diff --git a/.dockerignore b/.dockerignore
index 2e05d2c9b7d..d4e31f2c7a2 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -1,2 +1,3 @@
+.k8s_ci.Dockerfile
 .venv
 database
diff --git a/.gitignore b/.gitignore
index ea4673509d6..5f286aff736 100644
--- a/.gitignore
+++ b/.gitignore
@@ -162,10 +162,7 @@ client/galaxy
 doc/build
 doc/schema.md
 doc/source/admin/config_logging_default_yaml.rst
-doc/source/api/api.rst
-doc/source/api/ts_api.rst
 doc/source/dev/schema.md
-doc/source/dev/schema.rst
 client/styleguide
 
 # webpack stats
diff --git a/.k8s_ci.Dockerfile b/.k8s_ci.Dockerfile
index c2580717e7d..fab33a27f77 100644
--- a/.k8s_ci.Dockerfile
+++ b/.k8s_ci.Dockerfile
@@ -1,12 +1,18 @@
 # Stage 1:
 # - base: ubuntu (default) OR prebuilt image0
 # - install build tools
-# - run playbook (image0 avoids rerunning lengthy tasks)
+# - clone playbook
+# Stage 2: build galaxy client and server in parallel
+# Stage 2.1:
+# - run playbook with server build steps only
 # - remove build artifacts + files not needed in container
-# Stage 2:
+# Stage 2.2:
+# - run playbook with client build steps only
+# - remove build artifacts + files not needed in container
+# Stage 3:
 # - install python-virtualenv
 # - create galaxy user + group + directory
-# - copy galaxy files from stage 1
+# - copy galaxy files from stage 2.1 and 2.2
 # - finalize container (set path, user...)
 
 # Init ARGs
@@ -16,12 +22,14 @@ ARG SERVER_DIR=$ROOT_DIR/server
 # For much faster build time override this with image0 (Dockerfile.0 build):
 #   docker build --build-arg BASE=<image0 name>...
 ARG STAGE1_BASE=ubuntu:20.04
-ARG STAGE2_BASE=$STAGE1_BASE
+ARG FINAL_STAGE_BASE=$STAGE1_BASE
 # NOTE: the value of GALAXY_USER must be also hardcoded in COPY in final stage
 ARG GALAXY_USER=galaxy
 ARG GALAXY_PLAYBOOK_REPO=https://github.com/galaxyproject/galaxy-docker-k8s
 
-# Stage-1
+#======================================================
+# Stage 1 - Setup common requirements for build
+#======================================================
 FROM $STAGE1_BASE AS stage1
 ARG DEBIAN_FRONTEND=noninteractive
 ARG SERVER_DIR
@@ -61,7 +69,14 @@ RUN ansible-galaxy install -r requirements.yml -p roles --force-with-deps
 
 # Add Galaxy source code
 COPY . $SERVER_DIR/
-RUN ansible-playbook -i localhost, playbook.yml -v
+
+#======================================================
+# Stage 2.1 - Build galaxy server
+#======================================================
+FROM stage1 AS server_build
+ARG SERVER_DIR
+
+RUN ansible-playbook -i localhost, playbook.yml -v -e galaxy_build_client=False
 
 RUN cat /galaxy/server/lib/galaxy/dependencies/conditional-requirements.txt | grep psycopg2-binary | xargs /galaxy/server/.venv/bin/pip install
 
@@ -72,7 +87,6 @@ RUN git rev-parse HEAD > GITREVISION
 RUN rm -rf \
         .ci \
         .git \
-        .venv/bin/node \
         .venv/include/node \
         .venv/src/node* \
         doc \
@@ -81,8 +95,30 @@ RUN rm -rf \
 # Clean up *all* node_modules, including plugins.  Everything is already built+staged.
 RUN find . -name "node_modules" -type d -prune -exec rm -rf '{}' +
 
-# Stage-2
-FROM $STAGE2_BASE
+#======================================================
+# Stage 2.2 - Build galaxy client
+#======================================================
+FROM stage1 AS client_build
+ARG SERVER_DIR
+
+RUN ansible-playbook -i localhost, playbook.yml -v --tags "galaxy_build_client"
+
+WORKDIR $SERVER_DIR
+RUN rm -rf \
+        .ci \
+        .git \
+        .venv/include/node \
+        .venv/src/node* \
+        doc \
+        test \
+        test-data
+# Clean up *all* node_modules, including plugins.  Everything is already built+staged.
+RUN find . -name "node_modules" -type d -prune -exec rm -rf '{}' +
+
+#======================================================
+# Stage 3 - Build final image based on previous stages
+#======================================================
+FROM $FINAL_STAGE_BASE
 ARG DEBIAN_FRONTEND=noninteractive
 ARG ROOT_DIR
 ARG SERVER_DIR
@@ -115,7 +151,8 @@ RUN set -xe; \
 WORKDIR $ROOT_DIR
 # Copy galaxy files to final image
 # The chown value MUST be hardcoded (see #35018 at github.com/moby/moby)
-COPY --chown=galaxy:galaxy --from=stage1 $ROOT_DIR .
+COPY --chown=galaxy:galaxy --from=server_build $ROOT_DIR .
+COPY --chown=galaxy:galaxy --from=client_build $SERVER_DIR/static ./server/static
 
 WORKDIR $SERVER_DIR
 EXPOSE 8080
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 6af16ec22d2..50676c0f24d 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -41,7 +41,10 @@ Git](https://swcarpentry.github.io/git-novice/) tutorial is a good place to
 start.  More learning resources are listed at
 https://help.github.com/en/github/getting-started-with-github/git-and-github-learning-resources
 
-1. Make sure you have a free [GitHub](https://github.com/) account.
+1. Make sure you have a free [GitHub](https://github.com/) account. To increase
+   the security of your account, we strongly recommend that you configure
+   [two-factor authentication](https://docs.github.com/en/github/authenticating-to-github/securing-your-account-with-two-factor-authentication-2fa).
+   Additionally, you may want to [sign your commits](https://docs.github.com/en/github/authenticating-to-github/managing-commit-signature-verification).
 
 2. Fork the [galaxy repository](https://github.com/galaxyproject/galaxy) on
    GitHub to make your changes.  To keep your copy up to date with respect to
diff --git a/Makefile b/Makefile
index 0815ade564c..938f7bf63fd 100644
--- a/Makefile
+++ b/Makefile
@@ -30,6 +30,9 @@ docs: ## Generate HTML documentation.
 	$(IN_VENV) $(MAKE) -C doc clean
 	$(IN_VENV) $(MAKE) -C doc html
 
+docs-develop: ## Fast doc generation and more warnings (for development)
+	$(IN_VENV) GALAXY_DOCS_SKIP_VIEW_CODE=1 SPHINXOPTS='-j 4' $(MAKE) -C doc html
+
 setup-venv:
 	if [ ! -f $(VENV)/bin/activate ]; then bash scripts/common_startup.sh --dev-wheels; fi
 
diff --git a/client/gulpfile.js b/client/gulpfile.js
index 015f572fda8..727ea665282 100644
--- a/client/gulpfile.js
+++ b/client/gulpfile.js
@@ -22,6 +22,7 @@ const PLUGIN_BUILD_IDS = [
     "openlayers",
     "openseadragon",
     "pv",
+    "nora",
 ];
 
 const paths = {
diff --git a/client/src/components/DatasetInformation/DatasetInformation.test.js b/client/src/components/DatasetInformation/DatasetInformation.test.js
index 5fa47ff2e5f..dfc341eb83b 100644
--- a/client/src/components/DatasetInformation/DatasetInformation.test.js
+++ b/client/src/components/DatasetInformation/DatasetInformation.test.js
@@ -1,6 +1,7 @@
 import axios from "axios";
 import MockAdapter from "axios-mock-adapter";
 import { mount } from "@vue/test-utils";
+import { getLocalVue } from "jest/helpers";
 import DatasetInformation from "./DatasetInformation";
 import datasetResponse from "./testData/datasetResponse";
 import flushPromises from "flush-promises";
@@ -18,6 +19,8 @@ const mockDatasetProvider = {
     },
 };
 
+const localVue = getLocalVue();
+
 describe("DatasetInformation/DatasetInformation.vue", () => {
     let wrapper;
     let datasetInfoTable;
@@ -42,6 +45,7 @@ describe("DatasetInformation/DatasetInformation.vue", () => {
             stubs: {
                 DatasetProvider: mockDatasetProvider,
             },
+            localVue,
         });
         datasetInfoTable = wrapper.find("#dataset-details");
         await flushPromises();
diff --git a/client/src/components/FilesDialog/FilesInput.vue b/client/src/components/FilesDialog/FilesInput.vue
index a56a184af73..261eb807fb2 100644
--- a/client/src/components/FilesDialog/FilesInput.vue
+++ b/client/src/components/FilesDialog/FilesInput.vue
@@ -1,5 +1,6 @@
 <template>
-    <b-form-input v-model="localValue" :placeholder="placeholder" @click="selectFile"> </b-form-input>
+    <b-form-input class="directory-form-input" v-model="localValue" :placeholder="placeholder" @click="selectFile">
+    </b-form-input>
 </template>
 
 <script>
diff --git a/client/src/components/History/HistoryTopNav.vue b/client/src/components/History/HistoryTopNav.vue
index aa40697e733..1f3006f91c5 100644
--- a/client/src/components/History/HistoryTopNav.vue
+++ b/client/src/components/History/HistoryTopNav.vue
@@ -35,7 +35,7 @@
                 key="use-legacy-history"
                 title="Return to legacy history panel"
                 icon="fas fa-exchange-alt"
-                @click="useLegacyHistoryPanel"
+                @click="switchToLegacyHistoryPanel"
             />
         </PriorityMenu>
     </div>
@@ -48,6 +48,7 @@ import HistorySelector from "./HistorySelector";
 import { createNewHistory } from "./model/queries";
 import { wipeDatabase, clearHistoryDateStore } from "./caching";
 import { legacyNavigationMixin } from "components/plugins";
+import { switchToLegacyHistoryPanel } from "./adapters/betaToggle";
 
 export default {
     mixins: [legacyNavigationMixin],
@@ -72,10 +73,7 @@ export default {
     methods: {
         ...mapActions("betaHistory", ["storeHistory"]),
 
-        useLegacyHistoryPanel() {
-            sessionStorage.removeItem("useBetaHistory");
-            location.reload();
-        },
+        switchToLegacyHistoryPanel,
 
         // create new server, store in vuex, switch to it
         async createHistory() {
diff --git a/client/src/components/History/adapters/HistoryPanelProxy.js b/client/src/components/History/adapters/HistoryPanelProxy.js
index 7f39ca6c802..6b4dc223122 100644
--- a/client/src/components/History/adapters/HistoryPanelProxy.js
+++ b/client/src/components/History/adapters/HistoryPanelProxy.js
@@ -15,6 +15,7 @@ import Backbone from "backbone";
 import CurrentHistoryView from "mvc/history/history-view-edit-current";
 import { History } from "mvc/history/history-model";
 import "./HistoryPanelProxy.scss";
+import store from "store";
 
 // bypass polling while using the beta panel, skips contents loading
 const FakeHistoryViewModel = CurrentHistoryView.CurrentHistoryView.extend({
@@ -37,6 +38,7 @@ export const HistoryPanelProxy = Backbone.View.extend({
 
         // fake view of the current history
         this.historyView = new FakeHistoryViewModel({
+            fakeHistoryViewModel: true,
             className: `fake ${CurrentHistoryView.CurrentHistoryView.prototype.className} middle`,
             purgeAllowed: this.allow_user_dataset_purge,
             linkTarget: "galaxy_main",
@@ -59,6 +61,14 @@ export const HistoryPanelProxy = Backbone.View.extend({
                 url: `${Galaxy.user.urlRoot()}/${Galaxy.user.id || "current"}`,
             });
         });
+
+        // Watch the store, change the fake history model when it changs
+        store.subscribe(({ type, payload: newId }) => {
+            if (type == "betaHistory/setCurrentHistoryId") {
+                console.log("setCurrentHistoryId", newId);
+                Galaxy.currHistoryPanel.setModel(new History({ id: newId }));
+            }
+        });
     },
     render() {
         // Hack: For now, remove unused "unified-panel" elements until we can
diff --git a/client/src/components/History/adapters/betaToggle.js b/client/src/components/History/adapters/betaToggle.js
new file mode 100644
index 00000000000..0cf1fe6afd1
--- /dev/null
+++ b/client/src/components/History/adapters/betaToggle.js
@@ -0,0 +1,13 @@
+export const isBetaHistoryOpen = () => {
+    return sessionStorage.getItem("useBetaHistory");
+};
+
+export const switchToLegacyHistoryPanel = () => {
+    sessionStorage.removeItem("useBetaHistory");
+    location.reload();
+};
+
+export const switchToBetaHistoryPanel = () => {
+    sessionStorage.setItem("useBetaHistory", 1);
+    location.reload(false);
+};
diff --git a/client/src/components/History/model/syncCurrentHistoryToGalaxy.js b/client/src/components/History/model/syncCurrentHistoryToGalaxy.js
index be7ce846c14..7834bd84dec 100644
--- a/client/src/components/History/model/syncCurrentHistoryToGalaxy.js
+++ b/client/src/components/History/model/syncCurrentHistoryToGalaxy.js
@@ -1,9 +1,11 @@
 // Sync Galaxy store to legacy galaxy current history
 
-import { fromEvent } from "rxjs";
-import { map, filter, switchMap, pluck, distinctUntilChanged } from "rxjs/operators";
+import { concat, fromEvent, throwError } from "rxjs";
+import { tap, map, filter, switchMap, pluck, distinctUntilChanged, retryWhen, take, delay } from "rxjs/operators";
+
+export function syncCurrentHistoryToGalaxy(galaxy$, store, cfg = {}) {
+    const { retryPeriod = 500, retries = 20 } = cfg;
 
-export function syncCurrentHistoryToGalaxy(galaxy$, store) {
     // prettier-ignore
     const historyId$ = galaxy$.pipe(
         pluck("currHistoryPanel"),
@@ -14,15 +16,22 @@ export function syncCurrentHistoryToGalaxy(galaxy$, store) {
                 map(() => panel.model.id)
             );
         }),
+        retryWhen(err$ => {
+            const retries$ = err$.pipe(
+                delay(retryPeriod),
+                take(retries)
+            );
+            const errMsg$ = throwError("Unable to sync to currHistoryPanel because it never appeared");
+            return concat(retries$, errMsg$);
+        }),
         filter(Boolean),
-        distinctUntilChanged()
+        distinctUntilChanged(),
+        tap(() => console.log("Vuex is now tracking galaxy.currHistoryPanel")),
     );
 
     return historyId$.subscribe(
-        (id) => {
-            store.commit("betaHistory/setCurrentHistoryId", id);
-        },
-        (err) => console.log("syncCurrentHistoryToGalaxy error", err),
+        (id) => store.commit("betaHistory/setCurrentHistoryId", id),
+        (err) => console.warn("syncCurrentHistoryToGalaxy error", err),
         () => console.log("syncCurrentHistoryToGalaxy complete")
     );
 }
diff --git a/client/src/components/History/providers/HistoryContentProvider/loadContents.js b/client/src/components/History/providers/HistoryContentProvider/loadContents.js
index a18488e4028..6fa25efe372 100644
--- a/client/src/components/History/providers/HistoryContentProvider/loadContents.js
+++ b/client/src/components/History/providers/HistoryContentProvider/loadContents.js
@@ -1,33 +1,44 @@
-import { pipe, defer, of } from "rxjs";
-import { repeat, switchMap, catchError } from "rxjs/operators";
-import { tag } from "rxjs-spy/operators/tag";
-import { decay } from "../../../../utils/observable/decay";
+import { defer, of } from "rxjs";
+import { repeat, switchMap, switchMapTo, startWith, debounceTime } from "rxjs/operators";
+import { decay } from "utils/observable/decay";
+import { monitorXHR } from "utils/observable/monitorXHR";
 import { loadHistoryContents } from "../../caching";
 
 // prettier-ignore
 export const loadContents = (cfg = {}) => {
     const {
         windowSize,
-        initialInterval = 3 * 1000,
+        initialInterval = 2 * 1000,
         maxInterval = 10 * initialInterval,
-        disablePoll = false,
+        disablePoll = false
     } = cfg;
 
-    return pipe(
-        switchMap(([{id}, params, hid]) => {
-            const singleLoad$ = defer(() => of([id, params, hid]).pipe(
-                tag('ajaxLoadInputs'),
-                loadHistoryContents({ windowSize }),
-            ));
-            const poll$ = singleLoad$.pipe(
-                decay({ initialInterval, maxInterval }),
-                repeat(),
-            );
-            return disablePoll ? singleLoad$ : poll$;
-        }),
-        catchError(err => {
-            console.warn("Error in loadContents", err);
-            throw err;
-        })
-    );
-}
+    return switchMap(([{ id }, params, hid]) => {
+
+        // a single history update
+        const singleLoad$ = of([id, params, hid]).pipe(
+            loadHistoryContents({ windowSize })
+        );
+
+        // start repeating, delay gets longer over time until unsubscribed
+        const freshPoll$ = defer(() => singleLoad$.pipe(
+            decay({ initialInterval, maxInterval }),
+            repeat()
+        ));
+
+        // history, tools routes all refresh
+        // exclude our own polling url though
+        const routes = [/api\/(history|tools|histories)/];
+        const methods = ["POST", "PUT", "DELETE"];
+        const resetPoll$ = monitorXHR({ methods, routes });
+
+        // resets re-subscribe to freshPoll$ starting the decay over again
+        const poll$ = resetPoll$.pipe(
+            startWith(true),
+            debounceTime(100),
+            switchMapTo(freshPoll$)
+        );
+
+        return disablePoll ? singleLoad$ : poll$;
+    });
+};
diff --git a/client/src/components/HistoryExport/ExportLink.vue b/client/src/components/HistoryExport/ExportLink.vue
index f42627f2745..2b9ccd95edc 100644
--- a/client/src/components/HistoryExport/ExportLink.vue
+++ b/client/src/components/HistoryExport/ExportLink.vue
@@ -1,11 +1,12 @@
 <template>
     <span>
         <b
-            ><a :href="link">{{ link }}</a></b
+            ><a class="generated-export-link" :href="link">{{ link }}</a></b
         >
         <font-awesome-icon
             v-b-tooltip.hover
             title="Copy export URL to your clipboard"
+            class="copy-export-link"
             icon="link"
             style="cursor: pointer;"
             @click="copyUrl"
@@ -13,9 +14,9 @@
         <i
             title="Information about when the history export was generated is included in the job details. Additionally, if there are issues with export, the job details may help figure out the underlying problem or communicate issues to your Galaxy administrator."
         >
-            (<a href="#" @click="showDetails">view job details</a>)
+            (<a class="show-job-link" href="#" @click="showDetails">view job details</a>)
         </i>
-        <b-modal v-model="details" scrollable ok-only>
+        <b-modal v-model="details" modal-class="job-information-modal" scrollable ok-only hide-header>
             <job-information :job_id="historyExport.job_id" :include-times="true" />
         </b-modal>
     </span>
diff --git a/client/src/components/HistoryExport/Index.vue b/client/src/components/HistoryExport/Index.vue
index 51db0e2fccd..aa9b54c83bb 100644
--- a/client/src/components/HistoryExport/Index.vue
+++ b/client/src/components/HistoryExport/Index.vue
@@ -1,5 +1,5 @@
 <template>
-    <span>
+    <span class="history-export-component">
         <h2>Export history archive</h2>
         <span v-if="initializing">
             <loading-span message="Loading server configuration." />
@@ -7,13 +7,15 @@
         <span v-else-if="hasWritableFileSources">
             <b-card no-body>
                 <b-tabs pills card vertical>
-                    <b-tab title="to a link" active>
+                    <b-tab title="to a link" title-link-class="tab-export-to-link" active>
                         <b-card-text>
                             <ToLink :history-id="historyId" />
                         </b-card-text>
                     </b-tab>
-                    <b-tab title="to a remote file">
-                        <ToRemoteFile :history-id="historyId" />
+                    <b-tab title="to a remote file" title-link-class="tab-export-to-file">
+                        <b-card-text>
+                            <ToRemoteFile :history-id="historyId" />
+                        </b-card-text>
                     </b-tab>
                 </b-tabs>
             </b-card>
@@ -25,20 +27,20 @@
 </template>
 
 <script>
-import Vue from "vue";
-import BootstrapVue from "bootstrap-vue";
+import { BCard, BTabs, BTab } from "bootstrap-vue";
 import ToLink from "./ToLink.vue";
 import ToRemoteFile from "./ToRemoteFile.vue";
 import { Services } from "components/FilesDialog/services";
 import LoadingSpan from "components/LoadingSpan";
 
-Vue.use(BootstrapVue);
-
 export default {
     components: {
         LoadingSpan,
         ToLink,
         ToRemoteFile,
+        BCard,
+        BTabs,
+        BTab,
     },
     props: {
         historyId: {
@@ -59,7 +61,7 @@ export default {
         async initialize() {
             const fileSources = await new Services().getFileSources();
             this.hasWritableFileSources = fileSources.some((fs) => fs.writable);
-            console.log(fileSources);
+            // console.log(fileSources);
             this.initializing = false;
         },
     },
diff --git a/client/src/components/HistoryExport/ToLink.vue b/client/src/components/HistoryExport/ToLink.vue
index b45587bac26..a6b6d2c807c 100644
--- a/client/src/components/HistoryExport/ToLink.vue
+++ b/client/src/components/HistoryExport/ToLink.vue
@@ -153,10 +153,7 @@ export default {
             waitOnJob(jobId)
                 .then((jobResponse) => {
                     this.waitingOnJob = false;
-                    this.loadingExports = true;
-                    // Race condition, for some reasons the job API returns
-                    // ok before the JEHA...
-                    setTimeout(this.loadExports, 2000);
+                    this.loadExports();
                 })
                 .catch(this.handleError);
         },
diff --git a/client/src/components/HistoryExport/ToRemoteFile.vue b/client/src/components/HistoryExport/ToRemoteFile.vue
index 85ea86ad414..c78bdf6bf30 100644
--- a/client/src/components/HistoryExport/ToRemoteFile.vue
+++ b/client/src/components/HistoryExport/ToRemoteFile.vue
@@ -1,5 +1,5 @@
 <template>
-    <div>
+    <div class="export-to-remote-file">
         <b-alert v-if="errorMessage" show variant="danger" dismissible @dismissed="errorMessage = null">
             {{ errorMessage }}
             <JobError
@@ -20,14 +20,14 @@
         </div>
         <div v-else>
             <b-form-group
-                id="directory"
+                id="fieldset-directory"
                 label-for="directory"
                 description="Select a 'remote files' directory to export history archive to."
                 class="mt-3"
             >
-                <files-input v-model="directory" mode="directory" :requireWritable="true" />
+                <files-input id="directory" v-model="directory" mode="directory" :requireWritable="true" />
             </b-form-group>
-            <b-form-group id="name" label-for="name" description="Give the exported file a name." class="mt-3">
+            <b-form-group id="fieldset-name" label-for="name" description="Give the exported file a name." class="mt-3">
                 <b-form-input id="name" v-model="name" placeholder="Name" required></b-form-input>
             </b-form-group>
             <b-row align-h="end">
diff --git a/client/src/components/HistoryImport.vue b/client/src/components/HistoryImport.vue
index 305000896a0..34feb5c28a9 100644
--- a/client/src/components/HistoryImport.vue
+++ b/client/src/components/HistoryImport.vue
@@ -1,5 +1,5 @@
 <template>
-    <b-card title="Import a history from an archive">
+    <b-card body-class="history-import-component" title="Import a history from an archive">
         <b-alert v-if="errorMessage" variant="danger" dismissible @dismissed="errorMessage = null" show>
             {{ errorMessage }}
             <JobError
diff --git a/client/src/components/JobInformation/JobError.vue b/client/src/components/JobInformation/JobError.vue
index bab388d1f52..77b51119469 100644
--- a/client/src/components/JobInformation/JobError.vue
+++ b/client/src/components/JobInformation/JobError.vue
@@ -11,7 +11,7 @@
             </div>
             <!-- TODO: modal for reporting error. -->
         </b-card-text>
-        <b-modal v-model="showInfo" scrollable ok-only>
+        <b-modal v-model="showInfo" modal-class="job-information-modal" scrollable ok-only hide-header>
             <job-information :job_id="job.id" :include-times="true" />
         </b-modal>
     </b-card>
diff --git a/client/src/components/LibraryFolder/TopToolbar/FolderTopBar.vue b/client/src/components/LibraryFolder/TopToolbar/FolderTopBar.vue
index 6f759740bc0..ae06816d7d6 100644
--- a/client/src/components/LibraryFolder/TopToolbar/FolderTopBar.vue
+++ b/client/src/components/LibraryFolder/TopToolbar/FolderTopBar.vue
@@ -46,7 +46,7 @@
                                     from History</a
                                 >
                                 <a
-                                    v-if="user_library_import_dir"
+                                    v-if="user_library_import_dir_available"
                                     class="dropdown-item cursor-pointer"
                                     @click="addDatasets('userdir')"
                                 >
@@ -203,7 +203,7 @@ export default {
     data() {
         return {
             is_admin: false,
-            user_library_import_dir: false,
+            user_library_import_dir_available: false,
             library_import_dir: false,
             allow_library_path_paste: false,
             list_genomes: [],
@@ -225,7 +225,7 @@ export default {
         const Galaxy = getGalaxyInstance();
         this.services = new Services();
         this.is_admin = Galaxy.user.attributes.is_admin;
-        this.user_library_import_dir = Galaxy.config.user_library_import_dir;
+        this.user_library_import_dir_available = Galaxy.config.user_library_import_dir_available;
         this.library_import_dir = Galaxy.config.library_import_dir;
         this.allow_library_path_paste = Galaxy.config.allow_library_path_paste;
 
diff --git a/client/src/components/LibraryFolder/TopToolbar/add-datasets.js b/client/src/components/LibraryFolder/TopToolbar/add-datasets.js
index 7473509bbbe..9f3a2cc977c 100644
--- a/client/src/components/LibraryFolder/TopToolbar/add-datasets.js
+++ b/client/src/components/LibraryFolder/TopToolbar/add-datasets.js
@@ -411,6 +411,7 @@ var AddDatasets = Backbone.View.extend({
                 if (typeof response.responseJSON !== "undefined") {
                     if (response.responseJSON.err_code === 404001) {
                         Toast.warning(response.responseJSON.err_msg);
+                        getGalaxyInstance().modal.hide();
                     } else {
                         Toast.error(response.responseJSON.err_msg);
                     }
diff --git a/client/src/components/Panels/Buttons/FavoritesButton.vue b/client/src/components/Panels/Buttons/FavoritesButton.vue
index 82fb53f2251..a0b295b7ca5 100644
--- a/client/src/components/Panels/Buttons/FavoritesButton.vue
+++ b/client/src/components/Panels/Buttons/FavoritesButton.vue
@@ -8,7 +8,8 @@
         role="button"
         aria-label="Show favorite tools"
     >
-        <font-awesome-icon :icon="['far', 'star']" />
+        <font-awesome-icon v-if="toggle" :icon="['fas', 'star']" />
+        <font-awesome-icon v-else :icon="['far', 'star']" />
     </a>
 </template>
 
@@ -17,22 +18,52 @@ import { VBTooltip } from "bootstrap-vue";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { library } from "@fortawesome/fontawesome-svg-core";
 import { faStar } from "@fortawesome/free-regular-svg-icons";
+import { faStar as faStarSolid } from "@fortawesome/free-solid-svg-icons";
+
 library.add(faStar);
+library.add(faStarSolid);
 
 export default {
     name: "FavoritesButton",
+    props: {
+        query: {
+            type: String,
+        },
+    },
     components: { FontAwesomeIcon },
     data() {
         return {
-            tooltipText: "Show favorites",
+            searchKey: "#favorites",
+            tooltipToggle: "Show favorites",
+            tooltipUntoggle: "Clear",
+            toggle: false,
         };
     },
     directives: {
         "v-b-tooltip": VBTooltip,
     },
+    watch: {
+        query() {
+            this.toggle = this.query == this.searchKey;
+        },
+    },
+    computed: {
+        tooltipText() {
+            if (this.toggle) {
+                return this.tooltipUntoggle;
+            } else {
+                return this.tooltipToggle;
+            }
+        },
+    },
     methods: {
         onFavorites() {
-            this.$emit("onFavorites", "#favorites");
+            this.toggle = !this.toggle;
+            if (this.toggle) {
+                this.$emit("onFavorites", this.searchKey);
+            } else {
+                this.$emit("onFavorites", null);
+            }
         },
     },
 };
diff --git a/client/src/components/Panels/ToolBox.vue b/client/src/components/Panels/ToolBox.vue
index 472203b731e..14a66c8bf65 100644
--- a/client/src/components/Panels/ToolBox.vue
+++ b/client/src/components/Panels/ToolBox.vue
@@ -3,7 +3,7 @@
         <div class="unified-panel-header" unselectable="on">
             <div class="unified-panel-header-inner">
                 <div class="panel-header-buttons">
-                    <favorites-button @onFavorites="onFavorites" v-if="isUser" />
+                    <favorites-button :query="query" @onFavorites="onFavorites" v-if="isUser" />
                 </div>
                 <div class="panel-header-text">Tools</div>
             </div>
diff --git a/client/src/components/Panels/utilities.js b/client/src/components/Panels/utilities.js
index fe1913b3d33..3d5090edd9c 100644
--- a/client/src/components/Panels/utilities.js
+++ b/client/src/components/Panels/utilities.js
@@ -1,10 +1,14 @@
 export function filterToolSections(layout, results) {
     if (results) {
+        results = normalize_results(results);
         const filteredLayout = layout.map((section) => {
             var toolRes = [];
             if (section.elems) {
                 section.elems.forEach((el) => {
-                    if (!el.text && results.includes(el.id)) {
+                    if (
+                        (!el.text && results.includes(el.id)) ||
+                        (el.tool_shed_repository && results.includes(el.tool_shed_repository.name))
+                    ) {
                         toolRes.push(el);
                     }
                 });
@@ -41,6 +45,7 @@ export function filterTools(layout, results) {
     // do not consider expression tools, unless requested by the workflow editor
     layout = layout.filter((section) => section.name !== "Expression Tools");
     if (results) {
+        results = normalize_results(results);
         var toolsResults = [];
         if (results.length < 1) {
             return toolsResults;
@@ -50,7 +55,10 @@ export function filterTools(layout, results) {
         layout.map((section) => {
             if (section.elems) {
                 section.elems.forEach((el) => {
-                    if (!el.text && results.includes(el.id)) {
+                    if (
+                        (!el.text && results.includes(el.id)) ||
+                        (el.tool_shed_repository && results.includes(el.tool_shed_repository.name))
+                    ) {
                         toolsResults.push(el);
                     }
                 });
@@ -65,3 +73,15 @@ export function filterTools(layout, results) {
         return layout;
     }
 }
+
+function normalize_results(results) {
+    var norm_results = [];
+    results.forEach((result) => {
+        if (result.includes("/repos/")) {
+            norm_results.push(result.split("/")[3]);
+        } else {
+            norm_results.push(result);
+        }
+    });
+    return norm_results;
+}
diff --git a/client/src/components/ToolsView/ToolsSchemaJson/ToolsJson.test.js b/client/src/components/ToolsView/ToolsSchemaJson/ToolsJson.test.js
index a04f76e3769..da8a157f4e3 100644
--- a/client/src/components/ToolsView/ToolsSchemaJson/ToolsJson.test.js
+++ b/client/src/components/ToolsView/ToolsSchemaJson/ToolsJson.test.js
@@ -3,7 +3,10 @@ import ToolsJson from "./ToolsJson";
 import testToolsListResponse from "../testData/toolsList";
 import MockAdapter from "axios-mock-adapter";
 import axios from "axios";
-import { mount } from "@vue/test-utils";
+import { shallowMount } from "@vue/test-utils";
+import { getLocalVue } from "jest/helpers";
+
+const localVue = getLocalVue();
 
 describe("ToolsView/ToolsView.vue", () => {
     let wrapper;
@@ -12,7 +15,7 @@ describe("ToolsView/ToolsView.vue", () => {
 
     beforeEach(async () => {
         axiosMock = new MockAdapter(axios);
-        wrapper = mount(ToolsJson);
+        wrapper = shallowMount(ToolsJson, { localVue });
         axiosMock.onGet("/api/tools?tool_help=True").reply(200, testToolsListResponse);
         await wrapper.vm.$nextTick();
     });
diff --git a/client/src/components/Toolshed/InstalledList/Index.test.js b/client/src/components/Toolshed/InstalledList/Index.test.js
index 85f5285a68d..6342ea7e7c0 100644
--- a/client/src/components/Toolshed/InstalledList/Index.test.js
+++ b/client/src/components/Toolshed/InstalledList/Index.test.js
@@ -1,4 +1,5 @@
 import { mount } from "@vue/test-utils";
+import { getLocalVue } from "jest/helpers";
 import Index from "./Index";
 
 jest.mock("app");
@@ -10,6 +11,8 @@ getAppRoot.mockImplementation(() => "/");
 import { Services } from "../services";
 jest.mock("../services");
 
+const localVue = getLocalVue();
+
 Services.mockImplementation(() => {
     return {
         async getInstalledRepositories() {
@@ -42,6 +45,7 @@ describe("InstalledList", () => {
             stubs: {
                 RepositoryDetails: true,
             },
+            localVue,
         });
         expect(wrapper.find(".loading-message").text()).toBe("Loading installed repositories...");
         await wrapper.vm.$nextTick();
diff --git a/client/src/components/Toolshed/RepositoryDetails/InstallationButton.test.js b/client/src/components/Toolshed/RepositoryDetails/InstallationButton.test.js
index 71c62688fbc..7fae5f3d856 100644
--- a/client/src/components/Toolshed/RepositoryDetails/InstallationButton.test.js
+++ b/client/src/components/Toolshed/RepositoryDetails/InstallationButton.test.js
@@ -1,6 +1,9 @@
 import { mount } from "@vue/test-utils";
+import { getLocalVue } from "jest/helpers";
 import InstallationButton from "./InstallationButton";
 
+const localVue = getLocalVue();
+
 describe("InstallationButton", () => {
     it("test installed repository revision", () => {
         const wrapper = mount(InstallationButton, {
@@ -8,6 +11,7 @@ describe("InstallationButton", () => {
                 installed: true,
                 status: "Installed",
             },
+            localVue,
         });
         const $el = wrapper.find("button");
         expect($el.classes()).toEqual(expect.arrayContaining(["btn-danger"]));
diff --git a/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.test.js b/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.test.js
index fc19ab1aad0..f0b6aacf56d 100644
--- a/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.test.js
+++ b/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.test.js
@@ -1,8 +1,11 @@
 import { mount } from "@vue/test-utils";
+import { getLocalVue } from "jest/helpers";
 import InstallationSettings from "./InstallationSettings";
 
 jest.mock("app");
 
+const localVue = getLocalVue();
+
 describe("InstallationSettings", () => {
     it("test tool repository installer interface", () => {
         const wrapper = mount(InstallationSettings, {
@@ -18,6 +21,7 @@ describe("InstallationSettings", () => {
                 requiresPanel: true,
                 toolshedUrl: "toolshedUrl",
             },
+            localVue,
         });
         expect(wrapper.find(".title").text()).toBe("Installing 'name'");
         expect(wrapper.find(".description").text()).toBe("long_description");
diff --git a/client/src/components/Toolshed/RepositoryDetails/RepositoryTools.test.js b/client/src/components/Toolshed/RepositoryDetails/RepositoryTools.test.js
index 09b7c9aad4d..ab11cdc67c7 100644
--- a/client/src/components/Toolshed/RepositoryDetails/RepositoryTools.test.js
+++ b/client/src/components/Toolshed/RepositoryDetails/RepositoryTools.test.js
@@ -1,6 +1,9 @@
 import { mount } from "@vue/test-utils";
+import { getLocalVue } from "jest/helpers";
 import RepositoryTools from "./RepositoryTools";
 
+const localVue = getLocalVue();
+
 describe("RepositoryTools", () => {
     it("test tool version list in repository details", () => {
         const wrapper = mount(RepositoryTools, {
@@ -13,6 +16,7 @@ describe("RepositoryTools", () => {
                     },
                 ],
             },
+            localVue,
         });
         const $el = wrapper.findAll("td");
         const $first = $el.at(0);
diff --git a/client/src/components/Toolshed/SearchList/ServerSelection.test.js b/client/src/components/Toolshed/SearchList/ServerSelection.test.js
index 3ac7e5b4869..d3e138113fc 100644
--- a/client/src/components/Toolshed/SearchList/ServerSelection.test.js
+++ b/client/src/components/Toolshed/SearchList/ServerSelection.test.js
@@ -1,6 +1,9 @@
 import { mount } from "@vue/test-utils";
+import { getLocalVue } from "jest/helpers";
 import ServerSelection from "./ServerSelection";
 
+const localVue = getLocalVue();
+
 describe("ServerSelection", () => {
     it("test server selection dropdown", () => {
         const wrapper = mount(ServerSelection, {
@@ -10,6 +13,7 @@ describe("ServerSelection", () => {
                 loading: false,
                 total: "total",
             },
+            localVue,
         });
         expect(wrapper.find(".description").text()).toBe("total repositories available at");
         const $options = wrapper.findAll("a");
diff --git a/client/src/components/Upload/UploadModal.test.js b/client/src/components/Upload/UploadModal.test.js
index 82cf033a89e..5e2719d761c 100644
--- a/client/src/components/Upload/UploadModal.test.js
+++ b/client/src/components/Upload/UploadModal.test.js
@@ -3,7 +3,6 @@ import axios from "axios";
 import UploadModal from "./UploadModal.vue";
 import store from "../../store";
 import { shallowMount, createLocalVue } from "@vue/test-utils";
-import BootstrapVue from "bootstrap-vue";
 
 jest.mock("app");
 jest.mock("../History/caching");
@@ -39,7 +38,6 @@ describe("UploadModal.vue", () => {
         axiosMock.onGet(`/api/genomes`).reply(200, genomesResponse);
 
         const localVue = createLocalVue();
-        localVue.use(BootstrapVue);
 
         wrapper = await shallowMount(UploadModal, {
             store,
diff --git a/client/src/components/Upload/UploadModal.vue b/client/src/components/Upload/UploadModal.vue
index e303d55cba0..6e2e6ef3630 100644
--- a/client/src/components/Upload/UploadModal.vue
+++ b/client/src/components/Upload/UploadModal.vue
@@ -46,6 +46,7 @@ import RulesInput from "./RulesInput";
 import LoadingSpan from "components/LoadingSpan";
 import { mapState } from "vuex";
 import { BModal, BTabs, BTab } from "bootstrap-vue";
+import { isBetaHistoryOpen } from "components/History/adapters/betaToggle";
 
 const UploadModal = {
     components: {
@@ -336,8 +337,7 @@ const UploadModal = {
 };
 
 // Beta history patch
-const useBetaHistory = sessionStorage.getItem("useBetaHistory");
-if (useBetaHistory) {
+if (isBetaHistoryOpen()) {
     UploadModal.computed.currentHistoryId = function () {
         return this.$store.getters["betaHistory/currentHistoryId"];
     };
diff --git a/client/src/components/User/CloudAuth/CloudAuth.test.js b/client/src/components/User/CloudAuth/CloudAuth.test.js
index bc7751a4e74..91d9d17da45 100644
--- a/client/src/components/User/CloudAuth/CloudAuth.test.js
+++ b/client/src/components/User/CloudAuth/CloudAuth.test.js
@@ -5,9 +5,6 @@ import { getLocalVue } from "jest/helpers";
 import { default as CloudAuth } from "./CloudAuth";
 import CloudAuthItem from "./CloudAuthItem";
 
-import _l from "utils/localization";
-import BootstrapVue from "bootstrap-vue";
-
 jest.mock("./model/service", () => ({
     listCredentials: async () => {
         const listCredentials = require("./testdata/listCredentials.json");
@@ -17,8 +14,6 @@ jest.mock("./model/service", () => ({
 }));
 
 const localVue = getLocalVue();
-localVue.use(BootstrapVue);
-localVue.filter("localize", (value) => _l(value));
 
 describe("CloudAuth component", () => {
     let wrapper;
diff --git a/client/src/components/User/RecentInvocations.test.js b/client/src/components/User/RecentInvocations.test.js
index 82169267f06..0298f9cb066 100644
--- a/client/src/components/User/RecentInvocations.test.js
+++ b/client/src/components/User/RecentInvocations.test.js
@@ -1,5 +1,6 @@
 import Invocations from "../Workflow/Invocations";
 import { mount } from "@vue/test-utils";
+import { getLocalVue } from "jest/helpers";
 import flushPromises from "flush-promises";
 
 import RecentInvocations from "./RecentInvocations.vue";
@@ -7,13 +8,15 @@ import RecentInvocations from "./RecentInvocations.vue";
 jest.mock("../History/caching");
 jest.mock("./UserServices");
 
+const localVue = getLocalVue();
+
 describe("RecentInvocations.vue", () => {
     let wrapper;
     let fetchInvocationsSpy;
 
     beforeEach(async () => {
         fetchInvocationsSpy = jest.spyOn(RecentInvocations.methods, "fetchRecentInvocations");
-        wrapper = mount(RecentInvocations);
+        wrapper = mount(RecentInvocations, { localVue });
         await flushPromises();
     });
 
diff --git a/client/src/components/Workflow/Editor/RefactorConfirmationModal.test.js b/client/src/components/Workflow/Editor/RefactorConfirmationModal.test.js
index 037a1c418ad..68dcf0fe03a 100644
--- a/client/src/components/Workflow/Editor/RefactorConfirmationModal.test.js
+++ b/client/src/components/Workflow/Editor/RefactorConfirmationModal.test.js
@@ -1,11 +1,12 @@
 jest.mock("./modules/services");
 
-import { shallowMount, createLocalVue } from "@vue/test-utils";
+import { shallowMount } from "@vue/test-utils";
+import { getLocalVue } from "jest/helpers";
 import RefactorConfirmationModal from "./RefactorConfirmationModal";
 import { refactor } from "./modules/services";
 import flushPromises from "flush-promises";
 
-const localVue = createLocalVue();
+const localVue = getLocalVue();
 const TEST_WORKFLOW_ID = "test123";
 const TEST_ACTION_TYPE = "upgrade_subworkflow";
 
diff --git a/client/src/components/Workflow/Invocations.test.js b/client/src/components/Workflow/Invocations.test.js
index da4a5b1ad88..2590c0024ed 100644
--- a/client/src/components/Workflow/Invocations.test.js
+++ b/client/src/components/Workflow/Invocations.test.js
@@ -1,10 +1,13 @@
 import Invocations from "../Workflow/Invocations";
 import { mount } from "@vue/test-utils";
+import { getLocalVue } from "jest/helpers";
 import invocationData from "./test/json/invocation.json";
 import moment from "moment";
 
 jest.mock("../History/caching");
 
+const localVue = getLocalVue();
+
 describe("Invocations.vue without invocation", () => {
     let wrapper;
     let propsData;
@@ -16,6 +19,7 @@ describe("Invocations.vue without invocation", () => {
         };
         wrapper = mount(Invocations, {
             propsData,
+            localVue,
         });
     });
 
@@ -62,6 +66,7 @@ describe("Invocations.vue with invocation", () => {
                     template: "<span/>",
                 },
             },
+            localVue,
         });
     });
 
@@ -81,10 +86,10 @@ describe("Invocations.vue with invocation", () => {
     it("toggles detail rendering", async () => {
         let rows = wrapper.findAll("tbody > tr").wrappers;
         expect(rows.length).toBe(1);
-        await wrapper.find("#toggle-invocation-details").trigger("click");
+        await wrapper.find(".toggle-invocation-details").trigger("click");
         rows = wrapper.findAll("tbody > tr").wrappers;
         expect(rows.length).toBe(3);
-        await wrapper.find("#toggle-invocation-details").trigger("click");
+        await wrapper.find(".toggle-invocation-details").trigger("click");
         rows = wrapper.findAll("tbody > tr").wrappers;
         expect(rows.length).toBe(1);
     });
diff --git a/client/src/components/Workflow/Invocations.vue b/client/src/components/Workflow/Invocations.vue
index df40dd859b3..9e655d3da27 100644
--- a/client/src/components/Workflow/Invocations.vue
+++ b/client/src/components/Workflow/Invocations.vue
@@ -1,5 +1,5 @@
 <template>
-    <div>
+    <div class="invocations-list">
         <h2 class="mb-3">
             <span id="invocations-title">Workflow Invocations</span>
         </h2>
@@ -24,7 +24,7 @@
             >
                 <template v-slot:row-details="row">
                     <b-card>
-                        <small class="float-right">
+                        <small class="float-right" :data-invocation-id="row.item.id">
                             <b>Invocation: {{ row.item.id }}</b>
                         </small>
                         <workflow-invocation-state
@@ -35,7 +35,7 @@
                 </template>
                 <template v-slot:cell(workflow_id)="data">
                     <b-link
-                        id="toggle-invocation-details"
+                        class="toggle-invocation-details"
                         v-b-tooltip
                         title="Show Invocation details"
                         href="#"
diff --git a/client/src/components/WorkflowInvocationState/JobStep.test.js b/client/src/components/WorkflowInvocationState/JobStep.test.js
new file mode 100644
index 00000000000..ed21349cb4c
--- /dev/null
+++ b/client/src/components/WorkflowInvocationState/JobStep.test.js
@@ -0,0 +1,71 @@
+import BootstrapVue from "bootstrap-vue";
+import JobStep from "./JobStep";
+import { mount } from "@vue/test-utils";
+import jobs from "./test/json/jobs.json";
+
+jest.mock("../History/caching");
+
+import { createLocalVue } from "@vue/test-utils";
+
+// create an extended `Vue` constructor
+const localVue = createLocalVue();
+
+// install plugins as normal
+localVue.use(BootstrapVue);
+
+describe("DatasetUIWrapper.vue with Dataset", () => {
+    let wrapper;
+    let propsData;
+
+    beforeEach(async () => {
+        propsData = {
+            jobs: jobs,
+        };
+        wrapper = mount(JobStep, {
+            localVue,
+            propsData,
+            stubs: {
+                JobProvider: { template: "<div class='expanded'>I am expanded</div>" },
+            },
+        });
+    });
+    test("it renders a table with 2 jobs", async () => {
+        expect(wrapper.find("tbody").findAll("tr").length).toBe(2);
+    });
+    test("it expands on row click", async () => {
+        // verify no item is expanded
+        expect(wrapper.vm.toggledItems["1"]).toBe(undefined);
+        expect(wrapper.find(".expanded").exists()).toBeFalsy();
+        // expand
+        wrapper.find("tbody").find("tbody").find("tr").trigger("click");
+        await localVue.nextTick();
+        expect(wrapper.vm.toggledItems["1"]).toBeTruthy();
+        expect(wrapper.find(".expanded").exists()).toBeTruthy();
+        wrapper.find("tbody").find("tbody").find("tr").trigger("click");
+        // close again
+        await localVue.nextTick();
+        expect(wrapper.vm.toggledItems["1"]).toBeFalsy();
+        expect(wrapper.find(".expanded").exists()).toBeFalsy();
+    });
+    test("it sustains expanded on prop update", async () => {
+        // verify no item is expanded
+        expect(wrapper.vm.toggledItems["1"]).toBe(undefined);
+        expect(wrapper.find(".expanded").exists()).toBeFalsy();
+        // expand
+        wrapper.find("tbody").find("tbody").find("tr").trigger("click");
+        await localVue.nextTick();
+        expect(wrapper.vm.toggledItems["1"]).toBeTruthy();
+        expect(wrapper.find(".expanded").exists()).toBeTruthy();
+        // 2 collapsed rows, plus 1 expanded row
+        expect(wrapper.find("tbody").findAll("tr").length).toBe(3);
+        // update data
+        const additionalJob = { ...jobs[0], id: 3 };
+        wrapper.setProps({ jobs: [...jobs, additionalJob] });
+        await localVue.nextTick();
+        // verify new data is displayed
+        expect(wrapper.find("tbody").findAll("tr").length).toBe(4);
+        // verify first row is still expanded
+        expect(wrapper.vm.toggledItems["1"]).toBeTruthy();
+        expect(wrapper.find(".expanded").exists()).toBeTruthy();
+    });
+});
diff --git a/client/src/components/WorkflowInvocationState/JobStep.vue b/client/src/components/WorkflowInvocationState/JobStep.vue
index 459d3d2108c..f01ef24f404 100644
--- a/client/src/components/WorkflowInvocationState/JobStep.vue
+++ b/client/src/components/WorkflowInvocationState/JobStep.vue
@@ -1,13 +1,6 @@
 <template>
     <b-card v-if="jobs">
-        <b-table
-            small
-            caption-top
-            :items="jobs"
-            :fields="fields"
-            v-if="jobs"
-            @row-clicked="(item) => $set(item, '_showDetails', !item._showDetails)"
-        >
+        <b-table small caption-top :items="jobsProvider" :fields="fields" primary-key="id" @row-clicked="toggleDetails">
             <template v-slot:row-details="row">
                 <job-provider
                     :id="row.item.id"
@@ -53,6 +46,31 @@ export default {
     props: {
         jobs: { type: Array, required: true },
     },
+    methods: {
+        jobsProvider(ctx, callback) {
+            // It may seem unnecessary to use a provider here, since the jobs prop
+            // is being updated externally. However we need to keep track of the
+            // _showDetails attribute which determines whether the row is shown as expanded
+            this.$watch(
+                "jobs",
+                function () {
+                    // update new jobs array with current state
+                    const toggledJobs = this.jobs.map((e) => {
+                        return { ...e, _showDetails: !!this.toggledItems[e.id] };
+                    });
+                    callback(toggledJobs);
+                },
+                { immediate: true }
+            );
+            return null;
+        },
+        toggleDetails(item) {
+            // toggle item
+            item._showDetails = !item._showDetails;
+            // update state
+            this.toggledItems[item.id] = item._showDetails;
+        },
+    },
     data() {
         return {
             fields: [
@@ -60,6 +78,7 @@ export default {
                 { key: "update_time", label: "Updated", sortable: true },
                 { key: "create_time", label: "Created", sortable: true },
             ],
+            toggledItems: {},
         };
     },
 };
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationDetails.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationDetails.vue
index 2d8503973e1..a236a5fed03 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationDetails.vue
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationDetails.vue
@@ -1,22 +1,26 @@
 <template>
     <div v-if="invocation">
         <div v-if="Object.keys(invocation.input_step_parameters).length">
-            <details
+            <details class="invocation-parameters-details"
                 ><summary><b>Parameters</b></summary>
                 <parameter-step :parameters="Object.values(invocation.input_step_parameters)" />
             </details>
         </div>
         <div v-if="Object.keys(invocation.inputs).length">
-            <details
+            <details class="invocation-inputs-details"
                 ><summary><b>Inputs</b></summary>
-                <div v-for="(input, key) in invocation.inputs" :key="input.id">
+                <div
+                    v-for="(input, key) in invocation.inputs"
+                    :key="input.id"
+                    :data-label="dataInputStepLabel(key, input)"
+                >
                     <b>{{ dataInputStepLabel(key, input) }}</b>
                     <workflow-invocation-data-contents :data_item="input" />
                 </div>
             </details>
         </div>
         <div v-if="Object.keys(invocation.outputs).length">
-            <details
+            <details class="invocation-outputs-details"
                 ><summary><b>Outputs</b></summary>
                 <div v-for="(output, key) in invocation.outputs" :key="output.id">
                     <b>{{ key }}:</b>
@@ -25,7 +29,7 @@
             </details>
         </div>
         <div v-if="Object.keys(invocation.output_collections).length">
-            <details
+            <details class="invocation-output-collections-details"
                 ><summary><b>Output Collections</b></summary>
                 <div v-for="(output, key) in invocation.output_collections" :key="output.id">
                     <b>{{ key }}:</b>
@@ -34,7 +38,7 @@
             </details>
         </div>
         <div v-if="workflow">
-            <details v-if="workflow"
+            <details v-if="workflow" class="invocation-steps-details"
                 ><summary><b>Steps</b></summary>
                 <workflow-invocation-step
                     v-for="step in Object.values(workflow.steps)"
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.js b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.js
index 503dad6c25d..b0132f42033 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.js
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.js
@@ -1,5 +1,6 @@
 import WorkflowInvocationState from "./WorkflowInvocationState";
 import { shallowMount } from "@vue/test-utils";
+import { getLocalVue } from "jest/helpers";
 import Vuex from "vuex";
 import invocationData from "../Workflow/test/json/invocation.json";
 
@@ -11,6 +12,8 @@ const invocationJobsSummaryById = {
 };
 jest.mock("../History/caching");
 
+const localVue = getLocalVue();
+
 describe("WorkflowInvocationState.vue with terminal invocation", () => {
     let wrapper;
     let propsData;
@@ -25,6 +28,7 @@ describe("WorkflowInvocationState.vue with terminal invocation", () => {
                 invocation: () => invocationData,
                 getInvocationJobsSummaryById: () => () => invocationJobsSummaryById,
             },
+            localVue,
         });
     });
 
@@ -33,13 +37,13 @@ describe("WorkflowInvocationState.vue with terminal invocation", () => {
     });
 
     it("displays report links", async () => {
-        expect(wrapper.find("#invocation-pdf-link").exists()).toBeTruthy();
-        expect(wrapper.find("#invocation-link").exists()).toBeTruthy();
-        expect(wrapper.find("#bco-json").exists()).toBeTruthy();
+        expect(wrapper.find(".invocation-pdf-link").exists()).toBeTruthy();
+        expect(wrapper.find(".invocation-report-link").exists()).toBeTruthy();
+        expect(wrapper.find(".bco-json").exists()).toBeTruthy();
     });
 
     it("doesn't show cancel invocation button", async () => {
-        expect(wrapper.find("#cancel-workflow-scheduling").exists()).toBeFalsy();
+        expect(wrapper.find(".cancel-workflow-scheduling").exists()).toBeFalsy();
     });
 });
 
@@ -67,6 +71,7 @@ describe("WorkflowInvocationState.vue with no invocation", () => {
                 invocation: () => null,
                 getInvocationJobsSummaryById: () => () => invocationJobsSummaryById,
             },
+            localVue,
         });
     });
 
@@ -75,12 +80,12 @@ describe("WorkflowInvocationState.vue with no invocation", () => {
     });
 
     it("does not display report links", async () => {
-        expect(wrapper.find("#invocation-pdf-link").exists()).toBeFalsy();
-        expect(wrapper.find("#invocation-link").exists()).toBeFalsy();
-        expect(wrapper.find("#bco-json").exists()).toBeFalsy();
+        expect(wrapper.find(".invocation-pdf-link").exists()).toBeFalsy();
+        expect(wrapper.find(".invocation-report-link").exists()).toBeFalsy();
+        expect(wrapper.find(".bco-json").exists()).toBeFalsy();
     });
 
     it("shows cancel invocation button", async () => {
-        expect(wrapper.find("#cancel-workflow-scheduling").exists()).toBeTruthy();
+        expect(wrapper.find(".cancel-workflow-scheduling").exists()).toBeTruthy();
     });
 });
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
index aa5c940c09d..2c759605426 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
@@ -1,13 +1,12 @@
 <template>
-    <div class="mb-3">
+    <div class="mb-3 workflow-invocation-state-component">
         <div v-if="invocationAndJobTerminal">
             <span>
-                <a id="invocation-link" :href="invocationLink"
-                    ><b>View Report {{ index + 1 }}</b></a
+                <a class="invocation-report-link" :href="invocationLink"
+                    ><b>View Report {{ indexStr }}</b></a
                 >
                 <a
-                    id="invocation-pdf-link"
-                    class="fa fa-print ml-1"
+                    class="fa fa-print ml-1 invocation-pdf-link"
                     :href="invocationPdfLink"
                     v-b-tooltip
                     title="Download PDF"
@@ -16,26 +15,27 @@
         </div>
         <div v-else>
             <span class="fa fa-spinner fa-spin" />
-            <span>Invocation {{ index + 1 }}...</span>
+            <span>Invocation {{ indexStr }}...</span>
             <span
-                id="cancel-workflow-scheduling"
+                class="fa fa-times cancel-workflow-scheduling"
                 v-if="!invocationSchedulingTerminal"
                 v-b-tooltip.hover
                 title="Cancel scheduling of workflow invocation"
-                class="fa fa-times"
                 @click="cancelWorkflowScheduling"
             ></span>
         </div>
-        <progress-bar v-if="!stepCount" note="Loading step state summary..." :loading="true" />
+        <progress-bar v-if="!stepCount" note="Loading step state summary..." :loading="true" class="steps-progress" />
         <progress-bar
             v-else-if="invocationState == 'cancelled'"
             note="Invocation scheduling cancelled - expected jobs and outputs may not be generated."
             :error-count="1"
+            class="steps-progress"
         />
         <progress-bar
             v-else-if="invocationState == 'failed'"
             note="Invocation scheduling failed - Galaxy administrator may have additional details in logs."
             :error-count="1"
+            class="steps-progress"
         />
         <progress-bar
             v-else
@@ -43,6 +43,7 @@
             :total="stepCount"
             :ok-count="stepStates.scheduled"
             :loading="!invocationSchedulingTerminal"
+            class="steps-progress"
         />
         <progress-bar
             :note="jobStatesStr"
@@ -52,9 +53,10 @@
             :new-count="newCount"
             :error-count="errorCount"
             :loading="!invocationAndJobTerminal"
+            class="jobs-progress"
         />
         <span v-if="invocationAndJobTerminal">
-            <a id="bco-json" :href="bcoJSON"><b>Download BioCompute Object</b></a>
+            <a class="bco-json" :href="bcoJSON"><b>Download BioCompute Object</b></a>
         </span>
         <workflow-invocation-details
             v-if="invocation"
@@ -89,7 +91,7 @@ export default {
         },
         index: {
             type: Number,
-            default: 0,
+            optional: true,
         },
     },
     data() {
@@ -104,6 +106,13 @@ export default {
     },
     computed: {
         ...mapGetters(["getInvocationById", "getInvocationJobsSummaryById"]),
+        indexStr() {
+            if (this.index == null) {
+                return "";
+            } else {
+                return `${this.index + 1}`;
+            }
+        },
         invocation: function () {
             return this.getInvocationById(this.invocationId);
         },
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationStep.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationStep.vue
index c1ce5cfea39..6b5793bf92d 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationStep.vue
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationStep.vue
@@ -1,10 +1,10 @@
 <template>
-    <div class="d-flex">
+    <div class="d-flex" :data-step="workflowStep.id">
         <div class="ui-portlet-section" style="width: 100%;">
             <div class="portlet-header portlet-title portlet-operations" v-on:click="toggleStep">
                 <i :class="'portlet-title-icon fa mr-1 ' + stepIcon"></i>
                 <span class="portlet-title-text">
-                    <u>{{ stepLabel }}</u>
+                    <u class="step-title">{{ stepLabel }}</u>
                 </span>
             </div>
             <div class="portlet-content" v-if="expanded">
@@ -16,14 +16,18 @@
                     <div style="min-width: 1;">
                         <loading-span v-if="loading" :message="`Loading invocation step details`"> </loading-span>
                         <div v-else>
-                            <details v-if="Object.values(stepDetails.outputs).length > 0"
+                            <details
+                                v-if="Object.values(stepDetails.outputs).length > 0"
+                                class="invocation-step-output-details"
                                 ><summary><b>Output Datasets</b></summary>
                                 <div v-for="(value, name) in stepDetails.outputs" :key="value.id">
                                     <b>{{ name }}</b>
                                     <workflow-invocation-data-contents :data_item="value" />
                                 </div>
                             </details>
-                            <details v-if="Object.values(stepDetails.output_collections).length > 0"
+                            <details
+                                v-if="Object.values(stepDetails.output_collections).length > 0"
+                                class="invocation-step-output-collection-details"
                                 ><summary><b>Output Dataset Collections</b></summary>
                                 <div v-for="(value, name) in stepDetails.output_collections" :key="value.id">
                                     <b>{{ name }}</b>
@@ -31,7 +35,7 @@
                                 </div>
                             </details>
                             <div class="portlet-body" style="width: 100%; overflow-x: auto;">
-                                <details v-if="workflowStepType == 'tool'">
+                                <details v-if="workflowStepType == 'tool'" class="invocation-step-job-details">
                                     <summary><b>Jobs</b></summary>
                                     <job-step :jobs="stepDetails.jobs" />
                                 </details>
diff --git a/client/src/components/WorkflowInvocationState/test/json/jobs.json b/client/src/components/WorkflowInvocationState/test/json/jobs.json
new file mode 100644
index 00000000000..daacfc2e5b5
--- /dev/null
+++ b/client/src/components/WorkflowInvocationState/test/json/jobs.json
@@ -0,0 +1,24 @@
+[
+    {
+        "model_class": "Job",
+        "id": "1",
+        "state": "new",
+        "exit_code": 0,
+        "update_time": "2021-01-15T10:38:36.015269",
+        "create_time": "2021-01-15T10:38:21.462106",
+        "galaxy_version": "21.01",
+        "tool_id": "cat_data_and_sleep",
+        "history_id": "b6aaf20167e56df2"
+    },
+    {
+        "model_class": "Job",
+        "id": "2",
+        "state": "new",
+        "exit_code": 0,
+        "update_time": "2021-01-15T10:38:36.015269",
+        "create_time": "2021-01-15T10:38:21.462106",
+        "galaxy_version": "21.01",
+        "tool_id": "cat_data_and_sleep",
+        "history_id": "b6aaf20167e56df2"
+    }
+]
\ No newline at end of file
diff --git a/client/src/components/admin/BaseList.test.js b/client/src/components/admin/BaseList.test.js
index bf1a7344e01..4b1c7df8019 100644
--- a/client/src/components/admin/BaseList.test.js
+++ b/client/src/components/admin/BaseList.test.js
@@ -1,6 +1,9 @@
 import { mount } from "@vue/test-utils";
+import { getLocalVue } from "jest/helpers";
 import BaseList from "./BaseList";
 
+const localVue = getLocalVue();
+
 describe("Categories", () => {
     const getter = async () => {
         return {
@@ -30,6 +33,7 @@ describe("Categories", () => {
                 getter: getter,
                 setter: setter,
             },
+            localVue,
         });
         await wrapper.vm.$nextTick();
         expect(wrapper.find(".card-header").text()).toContain("There are 2");
diff --git a/client/src/entry/analysis/index.js b/client/src/entry/analysis/index.js
index aa54ee8244c..8898b967012 100644
--- a/client/src/entry/analysis/index.js
+++ b/client/src/entry/analysis/index.js
@@ -6,14 +6,14 @@ import Page from "layout/page";
 
 // Vue adapter emulates current features of backbone history panel
 import { HistoryPanelProxy } from "components/History";
+import { isBetaHistoryOpen } from "components/History/adapters/betaToggle";
 
 addInitialization((Galaxy, { options = {} }) => {
     console.log("Analysis custom page setup");
 
     // Handle beta history panel
     // Need to mock Galaxy.currHistoryPanel
-    const useBeta = sessionStorage.getItem("useBetaHistory");
-    const HistoryPanel = useBeta ? HistoryPanelProxy : MvcHistoryPanel;
+    const HistoryPanel = isBetaHistoryOpen() ? HistoryPanelProxy : MvcHistoryPanel;
 
     const pageOptions = Object.assign({}, options, {
         config: Object.assign({}, options.config, {
diff --git a/client/src/mvc/history/options-menu.js b/client/src/mvc/history/options-menu.js
index 3556ca5b8db..ff3d57f11c6 100644
--- a/client/src/mvc/history/options-menu.js
+++ b/client/src/mvc/history/options-menu.js
@@ -6,6 +6,7 @@ import _l from "utils/localization";
 import PopupMenu from "mvc/ui/popup-menu";
 import historyCopyDialog from "mvc/history/copy-dialog";
 import Webhooks from "mvc/webhooks";
+import { switchToBetaHistoryPanel } from "../../components/History/adapters/betaToggle";
 
 // ============================================================================
 var menu = [
@@ -165,8 +166,7 @@ var menu = [
         html: _l("Use Beta History Panel"),
         anon: false,
         func: function () {
-            sessionStorage.setItem("useBetaHistory", 1);
-            window.location.reload(false);
+            switchToBetaHistoryPanel();
         },
     },
 ];
diff --git a/client/src/store/syncVuextoGalaxy.js b/client/src/store/syncVuextoGalaxy.js
index 797a868b526..f2f99d1cc98 100644
--- a/client/src/store/syncVuextoGalaxy.js
+++ b/client/src/store/syncVuextoGalaxy.js
@@ -13,6 +13,7 @@ import { waitForInit } from "utils/observable/waitForInit";
 import { syncUserToGalaxy } from "store/userStore/syncUserToGalaxy";
 import { syncConfigToGalaxy } from "store/configStore/syncConfigToGalaxy";
 import { syncCurrentHistoryToGalaxy } from "components/History/model/syncCurrentHistoryToGalaxy";
+import { isBetaHistoryOpen } from "components/History/adapters/betaToggle";
 
 export const syncVuextoGalaxy = (store) => {
     const globalGalaxy$ = defer(() => {
@@ -25,6 +26,8 @@ export const syncVuextoGalaxy = (store) => {
     // configuration
     syncConfigToGalaxy(globalGalaxy$, store);
 
-    // Current History object (from legacy history panel)
-    syncCurrentHistoryToGalaxy(globalGalaxy$, store);
+    // Update Vuex with legacy galaxy history changes only when beta panel is closed.
+    if (!isBetaHistoryOpen()) {
+        syncCurrentHistoryToGalaxy(globalGalaxy$, store);
+    }
 };
diff --git a/client/src/utils/observable/decay.js b/client/src/utils/observable/decay.js
index 5d297b00d78..099d90b1512 100644
--- a/client/src/utils/observable/decay.js
+++ b/client/src/utils/observable/decay.js
@@ -1,14 +1,9 @@
 // Stateful delay gets longer with each repeated call
-import { pipe, of } from "rxjs";
+import { of } from "rxjs";
 import { mergeMap, delay } from "rxjs/operators";
 
-// prettier-ignore
 export const decay = (cfg = {}) => {
-    const {
-        initialInterval,
-        maxInterval = 60 * 1000,
-        lambda = 0.25
-    } = cfg;
+    const { initialInterval, maxInterval = 60 * 1000, lambda = 0.25 } = cfg;
 
     if (undefined === initialInterval) {
         throw new Error("provide an initialInterval to decay");
@@ -16,13 +11,10 @@ export const decay = (cfg = {}) => {
 
     let counter = 0;
 
-    return pipe(
-        mergeMap(val => {
-            let waitTime = Math.floor(initialInterval * Math.exp(lambda * counter++));
-            waitTime = Math.max(waitTime, initialInterval);
-            waitTime = Math.min(waitTime, maxInterval);
-            // console.log("decay time", waitTime);
-            return of(val).pipe(delay(waitTime))
-        })
-    );
-}
+    return mergeMap((val) => {
+        let waitTime = Math.floor(initialInterval * Math.exp(lambda * counter++));
+        waitTime = Math.max(waitTime, initialInterval);
+        waitTime = Math.min(waitTime, maxInterval);
+        return of(val).pipe(delay(waitTime));
+    });
+};
diff --git a/client/src/utils/observable/monitorXHR.js b/client/src/utils/observable/monitorXHR.js
new file mode 100644
index 00000000000..7c9ea274c45
--- /dev/null
+++ b/client/src/utils/observable/monitorXHR.js
@@ -0,0 +1,62 @@
+import { defer, Subject } from "rxjs";
+import { filter, finalize, share } from "rxjs/operators";
+
+// global XHR request feed, emits every time xhr fires
+const xhr$ = defer(() => {
+    const request$ = new Subject();
+
+    // patch
+    const originalOpen = XMLHttpRequest.prototype.open;
+    XMLHttpRequest.prototype.open = function (method, url) {
+        request$.next({ method, url });
+        return originalOpen.apply(this, arguments);
+    };
+
+    return request$.pipe(
+        // un-patch after all subscribers have left
+        finalize(() => {
+            XMLHttpRequest.prototype.open = originalOpen;
+        })
+    );
+}).pipe(share());
+
+/**
+ * Watch outgoing ajax calls for any of the indicated methods, filter to any of the provided route regexes
+ *
+ * @param {Object} cfg  Configure methods and routes to monitor
+ * @return {Observable} Observable that emits every time a matching outgoing request happens
+ */
+export const monitorXHR = (cfg = {}) => {
+    return xhr$.pipe(filter(matchRoutes(cfg)));
+};
+
+// matches incoming method/url against config
+export const matchRoutes = (cfg = {}) => ({ method, url }) => {
+    const { methods = ["GET", "POST", "PUT", "DELETE"], routes = [], exclude = [] } = cfg;
+
+    // match fun compares route def to current url
+    const matcher = matchUrlToRoute(url);
+
+    if (!methods.includes(method)) {
+        return false;
+    }
+    if (exclude.length && exclude.find(matcher)) {
+        return false;
+    }
+    if (routes.length) {
+        const routeMatch = routes.find(matcher);
+        return !!routeMatch;
+    }
+    return false;
+};
+
+const matchUrlToRoute = (url) => (rt) => {
+    let result = false;
+    if (rt instanceof RegExp) {
+        result = url.match(rt);
+    } else {
+        // simple matcher
+        result = url.includes(rt);
+    }
+    return result;
+};
diff --git a/client/src/utils/observable/monitorXHR.test.js b/client/src/utils/observable/monitorXHR.test.js
new file mode 100644
index 00000000000..fd8274e1240
--- /dev/null
+++ b/client/src/utils/observable/monitorXHR.test.js
@@ -0,0 +1,87 @@
+import { matchRoutes, monitorXHR } from "./monitorXHR";
+
+describe("monitorXhr", () => {
+    describe("monitorXHR", () => {
+        it("should import", () => {
+            expect(monitorXHR).toBeInstanceOf(Function);
+        });
+    });
+
+    // request matcher, XHR object emits objects of form { method, url } which get matched to a set
+    // of routes of interest
+
+    describe("matchRoutes", () => {
+        let matcher;
+
+        beforeEach(() => {
+            matcher = matchRoutes({ routes: ["api/foo"] });
+        });
+
+        it("matcher should be a function", () => {
+            expect(matcher).toBeInstanceOf(Function);
+        });
+
+        it("should recognize an exact route", () => {
+            const testPacket = { method: "POST", url: "api/foo" };
+            expect(matcher(testPacket)).toBe(true);
+        });
+
+        it("should recognize a subroute", () => {
+            const testPacket = { method: "POST", url: "api/foo/123" };
+            expect(matcher(testPacket)).toBe(true);
+        });
+
+        it("should recognize a subroute with some query params", () => {
+            const testPacket = { method: "POST", url: "api/foo/123?foo=bar" };
+            expect(matcher(testPacket)).toBe(true);
+        });
+
+        it("should not match unwatched urls", () => {
+            const testPacket = { method: "POST", url: "api/notinthelist" };
+            expect(matcher(testPacket)).toBe(false);
+        });
+
+        it("should not match unwatched methods", () => {
+            const testPacket = { method: "GET", url: "api/notinthelist" };
+            expect(matcher(testPacket)).toBe(false);
+        });
+    });
+
+    describe("matchRoutes: general regex", () => {
+        it("should match foo or bar", () => {
+            const matcher = matchRoutes({
+                routes: [/api\/(foo|bar)/gi],
+            });
+
+            const fooTest = { method: "POST", url: "api/foo/asdfasdf" };
+            expect(matcher(fooTest)).toBe(true);
+            const barTest = { method: "POST", url: "api/bar/asdfasdf" };
+            expect(matcher(barTest)).toBe(true);
+            const blechTest = { method: "POST", url: "api/blech/asdfasdf" };
+            expect(matcher(blechTest)).toBe(false);
+        });
+    });
+
+    describe("matchRoutes: excludes", () => {
+        const matcher = matchRoutes({
+            routes: ["api/histories"],
+            exclude: ["api/histories/ABC"],
+        });
+
+        // should exclude urls containing the restricted ID
+        it("should exclude history routes with id=ABC", () => {
+            const testRoute = { method: "POST", url: "api/histories/ABC" };
+            expect(matcher(testRoute)).toBe(false);
+            const testRouteWithParams = { method: "POST", url: "api/histories/ABC?hoohah=123" };
+            expect(matcher(testRouteWithParams)).toBe(false);
+        });
+
+        // should pass similar routes with different ids
+        it("should match other history routes", () => {
+            const testRoute = { method: "POST", url: "api/histories/DEF" };
+            expect(matcher(testRoute)).toBe(true);
+            const testRouteWithParams = { method: "POST", url: "api/histories/DEF?foo=sadfasd" };
+            expect(matcher(testRouteWithParams)).toBe(true);
+        });
+    });
+});
diff --git a/config/plugins/tours/core.galaxy_ui.yaml b/config/plugins/tours/core.galaxy_ui.yaml
index e981beb72fe..dfc9e56f418 100644
--- a/config/plugins/tours/core.galaxy_ui.yaml
+++ b/config/plugins/tours/core.galaxy_ui.yaml
@@ -1,4 +1,3 @@
-id: galaxy_ui
 name: Galaxy UI
 description: A gentle introduction to the Galaxy User Interface
 title_default: "Welcome to Galaxy"
diff --git a/config/plugins/tours/core.scratchbook.yaml b/config/plugins/tours/core.scratchbook.yaml
index 6b878772257..b3111a98088 100644
--- a/config/plugins/tours/core.scratchbook.yaml
+++ b/config/plugins/tours/core.scratchbook.yaml
@@ -1,6 +1,6 @@
 name: Scratchbook - Introduction
-title_default: "Scratchbook Introduction"
 description: "An introduction on how to display multiple datasets and visualizations next to each other."
+title_default: "Scratchbook Introduction"
 tags:
   - "core"
   - "UI"
diff --git a/config/plugins/visualizations/nora/config/nora.xml b/config/plugins/visualizations/nora/config/nora.xml
new file mode 100644
index 00000000000..f84da5b5056
--- /dev/null
+++ b/config/plugins/visualizations/nora/config/nora.xml
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
+<visualization name="Nora" embeddable="true">
+    <description>NORA's viewer. A medical image viewer and annotation tool.</description>
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test test_attr="ext" result_type="datatype">nrrd</test>
+            <test test_attr="ext" result_type="datatype">stl</test>
+            <test test_attr="ext" result_type="datatype">nii1</test>
+            <test test_attr="ext" result_type="datatype">nii1.gz</test>
+            <test test_attr="ext" result_type="datatype">gii</test>
+            <test test_attr="ext" result_type="datatype">gii.gz</test>
+            <test test_attr="ext" result_type="datatype">png</test>
+            <test test_attr="ext" result_type="datatype">jpg</test>
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
+    </data_sources>
+    <params>
+        <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
+    </params>
+    <entry_point entry_point_type="chart" src="dist/script.js"/>
+    <specs>
+        <tag>svg</tag>
+        <use_panels>optional</use_panels>
+    </specs>
+</visualization>
diff --git a/config/plugins/visualizations/nora/package.json b/config/plugins/visualizations/nora/package.json
new file mode 100644
index 00000000000..04adc1bd2ff
--- /dev/null
+++ b/config/plugins/visualizations/nora/package.json
@@ -0,0 +1,18 @@
+{
+  "name": "nora",
+  "license": "MIT",
+  "description": "NORA Medical Image Viewer",
+  "version": "1.1.0",
+  "keywords": [
+    "galaxy",
+    "visualization"
+  ],
+  "main": "index.js",
+  "dependencies": {
+    "@galaxyproject/nora": "^1.1.0",
+    "cpy-cli": "^3.1.1"
+  },
+  "scripts": {
+    "build": "cpy --cwd='node_modules/@galaxyproject/nora/static/dist' --parents './' '../../../../../static/dist'"
+  }
+}
diff --git a/config/plugins/visualizations/nora/static/logo.png b/config/plugins/visualizations/nora/static/logo.png
new file mode 100644
index 00000000000..987efb0a6d2
Binary files /dev/null and b/config/plugins/visualizations/nora/static/logo.png differ
diff --git a/config/plugins/webhooks/demo/tour_generator/__init__.py b/config/plugins/webhooks/demo/tour_generator/__init__.py
index f61ddaaf323..8e4d77e5bfc 100644
--- a/config/plugins/webhooks/demo/tour_generator/__init__.py
+++ b/config/plugins/webhooks/demo/tour_generator/__init__.py
@@ -44,7 +44,7 @@ class TourGenerator:
         }
 
         # Conditional datasets
-        for name, value in self._test.inputs.items():
+        for name in self._test.inputs.keys():
             if '|' in name:
                 input_name = name.split('|')[1]
                 if input_name in self._data_inputs.keys():
@@ -119,8 +119,8 @@ class TourGenerator:
 
         steps = [{
             'title': tour_name,
-            'content': 'This short tour will guide you through the <b>' +
-                       self._tool.name + '</b> tool.',
+            'content': 'This short tour will guide you through the <b>'
+                       + self._tool.name + '</b> tool.',
             'orphan': True
         }]
 
diff --git a/contrib/nagios/check_galaxy.py b/contrib/nagios/check_galaxy.py
index 6a5a9f6a138..753f671bfe3 100755
--- a/contrib/nagios/check_galaxy.py
+++ b/contrib/nagios/check_galaxy.py
@@ -138,9 +138,9 @@ class Browser:
 
     def runtool(self):
         path = '/api/tools'
-        data = {'tool_id' : self.tool,
-                'history_id' : self.history_id,
-                'inputs' : {'echo' : self.handler}}
+        data = {'tool_id': self.tool,
+                'history_id': self.history_id,
+                'inputs': {'echo': self.handler}}
         res = self.req(path, data=data)
         dprint(json.loads(res.read()))
 
@@ -158,7 +158,7 @@ class Browser:
         return self._history_id
 
     def create_history(self):
-        res = self.req('/api/histories', data={'name' : handler})
+        res = self.req('/api/histories', data={'name': handler})
         self._history_id = json.loads(res.read())['id']
 
     @property
diff --git a/doc/Makefile b/doc/Makefile
index 66e184a4e1b..de5921267ad 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -2,7 +2,7 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
+SPHINXOPTS    ?=
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = build
@@ -15,7 +15,7 @@ ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) sou
 # the i18n builder cannot share the environment and doctrees with the others
 I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
 
-GENERATED_RST = source/api/api.rst source/api/ts_api.rst source/dev/schema.md source/admin/config_logging_default_yaml.rst
+GENERATED_RST = source/dev/schema.md source/admin/config_logging_default_yaml.rst
 
 .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext updaterst
 
@@ -48,18 +48,6 @@ source/dev/run_tests_help.txt:
 source/dev/schema.md: parse_gx_xsd.py schema_template.md ../lib/galaxy/tool_util/xsd/galaxy.xsd ## Build Github-flavored Markdown from Galaxy Tool XSD (expects lxml in environment)
 	python parse_gx_xsd.py schema_template.md ../lib/galaxy/tool_util/xsd/galaxy.xsd > $@
 
-source/api/api.rst: source/lib/galaxy.webapps.galaxy.api.rst
-	printf "Galaxy API\n==========\n" > $@
-	tail -n +11 source/lib/galaxy.webapps.galaxy.api.rst >> $@
-	sed -i.bak -e 's/^galaxy\\\.webapps\\\.galaxy\\\.api\\\.//' $@
-	rm -f $@.bak
-
-source/api/ts_api.rst: source/lib/tool_shed.webapp.api.rst
-	printf "Tool Shed API\n=============\n" > $@
-	tail -n +11 source/lib/tool_shed.webapp.api.rst >> $@
-	sed -i.bak -e 's/^tool_shed\\\.webapp\\\.api\\\.//' $@
-	rm -f $@.bak
-
 source/admin/config_logging_default_yaml.rst: ../lib/galaxy/config/__init__.py
 	printf '.. code-block:: yaml\n\n' > $@
 	printf '    galaxy:\n' >> $@
diff --git a/doc/source/admin/cluster.md b/doc/source/admin/cluster.md
index e61bf49e451..7f9060a9cbe 100644
--- a/doc/source/admin/cluster.md
+++ b/doc/source/admin/cluster.md
@@ -2,7 +2,7 @@
 
 Galaxy is designed to run jobs on your local system by default, but it can be configured to run jobs on a cluster.  The front-end Galaxy application runs on a single server as usual, but tools are run on cluster nodes instead.
 
-A [general reference for the job configuration file](jobs.md) is also available.
+A [general reference for the job configuration file](./jobs.md) is also available.
 
 ## Distributed Resources Managers
 
@@ -70,7 +70,7 @@ You may also find that attribute caching in your filesystem causes problems with
 
 ## Runner Configuration
 
-**This documentation covers configuration of the various runner plugins, not how to distribute jobs to the various plugins.** Consult the [job configuration file documentation](jobs.md) for full details on the correct syntax, and for instructions on how to configure tools to actually use the runners explained below.
+**This documentation covers configuration of the various runner plugins, not how to distribute jobs to the various plugins.** Consult the [job configuration file documentation](./jobs.md) for full details on the correct syntax, and for instructions on how to configure tools to actually use the runners explained below.
 
 ### Local
 
diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 4d387d9e615..6469d27017f 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -677,8 +677,8 @@
 :Description:
     involucro is a tool used to build Docker or Singularity containers
     for tools from Conda dependencies referenced in tools as
-    `requirement`s. The following path is the location of involucro on
-    the Galaxy host. This is ignored if the relevant container
+    `requirement` s. The following path is the location of involucro
+    on the Galaxy host. This is ignored if the relevant container
     resolver isn't enabled, and will install on demand unless
     involucro_auto_init is set to false.
     The value of this option will be resolved with respect to
@@ -1049,6 +1049,21 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``enable_tool_document_cache``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Set this to false to disable the tool document cache. This cache
+    stores expanded xml strings. Disabling the tool cache results in
+    slower startup times. The tool cache is backed by sqlite database,
+    which cannot be stored on certain network disks. The cache
+    location is configurable using the ``tool_cache_data_dir``
+    setting, but can be disabled completely here.
+:Default: ``true``
+:Type: bool
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~
 ``tool_cache_data_dir``
 ~~~~~~~~~~~~~~~~~~~~~~~
@@ -3709,7 +3724,7 @@
     you can separate Galaxy into multiple processes.  There are more
     than one way to do this, and they are explained in detail in the
     documentation:
-      https://docs.galaxyproject.org/en/master/admin/scaling.html
+    https://docs.galaxyproject.org/en/master/admin/scaling.html
     By default, Galaxy manages and executes jobs from within a single
     process and notifies itself of new jobs via in-memory queues.
     Jobs are run locally on the system on which Galaxy is started.
@@ -4085,7 +4100,7 @@
 :Description:
     Prologue Markdown/HTML to apply to markdown exports to PDF.
     Allowing branded headers.
-:Default: ````
+:Default: ``""``
 :Type: str
 
 
@@ -4096,7 +4111,7 @@
 :Description:
     Prologue Markdown/HTML to apply to markdown exports to PDF.
     Allowing branded footers.
-:Default: ````
+:Default: ``""``
 :Type: str
 
 
@@ -4107,7 +4122,7 @@
 :Description:
     Alternative to markdown_export_prologue that applies just to page
     exports.
-:Default: ````
+:Default: ``""``
 :Type: str
 
 
@@ -4118,7 +4133,7 @@
 :Description:
     Alternative to markdown_export_prologue that applies just to
     invocation report exports.
-:Default: ````
+:Default: ``""``
 :Type: str
 
 
@@ -4129,7 +4144,7 @@
 :Description:
     Alternative to markdown_export_epilogue that applies just to page
     exports.
-:Default: ````
+:Default: ``""``
 :Type: str
 
 
@@ -4140,7 +4155,7 @@
 :Description:
     Alternative to markdown_export_epilogue that applies just to
     invocation report exports.
-:Default: ````
+:Default: ``""``
 :Type: str
 
 
diff --git a/doc/source/admin/index.rst b/doc/source/admin/index.rst
index 690774a1e66..79e79215658 100644
--- a/doc/source/admin/index.rst
+++ b/doc/source/admin/index.rst
@@ -18,6 +18,7 @@ This documentation is in the midst of being ported and unified based on resource
    jobs
    authentication
    tool_panel
+   mq
    dependency_resolvers
    conda_faq
    reports
diff --git a/doc/source/admin/mq.md b/doc/source/admin/mq.md
index b4167185898..07936d1ab69 100644
--- a/doc/source/admin/mq.md
+++ b/doc/source/admin/mq.md
@@ -1,3 +1,4 @@
+
 # Message queue
 
 Galaxy uses a message queue internally for communicating between processes. 
diff --git a/doc/source/admin/nginx.md b/doc/source/admin/nginx.md
index 95adad98664..917567f6b88 100644
--- a/doc/source/admin/nginx.md
+++ b/doc/source/admin/nginx.md
@@ -399,7 +399,7 @@ these paths need to exposed in the same way.
 
 You may find it useful to require authentication for access to certain paths on your server.  For example, Galaxy can
 run a separate reports app which gives useful information about your Galaxy instance. See the [Reports Configuration
-documentation](reports) and [Peter Briggs' blog post on the
+documentation](./reports) and [Peter Briggs' blog post on the
 subject](http://galacticengineer.blogspot.com/2015/06/exposing-galaxy-reports-via-nginx-in.html) for more.
 
 After successfully following the blog post, Galaxy reports should be available at e.g. `https://galaxy.example.org/reports`.
diff --git a/doc/source/admin/proxy_package_layout.rst b/doc/source/admin/proxy_package_layout.rst
index 7c038adf31f..1cde42234eb 100644
--- a/doc/source/admin/proxy_package_layout.rst
+++ b/doc/source/admin/proxy_package_layout.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 Proxy Package Layouts
 ========================================
 
diff --git a/doc/source/admin/scaling.md b/doc/source/admin/scaling.md
index e50aa6963ec..71f35ef2f9c 100644
--- a/doc/source/admin/scaling.md
+++ b/doc/source/admin/scaling.md
@@ -438,8 +438,8 @@ separated,  to the `job-handlers` farm. For example, 3 handlers are defined like
 
 By default, a job will be handled by whatever mule currently has the lock on the mule message queue. After receiving a
 message, it will release the lock, giving other mules a chance to handle future jobs.  Jobs can be explicitly mapped to
-specific mules as described in the [Job configuration documentation](jobs.md) by using the handler IDs
-`main.job-handlers.N`, where `N` is the mule's position in the farm, starting at 1 and incrementing for each mule in the
+specific mules as described in the [Galaxy Job Configuration](./jobs.md) documentation
+by using the handler IDs `main.job-handlers.N`, where `N` is the mule's position in the farm, starting at 1 and incrementing for each mule in the
 farm (this is not necessarily the mule ID, but it will be if you only define one farm and you add mules to that farm in
 sequential order).  Each worker that you wish to explicitly map jobs to should be defined in the `<handlers>` section
 of `job_conf.xml`. *Do not* define a default handler.
diff --git a/doc/source/admin/special_topics/index.rst b/doc/source/admin/special_topics/index.rst
index f2a33965e2e..a49416a3785 100644
--- a/doc/source/admin/special_topics/index.rst
+++ b/doc/source/admin/special_topics/index.rst
@@ -10,6 +10,7 @@ Special Topics
    interactive_environments
    mulled_containers
    grt
+   gtn
    job_metrics
    webhooks
    performance_tracking
diff --git a/doc/source/api/api.rst b/doc/source/api/api.rst
new file mode 100644
index 00000000000..4bb55ccb9c8
--- /dev/null
+++ b/doc/source/api/api.rst
@@ -0,0 +1,5 @@
+Galaxy API
+==========
+
+For a detailed description of the of Galaxy API controller please see
+the API module :py:mod:`galaxy.webapps.galaxy.api`.
diff --git a/doc/source/api/guidelines.rst b/doc/source/api/guidelines.rst
deleted file mode 100644
index 4260144da2f..00000000000
--- a/doc/source/api/guidelines.rst
+++ /dev/null
@@ -1,70 +0,0 @@
-API Design Guidelines
-=====================
-
-The following section outlines guidelines related to extending and/or modifying
-the Galaxy API. The Galaxy API has grown in an ad-hoc fashion over time by
-many contributors and so clients SHOULD NOT expect the API will conform to
-these guidelines - but developers contributing to the Galaxy API SHOULD follow
-these guidelines.
-
-    - API functionality should include docstring documentation for consumption
-      at docs.galaxyproject.org.
-    - Developers should familiarize themselves with the HTTP status code definitions
-      http://www.w3.org/Protocols/rfc2616/rfc2616-sec10.html. The API responses
-      should properly set the status code according to the result - in particular
-      2XX responses should be used for successful requests, 4XX for various
-      kinds of client errors, and 5XX for the errors on the server side.
-    - If there is an error processing some part of the request (one item in a list
-      for instance), the status code should be set to reflect the error and the
-      partial result may or may not be returned depending on the controller -
-      this behavior should be documented.
-    - API methods should throw a finite number of exceptions 
-      (defined in :mod:`galaxy.exceptions`) and these should subclass 
-      `MessageException` and not paste/wsgi HTTP exceptions. When possible, 
-      the framework itself should be responsible for catching these exceptions, 
-      setting the status code, and building an error response.
-    - Error responses should not consist of plain text strings - they should be
-      dictionaries describing the error and containing the following::
-
-          {
-            "status_code": 400,
-            "err_code": 400007,
-            "err_msg": "Request contained invalid parameter, action could not be completed.",
-            "type": "error",
-            "extra_error_info": "Extra information."
-          }
-
-      Various error conditions (once a format has been chosen and framework to
-      enforce it in place) should be spelled out in this document.
-    - Backward compatibility is important and should be maintained when possible.
-      If changing behavior in a non-backward compatible way please ensure one
-      of the following holds - there is a strong reason to believe no consumers
-      depend on a behavior, the behavior is effectively broken, or the API
-      method being modified has not been part of a tagged dist release.
-
-The following bullet points represent good practices more than guidelines, please
-consider them when modifying the API.
-
-    - Functionality should not be copied and pasted between controllers -
-      consider refactoring functionality into associated classes or short of
-      that into Mixins (http://en.wikipedia.org/wiki/Composition_over_inheritance)
-      or into Managers (:mod:`galaxy.managers`).
-    - API additions are more permanent changes to Galaxy than many other potential
-      changes and so a second opinion on API changes should be sought.
-    - New API functionality should include functional tests. These functional
-      tests should be implemented in Python and placed in
-      `lib/galaxy_test/api`.
-    - Changes to reflect modifications to the API should be pushed upstream to
-      the BioBlend project if possible.
-
-Longer term goals/notes.
-
-    - It would be advantageous to have a clearer separation of anonymous and
-      admin handling functionality.
-    - If at some point in the future, functionality needs to be added that
-      breaks backward compatibility in a significant way to a component used by
-      the community - a "dev" variant of the API will be established and
-      the community should be alerted and given a timeframe for when the old
-      behavior will be replaced with the new behavior.
-    - Consistent standards for range-based requests, batch requests, filtered
-      requests, etc... should be established and documented here.
diff --git a/doc/source/api/quickstart.rst b/doc/source/api/quickstart.rst
index bd517ba461d..d1a251cf7ae 100644
--- a/doc/source/api/quickstart.rst
+++ b/doc/source/api/quickstart.rst
@@ -1,186 +1,6 @@
 Quickstart
 ==========
 
-Log in as your user, navigate to the API Keys page in the User menu, and
-generate a new API key. Make a note of the API key, and then pull up a
-terminal.  Now we'll use the display.py script in your ``galaxy/scripts/api``
-directory for a short example, which assumes your local galaxy server is
-running on the default port 8080::
-
-        % ./display.py my_key http://localhost:8080/api/histories
-        Collection Members
-        ------------------
-        #1: /api/histories/8c49be448cfe29bc
-          name: Unnamed history
-          id: 8c49be448cfe29bc
-        #2: /api/histories/33b43b4e7093c91f
-          name: output test
-          id: 33b43b4e7093c91f
-
-The result is a Collection of the histories of the user specified by the API
-key (you).  To look at the details of a particular history, say #1 above, do
-the following::
-
-        % ./display.py my_key http://localhost:8080/api/histories/8c49be448cfe29bc
-        Member Information
-        ------------------
-        state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0}
-        state: ok
-        contents_url: /api/histories/8c49be448cfe29bc/contents
-        id: 8c49be448cfe29bc
-        name: Unnamed history
-
-This gives detailed information about the specific member in question, in this
-case the History.  To view history contents, do the following::
-
-
-        % ./display.py my_key http://localhost:8080/api/histories/8c49be448cfe29bc/contents
-        Collection Members
-        ------------------
-        #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
-          name: Pasted Entry
-          type: file
-          id: 6f91353f3eb0fa4a
-
-What we have here is another Collection of items containing all of the datasets
-in this particular history.  Finally, to view details of a particular dataset
-in this collection, execute the following::
-
-        % ./display.py my_key http://localhost:8080/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
-        Member Information
-        ------------------
-        misc_blurb: 1 line
-        name: Pasted Entry
-        data_type: txt
-        deleted: False
-        file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat
-        state: ok
-        download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt
-        visible: True
-        genome_build: ?
-        model_class: HistoryDatasetAssociation
-        file_size: 17
-        metadata_data_lines: 1
-        id: 6f91353f3eb0fa4a
-        misc_info: uploaded txt file
-        metadata_dbkey: ?
-
-And now you've successfully used the API to request and select a history,
-browse the contents of that history, and then look at detailed information
-about a particular dataset.
-
-For a more comprehensive Data Library example, set the following options in your
-galaxy.yml as well, and restart galaxy again::
-
-        admin_users: you@example.org
-        library_import_dir: /path/to/some/directory
-
-In the directory you specified for 'library_import_dir', create some
-subdirectories, and put (or symlink) files to import into Galaxy into those
-subdirectories.
-
-In Galaxy, create an account that matches the address you put in 'admin_users',
-then browse to that user's preferences and generate a new API Key.  Copy the
-key to your clipboard and then use these scripts::
-
-        % ./display.py my_key http://localhost:8080/api/libraries
-        Collection Members
-        ------------------
-
-        0 elements in collection
-
-        % ./library_create_library.py my_key http://localhost:8080/api/libraries api_test 'API Test Library'
-        Response
-        --------
-        /api/libraries/f3f73e481f432006
-          name: api_test
-          id: f3f73e481f432006
-
-        % ./display.py my_key http://localhost:8080/api/libraries
-        Collection Members
-        ------------------
-        /api/libraries/f3f73e481f432006
-          name: api_test
-          id: f3f73e481f432006
-
-        % ./display.py my_key http://localhost:8080/api/libraries/f3f73e481f432006
-        Member Information
-        ------------------
-        synopsis: None
-        contents_url: /api/libraries/f3f73e481f432006/contents
-        description: API Test Library
-        name: api_test
-
-        % ./display.py my_key http://localhost:8080/api/libraries/f3f73e481f432006/contents
-        Collection Members
-        ------------------
-        /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
-          name: /
-          type: folder
-          id: 28202595c0d2591f61ddda595d2c3670
-
-        % ./library_create_folder.py my_key http://localhost:8080/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1'
-        Response
-        --------
-        /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
-          name: api_test_folder1
-          id: 28202595c0d2591fa4f9089d2303fd89
-
-        % ./library_upload_from_import_dir.py my_key http://localhost:8080/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19
-        Response
-        --------
-        /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
-          name: 2.bed
-          id: e9ef7fdb2db87d7b
-        /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
-          name: 3.bed
-          id: 3b7f6a31f80a5018
-
-        % ./display.py my_key http://localhost:8080/api/libraries/f3f73e481f432006/contents 
-        Collection Members
-        ------------------
-        /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
-          name: /
-          type: folder
-          id: 28202595c0d2591f61ddda595d2c3670
-        /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
-          name: /api_test_folder1
-          type: folder
-          id: 28202595c0d2591fa4f9089d2303fd89
-        /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
-          name: /api_test_folder1/2.bed
-          type: file
-          id: e9ef7fdb2db87d7b
-        /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
-          name: /api_test_folder1/3.bed
-          type: file
-          id: 3b7f6a31f80a5018
-
-        % ./display.py my_key http://localhost:8080/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
-        Member Information
-        ------------------
-        misc_blurb: 68 regions
-        metadata_endCol: 3
-        data_type: bed
-        metadata_columns: 6
-        metadata_nameCol: 4
-        uploaded_by: nate@...
-        metadata_strandCol: 6
-        name: 2.bed
-        genome_build: hg19
-        metadata_comment_lines: None
-        metadata_startCol: 2
-        metadata_chromCol: 1
-        file_size: 4272
-        metadata_data_lines: 68
-        message:
-        metadata_dbkey: hg19
-        misc_info: uploaded bed file
-        date_uploaded: 2010-06-22T17:01:51.266119
-        metadata_column_types: str, int, int, str, int, str
-
-Other parameters are valid when uploading, they are the same parameters as are
-used in the web form, like 'link_data_only' and etc.
-
-The request and response format should be considered alpha and are subject to change.
-
+The Galaxy Training Network material has a tutorial designed
+to teach using the Galaxy API at
+https://training.galaxyproject.org/training-material/topics/dev/tutorials/bioblend-api/slides.html.
diff --git a/doc/source/api/ts_api.rst b/doc/source/api/ts_api.rst
new file mode 100644
index 00000000000..55ca735002f
--- /dev/null
+++ b/doc/source/api/ts_api.rst
@@ -0,0 +1,5 @@
+ToolShed API
+=============
+
+For a detailed description of the of Tool Shed API controller please see
+the API module :py:mod:`tool_shed.webapp.api`.
diff --git a/doc/source/api_doc.rst b/doc/source/api_doc.rst
index 379cb8d006b..85e56bc2afe 100644
--- a/doc/source/api_doc.rst
+++ b/doc/source/api_doc.rst
@@ -28,7 +28,4 @@ Overview of available API resources is available at https://galaxyproject.org/de
 
     Quickstart <api/quickstart>
 
-    Development Guidelines <api/guidelines>
-
     Documentation <api/api>
-
diff --git a/doc/source/conf.py b/doc/source/conf.py
index d44ee73b861..c983beef6a1 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -18,6 +18,10 @@ import sphinx_rtd_theme
 # Library to make .md to slideshow
 from recommonmark.transform import AutoStructify
 
+# Set GALAXY_DOCS_SKIP_VIEW_CODE=1 to skip embedding highlighted source
+# code into docs.
+SKIP_VIEW_CODE = os.environ.get("GALAXY_DOCS_SKIP_VIEW_CODE", False) == "1"
+
 # Set GALAXY_DOCS_SKIP_SOURCE=1 to skip building source information and
 # just build primary documentation. (Quicker to debug issues in most frequently updated
 # docs).
@@ -43,7 +47,9 @@ sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pa
 extensions = ['recommonmark', 'sphinx.ext.intersphinx', 'sphinx_markdown_tables']
 if not SKIP_SOURCE:
     # TODO: Add https://pypi.org/project/sphinx-autodoc-typehints
-    extensions += ['sphinx.ext.doctest', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.viewcode', 'sphinx.ext.autodoc']
+    extensions += ['sphinx.ext.doctest', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.autodoc']
+    if not SKIP_VIEW_CODE:
+        extensions.append('sphinx.ext.viewcode')
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -134,7 +140,10 @@ pygments_style = 'sphinx'
 #modindex_common_prefix = []
 
 # Intersphinx mapping to Python documentation
-intersphinx_mapping = {'python': ('https://docs.python.org/3', None)}
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3', None),
+    'requests': ("https://requests.readthedocs.io/en/master/", None),
+}
 
 # -- Options for HTML output ---------------------------------------------------
 
diff --git a/doc/source/dev/api_guidelines.rst b/doc/source/dev/api_guidelines.rst
new file mode 100644
index 00000000000..6e1c822b46a
--- /dev/null
+++ b/doc/source/dev/api_guidelines.rst
@@ -0,0 +1,172 @@
+API Design Guidelines
+=====================
+
+The following section outlines guidelines related to extending and/or modifying
+the Galaxy API. The Galaxy API has been developed over time in an ad-hoc fashion and by
+many contributors, so clients SHOULD NOT expect the API will conform to
+these guidelines - but developers contributing to the Galaxy API SHOULD follow
+these guidelines.
+
+Before Getting Started
+~~~~~~~~~~~~~~~~~~~~~~
+
+Developers should familiarize themselves with `HTTP method definitions
+<https://www.w3.org/Protocols/rfc2616/rfc2616-sec9.html#sec9>`__. While Galaxy
+follows these imperfectly - a serious effort should be made to use HTTP
+methods (GET, POST, PUT, DELETE, etc.) correctly and consistently. More
+information about these methods with a focus on RESTful APIs can be found
+at https://restfulapi.net/http-methods/.
+
+Developers should also familiarize themselves with the `HTTP status code definitions
+<http://www.w3.org/Protocols/rfc2616/rfc2616-sec10.html>`__. The API responses
+should properly set the status code according to the result - in particular
+2XX responses should be used for successful requests, 4XX for various
+kinds of client errors, and 5XX for the errors on the server side.
+
+Finally, developers should familiarize themselves with `RESTful API design
+<https://docs.microsoft.com/en-us/azure/architecture/best-practices/api-design>`__.
+Again, Galaxy follows generic RESTful guidelines imperfectly, but a serious
+effort should be made to design the API as RESTfully and consistently as possible.
+
+Documenting the API
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+An API endpoint implementation method should include high-level docstring documentation
+for consumption at docs.galaxyproject.org.
+
+API functionality should consume and produce Pydantic_ `models
+<https://pydantic-docs.helpmanual.io/usage/models/>`__ with typed and annotated
+`fields <https://pydantic-docs.helpmanual.io/usage/types/>`__. This information
+will be used to generate detailed OpenAPI_ documentation for APIs in
+the near future. Typed models also improve the quality and thoroughness
+of the static checking that can be done for the Galaxy backend.
+
+To further document your API and allow other developers to see how it functions,
+new API functionality should include functional tests. These functional
+tests should be implemented in Python and added to either the API test suite
+or the integration test suite. Checkout the :doc:`Writing Tests for Galaxy <writing_tests>`
+documentation for more information on developing tests for Galaxy.
+
+.. note::
+
+    The Galaxy documentation can be generated by running ``make docs-develop``
+    from the Galaxy root. Galaxy can be type checked by running ``tox -e mypy``
+    from the root of Galaxy after tox_ has been configured.
+
+Error Handling
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+API methods should throw a finite number of exceptions 
+(defined in :mod:`galaxy.exceptions`) and these should subclass 
+:class:`galaxy.exceptions.MessageException` and not paste/WSGI/FastAPI HTTP exceptions.
+When possible, the framework itself should be responsible for catching these exceptions,
+setting the status code, and building an error response. Throwing these exceptions
+will ensure the API responses are consistent across frameworks and across the API.
+These exceptions allow throwers to attach arbitrary extra information.
+
+Error responses should not consist of plain text strings - they should be
+dictionaries describing the error and containing the following:
+
+.. code-block: json
+
+    {
+      "status_code": 400,
+      "err_code": 400007,
+      "err_msg": "Request contained invalid parameter, action could not be completed.",
+      "type": "error",
+      "extra_error_info": "Extra information."
+    }
+
+The error code (``err_code``) is defined by the exception class
+and pulled from ``lig/galaxy/exceptions/error_codes.json``. This JSON
+document should be used to add new error conditions or improve
+default error messages.
+
+If there is an error processing some part of the request (one item in a list
+for instance), the status code should be set to reflect the error and the
+partial result may or may not be returned depending on the controller -
+this behavior should be documented.
+
+Backward Compatibility
+~~~~~~~~~~~~~~~~~~~~~~
+
+Backward compatibility is important and should be maintained when possible.
+If changing behavior in a non-backward compatible way please ensure one
+of the following holds - there is a strong reason to believe no consumers
+depend on the old behavior, the behavior is effectively broken, or the API
+method being modified has not been part of a tagged dist release. If these
+conditions do not hold, please help the Galaxy release manager ensure
+information about the breaking API is highlighted in the Galaxy release
+notes.
+
+Whenever functionality needs to be added, removed, or modified that
+breaks backward compatibility in a significant way to a component used by
+the community - a "dev" variant of the API should be established and
+the community should be alerted and given a time frame for when the old
+behavior will be replaced with the new behavior.
+
+Design
+~~~~~~
+
+Functionality should not be copied and pasted between controllers -
+consider refactoring functionality into associated classes or short of
+that into mixins_ or into managers (:mod:`galaxy.managers`).
+
+To whatever degree is possible, the Galaxy API controller classes
+(found in :mod:`galaxy.webapps.galaxy.api`) should be as lean as
+possible. Most of the logic should be pushed into components that
+are decoupled from the actual web application and the web framework.
+The role of the controller should be simply to adapt the web request
+(tied to the web framework) to simple objects (plain Python objects,
+Pydantic_ models, or SQLAlchemy models), send these objects to a
+Python component lower in the stack, and finally to translate the
+response to a web response. This design will ensure that Galaxy
+application logic is usable in as many contexts as possible and
+decouple the core "business logic" of Galaxy from the web framework
+hosting it.
+
+Going forward, we anticipate the most typical way this abstract
+advice translates to concrete code flow is that API controllers
+in :mod:`galaxy.webapps.galaxy.api` receive or produce Pydantic_
+models and pass them to manager components defined in
+:mod:`galaxy.managers`. The manager is then responsible for
+interacting with the whole backend or specific components to
+fullfil the desired request.
+
+Galaxy work contexts provide a way for API requests (and other
+components) to describe what they require from the framework
+in terms of the request (examples include the Galaxy app, a user
+to act on behalf of, or a user with a defined "current history").
+These objects describing the web request are passed around rather
+haphazardly as an argument named ``trans``. To design API methods
+to deal with ``trans`` in the most statically checkable and
+rigorous way - please review the docs for :mod:`galaxy.managers.context`.
+
+Examples
+~~~~~~~~
+
+A very clean, isolated example of a well documented controller
+and well annotated models is the licenses endpoint -
+:mod:`galaxy.webapps.galaxy.api.licenses`. A more complicated
+endpoint that demonstrates working with a manager and the
+Galaxy model backend is the roles endpoint - :mod:`galaxy.webapps.galaxy.api.roles`.
+
+BioBlend
+~~~~~~~~
+
+Changes to reflect modifications to the API should be pushed upstream to
+the BioBlend_ project if possible.
+
+Longer Term Goals
+~~~~~~~~~~~~~~~~~~
+
+    - It would be advantageous to have a clearer separation of anonymous and
+      admin handling functionality.
+    - Consistent standards for range-based requests, batch requests, filtered
+      requests, etc... should be established and documented here.
+
+.. _Pydantic: https://pydantic-docs.helpmanual.io/ 
+.. _BioBlend: https://github.com/galaxyproject/bioblend
+.. _mixins: http://en.wikipedia.org/wiki/Composition_over_inheritance
+.. _tox: https://tox.readthedocs.io/en/latest/
+.. _OpenAPI: https://www.openapis.org
diff --git a/doc/source/dev/index.rst b/doc/source/dev/index.rst
index d1d16374be1..74f48f5be70 100644
--- a/doc/source/dev/index.rst
+++ b/doc/source/dev/index.rst
@@ -12,6 +12,7 @@ A multi-hour long video playlist covering these slides can be found at
   :maxdepth: 1
 
   schema
+  api_guidelines
   interactive_environments
   build_a_job_runner
   finding_and_improving_slow_code
diff --git a/doc/source/lib/galaxy.schema.rst b/doc/source/lib/galaxy.schema.rst
new file mode 100644
index 00000000000..38ec22b6fdc
--- /dev/null
+++ b/doc/source/lib/galaxy.schema.rst
@@ -0,0 +1,26 @@
+galaxy.schema package
+=====================
+
+.. automodule:: galaxy.schema
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+galaxy.schema.fields module
+---------------------------
+
+.. automodule:: galaxy.schema.fields
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+galaxy.schema.schema module
+---------------------------
+
+.. automodule:: galaxy.schema.schema
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/source/lib/galaxy.tool_util.client.rst b/doc/source/lib/galaxy.tool_util.client.rst
new file mode 100644
index 00000000000..714007ba211
--- /dev/null
+++ b/doc/source/lib/galaxy.tool_util.client.rst
@@ -0,0 +1,18 @@
+galaxy.tool\_util.client package
+================================
+
+.. automodule:: galaxy.tool_util.client
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+galaxy.tool\_util.client.staging module
+---------------------------------------
+
+.. automodule:: galaxy.tool_util.client.staging
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/source/lib/galaxy.tool_util.deps.rst b/doc/source/lib/galaxy.tool_util.deps.rst
index ee9da16f461..947dddb4f28 100644
--- a/doc/source/lib/galaxy.tool_util.deps.rst
+++ b/doc/source/lib/galaxy.tool_util.deps.rst
@@ -51,14 +51,6 @@ galaxy.tool\_util.deps.conda\_compat module
    :undoc-members:
    :show-inheritance:
 
-galaxy.tool\_util.deps.conda\_init module
------------------------------------------
-
-.. automodule:: galaxy.tool_util.deps.conda_init
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 galaxy.tool\_util.deps.conda\_util module
 -----------------------------------------
 
diff --git a/doc/source/lib/galaxy.web.legacy_framework.rst b/doc/source/lib/galaxy.web.legacy_framework.rst
new file mode 100644
index 00000000000..ca7a526215e
--- /dev/null
+++ b/doc/source/lib/galaxy.web.legacy_framework.rst
@@ -0,0 +1,18 @@
+galaxy.web.legacy\_framework package
+====================================
+
+.. automodule:: galaxy.web.legacy_framework
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+galaxy.web.legacy\_framework.grids module
+-----------------------------------------
+
+.. automodule:: galaxy.web.legacy_framework.grids
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/source/lib/galaxy.webapps.reports.framework.rst b/doc/source/lib/galaxy.webapps.reports.framework.rst
deleted file mode 100644
index 1a39715bd9e..00000000000
--- a/doc/source/lib/galaxy.webapps.reports.framework.rst
+++ /dev/null
@@ -1,18 +0,0 @@
-galaxy.webapps.reports.framework package
-========================================
-
-.. automodule:: galaxy.webapps.reports.framework
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Submodules
-----------
-
-galaxy.webapps.reports.framework.grids module
----------------------------------------------
-
-.. automodule:: galaxy.webapps.reports.framework.grids
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/doc/source/lib/galaxy.workflow.refactor.rst b/doc/source/lib/galaxy.workflow.refactor.rst
new file mode 100644
index 00000000000..c498d156294
--- /dev/null
+++ b/doc/source/lib/galaxy.workflow.refactor.rst
@@ -0,0 +1,26 @@
+galaxy.workflow.refactor package
+================================
+
+.. automodule:: galaxy.workflow.refactor
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+galaxy.workflow.refactor.execute module
+---------------------------------------
+
+.. automodule:: galaxy.workflow.refactor.execute
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+galaxy.workflow.refactor.schema module
+--------------------------------------
+
+.. automodule:: galaxy.workflow.refactor.schema
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/source/releases/20.09-config.rst b/doc/source/releases/20.09-config.rst
index be7cb7d3852..e2657595b03 100644
--- a/doc/source/releases/20.09-config.rst
+++ b/doc/source/releases/20.09-config.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 Configuration Changes
 =====================
 
diff --git a/doc/source/releases/21.01_announce.rst b/doc/source/releases/21.01_announce.rst
index 631ca300a94..87b2347860b 100644
--- a/doc/source/releases/21.01_announce.rst
+++ b/doc/source/releases/21.01_announce.rst
@@ -1,3 +1,4 @@
+:orphan:
 
 ===========================================================
 January 2021 Galaxy Release (v 21.01)
diff --git a/doc/source/releases/index.rst b/doc/source/releases/index.rst
index 81c8b7c1978..3d6157b8b48 100644
--- a/doc/source/releases/index.rst
+++ b/doc/source/releases/index.rst
@@ -4,12 +4,12 @@ Releases
 .. toctree::
    :maxdepth: 1
 
-   20.09_announce
-   20.05_announce
-   20.01_announce
-   19.09_announce
-   19.05_announce
-   19.01_announce
+   20.09_announce_user
+   20.05_announce_user
+   20.01_announce_user
+   19.09_announce_user
+   19.05_announce_user
+   19.01_announce_user
    18.09_announce
    18.05_announce
    18.01_announce
diff --git a/hooks/build b/hooks/build
new file mode 100644
index 00000000000..2459dc31e93
--- /dev/null
+++ b/hooks/build
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+DOCKER_BUILDKIT=1 docker build -f $DOCKERFILE_PATH -t $IMAGE_NAME --build-arg GIT_USERNAME=$GIT_USERNAME --build-arg GIT_PASSWORD=$GIT_PASSWORD .
diff --git a/lib/galaxy/actions/library.py b/lib/galaxy/actions/library.py
index b9ee0d70734..bd3d6f009d9 100644
--- a/lib/galaxy/actions/library.py
+++ b/lib/galaxy/actions/library.py
@@ -85,7 +85,7 @@ class LibraryActions:
         populate_state(trans, tool.inputs, kwd, state.inputs)
         tool_params = state.inputs
         dataset_upload_inputs = []
-        for input_name, input in tool.inputs.items():
+        for input in tool.inputs.values():
             if input.type == "upload_dataset":
                 dataset_upload_inputs.append(input)
         # Library-specific params
@@ -203,7 +203,7 @@ class LibraryActions:
         if os.path.isfile(path):
             name = os.path.basename(path)
             files_and_folders.append((path, name, None))
-        for basedir, dirs, files in os.walk(line):
+        for basedir, _dirs, files in os.walk(line):
             for file in files:
                 file_path = os.path.abspath(os.path.join(basedir, file))
                 if preserve_dirs:
@@ -214,7 +214,7 @@ class LibraryActions:
         return files_and_folders
 
     def _paths_list(self, params):
-        return [(l.strip(), os.path.abspath(l.strip())) for l in params.get('filesystem_paths', '').splitlines() if l.strip()]
+        return [(line.strip(), os.path.abspath(line.strip())) for line in params.get('filesystem_paths', '').splitlines() if line.strip()]
 
     def _check_path_paste_params(self, params):
         if params.get('filesystem_paths', '') == '':
diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index 97c6b971a7b..400363852d5 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -2,6 +2,7 @@ import logging
 import signal
 import sys
 import time
+from typing import Any
 
 import galaxy.model
 import galaxy.model.security
@@ -12,6 +13,7 @@ from galaxy.config_watchers import ConfigWatchers
 from galaxy.containers import build_container_interfaces
 from galaxy.files import ConfiguredFileSources
 from galaxy.job_metrics import JobMetrics
+from galaxy.managers.api_keys import ApiKeyManager
 from galaxy.managers.collections import DatasetCollectionManager
 from galaxy.managers.folders import FolderManager
 from galaxy.managers.hdas import HDAManager
@@ -43,7 +45,7 @@ from galaxy.tools.cache import (
 from galaxy.tools.data_manager.manager import DataManagers
 from galaxy.tools.error_reports import ErrorReports
 from galaxy.tools.special_tools import load_lib_tools
-from galaxy.tours import ToursRegistry
+from galaxy.tours import build_tours_registry
 from galaxy.util import (
     ExecutionTimer,
     heartbeat,
@@ -57,15 +59,16 @@ from galaxy.web.proxy import ProxyManager
 from galaxy.web_stack import application_stack_instance
 from galaxy.webhooks import WebhooksRegistry
 from galaxy.workflow.trs_proxy import TrsProxy
+from .structured_app import StructuredApp
 
 log = logging.getLogger(__name__)
 app = None
 
 
-class UniverseApplication(config.ConfiguresGalaxyMixin):
+class UniverseApplication(StructuredApp, config.ConfiguresGalaxyMixin):
     """Encapsulates the state of a Universe application"""
 
-    def __init__(self, **kwargs):
+    def __init__(self, **kwargs) -> None:
         if not log.handlers:
             # Paste didn't handle it, so we need a temporary basic log
             # configured.  The handler added here gets dumped and replaced with
@@ -73,12 +76,11 @@ class UniverseApplication(config.ConfiguresGalaxyMixin):
             logging.basicConfig(level=logging.DEBUG)
         log.debug("python path is: %s", ", ".join(sys.path))
         self.name = 'galaxy'
-        # is_webapp will be set to true when building WSGI app
         self.is_webapp = False
-        self.startup_timer = ExecutionTimer()
+        startup_timer = ExecutionTimer()
         self.new_installation = False
         # Read config file and check for errors
-        self.config = config.Configuration(**kwargs)
+        self.config: Any = config.Configuration(**kwargs)
         self.config.check()
         config.configure_logging(self.config)
         self.execution_timer_factory = ExecutionTimerFactory(self.config)
@@ -116,6 +118,7 @@ class UniverseApplication(config.ConfiguresGalaxyMixin):
         self.library_manager = LibraryManager()
         self.role_manager = RoleManager(self)
         self.dynamic_tool_manager = DynamicToolManager(self)
+        self.api_keys_manager = ApiKeyManager(app)
 
         # ConfiguredFileSources
         self.file_sources = ConfiguredFileSources.from_app_config(self.config)
@@ -173,7 +176,7 @@ class UniverseApplication(config.ConfiguresGalaxyMixin):
             directories_setting=self.config.visualization_plugins_directory,
             template_cache_dir=self.config.template_cache_path)
         # Tours registry
-        self.tour_registry = ToursRegistry(self.config.tour_config_dir)
+        self.tour_registry = build_tours_registry(self.config.tour_config_dir)
         # Webhooks registry
         self.webhooks_registry = WebhooksRegistry(self.config.webhooks_dir)
         # Load security policy.
@@ -270,7 +273,7 @@ class UniverseApplication(config.ConfiguresGalaxyMixin):
         self.url_for = url_for
 
         self.server_starttime = int(time.time())  # used for cachebusting
-        log.info("Galaxy app startup finished %s" % self.startup_timer)
+        log.info("Galaxy app startup finished %s" % startup_timer)
 
     def shutdown(self):
         log.debug('Shutting down')
diff --git a/lib/galaxy/auth/providers/ldap_ad.py b/lib/galaxy/auth/providers/ldap_ad.py
index 9497ba61d4c..91088748f86 100644
--- a/lib/galaxy/auth/providers/ldap_ad.py
+++ b/lib/galaxy/auth/providers/ldap_ad.py
@@ -144,20 +144,22 @@ class LDAP(AuthProvider):
 
         if 'search-fields' in options:
             try:
-                l = ldap.initialize(_get_subs(options, 'server', params))
-                l.protocol_version = 3
+                conn = ldap.initialize(_get_subs(options, 'server', params))
+                conn.protocol_version = 3
 
                 if 'search-user' in options:
-                    l.simple_bind_s(_get_subs(options, 'search-user', params),
-                                    _get_subs(options, 'search-password', params))
+                    conn.simple_bind_s(
+                        _get_subs(options, 'search-user', params),
+                        _get_subs(options, 'search-password', params))
                 else:
-                    l.simple_bind_s()
+                    conn.simple_bind_s()
 
                 # setup search
                 attributes = {_.strip().format(**params) for _ in options['search-fields'].split(',')}
                 if 'search-memberof-filter' in options:
                     attributes.add('memberOf')
-                suser = l.search_ext_s(_get_subs(options, 'search-base', params),
+                suser = conn.search_ext_s(
+                    _get_subs(options, 'search-base', params),
                     ldap.SCOPE_SUBTREE,
                     _get_subs(options, 'search-filter', params), attributes,
                     timeout=60, sizelimit=1)
@@ -230,17 +232,17 @@ class LDAP(AuthProvider):
         Do the actual authentication by binding as the user to check their credentials
         """
         try:
-            l = ldap.initialize(_get_subs(options, 'server', params))
-            l.protocol_version = 3
+            conn = ldap.initialize(_get_subs(options, 'server', params))
+            conn.protocol_version = 3
             bind_user = _get_subs(options, 'bind-user', params)
             bind_password = _get_subs(options, 'bind-password', params)
         except Exception:
             log.exception('LDAP authenticate: initialize exception')
             return False
         try:
-            l.simple_bind_s(bind_user, bind_password)
+            conn.simple_bind_s(bind_user, bind_password)
             try:
-                whoami = l.whoami_s()
+                whoami = conn.whoami_s()
             except ldap.PROTOCOL_ERROR:
                 # The "Who am I?" extended operation is not supported by this LDAP server
                 pass
diff --git a/lib/galaxy/authnz/__init__.py b/lib/galaxy/authnz/__init__.py
index 00fbc428630..7087f96a8f2 100644
--- a/lib/galaxy/authnz/__init__.py
+++ b/lib/galaxy/authnz/__init__.py
@@ -26,12 +26,14 @@ class IdentityProvider:
 
         :type config: lxml.etree.ElementTree._Element
         :param config: Is the configuration element of the provider
-            from the configuration file (e.g., oidc_config.xml).
-            This element contains the all the provider-specific
-            configuration elements.
+                       from the configuration file (e.g., oidc_config.xml).
+                       This element contains the all the provider-specific
+                       configuration elements.
 
         :type backend_config: lxml.etree.ElementTree._Element
-        :param backend_config: Is the configuration element of the backend of
+        :param backend_config:
+
+            Is the configuration element of the backend of
             the provider from the configuration file (e.g.,
             oidc_backends_config.xml). This element contains all the
             backend-specific configuration elements.
@@ -47,24 +49,23 @@ class IdentityProvider:
         :type trans: GalaxyWebTransaction
         :param trans: Galaxy web transaction.
 
-        :return: a redirect URI to the provider's authentication
-            endpoint.
+        :returns: a redirect URI to the provider's authentication endpoint
         """
         raise NotImplementedError()
 
-    def callback(self, state_token, authz_code, trans, login_redirect_url):
-        """
-        Handles authentication call-backs from identity providers.
-        This process maps `state-token` to a user
-        :type state_token: string
+    def callback(self, state_token: str, authz_code: str, trans, login_redirect_url):
+        """Handles authentication call-backs from identity providers.
+
+        This process maps `state-token` to a user.
+
         :param state_token: is an anti-forgery token which identifies
-            a Galaxy user to whom the given authorization code belongs to.
-        :type authz_code: string
+                            a Galaxy user to whom the given authorization code belongs to.
         :param authz_code: a very short-lived, single-use token to
-            request a refresh token.
+                           request a refresh token.
         :type trans: GalaxyWebTransaction
         :param trans: Galaxy web transaction.
-        :return tuple: a tuple of redirect_url and user.
+        :rtype: tuple
+        :returns: a tuple of redirect_url and user.
         """
         raise NotImplementedError()
 
@@ -79,7 +80,7 @@ class IdentityProvider:
         :type trans: GalaxyWebTransaction
         :param trans: Galaxy web transaction.
 
-        :type trans: string
-        :param trans: Optional URL to redirect to after logging out of IDP.
+        :type post_logout_redirect_url: string
+        :param post_logout_redirect_url: Optional URL to redirect to after logging out of IDP.
         """
         raise NotImplementedError()
diff --git a/lib/galaxy/authnz/custos_authnz.py b/lib/galaxy/authnz/custos_authnz.py
index f2a22191dd3..32180411516 100644
--- a/lib/galaxy/authnz/custos_authnz.py
+++ b/lib/galaxy/authnz/custos_authnz.py
@@ -102,9 +102,9 @@ class CustosAuthnz(IdentityProvider):
                     # TODO: Future work will expand on this and provide an
                     # interface for when there are multiple auth providers
                     # allowing explicit authenticated association.
-                    if (trans.app.config.enable_oidc and
-                            len(trans.app.config.oidc) == 1 and
-                            len(trans.app.auth_manager.authenticators) == 0):
+                    if (trans.app.config.enable_oidc
+                            and len(trans.app.config.oidc) == 1
+                            and len(trans.app.auth_manager.authenticators) == 0):
                         user = existing_user
                     else:
                         message = "There already exists a user with email %s.  To associate this external login, you must first be logged in as that existing account." % email
diff --git a/lib/galaxy/authnz/psa_authnz.py b/lib/galaxy/authnz/psa_authnz.py
index 34dbb592181..3114b0b331f 100644
--- a/lib/galaxy/authnz/psa_authnz.py
+++ b/lib/galaxy/authnz/psa_authnz.py
@@ -282,9 +282,10 @@ def contains_required_data(response=None, is_new=False, **kwargs):
     and returns void if otherwise.
 
     :type  response: dict
-    :param response:    a dictionary containing decoded response from
-                        OIDC backend that contain the following keys
-                        among others:
+    :param response:  a dictionary containing decoded response from
+                      OIDC backend that contain the following keys
+                      among others:
+
                         -   id_token;       see: http://openid.net/specs/openid-connect-core-1_0.html#IDToken
                         -   access_token;   see: https://tools.ietf.org/html/rfc6749#section-1.4
                         -   refresh_token;  see: https://tools.ietf.org/html/rfc6749#section-1.5
@@ -297,6 +298,7 @@ def contains_required_data(response=None, is_new=False, **kwargs):
     :param is_new: has the user been authenticated?
 
     :param kwargs:      may contain the following keys among others:
+
                         -   uid:        user ID
                         -   user:       Galaxy user; if user is already authenticated
                         -   backend:    the backend that is used for user authentication.
diff --git a/lib/galaxy/config/config_manage.py b/lib/galaxy/config/config_manage.py
index 0bbaa64977e..bd061f6b14a 100644
--- a/lib/galaxy/config/config_manage.py
+++ b/lib/galaxy/config/config_manage.py
@@ -426,6 +426,8 @@ def _write_option_rst(args, rst, key, heading_level, option_value):
         default = "true"
     elif default is False:
         default = "false"
+    elif default == "":
+        default = '""'
     rst.write(":Default: ``%s``\n" % default)
     if type:
         rst.write(":Type: %s\n" % type)
@@ -686,7 +688,7 @@ def _build_sample_yaml(args, app_desc):
     description = getattr(schema, "description", None)
     if description:
         description = description.lstrip()
-        as_comment = "\n".join("# %s" % l for l in description.split("\n")) + "\n"
+        as_comment = "\n".join(f"# {line}" for line in description.split("\n")) + "\n"
         f.write(as_comment)
     _write_sample_section(args, f, 'uwsgi', Schema(UWSGI_OPTIONS), as_comment=False, uwsgi_hack=True)
     _write_sample_section(args, f, app_desc.app_name, schema)
@@ -700,7 +702,7 @@ def _write_to_file(args, f, path):
     else:
         contents = f
     if args.dry_run:
-        contents_indented = "\n".join(" |%s" % l for l in contents.splitlines())
+        contents_indented = "\n".join(f" |{line}" for line in contents.splitlines())
         print(f"Overwriting {path} with the following contents:\n{contents_indented}")
         print("... skipping because --dry-run is enabled.")
     else:
@@ -755,7 +757,7 @@ def _write_option(args, f, key, option_value, as_comment=False, uwsgi_hack=False
     else:
         key_val_str = yaml.dump({key: value}, width=float("inf")).lstrip("{").rstrip("\n}")
     lines = f"{comment}{as_comment_str}{key_val_str}"
-    lines_idented = "\n".join("  %s" % l for l in lines.split("\n"))
+    lines_idented = "\n".join(f"  {line}" for line in lines.split("\n"))
     f.write("%s\n\n" % lines_idented)
 
 
diff --git a/lib/galaxy/config/sample/container_resolvers_conf.xml.sample b/lib/galaxy/config/sample/container_resolvers_conf.xml.sample
index 1f6c32ed67c..78051d5cb64 100644
--- a/lib/galaxy/config/sample/container_resolvers_conf.xml.sample
+++ b/lib/galaxy/config/sample/container_resolvers_conf.xml.sample
@@ -52,7 +52,7 @@
        or more package requirements listed as part of the tool's definition.
        Set auto_install to False if Galaxy should build container images
        through the admin interface or API, but not automatically when
-       a tool is run.
+       a tool is run. WARNING: requires docker to be installed.
 
   -->
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index d0e86061f8f..7fccb510097 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -436,7 +436,7 @@ galaxy:
 
   # involucro is a tool used to build Docker or Singularity containers
   # for tools from Conda dependencies referenced in tools as
-  # `requirement`s. The following path is the location of involucro on
+  # `requirement` s. The following path is the location of involucro on
   # the Galaxy host. This is ignored if the relevant container resolver
   # isn't enabled, and will install on demand unless involucro_auto_init
   # is set to false.
@@ -617,6 +617,14 @@ galaxy:
   # generated commands run in sh.
   #default_job_shell: /bin/bash
 
+  # Set this to false to disable the tool document cache. This cache
+  # stores expanded xml strings. Disabling the tool cache results in
+  # slower startup times. The tool cache is backed by sqlite database,
+  # which cannot be stored on certain network disks. The cache location
+  # is configurable using the ``tool_cache_data_dir`` setting, but can
+  # be disabled completely here.
+  #enable_tool_document_cache: true
+
   # Tool related caching. Fully expanded tools and metadata will be
   # stored at this path. Per tool_conf cache locations can be configured
   # in (``shed_``)tool_conf.xml files using the tool_cache_data_dir
@@ -1830,7 +1838,7 @@ galaxy:
   # can separate Galaxy into multiple processes.  There are more than
   # one way to do this, and they are explained in detail in the
   # documentation:
-  #   https://docs.galaxyproject.org/en/master/admin/scaling.html
+  # https://docs.galaxyproject.org/en/master/admin/scaling.html
   # By default, Galaxy manages and executes jobs from within a single
   # process and notifies itself of new jobs via in-memory queues.  Jobs
   # are run locally on the system on which Galaxy is started.  Advanced
diff --git a/lib/galaxy/config/script.py b/lib/galaxy/config/script.py
index ee4c72db4eb..f5e3574568d 100644
--- a/lib/galaxy/config/script.py
+++ b/lib/galaxy/config/script.py
@@ -154,7 +154,8 @@ def _handle_galaxy_yml(args, config_dir, data_dir):
 
     galaxy_config_template = []
     with open(GALAXY_CONFIG_TEMPLATE_FILE) as fh:
-        for line in [l.rstrip('\n') for l in fh.readlines()]:
+        for line in fh:
+            line = line.rstrip('\n')
             for k, v in GALAXY_CONFIG_SUBSTITUTIONS.items():
                 if line == k:
                     line = v
diff --git a/lib/galaxy/containers/__init__.py b/lib/galaxy/containers/__init__.py
index 2d12bd9e06e..ac416914177 100644
--- a/lib/galaxy/containers/__init__.py
+++ b/lib/galaxy/containers/__init__.py
@@ -14,8 +14,7 @@ from abc import (
     abstractmethod,
     abstractproperty
 )
-from collections import namedtuple
-from typing import Any, Dict, Optional, Type
+from typing import Any, Dict, NamedTuple, Optional, Type
 
 import yaml
 
@@ -29,18 +28,12 @@ DEFAULT_CONF = {'_default_': {'type': DEFAULT_CONTAINER_TYPE}}
 log = logging.getLogger(__name__)
 
 
-class ContainerPort(namedtuple('ContainerPort', ('port', 'protocol', 'hostaddr', 'hostport'))):
-    """Named tuple representing ports published by a container, with attributes:
-
-    :ivar       port:       Port number (inside the container)
-    :vartype    port:       int
-    :ivar       protocol:   Port protocol, either ``tcp`` or ``udp``
-    :vartype    protocol:   str
-    :ivar       hostaddr:   Address or hostname where the published port can be accessed
-    :vartype    hostaddr:   str
-    :ivar       hostport:   Published port number on which the container can be accessed
-    :vartype    hostport:   int
-    """
+class ContainerPort(NamedTuple):
+    """Named tuple representing ports published by a container, with attributes"""
+    port: int  # Port number (inside the container)
+    protocol: str  # Port protocol, either ``tcp`` or ``udp``
+    hostaddr: str  # Address or hostname where the published port can be accessed
+    hostport: int  # Published port number on which the container can be accessed
 
 
 class ContainerVolume(metaclass=ABCMeta):
@@ -80,12 +73,15 @@ class ContainerVolume(metaclass=ABCMeta):
 class Container(metaclass=ABCMeta):
 
     def __init__(self, interface, id, name=None, **kwargs):
-        """:param   interface:  Container interface for the given container type
+        """
+
+        :param      interface:  Container interface for the given container type
         :type       interface:  :class:`ContainerInterface` subclass instance
         :param      id:         Container identifier
         :type       id:         str
         :param      name:       Container name
         :type       name:       str
+
         """
         self._interface = interface
         self._id = id
@@ -118,7 +114,7 @@ class Container(metaclass=ABCMeta):
         """Attribute for accessing details of ports published by the container.
 
         :returns:   Port details
-        :rtype:     list of :class:`ContainerPort`s
+        :rtype:     list of :class:`ContainerPort` s
         """
 
     @abstractproperty
@@ -246,25 +242,25 @@ class ContainerInterface(metaclass=ABCMeta):
     def _stringify_kwopt_list_of_kvpairs(self, flag, val):
         """
         """
-        l = []
+        kwopt_list = []
         if isinstance(val, list):
             # ['foo=bar', 'baz=quux']
-            l = val
+            kwopt_list = val
         else:
             # {'foo': 'bar', 'baz': 'quux'}
             for k, v in dict(val).items():
-                l.append(f'{k}={v}')
-        return self._stringify_kwopt_list(flag, l)
+                kwopt_list.append(f'{k}={v}')
+        return self._stringify_kwopt_list(flag, kwopt_list)
 
     def _stringify_kwopt_list_of_kovtrips(self, flag, val):
         """
         """
         if isinstance(val, str):
             return self._stringify_kwopt_string(flag, val)
-        l = []
+        kwopt_list = []
         for k, o, v in val:
-            l.append(f'{k}{o}{v}')
-        return self._stringify_kwopt_list(flag, l)
+            kwopt_list.append(f'{k}{o}{v}')
+        return self._stringify_kwopt_list(flag, kwopt_list)
 
     def _run_command(self, command, verbose=False):
         if verbose:
@@ -381,7 +377,7 @@ def _get_interface_modules():
     modules = import_submodules(sys.modules[__name__])
     for module in modules:
         module_names = [getattr(module, _) for _ in dir(module)]
-        classes = [_ for _ in module_names if inspect.isclass(_) and
-            not _ == ContainerInterface and issubclass(_, ContainerInterface)]
+        classes = [_ for _ in module_names if inspect.isclass(_)
+            and not _ == ContainerInterface and issubclass(_, ContainerInterface)]
         interfaces.extend(classes)
     return {x.container_type: x for x in interfaces}
diff --git a/lib/galaxy/containers/docker.py b/lib/galaxy/containers/docker.py
index c6a94cc7266..7b1d23d8594 100644
--- a/lib/galaxy/containers/docker.py
+++ b/lib/galaxy/containers/docker.py
@@ -152,25 +152,25 @@ class DockerCLIInterface(DockerInterface):
         """The docker API will take a volumes argument in many formats, try to
         deal with that for the command line
         """
-        l = []
+        kwopt_list = []
         if isinstance(val, list):
             # ['/host/vol']
-            l = val
+            kwopt_list = val
         else:
             for hostvol, guestopts in val.items():
                 if isinstance(guestopts, str):
                     # {'/host/vol': '/container/vol'}
-                    l.append(f'{hostvol}:{guestopts}')
+                    kwopt_list.append(f'{hostvol}:{guestopts}')
                 else:
                     # {'/host/vol': {'bind': '/container/vol'}}
                     # {'/host/vol': {'bind': '/container/vol', 'mode': 'rw'}}
                     mode = guestopts.get('mode', '')
-                    l.append('{vol}:{bind}{mode}'.format(
+                    kwopt_list.append('{vol}:{bind}{mode}'.format(
                         vol=hostvol,
                         bind=guestopts['bind'],
                         mode=':' + mode if mode else ''
                     ))
-        return self._stringify_kwopt_list(flag, l)
+        return self._stringify_kwopt_list(flag, kwopt_list)
 
     def _run_docker(self, subcommand, args=None, verbose=False):
         command = self._docker_command.format(subcommand=subcommand, args=args or '')
@@ -265,7 +265,6 @@ class DockerAPIClient:
         for tries in range(1, max_tries + 1):
             retry_time = DockerAPIClient._exception_retry_time
             reinit = False
-            exc = None
             # re-get the APIClient method every time as a different caller (such as the success test function) may have
             # already reinitialized the client, and we always want to use the current client
             f = DockerAPIClient._unwrapped_attr(fname)
@@ -275,42 +274,38 @@ class DockerAPIClient:
                 if tries > 1:
                     log.info('%s() succeeded on attempt %s', qualname, tries)
                 return r
-            except ConnectionError:
-                reinit = True
-            except docker.errors.APIError as exc:
-                if not DockerAPIClient._should_retry_request(exc.response.status_code):
-                    raise
-            except ReadTimeout:
-                reinit = True
-                retry_time = 0
-            finally:
-                # this is inside the finally context so we can do a bare raise when we give up (so the real stack for
-                # the exception is raised)
-                if exc is not None:
-                    log.warning("Caught exception on %s(): %s: %s",
-                                DockerAPIClient._qualname(f), exc.__class__.__name__, exc)
-                    if reinit:
-                        log.warning("Reinitializing Docker API client due to connection-oriented failure")
-                        DockerAPIClient._init_client()
-                        f = DockerAPIClient._unwrapped_attr(fname)
-                        qualname = DockerAPIClient._qualname(f)
-                    r = None
-                    if success_test is not None:
-                        log.info("Testing if %s() succeeded despite the exception", qualname)
-                        r = success_test()
-                    if r:
-                        log.warning("The request appears to have succeeded, will not retry. Response is: %s", str(r))
-                        return r
-                    elif tries >= max_tries:
-                        log.error("Maximum number of attempts (%s) exceeded", max_tries)
-                        if 'response' in exc and DockerAPIClient._nonfatal_error(exc.response.status_code):
-                            return None
-                        else:
-                            raise
+            except (ConnectionError, docker.errors.APIError, ReadTimeout) as exc:
+                if isinstance(exc, ConnectionError):
+                    reinit = True
+                elif isinstance(exc, docker.errors.APIError):
+                    if not DockerAPIClient._should_retry_request(exc.response.status_code):
+                        raise
+                else:  # ReadTimeout
+                    reinit = True
+                    retry_time = 0
+                log.warning("Caught exception on %s(): %s: %s",
+                            DockerAPIClient._qualname(f), exc.__class__.__name__, exc)
+                if reinit:
+                    log.warning("Reinitializing Docker API client due to connection-oriented failure")
+                    DockerAPIClient._init_client()
+                    f = DockerAPIClient._unwrapped_attr(fname)
+                    qualname = DockerAPIClient._qualname(f)
+                r = None
+                if success_test is not None:
+                    log.info("Testing if %s() succeeded despite the exception", qualname)
+                    r = success_test()
+                if r:
+                    log.warning("The request appears to have succeeded, will not retry. Response is: %s", str(r))
+                    return r
+                elif tries >= max_tries:
+                    log.error("Maximum number of attempts (%s) exceeded", max_tries)
+                    if 'response' in exc and DockerAPIClient._nonfatal_error(exc.response.status_code):
+                        return None
                     else:
-                        log.error("Retrying %s() in %s seconds (attempt: %s of %s)", qualname, retry_time, tries,
-                                  max_tries)
-                        sleep(retry_time)
+                        raise
+                else:
+                    log.error("Retrying %s() in %s seconds (attempt: %s of %s)", qualname, retry_time, tries, max_tries)
+                    sleep(retry_time)
 
     def __init__(self, *args, **kwargs):
         # Only initialize the host iterator once
diff --git a/lib/galaxy/datatypes/_schema.py b/lib/galaxy/datatypes/_schema.py
new file mode 100644
index 00000000000..6efb7cc4565
--- /dev/null
+++ b/lib/galaxy/datatypes/_schema.py
@@ -0,0 +1,129 @@
+from typing import (
+    Dict,
+    List,
+    Optional,
+)
+
+from pydantic import (
+    BaseModel,
+    Field,
+    HttpUrl
+)
+
+
+class CompositeFileInfo(BaseModel):
+    name: str = Field(
+        ...,  # Mark this field as required
+        title="Name",
+        description="The name of this composite file"
+    )
+    optional: bool = Field(
+        title="Optional",
+        description=""  # TODO add description
+    )
+    mimetype: Optional[str] = Field(
+        title="MIME type",
+        description="The MIME type of this file"
+    )
+    description: Optional[str] = Field(
+        title="Description",
+        description="Summary description of the purpouse of this file"
+    )
+    substitute_name_with_metadata: Optional[str] = Field(
+        title="Substitute name with metadata",
+        description=""  # TODO add description
+    )
+    is_binary: bool = Field(
+        title="Is binary",
+        description="Whether this file is a binary file"
+    )
+    to_posix_lines: bool = Field(
+        title="To posix lines",
+        description=""  # TODO add description
+    )
+    space_to_tab: bool = Field(
+        title="Spaces to tabulation",
+        description=""  # TODO add description
+    )
+
+
+class DatatypeDetails(BaseModel):
+    extension: str = Field(
+        ...,  # Mark this field as required
+        title="Extension",
+        description="The data type’s Dataset file extension",
+        example="bed"
+    )
+    description: Optional[str] = Field(
+        title="Description",
+        description="A summary description for this data type"
+    )
+    description_url: Optional[HttpUrl] = Field(
+        title="Description URL",
+        description="The URL to a detailed description for this datatype",
+        example="https://wiki.galaxyproject.org/Learn/Datatypes#Bed"
+    )
+    display_in_upload: bool = Field(
+        default=False,
+        title="Display in upload",
+        description="If True, the associated file extension will be displayed in the `File Format` select list in the `Upload File from your computer` tool in the `Get Data` tool section of the tool panel"
+    )
+    composite_files: Optional[List[CompositeFileInfo]] = Field(
+        default=None,
+        title="Composite files",
+        description="A collection of files composing this data type"
+    )
+
+
+class DatatypesMap(BaseModel):
+    ext_to_class_name: Dict[str, str] = Field(
+        ...,  # Mark this field as required
+        title="Extension Map",
+        description="Dictionary mapping datatype's extensions with implementation classes",
+    )
+    class_to_classes: Dict[str, Dict[str, bool]] = Field(
+        ...,  # Mark this field as required
+        title="Classes Map",
+        description="Dictionary mapping datatype's classes with their base classes",
+    )
+
+
+class DatatypesCombinedMap(BaseModel):
+    datatypes: List[str] = Field(
+        ...,  # Mark this field as required
+        title="Datatypes",
+        description="List of datatypes extensions",
+    )
+    datatypes_mapping: DatatypesMap = Field(
+        ...,  # Mark this field as required
+        title="Datatypes Mapping",
+        description="Dictionaries for mapping datatype's extensions/classes with their implementation classes",
+    )
+
+
+class DatatypeConverter(BaseModel):
+    source: str = Field(
+        ...,  # Mark this field as required
+        title="Source",
+        description="Source type for conversion",
+        example="bam",
+    )
+    target: str = Field(
+        ...,  # Mark this field as required
+        title="Target",
+        description="Target type for conversion",
+        example="bai",
+    )
+    tool_id: str = Field(
+        ...,  # Mark this field as required
+        title="Tool identifier",
+        description="The converter tool identifier",
+        example="CONVERTER_Bam_Bai_0",
+    )
+
+
+class DatatypeConverterList(BaseModel):
+    __root__: List[DatatypeConverter] = Field(
+        title='List of data type converters',
+        default=[]
+    )
diff --git a/lib/galaxy/datatypes/converters/fasta_to_len.py b/lib/galaxy/datatypes/converters/fasta_to_len.py
index f2d56948ed2..3447aba63c0 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_len.py
+++ b/lib/galaxy/datatypes/converters/fasta_to_len.py
@@ -49,5 +49,5 @@ def compute_fasta_length(fasta_file, out_file, keep_first_char, keep_first_word=
         out.write("%s\t%d\n" % (fasta_title[1:keep_first_char], seq_len))
 
 
-if __name__ == "__main__" :
+if __name__ == "__main__":
     compute_fasta_length(sys.argv[1], sys.argv[2], sys.argv[3], True)
diff --git a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
index 424a9fa90fa..f82e23d39d8 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
+++ b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
@@ -45,5 +45,5 @@ def __main__():
                 out.write("".join(sequence.split()) + '\n')
 
 
-if __name__ == "__main__" :
+if __name__ == "__main__":
     __main__()
diff --git a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
index 1e5b435b44a..686697c1e5e 100644
--- a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
+++ b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
@@ -23,7 +23,7 @@ def __main__():
                     spec_counts[spec] = 0
                 else:
                     spec_counts[spec] += 1
-                out.write("%s\n" % maf_utilities.get_fasta_header(c, {'block_index' : count, 'species' : spec, 'sequence_index' : spec_counts[spec]}, suffix="%s_%i_%i" % (spec, count, spec_counts[spec])))
+                out.write("%s\n" % maf_utilities.get_fasta_header(c, {'block_index': count, 'species': spec, 'sequence_index': spec_counts[spec]}, suffix="%s_%i_%i" % (spec, count, spec_counts[spec])))
                 out.write("%s\n" % c.text)
             out.write("\n")
     print("%i MAF blocks converted to FASTA." % (count))
diff --git a/lib/galaxy/datatypes/dataproviders/base.py b/lib/galaxy/datatypes/dataproviders/base.py
index 22cd392d930..4b087170e41 100644
--- a/lib/galaxy/datatypes/dataproviders/base.py
+++ b/lib/galaxy/datatypes/dataproviders/base.py
@@ -66,10 +66,11 @@ class HasSettings(type):
 class DataProvider(metaclass=HasSettings):
     """
     Base class for all data providers. Data providers:
-        (a) have a source (which must be another file-like object)
-        (b) implement both the iterator and context manager interfaces
-        (c) do not allow write methods
-            (but otherwise implement the other file object interface methods)
+
+    - have a source (which must be another file-like object)
+    - implement both the iterator and context manager interfaces
+    - do not allow write methods (but otherwise implement the other file object interface methods)
+
     """
     # a definition of expected types for keyword arguments sent to __init__
     #   useful for controlling how query string dictionaries can be parsed into correct types for __init__
@@ -77,10 +78,12 @@ class DataProvider(metaclass=HasSettings):
     settings: Dict[str, str] = {}
 
     def __init__(self, source, **kwargs):
-        """
+        """Sets up a data provider, validates supplied source.
+
         :param source: the source that this iterator will loop over.
-            (Should implement the iterable interface and ideally have the
-            context manager interface as well)
+                       (Should implement the iterable interface and ideally have the
+                       context manager interface as well)
+
         """
         self.source = self.validate_source(source)
 
diff --git a/lib/galaxy/datatypes/dataproviders/chunk.py b/lib/galaxy/datatypes/dataproviders/chunk.py
index 0923c93c767..16aa2016182 100644
--- a/lib/galaxy/datatypes/dataproviders/chunk.py
+++ b/lib/galaxy/datatypes/dataproviders/chunk.py
@@ -25,8 +25,8 @@ class ChunkDataProvider(base.DataProvider):
     MAX_CHUNK_SIZE = 2 ** 16
     DEFAULT_CHUNK_SIZE = MAX_CHUNK_SIZE
     settings = {
-        'chunk_index'   : 'int',
-        'chunk_size'    : 'int'
+        'chunk_index': 'int',
+        'chunk_size': 'int'
     }
 
     # TODO: subclass from LimitedOffsetDataProvider?
diff --git a/lib/galaxy/datatypes/dataproviders/column.py b/lib/galaxy/datatypes/dataproviders/column.py
index 1306338714d..6a94597bcf4 100644
--- a/lib/galaxy/datatypes/dataproviders/column.py
+++ b/lib/galaxy/datatypes/dataproviders/column.py
@@ -32,53 +32,52 @@ class ColumnarDataProvider(line.RegexLineDataProvider):
     are filled with None).
     """
     settings = {
-        'indeces'       : 'list:int',
-        'column_count'  : 'int',
-        'column_types'  : 'list:str',
-        'parse_columns' : 'bool',
-        'deliminator'   : 'str',
-        'filters'       : 'list:str'
+        'indeces': 'list:int',
+        'column_count': 'int',
+        'column_types': 'list:str',
+        'parse_columns': 'bool',
+        'deliminator': 'str',
+        'filters': 'list:str'
     }
 
     def __init__(self, source, indeces=None,
                  column_count=None, column_types=None, parsers=None, parse_columns=True,
                  deliminator='\t', filters=None, **kwargs):
         """
+
         :param indeces: a list of indeces of columns to gather from each row
-            Optional: will default to `None`.
-            If `None`, this provider will return all rows (even when a
-                particular row contains more/less than others).
-            If a row/line does not contain an element at a given index, the
-                provider will-return/fill-with a `None` value as the element.
+                        Optional: will default to `None`.
+                        If `None`, this provider will return all rows (even when a
+                        particular row contains more/less than others).
+                        If a row/line does not contain an element at a given index, the
+                        provider will-return/fill-with a `None` value as the element.
         :type indeces: list or None
 
         :param column_count: an alternate means of defining indeces, use an int
-            here to effectively provide the first N columns.
-            Optional: will default to `None`.
+                             here to effectively provide the first N columns.
+                             Optional: will default to `None`.
         :type column_count: int
 
         :param column_types: a list of string names of types that the
-            provider will use to look up an appropriate parser for the column.
-            (e.g. 'int', 'float', 'str', 'bool')
-            Optional: will default to parsing all columns as strings.
+                             provider will use to look up an appropriate parser for the column.
+                             (e.g. 'int', 'float', 'str', 'bool')
+                             Optional: will default to parsing all columns as strings.
         :type column_types: list of strings
 
         :param parsers: a dictionary keyed with column type strings
-            and with values that are functions to use when parsing those
-            types.
-            Optional: will default to using the function `_get_default_parsers`.
+                        and with values that are functions to use when parsing those
+                        types.
+                        Optional: will default to using the function `_get_default_parsers`.
         :type parsers: dictionary
 
-        :param parse_columns: attempt to parse columns?
-            Optional: defaults to `True`.
+        :param parse_columns: attempt to parse columns? Optional: defaults to `True`.
         :type parse_columns: bool
 
-        :param deliminator: character(s) used to split each row/line of the source.
-            Optional: defaults to the tab character.
+        :param deliminator: character(s) used to split each row/line of the source. Optional: defaults to the tab character.
         :type deliminator: str
 
         .. note:: that the subclass constructors are passed kwargs - so they're
-            params (limit, offset, etc.) are also applicable here.
+                  params (limit, offset, etc.) are also applicable here.
         """
         # TODO: other columnar formats: csv, etc.
         super().__init__(source, **kwargs)
@@ -224,9 +223,9 @@ class ColumnarDataProvider(line.RegexLineDataProvider):
         # TODO: move to module level (or datatypes, util)
         return {
             # str is default and not needed here
-            'int'   : int,
-            'float' : float,
-            'bool'  : bool,
+            'int': int,
+            'float': float,
+            'bool': bool,
 
             # unfortunately, 'list' is used in dataset metadata both for
             #   query style maps (9th col gff) AND comma-sep strings.
@@ -334,7 +333,7 @@ class DictDataProvider(ColumnarDataProvider):
         params (limit, offset, etc.) are also applicable here.
     """
     settings = {
-        'column_names'  : 'list:str',
+        'column_names': 'list:str',
     }
 
     def __init__(self, source, column_names=None, **kwargs):
diff --git a/lib/galaxy/datatypes/dataproviders/dataset.py b/lib/galaxy/datatypes/dataproviders/dataset.py
index 687f5f0062a..b9fcb6af37d 100644
--- a/lib/galaxy/datatypes/dataproviders/dataset.py
+++ b/lib/galaxy/datatypes/dataproviders/dataset.py
@@ -79,8 +79,8 @@ class DatasetDataProvider(base.DataProvider):
             Optional: defaults to None (return all types)
         :type indeces: list of ints
         """
-        metadata_column_types = (self.dataset.metadata.column_types or
-                                 getattr(self.dataset.datatype, 'column_types', None) or None)
+        metadata_column_types = (self.dataset.metadata.column_types
+                                 or getattr(self.dataset.datatype, 'column_types', None) or None)
         if not metadata_column_types:
             return metadata_column_types
         if indeces:
@@ -99,8 +99,8 @@ class DatasetDataProvider(base.DataProvider):
             Optional: defaults to None (return all names)
         :type indeces: list of ints
         """
-        metadata_column_names = (self.dataset.metadata.column_names or
-                                 getattr(self.dataset.datatype, 'column_names', None) or None)
+        metadata_column_names = (self.dataset.metadata.column_names
+                                 or getattr(self.dataset.datatype, 'column_names', None) or None)
         if not metadata_column_names:
             return metadata_column_names
         if indeces:
@@ -122,11 +122,11 @@ class DatasetDataProvider(base.DataProvider):
         :raises KeyError: if column_names are not found
         :raises ValueError: if an entry in list_of_column_names is not in column_names
         """
-        metadata_column_names = (self.dataset.metadata.column_names or
-                                 getattr(self.dataset.datatype, 'column_names', None) or None)
+        metadata_column_names = (self.dataset.metadata.column_names
+                                 or getattr(self.dataset.datatype, 'column_names', None) or None)
         if not metadata_column_names:
-            raise KeyError('No column_names found for ' +
-                           'datatype: {}, dataset: {}'.format(str(self.dataset.datatype), str(self.dataset)))
+            raise KeyError('No column_names found for '
+                           + 'datatype: {}, dataset: {}'.format(str(self.dataset.datatype), str(self.dataset)))
         indeces = []  # if indeces and column_names:
         # pull using indeces and re-name with given names - no need to alter (does as super would)
         #    pass
@@ -270,10 +270,10 @@ class GenomicRegionDataProvider(column.ColumnarDataProvider):
     # dictionary keys when named_columns=True
     COLUMN_NAMES = ['chrom', 'start', 'end']
     settings = {
-        'chrom_column'  : 'int',
-        'start_column'  : 'int',
-        'end_column'    : 'int',
-        'named_columns' : 'bool',
+        'chrom_column': 'int',
+        'start_column': 'int',
+        'end_column': 'int',
+        'named_columns': 'bool',
     }
 
     def __init__(self, dataset, chrom_column=None, start_column=None, end_column=None, named_columns=False, **kwargs):
@@ -304,12 +304,12 @@ class GenomicRegionDataProvider(column.ColumnarDataProvider):
             end_column = dataset_source.get_metadata_column_index_by_name('endCol')
         indeces = [chrom_column, start_column, end_column]
         if not all(_ is not None for _ in indeces):
-            raise ValueError("Could not determine proper column indeces for" +
-                             " chrom, start, end: %s" % (str(indeces)))
-        kwargs.update({'indeces' : indeces})
+            raise ValueError("Could not determine proper column indeces for"
+                             + " chrom, start, end: %s" % (str(indeces)))
+        kwargs.update({'indeces': indeces})
 
         if not kwargs.get('column_types', None):
-            kwargs.update({'column_types' : dataset_source.get_metadata_column_types(indeces=indeces)})
+            kwargs.update({'column_types': dataset_source.get_metadata_column_types(indeces=indeces)})
 
         self.named_columns = named_columns
         if self.named_columns:
@@ -338,12 +338,12 @@ class IntervalDataProvider(column.ColumnarDataProvider):
     """
     COLUMN_NAMES = ['chrom', 'start', 'end', 'strand', 'name']
     settings = {
-        'chrom_column'  : 'int',
-        'start_column'  : 'int',
-        'end_column'    : 'int',
-        'strand_column' : 'int',
-        'name_column'   : 'int',
-        'named_columns' : 'bool',
+        'chrom_column': 'int',
+        'start_column': 'int',
+        'end_column': 'int',
+        'strand_column': 'int',
+        'name_column': 'int',
+        'named_columns': 'bool',
     }
 
     def __init__(self, dataset, chrom_column=None, start_column=None, end_column=None,
@@ -390,9 +390,9 @@ class IntervalDataProvider(column.ColumnarDataProvider):
                 self.column_names.append('name')
                 indeces.append(name_column)
 
-        kwargs.update({'indeces' : indeces})
+        kwargs.update({'indeces': indeces})
         if not kwargs.get('column_types', None):
-            kwargs.update({'column_types' : dataset_source.get_metadata_column_types(indeces=indeces)})
+            kwargs.update({'column_types': dataset_source.get_metadata_column_types(indeces=indeces)})
 
         self.named_columns = named_columns
 
@@ -419,7 +419,7 @@ class FastaDataProvider(base.FilteredDataProvider):
         }
     """
     settings = {
-        'ids'  : 'list:str',
+        'ids': 'list:str',
     }
 
     def __init__(self, source, ids=None, **kwargs):
@@ -438,8 +438,8 @@ class FastaDataProvider(base.FilteredDataProvider):
         parent_gen = super().__iter__()
         for fasta_record in parent_gen:
             yield {
-                'id'  : fasta_record.name,
-                'seq' : fasta_record.text
+                'id': fasta_record.name,
+                'seq': fasta_record.text
             }
 
 
@@ -453,7 +453,7 @@ class TwoBitFastaDataProvider(DatasetDataProvider):
         }
     """
     settings = {
-        'ids'  : 'list:str',
+        'ids': 'list:str',
     }
 
     def __init__(self, source, ids=None, **kwargs):
@@ -483,8 +483,8 @@ class WiggleDataProvider(base.LimitedOffsetDataProvider):
     """
     COLUMN_NAMES = ['chrom', 'pos', 'value']
     settings = {
-        'named_columns' : 'bool',
-        'column_names'  : 'list:str',
+        'named_columns': 'bool',
+        'column_names': 'list:str',
     }
 
     def __init__(self, source, named_columns=False, column_names=None, **kwargs):
@@ -525,12 +525,13 @@ class BigWigDataProvider(base.LimitedOffsetDataProvider):
     """
     COLUMN_NAMES = ['chrom', 'pos', 'value']
     settings = {
-        'named_columns' : 'bool',
-        'column_names'  : 'list:str',
+        'named_columns': 'bool',
+        'column_names': 'list:str',
     }
 
     def __init__(self, source, chrom, start, end, named_columns=False, column_names=None, **kwargs):
         """
+
         :param chrom: which chromosome within the bigbed file to extract data for
         :type chrom: str
         :param start: the start of the region from which to extract data
@@ -539,15 +540,16 @@ class BigWigDataProvider(base.LimitedOffsetDataProvider):
         :type end: int
 
         :param named_columns: optionally return dictionaries keying each column
-            with 'chrom', 'start', 'end', 'strand', or 'name'.
-            Optional: defaults to False
+                              with 'chrom', 'start', 'end', 'strand', or 'name'.
+                              Optional: defaults to False
         :type named_columns: bool
 
         :param column_names: an ordered list of strings that will be used as the keys
-            for each column in the returned dictionaries.
-            The number of key, value pairs each returned dictionary has will
-            be as short as the number of column names provided.
+                             for each column in the returned dictionaries.
+                             The number of key, value pairs each returned dictionary has will
+                             be as short as the number of column names provided.
         :type column_names:
+
         """
         raise NotImplementedError('Work in progress')
         # TODO: validate is a wig
@@ -657,8 +659,8 @@ class SamtoolsDataProvider(line.RegexLineDataProvider):
 
         # if sam add -S
         # TODO: not the best test in the world...
-        if((self.dataset.ext == 'sam') and
-                ('S' not in validated_flag_list)):
+        if((self.dataset.ext == 'sam')
+                and ('S' not in validated_flag_list)):
             validated_flag_list.append('S')
 
         if validated_flag_list:
@@ -688,32 +690,6 @@ class SamtoolsDataProvider(line.RegexLineDataProvider):
         return options_dict, new_kwargs
 
 
-class BcftoolsDataProvider(line.RegexLineDataProvider):
-    """
-    Data provider that uses an bcftools on a bcf (or vcf?) file as its source.
-
-    This can be piped through other providers (column, map, genome region, etc.).
-    """
-
-    def __init__(self, dataset, **kwargs):
-        # TODO: as samtools
-        raise NotImplementedError()
-        # super(BcftoolsDataProvider, self).__init__(dataset, **kwargs)
-
-
-class BGzipTabixDataProvider(base.DataProvider):
-    """
-    Data provider that uses an g(un)zip on a file as its source.
-
-    This can be piped through other providers (column, map, genome region, etc.).
-    """
-
-    def __init__(self, dataset, **kwargs):
-        # TODO: as samtools - need more info on output format
-        raise NotImplementedError()
-        # super(BGzipTabixDataProvider, self).__init__(dataset, **kwargs)
-
-
 class SQliteDataProvider(base.DataProvider):
     """
     Data provider that uses a sqlite database file as its source.
diff --git a/lib/galaxy/datatypes/dataproviders/decorators.py b/lib/galaxy/datatypes/dataproviders/decorators.py
index 76d05776f4f..6a2579260b3 100644
--- a/lib/galaxy/datatypes/dataproviders/decorators.py
+++ b/lib/galaxy/datatypes/dataproviders/decorators.py
@@ -67,9 +67,9 @@ def has_dataproviders(cls):
     #       where it's possible to override a super's provider with a sub's
     for attr_key, attr_value in cls.__dict__.items():
         # can't use isinstance( attr_value, MethodType ) bc of wrapping
-        if((callable(attr_value)) and
-                (not attr_key.startswith("__")) and
-                (getattr(attr_value, _DATAPROVIDER_METHOD_NAME_KEY, None))):
+        if((callable(attr_value))
+                and (not attr_key.startswith("__"))
+                and (getattr(attr_value, _DATAPROVIDER_METHOD_NAME_KEY, None))):
             name = getattr(attr_value, _DATAPROVIDER_METHOD_NAME_KEY)
             dataproviders[name] = attr_value
     return cls
@@ -125,12 +125,12 @@ def _parse_query_string_settings(query_kwargs, settings=None):
         return s.split(',')
 
     parsers = {
-        'int'   : int,
-        'float' : float,
-        'bool'  : bool,
-        'list:str'      : lambda s: list_from_query_string(s),
-        'list:escaped'  : lambda s: [unquote(e) for e in list_from_query_string(s)],
-        'list:int'      : lambda s: [int(i) for i in list_from_query_string(s)],
+        'int': int,
+        'float': float,
+        'bool': bool,
+        'list:str': lambda s: list_from_query_string(s),
+        'list:escaped': lambda s: [unquote(e) for e in list_from_query_string(s)],
+        'list:int': lambda s: [int(i) for i in list_from_query_string(s)],
     }
     settings = settings or {}
     # yay! yet another set of query string parsers! <-- sarcasm
diff --git a/lib/galaxy/datatypes/dataproviders/hierarchy.py b/lib/galaxy/datatypes/dataproviders/hierarchy.py
index ffe060c62d9..7a52dd76b29 100644
--- a/lib/galaxy/datatypes/dataproviders/hierarchy.py
+++ b/lib/galaxy/datatypes/dataproviders/hierarchy.py
@@ -34,8 +34,8 @@ class XMLDataProvider(HierarchalDataProvider):
     # using lxml.etree's iterparse method to keep mem down
     # TODO:   this, however (AFAIK), prevents the use of xpath
     settings = {
-        'selector'  : 'str',  # urlencoded
-        'max_depth' : 'int',
+        'selector': 'str',  # urlencoded
+        'max_depth': 'int',
     }
     ITERPARSE_ALL_EVENTS = ('start', 'end', 'start-ns', 'end-ns')
     # TODO: move appropo into super
@@ -65,8 +65,8 @@ class XMLDataProvider(HierarchalDataProvider):
         # TODO: fails with '#' - browser thinks it's an anchor - use urlencode
         # TODO: need removal/replacement of etree namespacing here - then move to string match
         Element = getattr(etree, '_Element', etree.Element)
-        return bool((selector is None) or
-                    (isinstance(element, Element) and selector in element.tag))
+        return bool((selector is None)
+                    or (isinstance(element, Element) and selector in element.tag))
 
     def element_as_dict(self, element):
         """
@@ -76,10 +76,10 @@ class XMLDataProvider(HierarchalDataProvider):
         """
         # TODO: Key collision is unlikely here, but still should be better handled
         return {
-            'tag'      : element.tag,
-            'text'     : element.text.strip() if element.text else None,
+            'tag': element.tag,
+            'text': element.text.strip() if element.text else None,
             # needs shallow copy to protect v. element.clear()
-            'attrib'   : dict(element.attrib)
+            'attrib': dict(element.attrib)
         }
 
     def get_children(self, element, max_depth=None):
@@ -111,8 +111,8 @@ class XMLDataProvider(HierarchalDataProvider):
                 self.namespaces[ns] = uri
 
             elif event == 'start':
-                if((selected_element is None) and
-                        (self.matches_selector(element, self.selector))):
+                if((selected_element is None)
+                        and (self.matches_selector(element, self.selector))):
                     # start tag of selected element - wait for 'end' to emit/yield
                     selected_element = element
 
diff --git a/lib/galaxy/datatypes/dataproviders/line.py b/lib/galaxy/datatypes/dataproviders/line.py
index daf4519368f..c4707c553ce 100644
--- a/lib/galaxy/datatypes/dataproviders/line.py
+++ b/lib/galaxy/datatypes/dataproviders/line.py
@@ -25,10 +25,10 @@ class FilteredLineDataProvider(base.LimitedOffsetDataProvider):
     """
     DEFAULT_COMMENT_CHAR = '#'
     settings = {
-        'strip_lines'   : 'bool',
+        'strip_lines': 'bool',
         'strip_newlines': 'bool',
-        'provide_blank' : 'bool',
-        'comment_char'  : 'str',
+        'provide_blank': 'bool',
+        'comment_char': 'str',
     }
 
     def __init__(self, source, strip_lines=True, strip_newlines=False, provide_blank=False,
@@ -91,8 +91,8 @@ class RegexLineDataProvider(FilteredLineDataProvider):
         the line it is considered valid and will be provided).
     """
     settings = {
-        'regex_list'    : 'list:escaped',
-        'invert'        : 'bool',
+        'regex_list': 'list:escaped',
+        'invert': 'bool',
     }
 
     def __init__(self, source, regex_list=None, invert=False, **kwargs):
diff --git a/lib/galaxy/datatypes/genetics.py b/lib/galaxy/datatypes/genetics.py
index 24a60abb68d..cdf98ab32d1 100644
--- a/lib/galaxy/datatypes/genetics.py
+++ b/lib/galaxy/datatypes/genetics.py
@@ -179,7 +179,7 @@ class GenomeGraphs(Tabular):
         True
         """
         buf = file_prefix.contents_header
-        rows = [l.split() for l in buf.splitlines()[1:4]]  # break on lines and drop header, small sample
+        rows = [line.split() for line in buf.splitlines()[1:4]]  # break on lines and drop header, small sample
 
         if len(rows) < 1:
             return False
diff --git a/lib/galaxy/datatypes/graph.py b/lib/galaxy/datatypes/graph.py
index df3c2131437..c36deb26885 100644
--- a/lib/galaxy/datatypes/graph.py
+++ b/lib/galaxy/datatypes/graph.py
@@ -45,8 +45,8 @@ class Xgmml(xml.GenericXml):
         Merging multiple XML files is non-trivial and must be done in subclasses.
         """
         if len(split_files) > 1:
-            raise NotImplementedError("Merging multiple XML files is non-trivial " +
-                                      "and must be implemented for each XML type")
+            raise NotImplementedError("Merging multiple XML files is non-trivial "
+                                      + "and must be implemented for each XML type")
         # For one file only, use base class method (move/copy)
         data.Text.merge(split_files, output_file)
 
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index 638d8cd66a8..6edb651ea1c 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -393,9 +393,9 @@ class Bed(Interval):
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         """Sets the metadata information for datasets previously determined to be in bed format."""
-        i = 0
         if dataset.has_data():
-            for i, line in enumerate(open(dataset.file_name)):
+            i = 0
+            for i, line in enumerate(open(dataset.file_name)):  # noqa: B007
                 line = line.rstrip('\r\n')
                 if line and not line.startswith('#'):
                     elems = line.split('\t')
@@ -683,7 +683,7 @@ class Gff(Tabular, _RemoteCallMixin):
 
         i = 0
         with compression_utils.get_fileobj(dataset.file_name) as in_fh:
-            for i, line in enumerate(in_fh):
+            for i, line in enumerate(in_fh):  # noqa: B007
                 line = line.rstrip('\r\n')
                 if line and not line.startswith('#'):
                     elems = line.split('\t')
@@ -889,7 +889,7 @@ class Gff3(Gff):
         self.set_attribute_metadata(dataset)
         i = 0
         with compression_utils.get_fileobj(dataset.file_name) as in_fh:
-            for i, line in enumerate(in_fh):
+            for i, line in enumerate(in_fh):  # noqa: B007
                 line = line.rstrip('\r\n')
                 if line and not line.startswith('#'):
                     elems = line.split('\t')
@@ -1171,7 +1171,7 @@ class Wiggle(Tabular, _RemoteCallMixin):
     def set_meta(self, dataset, overwrite=True, **kwd):
         max_data_lines = None
         i = 0
-        for i, line in enumerate(open(dataset.file_name)):
+        for i, line in enumerate(open(dataset.file_name)):  # noqa: B007
             line = line.rstrip('\r\n')
             if line and not line.startswith('#'):
                 elems = line.split('\t')
diff --git a/lib/galaxy/datatypes/molecules.py b/lib/galaxy/datatypes/molecules.py
index 1eaa4fb81da..1f8a0dac099 100644
--- a/lib/galaxy/datatypes/molecules.py
+++ b/lib/galaxy/datatypes/molecules.py
@@ -107,8 +107,8 @@ class SDF(GenericMolFile):
             if idx < 4:
                 continue
             elif idx == 4:
-                if len(line) != 39 or not(line.endswith(' V2000') or
-                        line.endswith(' V3000')):
+                if len(line) != 39 or not(line.endswith(' V2000')
+                        or line.endswith(' V3000')):
                     return False
             elif not m_end_found:
                 if line == 'M  END':
diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py
index 2d495c05a53..94fa6b2a3b7 100644
--- a/lib/galaxy/datatypes/mothur.py
+++ b/lib/galaxy/datatypes/mothur.py
@@ -357,6 +357,7 @@ class LowerTriangleDistanceMatrix(DistanceMatrix):
         Determines whether the file is a lower-triangle distance matrix (phylip) format
         The first line has the number of sequences in the matrix.
         The remaining lines have the sequence name followed by a list of distances from all preceeding sequences
+
                 5  # possibly but not always preceded by a tab :/
                 U68589
                 U68590	0.3371
@@ -422,6 +423,7 @@ class SquareDistanceMatrix(DistanceMatrix):
         The first line has the number of sequences in the matrix.
         The following lines have the sequence name in the first column plus a column for the distance to each sequence
         in the row order in which they appear in the matrix.
+
                3
                U68589  0.0000  0.3371  0.3610
                U68590  0.3371  0.0000  0.3783
@@ -623,11 +625,14 @@ class Frequency(Tabular):
     def sniff_prefix(self, file_prefix):
         """
         Determines whether the file is a frequency tabular format for chimera analysis
-        #1.14.0
-        0	0.000
-        1	0.000
-        ...
-        155	0.975
+
+        .. code-block::
+
+            #1.14.0
+            0	0.000
+            1	0.000
+            ...
+            155	0.975
 
         >>> from galaxy.datatypes.sniff import get_test_fname
         >>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.freq' )
@@ -685,10 +690,13 @@ class Quantile(Tabular):
     def sniff_prefix(self, file_prefix):
         """
         Determines whether the file is a quantiles tabular format for chimera analysis
-        1	0	0	0	0	0	0
-        2       0.309198        0.309198        0.37161 0.37161 0.37161 0.37161
-        3       0.510982        0.563213        0.693529        0.858939        1.07442 1.20608
-        ...
+
+        .. code-block::
+
+            1	0	0	0	0	0	0
+            2       0.309198        0.309198        0.37161 0.37161 0.37161 0.37161
+            3       0.510982        0.563213        0.693529        0.858939        1.07442 1.20608
+            ...
 
         >>> from galaxy.datatypes.sniff import get_test_fname
         >>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.quan' )
@@ -805,17 +813,26 @@ class RefTaxonomy(Tabular):
 
         http://www.mothur.org/wiki/Taxonomy_outline
         A table with 2 or 3 columns:
+
         - SequenceName
         - Taxonomy (semicolon-separated taxonomy in descending order)
         - integer ?
+
         Example: 2-column (http://www.mothur.org/wiki/Taxonomy_outline)
-          X56533.1        Eukaryota;Alveolata;Ciliophora;Intramacronucleata;Oligohymenophorea;Hymenostomatida;Tetrahymenina;Glaucomidae;Glaucoma;
-          X97975.1        Eukaryota;Parabasalidea;Trichomonada;Trichomonadida;unclassified_Trichomonadida;
-          AF052717.1      Eukaryota;Parabasalidea;
+
+        .. code-block::
+
+            X56533.1        Eukaryota;Alveolata;Ciliophora;Intramacronucleata;Oligohymenophorea;Hymenostomatida;Tetrahymenina;Glaucomidae;Glaucoma;
+            X97975.1        Eukaryota;Parabasalidea;Trichomonada;Trichomonadida;unclassified_Trichomonadida;
+            AF052717.1      Eukaryota;Parabasalidea;
+
         Example: 3-column (http://vamps.mbl.edu/resources/databases.php)
-          v3_AA008	Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus	5
-          v3_AA016	Bacteria	120
-          v3_AA019	Archaea;Crenarchaeota;Marine_Group_I	1
+
+        .. code-block::
+
+            v3_AA008	Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus	5
+            v3_AA016	Bacteria	120
+            v3_AA019	Archaea;Crenarchaeota;Marine_Group_I	1
 
         >>> from galaxy.datatypes.sniff import get_test_fname
         >>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.ref.taxonomy' )
@@ -882,16 +899,19 @@ class Axes(Tabular):
         Determines whether the file is an axes format
         The first line may have column headings.
         The following lines have the name in the first column plus float columns for each axis.
-        ==> 98_sq_phylip_amazon.fn.unique.pca.axes <==
-           group   axis1   axis2
-           forest  0.000000        0.145743
-           pasture 0.145743        0.000000
 
-        ==> 98_sq_phylip_amazon.nmds.axes <==
-                   axis1   axis2
-           U68589  0.262608        -0.077498
-           U68590  0.027118        0.195197
-           U68591  0.329854        0.014395
+        .. code-block::
+
+            group   axis1   axis2
+            forest  0.000000        0.145743
+            pasture 0.145743        0.000000
+
+        .. code-block::
+
+                    axis1   axis2
+            U68589  0.262608        -0.077498
+            U68590  0.027118        0.195197
+            U68591  0.329854        0.014395
 
         >>> from galaxy.datatypes.sniff import get_test_fname
         >>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.axes' )
@@ -943,14 +963,20 @@ class SffFlow(Tabular):
         https://mothur.org/wiki/flow_file/
         The first line is the total number of flow values - 800 for Titanium data. For GS FLX it would be 400.
         Following lines contain:
+
         - SequenceName
         - the number of useable flows as defined by 454's software
         - the flow intensity for each base going in the order of TACG.
+
         Example:
+
+        .. code-block::
+
           800
           GQY1XT001CQL4K 85 1.04 0.00 1.00 0.02 0.03 1.02 0.05 ...
           GQY1XT001CQIRF 84 1.02 0.06 0.98 0.06 0.09 1.05 0.07 ...
           GQY1XT001CF5YW 88 1.02 0.02 1.01 0.04 0.06 1.02 0.03 ...
+
     """
 
     def __init__(self, **kwd):
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 379991778c5..58669790336 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -756,73 +756,73 @@ class Registry:
         # Default values.
         if not self.datatypes_by_extension:
             self.datatypes_by_extension = {
-                'ab1'           : binary.Ab1(),
-                'axt'           : sequence.Axt(),
-                'bam'           : binary.Bam(),
-                'bed'           : interval.Bed(),
-                'coverage'      : coverage.LastzCoverage(),
-                'customtrack'   : interval.CustomTrack(),
-                'csfasta'       : sequence.csFasta(),
-                'fasta'         : sequence.Fasta(),
-                'eland'         : tabular.Eland(),
-                'fastq'         : sequence.Fastq(),
-                'fastqsanger'   : sequence.FastqSanger(),
-                'gtf'           : interval.Gtf(),
-                'gff'           : interval.Gff(),
-                'gff3'          : interval.Gff3(),
-                'genetrack'     : tracks.GeneTrack(),
-                'h5'            : binary.H5(),
-                'interval'      : interval.Interval(),
-                'laj'           : images.Laj(),
-                'lav'           : sequence.Lav(),
-                'maf'           : sequence.Maf(),
-                'pileup'        : tabular.Pileup(),
-                'qualsolid'     : qualityscore.QualityScoreSOLiD(),
-                'qualsolexa'    : qualityscore.QualityScoreSolexa(),
-                'qual454'       : qualityscore.QualityScore454(),
-                'sam'           : tabular.Sam(),
-                'scf'           : binary.Scf(),
-                'sff'           : binary.Sff(),
-                'tabular'       : tabular.Tabular(),
-                'csv'           : tabular.CSV(),
-                'taxonomy'      : tabular.Taxonomy(),
-                'txt'           : data.Text(),
-                'wig'           : interval.Wiggle(),
-                'xml'           : xml.GenericXml(),
+                'ab1': binary.Ab1(),
+                'axt': sequence.Axt(),
+                'bam': binary.Bam(),
+                'bed': interval.Bed(),
+                'coverage': coverage.LastzCoverage(),
+                'customtrack': interval.CustomTrack(),
+                'csfasta': sequence.csFasta(),
+                'fasta': sequence.Fasta(),
+                'eland': tabular.Eland(),
+                'fastq': sequence.Fastq(),
+                'fastqsanger': sequence.FastqSanger(),
+                'gtf': interval.Gtf(),
+                'gff': interval.Gff(),
+                'gff3': interval.Gff3(),
+                'genetrack': tracks.GeneTrack(),
+                'h5': binary.H5(),
+                'interval': interval.Interval(),
+                'laj': images.Laj(),
+                'lav': sequence.Lav(),
+                'maf': sequence.Maf(),
+                'pileup': tabular.Pileup(),
+                'qualsolid': qualityscore.QualityScoreSOLiD(),
+                'qualsolexa': qualityscore.QualityScoreSolexa(),
+                'qual454': qualityscore.QualityScore454(),
+                'sam': tabular.Sam(),
+                'scf': binary.Scf(),
+                'sff': binary.Sff(),
+                'tabular': tabular.Tabular(),
+                'csv': tabular.CSV(),
+                'taxonomy': tabular.Taxonomy(),
+                'txt': data.Text(),
+                'wig': interval.Wiggle(),
+                'xml': xml.GenericXml(),
             }
             self.mimetypes_by_extension = {
-                'ab1'           : 'application/octet-stream',
-                'axt'           : 'text/plain',
-                'bam'           : 'application/octet-stream',
-                'bed'           : 'text/plain',
-                'customtrack'   : 'text/plain',
-                'csfasta'       : 'text/plain',
-                'eland'         : 'application/octet-stream',
-                'fasta'         : 'text/plain',
-                'fastq'         : 'text/plain',
-                'fastqsanger'   : 'text/plain',
-                'gtf'           : 'text/plain',
-                'gff'           : 'text/plain',
-                'gff3'          : 'text/plain',
-                'h5'            : 'application/octet-stream',
-                'interval'      : 'text/plain',
-                'laj'           : 'text/plain',
-                'lav'           : 'text/plain',
-                'maf'           : 'text/plain',
-                'memexml'       : 'application/xml',
-                'pileup'        : 'text/plain',
-                'qualsolid'     : 'text/plain',
-                'qualsolexa'    : 'text/plain',
-                'qual454'       : 'text/plain',
-                'sam'           : 'text/plain',
-                'scf'           : 'application/octet-stream',
-                'sff'           : 'application/octet-stream',
-                'tabular'       : 'text/plain',
-                'csv'           : 'text/plain',
-                'taxonomy'      : 'text/plain',
-                'txt'           : 'text/plain',
-                'wig'           : 'text/plain',
-                'xml'           : 'application/xml',
+                'ab1': 'application/octet-stream',
+                'axt': 'text/plain',
+                'bam': 'application/octet-stream',
+                'bed': 'text/plain',
+                'customtrack': 'text/plain',
+                'csfasta': 'text/plain',
+                'eland': 'application/octet-stream',
+                'fasta': 'text/plain',
+                'fastq': 'text/plain',
+                'fastqsanger': 'text/plain',
+                'gtf': 'text/plain',
+                'gff': 'text/plain',
+                'gff3': 'text/plain',
+                'h5': 'application/octet-stream',
+                'interval': 'text/plain',
+                'laj': 'text/plain',
+                'lav': 'text/plain',
+                'maf': 'text/plain',
+                'memexml': 'application/xml',
+                'pileup': 'text/plain',
+                'qualsolid': 'text/plain',
+                'qualsolexa': 'text/plain',
+                'qual454': 'text/plain',
+                'sam': 'text/plain',
+                'scf': 'application/octet-stream',
+                'sff': 'application/octet-stream',
+                'tabular': 'text/plain',
+                'csv': 'text/plain',
+                'taxonomy': 'text/plain',
+                'txt': 'text/plain',
+                'wig': 'text/plain',
+                'xml': 'application/xml',
             }
         # super supertype fix for input steps in workflows.
         if 'data' not in self.datatypes_by_extension:
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index efcd99cbfcc..d94d77ee669 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -547,7 +547,7 @@ class Sam(Tabular):
                             break
                 else:
                     # Otherwise, read the whole thing and set num data lines.
-                    for i, l in enumerate(dataset_fh):
+                    for i, l in enumerate(dataset_fh):  # noqa: B007
                         if l.startswith('@'):
                             comment_lines += 1
                     dataset.metadata.data_lines = i + 1 - comment_lines
@@ -1238,18 +1238,20 @@ class MatrixMarket(TabularData):
     suitable for representing sparse matrices. Only nonzero entries need
     be encoded, and the coordinates of each are given explicitly.
 
-    The tabular file format is defined as follows::
+    The tabular file format is defined as follows:
 
-    %%MatrixMarket matrix coordinate real general <--- header line
-    %                                             <--+
-    % comments                                       |-- 0 or more comment lines
-    %                                             <--+
-        M  N  L                                   <--- rows, columns, entries
-        I1  J1  A(I1, J1)                         <--+
-        I2  J2  A(I2, J2)                            |
-        I3  J3  A(I3, J3)                            |-- L lines
-            . . .                                    |
-        IL JL  A(IL, JL)                          <--+
+    .. code-block::
+
+        %%MatrixMarket matrix coordinate real general <--- header line
+        %                                             <--+
+        % comments                                       |-- 0 or more comment lines
+        %                                             <--+
+            M  N  L                                   <--- rows, columns, entries
+            I1  J1  A(I1, J1)                         <--+
+            I2  J2  A(I2, J2)                            |
+            I3  J3  A(I3, J3)                            |-- L lines
+                . . .                                    |
+            IL JL  A(IL, JL)                          <--+
 
     Indices are 1-based, i.e. A(1,1) is the first element.
 
@@ -1286,7 +1288,7 @@ class MatrixMarket(TabularData):
                             dataset.metadata.data_lines = None
                             break
                 else:
-                    for i, l in enumerate(dataset_fh):
+                    for i, l in enumerate(dataset_fh):  # noqa: B007
                         if l.startswith('%'):
                             comment_lines += 1
                     dataset.metadata.data_lines = i + 1 - comment_lines
diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py
index 48b54c6d080..56fa5b863b9 100644
--- a/lib/galaxy/datatypes/text.py
+++ b/lib/galaxy/datatypes/text.py
@@ -849,7 +849,7 @@ class Gfa2(Text):
             elif line[0] == 'G':
                 if len(line) < 6:
                     return False
-            elif line[0] == 'O' or line[0] == 'U' :
+            elif line[0] == 'O' or line[0] == 'U':
                 if len(line) < 3:
                     return False
             else:
diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py
index 95360b10c50..c15e872a993 100644
--- a/lib/galaxy/dependencies/__init__.py
+++ b/lib/galaxy/dependencies/__init__.py
@@ -172,9 +172,9 @@ class ConditionalDependencies:
         return self.config["database_connection"].startswith("mysql")
 
     def check_drmaa(self):
-        return ("galaxy.jobs.runners.drmaa:DRMAAJobRunner" in self.job_runners or
-                "galaxy.jobs.runners.slurm:SlurmJobRunner" in self.job_runners or
-                "galaxy.jobs.runners.univa:UnivaJobRunner" in self.job_runners)
+        return ("galaxy.jobs.runners.drmaa:DRMAAJobRunner" in self.job_runners
+                or "galaxy.jobs.runners.slurm:SlurmJobRunner" in self.job_runners
+                or "galaxy.jobs.runners.univa:UnivaJobRunner" in self.job_runners)
 
     def check_galaxycloudrunner(self):
         return ("galaxycloudrunner.rules" in self.job_rule_modules)
@@ -198,8 +198,8 @@ class ConditionalDependencies:
         return self.config.get("statsd_host", None) is not None
 
     def check_python_ldap(self):
-        return ('ldap' in self.authenticators or
-                'activedirectory' in self.authenticators)
+        return ('ldap' in self.authenticators
+                or 'activedirectory' in self.authenticators)
 
     def check_python_pam(self):
         return 'PAM' in self.authenticators
@@ -221,13 +221,13 @@ class ConditionalDependencies:
 
     def check_watchdog(self):
         install_set = {'auto', 'True', 'true', 'polling'}
-        return (self.config['watch_tools'] in install_set or
-                self.config['watch_tool_data_dir'] in install_set)
+        return (self.config['watch_tools'] in install_set
+                or self.config['watch_tool_data_dir'] in install_set)
 
     def check_docker(self):
-        return (self.config.get("enable_beta_containers_interface", False) and
-                ('docker' in self.container_interface_types or
-                 'docker_swarm' in self.container_interface_types))
+        return (self.config.get("enable_beta_containers_interface", False)
+                and ('docker' in self.container_interface_types
+                     or 'docker_swarm' in self.container_interface_types))
 
     def check_python_gitlab(self):
         return 'gitlab' in self.error_report_modules
diff --git a/lib/galaxy/dependencies/pipfiles/default/Pipfile b/lib/galaxy/dependencies/pipfiles/default/Pipfile
index f914d1b606c..fc391f87850 100644
--- a/lib/galaxy/dependencies/pipfiles/default/Pipfile
+++ b/lib/galaxy/dependencies/pipfiles/default/Pipfile
@@ -56,6 +56,7 @@ docutils = "*"
 uvicorn = "*"
 fastapi = "*"
 fastapi-utils = "*"
+aiofiles = "*"
 Routes = "*"
 WebOb = "*"
 Mako = "*"
@@ -84,7 +85,7 @@ pyparsing = "*"
 "Fabric3" = "*"
 paramiko = "*"
 cloudbridge = "*"
-social_auth_core = {version = "==3.3.0", extras = ['openidconnect']}
+social-auth-core = {version = "==3.3.0", extras = ['openidconnect']}
 cloudauthz = "==0.6.0"
 gxformat2 = "*"
 refgenconf = ">=0.7.0"
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index 09324d1cd95..672dc270335 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -8,6 +8,7 @@
 -i https://wheels.galaxyproject.org/simple
 --extra-index-url https://pypi.python.org/simple
 adal==1.2.5
+aiofiles==0.6.0
 amqp==5.0.2; python_version >= '3.6'
 appdirs==1.4.4
 argcomplete==1.12.2
diff --git a/lib/galaxy/dependencies/pipfiles/flake8/Pipfile b/lib/galaxy/dependencies/pipfiles/flake8/Pipfile
index 75dd9343030..37e5ba2e60b 100644
--- a/lib/galaxy/dependencies/pipfiles/flake8/Pipfile
+++ b/lib/galaxy/dependencies/pipfiles/flake8/Pipfile
@@ -1,15 +1,15 @@
 [[source]]
-
 url = "https://pypi.python.org/simple"
 verify_ssl = true
 name = "pypi"
 
-
 [dev-packages]
 
 
-
 [packages]
+flake8 = "*"
+flake8-bugbear = "*"
+flake8-import-order = "*"
 
-"flake8" = "*"
-"flake8-import-order" = "*"
+[requires]
+python_version = "3.6"
diff --git a/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
index fb7b14ca23a..2f35a72138d 100644
--- a/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
@@ -6,10 +6,13 @@
 #
 
 -i https://pypi.python.org/simple
+attrs==20.3.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+flake8-bugbear==20.11.1
 flake8-import-order==0.18.1
 flake8==3.8.4
 importlib-metadata==3.1.1; python_version < '3.8'
 mccabe==0.6.1
 pycodestyle==2.6.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 pyflakes==2.2.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+typing-extensions==3.7.4.3; python_version < '3.8'
 zipp==3.4.0; python_version >= '3.6'
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index fb46d84a86f..3ab20ea94e6 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1731,7 +1731,11 @@ class JobWrapper(HasResourceParameters):
         # Certain tools require tasks to be completed after job execution
         # ( this used to be performed in the "exec_after_process" hook, but hooks are deprecated ).
         param_dict = self.get_param_dict(job)
-        self.tool.exec_after_process(self.app, inp_data, out_data, param_dict, job=job, final_job_state=final_job_state)
+        try:
+            self.tool.exec_after_process(self.app, inp_data, out_data, param_dict, job=job, final_job_state=final_job_state)
+        except Exception:
+            log.exception(f"exec_after_process hook failed for job {self.job_id}")
+            final_job_state = job.states.ERROR
         # Call 'exec_after_process' hook
         self.tool.call_hook('exec_after_process', self.app, inp_data=inp_data,
                             out_data=out_data, param_dict=param_dict,
@@ -1834,7 +1838,6 @@ class JobWrapper(HasResourceParameters):
                         if e.errno != errno.ENOENT:
                             raise
                 self.external_output_metadata.cleanup_external_metadata(self.sa_session)
-            galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper(self.app, self.job_id).cleanup_after_job()
             if delete_files:
                 self.object_store.delete(self.get_job(), base_dir='job_work', entire_dir=True, dir_only=True, obj_dir=True)
         except Exception:
diff --git a/lib/galaxy/jobs/dynamic_tool_destination.py b/lib/galaxy/jobs/dynamic_tool_destination.py
index 36832cd5c6a..bc728b1ea8e 100755
--- a/lib/galaxy/jobs/dynamic_tool_destination.py
+++ b/lib/galaxy/jobs/dynamic_tool_destination.py
@@ -83,21 +83,17 @@ class RuleValidator:
     """
 
     @classmethod
-    def validate_rule(cls, rule_type, app, return_bool=False, *args, **kwargs):
+    def validate_rule(cls, rule_type: str, app, return_bool: bool = False, *args, **kwargs):
         """
         This function is responsible for passing each rule to its relevant
         function.
 
-        @type rule_type: str
-        @param rule_type: the current rule's type
-
-        @type return_bool: bool
-        @param return_bool: True when we are only interested in the result of
+        :param rule_type: the current rule's type
+        :param return_bool: True when we are only interested in the result of
                             the validation, and not the validated rule itself.
-
-        @rtype: bool, dict (depending on return_bool)
-        @return: validated rule or result of validation (depending on
-                 return_bool)
+        :rtype: bool, dict (depending on return_bool)
+        :returns: validated rule or result of validation (depending on
+                  return_bool)
         """
         if rule_type == 'file_size':
             return cls.__validate_file_size_rule(app, return_bool, *args, **kwargs)
@@ -380,30 +376,20 @@ class RuleValidator:
         return valid_rule, rule
 
     @classmethod
-    def __validate_destination(cls, valid_rule, app, return_bool, rule, tool, counter):
+    def __validate_destination(cls, valid_rule: bool, app, return_bool: bool, rule: dict, tool: str, counter: int):
         """
         This function is responsible for validating destination.
 
-        @type valid_rule: bool
-        @param valid_rule: returns True if everything is valid. False if it
+        :param valid_rule: returns True if everything is valid. False if it
                            encounters any abnormalities in the config.
-
-        @type return_bool: bool
-        @param return_bool: True when we are only interested in the result of
+        :param return_bool: True when we are only interested in the result of
                             the validation, and not the validated rule itself.
-
-        @type rule: dict
-        @param rule: contains the original received rule
-
-        @type tool: str
-        @param tool: the name of the current tool. Necessary for log output.
-
-        @type counter: int
-        @param counter: this counter is used to identify what rule # is
+        :param rule: contains the original received rule
+        :param tool: the name of the current tool. Necessary for log output.
+        :param counter: this counter is used to identify what rule # is
                         currently being validated. Necessary for log output.
-
-        @rtype: bool, dict (tuple)
-        @return: validated rule and result of validation
+        :rtype: bool, dict (tuple)
+        :returns: validated rule and result of validation
         """
 
         if "fail_message" in rule:
@@ -698,27 +684,20 @@ class RuleValidator:
         return valid_rule, rule
 
 
-def parse_yaml(path="/config/tool_destinations.yml",
-               job_conf_path="/config/job_conf.xml", app=None, test=False,
-               return_bool=False):
+def parse_yaml(path: str = "/config/tool_destinations.yml",
+               job_conf_path: str = "/config/job_conf.xml", app=None, test: bool = False,
+               return_bool: bool = False):
     """
     Get a yaml file from path and send it to validate_config for validation.
 
-    @type path: str
-    @param path: the path to the tool destinations config file
-
-    @type job_conf_path: str
-    @param job_conf_path: the path to the job config file
-
-    @type test: bool
-    @param test: indicates whether to run in test mode or production mode
-
-    @type return_bool: bool
-    @param return_bool: True when we are only interested in the result of the
+    :param path: the path to the tool destinations config file
+    :param job_conf_path: the path to the job config file
+    :param test: indicates whether to run in test mode or production mode
+    :type return_bool: bool
+    :param return_bool: True when we are only interested in the result of the
                           validation, and not the validated rule itself.
-
-    @rtype: bool, dict (depending on return_bool)
-    @return: validated rule or result of validation (depending on return_bool)
+    :rtype: bool, dict (depending on return_bool)
+    :returns: validated rule or result of validation (depending on return_bool)
 
     """
 
@@ -754,7 +733,7 @@ def parse_yaml(path="/config/tool_destinations.yml",
                 config = validate_config(config, app)
         except MalformedYMLException:
             if verbose:
-                log.error(str(sys.exc_value))
+                log.exception("Failed to parse YAML for dynamic job destination")
             raise
     except ScannerError:
         if verbose:
@@ -768,34 +747,26 @@ def parse_yaml(path="/config/tool_destinations.yml",
         return config
 
 
-def validate_destination(app, destination, err_message, err_message_contents,
-                         return_bool=True):
+def validate_destination(app, destination: str, err_message: str, err_message_contents,
+                         return_bool: bool = True):
     """
     Validate received destination id.
 
-    @type app:
-    @param app: Current app
-
-    @type destination: str
-    @param destination: string containing the destination id that is being
+    :param app: Current app
+    :param destination: string containing the destination id that is being
                         validated
-
-    @type err_message: str
-    @param err_message: Error message to be formatted with the contents of
+    :param err_message: Error message to be formatted with the contents of
                         `err_message_contents` upon the event of invalid
                         destination
-
-    @type err_message_contents: tuple
-    @param err_message_contents: A tuple of strings to be placed in
-                                 `err_message`
-
-    @type return_bool: bool
-    @param return_bool: Whether or not the calling function has been told to
+    :type err_message_contents: tuple
+    :param err_message_contents: A tuple of strings to be placed in
+                                 ``err_message``
+    :param return_bool: Whether or not the calling function has been told to
                         return a boolean value or not. Determines whether or
                         not to print 'Ignoring...' after error messages.
 
-    @rtype: bool
-    @return: True if the destination is valid and False otherwise.
+    :rtype: bool
+    :returns: True if the destination is valid and False otherwise.
     """
 
     valid_destination = False
@@ -824,19 +795,15 @@ def validate_destination(app, destination, err_message, err_message_contents,
     return valid_destination
 
 
-def validate_config(obj, app=None, return_bool=False,):
+def validate_config(obj: dict, app=None, return_bool: bool = False):
     """
     Validate received config.
 
-    @type obj: dict
-    @param obj: the entire contents of the config
-
-    @type return_bool: bool
-    @param return_bool: True when we are only interested in the result of the
-                          validation, and not the validated rule itself.
-
-    @rtype: bool, dict (depending on return_bool)
-    @return: validated rule or result of validation (depending on return_bool)
+    :param obj: the entire contents of the config
+    :param return_bool: True when we are only interested in the result of the
+                        validation, and not the validated rule itself.
+    :rtype: bool, dict (depending on return_bool)
+    :returns: validated rule or result of validation (depending on return_bool)
     """
 
     global priority_list
@@ -1625,21 +1592,22 @@ def map_tool_to_destination(
     return destination
 
 
-def get_destination_list_from_job_config(job_config_location):
+def get_destination_list_from_job_config(job_config_location) -> set:
     """
     returns A list of all destination IDs declared in the job configuration
 
-    @type job_config_location: str
-    @param job_config_location: The location of the job config file relative
-                to the galaxy root directory. If NoneType, defaults to
-                galaxy/config/job_conf.xml,
-                galaxy/config/job_conf.xml.sample_advanced, or
-                galaxy/config/job_conf.xml.sample_basic
-                (first one that exists)
+    :type job_config_location: str
+    :param job_config_location:
 
-    @rtype: list
-    @return: A list of all of the destination IDs declared in the job
-                configuration file.
+        The location of the job config file relative
+        to the galaxy root directory. If NoneType, defaults to
+        galaxy/config/job_conf.xml,
+        galaxy/config/job_conf.xml.sample_advanced, or
+        galaxy/config/job_conf.xml.sample_basic
+        (first one that exists)
+
+    :return: A list of all of the destination IDs declared in the job
+             configuration file.
     """
     global destination_list
 
@@ -1751,20 +1719,18 @@ def get_typo_correction(typo_str, word_set, max_dist):
     the same when case is not considered. If there are no
     appropriate matches, nothing is returned instead.
 
-    @type typo_str: str
-    @param typo_str: The string to be compared
+    :type typo_str: str
+    :param typo_str: The string to be compared
+    :type word_set: set of str
+    :param word_set: The set of strings to compare to
+    :type max_dist: int
+    :param max_dist: the largest allowed edit distance between
+                     the word and the result. If nothing is
+                     within this range, nothing is returned
 
-    @type word_set: set of str
-    @param word_set: The set of strings to compare to
-
-    @type max_dist: int
-    @param max_dist: the largest allowed edit distance between
-                    the word and the result. If nothing is
-                    within this range, nothing is returned
-
-    @rtype: str or NoneType
-    @return: The closest matching string, or None, if no strings
-    being compared to are within max_dist edit distance.
+    :rtype: str or NoneType
+    :returns: The closest matching string, or None, if no strings
+              being compared to are within max_dist edit distance.
     """
 
     # Start curr_best out as the largest
diff --git a/lib/galaxy/jobs/handler.py b/lib/galaxy/jobs/handler.py
index 4cff86a0308..101c66a9c1b 100644
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -209,13 +209,13 @@ class JobHandlerQueue(Monitors):
         if self.app.config.user_activation_on:
             jobs_at_startup = self.sa_session.query(model.Job).enable_eagerloads(False) \
                 .outerjoin(model.User) \
-                .filter(model.Job.state.in_(in_list) &
-                        (model.Job.handler == self.app.config.server_name) &
-                        or_((model.Job.user_id == null()), (model.User.active == true()))).all()
+                .filter(model.Job.state.in_(in_list)
+                        & (model.Job.handler == self.app.config.server_name)
+                        & or_((model.Job.user_id == null()), (model.User.active == true()))).all()
         else:
             jobs_at_startup = self.sa_session.query(model.Job).enable_eagerloads(False) \
-                .filter(model.Job.state.in_(in_list) &
-                        (model.Job.handler == self.app.config.server_name)).all()
+                .filter(model.Job.state.in_(in_list)
+                        & (model.Job.handler == self.app.config.server_name)).all()
 
         for job in jobs_at_startup:
             if not self.app.toolbox.has_tool(job.tool_id, job.tool_version, exact=True):
@@ -582,14 +582,10 @@ class JobHandlerQueue(Monitors):
         if state == JOB_READY and self.app.quota_agent.is_over_quota(self.app, job, job_destination):
             return JOB_USER_OVER_QUOTA, job_destination
         # Check total walltime limits
-        if (state == JOB_READY and
-                "delta" in self.app.job_config.limits.total_walltime):
+        if (state == JOB_READY and "delta" in self.app.job_config.limits.total_walltime):
             jobs_to_check = self.sa_session.query(model.Job).filter(
                 model.Job.user_id == job.user.id,
-                model.Job.update_time >= datetime.datetime.now() -
-                datetime.timedelta(
-                    self.app.job_config.limits.total_walltime["window"]
-                ),
+                model.Job.update_time >= datetime.datetime.now() - datetime.timedelta(self.app.job_config.limits.total_walltime["window"]),
                 model.Job.state == 'ok'
             ).all()
             time_spent = datetime.timedelta(0)
@@ -919,8 +915,8 @@ class JobHandlerStopQueue(Monitors):
             newly_deleted_jobs = self.sa_session.query(model.Job).enable_eagerloads(False) \
                                      .filter((model.Job.state.in_((model.Job.states.DELETED_NEW,
                                                                    model.Job.states.DELETING,
-                                                                   model.Job.states.STOPPING))) &
-                                             (model.Job.handler == self.app.config.server_name)).all()
+                                                                   model.Job.states.STOPPING)))
+                                             & (model.Job.handler == self.app.config.server_name)).all()
             for job in newly_deleted_jobs:
                 # job.stderr is always a string (job.job_stderr + job.tool_stderr, possibly `''`),
                 # while any `not None` message returned in self.queue.get_nowait() is interpreted
@@ -944,8 +940,8 @@ class JobHandlerStopQueue(Monitors):
                      job.states.DELETING,
                      job.states.DELETED,
                      job.states.STOPPING,
-                     job.states.STOPPED) and
-                    job.finished):
+                     job.states.STOPPED)
+                    and job.finished):
                 # terminated before it got here
                 log.debug('Job %s already finished, not deleting or stopping', job.id)
                 continue
diff --git a/lib/galaxy/jobs/manager.py b/lib/galaxy/jobs/manager.py
index 1bcd87c2fcb..0f90e5a9e24 100644
--- a/lib/galaxy/jobs/manager.py
+++ b/lib/galaxy/jobs/manager.py
@@ -54,7 +54,7 @@ class JobManager:
 
         Due to the nature of some handler assignment methods which are wholly DB-based, the enqueue method will flush
         the job. Callers who create the job typically should not flush the job before handing it off to ``enqueue()``.
-        If a job handler cannot be assigned, :exception:`ToolExecutionError` is raised.
+        If a job handler cannot be assigned, py:class:`ToolExecutionError` is raised.
 
         :param job:     Job to enqueue.
         :type job:      Instance of :class:`galaxy.model.Job`.
@@ -62,7 +62,7 @@ class JobManager:
         :type tool:     Instance of :class:`galaxy.tools.Tool`.
 
         :raises ToolExecutionError: if a handler was unable to be assigned.
-        returns: str or None -- Handler ID, tag, or pool assigned to the job.
+        :returns: str or None -- Handler ID, tag, or pool assigned to the job.
         """
         tool_id = None
         configured_handler = None
diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py
index ee7b9758974..79d0f2ecd4c 100644
--- a/lib/galaxy/jobs/runners/__init__.py
+++ b/lib/galaxy/jobs/runners/__init__.py
@@ -350,7 +350,7 @@ class BaseJobRunner:
                                                                            set_extension=True,
                                                                            tmp_dir=job_wrapper.working_directory,
                                                                            # We don't want to overwrite metadata that was copied over in init_meta(), as per established behavior
-                                                                           kwds={'overwrite' : False})
+                                                                           kwds={'overwrite': False})
             external_metadata_script = f"{lib_adjust} {venv} {external_metadata_script}"
             if resolve_requirements:
                 dependency_shell_commands = self.app.datatypes_registry.set_external_metadata_tool.build_dependency_shell_commands(job_directory=job_wrapper.working_directory)
diff --git a/lib/galaxy/jobs/runners/drmaa.py b/lib/galaxy/jobs/runners/drmaa.py
index b0b7509fda3..d35a1ac71d1 100644
--- a/lib/galaxy/jobs/runners/drmaa.py
+++ b/lib/galaxy/jobs/runners/drmaa.py
@@ -261,13 +261,17 @@ class DRMAAJobRunner(AsynchronousJobRunner):
         that could happen in this process. to be called from check_watched_items()
         returns the state or None if exceptions occurred
         in the latter case the job is appended to new_watched if a
+
         1 drmaa.InternalException,
         2 drmaa.InvalidJobExceptionnot, or
         3 drmaa.DrmCommunicationException occurred
+
         (which causes the job to be tested again in the next iteration of check_watched_items)
+
         - the job is finished as errored if any other exception occurs
         - the job is finished OK or errored after the maximum number of retries
           depending on the exception
+
         Note that None is returned in all cases where the loop in check_watched_items
         is to be continued
         """
diff --git a/lib/galaxy/jobs/runners/pbs.py b/lib/galaxy/jobs/runners/pbs.py
index 3074bac6b5d..c96b4020b30 100644
--- a/lib/galaxy/jobs/runners/pbs.py
+++ b/lib/galaxy/jobs/runners/pbs.py
@@ -43,26 +43,26 @@ mkdir -p %s
 """
 
 PBS_ARGMAP = {
-    'destination'           : '-q',
-    'Execution_Time'        : '-a',
-    'Account_Name'          : '-A',
-    'Checkpoint'            : '-c',
-    'Error_Path'            : '-e',
-    'Group_List'            : '-g',
-    'Hold_Types'            : '-h',
-    'Join_Paths'            : '-j',
-    'Keep_Files'            : '-k',
-    'Resource_List'         : '-l',
-    'Mail_Points'           : '-m',
-    'Mail_Users'            : '-M',
-    'Job_Name'              : '-N',
-    'Output_Path'           : '-o',
-    'Priority'              : '-p',
-    'Rerunable'             : '-r',
-    'Shell_Path_List'       : '-S',
-    'job_array_request'     : '-t',
-    'User_List'             : '-u',
-    'Variable_List'         : '-v',
+    'destination': '-q',
+    'Execution_Time': '-a',
+    'Account_Name': '-A',
+    'Checkpoint': '-c',
+    'Error_Path': '-e',
+    'Group_List': '-g',
+    'Hold_Types': '-h',
+    'Join_Paths': '-j',
+    'Keep_Files': '-k',
+    'Resource_List': '-l',
+    'Mail_Points': '-m',
+    'Mail_Users': '-M',
+    'Job_Name': '-N',
+    'Output_Path': '-o',
+    'Priority': '-p',
+    'Rerunable': '-r',
+    'Shell_Path_List': '-S',
+    'job_array_request': '-t',
+    'User_List': '-u',
+    'Variable_List': '-v',
 }
 
 # From pbs' pbs_job.h
diff --git a/lib/galaxy/jobs/runners/univa.py b/lib/galaxy/jobs/runners/univa.py
index 0db05fd3de9..742c7669e38 100644
--- a/lib/galaxy/jobs/runners/univa.py
+++ b/lib/galaxy/jobs/runners/univa.py
@@ -4,9 +4,12 @@ Job control via the DRMAA API / qstat and qacct.
 Known to work on the UNIVA grid engine.
 
 known bugs/problems:
+
 - if a job runs longer than the time limits of the queue two things happen
+
   1. at the soft limit (s_rt) SIGUSR1 is sent to the job
   2. at the hard limit (h_rt) SIGKILL is sent to the job
+
   The second case is covered by the runner -- it's the same mechanism that
   kills a job when the job time limit is reached. The first case is currently
   not covered. The good thing is that most programs ignore SIGUSR1.
@@ -14,11 +17,12 @@ known bugs/problems:
   at random.
 
   Possible solutions:
+
   - configure the job destinations such that the queue limits are never reached.
     the time limits can be determined with
     `for i in `qconf -sql`; do qconf -sq $i | grep -E '(h|s)_rt'; done`
-
   - extend the job runner to cover s_rt cases (some ideas):
+
     * I'm unsure if the programs reaction to SIGUSR1 can be determined easily
       because it depends on the program. It seems that exit code is in most
       cases 10.
diff --git a/lib/galaxy/main_config.py b/lib/galaxy/main_config.py
new file mode 100644
index 00000000000..c1f981ab148
--- /dev/null
+++ b/lib/galaxy/main_config.py
@@ -0,0 +1,36 @@
+"""Utilities for finding Galaxy's configuration file.
+
+This is for use by web framework code and scripts (e.g. scripts/galaxy_main.py).
+"""
+import os
+
+DEFAULT_INIS = ["config/galaxy.yml", "config/galaxy.ini", "universe_wsgi.ini", "config/galaxy.yml.sample"]
+DEFAULT_INI_APP = "main"
+DEFAULT_CONFIG_SECTION = "galaxy"
+
+
+def absolute_config_path(path, galaxy_root):
+    if path and not os.path.isabs(path):
+        path = os.path.join(galaxy_root, path)
+    return path
+
+
+def config_is_ini(config_file):
+    return config_file and (config_file.endswith('.ini') or config_file.endswith('.ini.sample'))
+
+
+def find_config(supplied_config, galaxy_root):
+    if supplied_config:
+        return supplied_config
+
+    if galaxy_root is None:
+        return os.path.abspath('galaxy.yml')
+
+    # If not explicitly supplied an config, check galaxy.ini and then
+    # just resort to sample if that has not been configured.
+    for guess in DEFAULT_INIS:
+        config_path = os.path.join(galaxy_root, guess)
+        if os.path.exists(config_path):
+            return config_path
+
+    return guess
diff --git a/lib/galaxy/managers/annotatable.py b/lib/galaxy/managers/annotatable.py
index 5e34e941ef7..017d8dd9f29 100644
--- a/lib/galaxy/managers/annotatable.py
+++ b/lib/galaxy/managers/annotatable.py
@@ -103,7 +103,13 @@ class AnnotatableFilterMixin:
         return val in owner_annotation
 
     def _add_parsers(self):
-        self.fn_filter_parsers.update({
-            'annotation'    : {'op': {'has': self.filter_annotation_contains,
-                                      'contains': self.filter_annotation_contains}},
-        })
+        self.fn_filter_parsers.update(
+            {
+                'annotation': {
+                    'op': {
+                        'has': self.filter_annotation_contains,
+                        'contains': self.filter_annotation_contains,
+                    },
+                },
+            }
+        )
diff --git a/lib/galaxy/managers/base.py b/lib/galaxy/managers/base.py
index 6f70db08678..2eb1fd2bbc5 100644
--- a/lib/galaxy/managers/base.py
+++ b/lib/galaxy/managers/base.py
@@ -567,9 +567,9 @@ class ModelSerializer(HasAModelManager):
         the attribute.
         """
         self.serializers.update({
-            'id'            : self.serialize_id,
-            'create_time'   : self.serialize_date,
-            'update_time'   : self.serialize_date,
+            'id': self.serialize_id,
+            'create_time': self.serialize_date,
+            'update_time': self.serialize_date,
         })
 
     def add_view(self, view_name, key_list, include_keys_from=None):
@@ -925,12 +925,12 @@ class ModelFilterParser(HasAModelManager):
         # note: these are the default filters for all models
         self.orm_filter_parsers.update({
             # (prob.) applicable to all models
-            'id'            : {'op': ('in')},
-            'encoded_id'    : {'column' : 'id', 'op': ('in'), 'val': self.parse_id_list},
+            'id': {'op': ('in')},
+            'encoded_id': {'column': 'id', 'op': ('in'), 'val': self.parse_id_list},
             # dates can be directly passed through the orm into a filter (no need to parse into datetime object)
-            'extension'     : {'op': ('eq', 'like', 'in')},
-            'create_time'   : {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
-            'update_time'   : {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
+            'extension': {'op': ('eq', 'like', 'in')},
+            'create_time': {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
+            'update_time': {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
         })
 
     def parse_filters(self, filter_tuple_list):
@@ -1064,9 +1064,9 @@ class ModelFilterParser(HasAModelManager):
     # ---- preset fn_filters: dictionaries of standard filter ops for standard datatypes
     def string_standard_ops(self, key):
         return {
-            'op' : {
-                'eq'        : lambda i, v: v == getattr(i, key),
-                'contains'  : lambda i, v: v in getattr(i, key),
+            'op': {
+                'eq': lambda i, v: v == getattr(i, key),
+                'contains': lambda i, v: v in getattr(i, key),
             }
         }
 
diff --git a/lib/galaxy/managers/cloud.py b/lib/galaxy/managers/cloud.py
index cc0733940a9..e4cb42243e9 100644
--- a/lib/galaxy/managers/cloud.py
+++ b/lib/galaxy/managers/cloud.py
@@ -61,11 +61,11 @@ class CloudManager(sharable.SharableModelManager):
 
         :type  provider: string
         :param provider: the name of cloud-based resource provided. A list of supported providers is given in
-        `SUPPORTED_PROVIDERS` variable.
+                         `SUPPORTED_PROVIDERS` variable.
 
         :type  credentials: dict
         :param credentials: a dictionary containing all the credentials required to authenticated to the
-        specified provider.
+                            specified provider.
 
         :rtype: provider specific, e.g., `cloudbridge.cloud.providers.aws.provider.AWSCloudProvider` for AWS.
         :return: a cloudbridge connection to the specified provider.
diff --git a/lib/galaxy/managers/cloudauthzs.py b/lib/galaxy/managers/cloudauthzs.py
index 789dd54335c..b206f7cc755 100644
--- a/lib/galaxy/managers/cloudauthzs.py
+++ b/lib/galaxy/managers/cloudauthzs.py
@@ -53,16 +53,16 @@ class CloudAuthzsSerializer(base.ModelSerializer):
         # k  : serialized dictionary key (e.g., 'model_class', 'provider').
         # **c: a dictionary containing 'trans' and 'user' objects.
         self.serializers.update({
-            'id'           : lambda i, k, **c: self.app.security.encode_id(i.id),
-            'model_class'  : lambda *a, **c: 'CloudAuthz',
-            'user_id'      : lambda i, k, **c: self.app.security.encode_id(i.user_id),
-            'provider'     : lambda i, k, **c: str(i.provider),
-            'config'       : lambda i, k, **c: i.config,
-            'authn_id'     : lambda i, k, **c: self.app.security.encode_id(i.authn_id) if i.authn_id else None,
-            'last_update'  : lambda i, k, **c: str(i.last_update),
+            'id': lambda i, k, **c: self.app.security.encode_id(i.id),
+            'model_class': lambda *a, **c: 'CloudAuthz',
+            'user_id': lambda i, k, **c: self.app.security.encode_id(i.user_id),
+            'provider': lambda i, k, **c: str(i.provider),
+            'config': lambda i, k, **c: i.config,
+            'authn_id': lambda i, k, **c: self.app.security.encode_id(i.authn_id) if i.authn_id else None,
+            'last_update': lambda i, k, **c: str(i.last_update),
             'last_activity': lambda i, k, **c: str(i.last_activity),
-            'create_time'  : lambda i, k, **c: str(i.create_time),
-            'description'  : lambda i, k, **c: str(i.description)
+            'create_time': lambda i, k, **c: str(i.create_time),
+            'description': lambda i, k, **c: str(i.description)
         })
 
 
diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py
index c9e8a61065f..374e691ee62 100644
--- a/lib/galaxy/managers/configuration.py
+++ b/lib/galaxy/managers/configuration.py
@@ -40,74 +40,75 @@ class ConfigSerializer(base.ModelSerializer):
 
         self.serializers = {
             # TODO: this is available from user data, remove
-            'is_admin_user'                     : lambda *a, **c: False,
-            'brand'                             : _use_config,
-            'display_galaxy_brand'              : _use_config,
-            'logo_url'                          : lambda config, key, **context: self.url_for(config.get(key, '/')),
-            'logo_src'                          : lambda config, key, **context: self.url_for(config.get(key, '/static/favicon.png')),
-            'logo_src_secondary'                : lambda config, key, **context: self.url_for(config.get(key)) if config.get(key) else None,
-            'terms_url'                         : _use_config,
-            'myexperiment_target_url'           : _use_config,
-            'wiki_url'                          : _use_config,
-            'search_url'                        : _use_config,
-            'mailing_lists'                     : _defaults_to(self.app.config.mailing_lists_url),
-            'screencasts_url'                   : _use_config,
-            'citation_url'                      : _use_config,
-            'support_url'                       : _use_config,
-            'quota_url'                         : _use_config,
-            'helpsite_url'                      : _use_config,
-            'lims_doc_url'                      : _defaults_to("https://usegalaxy.org/u/rkchak/p/sts"),
-            'default_locale'                    : _use_config,
-            'enable_openid'                     : _use_config,
-            'enable_tool_recommendations'       : _use_config,
-            'tool_recommendation_model_path'    : _use_config,
-            'admin_tool_recommendations_path'   : _use_config,
-            'overwrite_model_recommendations'   : _use_config,
-            'topk_recommendations'              : _use_config,
-            'allow_user_impersonation'          : _use_config,
-            'allow_user_creation'               : _defaults_to(False),  # schema default is True
-            'use_remote_user'                   : _defaults_to(None),  # schema default is False; or config.single_user
-            'enable_oidc'                       : _use_config,
-            'oidc'                              : _use_config,
-            'enable_quotas'                     : _use_config,
-            'remote_user_logout_href'           : _use_config,
-            'datatypes_disable_auto'            : _use_config,
-            'allow_user_dataset_purge'          : _defaults_to(False),  # schema default is True
-            'ga_code'                           : _use_config,
-            'enable_unique_workflow_defaults'   : _use_config,
-            'enable_beta_markdown_export'       : _use_config,
-            'simplified_workflow_run_ui'        : _use_config,
+            'is_admin_user': lambda *a, **c: False,
+            'brand': _use_config,
+            'display_galaxy_brand': _use_config,
+            'logo_url': lambda config, key, **context: self.url_for(config.get(key, '/')),
+            'logo_src': lambda config, key, **context: self.url_for(config.get(key, '/static/favicon.png')),
+            'logo_src_secondary': lambda config, key, **context: self.url_for(config.get(key)) if config.get(key) else None,
+            'terms_url': _use_config,
+            'myexperiment_target_url': _use_config,
+            'wiki_url': _use_config,
+            'search_url': _use_config,
+            'mailing_lists': _defaults_to(self.app.config.mailing_lists_url),
+            'screencasts_url': _use_config,
+            'citation_url': _use_config,
+            'support_url': _use_config,
+            'quota_url': _use_config,
+            'helpsite_url': _use_config,
+            'lims_doc_url': _defaults_to("https://usegalaxy.org/u/rkchak/p/sts"),
+            'default_locale': _use_config,
+            'enable_openid': _use_config,
+            'enable_tool_recommendations': _use_config,
+            'tool_recommendation_model_path': _use_config,
+            'admin_tool_recommendations_path': _use_config,
+            'overwrite_model_recommendations': _use_config,
+            'topk_recommendations': _use_config,
+            'allow_user_impersonation': _use_config,
+            'allow_user_creation': _defaults_to(False),  # schema default is True
+            'use_remote_user': _defaults_to(None),  # schema default is False; or config.single_user
+            'enable_oidc': _use_config,
+            'oidc': _use_config,
+            'enable_quotas': _use_config,
+            'remote_user_logout_href': _use_config,
+            'datatypes_disable_auto': _use_config,
+            'allow_user_dataset_purge': _defaults_to(False),  # schema default is True
+            'ga_code': _use_config,
+            'enable_unique_workflow_defaults': _use_config,
+            'enable_beta_markdown_export': _use_config,
+            'simplified_workflow_run_ui': _use_config,
             'simplified_workflow_run_ui_target_history': _use_config,
             'simplified_workflow_run_ui_job_cache': _use_config,
-            'has_user_tool_filters'             : _defaults_to(False),
+            'has_user_tool_filters': _defaults_to(False),
             # TODO: is there no 'correct' way to get an api url? controller='api', action='tools' is a hack
             # at any rate: the following works with path_prefix but is still brittle
             # TODO: change this to (more generic) upload_path and incorporate config.nginx_upload_path into building it
-            'nginx_upload_path'                 : lambda config, key, **context: getattr(config, key, False),
-            'chunk_upload_size'                 : _use_config,
-            'ftp_upload_site'                   : _use_config,
-            'version_major'                     : _defaults_to(None),
-            'version_minor'                     : _defaults_to(None),
-            'require_login'                     : _use_config,
-            'inactivity_box_content'            : _use_config,
-            'visualizations_visible'            : _use_config,
-            'interactivetools_enable'           : _use_config,
-            'aws_estimate'                      : _use_config,
-            'message_box_content'               : _use_config,
-            'message_box_visible'               : _use_config,
-            'message_box_class'                 : _use_config,
-            'server_startttime'                 : lambda config, key, **context: server_starttime,
-            'mailing_join_addr'                 : _defaults_to('galaxy-announce-join@bx.psu.edu'),  # should this be the schema default?
-            'server_mail_configured'            : lambda config, key, **context: bool(config.smtp_server),
-            'registration_warning_message'      : _use_config,
-            'welcome_url'                       : _use_config,
-            'show_welcome_with_login'           : _defaults_to(True),  # schema default is False
-            'cookie_domain'                     : _use_config,
-            'python'                            : _defaults_to((sys.version_info.major, sys.version_info.minor)),
-            'select_type_workflow_threshold'    : _use_config,
-            'file_sources_configured'           : lambda config, key, **context: self.app.file_sources.custom_sources_configured,
-            'upload_from_form_button'           : _use_config,
-            'release_doc_base_url'              : _use_config,
+            'nginx_upload_path': lambda config, key, **context: getattr(config, key, False),
+            'chunk_upload_size': _use_config,
+            'ftp_upload_site': _use_config,
+            'version_major': _defaults_to(None),
+            'version_minor': _defaults_to(None),
+            'require_login': _use_config,
+            'inactivity_box_content': _use_config,
+            'visualizations_visible': _use_config,
+            'interactivetools_enable': _use_config,
+            'aws_estimate': _use_config,
+            'message_box_content': _use_config,
+            'message_box_visible': _use_config,
+            'message_box_class': _use_config,
+            'server_startttime': lambda config, key, **context: server_starttime,
+            'mailing_join_addr': _defaults_to('galaxy-announce-join@bx.psu.edu'),  # should this be the schema default?
+            'server_mail_configured': lambda config, key, **context: bool(config.smtp_server),
+            'registration_warning_message': _use_config,
+            'welcome_url': _use_config,
+            'show_welcome_with_login': _defaults_to(True),  # schema default is False
+            'cookie_domain': _use_config,
+            'python': _defaults_to((sys.version_info.major, sys.version_info.minor)),
+            'select_type_workflow_threshold': _use_config,
+            'file_sources_configured': lambda config, key, **context: self.app.file_sources.custom_sources_configured,
+            'upload_from_form_button': _use_config,
+            'release_doc_base_url': _use_config,
+            'user_library_import_dir_available': lambda config, key, **context: bool(config.get('user_library_import_dir')),
         }
 
 
@@ -122,10 +123,10 @@ class AdminConfigSerializer(ConfigSerializer):
 
         self.serializers.update({
             # TODO: this is available from user serialization: remove
-            'is_admin_user'                     : lambda *a: True,
+            'is_admin_user': lambda *a: True,
 
-            'library_import_dir'                : _defaults_to(None),
-            'user_library_import_dir'           : _defaults_to(None),
-            'allow_library_path_paste'          : _defaults_to(False),
-            'allow_user_deletion'               : _defaults_to(False),
+            'library_import_dir': _defaults_to(None),
+            'user_library_import_dir': _defaults_to(None),
+            'allow_library_path_paste': _defaults_to(False),
+            'allow_user_deletion': _defaults_to(False),
         })
diff --git a/lib/galaxy/managers/context.py b/lib/galaxy/managers/context.py
index d927316571e..16f74881e32 100644
--- a/lib/galaxy/managers/context.py
+++ b/lib/galaxy/managers/context.py
@@ -1,21 +1,74 @@
+"""Interfaces/mixins for transaction-like objects.
+
+These objects describe the context around a unit of work. This unit of work
+is very broad and can be anything from the response to a web request, the
+scheduling of a workflow, the reloading the toolbox, etc.. Traditionally,
+Galaxy has simply passed around a GalaxyWebTransaction object through
+all layers and large components of the Galaxy app. Having random backend
+components define explicit dependencies on this however is inappropriate
+because Galaxy may not be used in all sort of non-web contexts. The future
+use of message queues and web sockets as well as the decomposition of the
+backend into packages only further make this heavy reliance on
+GalaxyWebTransaction inappropriate.
+
+A better approach is for components to annotate their reliance on much
+narrower, typed views of the GalaxyWebTransaction. This allows explicit
+declaration of what is being required in the context of a method or class
+and allows the Python type system to ensure the transaction supplied to
+the method is appropriate for the context. For instance, an effective
+use of the type system in this way can prevent the backend work context
+used to schedule workflow from being supplied to a method that requires
+an older-style WSGI web response object.
+
+There are various levels of transactions defined in this file - these
+include :class:`galaxy.managers.context.ProvidesAppContext`,
+:class:`galaxy.managers.context.ProvidesUserContext`,
+and :class:`galaxy.managers.context.ProvidesHistoryContext`. Methods
+should annotate their dependency on the narrowest context they require.
+A method that requires a user but not a history should declare its
+``trans`` argument as requiring type :class:`galaxy.managers.context.ProvidesUserContext`.
 """
-Mixins for transaction-like objects.
-"""
+# TODO: Refactor this class so that galaxy.managers depends on a package
+# containing this.
+# TODO: Provide different classes for real users and potentially bootstrapped
+# users so the framework can provide consistent web exceptions for incorrect
+# user being used in that context and so that the type system can provide
+# more checks against this issue.
+import abc
 import string
 from json import dumps
+from typing import List, Optional
 
+from sqlalchemy.orm.scoping import scoped_session
 
 from galaxy.exceptions import UserActivationRequiredException
+from galaxy.model import Dataset, History, HistoryDatasetAssociation, Role
+from galaxy.model.base import ModelMapping
+from galaxy.security.idencoding import IdEncodingHelper
+from galaxy.structured_app import StructuredApp
 from galaxy.util import bunch
 
 
 class ProvidesAppContext:
-    """ For transaction-like objects to provide Galaxy convience layer for
+    """ For transaction-like objects to provide Galaxy convenience layer for
     database and event handling.
 
     Mixed in class must provide `app` property.
     """
 
+    @abc.abstractproperty
+    def app(self) -> StructuredApp:
+        """Provide access to the Galaxy ``app`` object.
+        """
+
+    @property
+    def security(self) -> IdEncodingHelper:
+        """Provide access to Galaxy app's id encoding helper.
+
+        :rtype: IdEncodingHelper
+        """
+        return self.app.security
+
     def log_action(self, user=None, action=None, context=None, params=None):
         """
         Application-level logging of user actions.
@@ -68,15 +121,15 @@ class ProvidesAppContext:
             self.sa_session.flush()
 
     @property
-    def sa_session(self):
-        """
-        Returns a SQLAlchemy session -- currently just gets the current
-        session from the threadlocal session context, but this is provided
-        to allow migration toward a more SQLAlchemy 0.4 style of use.
+    def sa_session(self) -> scoped_session:
+        """Provide access to Galaxy's SQLAlchemy session.
+
+        :rtype: sqlalchemy.orm.scoping.scoped_session
         """
         return self.app.model.context.current
 
     def expunge_all(self):
+        """Expunge all the objects in Galaxy's SQLAlchemy sessions."""
         app = self.app
         context = app.model.context
         context.expunge_all()
@@ -87,31 +140,54 @@ class ProvidesAppContext:
                 install_model.context.expunge_all()
 
     def get_toolbox(self):
-        """Returns the application toolbox"""
+        """Returns the application toolbox.
+
+        :rtype: galaxy.tools.ToolBox
+        """
         return self.app.toolbox
 
     @property
-    def model(self):
+    def model(self) -> ModelMapping:
+        """Provide access to Galaxy's model mapping class.
+
+        This is sometimes used for quick access to classes in
+        :mod:`galaxy.model` but this is discouraged. Those classes
+        should be imported by the consumer for stronger static
+        checking.
+
+        This is more proper use for this is accessing the threadbound
+        SQLAlchemy session or engine.
+
+        :rtype: galaxy.model.base.ModelMapping
+        """
         return self.app.model
 
     @property
-    def install_model(self):
+    def install_model(self) -> ModelMapping:
+        """Provide access to Galaxy's install mapping.
+
+        Comments on the ``model`` property apply here also.
+        """
         return self.app.install_model
 
 
-class ProvidesUserContext:
-    """ For transaction-like objects to provide Galaxy convience layer for
+class ProvidesUserContext(ProvidesAppContext):
+    """ For transaction-like objects to provide Galaxy convenience layer for
     reasoning about users.
 
     Mixed in class must provide `user` and `app`
     properties.
     """
 
+    @abc.abstractproperty
+    def user(self):
+        """Provide access to the user object."""
+
     @property
-    def anonymous(self):
+    def anonymous(self) -> bool:
         return self.user is None
 
-    def get_current_user_roles(self):
+    def get_current_user_roles(self) -> List[Role]:
         user = self.user
         if user:
             roles = user.all_roles()
@@ -120,11 +196,11 @@ class ProvidesUserContext:
         return roles
 
     @property
-    def user_is_admin(self):
+    def user_is_admin(self) -> bool:
         return self.app.config.is_admin_user(self.user)
 
     @property
-    def user_can_do_run_as(self):
+    def user_can_do_run_as(self) -> bool:
         run_as_users = [user for user in self.app.config.get("api_allow_run_as", "").split(",") if user]
         if not run_as_users:
             return False
@@ -134,7 +210,7 @@ class ProvidesUserContext:
         return can_do_run_as
 
     @property
-    def user_is_active(self):
+    def user_is_active(self) -> bool:
         return not self.app.config.user_activation_on or self.user is None or self.user.active
 
     def check_user_activation(self):
@@ -143,7 +219,7 @@ class ProvidesUserContext:
             raise UserActivationRequiredException()
 
     @property
-    def user_ftp_dir(self):
+    def user_ftp_dir(self) -> Optional[str]:
         base_dir = self.app.config.ftp_upload_dir
         if base_dir is None or self.user is None:
             return None
@@ -159,17 +235,23 @@ class ProvidesUserContext:
             return path
 
 
-class ProvidesHistoryContext:
-    """ For transaction-like objects to provide Galaxy convience layer for
+class ProvidesHistoryContext(ProvidesUserContext):
+    """ For transaction-like objects to provide Galaxy convenience layer for
     reasoning about histories.
 
     Mixed in class must provide `user`, `history`, and `app`
     properties.
     """
 
-    def db_dataset_for(self, dbkey):
+    @abc.abstractproperty
+    def history(self) -> Optional[History]:
+        """Provide access to the user's current history model object.
+
+        :rtype: Optional[galaxy.model.History]
         """
-        Returns the db_file dataset associated/needed by `dataset`, or `None`.
+
+    def db_dataset_for(self, dbkey) -> Optional[HistoryDatasetAssociation]:
+        """Optionally return the db_file dataset associated/needed by `dataset`.
         """
         # If no history, return None.
         if self.history is None:
@@ -179,21 +261,21 @@ class ProvidesHistoryContext:
             # The API presents a Bunch for a history.  Until the API is
             # more fully featured for handling this, also return None.
             return None
-        non_ready_or_ok = set(self.app.model.Dataset.non_ready_states)
-        non_ready_or_ok.add(self.app.model.HistoryDatasetAssociation.states.OK)
+        non_ready_or_ok = set(Dataset.non_ready_states)
+        non_ready_or_ok.add(HistoryDatasetAssociation.states.OK)
         datasets = self.sa_session.query(
-            self.app.model.HistoryDatasetAssociation
+            HistoryDatasetAssociation
         ).filter_by(
             deleted=False,
             history_id=self.history.id,
             extension="len"
         ).filter(
-            self.app.model.HistoryDatasetAssociation._state.in_(non_ready_or_ok),
+            HistoryDatasetAssociation.table.c._state.in_(non_ready_or_ok),
         )
         valid_ds = None
         for ds in datasets:
             if ds.dbkey == dbkey:
-                if ds.state == self.app.model.HistoryDatasetAssociation.states.OK:
+                if ds.state == HistoryDatasetAssociation.states.OK:
                     return ds
                 valid_ds = ds
         return valid_ds
diff --git a/lib/galaxy/managers/datasets.py b/lib/galaxy/managers/datasets.py
index a040cb8061c..3bb6e901130 100644
--- a/lib/galaxy/managers/datasets.py
+++ b/lib/galaxy/managers/datasets.py
@@ -171,16 +171,16 @@ class DatasetSerializer(base.ModelSerializer, deletable.PurgableSerializerMixin)
         deletable.PurgableSerializerMixin.add_serializers(self)
 
         self.serializers.update({
-            'create_time'   : self.serialize_date,
-            'update_time'   : self.serialize_date,
+            'create_time': self.serialize_date,
+            'update_time': self.serialize_date,
 
-            'uuid'          : lambda i, k, **c: str(i.uuid) if i.uuid else None,
-            'file_name'     : self.serialize_file_name,
-            'extra_files_path' : self.serialize_extra_files_path,
-            'permissions'   : self.serialize_permissions,
+            'uuid': lambda i, k, **c: str(i.uuid) if i.uuid else None,
+            'file_name': self.serialize_file_name,
+            'extra_files_path': self.serialize_extra_files_path,
+            'permissions': self.serialize_permissions,
 
-            'total_size'    : lambda i, k, **c: int(i.get_total_size()),
-            'file_size'     : lambda i, k, **c: int(i.get_size())
+            'total_size': lambda i, k, **c: int(i.get_total_size()),
+            'file_size': lambda i, k, **c: int(i.get_size())
         })
 
     def serialize_file_name(self, dataset, key, user=None, **context):
@@ -216,8 +216,8 @@ class DatasetSerializer(base.ModelSerializer, deletable.PurgableSerializerMixin)
         management_permissions = self.dataset_manager.permissions.manage.by_dataset(dataset)
         access_permissions = self.dataset_manager.permissions.access.by_dataset(dataset)
         permissions = {
-            'manage' : [self.app.security.encode_id(perm.role.id) for perm in management_permissions],
-            'access' : [self.app.security.encode_id(perm.role.id) for perm in access_permissions],
+            'manage': [self.app.security.encode_id(perm.role.id) for perm in management_permissions],
+            'access': [self.app.security.encode_id(perm.role.id) for perm in access_permissions],
         }
         return permissions
 
@@ -446,49 +446,49 @@ class _UnflattenedMetadataDatasetAssociationSerializer(base.ModelSerializer,
         deletable.PurgableSerializerMixin.add_serializers(self)
 
         self.serializers.update({
-            'create_time'   : self.serialize_date,
-            'update_time'   : self.serialize_date,
+            'create_time': self.serialize_date,
+            'update_time': self.serialize_date,
 
             # underlying dataset
-            'dataset'       : lambda i, k, **c: self.dataset_serializer.serialize_to_view(i.dataset, view='summary', **c),
-            'dataset_id'    : self._proxy_to_dataset(key='id'),
+            'dataset': lambda i, k, **c: self.dataset_serializer.serialize_to_view(i.dataset, view='summary', **c),
+            'dataset_id': self._proxy_to_dataset(key='id'),
             # TODO: why is this named uuid!? The da doesn't have a uuid - it's the underlying dataset's uuid!
-            'uuid'          : self._proxy_to_dataset(key='uuid'),
-            # 'dataset_uuid'  : self._proxy_to_dataset( key='uuid' ),
-            'file_name'     : self._proxy_to_dataset(serializer=self.dataset_serializer.serialize_file_name),
-            'extra_files_path' : self._proxy_to_dataset(serializer=self.dataset_serializer.serialize_extra_files_path),
-            'permissions'   : self._proxy_to_dataset(serializer=self.dataset_serializer.serialize_permissions),
+            'uuid': self._proxy_to_dataset(key='uuid'),
+            # 'dataset_uuid': self._proxy_to_dataset( key='uuid' ),
+            'file_name': self._proxy_to_dataset(serializer=self.dataset_serializer.serialize_file_name),
+            'extra_files_path': self._proxy_to_dataset(serializer=self.dataset_serializer.serialize_extra_files_path),
+            'permissions': self._proxy_to_dataset(serializer=self.dataset_serializer.serialize_permissions),
             # TODO: do the sizes proxy accurately/in the same way?
-            'size'          : lambda i, k, **c: int(i.get_size()),
-            'file_size'     : lambda i, k, **c: self.serializers['size'](i, k, **c),
-            'nice_size'     : lambda i, k, **c: i.get_size(nice_size=True),
+            'size': lambda i, k, **c: int(i.get_size()),
+            'file_size': lambda i, k, **c: self.serializers['size'](i, k, **c),
+            'nice_size': lambda i, k, **c: i.get_size(nice_size=True),
 
             # common to lddas and hdas - from mapping.py
-            'copied_from_history_dataset_association_id'        : self.serialize_id,
+            'copied_from_history_dataset_association_id': self.serialize_id,
             'copied_from_library_dataset_dataset_association_id': self.serialize_id,
-            'info'          : lambda i, k, **c: i.info.strip() if isinstance(i.info, str) else i.info,
-            'blurb'         : lambda i, k, **c: i.blurb,
-            'peek'          : lambda i, k, **c: i.display_peek() if i.peek and i.peek != 'no peek' else None,
+            'info': lambda i, k, **c: i.info.strip() if isinstance(i.info, str) else i.info,
+            'blurb': lambda i, k, **c: i.blurb,
+            'peek': lambda i, k, **c: i.display_peek() if i.peek and i.peek != 'no peek' else None,
 
-            'meta_files'    : self.serialize_meta_files,
-            'metadata'      : self.serialize_metadata,
+            'meta_files': self.serialize_meta_files,
+            'metadata': self.serialize_metadata,
 
-            'creating_job'  : self.serialize_creating_job,
-            'rerunnable'    : self.serialize_rerunnable,
+            'creating_job': self.serialize_creating_job,
+            'rerunnable': self.serialize_rerunnable,
 
-            'parent_id'     : self.serialize_id,
-            'designation'   : lambda i, k, **c: i.designation,
+            'parent_id': self.serialize_id,
+            'designation': lambda i, k, **c: i.designation,
 
-            # 'extended_metadata'     : self.serialize_extended_metadata,
-            # 'extended_metadata_id'  : self.serialize_id,
+            # 'extended_metadata': self.serialize_extended_metadata,
+            # 'extended_metadata_id': self.serialize_id,
 
             # remapped
-            'genome_build'  : lambda i, k, **c: i.dbkey,
+            'genome_build': lambda i, k, **c: i.dbkey,
 
             # derived (not mapped) attributes
-            'data_type'     : lambda i, k, **c: i.datatype.__class__.__module__ + '.' + i.datatype.__class__.__name__,
+            'data_type': lambda i, k, **c: i.datatype.__class__.__module__ + '.' + i.datatype.__class__.__name__,
 
-            'converted'     : self.serialize_converted_datasets,
+            'converted': self.serialize_converted_datasets,
             # TODO: metadata/extra files
         })
         # this an abstract superclass, so no views created
@@ -609,15 +609,15 @@ class DatasetAssociationSerializer(_UnflattenedMetadataDatasetAssociationSeriali
         return serialized
 
     # TODO: this is more util/gen. use
-    def _pluck_from_list(self, l, elems):
+    def _pluck_from_list(self, list_, elems):
         """
-        Removes found elems from list l and returns list of found elems if found.
+        Removes found elems from list list_ and returns list of found elems if found.
         """
         found = []
         for elem in elems:
             try:
-                index = l.index(elem)
-                found.append(l.pop(index))
+                index = list_.index(elem)
+                found.append(list_.pop(index))
             except ValueError:
                 pass
         return found
@@ -645,9 +645,9 @@ class DatasetAssociationDeserializer(base.ModelDeserializer, deletable.PurgableD
         deletable.PurgableDeserializerMixin.add_deserializers(self)
 
         self.deserializers.update({
-            'name' : self.deserialize_basestring,
-            'info' : self.deserialize_basestring,
-            'datatype' : self.deserialize_datatype,
+            'name': self.deserialize_basestring,
+            'info': self.deserialize_basestring,
+            'datatype': self.deserialize_datatype,
         })
         self.deserializable_keyset.update(self.deserializers.keys())
 
@@ -699,16 +699,16 @@ class DatasetAssociationFilterParser(base.ModelFilterParser, deletable.PurgableF
         deletable.PurgableFiltersMixin._add_parsers(self)
 
         self.orm_filter_parsers.update({
-            'name'      : {'op': ('eq', 'contains', 'like')},
-            'state'     : {'column' : '_state', 'op': ('eq', 'in')},
-            'visible'   : {'op': ('eq'), 'val': self.parse_bool},
+            'name': {'op': ('eq', 'contains', 'like')},
+            'state': {'column': '_state', 'op': ('eq', 'in')},
+            'visible': {'op': ('eq'), 'val': self.parse_bool},
         })
         self.fn_filter_parsers.update({
-            'genome_build' : self.string_standard_ops('dbkey'),
-            'data_type' : {
+            'genome_build': self.string_standard_ops('dbkey'),
+            'data_type': {
                 'op': {
-                    'eq' : self.eq_datatype,
-                    'isinstance' : self.isinstance_datatype
+                    'eq': self.eq_datatype,
+                    'isinstance': self.isinstance_datatype
                 }
             }
         })
@@ -718,8 +718,7 @@ class DatasetAssociationFilterParser(base.ModelFilterParser, deletable.PurgableF
         Is the `dataset_assoc` datatype equal to the registered datatype `class_str`?
         """
         comparison_class = self.app.datatypes_registry.get_datatype_class_by_name(class_str)
-        return (comparison_class and
-            dataset_assoc.datatype.__class__ == comparison_class)
+        return comparison_class and dataset_assoc.datatype.__class__ == comparison_class
 
     def isinstance_datatype(self, dataset_assoc, class_strs):
         """
@@ -732,5 +731,4 @@ class DatasetAssociationFilterParser(base.ModelFilterParser, deletable.PurgableF
             datatype_class = parse_datatype_fn(class_str)
             if datatype_class:
                 comparison_classes.append(datatype_class)
-        return (comparison_classes and
-            isinstance(dataset_assoc.datatype, comparison_classes))
+        return comparison_classes and isinstance(dataset_assoc.datatype, comparison_classes)
diff --git a/lib/galaxy/managers/datatypes.py b/lib/galaxy/managers/datatypes.py
new file mode 100644
index 00000000000..6913bc32104
--- /dev/null
+++ b/lib/galaxy/managers/datatypes.py
@@ -0,0 +1,99 @@
+from typing import (
+    Dict,
+    List,
+    Optional,
+    Union,
+)
+
+from pydantic.tools import parse_obj_as
+
+from galaxy.datatypes._schema import (
+    DatatypeConverterList,
+    DatatypeDetails,
+    DatatypesCombinedMap,
+    DatatypesMap,
+)
+from galaxy.datatypes.data import Data
+from galaxy.datatypes.registry import Registry
+
+
+def view_index(
+    datatypes_registry: Registry,
+    extension_only: Optional[bool] = True,
+    upload_only: Optional[bool] = True
+) -> Union[List[DatatypeDetails], List[str]]:
+    if extension_only:
+        if upload_only:
+            return datatypes_registry.upload_file_formats
+        else:
+            return [ext for ext in datatypes_registry.datatypes_by_extension]
+    else:
+        rval = []
+        for datatype_info_dict in datatypes_registry.datatype_info_dicts:
+            if upload_only and not datatype_info_dict.get('display_in_upload'):
+                continue
+            rval.append(datatype_info_dict)
+        return rval
+
+
+def view_mapping(datatypes_registry: Registry) -> DatatypesMap:
+    ext_to_class_name: Dict[str, str] = {}
+    classes = []
+    for k, v in datatypes_registry.datatypes_by_extension.items():
+        c = v.__class__
+        ext_to_class_name[k] = f"{c.__module__}.{c.__name__}"
+        classes.append(c)
+    class_to_classes: Dict[str, Dict[str, bool]] = {}
+
+    def visit_bases(types, cls):
+        for base in cls.__bases__:
+            if issubclass(base, Data):
+                types.add(f"{base.__module__}.{base.__name__}")
+            visit_bases(types, base)
+
+    for c in classes:
+        n = f"{c.__module__}.{c.__name__}"
+        types = {n}
+        visit_bases(types, c)
+        class_to_classes[n] = {t: True for t in types}
+    return DatatypesMap(ext_to_class_name=ext_to_class_name, class_to_classes=class_to_classes)
+
+
+def view_types_and_mapping(
+    datatypes_registry: Registry,
+    extension_only: Optional[bool] = True,
+    upload_only: Optional[bool] = True
+) -> DatatypesCombinedMap:
+    return DatatypesCombinedMap(
+        datatypes=view_index(datatypes_registry, extension_only, upload_only),
+        datatypes_mapping=view_mapping(datatypes_registry)
+    )
+
+
+def view_sniffers(datatypes_registry: Registry) -> List[str]:
+    rval: List[str] = []
+    for sniffer_elem in datatypes_registry.sniffer_elems:
+        datatype = sniffer_elem.get('type')
+        if datatype is not None:
+            rval.append(datatype)
+    return rval
+
+
+def view_converters(datatypes_registry: Registry) -> DatatypeConverterList:
+    converters = []
+    for (source_type, targets) in datatypes_registry.datatype_converters.items():
+        for target_type in targets:
+            converters.append({
+                'source': source_type,
+                'target': target_type,
+                'tool_id': targets[target_type].id,
+            })
+    return parse_obj_as(DatatypeConverterList, converters)
+
+
+def view_edam_formats(datatypes_registry: Registry) -> Dict[str, str]:
+    return datatypes_registry.edam_formats
+
+
+def view_edam_data(datatypes_registry: Registry) -> Dict[str, str]:
+    return datatypes_registry.edam_data
diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index 7c3f20481b8..f6b664fb2db 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -372,42 +372,42 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
         annotatable.AnnotatableSerializerMixin.add_serializers(self)
 
         self.serializers.update({
-            'model_class'   : lambda *a, **c: 'HistoryDatasetAssociation',
+            'model_class': lambda *a, **c: 'HistoryDatasetAssociation',
             'history_content_type': lambda *a, **c: 'dataset',
-            'hda_ldda'      : lambda *a, **c: 'hda',
-            'type_id'       : self.serialize_type_id,
+            'hda_ldda': lambda *a, **c: 'hda',
+            'type_id': self.serialize_type_id,
 
-            'history_id'    : self.serialize_id,
+            'history_id': self.serialize_id,
 
             # remapped
-            'misc_info'     : self._remap_from('info'),
-            'misc_blurb'    : self._remap_from('blurb'),
-            'file_ext'      : self._remap_from('extension'),
-            'file_path'     : self._remap_from('file_name'),
-            'resubmitted'   : lambda i, k, **c: self.hda_manager.has_been_resubmitted(i),
-            'display_apps'  : self.serialize_display_apps,
-            'display_types' : self.serialize_old_display_applications,
+            'misc_info': self._remap_from('info'),
+            'misc_blurb': self._remap_from('blurb'),
+            'file_ext': self._remap_from('extension'),
+            'file_path': self._remap_from('file_name'),
+            'resubmitted': lambda i, k, **c: self.hda_manager.has_been_resubmitted(i),
+            'display_apps': self.serialize_display_apps,
+            'display_types': self.serialize_old_display_applications,
             'visualizations': self.serialize_visualization_links,
 
             # 'url'   : url_for( 'history_content_typed', history_id=encoded_history_id, id=encoded_id, type="dataset" ),
             # TODO: this intermittently causes a routes.GenerationException - temp use the legacy route to prevent this
             #   see also: https://trello.com/c/5d6j4X5y
             #   see also: https://sentry.galaxyproject.org/galaxy/galaxy-main/group/20769/events/9352883/
-            'url'           : lambda i, k, **c: self.url_for('history_content',
-                                                             history_id=self.app.security.encode_id(i.history_id),
-                                                             id=self.app.security.encode_id(i.id)),
-            'urls'          : self.serialize_urls,
+            'url': lambda i, k, **c: self.url_for('history_content',
+                                                  history_id=self.app.security.encode_id(i.history_id),
+                                                  id=self.app.security.encode_id(i.id)),
+            'urls': self.serialize_urls,
 
             # TODO: backwards compat: need to go away
-            'download_url'  : lambda i, k, **c: self.url_for('history_contents_display',
-                                                             history_id=self.app.security.encode_id(i.history.id),
-                                                             history_content_id=self.app.security.encode_id(i.id)),
-            'parent_id'     : self.serialize_id,
+            'download_url': lambda i, k, **c: self.url_for('history_contents_display',
+                                                           history_id=self.app.security.encode_id(i.history.id),
+                                                           history_content_id=self.app.security.encode_id(i.id)),
+            'parent_id': self.serialize_id,
             # TODO: to DatasetAssociationSerializer
-            'accessible'    : lambda i, k, user=None, **c: self.manager.is_accessible(i, user, **c),
-            'api_type'      : lambda *a, **c: 'file',
-            'type'          : lambda *a, **c: 'file',
-            'created_from_basename' : lambda i, k, **c: i.created_from_basename,
+            'accessible': lambda i, k, user=None, **c: self.manager.is_accessible(i, user, **c),
+            'api_type': lambda *a, **c: 'file',
+            'type': lambda *a, **c: 'file',
+            'created_from_basename': lambda i, k, **c: i.created_from_basename,
         })
 
     def serialize(self, hda, keys, user=None, **context):
@@ -482,18 +482,18 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
         url_for = self.url_for
         encoded_id = self.app.security.encode_id(hda.id)
         urls = {
-            'purge'         : url_for(controller='dataset', action='purge_async', dataset_id=encoded_id),
-            'display'       : url_for(controller='dataset', action='display', dataset_id=encoded_id, preview=True),
-            'edit'          : url_for(controller='dataset', action='edit', dataset_id=encoded_id),
-            'download'      : url_for(controller='dataset', action='display',
-                                      dataset_id=encoded_id, to_ext=hda.extension),
-            'report_error'  : url_for(controller='dataset', action='errors', id=encoded_id),
-            'rerun'         : url_for(controller='tool_runner', action='rerun', id=encoded_id),
-            'show_params'   : url_for(controller='dataset', action='show_params', dataset_id=encoded_id),
-            'visualization' : url_for(controller='visualization', action='index',
-                                      id=encoded_id, model='HistoryDatasetAssociation'),
-            'meta_download' : url_for(controller='dataset', action='get_metadata_file',
-                                      hda_id=encoded_id, metadata_name=''),
+            'purge': url_for(controller='dataset', action='purge_async', dataset_id=encoded_id),
+            'display': url_for(controller='dataset', action='display', dataset_id=encoded_id, preview=True),
+            'edit': url_for(controller='dataset', action='edit', dataset_id=encoded_id),
+            'download': url_for(controller='dataset', action='display',
+                                dataset_id=encoded_id, to_ext=hda.extension),
+            'report_error': url_for(controller='dataset', action='errors', id=encoded_id),
+            'rerun': url_for(controller='tool_runner', action='rerun', id=encoded_id),
+            'show_params': url_for(controller='dataset', action='show_params', dataset_id=encoded_id),
+            'visualization': url_for(controller='visualization', action='index',
+                                     id=encoded_id, model='HistoryDatasetAssociation'),
+            'meta_download': url_for(controller='dataset', action='get_metadata_file',
+                                     hda_id=encoded_id, metadata_name=''),
         }
         return urls
 
@@ -516,11 +516,11 @@ class HDADeserializer(datasets.DatasetAssociationDeserializer,
         annotatable.AnnotatableDeserializerMixin.add_deserializers(self)
 
         self.deserializers.update({
-            'visible'       : self.deserialize_bool,
+            'visible': self.deserialize_bool,
             # remapped
-            'genome_build'  : lambda i, k, v, **c: self.deserialize_genome_build(i, 'dbkey', v),
-            'misc_info'     : lambda i, k, v, **c: self.deserialize_basestring(i, 'info', v,
-                                                                               convert_none_to_empty=True),
+            'genome_build': lambda i, k, v, **c: self.deserialize_genome_build(i, 'dbkey', v),
+            'misc_info': lambda i, k, v, **c: self.deserialize_basestring(i, 'info', v,
+                                                                          convert_none_to_empty=True),
         })
         self.deserializable_keyset.update(self.deserializers.keys())
 
diff --git a/lib/galaxy/managers/hdcas.py b/lib/galaxy/managers/hdcas.py
index 5f003549c90..7aa696676bd 100644
--- a/lib/galaxy/managers/hdcas.py
+++ b/lib/galaxy/managers/hdcas.py
@@ -109,8 +109,8 @@ class DCESerializer(base.ModelSerializer):
     def add_serializers(self):
         super().add_serializers()
         self.serializers.update({
-            'model_class'   : lambda *a, **c: 'DatasetCollectionElement',
-            'object'        : self.serialize_object
+            'model_class': lambda *a, **c: 'DatasetCollectionElement',
+            'object': self.serialize_object
         })
 
     def serialize_object(self, item, key, **context):
@@ -148,8 +148,8 @@ class DCSerializer(base.ModelSerializer):
     def add_serializers(self):
         super().add_serializers()
         self.serializers.update({
-            'model_class'   : lambda *a, **c: 'DatasetCollection',
-            'elements'      : self.serialize_elements,
+            'model_class': lambda *a, **c: 'DatasetCollection',
+            'elements': self.serialize_elements,
         })
 
     def serialize_elements(self, item, key, **context):
@@ -290,21 +290,21 @@ class HDCASerializer(
         annotatable.AnnotatableSerializerMixin.add_serializers(self)
 
         self.serializers.update({
-            'model_class'               : lambda *a, **c: self.hdca_manager.model_class.__class__.__name__,
+            'model_class': lambda *a, **c: self.hdca_manager.model_class.__class__.__name__,
             # TODO: remove
-            'type'                      : lambda *a, **c: 'collection',
+            'type': lambda *a, **c: 'collection',
             # part of a history and container
-            'history_id'                : self.serialize_id,
-            'history_content_type'      : lambda *a, **c: self.hdca_manager.model_class.content_type,
-            'type_id'                   : self.serialize_type_id,
-            'job_source_id'             : self.serialize_id,
+            'history_id': self.serialize_id,
+            'history_content_type': lambda *a, **c: self.hdca_manager.model_class.content_type,
+            'type_id': self.serialize_type_id,
+            'job_source_id': self.serialize_id,
 
-            'url'   : lambda i, k, **c: self.url_for('history_content_typed',
-                                                     history_id=self.app.security.encode_id(i.history_id),
-                                                     id=self.app.security.encode_id(i.id),
-                                                     type=self.hdca_manager.model_class.content_type),
-            'contents_url'              : self.generate_contents_url,
-            'job_state_summary'         : self.serialize_job_state_summary
+            'url': lambda i, k, **c: self.url_for('history_content_typed',
+                                                  history_id=self.app.security.encode_id(i.history_id),
+                                                  id=self.app.security.encode_id(i.id),
+                                                  type=self.hdca_manager.model_class.content_type),
+            'contents_url': self.generate_contents_url,
+            'job_state_summary': self.serialize_job_state_summary
         })
 
     def generate_contents_url(self, hdca, key, **context):
diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py
index f5ead283371..6649139a0b9 100644
--- a/lib/galaxy/managers/histories.py
+++ b/lib/galaxy/managers/histories.py
@@ -314,21 +314,21 @@ class HistorySerializer(sharable.SharableModelSerializer, deletable.PurgableSeri
         deletable.PurgableSerializerMixin.add_serializers(self)
 
         self.serializers.update({
-            'model_class'   : lambda *a, **c: 'History',
-            'size'          : lambda i, k, **c: int(i.disk_size),
-            'nice_size'     : lambda i, k, **c: i.disk_nice_size,
-            'state'         : self.serialize_history_state,
+            'model_class': lambda *a, **c: 'History',
+            'size': lambda i, k, **c: int(i.disk_size),
+            'nice_size': lambda i, k, **c: i.disk_nice_size,
+            'state': self.serialize_history_state,
 
-            'url'           : lambda i, k, **c: self.url_for('history', id=self.app.security.encode_id(i.id)),
-            'contents_url'  : lambda i, k, **c: self.url_for('history_contents',
-                                                             history_id=self.app.security.encode_id(i.id)),
+            'url': lambda i, k, **c: self.url_for('history', id=self.app.security.encode_id(i.id)),
+            'contents_url': lambda i, k, **c: self.url_for('history_contents',
+                                                           history_id=self.app.security.encode_id(i.id)),
 
-            'empty'         : lambda i, k, **c: (len(i.datasets) + len(i.dataset_collections)) <= 0,
-            'count'         : lambda i, k, **c: len(i.datasets),
-            'hdas'          : lambda i, k, **c: [self.app.security.encode_id(hda.id) for hda in i.datasets],
-            'state_details' : self.serialize_state_counts,
-            'state_ids'     : self.serialize_state_ids,
-            'contents'      : self.serialize_contents,
+            'empty': lambda i, k, **c: (len(i.datasets) + len(i.dataset_collections)) <= 0,
+            'count': lambda i, k, **c: len(i.datasets),
+            'hdas': lambda i, k, **c: [self.app.security.encode_id(hda.id) for hda in i.datasets],
+            'state_details': self.serialize_state_counts,
+            'state_ids': self.serialize_state_ids,
+            'contents': self.serialize_contents,
             'non_ready_jobs': lambda i, k, **c: [self.app.security.encode_id(job.id) for job
                                                  in self.manager.non_ready_jobs(i)],
 
@@ -336,7 +336,7 @@ class HistorySerializer(sharable.SharableModelSerializer, deletable.PurgableSeri
             'contents_active': self.serialize_contents_active,
             #  TODO: Use base manager's serialize_id for user_id (and others)
             #  after refactoring hierarchy here?
-            'user_id'       : lambda i, k, **c: self.app.security.encode_id(i.user_id) if i.user_id is not None else None
+            'user_id': lambda i, k, **c: self.app.security.encode_id(i.user_id) if i.user_id is not None else None
         })
 
     # remove this
@@ -392,16 +392,16 @@ class HistorySerializer(sharable.SharableModelSerializer, deletable.PurgableSeri
             state = states.NEW
 
         else:
-            if (hda_state_counts[states.RUNNING] > 0 or
-                    hda_state_counts[states.SETTING_METADATA] > 0 or
-                    hda_state_counts[states.UPLOAD] > 0):
+            if (hda_state_counts[states.RUNNING] > 0
+                    or hda_state_counts[states.SETTING_METADATA] > 0
+                    or hda_state_counts[states.UPLOAD] > 0):
                 state = states.RUNNING
             # TODO: this method may be more useful if we *also* polled the histories jobs here too
-            elif (hda_state_counts[states.QUEUED] > 0 or
-                    hda_state_counts[states.NEW] > 0):
+            elif (hda_state_counts[states.QUEUED] > 0
+                    or hda_state_counts[states.NEW] > 0):
                 state = states.QUEUED
-            elif (hda_state_counts[states.ERROR] > 0 or
-                    hda_state_counts[states.FAILED_METADATA] > 0):
+            elif (hda_state_counts[states.ERROR] > 0
+                    or hda_state_counts[states.FAILED_METADATA] > 0):
                 state = states.ERROR
             elif hda_state_counts[states.OK] == num_hdas:
                 state = states.OK
@@ -451,8 +451,8 @@ class HistoryDeserializer(sharable.SharableModelDeserializer, deletable.Purgable
         deletable.PurgableDeserializerMixin.add_deserializers(self)
 
         self.deserializers.update({
-            'name'          : self.deserialize_basestring,
-            'genome_build'  : self.deserialize_genome_build,
+            'name': self.deserialize_basestring,
+            'genome_build': self.deserialize_genome_build,
         })
 
 
@@ -465,8 +465,8 @@ class HistoryFilters(sharable.SharableModelFilters, deletable.PurgableFiltersMix
         deletable.PurgableFiltersMixin._add_parsers(self)
         self.orm_filter_parsers.update({
             # history specific
-            'name'          : {'op': ('eq', 'contains', 'like')},
-            'genome_build'  : {'op': ('eq', 'contains', 'like')},
-            'create_time'   : {'op': ('le', 'ge', 'gt', 'lt'), 'val': self.parse_date},
-            'update_time'   : {'op': ('le', 'ge', 'gt', 'lt'), 'val': self.parse_date},
+            'name': {'op': ('eq', 'contains', 'like')},
+            'genome_build': {'op': ('eq', 'contains', 'like')},
+            'create_time': {'op': ('le', 'ge', 'gt', 'lt'), 'val': self.parse_date},
+            'update_time': {'op': ('le', 'ge', 'gt', 'lt'), 'val': self.parse_date},
         })
diff --git a/lib/galaxy/managers/history_contents.py b/lib/galaxy/managers/history_contents.py
index 71a39b1b1b4..23e2f72e477 100644
--- a/lib/galaxy/managers/history_contents.py
+++ b/lib/galaxy/managers/history_contents.py
@@ -453,10 +453,10 @@ class HistoryContentsSerializer(base.ModelSerializer, deletable.PurgableSerializ
         deletable.PurgableSerializerMixin.add_serializers(self)
 
         self.serializers.update({
-            'type_id'       : self.serialize_type_id,
-            'history_id'    : self.serialize_id,
-            'dataset_id'    : self.serialize_id_or_skip,
-            'collection_id' : self.serialize_id_or_skip,
+            'type_id': self.serialize_type_id,
+            'history_id': self.serialize_id,
+            'dataset_id': self.serialize_id_or_skip,
+            'collection_id': self.serialize_id_or_skip,
         })
 
     def serialize_id_or_skip(self, content, key, **context):
@@ -542,14 +542,14 @@ class HistoryContentsFilters(base.ModelFilterParser,
         taggable.TaggableFilterMixin._add_parsers(self)
         tools.ToolFilterMixin._add_parsers(self)
         self.orm_filter_parsers.update({
-            'history_content_type' : {'op': ('eq')},
-            'type_id'       : {'op': ('eq', 'in'), 'val': self.parse_type_id_list},
-            'hid'           : {'op': ('eq', 'ge', 'le', 'gt', 'lt'), 'val': int},
+            'history_content_type': {'op': ('eq')},
+            'type_id': {'op': ('eq', 'in'), 'val': self.parse_type_id_list},
+            'hid': {'op': ('eq', 'ge', 'le', 'gt', 'lt'), 'val': int},
             # TODO: needs a different val parser - but no way to add to the above
             # 'hid-in'        : { 'op': ( 'in' ), 'val': self.parse_int_list },
-            'name'          : {'op': ('eq', 'contains', 'like')},
-            'state'         : {'op': ('eq', 'in')},
-            'visible'       : {'op': ('eq'), 'val': self.parse_bool},
-            'create_time'   : {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
-            'update_time'   : {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
+            'name': {'op': ('eq', 'contains', 'like')},
+            'state': {'op': ('eq', 'in')},
+            'visible': {'op': ('eq'), 'val': self.parse_bool},
+            'create_time': {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
+            'update_time': {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
         })
diff --git a/lib/galaxy/managers/libraries.py b/lib/galaxy/managers/libraries.py
index 141240e10bf..53544a21e85 100644
--- a/lib/galaxy/managers/libraries.py
+++ b/lib/galaxy/managers/libraries.py
@@ -174,7 +174,7 @@ class LibraryManager:
         :type   check_accessible:        bool
 
         :returns:   the original library
-        :rtype:     Library
+        :rtype:     galaxy.model.Library
         """
         # all libraries are accessible to an admin
         if trans.user_is_admin:
diff --git a/lib/galaxy/managers/markdown_util.py b/lib/galaxy/managers/markdown_util.py
index 43e0a48f8f9..76b65d43c32 100644
--- a/lib/galaxy/managers/markdown_util.py
+++ b/lib/galaxy/managers/markdown_util.py
@@ -518,7 +518,7 @@ class MarkdownFormatHelpers:
 
     @staticmethod
     def literal_via_fence(content):
-        return "\n%s\n" % "\n".join("    %s" % l for l in content.splitlines())
+        return "\n%s\n" % "\n".join(f"    {line}" for line in content.splitlines())
 
     @staticmethod
     def indicate_data_truncated():
diff --git a/lib/galaxy/managers/ratable.py b/lib/galaxy/managers/ratable.py
index 42279f5f2ed..b1bf4a08e67 100644
--- a/lib/galaxy/managers/ratable.py
+++ b/lib/galaxy/managers/ratable.py
@@ -84,8 +84,8 @@ class RatableSerializerMixin:
         # than getting the rows and calc'ing both here with one query
         manager = self.manager
         return {
-            'average' : manager.ratings_avg(item),
-            'count'   : manager.ratings_count(item),
+            'average': manager.ratings_avg(item),
+            'count': manager.ratings_count(item),
         }
 
 
@@ -115,11 +115,11 @@ class RatableFilterMixin:
         self.fn_filter_parsers.update({
             'community_rating': {
                 'op': {
-                    'eq' : lambda i, v: self._ratings_avg_accessor(i) == v,
+                    'eq': lambda i, v: self._ratings_avg_accessor(i) == v,
                     # TODO: default to greater than (currently 'eq' due to base/controller.py)
-                    'ge' : lambda i, v: self._ratings_avg_accessor(i) >= v,
-                    'le' : lambda i, v: self._ratings_avg_accessor(i) <= v,
+                    'ge': lambda i, v: self._ratings_avg_accessor(i) >= v,
+                    'le': lambda i, v: self._ratings_avg_accessor(i) <= v,
                 },
-                'val' : float
+                'val': float
             }
         })
diff --git a/lib/galaxy/managers/rbac_secured.py b/lib/galaxy/managers/rbac_secured.py
index 4ccda187aa3..640b4804292 100644
--- a/lib/galaxy/managers/rbac_secured.py
+++ b/lib/galaxy/managers/rbac_secured.py
@@ -16,7 +16,7 @@ class RBACPermissionFailedException(galaxy.exceptions.InsufficientPermissionsExc
 
 class RBACPermission:
     """
-    Base class for wrangling/controlling the permissions ORM models (*Permissions, Roles)
+    Base class for wrangling/controlling the permissions ORM models (Permissions, Roles)
     that control which users can perform certain actions on their associated models
     (Libraries, Datasets).
     """
@@ -238,10 +238,9 @@ class AccessDatasetRBACPermission(DatasetRBACPermission):
         current_roles = self._roles(dataset)
         # NOTE: that because of short circuiting this allows
         #   anonymous access to public datasets
-        return (self._is_public_based_on_roles(current_roles) or
-                # admin is always permitted
-                self.user_manager.is_admin(user) or
-                self._user_has_all_roles(user, current_roles))
+        return (self._is_public_based_on_roles(current_roles)
+                or self.user_manager.is_admin(user)  # admin is always permitted
+                or self._user_has_all_roles(user, current_roles))
 
     def grant(self, item, user):
         pass
@@ -274,6 +273,6 @@ class AccessDatasetRBACPermission(DatasetRBACPermission):
 
     def _role_is_permitted(self, dataset, role):
         current_roles = self._roles(dataset)
-        return (self._is_public_based_on_roles(current_roles) or
+        return (self._is_public_based_on_roles(current_roles)
                 # if there's only one role and this is it, let em in
-                ((len(current_roles) == 1) and (role == current_roles[0])))
+                or ((len(current_roles) == 1) and (role == current_roles[0])))
diff --git a/lib/galaxy/managers/roles.py b/lib/galaxy/managers/roles.py
index d1d709be029..088e637fd7b 100644
--- a/lib/galaxy/managers/roles.py
+++ b/lib/galaxy/managers/roles.py
@@ -15,6 +15,8 @@ import galaxy.exceptions
 from galaxy import model
 from galaxy.exceptions import RequestParameterInvalidException
 from galaxy.managers import base
+from galaxy.managers.context import ProvidesUserContext
+from galaxy.model import Role
 from galaxy.schema.fields import EncodedDatabaseIdField
 from galaxy.util import unicodify
 
@@ -54,7 +56,7 @@ class RoleManager(base.ModelManager):
     def __init__(self, app):
         super().__init__(app)
 
-    def get(self, trans, decoded_role_id):
+    def get(self, trans: ProvidesUserContext, decoded_role_id):
         """
         Method loads the role from the DB based on the given role id.
 
@@ -81,28 +83,28 @@ class RoleManager(base.ModelManager):
 
         return role
 
-    def list_displayable_roles(self, trans):
+    def list_displayable_roles(self, trans: ProvidesUserContext):
         roles = []
-        for role in trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.table.c.deleted == false()):
+        for role in trans.sa_session.query(Role).filter(Role.table.c.deleted == false()):
             if trans.user_is_admin or trans.app.security_agent.ok_to_display(trans.user, role):
                 roles.append(role)
         return roles
 
-    def create(self, trans, role_definition_model):
+    def create_role(self, trans: ProvidesUserContext, role_definition_model) -> model.Role:
         name = role_definition_model.name
         description = role_definition_model.description
         user_ids = role_definition_model.user_ids or []
         group_ids = role_definition_model.group_ids or []
 
-        if trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.table.c.name == name).first():
+        if trans.sa_session.query(Role).filter(Role.table.c.name == name).first():
             raise RequestParameterInvalidException(f"A role with that name already exists [{name}]")
 
-        role_type = trans.app.model.Role.types.ADMIN  # TODO: allow non-admins to create roles
+        role_type = Role.types.ADMIN  # TODO: allow non-admins to create roles
 
-        role = trans.app.model.Role(name=name, description=description, type=role_type)
+        role = Role(name=name, description=description, type=role_type)
         trans.sa_session.add(role)
-        users = [trans.sa_session.query(trans.model.User).get(trans.security.decode_id(i)) for i in user_ids]
-        groups = [trans.sa_session.query(trans.model.Group).get(trans.security.decode_id(i)) for i in group_ids]
+        users = [trans.sa_session.query(model.User).get(trans.security.decode_id(i)) for i in user_ids]
+        groups = [trans.sa_session.query(model.Group).get(trans.security.decode_id(i)) for i in group_ids]
 
         # Create the UserRoleAssociations
         for user in users:
diff --git a/lib/galaxy/managers/sharable.py b/lib/galaxy/managers/sharable.py
index 983c6c0636b..8b60017f573 100644
--- a/lib/galaxy/managers/sharable.py
+++ b/lib/galaxy/managers/sharable.py
@@ -337,10 +337,10 @@ class SharableModelSerializer(base.ModelSerializer,
         annotatable.AnnotatableSerializerMixin.add_serializers(self)
         ratable.RatableSerializerMixin.add_serializers(self)
         self.serializers.update({
-            'id'                : self.serialize_id,
-            'title'             : self.serialize_title,
-            'username_and_slug' : self.serialize_username_and_slug,
-            'users_shared_with' : self.serialize_users_shared_with
+            'id': self.serialize_id,
+            'title': self.serialize_title,
+            'username_and_slug': self.serialize_username_and_slug,
+            'users_shared_with': self.serialize_users_shared_with
         })
         # these use the default serializer but must still be white-listed
         self.serializable_keyset.update([
@@ -387,9 +387,9 @@ class SharableModelDeserializer(base.ModelDeserializer,
         ratable.RatableDeserializerMixin.add_deserializers(self)
 
         self.deserializers.update({
-            'published'         : self.deserialize_published,
-            'importable'        : self.deserialize_importable,
-            'users_shared_with' : self.deserialize_users_shared_with,
+            'published': self.deserialize_published,
+            'importable': self.deserialize_importable,
+            'users_shared_with': self.deserialize_users_shared_with,
         })
 
     def deserialize_published(self, item, key, val, **context):
@@ -454,9 +454,9 @@ class SharableModelFilters(base.ModelFilterParser,
         ratable.RatableFilterMixin._add_parsers(self)
 
         self.orm_filter_parsers.update({
-            'importable'    : {'op': ('eq'), 'val': self.parse_bool},
-            'published'     : {'op': ('eq'), 'val': self.parse_bool},
-            'slug'          : {'op': ('eq', 'contains', 'like')},
+            'importable': {'op': ('eq'), 'val': self.parse_bool},
+            'published': {'op': ('eq'), 'val': self.parse_bool},
+            'slug': {'op': ('eq', 'contains', 'like')},
             # chose by user should prob. only be available for admin? (most often we'll only need trans.user)
             # 'user'          : { 'op': ( 'eq' ), 'val': self.parse_id_list },
         })
diff --git a/lib/galaxy/managers/tool_data.py b/lib/galaxy/managers/tool_data.py
new file mode 100644
index 00000000000..6b516e670da
--- /dev/null
+++ b/lib/galaxy/managers/tool_data.py
@@ -0,0 +1,96 @@
+
+from pathlib import Path
+from typing import (
+    Dict,
+    Optional,
+)
+
+from galaxy import exceptions
+from galaxy.app import StructuredApp
+from galaxy.tools.data import (
+    TabularToolDataField,
+    TabularToolDataTable,
+)
+from galaxy.tools.data._schema import (
+    ToolDataDetails,
+    ToolDataEntryList,
+    ToolDataField,
+)
+
+
+class ToolDataManager:
+    """
+    Interface/service object for interacting with tool data.
+    """
+
+    def __init__(self, app: StructuredApp):
+        self._app = app
+
+    @property
+    def data_tables(self) -> Dict[str, TabularToolDataTable]:
+        return self._app.tool_data_tables.data_tables
+
+    def index(self) -> ToolDataEntryList:
+        """Return all tool data tables."""
+        data_tables = [table.to_dict() for table in self.data_tables.values()]
+        return ToolDataEntryList.parse_obj(data_tables)
+
+    def show(self, table_name: str) -> ToolDataDetails:
+        """Get details of a given data table"""
+        data_table = self._data_table(table_name)
+        element_view = data_table.to_dict(view='element')
+        return ToolDataDetails.parse_obj(element_view)
+
+    def show_field(self, table_name: str, field_name: str) -> ToolDataField:
+        """Get information about a partiular field in a tool data table"""
+        field = self._data_table_field(table_name, field_name)
+        return ToolDataField.parse_obj(field.to_dict())
+
+    def reload(self, table_name: str) -> ToolDataDetails:
+        """Reloads a tool data table."""
+        data_table = self._data_table(table_name)
+        data_table.reload_from_files()
+        return self._reload_data_table(table_name)
+
+    def get_field_file_path(self, table_name: str, field_name: str, file_name: str) -> Path:
+        """Get the absolute path to a given file name in the table field"""
+        field_value = self._data_table_field(table_name, field_name)
+        base_dir = Path(field_value.get_base_dir())
+        full_path = base_dir / file_name
+        if str(full_path) not in field_value.get_files():
+            raise exceptions.ObjectNotFound("No such path in data table field.")
+        return full_path.absolute()
+
+    def delete(self, table_name: str, values: Optional[str] = None) -> ToolDataDetails:
+        """Removes an item from a data table"""
+        data_table = self._data_table(table_name)
+        if not values:
+            raise exceptions.RequestParameterInvalidException("Invalid values for data table item specified.")
+
+        split_values = values.split("\t")
+
+        if len(split_values) != len(data_table.get_column_name_list()):
+            raise exceptions.RequestParameterInvalidException(f"Invalid data table item ( {values} ) specified. Wrong number of columns ({len(split_values)} given, {len(data_table.get_column_name_list())} required).")
+
+        data_table.remove_entry(split_values)
+        return self._reload_data_table(table_name)
+
+    def _data_table(self, table_name: str) -> TabularToolDataTable:
+        try:
+            return self.data_tables[table_name]
+        except KeyError:
+            raise exceptions.ObjectNotFound(f"No such data table {table_name}")
+
+    def _data_table_field(self, table_name: str, field_name: str) -> TabularToolDataField:
+        out = self._data_table(table_name).get_field(field_name)
+        if out is None:
+            raise exceptions.ObjectNotFound(f"No such field {field_name} in data table {table_name}.")
+        return out
+
+    def _reload_data_table(self, name: str) -> ToolDataDetails:
+        self._app.queue_worker.send_control_task(
+            'reload_tool_data_tables',
+            noop_self=True,
+            kwargs={'table_name': name}
+        )
+        return self.show(name)
diff --git a/lib/galaxy/managers/users.py b/lib/galaxy/managers/users.py
index 8754a4df409..95f031adb77 100644
--- a/lib/galaxy/managers/users.py
+++ b/lib/galaxy/managers/users.py
@@ -628,18 +628,18 @@ class UserSerializer(base.ModelSerializer, deletable.PurgableSerializerMixin):
         deletable.PurgableSerializerMixin.add_serializers(self)
 
         self.serializers.update({
-            'id'            : self.serialize_id,
-            'create_time'   : self.serialize_date,
-            'update_time'   : self.serialize_date,
-            'is_admin'      : lambda i, k, **c: self.user_manager.is_admin(i),
+            'id': self.serialize_id,
+            'create_time': self.serialize_date,
+            'update_time': self.serialize_date,
+            'is_admin': lambda i, k, **c: self.user_manager.is_admin(i),
 
-            'preferences'   : lambda i, k, **c: self.user_manager.preferences(i),
+            'preferences': lambda i, k, **c: self.user_manager.preferences(i),
 
-            'total_disk_usage' : lambda i, k, **c: float(i.total_disk_usage),
-            'quota_percent' : lambda i, k, **c: self.user_manager.quota(i),
-            'quota'         : lambda i, k, **c: self.user_manager.quota(i, total=True),
+            'total_disk_usage': lambda i, k, **c: float(i.total_disk_usage),
+            'quota_percent': lambda i, k, **c: self.user_manager.quota(i),
+            'quota': lambda i, k, **c: self.user_manager.quota(i, total=True),
 
-            'tags_used'     : lambda i, k, **c: self.user_manager.tags_used(i),
+            'tags_used': lambda i, k, **c: self.user_manager.tags_used(i),
         })
 
 
@@ -653,7 +653,7 @@ class UserDeserializer(base.ModelDeserializer):
     def add_deserializers(self):
         super().add_deserializers()
         self.deserializers.update({
-            'username'  : self.deserialize_username,
+            'username': self.deserialize_username,
         })
 
     def deserialize_username(self, item, key, username, trans=None, **context):
@@ -690,10 +690,10 @@ class CurrentUserSerializer(UserSerializer):
 
         # a very small subset of keys available
         values = {
-            'id'                    : None,
-            'total_disk_usage'      : float(usage),
-            'nice_total_disk_usage' : util.nice_size(usage),
-            'quota_percent'         : percent,
+            'id': None,
+            'total_disk_usage': float(usage),
+            'nice_total_disk_usage': util.nice_size(usage),
+            'quota_percent': percent,
         }
         serialized = {}
         for key in keys:
@@ -712,10 +712,10 @@ class AdminUserFilterParser(base.ModelFilterParser, deletable.PurgableFiltersMix
 
         # PRECONDITION: user making the query has been verified as an admin
         self.orm_filter_parsers.update({
-            'email'         : {'op': ('eq', 'contains', 'like')},
-            'username'      : {'op': ('eq', 'contains', 'like')},
-            'active'        : {'op': ('eq')},
-            'disk_usage'    : {'op': ('le', 'ge')}
+            'email': {'op': ('eq', 'contains', 'like')},
+            'username': {'op': ('eq', 'contains', 'like')},
+            'active': {'op': ('eq')},
+            'disk_usage': {'op': ('le', 'ge')}
         })
 
         self.fn_filter_parsers.update({})
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index c83769989f0..71c762fdf1f 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -101,6 +101,8 @@ else:
 
 
 class RepresentById(_HasTable):
+    id: int
+
     def __repr__(self):
         try:
             r = '<galaxy.model.{}({}) at {}>'.format(self.__class__.__name__, cached_id(self), hex(id(self)))
@@ -1147,13 +1149,13 @@ class Job(JobLike, UsesCreateAndUpdateTime, Dictifiable, RepresentById):
             for i in self.input_datasets:
                 if i.dataset is not None:
                     input_dict[i.name] = {
-                        "id" : i.dataset.id, "src" : "hda",
-                        "uuid" : str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
+                        "id": i.dataset.id, "src": "hda",
+                        "uuid": str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
                     }
             for i in self.input_library_datasets:
                 if i.dataset is not None:
                     input_dict[i.name] = {
-                        "id" : i.dataset.id, "src" : "ldda",
+                        "id": i.dataset.id, "src": "ldda",
                         "uuid": str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
                     }
             for k in input_dict:
@@ -1165,14 +1167,14 @@ class Job(JobLike, UsesCreateAndUpdateTime, Dictifiable, RepresentById):
             for i in self.output_datasets:
                 if i.dataset is not None:
                     output_dict[i.name] = {
-                        "id" : i.dataset.id, "src" : "hda",
-                        "uuid" : str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
+                        "id": i.dataset.id, "src": "hda",
+                        "uuid": str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
                     }
             for i in self.output_library_datasets:
                 if i.dataset is not None:
                     output_dict[i.name] = {
-                        "id" : i.dataset.id, "src" : "ldda",
-                        "uuid" : str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
+                        "id": i.dataset.id, "src": "ldda",
+                        "uuid": str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
                     }
             rval['outputs'] = output_dict
 
@@ -1585,7 +1587,7 @@ class JobExternalOutputMetadata(RepresentById):
 # uses a Dataset rather than an HDA or LDA, it's necessary to set up a
 # fake dataset association that provides the needed attributes for
 # preparing a job.
-class FakeDatasetAssociation :
+class FakeDatasetAssociation:
     fake_dataset_association = True
 
     def __init__(self, dataset=None):
@@ -5887,14 +5889,14 @@ class FormDefinition(Dictifiable, RepresentById):
         values = values or {}
         form_def = {'id': security.encode_id(self.id) if security else self.id, 'name': self.name, 'inputs': []}
         for field in self.fields:
-            FieldClass = ({'AddressField'         : AddressField,
-                           'CheckboxField'        : CheckboxField,
-                           'HistoryField'         : HistoryField,
-                           'PasswordField'        : PasswordField,
-                           'SelectField'          : SelectField,
-                           'TextArea'             : TextArea,
-                           'TextField'            : TextField,
-                           'WorkflowField'        : WorkflowField}).get(field['type'], TextField)
+            FieldClass = ({'AddressField': AddressField,
+                           'CheckboxField': CheckboxField,
+                           'HistoryField': HistoryField,
+                           'PasswordField': PasswordField,
+                           'SelectField': SelectField,
+                           'TextArea': TextArea,
+                           'TextField': TextField,
+                           'WorkflowField': WorkflowField}).get(field['type'], TextField)
             form_def['inputs'].append(FieldClass(user=user, value=values.get(field['name'], field['default']), security=security, **field).to_dict())
         return form_def
 
@@ -5935,16 +5937,16 @@ class UserAddress(RepresentById):
         self.phone = phone
 
     def to_dict(self, trans):
-        return {'id'           : trans.security.encode_id(self.id),
-                'name'         : sanitize_html(self.name),
-                'desc'         : sanitize_html(self.desc),
-                'institution'  : sanitize_html(self.institution),
-                'address'      : sanitize_html(self.address),
-                'city'         : sanitize_html(self.city),
-                'state'        : sanitize_html(self.state),
-                'postal_code'  : sanitize_html(self.postal_code),
-                'country'      : sanitize_html(self.country),
-                'phone'        : sanitize_html(self.phone)}
+        return {'id': trans.security.encode_id(self.id),
+                'name': sanitize_html(self.name),
+                'desc': sanitize_html(self.desc),
+                'institution': sanitize_html(self.institution),
+                'address': sanitize_html(self.address),
+                'city': sanitize_html(self.city),
+                'state': sanitize_html(self.state),
+                'postal_code': sanitize_html(self.postal_code),
+                'country': sanitize_html(self.country),
+                'phone': sanitize_html(self.phone)}
 
 
 class PSAAssociation(AssociationMixin, RepresentById):
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index db48b9b64c1..d5db8da3e7e 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -4,6 +4,8 @@ are encapsulated here.
 """
 
 import logging
+from threading import local
+from typing import Optional
 
 from sqlalchemy import (
     and_,
@@ -1723,24 +1725,24 @@ simple_mapping(model.HistoryDatasetAssociation,
         primaryjoin=(model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id), lazy=False),
     # .history defined in History mapper
     copied_from_history_dataset_association=relation(model.HistoryDatasetAssociation,
-        primaryjoin=(model.HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id ==
-                     model.HistoryDatasetAssociation.table.c.id),
+        primaryjoin=(model.HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id
+                     == model.HistoryDatasetAssociation.table.c.id),
         remote_side=[model.HistoryDatasetAssociation.table.c.id],
         uselist=False),
     copied_to_history_dataset_associations=relation(model.HistoryDatasetAssociation,
-        primaryjoin=(model.HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id ==
-                     model.HistoryDatasetAssociation.table.c.id)),
+        primaryjoin=(model.HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id
+                     == model.HistoryDatasetAssociation.table.c.id)),
     copied_from_library_dataset_dataset_association=relation(
         model.LibraryDatasetDatasetAssociation,
-        primaryjoin=(model.HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id ==
-                     model.LibraryDatasetDatasetAssociation.table.c.id),
+        primaryjoin=(model.HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id
+                     == model.LibraryDatasetDatasetAssociation.table.c.id),
         uselist=False),
     copied_to_library_dataset_dataset_associations=relation(model.LibraryDatasetDatasetAssociation,
-        primaryjoin=(model.HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id ==
-                     model.LibraryDatasetDatasetAssociation.table.c.id)),
+        primaryjoin=(model.HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id
+                     == model.LibraryDatasetDatasetAssociation.table.c.id)),
     implicitly_converted_datasets=relation(model.ImplicitlyConvertedDatasetAssociation,
-        primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id ==
-                     model.HistoryDatasetAssociation.table.c.id)),
+        primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id
+                     == model.HistoryDatasetAssociation.table.c.id)),
     tags=relation(model.HistoryDatasetAssociationTagAssociation,
         order_by=model.HistoryDatasetAssociationTagAssociation.table.c.id,
         backref='history_tag_associations'),
@@ -1751,11 +1753,11 @@ simple_mapping(model.HistoryDatasetAssociation,
         order_by=model.HistoryDatasetAssociationRatingAssociation.table.c.id,
         backref="hdas"),
     extended_metadata=relation(model.ExtendedMetadata,
-        primaryjoin=(model.HistoryDatasetAssociation.table.c.extended_metadata_id ==
-                     model.ExtendedMetadata.table.c.id)),
+        primaryjoin=(model.HistoryDatasetAssociation.table.c.extended_metadata_id
+                     == model.ExtendedMetadata.table.c.id)),
     hidden_beneath_collection_instance=relation(model.HistoryDatasetCollectionAssociation,
-        primaryjoin=(model.HistoryDatasetAssociation.table.c.hidden_beneath_collection_instance_id ==
-                     model.HistoryDatasetCollectionAssociation.table.c.id),
+        primaryjoin=(model.HistoryDatasetAssociation.table.c.hidden_beneath_collection_instance_id
+                     == model.HistoryDatasetCollectionAssociation.table.c.id),
         uselist=False,
         backref="hidden_dataset_instances"),
     _metadata=deferred(model.HistoryDatasetAssociation.table.c._metadata)
@@ -1766,19 +1768,19 @@ simple_mapping(model.Dataset,
         primaryjoin=(model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id)),
     active_history_associations=relation(model.HistoryDatasetAssociation,
         primaryjoin=(
-            (model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id) &
-            (model.HistoryDatasetAssociation.table.c.deleted == false()) &
-            (model.HistoryDatasetAssociation.table.c.purged == false()))),
+            (model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id)
+            & (model.HistoryDatasetAssociation.table.c.deleted == false())
+            & (model.HistoryDatasetAssociation.table.c.purged == false()))),
     purged_history_associations=relation(model.HistoryDatasetAssociation,
         primaryjoin=(
-            (model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id) &
-            (model.HistoryDatasetAssociation.table.c.purged == true()))),
+            (model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id)
+            & (model.HistoryDatasetAssociation.table.c.purged == true()))),
     library_associations=relation(model.LibraryDatasetDatasetAssociation,
         primaryjoin=(model.Dataset.table.c.id == model.LibraryDatasetDatasetAssociation.table.c.dataset_id)),
     active_library_associations=relation(model.LibraryDatasetDatasetAssociation,
         primaryjoin=(
-            (model.Dataset.table.c.id == model.LibraryDatasetDatasetAssociation.table.c.dataset_id) &
-            (model.LibraryDatasetDatasetAssociation.table.c.deleted == false()))),
+            (model.Dataset.table.c.id == model.LibraryDatasetDatasetAssociation.table.c.dataset_id)
+            & (model.LibraryDatasetDatasetAssociation.table.c.deleted == false()))),
 )
 
 mapper(model.DatasetHash, model.DatasetHash.table, properties=dict(
@@ -1802,27 +1804,27 @@ mapper(model.HistoryDatasetAssociationDisplayAtAuthorization, model.HistoryDatas
 
 mapper(model.HistoryDatasetAssociationSubset, model.HistoryDatasetAssociationSubset.table, properties=dict(
     hda=relation(model.HistoryDatasetAssociation,
-        primaryjoin=(model.HistoryDatasetAssociationSubset.table.c.history_dataset_association_id ==
-                     model.HistoryDatasetAssociation.table.c.id)),
+        primaryjoin=(model.HistoryDatasetAssociationSubset.table.c.history_dataset_association_id
+                     == model.HistoryDatasetAssociation.table.c.id)),
     subset=relation(model.HistoryDatasetAssociation,
-        primaryjoin=(model.HistoryDatasetAssociationSubset.table.c.history_dataset_association_subset_id ==
-                     model.HistoryDatasetAssociation.table.c.id))
+        primaryjoin=(model.HistoryDatasetAssociationSubset.table.c.history_dataset_association_subset_id
+                     == model.HistoryDatasetAssociation.table.c.id))
 ))
 
 mapper(model.ImplicitlyConvertedDatasetAssociation, model.ImplicitlyConvertedDatasetAssociation.table, properties=dict(
     parent_hda=relation(model.HistoryDatasetAssociation,
-        primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id ==
-                     model.HistoryDatasetAssociation.table.c.id)),
+        primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id
+                     == model.HistoryDatasetAssociation.table.c.id)),
     parent_ldda=relation(model.LibraryDatasetDatasetAssociation,
-        primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.ldda_parent_id ==
-                     model.LibraryDatasetDatasetAssociation.table.c.id)),
+        primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.ldda_parent_id
+                     == model.LibraryDatasetDatasetAssociation.table.c.id)),
     dataset_ldda=relation(model.LibraryDatasetDatasetAssociation,
-        primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.ldda_id ==
-                     model.LibraryDatasetDatasetAssociation.table.c.id),
+        primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.ldda_id
+                     == model.LibraryDatasetDatasetAssociation.table.c.id),
         backref="implicitly_converted_parent_datasets"),
     dataset=relation(model.HistoryDatasetAssociation,
-        primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.hda_id ==
-                     model.HistoryDatasetAssociation.table.c.id),
+        primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.hda_id
+                     == model.HistoryDatasetAssociation.table.c.id),
         backref="implicitly_converted_parent_datasets")
 ))
 
@@ -1836,31 +1838,31 @@ mapper(model.History, model.History.table, properties=dict(
         order_by=desc(model.JobExportHistoryArchive.table.c.id)),
     active_datasets=relation(model.HistoryDatasetAssociation,
         primaryjoin=(
-            (model.HistoryDatasetAssociation.table.c.history_id == model.History.table.c.id) &
-            not_(model.HistoryDatasetAssociation.table.c.deleted)
+            (model.HistoryDatasetAssociation.table.c.history_id == model.History.table.c.id)
+            & not_(model.HistoryDatasetAssociation.table.c.deleted)
         ),
         order_by=asc(model.HistoryDatasetAssociation.table.c.hid),
         viewonly=True),
     active_dataset_collections=relation(model.HistoryDatasetCollectionAssociation,
         primaryjoin=(
-            (model.HistoryDatasetCollectionAssociation.table.c.history_id == model.History.table.c.id) &
-            not_(model.HistoryDatasetCollectionAssociation.table.c.deleted)
+            (model.HistoryDatasetCollectionAssociation.table.c.history_id == model.History.table.c.id)
+            & not_(model.HistoryDatasetCollectionAssociation.table.c.deleted)
         ),
         order_by=asc(model.HistoryDatasetCollectionAssociation.table.c.hid),
         viewonly=True),
     visible_datasets=relation(model.HistoryDatasetAssociation,
         primaryjoin=(
-            (model.HistoryDatasetAssociation.table.c.history_id == model.History.table.c.id) &
-            not_(model.HistoryDatasetAssociation.table.c.deleted) &
-            model.HistoryDatasetAssociation.table.c.visible
+            (model.HistoryDatasetAssociation.table.c.history_id == model.History.table.c.id)
+            & not_(model.HistoryDatasetAssociation.table.c.deleted)
+            & model.HistoryDatasetAssociation.table.c.visible
         ),
         order_by=asc(model.HistoryDatasetAssociation.table.c.hid),
         viewonly=True),
     visible_dataset_collections=relation(model.HistoryDatasetCollectionAssociation,
         primaryjoin=(
-            (model.HistoryDatasetCollectionAssociation.table.c.history_id == model.History.table.c.id) &
-            not_(model.HistoryDatasetCollectionAssociation.table.c.deleted) &
-            model.HistoryDatasetCollectionAssociation.table.c.visible
+            (model.HistoryDatasetCollectionAssociation.table.c.history_id == model.History.table.c.id)
+            & not_(model.HistoryDatasetCollectionAssociation.table.c.deleted)
+            & model.HistoryDatasetCollectionAssociation.table.c.visible
         ),
         order_by=asc(model.HistoryDatasetCollectionAssociation.table.c.hid),
         viewonly=True),
@@ -1899,8 +1901,8 @@ mapper(model.User, model.User.table, properties=dict(
         order_by=desc(model.History.table.c.update_time)),
     active_histories=relation(model.History,
         primaryjoin=(
-            (model.History.table.c.user_id == model.User.table.c.id) &
-            (not_(model.History.table.c.deleted))
+            (model.History.table.c.user_id == model.User.table.c.id)
+            & (not_(model.History.table.c.deleted))
         ),
         order_by=desc(model.History.table.c.update_time)),
 
@@ -1908,9 +1910,9 @@ mapper(model.User, model.User.table, properties=dict(
         order_by=desc(model.GalaxySession.table.c.update_time)),
     stored_workflow_menu_entries=relation(model.StoredWorkflowMenuEntry,
         primaryjoin=(
-            (model.StoredWorkflowMenuEntry.table.c.user_id == model.User.table.c.id) &
-            (model.StoredWorkflowMenuEntry.table.c.stored_workflow_id == model.StoredWorkflow.table.c.id) &
-            not_(model.StoredWorkflow.table.c.deleted)
+            (model.StoredWorkflowMenuEntry.table.c.user_id == model.User.table.c.id)
+            & (model.StoredWorkflowMenuEntry.table.c.stored_workflow_id == model.StoredWorkflow.table.c.id)
+            & not_(model.StoredWorkflow.table.c.deleted)
         ),
         backref="user",
         cascade="all, delete-orphan",
@@ -1967,9 +1969,9 @@ mapper(model.UserRoleAssociation, model.UserRoleAssociation.table, properties=di
         model.User,
         backref="non_private_roles",
         primaryjoin=(
-            (model.User.table.c.id == model.UserRoleAssociation.table.c.user_id) &
-            (model.UserRoleAssociation.table.c.role_id == model.Role.table.c.id) &
-            not_(model.Role.table.c.name == model.User.table.c.email))
+            (model.User.table.c.id == model.UserRoleAssociation.table.c.user_id)
+            & (model.UserRoleAssociation.table.c.role_id == model.Role.table.c.id)
+            & not_(model.Role.table.c.name == model.User.table.c.email))
     ),
     role=relation(model.Role)
 ))
@@ -2043,8 +2045,8 @@ mapper(model.ExtendedMetadataIndex, model.ExtendedMetadataIndex.table, propertie
 mapper(model.LibraryInfoAssociation, model.LibraryInfoAssociation.table, properties=dict(
     library=relation(model.Library,
         primaryjoin=(
-            (model.LibraryInfoAssociation.table.c.library_id == model.Library.table.c.id) &
-            (not_(model.LibraryInfoAssociation.table.c.deleted))
+            (model.LibraryInfoAssociation.table.c.library_id == model.Library.table.c.id)
+            & (not_(model.LibraryInfoAssociation.table.c.deleted))
         ),
         backref="info_association"),
     template=relation(model.FormDefinition,
@@ -2062,8 +2064,8 @@ mapper(model.LibraryFolder, model.LibraryFolder.table, properties=dict(
             remote_side=[model.LibraryFolder.table.c.id])),
     active_folders=relation(model.LibraryFolder,
         primaryjoin=(
-            (model.LibraryFolder.table.c.parent_id == model.LibraryFolder.table.c.id) &
-            (not_(model.LibraryFolder.table.c.deleted))
+            (model.LibraryFolder.table.c.parent_id == model.LibraryFolder.table.c.id)
+            & (not_(model.LibraryFolder.table.c.deleted))
         ),
         order_by=asc(model.LibraryFolder.table.c.name),
         # """sqlalchemy.exc.ArgumentError: Error creating eager relationship 'active_folders'
@@ -2078,8 +2080,8 @@ mapper(model.LibraryFolder, model.LibraryFolder.table, properties=dict(
         viewonly=True),
     active_datasets=relation(model.LibraryDataset,
         primaryjoin=(
-            (model.LibraryDataset.table.c.folder_id == model.LibraryFolder.table.c.id) &
-            (not_(model.LibraryDataset.table.c.deleted))
+            (model.LibraryDataset.table.c.folder_id == model.LibraryFolder.table.c.id)
+            & (not_(model.LibraryDataset.table.c.deleted))
         ),
         order_by=asc(model.LibraryDataset.table.c._name),
         lazy=True,
@@ -2089,8 +2091,8 @@ mapper(model.LibraryFolder, model.LibraryFolder.table, properties=dict(
 mapper(model.LibraryFolderInfoAssociation, model.LibraryFolderInfoAssociation.table, properties=dict(
     folder=relation(model.LibraryFolder,
         primaryjoin=(
-            (model.LibraryFolderInfoAssociation.table.c.library_folder_id == model.LibraryFolder.table.c.id) &
-            (not_(model.LibraryFolderInfoAssociation.table.c.deleted))
+            (model.LibraryFolderInfoAssociation.table.c.library_folder_id == model.LibraryFolder.table.c.id)
+            & (not_(model.LibraryFolderInfoAssociation.table.c.deleted))
         ),
         backref="info_association"),
     template=relation(model.FormDefinition,
@@ -2107,9 +2109,9 @@ mapper(model.LibraryDataset, model.LibraryDataset.table, properties=dict(
     expired_datasets=relation(model.LibraryDatasetDatasetAssociation,
         foreign_keys=[model.LibraryDataset.table.c.id, model.LibraryDataset.table.c.library_dataset_dataset_association_id],
         primaryjoin=(
-            (model.LibraryDataset.table.c.id == model.LibraryDatasetDatasetAssociation.table.c.library_dataset_id) &
-            (not_(model.LibraryDataset.table.c.library_dataset_dataset_association_id ==
-                  model.LibraryDatasetDatasetAssociation.table.c.id))
+            (model.LibraryDataset.table.c.id == model.LibraryDatasetDatasetAssociation.table.c.library_dataset_id)
+            & (not_(model.LibraryDataset.table.c.library_dataset_dataset_association_id
+                  == model.LibraryDatasetDatasetAssociation.table.c.id))
         ),
         viewonly=True,
         uselist=True)
@@ -2122,23 +2124,23 @@ mapper(model.LibraryDatasetDatasetAssociation, model.LibraryDatasetDatasetAssoci
     # user=relation( model.User.mapper ),
     user=relation(model.User),
     copied_from_library_dataset_dataset_association=relation(model.LibraryDatasetDatasetAssociation,
-        primaryjoin=(model.LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id ==
-                     model.LibraryDatasetDatasetAssociation.table.c.id),
+        primaryjoin=(model.LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id
+                     == model.LibraryDatasetDatasetAssociation.table.c.id),
         remote_side=[model.LibraryDatasetDatasetAssociation.table.c.id],
         uselist=False),
     copied_to_library_dataset_dataset_associations=relation(model.LibraryDatasetDatasetAssociation,
-        primaryjoin=(model.LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id ==
-                     model.LibraryDatasetDatasetAssociation.table.c.id)),
+        primaryjoin=(model.LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id
+                     == model.LibraryDatasetDatasetAssociation.table.c.id)),
     copied_from_history_dataset_association=relation(model.HistoryDatasetAssociation,
-        primaryjoin=(model.LibraryDatasetDatasetAssociation.table.c.copied_from_history_dataset_association_id ==
-                     model.HistoryDatasetAssociation.table.c.id),
+        primaryjoin=(model.LibraryDatasetDatasetAssociation.table.c.copied_from_history_dataset_association_id
+                     == model.HistoryDatasetAssociation.table.c.id),
         uselist=False),
     copied_to_history_dataset_associations=relation(model.HistoryDatasetAssociation,
-        primaryjoin=(model.HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id ==
-                     model.LibraryDatasetDatasetAssociation.table.c.id)),
+        primaryjoin=(model.HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id
+                     == model.LibraryDatasetDatasetAssociation.table.c.id)),
     implicitly_converted_datasets=relation(model.ImplicitlyConvertedDatasetAssociation,
-        primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.ldda_parent_id ==
-                     model.LibraryDatasetDatasetAssociation.table.c.id)),
+        primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.ldda_parent_id
+                     == model.LibraryDatasetDatasetAssociation.table.c.id)),
     tags=relation(model.LibraryDatasetDatasetAssociationTagAssociation,
                   order_by=model.LibraryDatasetDatasetAssociationTagAssociation.table.c.id,
                   backref='history_tag_associations'),
@@ -2151,9 +2153,9 @@ mapper(model.LibraryDatasetDatasetAssociation, model.LibraryDatasetDatasetAssoci
 mapper(model.LibraryDatasetDatasetInfoAssociation, model.LibraryDatasetDatasetInfoAssociation.table, properties=dict(
     library_dataset_dataset_association=relation(model.LibraryDatasetDatasetAssociation,
         primaryjoin=(
-            (model.LibraryDatasetDatasetInfoAssociation.table.c.library_dataset_dataset_association_id ==
-             model.LibraryDatasetDatasetAssociation.table.c.id) &
-            (not_(model.LibraryDatasetDatasetInfoAssociation.table.c.deleted))
+            (model.LibraryDatasetDatasetInfoAssociation.table.c.library_dataset_dataset_association_id
+             == model.LibraryDatasetDatasetAssociation.table.c.id)
+            & (not_(model.LibraryDatasetDatasetInfoAssociation.table.c.deleted))
         ),
         backref="info_association"),
     template=relation(model.FormDefinition,
@@ -2230,8 +2232,8 @@ simple_mapping(model.TaskMetricNumeric,
 
 simple_mapping(model.ImplicitlyCreatedDatasetCollectionInput,
     input_dataset_collection=relation(model.HistoryDatasetCollectionAssociation,
-        primaryjoin=(model.HistoryDatasetCollectionAssociation.table.c.id ==
-                     model.ImplicitlyCreatedDatasetCollectionInput.table.c.input_dataset_collection_id),
+        primaryjoin=(model.HistoryDatasetCollectionAssociation.table.c.id
+                     == model.ImplicitlyCreatedDatasetCollectionInput.table.c.input_dataset_collection_id),
         # backref="implicitly_created_dataset_collections",
     ),
 )
@@ -2329,16 +2331,16 @@ simple_mapping(model.HistoryDatasetCollectionAssociation,
     history=relation(model.History,
         backref='dataset_collections'),
     copied_from_history_dataset_collection_association=relation(model.HistoryDatasetCollectionAssociation,
-        primaryjoin=(model.HistoryDatasetCollectionAssociation.table.c.copied_from_history_dataset_collection_association_id ==
-                     model.HistoryDatasetCollectionAssociation.table.c.id),
+        primaryjoin=(model.HistoryDatasetCollectionAssociation.table.c.copied_from_history_dataset_collection_association_id
+                     == model.HistoryDatasetCollectionAssociation.table.c.id),
         remote_side=[model.HistoryDatasetCollectionAssociation.table.c.id],
         uselist=False),
     copied_to_history_dataset_collection_associations=relation(model.HistoryDatasetCollectionAssociation,
-        primaryjoin=(model.HistoryDatasetCollectionAssociation.table.c.copied_from_history_dataset_collection_association_id ==
-                     model.HistoryDatasetCollectionAssociation.table.c.id)),
+        primaryjoin=(model.HistoryDatasetCollectionAssociation.table.c.copied_from_history_dataset_collection_association_id
+                     == model.HistoryDatasetCollectionAssociation.table.c.id)),
     implicit_input_collections=relation(model.ImplicitlyCreatedDatasetCollectionInput,
-        primaryjoin=(model.HistoryDatasetCollectionAssociation.table.c.id ==
-                     model.ImplicitlyCreatedDatasetCollectionInput.table.c.dataset_collection_id),
+        primaryjoin=(model.HistoryDatasetCollectionAssociation.table.c.id
+                     == model.ImplicitlyCreatedDatasetCollectionInput.table.c.dataset_collection_id),
         backref="dataset_collection",
     ),
     implicit_collection_jobs=relation(
@@ -2865,9 +2867,15 @@ def _workflow_invocation_update(self):
 model.WorkflowInvocation.update = _workflow_invocation_update  # type: ignore
 
 
+class GalaxyModelMapping(ModelMapping):
+    security_agent: GalaxyRBACAgent
+    thread_local_log: Optional[local]
+    create_tables: bool
+
+
 def init(file_path, url, engine_options=None, create_tables=False, map_install_models=False,
         database_query_profiling_proxy=False, object_store=None, trace_logger=None, use_pbkdf2=True,
-        slow_query_log_threshold=0, thread_local_log=None, log_query_counts=False):
+        slow_query_log_threshold=0, thread_local_log: Optional[local] = None, log_query_counts=False) -> GalaxyModelMapping:
     """Connect mappings to the database"""
     if engine_options is None:
         engine_options = {}
@@ -2890,7 +2898,7 @@ def init(file_path, url, engine_options=None, create_tables=False, map_install_m
         galaxy.model.tool_shed_install.mapping.init(url=url, engine_options=engine_options, create_tables=create_tables)
         model_modules.append(tool_shed_install)
 
-    result = ModelMapping(model_modules, engine=engine)
+    result = GalaxyModelMapping(model_modules, engine=engine)
 
     # Create tables if needed
     if create_tables:
diff --git a/lib/galaxy/model/metadata.py b/lib/galaxy/model/metadata.py
index c732282b8bc..b570f05af54 100644
--- a/lib/galaxy/model/metadata.py
+++ b/lib/galaxy/model/metadata.py
@@ -132,12 +132,13 @@ class MetadataCollection(Mapping):
     def element_is_set(self, name):
         """
         check if the meta data with the given name is set, i.e.
+
         - if the such a metadata actually exists and
         - if its value differs from no_value
 
-        param name the name of the metadata element
-        return True if the value differes from the no_value
-            False if its equal of if no metadata with the name is specified
+        :param name: the name of the metadata element
+        :returns: True if the value differes from the no_value
+                  False if its equal of if no metadata with the name is specified
         """
         try:
             meta_val = self.parent._metadata[name]
diff --git a/lib/galaxy/model/migrate/versions/util.py b/lib/galaxy/model/migrate/versions/util.py
index c737d18efec..a9265f9a5e1 100644
--- a/lib/galaxy/model/migrate/versions/util.py
+++ b/lib/galaxy/model/migrate/versions/util.py
@@ -53,7 +53,7 @@ def truncate_index_name(index_name, engine):
     max_index_name_length = engine.dialect.max_index_name_length or engine.dialect.max_identifier_length
     if len(index_name) > max_index_name_length:
         suffix = hashlib.md5(index_name.encode('utf-8')).hexdigest()[-4:]
-        index_name = "{trunc}_{suffix}".format(trunc=index_name[0 : max_index_name_length - 8], suffix=suffix)
+        index_name = "{trunc}_{suffix}".format(trunc=index_name[0:max_index_name_length - 8], suffix=suffix)
     return index_name
 
 
diff --git a/lib/galaxy/model/security.py b/lib/galaxy/model/security.py
index 889363e8e83..ebfbddf0741 100644
--- a/lib/galaxy/model/security.py
+++ b/lib/galaxy/model/security.py
@@ -1211,21 +1211,20 @@ class GalaxyRBACAgent(RBACAgent):
                     permissions[role_assoc.action] = [role_assoc.role]
         self.set_all_library_permissions(trans, target_library_item, permissions)
         if user:
-            item_class = None
             for item_class, permission_class in self.library_item_assocs:
                 if isinstance(target_library_item, item_class):
+                    found_permission_class = permission_class
                     break
-            if item_class:
-                # Make sure user's private role is included
-                private_role = self.model.security_agent.get_private_user_role(user)
-                for action in self.permitted_actions.values():
-                    if not permission_class.filter_by(role_id=private_role.id, action=action.action).first():
-                        lp = permission_class(action.action, target_library_item, private_role)
-                        self.sa_session.add(lp)
-                        self.sa_session.flush()
             else:
                 raise Exception('Invalid class (%s) specified for target_library_item (%s)' %
                                 (target_library_item.__class__, target_library_item.__class__.__name__))
+            # Make sure user's private role is included
+            private_role = self.model.security_agent.get_private_user_role(user)
+            for action in self.permitted_actions.values():
+                if not found_permission_class.filter_by(role_id=private_role.id, action=action.action).first():
+                    lp = found_permission_class(action.action, target_library_item, private_role)
+                    self.sa_session.add(lp)
+                    self.sa_session.flush()
 
     def get_permitted_libraries(self, trans, user, actions):
         """
diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index fa2d6443463..525db57c0d4 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -626,7 +626,7 @@ class ModelImportStore(metaclass=abc.ABCMeta):
             if input_key in object_import_tracker.hdcas_by_key:
                 hdca = object_import_tracker.hdcas_by_key[input_key]
             if input_key in object_import_tracker.hdca_copied_from_sinks:
-                hdca = object_import_tracker.hdca_copied_from_sinks[input_key]
+                hdca = object_import_tracker.hdcas_by_key[object_import_tracker.hdca_copied_from_sinks[input_key]]
             return hdca
 
         def _find_dce(input_key):
diff --git a/lib/galaxy/model/store/discover.py b/lib/galaxy/model/store/discover.py
index 6d61479b47e..482b4e2b81e 100644
--- a/lib/galaxy/model/store/discover.py
+++ b/lib/galaxy/model/store/discover.py
@@ -460,7 +460,7 @@ def persist_extra_files(object_store, src_extra_files_path, primary_data):
     if src_extra_files_path and os.path.exists(src_extra_files_path):
         primary_data.dataset.create_extra_files_path()
         target_extra_files_path = primary_data.extra_files_path
-        for root, dirs, files in os.walk(src_extra_files_path):
+        for root, _dirs, files in os.walk(src_extra_files_path):
             extra_dir = os.path.join(target_extra_files_path, root.replace(src_extra_files_path, '', 1).lstrip(os.path.sep))
             extra_dir = os.path.normpath(extra_dir)
             for f in files:
diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index 01ee230377e..c6505af9c51 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -94,7 +94,7 @@ def parse_config_xml(config_xml):
                 'port': port,
                 'timeout': timeout,
                 'poolsize': poolsize,
-                'refresh_time' : refresh_time
+                'refresh_time': refresh_time,
             },
             'cache': {
                 'size': cache_size,
diff --git a/lib/galaxy/queues.py b/lib/galaxy/queues.py
index f858b656d5f..b9191d2f993 100644
--- a/lib/galaxy/queues.py
+++ b/lib/galaxy/queues.py
@@ -4,6 +4,7 @@ All message queues used by Galaxy
 
 """
 import socket
+from typing import Optional
 
 from kombu import (
     Connection,
@@ -37,7 +38,7 @@ def control_queues_from_config(config):
     return exchange_queue, non_exchange_queue
 
 
-def connection_from_config(config):
+def connection_from_config(config) -> Optional[Connection]:
     if config.amqp_internal_connection:
         return Connection(config.amqp_internal_connection)
     else:
diff --git a/lib/galaxy/schema/__init__.py b/lib/galaxy/schema/__init__.py
index 0533680cb97..174c87af56d 100644
--- a/lib/galaxy/schema/__init__.py
+++ b/lib/galaxy/schema/__init__.py
@@ -1,12 +1,15 @@
-import typing
+from typing import (
+    Dict,
+    Optional,
+)
 
 from pydantic import BaseModel
 
 
 class BootstrapAdminUser(BaseModel):
     id = 0
-    email: typing.Optional[str] = None
-    preferences: typing.Dict[str, str] = {}
+    email: Optional[str] = None
+    preferences: Dict[str, str] = {}
     bootstrap_admin_user = True
 
     def all_roles(*args) -> list:
diff --git a/lib/galaxy/selenium/context.py b/lib/galaxy/selenium/context.py
index 1b759128a1c..0419b7c54c4 100644
--- a/lib/galaxy/selenium/context.py
+++ b/lib/galaxy/selenium/context.py
@@ -1,3 +1,6 @@
+from abc import abstractmethod
+from typing import Optional
+
 from six.moves.urllib.parse import urljoin
 
 from .driver_factory import ConfiguredDriver
@@ -5,8 +8,10 @@ from .navigates_galaxy import NavigatesGalaxy
 
 
 class GalaxySeleniumContext(NavigatesGalaxy):
+    url: str
+    target_url_from_selenium: str
 
-    def build_url(self, url, for_selenium=True):
+    def build_url(self, url: str, for_selenium: bool = True) -> str:
         if for_selenium:
             base = self.target_url_from_selenium
         else:
@@ -17,7 +22,7 @@ class GalaxySeleniumContext(NavigatesGalaxy):
     def driver(self):
         return self.configured_driver.driver
 
-    def screenshot(self, label):
+    def screenshot(self, label: str):
         """If GALAXY_TEST_SCREENSHOTS_DIRECTORY is set create a screenshot there named <label>.png.
 
         Unlike the above "snapshot" feature, this will be written out regardless and not in a per-test
@@ -32,11 +37,19 @@ class GalaxySeleniumContext(NavigatesGalaxy):
         self.driver.save_screenshot(target)
         return target
 
+    @abstractmethod
+    def _screenshot_path(self, label: str, extension=".png") -> str:
+        """Path to store screenshots in."""
+
 
 class GalaxySeleniumContextImpl(GalaxySeleniumContext):
-    """Minimal, simplified GalaxySeleniumContext useful outside the context of test cases."""
+    """Minimal, simplified GalaxySeleniumContext useful outside the context of test cases.
 
-    def __init__(self, from_dict=None):
+    A variant of this concept that can also populate content via the API
+    to then interact with via the Selenium is :class:galaxy_test.selenium.framework:`GalaxySeleniumContextImpl`.
+    """
+
+    def __init__(self, from_dict: Optional[dict] = None) -> None:
         from_dict = from_dict or {}
         self.configured_driver = ConfiguredDriver(**from_dict.get("driver", {}))
         self.url = from_dict.get("local_galaxy_url", "http://localhost:8080")
diff --git a/lib/galaxy/selenium/driver_factory.py b/lib/galaxy/selenium/driver_factory.py
index 19c41ca974e..03ceacaab72 100644
--- a/lib/galaxy/selenium/driver_factory.py
+++ b/lib/galaxy/selenium/driver_factory.py
@@ -8,6 +8,7 @@ except ImportError:
 from selenium import webdriver
 from selenium.webdriver.chrome.options import Options as ChromeOptions
 from selenium.webdriver.common.desired_capabilities import DesiredCapabilities
+from selenium.webdriver.remote.webdriver import WebDriver
 
 
 DEFAULT_BROWSER = "auto"
@@ -25,6 +26,7 @@ VALID_LOCAL_BROWSERS = ["CHROME", "FIREFOX", "OPERA", "PHANTOMJS"]
 
 
 class ConfiguredDriver:
+    driver: WebDriver
 
     def __init__(
         self,
@@ -75,7 +77,7 @@ def get_local_browser(browser):
     return browser
 
 
-def get_local_driver(browser=DEFAULT_BROWSER, headless=False):
+def get_local_driver(browser=DEFAULT_BROWSER, headless=False) -> WebDriver:
     browser = get_local_browser(browser)
     if browser not in VALID_LOCAL_BROWSERS:
         raise AssertionError(f"{browser} not in VALID_LOCAL_BROWSERS ({VALID_LOCAL_BROWSERS})")
@@ -111,7 +113,7 @@ def get_remote_driver(
     host,
     port,
     browser=DEFAULT_BROWSER
-):
+) -> WebDriver:
     # docker run -d -p 4444:4444 -v /dev/shm:/dev/shm selenium/standalone-chrome:3.0.1-aluminum
     if browser == "auto":
         browser = "CHROME"
diff --git a/lib/galaxy/selenium/navigates_galaxy.py b/lib/galaxy/selenium/navigates_galaxy.py
index 7071d0e9fcc..104240fc525 100644
--- a/lib/galaxy/selenium/navigates_galaxy.py
+++ b/lib/galaxy/selenium/navigates_galaxy.py
@@ -112,14 +112,14 @@ class NavigatesGalaxy(HasDriver):
 
     In most cases, methods for interacting with Galaxy components that appear in
     multiple tests or applications should be refactored into this class for now.
-    Keep in mind that this class is used outside the context of ``TestCase``s as
+    Keep in mind that this class is used outside the context of ``TestCase`` s as
     well - so some methods more explicitly related to test data or assertion checking
     may make more sense in SeleniumTestCase for instance.
 
     Some day this class will likely be split up into smaller mixins for particular
     components of Galaxy, but until that day the best practice is to prefix methods
     for driving or querying the interface with the name of the component or page
-    the method operates on. These serve as psedu-namespaces until we decompose this
+    the method operates on. These serve as pseudo-namespaces until we decompose this
     class. For instance, the method for clicking an option in the workflow editor is
     workflow_editor_click_option instead of click_workflow_editor_option.
     """
@@ -517,14 +517,24 @@ class NavigatesGalaxy(HasDriver):
         center_element = self.driver.find_element_by_css_selector("#center")
         action_chains.move_to_element(center_element).click().perform()
 
-    def perform_upload(self, test_path, ext=None, genome=None, ext_all=None, genome_all=None):
+    def perform_upload(self, test_path, **kwd):
+        self._perform_upload(test_path=test_path, **kwd)
+
+    def perform_upload_of_pasted_content(self, paste_data, **kwd):
+        self._perform_upload(paste_data=paste_data, **kwd)
+
+    def _perform_upload(self, test_path=None, paste_data=None, ext=None, genome=None, ext_all=None, genome_all=None):
         self.home()
         self.upload_start_click()
 
         self.upload_set_footer_extension(ext_all)
         self.upload_set_footer_genome(genome_all)
 
-        self.upload_queue_local_file(test_path)
+        if test_path:
+            self.upload_queue_local_file(test_path)
+        else:
+            assert paste_data is not None
+            self.upload_paste_data(paste_data)
 
         if ext is not None:
             self.wait_for_selector_visible('.upload-extension')
@@ -635,6 +645,13 @@ class NavigatesGalaxy(HasDriver):
         file_upload = self.wait_for_selector('div#%s input[type="file"]' % tab_id)
         file_upload.send_keys(test_path)
 
+    def upload_paste_data(self, pasted_content, tab_id="regular"):
+        tab_locator = f"div#{tab_id}"
+        self.wait_for_and_click_selector(f"{tab_locator} button#btn-new")
+
+        textarea = self.wait_for_selector(f"{tab_locator} .upload-text-content")
+        textarea.send_keys(pasted_content)
+
     def upload_rule_start(self):
         self.upload_start_click()
         self.upload_tab_click("rule-based")
@@ -865,11 +882,21 @@ class NavigatesGalaxy(HasDriver):
         self.wait_for_and_click_selector("#workflow-save-button")
         self.sleep_for(self.wait_types.DATABASE_OPERATION)
 
+    def navigate_to_histories_page(self):
+        self.home()
+        self.click_masthead_user()
+        self.components.masthead.histories.wait_for_and_click()
+
     def navigate_to_user_preferences(self):
         self.home()
         self.click_masthead_user()
         self.components.masthead.preferences.wait_for_and_click()
 
+    def navigate_to_invocations(self):
+        self.home()
+        self.click_masthead_user()
+        self.components.masthead.invocations.wait_for_and_click()
+
     def admin_open(self):
         self.components.masthead.admin.wait_for_and_click()
 
@@ -935,19 +962,20 @@ class NavigatesGalaxy(HasDriver):
 
     def libraries_click_dataset_import(self):
         self.wait_for_and_click(self.navigation.libraries.folder.selectors.add_items_button)
+        self.wait_for_visible(self.navigation.libraries.folder.selectors.add_items_menu)
 
     def libraries_dataset_import_from_history(self):
         self.libraries_click_dataset_import()
-
-        self.wait_for_visible(self.navigation.libraries.folder.selectors.add_items_menu)
         self.wait_for_and_click(self.navigation.libraries.folder.labels.from_history)
 
     def libraries_dataset_import_from_path(self):
         self.libraries_click_dataset_import()
-
-        self.wait_for_visible(self.navigation.libraries.folder.selectors.add_items_menu)
         self.wait_for_and_click(self.navigation.libraries.folder.labels.from_path)
 
+    def libraries_dataset_import_from_import_dir(self):
+        self.libraries_click_dataset_import()
+        self.wait_for_and_click(self.navigation.libraries.folder.labels.from_import_dir)
+
     def libraries_dataset_import_from_history_select(self, to_select_items):
         self.wait_for_visible(self.navigation.libraries.folder.selectors.import_history_content)
         history_elements = self.find_elements(self.navigation.libraries.folder.selectors.import_history_contents_items)
@@ -1164,6 +1192,18 @@ class NavigatesGalaxy(HasDriver):
         search_selector = '#standard-search .advanced-search-toggle'
         self.wait_for_and_click_selector(search_selector)
 
+    @retry_during_transitions
+    def histories_get_history_names(self):
+        self.sleep_for(self.wait_types.UX_RENDER)
+        names = []
+        grid = self.wait_for_selector('#grid-table-body')
+        for row in grid.find_elements_by_tag_name('tr'):
+            td = row.find_elements_by_tag_name('td')
+            name = td[1].text if td[0].text == '' else td[0].text
+            if name != "No items" and not name.startswith("No matching entries found"):
+                names.append(name)
+        return names
+
     def history_panel_add_tags(self, tags):
         tag_icon_selector = self.components.history_panel.tag_icon
         tag_area_selector = self.components.history_panel.tag_area
diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index a8a0781112f..d840efa160d 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -60,6 +60,7 @@ masthead:
     custom_builds: 'Custom Builds'
     preferences: 'Preferences'
     histories: 'Histories'
+    invocations: 'Workflow Invocations'
     pages: 'Pages'
 
     # Shared data
@@ -187,6 +188,9 @@ history_panel:
     options_show_history_structure:
       type: xpath
       selector: '//a[text()="Show Structure"]'
+    options_show_export_history_to_file:
+      type: xpath
+      selector: '//a[text()="Export History to File"]'
     new_history_button: '#history-new-button'
     multi_view_button: '#history-view-multi-button'
 
@@ -282,6 +286,9 @@ collection_builders:
     reverse_datasets: ".reverse-column .column-datasets"
 
 histories:
+  labels:
+    import_button: 'Import from file'
+
   sharing:
     selectors:
       unshare_user_button: '.unshare_user'
@@ -291,6 +298,33 @@ histories:
     labels:
       unshare: 'Unshare'
 
+files_dialog:
+  selectors:
+    ftp_row: 'span[title="gxftp://"]'
+    row: 'span[title="${uri}"]'
+
+history_export:
+  selectors:
+    export_link: '.export-link'
+    running: '.history-export-component .loading-icon'
+    generated_export_link: '.generated-export-link'
+    copy_export_link: '.copy-export-link'
+    show_job_link: '.show-job-link'
+    job_table: '.info_data_table'
+    job_table_ok: '.job-information-modal .btn-primary'
+    tab_export_to_file: '.tab-export-to-file'
+    directory_input: '.directory-form-input'
+    name_input: '.export-to-remote-file #name'
+    export_button: '.export-button'
+    success_message: '.history-export-component .alert-success'
+
+history_import:
+  selectors:
+    radio_button_remote_files: '.history-import-component .fa-folder-open'
+    import_button: '.import-button'
+    running: '.history-import-component .loading-icon'
+    success_message: '.history-import-component .alert-success'
+
 pages:
   selectors:
     create: '.manage-table-actions .action-button'
@@ -386,6 +420,27 @@ workflow_editor:
     save_button: '.editor-button-save'
     state_modal_body: '.state-upgrade-modal'
 
+invocations:
+  selectors:
+    invocations_table: '.invocations-list table'
+    invocations_table_rows: '.invocations-list table tbody tr'
+    state_details: '.workflow-invocation-state-component'
+    toggle_invocation_details: '.toggle-invocation-details'
+    progress_steps_note: '.workflow-invocation-state-component .steps-progress .progressNote'
+    progress_jobs_note: '.workflow-invocation-state-component .jobs-progress .progressNote'
+    input_details: '.workflow-invocation-state-component .invocation-inputs-details'
+    input_details_title: '.workflow-invocation-state-component .invocation-inputs-details [data-label="${label}"]'
+    input_details_name:  '.workflow-invocation-state-component .invocation-inputs-details [data-label="${label}"] .name'
+
+    steps_details: '.workflow-invocation-state-component .invocation-steps-details'
+    step_title: '.workflow-invocation-state-component .invocation-steps-details [data-step="${order_index}"] .step-title'
+    step_details: '.workflow-invocation-state-component .invocation-steps-details [data-step="${order_index}"] .portlet-operations'
+    step_job_details: '.workflow-invocation-state-component .invocation-steps-details [data-step="${order_index}"] .invocation-step-job-details'
+    step_job_table: '.workflow-invocation-state-component .invocation-steps-details [data-step="${order_index}"] .invocation-step-job-details table'
+    step_job_table_rows: '.workflow-invocation-state-component .invocation-steps-details [data-step="${order_index}"] .invocation-step-job-details table tbody tr'
+    step_job_information: '.workflow-invocation-state-component .invocation-steps-details [data-step="${order_index}"] .invocation-step-job-details table tbody .b-table-details .info_data_table'
+    step_job_information_tool_id: '.workflow-invocation-state-component .invocation-steps-details [data-step="${order_index}"] .invocation-step-job-details table tbody .b-table-details .info_data_table #galaxy-tool-id'
+
 tour:
   popover:
     selectors:
@@ -508,10 +563,15 @@ libraries:
       download_button: '#download-btn'
       delete_btn: '.toolbtn-bulk-delete'
       toast_msg: '.toast-message'
+      select_import_dir_item: 'li[full_path="${name}"] .jstree-anchor'
+      import_dir_btn:
+        type: xpath
+        selector: '//button[contains(text(), "Import")]'
 
     labels:
       from_history: 'from History'
       from_path: 'from Path'
+      from_import_dir: 'from Import Directory'
 
   dataset:
     selectors:
diff --git a/lib/galaxy/selenium/sizzle.py b/lib/galaxy/selenium/sizzle.py
index 172c6ac7ca2..1e71e9e25f1 100644
--- a/lib/galaxy/selenium/sizzle.py
+++ b/lib/galaxy/selenium/sizzle.py
@@ -62,13 +62,11 @@ def sizzle_presence_of_selector(selector):
     return ec
 
 
-def find_element_by_sizzle(driver, sizzle_selector):
+def find_element_by_sizzle(driver, sizzle_selector: str):
     """
     Finds an element by sizzle selector.
-    :Args:
-     - sizzle_selector: The sizzle selector to use when finding element.
-    :Usage:
-        driver.find_element_by_sizzle('#foo')
+
+    :param sizzle_selector: The sizzle selector to use when finding element.
     """
     elements = driver.find_elements_by_sizzle(sizzle_selector)
     if elements:
@@ -79,13 +77,11 @@ def find_element_by_sizzle(driver, sizzle_selector):
         )
 
 
-def find_elements_by_sizzle(driver, sizzle_selector):
+def find_elements_by_sizzle(driver, sizzle_selector: str):
     """
     Finds elements by sizzle selector.
-    :Args:
-     - sizzle_selector: The sizzle selector to use when finding elements.
-    :Usage:
-        driver.find_elements_by_sizzle('.foo')
+
+    :param sizzle_selector: The sizzle selector to use when finding elements.
     """
     if not _is_sizzle_loaded(driver):
         _inject_sizzle(driver, SIZZLE_URL, SIZZLE_LOAD_TIMEOUT)
diff --git a/lib/galaxy/structured_app.py b/lib/galaxy/structured_app.py
new file mode 100644
index 00000000000..81f337a322c
--- /dev/null
+++ b/lib/galaxy/structured_app.py
@@ -0,0 +1,78 @@
+"""Typed description of Galaxy's app object."""
+from typing import Any, Optional
+
+from kombu import Connection
+
+from galaxy.auth import AuthManager
+from galaxy.files import ConfiguredFileSources
+from galaxy.job_metrics import JobMetrics
+from galaxy.model.base import ModelMapping
+from galaxy.model.mapping import GalaxyModelMapping
+from galaxy.model.security import GalaxyRBACAgent
+from galaxy.model.security import HostAgent
+from galaxy.model.tags import GalaxyTagHandler
+from galaxy.security.idencoding import IdEncodingHelper
+from galaxy.tool_util.deps.views import DependencyResolversView
+from galaxy.tool_util.verify import test_data
+from galaxy.util.dbkeys import GenomeBuilds
+from galaxy.web_stack import ApplicationStack
+from galaxy.webhooks import WebhooksRegistry
+from galaxy.workflow.trs_proxy import TrsProxy
+
+
+class StructuredApp:
+    """Interface defining typed description of the Galaxy UniverseApplication.
+
+    Ideally nothing that depends on StructuredApp should require
+    StructuredApp so we can have a clean import dag. This will
+    require setting up a lot more distinction between interfaces
+    and implementations in Galaxy though. In the meantime, for
+    imports that would bring in StructuredApp if properly type
+    (cyclical imports), we're just setting the class attributes to
+    Any.
+    """
+    name: str
+    is_webapp: bool  # is_webapp will be set to true when building WSGI app
+    new_installation: bool
+    config: Any
+    tag_handler: GalaxyTagHandler
+    application_stack: ApplicationStack
+    amqp_internal_connection_obj: Optional[Connection]
+    dependency_resolvers_view: DependencyResolversView
+    test_data_resolver: test_data.TestDataResolver
+    file_sources: ConfiguredFileSources
+    genome_builds: GenomeBuilds
+    job_metrics: JobMetrics
+    model: GalaxyModelMapping
+    install_model: ModelMapping
+    security: IdEncodingHelper
+    security_agent: GalaxyRBACAgent
+    host_security_agent: HostAgent
+    auth_manager: AuthManager
+    trs_proxy: TrsProxy
+    webhooks_registry: WebhooksRegistry
+
+    queue_worker: Any  # 'galaxy.queue_worker.GalaxyQueueWorker'
+    dataset_collections_service: Any  # 'galaxy.managers.collections.DatasetCollectionManager'
+    history_manager: Any  # 'galaxy.managers.histories.HistoryManager'
+    hda_manager: Any  # 'galaxy.managers.hdas.HDAManager'
+    workflow_manager: Any  # 'galaxy.managers.workflows.WorkflowsManager'
+    workflow_contents_manager: Any  # 'galaxy.managers.workflows.WorkflowContentsManager'
+    library_folder_manager: Any  # 'galaxy.managers.folders.FolderManager'
+    library_manager: Any  # 'galaxy.managers.libraries.LibraryManager'
+    role_manager: Any  # 'galaxy.managers.roles.RoleManager'
+    dynamic_tool_manager: Any  # 'galaxy.managers.tools.DynamicToolManager'
+    data_provider_registry: Any  # 'galaxy.visualization.data_providers.registry.DataProviderRegistry'
+    tool_data_tables: Any  # 'galaxy.tools.data.ToolDataTableManager'
+    genomes: Any  # 'galaxy.visualization.genomes.Genomes'
+    error_reports: Any  # 'galaxy.tools.error_reports.ErrorReports'
+    job_config: Any  # 'galaxy.jobs.JobConfiguration'
+    tool_cache: Any  # 'galaxy.tools.cache.ToolCache'
+    tool_shed_repository_cache: Any  # 'galaxy.tools.cache.ToolShedRepositoryCache'
+    watchers: Any  # 'galaxy.config_watchers.ConfigWatchers'
+    installed_repository_manager: Any  # 'galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager'
+    workflow_scheduling_manager: Any  # 'galaxy.workflow.scheduling_manager.WorkflowSchedulingManager'
+    interactivetool_manager: Any
+    user_manager: Any
+    api_keys_manager: Any
+    toolbox: Any
diff --git a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
index f28ed4d2ca6..06558b4e497 100644
--- a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
@@ -56,24 +56,6 @@ class InstalledRepositoryManager:
         # and whose values are a list of tuples defining tool_shed_repository objects (whose status is 'Installed') that require
         # the key.
         self.installed_dependent_repositories_of_installed_repositories = {}
-        # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed')
-        # and whose values are a list of tuples defining its immediate tool_dependency objects (whose status can be anything).
-        # The value defines only the immediate tool dependencies of the repository and does not include any dependencies of the
-        # tool dependencies.
-        self.tool_dependencies_of_installed_repositories = {}
-        # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed')
-        # and whose values are a list of tuples defining its immediate tool_dependency objects (whose status is 'Installed').
-        # The value defines only the immediate tool dependencies of the repository and does not include any dependencies of the
-        # tool dependencies.
-        self.installed_tool_dependencies_of_installed_repositories = {}
-        # Keep an in-memory dictionary whose keys are tuples defining tool_dependency objects (whose status is 'Installed') and
-        # whose values are a list of tuples defining tool_dependency objects (whose status can be anything) required by the
-        # installed tool dependency at runtime.  The value defines the entire tool dependency tree.
-        self.runtime_tool_dependencies_of_installed_tool_dependencies = {}
-        # Keep an in-memory dictionary whose keys are tuples defining tool_dependency objects (whose status is 'Installed') and
-        # whose values are a list of tuples defining tool_dependency objects (whose status is 'Installed') that require the key
-        # at runtime.  The value defines the entire tool dependency tree.
-        self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {}
 
     @property
     def tool_paths(self):
@@ -176,35 +158,6 @@ class InstalledRepositoryManager:
             else:
                 self.installed_dependent_repositories_of_installed_repositories[required_repository_tup] = [repository_tup]
 
-    def add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(self, tool_dependency):
-        """Add an entry to self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies."""
-        tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
-        if tool_dependency_tup not in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies:
-            tool_shed_repository_id, name, version, type = tool_dependency_tup
-            debug_msg = f"Adding an entry for version {version} of {type} {name} "
-            debug_msg += "to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies."
-            log.debug(debug_msg)
-            status = self.install_model.ToolDependency.installation_status.INSTALLED
-            installed_runtime_dependent_tool_dependency_tups = self.get_runtime_dependent_tool_dependency_tuples(tool_dependency,
-                                                                                                                 status=status)
-            self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[tool_dependency_tup] = \
-                installed_runtime_dependent_tool_dependency_tups
-
-    def add_entry_to_installed_tool_dependencies_of_installed_repositories(self, repository):
-        """Add an entry to self.installed_tool_dependencies_of_installed_repositories."""
-        repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
-        if repository_tup not in self.installed_tool_dependencies_of_installed_repositories:
-            tool_shed, name, owner, installed_changeset_revision = repository_tup
-            debug_msg = f"Adding an entry for revision {installed_changeset_revision} of repository {name} owned by {owner} "
-            debug_msg += "to installed_tool_dependencies_of_installed_repositories."
-            log.debug(debug_msg)
-            installed_tool_dependency_tups = []
-            for tool_dependency in repository.tool_dependencies:
-                if tool_dependency.status == self.app.install_model.ToolDependency.installation_status.INSTALLED:
-                    tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
-                    installed_tool_dependency_tups.append(tool_dependency_tup)
-            self.installed_tool_dependencies_of_installed_repositories[repository_tup] = installed_tool_dependency_tups
-
     def add_entry_to_repository_dependencies_of_installed_repositories(self, repository):
         """Add an entry to self.repository_dependencies_of_installed_repositories."""
         repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
@@ -216,33 +169,6 @@ class InstalledRepositoryManager:
             repository_dependency_tups = self.get_repository_dependency_tups_for_installed_repository(repository, status=None)
             self.repository_dependencies_of_installed_repositories[repository_tup] = repository_dependency_tups
 
-    def add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies(self, tool_dependency):
-        """Add an entry to self.runtime_tool_dependencies_of_installed_tool_dependencies."""
-        tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
-        if tool_dependency_tup not in self.runtime_tool_dependencies_of_installed_tool_dependencies:
-            tool_shed_repository_id, name, version, type = tool_dependency_tup
-            debug_msg = f"Adding an entry for version {version} of {type} {name} "
-            debug_msg += "to runtime_tool_dependencies_of_installed_tool_dependencies."
-            log.debug(debug_msg)
-            runtime_dependent_tool_dependency_tups = self.get_runtime_dependent_tool_dependency_tuples(tool_dependency,
-                                                                                                       status=None)
-            self.runtime_tool_dependencies_of_installed_tool_dependencies[tool_dependency_tup] = \
-                runtime_dependent_tool_dependency_tups
-
-    def add_entry_to_tool_dependencies_of_installed_repositories(self, repository):
-        """Add an entry to self.tool_dependencies_of_installed_repositories."""
-        repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
-        if repository_tup not in self.tool_dependencies_of_installed_repositories:
-            tool_shed, name, owner, installed_changeset_revision = repository_tup
-            debug_msg = f"Adding an entry for revision {installed_changeset_revision} of repository {name} owned by {owner} "
-            debug_msg += "to tool_dependencies_of_installed_repositories."
-            log.debug(debug_msg)
-            tool_dependency_tups = []
-            for tool_dependency in repository.tool_dependencies:
-                tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
-                tool_dependency_tups.append(tool_dependency_tup)
-            self.tool_dependencies_of_installed_repositories[repository_tup] = tool_dependency_tups
-
     def get_containing_repository_for_tool_dependency(self, tool_dependency_tup):
         tool_shed_repository_id, name, version, type = tool_dependency_tup
         return self.app.install_model.context.query(self.app.install_model.ToolShedRepository).get(tool_shed_repository_id)
@@ -883,26 +809,6 @@ class InstalledRepositoryManager:
             log.debug(debug_msg)
             del self.installed_repository_dependencies_of_installed_repositories[repository_tup]
 
-    def remove_entry_from_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(self, tool_dependency):
-        """Remove an entry from self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies."""
-        tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
-        if tool_dependency_tup in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies:
-            tool_shed_repository_id, name, version, type = tool_dependency_tup
-            debug_msg = f"Removing entry for version {version} of {type} {name} "
-            debug_msg += "from installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies."
-            log.debug(debug_msg)
-            del self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[tool_dependency_tup]
-
-    def remove_entry_from_installed_tool_dependencies_of_installed_repositories(self, repository):
-        """Remove an entry from self.installed_tool_dependencies_of_installed_repositories."""
-        repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
-        if repository_tup in self.installed_tool_dependencies_of_installed_repositories:
-            tool_shed, name, owner, installed_changeset_revision = repository_tup
-            debug_msg = f"Removing entry for revision {installed_changeset_revision} of repository {name} owned by {owner} "
-            debug_msg += "from installed_tool_dependencies_of_installed_repositories."
-            log.debug(debug_msg)
-            del self.installed_tool_dependencies_of_installed_repositories[repository_tup]
-
     def remove_entry_from_repository_dependencies_of_installed_repositories(self, repository):
         """Remove an entry from self.repository_dependencies_of_installed_repositories."""
         repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
@@ -913,26 +819,6 @@ class InstalledRepositoryManager:
             log.debug(debug_msg)
             del self.repository_dependencies_of_installed_repositories[repository_tup]
 
-    def remove_entry_from_runtime_tool_dependencies_of_installed_tool_dependencies(self, tool_dependency):
-        """Remove an entry from self.runtime_tool_dependencies_of_installed_tool_dependencies."""
-        tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
-        if tool_dependency_tup in self.runtime_tool_dependencies_of_installed_tool_dependencies:
-            tool_shed_repository_id, name, version, type = tool_dependency_tup
-            debug_msg = "Removing entry for version %s of %s %s from runtime_tool_dependencies_of_installed_tool_dependencies." % \
-                (version, type, name)
-            log.debug(debug_msg)
-            del self.runtime_tool_dependencies_of_installed_tool_dependencies[tool_dependency_tup]
-
-    def remove_entry_from_tool_dependencies_of_installed_repositories(self, repository):
-        """Remove an entry from self.tool_dependencies_of_installed_repositories."""
-        repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
-        if repository_tup in self.tool_dependencies_of_installed_repositories:
-            tool_shed, name, owner, installed_changeset_revision = repository_tup
-            debug_msg = "Removing entry for revision %s of repository %s owned by %s from tool_dependencies_of_installed_repositories." % \
-                (installed_changeset_revision, name, owner)
-            log.debug(debug_msg)
-            del self.tool_dependencies_of_installed_repositories[repository_tup]
-
     def repository_dependency_needed_only_for_compiling_tool_dependency(self, repository, repository_dependency):
         for rd_tup in repository.tuples_of_repository_dependencies_needed_for_compiling_td:
             tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = rd_tup
@@ -944,8 +830,8 @@ class InstalledRepositoryManager:
             if cleaned_repository_dependency_tool_shed == cleaned_tool_shed and \
                 repository_dependency.name == name and \
                 repository_dependency.owner == owner and \
-                (repository_dependency.installed_changeset_revision == changeset_revision or
-                 repository_dependency.changeset_revision == changeset_revision):
+                (repository_dependency.installed_changeset_revision == changeset_revision
+                 or repository_dependency.changeset_revision == changeset_revision):
                 return True
         return False
 
diff --git a/lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py b/lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py
index 136eabb6d20..ccc933a7044 100644
--- a/lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py
@@ -56,7 +56,22 @@ class ToolPanelManager:
                 config_elems.append(elem)
             # Add the new elements to the in-memory list of config_elems.
             for elem_entry in elem_list:
-                config_elems.append(elem_entry)
+                if elem_entry.tag == 'section':
+                    # Loop through section entries in the in-memory tool panel.
+                    for existing_elem in config_elems:
+                        # Compare the section ID for each one to the section ID for the tool being installed.
+                        if existing_elem.tag == 'section' and existing_elem.attrib.get('id', None) == elem_entry.attrib.get('id', None):
+                            # We've found a section, add the incoming tools to it.
+                            for child in elem_entry:
+                                existing_elem.append(child)
+                            # Break out of the config_elems loop back to the elem_list loop.
+                            break
+                    # If we reach this point, no section was found. Create one with contents.
+                    else:
+                        config_elems.append(elem_entry)
+                # This is not a section, but a tool or label. No need to search for matching sections, just add it.
+                else:
+                    config_elems.append(elem_entry)
             # Persist the altered shed_tool_config file.
             self.config_elems_to_xml_file(config_elems, shed_tool_conf, tool_path, tool_cache_data_dir)
             self.app.wait_for_toolbox_reload(old_toolbox)
@@ -168,11 +183,15 @@ class ToolPanelManager:
         The intent is to call this method for every tool config in a repository and
         append each of these as entries to a tool panel dictionary for the repository.
         This enables each tool to be loaded into a different section in the tool panel.
-        {<Tool guid> :
-           [{ tool_config : <tool_config_file>,
-              id: <ToolSection id>,
-              version : <ToolSection version>,
-              name : <TooSection name>}]}
+
+        .. code-block::
+
+            {<Tool guid> :
+                [{ tool_config : <tool_config_file>,
+                    id: <ToolSection id>,
+                    version : <ToolSection version>,
+                    name : <TooSection name>}]}
+
         """
         tool_panel_dict = {}
         file_name = strip_path(tool_config)
diff --git a/lib/galaxy/tool_shed/util/tool_util.py b/lib/galaxy/tool_shed/util/tool_util.py
index b5ff1a8bcd2..6614883447c 100644
--- a/lib/galaxy/tool_shed/util/tool_util.py
+++ b/lib/galaxy/tool_shed/util/tool_util.py
@@ -233,7 +233,7 @@ def panel_entry_per_tool(tool_section_dict):
         return False
     if len(tool_section_dict) != 3:
         return True
-    for k, v in tool_section_dict:
+    for k in tool_section_dict.keys():
         if k not in ['id', 'version', 'name']:
             return True
     return False
diff --git a/lib/galaxy/tool_util/cwl/representation.py b/lib/galaxy/tool_util/cwl/representation.py
index d428db4fa39..c94f56bf09a 100644
--- a/lib/galaxy/tool_util/cwl/representation.py
+++ b/lib/galaxy/tool_util/cwl/representation.py
@@ -114,8 +114,8 @@ def type_representation_from_name(type_representation_name):
     for type_representation in TYPE_REPRESENTATIONS:
         if type_representation.name == type_representation_name:
             return type_representation
-
-    assert False
+    else:
+        raise ValueError(f"No type representation for {type_representation_name}")
 
 
 def type_descriptions_for_field_types(field_types):
@@ -343,7 +343,7 @@ def to_galaxy_parameters(tool, as_dict):
                 continue
 
             only_input = next(iter(input.inputs.values()))
-            for index, value in enumerate(as_dict_value):
+            for value in as_dict_value:
                 key = f"{input_name}_repeat_0|{only_input.name}"
                 galaxy_value = from_simple_value(only_input, value)
                 galaxy_request[key] = galaxy_value
diff --git a/lib/galaxy/tool_util/deps/container_resolvers/mulled.py b/lib/galaxy/tool_util/deps/container_resolvers/mulled.py
index 486e890ea1a..dce5f6eb60d 100644
--- a/lib/galaxy/tool_util/deps/container_resolvers/mulled.py
+++ b/lib/galaxy/tool_util/deps/container_resolvers/mulled.py
@@ -6,8 +6,10 @@ import subprocess
 from typing import NamedTuple, Optional
 
 from galaxy.util import (
+    safe_makedirs,
     string_as_bool,
     unicodify,
+    which,
 )
 from galaxy.util.commands import shell
 from ..container_classes import CONTAINER_CLASSES
@@ -84,7 +86,7 @@ def list_docker_cached_mulled_images(namespace=None, hash_func="v2", resolution_
         except subprocess.CalledProcessError:
             log.info("Call to `docker images` failed, configured container resolution may be broken")
             return []
-        images_and_versions = [":".join(l.split()[0:2]) for l in images_and_versions[1:]]
+        images_and_versions = [":".join(line.split()[0:2]) for line in images_and_versions[1:]]
         if resolution_cache is not None:
             resolution_cache[cache_key] = images_and_versions
 
@@ -334,19 +336,49 @@ def targets_to_mulled_name(targets, hash_func, namespace, resolution_cache=None,
     return name
 
 
-class CachedMulledDockerContainerResolver(ContainerResolver):
+class CliContainerResolver(ContainerResolver):
+
+    container_type = 'docker'
+    cli = 'docker'
+
+    def __init__(self, *args, **kwargs):
+        self._cli_available = bool(which(self.cli))
+        super().__init__(*args, **kwargs)
+
+    @property
+    def cli_available(self):
+        return self._cli_available
+
+    @cli_available.setter
+    def cli_available(self, value):
+        if not value:
+            log.info('{} CLI not available, cannot list or pull images in Galaxy process. Does not impact kubernetes.'.format(self.cli))
+        self._cli_available = value
+
+
+class SingularityCliContainerResolver(CliContainerResolver):
+
+    container_type = 'singularity'
+    cli = 'singularity'
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.cache_directory = kwargs.get("cache_directory", os.path.join(kwargs['app_info'].container_image_cache_path, "singularity", "mulled"))
+        safe_makedirs(self.cache_directory)
+
+
+class CachedMulledDockerContainerResolver(CliContainerResolver):
 
     resolver_type = "cached_mulled"
-    container_type = "docker"
     shell = '/bin/bash'
 
     def __init__(self, app_info=None, namespace="biocontainers", hash_func="v2", **kwds):
-        super().__init__(app_info)
+        super().__init__(app_info=app_info, **kwds)
         self.namespace = namespace
         self.hash_func = hash_func
 
     def resolve(self, enabled_container_types, tool_info, **kwds):
-        if tool_info.requires_galaxy_python_environment or self.container_type not in enabled_container_types:
+        if not self.cli_available or tool_info.requires_galaxy_python_environment or self.container_type not in enabled_container_types:
             return None
 
         targets = mulled_targets(tool_info)
@@ -357,15 +389,13 @@ class CachedMulledDockerContainerResolver(ContainerResolver):
         return "CachedMulledDockerContainerResolver[namespace=%s]" % self.namespace
 
 
-class CachedMulledSingularityContainerResolver(ContainerResolver):
+class CachedMulledSingularityContainerResolver(SingularityCliContainerResolver):
 
     resolver_type = "cached_mulled_singularity"
-    container_type = "singularity"
     shell = '/bin/bash'
 
     def __init__(self, app_info=None, hash_func="v2", **kwds):
-        super().__init__(app_info)
-        self.cache_directory = kwds.get("cache_directory", os.path.join(app_info.container_image_cache_path, "singularity", "mulled"))
+        super().__init__(app_info=app_info, **kwds)
         self.hash_func = hash_func
 
     def resolve(self, enabled_container_types, tool_info, **kwds):
@@ -379,26 +409,36 @@ class CachedMulledSingularityContainerResolver(ContainerResolver):
         return "CachedMulledSingularityContainerResolver[cache_directory=%s]" % self.cache_directory
 
 
-class MulledDockerContainerResolver(ContainerResolver):
+class MulledDockerContainerResolver(CliContainerResolver):
     """Look for mulled images matching tool dependencies."""
 
     resolver_type = "mulled"
-    container_type = "docker"
     shell = '/bin/bash'
     protocol: Optional[str] = None
 
     def __init__(self, app_info=None, namespace="biocontainers", hash_func="v2", auto_install=True, **kwds):
-        super().__init__(app_info)
+        super().__init__(app_info=app_info, **kwds)
         self.namespace = namespace
         self.hash_func = hash_func
         self.auto_install = string_as_bool(auto_install)
 
     def cached_container_description(self, targets, namespace, hash_func, resolution_cache):
-        return docker_cached_container_description(targets, namespace, hash_func, resolution_cache)
+        try:
+            return docker_cached_container_description(targets, namespace, hash_func, resolution_cache)
+        except subprocess.CalledProcessError:
+            # We should only get here if a docker binary is available, but command quits with a non-zero exit code,
+            # e.g if the docker daemon is not available
+            log.exception('An error occured while listing cached docker image. Docker daemon may need to be restarted.')
+            return None
 
     def pull(self, container):
-        command = container.build_pull_command()
-        shell(command)
+        if self.cli_available:
+            command = container.build_pull_command()
+            shell(command)
+
+    @property
+    def can_list_containers(self):
+        return self.cli_available
 
     def resolve(self, enabled_container_types, tool_info, install=False, session=None, **kwds):
         resolution_cache = kwds.get("resolution_cache")
@@ -419,45 +459,44 @@ class MulledDockerContainerResolver(ContainerResolver):
                 type=self.container_type,
                 shell=self.shell,
             )
-            if install and not self.cached_container_description(
-                    targets,
-                    namespace=self.namespace,
-                    hash_func=self.hash_func,
-                    resolution_cache=resolution_cache,
-            ):
-                destination_info = {}
-                destination_for_container_type = kwds.get('destination_for_container_type')
-                if destination_for_container_type:
-                    destination_info = destination_for_container_type(self.container_type)
-                container = CONTAINER_CLASSES[self.container_type](container_description.identifier,
-                                                                   self.app_info,
-                                                                   tool_info,
-                                                                   destination_info,
-                                                                   {},
-                                                                   container_description)
-                self.pull(container)
-            if not self.auto_install:
-                container_description = self.cached_container_description(
-                    targets,
-                    namespace=self.namespace,
-                    hash_func=self.hash_func,
-                    resolution_cache=resolution_cache,
-                )
+            if self.can_list_containers:
+                if install and not self.cached_container_description(
+                        targets,
+                        namespace=self.namespace,
+                        hash_func=self.hash_func,
+                        resolution_cache=resolution_cache,
+                ):
+                    destination_info = {}
+                    destination_for_container_type = kwds.get('destination_for_container_type')
+                    if destination_for_container_type:
+                        destination_info = destination_for_container_type(self.container_type)
+                    container = CONTAINER_CLASSES[self.container_type](container_description.identifier,
+                                                                       self.app_info,
+                                                                       tool_info,
+                                                                       destination_info,
+                                                                       {},
+                                                                       container_description)
+                    self.pull(container)
+                if not self.auto_install:
+                    container_description = self.cached_container_description(
+                        targets,
+                        namespace=self.namespace,
+                        hash_func=self.hash_func,
+                        resolution_cache=resolution_cache,
+                    ) or container_description
             return container_description
 
     def __str__(self):
         return "MulledDockerContainerResolver[namespace=%s]" % self.namespace
 
 
-class MulledSingularityContainerResolver(MulledDockerContainerResolver):
+class MulledSingularityContainerResolver(SingularityCliContainerResolver, MulledDockerContainerResolver):
 
     resolver_type = "mulled_singularity"
-    container_type = "singularity"
     protocol = 'docker://'
 
     def __init__(self, app_info=None, namespace="biocontainers", hash_func="v2", auto_install=True, **kwds):
-        super().__init__(app_info)
-        self.cache_directory = kwds.get("cache_directory", os.path.join(app_info.container_image_cache_path, "singularity", "mulled"))
+        super().__init__(app_info=app_info, **kwds)
         self.namespace = namespace
         self.hash_func = hash_func
         self.auto_install = string_as_bool(auto_install)
@@ -467,24 +506,29 @@ class MulledSingularityContainerResolver(MulledDockerContainerResolver):
                                                         cache_directory=self.cache_directory,
                                                         hash_func=hash_func)
 
+    @property
+    def can_list_containers(self):
+        # Only needs access to path, doesn't require CLI
+        return True
+
     def pull(self, container):
-        cmds = container.build_mulled_singularity_pull_command(cache_directory=self.cache_directory, namespace=self.namespace)
-        shell(cmds=cmds)
+        if self.cli_available:
+            cmds = container.build_mulled_singularity_pull_command(cache_directory=self.cache_directory, namespace=self.namespace)
+            shell(cmds=cmds)
 
     def __str__(self):
         return "MulledSingularityContainerResolver[namespace=%s]" % self.namespace
 
 
-class BuildMulledDockerContainerResolver(ContainerResolver):
+class BuildMulledDockerContainerResolver(CliContainerResolver):
     """Build for Docker mulled images matching tool dependencies."""
 
     resolver_type = "build_mulled"
-    container_type = "docker"
     shell = '/bin/bash'
     builds_on_resolution = True
 
     def __init__(self, app_info=None, namespace="local", hash_func="v2", auto_install=True, **kwds):
-        super().__init__(app_info)
+        super().__init__(app_info=app_info, **kwds)
         self._involucro_context_kwds = {
             'involucro_bin': self._get_config_option("involucro_path", None)
         }
@@ -523,20 +567,18 @@ class BuildMulledDockerContainerResolver(ContainerResolver):
         return "BuildDockerContainerResolver[namespace=%s]" % self.namespace
 
 
-class BuildMulledSingularityContainerResolver(ContainerResolver):
+class BuildMulledSingularityContainerResolver(SingularityCliContainerResolver):
     """Build for Singularity mulled images matching tool dependencies."""
 
     resolver_type = "build_mulled_singularity"
-    container_type = "singularity"
     shell = '/bin/bash'
     builds_on_resolution = True
 
     def __init__(self, app_info=None, hash_func="v2", auto_install=True, **kwds):
-        super().__init__(app_info)
+        super().__init__(app_info=app_info, **kwds)
         self._involucro_context_kwds = {
             'involucro_bin': self._get_config_option("involucro_path", None)
         }
-        self.cache_directory = kwds.get("cache_directory", os.path.join(app_info.container_image_cache_path, "singularity", "mulled"))
         self.hash_func = hash_func
         self.auto_install = string_as_bool(auto_install)
         self._mulled_kwds = {
diff --git a/lib/galaxy/tool_util/deps/containers.py b/lib/galaxy/tool_util/deps/containers.py
index d6bda37a3e3..63b06f385f8 100644
--- a/lib/galaxy/tool_util/deps/containers.py
+++ b/lib/galaxy/tool_util/deps/containers.py
@@ -222,9 +222,15 @@ class ContainerRegistry:
                 CachedMulledSingularityContainerResolver(self.app_info, namespace="local"),
                 MulledDockerContainerResolver(self.app_info, namespace="biocontainers"),
                 MulledSingularityContainerResolver(self.app_info, namespace="biocontainers"),
-                BuildMulledDockerContainerResolver(self.app_info),
-                BuildMulledSingularityContainerResolver(self.app_info),
             ])
+            # BuildMulledDockerContainerResolver and BuildMulledSingularityContainerResolver both need the docker daemon to build images.
+            # If docker is not available, we don't load them.
+            build_mulled_docker_container_resolver = BuildMulledDockerContainerResolver(self.app_info)
+            if build_mulled_docker_container_resolver.cli_available:
+                default_resolvers.extend([
+                    build_mulled_docker_container_resolver,
+                    BuildMulledSingularityContainerResolver(self.app_info),
+                ])
         return default_resolvers
 
     def __resolvers_dict(self):
diff --git a/lib/galaxy/tool_util/deps/mulled/get_tests.py b/lib/galaxy/tool_util/deps/mulled/get_tests.py
index c30630ee80e..a0cf52e5e51 100644
--- a/lib/galaxy/tool_util/deps/mulled/get_tests.py
+++ b/lib/galaxy/tool_util/deps/mulled/get_tests.py
@@ -162,7 +162,7 @@ def open_recipe_file(file, recipes_path=None, github_repo='bioconda/bioconda-rec
 
 def get_alternative_versions(filepath, filename, recipes_path=None, github_repo='bioconda/bioconda-recipes'):
     """
-    Return files that match 'filepath/*/filename' in the bioconda-recipes repository
+    Return files that match ``filepath/*/filename`` in the bioconda-recipes repository
     """
     if recipes_path:
         return [n.replace('%s/' % recipes_path, '') for n in glob(f'{recipes_path}/{filepath}/*/{filename}')]
diff --git a/lib/galaxy/tool_util/deps/mulled/mulled_search.py b/lib/galaxy/tool_util/deps/mulled/mulled_search.py
index 797da5eb8e7..cf83a945235 100755
--- a/lib/galaxy/tool_util/deps/mulled/mulled_search.py
+++ b/lib/galaxy/tool_util/deps/mulled/mulled_search.py
@@ -228,15 +228,15 @@ def readable_output(json, organization='biocontainers', channel='bioconda'):
         sys.stdout.write("The query returned the following result(s).\n")
         # put quay, conda etc results as lists in lines
         lines = [['LOCATION', 'NAME', 'VERSION', 'COMMAND\n']]
-        for search_string, results in json.get('quay', {}).items():
+        for results in json.get('quay', {}).values():
             for result in results:
                 lines.append(['quay', result['package'], result['version'], 'docker pull quay.io/%s/%s:%s\n' %
                               (organization, result['package'], result['version'])])  # NOT a real solution
-        for search_string, results in json.get('conda', {}).items():
+        for results in json.get('conda', {}).values():
             for result in results:
                 lines.append(['conda', result['package'], '{}--{}'.format(result['version'], result['build']),
                               'conda install -c {} {}={}={}\n'.format(channel, result['package'], result['version'], result['build'])])
-        for search_string, results in json.get('singularity', {}).items():
+        for results in json.get('singularity', {}).values():
             for result in results:
                 lines.append(['singularity', result['package'], result['version'],
                               'wget https://depot.galaxyproject.org/singularity/{}:{}\n'.format(result['package'], result['version'])])
diff --git a/lib/galaxy/tool_util/deps/resolvers/unlinked_tool_shed_packages.py b/lib/galaxy/tool_util/deps/resolvers/unlinked_tool_shed_packages.py
index af2d8642042..eafa3b685ad 100644
--- a/lib/galaxy/tool_util/deps/resolvers/unlinked_tool_shed_packages.py
+++ b/lib/galaxy/tool_util/deps/resolvers/unlinked_tool_shed_packages.py
@@ -3,13 +3,15 @@ Backup resolvers for when dependencies can not be loaded from the database.
 Mainly suited for testing stage.
 
 Ideally all dependencies will be stored in the database
-    when a tool is added from a Tool Shed.
+when a tool is added from a Tool Shed.
+
 That should remain the preferred way of locating dependencies.
 
 In cases where that is not possible
-    for example during testing this resolver can act as a backup.
+for example during testing this resolver can act as a backup.
+
 This resolver looks not just for manually added dependencies
-    but also ones added from a Tool Shed.
+but also ones added from a Tool Shed.
 
 This tool is still under development so the default behaviour could change.
 It has been tested when placed in the same directory as galaxy_packages.py
diff --git a/lib/galaxy/tool_util/loader_directory.py b/lib/galaxy/tool_util/loader_directory.py
index 92b445272e9..056ec577447 100644
--- a/lib/galaxy/tool_util/loader_directory.py
+++ b/lib/galaxy/tool_util/loader_directory.py
@@ -164,11 +164,11 @@ def looks_like_xml(path, regex=TOOL_REGEX):
     if not os.path.getsize(full_path):
         return False
 
-    if(checkers.check_binary(full_path) or
-       checkers.check_image(full_path) or
-       checkers.is_gzip(full_path) or
-       checkers.is_bz2(full_path) or
-       checkers.is_zip(full_path)):
+    if(checkers.check_binary(full_path)
+       or checkers.check_image(full_path)
+       or checkers.is_gzip(full_path)
+       or checkers.is_bz2(full_path)
+       or checkers.is_zip(full_path)):
         return False
 
     with open(path, encoding='utf-8') as f:
@@ -250,7 +250,7 @@ def _find_tool_files(path_or_uri_like, recursive, enable_beta_formats):
 
     is_file = not os.path.isdir(path)
     if not os.path.exists(path):
-        raise Exception(PATH_DOES_NOT_EXIST_ERROR)
+        raise Exception(PATH_DOES_NOT_EXIST_ERROR % path)
     elif is_file and recursive:
         raise Exception(PATH_AND_RECURSIVE_ERROR)
     elif is_file:
diff --git a/lib/galaxy/tool_util/output_checker.py b/lib/galaxy/tool_util/output_checker.py
index 46b61334b5b..7cdbc2681ed 100644
--- a/lib/galaxy/tool_util/output_checker.py
+++ b/lib/galaxy/tool_util/output_checker.py
@@ -77,8 +77,8 @@ def check_output(stdio_regexes, stdio_exit_codes, stdout, stderr, tool_exit_code
             max_error_level = StdioErrorLevel.NO_ERROR
             if tool_exit_code is not None:
                 for stdio_exit_code in stdio_exit_codes:
-                    if (tool_exit_code >= stdio_exit_code.range_start and
-                            tool_exit_code <= stdio_exit_code.range_end):
+                    if (tool_exit_code >= stdio_exit_code.range_start
+                            and tool_exit_code <= stdio_exit_code.range_end):
                         # Tack on a generic description of the code
                         # plus a specific code description. For example,
                         # this might prepend "Job 42: Warning (Out of Memory)\n".
@@ -166,9 +166,9 @@ def __regex_err_msg(match, stream, regex):
     mstart = match.start()
     mend = match.end()
     if mend - mstart > 256:
-        match_str = match.string[mstart : mstart + 256] + "..."
+        match_str = match.string[mstart:mstart + 256] + "..."
     else:
-        match_str = match.string[mstart: mend]
+        match_str = match.string[mstart:mend]
 
     # If there's a description for the regular expression, then use it.
     # Otherwise, we'll take the first 256 characters of the match.
diff --git a/lib/galaxy/tool_util/parser/output_objects.py b/lib/galaxy/tool_util/parser/output_objects.py
index c6084b62e88..1827f2cc710 100644
--- a/lib/galaxy/tool_util/parser/output_objects.py
+++ b/lib/galaxy/tool_util/parser/output_objects.py
@@ -25,7 +25,7 @@ class ToolOutput(ToolOutputBase):
     Represents an output datasets produced by a tool. For backward
     compatibility this behaves as if it were the tuple::
 
-      (format, metadata_source, parent)
+    (format, metadata_source, parent)
     """
 
     dict_collection_visible_keys = ['name', 'format', 'label', 'hidden', 'output_type', 'format_source',
@@ -123,15 +123,17 @@ class ToolOutputCollection(ToolOutputBase):
     Represents a HistoryDatasetCollectionAssociation of output datasets produced
     by a tool.
 
-    <outputs>
-      <collection type="list" label="${tool.name} on ${on_string} fasta">
-        <discover_datasets pattern="__name__" ext="fasta" visible="True" directory="outputFiles" />
-      </collection>
-      <collection type="paired" label="${tool.name} on ${on_string} paired reads">
-        <data name="forward" format="fastqsanger" />
-        <data name="reverse" format="fastqsanger"/>
-      </collection>
-    <outputs>
+    .. code-block::
+
+        <outputs>
+        <collection type="list" label="${tool.name} on ${on_string} fasta">
+            <discover_datasets pattern="__name__" ext="fasta" visible="True" directory="outputFiles" />
+        </collection>
+        <collection type="paired" label="${tool.name} on ${on_string} paired reads">
+            <data name="forward" format="fastqsanger" />
+            <data name="reverse" format="fastqsanger"/>
+        </collection>
+        <outputs>
     """
     dict_collection_visible_keys = ['name', 'format', 'label', 'hidden', 'output_type', 'default_format',
                                     'default_format_source', 'default_metadata_source', 'inherit_format', 'inherit_metadata']
diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index 957cb05d6ee..e5573820c45 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -443,6 +443,7 @@ class XmlToolSource(ToolSource):
         parse error handling from command and stdio tag
 
         returns list of exit codes, list of regexes
+
         - exit_codes contain all non-zero exit codes (:-1 and 1:) if
           detect_errors is default (if not legacy), exit_code, or aggressive
         - the oom_exit_code if given and detect_errors is exit_code
@@ -451,6 +452,7 @@ class XmlToolSource(ToolSource):
           and exit codes derived from the properties of the command tag.
           thus more specific regexes of the same or more severe error level
           are triggered first.
+
         """
 
         command_el = self._command_el
diff --git a/lib/galaxy/tool_util/verify/__init__.py b/lib/galaxy/tool_util/verify/__init__.py
index 1d814cf7017..1da03455385 100644
--- a/lib/galaxy/tool_util/verify/__init__.py
+++ b/lib/galaxy/tool_util/verify/__init__.py
@@ -253,8 +253,8 @@ def files_diff(file1, file2, attributes=None):
                 is_pdf = True
                 # Replace non-Unicode characters using unicodify(),
                 # difflib.unified_diff doesn't work on list of bytes
-                history_data = [unicodify(l) for l in get_fileobj(file2, mode='rb', compressed_formats=compressed_formats)]
-                local_file = [unicodify(l) for l in get_fileobj(file1, mode='rb', compressed_formats=compressed_formats)]
+                history_data = [unicodify(line) for line in get_fileobj(file2, mode='rb', compressed_formats=compressed_formats)]
+                local_file = [unicodify(line) for line in get_fileobj(file1, mode='rb', compressed_formats=compressed_formats)]
             else:
                 raise AssertionError("Binary data detected, not displaying diff")
         if attributes.get('sort', False):
diff --git a/lib/galaxy/tool_util/verify/interactor.py b/lib/galaxy/tool_util/verify/interactor.py
index 0c110414a78..22055d75286 100644
--- a/lib/galaxy/tool_util/verify/interactor.py
+++ b/lib/galaxy/tool_util/verify/interactor.py
@@ -562,7 +562,7 @@ class GalaxyInteractorApi:
                 print("| Dataset Info:")
                 print(self.format_for_summary(dataset_info.get("misc_info", ""), "Dataset info is empty."))
                 print("| Peek:")
-                print(self.format_for_summary(dataset_info.get("peek", ""), "Peek unavilable."))
+                print(self.format_for_summary(dataset_info.get("peek", ""), "Peek unavailable."))
             except Exception:
                 print("| *TEST FRAMEWORK ERROR FETCHING DATASET DETAILS*")
             try:
@@ -883,7 +883,7 @@ def _verify_extra_files_content(extra_files, hda_id, dataset_fetcher, test_data_
         elif extra_file_type == 'directory':
             extracted_path = test_data_downloader(extra_file_value, mode='directory')
             cleanup_directories.append(extracted_path)
-            for root, directories, files in util.path.safe_walk(extracted_path):
+            for root, _directories, files in util.path.safe_walk(extracted_path):
                 for filename in files:
                     filename = os.path.join(root, filename)
                     filename = os.path.relpath(filename, extracted_path)
diff --git a/lib/galaxy/tool_util/verify/wait.py b/lib/galaxy/tool_util/verify/wait.py
index 33f71427e4a..0ef1f5d57b1 100644
--- a/lib/galaxy/tool_util/verify/wait.py
+++ b/lib/galaxy/tool_util/verify/wait.py
@@ -1,14 +1,16 @@
 """Abstraction for waiting on API conditions to become true."""
 
 import time
+from typing import Callable, Optional, Union
 
 DEFAULT_POLLING_BACKOFF = 0
 DEFAULT_POLLING_DELTA = 0.25
 
 TIMEOUT_MESSAGE_TEMPLATE = "Timed out after {} seconds waiting on {}."
+timeout_type = Union[int, float]
 
 
-def wait_on(function, desc, timeout, delta=DEFAULT_POLLING_DELTA, polling_backoff=DEFAULT_POLLING_BACKOFF, sleep_=None):
+def wait_on(function: Callable, desc: str, timeout: timeout_type, delta: timeout_type = DEFAULT_POLLING_DELTA, polling_backoff: timeout_type = DEFAULT_POLLING_BACKOFF, sleep_: Optional[Callable] = None):
     """Wait for function to return non-None value.
 
     Grow the polling interval (initially ``delta`` defaulting to 0.25 seconds)
@@ -18,7 +20,7 @@ def wait_on(function, desc, timeout, delta=DEFAULT_POLLING_DELTA, polling_backof
     supplied function ever returning a non-None value.
     """
     sleep = sleep_ or time.sleep
-    total_wait = 0
+    total_wait = 0.0
     while True:
         if total_wait > timeout:
             raise TimeoutAssertionError(TIMEOUT_MESSAGE_TEMPLATE.format(total_wait, desc))
diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index d9b991bab28..4e91a32ab97 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -414,47 +414,47 @@ This tag set is contained within the ``<entry_point>`` tag set. It contains the
   <xs:attributeGroup name="Thing">
     <xs:attribute name="name" type="xs:string" use="optional">
       <xs:annotation>
-        <xs:documentation>https://schema.org/name</xs:documentation>
+        <xs:documentation xml:lang="en">https://schema.org/name</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="url" type="xs:string" use="optional">
       <xs:annotation>
-      <xs:documentation>https://schema.org/url</xs:documentation>
+      <xs:documentation xml:lang="en">https://schema.org/url</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="identifier" type="xs:string" use="optional">
       <xs:annotation>
-        <xs:documentation>https://schema.org/identifier</xs:documentation>
+        <xs:documentation xml:lang="en">https://schema.org/identifier</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="image" type="xs:string" use="optional">
       <xs:annotation>
-        <xs:documentation>https://schema.org/image</xs:documentation>
+        <xs:documentation xml:lang="en">https://schema.org/image</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="address" type="xs:string" use="optional">
       <xs:annotation>
-        <xs:documentation>https://schema.org/address</xs:documentation>
+        <xs:documentation xml:lang="en">https://schema.org/address</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="email" type="xs:string" use="optional">
       <xs:annotation>
-        <xs:documentation>https://schema.org/email</xs:documentation>
+        <xs:documentation xml:lang="en">https://schema.org/email</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="telephone" type="xs:string" use="optional">
       <xs:annotation>
-        <xs:documentation>https://schema.org/telephone</xs:documentation>
+        <xs:documentation xml:lang="en">https://schema.org/telephone</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="faxNumber" type="xs:string" use="optional">
       <xs:annotation>
-        <xs:documentation>https://schema.org/faxNumber</xs:documentation>
+        <xs:documentation xml:lang="en">https://schema.org/faxNumber</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="alternateName" type="xs:string" use="optional">
       <xs:annotation>
-        <xs:documentation>https://schema.org/alternateName</xs:documentation>
+        <xs:documentation xml:lang="en">https://schema.org/alternateName</xs:documentation>
       </xs:annotation>
     </xs:attribute>
   </xs:attributeGroup>
@@ -468,27 +468,27 @@ Describes a person. Tries to stay close to schema.org data model - see https://s
     <xs:attributeGroup ref="Thing"/>
     <xs:attribute name="givenName" type="xs:string" use="optional">
       <xs:annotation>
-        <xs:documentation>https://schema.org/givenName</xs:documentation>
+        <xs:documentation xml:lang="en">https://schema.org/givenName</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="familyName" type="xs:string" use="optional">
       <xs:annotation>
-        <xs:documentation>https://schema.org/familyName</xs:documentation>
+        <xs:documentation xml:lang="en">https://schema.org/familyName</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="honorificPrefix" type="xs:string" use="optional">
       <xs:annotation>
-        <xs:documentation>https://schema.org/honorificPrefix</xs:documentation>
+        <xs:documentation xml:lang="en">https://schema.org/honorificPrefix</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="honorificSuffix" type="xs:string" use="optional">
       <xs:annotation>
-        <xs:documentation>https://schema.org/honorificSuffix</xs:documentation>
+        <xs:documentation xml:lang="en">https://schema.org/honorificSuffix</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="jobTitle" type="xs:string" use="optional">
       <xs:annotation>
-        <xs:documentation>https://schema.org/jobTitle</xs:documentation>
+        <xs:documentation xml:lang="en">https://schema.org/jobTitle</xs:documentation>
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
@@ -1354,6 +1354,38 @@ This tag set defines the tool's input parameters for executing the tool via the
 functional test framework. See [test](#tool-tests-test) documentation for
 some simple examples of parameters.
 
+### Parameter Types
+
+#### ``text``, ``integer``, and ``float``
+
+Values for these parameters are simply given by the desired value.
+
+#### ``boolean``
+
+The value of the test parameter should be set to `true` or `false` corresponding
+to the cases that the parameter is checked or not. Alternatively the value
+specified as `truevalue` or `falsevalue` can be given.
+
+#### ``data``
+
+Data input parameters can be given as a file name. The file should exist in the
+`test-data` folder. Multiple files can be specified as comma separated list.
+
+#### ``select``
+
+The value of a select parameter should be specified as the value of one of the
+legal options. If more than one option is selected (`multiple="true"`) they
+should be given as comma separated list. For optional selects
+(`optional="true"`) the case that no option is selected can be specified with
+`value=""`.
+
+While in general it is preferred to specify the selected cases by their values it
+is also possible to specify them by their name (i.e. the content of the
+`option` tag that is shown to the user). One use case is a dynamic select that is
+generated from a data table with two columns: name and value where the value is
+a path. Since the path changes with the test environment it can not be used to
+select an option for a test.
+
 ]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
@@ -1560,7 +1592,7 @@ When this attribute is true and ``compare`` is set to ``diff``, try to decompres
       <!-- TODO: To be more percise only one assert_contents is allowed - this should not be in here. -->
       <xs:element name="assert_contents" type="TestAssertions">
         <xs:annotation>
-          <xs:documentation><![CDATA[
+          <xs:documentation xml:lang="en"><![CDATA[
 $assertions
 
 ### Examples
@@ -1669,7 +1701,7 @@ provides a demonstration of using this tag.
   </xs:complexType>
   <xs:complexType name="TestDiscoveredDataset">
     <xs:annotation>
-      <xs:documentation><![CDATA[
+      <xs:documentation xml:lang="en"><![CDATA[
 
 This directive specifies a test for an output's discovered dataset. It acts as an
 ``output`` test tag in many ways and can define any tests of that tag (e.g.
@@ -1877,7 +1909,7 @@ or ``list:paired``).</xs:documentation>
 
   <xs:complexType name="TestAssertions">
     <xs:annotation>
-      <xs:documentation><![CDATA[
+      <xs:documentation xml:lang="en"><![CDATA[
 This tag set defines a sequence of checks or assertions to run against the
 target output. This tag requires no attributes, but child tags should be used to
 define the assertions to make about the output. The functional test framework
@@ -1899,90 +1931,90 @@ module.
     <xs:choice>
       <xs:element name="has_text" type="xs:anyType">
         <xs:annotation>
-          <xs:documentation><![CDATA[Asserts the specified ``text`` appears in the output (e.g. ``<has_text text="chr7">``). If the ``text`` is expected to occur a particular number of times, this value can be specified using ``n``.]]>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the specified ``text`` appears in the output (e.g. ``<has_text text="chr7">``). If the ``text`` is expected to occur a particular number of times, this value can be specified using ``n``.]]>
           </xs:documentation>
         </xs:annotation>
       </xs:element>
       <xs:element name="not_has_text" type="xs:anyType">
         <xs:annotation>
-          <xs:documentation><![CDATA[Asserts the specified ``text`` does not appear in the output (e.g. ``<not_has_text text="chr8" />``).]]>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the specified ``text`` does not appear in the output (e.g. ``<not_has_text text="chr8" />``).]]>
           </xs:documentation>
         </xs:annotation>
       </xs:element>
       <xs:element name="has_text_matching" type="xs:anyType">
         <xs:annotation>
-          <xs:documentation><![CDATA[Asserts text matching the specified regular expression (``expression``) appears in the output (e.g. ``<has_text_matching expression="1274\d+53" />`` ).]]>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts text matching the specified regular expression (``expression``) appears in the output (e.g. ``<has_text_matching expression="1274\d+53" />`` ).]]>
           </xs:documentation>
         </xs:annotation>
       </xs:element>
       <xs:element name="has_line" type="xs:anyType">
         <xs:annotation>
-          <xs:documentation><![CDATA[Asserts a line matching the specified string (``line``) appears in the output (e.g. ``<has_line line="A full example line." />``). If the ``line`` is expected to occur a particular number of times, this value can be specified using ``n``.]]>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts a line matching the specified string (``line``) appears in the output (e.g. ``<has_line line="A full example line." />``). If the ``line`` is expected to occur a particular number of times, this value can be specified using ``n``.]]>
           </xs:documentation>
         </xs:annotation>
       </xs:element>
       <xs:element name="has_n_lines" type="xs:anyType">
         <xs:annotation>
-          <xs:documentation><![CDATA[Asserts that an output contains ``n`` lines, e.g. ``<has_n_lines n="3" />``.]]>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts that an output contains ``n`` lines, e.g. ``<has_n_lines n="3" />``.]]>
           </xs:documentation>
         </xs:annotation>
       </xs:element>
       <xs:element name="has_line_matching" type="xs:anyType">
         <xs:annotation>
-          <xs:documentation><![CDATA[Asserts a line matching the specified regular expression (``expression``) appears in the output (e.g. ``<has_line_matching expression=".*\s+127489808\s+127494553" />``).]]>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts a line matching the specified regular expression (``expression``) appears in the output (e.g. ``<has_line_matching expression=".*\s+127489808\s+127494553" />``).]]>
           </xs:documentation>
         </xs:annotation>
       </xs:element>
       <xs:element name="has_n_columns" type="xs:anyType">
         <xs:annotation>
-          <xs:documentation><![CDATA[Asserts tabular output contains the specified number (``n``) of columns (e.g. ``<has_n_columns n="3" />``).]]>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts tabular output contains the specified number (``n``) of columns (e.g. ``<has_n_columns n="3" />``).]]>
           </xs:documentation>
         </xs:annotation>
       </xs:element>
       <xs:element name="is_valid_xml" type="xs:anyType">
         <xs:annotation>
-          <xs:documentation><![CDATA[Asserts the output is a valid XML file (e.g. ``<is_valid_xml />``).]]>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the output is a valid XML file (e.g. ``<is_valid_xml />``).]]>
           </xs:documentation>
         </xs:annotation>
       </xs:element>
       <xs:element name="has_element_with_path" type="xs:anyType">
         <xs:annotation>
-          <xs:documentation><![CDATA[Asserts the XML output contains at least one element (or tag) with the specified XPath-like ``path`` (e.g. ``<has_element_with_path path="BlastOutput_param/Parameters/Parameters_matrix" />``).]]>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the XML output contains at least one element (or tag) with the specified XPath-like ``path`` (e.g. ``<has_element_with_path path="BlastOutput_param/Parameters/Parameters_matrix" />``).]]>
           </xs:documentation>
         </xs:annotation>
       </xs:element>
       <xs:element name="has_n_elements_with_path" type="xs:anyType">
         <xs:annotation>
-          <xs:documentation><![CDATA[Asserts the XML output contains the specified number (``n``) of elements (or tags) with the specified XPath-like ``path`` (e.g. ``<has_n_elements_with_path n="9" path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_num" />``).]]>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the XML output contains the specified number (``n``) of elements (or tags) with the specified XPath-like ``path`` (e.g. ``<has_n_elements_with_path n="9" path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_num" />``).]]>
           </xs:documentation>
         </xs:annotation>
       </xs:element>
       <xs:element name="element_text_is" type="xs:anyType">
         <xs:annotation>
-          <xs:documentation><![CDATA[Asserts the text of the XML element with the specified XPath-like ``path`` is the specified ``text`` (e.g. ``<element_text_is path="BlastOutput_program" text="blastp" />``).]]>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the text of the XML element with the specified XPath-like ``path`` is the specified ``text`` (e.g. ``<element_text_is path="BlastOutput_program" text="blastp" />``).]]>
           </xs:documentation>
         </xs:annotation>
       </xs:element>
       <xs:element name="element_text_matches">
         <xs:annotation>
-          <xs:documentation><![CDATA[Asserts the text of the XML element with the specified XPath-like ``path`` matches the regular expression defined by ``expression`` (e.g. ``<element_text_matches path="BlastOutput_version" expression="BLASTP\s+2\.2.*" />``).]]>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the text of the XML element with the specified XPath-like ``path`` matches the regular expression defined by ``expression`` (e.g. ``<element_text_matches path="BlastOutput_version" expression="BLASTP\s+2\.2.*" />``).]]>
           </xs:documentation>
         </xs:annotation>
       </xs:element>
       <xs:element name="attribute_is" type="xs:anyType">
         <xs:annotation>
-          <xs:documentation><![CDATA[Asserts the XML ``attribute`` for the element (or tag) with the specified XPath-like ``path`` is the specified ``text`` (e.g. ``<attribute_is path="outerElement/innerElement1" attribute="foo" text="bar" />`` ).]]>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the XML ``attribute`` for the element (or tag) with the specified XPath-like ``path`` is the specified ``text`` (e.g. ``<attribute_is path="outerElement/innerElement1" attribute="foo" text="bar" />`` ).]]>
           </xs:documentation>
         </xs:annotation>
       </xs:element>
       <xs:element name="attribute_matches" type="xs:anyType">
         <xs:annotation>
-          <xs:documentation><![CDATA[Asserts the XML ``attribute`` for the element (or tag) with the specified XPath-like ``path`` matches the regular expression specified by ``expression`` (e.g. ``<attribute_matches path="outerElement/innerElement2" attribute="foo2" expression="bar\d+" />``).]]></xs:documentation>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the XML ``attribute`` for the element (or tag) with the specified XPath-like ``path`` matches the regular expression specified by ``expression`` (e.g. ``<attribute_matches path="outerElement/innerElement2" attribute="foo2" expression="bar\d+" />``).]]></xs:documentation>
         </xs:annotation>
       </xs:element>
       <xs:element name="element_text" type="xs:anyType">
         <xs:annotation>
-          <xs:documentation><![CDATA[This tag allows the developer to recurisively specify additional assertions as child elements about just the text contained in the element specified by the XPath-like ``path`` (e.g. ``<element_text path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def"><not_has_text text="EDK72998.1" /></element_text>``).]]></xs:documentation>
+          <xs:documentation xml:lang="en"><![CDATA[This tag allows the developer to recurisively specify additional assertions as child elements about just the text contained in the element specified by the XPath-like ``path`` (e.g. ``<element_text path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def"><not_has_text text="EDK72998.1" /></element_text>``).]]></xs:documentation>
         </xs:annotation>
       </xs:element>
       <xs:element name="has_h5_keys" type="AssertHasH5Keys">
@@ -1993,7 +2025,7 @@ module.
       </xs:element>
       <xs:element name="has_size" type="xs:anyType">
         <xs:annotation>
-          <xs:documentation><![CDATA[Asserts the output has a size (in bytes) of the specified ``value``; if the size is allowed to deviate from this value, the maximum difference can be optionally specified with ``delta`` (e.g. ``<has_size value="10000" delta="100">``).]]>
+          <xs:documentation xml:lang="en"><![CDATA[Asserts the output has a size (in bytes) of the specified ``value``; if the size is allowed to deviate from this value, the maximum difference can be optionally specified with ``delta`` (e.g. ``<has_size value="10000" delta="100">``).]]>
           </xs:documentation>
         </xs:annotation>
       </xs:element>
@@ -2199,21 +2231,21 @@ between paired inputs of single stranded inputs.
         </xs:attribute>
         <xs:attribute name="value_from" type="xs:string">
           <xs:annotation>
-            <xs:documentation><![CDATA[Infrequently used option to dynamically access Galaxy internals, this should be avoided.
+            <xs:documentation xml:lang="en"><![CDATA[Infrequently used option to dynamically access Galaxy internals, this should be avoided.
 
 Galaxy method to execute.]]></xs:documentation>
           </xs:annotation>
         </xs:attribute>
         <xs:attribute name="value_ref" type="xs:string">
           <xs:annotation>
-            <xs:documentation><![CDATA[Infrequently used option to dynamically access Galaxy internals, this should be avoided.
+            <xs:documentation xml:lang="en"><![CDATA[Infrequently used option to dynamically access Galaxy internals, this should be avoided.
 
 Referenced parameter to pass method.]]></xs:documentation>
           </xs:annotation>
         </xs:attribute>
         <xs:attribute name="value_ref_in_group" type="PermissiveBoolean">
           <xs:annotation>
-            <xs:documentation><![CDATA[Infrequently used option to dynamically access Galaxy internals, this should be avoided.
+            <xs:documentation xml:lang="en"><![CDATA[Infrequently used option to dynamically access Galaxy internals, this should be avoided.
 
 Is referenced parameter is the same group.]]></xs:documentation>
           </xs:annotation>
@@ -2383,8 +2415,8 @@ The XML configuration is relatively trivial for sections:
 
 ```xml
 <inputs>
-    <section name="adv" title="Advanced Options" expanded="false">
-        <param name="plot_color" type="color" label="Track color" />
+    <section name="section_name" title="Section Title" >
+        <param name="parameter_name" type="text" label="A parameter  label" />
     </section>
 </inputs>
 ```
@@ -2393,7 +2425,44 @@ In your command template, you'll need to include the section name to access the
 variable:
 
 ```
---color $adv.plot_color
+$section_name.parameter_name
+```
+
+In output filters sections are represented as dictionary with the same name as the section:
+
+```
+<filter>section_name['parameter_name']</filter>
+```
+
+In order to reference parameters in sections from tags in the `<outputs>` section, e.g. in the `format_source` attribute of `<data>` tags, the syntax is:
+
+```
+<data name="output" format_source="section_name|parameter_name" metadata_source="section_name|parameter_name"/>
+```
+
+Until profile 21.01 `parameter_name` was sufficient (https://github.com/galaxyproject/galaxy/pull/9493/files).
+
+Note that references to other parameters in the `<inputs>` section are only possible if the reference is in the same section or its parents (and is defined earlier), therefore only `parameter_name` is used.
+
+```
+    <param name="foo" type="data" format="tabular"/>
+    <param name="bar" type="data_column" data_ref="foo"/>
+    <section>
+        <param name="qux" type="data_column" data_ref="foo"/>
+        <param name="foo" type="data" format="tabular"/>
+        <param name="baz" type="data_column" data_ref="foo"/>
+    </section>
+```
+
+In the above example `bar` and `qux` will refer to the first foo outside of the section and `baz` to the `foo` inside the section. This illustrates why non-unique parameter names are strongly discouraged. 
+
+The following will not work:
+
+```
+    <section>
+        <param name="foo" type="data" format="tabular"/>
+    </section>
+    <param name="bar" type="data_column" data_ref="foo"/>
 ```
 
 Further examples can be found in the [test case](https://github.com/galaxyproject/galaxy/blob/master/test/functional/tools/section.xml) from [pull request #35](https://github.com/galaxyproject/galaxy/pull/35).
@@ -3124,12 +3193,12 @@ The ``detect_errors`` attribute of ``command``, if present, loads a preset of er
         </xs:attribute>
         <xs:attribute name="oom_exit_code" type="xs:integer">
           <xs:annotation>
-            <xs:documentation>Only used if ``detect_errors="exit_code"``, tells Galaxy the specified exit code indicates an out of memory error. Galaxy instances may be configured to retry such jobs on resources with more memory.</xs:documentation>
+            <xs:documentation xml:lang="en">Only used if ``detect_errors="exit_code"``, tells Galaxy the specified exit code indicates an out of memory error. Galaxy instances may be configured to retry such jobs on resources with more memory.</xs:documentation>
           </xs:annotation>
         </xs:attribute>
         <xs:attribute name="use_shared_home" type="xs:string">
           <xs:annotation>
-            <xs:documentation>When running a job for this tool, do not isolate its ``$HOME`` directory within the job's directory - use either the ``shared_home_dir`` setting in Galaxy or the default ``$HOME`` specified in the job's default environment.</xs:documentation>
+            <xs:documentation xml:lang="en">When running a job for this tool, do not isolate its ``$HOME`` directory within the job's directory - use either the ``shared_home_dir`` setting in Galaxy or the default ``$HOME`` specified in the job's default environment.</xs:documentation>
           </xs:annotation>
         </xs:attribute>
         <xs:attribute name="interpreter" type="xs:string" gxdocs:deprecated="true">
@@ -3158,7 +3227,7 @@ of "type" specified for this expression block.
       <xs:extension base="xs:string">
         <xs:attribute name="type" type="ExpressionType">
           <xs:annotation>
-            <xs:documentation>Type of expression defined by this expression block. The only current valid option is ecma5.1 - which will evaluate the expression in a sandbox using node. The option still must be specified to allow a different default in the future.</xs:documentation>
+            <xs:documentation xml:lang="en">Type of expression defined by this expression block. The only current valid option is ecma5.1 - which will evaluate the expression in a sandbox using node. The option still must be specified to allow a different default in the future.</xs:documentation>
           </xs:annotation>
         </xs:attribute>
       </xs:extension>
@@ -4436,6 +4505,7 @@ parameters appear as booleans, not the value of their ``truevalue`` and
 appear as ``$options.selection_mode`` in Cheetah. Similarly ``options["vcf_output"]``
 would appear as ``$options.vcf_output`` having the values ``'--vcf'`` when true and
 ``''`` when false in Cheetah.
+Note that also parameters in sections are accessed via a dictionary.
 
 ### Example
 
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index d2e12068563..1a9d6c20d77 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -55,6 +55,7 @@ from galaxy.tools.actions.data_manager import DataManagerToolAction
 from galaxy.tools.actions.data_source import DataSourceToolAction
 from galaxy.tools.actions.model_operations import ModelOperationToolAction
 from galaxy.tools.cache import ToolDocumentCache
+from galaxy.tools.imp_exp import JobImportHistoryArchiveWrapper
 from galaxy.tools.parameters import (
     check_param,
     params_from_strings,
@@ -304,13 +305,14 @@ class ToolBox(BaseGalaxyToolBox):
         return self._tools_by_id
 
     def get_cache_region(self, tool_cache_data_dir):
-        if tool_cache_data_dir not in self.cache_regions:
-            self.cache_regions[tool_cache_data_dir] = ToolDocumentCache(cache_dir=tool_cache_data_dir)
-        return self.cache_regions[tool_cache_data_dir]
+        if self.app.config.enable_tool_document_cache:
+            if tool_cache_data_dir not in self.cache_regions:
+                self.cache_regions[tool_cache_data_dir] = ToolDocumentCache(cache_dir=tool_cache_data_dir)
+            return self.cache_regions[tool_cache_data_dir]
 
     def create_tool(self, config_file, tool_cache_data_dir=None, **kwds):
         cache = self.get_cache_region(tool_cache_data_dir or self.app.config.tool_cache_data_dir)
-        if config_file.endswith('.xml') and not cache.disabled:
+        if config_file.endswith('.xml') and cache and not cache.disabled:
             tool_document = cache.get(config_file)
             if tool_document:
                 tool_source = self.get_expanded_tool_source(
@@ -1117,7 +1119,7 @@ class Tool(Dictifiable):
 
     def parse_inputs(self, tool_source):
         """
-        Parse the "<inputs>" element and create appropriate `ToolParameter`s.
+        Parse the "<inputs>" element and create appropriate `ToolParameter` s.
         This implementation supports multiple pages and grouping constructs.
         """
         # Load parameters (optional)
@@ -2181,26 +2183,26 @@ class Tool(Dictifiable):
 
         # update tool model
         tool_model.update({
-            'id'            : self.id,
-            'help'          : tool_help,
-            'citations'     : bool(self.citations),
-            'sharable_url'  : self.sharable_url,
-            'message'       : tool_message,
-            'warnings'      : tool_warnings,
-            'versions'      : self.tool_versions,
-            'requirements'  : [{'name' : r.name, 'version' : r.version} for r in self.requirements],
-            'errors'        : state_errors,
-            'tool_errors'   : self.tool_errors,
-            'state_inputs'  : params_to_strings(self.inputs, state_inputs, self.app, use_security=True, nested=True),
-            'job_id'        : trans.security.encode_id(job.id) if job else None,
-            'job_remap'     : job.remappable() if job else None,
-            'history_id'    : trans.security.encode_id(history.id) if history else None,
-            'display'       : self.display_interface,
-            'action'        : action,
-            'license'       : self.license,
-            'creator'       : self.creator,
-            'method'        : self.method,
-            'enctype'       : self.enctype
+            'id': self.id,
+            'help': tool_help,
+            'citations': bool(self.citations),
+            'sharable_url': self.sharable_url,
+            'message': tool_message,
+            'warnings': tool_warnings,
+            'versions': self.tool_versions,
+            'requirements': [{'name': r.name, 'version': r.version} for r in self.requirements],
+            'errors': state_errors,
+            'tool_errors': self.tool_errors,
+            'state_inputs': params_to_strings(self.inputs, state_inputs, self.app, use_security=True, nested=True),
+            'job_id': trans.security.encode_id(job.id) if job else None,
+            'job_remap': job.remappable() if job else None,
+            'history_id': trans.security.encode_id(history.id) if history else None,
+            'display': self.display_interface,
+            'action': action,
+            'license': self.license,
+            'creator': self.creator,
+            'method': self.method,
+            'enctype': self.enctype
         })
         return tool_model
 
@@ -2649,6 +2651,12 @@ class ExportHistoryTool(Tool):
 class ImportHistoryTool(Tool):
     tool_type = 'import_history'
 
+    def exec_after_process(self, app, inp_data, out_data, param_dict, job, final_job_state=None, **kwds):
+        super().exec_after_process(app, inp_data, out_data, param_dict, job=job, **kwds)
+        if final_job_state != DETECTED_JOB_STATE.OK:
+            return
+        JobImportHistoryArchiveWrapper(self.app, job.id).cleanup_after_job()
+
 
 class InteractiveTool(Tool):
     tool_type = 'interactive'
@@ -2728,17 +2736,18 @@ class DataManagerTool(OutputParameterJSONTool):
                     history = None
         return history
 
-    def allow_user_access(self, user, attempting_access=True):
-        """
+    def allow_user_access(self, user, attempting_access=True) -> bool:
+        """Check user access to this tool.
+
         :param user: model object representing user.
         :type user: galaxy.model.User
         :param attempting_access: is the user attempting to do something with the
-                               the tool (set false for incidental checks like toolbox
-                               listing)
+                                  the tool (set false for incidental checks like toolbox
+                                  listing)
         :type attempting_access:  bool
 
-        :returns: bool -- Whether the user is allowed to access the tool.
-        Data Manager tools are only accessible to admins.
+        :returns: Whether the user is allowed to access the tool.
+                  Data Manager tools are only accessible to admins.
         """
         if super().allow_user_access(user) and self.app.config.is_admin_user(user):
             return True
diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 015a7b93ed5..f2b98a2489f 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -467,7 +467,7 @@ class DefaultToolAction:
             return data
 
         for name, output in tool.outputs.items():
-            if not filter_output(output, incoming):
+            if not filter_output(tool, output, incoming):
                 handle_output_timer = ExecutionTimer()
                 if output.collection:
                     if completed_job and dataset_collection_elements and name in dataset_collection_elements:
@@ -785,11 +785,13 @@ class DefaultToolAction:
         """
         This allows to map names of input files to metadata default values. Example:
 
-        <data format="tabular" name="output" label="Tabular output, aggregates data from individual_inputs" >
-            <actions>
-                <action name="column_names" type="metadata" default="${','.join(input.name for input in $individual_inputs)}" />
-            </actions>
-        </data>
+        .. code-block::
+
+            <data format="tabular" name="output" label="Tabular output, aggregates data from individual_inputs" >
+                <actions>
+                    <action name="column_names" type="metadata" default="${','.join(input.name for input in $individual_inputs)}" />
+                </actions>
+            </data>
         """
         if output.actions:
             for action in output.actions.actions:
@@ -942,13 +944,13 @@ def on_text_for_names(input_names):
     return on_text
 
 
-def filter_output(output, incoming):
+def filter_output(tool, output, incoming):
     for filter in output.filters:
         try:
             if not eval(filter.text.strip(), globals(), incoming):
                 return True  # do not create this dataset
         except Exception as e:
-            log.debug('Dataset output filter failed: %s' % e)
+            log.debug('Tool %s output %s: dataset output filter (%s) failed: %s' % (tool.id, output.name, filter.text, e))
     return False
 
 
diff --git a/lib/galaxy/tools/data/__init__.py b/lib/galaxy/tools/data/__init__.py
index 20dc67e7353..1f5f169d750 100644
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -264,7 +264,7 @@ class ToolDataTable:
         # increment this variable any time a new entry is added, or when the table is totally reloaded
         # This value has no external meaning, and does not represent an abstract version of the underlying data
         self._loaded_content_version = 1
-        self._load_info = ([config_element, tool_data_path], {'from_shed_config': from_shed_config, 'tool_data_path_files': self.tool_data_path_files, 'other_config_dict': other_config_dict})
+        self._load_info = ([config_element, tool_data_path], {'from_shed_config': from_shed_config, 'tool_data_path_files': self.tool_data_path_files, 'other_config_dict': other_config_dict, 'filename': filename})
         self._merged_load_info = []
 
     def _update_version(self, version=None):
@@ -315,7 +315,9 @@ class ToolDataTable:
 class TabularToolDataTable(ToolDataTable, Dictifiable):
     """
     Data stored in a tabular / separated value format on disk, allows multiple
-    files to be merged but all must have the same column definitions::
+    files to be merged but all must have the same column definitions:
+
+    .. code-block:: xml
 
         <table type="tabular" name="test">
             <column name='...' index = '...' />
@@ -798,13 +800,16 @@ class TabularToolDataField(Dictifiable):
 class RefgenieToolDataTable(TabularToolDataTable):
     """
     Data stored in refgenie
-    <table name="all_fasta" type="refgenie" asset="fasta" >
-        <file path="refgenie.yml" />
-        <field name="value" template="true">${__REFGENIE_UUID__}</field>
-        <field name="dbkey" template="true">${__REFGENIE_GENOME__}</field>
-        <field name="name" template="true">${__REFGENIE_DISPLAY_NAME__}</field>
-        <field name="path" template="true">${__REFGENIE_ASSET__}</field>
-    </table>
+
+    .. code-block:: xml
+
+        <table name="all_fasta" type="refgenie" asset="fasta" >
+            <file path="refgenie.yml" />
+            <field name="value" template="true">${__REFGENIE_UUID__}</field>
+            <field name="dbkey" template="true">${__REFGENIE_GENOME__}</field>
+            <field name="name" template="true">${__REFGENIE_DISPLAY_NAME__}</field>
+            <field name="path" template="true">${__REFGENIE_ASSET__}</field>
+        </table>
     """
     dict_collection_visible_keys = ['name']
 
diff --git a/lib/galaxy/tools/data/_schema.py b/lib/galaxy/tools/data/_schema.py
new file mode 100644
index 00000000000..f9eed32570d
--- /dev/null
+++ b/lib/galaxy/tools/data/_schema.py
@@ -0,0 +1,101 @@
+from typing import (
+    Dict,
+    List,
+)
+
+from pydantic import (
+    BaseModel,
+    Field,
+)
+
+
+class ToolDataEntry(BaseModel):
+    name: str = Field(
+        ...,  # Mark this field as required
+        title="Name",
+        description="The name of this tool data entry",
+        example="all_fasta",
+    )
+    model_class: str = Field(
+        ...,  # Mark this field as required
+        title="Model class",
+        description="The name of class modelling this tool data",
+        example="TabularToolDataTable",
+    )
+
+
+class ToolDataEntryList(BaseModel):
+    __root__: List[ToolDataEntry] = Field(
+        title="A list with details on individual data tables.",
+    )
+
+
+class ToolDataDetails(ToolDataEntry):
+    columns: List[str] = Field(
+        ...,  # Mark this field as required
+        title="Columns",
+        description="A list of column names",
+        example=[
+            "value",
+            "dbkey",
+            "name",
+            "path"
+        ],
+    )
+    # We must use an alias since the name 'fields'
+    # shadows a BaseModel attribute
+    fields_value: List[List[str]] = Field(
+        alias='fields',
+        default=[],
+        title="Fields",
+        description="",  # TODO add documentation
+    )
+
+
+class ToolDataField(BaseModel):
+    name: str = Field(
+        ...,  # Mark this field as required
+        title="Name",
+        description="The name of the field",
+    )
+    model_class: str = Field(
+        ...,  # Mark this field as required
+        title="Model class",
+        description="The name of class modelling this tool data field",
+        example="TabularToolDataField",
+    )
+    # We must use an alias since the name 'fields'
+    # shadows a BaseModel attribute
+    fields_value: Dict[str, str] = Field(
+        ...,  # Mark this field as required
+        alias='fields',
+        title="Fields",
+        description="",  # TODO add documentation
+    )
+    base_dir: List[str] = Field(
+        ...,  # Mark this field as required
+        title="Base directories",
+        description="A list of directories where the data files are stored",
+    )
+    files: Dict[str, int] = Field(
+        ...,  # Mark this field as required
+        title="Files",
+        description="A dictionary of file names and their size in bytes",
+        example={"file.txt": 136},
+    )
+    fingerprint: str = Field(
+        ...,  # Mark this field as required
+        title="Fingerprint",
+        description="SHA1 Hash",
+        example="22b45237a85c2b3f474bf66888c534387ffe0ced",
+    )
+
+
+class ToolDataItem(BaseModel):
+    values: str = Field(
+        ...,  # Mark this field as required
+        title="Values",
+        description=("A `\\t` (TAB) separated list of column __contents__."
+        " You must specify a value for each of the columns of the data table."),
+        example="value\tdbkey\tname\tpath",
+    )
diff --git a/lib/galaxy/tools/data_fetch.py b/lib/galaxy/tools/data_fetch.py
index 9ecfc29f010..2a571be51ce 100644
--- a/lib/galaxy/tools/data_fetch.py
+++ b/lib/galaxy/tools/data_fetch.py
@@ -451,7 +451,7 @@ class UploadConfig:
         self.registry = registry
         self.working_directory = working_directory
         self.allow_failed_collections = allow_failed_collections
-        self.check_content = request.get("check_content" , True)
+        self.check_content = request.get("check_content", True)
         self.to_posix_lines = request.get("to_posix_lines", False)
         self.space_to_tab = request.get("space_to_tab", False)
         self.auto_decompress = request.get("auto_decompress", False)
diff --git a/lib/galaxy/tools/error_reports/plugins/json.py b/lib/galaxy/tools/error_reports/plugins/json.py
index a69a2c715b8..d9b4c1f9061 100644
--- a/lib/galaxy/tools/error_reports/plugins/json.py
+++ b/lib/galaxy/tools/error_reports/plugins/json.py
@@ -31,11 +31,11 @@ class JsonPlugin(ErrorPlugin):
         path = os.path.join(self.report_directory, str(dataset.id))
         with open(path, 'w') as handle:
             data = {
-                'info' : job.info,
-                'id' : job.id,
-                'command_line' : job.command_line,
+                'info': job.info,
+                'id': job.id,
+                'command_line': job.command_line,
                 'destination_id': job.destination_id,
-                'stderr' : job.stderr,
+                'stderr': job.stderr,
                 'traceback': job.traceback,
                 'exit_code': job.exit_code,
                 'stdout': job.stdout,
diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py
index cfd97a7d07e..ef49531e11c 100644
--- a/lib/galaxy/tools/execute.py
+++ b/lib/galaxy/tools/execute.py
@@ -107,10 +107,11 @@ def execute(trans, tool, mapping_params, history, rerun_remap_job_id=None, colle
     else:
         # Make sure collections, implicit jobs etc are flushed even if there are no precreated output datasets
         trans.sa_session.flush()
+    tool_id = tool.id
     for job in execution_tracker.successful_jobs:
         # Put the job in the queue if tracking in memory
         tool.app.job_manager.enqueue(job, tool=tool, flush=False)
-        trans.log_event("Added job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id)
+        trans.log_event("Added job to the job queue, id: %s" % str(job.id), tool_id=tool_id)
     trans.sa_session.flush()
 
     if has_remaining_jobs:
@@ -286,7 +287,7 @@ class ExecutionTracker:
 
         implicit_collection_jobs = model.ImplicitCollectionJobs()
         for output_name, output in self.tool.outputs.items():
-            if filter_output(output, self.example_params):
+            if filter_output(self.tool, output, self.example_params):
                 continue
             output_collection_name = self.output_name(trans, history, params, output)
             effective_structure = self._mapped_output_structure(trans, output)
diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py
index c9750b83dd1..26ea6c058a8 100644
--- a/lib/galaxy/tools/parameters/__init__.py
+++ b/lib/galaxy/tools/parameters/__init__.py
@@ -117,14 +117,14 @@ def visit_input_values(inputs, input_values, callback, name_prefix='', label_pre
     def callback_helper(input, input_values, name_prefix, label_prefix, parent_prefix, context=None, error=None):
         value = input_values.get(input.name)
         args = {
-            'input'             : input,
-            'parent'            : input_values,
-            'value'             : value,
-            'prefixed_name'     : f'{name_prefix}{input.name}',
-            'prefixed_label'    : '{}{}'.format(label_prefix, input.label or input.name),
-            'prefix'            : parent_prefix,
-            'context'           : context,
-            'error'             : error
+            'input': input,
+            'parent': input_values,
+            'value': value,
+            'prefixed_name': f'{name_prefix}{input.name}',
+            'prefixed_label': '{}{}'.format(label_prefix, input.label or input.name),
+            'prefix': parent_prefix,
+            'context': context,
+            'error': error
         }
         if input.name not in input_values:
             args['error'] = 'No value found for \'%s\'.' % args.get('prefixed_label')
@@ -401,7 +401,7 @@ def _populate_state_legacy(request_context, inputs, incoming, state, errors, pre
                 if not any(incoming_key.startswith(rep_prefix) for incoming_key in incoming.keys()) and rep_index >= input.min:
                     break
                 if rep_index < input.max:
-                    new_state = {'__index__' : rep_index}
+                    new_state = {'__index__': rep_index}
                     group_state.append(new_state)
                     _populate_state_legacy(request_context, input.inputs, incoming, new_state, errors, prefix=rep_prefix + '|', context=context, check=check, simple_errors=simple_errors)
                 rep_index += 1
@@ -430,7 +430,7 @@ def _populate_state_legacy(request_context, inputs, incoming, state, errors, pre
             while len(group_state) > file_count:
                 del group_state[-1]
             while file_count > len(group_state):
-                new_state = {'__index__' : len(group_state)}
+                new_state = {'__index__': len(group_state)}
                 for upload_item in input.inputs.values():
                     new_state[upload_item.name] = upload_item.get_initial_value(request_context, context)
                 group_state.append(new_state)
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 4fe24d9c4b3..b81d41d6a45 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -21,7 +21,6 @@ from galaxy.util import (
     unicodify,
     XML,
 )
-from galaxy.util.bunch import Bunch
 from galaxy.util.dictifiable import Dictifiable
 from galaxy.util.expressions import ExpressionContext
 from galaxy.util.rules_dsl import RuleSet
@@ -38,7 +37,12 @@ from .sanitize import ToolParameterSanitizer
 
 log = logging.getLogger(__name__)
 
-workflow_building_modes = Bunch(DISABLED=False, ENABLED=True, USE_HISTORY=1)
+
+class workflow_building_modes:
+    DISABLED = False
+    ENABLED = True
+    USE_HISTORY = 1
+
 
 WORKFLOW_PARAMETER_REGULAR_EXPRESSION = re.compile(r'\$\{.+?\}')
 
@@ -58,8 +62,8 @@ def contains_workflow_parameter(value, search=False):
 
 
 def is_runtime_value(value):
-    return isinstance(value, RuntimeValue) or (isinstance(value, dict) and
-        value.get("__class__") in ["RuntimeValue", "ConnectedValue"])
+    return isinstance(value, RuntimeValue) or (isinstance(value, dict)
+        and value.get("__class__") in ["RuntimeValue", "ConnectedValue"])
 
 
 def is_runtime_context(trans, other_values):
@@ -70,8 +74,8 @@ def is_runtime_context(trans, other_values):
             return True
         for v in util.listify(context_value):
             if isinstance(v, trans.app.model.HistoryDatasetAssociation) and \
-                    ((hasattr(v, 'state') and v.state != galaxy.model.Dataset.states.OK) or
-                    hasattr(v, 'implicit_conversion')):
+                    ((hasattr(v, 'state') and v.state != galaxy.model.Dataset.states.OK)
+                    or hasattr(v, 'implicit_conversion')):
                 return True
     return False
 
@@ -878,17 +882,16 @@ class SelectToolParameter(ToolParameter):
             return self.static_options
 
     def get_legal_values(self, trans, other_values):
-        if self.options:
-            return {v for _, v, _ in self.options.get_options(trans, other_values)}
-        elif self.dynamic_options:
-            try:
-                call_other_values = self._get_dynamic_options_call_other_values(trans, other_values)
-                return {v for _, v, _ in eval(self.dynamic_options, self.tool.code_namespace, call_other_values)}
-            except Exception as e:
-                log.debug("Determining legal values failed for '%s': %s", self.name, unicodify(e))
-                return set()
-        else:
-            return self.legal_values
+        """
+        determine the set of values of legal options
+        """
+        return {v for _, v, _ in self.get_options(trans, other_values)}
+
+    def get_legal_names(self, trans, other_values):
+        """
+        determine a mapping from names to values for all legal options
+        """
+        return {n: v for n, v, _ in self.get_options(trans, other_values)}
 
     def from_json(self, value, trans, other_values=None, require_legal_value=True):
         other_values = other_values or {}
@@ -896,6 +899,11 @@ class SelectToolParameter(ToolParameter):
             legal_values = self.get_legal_values(trans, other_values)
         except ImplicitConversionRequired:
             return value
+        # if the given value is not found in the set of values of the legal
+        # options we fall back to check if the value is in the set of names of
+        # the legal options. this is done with the fallback_values dict which
+        # allows to determine the corresponding legal values
+        fallback_values = self.get_legal_names(trans, other_values)
         if (not legal_values or not require_legal_value) and is_runtime_context(trans, other_values):
             if self.multiple:
                 # While it is generally allowed that a select value can be '',
@@ -924,12 +932,12 @@ class SelectToolParameter(ToolParameter):
         if isinstance(value, list):
             if not self.multiple:
                 raise ParameterValueError("multiple values provided but parameter is not expecting multiple values", self.name, is_dynamic=self.is_dynamic)
-            rval = []
-            for v in value:
-                if v not in legal_values:
-                    raise ParameterValueError("an invalid option ({!r}) was selected (valid options: {})".format(v, ",".join(legal_values)), self.name, v, is_dynamic=self.is_dynamic)
-                rval.append(v)
-            return rval
+            if set(value).issubset(legal_values):
+                return value
+            elif set(value).issubset(set(fallback_values.keys())):
+                return [fallback_values[v] for v in value]
+            else:
+                raise ParameterValueError("invalid options ({!r}) were selected (valid options: {})".format(",".join(set(value) - set(legal_values)), ",".join(legal_values)), self.name, is_dynamic=self.is_dynamic)
         else:
             value_is_none = (value == "None" and "None" not in legal_values)
             if value_is_none or not value:
@@ -940,9 +948,14 @@ class SelectToolParameter(ToolParameter):
                         raise ParameterValueError("no option was selected for non optional parameter", self.name, is_dynamic=self.is_dynamic)
             if is_runtime_value(value):
                 return None
-            if value not in legal_values and require_legal_value:
+            if value in legal_values:
+                return value
+            elif value in fallback_values:
+                return fallback_values[value]
+            elif not require_legal_value:
+                return value
+            else:
                 raise ParameterValueError("an invalid option ({!r}) was selected (valid options: {})".format(value, ",".join(legal_values)), self.name, value, is_dynamic=self.is_dynamic)
-            return value
 
     def to_param_dict_string(self, value, other_values=None):
         if value in (None, []):
@@ -1345,7 +1358,22 @@ class ColumnListParameter(SelectToolParameter):
     def get_legal_values(self, trans, other_values):
         if self.data_ref not in other_values:
             raise ValueError("Value for associated data reference not found (data_ref).")
-        return set(self.get_column_list(trans, other_values))
+        legal_values = self.get_column_list(trans, other_values)
+
+        value = other_values.get(self.name)
+        if value is not None and value not in legal_values and self.is_file_empty(trans, other_values):
+            legal_values.extend(value)
+
+        return set(legal_values)
+
+    def is_file_empty(self, trans, other_values):
+        for dataset in util.listify(other_values.get(self.data_ref)):
+            # Use representative dataset if a dataset collection is parsed
+            if isinstance(dataset, trans.app.model.HistoryDatasetCollectionAssociation):
+                dataset = dataset.to_hda_representative()
+            if is_runtime_value(dataset) or not dataset.has_data():
+                return True
+        return False
 
     def get_dependencies(self):
         return [self.data_ref]
diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py
index fda72b643fc..037a71e285b 100644
--- a/lib/galaxy/tools/parameters/grouping.py
+++ b/lib/galaxy/tools/parameters/grouping.py
@@ -433,8 +433,8 @@ class UploadDataset(Group):
                             if ftp_filename == filename:
                                 path = relpath(os.path.join(dirpath, filename), user_ftp_dir)
                                 if not os.path.islink(os.path.join(dirpath, filename)):
-                                    ftp_data_file = {'local_filename' : os.path.abspath(os.path.join(user_ftp_dir, path)),
-                                                     'filename' : os.path.basename(path)}
+                                    ftp_data_file = {'local_filename': os.path.abspath(os.path.join(user_ftp_dir, path)),
+                                                     'filename': os.path.basename(path)}
                                     purge = getattr(trans.app.config, 'ftp_upload_purge', True)
                                     file_bunch = get_data_file_filename(
                                         ftp_data_file,
@@ -530,8 +530,8 @@ class UploadDataset(Group):
                     log.warning('User passed an invalid file path in ftp_files: %s' % ftp_file)
                     continue
                     # TODO: warning to the user (could happen if file is already imported)
-                ftp_data_file = {'local_filename' : os.path.abspath(os.path.join(user_ftp_dir, ftp_file)),
-                                 'filename' : os.path.basename(ftp_file)}
+                ftp_data_file = {'local_filename': os.path.abspath(os.path.join(user_ftp_dir, ftp_file)),
+                                 'filename': os.path.basename(ftp_file)}
                 purge = getattr(trans.app.config, 'ftp_upload_purge', True)
                 file_bunch = get_data_file_filename(ftp_data_file, override_name=name, override_info=info, purge=purge)
                 if file_bunch.path:
diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index 8d14362f9f7..d4993c7ca28 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -150,7 +150,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         with open(self.app.config.beta_edam_toolbox_ontology_path, 'r') as handle:
             log.debug(f'Processing {handle}')
             self.edam = {}
-            for idx, line in enumerate(handle.readlines()):
+            for line in handle.readlines():
                 fields = line.split('\t')
                 if not fields[0].startswith('http://edamontology.org/'):
                     continue
@@ -432,11 +432,11 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                     log.warning("Could not find lineage for tool '%s'", tool.id)
                 if not inserted:
                     if (
-                        tool.guid is None or
-                        tool.tool_shed is None or
-                        tool.repository_name is None or
-                        tool.repository_owner is None or
-                        tool.installed_changeset_revision is None
+                        tool.guid is None
+                        or tool.tool_shed is None
+                        or tool.repository_name is None
+                        or tool.repository_owner is None
+                        or tool.installed_changeset_revision is None
                     ):
                         # We have a tool that was not installed from the Tool
                         # Shed, but is also not yet defined in
@@ -459,9 +459,9 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         edam = tool.edam_operations + tool.edam_topics
         if len(edam) > 0:
             for term in edam:
-                yield term, self.edam.get(term, {'label': f'Unknown EDAM Term {term}'})['label']
+                yield term
         else:
-            yield 'uncategorized', 'Uncategorized'
+            yield 'uncategorized'
 
     def _get_section(self, sec_id, sec_nm):
         if sec_id not in self._tool_panel:
@@ -503,7 +503,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                 tool_id = key.replace('tool_', '', 1)
                 if tool_id in self._tools_by_id:
                     if tool_id in self._tools_by_id:
-                        for term, label in self._get_edam_sec(val):
+                        for term in self._get_edam_sec(val):
                             if term == 'uncategorized':
                                 uncategorized.append((tool_id, key, val, val.name))
                             else:
@@ -528,7 +528,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                     if section_item_type == panel_item_types.TOOL:
                         tool_id = section_key.replace('tool_', '', 1)
                         if tool_id in self._tools_by_id:
-                            for term, label in self._get_edam_sec(section_val):
+                            for term in self._get_edam_sec(section_val):
                                 if term == 'uncategorized':
                                     uncategorized.append((tool_id, key, section_val, val.name))
                                 else:
diff --git a/lib/galaxy/tools/toolbox/integrated_panel.py b/lib/galaxy/tools/toolbox/integrated_panel.py
index b96a24a698a..5edcbcb1a0a 100644
--- a/lib/galaxy/tools/toolbox/integrated_panel.py
+++ b/lib/galaxy/tools/toolbox/integrated_panel.py
@@ -90,7 +90,7 @@ $INTEGRATED_TOOL_PANEL
                     section_name = item.name or ''
                     section_version = item.version or ''
                     integrated_tool_panel.append('    <section id="{}" name="{}" version="{}">\n'.format(escape(section_id), escape(section_name), section_version))
-                    for section_key, section_item_type, section_item in item.panel_items_iter():
+                    for _section_key, section_item_type, section_item in item.panel_items_iter():
                         if section_item_type == panel_item_types.TOOL:
                             if section_item:
                                 integrated_tool_panel.append('        <tool id="%s" />\n' % section_item.id)
@@ -104,7 +104,7 @@ $INTEGRATED_TOOL_PANEL
                                 label_version = section_item.version or ''
                                 integrated_tool_panel.append(f'        <label id="{label_id}" text="{label_text}" version="{label_version}" />\n')
                     integrated_tool_panel.append('    </section>\n')
-        tool_panel_description = '\n    '.join(l for l in INTEGRATED_TOOL_PANEL_DESCRIPTION.split("\n") if l)
+        tool_panel_description = '\n    '.join(line for line in INTEGRATED_TOOL_PANEL_DESCRIPTION.split("\n") if line)
         tp_string = template.substitute(INTEGRATED_TOOL_PANEL_DESCRIPTION=tool_panel_description,
                                         INTEGRATED_TOOL_PANEL='\n'.join(integrated_tool_panel))
         with RenamedTemporaryFile(filename, mode='w') as f:
diff --git a/lib/galaxy/tours/__init__.py b/lib/galaxy/tours/__init__.py
index 2239caf4804..b8549dc9a45 100644
--- a/lib/galaxy/tours/__init__.py
+++ b/lib/galaxy/tours/__init__.py
@@ -1,87 +1,17 @@
-"""
-This module manages loading/etc of Galaxy interactive tours.
-"""
-import logging
-import os
+from ._impl import build_tours_registry
+from ._interface import ToursRegistry
+from ._schema import Tour
+from ._schema import TourCore
+from ._schema import TourDetails
+from ._schema import TourList
+from ._schema import TourStep
 
-import yaml
-
-from galaxy import util
-
-log = logging.getLogger(__name__)
-
-
-def tour_loader(contents_dict):
-    #  Some of this can be done on the clientside.  Maybe even should?
-    title_default = contents_dict.get('title_default', None)
-    for step in contents_dict['steps']:
-        if 'intro' in step:
-            step['content'] = step.pop('intro')
-        if 'position' in step:
-            step['placement'] = step.pop('position')
-        if 'element' not in step:
-            step['orphan'] = True
-        if title_default and 'title' not in step:
-            step['title'] = title_default
-    return contents_dict
-
-
-class ToursRegistry:
-    def __init__(self, tour_directories):
-        self.tour_directories = util.config_directories_from_setting(tour_directories)
-        self.load_tours()
-
-    def tours_by_id_with_description(self):
-        return [{'id': k,
-                 'description': self.tours[k].get('description', None),
-                 'name': self.tours[k].get('name', None),
-                 'tags': self.tours[k].get('tags', None)}
-                for k in self.tours.keys()]
-
-    def load_tour(self, tour_id):
-        for tour_dir in self.tour_directories:
-            tour_path = os.path.join(tour_dir, tour_id + ".yaml")
-            if not os.path.exists(tour_path):
-                tour_path = os.path.join(tour_dir, tour_id + ".yml")
-            if os.path.exists(tour_path):
-                return self._load_tour_from_path(tour_path)
-
-    def load_tours(self):
-        self.tours = {}
-        for tour_dir in self.tour_directories:
-            for filename in os.listdir(tour_dir):
-                if self._is_yaml(filename):
-                    self._load_tour_from_path(os.path.join(tour_dir, filename))
-        return self.tours_by_id_with_description()
-
-    def reload_tour(self, path):
-        # We may safely assume that the path is within the tour directory
-        filename = os.path.basename(path)
-        if self._is_yaml(filename):
-            self._load_tour_from_path(path)
-
-    def tour_contents(self, tour_id):
-        # Extra format translation could happen here (like the previous intro_to_tour)
-        # For now just return the loaded contents.
-        return self.tours.get(tour_id, None)
-
-    def _is_yaml(self, filename):
-        return filename.endswith('.yaml') or filename.endswith('.yml')
-
-    def _load_tour_from_path(self, tour_path):
-        filename = os.path.basename(tour_path)
-        tour_id = os.path.splitext(filename)[0]
-        try:
-            with open(tour_path) as handle:
-                conf = yaml.safe_load(handle)
-                tour = tour_loader(conf)
-                self.tours[tour_id] = tour_loader(conf)
-                log.info("Loaded tour '%s'" % tour_id)
-                return tour
-        except OSError:
-            log.exception("Tour '%s' could not be loaded, error reading file.", tour_id)
-        except yaml.error.YAMLError:
-            log.exception("Tour '%s' could not be loaded, error within file.  Please check your yaml syntax.", tour_id)
-        except TypeError:
-            log.exception("Tour '%s' could not be loaded, error within file. Possibly spacing related. Please check your yaml syntax.", tour_id)
-        return None
+__all__ = [
+    'build_tours_registry',
+    'ToursRegistry',
+    'Tour',
+    'TourCore',
+    'TourDetails',
+    'TourList',
+    'TourStep'
+]
diff --git a/lib/galaxy/tours/_impl.py b/lib/galaxy/tours/_impl.py
new file mode 100644
index 00000000000..be413f9d498
--- /dev/null
+++ b/lib/galaxy/tours/_impl.py
@@ -0,0 +1,115 @@
+"""
+This module manages loading/etc of Galaxy interactive tours.
+"""
+import logging
+import os
+
+import yaml
+from pydantic import parse_obj_as
+
+from galaxy.util import config_directories_from_setting
+from ._interface import ToursRegistry
+from ._schema import TourList
+
+
+log = logging.getLogger(__name__)
+
+
+def build_tours_registry(tour_directories: str):
+    return ToursRegistryImpl(tour_directories)
+
+
+def load_tour_steps(contents_dict):
+    #  Some of this can be done on the clientside.  Maybe even should?
+    title_default = contents_dict.get('title_default')
+    for step in contents_dict['steps']:
+        if 'intro' in step:
+            step['content'] = step.pop('intro')
+        if 'position' in step:
+            step['placement'] = step.pop('position')
+        if 'element' not in step:
+            step['orphan'] = True
+        if title_default and 'title' not in step:
+            step['title'] = title_default
+
+
+@ToursRegistry.register
+class ToursRegistryImpl:
+
+    def __init__(self, tour_directories):
+        self.tour_directories = config_directories_from_setting(tour_directories)
+        self._extensions = ('.yml', '.yaml')
+        self._load_tours()
+
+    def get_tours(self):
+        """Return list of tours."""
+        tours = []
+        for k in self.tours.keys():
+            tourdata = {
+                'id': k,
+                'name': self.tours[k].get('name'),
+                'description': self.tours[k].get('description'),
+                'tags': self.tours[k].get('tags')
+            }
+            tours.append(tourdata)
+        return parse_obj_as(TourList, tours)
+
+    def tour_contents(self, tour_id):
+        """Return tour contents."""
+        # Extra format translation could happen here (like the previous intro_to_tour)
+        # For now just return the loaded contents.
+        return self.tours.get(tour_id)
+
+    def load_tour(self, tour_id):
+        """Reload tour and return its contents."""
+        tour_path = self._get_path_from_tour_id(tour_id)
+        self._load_tour_from_path(tour_path)
+        return self.tours.get(tour_id)
+
+    def reload_tour(self, path):
+        """Reload tour."""
+        # We may safely assume that the path is within the tour directory
+        filename = os.path.basename(path)
+        if self._is_yaml(filename):
+            self._load_tour_from_path(path)
+
+    def _load_tours(self):
+        self.tours = {}
+        for tour_dir in self.tour_directories:
+            for filename in os.listdir(tour_dir):
+                if self._is_yaml(filename):
+                    tour_path = os.path.join(tour_dir, filename)
+                    self._load_tour_from_path(tour_path)
+
+    def _is_yaml(self, filename):
+        for ext in self._extensions:
+            if filename.endswith(ext):
+                return True
+
+    def _load_tour_from_path(self, tour_path):
+        tour_id = self._get_tour_id_from_path(tour_path)
+        try:
+            with open(tour_path) as f:
+                tour = yaml.safe_load(f)
+                load_tour_steps(tour)
+                self.tours[tour_id] = tour
+                log.info("Loaded tour '%s'" % tour_id)
+        except OSError:
+            log.exception("Tour '%s' could not be loaded, error reading file." % tour_id)
+        except yaml.error.YAMLError:
+            log.exception("Tour '%s' could not be loaded, error within file."
+                " Please check your yaml syntax." % tour_id)
+        except TypeError:
+            log.exception("Tour '%s' could not be loaded, error within file."
+                " Possibly spacing related. Please check your yaml syntax." % tour_id)
+
+    def _get_tour_id_from_path(self, tour_path):
+        filename = os.path.basename(tour_path)
+        return os.path.splitext(filename)[0]
+
+    def _get_path_from_tour_id(self, tour_id):
+        for tour_dir in self.tour_directories:
+            for ext in self._extensions:
+                tour_path = os.path.join(tour_dir, tour_id + ext)
+                if os.path.exists(tour_path):
+                    return tour_path
diff --git a/lib/galaxy/tours/_interface.py b/lib/galaxy/tours/_interface.py
new file mode 100644
index 00000000000..33cd2f76168
--- /dev/null
+++ b/lib/galaxy/tours/_interface.py
@@ -0,0 +1,21 @@
+from abc import ABC, abstractmethod
+
+from ._schema import (
+    TourDetails,
+    TourList,
+)
+
+
+class ToursRegistry(ABC):
+
+    @abstractmethod
+    def get_tours(self) -> TourList:
+        """Return list of tours."""
+
+    @abstractmethod
+    def tour_contents(self, tour_id: str) -> TourDetails:
+        """Return tour contents."""
+
+    @abstractmethod
+    def load_tour(self, tour_id: str) -> TourDetails:
+        """Reload tour and return its contents."""
diff --git a/lib/galaxy/tours/_schema.py b/lib/galaxy/tours/_schema.py
new file mode 100644
index 00000000000..bf5d1274fef
--- /dev/null
+++ b/lib/galaxy/tours/_schema.py
@@ -0,0 +1,82 @@
+from typing import (
+    List,
+    Optional,
+)
+
+from pydantic import BaseModel, Field
+
+
+class TourCore(BaseModel):
+    name: str = Field(
+        title='Name',
+        description='Name of tour'
+    )
+    description: str = Field(
+        title='Description',
+        description='Tour description'
+    )
+    tags: List[str] = Field(
+        title='Tags',
+        description='Topic topic tags'
+    )
+
+
+class Tour(TourCore):
+    id: str = Field(
+        title='Identifier',
+        description='Tour identifier'
+    )
+
+
+class TourList(BaseModel):
+    __root__: List[Tour] = Field(
+        title='List of tours',
+        default=[]
+    )
+
+
+class TourStep(BaseModel):
+    title: Optional[str] = Field(
+        title='Title',
+        description='Title displayed in the header of the step container'
+    )
+    content: Optional[str] = Field(
+        title='Content',
+        description='Text shown to the user'
+    )
+    element: Optional[str] = Field(
+        title='Element',
+        description='JQuery selector for the element to be described/clicked'
+    )
+    placement: Optional[str] = Field(
+        title='Placement',
+        description='Placement of the text box relative to the selected element'
+    )
+    preclick: Optional[list] = Field(
+        title='Pre-click',
+        description='Elements that receive a click() event before the step is shown'
+    )
+    postclick: Optional[list] = Field(
+        title='Post-click',
+        description='Elements that receive a click() event after the step is shown'
+    )
+    textinsert: Optional[str] = Field(
+        title='Text-insert',
+        description='Text to insert if element is a text box (e.g. tool search or upload)'
+    )
+    backdrop: Optional[bool] = Field(
+        title='Backdrop',
+        description=('Show a dark backdrop behind the popover and its element,'
+            'highlighting the current step')
+    )
+
+
+class TourDetails(TourCore):
+    title_default: Optional[str] = Field(
+        title='Default title',
+        description='Default title for each step'
+    )
+    steps: List[TourStep] = Field(
+        title='Steps',
+        description='Tour steps'
+    )
diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index e65c00dc1f2..0e34ff70a9a 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -159,13 +159,13 @@ def directory_hash_id(id):
     ['1', '3', '5']
     """
     s = str(id)
-    l = len(s)
+    len_s = len(s)
     # Shortcut -- ids 0-999 go under ../000/
-    if l < 4:
+    if len_s < 4:
         return ["000"]
     if not is_uuid(s):
         # Pad with zeros until a multiple of three
-        padded = ((3 - len(s) % 3) * "0") + s
+        padded = ((3 - len_s % 3) * "0") + s
         # Drop the last three digits -- 1000 files per directory
         padded = padded[:-3]
         # Break into chunks of three
diff --git a/lib/galaxy/util/form_builder.py b/lib/galaxy/util/form_builder.py
index f2ec106d7cf..758af3c3599 100644
--- a/lib/galaxy/util/form_builder.py
+++ b/lib/galaxy/util/form_builder.py
@@ -25,12 +25,12 @@ class BaseField:
 
     def to_dict(self):
         return {
-            'name'      : self.name,
-            'label'     : self.label,
-            'disabled'  : self.disabled,
-            'optional'  : self.optional,
-            'value'     : self.value,
-            'help'      : self.help
+            'name': self.name,
+            'label': self.label,
+            'disabled': self.disabled,
+            'optional': self.optional,
+            'value': self.value,
+            'help': self.help
         }
 
 
diff --git a/lib/galaxy/util/json.py b/lib/galaxy/util/json.py
index 1acc9e55146..245da0858fe 100644
--- a/lib/galaxy/util/json.py
+++ b/lib/galaxy/util/json.py
@@ -1,4 +1,3 @@
-import copy
 import json
 import logging
 import math
@@ -70,7 +69,7 @@ def safe_dumps(*args, **kwargs):
     try:
         dumped = json.dumps(*args, allow_nan=False, **kwargs)
     except ValueError:
-        obj = swap_inf_nan(copy.deepcopy(args[0]))
+        obj = swap_inf_nan(args[0])
         dumped = json.dumps(obj, allow_nan=False, **kwargs)
     if kwargs.get('escape_closing_tags', True):
         return dumped.replace('</', '<\\/')
diff --git a/lib/galaxy/util/pastescript/loadwsgi.py b/lib/galaxy/util/pastescript/loadwsgi.py
index f0a8dc57d1f..f7a7226864c 100644
--- a/lib/galaxy/util/pastescript/loadwsgi.py
+++ b/lib/galaxy/util/pastescript/loadwsgi.py
@@ -54,9 +54,9 @@ def fix_type_error(exc_info, callable, varargs, kwargs):
     """
     if exc_info is None:
         exc_info = sys.exc_info()
-    if (exc_info[0] != TypeError or
-            str(exc_info[1]).find('argument') == -1 or
-            getattr(exc_info[1], '_type_error_fixed', False)):
+    if (exc_info[0] != TypeError
+            or str(exc_info[1]).find('argument') == -1
+            or getattr(exc_info[1], '_type_error_fixed', False)):
         return exc_info
     exc_info[1]._type_error_fixed = True
     argspec = inspect.formatargspec(*getfullargspec(callable))
diff --git a/lib/galaxy/util/pastescript/serve.py b/lib/galaxy/util/pastescript/serve.py
index 6e40b099fca..a30fca3f032 100644
--- a/lib/galaxy/util/pastescript/serve.py
+++ b/lib/galaxy/util/pastescript/serve.py
@@ -514,8 +514,8 @@ class ServeCommand(Command):
                 cmd = None
                 restvars = self.args[:]
 
-        if (getattr(self.options, 'daemon', False) and
-                getattr(self.options, 'reload', False)):
+        if (getattr(self.options, 'daemon', False)
+                and getattr(self.options, 'reload', False)):
             raise BadCommand('The --daemon and --reload options may not be used together')
 
         jython_monitor = False
@@ -1025,8 +1025,8 @@ commands = {
 
 
 def run(args=None):
-    if (not args and len(sys.argv) >= 2 and os.environ.get('_') and
-            sys.argv[0] != os.environ['_'] and os.environ['_'] == sys.argv[1]):
+    if (not args and len(sys.argv) >= 2 and os.environ.get('_')
+            and sys.argv[0] != os.environ['_'] and os.environ['_'] == sys.argv[1]):
         # probably it's an exe execution
         args = ['exe', os.environ['_']] + sys.argv[2:]
     if args is None:
diff --git a/lib/galaxy/util/properties.py b/lib/galaxy/util/properties.py
index 76c4557ba47..535426872b5 100644
--- a/lib/galaxy/util/properties.py
+++ b/lib/galaxy/util/properties.py
@@ -142,6 +142,7 @@ class NicerConfigParser(ConfigParser):
             self._interpolation = self.InterpolateWrapper(self._interpolation)
 
     read_file = getattr(ConfigParser, 'read_file', ConfigParser.readfp)
+    read_file.__doc__ = ""
 
     def defaults(self):
         """Return the defaults, with their values interpolated (with the
diff --git a/lib/galaxy/util/tool_shed/common_util.py b/lib/galaxy/util/tool_shed/common_util.py
index 846b121247d..0593cd5e51e 100644
--- a/lib/galaxy/util/tool_shed/common_util.py
+++ b/lib/galaxy/util/tool_shed/common_util.py
@@ -155,9 +155,9 @@ def get_non_shed_tool_panel_configs(app):
         try:
             tree, error_message = xml_util.parse_xml(config_filename)
         except OSError as exc:
-            if (config_filename == app.config.shed_tool_conf and not
-                    app.config.shed_tool_conf_set and
-                    exc.errno == errno.ENOENT):
+            if (config_filename == app.config.shed_tool_conf
+                    and not app.config.shed_tool_conf_set
+                    and exc.errno == errno.ENOENT):
                 continue
             raise
         if tree is None:
diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py
index 93b5057948d..803342840aa 100644
--- a/lib/galaxy/version.py
+++ b/lib/galaxy/version.py
@@ -1,3 +1,3 @@
-VERSION_MAJOR = "21.01"
+VERSION_MAJOR = "21.05"
 VERSION_MINOR = "dev"
 VERSION = VERSION_MAJOR + ('.' + VERSION_MINOR if VERSION_MINOR else '')
diff --git a/lib/galaxy/visualization/data_providers/basic.py b/lib/galaxy/visualization/data_providers/basic.py
index c22eac0baf0..e6a704197c1 100644
--- a/lib/galaxy/visualization/data_providers/basic.py
+++ b/lib/galaxy/visualization/data_providers/basic.py
@@ -6,8 +6,11 @@ from galaxy.datatypes.tabular import Tabular
 
 class BaseDataProvider:
     """
-    Base class for data providers. Data providers (a) read and package data from datasets;
-    and (b) write subsets of data to new datasets.
+    Base class for data providers. Data providers both:
+
+    - read and package data from datasets
+    - write subsets of data to new datasets
+
     """
 
     def __init__(self, converted_dataset=None, original_dataset=None, dependencies=None,
@@ -92,27 +95,27 @@ class ColumnDataProvider(BaseDataProvider):
 
         # skip comment lines (if any/avail)
         # pre: should have original_dataset and
-        if(skip_comments and
-                self.original_dataset.metadata.comment_lines and
-                start_val < self.original_dataset.metadata.comment_lines):
+        if(skip_comments
+                and self.original_dataset.metadata.comment_lines
+                and start_val < self.original_dataset.metadata.comment_lines):
             start_val = int(self.original_dataset.metadata.comment_lines)
 
         # columns is an array of ints for now (should handle column names later)
         columns = loads(columns)
         for column in columns:
-            assert((column < self.original_dataset.metadata.columns) and
-                   (column >= 0)), (
-                "column index (%d) must be positive and less" % (column) +
-                " than the number of columns: %d" % (self.original_dataset.metadata.columns))
+            assert((column < self.original_dataset.metadata.columns)
+                   and (column >= 0)), (
+                "column index (%d) must be positive and less" % (column)
+                + " than the number of columns: %d" % (self.original_dataset.metadata.columns))
 
         # set up the response, column lists
         response = {}
         response['data'] = data = [[] for column in columns]
         response['meta'] = meta = [{
-            'min'   : None,
-            'max'   : None,
-            'count' : 0,
-            'sum'   : 0
+            'min': None,
+            'max': None,
+            'count': 0,
+            'sum': 0
         } for column in columns]
 
         column_types = [self.original_dataset.metadata.column_types[column] for column in columns]
diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py
index 57a8e9090d8..3393db81073 100644
--- a/lib/galaxy/visualization/data_providers/genome.py
+++ b/lib/galaxy/visualization/data_providers/genome.py
@@ -586,6 +586,7 @@ class VcfDataProvider(GenomeDataProvider):
 
     Payload format: An array of entries for each locus in the file. Each array
     has the following entries:
+
         1. GUID (unused)
         2. location (0-based)
         3. reference base(s)
@@ -594,7 +595,8 @@ class VcfDataProvider(GenomeDataProvider):
         6. whether variant passed filter
         7. sample genotypes -- a single string with samples separated by commas; empty string
            denotes the reference genotype
-        8-end: allele counts for each alternative
+        8. allele counts for each alternative
+
     """
 
     col_name_data_attr_mapping: Dict[Union[str, int], Dict] = {'Qual': {'index': 6, 'name': 'Qual'}}
@@ -1268,7 +1270,7 @@ class IntervalIndexDataProvider(GenomeDataProvider, FilterableMixin):
                 chrom = region.chrom
                 start = region.start
                 end = region.end
-                for start, end, offset in index.find(chrom, start, end):
+                for _start, _end, offset in index.find(chrom, start, end):
                     source.seek(offset)
 
                     # HACK: write differently depending on original dataset format.
diff --git a/lib/galaxy/visualization/data_providers/phyloviz/baseparser.py b/lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
index 0e37a5bbefa..a7c499bc231 100644
--- a/lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
+++ b/lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
@@ -31,10 +31,10 @@ class Node:
     def toJson(self):
         """Converts the data in the node to a dict representation of json"""
         thisJson = {
-            "name"      : self.name,
-            "id"        : self.id,
-            "depth"     : self.depth,
-            "dist"      : self.length
+            "name": self.name,
+            "id": self.id,
+            "depth": self.depth,
+            "dist": self.length
         }
         thisJson = self.addChildrenToJson(thisJson)
         thisJson = self.addMiscToJson(thisJson)
diff --git a/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py b/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
index 9c5548be1fa..4144b612344 100644
--- a/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
+++ b/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
@@ -94,7 +94,7 @@ class Newick_Parser(Base_Parser):
                         if enclosingSymbol == ")" or enclosingSymbol == ":" or enclosingSymbol == ",":
                             termToReplace = newickString[end:j]
 
-                            newString += newickString[start : end] + nameMap[termToReplace]  # + "'"  "'" +
+                            newString += newickString[start:end] + nameMap[termToReplace]  # + "'"  "'" +
                             start = j
                             break
 
@@ -159,7 +159,7 @@ class Newick_Parser(Base_Parser):
                         lenOfPreceedingInternalNodeString = 0
 
                     # recussive call to make the internal claude
-                    childSubString = string[i + 1 : j]
+                    childSubString = string[i + 1:j]
                     InternalNode.addChildNode(self.parseNode(childSubString, depth + 1))
 
                     nodes.append(InternalNode)  # we append the internal node later to preserve order
diff --git a/lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py b/lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py
index 59288acba60..2fac57800f2 100644
--- a/lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py
+++ b/lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py
@@ -35,7 +35,7 @@ class Nexus_Parser(Newick_Parser):
             line = line.replace(";\n", "")
             lline = line.lower()
 
-            if rowCount > MAX_READLINES or (not nex_file) :
+            if rowCount > MAX_READLINES or (not nex_file):
                 break
             rowCount += 1
             # We are only interested in the tree block.
@@ -92,7 +92,7 @@ class Nexus_Parser(Newick_Parser):
                     self.inCommentBlock = True
                 else:
                     return "Nextline"   # need to move on to the nextline after getting out of comment
-        else :
+        else:
             if "]" in line:
                 if line.rfind("[") > line.rfind("]"):
                     pass                # a comment block is closed but another is open.
diff --git a/lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py b/lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py
index b2786434130..84ee9303597 100644
--- a/lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py
+++ b/lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py
@@ -14,10 +14,10 @@ class Phyloxml_Parser(Base_Parser):
         self.phyloTree = PhyloTree()
         self.tagsOfInterest = {
             "clade": "",
-            "name" : "name",
-            "branch_length" : "length",
-            "confidence"    : "bootstrap",
-            "events"        : "events"
+            "name": "name",
+            "branch_length": "length",
+            "confidence": "bootstrap",
+            "events": "events"
         }
 
     def parseFile(self, filePath):
@@ -85,9 +85,9 @@ class Phyloxml_Parser(Base_Parser):
             """Returns the name of a taxonomy node. A taxonomy node have to be treated differently as the name
             is embedded one level deeper"""
             phyloxmlTaxoNames = {
-                "common_name" : "",
-                "scientific_name" : "",
-                "code"  : ""
+                "common_name": "",
+                "scientific_name": "",
+                "code": ""
             }
             for child in node:
                 childTag = self.cleanTag(child.tag)
@@ -98,7 +98,7 @@ class Phyloxml_Parser(Base_Parser):
         nodeName = ""
         for child in node:
             childTag = self.cleanTag(child.tag)
-            if childTag == "name" :
+            if childTag == "name":
                 nodeName = child.text
                 break
             elif childTag == "taxonomy":
diff --git a/lib/galaxy/visualization/genomes.py b/lib/galaxy/visualization/genomes.py
index 1db30e3efc8..ed1b8cd30d1 100644
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -176,9 +176,9 @@ class Genome:
             'id': self.key,
             'reference': self.twobit_file is not None,
             'chrom_info': to_sort,
-            'prev_chroms' : prev_chroms,
-            'next_chroms' : next_chroms,
-            'start_index' : start_index
+            'prev_chroms': prev_chroms,
+            'next_chroms': next_chroms,
+            'start_index': start_index
         }
 
 
diff --git a/lib/galaxy/visualization/plugins/config_parser.py b/lib/galaxy/visualization/plugins/config_parser.py
index 3ee7da3a473..21a1beb10bb 100644
--- a/lib/galaxy/visualization/plugins/config_parser.py
+++ b/lib/galaxy/visualization/plugins/config_parser.py
@@ -137,8 +137,8 @@ class VisualizationsConfigParser:
         # render_target: where in the browser to open the rendered visualization
         # defaults to: galaxy_main
         render_target = xml_tree.find('render_target')
-        if((render_target is not None and render_target.text) and
-                (render_target.text in self.VALID_RENDER_TARGETS)):
+        if((render_target is not None and render_target.text)
+                and (render_target.text in self.VALID_RENDER_TARGETS)):
             returned['render_target'] = render_target.text
         else:
             returned['render_target'] = 'galaxy_main'
@@ -164,7 +164,7 @@ class VisualizationsConfigParser:
     def parse_entry_point(self, xml_tree):
         """
         Parse the config file for an appropriate entry point: a mako template, a script tag,
-        or an html file, returning as dictionary with: `type`, `file`, and `attr`ibutes of
+        or an html file, returning as dictionary with: ``type``, ``file``, and ``attr`` (-ibutes) of
         the element.
         """
         # (older) mako-only syntax: the template to use in rendering the visualization
@@ -172,9 +172,9 @@ class VisualizationsConfigParser:
         if template is not None and template.text:
             log.info('template syntax is deprecated: use entry_point instead')
             return {
-                'type' : 'mako',
-                'file' : template.text,
-                'attr' : {}
+                'type': 'mako',
+                'file': template.text,
+                'attr': {}
             }
 
         # need one of the two: (the deprecated) template or entry_point
@@ -188,9 +188,9 @@ class VisualizationsConfigParser:
         if entry_point_type not in self.ALLOWED_ENTRY_POINT_TYPES:
             raise ParsingException('Unknown entry_point type: ' + entry_point_type)
         return {
-            'type' : entry_point_type,
-            'file' : entry_point.text,
-            'attr' : entry_point_attrib
+            'type': entry_point_type,
+            'file': entry_point.text,
+            'attr': entry_point_attrib
         }
 
 
@@ -295,8 +295,8 @@ class DataSourceParser:
             test_type = test_elem.get('type', 'eq')
             test_result = test_elem.text.strip() if test_elem.text else None
             if not test_type or not test_result:
-                log.warning('Skipping test. Needs both type attribute and text node to be parsed: ' +
-                          f'{test_type}, {test_elem.text}')
+                log.warning('Skipping test. Needs both type attribute and text node to be parsed: '
+                          + f'{test_type}, {test_elem.text}')
                 continue
             test_result = test_result.strip()
 
@@ -322,8 +322,8 @@ class DataSourceParser:
             elif test_type == 'has_dataprovider':
                 # does the object itself have a datatype attr and does that datatype have the given dataprovider
                 def test_fn(o, result):
-                    return (hasattr(getter(o), 'has_dataprovider') and
-                            getter(o).has_dataprovider(result))
+                    return (hasattr(getter(o), 'has_dataprovider')
+                            and getter(o).has_dataprovider(result))
 
             elif test_type == 'has_attribute':
                 # does the object itself have attr in 'result' (no equivalence checking)
@@ -340,10 +340,10 @@ class DataSourceParser:
                     return str(getter(o)) == result
 
             tests.append({
-                'type'          : test_type,
-                'result'        : test_result,
-                'result_type'   : test_result_type,
-                'fn'            : test_fn
+                'type': test_type,
+                'result': test_result,
+                'result_type': test_result_type,
+                'fn': test_fn
             })
 
         return tests
diff --git a/lib/galaxy/visualization/plugins/interactive_environments.py b/lib/galaxy/visualization/plugins/interactive_environments.py
index 54afd0db041..da160d94b19 100644
--- a/lib/galaxy/visualization/plugins/interactive_environments.py
+++ b/lib/galaxy/visualization/plugins/interactive_environments.py
@@ -322,13 +322,13 @@ class InteractiveEnvironmentRequest:
             volumes.insert(0, import_volume_def)
 
         return (
-            self.base_docker_cmd('run') +
-            shlex.split(command_inject) +
-            name +
-            _flag_opts('-e', ['='.join(map(str, t)) for t in env.items()]) +
-            ['-d', '-P'] +
-            _flag_opts('-v', map(str, volumes)) +
-            [image]
+            self.base_docker_cmd('run')
+            + shlex.split(command_inject)
+            + name
+            + _flag_opts('-e', ['='.join(map(str, t)) for t in env.items()])
+            + ['-d', '-P']
+            + _flag_opts('-v', map(str, volumes))
+            + [image]
         )
 
     @property
@@ -510,7 +510,7 @@ class InteractiveEnvironmentRequest:
         :type env_override: dict
         :param env_override: dictionary of environment variables to add.
 
-        :type volumes: list of :class:`galaxy.containers.docker_model.DockerVolume`s
+        :type volumes: list of py:class:`galaxy.containers.docker_model.DockerVolume` s
         :param volumes: dictionary of docker volume mounts
 
         """
diff --git a/lib/galaxy/visualization/plugins/plugin.py b/lib/galaxy/visualization/plugins/plugin.py
index 0326df7b95d..aeda3ffeabe 100644
--- a/lib/galaxy/visualization/plugins/plugin.py
+++ b/lib/galaxy/visualization/plugins/plugin.py
@@ -108,18 +108,18 @@ class VisualizationPlugin(ServesTemplatesPluginMixin):
 
     def to_dict(self):
         return {
-            'name'          : self.name,
-            'html'          : self.config.get('name'),
-            'description'   : self.config.get('description'),
-            'logo'          : self.config.get('logo'),
-            'title'         : self.config.get('title'),
-            'target'        : self.config.get('render_target', 'galaxy_main'),
-            'embeddable'    : self.config.get('embeddable'),
-            'entry_point'   : self.config.get('entry_point'),
-            'settings'      : self.config.get('settings'),
-            'groups'        : self.config.get('groups'),
-            'specs'         : self.config.get('specs'),
-            'href'          : self._get_url()
+            'name': self.name,
+            'html': self.config.get('name'),
+            'description': self.config.get('description'),
+            'logo': self.config.get('logo'),
+            'title': self.config.get('title'),
+            'target': self.config.get('render_target', 'galaxy_main'),
+            'embeddable': self.config.get('embeddable'),
+            'entry_point': self.config.get('entry_point'),
+            'settings': self.config.get('settings'),
+            'groups': self.config.get('groups'),
+            'specs': self.config.get('specs'),
+            'href': self._get_url()
         }
 
     def _get_url(self):
@@ -308,7 +308,7 @@ class ScriptVisualizationPlugin(VisualizationPlugin):
         render_vars['static_url'] = url_for('/%s/' % self.static_path)
         render_vars.update(vars={})
         render_vars.update({
-            "script_attributes" : self.config['entry_point']['attr']
+            "script_attributes": self.config['entry_point']['attr']
         })
         template_filename = os.path.join(self.MAKO_TEMPLATE)
         return trans.fill_template(template_filename, template_lookup=self.template_lookup, **render_vars)
diff --git a/lib/galaxy/visualization/plugins/registry.py b/lib/galaxy/visualization/plugins/registry.py
index 4f1dc1cea9f..12460ef24c1 100644
--- a/lib/galaxy/visualization/plugins/registry.py
+++ b/lib/galaxy/visualization/plugins/registry.py
@@ -51,7 +51,7 @@ class VisualizationsRegistry:
         """
         Set up the manager and load all visualization plugins.
 
-        :type   app:        UniverseApplication
+        :type   app:        galaxy.app.UniverseApplication
         :param  app:        the application (and its configuration) using this manager
         :type   base_url:   string
         :param  base_url:   url to prefix all plugin urls with
diff --git a/lib/galaxy/visualization/plugins/resource_parser.py b/lib/galaxy/visualization/plugins/resource_parser.py
index 07cfdd7b522..58d5893db35 100644
--- a/lib/galaxy/visualization/plugins/resource_parser.py
+++ b/lib/galaxy/visualization/plugins/resource_parser.py
@@ -29,12 +29,12 @@ class ResourceParser:
     new keys (e.g. dataset_id="NNN" -> hda=<HistoryDatasetAssociation>).
     """
     primitive_parsers = {
-        'str'   : lambda param: galaxy.util.sanitize_html.sanitize_html(param),
-        'bool'  : lambda param: galaxy.util.string_as_bool(param),
-        'int'   : int,
-        'float' : float,
+        'str': lambda param: galaxy.util.sanitize_html.sanitize_html(param),
+        'bool': lambda param: galaxy.util.string_as_bool(param),
+        'int': int,
+        'float': float,
         # 'date'  : lambda param: ,
-        'json'  : (lambda param: json.loads(
+        'json': (lambda param: json.loads(
             galaxy.util.sanitize_html.sanitize_html(param))),
     }
 
@@ -111,8 +111,8 @@ class ResourceParser:
                     config_val = self.parse_parameter(trans, param_config, config_val)
 
                 except Exception as exception:
-                    log.warning('Exception parsing visualization param from query: ' +
-                              '{}, {}, ({}) {}'.format(param_name, config_val, str(type(exception)), str(exception)))
+                    log.warning('Exception parsing visualization param from query: '
+                              + '{}, {}, ({}) {}'.format(param_name, config_val, str(type(exception)), str(exception)))
                     config_val = None
 
             # here - we've either had no value in the query_params or there was a failure to parse
diff --git a/lib/galaxy/web/__init__.py b/lib/galaxy/web/__init__.py
index 6ab1bd9218a..696fd07f2b3 100644
--- a/lib/galaxy/web/__init__.py
+++ b/lib/galaxy/web/__init__.py
@@ -25,10 +25,10 @@ from .framework.decorators import (
     require_login,
 )
 
-__all__ = ('FormBuilder', 'do_not_cache', 'error', 'expose', 'expose_api',
+__all__ = ('do_not_cache', 'error', 'expose', 'expose_api',
         'expose_api_anonymous', 'expose_api_anonymous_and_sessionless',
         'expose_api_raw', 'expose_api_raw_anonymous',
-        'expose_api_raw_anonymous_and_sessionless', 'form',
+        'expose_api_raw_anonymous_and_sessionless',
         'format_return_as_json', 'httpexceptions', 'json', 'json_pretty',
         'legacy_expose_api', 'legacy_expose_api_anonymous',
         'legacy_expose_api_raw', 'legacy_expose_api_raw_anonymous',
diff --git a/lib/galaxy/web/framework/base.py b/lib/galaxy/web/framework/base.py
index 461a7ea7f41..d29fddf73c1 100644
--- a/lib/galaxy/web/framework/base.py
+++ b/lib/galaxy/web/framework/base.py
@@ -3,13 +3,14 @@ A simple WSGI application/framework.
 """
 import io
 import logging
-import os.path
+import os
 import socket
 import tarfile
 import tempfile
 import time
 import types
 from http.cookies import CookieError, SimpleCookie
+from importlib import import_module
 
 import routes
 import webob.compat
@@ -520,3 +521,14 @@ def flatten(seq):
                 yield smart_str(y)
         else:
             yield smart_str(x)
+
+
+def walk_controller_modules(package_name):
+    package = import_module(package_name)
+    controller_dir = package.__path__[0]
+    for fname in os.listdir(controller_dir):
+        if not(fname.startswith("_")) and fname.endswith(".py"):
+            name = fname[:-3]
+            module_name = package_name + "." + name
+            module = import_module(module_name)
+            yield name, module
diff --git a/lib/galaxy/web/framework/helpers/grids.py b/lib/galaxy/web/framework/helpers/grids.py
index 31db02a9262..1c77acf36f4 100644
--- a/lib/galaxy/web/framework/helpers/grids.py
+++ b/lib/galaxy/web/framework/helpers/grids.py
@@ -801,32 +801,32 @@ class Grid:
         # results via a controller method, which is require substantial changes. Hence, for now, return grid
         # as str.
         grid_config = {
-            'title'                         : self.title,
-            'title_id'                      : getattr(self, "title_id", None),
-            'url_base'                      : trans.request.path_url,
-            'async_ops'                     : [],
-            'categorical_filters'           : {},
-            'filters'                       : cur_filter_dict,
-            'sort_key'                      : sort_key,
-            'show_item_checkboxes'          : self.show_item_checkboxes or kwargs.get('show_item_checkboxes', '') in ['True', 'true'],
-            'cur_page_num'                  : page_num,
-            'num_page_links'                : self.num_page_links,
-            'status'                        : status,
-            'message'                       : restore_text(message),
-            'global_actions'                : [],
-            'operations'                    : [],
-            'items'                         : [],
-            'columns'                       : [],
-            'model_class'                   : str(self.model_class),
-            'use_paging'                    : self.use_paging,
-            'legend'                        : self.legend,
-            'current_item_id'               : False,
-            'use_hide_message'              : self.use_hide_message,
-            'default_filter_dict'           : self.default_filter,
-            'advanced_search'               : self.advanced_search,
-            'info_text'                     : self.info_text,
-            'url'                           : url(dict()),
-            'refresh_frames'                : kwargs.get('refresh_frames', [])
+            'title': self.title,
+            'title_id': getattr(self, "title_id", None),
+            'url_base': trans.request.path_url,
+            'async_ops': [],
+            'categorical_filters': {},
+            'filters': cur_filter_dict,
+            'sort_key': sort_key,
+            'show_item_checkboxes': self.show_item_checkboxes or kwargs.get('show_item_checkboxes', '') in ['True', 'true'],
+            'cur_page_num': page_num,
+            'num_page_links': self.num_page_links,
+            'status': status,
+            'message': restore_text(message),
+            'global_actions': [],
+            'operations': [],
+            'items': [],
+            'columns': [],
+            'model_class': str(self.model_class),
+            'use_paging': self.use_paging,
+            'legend': self.legend,
+            'current_item_id': False,
+            'use_hide_message': self.use_hide_message,
+            'default_filter_dict': self.default_filter,
+            'advanced_search': self.advanced_search,
+            'info_text': self.info_text,
+            'url': url(dict()),
+            'refresh_frames': kwargs.get('refresh_frames', [])
         }
         if current_item:
             grid_config['current_item_id'] = current_item.id
diff --git a/lib/galaxy/web/framework/middleware/batch.py b/lib/galaxy/web/framework/middleware/batch.py
index 722e8bb8da4..468a57f5143 100644
--- a/lib/galaxy/web/framework/middleware/batch.py
+++ b/lib/galaxy/web/framework/middleware/batch.py
@@ -2,6 +2,7 @@
 Batch API middleware
 
 Adds a single route to the installation that:
+
   1. accepts a POST call containing a JSON array of 'http-like' JSON
      dictionaries.
   2. Each dictionary describes a single API call within the batch and is routed
@@ -40,24 +41,28 @@ class BatchMiddleware:
     """
     Adds a URL endpoint for processing batch API calls formatted as a JSON
     array of JSON dictionaries. These dictionaries are in the form:
-    [
-        {
-            "url": "/api/histories",
-            "type": "POST",
-            "body": "{ \"name\": \"New History Name\" }"
-        },
-        ...
-    ]
+
+    .. code-block: json
+
+        [
+            {
+                "url": "/api/histories",
+                "type": "POST",
+                "body": "{ \"name\": \"New History Name\" }"
+            },
+            ...
+        ]
 
     where:
+
       * `url` is the url for the API call to be made including any query string
       * `type` is the HTTP method used (e.g. 'POST', 'PUT') - defaults to 'GET'
       * `body` is the text body of the request (optional)
       * `contentType` content-type request header (defaults to application/json)
     """
     DEFAULT_CONFIG = {
-        'route' : '/api/batch',
-        'allowed_routes' : [
+        'route': '/api/batch',
+        'allowed_routes': [
             r'^api\/users.*',
             r'^api\/histories.*',
             r'^api\/jobs.*',
@@ -121,9 +126,9 @@ class BatchMiddleware:
 
     def _disallowed_route_response(self, route):
         return dict(status=403, headers=self._default_headers(), body={
-            'err_msg'   : 'Disallowed route used for batch operation',
-            'route'     : route,
-            'allowed'   : self.config['allowed_routes']
+            'err_msg': 'Disallowed route used for batch operation',
+            'route': route,
+            'allowed': self.config['allowed_routes']
         })
 
     def _build_request_environ(self, original_environ, request):
@@ -179,8 +184,8 @@ class BatchMiddleware:
     def _default_headers(self):
         return {
             'x-frame-options': 'SAMEORIGIN',
-            'content-type'   : 'application/json',
-            'cache-control'  : 'max-age=0,no-cache,no-store'
+            'content-type': 'application/json',
+            'cache-control': 'max-age=0,no-cache,no-store'
         }
 
     def handle_exception(self, environ):
diff --git a/lib/galaxy/web/framework/middleware/error.py b/lib/galaxy/web/framework/middleware/error.py
index c0dc570711d..455b28982c0 100644
--- a/lib/galaxy/web/framework/middleware/error.py
+++ b/lib/galaxy/web/framework/middleware/error.py
@@ -113,10 +113,10 @@ class ErrorMiddleware:
             show_exceptions_in_wsgi_errors = converters.asbool(global_conf.get('show_exceptions_in_wsgi_errors'))
         self.debug_mode = converters.asbool(debug)
         if error_email is None:
-            error_email = (global_conf.get('error_email') or
-                           global_conf.get('admin_email') or
-                           global_conf.get('webmaster_email') or
-                           global_conf.get('sysadmin_email'))
+            error_email = (global_conf.get('error_email')
+                           or global_conf.get('admin_email')
+                           or global_conf.get('webmaster_email')
+                           or global_conf.get('sysadmin_email'))
         self.error_email = converters.aslist(error_email)
         self.error_log = error_log
         self.show_exceptions_in_wsgi_errors = show_exceptions_in_wsgi_errors
diff --git a/lib/galaxy/web/framework/middleware/translogger.py b/lib/galaxy/web/framework/middleware/translogger.py
index 161666a605a..e11a0709d80 100644
--- a/lib/galaxy/web/framework/middleware/translogger.py
+++ b/lib/galaxy/web/framework/middleware/translogger.py
@@ -50,8 +50,8 @@ class TransLogger:
 
     def __call__(self, environ, start_response):
         start = time.localtime()
-        req_uri = quote(environ.get('SCRIPT_NAME', '') +
-                        environ.get('PATH_INFO', ''))
+        req_uri = quote(environ.get('SCRIPT_NAME', '')
+                        + environ.get('PATH_INFO', ''))
         if environ.get('QUERY_STRING'):
             req_uri += '?' + environ['QUERY_STRING']
         method = environ['REQUEST_METHOD']
diff --git a/lib/galaxy/web/legacy_framework/grids.py b/lib/galaxy/web/legacy_framework/grids.py
index 13b03171e35..67ce975babf 100644
--- a/lib/galaxy/web/legacy_framework/grids.py
+++ b/lib/galaxy/web/legacy_framework/grids.py
@@ -810,8 +810,8 @@ class Grid:
                                    use_panels=self.use_panels,
                                    use_hide_message=self.use_hide_message,
                                    advanced_search=self.advanced_search,
-                                   show_item_checkboxes=(self.show_item_checkboxes or
-                                                         kwargs.get('show_item_checkboxes', '') in ['True', 'true']),
+                                   show_item_checkboxes=(self.show_item_checkboxes
+                                                         or kwargs.get('show_item_checkboxes', '') in ['True', 'true']),
                                    # Pass back kwargs so that grid template can set and use args without
                                    # grid explicitly having to pass them.
                                    kwargs=kwargs)
diff --git a/lib/galaxy/web_stack/__init__.py b/lib/galaxy/web_stack/__init__.py
index 4b358282b1f..fb75427b539 100644
--- a/lib/galaxy/web_stack/__init__.py
+++ b/lib/galaxy/web_stack/__init__.py
@@ -573,7 +573,7 @@ class WeblessApplicationStack(ApplicationStack):
         return (self.config.server_name,) if self.in_pool(pool_name) else None
 
 
-def application_stack_class():
+def application_stack_class() -> Type[ApplicationStack]:
     """Returns the correct ApplicationStack class for the stack under which
     this Galaxy process is running.
     """
@@ -587,7 +587,7 @@ def application_stack_class():
     return WeblessApplicationStack
 
 
-def application_stack_instance(app=None, config=None):
+def application_stack_instance(app=None, config=None) -> ApplicationStack:
     stack_class = application_stack_class()
     return stack_class(app=app, config=config)
 
diff --git a/lib/galaxy/web_stack/handlers.py b/lib/galaxy/web_stack/handlers.py
index 042cfc0d518..3213c9e3c15 100644
--- a/lib/galaxy/web_stack/handlers.py
+++ b/lib/galaxy/web_stack/handlers.py
@@ -425,7 +425,7 @@ class ConfiguresHandlers:
             log.debug("(%s) No handler pool (uWSGI farm) for '%s' found", obj.log_str(), tag)
             raise HandlerAssignmentSkip()
         else:
-            if flush:
+            if flush or not obj.id:
                 _timed_flush_obj(obj)
             message = message_callback()
             self.app.application_stack.send_message(pool, message)
@@ -434,7 +434,7 @@ class ConfiguresHandlers:
     def assign_handler(self, obj, configured=None, **kwargs):
         """Set a job handler, flush obj
 
-        Called assignment methods should raise :exception:`HandlerAssignmentSkip` to indicate that the next method
+        Called assignment methods should raise py:class:`HandlerAssignmentSkip` to indicate that the next method
         should be tried.
 
         :param obj:         Object to assign a handler to (must be a model object with ``handler`` attribute and
diff --git a/lib/galaxy/webapps/base/controller.py b/lib/galaxy/webapps/base/controller.py
index 07d49494552..eac3e994319 100644
--- a/lib/galaxy/webapps/base/controller.py
+++ b/lib/galaxy/webapps/base/controller.py
@@ -2,6 +2,7 @@
 Contains functionality needed in every web interface
 """
 import logging
+from typing import Optional
 
 from sqlalchemy import true
 from webob.exc import (
@@ -33,6 +34,7 @@ from galaxy.model import (
     tags,
 )
 from galaxy.model.item_attrs import UsesAnnotations
+from galaxy.structured_app import StructuredApp
 from galaxy.util.dictifiable import Dictifiable
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web import (
@@ -56,8 +58,9 @@ class BaseController:
     """
     Base class for Galaxy web application controllers.
     """
+    app: StructuredApp
 
-    def __init__(self, app):
+    def __init__(self, app: StructuredApp) -> None:
         """Initialize an interface for application 'app'"""
         self.app = app
         self.sa_session = app.model.context
@@ -291,24 +294,24 @@ class JSAppLauncher(BaseUIController):
         """
         root = root or web.url_for('/')
         js_options = {
-            'root'               : root,
-            'user'               : self.user_serializer.serialize(trans.user, self.USER_BOOTSTRAP_KEYS, trans=trans),
-            'config'             : self._get_site_configuration(trans),
-            'params'             : dict(trans.request.params),
-            'session_csrf_token' : trans.session_csrf_token,
+            'root': root,
+            'user': self.user_serializer.serialize(trans.user, self.USER_BOOTSTRAP_KEYS, trans=trans),
+            'config': self._get_site_configuration(trans),
+            'params': dict(trans.request.params),
+            'session_csrf_token': trans.session_csrf_token,
         }
         return js_options
 
     def _get_extended_config(self, trans):
         config = {
-            'active_view'                   : 'analysis',
-            'enable_cloud_launch'           : trans.app.config.get_bool('enable_cloud_launch', False),
-            'enable_webhooks'               : True if trans.app.webhooks_registry.webhooks else False,
-            'toolbox'                       : trans.app.toolbox.to_dict(trans),
-            'message_box_visible'           : trans.app.config.message_box_visible,
-            'show_inactivity_warning'       : trans.app.config.user_activation_on and trans.user and not trans.user.active,
-            'tool_shed_urls'                : list(trans.app.tool_shed_registry.tool_sheds.values()) if trans.app.tool_shed_registry else [],
-            'tool_dynamic_configs'          : list(trans.app.toolbox.dynamic_conf_filenames())
+            'active_view': 'analysis',
+            'enable_cloud_launch': trans.app.config.get_bool('enable_cloud_launch', False),
+            'enable_webhooks': True if trans.app.webhooks_registry.webhooks else False,
+            'toolbox': trans.app.toolbox.to_dict(trans),
+            'message_box_visible': trans.app.config.message_box_visible,
+            'show_inactivity_warning': trans.app.config.user_activation_on and trans.user and not trans.user.active,
+            'tool_shed_urls': list(trans.app.tool_shed_registry.tool_sheds.values()) if trans.app.tool_shed_registry else [],
+            'tool_dynamic_configs': list(trans.app.toolbox.dynamic_conf_filenames())
         }
 
         # TODO: move to user
@@ -338,18 +341,17 @@ class JSAppLauncher(BaseUIController):
             log.exception(exc)
             return {}
 
-    def template(self, trans, app_name, entry_fn='app', options=None, bootstrapped_data=None, masthead=True, **additional_options):
+    def template(self, trans, app_name: str, entry_fn: str = 'app', options=None, bootstrapped_data: Optional[dict] = None, masthead: Optional[bool] = True, **additional_options):
         """
         Render and return the single page mako template that starts the app.
 
-        `app_name` (string): the first portion of the webpack bundle to as the app.
-        `entry_fn` (string): the name of the window-scope function that starts the
-            app. Defaults to 'app'.
-        `bootstrapped_data` (dict): (optional) update containing any more data
-            the app may need.
-        `masthead` (boolean): (optional, default=True) include masthead elements in
-            the initial page dom.
-        `additional_options` (kwargs): update to the options sent to the app.
+        :param app_name: the first portion of the webpack bundle to as the app.
+        :param entry_fn: the name of the window-scope function that starts the
+                         app. Defaults to 'app'.
+        :param bootstrapped_data: update containing any more data
+                                  the app may need.
+        :param masthead: include masthead elements in the initial page dom.
+        :param additional_options: update to the options sent to the app.
         """
         options = options or self._get_js_options(trans)
         options.update(additional_options)
@@ -444,7 +446,7 @@ class ImportsHistoryMixin:
     def queue_history_import(self, trans, archive_type, archive_source):
         # Run job to do import.
         history_imp_tool = trans.app.toolbox.get_tool('__IMPORT_HISTORY__')
-        incoming = {'__ARCHIVE_SOURCE__' : archive_source, '__ARCHIVE_TYPE__' : archive_type}
+        incoming = {'__ARCHIVE_SOURCE__': archive_source, '__ARCHIVE_TYPE__': archive_type}
         job, _ = history_imp_tool.execute(trans, incoming=incoming)
         return job
 
@@ -452,10 +454,10 @@ class ImportsHistoryMixin:
 class UsesLibraryMixin:
 
     def get_library(self, trans, id, check_ownership=False, check_accessible=True):
-        l = self.get_object(trans, id, 'Library')
-        if check_accessible and not (trans.user_is_admin or trans.app.security_agent.can_access_library(trans.get_current_user_roles(), l)):
-            error("LibraryFolder is not accessible to the current user")
-        return l
+        library = self.get_object(trans, id, 'Library')
+        if check_accessible and not (trans.user_is_admin or trans.app.security_agent.can_access_library(trans.get_current_user_roles(), library)):
+            error("Library is not accessible to the current user")
+        return library
 
 
 class UsesLibraryMixinItems(SharableItemSecurityMixin):
@@ -484,8 +486,8 @@ class UsesLibraryMixinItems(SharableItemSecurityMixin):
     def can_current_user_add_to_library_item(self, trans, item):
         if not trans.user:
             return False
-        return (trans.user_is_admin or
-                trans.app.security_agent.can_add_library_item(trans.get_current_user_roles(), item))
+        return (trans.user_is_admin
+                or trans.app.security_agent.can_add_library_item(trans.get_current_user_roles(), item))
 
     def check_user_can_add_to_library_item(self, trans, item, check_accessible=True):
         """
@@ -744,10 +746,10 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
         # TODO: deleted
         # TODO: importable
         return {
-            'id'        : visualization.id,
-            'title'     : visualization.title,
-            'type'      : visualization.type,
-            'dbkey'     : visualization.dbkey,
+            'id': visualization.id,
+            'title': visualization.title,
+            'type': visualization.type,
+            'dbkey': visualization.dbkey,
         }
 
     def get_visualization_dict(self, visualization):
@@ -758,15 +760,15 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
         """
         return {
             'model_class': 'Visualization',
-            'id'         : visualization.id,
-            'title'      : visualization.title,
-            'type'       : visualization.type,
-            'user_id'    : visualization.user.id,
-            'dbkey'      : visualization.dbkey,
-            'slug'       : visualization.slug,
+            'id': visualization.id,
+            'title': visualization.title,
+            'type': visualization.type,
+            'user_id': visualization.user.id,
+            'dbkey': visualization.dbkey,
+            'slug': visualization.slug,
             # to_dict only the latest revision (allow older to be fetched elsewhere)
-            'latest_revision' : self.get_visualization_revision_dict(visualization.latest_revision),
-            'revisions' : [r.id for r in visualization.revisions],
+            'latest_revision': self.get_visualization_revision_dict(visualization.latest_revision),
+            'revisions': [r.id for r in visualization.revisions],
         }
 
     def get_visualization_revision_dict(self, revision):
@@ -775,12 +777,12 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
         NOTE: that encoding ids isn't done here should happen at the caller level.
         """
         return {
-            'model_class'      : 'VisualizationRevision',
-            'id'               : revision.id,
-            'visualization_id' : revision.visualization.id,
-            'title'            : revision.title,
-            'dbkey'            : revision.dbkey,
-            'config'           : revision.config,
+            'model_class': 'VisualizationRevision',
+            'id': revision.id,
+            'visualization_id': revision.visualization.id,
+            'title': revision.title,
+            'dbkey': revision.dbkey,
+            'config': revision.config,
         }
 
     def import_visualization(self, trans, id, user=None):
@@ -993,7 +995,7 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
                     "dataset": trans.security.encode_dict_ids(dataset.to_dict()),
                     "prefs": prefs,
                     "mode": track_dict.get('mode', 'Auto'),
-                    "filters": track_dict.get('filters', {'filters' : track_data_provider.get_filters()}),
+                    "filters": track_dict.get('filters', {'filters': track_data_provider.get_filters()}),
                     "tool": self.get_tool_def(trans, dataset),
                     "tool_state": track_dict.get('tool_state', {})
                 }
@@ -1065,7 +1067,7 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
             "name": dataset.name,
             "dataset": trans.security.encode_dict_ids(dataset.to_dict()),
             "prefs": {},
-            "filters": {'filters' : track_data_provider.get_filters()},
+            "filters": {'filters': track_data_provider.get_filters()},
             "tool": self.get_tool_def(trans, dataset),
             "tool_state": {}
         }
@@ -1112,8 +1114,8 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
                 error("You are not allowed to access this dataset")
 
             if check_state and data.state == trans.model.Dataset.states.UPLOAD:
-                return trans.show_error_message("Please wait until this dataset finishes uploading " +
-                                                "before attempting to view it.")
+                return trans.show_error_message("Please wait until this dataset finishes uploading "
+                                                + "before attempting to view it.")
         return data
 
     # -- Helper functions --
@@ -1669,14 +1671,6 @@ class UsesExtendedMetadataMixin(SharableItemSecurityMixin):
             yield prefix, ("%s" % (meta)).encode("utf8", errors='replace')
 
 
-class ControllerUnavailable(Exception):
-    """
-    Deprecated: `BaseController` used to be available under the name `Root`
-    """
-
-# ---- Utility methods -------------------------------------------------------
-
-
 def sort_by_attr(seq, attr):
     """
     Sort the sequence of objects by object's attribute
diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index 2fab4d18435..ead9ccee1f1 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -9,7 +9,6 @@ import socket
 import string
 import time
 from http.cookies import CookieError
-from importlib import import_module
 from urllib.parse import urlparse
 
 import mako.lookup
@@ -70,8 +69,9 @@ class WebApplication(base.WebApplication):
     Base WSGI application instantiated for all Galaxy webapps.
 
     A web application that:
+
         * adds API and UI controllers by scanning given directories and
-        importing all modules found there.
+          importing all modules found there.
         * has a security object.
         * builds mako template lookups.
         * generates GalaxyWebTransactions.
@@ -123,24 +123,13 @@ class WebApplication(base.WebApplication):
         them to the webapp.
         """
         from galaxy.webapps.base.controller import BaseUIController
-        from galaxy.webapps.base.controller import ControllerUnavailable
-        package = import_module(package_name)
-        controller_dir = package.__path__[0]
-        for fname in os.listdir(controller_dir):
-            if not(fname.startswith("_")) and fname.endswith(".py"):
-                name = fname[:-3]
-                module_name = package_name + "." + name
-                try:
-                    module = import_module(module_name)
-                except ControllerUnavailable as exc:
-                    log.debug("%s could not be loaded: %s", module_name, unicodify(exc))
-                    continue
-                # Look for a controller inside the modules
-                for key in dir(module):
-                    T = getattr(module, key)
-                    if inspect.isclass(T) and T is not BaseUIController and issubclass(T, BaseUIController):
-                        controller = self._instantiate_controller(T, app)
-                        self.add_ui_controller(name, controller)
+        for name, module in base.walk_controller_modules(package_name):
+            # Look for a controller inside the modules
+            for key in dir(module):
+                T = getattr(module, key)
+                if inspect.isclass(T) and T is not BaseUIController and issubclass(T, BaseUIController):
+                    controller = self._instantiate_controller(T, app)
+                    self.add_ui_controller(name, controller)
 
     def add_api_controllers(self, package_name, app):
         """
@@ -148,26 +137,15 @@ class WebApplication(base.WebApplication):
         them to the webapp.
         """
         from galaxy.webapps.base.controller import BaseAPIController
-        from galaxy.webapps.base.controller import ControllerUnavailable
-        package = import_module(package_name)
-        controller_dir = package.__path__[0]
-        for fname in os.listdir(controller_dir):
-            if not(fname.startswith("_")) and fname.endswith(".py"):
-                name = fname[:-3]
-                module_name = package_name + "." + name
-                try:
-                    module = import_module(module_name)
-                except ControllerUnavailable as exc:
-                    log.debug("%s could not be loaded: %s", module_name, unicodify(exc))
-                    continue
-                for key in dir(module):
-                    T = getattr(module, key)
-                    # Exclude classes such as BaseAPIController and BaseTagItemsController
-                    if inspect.isclass(T) and not key.startswith("Base") and issubclass(T, BaseAPIController):
-                        # By default use module_name, but allow controller to override name
-                        controller_name = getattr(T, "controller_name", name)
-                        controller = self._instantiate_controller(T, app)
-                        self.add_api_controller(controller_name, controller)
+        for name, module in base.walk_controller_modules(package_name):
+            for key in dir(module):
+                T = getattr(module, key)
+                # Exclude classes such as BaseAPIController and BaseTagItemsController
+                if inspect.isclass(T) and not key.startswith("Base") and issubclass(T, BaseAPIController):
+                    # By default use module_name, but allow controller to override name
+                    controller_name = getattr(T, "controller_name", name)
+                    controller = self._instantiate_controller(T, app)
+                    self.add_api_controller(controller_name, controller)
 
     def _instantiate_controller(self, T, app):
         """ Extension point, allow apps to construct controllers differently,
@@ -176,17 +154,15 @@ class WebApplication(base.WebApplication):
         return T(app)
 
 
-class GalaxyWebTransaction(base.DefaultWebTransaction,
-                           context.ProvidesAppContext, context.ProvidesUserContext, context.ProvidesHistoryContext):
+class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryContext):
     """
     Encapsulates web transaction specific state for the Galaxy application
     (specifically the user's "cookie" session and history)
     """
 
     def __init__(self, environ, app, webapp, session_cookie=None):
-        self.app = app
+        self._app = app
         self.webapp = webapp
-        self.security = webapp.security
         self.user_manager = UserManager(app)
         self.session_manager = GalaxySessionManager(app.model)
         base.DefaultWebTransaction.__init__(self, environ)
@@ -263,6 +239,10 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
                     self.sa_session.add(self.galaxy_session)
                     self.sa_session.flush()
 
+    @property
+    def app(self):
+        return self._app
+
     def setup_i18n(self):
         locales = []
         if 'HTTP_ACCEPT_LANGUAGE' in self.environ:
@@ -429,9 +409,6 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
         """
         Ensure that a valid Galaxy session exists and is available as
         trans.session (part of initialization)
-
-        Support for universe_session and universe_user cookies has been
-        removed as of 31 Oct 2008.
         """
         # Try to load an existing session
         secure_id = self.get_cookie(name=session_cookie)
@@ -461,10 +438,10 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
                     # No user, associate
                     galaxy_session.user = self.get_or_create_remote_user(remote_user_email)
                     galaxy_session_requires_flush = True
-                elif (remote_user_email and
-                      (galaxy_session.user.email != remote_user_email) and
-                      ((not self.app.config.allow_user_impersonation) or
-                       (remote_user_email not in self.app.config.admin_users_list))):
+                elif (remote_user_email
+                      and galaxy_session.user.email != remote_user_email
+                      and (not self.app.config.allow_user_impersonation
+                           or remote_user_email not in self.app.config.admin_users_list)):
                     # Session exists but is not associated with the correct
                     # remote user, and the currently set remote_user is not a
                     # potentially impersonating admin.
@@ -554,9 +531,9 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
             if self.request.path.startswith(external_display_path):
                 request_path_split = self.request.path.split('/')
                 try:
-                    if (self.app.datatypes_registry.display_applications.get(request_path_split[-5]) and
-                            request_path_split[-4] in self.app.datatypes_registry.display_applications.get(request_path_split[-5]).links and
-                            request_path_split[-3] != 'None'):
+                    if (self.app.datatypes_registry.display_applications.get(request_path_split[-5])
+                            and request_path_split[-4] in self.app.datatypes_registry.display_applications.get(request_path_split[-5]).links
+                            and request_path_split[-3] != 'None'):
                         return
                 except IndexError:
                     pass
@@ -671,12 +648,12 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
             users_last_session = user.galaxy_sessions[0]
         except Exception:
             users_last_session = None
-        if (prev_galaxy_session and
-                prev_galaxy_session.current_history and not
-                prev_galaxy_session.current_history.deleted and
-                prev_galaxy_session.current_history.datasets and
-                (prev_galaxy_session.current_history.user is None or
-                 prev_galaxy_session.current_history.user == user)):
+        if (prev_galaxy_session
+                and prev_galaxy_session.current_history
+                and not prev_galaxy_session.current_history.deleted
+                and prev_galaxy_session.current_history.datasets
+                and (prev_galaxy_session.current_history.user is None
+                     or prev_galaxy_session.current_history.user == user)):
             # If the previous galaxy session had a history, associate it with the new session, but only if it didn't
             # belong to a different user.
             history = prev_galaxy_session.current_history
@@ -689,8 +666,8 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
                 set_permissions = True
         elif self.galaxy_session.current_history:
             history = self.galaxy_session.current_history
-        if (not history and users_last_session and
-                users_last_session.current_history and not
+        if (not history and users_last_session
+                and users_last_session.current_history and not
                 users_last_session.current_history.deleted):
             history = users_last_session.current_history
         elif not history:
@@ -765,8 +742,10 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
     def get_history(self, create=False, most_recent=False):
         """
         Load the current history.
+
             - If that isn't available, we find the most recently updated history.
             - If *that* isn't available, we get or create the default history.
+
         Transactions will not always have an active history (API requests), so
         None is a valid response.
         """
@@ -786,7 +765,9 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
         self.sa_session.add(self.galaxy_session)
         self.sa_session.flush()
 
-    history = property(get_history, set_history)
+    @property
+    def history(self):
+        return self.get_history()
 
     def get_or_create_default_history(self):
         """
diff --git a/lib/galaxy/webapps/galaxy/api/annotations.py b/lib/galaxy/webapps/galaxy/api/annotations.py
index 155ef385803..b9d323c90d4 100644
--- a/lib/galaxy/webapps/galaxy/api/annotations.py
+++ b/lib/galaxy/webapps/galaxy/api/annotations.py
@@ -2,11 +2,13 @@
 API operations on annotations.
 """
 import logging
+from abc import abstractmethod
 
 from galaxy import (
     exceptions,
     managers
 )
+from galaxy.managers.context import ProvidesHistoryContext
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web import expose_api
@@ -19,16 +21,17 @@ log = logging.getLogger(__name__)
 
 
 class BaseAnnotationsController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnnotations):
+    tagged_item_id: str
 
     @expose_api
-    def index(self, trans, **kwd):
+    def index(self, trans: ProvidesHistoryContext, **kwd):
         idnum = kwd[self.tagged_item_id]
         item = self._get_item_from_id(trans, idnum)
         if item is not None:
-            return self.get_item_annotation_str(trans.sa_session, trans.get_user(), item)
+            return self.get_item_annotation_str(trans.sa_session, trans.user, item)
 
     @expose_api
-    def create(self, trans, payload, **kwd):
+    def create(self, trans: ProvidesHistoryContext, payload: dict, **kwd):
         if "text" not in payload:
             return ""
         idnum = kwd[self.tagged_item_id]
@@ -38,22 +41,26 @@ class BaseAnnotationsController(BaseAPIController, UsesStoredWorkflowMixin, Uses
             # TODO: sanitize on display not entry
             new_annotation = sanitize_html(new_annotation)
 
-            self.add_item_annotation(trans.sa_session, trans.get_user(), item, new_annotation)
+            self.add_item_annotation(trans.sa_session, trans.user, item, new_annotation)
             trans.sa_session.flush()
             return new_annotation
         return ""
 
     @expose_api
-    def delete(self, trans, **kwd):
+    def delete(self, trans: ProvidesHistoryContext, **kwd):
         idnum = kwd[self.tagged_item_id]
         item = self._get_item_from_id(trans, idnum)
         if item is not None:
-            return self.delete_item_annotation(trans.sa_session, trans.get_user(), item)
+            return self.delete_item_annotation(trans.sa_session, trans.user, item)
 
     @expose_api
-    def undelete(self, trans, **kwd):
+    def undelete(self, trans: ProvidesHistoryContext, **kwd):
         raise exceptions.NotImplemented()
 
+    @abstractmethod
+    def _get_item_from_id(self, trans: ProvidesHistoryContext, idstr):
+        """Return item with annotation association."""
+
 
 class HistoryAnnotationsController(BaseAnnotationsController):
     controller_name = "history_annotations"
@@ -63,7 +70,7 @@ class HistoryAnnotationsController(BaseAnnotationsController):
         super().__init__(app)
         self.history_manager = managers.histories.HistoryManager(app)
 
-    def _get_item_from_id(self, trans, idstr):
+    def _get_item_from_id(self, trans: ProvidesHistoryContext, idstr):
         decoded_idstr = self.decode_id(idstr)
         history = self.history_manager.get_accessible(decoded_idstr, trans.user, current_history=trans.history)
         return history
@@ -77,7 +84,7 @@ class HistoryContentAnnotationsController(BaseAnnotationsController):
         super().__init__(app)
         self.hda_manager = managers.hdas.HDAManager(app)
 
-    def _get_item_from_id(self, trans, idstr):
+    def _get_item_from_id(self, trans: ProvidesHistoryContext, idstr):
         decoded_idstr = self.decode_id(idstr)
         hda = self.hda_manager.get_accessible(decoded_idstr, trans.user)
         hda = self.hda_manager.error_if_uploading(hda)
@@ -88,6 +95,6 @@ class WorkflowAnnotationsController(BaseAnnotationsController):
     controller_name = "workflow_annotations"
     tagged_item_id = "workflow_id"
 
-    def _get_item_from_id(self, trans, idstr):
+    def _get_item_from_id(self, trans: ProvidesHistoryContext, idstr):
         hda = self.get_stored_workflow(trans, idstr)
         return hda
diff --git a/lib/galaxy/webapps/galaxy/api/authenticate.py b/lib/galaxy/webapps/galaxy/api/authenticate.py
index df34bc3ddc6..52a08de6239 100644
--- a/lib/galaxy/webapps/galaxy/api/authenticate.py
+++ b/lib/galaxy/webapps/galaxy/api/authenticate.py
@@ -8,7 +8,6 @@ Sample usage
 
 Returns
 
-.. highlight:: json
 .. code-block:: json
 
     {
@@ -21,29 +20,21 @@ from base64 import b64decode
 from urllib.parse import unquote
 
 from galaxy import exceptions
-from galaxy.managers import (
-    api_keys,
-    users,
-)
 from galaxy.util import (
     smart_str,
     unicodify
 )
 from galaxy.web import expose_api_anonymous_and_sessionless
 from galaxy.webapps.base.controller import BaseAPIController
+from galaxy.webapps.base.webapp import GalaxyWebTransaction
 
 log = logging.getLogger(__name__)
 
 
 class AuthenticationController(BaseAPIController):
 
-    def __init__(self, app):
-        super().__init__(app)
-        self.user_manager = users.UserManager(app)
-        self.api_keys_manager = api_keys.ApiKeyManager(app)
-
     @expose_api_anonymous_and_sessionless
-    def options(self, trans, **kwd):
+    def options(self, trans: GalaxyWebTransaction, **kwd):
         """
         A no-op endpoint to return generic OPTIONS for the API.
         Any OPTIONS request to /api/* maps here.
@@ -57,7 +48,7 @@ class AuthenticationController(BaseAPIController):
         # trans.response.headers['Access-Control-Allow-Methods'] = 'POST, PUT, GET, OPTIONS, DELETE'
 
     @expose_api_anonymous_and_sessionless
-    def get_api_key(self, trans, **kwd):
+    def get_api_key(self, trans: GalaxyWebTransaction, **kwd):
         """
         GET /api/authenticate/baseauth
           returns an API key for authenticated user based on BaseAuth headers
@@ -69,12 +60,12 @@ class AuthenticationController(BaseAPIController):
         """
         identity, password = self._decode_baseauth(trans.environ.get('HTTP_AUTHORIZATION'))
         # check if this is an email address or username
-        user = self.user_manager.get_user_by_identity(identity)
+        user = self.app.user_manager.get_user_by_identity(identity)
         if not user:
             raise exceptions.ObjectNotFound('The user does not exist.')
         is_valid_user = self.app.auth_manager.check_password(user, password)
         if is_valid_user:
-            key = self.api_keys_manager.get_or_create_api_key(user)
+            key = self.app.api_keys_manager.get_or_create_api_key(user)
             return dict(api_key=key)
         else:
             raise exceptions.AuthenticationFailed('Invalid password.')
@@ -95,7 +86,10 @@ class AuthenticationController(BaseAPIController):
 
         :raises: HTTPBadRequest
         """
-        split = encoded_str.strip().split(' ')
+        try:
+            split = encoded_str.strip().split(' ')
+        except AttributeError:
+            raise exceptions.RequestParameterInvalidException('Authentication is missing')
 
         # If split is only one element, try to decode the email and password
         # directly.
diff --git a/lib/galaxy/webapps/galaxy/api/dataset_collections.py b/lib/galaxy/webapps/galaxy/api/dataset_collections.py
index ffc0ebbb85a..43d8dd20aad 100644
--- a/lib/galaxy/webapps/galaxy/api/dataset_collections.py
+++ b/lib/galaxy/webapps/galaxy/api/dataset_collections.py
@@ -2,14 +2,15 @@ from logging import getLogger
 
 import routes
 
-from galaxy import managers
-from galaxy.exceptions import ObjectNotFound
+from galaxy.exceptions import ObjectNotFound, RequestParameterInvalidException
 from galaxy.managers.base import decode_id
+from galaxy.managers.collections import DatasetCollectionManager
 from galaxy.managers.collections_util import (
     api_payload_to_create_params,
     dictify_dataset_collection_instance,
     dictify_element_reference
 )
+from galaxy.managers.context import ProvidesHistoryContext
 from galaxy.web import expose_api
 from galaxy.webapps.base.controller import (
     BaseAPIController,
@@ -26,7 +27,7 @@ class DatasetCollectionsController(
 
     def __init__(self, app):
         super().__init__(app)
-        self.history_manager = managers.histories.HistoryManager(app)
+        self.history_manager = app.history_manager
 
     @expose_api
     def index(self, trans, **kwd):
@@ -34,7 +35,7 @@ class DatasetCollectionsController(
         return 'not implemented'
 
     @expose_api
-    def create(self, trans, payload, **kwd):
+    def create(self, trans: ProvidesHistoryContext, payload: dict, **kwd):
         """
         * POST /api/dataset_collections:
             create a new dataset collection instance.
@@ -62,15 +63,15 @@ class DatasetCollectionsController(
             self.check_user_can_add_to_library_item(trans, library_folder, check_accessible=False)
             create_params["parent"] = library_folder
         else:
-            trans.status = 501
-            return
-        dataset_collection_instance = self.__service(trans).create(trans=trans, **create_params)
+            raise RequestParameterInvalidException()
+
+        dataset_collection_instance = self.__service.create(trans=trans, **create_params)
         return dictify_dataset_collection_instance(dataset_collection_instance,
                                                    security=trans.security, parent=create_params["parent"])
 
     @expose_api
-    def show(self, trans, instance_type, id, **kwds):
-        dataset_collection_instance = self.__service(trans).get_dataset_collection_instance(
+    def show(self, trans: ProvidesHistoryContext, instance_type, id, **kwds):
+        dataset_collection_instance = self.__service.get_dataset_collection_instance(
             trans,
             id=id,
             instance_type=instance_type,
@@ -80,8 +81,8 @@ class DatasetCollectionsController(
         elif instance_type == 'library':
             parent = dataset_collection_instance.folder
         else:
-            trans.status = 501
-            return
+            raise RequestParameterInvalidException()
+
         return dictify_dataset_collection_instance(
             dataset_collection_instance,
             security=trans.security,
@@ -90,7 +91,7 @@ class DatasetCollectionsController(
         )
 
     @expose_api
-    def contents(self, trans, hdca_id, parent_id, instance_type='history', limit=None, offset=None, **kwds):
+    def contents(self, trans: ProvidesHistoryContext, hdca_id, parent_id, instance_type='history', limit=None, offset=None, **kwds):
         """
         GET /api/dataset_collection/{hdca_id}/contents/{parent_id}?limit=100&offset=0
 
@@ -107,7 +108,7 @@ class DatasetCollectionsController(
         :rtype:     list
         :returns:   list of dataset collection elements and contents
         """
-        svc = self.__service(trans)
+        svc = self.__service
         encode_id = trans.app.security.encode_id
 
         # validate HDCA for current user, will throw error if not permitted
@@ -138,6 +139,7 @@ class DatasetCollectionsController(
         results = contents_qry.with_session(trans.sa_session()).all()
         return [process_element(el) for el in results]
 
-    def __service(self, trans):
-        service = trans.app.dataset_collections_service
+    @property
+    def __service(self) -> DatasetCollectionManager:
+        service = self.app.dataset_collections_service
         return service
diff --git a/lib/galaxy/webapps/galaxy/api/datatypes.py b/lib/galaxy/webapps/galaxy/api/datatypes.py
index 3f17f881df6..bd089330d5d 100644
--- a/lib/galaxy/webapps/galaxy/api/datatypes.py
+++ b/lib/galaxy/webapps/galaxy/api/datatypes.py
@@ -2,14 +2,141 @@
 API operations allowing clients to determine datatype supported by Galaxy.
 """
 import logging
+from typing import (
+    Dict,
+    List,
+    Optional,
+    Union,
+)
 
-from galaxy.datatypes.data import Data
+from fastapi import (
+    Depends,
+    Query,
+)
+from fastapi_utils.cbv import cbv
+from fastapi_utils.inferring_router import InferringRouter as APIRouter
+
+from galaxy.app import UniverseApplication
+from galaxy.datatypes.registry import Registry
+from galaxy.managers.datatypes import (
+    DatatypeConverterList,
+    DatatypeDetails,
+    DatatypesCombinedMap,
+    DatatypesMap,
+    view_converters,
+    view_edam_data,
+    view_edam_formats,
+    view_index,
+    view_mapping,
+    view_sniffers,
+    view_types_and_mapping
+)
 from galaxy.util import asbool
 from galaxy.web import expose_api_anonymous_and_sessionless
 from galaxy.webapps.base.controller import BaseAPIController
+from . import get_app
 
 log = logging.getLogger(__name__)
 
+router = APIRouter(tags=['datatypes'])
+
+ExtensionOnlyQueryParam: Optional[bool] = Query(
+    default=True,
+    title="Extension only",
+    description="Whether to return only the datatype's extension rather than the datatype's details",
+)
+
+UploadOnlyQueryParam: Optional[bool] = Query(
+    default=True,
+    title="Upload only",
+    description="Whether to return only datatypes which can be uploaded",
+)
+
+
+def get_datatypes_registry(app: UniverseApplication = Depends(get_app)) -> Registry:
+    return app.datatypes_registry
+
+
+@cbv(router)
+class FastAPIDatatypes:
+    datatypes_registry: Registry = Depends(get_datatypes_registry)
+
+    @router.get(
+        '/api/datatypes',
+        summary="Lists all available data types",
+        response_description="List of data types",
+    )
+    async def index(
+        self,
+        extension_only: Optional[bool] = ExtensionOnlyQueryParam,
+        upload_only: Optional[bool] = UploadOnlyQueryParam
+    ) -> Union[List[DatatypeDetails], List[str]]:
+        """Gets the list of all available data types."""
+        return view_index(self.datatypes_registry, extension_only, upload_only)
+
+    @router.get(
+        '/api/datatypes/mapping',
+        summary="Returns mappings for data types and their implementing classes",
+        response_description="Dictionary to map data types with their classes"
+    )
+    async def mapping(self) -> DatatypesMap:
+        """Gets mappings for data types."""
+        return view_mapping(self.datatypes_registry)
+
+    @router.get(
+        '/api/datatypes/types_and_mapping',
+        summary="Returns all the data types extensions and their mappings",
+        response_description="Dictionary to map data types with their classes"
+    )
+    async def types_and_mapping(
+        self,
+        extension_only: Optional[bool] = ExtensionOnlyQueryParam,
+        upload_only: Optional[bool] = UploadOnlyQueryParam
+    ) -> DatatypesCombinedMap:
+        """Combines the datatype information from (/api/datatypes) and the
+        mapping information from (/api/datatypes/mapping) into a single
+        response."""
+        return DatatypesCombinedMap(
+            datatypes=view_index(self.datatypes_registry, extension_only, upload_only),
+            datatypes_mapping=view_mapping(self.datatypes_registry)
+        )
+
+    @router.get(
+        '/api/datatypes/sniffers',
+        summary="Returns the list of all installed sniffers",
+        response_description="List of datatype sniffers"
+    )
+    async def sniffers(self) -> List[str]:
+        """Gets the list of all installed data type sniffers."""
+        return view_sniffers(self.datatypes_registry)
+
+    @router.get(
+        '/api/datatypes/converters',
+        summary="Returns the list of all installed converters",
+        response_description="List of all datatype converters"
+    )
+    async def converters(self) -> DatatypeConverterList:
+        """Gets the list of all installed converters."""
+        return view_converters(self.datatypes_registry)
+
+    @router.get(
+        '/api/datatypes/edam_formats',
+        summary="Returns a dictionary/map of datatypes and EDAM formats",
+        response_description="Dictionary/map of datatypes and EDAM formats"
+    )
+    async def edam_formats(self) -> Dict[str, str]:
+        """Gets a map of datatypes and their corresponding EDAM formats."""
+        return self.datatypes_registry.edam_formats
+
+    @router.get(
+        '/api/datatypes/edam_data',
+        summary="Returns a dictionary/map of datatypes and EDAM data",
+        response_description="Dictionary/map of datatypes and EDAM data"
+    )
+    async def edam_data(self) -> Dict[str, str]:
+        """Gets a map of datatypes and their corresponding EDAM data."""
+        return self.datatypes_registry.edam_data
+
 
 class DatatypesController(BaseAPIController):
 
@@ -19,28 +146,9 @@ class DatatypesController(BaseAPIController):
         GET /api/datatypes
         Return an object containing upload datatypes.
         """
-        try:
-            return self._index(trans, **kwd)
-        except Exception as e:
-            log.exception('Could not get datatypes')
-            raise e
-
-    def _index(self, trans, **kwd):
-        datatypes_registry = self._datatypes_registry
         extension_only = asbool(kwd.get('extension_only', True))
         upload_only = asbool(kwd.get('upload_only', True))
-        if extension_only:
-            if upload_only:
-                return datatypes_registry.upload_file_formats
-            else:
-                return [ext for ext in datatypes_registry.datatypes_by_extension]
-        else:
-            rval = []
-            for datatype_info_dict in datatypes_registry.datatype_info_dicts:
-                if not datatype_info_dict.get('display_in_upload') and upload_only:
-                    continue
-                rval.append(datatype_info_dict)
-            return rval
+        return view_index(self._datatypes_registry, extension_only, upload_only)
 
     @expose_api_anonymous_and_sessionless
     def mapping(self, trans, **kwd):
@@ -48,32 +156,7 @@ class DatatypesController(BaseAPIController):
         GET /api/datatypes/mapping
         Return a dictionary of class to class mappings.
         '''
-        try:
-            return self._mapping()
-        except Exception as e:
-            log.exception('Could not get datatype mapping')
-            raise e
-
-    def _mapping(self):
-        ext_to_class_name = dict()
-        classes = []
-        for k, v in self._datatypes_registry.datatypes_by_extension.items():
-            c = v.__class__
-            ext_to_class_name[k] = c.__module__ + "." + c.__name__
-            classes.append(c)
-        class_to_classes = dict()
-
-        def visit_bases(types, cls):
-            for base in cls.__bases__:
-                if issubclass(base, Data):
-                    types.add(base.__module__ + "." + base.__name__)
-                visit_bases(types, base)
-        for c in classes:
-            n = c.__module__ + "." + c.__name__
-            types = {n}
-            visit_bases(types, c)
-            class_to_classes[n] = {t: True for t in types}
-        return dict(ext_to_class_name=ext_to_class_name, class_to_classes=class_to_classes)
+        return view_mapping(self._datatypes_registry)
 
     @expose_api_anonymous_and_sessionless
     def types_and_mapping(self, trans, **kwd):
@@ -84,10 +167,9 @@ class DatatypesController(BaseAPIController):
         mapping information from (/api/datatypes/mapping) into a single
         response.
         """
-        return {
-            "datatypes": self._index(trans, **kwd),
-            "datatypes_mapping": self._mapping(),
-        }
+        extension_only = asbool(kwd.get('extension_only', True))
+        upload_only = asbool(kwd.get('upload_only', True))
+        return view_types_and_mapping(self._datatypes_registry, extension_only, upload_only)
 
     @expose_api_anonymous_and_sessionless
     def sniffers(self, trans, **kwd):
@@ -95,37 +177,19 @@ class DatatypesController(BaseAPIController):
         GET /api/datatypes/sniffers
         Return a list of sniffers.
         '''
-        try:
-            rval = []
-            for sniffer_elem in self._datatypes_registry.sniffer_elems:
-                datatype = sniffer_elem.get('type')
-                if datatype is not None:
-                    rval.append(datatype)
-            return rval
-        except Exception as e:
-            log.exception('Could not get datatypes')
-            raise e
+        return view_sniffers(self._datatypes_registry)
 
     @expose_api_anonymous_and_sessionless
     def converters(self, trans, **kwd):
-        converters = []
-        for (source_type, targets) in self._datatypes_registry.datatype_converters.items():
-            for target_type in targets:
-                converters.append({
-                    'source': source_type,
-                    'target': target_type,
-                    'tool_id': targets[target_type].id,
-                })
-
-        return converters
+        return view_converters(self._datatypes_registry)
 
     @expose_api_anonymous_and_sessionless
     def edam_formats(self, trans, **kwds):
-        return self._datatypes_registry.edam_formats
+        return view_edam_formats(self._datatypes_registry)
 
     @expose_api_anonymous_and_sessionless
     def edam_data(self, trans, **kwds):
-        return self._datatypes_registry.edam_data
+        return view_edam_data(self._datatypes_registry)
 
     @property
     def _datatypes_registry(self):
diff --git a/lib/galaxy/webapps/galaxy/api/histories.py b/lib/galaxy/webapps/galaxy/api/histories.py
index e7fd32d92a8..701542b4935 100644
--- a/lib/galaxy/webapps/galaxy/api/histories.py
+++ b/lib/galaxy/webapps/galaxy/api/histories.py
@@ -475,9 +475,10 @@ class HistoriesController(BaseAPIController, ExportsHistoryMixin, ImportsHistory
     @expose_api
     def index_exports(self, trans, id):
         """
-        index_exports(self, trans, id)
-        * GET /api/histories/{id}/exports:
-            Get history exports.
+        GET /api/histories/{id}/exports
+
+        Get previous history exports (to links). Effectively returns serialized
+        JEHA objects.
         """
         return self.history_export_view.get_exports(trans, id)
 
@@ -576,6 +577,6 @@ class HistoriesController(BaseAPIController, ExportsHistoryMixin, ImportsHistory
             .filter_by(history=history, extension="fasta", deleted=False) \
             .order_by(model.HistoryDatasetAssociation.hid.desc())
         return {
-            'installed_builds'  : [{'label' : ins, 'value' : ins} for ins in installed_builds],
-            'fasta_hdas'        : [{'label' : f'{hda.hid}: {hda.name}', 'value' : trans.security.encode_id(hda.id)} for hda in fasta_hdas],
+            'installed_builds': [{'label': ins, 'value': ins} for ins in installed_builds],
+            'fasta_hdas': [{'label': f'{hda.hid}: {hda.name}', 'value': trans.security.encode_id(hda.id)} for hda in fasta_hdas],
         }
diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py
index a39a65cc130..dc56cddb868 100644
--- a/lib/galaxy/webapps/galaxy/api/jobs.py
+++ b/lib/galaxy/webapps/galaxy/api/jobs.py
@@ -21,6 +21,7 @@ from galaxy import (
 )
 from galaxy.app import UniverseApplication
 from galaxy.managers import hdas
+from galaxy.managers.context import ProvidesHistoryContext, ProvidesUserContext
 from galaxy.managers.jobs import (
     JobLock,
     JobManager,
@@ -30,6 +31,7 @@ from galaxy.managers.jobs import (
     summarize_job_parameters,
     view_show_job,
 )
+from galaxy.model import Job
 from galaxy.schema.fields import EncodedDatabaseIdField
 from galaxy.web import (
     expose_api,
@@ -41,7 +43,6 @@ from galaxy.webapps.base.controller import (
     UsesVisualizationMixin
 )
 from galaxy.work.context import (
-    SessionRequestContext,
     WorkRequestContext,
 )
 from . import (
@@ -70,7 +71,7 @@ class FastAPIJobs:
     hda_manager: hdas.HDAManager = Depends(get_hda_manager)
 
     @router.get("/api/job/{id}")
-    def show(self, id: EncodedDatabaseIdField, trans: SessionRequestContext = Depends(get_trans), full: typing.Optional[bool] = False) -> typing.Dict:
+    def show(self, id: EncodedDatabaseIdField, trans: ProvidesUserContext = Depends(get_trans), full: typing.Optional[bool] = False) -> typing.Dict:
         """
         Return dictionary containing description of job data
 
@@ -92,7 +93,7 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
         self.hda_manager = hdas.HDAManager(app)
 
     @expose_api
-    def index(self, trans, **kwd):
+    def index(self, trans: ProvidesUserContext, **kwd):
         """
         GET /api/jobs
 
@@ -127,9 +128,9 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
         user_details = kwd.get('user_details', False)
 
         if is_admin:
-            query = trans.sa_session.query(trans.app.model.Job)
+            query = trans.sa_session.query(Job)
         else:
-            query = trans.sa_session.query(trans.app.model.Job).filter(trans.app.model.Job.user == trans.user)
+            query = trans.sa_session.query(Job).filter(Job.table.c.user_id == trans.user.id)
 
         def build_and_apply_filters(query, objects, filter_func):
             if objects is not None:
@@ -142,27 +143,27 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
                     query = query.filter(or_(*t))
             return query
 
-        query = build_and_apply_filters(query, state, lambda s: trans.app.model.Job.state == s)
+        query = build_and_apply_filters(query, state, lambda s: Job.table.c.state == s)
 
-        query = build_and_apply_filters(query, kwd.get('tool_id', None), lambda t: trans.app.model.Job.tool_id == t)
-        query = build_and_apply_filters(query, kwd.get('tool_id_like', None), lambda t: trans.app.model.Job.tool_id.like(t))
+        query = build_and_apply_filters(query, kwd.get('tool_id', None), lambda t: Job.tool_id == t)
+        query = build_and_apply_filters(query, kwd.get('tool_id_like', None), lambda t: Job.tool_id.like(t))
 
-        query = build_and_apply_filters(query, kwd.get('date_range_min', None), lambda dmin: trans.app.model.Job.table.c.update_time >= dmin)
-        query = build_and_apply_filters(query, kwd.get('date_range_max', None), lambda dmax: trans.app.model.Job.table.c.update_time <= dmax)
+        query = build_and_apply_filters(query, kwd.get('date_range_min', None), lambda dmin: Job.table.c.update_time >= dmin)
+        query = build_and_apply_filters(query, kwd.get('date_range_max', None), lambda dmax: Job.table.c.update_time <= dmax)
 
         history_id = kwd.get('history_id', None)
         if history_id is not None:
             try:
                 decoded_history_id = self.decode_id(history_id)
-                query = query.filter(trans.app.model.Job.history_id == decoded_history_id)
+                query = query.filter(Job.table.c.history_id == decoded_history_id)
             except Exception:
                 raise exceptions.ObjectAttributeInvalidException()
 
         out = []
         if kwd.get('order_by') == 'create_time':
-            order_by = trans.app.model.Job.create_time.desc()
+            order_by = Job.table.c.create_time.desc()
         else:
-            order_by = trans.app.model.Job.update_time.desc()
+            order_by = Job.table.c.update_time.desc()
         for job in query.order_by(order_by).all():
             job_dict = job.to_dict('collection', system_details=is_admin)
             j = self.encode_all_ids(trans, job_dict, True)
@@ -173,7 +174,7 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
         return out
 
     @expose_api_anonymous
-    def show(self, trans, id, **kwd):
+    def show(self, trans: ProvidesUserContext, id, **kwd):
         """
         show( trans, id )
         * GET /api/jobs/{id}:
@@ -193,7 +194,7 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
         return view_show_job(trans, job, full_output)
 
     @expose_api
-    def common_problems(self, trans, id, **kwd):
+    def common_problems(self, trans: ProvidesUserContext, id, **kwd):
         """
         * GET /api/jobs/{id}/common_problems
             check inputs and job for common potential problems to aid in error reporting
@@ -219,7 +220,7 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
         return {"has_empty_inputs": has_empty_inputs, "has_duplicate_inputs": has_duplicate_inputs}
 
     @expose_api
-    def inputs(self, trans, id, **kwd):
+    def inputs(self, trans: ProvidesUserContext, id, **kwd):
         """
         GET /api/jobs/{id}/inputs
 
@@ -235,7 +236,7 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
         return self.__dictify_associations(trans, job.input_datasets, job.input_library_datasets)
 
     @expose_api
-    def outputs(self, trans, id, **kwd):
+    def outputs(self, trans: ProvidesUserContext, id, **kwd):
         """
         outputs( trans, id )
         * GET /api/jobs/{id}/outputs
@@ -251,7 +252,7 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
         return self.__dictify_associations(trans, job.output_datasets, job.output_library_datasets)
 
     @expose_api
-    def delete(self, trans, id, **kwd):
+    def delete(self, trans: ProvidesUserContext, id, **kwd):
         """
         delete( trans, id )
         * Delete /api/jobs/{id}
@@ -268,7 +269,7 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
         return self.job_manager.stop(job, message=message)
 
     @expose_api
-    def resume(self, trans, id, **kwd):
+    def resume(self, trans: ProvidesUserContext, id, **kwd):
         """
         * PUT /api/jobs/{id}/resume
             Resumes a paused job
@@ -289,7 +290,7 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
         return self.__dictify_associations(trans, job.output_datasets, job.output_library_datasets)
 
     @expose_api_anonymous
-    def metrics(self, trans, **kwd):
+    def metrics(self, trans: ProvidesUserContext, **kwd):
         """
         * GET /api/jobs/{job_id}/metrics
         * GET /api/datasets/{dataset_id}/metrics
@@ -314,7 +315,7 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
 
     @require_admin
     @expose_api
-    def destination_params(self, trans, **kwd):
+    def destination_params(self, trans: ProvidesUserContext, **kwd):
         """
         * GET /api/jobs/{job_id}/destination_params
             Return destination parameters for specified job.
@@ -329,7 +330,7 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
         return summarize_destination_params(trans, job)
 
     @expose_api_anonymous
-    def parameters_display(self, trans, **kwd):
+    def parameters_display(self, trans: ProvidesUserContext, **kwd):
         """
         * GET /api/jobs/{job_id}/parameters_display
         * GET /api/datasets/{dataset_id}/parameters_display
@@ -360,7 +361,7 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
         return summarize_job_parameters(trans, job)
 
     @expose_api_anonymous
-    def build_for_rerun(self, trans, id, **kwd):
+    def build_for_rerun(self, trans: ProvidesHistoryContext, id, **kwd):
         """
         * GET /api/jobs/{id}/build_for_rerun
             returns a tool input/param template prepopulated with this job's
@@ -411,12 +412,12 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
             return dataset_instance.creating_job
 
     @expose_api
-    def create(self, trans, payload, **kwd):
+    def create(self, trans: ProvidesUserContext, payload, **kwd):
         """ See the create method in tools.py in order to submit a job. """
         raise exceptions.NotImplemented('Please POST to /api/tools instead.')
 
     @expose_api
-    def search(self, trans, payload, **kwd):
+    def search(self, trans: ProvidesHistoryContext, payload: dict, **kwd):
         """
         search( trans, payload )
         * POST /api/jobs/search:
@@ -464,7 +465,7 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
         return [self.encode_all_ids(trans, single_job.to_dict('element'), True) for single_job in jobs]
 
     @expose_api_anonymous
-    def error(self, trans, id, payload, **kwd):
+    def error(self, trans: ProvidesUserContext, id, payload, **kwd):
         """
         error( trans, id )
         * POST /api/jobs/{id}/error
@@ -505,7 +506,7 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
 
     @require_admin
     @expose_api
-    def show_job_lock(self, trans, **kwd):
+    def show_job_lock(self, trans: ProvidesUserContext, **kwd):
         """
         * GET /api/job_lock
             return boolean indicating if job lock active.
@@ -514,7 +515,7 @@ class JobController(BaseAPIController, UsesVisualizationMixin):
 
     @require_admin
     @expose_api
-    def update_job_lock(self, trans, payload, **kwd):
+    def update_job_lock(self, trans: ProvidesUserContext, payload, **kwd):
         """
         * PUT /api/job_lock
             return boolean indicating if job lock active.
diff --git a/lib/galaxy/webapps/galaxy/api/library_datasets.py b/lib/galaxy/webapps/galaxy/api/library_datasets.py
index 98734c31c6f..dfe82e65437 100644
--- a/lib/galaxy/webapps/galaxy/api/library_datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/library_datasets.py
@@ -436,7 +436,6 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin, Libra
                 raise exceptions.RequestParameterInvalidException('The given path is invalid.')
             path = os.path.join(import_base_dir, path)
         elif source in ['userdir_file', 'userdir_folder']:
-            unsafe = None
             username = trans.user.username if trans.app.config.user_library_import_check_permissions else None
             user_login = trans.user.email
             user_base_dir = trans.app.config.user_library_import_dir
@@ -454,14 +453,13 @@ class LibraryDatasetsController(BaseAPIController, UsesVisualizationMixin, Libra
                         '%s -> %s and cannot be read by them.', path, os.path.realpath(path))
                 raise exceptions.RequestParameterInvalidException('The given path is invalid.')
             path = os.path.join(full_dir, path)
-            for unsafe in unsafe_walk(path, allowlist=[full_dir] + trans.app.config.user_library_import_symlink_allowlist, username=username):
+            if unsafe_walk(path, allowlist=[full_dir] + trans.app.config.user_library_import_symlink_allowlist, username=username):
                 # the path is a dir and contains files that symlink outside the user dir
                 error = 'User attempted to import a path that resolves to a path outside of their import dir: %s -> %s', \
                         path, os.path.realpath(path)
                 if trans.app.config.user_library_import_check_permissions:
                     error += ' or is not readable for them.'
                 log.error(error)
-            if unsafe:
                 raise exceptions.RequestParameterInvalidException('The given path is invalid.')
             if not os.path.exists(path):
                 raise exceptions.RequestParameterInvalidException('Given path does not exist on the host.')
diff --git a/lib/galaxy/webapps/galaxy/api/licenses.py b/lib/galaxy/webapps/galaxy/api/licenses.py
index c058acad185..e7e6f09df93 100644
--- a/lib/galaxy/webapps/galaxy/api/licenses.py
+++ b/lib/galaxy/webapps/galaxy/api/licenses.py
@@ -4,8 +4,8 @@ from fastapi import (
     Depends,
     Path
 )
-from fastapi.routing import APIRouter
 from fastapi_utils.cbv import cbv
+from fastapi_utils.inferring_router import InferringRouter as APIRouter
 
 from galaxy.managers.licenses import (
     LicenseMetadataModel,
@@ -34,7 +34,6 @@ class FastAPILicenses:
 
     @router.get('/api/licenses',
         summary="Lists all available SPDX licenses",
-        response_model=List[LicenseMetadataModel],
         response_description="List of SPDX licenses")
     async def index(self) -> List[LicenseMetadataModel]:
         """Returns an index with all the available [SPDX licenses](https://spdx.org/licenses/)."""
@@ -42,7 +41,6 @@ class FastAPILicenses:
 
     @router.get('/api/licenses/{id}',
         summary="Gets the SPDX license metadata associated with the short identifier",
-        response_model=LicenseMetadataModel,
         response_description="SPDX license metadata")
     async def get(self, id=LicenseIdPath) -> LicenseMetadataModel:
         """Returns the license metadata associated with the given
diff --git a/lib/galaxy/webapps/galaxy/api/metrics.py b/lib/galaxy/webapps/galaxy/api/metrics.py
index ca5d8a93db5..699551a7d1e 100644
--- a/lib/galaxy/webapps/galaxy/api/metrics.py
+++ b/lib/galaxy/webapps/galaxy/api/metrics.py
@@ -71,10 +71,10 @@ class MetricsController(BaseAPIController):
             label = metric['namespace']
             time = self._deserialize_isoformat_date(metric['time'])
             kwargs = {
-                'level'   : metric['level'],
-                'args'    : metric['args'],
-                'user'    : user_id,
-                'session' : session_id
+                'level': metric['level'],
+                'args': metric['args'],
+                'user': user_id,
+                'session': session_id
             }
             yield (label, time, kwargs)
 
diff --git a/lib/galaxy/webapps/galaxy/api/remote_files.py b/lib/galaxy/webapps/galaxy/api/remote_files.py
index cd08d871f39..d7a7c074601 100644
--- a/lib/galaxy/webapps/galaxy/api/remote_files.py
+++ b/lib/galaxy/webapps/galaxy/api/remote_files.py
@@ -7,6 +7,7 @@ from operator import itemgetter
 
 from galaxy import exceptions
 from galaxy.files import ProvidesUserFileSourcesUserContext
+from galaxy.managers.context import ProvidesUserContext
 from galaxy.util import (
     jstree,
     smart_str,
@@ -20,7 +21,7 @@ log = logging.getLogger(__name__)
 class RemoteFilesAPIController(BaseAPIController):
 
     @expose_api
-    def index(self, trans, **kwd):
+    def index(self, trans: ProvidesUserContext, **kwd):
         """
         GET /api/remote_files/
 
@@ -94,7 +95,7 @@ class RemoteFilesAPIController(BaseAPIController):
         return index
 
     @expose_api
-    def plugins(self, trans, **kwd):
+    def plugins(self, trans: ProvidesUserContext, **kwd):
         """
         GET /api/remote_files/plugins
 
diff --git a/lib/galaxy/webapps/galaxy/api/roles.py b/lib/galaxy/webapps/galaxy/api/roles.py
index 41a42b0703d..0414bd39116 100644
--- a/lib/galaxy/webapps/galaxy/api/roles.py
+++ b/lib/galaxy/webapps/galaxy/api/roles.py
@@ -18,6 +18,7 @@ from pydantic import (
 from galaxy import web
 from galaxy.app import UniverseApplication
 from galaxy.managers.base import decode_id
+from galaxy.managers.context import ProvidesUserContext
 from galaxy.managers.roles import (
     RoleDefinitionModel,
     RoleManager,
@@ -25,9 +26,6 @@ from galaxy.managers.roles import (
 )
 from galaxy.schema.fields import EncodedDatabaseIdField
 from galaxy.webapps.base.controller import BaseAPIController, url_for
-from galaxy.work.context import (
-    SessionRequestContext,
-)
 from . import (
     get_admin_user,
     get_app,
@@ -65,26 +63,26 @@ class FastAPIRoles:
     role_manager: RoleManager = Depends(get_role_manager)
 
     @router.get('/api/roles')
-    def index(self, trans: SessionRequestContext = Depends(get_trans)) -> RoleListModel:
+    def index(self, trans: ProvidesUserContext = Depends(get_trans)) -> RoleListModel:
         roles = self.role_manager.list_displayable_roles(trans)
         return RoleListModel(__root__=[role_to_model(trans, r) for r in roles])
 
     @router.get('/api/roles/{id}')
-    def show(self, id: EncodedDatabaseIdField, trans: SessionRequestContext = Depends(get_trans)) -> RoleModel:
+    def show(self, id: EncodedDatabaseIdField, trans: ProvidesUserContext = Depends(get_trans)) -> RoleModel:
         role_id = trans.app.security.decode_id(id)
         role = self.role_manager.get(trans, role_id)
         return role_to_model(trans, role)
 
     @router.post("/api/roles")
-    def create(self, trans: SessionRequestContext = Depends(get_trans), admin_user=Depends(get_admin_user), role_definition_model: RoleDefinitionModel = Body(...)) -> RoleModel:
-        role = self.role_manager.create(trans, role_definition_model)
+    def create(self, trans: ProvidesUserContext = Depends(get_trans), admin_user=Depends(get_admin_user), role_definition_model: RoleDefinitionModel = Body(...)) -> RoleModel:
+        role = self.role_manager.create_role(trans, role_definition_model)
         return role_to_model(trans, role)
 
 
 class RoleAPIController(BaseAPIController):
 
     @web.expose_api
-    def index(self, trans, **kwd):
+    def index(self, trans: ProvidesUserContext, **kwd):
         """
         GET /api/roles
         Displays a collection (list) of roles.
@@ -93,7 +91,7 @@ class RoleAPIController(BaseAPIController):
         return RoleListModel(__root__=[role_to_model(trans, r) for r in roles])
 
     @web.expose_api
-    def show(self, trans, id, **kwd):
+    def show(self, trans: ProvidesUserContext, id: str, **kwd):
         """
         GET /api/roles/{encoded_role_id}
         Displays information about a role.
@@ -104,14 +102,14 @@ class RoleAPIController(BaseAPIController):
 
     @web.require_admin
     @web.expose_api
-    def create(self, trans, payload, **kwd):
+    def create(self, trans: ProvidesUserContext, payload, **kwd):
         """
         POST /api/roles
         Creates a new role.
         """
         expand_json_keys(payload, ["user_ids", "group_ids"])
         role_definition_model = RoleDefinitionModel(**payload)
-        role = self._role_manager.create(trans, role_definition_model)
+        role = self._role_manager.create_role(trans, role_definition_model)
         return role_to_model(trans, role)
 
     @property
@@ -119,7 +117,7 @@ class RoleAPIController(BaseAPIController):
         return self.app.role_manager
 
 
-def expand_json_keys(payload, keys):
+def expand_json_keys(payload: dict, keys):
     for key in keys:
         value = payload.get(key)
         if isinstance(value, str):
diff --git a/lib/galaxy/webapps/galaxy/api/search.py b/lib/galaxy/webapps/galaxy/api/search.py
index 7c5f4bead44..3b2871069ff 100644
--- a/lib/galaxy/webapps/galaxy/api/search.py
+++ b/lib/galaxy/webapps/galaxy/api/search.py
@@ -3,8 +3,9 @@ API for searching Galaxy Datasets
 """
 import logging
 
-from galaxy import web
+from galaxy import model, web
 from galaxy.exceptions import ItemAccessibilityException
+from galaxy.managers.context import ProvidesUserContext
 from galaxy.model.search import GalaxySearchEngine
 from galaxy.util import unicodify
 from galaxy.webapps.base.controller import (
@@ -18,7 +19,7 @@ log = logging.getLogger(__name__)
 class SearchController(BaseAPIController, SharableItemSecurityMixin):
 
     @web.legacy_expose_api
-    def create(self, trans, payload, **kwd):
+    def create(self, trans: ProvidesUserContext, payload: dict, **kwd):
         """
         POST /api/search
         Do a search of the various elements of Galaxy.
@@ -43,19 +44,19 @@ class SearchController(BaseAPIController, SharableItemSecurityMixin):
                     if trans.user_is_admin:
                         append = True
                     if not append:
-                        if type(item) in [trans.app.model.LibraryFolder, trans.app.model.LibraryDatasetDatasetAssociation, trans.app.model.LibraryDataset]:
+                        if type(item) in [model.LibraryFolder, model.LibraryDatasetDatasetAssociation, model.LibraryDataset]:
                             if (trans.app.security_agent.can_access_library_item(trans.get_current_user_roles(), item, trans.user)):
                                 append = True
-                        elif type(item) in [trans.app.model.Job]:
+                        elif type(item) in [model.Job]:
                             if item.used_id == trans.user or trans.user_is_admin:
                                 append = True
-                        elif type(item) in [trans.app.model.Page, trans.app.model.StoredWorkflow]:
+                        elif type(item) in [model.Page, model.StoredWorkflow]:
                             try:
                                 if self.security_check(trans, item, False, True):
                                     append = True
                             except ItemAccessibilityException:
                                 append = False
-                        elif type(item) in [trans.app.model.PageRevision]:
+                        elif type(item) in [model.PageRevision]:
                             try:
                                 if self.security_check(trans, item.page, False, True):
                                     append = True
diff --git a/lib/galaxy/webapps/galaxy/api/tags.py b/lib/galaxy/webapps/galaxy/api/tags.py
index 3fd9b51936d..9f0639f486c 100644
--- a/lib/galaxy/webapps/galaxy/api/tags.py
+++ b/lib/galaxy/webapps/galaxy/api/tags.py
@@ -6,6 +6,7 @@ import logging
 from galaxy.exceptions import MessageException
 from galaxy.web import expose_api
 from galaxy.webapps.base.controller import BaseAPIController, UsesTagsMixin
+from galaxy.webapps.base.webapp import GalaxyWebTransaction
 
 log = logging.getLogger(__name__)
 
@@ -14,7 +15,7 @@ class TagsController(BaseAPIController, UsesTagsMixin):
 
     # Retag an item. All previous tags are deleted and new tags are applied.
     @expose_api
-    def update(self, trans, payload, **kwd):
+    def update(self, trans: GalaxyWebTransaction, payload: dict, **kwd):
         """
         PUT /api/tags/
 
@@ -35,7 +36,7 @@ class TagsController(BaseAPIController, UsesTagsMixin):
         self.get_tag_handler(trans).apply_item_tags(user, item, item_tags)
         trans.sa_session.flush()
 
-    def _get_item(self, trans, item_class_name, id):
+    def _get_item(self, trans: GalaxyWebTransaction, item_class_name, id):
         """
         Get an item based on type and id.
         """
diff --git a/lib/galaxy/webapps/galaxy/api/tool_data.py b/lib/galaxy/webapps/galaxy/api/tool_data.py
index 9f3eb5d7a27..2d3a2098619 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_data.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_data.py
@@ -1,14 +1,137 @@
-import os
+from typing import Optional
 
-from galaxy import (
-    exceptions,
-    web
+from fastapi import (
+    Depends,
+    Path,
+)
+from fastapi.responses import FileResponse
+from fastapi_utils.cbv import cbv
+from fastapi_utils.inferring_router import InferringRouter as APIRouter
+
+from galaxy import web
+from galaxy.app import StructuredApp
+from galaxy.managers.context import ProvidesAppContext
+from galaxy.managers.tool_data import ToolDataManager
+from galaxy.tools.data._schema import (
+    ToolDataDetails,
+    ToolDataEntryList,
+    ToolDataField,
+    ToolDataItem,
 )
 from galaxy.web import (
     expose_api,
-    expose_api_raw
+    expose_api_raw,
 )
 from galaxy.webapps.base.controller import BaseAPIController
+from . import (
+    get_admin_user,
+    get_app,
+)
+
+router = APIRouter(tags=['tool data tables'])
+
+AdminUserRequired = Depends(get_admin_user)
+
+ToolDataTableName = Path(
+    ...,  # Mark this field as required
+    title="Data table name",
+    description="The name of the tool data table",
+    example="all_fasta",
+)
+
+ToolDataTableFieldName = Path(
+    ...,  # Mark this field as required
+    title="Field name",
+    description="The name of the tool data table field",
+)
+
+
+def get_tool_data_manager(app: StructuredApp = Depends(get_app)) -> ToolDataManager:
+    return ToolDataManager(app)
+
+
+@cbv(router)
+class FastAPIToolData:
+    tool_data_manager: ToolDataManager = Depends(get_tool_data_manager)
+
+    @router.get(
+        '/api/tool_data',
+        summary="Lists all available data tables",
+        response_description="A list with details on individual data tables.",
+        dependencies=[AdminUserRequired],
+    )
+    async def index(self) -> ToolDataEntryList:
+        """Get the list of all available data tables."""
+        return self.tool_data_manager.index()
+
+    @router.get(
+        '/api/tool_data/{table_name}',
+        summary="Get details of a given data table",
+        response_description="A description of the given data table and its content",
+        dependencies=[AdminUserRequired],
+    )
+    async def show(self, table_name: str = ToolDataTableName) -> ToolDataDetails:
+        """Get details of a given tool data table."""
+        return self.tool_data_manager.show(table_name)
+
+    @router.get(
+        '/api/tool_data/{table_name}/reload',
+        summary="Reloads a tool data table",
+        response_description="A description of the reloaded data table and its content",
+        dependencies=[AdminUserRequired],
+    )
+    async def reload(self, table_name: str = ToolDataTableName) -> ToolDataDetails:
+        """Reloads a data table and return its details."""
+        return self.tool_data_manager.reload(table_name)
+
+    @router.get(
+        '/api/tool_data/{table_name}/fields/{field_name}',
+        summary="Get information about a particular field in a tool data table",
+        response_description="Information about a data table field",
+        dependencies=[AdminUserRequired],
+    )
+    async def show_field(
+        self,
+        table_name: str = ToolDataTableName,
+        field_name: str = ToolDataTableFieldName,
+    ) -> ToolDataField:
+        """Reloads a data table and return its details."""
+        return self.tool_data_manager.show_field(table_name, field_name)
+
+    @router.get(
+        '/api/tool_data/{table_name}/fields/{field_name}/files/{file_name}',
+        summary="Get information about a particular field in a tool data table",
+        response_description="Information about a data table field",
+        response_class=FileResponse,
+        dependencies=[AdminUserRequired],
+    )
+    async def download_field_file(
+        self,
+        table_name: str = ToolDataTableName,
+        field_name: str = ToolDataTableFieldName,
+        file_name: str = Path(
+            ...,  # Mark this field as required
+            title="File name",
+            description="The name of a file associated with this data table field",
+        ),
+    ):
+        """Download a file associated with the data table field."""
+        path = self.tool_data_manager.get_field_file_path(table_name, field_name, file_name)
+        return FileResponse(str(path))
+
+    @router.delete(
+        '/api/tool_data/{table_name}',
+        summary="Removes an item from a data table",
+        response_description="A description of the affected data table and its content",
+        dependencies=[AdminUserRequired],
+    )
+    async def delete(
+        self,
+        payload: ToolDataItem,
+        table_name: str = ToolDataTableName,
+    ) -> ToolDataDetails:
+        """Removes an item from a data table and reloads it to return its updated details."""
+        return self.tool_data_manager.delete(table_name, payload.values)
 
 
 class ToolData(BaseAPIController):
@@ -16,20 +139,29 @@ class ToolData(BaseAPIController):
     RESTful controller for interactions with tool data
     """
 
+    def __init__(self, app):
+        super().__init__(app)
+        self.tool_data_manager = ToolDataManager(app)
+
     @web.require_admin
     @expose_api
-    def index(self, trans, **kwds):
+    def index(self, trans: ProvidesAppContext, **kwds):
         """
         GET /api/tool_data
 
         Return a list tool_data tables.
         """
-        return list(a.to_dict() for a in self._data_tables.values())
+        return self.tool_data_manager.index()
 
     @web.require_admin
     @expose_api
-    def show(self, trans, id, **kwds):
-        return self._data_table(id).to_dict(view='element')
+    def show(self, trans: ProvidesAppContext, id, **kwds):
+        details = self.tool_data_manager.show(id)
+        # Here dict(by_alias=True) is required to return
+        # `field_value` as `field` since `field` can not be directly
+        # used in the pydantic BaseModel and needs to be aliased
+        # For more details see: https://github.com/samuelcolvin/pydantic/issues/1250
+        return details.dict(by_alias=True)
 
     @web.require_admin
     @expose_api
@@ -39,19 +171,16 @@ class ToolData(BaseAPIController):
 
         Reloads a tool_data table.
         """
-        decoded_tool_data_id = id
-        data_table = trans.app.tool_data_tables.data_tables.get(decoded_tool_data_id)
-        data_table.reload_from_files()
-        trans.app.queue_worker.send_control_task(
-            'reload_tool_data_tables',
-            noop_self=True,
-            kwargs={'table_name': decoded_tool_data_id}
-        )
-        return self._data_table(decoded_tool_data_id).to_dict(view='element')
+        details = self.tool_data_manager.reload(id)
+        # Here dict(by_alias=True) is required to return
+        # `field_value` as `field` since `field` can not be directly
+        # used in the pydantic BaseModel and needs to be aliased
+        # For more details see: https://github.com/samuelcolvin/pydantic/issues/1250
+        return details.dict(by_alias=True)
 
     @web.require_admin
     @expose_api
-    def delete(self, trans, id, **kwd):
+    def delete(self, trans: ProvidesAppContext, id, **kwd):
         """
         DELETE /api/tool_data/{id}
         Removes an item from a data table
@@ -64,70 +193,32 @@ class ToolData(BaseAPIController):
             * payload:     a dictionary itself containing:
                 * values:   <TAB> separated list of column contents, there must be a value for all the columns of the data table
         """
-        decoded_tool_data_id = id
-
-        try:
-            data_table = trans.app.tool_data_tables.data_tables.get(decoded_tool_data_id)
-        except Exception:
-            data_table = None
-        if not data_table:
-            trans.response.status = 400
-            return "Invalid data table id ( %s ) specified." % str(decoded_tool_data_id)
-
-        values = None
+        values: Optional[str] = None
         if kwd.get('payload', None):
             values = kwd['payload'].get('values', '')
-
-        if not values:
-            trans.response.status = 400
-            return "Invalid data table item ( %s ) specified." % str(values)
-
-        split_values = values.split("\t")
-
-        if len(split_values) != len(data_table.get_column_name_list()):
-            trans.response.status = 400
-            return "Invalid data table item ( {} ) specified. Wrong number of columns ({} given, {} required).".format(str(values), str(len(split_values)), str(len(data_table.get_column_name_list())))
-
-        data_table.remove_entry(split_values)
-        trans.app.queue_worker.send_control_task(
-            'reload_tool_data_tables',
-            noop_self=True,
-            kwargs={'table_name': decoded_tool_data_id}
-        )
-        return self._data_table(decoded_tool_data_id).to_dict(view='element')
+        # Here dict(by_alias=True) is required to return
+        # `field_value` as `field` since `field` can not be directly
+        # used in the pydantic BaseModel and needs to be aliased
+        # For more details see: https://github.com/samuelcolvin/pydantic/issues/1250
+        return self.tool_data_manager.delete(id, values).dict(by_alias=True)
 
     @web.require_admin
     @expose_api
-    def show_field(self, trans, id, value, **kwds):
+    def show_field(self, trans: ProvidesAppContext, id, value, **kwds):
         """
         GET /api/tool_data/<id>/fields/<value>
 
         Get information about a partiular field in a tool_data table
         """
-        return self._data_table_field(id, value).to_dict()
+        field = self.tool_data_manager.show_field(id, value)
+        # Here dict(by_alias=True) is required to return
+        # `field_value` as `field` since `field` can not be directly
+        # used in the pydantic BaseModel and needs to be aliased
+        # For more details see: https://github.com/samuelcolvin/pydantic/issues/1250
+        return field.dict(by_alias=True)
 
     @web.require_admin
     @expose_api_raw
-    def download_field_file(self, trans, id, value, path, **kwds):
-        field_value = self._data_table_field(id, value)
-        base_dir = field_value.get_base_dir()
-        full_path = os.path.join(base_dir, path)
-        if full_path not in field_value.get_files():
-            raise exceptions.ObjectNotFound("No such path in data table field.")
+    def download_field_file(self, trans: ProvidesAppContext, id: str, value, path, **kwds):
+        full_path = self.tool_data_manager.get_field_file_path(id, value, path)
         return open(full_path, "rb")
-
-    def _data_table_field(self, id, value):
-        out = self._data_table(id).get_field(value)
-        if out is None:
-            raise exceptions.ObjectNotFound(f"No such field {value} in data table {id}.")
-        return out
-
-    def _data_table(self, id):
-        try:
-            return self._data_tables[id]
-        except IndexError:
-            raise exceptions.ObjectNotFound("No such data table %s" % id)
-
-    @property
-    def _data_tables(self):
-        return self.app.tool_data_tables.data_tables
diff --git a/lib/galaxy/webapps/galaxy/api/tool_dependencies.py b/lib/galaxy/webapps/galaxy/api/tool_dependencies.py
index c1b171c81c9..d4a28781e1b 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_dependencies.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_dependencies.py
@@ -2,7 +2,9 @@
 API operations allowing clients to manage tool dependencies.
 """
 import logging
+from typing import Optional
 
+from galaxy.managers.context import ProvidesAppContext
 from galaxy.tool_util.deps import views
 from galaxy.web import (
     expose_api,
@@ -21,7 +23,7 @@ class ToolDependenciesAPIController(BaseAPIController):
 
     @require_admin
     @expose_api
-    def index(self, trans, **kwd):
+    def index(self, trans: ProvidesAppContext, **kwd):
         """
         GET /api/dependency_resolvers
         """
@@ -29,7 +31,7 @@ class ToolDependenciesAPIController(BaseAPIController):
 
     @require_admin
     @expose_api
-    def show(self, trans, id):
+    def show(self, trans: ProvidesAppContext, id: str):
         """
         GET /api/dependency_resolvers/<id>
         """
@@ -47,7 +49,7 @@ class ToolDependenciesAPIController(BaseAPIController):
 
     @require_admin
     @expose_api
-    def resolver_dependency(self, trans, id, **kwds):
+    def resolver_dependency(self, trans: ProvidesAppContext, id: str, **kwds):
         """
         GET /api/dependency_resolvers/{index}/dependency
 
@@ -73,7 +75,7 @@ class ToolDependenciesAPIController(BaseAPIController):
 
     @require_admin
     @expose_api
-    def install_dependency(self, trans, id=None, **kwds):
+    def install_dependency(self, trans: ProvidesAppContext, id: Optional[str] = None, **kwds):
         """
         POST /api/dependency_resolvers/{index}/dependency
         POST /api/dependency_resolvers/dependency
@@ -103,7 +105,7 @@ class ToolDependenciesAPIController(BaseAPIController):
 
     @require_admin
     @expose_api
-    def manager_dependency(self, trans, **kwds):
+    def manager_dependency(self, trans: ProvidesAppContext, **kwds):
         """
         GET /api/dependency_resolvers/dependency
 
@@ -130,7 +132,7 @@ class ToolDependenciesAPIController(BaseAPIController):
 
     @require_admin
     @expose_api
-    def resolver_requirements(self, trans, id, **kwds):
+    def resolver_requirements(self, trans: ProvidesAppContext, id, **kwds):
         """
         GET /api/dependency_resolvers/{index}/requirements
 
@@ -149,7 +151,7 @@ class ToolDependenciesAPIController(BaseAPIController):
 
     @require_admin
     @expose_api
-    def manager_requirements(self, trans, **kwds):
+    def manager_requirements(self, trans: ProvidesAppContext, **kwds):
         """
         GET /api/dependency_resolvers/requirements
 
@@ -168,7 +170,7 @@ class ToolDependenciesAPIController(BaseAPIController):
 
     @require_admin
     @expose_api
-    def clean(self, trans, id=None, **kwds):
+    def clean(self, trans: ProvidesAppContext, id=None, **kwds):
         """
         POST /api/dependency_resolvers/{index}/clean
 
@@ -187,7 +189,7 @@ class ToolDependenciesAPIController(BaseAPIController):
 
     @expose_api
     @require_admin
-    def summarize_toolbox(self, trans, **kwds):
+    def summarize_toolbox(self, trans: ProvidesAppContext, **kwds):
         """
         GET /api/dependency_resolvers/toolbox
 
@@ -225,7 +227,7 @@ class ToolDependenciesAPIController(BaseAPIController):
 
     @expose_api
     @require_admin
-    def toolbox_install(self, trans, payload, index=None, **kwds):
+    def toolbox_install(self, trans: ProvidesAppContext, payload, index=None, **kwds):
         """
         POST /api/dependency_resolvers/{index}/toolbox/install
         POST /api/dependency_resolvers/toolbox/install
@@ -259,7 +261,7 @@ class ToolDependenciesAPIController(BaseAPIController):
 
     @expose_api
     @require_admin
-    def toolbox_uninstall(self, trans, payload, index=None, **kwds):
+    def toolbox_uninstall(self, trans: ProvidesAppContext, payload, index=None, **kwds):
         """
         POST /api/dependency_resolvers/{index}/toolbox/uninstall
         POST /api/dependency_resolvers/toolbox/uninstall
@@ -278,7 +280,7 @@ class ToolDependenciesAPIController(BaseAPIController):
         :type   resolver_type:  str
         :param  resolver_type:  restrict to uninstall to specified resolver type
         """
-        tools_by_id = trans.app.toolbox.tools_by_id.copy()
+        tools_by_id = self.app.toolbox.tools_by_id.copy()
         tool_ids = payload.get("tool_ids")
         requirements = {tools_by_id[tid].tool_requirements for tid in tool_ids}
         install_kwds = {}
@@ -294,7 +296,7 @@ class ToolDependenciesAPIController(BaseAPIController):
 
     @expose_api
     @require_admin
-    def unused_dependency_paths(self, trans, **kwds):
+    def unused_dependency_paths(self, trans: ProvidesAppContext, **kwds):
         """
         GET /api/dependency_resolvers/unused_paths
         """
@@ -302,7 +304,7 @@ class ToolDependenciesAPIController(BaseAPIController):
 
     @expose_api
     @require_admin
-    def delete_unused_dependency_paths(self, trans, payload, **kwds):
+    def delete_unused_dependency_paths(self, trans: ProvidesAppContext, payload, **kwds):
         """
         PUT /api/dependency_resolvers/unused_paths
         """
diff --git a/lib/galaxy/webapps/galaxy/api/tool_entry_points.py b/lib/galaxy/webapps/galaxy/api/tool_entry_points.py
index 59f60c71a13..6d792cabc08 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_entry_points.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_entry_points.py
@@ -4,7 +4,11 @@ related to running and queued jobs.
 import logging
 
 from galaxy import exceptions, util
-from galaxy.managers.interactivetool import InteractiveToolManager
+from galaxy.managers.context import ProvidesUserContext
+from galaxy.model import (
+    InteractiveToolEntryPoint,
+    Job,
+)
 from galaxy.web import expose_api_anonymous_and_sessionless
 from galaxy.webapps.base.controller import BaseAPIController
 
@@ -15,10 +19,10 @@ class ToolEntryPointsAPIController(BaseAPIController):
 
     def __init__(self, app):
         self.app = app
-        self.interactivetool_manager = InteractiveToolManager(app)
+        self.interactivetool_manager = app.interactivetool_manager
 
     @expose_api_anonymous_and_sessionless
-    def index(self, trans, running=False, job_id=None, **kwd):
+    def index(self, trans: ProvidesUserContext, running=False, job_id=None, **kwd):
         """
         * GET /api/entry_points
             Returns tool entry point information. Currently passing a job_id
@@ -42,7 +46,7 @@ class ToolEntryPointsAPIController(BaseAPIController):
             raise exceptions.RequestParameterInvalidException("Currently this API must passed only a job id or running=true")
 
         if job_id is not None:
-            job = trans.sa_session.query(trans.app.model.Job).get(self.decode_id(job_id))
+            job = trans.sa_session.query(Job).get(self.decode_id(job_id))
             if not self.interactivetool_manager.can_access_job(trans, job):
                 raise exceptions.ItemAccessibilityException()
             entry_points = job.interactivetool_entry_points
@@ -59,7 +63,7 @@ class ToolEntryPointsAPIController(BaseAPIController):
         return rval
 
     @expose_api_anonymous_and_sessionless
-    def access_entry_point(self, trans, id, **kwd):
+    def access_entry_point(self, trans: ProvidesUserContext, id, **kwd):
         """
         * GET /api/entry_points/{id}/access
             Return the URL target described by the entry point.
@@ -77,7 +81,7 @@ class ToolEntryPointsAPIController(BaseAPIController):
         return {"target": self.interactivetool_manager.access_entry_point_target(trans, entry_point_id)}
 
     @expose_api_anonymous_and_sessionless
-    def stop_entry_point(self, trans, id, **kwds):
+    def stop_entry_point(self, trans: ProvidesUserContext, id, **kwds):
         """
         DELETE /api/entry_points/{id}
         """
@@ -85,10 +89,10 @@ class ToolEntryPointsAPIController(BaseAPIController):
             raise exceptions.RequestParameterMissingException("Must supply entry point id")
         try:
             entry_point_id = self.decode_id(id)
-            entry_point = trans.sa_session.query(trans.app.model.InteractiveToolEntryPoint).get(entry_point_id)
+            entry_point = trans.sa_session.query(InteractiveToolEntryPoint).get(entry_point_id)
         except Exception:
             raise exceptions.RequestParameterInvalidException("entry point '{id}' invalid")
-        if trans.app.interactivetool_manager.can_access_entry_point(trans, entry_point):
-            trans.app.interactivetool_manager.stop(trans, entry_point)
+        if self.app.interactivetool_manager.can_access_entry_point(trans, entry_point):
+            self.app.interactivetool_manager.stop(trans, entry_point)
         else:
             raise exceptions.ItemAccessibilityException(f"entry point '{id}' is not accessible")
diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
index d15a9bd4188..ade2cad3315 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
@@ -16,6 +16,8 @@ from galaxy import (
     exceptions,
     util
 )
+from galaxy.managers.context import ProvidesUserContext
+from galaxy.model.tool_shed_install import ToolShedRepository
 from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager
 from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
 from galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager
@@ -67,7 +69,7 @@ class ToolShedRepositoriesController(BaseAPIController):
         return value_mapper
 
     @expose_api
-    def index(self, trans, **kwd):
+    def index(self, trans: ProvidesUserContext, **kwd):
         """
         GET /api/tool_shed_repositories
         Display a list of dictionaries containing information about installed tool shed repositories.
@@ -75,19 +77,19 @@ class ToolShedRepositoriesController(BaseAPIController):
         # Example URL: http://localhost:8763/api/tool_shed_repositories
         clause_list = []
         if 'name' in kwd:
-            clause_list.append(self.app.install_model.ToolShedRepository.table.c.name == kwd.get('name'))
+            clause_list.append(ToolShedRepository.table.c.name == kwd.get('name'))
         if 'owner' in kwd:
-            clause_list.append(self.app.install_model.ToolShedRepository.table.c.owner == kwd.get('owner'))
+            clause_list.append(ToolShedRepository.table.c.owner == kwd.get('owner'))
         if 'changeset' in kwd:
-            clause_list.append(self.app.install_model.ToolShedRepository.table.c.changeset_revision == kwd.get('changeset'))
+            clause_list.append(ToolShedRepository.table.c.changeset_revision == kwd.get('changeset'))
         if 'deleted' in kwd:
-            clause_list.append(self.app.install_model.ToolShedRepository.table.c.deleted == util.asbool(kwd.get('deleted')))
+            clause_list.append(ToolShedRepository.table.c.deleted == util.asbool(kwd.get('deleted')))
         if 'uninstalled' in kwd:
-            clause_list.append(self.app.install_model.ToolShedRepository.table.c.uninstalled == util.asbool(kwd.get('uninstalled')))
+            clause_list.append(ToolShedRepository.table.c.uninstalled == util.asbool(kwd.get('uninstalled')))
         tool_shed_repository_dicts = []
-        query = trans.install_model.context.query(self.app.install_model.ToolShedRepository) \
-                                           .order_by(self.app.install_model.ToolShedRepository.table.c.name) \
-                                           .order_by(cast(self.app.install_model.ToolShedRepository.ctx_rev, Integer).desc())
+        query = trans.install_model.context.query(ToolShedRepository) \
+                                           .order_by(ToolShedRepository.table.c.name) \
+                                           .order_by(cast(ToolShedRepository.ctx_rev, Integer).desc())
         if len(clause_list) > 0:
             query = query.filter(and_(*clause_list))
         for tool_shed_repository in query.all():
@@ -101,7 +103,7 @@ class ToolShedRepositoriesController(BaseAPIController):
 
     @require_admin
     @expose_api
-    def install_repository_revision(self, trans, payload, **kwd):
+    def install_repository_revision(self, trans: ProvidesUserContext, payload, **kwd):
         """
         POST /api/tool_shed_repositories/install_repository_revision
         Install a specified repository revision from a specified tool shed into Galaxy.
@@ -420,10 +422,9 @@ class ToolShedRepositoriesController(BaseAPIController):
         """
         GET /api/tool_shed_repositories/{encoded_tool_shed_repsository_id}
 
-        Display a dictionary containing information about a specified tool_shed_repository
+        Display a dictionary containing information about a specified tool_shed_repository.
 
-        .. highlight:: json
-        .. code-block:: json
+        .. code-block::
 
             {
                 id: (string) Galaxy ID
diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index b5cc2992f76..41e2c51b0ed 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -1,9 +1,11 @@
 import logging
 import os
 from json import dumps, loads
+from typing import Any, cast, Dict, Optional
 
-from galaxy import exceptions, managers, util, web
+from galaxy import exceptions, util, web
 from galaxy.managers.collections_util import dictify_dataset_collection_instance
+from galaxy.model import PostJobAction
 from galaxy.tools import global_tool_errors
 from galaxy.util.zipstream import ZipstreamWrapper
 from galaxy.web import (
@@ -14,6 +16,7 @@ from galaxy.web import (
 )
 from galaxy.webapps.base.controller import BaseAPIController
 from galaxy.webapps.base.controller import UsesVisualizationMixin
+from galaxy.webapps.base.webapp import GalaxyWebTransaction
 from ._fetch_util import validate_and_normalize_targets
 
 log = logging.getLogger(__name__)
@@ -32,23 +35,23 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
 
     def __init__(self, app):
         super().__init__(app)
-        self.history_manager = managers.histories.HistoryManager(app)
-        self.hda_manager = managers.hdas.HDAManager(app)
+        self.history_manager = app.history_manager
+        self.hda_manager = app.hda_manager
 
     @expose_api_anonymous_and_sessionless
-    def index(self, trans, **kwds):
+    def index(self, trans: GalaxyWebTransaction, **kwds):
         """
-        GET /api/tools: returns a list of tools defined by parameters::
+        GET /api/tools
 
-            parameters:
+        returns a list of tools defined by parameters
 
-                in_panel  - if true, tools are returned in panel structure,
-                            including sections and labels
-                trackster - if true, only tools that are compatible with
-                            Trackster are returned
-                q         - if present search on the given query will be performed
-                tool_id   - if present the given tool_id will be searched for
-                            all installed versions
+        :param in_panel: if true, tools are returned in panel structure,
+                         including sections and labels
+        :param trackster: if true, only tools that are compatible with
+                          Trackster are returned
+        :param q: if present search on the given query will be performed
+        :param tool_id: if present the given tool_id will be searched for
+                        all installed versions
         """
 
         # Read params.
@@ -93,7 +96,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
             raise exceptions.InternalServerError("Error: Could not convert toolbox to dictionary")
 
     @expose_api_anonymous_and_sessionless
-    def show(self, trans, id, **kwd):
+    def show(self, trans: GalaxyWebTransaction, id, **kwd):
         """
         GET /api/tools/{tool_id}
 
@@ -112,13 +115,12 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
         return tool.to_dict(trans, io_details=io_details, link_details=link_details)
 
     @expose_api_anonymous
-    def build(self, trans, id, **kwd):
+    def build(self, trans: GalaxyWebTransaction, id, **kwd):
         """
         GET /api/tools/{tool_id}/build
         Returns a tool model including dynamic parameters and updated values, repeats block etc.
         """
-        if 'payload' in kwd:
-            kwd = kwd.get('payload')
+        kwd = _kwd_or_payload(kwd)
         tool_version = kwd.get('tool_version')
         history_id = kwd.pop('history_id', None)
         history = None
@@ -129,13 +131,11 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
 
     @web.require_admin
     @expose_api
-    def test_data_path(self, trans, id, **kwd):
+    def test_data_path(self, trans: GalaxyWebTransaction, id, **kwd):
         """
         GET /api/tools/{tool_id}/test_data_path?tool_version={tool_version}
         """
-        # TODO: eliminate copy and paste with above code.
-        if 'payload' in kwd:
-            kwd = kwd.get('payload')
+        kwd = _kwd_or_payload(kwd)
         tool_version = kwd.get('tool_version', None)
         tool = self._get_tool(id, tool_version=tool_version, user=trans.user)
         path = tool.test_data_path(kwd.get("filename"))
@@ -145,7 +145,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
             raise exceptions.ObjectNotFound("Specified test data path not found.")
 
     @expose_api_raw_anonymous_and_sessionless
-    def test_data_download(self, trans, id, **kwd):
+    def test_data_download(self, trans: GalaxyWebTransaction, id, **kwd):
         """
         GET /api/tools/{tool_id}/test_data_download?tool_version={tool_version}&filename={filename}
         """
@@ -172,7 +172,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
         raise exceptions.ObjectNotFound("Specified test data path not found.")
 
     @expose_api_anonymous_and_sessionless
-    def tests_summary(self, trans, **kwd):
+    def tests_summary(self, trans: GalaxyWebTransaction, **kwd):
         """
         GET /api/tools/tests_summary
 
@@ -182,7 +182,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
 
         Fetch complete test data for each tool with /api/tools/{tool_id}/test_data?tool_version=<tool_version>
         """
-        test_counts_by_tool = {}
+        test_counts_by_tool: Dict[str, Dict] = {}
         for _id, tool in self.app.toolbox.tools():
             if not tool.is_datatype_converter:
                 tests = tool.tests
@@ -197,7 +197,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
         return test_counts_by_tool
 
     @expose_api_anonymous_and_sessionless
-    def test_data(self, trans, id, **kwd):
+    def test_data(self, trans: GalaxyWebTransaction, id, **kwd):
         """
         GET /api/tools/{tool_id}/test_data?tool_version={tool_version}
 
@@ -210,8 +210,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
         If tool version is not passed, it is assumed to be latest. Tool version can be
         set as '*' to get tests for all configured versions.
         """
-        if 'payload' in kwd:
-            kwd = kwd.get('payload')
+        kwd = _kwd_or_payload(kwd)
         tool_version = kwd.get('tool_version', None)
         if tool_version == "*":
             tools = self.app.toolbox.get_tool(id, get_all_versions=True)
@@ -228,7 +227,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
 
     @web.require_admin
     @expose_api
-    def reload(self, trans, id, **kwd):
+    def reload(self, trans: GalaxyWebTransaction, id, **kwd):
         """
         GET /api/tools/{tool_id}/reload
         Reload specified tool.
@@ -241,7 +240,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
 
     @web.require_admin
     @expose_api
-    def all_requirements(self, trans, **kwds):
+    def all_requirements(self, trans: GalaxyWebTransaction, **kwds):
         """
         GET /api/tools/all_requirements
         Return list of unique requirements for all tools.
@@ -251,7 +250,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
 
     @web.require_admin
     @expose_api
-    def requirements(self, trans, id, **kwds):
+    def requirements(self, trans: GalaxyWebTransaction, id, **kwds):
         """
         GET /api/tools/{tool_id}/requirements
         Return the resolver status for a specific tool id.
@@ -262,7 +261,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
 
     @web.require_admin
     @expose_api
-    def install_dependencies(self, trans, id, **kwds):
+    def install_dependencies(self, trans: GalaxyWebTransaction, id, **kwds):
         """
         POST /api/tools/{tool_id}/dependencies
 
@@ -290,7 +289,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
 
     @web.require_admin
     @expose_api
-    def uninstall_dependencies(self, trans, id, **kwds):
+    def uninstall_dependencies(self, trans: GalaxyWebTransaction, id, **kwds):
         """
         DELETE /api/tools/{tool_id}/dependencies
 
@@ -312,7 +311,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
 
     @web.require_admin
     @expose_api
-    def build_dependency_cache(self, trans, id, **kwds):
+    def build_dependency_cache(self, trans: GalaxyWebTransaction, id, **kwds):
         """
         POST /api/tools/{tool_id}/build_dependency_cache
         Attempts to cache installed dependencies.
@@ -327,7 +326,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
 
     @web.require_admin
     @expose_api
-    def diagnostics(self, trans, id, **kwd):
+    def diagnostics(self, trans: GalaxyWebTransaction, id, **kwd):
         """
         GET /api/tools/{tool_id}/diagnostics
         Return diagnostic information to help debug panel
@@ -343,10 +342,9 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
         else:
             lineage_dict = None
         tool_shed_dependencies = tool.installed_tool_dependencies
+        tool_shed_dependencies_dict: Optional[list] = None
         if tool_shed_dependencies:
             tool_shed_dependencies_dict = list(map(to_dict, tool_shed_dependencies))
-        else:
-            tool_shed_dependencies_dict = None
         return {
             "tool_id": tool.id,
             "tool_version": tool.version,
@@ -362,7 +360,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
             "guid": tool.guid,
         }
 
-    def _detect(self, trans, tool_id):
+    def _detect(self, trans: GalaxyWebTransaction, tool_id):
         """
         Detect whether the tool with the given id is installed.
 
@@ -418,7 +416,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
         return results
 
     @expose_api_anonymous_and_sessionless
-    def citations(self, trans, id, **kwds):
+    def citations(self, trans: GalaxyWebTransaction, id, **kwds):
         tool = self._get_tool(id, user=trans.user)
         rval = []
         for citation in tool.citations:
@@ -426,13 +424,13 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
         return rval
 
     @expose_api_anonymous_and_sessionless
-    def xrefs(self, trans, id, **kwds):
+    def xrefs(self, trans: GalaxyWebTransaction, id, **kwds):
         tool = self._get_tool(id, user=trans.user)
         return tool.xrefs
 
     @web.require_admin
     @web.legacy_expose_api_raw
-    def download(self, trans, id, **kwds):
+    def download(self, trans: GalaxyWebTransaction, id, **kwds):
         tool_tarball = trans.app.toolbox.package_tool(trans, id)
         trans.response.set_content_type('application/x-gzip')
         download_file = open(tool_tarball, "rb")
@@ -440,7 +438,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
         return download_file
 
     @expose_api_anonymous
-    def fetch(self, trans, payload, **kwd):
+    def fetch(self, trans: GalaxyWebTransaction, payload, **kwd):
         """Adapt clean API to tool-constrained API.
         """
         request_version = '1'
@@ -473,7 +471,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
 
     @web.require_admin
     @expose_api
-    def error_stack(self, trans, **kwd):
+    def error_stack(self, trans: GalaxyWebTransaction, **kwd):
         """
         GET /api/tools/error_stack
         Returns global tool error stack
@@ -481,7 +479,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
         return global_tool_errors.error_stack
 
     @expose_api_anonymous
-    def create(self, trans, payload, **kwd):
+    def create(self, trans: GalaxyWebTransaction, payload, **kwd):
         """
         POST /api/tools
         Execute tool with a given parameter payload
@@ -497,7 +495,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
             raise exceptions.RequestParameterInvalidException("Must specify a valid tool_id to use this endpoint.")
         return self._create(trans, payload, **kwd)
 
-    def _create(self, trans, payload, **kwd):
+    def _create(self, trans: GalaxyWebTransaction, payload, **kwd):
         action = payload.get('action')
         if action == 'rerun':
             raise Exception("'rerun' action has been deprecated")
@@ -565,7 +563,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
 
         # TODO: check for errors and ensure that output dataset(s) are available.
         output_datasets = vars.get('out_data', [])
-        rval = {'outputs': [], 'output_collections': [], 'jobs': [], 'implicit_collections': []}
+        rval: Dict[str, Any] = {'outputs': [], 'output_collections': [], 'jobs': [], 'implicit_collections': []}
         rval['produces_entry_points'] = tool.produces_entry_points
         job_errors = vars.get('job_errors', [])
         if job_errors:
@@ -591,7 +589,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
                 if trans.user is None:
                     raise exceptions.ToolExecutionError("Anonymously run jobs cannot send an email notification.")
                 else:
-                    job_email_action = trans.model.PostJobAction('EmailAction')
+                    job_email_action = PostJobAction('EmailAction')
                     job.add_post_job_action(job_email_action)
                     new_pja_flush = True
 
@@ -612,7 +610,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
 
         return rval
 
-    def _patch_library_inputs(self, trans, inputs, target_history):
+    def _patch_library_inputs(self, trans: GalaxyWebTransaction, inputs, target_history):
         """
         Transform inputs from the data libaray to history items.
         """
@@ -627,7 +625,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
                         v['values'][index] = patched
             inputs[k] = v
 
-    def _patch_library_dataset(self, trans, v, target_history):
+    def _patch_library_dataset(self, trans: GalaxyWebTransaction, v, target_history):
         if isinstance(v, dict) and 'id' in v and v.get('src') == 'ldda':
             ldda = trans.sa_session.query(trans.app.model.LibraryDatasetDatasetAssociation).get(self.decode_id(v['id']))
             if trans.user_is_admin or trans.app.security_agent.can_access_dataset(trans.get_current_user_roles(), ldda.dataset):
@@ -643,3 +641,9 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
         if not tool.allow_user_access(user):
             raise exceptions.AuthenticationFailed("Access denied, please login for tool with id '%s'." % id)
         return tool
+
+
+def _kwd_or_payload(kwd: Dict[str, Any]) -> Dict[str, Any]:
+    if 'payload' in kwd:
+        kwd = cast(Dict[str, Any], kwd.get('payload'))
+    return kwd
diff --git a/lib/galaxy/webapps/galaxy/api/tours.py b/lib/galaxy/webapps/galaxy/api/tours.py
index 9c7e36c9025..22c63da34c9 100644
--- a/lib/galaxy/webapps/galaxy/api/tours.py
+++ b/lib/galaxy/webapps/galaxy/api/tours.py
@@ -3,16 +3,56 @@ API Controller providing Galaxy Tours
 """
 import logging
 
+from fastapi import Depends
+from fastapi_utils.cbv import cbv
+from fastapi_utils.inferring_router import InferringRouter as APIRouter
+
+from galaxy.tours import (
+    TourDetails,
+    TourList,
+    ToursRegistry,
+)
 from galaxy.web import (
     expose_api_anonymous_and_sessionless,
     legacy_expose_api,
     require_admin
 )
 from galaxy.webapps.base.controller import BaseAPIController
+from . import (
+    get_admin_user,
+    get_app,
+)
 
 log = logging.getLogger(__name__)
 
 
+router = APIRouter(tags=['tours'])
+
+
+def get_tours_registry(app=Depends(get_app)) -> ToursRegistry:
+    return app.tour_registry
+
+
+@cbv(router)
+class FastAPITours:
+    registry: ToursRegistry = Depends(get_tours_registry)
+
+    @router.get('/api/tours')
+    def index(self) -> TourList:
+        """Return list of available tours."""
+        return self.registry.get_tours()
+
+    @router.get('/api/tours/{tour_id}')
+    def show(self, tour_id: str) -> TourDetails:
+        """Return a tour definition."""
+        return self.registry.tour_contents(tour_id)
+
+    @router.post('/api/tours/{tour_id}', dependencies=[Depends(get_admin_user)])
+    def update_tour(self, tour_id: str) -> TourDetails:
+        """Return a tour definition."""
+        return self.registry.load_tour(tour_id)
+
+
 class ToursController(BaseAPIController):
 
     def __init__(self, app):
@@ -25,7 +65,7 @@ class ToursController(BaseAPIController):
 
         Displays available tours
         """
-        return self.app.tour_registry.tours_by_id_with_description()
+        return self.app.tour_registry.get_tours()
 
     @expose_api_anonymous_and_sessionless
     def show(self, trans, tour_id, **kwd):
diff --git a/lib/galaxy/webapps/galaxy/api/users.py b/lib/galaxy/webapps/galaxy/api/users.py
index c7184b8f00a..10afdd28f41 100644
--- a/lib/galaxy/webapps/galaxy/api/users.py
+++ b/lib/galaxy/webapps/galaxy/api/users.py
@@ -20,7 +20,12 @@ from galaxy import (
     web
 )
 from galaxy.exceptions import ObjectInvalid
-from galaxy.managers import users
+from galaxy.managers import (
+    api_keys,
+    users
+)
+from galaxy.managers.context import ProvidesUserContext
+from galaxy.model import User, UserAddress
 from galaxy.security.validate_user_input import (
     validate_email,
     validate_password,
@@ -39,25 +44,26 @@ from galaxy.web.form_builder import AddressField
 from galaxy.webapps.base.controller import (
     BaseAPIController,
     BaseUIController,
-    CreatesApiKeysMixin,
     UsesFormDefinitionsMixin,
     UsesTagsMixin
 )
+from galaxy.webapps.base.webapp import GalaxyWebTransaction
 
 
 log = logging.getLogger(__name__)
 
 
-class UserAPIController(BaseAPIController, UsesTagsMixin, CreatesApiKeysMixin, BaseUIController, UsesFormDefinitionsMixin):
+class UserAPIController(BaseAPIController, UsesTagsMixin, BaseUIController, UsesFormDefinitionsMixin):
 
     def __init__(self, app):
         super().__init__(app)
         self.user_manager = users.UserManager(app)
         self.user_serializer = users.UserSerializer(app)
         self.user_deserializer = users.UserDeserializer(app)
+        self.api_key_manager = api_keys.ApiKeyManager(app)
 
     @expose_api
-    def index(self, trans, deleted='False', f_email=None, f_name=None, f_any=None, **kwd):
+    def index(self, trans: ProvidesUserContext, deleted='False', f_email=None, f_name=None, f_any=None, **kwd):
         """
         GET /api/users
         GET /api/users/deleted
@@ -83,37 +89,37 @@ class UserAPIController(BaseAPIController, UsesTagsMixin, CreatesApiKeysMixin, B
         :type  f_any: str
         """
         rval = []
-        query = trans.sa_session.query(trans.app.model.User)
+        query = trans.sa_session.query(User)
         deleted = util.string_as_bool(deleted)
 
         if f_email and (trans.user_is_admin or trans.app.config.expose_user_email):
-            query = query.filter(trans.app.model.User.email.like("%%%s%%" % f_email))
+            query = query.filter(User.email.like("%%%s%%" % f_email))
 
         if f_name and (trans.user_is_admin or trans.app.config.expose_user_name):
-            query = query.filter(trans.app.model.User.username.like("%%%s%%" % f_name))
+            query = query.filter(User.username.like("%%%s%%" % f_name))
 
         if f_any:
             if trans.user_is_admin:
                 query = query.filter(or_(
-                    trans.app.model.User.email.like("%%%s%%" % f_any),
-                    trans.app.model.User.username.like("%%%s%%" % f_any)
+                    User.email.like("%%%s%%" % f_any),
+                    User.username.like("%%%s%%" % f_any)
                 ))
             else:
                 if trans.app.config.expose_user_email and trans.app.config.expose_user_name:
                     query = query.filter(or_(
-                        trans.app.model.User.email.like("%%%s%%" % f_any),
-                        trans.app.model.User.username.like("%%%s%%" % f_any)
+                        User.email.like("%%%s%%" % f_any),
+                        User.username.like("%%%s%%" % f_any)
                     ))
                 elif trans.app.config.expose_user_email:
-                    query = query.filter(trans.app.model.User.email.like("%%%s%%" % f_any))
+                    query = query.filter(User.email.like("%%%s%%" % f_any))
                 elif trans.app.config.expose_user_name:
-                    query = query.filter(trans.app.model.User.username.like("%%%s%%" % f_any))
+                    query = query.filter(User.username.like("%%%s%%" % f_any))
 
         if deleted:
             # only admins can see deleted users
             if not trans.user_is_admin:
                 return []
-            query = query.filter(trans.app.model.User.table.c.deleted == true())
+            query = query.filter(User.table.c.deleted == true())
         else:
             # special case: user can see only their own user
             # special case2: if the galaxy admin has specified that other user email/names are
@@ -121,7 +127,7 @@ class UserAPIController(BaseAPIController, UsesTagsMixin, CreatesApiKeysMixin, B
             if not trans.user_is_admin and not trans.app.config.expose_user_name and not trans.app.config.expose_user_email:
                 item = trans.user.to_dict(value_mapper={'id': trans.security.encode_id})
                 return [item]
-            query = query.filter(trans.app.model.User.table.c.deleted == false())
+            query = query.filter(User.table.c.deleted == false())
         for user in query:
             item = user.to_dict(value_mapper={'id': trans.security.encode_id})
             # If NOT configured to expose_email, do not expose email UNLESS the user is self, or
@@ -143,7 +149,7 @@ class UserAPIController(BaseAPIController, UsesTagsMixin, CreatesApiKeysMixin, B
         return rval
 
     @expose_api_anonymous
-    def show(self, trans, id, deleted='False', **kwd):
+    def show(self, trans: ProvidesUserContext, id, deleted='False', **kwd):
         """
         GET /api/users/{encoded_id}
         GET /api/users/deleted/{encoded_id}
@@ -175,7 +181,7 @@ class UserAPIController(BaseAPIController, UsesTagsMixin, CreatesApiKeysMixin, B
         return self.user_serializer.serialize_to_view(user, view='detailed')
 
     @expose_api
-    def create(self, trans, payload, **kwd):
+    def create(self, trans: GalaxyWebTransaction, payload: dict, **kwd):
         """
         POST /api/users
         Creates a new Galaxy user.
@@ -202,7 +208,7 @@ class UserAPIController(BaseAPIController, UsesTagsMixin, CreatesApiKeysMixin, B
         return item
 
     @expose_api
-    def update(self, trans, id, payload, **kwd):
+    def update(self, trans: ProvidesUserContext, id: str, payload: dict, **kwd):
         """
         update( self, trans, id, payload, **kwd )
         * PUT /api/users/{id}
@@ -492,11 +498,11 @@ class UserAPIController(BaseAPIController, UsesTagsMixin, CreatesApiKeysMixin, B
             d = address_dicts[index]
             if d.get('id'):
                 try:
-                    user_address = trans.sa_session.query(trans.app.model.UserAddress).get(trans.security.decode_id(d['id']))
+                    user_address = trans.sa_session.query(UserAddress).get(trans.security.decode_id(d['id']))
                 except Exception as e:
                     raise exceptions.ObjectNotFound('Failed to access user address ({}). {}'.format(d['id'], e))
             else:
-                user_address = trans.model.UserAddress()
+                user_address = UserAddress()
                 trans.log_event('User address added')
             for field in AddressField.fields():
                 if str(field[2]).lower() == 'required' and not d.get(field[0]):
@@ -731,7 +737,16 @@ class UserAPIController(BaseAPIController, UsesTagsMixin, CreatesApiKeysMixin, B
         """
         payload = payload or {}
         user = self._get_user(trans, id)
-        return self.create_api_key(trans, user)
+        return self.api_key_manager.create_api_key(user)
+
+    @expose_api
+    def get_or_create_api_key(self, trans, id, payload=None, **kwd):
+        """
+        Unified 'get or create' for API key
+        """
+        payload = payload or {}
+        user = self._get_user(trans, id)
+        return self.api_key_manager.get_or_create_api_key(user)
 
     @expose_api
     def get_api_key(self, trans, id, payload=None, **kwd):
@@ -749,7 +764,7 @@ class UserAPIController(BaseAPIController, UsesTagsMixin, CreatesApiKeysMixin, B
         """
         payload = payload or {}
         user = self._get_user(trans, id)
-        self.create_api_key(trans, user)
+        self.api_key_manager.create_api_key(trans, user)
         return self._build_inputs_api_key(user, message='Generated a new web API key.')
 
     def _build_inputs_api_key(self, user, message=''):
diff --git a/lib/galaxy/webapps/galaxy/api/visualizations.py b/lib/galaxy/webapps/galaxy/api/visualizations.py
index 9e278a83c2c..dc14e6fa6d1 100644
--- a/lib/galaxy/webapps/galaxy/api/visualizations.py
+++ b/lib/galaxy/webapps/galaxy/api/visualizations.py
@@ -24,6 +24,7 @@ from galaxy.webapps.base.controller import (
     SharableMixin,
     UsesVisualizationMixin
 )
+from galaxy.webapps.base.webapp import GalaxyWebTransaction
 
 log = logging.getLogger(__name__)
 
@@ -39,7 +40,7 @@ class VisualizationsController(BaseAPIController, UsesVisualizationMixin, Sharab
         self.serializer = VisualizationSerializer(app)
 
     @expose_api
-    def index(self, trans, **kwargs):
+    def index(self, trans: GalaxyWebTransaction, **kwargs):
         """
         GET /api/visualizations:
         """
@@ -65,7 +66,7 @@ class VisualizationsController(BaseAPIController, UsesVisualizationMixin, Sharab
         return rval
 
     @expose_api
-    def show(self, trans, id, **kwargs):
+    def show(self, trans: GalaxyWebTransaction, id: str, **kwargs):
         """
         GET /api/visualizations/{viz_id}
         """
@@ -90,7 +91,7 @@ class VisualizationsController(BaseAPIController, UsesVisualizationMixin, Sharab
         return dictionary
 
     @expose_api
-    def create(self, trans, payload, **kwargs):
+    def create(self, trans: GalaxyWebTransaction, payload: dict, **kwargs):
         """
         POST /api/visualizations
         creates a new visualization using the given payload
@@ -101,7 +102,7 @@ class VisualizationsController(BaseAPIController, UsesVisualizationMixin, Sharab
         rval = None
 
         if 'import_id' in payload:
-            import_id = payload('import_id')
+            import_id = payload['import_id']
             visualization = self.import_visualization(trans, import_id, user=trans.user)
 
         else:
@@ -118,12 +119,12 @@ class VisualizationsController(BaseAPIController, UsesVisualizationMixin, Sharab
             except ValueError as val_err:
                 raise exceptions.RequestParameterMissingException(str(val_err))
 
-        rval = {'id' : trans.security.encode_id(visualization.id)}
+        rval = {'id': trans.security.encode_id(visualization.id)}
 
         return rval
 
     @expose_api
-    def update(self, trans, id, payload, **kwargs):
+    def update(self, trans: GalaxyWebTransaction, id: str, payload: dict, **kwargs):
         """
         PUT /api/visualizations/{encoded_visualization_id}
         """
@@ -145,11 +146,11 @@ class VisualizationsController(BaseAPIController, UsesVisualizationMixin, Sharab
         config = payload.get('config', visualization.latest_revision.config)
 
         latest_config = visualization.latest_revision.config
-        if((title != visualization.latest_revision.title) or
-                (dbkey != visualization.latest_revision.dbkey) or
-                (json.dumps(config) != json.dumps(latest_config))):
+        if((title != visualization.latest_revision.title)
+                or (dbkey != visualization.latest_revision.dbkey)
+                or (json.dumps(config) != json.dumps(latest_config))):
             revision = self.add_visualization_revision(trans, visualization, config, title, dbkey)
-            rval = {'id' : id, 'revision' : revision.id}
+            rval = {'id': id, 'revision': revision.id}
 
         # allow updating vis title
         visualization.title = title
diff --git a/lib/galaxy/webapps/galaxy/api/webhooks.py b/lib/galaxy/webapps/galaxy/api/webhooks.py
index 957759e85eb..cec2a6201e8 100644
--- a/lib/galaxy/webapps/galaxy/api/webhooks.py
+++ b/lib/galaxy/webapps/galaxy/api/webhooks.py
@@ -3,19 +3,19 @@ API Controller providing Galaxy Webhooks
 """
 import imp
 import logging
+from typing import Any
 
 from galaxy.web import expose_api_anonymous_and_sessionless
 from galaxy.webapps.base.controller import BaseAPIController
+from galaxy.webapps.base.webapp import GalaxyWebTransaction
 
 log = logging.getLogger(__name__)
 
 
 class WebhooksController(BaseAPIController):
-    def __init__(self, app):
-        super().__init__(app)
 
     @expose_api_anonymous_and_sessionless
-    def all_webhooks(self, trans, **kwd):
+    def all_webhooks(self, trans: GalaxyWebTransaction, **kwd):
         """
         GET /api/webhooks/
 
@@ -27,7 +27,7 @@ class WebhooksController(BaseAPIController):
         ]
 
     @expose_api_anonymous_and_sessionless
-    def webhook_data(self, trans, webhook_id, **kwd):
+    def webhook_data(self, trans: Any, webhook_id, **kwd):
         """
         GET /api/webhooks/{webhook_id}/data/{params}
 
@@ -44,6 +44,9 @@ class WebhooksController(BaseAPIController):
             if webhook.id == webhook_id
         )
 
-        return imp.load_source(webhook.path, webhook.helper).main(
-            trans, webhook, params,
-        ) if webhook and webhook.helper != '' else {}
+        if webhook and webhook.helper != '':
+            return imp.load_source(webhook.path, webhook.helper).main(  # type: ignore
+                trans, webhook, params,
+            )
+        else:
+            return {}
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 7420de8cadc..dcaae8435fd 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -6,6 +6,7 @@ import hashlib
 import json
 import logging
 import os
+from typing import Any, Dict
 
 import requests
 from gxformat2._yaml import ordered_dump
@@ -18,9 +19,7 @@ from galaxy import (
     model,
     util
 )
-from galaxy.managers import (
-    histories,
-)
+from galaxy.managers.context import ProvidesUserContext
 from galaxy.managers.jobs import fetch_job_states, invocation_job_source_iter, summarize_job_metrics
 from galaxy.managers.workflows import (
     MissingToolsException,
@@ -48,6 +47,7 @@ from galaxy.webapps.base.controller import (
     url_for,
     UsesStoredWorkflowMixin
 )
+from galaxy.webapps.base.webapp import GalaxyWebTransaction
 from galaxy.workflow.extract import extract_workflow
 from galaxy.workflow.modules import module_factory
 from galaxy.workflow.run import invoke, queue_invoke
@@ -60,7 +60,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
 
     def __init__(self, app):
         super().__init__(app)
-        self.history_manager = histories.HistoryManager(app)
+        self.history_manager = app.history_manager
         self.workflow_manager = app.workflow_manager
         self.workflow_contents_manager = app.workflow_contents_manager
         self.tool_recommendations = recommendations.ToolRecommendations()
@@ -72,19 +72,19 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         return None
 
     @expose_api_anonymous_and_sessionless
-    def index(self, trans, **kwd):
+    def index(self, trans: ProvidesUserContext, **kwd):
         """
         GET /api/workflows
         """
         return self.get_workflows_list(trans, **kwd)
 
     @expose_api
-    def get_workflow_menu(self, trans, **kwd):
+    def get_workflow_menu(self, trans: ProvidesUserContext, **kwd):
         """
         Get workflows present in the tools panel
         GET /api/workflows/menu
         """
-        user = trans.get_user()
+        user = trans.user
         ids_in_menu = [x.stored_workflow_id for x in user.stored_workflow_menu_entries]
         return {
             'ids_in_menu': ids_in_menu,
@@ -92,13 +92,13 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         }
 
     @expose_api
-    def set_workflow_menu(self, trans, **kwd):
+    def set_workflow_menu(self, trans: GalaxyWebTransaction, payload=None, **kwd):
         """
         Save workflow menu to be shown in the tool panel
         PUT /api/workflows/menu
         """
-        payload = kwd.get('payload')
-        user = trans.get_user()
+        payload = payload or {}
+        user = trans.user
         workflow_ids = payload.get('workflow_ids')
         if workflow_ids is None:
             workflow_ids = []
@@ -130,7 +130,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         trans.set_message(message)
         return {'message': message, 'status': 'done'}
 
-    def get_workflows_list(self, trans, missing_tools=False, show_published=None, show_hidden=False, show_deleted=False, **kwd):
+    def get_workflows_list(self, trans: ProvidesUserContext, missing_tools=False, show_published=None, show_hidden=False, show_deleted=False, **kwd):
         """
         Displays a collection of workflows.
 
@@ -144,17 +144,17 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         :type   missing_tools:       boolean
         """
         rval = []
-        filter1 = trans.app.model.StoredWorkflow.user == trans.user
-        user = trans.get_user()
+        filter1 = model.StoredWorkflow.user == trans.user
+        user = trans.user
         if show_published or user is None and show_published is None:
-            filter1 = or_(filter1, (trans.app.model.StoredWorkflow.published == true()))
-        query = trans.sa_session.query(trans.app.model.StoredWorkflow).options(
+            filter1 = or_(filter1, (model.StoredWorkflow.published == true()))
+        query = trans.sa_session.query(model.StoredWorkflow).options(
             joinedload("annotations")).options(
             joinedload("latest_workflow").undefer("step_count").lazyload("steps")).options(
             joinedload("tags")
         ).filter(filter1)
         query = query.filter_by(hidden=true() if show_hidden else false(), deleted=true() if show_deleted else false())
-        for wf in query.order_by(desc(trans.app.model.StoredWorkflow.table.c.update_time)).all():
+        for wf in query.order_by(desc(model.StoredWorkflow.table.c.update_time)).all():
             item = wf.to_dict(value_mapper={'id': trans.security.encode_id})
             encoded_id = trans.security.encode_id(wf.id)
             item['annotations'] = [x.annotation for x in wf.annotations]
@@ -171,7 +171,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
                 joinedload("stored_workflow").joinedload("latest_workflow").undefer("step_count").lazyload("steps")).options(
                 joinedload("stored_workflow").joinedload("user")).options(
                 joinedload("stored_workflow").joinedload("tags")).filter(model.StoredWorkflowUserShareAssociation.user == trans.user).filter(
-                model.StoredWorkflow.deleted == false()).order_by(
+                model.StoredWorkflow.table.c.deleted == false()).order_by(
                 desc(model.StoredWorkflow.update_time)).all():
             item = wf_sa.stored_workflow.to_dict(value_mapper={'id': trans.security.encode_id})
             encoded_id = trans.security.encode_id(wf_sa.stored_workflow.id)
@@ -217,7 +217,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         return rval
 
     @expose_api_anonymous_and_sessionless
-    def show(self, trans, id, **kwd):
+    def show(self, trans: GalaxyWebTransaction, id, **kwd):
         """
         GET /api/workflows/{encoded_workflow_id}
 
@@ -229,7 +229,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         """
         stored_workflow = self.__get_stored_workflow(trans, id, **kwd)
         if stored_workflow.importable is False and stored_workflow.user != trans.user and not trans.user_is_admin:
-            if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0:
+            if trans.sa_session.query(model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0:
                 message = "Workflow is neither importable, nor owned by or shared with current user"
                 raise exceptions.ItemAccessibilityException(message)
         if kwd.get("legacy", False):
@@ -241,13 +241,14 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
             # A Workflow instance may not be the latest workflow version attached to StoredWorkflow.
             # This figures out the correct version so that we return the correct Workflow and version.
             workflow_id = self.decode_id(id)
-            for version, workflow in enumerate(reversed(stored_workflow.workflows)):
+            for i, workflow in enumerate(reversed(stored_workflow.workflows)):
                 if workflow.id == workflow_id:
+                    version = i
                     break
         return self.workflow_contents_manager.workflow_to_dict(trans, stored_workflow, style=style, version=version)
 
     @expose_api
-    def show_versions(self, trans, workflow_id, **kwds):
+    def show_versions(self, trans: GalaxyWebTransaction, workflow_id, **kwds):
         """
         GET /api/workflows/{encoded_workflow_id}/versions
 
@@ -261,7 +262,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         return [{'version': i, 'update_time': str(w.update_time), 'steps': len(w.steps)} for i, w in enumerate(reversed(stored_workflow.workflows))]
 
     @expose_api
-    def create(self, trans, payload=None, **kwd):
+    def create(self, trans: GalaxyWebTransaction, payload=None, **kwd):
         """
         POST /api/workflows
 
@@ -391,7 +392,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
             workflow_name = payload['workflow_name']
             stored_workflow = extract_workflow(
                 trans=trans,
-                user=trans.get_user(),
+                user=trans.user,
                 history=history,
                 job_ids=job_ids,
                 dataset_ids=dataset_ids,
@@ -462,7 +463,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         return invocation_response
 
     @expose_api_raw_anonymous_and_sessionless
-    def workflow_dict(self, trans, workflow_id, **kwd):
+    def workflow_dict(self, trans: GalaxyWebTransaction, workflow_id, **kwd):
         """
         GET /api/workflows/{encoded_workflow_id}/download
 
@@ -507,7 +508,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
             return format_return_as_json(ret_dict, pretty=True)
 
     @expose_api
-    def delete(self, trans, id, **kwd):
+    def delete(self, trans: ProvidesUserContext, id, **kwd):
         """
         DELETE /api/workflows/{encoded_workflow_id}
         Deletes a specified workflow
@@ -515,18 +516,11 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
 
         copied from galaxy.web.controllers.workflows.py (delete)
         """
-        workflow_id = id
-
-        try:
-            stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(self.decode_id(workflow_id))
-        except Exception as e:
-            trans.response.status = 400
-            return ("Workflow with ID='%s' can not be found\n Exception: %s") % (workflow_id, util.unicodify(e))
+        stored_workflow = self.__get_stored_workflow(trans, id, **kwd)
 
         # check to see if user has permissions to selected workflow
         if stored_workflow.user != trans.user and not trans.user_is_admin:
-            trans.response.status = 403
-            return("Workflow is not owned by current user")
+            raise exceptions.InsufficientPermissionsException()
 
         # Mark a workflow as deleted
         stored_workflow.deleted = True
@@ -536,7 +530,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         return ("Workflow '%s' successfully deleted" % stored_workflow.name)
 
     @expose_api
-    def import_new_workflow_deprecated(self, trans, payload, **kwd):
+    def import_new_workflow_deprecated(self, trans: GalaxyWebTransaction, payload, **kwd):
         """
         POST /api/workflows/upload
         Importing dynamic workflows from the api. Return newly generated workflow id.
@@ -550,7 +544,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         return self.__api_import_new_workflow(trans, payload, **kwd)
 
     @expose_api
-    def update(self, trans, id, payload, **kwds):
+    def update(self, trans: GalaxyWebTransaction, id, payload, **kwds):
         """
         PUT /api/workflows/{id}
 
@@ -629,19 +623,19 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
 
             if 'annotation' in workflow_dict and not steps_updated:
                 newAnnotation = sanitize_html(workflow_dict['annotation'])
-                self.add_item_annotation(trans.sa_session, trans.get_user(), stored_workflow, newAnnotation)
+                self.add_item_annotation(trans.sa_session, trans.user, stored_workflow, newAnnotation)
                 trans.sa_session.flush()
 
             if 'menu_entry' in workflow_dict or 'show_in_tool_panel' in workflow_dict:
                 if workflow_dict.get('menu_entry') or workflow_dict.get('show_in_tool_panel'):
                     menuEntry = model.StoredWorkflowMenuEntry()
                     menuEntry.stored_workflow = stored_workflow
-                    trans.get_user().stored_workflow_menu_entries.append(menuEntry)
+                    trans.user.stored_workflow_menu_entries.append(menuEntry)
                 else:
                     # remove if in list
-                    entries = {x.stored_workflow_id: x for x in trans.get_user().stored_workflow_menu_entries}
+                    entries = {x.stored_workflow_id: x for x in trans.user.stored_workflow_menu_entries}
                     if trans.security.decode_id(id) in entries:
-                        trans.get_user().stored_workflow_menu_entries.remove(entries[trans.security.decode_id(id)])
+                        trans.user.stored_workflow_menu_entries.remove(entries[trans.security.decode_id(id)])
             # set tags
             if 'tags' in workflow_dict:
                 trans.app.tag_handler.set_tags_from_list(user=trans.user, item=stored_workflow, new_tags_list=workflow_dict['tags'])
@@ -686,7 +680,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         )
 
     @expose_api
-    def build_module(self, trans, payload=None):
+    def build_module(self, trans: GalaxyWebTransaction, payload=None):
         """
         POST /api/workflows/build_module
         Builds module models for the workflow editor.
@@ -697,22 +691,22 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         trans.workflow_building_mode = workflow_building_modes.ENABLED
         module = module_factory.from_dict(trans, payload, from_tool_form=True)
         if 'tool_state' not in payload:
-            module_state = {}
+            module_state: Dict[str, Any] = {}
             populate_state(trans, module.get_inputs(), inputs, module_state, check=False)
             module.recover_state(module_state, from_tool_form=True)
         return {
-            'label'             : inputs.get('__label', ''),
-            'annotation'        : inputs.get('__annotation', ''),
-            'name'              : module.get_name(),
-            'tool_state'        : module.get_state(),
-            'inputs'            : module.get_all_inputs(connectable_only=True),
-            'outputs'           : module.get_all_outputs(),
-            'config_form'       : module.get_config_form(),
-            'post_job_actions'  : module.get_post_job_actions(inputs)
+            'label': inputs.get('__label', ''),
+            'annotation': inputs.get('__annotation', ''),
+            'name': module.get_name(),
+            'tool_state': module.get_state(),
+            'inputs': module.get_all_inputs(connectable_only=True),
+            'outputs': module.get_all_outputs(),
+            'config_form': module.get_config_form(),
+            'post_job_actions': module.get_post_job_actions(inputs)
         }
 
     @expose_api
-    def get_tool_predictions(self, trans, payload, **kwd):
+    def get_tool_predictions(self, trans: ProvidesUserContext, payload, **kwd):
         """
         POST /api/workflows/get_tool_predictions
 
@@ -738,7 +732,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
     #
     # -- Helper methods --
     #
-    def __api_import_from_archive(self, trans, archive_data, source=None, payload=None):
+    def __api_import_from_archive(self, trans: GalaxyWebTransaction, archive_data, source=None, payload=None):
         payload = payload or {}
         try:
             data = json.loads(archive_data)
@@ -768,7 +762,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
             response["status"] = "error"
         return response
 
-    def __api_import_new_workflow(self, trans, payload, **kwd):
+    def __api_import_new_workflow(self, trans: GalaxyWebTransaction, payload, **kwd):
         data = payload['workflow']
         raw_workflow_description = self.__normalize_workflow(trans, data)
         workflow_create_options = WorkflowCreateOptions(**payload)
@@ -788,11 +782,11 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         item['number_of_steps'] = len(workflow.latest_workflow.steps)
         return item
 
-    def __normalize_workflow(self, trans, as_dict):
+    def __normalize_workflow(self, trans: GalaxyWebTransaction, as_dict):
         return self.workflow_contents_manager.normalize_workflow_format(trans, as_dict)
 
     @expose_api
-    def import_shared_workflow_deprecated(self, trans, payload, **kwd):
+    def import_shared_workflow_deprecated(self, trans: GalaxyWebTransaction, payload, **kwd):
         """
         POST /api/workflows/import
         Import a workflow shared by other users.
@@ -808,7 +802,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
             raise exceptions.ObjectAttributeMissingException("Missing required parameter 'workflow_id'.")
         self.__api_import_shared_workflow(trans, workflow_id, payload)
 
-    def __api_import_shared_workflow(self, trans, workflow_id, payload, **kwd):
+    def __api_import_shared_workflow(self, trans: GalaxyWebTransaction, workflow_id, payload, **kwd):
         try:
             stored_workflow = self.get_stored_workflow(trans, workflow_id, check_ownership=False)
         except Exception:
@@ -824,7 +818,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         return item
 
     @expose_api
-    def invoke(self, trans, workflow_id, payload, **kwd):
+    def invoke(self, trans: GalaxyWebTransaction, workflow_id, payload, **kwd):
         """
         POST /api/workflows/{encoded_workflow_id}/invocations
 
@@ -864,7 +858,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
             return invocations[0]
 
     @expose_api
-    def index_invocations(self, trans, workflow_id=None, **kwd):
+    def index_invocations(self, trans: GalaxyWebTransaction, workflow_id=None, **kwd):
         """
         GET /api/workflows/{workflow_id}/invocations
         GET /api/invocations
@@ -930,7 +924,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         return self.workflow_manager.serialize_workflow_invocations(invocations, **kwd)
 
     @expose_api
-    def show_invocation(self, trans, invocation_id, **kwd):
+    def show_invocation(self, trans: GalaxyWebTransaction, invocation_id, **kwd):
         """
         GET /api/workflows/{workflow_id}/invocations/{invocation_id}
         GET /api/invocations/{invocation_id}
@@ -967,7 +961,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         return None
 
     @expose_api
-    def cancel_invocation(self, trans, invocation_id, **kwd):
+    def cancel_invocation(self, trans: ProvidesUserContext, invocation_id, **kwd):
         """
         DELETE /api/workflows/{workflow_id}/invocations/{invocation_id}
         DELETE /api/invocations/{invocation_id}
@@ -983,7 +977,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         return self.__encode_invocation(workflow_invocation, **kwd)
 
     @expose_api
-    def show_invocation_report(self, trans, invocation_id, **kwd):
+    def show_invocation_report(self, trans: GalaxyWebTransaction, invocation_id, **kwd):
         """
         GET /api/workflows/{workflow_id}/invocations/{invocation_id}/report
         GET /api/invocations/{invocation_id}/report
@@ -994,7 +988,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         return self.workflow_manager.get_invocation_report(trans, invocation_id, **kwd)
 
     @expose_api_raw
-    def show_invocation_report_pdf(self, trans, invocation_id, **kwd):
+    def show_invocation_report_pdf(self, trans: GalaxyWebTransaction, invocation_id, **kwd):
         """
         GET /api/workflows/{workflow_id}/invocations/{invocation_id}/report.pdf
         GET /api/invocations/{invocation_id}/report.pdf
@@ -1005,7 +999,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         trans.response.set_content_type("application/pdf")
         return self.workflow_manager.get_invocation_report(trans, invocation_id, **kwd)
 
-    def _generate_invocation_bco(self, trans, invocation_id, **kwd):
+    def _generate_invocation_bco(self, trans: GalaxyWebTransaction, invocation_id, **kwd):
         decoded_workflow_invocation_id = self.decode_id(invocation_id)
         workflow_invocation = self.workflow_manager.get_invocation(trans, decoded_workflow_invocation_id)
         history = workflow_invocation.history
@@ -1076,7 +1070,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         tools, input_subdomain, output_subdomain, pipeline_steps, software_prerequisites = [], [], [], [], []
         for step in workflow_invocation.steps:
             if step.workflow_step.type == 'tool':
-                workflow_outputs_list , output_list, input_list = set(), [], []
+                workflow_outputs_list, output_list, input_list = set(), [], []
                 for wo in step.workflow_step.workflow_outputs:
                     workflow_outputs_list.add(wo.output_name)
                 for job in step.jobs:
@@ -1237,7 +1231,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         return bco_dict
 
     @expose_api
-    def export_invocation_bco(self, trans, invocation_id, **kwd):
+    def export_invocation_bco(self, trans: GalaxyWebTransaction, invocation_id, **kwd):
         '''
         GET /api/invocations/{invocations_id}/biocompute
 
@@ -1251,7 +1245,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         return self._generate_invocation_bco(trans, invocation_id, **kwd)
 
     @expose_api_raw
-    def download_invocation_bco(self, trans, invocation_id, **kwd):
+    def download_invocation_bco(self, trans: GalaxyWebTransaction, invocation_id, **kwd):
         """
         GET /api/invocations/{invocations_id}/biocompute/download
 
@@ -1293,7 +1287,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         return self.__encode_invocation_step(trans, invocation_step)
 
     @expose_api_anonymous_and_sessionless
-    def invocation_step_jobs_summary(self, trans, invocation_id, **kwd):
+    def invocation_step_jobs_summary(self, trans: GalaxyWebTransaction, invocation_id, **kwd):
         """
         GET /api/workflows/{workflow_id}/invocations/{invocation_id}/step_jobs_summary
         GET /api/invocations/{invocation_id}/step_jobs_summary
@@ -1320,7 +1314,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         return [self.encode_all_ids(trans, s) for s in fetch_job_states(trans.sa_session, ids, types)]
 
     @expose_api_anonymous_and_sessionless
-    def invocation_jobs_summary(self, trans, invocation_id, **kwd):
+    def invocation_jobs_summary(self, trans: GalaxyWebTransaction, invocation_id, **kwd):
         """
         GET /api/workflows/{workflow_id}/invocations/{invocation_id}/jobs_summary
         GET /api/invocations/{invocation_id}/jobs_summary
@@ -1343,7 +1337,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         return [self.encode_all_ids(trans, s) for s in fetch_job_states(trans.sa_session, ids, types)][0]
 
     @expose_api
-    def update_invocation_step(self, trans, invocation_id, step_id, payload, **kwd):
+    def update_invocation_step(self, trans: GalaxyWebTransaction, invocation_id, step_id, payload, **kwd):
         """
         PUT /api/workflows/{workflow_id}/invocations/{invocation_id}/steps/{step_id}
         PUT /api/invocations/{invocation_id}/steps/{step_id}
@@ -1431,7 +1425,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
                         changeset_revision,
                         install_options)
 
-    def __encode_invocation_step(self, trans, invocation_step):
+    def __encode_invocation_step(self, trans: ProvidesUserContext, invocation_step):
         return self.encode_all_ids(
             trans,
             invocation_step.to_dict('element'),
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 225d37da7d8..6e2e75d1ade 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -756,6 +756,12 @@ def populate_api_routes(webapp, app):
                           action='api_key',
                           conditions=dict(method=["POST"]))
 
+    webapp.mapper.connect('api_key',
+                          '/api/users/{id}/api_key',
+                          controller='users',
+                          action='get_or_create_api_key',
+                          conditions=dict(method=["GET"]))
+
     webapp.mapper.connect('get_api_key',
                           '/api/users/{id}/api_key/inputs',
                           controller='users',
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 250a771a41d..5471ac209ae 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -505,7 +505,7 @@ mapping:
         required: false
         desc: |
           involucro is a tool used to build Docker or Singularity containers for tools from Conda
-          dependencies referenced in tools as `requirement`s. The following path is
+          dependencies referenced in tools as `requirement` s. The following path is
           the location of involucro on the Galaxy host. This is ignored if the relevant
           container resolver isn't enabled, and will install on demand unless
           involucro_auto_init is set to false.
@@ -765,6 +765,17 @@ mapping:
           should be disabled. Containerized jobs always use /bin/sh - so more maximum
           portability tool authors should assume generated commands run in sh.
 
+      enable_tool_document_cache:
+        type: bool
+        default: true
+        required: false
+        desc: |
+          Set this to false to disable the tool document cache. This cache stores
+          expanded xml strings. Disabling the tool cache results in slower startup
+          times. The tool cache is backed by sqlite database, which cannot
+          be stored on certain network disks. The cache location is configurable
+          using the ``tool_cache_data_dir`` setting, but can be disabled completely here.
+
       tool_cache_data_dir:
         type: str
         default: tool_cache
@@ -2704,7 +2715,7 @@ mapping:
           separate Galaxy into multiple processes.  There are more than one way to do
           this, and they are explained in detail in the documentation:
 
-            https://docs.galaxyproject.org/en/master/admin/scaling.html
+          https://docs.galaxyproject.org/en/master/admin/scaling.html
 
           By default, Galaxy manages and executes jobs from within a single process and
           notifies itself of new jobs via in-memory queues.  Jobs are run locally on
diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index 8d7fc8ea926..78fd4fb931d 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -207,44 +207,44 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             can_manage_dataset = trans.app.security_agent.can_manage_dataset(trans.get_current_user_roles(), data.dataset)
             # attribute editing
             attribute_inputs = [{
-                'name' : 'name',
-                'type' : 'text',
+                'name': 'name',
+                'type': 'text',
                 'label': 'Name',
                 'value': data.get_display_name()
             }, {
-                'name' : 'info',
-                'type' : 'text',
-                'area' : True,
+                'name': 'info',
+                'type': 'text',
+                'area': True,
                 'label': 'Info',
                 'value': data.info
             }, {
-                'name' : 'annotation',
-                'type' : 'text',
-                'area' : True,
+                'name': 'annotation',
+                'type': 'text',
+                'area': True,
                 'label': 'Annotation',
                 'value': self.get_item_annotation_str(trans.sa_session, trans.user, data),
-                'help' : 'Add an annotation or notes to a dataset; annotations are available when a history is viewed.'
+                'help': 'Add an annotation or notes to a dataset; annotations are available when a history is viewed.'
             }]
             for name, spec in data_metadata:
                 if spec.visible:
                     attributes = data.metadata.get_metadata_parameter(name, trans=trans)
                     if type(attributes) is form_builder.SelectField:
                         attribute_inputs.append({
-                            'type'      : 'select',
-                            'multiple'  : attributes.multiple,
-                            'optional'  : spec.get('optional'),
-                            'name'      : name,
-                            'label'     : spec.desc,
-                            'options'   : attributes.options,
-                            'value'     : attributes.value if attributes.multiple else [attributes.value]
+                            'type': 'select',
+                            'multiple': attributes.multiple,
+                            'optional': spec.get('optional'),
+                            'name': name,
+                            'label': spec.desc,
+                            'options': attributes.options,
+                            'value': attributes.value if attributes.multiple else [attributes.value]
                         })
                     elif type(attributes) is form_builder.TextField:
                         attribute_inputs.append({
-                            'type'      : 'text',
-                            'name'      : name,
-                            'label'     : spec.desc,
-                            'value'     : attributes.value,
-                            'readonly'  : spec.get('readonly')
+                            'type': 'text',
+                            'name': name,
+                            'label': spec.desc,
+                            'value': attributes.value,
+                            'readonly': spec.get('readonly')
                         })
             if data.missing_meta():
                 message = 'Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.'
@@ -253,22 +253,22 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             conversion_options = [(convert_name, convert_id) for convert_id, convert_name in converters_collection]
             conversion_disable = len(conversion_options) == 0
             conversion_inputs = [{
-                'type'      : 'select',
-                'name'      : 'target_type',
-                'label'     : 'Name',
-                'help'      : 'This will create a new dataset with the contents of this dataset converted to a new format.',
-                'options'   : conversion_options
+                'type': 'select',
+                'name': 'target_type',
+                'label': 'Name',
+                'help': 'This will create a new dataset with the contents of this dataset converted to a new format.',
+                'options': conversion_options
             }]
             # datatype changing
             datatype_options = [(ext_name, ext_id) for ext_id, ext_name in ldatatypes]
             datatype_disable = len(datatype_options) == 0
             datatype_inputs = [{
-                'type'      : 'select',
-                'name'      : 'datatype',
-                'label'     : 'New Type',
-                'options'   : datatype_options,
-                'value'     : [ext_id for ext_id, ext_name in ldatatypes if ext_id == data.ext],
-                'help'      : 'This will change the datatype of the existing dataset but not modify its contents. Use this if Galaxy has incorrectly guessed the type of your dataset.',
+                'type': 'select',
+                'name': 'datatype',
+                'label': 'New Type',
+                'options': datatype_options,
+                'value': [ext_id for ext_id, ext_name in ldatatypes if ext_id == data.ext],
+                'help': 'This will change the datatype of the existing dataset but not modify its contents. Use this if Galaxy has incorrectly guessed the type of your dataset.',
             }]
             # permissions
             permission_disable = True
@@ -284,42 +284,42 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                         else:
                             help_text = action.description
                         permission_inputs.append({
-                            'type'      : 'select',
-                            'multiple'  : True,
-                            'optional'  : True,
-                            'name'      : index,
-                            'label'     : action.action,
-                            'help'      : help_text,
-                            'options'   : all_roles,
-                            'value'     : in_roles.get(action.action),
-                            'readonly'  : not can_manage_dataset
+                            'type': 'select',
+                            'multiple': True,
+                            'optional': True,
+                            'name': index,
+                            'label': action.action,
+                            'help': help_text,
+                            'options': all_roles,
+                            'value': in_roles.get(action.action),
+                            'readonly': not can_manage_dataset
                         })
                     permission_disable = not can_manage_dataset
                 else:
                     permission_inputs.append({
-                        'name'      : 'access_public',
-                        'type'      : 'hidden',
-                        'label'     : 'This dataset is accessible by everyone (it is public).',
-                        'readonly'  : True
+                        'name': 'access_public',
+                        'type': 'hidden',
+                        'label': 'This dataset is accessible by everyone (it is public).',
+                        'readonly': True
                     })
             else:
                 permission_inputs.append({
-                    'name'      : 'no_access',
-                    'type'      : 'hidden',
-                    'label'     : 'Permissions not available (not logged in).',
-                    'readonly'  : True
+                    'name': 'no_access',
+                    'type': 'hidden',
+                    'label': 'Permissions not available (not logged in).',
+                    'readonly': True
                 })
             return {
-                'display_name'      : data.get_display_name(),
-                'message'           : message,
-                'status'            : status,
-                'dataset_id'        : dataset_id,
-                'attribute_inputs'  : attribute_inputs,
-                'conversion_inputs' : conversion_inputs,
+                'display_name': data.get_display_name(),
+                'message': message,
+                'status': status,
+                'dataset_id': dataset_id,
+                'attribute_inputs': attribute_inputs,
+                'conversion_inputs': conversion_inputs,
                 'conversion_disable': conversion_disable,
-                'datatype_inputs'   : datatype_inputs,
-                'datatype_disable'  : datatype_disable,
-                'permission_inputs' : permission_inputs,
+                'datatype_inputs': datatype_inputs,
+                'datatype_disable': datatype_disable,
+                'permission_inputs': permission_inputs,
                 'permission_disable': permission_disable
             }
         else:
@@ -423,7 +423,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             # so it is possible that some Datasets have no roles associated with the DATASET_MANAGE_PERMISSIONS
             # permission.  In this case, we'll reset this permission to the hda user's private role.
             manage_permissions_action = trans.app.security_agent.get_action(trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action)
-            permissions = {manage_permissions_action : [trans.app.security_agent.get_private_user_role(data.history.user)]}
+            permissions = {manage_permissions_action: [trans.app.security_agent.get_private_user_role(data.history.user)]}
             trans.app.security_agent.set_dataset_permission(data.dataset, permissions)
         return data, None
 
@@ -453,7 +453,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         decoded_id = self.decode_id(id)
         dataset = self.hda_manager.get_accessible(decoded_id, trans.user)
         dataset = self.hda_manager.error_if_uploading(dataset)
-        return_dict = {"name" : dataset.name, "link" : url_for(controller='dataset', action="display_by_username_and_slug", username=dataset.history.user.username, slug=trans.security.encode_id(dataset.id))}
+        return_dict = {"name": dataset.name, "link": url_for(controller='dataset', action="display_by_username_and_slug", username=dataset.history.user.username, slug=trans.security.encode_id(dataset.id))}
         return return_dict
 
     @web.expose
diff --git a/lib/galaxy/webapps/galaxy/controllers/forms.py b/lib/galaxy/webapps/galaxy/controllers/forms.py
index 4812214c3a3..01063a875a5 100644
--- a/lib/galaxy/webapps/galaxy/controllers/forms.py
+++ b/lib/galaxy/webapps/galaxy/controllers/forms.py
@@ -105,24 +105,24 @@ class Forms(BaseUIController):
         if trans.request.method == 'GET':
             fd_types = sorted(trans.app.model.FormDefinition.types.items())
             return {
-                'title'         : 'Create new form',
-                'submit_title'  : 'Create',
-                'inputs'        : [{
-                    'name'    : 'name',
-                    'label'   : 'Name'
+                'title': 'Create new form',
+                'submit_title': 'Create',
+                'inputs': [{
+                    'name': 'name',
+                    'label': 'Name'
                 }, {
-                    'name'    : 'desc',
-                    'label'   : 'Description'
+                    'name': 'desc',
+                    'label': 'Description'
                 }, {
-                    'name'    : 'type',
-                    'type'    : 'select',
-                    'options' : [('None', 'none')] + [(ft[1], ft[1]) for ft in fd_types],
-                    'label'   : 'Type'
+                    'name': 'type',
+                    'type': 'select',
+                    'options': [('None', 'none')] + [(ft[1], ft[1]) for ft in fd_types],
+                    'label': 'Type'
                 }, {
-                    'name'    : 'csv_file',
-                    'label'   : 'Import from CSV',
-                    'type'    : 'upload',
-                    'help'    : 'Import fields from CSV-file with the following format: Label, Help, Type, Value, Options, Required=True/False.'
+                    'name': 'csv_file',
+                    'label': 'Import from CSV',
+                    'type': 'upload',
+                    'help': 'Import fields from CSV-file with the following format: Label, Help, Type, Value, Options, Required=True/False.'
                 }]
             }
         else:
@@ -163,57 +163,57 @@ class Forms(BaseUIController):
             ff_types = [(t.__name__.replace('Field', ''), t.__name__) for t in trans.model.FormDefinition.supported_field_types]
             field_cache = []
             field_inputs = [{
-                'name'    : 'name',
-                'label'   : 'Name',
-                'value'   : 'field_name',
-                'help'    : 'The field name must be unique for each field and must contain only alphanumeric characters and underscore.'
+                'name': 'name',
+                'label': 'Name',
+                'value': 'field_name',
+                'help': 'The field name must be unique for each field and must contain only alphanumeric characters and underscore.'
             }, {
-                'name'    : 'label',
-                'label'   : 'Label',
-                'value'   : 'Field label'
+                'name': 'label',
+                'label': 'Label',
+                'value': 'Field label'
             }, {
-                'name'    : 'helptext',
-                'label'   : 'Help text'
+                'name': 'helptext',
+                'label': 'Help text'
             }, {
-                'name'    : 'type',
-                'label'   : 'Type',
-                'type'    : 'select',
-                'options' : ff_types
+                'name': 'type',
+                'label': 'Type',
+                'type': 'select',
+                'options': ff_types
             }, {
-                'name'    : 'default',
-                'label'   : 'Default value'
+                'name': 'default',
+                'label': 'Default value'
             }, {
-                'name'    : 'selectlist',
-                'label'   : 'Options',
-                'help'    : '*Only for fields which allow multiple selections, provide comma-separated values.'
+                'name': 'selectlist',
+                'label': 'Options',
+                'help': '*Only for fields which allow multiple selections, provide comma-separated values.'
             }, {
-                'name'    : 'required',
-                'label'   : 'Required',
-                'type'    : 'boolean',
-                'value'   : 'false'
+                'name': 'required',
+                'label': 'Required',
+                'type': 'boolean',
+                'value': 'false'
             }]
             form_dict = {
-                'title'  : 'Edit form for \'%s\'' % (util.sanitize_text(latest_form.name)),
-                'inputs' : [{
-                    'name'    : 'name',
-                    'label'   : 'Name',
-                    'value'   : latest_form.name
+                'title': 'Edit form for \'%s\'' % (util.sanitize_text(latest_form.name)),
+                'inputs': [{
+                    'name': 'name',
+                    'label': 'Name',
+                    'value': latest_form.name
                 }, {
-                    'name'    : 'desc',
-                    'label'   : 'Description',
-                    'value'   : latest_form.desc
+                    'name': 'desc',
+                    'label': 'Description',
+                    'value': latest_form.desc
                 }, {
-                    'name'    : 'type',
-                    'type'    : 'select',
-                    'options' : [('None', 'none')] + [(ft[1], ft[1]) for ft in fd_types],
-                    'label'   : 'Type',
-                    'value'   : latest_form.type
+                    'name': 'type',
+                    'type': 'select',
+                    'options': [('None', 'none')] + [(ft[1], ft[1]) for ft in fd_types],
+                    'label': 'Type',
+                    'value': latest_form.type
                 }, {
-                    'name'    : 'fields',
-                    'title'   : 'Field',
-                    'type'    : 'repeat',
-                    'cache'   : field_cache,
-                    'inputs'  : field_inputs
+                    'name': 'fields',
+                    'title': 'Field',
+                    'type': 'repeat',
+                    'cache': field_cache,
+                    'inputs': field_inputs
                 }]
             }
             for field in latest_form.fields:
diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py
index 3d83ea8dfbd..f48eb3d1c7a 100644
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -475,9 +475,9 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
         history = trans.sa_session.query(model.History).options(
             joinedload('active_datasets').joinedload('creating_job_associations').joinedload('job').joinedload('workflow_invocation_step').joinedload('workflow_invocation').joinedload('workflow'),
         ).get(id)
-        if not (history and ((history.user and trans.user and history.user.id == trans.user.id) or
-                             (trans.history and history.id == trans.history.id) or
-                             trans.user_is_admin)):
+        if not (history and ((history.user and trans.user and history.user.id == trans.user.id)
+                             or (trans.history and history.id == trans.history.id)
+                             or trans.user_is_admin)):
             return trans.show_error_message("Cannot display history structure.")
         # Resolve jobs and workflow invocations for the datasets in the history
         # items is filled with items (hdas, jobs, or workflows) that go at the
@@ -579,8 +579,8 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
             if isinstance(exc, exceptions.ItemAccessibilityException):
                 error_msg = 'You do not have permission to view this history.'
             else:
-                error_msg = ('An error occurred getting the history data from the server. ' +
-                             'Please contact a Galaxy administrator if the problem persists.')
+                error_msg = ('An error occurred getting the history data from the server. '
+                             + 'Please contact a Galaxy administrator if the problem persists.')
             return trans.show_error_message(error_msg, use_panels=use_panels)
 
         return {
@@ -661,16 +661,16 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
                 for a in current_actions:
                     if a.action == action.action:
                         in_roles.add(a.role)
-                inputs.append({'type'      : 'select',
-                               'multiple'  : True,
-                               'optional'  : True,
+                inputs.append({'type': 'select',
+                               'multiple': True,
+                               'optional': True,
                                'individual': True,
-                               'name'      : action_key,
-                               'label'     : action.action,
-                               'help'      : action.description,
-                               'options'   : [(role.name, trans.security.encode_id(role.id)) for role in set(all_roles)],
-                               'value'     : [trans.security.encode_id(role.id) for role in in_roles]})
-            return {'title'  : 'Change default dataset permissions for history \'%s\'' % history.name, 'inputs' : inputs}
+                               'name': action_key,
+                               'label': action.action,
+                               'help': action.description,
+                               'options': [(role.name, trans.security.encode_id(role.id)) for role in set(all_roles)],
+                               'value': [trans.security.encode_id(role.id) for role in in_roles]})
+            return {'title': 'Change default dataset permissions for history \'%s\'' % history.name, 'inputs': inputs}
         else:
             permissions = {}
             for action_key, action in trans.app.model.Dataset.permitted_actions.items():
@@ -1152,11 +1152,11 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
                 histories.append(history)
         if trans.request.method == 'GET':
             return {
-                'title'  : 'Change history name(s)',
-                'inputs' : [{
-                    'name'  : 'name_%i' % i,
-                    'label' : 'Current: %s' % h.name,
-                    'value' : h.name
+                'title': 'Change history name(s)',
+                'inputs': [{
+                    'name': 'name_%i' % i,
+                    'label': 'Current: %s' % h.name,
+                    'value': h.name
                 } for i, h in enumerate(histories)]
             }
         else:
diff --git a/lib/galaxy/webapps/galaxy/controllers/library.py b/lib/galaxy/webapps/galaxy/controllers/library.py
index 73c5106ba49..2d2630f19af 100644
--- a/lib/galaxy/webapps/galaxy/controllers/library.py
+++ b/lib/galaxy/webapps/galaxy/controllers/library.py
@@ -13,7 +13,7 @@ class Library(BaseUIController):
     def list(self, trans, **kwd):
         # define app configuration for generic mako template
         app = {
-            'jscript'       : "library"
+            'jscript': "library"
         }
         return trans.fill_template('galaxy.panels.mako',
                                    config={
diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py
index 0ebf8f46e70..2a5c70117a6 100644
--- a/lib/galaxy/webapps/galaxy/controllers/page.py
+++ b/lib/galaxy/webapps/galaxy/controllers/page.py
@@ -315,9 +315,9 @@ class PageController(BaseUIController, SharableMixin,
             .filter(model.Page.deleted == false()) \
             .order_by(desc(model.Page.update_time)) \
             .all()
-        return [{'username' : p.page.user.username,
-                 'slug'     : p.page.slug,
-                 'title'    : p.page.title} for p in shared_by_others]
+        return [{'username': p.page.user.username,
+                 'slug': p.page.slug,
+                 'title': p.page.title} for p in shared_by_others]
 
     @web.legacy_expose_api
     @web.require_login("create pages")
@@ -342,33 +342,33 @@ class PageController(BaseUIController, SharableMixin,
                 content_format_hide = True
                 content_hide = False
             return {
-                'title'  : form_title,
-                'inputs' : [{
-                    'name'      : 'title',
-                    'label'     : 'Name',
-                    'value'     : title,
+                'title': form_title,
+                'inputs': [{
+                    'name': 'title',
+                    'label': 'Name',
+                    'value': title,
                 }, {
-                    'name'      : 'slug',
-                    'label'     : 'Identifier',
-                    'help'      : 'A unique identifier that will be used for public links to this page. This field can only contain lowercase letters, numbers, and dashes (-).',
-                    'value'     : slug,
+                    'name': 'slug',
+                    'label': 'Identifier',
+                    'help': 'A unique identifier that will be used for public links to this page. This field can only contain lowercase letters, numbers, and dashes (-).',
+                    'value': slug,
                 }, {
-                    'name'      : 'annotation',
-                    'label'     : 'Annotation',
-                    'help'      : 'A description of the page. The annotation is shown alongside published pages.'
+                    'name': 'annotation',
+                    'label': 'Annotation',
+                    'help': 'A description of the page. The annotation is shown alongside published pages.'
                 }, {
-                    'name'      : 'content_format',
-                    'label'     : 'Content Format',
-                    'type'      : 'select',
-                    'hidden'    : content_format_hide,
-                    'options'   : [('Markdown', 'markdown'), ('HTML', 'html')],
-                    'help'      : 'Use the traditional rich HTML editor or the newer experimental Markdown editor to create the page content. The HTML editor has several known bugs, is unmaintained and pages created with it will be read-only in future releases of Galaxy.'
+                    'name': 'content_format',
+                    'label': 'Content Format',
+                    'type': 'select',
+                    'hidden': content_format_hide,
+                    'options': [('Markdown', 'markdown'), ('HTML', 'html')],
+                    'help': 'Use the traditional rich HTML editor or the newer experimental Markdown editor to create the page content. The HTML editor has several known bugs, is unmaintained and pages created with it will be read-only in future releases of Galaxy.'
                 }, {
-                    'name'      : 'content',
-                    'label'     : 'Content',
-                    'area'      : True,
-                    'value'     : content,
-                    'hidden'    : content_hide,
+                    'name': 'content',
+                    'label': 'Content',
+                    'area': True,
+                    'value': content,
+                    'hidden': content_hide,
                 }]
             }
         else:
@@ -394,21 +394,21 @@ class PageController(BaseUIController, SharableMixin,
             if p.slug is None:
                 self.create_item_slug(trans.sa_session, p)
             return {
-                'title'  : 'Edit page attributes',
-                'inputs' : [{
-                    'name'      : 'title',
-                    'label'     : 'Name',
-                    'value'     : p.title
+                'title': 'Edit page attributes',
+                'inputs': [{
+                    'name': 'title',
+                    'label': 'Name',
+                    'value': p.title
                 }, {
-                    'name'      : 'slug',
-                    'label'     : 'Identifier',
-                    'value'     : p.slug,
-                    'help'      : 'A unique identifier that will be used for public links to this page. This field can only contain lowercase letters, numbers, and dashes (-).'
+                    'name': 'slug',
+                    'label': 'Identifier',
+                    'value': p.slug,
+                    'help': 'A unique identifier that will be used for public links to this page. This field can only contain lowercase letters, numbers, and dashes (-).'
                 }, {
-                    'name'      : 'annotation',
-                    'label'     : 'Annotation',
-                    'value'     : self.get_item_annotation_str(trans.sa_session, user, p),
-                    'help'      : 'A description of the page. The annotation is shown alongside published pages.'
+                    'name': 'annotation',
+                    'label': 'Annotation',
+                    'value': self.get_item_annotation_str(trans.sa_session, user, p),
+                    'help': 'A description of the page. The annotation is shown alongside published pages.'
                 }]
             }
         else:
@@ -676,8 +676,8 @@ class PageController(BaseUIController, SharableMixin,
             return None
 
         # Fork to template based on visualization.type (registry or builtin).
-        if((trans.app.visualizations_registry and visualization.type in trans.app.visualizations_registry.plugins) and
-                (visualization.type not in trans.app.visualizations_registry.BUILT_IN_VISUALIZATIONS)):
+        if((trans.app.visualizations_registry and visualization.type in trans.app.visualizations_registry.plugins)
+                and (visualization.type not in trans.app.visualizations_registry.BUILT_IN_VISUALIZATIONS)):
             # if a registry visualization, load a version into an iframe :(
             # TODO: simplest path from A to B but not optimal - will be difficult to do reg visualizations any other way
             # TODO: this will load the visualization twice (once above, once when the iframe src calls 'saved')
diff --git a/lib/galaxy/webapps/galaxy/controllers/root.py b/lib/galaxy/webapps/galaxy/controllers/root.py
index 8b57c574f4c..3109a0519cb 100644
--- a/lib/galaxy/webapps/galaxy/controllers/root.py
+++ b/lib/galaxy/webapps/galaxy/controllers/root.py
@@ -84,9 +84,9 @@ class RootController(controller.JSAppLauncher, UsesAnnotations):
         """
         # directly redirect to oidc provider if 1) enable_oidc is True, 2)
         # there is only one oidc provider, 3) auth_conf.xml has no authenticators
-        if (trans.app.config.enable_oidc and
-                len(trans.app.config.oidc) == 1 and
-                len(trans.app.auth_manager.authenticators) == 0
+        if (trans.app.config.enable_oidc
+                and len(trans.app.config.oidc) == 1
+                and len(trans.app.auth_manager.authenticators) == 0
                 and is_logout_redirect is False):
             provider = next(iter(trans.app.config.oidc.keys()))
             success, message, redirect_uri = trans.app.authnz_manager.authenticate(provider, trans)
diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py
index ea5c28c03a3..e4a1056a560 100644
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -308,9 +308,9 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
             .filter(model.Visualization.deleted == false()) \
             .order_by(desc(model.Visualization.update_time)) \
             .all()
-        return [{'username' : v.visualization.user.username,
-                 'slug'     : v.visualization.slug,
-                 'title'    : v.visualization.title} for v in shared_by_others]
+        return [{'username': v.visualization.user.username,
+                 'slug': v.visualization.slug,
+                 'title': v.visualization.title} for v in shared_by_others]
 
     #
     # -- Functions for operating on visualizations. --
@@ -474,8 +474,8 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         ave_item_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, visualization)
 
         # Fork to template based on visualization.type (registry or builtin).
-        if((trans.app.visualizations_registry and visualization.type in trans.app.visualizations_registry.plugins) and
-                (visualization.type not in trans.app.visualizations_registry.BUILT_IN_VISUALIZATIONS)):
+        if((trans.app.visualizations_registry and visualization.type in trans.app.visualizations_registry.plugins)
+                and (visualization.type not in trans.app.visualizations_registry.BUILT_IN_VISUALIZATIONS)):
             # if a registry visualization, load a version of display.mako that will load the vis into an iframe :(
             # TODO: simplest path from A to B but not optimal - will be difficult to do reg visualizations any other way
             # TODO: this will load the visualization twice (once above, once when the iframe src calls 'saved')
@@ -546,29 +546,29 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
             if v.slug is None:
                 self.create_item_slug(trans.sa_session, v)
             return {
-                'title'  : 'Edit visualization attributes',
-                'inputs' : [{
-                    'name'      : 'title',
-                    'label'     : 'Name',
-                    'value'     : v.title
+                'title': 'Edit visualization attributes',
+                'inputs': [{
+                    'name': 'title',
+                    'label': 'Name',
+                    'value': v.title
                 }, {
-                    'name'      : 'slug',
-                    'label'     : 'Identifier',
-                    'value'     : v.slug,
-                    'help'      : 'A unique identifier that will be used for public links to this visualization. This field can only contain lowercase letters, numbers, and dashes (-).'
+                    'name': 'slug',
+                    'label': 'Identifier',
+                    'value': v.slug,
+                    'help': 'A unique identifier that will be used for public links to this visualization. This field can only contain lowercase letters, numbers, and dashes (-).'
                 }, {
-                    'name'      : 'dbkey',
-                    'label'     : 'Build',
-                    'type'      : 'select',
-                    'optional'  : True,
-                    'value'     : v.dbkey,
-                    'options'   : trans.app.genomes.get_dbkeys(trans, chrom_info=True),
-                    'help'      : 'Parameter to associate your visualization with a database key.'
+                    'name': 'dbkey',
+                    'label': 'Build',
+                    'type': 'select',
+                    'optional': True,
+                    'value': v.dbkey,
+                    'options': trans.app.genomes.get_dbkeys(trans, chrom_info=True),
+                    'help': 'Parameter to associate your visualization with a database key.'
                 }, {
-                    'name'      : 'annotation',
-                    'label'     : 'Annotation',
-                    'value'     : self.get_item_annotation_str(trans.sa_session, trans.user, v),
-                    'help'      : 'A description of the visualization. The annotation is shown alongside published visualizations.'
+                    'name': 'annotation',
+                    'label': 'Annotation',
+                    'value': self.get_item_annotation_str(trans.sa_session, trans.user, v),
+                    'help': 'A description of the visualization. The annotation is shown alongside published visualizations.'
                 }]
             }
         else:
@@ -630,9 +630,9 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         if trans.debug:
             raise exception
         return trans.show_error_message(
-            "There was an error rendering the visualization. " +
-            "Contact your Galaxy administrator if the problem persists." +
-            "<br/>Details: " + unicodify(exception), use_panels=False)
+            "There was an error rendering the visualization. "
+            + "Contact your Galaxy administrator if the problem persists."
+            + "<br/>Details: " + unicodify(exception), use_panels=False)
 
     @web.expose
     @web.require_login("use Galaxy visualizations", use_panels=True)
@@ -698,7 +698,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         """
 
         # define app configuration
-        app = {"jscript" : "trackster"}
+        app = {"jscript": "trackster"}
 
         # get dataset to add
         id = kwargs.get("id", None)
@@ -736,9 +736,9 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         # update gene region of saved visualization if user parses a new gene region in the url
         if gene_region.chrom is not None:
             app['gene_region'] = {
-                'chrom' : gene_region.chrom,
-                'start' : gene_region.start,
-                'end'   : gene_region.end
+                'chrom': gene_region.chrom,
+                'start': gene_region.start,
+                'end': gene_region.end
             }
 
         # fill template
@@ -798,13 +798,13 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
 
         # define app configuration for generic mako template
         app = {
-            'jscript'       : "circster",
-            'viz_config'    : viz_config,
-            'genome'        : genome
+            'jscript': "circster",
+            'viz_config': viz_config,
+            'genome': genome
         }
 
         # fill template
-        return trans.fill_template('galaxy.panels.mako', config={'app' : app, 'bundle': 'extended'})
+        return trans.fill_template('galaxy.panels.mako', config={'app': app, 'bundle': 'extended'})
 
     @web.expose
     def sweepster(self, trans, id=None, hda_ldda=None, dataset_id=None, regions=None):
@@ -869,10 +869,10 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         if not config:
             config = {
                 'dataset_id': dataset_id,
-                'title'     : hda.display_name(),
-                'ext'       : hda.datatype.file_ext,
-                'treeIndex' : tree_index,
-                'saved_visualization' : False
+                'title': hda.display_name(),
+                'ext': hda.datatype.file_ext,
+                'treeIndex': tree_index,
+                'saved_visualization': False
             }
         return trans.fill_template_mako("visualization/phyloviz.mako", data=data, config=config)
 
diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py
index 79ec11dc8e5..f2d2e04e7ca 100644
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -544,15 +544,15 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
     def create(self, trans, payload=None, **kwd):
         if trans.request.method == 'GET':
             return {
-                'title'  : 'Create Workflow',
-                'inputs' : [{
-                    'name'  : 'workflow_name',
-                    'label' : 'Name',
-                    'value' : 'Unnamed workflow'
+                'title': 'Create Workflow',
+                'inputs': [{
+                    'name': 'workflow_name',
+                    'label': 'Name',
+                    'value': 'Unnamed workflow'
                 }, {
-                    'name'  : 'workflow_annotation',
-                    'label' : 'Annotation',
-                    'help'  : 'A description of the workflow; annotation is shown alongside shared or published workflows.'
+                    'name': 'workflow_annotation',
+                    'label': 'Annotation',
+                    'help': 'A description of the workflow; annotation is shown alongside shared or published workflows.'
                 }]}
         else:
             user = trans.get_user()
@@ -703,10 +703,10 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
 
         # create workflow models
         workflows = [{
-            'id'                  : trans.security.encode_id(workflow.id),
-            'latest_id'           : trans.security.encode_id(workflow.latest_workflow.id),
-            'step_count'          : len(workflow.latest_workflow.steps),
-            'name'                : workflow.name
+            'id': trans.security.encode_id(workflow.id),
+            'latest_id': trans.security.encode_id(workflow.latest_workflow.id),
+            'step_count': len(workflow.latest_workflow.steps),
+            'name': workflow.name
         } for workflow in workflows if workflow.id != stored.id]
 
         # identify item tags
@@ -717,15 +717,15 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
 
         # build workflow editor model
         editor_config = {
-            'id'                      : trans.security.encode_id(stored.id),
-            'name'                    : stored.name,
-            'tags'                    : item_tag_names,
-            'version'                 : version,
-            'annotation'              : self.get_item_annotation_str(trans.sa_session, trans.user, stored),
-            'toolbox'                 : trans.app.toolbox.to_dict(trans),
-            'moduleSections'          : module_sections,
-            'dataManagers'            : data_managers,
-            'workflows'               : workflows
+            'id': trans.security.encode_id(stored.id),
+            'name': stored.name,
+            'tags': item_tag_names,
+            'version': version,
+            'annotation': self.get_item_annotation_str(trans.sa_session, trans.user, stored),
+            'toolbox': trans.app.toolbox.to_dict(trans),
+            'moduleSections': module_sections,
+            'dataManagers': data_managers,
+            'workflows': workflows
         }
 
         # parse to mako
diff --git a/lib/galaxy/webapps/galaxy/fast_app.py b/lib/galaxy/webapps/galaxy/fast_app.py
index 64ad1e29329..c4d7234529b 100644
--- a/lib/galaxy/webapps/galaxy/fast_app.py
+++ b/lib/galaxy/webapps/galaxy/fast_app.py
@@ -5,6 +5,7 @@ from fastapi.responses import JSONResponse
 from starlette.responses import Response
 
 from galaxy.exceptions import MessageException
+from galaxy.web.framework.base import walk_controller_modules
 from galaxy.web.framework.decorators import (
     api_error_message,
     validation_error_to_message_exception
@@ -12,10 +13,22 @@ from galaxy.web.framework.decorators import (
 
 # https://fastapi.tiangolo.com/tutorial/metadata/#metadata-for-tags
 api_tags_metadata = [
+    {
+        "name": "datatypes",
+        "description": "Operations with supported data types.",
+    },
     {
         "name": "licenses",
         "description": "Operations with [SPDX licenses](https://spdx.org/licenses/).",
     },
+    {
+        "name": "tool data tables",
+        "description": "Operations with tool [Data Tables](https://galaxyproject.org/admin/tools/data-tables/).",
+    },
+    {
+        "name": "tours",
+        "description": "Operations with interactive tours.",
+    },
 ]
 
 
@@ -46,15 +59,9 @@ def initialize_fast_app(gx_app):
 
     add_exception_handler(app)
     wsgi_handler = WSGIMiddleware(gx_app)
-    from galaxy.webapps.galaxy.api import (
-        job_lock,
-        jobs,
-        roles,
-        licenses
-    )
-    app.include_router(jobs.router)
-    app.include_router(job_lock.router)
-    app.include_router(roles.router)
-    app.include_router(licenses.router)
+    for _, module in walk_controller_modules('galaxy.webapps.galaxy.api'):
+        router = getattr(module, "router", None)
+        if router:
+            app.include_router(router)
     app.mount('/', wsgi_handler)
     return app
diff --git a/lib/galaxy/webapps/galaxy/fast_factory.py b/lib/galaxy/webapps/galaxy/fast_factory.py
new file mode 100644
index 00000000000..4480c7a397f
--- /dev/null
+++ b/lib/galaxy/webapps/galaxy/fast_factory.py
@@ -0,0 +1,82 @@
+"""Module containing factory class for building uvicorn app for Galaxy.
+
+Information on uvicorn, its various settings, and how to invoke it can
+be found at https://www.uvicorn.org/.
+
+Galaxy can be launched with uvicorn using the following invocation:
+
+::
+
+    uvicorn --app-dir lib --factory galaxy.webapps.galaxy.fast_factory:factory
+
+Use the environment variable ``GALAXY_CONFIG_FILE`` to specify a Galaxy
+configuration file. Galaxy configuration can be loading from a YAML
+or an .ini file (reads app:main currently but can be overridden with
+GALAXY_CONFIG_SECTION).
+
+::
+
+    GALAXY_CONFIG_FILE=config/galaxy.yml uvicorn --app-dir lib --factory galaxy.webapps.galaxy.fast_factory:factory
+
+.. note::
+
+    Information on additional ways to configure uvicorn can be found at
+    https://www.uvicorn.org/.
+
+.. warning::
+
+    If an ini file is supplied via GALAXY_CONFIG_FILE, the server properties
+    such as host and port are not read from the file like older forms of
+    configuring Galaxy.
+
+`Gunicorn <https://docs.gunicorn.org/en/stable/index.html>`__ is a server with
+more complex management options.
+
+This factory function can be executed as a uvicorn worker managed with gunicorn
+with the following command-line.
+
+::
+
+    gunicorn 'galaxy.webapps.galaxy.fast_factory:factory()' --env GALAXY_CONFIG_FILE=config/galaxy.ini --pythonpath lib -w 4 -k uvicorn.workers.UvicornWorker
+
+"""
+import os
+
+from galaxy.main_config import (
+    absolute_config_path,
+    config_is_ini,
+    DEFAULT_CONFIG_SECTION,
+    DEFAULT_INI_APP,
+    find_config,
+)
+from galaxy.web_stack import get_app_kwds
+from galaxy.webapps.galaxy.buildapp import app_factory
+from .fast_app import initialize_fast_app
+
+
+def factory():
+    kwds = get_app_kwds("galaxy", "galaxy")
+    config_file = kwds.get("config_file")
+    if not config_file and "GALAXY_CONFIG_FILE" in os.environ:
+        config_file = os.path.abspath(os.environ["GALAXY_CONFIG_FILE"])
+    else:
+        galaxy_root = kwds.get("galaxy_root")
+        config_file = find_config(config_file, galaxy_root)
+        config_file = absolute_config_path(config_file, galaxy_root=galaxy_root)
+
+    if "GALAXY_CONFIG_SECTION" in os.environ:
+        config_section = os.environ["GALAXY_CONFIG_SECTION"]
+    elif config_is_ini(config_file):
+        config_section = "app:%s" % DEFAULT_INI_APP
+    else:
+        config_section = DEFAULT_CONFIG_SECTION
+
+    if 'config_file' not in kwds:
+        kwds['config_file'] = config_file
+    if 'config_section' not in kwds:
+        kwds['config_section'] = config_section
+    global_conf = {}
+    if config_is_ini(config_file):
+        global_conf["__file__"] = config_file
+    gx = app_factory(global_conf=global_conf, load_app_kwds=kwds)
+    return initialize_fast_app(gx)
diff --git a/lib/galaxy/webapps/reports/controllers/home.py b/lib/galaxy/webapps/reports/controllers/home.py
index 6c59fd0294f..4f3136ac774 100644
--- a/lib/galaxy/webapps/reports/controllers/home.py
+++ b/lib/galaxy/webapps/reports/controllers/home.py
@@ -37,10 +37,10 @@ class HomePage(BaseUIController, ReportQueryBuilder):
         )
 
         for job in recent_jobs.execute():
-            if(job.create_time >= start_days and
-               job.create_time < end_date_buffer):
-                if(job.create_time >= start_hours and
-                   job.create_time < end_date_buffer):
+            if(job.create_time >= start_days
+               and job.create_time < end_date_buffer):
+                if(job.create_time >= start_hours
+                   and job.create_time < end_date_buffer):
                     # Get the creation time for the jobs in the past day
                     end_day = end_date.day
                     start_day = job.create_time.day
@@ -71,10 +71,10 @@ class HomePage(BaseUIController, ReportQueryBuilder):
                 if(day < 30):
                     jc_dy_data[int(day)] += 1
 
-            if(job.update_time >= start_days and
-               job.update_time < end_date_buffer):
-                if(job.update_time >= start_hours and
-                   job.update_time < end_date_buffer):
+            if(job.update_time >= start_days
+               and job.update_time < end_date_buffer):
+                if(job.update_time >= start_hours
+                   and job.update_time < end_date_buffer):
                     # Get the time finishedfor the jobs in the past day
                     end_day = end_date.day
                     start_day = job.update_time.day
diff --git a/lib/galaxy/webapps/util.py b/lib/galaxy/webapps/util.py
index 7d82610aed5..94ca01e864e 100644
--- a/lib/galaxy/webapps/util.py
+++ b/lib/galaxy/webapps/util.py
@@ -36,7 +36,7 @@ def wrap_if_allowed_or_fail(app, stack, wrap, name=None, args=None, kwargs=None)
 
     Arguments are the same as for :func:`wrap_if_allowed`.
 
-    Raises :exception:`MiddlewareWrapUnsupported` if the stack does not allow the middleware.
+    Raises py:class:`MiddlewareWrapUnsupported` if the stack does not allow the middleware.
     """
     name = name or wrap.__name__
     if not stack.allowed_middleware(wrap):
diff --git a/lib/galaxy/work/context.py b/lib/galaxy/work/context.py
index 873d714301f..caa216ad0ca 100644
--- a/lib/galaxy/work/context.py
+++ b/lib/galaxy/work/context.py
@@ -1,14 +1,12 @@
 from galaxy.managers.context import (
-    ProvidesAppContext,
     ProvidesHistoryContext,
-    ProvidesUserContext
 )
 
 
-class WorkRequestContext(ProvidesAppContext, ProvidesUserContext, ProvidesHistoryContext):
+class WorkRequestContext(ProvidesHistoryContext):
     """ Stripped down implementation of Galaxy web transaction god object for
     work request handling outside of web threads - uses mix-ins shared with
-    GalaxyWebTransaction to provide app, user, and history context convience
+    GalaxyWebTransaction to provide app, user, and history context convenience
     methods - but nothing related to HTTP handling, mako views, etc....
 
     Things that only need app shouldn't be consuming trans - but there is a
@@ -19,20 +17,22 @@ class WorkRequestContext(ProvidesAppContext, ProvidesUserContext, ProvidesHistor
     """
 
     def __init__(self, app, user=None, history=None, workflow_building_mode=False):
-        self.app = app
-        self.security = app.security
+        self._app = app
         self.__user = user
         self.__user_current_roles = None
         self.__history = history
         self.workflow_building_mode = workflow_building_mode
 
+    @property
+    def app(self):
+        return self._app
+
     def get_history(self, create=False):
         return self.__history
 
-    def set_history(self, history):
-        raise NotImplementedError("Cannot change histories from a work request context.")
-
-    history = property(get_history, set_history)
+    @property
+    def history(self):
+        return self.get_history()
 
     def get_user(self):
         """Return the current user if logged in or None."""
diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py
index cf0f4a96b7b..a6c3354513d 100644
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -129,12 +129,14 @@ def extract_steps(trans, history=None, job_ids=None, dataset_ids=None, dataset_c
             assoc_name = assoc.name
             if ToolOutputCollectionPart.is_named_collection_part_name(assoc_name):
                 continue
+            if assoc_name.startswith("__new_primary_file"):
+                continue
             if job in summary.implicit_map_jobs:
                 hid = None
                 for implicit_pair in jobs[job]:
                     query_assoc_name, dataset_collection = implicit_pair
                     if query_assoc_name == assoc_name or assoc_name.startswith("__new_primary_file_%s|" % query_assoc_name):
-                        hid = dataset_collection.hid
+                        hid = summary.hid(dataset_collection)
                 if hid is None:
                     template = "Failed to find matching implicit job - job id is %s, implicit pairs are %s, assoc_name is %s."
                     message = template % (job.id, jobs[job], assoc_name)
@@ -142,9 +144,12 @@ def extract_steps(trans, history=None, job_ids=None, dataset_ids=None, dataset_c
                     raise Exception("Failed to extract job.")
             else:
                 if hasattr(assoc, "dataset"):
-                    hid = assoc.dataset.hid
+                    has_hid = assoc.dataset
                 else:
-                    hid = assoc.dataset_collection_instance.hid
+                    has_hid = assoc.dataset_collection_instance
+                hid = summary.hid(has_hid)
+            if hid in hid_to_output_pair:
+                log.warning("duplicate hid found in extract_steps [%s]" % hid)
             hid_to_output_pair[hid] = (step, assoc.name)
     return steps
 
@@ -196,8 +201,29 @@ class WorkflowSummary:
         self.implicit_map_jobs = []
         self.collection_types = {}
 
+        self.hda_hid_in_history = {}
+        self.hdca_hid_in_history = {}
+
         self.__summarize()
 
+    def hid(self, object):
+        if object.history_content_type == "dataset_collection":
+            if object.id in self.hdca_hid_in_history:
+                return self.hdca_hid_in_history[object.id]
+            elif object.history == self.history:
+                return object.hid
+            else:
+                log.warning("extraction issue, using hdca hid from outside current history and unmapped")
+                return object.hid
+        else:
+            if object.id in self.hda_hid_in_history:
+                return self.hda_hid_in_history[object.id]
+            elif object.history == self.history:
+                return object.hid
+            else:
+                log.warning("extraction issue, using hda hid from outside current history and unmapped")
+                return object.hid
+
     def __summarize(self):
         # Make a first pass handle all singleton jobs, input dataset and dataset collections
         # just grab the implicitly mapped jobs and handle in second pass. Second pass is
@@ -215,7 +241,10 @@ class WorkflowSummary:
             self.__summarize_dataset(content)
 
     def __summarize_dataset_collection(self, dataset_collection):
+        hid_in_history = dataset_collection.hid
         dataset_collection = self.__original_hdca(dataset_collection)
+        self.hdca_hid_in_history[dataset_collection.id] = hid_in_history
+
         hid = dataset_collection.hid
         self.collection_types[hid] = dataset_collection.collection.collection_type
         cja = dataset_collection.creating_job_associations
@@ -264,7 +293,9 @@ class WorkflowSummary:
         if not self.__check_state(dataset):
             return
 
+        hid_in_history = dataset.hid
         original_hda = self.__original_hda(dataset)
+        self.hda_hid_in_history[original_hda.id] = hid_in_history
 
         if not original_hda.creating_job_associations:
             self.jobs[FakeJob(dataset)] = [(None, dataset)]
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index ca526f45008..56f3ffe4af3 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -215,7 +215,7 @@ class WorkflowModule:
     def get_config_form(self, step=None):
         """ Serializes input parameters of a module into input dictionaries. """
         return {
-            'title' : self.name,
+            'title': self.name,
             'inputs': [param.to_dict(self.trans) for param in self.get_inputs().values()]
         }
 
@@ -1434,7 +1434,7 @@ class ToolModule(WorkflowModule):
         data_outputs = []
         if self.tool:
             for name, tool_output in self.tool.outputs.items():
-                if filter_output(tool_output, self.state.inputs):
+                if filter_output(self.tool, tool_output, self.state.inputs):
                     continue
                 extra_kwds = {}
                 if isinstance(tool_output, ToolExpressionOutput):
diff --git a/lib/galaxy/workflow/refactor/execute.py b/lib/galaxy/workflow/refactor/execute.py
index 89ee398efb1..dc6b3067eff 100644
--- a/lib/galaxy/workflow/refactor/execute.py
+++ b/lib/galaxy/workflow/refactor/execute.py
@@ -135,7 +135,7 @@ class WorkflowRefactorExecutor:
         if input_type in ["data", "dataset"]:
             module_type = "data_input"
         elif input_type in ["data_collection", "dataset_collection"]:
-            module_type == "data_collection_input"
+            module_type = "data_collection_input"
             tool_state["collection_type"] = action.collection_type
         else:
             if input_type not in InputParameterModule.POSSIBLE_PARAMETER_TYPES:
@@ -336,7 +336,7 @@ class WorkflowRefactorExecutor:
         )
         new_input_order_index = self._add_input_get_order_index(input_action, execution)
 
-        for order_index, tool_input, prefixed_name in target_tool_inputs:
+        for order_index, _tool_input, prefixed_name in target_tool_inputs:
             connect_input = InputReferenceByOrderIndex(order_index=order_index, input_name=prefixed_name)
             connect_action = ConnectAction(
                 action_type="connect",
diff --git a/lib/galaxy/workflow/resources/__init__.py b/lib/galaxy/workflow/resources/__init__.py
index 8567a98263e..282fa596d74 100644
--- a/lib/galaxy/workflow/resources/__init__.py
+++ b/lib/galaxy/workflow/resources/__init__.py
@@ -123,8 +123,8 @@ def validate_by_group_workflow_parameters_mapper(by_group, workflow_resource_par
         if 'groups' not in by_group:
             raise Exception("'workflow_resource_params_mapper' YAML file is malformed, 'groups' attribute not found!")
         if default_group not in by_group['groups']:
-            raise Exception("'workflow_resource_params_mapper' YAML file is malformed, default group with title '" +
-                            default_group + "' not found in 'groups'!")
+            raise Exception("'workflow_resource_params_mapper' YAML file is malformed, default group with title '"
+                            + default_group + "' not found in 'groups'!")
         for group in by_group['groups']:
             for attrib in by_group['groups'][group]:
                 if type(attrib) is dict:
@@ -132,8 +132,8 @@ def validate_by_group_workflow_parameters_mapper(by_group, workflow_resource_par
                         raise Exception("'workflow_resource_params_mapper' YAML file is malformed, "
                                         "'name' attribute not found in attribute of group '" + group + "'!")
                     if attrib['name'] not in workflow_resource_params:
-                        raise Exception("'workflow_resource_params_mapper' YAML file is malformed, group with name '" +
-                                        attrib['name'] + "' not found in 'workflow_resource_params'!")
+                        raise Exception("'workflow_resource_params_mapper' YAML file is malformed, group with name '"
+                                        + attrib['name'] + "' not found in 'workflow_resource_params'!")
                     if 'options' not in attrib:
                         raise Exception("'workflow_resource_params_mapper' YAML file is malformed, "
                                         "'options' attribute not found in attribute of group '" + group + "'!")
@@ -143,8 +143,8 @@ def validate_by_group_workflow_parameters_mapper(by_group, workflow_resource_par
                         valid_options.append(param_option.attrib['value'])
                     for option in attrib['options']:
                         if option not in valid_options:
-                            raise Exception("'workflow_resource_params_mapper' YAML file is malformed, '" + option +
-                                            "' in 'options' of '" + attrib['name'] + "' not found in attribute of group '" + group + "'!")
+                            raise Exception("'workflow_resource_params_mapper' YAML file is malformed, '" + option
+                                            + "' in 'options' of '" + attrib['name'] + "' not found in attribute of group '" + group + "'!")
                 else:
                     if attrib not in workflow_resource_params:
                         raise Exception("'workflow_resource_params_mapper' YAML file is malformed, attribute with name "
diff --git a/lib/galaxy/workflow/steps.py b/lib/galaxy/workflow/steps.py
index f6d50d712ae..1ff7e7e2bd8 100644
--- a/lib/galaxy/workflow/steps.py
+++ b/lib/galaxy/workflow/steps.py
@@ -44,8 +44,8 @@ def order_workflow_steps(steps):
 
 def edgelist_for_workflow_steps(steps):
     """
-    Create a list of tuples representing edges between ``WorkflowSteps`` based
-    on associated ``WorkflowStepConnection``s
+    Create a list of tuples representing edges between ``WorkflowStep`` s based
+    on associated ``WorkflowStepConnection`` s
     """
     edges = []
     steps_to_index = {step: i for i, step in enumerate(steps)}
diff --git a/lib/galaxy_test/api/test_api_batch.py b/lib/galaxy_test/api/test_api_batch.py
index c849ee71c47..18bcdabc99a 100644
--- a/lib/galaxy_test/api/test_api_batch.py
+++ b/lib/galaxy_test/api/test_api_batch.py
@@ -15,7 +15,7 @@ class ApiBatchTestCase(ApiTestCase):
         return url + sep + 'key=' + self._get_api_key(admin=admin)
 
     def _post_batch(self, batch):
-        data = json.dumps({"batch" : batch})
+        data = json.dumps({"batch": batch})
         return post("%s/batch" % (self.galaxy_interactor.api_url), data=data)
 
     # ---- tests
diff --git a/lib/galaxy_test/api/test_datatypes.py b/lib/galaxy_test/api/test_datatypes.py
index bc174af2448..3cc25f8eadf 100644
--- a/lib/galaxy_test/api/test_datatypes.py
+++ b/lib/galaxy_test/api/test_datatypes.py
@@ -84,6 +84,20 @@ class DatatypesApiTestCase(ApiTestCase):
         self._assert_status_code_is(response, 200)
         assert converters == len(response.json())
 
+    def test_edam_formats(self):
+        response = self._get("datatypes/edam_formats")
+        self._assert_status_code_is(response, 200)
+        edam_formats = response.json()
+        assert isinstance(edam_formats, dict)
+        assert edam_formats["ab1"] == "format_3000"
+
+    def test_edam_data(self):
+        response = self._get("datatypes/edam_data")
+        self._assert_status_code_is(response, 200)
+        edam_data = response.json()
+        assert isinstance(edam_data, dict)
+        assert edam_data["ab1"] == "data_0924"
+
     def _index_datatypes(self, data=None):
         data = data or {}
         response = self._get("datatypes", data=data)
diff --git a/lib/galaxy_test/api/test_history_contents.py b/lib/galaxy_test/api/test_history_contents.py
index 65c0f9aa304..da1908c5692 100644
--- a/lib/galaxy_test/api/test_history_contents.py
+++ b/lib/galaxy_test/api/test_history_contents.py
@@ -7,23 +7,22 @@ from galaxy_test.base.populators import (
     DatasetPopulator,
     LibraryPopulator,
     skip_without_tool,
-    TestsDatasets,
 )
 from ._framework import ApiTestCase
 
 
 # TODO: Test anonymous access.
-class HistoryContentsApiTestCase(ApiTestCase, TestsDatasets):
+class HistoryContentsApiTestCase(ApiTestCase):
 
     def setUp(self):
         super().setUp()
-        self.history_id = self._new_history()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
         self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
         self.library_populator = LibraryPopulator(self.galaxy_interactor)
+        self.history_id = self.dataset_populator.new_history()
 
     def test_index_hda_summary(self):
-        hda1 = self._new_dataset(self.history_id)
+        hda1 = self.dataset_populator.new_dataset(self.history_id)
         contents_response = self._get("histories/%s/contents" % self.history_id)
         hda_summary = self.__check_for_hda(contents_response, hda1)
         assert "display_types" not in hda_summary  # Quick summary, not full details
@@ -142,30 +141,30 @@ class HistoryContentsApiTestCase(ApiTestCase, TestsDatasets):
             assert "name" in contents_response.json()
 
     def test_index_hda_all_details(self):
-        hda1 = self._new_dataset(self.history_id)
+        hda1 = self.dataset_populator.new_dataset(self.history_id)
         contents_response = self._get("histories/%s/contents?details=all" % self.history_id)
         hda_details = self.__check_for_hda(contents_response, hda1)
         self.__assert_hda_has_full_details(hda_details)
 
     def test_index_hda_detail_by_id(self):
-        hda1 = self._new_dataset(self.history_id)
+        hda1 = self.dataset_populator.new_dataset(self.history_id)
         contents_response = self._get("histories/{}/contents?details={}".format(self.history_id, hda1["id"]))
         hda_details = self.__check_for_hda(contents_response, hda1)
         self.__assert_hda_has_full_details(hda_details)
 
     def test_show_hda(self):
-        hda1 = self._new_dataset(self.history_id)
+        hda1 = self.dataset_populator.new_dataset(self.history_id)
         show_response = self.__show(hda1)
         self._assert_status_code_is(show_response, 200)
         self.__assert_matches_hda(hda1, show_response.json())
 
     def test_hda_copy(self):
-        hda1 = self._new_dataset(self.history_id)
+        hda1 = self.dataset_populator.new_dataset(self.history_id)
         create_data = dict(
             source='hda',
             content=hda1["id"],
         )
-        second_history_id = self._new_history()
+        second_history_id = self.dataset_populator.new_history()
         assert self.__count_contents(second_history_id) == 0
         create_response = self._post("histories/%s/contents" % second_history_id, create_data)
         self._assert_status_code_is(create_response, 200)
@@ -235,8 +234,8 @@ class HistoryContentsApiTestCase(ApiTestCase, TestsDatasets):
         self._assert_status_code_is(update_response, 400)
 
     def _wait_for_new_hda(self):
-        hda1 = self._new_dataset(self.history_id)
-        self._wait_for_history(self.history_id)
+        hda1 = self.dataset_populator.new_dataset(self.history_id)
+        self.dataset_populator.wait_for_history(self.history_id)
         return hda1
 
     def _set_edit_update(self, json):
@@ -263,16 +262,16 @@ class HistoryContentsApiTestCase(ApiTestCase, TestsDatasets):
         return update_response
 
     def test_delete(self):
-        hda1 = self._new_dataset(self.history_id)
-        self._wait_for_history(self.history_id)
+        hda1 = self.dataset_populator.new_dataset(self.history_id)
+        self.dataset_populator.wait_for_history(self.history_id)
         assert str(self.__show(hda1).json()["deleted"]).lower() == "false"
         delete_response = self._delete("histories/{}/contents/{}".format(self.history_id, hda1["id"]))
         assert delete_response.status_code < 300  # Something in the 200s :).
         assert str(self.__show(hda1).json()["deleted"]).lower() == "true"
 
     def test_purge(self):
-        hda1 = self._new_dataset(self.history_id)
-        self._wait_for_history(self.history_id)
+        hda1 = self.dataset_populator.new_dataset(self.history_id)
+        self.dataset_populator.wait_for_history(self.history_id)
         assert str(self.__show(hda1).json()["deleted"]).lower() == "false"
         assert str(self.__show(hda1).json()["purged"]).lower() == "false"
         data = {'purge': True}
@@ -427,7 +426,7 @@ class HistoryContentsApiTestCase(ApiTestCase, TestsDatasets):
     def test_hdca_copy(self):
         hdca = self.dataset_collection_populator.create_pair_in_history(self.history_id).json()
         hdca_id = hdca["id"]
-        second_history_id = self._new_history()
+        second_history_id = self.dataset_populator.new_history()
         create_data = dict(
             source='hdca',
             content=hdca_id,
@@ -444,7 +443,7 @@ class HistoryContentsApiTestCase(ApiTestCase, TestsDatasets):
     def test_hdca_copy_and_elements(self):
         hdca = self.dataset_collection_populator.create_pair_in_history(self.history_id).json()
         hdca_id = hdca["id"]
-        second_history_id = self._new_history()
+        second_history_id = self.dataset_populator.new_history()
         create_data = dict(
             source='hdca',
             content=hdca_id,
@@ -476,7 +475,7 @@ class HistoryContentsApiTestCase(ApiTestCase, TestsDatasets):
         ld = self.library_populator.new_library_dataset("el1")
         ldda_id = ld["ldda_id"]
         element_identifiers = [{"name": "el1", "src": "ldda", "id": ldda_id}]
-        history_id = self._new_history()
+        history_id = self.dataset_populator.new_history()
         create_data = dict(
             history_id=history_id,
             type="dataset_collection",
@@ -506,7 +505,7 @@ class HistoryContentsApiTestCase(ApiTestCase, TestsDatasets):
             collection_type="list",
         )
         with self._different_user():
-            second_history_id = self._new_history()
+            second_history_id = self.dataset_populator.new_history()
             create_response = self._post("histories/%s/contents/dataset_collections" % second_history_id, create_data)
             self._assert_status_code_is(create_response, 403)
 
diff --git a/lib/galaxy_test/api/test_libraries.py b/lib/galaxy_test/api/test_libraries.py
index 08f752d7d97..73a1cd24274 100644
--- a/lib/galaxy_test/api/test_libraries.py
+++ b/lib/galaxy_test/api/test_libraries.py
@@ -6,7 +6,6 @@ from galaxy_test.base.populators import (
     DatasetCollectionPopulator,
     DatasetPopulator,
     LibraryPopulator,
-    TestsDatasets,
 )
 from ._framework import ApiTestCase
 
@@ -14,7 +13,7 @@ FILE_URL = 'https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data
 FILE_MD5 = "37b59762b59fff860460522d271bc111"
 
 
-class LibrariesApiTestCase(ApiTestCase, TestsDatasets):
+class LibrariesApiTestCase(ApiTestCase):
 
     def setUp(self):
         super().setUp()
diff --git a/lib/galaxy_test/api/test_pages.py b/lib/galaxy_test/api/test_pages.py
index b918511db56..f992c336c0f 100644
--- a/lib/galaxy_test/api/test_pages.py
+++ b/lib/galaxy_test/api/test_pages.py
@@ -71,7 +71,7 @@ steps:
             invocation_id = summary.invocation_id
             report_json = workflow_populator.workflow_report_json(workflow_id, invocation_id)
             assert "markdown" in report_json
-            self._assert_has_keys(report_json , "markdown", "render_format")
+            self._assert_has_keys(report_json, "markdown", "render_format")
             assert report_json["render_format"] == "markdown"
             markdown_content = report_json["markdown"]
             page_request = dict(
diff --git a/lib/galaxy_test/api/test_tool_data.py b/lib/galaxy_test/api/test_tool_data.py
index 1792f30c015..2b767c998fb 100644
--- a/lib/galaxy_test/api/test_tool_data.py
+++ b/lib/galaxy_test/api/test_tool_data.py
@@ -1,4 +1,8 @@
-""" Tests for the tool data API.
+"""Tests for the tool data API.
+
+The tests for the DELETE endpoint can be found in the
+integration tests directory (tests/integration/test_tool_data_delete.py)
+since these tests can mutate the server config state.
 """
 
 import operator
@@ -44,32 +48,39 @@ class ToolDataApiTestCase(ApiTestCase):
         content = show_field_response.text
         assert content == "This is data 1.", content
 
-    # Following test case rendered invalid by the fix in
-    # https://github.com/galaxyproject/galaxy/commit/48f77dc742acf01ddbafafcc4634e69378f1f020#diff-bfb557a99c1f7d646d4968d8d680b885R154.
-    # TODO: Restore the test case when test framework allows actions from
-    # admin users.
+    def test_reload(self):
+        show_response = self._get("tool_data/test_fasta_indexes/reload", admin=True)
+        self._assert_status_code_is(show_response, 200)
+        print(show_response.content)
+        data_table = show_response.json()
+        assert data_table["columns"] == ['value', 'dbkey', 'name', 'path']
 
-    # def test_delete_entry(self):
-    #     show_response = self._get( "tool_data/testbeta", admin=True )
-    #     original_count = len(show_response.json()["fields"])
+    def test_show_unknown_raises_404(self):
+        show_response = self._get("tool_data/unknown", admin=True)
+        self._assert_status_code_is(show_response, 404)
 
-    #     dataset_populator = DatasetPopulator( self.galaxy_interactor )
-    #     history_id = dataset_populator.new_history()
-    #     payload = dataset_populator.run_tool_payload(
-    #         tool_id="data_manager",
-    #         inputs={"ignored_value": "moo"},
-    #         history_id=history_id,
-    #     )
-    #     create_response = self._post( "tools", data=payload )
-    #     self._assert_status_code_is( create_response, 200 )
-    #     dataset_populator.wait_for_history( history_id, assert_ok=True )
-    #     show_response = self._get( "tool_data/testbeta", admin=True )
-    #     updated_fields = show_response.json()["fields"]
-    #     assert len(updated_fields) == original_count + 1
-    #     field0 = updated_fields[0]
-    #     url = self._api_url( "tool_data/testbeta?key=%s" % self.galaxy_interactor.master_api_key )
-    #     delete( url, data=json.dumps({"values": "\t".join(field0)}) )
+    def test_show_unknown_field_raises_404(self):
+        show_response = self._get("tool_data/testalpha/fields/unknown", admin=True)
+        self._assert_status_code_is(show_response, 404)
 
-    #     show_response = self._get( "tool_data/testbeta", admin=True )
-    #     updated_fields = show_response.json()["fields"]
-    #     assert len(updated_fields) == original_count
+    def test_reload_unknown_raises_404(self):
+        show_response = self._get("tool_data/unknown/reload", admin=True)
+        self._assert_status_code_is(show_response, 404)
+
+    def test_download_field_unknown_file_raises_404(self):
+        show_field_response = self._get("tool_data/testalpha/fields/data1/files/unknown.txt", admin=True)
+        self._assert_status_code_is(show_field_response, 404)
+
+    def test_delete_without_payload_raises_400(self):
+        delete_response = self._delete("tool_data/testbeta", admin=True)
+        self._assert_status_code_is(delete_response, 400)
+
+    def test_delete_without_values_raises_400(self):
+        payload = {"unknown": "test"}
+        delete_response = self._delete("tool_data/testbeta", data=payload, admin=True)
+        self._assert_status_code_is(delete_response, 400)
+
+    def test_delete_with_wrong_values_raises_400(self):
+        payload = {"values": "wrong"}
+        delete_response = self._delete("tool_data/testbeta", data=payload, admin=True)
+        self._assert_status_code_is(delete_response, 400)
diff --git a/lib/galaxy_test/api/test_tools.py b/lib/galaxy_test/api/test_tools.py
index e8c5d8f9e00..6a81373ebb4 100644
--- a/lib/galaxy_test/api/test_tools.py
+++ b/lib/galaxy_test/api/test_tools.py
@@ -1217,7 +1217,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         tool_test_dicts = [{
             "inputs": {
                 "input": ["simple_line.txt"],
-                "index": ["hg18"],
+                "index": ["hg18_value"],
             },
             "outputs": {},
             "required_files": [['simple_line.txt', {'value': 'simple_line.txt', 'dbkey': 'hg18'}]],
@@ -1235,7 +1235,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         tool_test_dicts = [{
             "inputs": {
                 "input": ["simple_line.txt"],
-                "index": ["hg18"],
+                "index": ["hg18_value"],
             },
             "outputs": {},
             "required_files": [['simple_line.txt', {'value': 'simple_line.txt', 'dbkey': 'hgnot18'}]],
diff --git a/lib/galaxy_test/api/test_tours.py b/lib/galaxy_test/api/test_tours.py
index b15a1e71442..6c2ecde6836 100644
--- a/lib/galaxy_test/api/test_tours.py
+++ b/lib/galaxy_test/api/test_tours.py
@@ -9,9 +9,20 @@ class TourApiTestCase(ApiTestCase):
         tours = response.json()
         tour_keys = map(lambda t: t["id"], tours)
         assert "core.history" in tour_keys
+        for tour in tours:
+            self._assert_has_keys(tour, "id", "name", "description", "tags")
 
     def test_show(self):
         response = self._get("tours/core.history")
         self._assert_status_code_is(response, 200)
         tour = response.json()
+        self._assert_tour(tour)
+
+    def test_update(self):
+        response = self._post("tours/core.history", admin=True)
+        self._assert_status_code_is(response, 200)
+        tour = response.json()
+        self._assert_tour(tour)
+
+    def _assert_tour(self, tour):
         self._assert_has_keys(tour, "name", "description", "title_default", "steps")
diff --git a/lib/galaxy_test/api/test_users.py b/lib/galaxy_test/api/test_users.py
index 33366fbbeed..3dd0dea8f66 100644
--- a/lib/galaxy_test/api/test_users.py
+++ b/lib/galaxy_test/api/test_users.py
@@ -122,7 +122,7 @@ class UsersApiTestCase(ApiTestCase):
         response = get(url).json()
         self.assertEqual(response["username"], user["username"])
         self.assertEqual(response["email"], TEST_USER_EMAIL)
-        put(url, data=json.dumps({"address_0|desc" : "_desc"}))
+        put(url, data=json.dumps({"address_0|desc": "_desc"}))
         response = get(url).json()
         self.assertEqual(len(response["addresses"]), 1)
         self.assertEqual(response["addresses"][0]["desc"], "_desc")
@@ -132,12 +132,12 @@ class UsersApiTestCase(ApiTestCase):
         user = self._setup_user(TEST_USER_EMAIL)
         # adding a tool to favorites
         url = self._api_url("users/%s/favorites/tools" % user["id"], params=dict(key=self.master_api_key))
-        put_response = put(url, data=json.dumps({"object_id" : "cat1"}))
+        put_response = put(url, data=json.dumps({"object_id": "cat1"}))
         self._assert_status_code_is_ok(put_response)
         self.assertEqual(put_response.json()["tools"][0], "cat1")
         # not implemented for workflows yet
         url = self._api_url("users/%s/favorites/workflows" % user["id"], params=dict(key=self.master_api_key))
-        put_response = put(url, data=json.dumps({"object_id" : "14ds68f4sda68gf46dsag4"}))
+        put_response = put(url, data=json.dumps({"object_id": "14ds68f4sda68gf46dsag4"}))
         self._assert_status_code_is(put_response, 400)
         # delete existing tool favorite
         url = self._api_url("users/%s/favorites/tools/cat1" % user["id"], params=dict(key=self.master_api_key))
@@ -157,7 +157,7 @@ class UsersApiTestCase(ApiTestCase):
     def test_search_favorites(self):
         user, user_key = self._setup_user_get_key(TEST_USER_EMAIL)
         url = self._api_url("users/%s/favorites/tools" % user["id"], params=dict(key=user_key))
-        fav_response = put(url, data=json.dumps({"object_id" : "cat1"}))
+        fav_response = put(url, data=json.dumps({"object_id": "cat1"}))
         self._assert_status_code_is_ok(fav_response)
         assert "cat1" in fav_response.json()["tools"]
         url = self._api_url("tools", params=dict(q="#favs", key=user_key))
diff --git a/lib/galaxy_test/api/test_workflow_extraction.py b/lib/galaxy_test/api/test_workflow_extraction.py
index 5da4408a098..76946ef3405 100644
--- a/lib/galaxy_test/api/test_workflow_extraction.py
+++ b/lib/galaxy_test/api/test_workflow_extraction.py
@@ -523,7 +523,7 @@ test_data:
                 if "job_ids" in extract_payload:
                     job_ids = extract_payload["job_ids"]
                     new_job_ids = []
-                    for i, job_id in enumerate(job_ids):
+                    for job_id in job_ids:
                         new_job_ids.append(new_history_job_ids[history_job_ids.index(job_id)])
 
                     extract_payload["job_ids"] = new_job_ids
diff --git a/lib/galaxy_test/base/api.py b/lib/galaxy_test/base/api.py
index a9c4fdbcd5d..f7a3ec5565b 100644
--- a/lib/galaxy_test/base/api.py
+++ b/lib/galaxy_test/base/api.py
@@ -11,7 +11,7 @@ from .api_asserts import (
 )
 from .api_util import (
     ADMIN_TEST_USER,
-    get_master_api_key,
+    get_admin_api_key,
     get_user_api_key,
     OTHER_USER,
     TEST_USER,
@@ -42,7 +42,7 @@ class UsesApiTestCaseMixin:
 
     def _setup_interactor(self):
         self.user_api_key = get_user_api_key()
-        self.master_api_key = get_master_api_key()
+        self.master_api_key = get_admin_api_key()
         self.galaxy_interactor = self._get_interactor()
 
     def _get_interactor(self, api_key=None):
@@ -60,10 +60,13 @@ class UsesApiTestCaseMixin:
 
     @contextmanager
     def _different_user(self, email=OTHER_USER):
-        """ Use in test cases to switch get/post operations to act as new user,
+        """ Use in test cases to switch get/post operations to act as new user
+
+        ..code-block:: python
 
             with self._different_user("other_user@bx.psu.edu"):
                 self._get("histories")  # Gets other_user@bx.psu.edu histories.
+
         """
         original_api_key = self.user_api_key
         original_interactor_key = self.galaxy_interactor.api_key
diff --git a/lib/galaxy_test/base/api_asserts.py b/lib/galaxy_test/base/api_asserts.py
index 3a0071dd6ef..95f775bb38f 100644
--- a/lib/galaxy_test/base/api_asserts.py
+++ b/lib/galaxy_test/base/api_asserts.py
@@ -1,50 +1,74 @@
-""" Utility methods for making assertions about Galaxy API responses, etc...
+"""Utility methods for making assertions about Galaxy API responses, etc...
 """
+from typing import Any, cast, Dict, Union
+
+from requests import Response
+
 ASSERT_FAIL_ERROR_CODE = "Expected Galaxy error code %d, obtained %d"
 ASSERT_FAIL_STATUS_CODE = "Request status code (%d) was not expected value %s. Body was %s"
 
 
-def assert_status_code_is(response, expected_status_code):
+def assert_status_code_is(response: Response, expected_status_code: int):
+    """Assert that the supplied response has the expect status code."""
     response_status_code = response.status_code
     if expected_status_code != response_status_code:
         _report_status_code_error(response, expected_status_code)
 
 
-def assert_status_code_is_ok(response):
+def assert_status_code_is_ok(response: Response):
+    """Assert that the supplied response is okay.
+
+    The easier alternative ``response.raise_for_status()`` might be
+    perferable generally.
+
+    .. seealso:: :py:meth:`requests.Response.raise_for_status()`
+    """
     response_status_code = response.status_code
     is_two_hundred_status_code = response_status_code >= 200 and response_status_code <= 300
     if not is_two_hundred_status_code:
         _report_status_code_error(response, "2XX")
 
 
-def _report_status_code_error(response, expected_status_code):
+def _report_status_code_error(response: Response, expected_status_code: Union[str, int]):
     try:
         body = response.json()
     except Exception:
-        body = "INVALID JSON RESPONSE <%s>" % response.content
+        body = f"INVALID JSON RESPONSE <{response.text}>"
     assertion_message = ASSERT_FAIL_STATUS_CODE % (response.status_code, expected_status_code, body)
     raise AssertionError(assertion_message)
 
 
-def assert_has_keys(response, *keys):
+def assert_has_keys(response: dict, *keys: str):
+    """Assert that the supplied response (dict) has the supplied keys."""
     for key in keys:
         assert key in response, f"Response [{response}] does not contain key [{key}]"
 
 
-def assert_not_has_keys(response, *keys):
+def assert_not_has_keys(response: dict, *keys: str):
+    """Assert that the supplied response (dict) does not have the supplied keys."""
     for key in keys:
         assert key not in response, f"Response [{response}] contains invalid key [{key}]"
 
 
-def assert_error_code_is(response, error_code):
-    if hasattr(response, "json"):
-        response = response.json()
-    assert_has_keys(response, "err_code")
-    err_code = response["err_code"]
+def assert_error_code_is(response: Union[Response, dict], error_code: int):
+    """Assert that the supplied response has the supplied Galaxy error code.
+
+    Galaxy error codes can be imported from :py:mod:`galaxy.exceptions.error_codes`
+    to test against.
+
+    ::
+
+        from galaxy.exceptions import error_codes
+        assert_error_code_is(response, error_codes.USER_REQUEST_MISSING_PARAMETER)
+
+    """
+    as_dict = _as_dict(response)
+    assert_has_keys(as_dict, "err_code")
+    err_code = as_dict["err_code"]
     assert err_code == int(error_code), ASSERT_FAIL_ERROR_CODE % (err_code, int(error_code))
 
 
-def assert_object_id_error(response):
+def assert_object_id_error(response: Response):
     # for tests that use fake object IDs - API might throw MalformedId (400) or
     # or ObjectNotFound (404) - depending if the ID happens to be parseable with
     # servers API key.
@@ -56,12 +80,20 @@ def assert_object_id_error(response):
         assert_error_code_is(response, 404001)
 
 
-def assert_error_message_contains(response, expected_contains):
-    if hasattr(response, "json"):
-        response = response.json()
-    assert_has_keys(response, "err_msg")
-    err_msg = response["err_msg"]
+def assert_error_message_contains(response: Union[Response, dict], expected_contains: str):
+    as_dict = _as_dict(response)
+    assert_has_keys(as_dict, "err_msg")
+    err_msg = as_dict["err_msg"]
     assert expected_contains in err_msg
 
 
+def _as_dict(response: Union[Response, dict]) -> Dict[str, Any]:
+    as_dict: Dict[str, Any]
+    if isinstance(response, Response):
+        as_dict = cast(dict, response.json())
+    else:
+        as_dict = response
+    return as_dict
+
+
 assert_has_key = assert_has_keys
diff --git a/lib/galaxy_test/base/api_util.py b/lib/galaxy_test/base/api_util.py
index d97377d1374..ace95c9b9d4 100644
--- a/lib/galaxy_test/base/api_util.py
+++ b/lib/galaxy_test/base/api_util.py
@@ -1,4 +1,5 @@
 import os
+from typing import Optional
 
 DEFAULT_GALAXY_MASTER_API_KEY = "TEST123"
 DEFAULT_GALAXY_USER_API_KEY = None
@@ -12,10 +13,11 @@ ADMIN_TEST_USER = os.environ.get("GALAXY_TEST_ADMIN_USER_EMAIL", DEFAULT_ADMIN_T
 OTHER_USER = os.environ.get("GALAXY_TEST_OTHER_USER_EMAIL", DEFAULT_OTHER_USER)
 
 
-def get_master_api_key():
-    """ Test master API key to use for functional test. This key should be
-    configured as a master API key and should be able to create additional
-    users and keys.
+def get_admin_api_key() -> str:
+    """Test admin API key to use for functional tests.
+
+    This key should be configured as a admin API key and should be able
+    to create additional users and keys.
     """
     for key in ["GALAXY_CONFIG_MASTER_API_KEY", "GALAXY_CONFIG_OVERRIDE_MASTER_API_KEY"]:
         value = os.environ.get(key, None)
@@ -24,9 +26,10 @@ def get_master_api_key():
     return DEFAULT_GALAXY_MASTER_API_KEY
 
 
-def get_user_api_key():
-    """ Test user API key to use for functional tests. If set, this should drive
-    API based testing - if not set master API key should be used to create a new
-    user and API key for tests.
+def get_user_api_key() -> Optional[str]:
+    """Test user API key to use for functional tests.
+
+    If set, this should drive API based testing - if not set an admin API key will
+    be used to create a new user and API key for tests.
     """
     return os.environ.get("GALAXY_TEST_USER_API_KEY", DEFAULT_GALAXY_USER_API_KEY)
diff --git a/lib/galaxy_test/base/env.py b/lib/galaxy_test/base/env.py
index 767d132c945..bd6014281a4 100644
--- a/lib/galaxy_test/base/env.py
+++ b/lib/galaxy_test/base/env.py
@@ -4,11 +4,12 @@ import fcntl
 import os
 import socket
 import struct
+from typing import Optional, Tuple
 
 DEFAULT_WEB_HOST = socket.gethostbyname('localhost')
 
 
-def setup_keep_outdir():
+def setup_keep_outdir() -> str:
     keep_outdir = os.environ.get('GALAXY_TEST_SAVE', '')
     if keep_outdir > '':
         try:
@@ -18,15 +19,18 @@ def setup_keep_outdir():
     return keep_outdir
 
 
-def target_url_parts():
+def target_url_parts() -> Tuple[str, Optional[str], str]:
     host = socket.gethostbyname(os.environ.get('GALAXY_TEST_HOST', DEFAULT_WEB_HOST))
     port = os.environ.get('GALAXY_TEST_PORT')
-    default_url = f"http://{host}:{port}"
+    if port:
+        default_url = f"http://{host}:{port}"
+    else:
+        default_url = f"http://{host}"
     url = os.environ.get('GALAXY_TEST_EXTERNAL', default_url)
     return host, port, url
 
 
-def get_ip_address(ifname):
+def get_ip_address(ifname: str) -> str:
     s = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
     return socket.inet_ntoa(fcntl.ioctl(
         s.fileno(),
diff --git a/lib/galaxy_test/base/populators.py b/lib/galaxy_test/base/populators.py
index dcfc2dee805..0a596882a75 100644
--- a/lib/galaxy_test/base/populators.py
+++ b/lib/galaxy_test/base/populators.py
@@ -1,36 +1,76 @@
+"""Abstractions used by the Galaxy testing frameworks for interacting with the Galaxy API.
+
+These abstractions are geared toward testing use cases and populating fixtures.
+For a more general framework for working with the Galaxy API checkout `bioblend
+<https://github.com/galaxyproject/bioblend>`__.
+
+The populators are broken into different categories of data one might want to populate
+and work with (datasets, histories, libraries, and workflows). Within each populator
+type abstract classes describe high-level functionality that depend on abstract
+HTTP verbs executions (e.g. methods for executing GET, POST, DELETE). The abstract
+classes are :class:`galaxy_test.base.populators.BaseDatasetPopulator`,
+:class:`galaxy_test.base.populators.BaseWorkflowPopulator`, and
+:class:`galaxy_test.base.populators.BaseDatasetCollectionPopulator`.
+
+There are a few different concrete ways to supply these low-level verb executions.
+For instance :class:`galaxy_test.base.populators.DatasetPopulator` implements the abstract
+:class:`galaxy_test.base.populators.BaseDatasetPopulator` by leveraging a galaxy interactor
+:class:`galaxy.tool_util.interactor.GalaxyInteractorApi`. It is non-intuitive
+that the Galaxy testing framework uses the tool testing code inside Galaxy's code
+base for a lot of heavy lifting. This is due to the API testing framework organically
+growing from the tool testing framework that predated it and then the tool testing
+framework being extracted for re-use in `Planemo <https://github.com/galaxyproject/planemo>`__, etc..
+
+These other two concrete implementation of the populators are much more
+direct and intuitive. :class:`galaxy_test.base.populators.GiDatasetPopulator`, et. al.
+are populators built based on Bioblend ``gi`` objects to build URLs and describe
+API keys. :class:`galaxy_test.selenium.framework.SeleniumSessionDatasetPopulator`,
+et al. are populators built based on Selenium sessions to leverage Galaxy cookies
+for auth for instance.
+
+All three of these implementations are now effectively light wrappers around
+`requests <https://requests.readthedocs.io/>`__. Not leveraging requests directly
+is a bit ugly and this ugliness again stems from these organically growing from a
+framework that originally didn't use requests at all.
+
+API tests and Selenium tests routinely use requests directly and that is totally fine,
+requests should just be filtered through the verb abstractions if that functionality
+is then added to populators to be shared across tests or across testing frameworks.
+"""
 import contextlib
 import json
 import os
 import random
 import string
 import unittest
+from abc import ABCMeta, abstractmethod
 from collections import namedtuple
 from functools import wraps
 from io import StringIO
 from operator import itemgetter
+from typing import Any, Callable, Dict, Optional
 
-try:
-    from nose.tools import nottest
-except ImportError:
-    def nottest(x):
-        return x
 import requests
 import yaml
+from bioblend.galaxy import GalaxyClient
 from gxformat2 import (
     convert_and_import_workflow,
     ImporterGalaxyInterface,
 )
 from gxformat2._yaml import ordered_load
 from pkg_resources import resource_string
+from requests.models import Response
 
 from galaxy.tool_util.client.staging import InteractorStaging
 from galaxy.tool_util.verify.test_data import TestDataResolver
 from galaxy.tool_util.verify.wait import (
+    timeout_type,
     TimeoutAssertionError,
     wait_on as tool_util_wait_on,
 )
 from galaxy.util import unicodify
 from . import api_asserts
+from .api import ApiTestInteractor
 
 
 # Simple workflow that takes an input and call cat wrapper on it.
@@ -148,7 +188,6 @@ def summarize_instance_history_on_error(method):
     return wrapped_method
 
 
-@nottest
 def uses_test_history(**test_history_kwd):
     """Can override require_new and cancel_executions using kwds to decorator.
     """
@@ -170,37 +209,42 @@ def _raise_skip_if(check, *args):
         raise SkipTest(*args)
 
 
-# Deprecated mixin, use dataset populator instead.
-# TODO: Rework existing tests to target DatasetPopulator in a setup method instead.
-class TestsDatasets:
+class BasePopulator(metaclass=ABCMeta):
 
-    def _new_dataset(self, history_id, content='TestData123', **kwds):
-        return DatasetPopulator(self.galaxy_interactor).new_dataset(history_id, content=content, **kwds)
+    @abstractmethod
+    def _post(self, route, data=None, files=None, admin=False, json: bool = False) -> Response:
+        """POST data to target Galaxy instance on specified route."""
 
-    def _wait_for_history(self, history_id, assert_ok=False):
-        return DatasetPopulator(self.galaxy_interactor).wait_for_history(history_id, assert_ok=assert_ok)
+    @abstractmethod
+    def _put(self, route, data=None, admin=False) -> Response:
+        """PUT data to target Galaxy instance on specified route."""
 
-    def _new_history(self, **kwds):
-        return DatasetPopulator(self.galaxy_interactor).new_history(**kwds)
+    @abstractmethod
+    def _get(self, route, data=None, admin=False) -> Response:
+        """GET data from target Galaxy instance on specified route."""
 
-    def _upload_payload(self, history_id, content, **kwds):
-        return DatasetPopulator(self.galaxy_interactor).upload_payload(history_id, content, **kwds)
-
-    def _run_tool_payload(self, tool_id, inputs, history_id, **kwds):
-        return DatasetPopulator(self.galaxy_interactor).run_tool_payload(tool_id, inputs, history_id, **kwds)
+    @abstractmethod
+    def _delete(self, route, data=None, admin=False) -> Response:
+        """DELETE against target Galaxy instance on specified route."""
 
 
-class BaseDatasetPopulator:
+class BaseDatasetPopulator(BasePopulator):
     """ Abstract description of API operations optimized for testing
     Galaxy - implementations must implement _get, _post and _delete.
     """
 
-    def new_dataset(self, history_id, content=None, wait=False, **kwds):
+    def new_dataset(self, history_id: str, content=None, wait: bool = False, **kwds) -> str:
+        """Create a new history dataset instance (HDA) and return its ID.
+
+        :returns: the HDA id of the new object
+        """
         run_response = self.new_dataset_request(history_id, content=content, wait=wait, **kwds)
-        assert run_response.status_code == 200, "Failed to create new dataset with response: %s" % run_response.content
+        assert run_response.status_code == 200, "Failed to create new dataset with response: %s" % run_response.text
         return run_response.json()["outputs"][0]
 
-    def new_dataset_request(self, history_id, content=None, wait=False, **kwds):
+    def new_dataset_request(self, history_id: str, content=None, wait: bool = False, **kwds) -> requests.Response:
+        """Lower-level dataset creation that returns the upload tool response object.
+        """
         if content is None and "ftp_files" not in kwds:
             content = "TestData123"
         payload = self.upload_payload(history_id, content=content, **kwds)
@@ -209,7 +253,7 @@ class BaseDatasetPopulator:
             self.wait_for_tool_run(history_id, run_response, assert_ok=kwds.get('assert_ok', True))
         return run_response
 
-    def fetch(self, payload, assert_ok=True, timeout=DEFAULT_TIMEOUT, wait=None):
+    def fetch(self, payload: dict, assert_ok: bool = True, timeout: timeout_type = DEFAULT_TIMEOUT, wait: Optional[bool] = None):
         tool_response = self._post("tools/fetch", data=payload)
         if wait is None:
             wait = assert_ok
@@ -223,26 +267,26 @@ class BaseDatasetPopulator:
 
         return tool_response
 
-    def wait_for_tool_run(self, history_id, run_response, timeout=DEFAULT_TIMEOUT, assert_ok=True):
+    def wait_for_tool_run(self, history_id: str, run_response: requests.Response, timeout: timeout_type = DEFAULT_TIMEOUT, assert_ok: bool = True):
         job = self.check_run(run_response)
         self.wait_for_job(job["id"], timeout=timeout)
         self.wait_for_history(history_id, assert_ok=assert_ok, timeout=timeout)
         return run_response
 
-    def check_run(self, run_response):
+    def check_run(self, run_response: requests.Response) -> dict:
         run = run_response.json()
         assert run_response.status_code == 200, run
         job = run["jobs"][0]
         return job
 
-    def wait_for_history(self, history_id, assert_ok=False, timeout=DEFAULT_TIMEOUT):
+    def wait_for_history(self, history_id: str, assert_ok: bool = False, timeout: timeout_type = DEFAULT_TIMEOUT) -> str:
         try:
             return wait_on_state(lambda: self._get("histories/%s" % history_id), desc="history state", assert_ok=assert_ok, timeout=timeout)
         except AssertionError:
             self._summarize_history(history_id)
             raise
 
-    def wait_for_history_jobs(self, history_id, assert_ok=False, timeout=DEFAULT_TIMEOUT):
+    def wait_for_history_jobs(self, history_id: str, assert_ok: bool = False, timeout: timeout_type = DEFAULT_TIMEOUT):
 
         def has_active_jobs():
             active_jobs = self.active_history_jobs(history_id)
@@ -261,40 +305,40 @@ class BaseDatasetPopulator:
         if assert_ok:
             return self.wait_for_history(history_id, assert_ok=True, timeout=timeout)
 
-    def wait_for_job(self, job_id, assert_ok=False, timeout=DEFAULT_TIMEOUT):
+    def wait_for_job(self, job_id: str, assert_ok: bool = False, timeout: timeout_type = DEFAULT_TIMEOUT):
         return wait_on_state(lambda: self.get_job_details(job_id), desc="job state", assert_ok=assert_ok, timeout=timeout)
 
-    def get_job_details(self, job_id, full=False):
+    def get_job_details(self, job_id: str, full: bool = False) -> Response:
         return self._get(f"jobs/{job_id}?full={full}")
 
-    def cancel_history_jobs(self, history_id, wait=True):
+    def cancel_history_jobs(self, history_id: str, wait=True) -> None:
         active_jobs = self.active_history_jobs(history_id)
         for active_job in active_jobs:
             self.cancel_job(active_job["id"])
 
-    def history_jobs(self, history_id):
+    def history_jobs(self, history_id: str) -> dict:
         query_params = {"history_id": history_id, "order_by": "create_time"}
         jobs_response = self._get("jobs", query_params)
         assert jobs_response.status_code == 200
         return jobs_response.json()
 
-    def active_history_jobs(self, history_id):
+    def active_history_jobs(self, history_id: str) -> list:
         all_history_jobs = self.history_jobs(history_id)
         active_jobs = [j for j in all_history_jobs if j["state"] in ["new", "upload", "waiting", "queued", "running"]]
         return active_jobs
 
-    def cancel_job(self, job_id):
+    def cancel_job(self, job_id: str) -> Response:
         return self._delete("jobs/%s" % job_id)
 
-    def delete_history(self, history_id):
+    def delete_history(self, history_id: str) -> None:
         delete_response = self._delete(f"histories/{history_id}")
         delete_response.raise_for_status()
 
-    def delete_dataset(self, history_id, content_id):
+    def delete_dataset(self, history_id: str, content_id: str) -> Response:
         delete_response = self._delete(f"histories/{history_id}/contents/{content_id}")
         return delete_response
 
-    def create_tool_from_path(self, tool_path):
+    def create_tool_from_path(self, tool_path: str) -> Response:
         tool_directory = os.path.dirname(os.path.abspath(tool_path))
         payload = dict(
             src="from_path",
@@ -303,7 +347,7 @@ class BaseDatasetPopulator:
         )
         return self._create_tool_raw(payload)
 
-    def create_tool(self, representation, tool_directory=None):
+    def create_tool(self, representation, tool_directory: Optional[str] = None) -> Response:
         if isinstance(representation, dict):
             representation = json.dumps(representation)
         payload = dict(
@@ -312,7 +356,7 @@ class BaseDatasetPopulator:
         )
         return self._create_tool_raw(payload)
 
-    def _create_tool_raw(self, payload):
+    def _create_tool_raw(self, payload) -> Response:
         try:
             create_response = self._post("dynamic_tools", data=payload, admin=True)
         except TypeError:
@@ -320,35 +364,33 @@ class BaseDatasetPopulator:
         assert create_response.status_code == 200, create_response.text
         return create_response.json()
 
-    def list_dynamic_tools(self):
+    def list_dynamic_tools(self) -> list:
         list_response = self._get("dynamic_tools", admin=True)
         assert list_response.status_code == 200, list_response
         return list_response.json()
 
-    def show_dynamic_tool(self, uuid):
+    def show_dynamic_tool(self, uuid) -> dict:
         show_response = self._get("dynamic_tools/%s" % uuid, admin=True)
         assert show_response.status_code == 200, show_response
         return show_response.json()
 
-    def deactivate_dynamic_tool(self, uuid):
+    def deactivate_dynamic_tool(self, uuid) -> dict:
         delete_response = self._delete("dynamic_tools/%s" % uuid, admin=True)
         return delete_response.json()
 
-    def _summarize_history(self, history_id):
-        pass
+    def _summarize_history(self, history_id: str) -> None:
+        """Abstract method for summarizing a target history - override to provide details."""
 
     @contextlib.contextmanager
-    def test_history(self, **kwds):
+    def test_history(self, cancel_executions: bool = True, require_new: bool = True, **kwds):
         cleanup = "GALAXY_TEST_NO_CLEANUP" not in os.environ
+        history_id = None
 
         def wrap_up():
-            cancel_executions = kwds.get("cancel_executions", True)
             if cleanup and cancel_executions:
                 self.cancel_history_jobs(history_id)
 
-        require_new = kwds.get("require_new", True)
         try:
-            history_id = None
             if not require_new:
                 history_id = kwds.get("GALAXY_TEST_HISTORY_ID", None)
 
@@ -356,18 +398,18 @@ class BaseDatasetPopulator:
             yield history_id
             wrap_up()
         except Exception:
-            self._summarize_history(history_id)
+            if history_id:
+                self._summarize_history(history_id)
             wrap_up()
             raise
 
-    def new_history(self, **kwds):
-        name = kwds.get("name", "API Test History")
+    def new_history(self, name="API Test History", **kwds) -> str:
         create_history_response = self._post("histories", data=dict(name=name))
         assert "id" in create_history_response.json(), create_history_response.text
         history_id = create_history_response.json()["id"]
         return history_id
 
-    def upload_payload(self, history_id, content=None, **kwds):
+    def upload_payload(self, history_id: str, content: str = None, **kwds) -> dict:
         name = kwds.get("name", "Test_Dataset")
         dbkey = kwds.get("dbkey", "?")
         file_type = kwds.get("file_type", 'txt')
@@ -399,10 +441,12 @@ class BaseDatasetPopulator:
             upload_type='upload_dataset'
         )
 
-    def get_remote_files(self, target="ftp"):
-        return self._get("remote_files", data={"target": target}).json()
+    def get_remote_files(self, target: str = "ftp") -> dict:
+        response = self._get("remote_files", data={"target": target})
+        response.raise_for_status()
+        return response.json()
 
-    def run_tool_payload(self, tool_id, inputs, history_id, **kwds):
+    def run_tool_payload(self, tool_id: str, inputs: dict, history_id: str, **kwds) -> dict:
         # Remove files_%d|file_data parameters from inputs dict and attach
         # as __files dictionary.
         for key, value in list(inputs.items()):
@@ -419,7 +463,7 @@ class BaseDatasetPopulator:
             **kwds
         )
 
-    def run_tool(self, tool_id, inputs, history_id, assert_ok=True, **kwds):
+    def run_tool(self, tool_id: str, inputs: dict, history_id: str, assert_ok: bool = True, **kwds):
         payload = self.run_tool_payload(tool_id, inputs, history_id, **kwds)
         tool_response = self.tools_post(payload)
         if assert_ok:
@@ -428,11 +472,11 @@ class BaseDatasetPopulator:
         else:
             return tool_response
 
-    def tools_post(self, payload, url="tools"):
+    def tools_post(self, payload: dict, url="tools") -> Response:
         tool_response = self._post(url, data=payload)
         return tool_response
 
-    def get_history_dataset_content(self, history_id, wait=True, filename=None, type='text', raw=False, **kwds):
+    def get_history_dataset_content(self, history_id: str, wait=True, filename=None, type='text', raw=False, **kwds):
         dataset_id = self.__history_content_id(history_id, wait=wait, **kwds)
         data = {}
         if filename:
@@ -446,36 +490,36 @@ class BaseDatasetPopulator:
         else:
             return display_response.content
 
-    def get_history_dataset_details(self, history_id, **kwds):
+    def get_history_dataset_details(self, history_id: str, **kwds) -> dict:
         dataset_id = self.__history_content_id(history_id, **kwds)
         details_response = self.get_history_dataset_details_raw(history_id, dataset_id)
         details_response.raise_for_status()
         return details_response.json()
 
-    def get_history_dataset_details_raw(self, history_id, dataset_id):
+    def get_history_dataset_details_raw(self, history_id: str, dataset_id: str) -> Response:
         details_response = self._get_contents_request(history_id, f"/datasets/{dataset_id}")
         return details_response
 
-    def get_history_dataset_extra_files(self, history_id, **kwds):
+    def get_history_dataset_extra_files(self, history_id: str, **kwds) -> list:
         dataset_id = self.__history_content_id(history_id, **kwds)
         details_response = self._get_contents_request(history_id, "/%s/extra_files" % dataset_id)
         assert details_response.status_code == 200, details_response.content
         return details_response.json()
 
-    def get_history_collection_details(self, history_id, **kwds):
+    def get_history_collection_details(self, history_id: str, **kwds) -> dict:
         hdca_id = self.__history_content_id(history_id, **kwds)
         details_response = self._get_contents_request(history_id, "/dataset_collections/%s" % hdca_id)
         assert details_response.status_code == 200, details_response.content
         return details_response.json()
 
-    def run_collection_creates_list(self, history_id, hdca_id):
+    def run_collection_creates_list(self, history_id: str, hdca_id: str) -> Response:
         inputs = {
             "input1": {"src": "hdca", "id": hdca_id},
         }
         self.wait_for_history(history_id, assert_ok=True)
         return self.run_tool("collection_creates_list", inputs, history_id)
 
-    def run_exit_code_from_file(self, history_id, hdca_id):
+    def run_exit_code_from_file(self, history_id: str, hdca_id: str) -> dict:
         exit_code_inputs = {
             "input": {'batch': True, 'values': [{"src": "hdca", "id": hdca_id}]},
         }
@@ -483,7 +527,7 @@ class BaseDatasetPopulator:
         self.wait_for_history(history_id, assert_ok=False)
         return response
 
-    def __history_content_id(self, history_id, wait=True, **kwds):
+    def __history_content_id(self, history_id: str, wait=True, **kwds) -> str:
         if wait:
             assert_ok = kwds.get("assert_ok", True)
             self.wait_for_history(history_id, assert_ok=assert_ok)
@@ -510,7 +554,7 @@ class BaseDatasetPopulator:
                 history_content_id = history_contents[-1]["id"]
         return history_content_id
 
-    def _get_contents_request(self, history_id, suffix="", data=None):
+    def _get_contents_request(self, history_id: str, suffix: str = "", data=None) -> Response:
         if data is None:
             data = {}
         url = "histories/%s/contents" % history_id
@@ -518,35 +562,35 @@ class BaseDatasetPopulator:
             url = f"{url}{suffix}"
         return self._get(url, data=data)
 
-    def ds_entry(self, history_content):
+    def ds_entry(self, history_content: dict) -> dict:
         src = 'hda'
         if 'history_content_type' in history_content and history_content['history_content_type'] == "dataset_collection":
             src = 'hdca'
         return dict(src=src, id=history_content["id"])
 
-    def dataset_storage_info(self, dataset_id):
-        storage_response = self.galaxy_interactor.get(f"datasets/{dataset_id}/storage")
+    def dataset_storage_info(self, dataset_id: str) -> dict:
+        storage_response = self._get(f"datasets/{dataset_id}/storage")
         storage_response.raise_for_status()
         return storage_response.json()
 
-    def get_roles(self):
-        roles_response = self.galaxy_interactor.get("roles", admin=True)
+    def get_roles(self) -> list:
+        roles_response = self._get("roles", admin=True)
         assert roles_response.status_code == 200
         return roles_response.json()
 
-    def user_email(self):
-        users_response = self.galaxy_interactor.get("users")
+    def user_email(self) -> str:
+        users_response = self._get("users")
         users = users_response.json()
         assert len(users) == 1
         return users[0]["email"]
 
-    def user_id(self):
-        users_response = self.galaxy_interactor.get("users")
+    def user_id(self) -> str:
+        users_response = self._get("users")
         users = users_response.json()
         assert len(users) == 1
         return users[0]["id"]
 
-    def user_private_role_id(self):
+    def user_private_role_id(self) -> str:
         user_email = self.user_email()
         roles = self.get_roles()
         users_roles = [r for r in roles if r["name"] == user_email]
@@ -555,27 +599,27 @@ class BaseDatasetPopulator:
         assert "id" in role, role
         return role["id"]
 
-    def create_role(self, user_ids, description=None):
+    def create_role(self, user_ids: list, description: str = None) -> dict:
         payload = {
             "name": self.get_random_name(prefix="testpop"),
             "description": description or "Test Role",
             "user_ids": user_ids,
         }
-        role_response = self.galaxy_interactor.post("roles", data=payload, admin=True, json=True)
+        role_response = self._post("roles", data=payload, admin=True, json=True)
         assert role_response.status_code == 200
         return role_response.json()
 
-    def create_quota(self, quota_payload):
-        quota_response = self.galaxy_interactor.post("quotas", data=quota_payload, admin=True)
+    def create_quota(self, quota_payload: dict) -> dict:
+        quota_response = self._post("quotas", data=quota_payload, admin=True)
         quota_response.raise_for_status()
         return quota_response.json()
 
-    def get_quotas(self):
-        quota_response = self.galaxy_interactor.get("quotas", admin=True)
+    def get_quotas(self) -> list:
+        quota_response = self._get("quotas", admin=True)
         quota_response.raise_for_status()
         return quota_response.json()
 
-    def make_private(self, history_id, dataset_id):
+    def make_private(self, history_id: str, dataset_id: str) -> dict:
         role_id = self.user_private_role_id()
         # Give manage permission to the user.
         payload = {
@@ -583,7 +627,7 @@ class BaseDatasetPopulator:
             "manage": json.dumps([role_id]),
         }
         url = f"histories/{history_id}/contents/{dataset_id}/permissions"
-        update_response = self.galaxy_interactor._put(url, payload, admin=True)
+        update_response = self._put(url, payload, admin=True)
         assert update_response.status_code == 200, update_response.content
         return update_response.json()
 
@@ -729,21 +773,22 @@ class BaseDatasetPopulator:
             suffix or '',
         )
 
+    def wait_for_dataset(self, history_id, dataset_id, assert_ok=False, timeout=DEFAULT_TIMEOUT):
+        return wait_on_state(lambda: self._get(f"histories/{history_id}/contents/{dataset_id}"), desc="dataset state", assert_ok=assert_ok, timeout=timeout)
 
-class DatasetPopulator(BaseDatasetPopulator):
 
-    def __init__(self, galaxy_interactor):
-        self.galaxy_interactor = galaxy_interactor
+class GalaxyInteractorHttpMixin:
+    galaxy_interactor: ApiTestInteractor
 
     @property
     def _api_key(self):
         return self.galaxy_interactor.api_key
 
-    def _post(self, route, data=None, files=None, admin=False):
-        return self.galaxy_interactor.post(route, data, files=files, admin=admin)
+    def _post(self, route, data=None, files=None, admin=False, json: bool = False) -> Response:
+        return self.galaxy_interactor.post(route, data, files=files, admin=admin, json=json)
 
-    def _put(self, route, data=None):
-        return self.galaxy_interactor.put(route, data)
+    def _put(self, route, data=None, admin=False):
+        return self.galaxy_interactor.put(route, data, admin=admin)
 
     def _get(self, route, data=None, admin=False):
         if data is None:
@@ -757,16 +802,19 @@ class DatasetPopulator(BaseDatasetPopulator):
 
         return self.galaxy_interactor.delete(route, data=data, admin=admin)
 
+
+class DatasetPopulator(GalaxyInteractorHttpMixin, BaseDatasetPopulator):
+
+    def __init__(self, galaxy_interactor):
+        self.galaxy_interactor = galaxy_interactor
+
     def _summarize_history(self, history_id):
         self.galaxy_interactor._summarize_history(history_id)
 
-    def wait_for_dataset(self, history_id, dataset_id, assert_ok=False, timeout=DEFAULT_TIMEOUT):
-        return wait_on_state(lambda: self._get(f"histories/{history_id}/contents/{dataset_id}"), desc="dataset state", assert_ok=assert_ok, timeout=timeout)
 
+class BaseWorkflowPopulator(BasePopulator):
 
-class BaseWorkflowPopulator:
-
-    def load_workflow(self, name, content=workflow_str, add_pja=False):
+    def load_workflow(self, name: str, content: str = workflow_str, add_pja=False) -> dict:
         workflow = json.loads(content)
         workflow["name"] = name
         if add_pja:
@@ -778,20 +826,20 @@ class BaseWorkflowPopulator:
             )
         return workflow
 
-    def load_random_x2_workflow(self, name):
+    def load_random_x2_workflow(self, name: str) -> dict:
         return self.load_workflow(name, content=workflow_random_x2_str)
 
-    def load_workflow_from_resource(self, name, filename=None):
+    def load_workflow_from_resource(self, name: str, filename: Optional[str] = None) -> dict:
         if filename is None:
             filename = "data/%s.ga" % name
         content = unicodify(resource_string(__name__, filename))
         return self.load_workflow(name, content=content)
 
-    def simple_workflow(self, name, **create_kwds):
+    def simple_workflow(self, name: str, **create_kwds) -> str:
         workflow = self.load_workflow(name)
         return self.create_workflow(workflow, **create_kwds)
 
-    def import_workflow_from_path(self, from_path):
+    def import_workflow_from_path(self, from_path: str) -> str:
         data = dict(
             from_path=from_path
         )
@@ -799,12 +847,12 @@ class BaseWorkflowPopulator:
         api_asserts.assert_status_code_is(import_response, 200)
         return import_response.json()["id"]
 
-    def create_workflow(self, workflow, **create_kwds):
+    def create_workflow(self, workflow: dict, **create_kwds) -> str:
         upload_response = self.create_workflow_response(workflow, **create_kwds)
         uploaded_workflow_id = upload_response.json()["id"]
         return uploaded_workflow_id
 
-    def create_workflow_response(self, workflow, **create_kwds):
+    def create_workflow_response(self, workflow: dict, **create_kwds) -> Response:
         data = dict(
             workflow=json.dumps(workflow),
             **create_kwds
@@ -812,7 +860,7 @@ class BaseWorkflowPopulator:
         upload_response = self._post("workflows/upload", data=data)
         return upload_response
 
-    def upload_yaml_workflow(self, has_yaml, **kwds):
+    def upload_yaml_workflow(self, has_yaml, **kwds) -> str:
         round_trip_conversion = kwds.get("round_trip_format_conversion", False)
         client_convert = kwds.pop("client_convert", not round_trip_conversion)
         kwds["convert"] = client_convert
@@ -826,7 +874,7 @@ class BaseWorkflowPopulator:
 
         return workflow_id
 
-    def wait_for_invocation(self, workflow_id, invocation_id, timeout=DEFAULT_TIMEOUT, assert_ok=True):
+    def wait_for_invocation(self, workflow_id: str, invocation_id: str, timeout: timeout_type = DEFAULT_TIMEOUT, assert_ok: bool = True):
         url = f"workflows/{workflow_id}/usage/{invocation_id}"
 
         def workflow_state():
@@ -834,7 +882,7 @@ class BaseWorkflowPopulator:
 
         return wait_on_state(workflow_state, desc="workflow invocation state", timeout=timeout, assert_ok=assert_ok)
 
-    def history_invocations(self, history_id):
+    def history_invocations(self, history_id: str) -> list:
         history_invocations_response = self._get("invocations", {"history_id": history_id})
         api_asserts.assert_status_code_is(history_invocations_response, 200)
         return history_invocations_response.json()
@@ -878,12 +926,12 @@ class BaseWorkflowPopulator:
             api_asserts.assert_has_keys(p, "param", "value", "step")
         api_asserts.assert_has_keys(bco['io_domain'], "input_subdomain", "output_subdomain")
 
-    def invoke_workflow_raw(self, workflow_id, request):
+    def invoke_workflow_raw(self, workflow_id, request: dict) -> Response:
         url = "workflows/%s/usage" % (workflow_id)
         invocation_response = self._post(url, data=request)
         return invocation_response
 
-    def invoke_workflow(self, history_id, workflow_id, inputs=None, request=None, assert_ok=True):
+    def invoke_workflow(self, history_id: str, workflow_id: str, inputs: Optional[dict] = None, request: Optional[dict] = None, assert_ok: bool = True):
         if inputs is None:
             inputs = {}
 
@@ -902,12 +950,12 @@ class BaseWorkflowPopulator:
         else:
             return invocation_response
 
-    def workflow_report_json(self, workflow_id, invocation_id):
+    def workflow_report_json(self, workflow_id: str, invocation_id: str) -> dict:
         response = self._get(f"workflows/{workflow_id}/invocations/{invocation_id}/report")
         api_asserts.assert_status_code_is(response, 200)
         return response.json()
 
-    def download_workflow(self, workflow_id, style=None, history_id=None):
+    def download_workflow(self, workflow_id: str, style: Optional[str] = None, history_id: Optional[str] = None) -> dict:
         params = {}
         if style is not None:
             params["style"] = style
@@ -920,16 +968,16 @@ class BaseWorkflowPopulator:
         else:
             return ordered_load(response.text)
 
-    def update_workflow(self, workflow_id, workflow_object):
+    def update_workflow(self, workflow_id: str, workflow_object: dict) -> Response:
         data = dict(
             workflow=workflow_object
         )
         raw_url = 'workflows/%s' % workflow_id
-        put_response = self.galaxy_interactor._put(raw_url, data=json.dumps(data))
+        put_response = self._put(raw_url, json.dumps(data))
         return put_response
 
-    def refactor_workflow(self, workflow_id, actions, dry_run=None, style=None):
-        data = dict(
+    def refactor_workflow(self, workflow_id: str, actions: list, dry_run: Optional[bool] = None, style: Optional[str] = None) -> Response:
+        data: Dict[str, Any] = dict(
             actions=actions,
         )
         if style is not None:
@@ -937,7 +985,7 @@ class BaseWorkflowPopulator:
         if dry_run is not None:
             data["dry_run"] = dry_run
         raw_url = 'workflows/%s/refactor' % workflow_id
-        put_response = self.galaxy_interactor._put(raw_url, data=json.dumps(data))
+        put_response = self._put(raw_url, json.dumps(data))
         return put_response
 
     @contextlib.contextmanager
@@ -1015,26 +1063,14 @@ class BaseWorkflowPopulator:
 RunJobsSummary = namedtuple('RunJobsSummary', ['history_id', 'workflow_id', 'invocation_id', 'inputs', 'jobs', 'invocation', 'workflow_request'])
 
 
-class WorkflowPopulator(BaseWorkflowPopulator, ImporterGalaxyInterface):
+class WorkflowPopulator(GalaxyInteractorHttpMixin, BaseWorkflowPopulator, ImporterGalaxyInterface):
 
     def __init__(self, galaxy_interactor):
         self.galaxy_interactor = galaxy_interactor
         self.dataset_populator = DatasetPopulator(galaxy_interactor)
         self.dataset_collection_populator = DatasetCollectionPopulator(galaxy_interactor)
 
-    def _post(self, route, data=None, admin=False):
-        if data is None:
-            data = {}
-
-        return self.galaxy_interactor.post(route, data, admin=admin)
-
-    def _get(self, route, data=None):
-        if data is None:
-            data = {}
-
-        return self.galaxy_interactor.get(route, data=data)
-
-    # Required for ImporterGalaxyInterface interface - so we can recurisvely import
+    # Required for ImporterGalaxyInterface interface - so we can recursively import
     # nested workflows.
     def import_workflow(self, workflow, **kwds):
         workflow_str = json.dumps(workflow, indent=4)
@@ -1448,14 +1484,18 @@ class BaseDatasetCollectionPopulator:
             elif element['element_type'] == 'dataset_collection':
                 self.wait_for_dataset_collection(element['object'], assert_ok=assert_ok, timeout=timeout)
 
+    @abstractmethod
+    def _create_collection(self, payload: dict) -> Response:
+        """Create collection from specified payload."""
+
 
 class DatasetCollectionPopulator(BaseDatasetCollectionPopulator):
 
-    def __init__(self, galaxy_interactor):
+    def __init__(self, galaxy_interactor: ApiTestInteractor):
         self.galaxy_interactor = galaxy_interactor
         self.dataset_populator = DatasetPopulator(galaxy_interactor)
 
-    def _create_collection(self, payload):
+    def _create_collection(self, payload: dict) -> Response:
         create_response = self.galaxy_interactor.post("dataset_collections", data=payload)
         return create_response
 
@@ -1557,7 +1597,7 @@ def stage_rules_example(galaxy_interactor, history_id, example):
     return inputs
 
 
-def wait_on_state(state_func, desc="state", skip_states=None, ok_states=None, assert_ok=False, timeout=DEFAULT_TIMEOUT):
+def wait_on_state(state_func: Callable, desc="state", skip_states=None, ok_states=None, assert_ok=False, timeout=DEFAULT_TIMEOUT) -> str:
     def get_state():
         response = state_func()
         assert response.status_code == 200, "Failed to fetch state update while waiting. [%s]" % response.content
@@ -1580,8 +1620,9 @@ def wait_on_state(state_func, desc="state", skip_states=None, ok_states=None, as
         raise TimeoutAssertionError(f"{e} Current response containing state [{response.json()}].")
 
 
-class GiPostGetMixin:
+class GiHttpMixin:
     """Mixin for adapting Galaxy testing populators helpers to bioblend."""
+    _gi: GalaxyClient
 
     @property
     def _api_key(self):
@@ -1595,14 +1636,14 @@ class GiPostGetMixin:
             data = {}
         return self._gi.make_get_request(self._url(route), data=data)
 
-    def _post(self, route, data=None):
+    def _post(self, route, data=None, files=None, admin=False, json: bool = False) -> Response:
         if data is None:
             data = {}
         data = data.copy()
         data['key'] = self._gi.key
         return requests.post(self._url(route), data=data)
 
-    def _put(self, route, data=None):
+    def _put(self, route, data=None, admin=False):
         if data is None:
             data = {}
         data = data.copy()
@@ -1623,7 +1664,7 @@ class GiPostGetMixin:
         return self._api_url() + "/" + route
 
 
-class GiDatasetPopulator(BaseDatasetPopulator, GiPostGetMixin):
+class GiDatasetPopulator(BaseDatasetPopulator, GiHttpMixin):
 
     """Implementation of BaseDatasetPopulator backed by bioblend."""
 
@@ -1632,7 +1673,7 @@ class GiDatasetPopulator(BaseDatasetPopulator, GiPostGetMixin):
         self._gi = gi
 
 
-class GiDatasetCollectionPopulator(BaseDatasetCollectionPopulator, GiPostGetMixin):
+class GiDatasetCollectionPopulator(BaseDatasetCollectionPopulator, GiHttpMixin):
 
     """Implementation of BaseDatasetCollectionPopulator backed by bioblend."""
 
@@ -1647,7 +1688,7 @@ class GiDatasetCollectionPopulator(BaseDatasetCollectionPopulator, GiPostGetMixi
         return create_response
 
 
-class GiWorkflowPopulator(BaseWorkflowPopulator, GiPostGetMixin):
+class GiWorkflowPopulator(BaseWorkflowPopulator, GiHttpMixin):
 
     """Implementation of BaseWorkflowPopulator backed by bioblend."""
 
diff --git a/lib/galaxy_test/base/testcase.py b/lib/galaxy_test/base/testcase.py
index c5bdea69270..1d84752ea73 100644
--- a/lib/galaxy_test/base/testcase.py
+++ b/lib/galaxy_test/base/testcase.py
@@ -17,8 +17,14 @@ class FunctionalTestCase(unittest.TestCase):
     server is already running.
     """
     galaxy_driver_class: Optional[type] = None
+    history_id: Optional[str]
+    host: str
+    port: Optional[str]
+    url: str
+    keepOutdir: str
+    test_data_resolver: TestDataResolver
 
-    def setUp(self):
+    def setUp(self) -> None:
         self.history_id = os.environ.get('GALAXY_TEST_HISTORY_ID', None)
         self.host, self.port, self.url = target_url_parts()
         self.test_data_resolver = TestDataResolver()
@@ -39,6 +45,6 @@ class FunctionalTestCase(unittest.TestCase):
         if cls._test_driver:
             cls._test_driver.tear_down()
 
-    def get_filename(self, filename):
+    def get_filename(self, filename: str) -> str:
         # No longer used by tool tests - drop if isn't used else where.
         return self.test_data_resolver.get_filename(filename)
diff --git a/lib/galaxy_test/driver/driver_util.py b/lib/galaxy_test/driver/driver_util.py
index 98751f28ab0..b3a24eab131 100644
--- a/lib/galaxy_test/driver/driver_util.py
+++ b/lib/galaxy_test/driver/driver_util.py
@@ -35,7 +35,7 @@ from galaxy.tool_util.verify.interactor import GalaxyInteractorApi, verify_tool
 from galaxy.util import asbool, download_to_file, galaxy_directory
 from galaxy.util.properties import load_app_properties
 from galaxy.web import buildapp
-from galaxy_test.base.api_util import get_master_api_key, get_user_api_key
+from galaxy_test.base.api_util import get_admin_api_key, get_user_api_key
 from galaxy_test.base.env import (
     DEFAULT_WEB_HOST,
     target_url_parts,
@@ -188,9 +188,9 @@ def setup_galaxy_config(
     data_manager_config_file = 'test/functional/tools/sample_data_manager_conf.xml'
     if default_data_manager_config is not None:
         data_manager_config_file = f"{default_data_manager_config},{data_manager_config_file}"
-    master_api_key = get_master_api_key()
-    cleanup_job = 'never' if ("GALAXY_TEST_NO_CLEANUP" in os.environ or
-                              "TOOL_SHED_TEST_NO_CLEANUP" in os.environ) else 'onsuccess'
+    master_api_key = get_admin_api_key()
+    cleanup_job = 'never' if ("GALAXY_TEST_NO_CLEANUP" in os.environ
+                              or "TOOL_SHED_TEST_NO_CLEANUP" in os.environ) else 'onsuccess'
 
     # Data Manager testing temp path
     # For storing Data Manager outputs and .loc files so that real ones don't get clobbered
@@ -1126,7 +1126,7 @@ class GalaxyTestDriver(TestDriver):
         test_classes = functional.test_toolbox.build_tests(
             app=self.app,
             testing_shed_tools=testing_shed_tools,
-            master_api_key=get_master_api_key(),
+            master_api_key=get_admin_api_key(),
             user_api_key=get_user_api_key(),
         )
         if return_test_classes:
@@ -1139,7 +1139,7 @@ class GalaxyTestDriver(TestDriver):
         host, port, url = target_url_parts()
         galaxy_interactor_kwds = {
             "galaxy_url": url,
-            "master_api_key": get_master_api_key(),
+            "master_api_key": get_admin_api_key(),
             "api_key": get_user_api_key(),
             "keep_outputs_dir": None,
         }
diff --git a/lib/galaxy_test/selenium/framework.py b/lib/galaxy_test/selenium/framework.py
index 9fab7520d88..9067c18d324 100644
--- a/lib/galaxy_test/selenium/framework.py
+++ b/lib/galaxy_test/selenium/framework.py
@@ -12,10 +12,7 @@ from gxformat2 import (
     convert_and_import_workflow,
     ImporterGalaxyInterface,
 )
-try:
-    from pyvirtualdisplay import Display
-except ImportError:
-    Display = None
+from requests.models import Response
 
 from galaxy.selenium import (
     driver_factory,
@@ -29,6 +26,7 @@ from galaxy.selenium.navigates_galaxy import (
 from galaxy.util import asbool, classproperty
 from galaxy_test.base import populators
 from galaxy_test.base.api import UsesApiTestCaseMixin
+from galaxy_test.base.api_util import get_admin_api_key
 from galaxy_test.base.env import DEFAULT_WEB_HOST, get_ip_address
 from galaxy_test.base.testcase import FunctionalTestCase
 try:
@@ -184,7 +182,26 @@ class TestSnapshot:
         write_file_func("%s-stack.txt" % prefix, str(self.stack))
 
 
-class TestWithSeleniumMixin(GalaxySeleniumContext, UsesApiTestCaseMixin):
+class GalaxyTestSeleniumContext(GalaxySeleniumContext):
+    """Extend GalaxySeleniumContext with Selenium-aware galaxy_test.base.populators."""
+
+    @property
+    def dataset_populator(self) -> populators.BaseDatasetPopulator:
+        """A dataset populator connected to the Galaxy session described by Selenium context."""
+        return SeleniumSessionDatasetPopulator(self)
+
+    @property
+    def dataset_collection_populator(self) -> populators.BaseDatasetCollectionPopulator:
+        """A dataset collection populator connected to the Galaxy session described by Selenium context."""
+        return SeleniumSessionDatasetCollectionPopulator(self)
+
+    @property
+    def workflow_populator(self) -> populators.BaseWorkflowPopulator:
+        """A workflow populator connected to the Galaxy session described by Selenium context."""
+        return SeleniumSessionWorkflowPopulator(self)
+
+
+class TestWithSeleniumMixin(GalaxyTestSeleniumContext, UsesApiTestCaseMixin):
     # If run one-off via nosetests, the next line ensures test
     # tools and datatypes are used instead of configured tools.
     framework_tool_and_types = True
@@ -354,18 +371,6 @@ class TestWithSeleniumMixin(GalaxySeleniumContext, UsesApiTestCaseMixin):
         with self.main_panel():
             self.assert_no_error_message()
 
-    @property
-    def dataset_populator(self):
-        return SeleniumSessionDatasetPopulator(self)
-
-    @property
-    def dataset_collection_populator(self):
-        return SeleniumSessionDatasetCollectionPopulator(self)
-
-    @property
-    def workflow_populator(self):
-        return SeleniumSessionWorkflowPopulator(self)
-
     def workflow_upload_yaml_with_random_name(self, content, **kwds):
         workflow_populator = self.workflow_populator
         name = self._get_random_name()
@@ -388,6 +393,7 @@ class SeleniumTestCase(FunctionalTestCase, TestWithSeleniumMixin):
     def setUp(self):
         super().setUp()
         self.setup_selenium()
+        self.admin_api_key = get_admin_api_key()
 
     def tearDown(self):
         exception = None
@@ -519,15 +525,25 @@ def use_virtual_display():
 
 class SeleniumSessionGetPostMixin:
     """Mixin for adapting Galaxy testing populators helpers to Selenium session backed bioblend."""
+    selenium_context: GalaxySeleniumContext
 
-    def _get(self, route, data=None):
+    @property
+    def _mixin_admin_api_key(self) -> str:
+        return getattr(self, "admin_api_key", get_admin_api_key())
+
+    def _get(self, route, data=None, admin=False) -> Response:
         data = data or {}
-        full_url = self.selenium_test_case.build_url("api/" + route, for_selenium=False)
-        response = requests.get(full_url, data=data, cookies=self.selenium_test_case.selenium_to_requests_cookies())
+        full_url = self.selenium_context.build_url("api/" + route, for_selenium=False)
+        cookies = None
+        if admin:
+            full_url = f"{full_url}?key={self._mixin_admin_api_key}"
+        else:
+            cookies = self.selenium_context.selenium_to_requests_cookies()
+        response = requests.get(full_url, params=data, cookies=cookies)
         return response
 
-    def _post(self, route, data=None, files=None):
-        full_url = self.selenium_test_case.build_url("api/" + route, for_selenium=False)
+    def _post(self, route, data=None, files=None, admin=False, json: bool = False) -> Response:
+        full_url = self.selenium_context.build_url("api/" + route, for_selenium=False)
         if data is None:
             data = {}
 
@@ -536,61 +552,80 @@ class SeleniumSessionGetPostMixin:
             if files is not None:
                 del data["__files"]
 
-        response = requests.post(full_url, data=data, cookies=self.selenium_test_case.selenium_to_requests_cookies(), files=files)
+        cookies = None
+        if admin:
+            full_url = f"{full_url}?key={self._mixin_admin_api_key}"
+        else:
+            cookies = self.selenium_context.selenium_to_requests_cookies()
+        response = requests.post(full_url, data=data, cookies=cookies, files=files)
         return response
 
-    def _delete(self, route, data=None):
+    def _delete(self, route, data=None, admin=False) -> Response:
         data = data or {}
-        full_url = self.selenium_test_case.build_url("api/" + route, for_selenium=False)
-        response = requests.delete(full_url, data=data, cookies=self.selenium_test_case.selenium_to_requests_cookies())
+        full_url = self.selenium_context.build_url("api/" + route, for_selenium=False)
+        cookies = None
+        if admin:
+            full_url = f"{full_url}?key={self._mixin_admin_api_key}"
+        else:
+            cookies = self.selenium_context.selenium_to_requests_cookies()
+        response = requests.delete(full_url, data=data, cookies=cookies)
         return response
 
-    def __url(self, route):
-        return self._gi.url + "/" + route
+    def _put(self, route, data=None, admin=False) -> Response:
+        data = data or {}
+        full_url = self.selenium_context.build_url("api/" + route, for_selenium=False)
+        cookies = None
+        if admin:
+            full_url = f"{full_url}?key={self._mixin_admin_api_key}"
+        else:
+            cookies = self.selenium_context.selenium_to_requests_cookies()
+        response = requests.put(full_url, data=data, cookies=cookies)
+        return response
 
 
-class SeleniumSessionDatasetPopulator(populators.BaseDatasetPopulator, SeleniumSessionGetPostMixin):
+class SeleniumSessionDatasetPopulator(SeleniumSessionGetPostMixin, populators.BaseDatasetPopulator):
 
     """Implementation of BaseDatasetPopulator backed by bioblend."""
 
-    def __init__(self, selenium_test_case):
+    def __init__(self, selenium_context: GalaxySeleniumContext):
         """Construct a dataset populator from a bioblend GalaxyInstance."""
-        self.selenium_test_case = selenium_test_case
+        self.selenium_context = selenium_context
 
 
-class SeleniumSessionDatasetCollectionPopulator(populators.BaseDatasetCollectionPopulator, SeleniumSessionGetPostMixin):
+class SeleniumSessionDatasetCollectionPopulator(SeleniumSessionGetPostMixin, populators.BaseDatasetCollectionPopulator):
 
     """Implementation of BaseDatasetCollectionPopulator backed by bioblend."""
 
-    def __init__(self, selenium_test_case):
+    def __init__(self, selenium_context: GalaxySeleniumContext):
         """Construct a dataset collection populator from a bioblend GalaxyInstance."""
-        self.selenium_test_case = selenium_test_case
-        self.dataset_populator = SeleniumSessionDatasetPopulator(selenium_test_case)
+        self.selenium_context = selenium_context
+        self.dataset_populator = SeleniumSessionDatasetPopulator(selenium_context)
 
-    def _create_collection(self, payload):
+    def _create_collection(self, payload: dict) -> Response:
         create_response = self._post("dataset_collections", data=payload)
         return create_response
 
 
-class SeleniumSessionWorkflowPopulator(populators.BaseWorkflowPopulator, SeleniumSessionGetPostMixin, ImporterGalaxyInterface):
+class SeleniumSessionWorkflowPopulator(SeleniumSessionGetPostMixin, populators.BaseWorkflowPopulator, ImporterGalaxyInterface):
 
     """Implementation of BaseWorkflowPopulator backed by bioblend."""
 
-    def __init__(self, selenium_test_case):
+    def __init__(self, selenium_context: GalaxySeleniumContext):
         """Construct a workflow populator from a bioblend GalaxyInstance."""
-        self.selenium_test_case = selenium_test_case
-        self.dataset_populator = SeleniumSessionDatasetPopulator(selenium_test_case)
+        self.selenium_context = selenium_context
+        self.dataset_populator = SeleniumSessionDatasetPopulator(selenium_context)
+        self.dataset_collection_populator = SeleniumSessionDatasetPopulator(selenium_context)
 
-    def import_workflow(self, workflow, **kwds):
+    def import_workflow(self, workflow: dict, **kwds) -> dict:
         workflow_str = json.dumps(workflow, indent=4)
         data = {
             'workflow': workflow_str,
         }
         data.update(**kwds)
         upload_response = self._post("workflows", data=data)
-        assert upload_response.status_code == 200
+        upload_response.raise_for_status()
         return upload_response.json()
 
-    def upload_yaml_workflow(self, has_yaml, **kwds):
+    def upload_yaml_workflow(self, has_yaml, **kwds) -> str:
         workflow = convert_and_import_workflow(has_yaml, galaxy_interface=self, **kwds)
         return workflow["id"]
diff --git a/lib/galaxy_test/selenium/test_histories_list.py b/lib/galaxy_test/selenium/test_histories_list.py
index ff4749529af..0cd9848c8ce 100644
--- a/lib/galaxy_test/selenium/test_histories_list.py
+++ b/lib/galaxy_test/selenium/test_histories_list.py
@@ -1,6 +1,5 @@
 from .framework import (
     retry_assertion_during_transitions,
-    retry_during_transitions,
     selenium_test,
     SharedStateSeleniumTestCase,
 )
@@ -251,17 +250,8 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
         else:
             self.assertEqual(intersection, set())
 
-    @retry_during_transitions
     def get_histories(self):
-        self.sleep_for(self.wait_types.UX_RENDER)
-        names = []
-        grid = self.wait_for_selector('#grid-table-body')
-        for row in grid.find_elements_by_tag_name('tr'):
-            td = row.find_elements_by_tag_name('td')
-            name = td[1].text if td[0].text == '' else td[0].text
-            if name != "No items" and not name.startswith("No matching entries found"):
-                names.append(name)
-        return names
+        return self.histories_get_history_names()
 
     def set_filter(self, selector, value):
         filter_input = self.wait_for_selector_clickable(selector)
@@ -275,11 +265,6 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase):
         self.wait_for_and_click_selector(close_button_selector)
         self.sleep_for(self.wait_types.UX_RENDER)
 
-    def navigate_to_histories_page(self):
-        self.home()
-        self.click_masthead_user()  # Open masthead menu
-        self.components.masthead.histories.wait_for_and_click()
-
     def setup_shared_state(self):
         SavedHistoriesTestCase.user_email = self._get_random_email()
         SavedHistoriesTestCase.history1_name = self._get_random_name()
diff --git a/lib/galaxy_test/selenium/test_history_export.py b/lib/galaxy_test/selenium/test_history_export.py
new file mode 100644
index 00000000000..d55d0105ffd
--- /dev/null
+++ b/lib/galaxy_test/selenium/test_history_export.py
@@ -0,0 +1,44 @@
+from .framework import (
+    selenium_test,
+    SeleniumTestCase
+)
+
+
+class HistoryExportTestCase(SeleniumTestCase):
+    ensure_registered = True
+
+    @selenium_test
+    def test_history_export(self):
+        gx_selenium_context = self
+        gx_selenium_context.perform_upload_of_pasted_content("my cool content")
+        gx_selenium_context.history_panel_wait_for_hid_ok(1)
+        gx_selenium_context.click_history_options()
+        gx_selenium_context.components.history_panel.options_show_export_history_to_file.wait_for_and_click()
+        history_export = gx_selenium_context.components.history_export
+        history_export.export_link.wait_for_and_click()
+        history_export.running.wait_for_visible()
+        history_export.running.wait_for_absent(wait_type=gx_selenium_context.wait_types.JOB_COMPLETION)
+        history_export.generated_export_link.wait_for_visible()
+        history_export.copy_export_link.wait_for_visible()
+        history_export.job_table.assert_absent_or_hidden()
+        history_export.show_job_link.wait_for_and_click()
+        history_export.job_table.wait_for_present()
+        history_export.job_table_ok.wait_for_and_click()
+        history_export.job_table.wait_for_absent()
+
+        gx_selenium_context.click_history_options()
+        gx_selenium_context.components.history_panel.options_show_export_history_to_file.wait_for_and_click()
+
+        # this time the exported link is still there
+        history_export.generated_export_link.wait_for_visible()
+        history_export.export_link.assert_absent()
+
+        gx_selenium_context.perform_upload_of_pasted_content("my cool content part 2")
+        gx_selenium_context.history_panel_wait_for_hid_ok(2)
+
+        gx_selenium_context.click_history_options()
+        gx_selenium_context.components.history_panel.options_show_export_history_to_file.wait_for_and_click()
+
+        # now we have a generated link and a link to update to the newest export
+        history_export.generated_export_link.wait_for_visible()
+        history_export.export_link.wait_for_visible()
diff --git a/lib/galaxy_test/selenium/test_library_contents.py b/lib/galaxy_test/selenium/test_library_contents.py
index 6823fa985f5..d6840f8bc03 100644
--- a/lib/galaxy_test/selenium/test_library_contents.py
+++ b/lib/galaxy_test/selenium/test_library_contents.py
@@ -145,6 +145,15 @@ class LibraryContentsTestCase(SeleniumTestCase):
         assert table_as_dict["Name"] == "1.txt", table_as_dict
         assert table_as_dict["Genome build"] == "?", table_as_dict
 
+    @selenium_test
+    def test_import_dataset_from_import_dir(self):
+        self._navigate_to_new_library()
+        self._assert_num_displayed_items_is(0)
+        self.libraries_dataset_import_from_import_dir()
+        self.components.libraries.folder.select_import_dir_item(name="1.axt").wait_for_and_click()
+        self.components.libraries.folder.import_dir_btn.wait_for_and_click()
+        self._assert_num_displayed_items_is(1)
+
     @selenium_test
     def test_show_details(self):
         self._navigate_to_new_library()
diff --git a/lib/galaxy_test/selenium/test_tool_form.py b/lib/galaxy_test/selenium/test_tool_form.py
index 4b7b01e34f2..e9bbcf16976 100644
--- a/lib/galaxy_test/selenium/test_tool_form.py
+++ b/lib/galaxy_test/selenium/test_tool_form.py
@@ -1,5 +1,7 @@
 import json
 
+import pytest
+
 from galaxy.selenium.navigates_galaxy import retry_call_during_transitions
 from galaxy_test.base import rules_test_data
 from galaxy_test.base.populators import (
@@ -183,6 +185,8 @@ class LoggedInToolFormTestCase(SeleniumTestCase):
     @selenium_test
     @managed_history
     @skip_if_github_down
+    @pytest.mark.gtn_screenshot
+    @pytest.mark.local
     def test_run_apply_rules_tutorial(self):
         self.home()
         self.upload_rule_start()
diff --git a/lib/galaxy_test/selenium/test_uploads.py b/lib/galaxy_test/selenium/test_uploads.py
index 2c26f08efea..c1153051a09 100644
--- a/lib/galaxy_test/selenium/test_uploads.py
+++ b/lib/galaxy_test/selenium/test_uploads.py
@@ -213,6 +213,8 @@ PRJDA60709  SAMD00016382    DRX000480   ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR0
         self.screenshot("rules_example_3_14_paired_identifier_set")
 
     @selenium_test
+    @pytest.mark.gtn_screenshot
+    @pytest.mark.local
     def test_rules_example_4_accessions(self):
         # http://www.uniprot.org/uniprot/?query=proteome:UP000052092+AND+proteomecomponent:%22Genome%22
         self._setup_uniprot_example()
@@ -245,6 +247,8 @@ PRJDA60709  SAMD00016382    DRX000480   ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR0
         rule_builder.view_source.wait_for_visible()
 
     @selenium_test
+    @pytest.mark.gtn_screenshot
+    @pytest.mark.local
     def test_rules_example_5_matching_collections(self):
         self._setup_uniprot_example()
         self.screenshot("rules_example_5_1_inputs")
@@ -273,6 +277,8 @@ PRJDA60709  SAMD00016382    DRX000480   ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR0
         self.screenshot("rules_example_5_9_mapping")
 
     @selenium_test
+    @pytest.mark.gtn_screenshot
+    @pytest.mark.local
     def test_rules_example_6_nested_lists(self):
         self.home()
         self.perform_upload(self.get_filename("rules/PRJNA355367.tsv"))
diff --git a/lib/galaxy_test/selenium/test_workflow_invocation_details.py b/lib/galaxy_test/selenium/test_workflow_invocation_details.py
new file mode 100644
index 00000000000..39e1952a1ec
--- /dev/null
+++ b/lib/galaxy_test/selenium/test_workflow_invocation_details.py
@@ -0,0 +1,68 @@
+from galaxy_test.base.workflow_fixtures import (
+    WORKFLOW_WITH_OUTPUT_COLLECTION,
+)
+from .framework import (
+    retry_assertion_during_transitions,
+    selenium_test,
+    SeleniumTestCase
+)
+
+
+class WorkflowInvocationDetailsTestCase(SeleniumTestCase):
+
+    ensure_registered = True
+
+    @selenium_test
+    def test_job_details(self):
+        gx_selenium_context = self
+        history_id = gx_selenium_context.dataset_populator.new_history()
+        gx_selenium_context.workflow_populator.run_workflow(WORKFLOW_WITH_OUTPUT_COLLECTION, history_id=history_id, assert_ok=True, wait=True)
+        gx_selenium_context.navigate_to_invocations()
+        invocations = gx_selenium_context.components.invocations
+        invocations.invocations_table.wait_for_visible()
+
+        @retry_assertion_during_transitions
+        def assert_has_row():
+            invocations.invocations_table_rows.wait_for_visible()
+            invocation_rows = invocations.invocations_table_rows.all()
+            assert len(invocation_rows) > 0
+            return invocation_rows[0]
+
+        first_row = assert_has_row()
+        print(first_row)
+        invocations.state_details.assert_absent()
+        invocations.toggle_invocation_details.wait_for_visible()
+        details = invocations.toggle_invocation_details.all()[0]
+        details.click()
+        invocations.state_details.wait_for_visible()
+
+        @retry_assertion_during_transitions
+        def assert_progress_steps_note_contains(text):
+            assert text in invocations.progress_steps_note.wait_for_visible().text
+
+        assert_progress_steps_note_contains("3 of 3 steps successfully scheduled.")
+        assert "2 of 2 jobs complete." in invocations.progress_jobs_note.wait_for_visible().text
+
+        invocations.input_details.wait_for_and_click()
+        invocations.input_details_title(label="text_input").wait_for_visible()
+        assert "Test_Dataset" in invocations.input_details_name(label="text_input").wait_for_visible().text
+
+        invocations.steps_details.wait_for_and_click()
+        assert "Step 1: text_input" in invocations.step_title(order_index="0").wait_for_visible().text
+        assert "Step 2: split_up" in invocations.step_title(order_index="1").wait_for_visible().text
+        assert "Step 3: paired" in invocations.step_title(order_index="2").wait_for_visible().text
+
+        invocations.step_details(order_index="1").wait_for_and_click()
+        invocations.step_job_details(order_index="1").wait_for_and_click()
+        invocations.step_job_table(order_index="1").wait_for_visible()
+        invocations.step_job_table_rows(order_index="1").wait_for_visible()
+        job_rows = invocations.step_job_table_rows(order_index="1").all()
+        assert len(job_rows) == 1
+
+        invocations.step_job_information(order_index="1").assert_absent()
+        job_rows[0].click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.screenshot("invocations_job_table")
+
+        invocations.step_job_information(order_index="1").wait_for_visible()
+        assert "collection_creates_pair" in invocations.step_job_information_tool_id(order_index="1").wait_for_visible().text
diff --git a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
index 4ac59baf882..c0af8ad72c1 100644
--- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
+++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
@@ -154,9 +154,9 @@ class InstalledRepositoryGrid(grids.Grid):
                                       allow_multiple=False),
                   grids.GridOperation(label="Get updates",
                                       condition=(lambda item:
-                                                 not item.deleted and
-                                                 item.revision_update_available and
-                                                 item.status not in [
+                                                 not item.deleted
+                                                 and item.revision_update_available
+                                                 and item.status not in [
                                                      tool_shed_install.ToolShedRepository.installation_status.ERROR,
                                                      tool_shed_install.ToolShedRepository.installation_status.NEW]),
                                       allow_multiple=False,
@@ -171,8 +171,8 @@ class InstalledRepositoryGrid(grids.Grid):
                                                     action='install_latest_repository_revision')),
                   grids.GridOperation(label="Install",
                                       condition=(lambda item:
-                                                 not item.deleted and
-                                                 item.status == tool_shed_install.ToolShedRepository.installation_status.NEW),
+                                                 not item.deleted
+                                                 and item.status == tool_shed_install.ToolShedRepository.installation_status.NEW),
                                       allow_multiple=False,
                                       target='center',
                                       url_args=dict(controller='admin_toolshed',
@@ -180,8 +180,8 @@ class InstalledRepositoryGrid(grids.Grid):
                                                     operation='install')),
                   grids.GridOperation(label="Deactivate or uninstall",
                                       condition=(lambda item:
-                                                 not item.deleted and
-                                                 item.status != tool_shed_install.ToolShedRepository.installation_status.NEW),
+                                                 not item.deleted
+                                                 and item.status != tool_shed_install.ToolShedRepository.installation_status.NEW),
                                       allow_multiple=True,
                                       target="center",
                                       url_args=dict(controller='admin_toolshed',
diff --git a/lib/tool_shed/grids/util.py b/lib/tool_shed/grids/util.py
index 39b54089472..5b5d4b6d79f 100644
--- a/lib/tool_shed/grids/util.py
+++ b/lib/tool_shed/grids/util.py
@@ -109,7 +109,7 @@ def get_latest_downloadable_repository_metadata(trans, repository):
     """
     Return the latest downloadable repository_metadata record for the received repository.  This will
     return repositories of type unrestricted as well as types repository_suite_definition and
-     tool_dependency_definition.
+    tool_dependency_definition.
     """
     encoded_repository_id = trans.security.encode_id(repository.id)
     repo = repository.hg_repo
@@ -148,7 +148,7 @@ def get_latest_repository_metadata(trans, repository):
     """
     Return the latest repository_metadata record for the received repository if it exists.  This will
     return repositories of type unrestricted as well as types repository_suite_definition and
-     tool_dependency_definition.
+    tool_dependency_definition.
     """
     encoded_repository_id = trans.security.encode_id(repository.id)
     repo = repository.hg_repo
diff --git a/lib/tool_shed/managers/groups.py b/lib/tool_shed/managers/groups.py
index b6093479cb3..45b3104e2f1 100644
--- a/lib/tool_shed/managers/groups.py
+++ b/lib/tool_shed/managers/groups.py
@@ -34,7 +34,7 @@ class GroupManager:
         :type   decoded_group_id:       int
 
         :returns:   the requested group
-        :rtype:     Group
+        :rtype:     tool_shed.model.Group
         """
         if decoded_group_id is None and name is None:
             raise RequestParameterInvalidException('You must supply either ID or a name of the group.')
diff --git a/lib/tool_shed/managers/repositories.py b/lib/tool_shed/managers/repositories.py
index 9efcce4e270..d1734251c3e 100644
--- a/lib/tool_shed/managers/repositories.py
+++ b/lib/tool_shed/managers/repositories.py
@@ -28,7 +28,7 @@ class RepoManager:
         :type   decoded_repo_id:       int
 
         :returns:   the requested repo
-        :rtype:     Repository
+        :rtype:     tool_shed.webapp.model.Repository
         """
         try:
             repo = trans.sa_session.query(trans.app.model.Repository).filter(trans.app.model.Repository.table.c.id == decoded_repo_id).one()
diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 2da7a490bb5..35008207c3d 100644
--- a/lib/tool_shed/test/base/twilltestcase.py
+++ b/lib/tool_shed/test/base/twilltestcase.py
@@ -20,7 +20,7 @@ import galaxy.model.tool_shed_install as galaxy_model
 import galaxy.util
 from galaxy.security import idencoding
 from galaxy.util import smart_str, unicodify
-from galaxy_test.base.api_util import get_master_api_key
+from galaxy_test.base.api_util import get_admin_api_key
 from galaxy_test.driver.testcase import DrivenFunctionalTestCase
 from tool_shed.util import (
     hg_util,
@@ -529,7 +529,7 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
 
     def deactivate_repository(self, installed_repository, strings_displayed=None, strings_not_displayed=None):
         encoded_id = self.security.encode_id(installed_repository.id)
-        api_key = get_master_api_key()
+        api_key = get_admin_api_key()
         response = requests.delete(self.galaxy_url + "/api/tool_shed_repositories/" + encoded_id, data={'remove_from_disk': False, 'key': api_key})
         assert response.status_code != 403, response.content
 
@@ -1258,7 +1258,7 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
 
     def reset_installed_repository_metadata(self, repository):
         encoded_id = self.security.encode_id(repository.id)
-        api_key = get_master_api_key()
+        api_key = get_admin_api_key()
         response = requests.post(self.galaxy_url + "/api/tool_shed_repositories/reset_metadata_on_selected_installed_repositories", data={'repository_ids': [encoded_id], 'key': api_key})
         assert response.status_code != 403, response.content
 
@@ -1268,7 +1268,7 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         self.submit_form(button="reset_metadata_on_selected_repositories_button", **kwd)
 
     def reset_metadata_on_selected_installed_repositories(self, repository_ids):
-        api_key = get_master_api_key()
+        api_key = get_admin_api_key()
         response = requests.post(self.galaxy_url + "/api/tool_shed_repositories/reset_metadata_on_selected_installed_repositories", data={'repository_ids': repository_ids, 'key': api_key})
         assert response.status_code != 403, response.content
 
@@ -1375,7 +1375,7 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
 
     def uninstall_repository(self, installed_repository, strings_displayed=None, strings_not_displayed=None):
         encoded_id = self.security.encode_id(installed_repository.id)
-        api_key = get_master_api_key()
+        api_key = get_admin_api_key()
         response = requests.delete(self.galaxy_url + "/api/tool_shed_repositories/" + encoded_id, data={'remove_from_disk': True, 'key': api_key})
         assert response.status_code != 403, response.content
 
@@ -1390,7 +1390,7 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def update_tool_shed_status(self):
-        api_key = get_master_api_key()
+        api_key = get_admin_api_key()
         response = requests.get(self.galaxy_url + "/api/tool_shed_repositories/check_for_updates?key=" + api_key)
         assert response.status_code != 403, response.content
 
diff --git a/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py b/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py
index f182b205da7..411512cf60f 100644
--- a/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py
+++ b/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py
@@ -22,6 +22,7 @@ bwa_tool_dependency_repository_long_description = "NT space mapping with BWA"
 
 '''
 Simple repository dependencies:
+
 1. Create and populate column_maker_0440 so that it has an installable revision 0.
 2. Create and populate convert_chars_0440 so that it has an installable revision 0.
 3. Add a valid simple repository_dependencies.xml to convert_chars_0440 that points to the installable revision of column_maker_0440.
@@ -29,6 +30,7 @@ Simple repository dependencies:
 5. Delete repository_dependencies.xml from convert_chars_0440, and make sure convert_chars_0440 now has two installable revisions: 1 and 2
 
 Complex repository dependencies:
+
 1. Create and populate bwa_package_0440 so that it has a valid tool dependency definition and an installable revision 0.
 2. Create and populate bwa_base_0440 so that it has an installable revision 0.
 3. Add a valid complex repository dependency tool_dependencies.xml to bwa_base_0440 that points to the installable revision 0 of bwa_package_0440.
@@ -36,11 +38,13 @@ Complex repository dependencies:
 5. Delete tool_dependencies.xml from bwa_base_0440, and make sure bwa_base_0440 now has two installable revisions: 1 and 2
 
 Tool dependencies:
+
 1. Create and populate bwa_tool_dependency_0440 so that it has a valid tool dependency definition and an installable revision 0.
 2. Delete tool_dependencies.xml from bwa_tool_dependency_0440, and make sure that bwa_tool_dependency_0440 still has
    a single installable revision 0.
 3. Add the same tool_dependencies.xml file to bwa_tool_dependency_0440, and make sure that bwa_tool_dependency_0440
    still has a single installable revision 0.
+
 '''
 
 
diff --git a/lib/tool_shed/test/functional/test_1160_tool_help_images.py b/lib/tool_shed/test/functional/test_1160_tool_help_images.py
index 5cdaf04d1e1..754cba287b8 100644
--- a/lib/tool_shed/test/functional/test_1160_tool_help_images.py
+++ b/lib/tool_shed/test/functional/test_1160_tool_help_images.py
@@ -11,13 +11,10 @@ repository_long_description = "Convert bed to gff"
 category_name = 'Test 0140 Tool Help Images'
 category_description = 'Test 0140 Tool Help Images'
 
-'''
-1) Create and populate the htseq_count_0140 repository.
-2) Visit the manage_repository page, then the tool page, and look for the image string
-similar to the following string where the encoded repository_id is previously determined:
-
-src="/repository/static/images/<id>/count_modes.png"
-'''
+# 1) Create and populate the htseq_count_0140 repository.
+# 2) Visit the manage_repository page, then the tool page, and look for the image string
+# similar to the following string where the encoded repository_id is previously determined:
+# src="/repository/static/images/<id>/count_modes.png"
 
 
 class TestToolHelpImages(ShedTwillTestCase):
diff --git a/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py b/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py
index cf0f41617de..6dd5829ffc5 100644
--- a/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py
+++ b/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py
@@ -24,8 +24,7 @@ category_0060_name = 'Test 0060 Workflow Features'
 '''
 This script will run in one of two possible ways:
 
-1. Directly, by calling sh run_functional_tests.sh -toolshed test/tool_shed/functional/test_1300_reset_all_metadata.py.
- -OR-
+1. Directly, by calling sh run_functional_tests.sh -toolshed test/tool_shed/functional/test_1300_reset_all_metadata.py. -or-
 2. After the previous test scripts have completed.
 
 In the first case, it is desirable to have the Galaxy database in a state that is as close as possible to the state it would
diff --git a/lib/tool_shed/util/repository_util.py b/lib/tool_shed/util/repository_util.py
index c2a555e81bf..504de162c50 100644
--- a/lib/tool_shed/util/repository_util.py
+++ b/lib/tool_shed/util/repository_util.py
@@ -420,8 +420,8 @@ def update_repository(app, trans, id, **kwds):
     if repository is None:
         return None, "Unknown repository ID"
 
-    if not (trans.user_is_admin or
-            trans.app.security_agent.user_can_administer_repository(trans.user, repository)):
+    if not (trans.user_is_admin
+            or trans.app.security_agent.user_can_administer_repository(trans.user, repository)):
         message = "You are not the owner of this repository, so you cannot administer it."
         return None, message
 
diff --git a/lib/tool_shed/util/search_util.py b/lib/tool_shed/util/search_util.py
index 83f8846df53..7cbc2996de4 100644
--- a/lib/tool_shed/util/search_util.py
+++ b/lib/tool_shed/util/search_util.py
@@ -38,13 +38,13 @@ def in_tool_dict(tool_dict, exact_matches_checked, tool_id=None, tool_name=None,
         tool_dict_tool_version = tool_dict['version'].lower()
         tool_dict_tool_name = tool_dict['name'].lower()
         tool_dict_tool_id = tool_dict['id'].lower()
-        found = (tool_version == tool_dict_tool_version and
-                 tool_name == tool_dict_tool_name and
-                 tool_id == tool_dict_tool_id) or \
-                (not exact_matches_checked and
-                 tool_dict_tool_version.find(tool_version) >= 0 and
-                 tool_dict_tool_name.find(tool_name) >= 0 and
-                 tool_dict_tool_id.find(tool_id) >= 0)
+        found = (tool_version == tool_dict_tool_version
+                 and tool_name == tool_dict_tool_name
+                 and tool_id == tool_dict_tool_id) or \
+                (not exact_matches_checked
+                 and tool_dict_tool_version.find(tool_version) >= 0
+                 and tool_dict_tool_name.find(tool_name) >= 0
+                 and tool_dict_tool_id.find(tool_id) >= 0)
     return found
 
 
diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index 21aedfbbead..747041ab96c 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -303,6 +303,7 @@ def get_tool_path_by_shed_tool_conf_filename(app, shed_tool_conf):
 def handle_email_alerts(app, host, repository, content_alert_str='', new_repo_alert=False, admin_only=False):
     """
     There are 2 complementary features that enable a tool shed user to receive email notification:
+
     1. Within User Preferences, they can elect to receive email when the first (or first valid)
        change set is produced for a new repository.
     2. When viewing or managing a repository, they can check the box labeled "Receive email alerts"
@@ -310,18 +311,20 @@ def handle_email_alerts(app, host, repository, content_alert_str='', new_repo_al
        is available on a per-repository basis on the repository grid within the tool shed.
 
     There are currently 4 scenarios for sending email notification when a change is made to a repository:
+
     1. An admin user elects to receive email when the first change set is produced for a new repository
        from User Preferences.  The change set does not have to include any valid content.  This allows for
        the capture of inappropriate content being uploaded to new repositories.
     2. A regular user elects to receive email when the first valid change set is produced for a new repository
        from User Preferences.  This differs from 1 above in that the user will not receive email until a
-       change set tha tincludes valid content is produced.
+       change set that includes valid content is produced.
     3. An admin user checks the "Receive email alerts" check box on the manage repository page.  Since the
        user is an admin user, the email will include information about both HTML and image content that was
        included in the change set.
     4. A regular user checks the "Receive email alerts" check box on the manage repository page.  Since the
        user is not an admin user, the email will not include any information about both HTML and image content
        that was included in the change set.
+
     """
     sa_session = app.model.context.current
     repo = repository.hg_repo
diff --git a/lib/tool_shed/utility_containers/utility_container_manager.py b/lib/tool_shed/utility_containers/utility_container_manager.py
index 3e2ce367d99..1b147b4aefd 100644
--- a/lib/tool_shed/utility_containers/utility_container_manager.py
+++ b/lib/tool_shed/utility_containers/utility_container_manager.py
@@ -818,11 +818,11 @@ class UtilityContainerManager:
         elif len(components_list) == 6:
             key_prior_installation_required = components_list[4]
             key_only_if_compiling_contained_td = components_list[5]
-        if (repository_name == key_name and
-                repository_owner == key_owner and
-                changeset_revision == key_changeset_revision and
-                prior_installation_required == key_prior_installation_required and
-                only_if_compiling_contained_td == key_only_if_compiling_contained_td):
+        if (repository_name == key_name
+                and repository_owner == key_owner
+                and changeset_revision == key_changeset_revision
+                and prior_installation_required == key_prior_installation_required
+                and only_if_compiling_contained_td == key_only_if_compiling_contained_td):
             return True
         return False
 
diff --git a/lib/tool_shed/webapp/api/authenticate.py b/lib/tool_shed/webapp/api/authenticate.py
index 9161107639f..e1a7bb865d6 100644
--- a/lib/tool_shed/webapp/api/authenticate.py
+++ b/lib/tool_shed/webapp/api/authenticate.py
@@ -8,11 +8,10 @@ Sample usage:
 
 Returns
 
-.. highlight:: json
 .. code-block:: json
 
     {
-        "api_key": <some api key>
+        "api_key": "<some api key>"
     }
 
 """
diff --git a/lib/tool_shed/webapp/api/groups.py b/lib/tool_shed/webapp/api/groups.py
index 6b510f244f0..ff38ed6c81d 100644
--- a/lib/tool_shed/webapp/api/groups.py
+++ b/lib/tool_shed/webapp/api/groups.py
@@ -29,7 +29,7 @@ class GroupsController(BaseAPIController):
         self.group_manager = groups.GroupManager()
 
     def __get_value_mapper(self, trans):
-        value_mapper = {'id' : trans.security.encode_id}
+        value_mapper = {'id': trans.security.encode_id}
         return value_mapper
 
     @expose_api_anonymous_and_sessionless
@@ -141,7 +141,7 @@ class GroupsController(BaseAPIController):
                                     'description': repo.description,
                                     'approved': approved,
                                     'ratings_mean': ratings_mean,
-                                    'categories' : categories})
+                                    'categories': categories})
                 user_repos_count += 1
             encoded_user_id = trans.app.security.encode_id(user.id)
             user_repos_url = web.url_for(controller='repository', action='browse_repositories_by_user', user_id=encoded_user_id)
diff --git a/lib/tool_shed/webapp/api/repositories.py b/lib/tool_shed/webapp/api/repositories.py
index 1520ae43aaa..00a4a84e1ff 100644
--- a/lib/tool_shed/webapp/api/repositories.py
+++ b/lib/tool_shed/webapp/api/repositories.py
@@ -976,9 +976,9 @@ class RepositoriesController(BaseAPIController):
 
         repository = repository_util.get_repository_in_tool_shed(self.app, id)
 
-        if not (trans.user_is_admin or
-                self.app.security_agent.user_can_administer_repository(trans.user, repository) or
-                self.app.security_agent.can_push(self.app, trans.user, repository)):
+        if not (trans.user_is_admin
+                or self.app.security_agent.user_can_administer_repository(trans.user, repository)
+                or self.app.security_agent.can_push(self.app, trans.user, repository)):
             trans.response.status = 400
             return {
                 "err_msg": "You do not have permission to update this repository.",
diff --git a/lib/tool_shed/webapp/api/repository_revisions.py b/lib/tool_shed/webapp/api/repository_revisions.py
index 185ebfa19c1..100a48a8b0b 100644
--- a/lib/tool_shed/webapp/api/repository_revisions.py
+++ b/lib/tool_shed/webapp/api/repository_revisions.py
@@ -15,9 +15,9 @@ class RepositoryRevisionsController(BaseAPIController):
     """RESTful controller for interactions with tool shed repository revisions."""
 
     def __get_value_mapper(self, trans):
-        value_mapper = {'id' : trans.security.encode_id,
-                        'repository_id' : trans.security.encode_id,
-                        'user_id' : trans.security.encode_id}
+        value_mapper = {'id': trans.security.encode_id,
+                        'repository_id': trans.security.encode_id,
+                        'user_id': trans.security.encode_id}
         return value_mapper
 
     @web.legacy_expose_api_anonymous
diff --git a/lib/tool_shed/webapp/api/tools.py b/lib/tool_shed/webapp/api/tools.py
index d5f378788b4..794eaecb023 100644
--- a/lib/tool_shed/webapp/api/tools.py
+++ b/lib/tool_shed/webapp/api/tools.py
@@ -176,13 +176,13 @@ class ToolsController(BaseAPIController):
         tool_dict['inputs'] = {}
         tool.populate_model(trans, tool.inputs, {}, tool_dict['inputs'])
         tool_dict.update({
-            'help'          : tool_help,
-            'citations'     : bool(tool.citations),
-            'requirements'  : [{'name' : r.name, 'version' : r.version} for r in tool.requirements],
-            'state_inputs'  : params_to_strings(tool.inputs, {}, trans.app),
-            'display'       : tool.display_interface,
-            'action'        : web.url_for(tool.action),
-            'method'        : tool.method,
-            'enctype'       : tool.enctype
+            'help': tool_help,
+            'citations': bool(tool.citations),
+            'requirements': [{'name': r.name, 'version': r.version} for r in tool.requirements],
+            'state_inputs': params_to_strings(tool.inputs, {}, trans.app),
+            'display': tool.display_interface,
+            'action': web.url_for(tool.action),
+            'method': tool.method,
+            'enctype': tool.enctype
         })
         return json.dumps(tool_dict)
diff --git a/lib/tool_shed/webapp/api/users.py b/lib/tool_shed/webapp/api/users.py
index 60fba03f199..748ff5b487b 100644
--- a/lib/tool_shed/webapp/api/users.py
+++ b/lib/tool_shed/webapp/api/users.py
@@ -72,7 +72,7 @@ class UsersController(BaseAPIController):
         return user
 
     def __get_value_mapper(self, trans):
-        value_mapper = {'id' : trans.security.encode_id}
+        value_mapper = {'id': trans.security.encode_id}
         return value_mapper
 
     @web.legacy_expose_api_anonymous
diff --git a/lib/tool_shed/webapp/controllers/admin.py b/lib/tool_shed/webapp/controllers/admin.py
index 9e1bc210af2..20ecf733721 100644
--- a/lib/tool_shed/webapp/controllers/admin.py
+++ b/lib/tool_shed/webapp/controllers/admin.py
@@ -51,7 +51,7 @@ class AdminController(BaseUIController, Admin):
                                                                 **kwd))
             elif operation == "repositories_by_user":
                 # Eliminate the current filters if any exist.
-                for k, v in list(kwd.items()):
+                for k in list(kwd.keys()):
                     if k.startswith('f-'):
                         del kwd[k]
                 if 'user_id' in kwd:
@@ -66,7 +66,7 @@ class AdminController(BaseUIController, Admin):
                     kwd['f-email'] = repository.user.email
             elif operation == "repositories_by_category":
                 # Eliminate the current filters if any exist.
-                for k, v in list(kwd.items()):
+                for k in list(kwd.keys()):
                     if k.startswith('f-'):
                         del kwd[k]
                 category_id = kwd.get('id', None)
diff --git a/lib/tool_shed/webapp/controllers/groups.py b/lib/tool_shed/webapp/controllers/groups.py
index b41ad39e17f..2fbbef9e5bb 100644
--- a/lib/tool_shed/webapp/controllers/groups.py
+++ b/lib/tool_shed/webapp/controllers/groups.py
@@ -12,7 +12,7 @@ class Group(BaseUIController):
     def index(self, trans, **kwd):
         # define app configuration for generic mako template
         app = {
-            'jscript'       : "../toolshed/scripts/toolshed.groups"
+            'jscript': "../toolshed/scripts/toolshed.groups"
         }
         return trans.fill_template('/webapps/tool_shed/group/index.mako',
                                    config={
diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py
index 13ac6bf5987..aad5dadda05 100644
--- a/lib/tool_shed/webapp/controllers/repository.py
+++ b/lib/tool_shed/webapp/controllers/repository.py
@@ -132,7 +132,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
             operation = kwd['operation'].lower()
             if operation in ["repositories_by_category", "repositories_by_user"]:
                 # Eliminate the current filters if any exist.
-                for k, v in list(kwd.items()):
+                for k in list(kwd.keys()):
                     if k.startswith('f-'):
                         del kwd[k]
                 return trans.response.send_redirect(web.url_for(controller='repository',
@@ -286,7 +286,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
     def browse_repositories_by_user(self, trans, **kwd):
         """Display the list of repositories owned by a specified user."""
         # Eliminate the current search filters if any exist.
-        for k, v in list(kwd.items()):
+        for k in list(kwd.keys()):
             if k.startswith('f-'):
                 del kwd[k]
         if 'operation' in kwd:
@@ -534,7 +534,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
             operation = kwd['operation'].lower()
             if operation in ["valid_repositories_by_category", "valid_repositories_by_user"]:
                 # Eliminate the current filters if any exist.
-                for k, v in list(kwd.items()):
+                for k in list(kwd.keys()):
                     if k.startswith('f-'):
                         del kwd[k]
                 return trans.response.send_redirect(web.url_for(controller='repository',
@@ -572,7 +572,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                                                                 changeset_revision=latest_installable_changeset_revision))
             elif operation == "valid_repositories_by_category":
                 # Eliminate the current filters if any exist.
-                for k, v in list(kwd.items()):
+                for k in list(kwd.keys()):
                     if k.startswith('f-'):
                         del kwd[k]
                 category_id = kwd.get('id', None)
@@ -2542,8 +2542,8 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
             repository = repository_util.get_repository_in_tool_shed(trans.app, repository_id)
             user = trans.user
             if repository:
-                if user is not None and (trans.user_is_admin or
-                                         trans.app.security_agent.user_can_administer_repository(user, repository)):
+                if user is not None and (trans.user_is_admin
+                                         or trans.app.security_agent.user_can_administer_repository(user, repository)):
                     return trans.response.send_redirect(web.url_for(controller='repository',
                                                                     action='manage_repository',
                                                                     **kwd))
diff --git a/lib/tool_shed/webapp/controllers/repository_review.py b/lib/tool_shed/webapp/controllers/repository_review.py
index fa694bc70ea..975571fcb54 100644
--- a/lib/tool_shed/webapp/controllers/repository_review.py
+++ b/lib/tool_shed/webapp/controllers/repository_review.py
@@ -389,6 +389,7 @@ class RepositoryReviewController(BaseUIController, ratings_util.ItemRatings):
     def manage_repositories_ready_for_review(self, trans, **kwd):
         """
         A repository is ready to be reviewed if one of the following conditions is met:
+
         1) It contains no tools
         2) It contains tools the tools_functionally_correct flag is set to True.  This implies that the repository metadata revision was installed and tested
            by the Tool Shed's install and test framework.
diff --git a/lib/tool_shed/webapp/search/repo_search.py b/lib/tool_shed/webapp/search/repo_search.py
index 5dbff48efbc..d78160df649 100644
--- a/lib/tool_shed/webapp/search/repo_search.py
+++ b/lib/tool_shed/webapp/search/repo_search.py
@@ -85,13 +85,13 @@ class RepoSearch:
                 # http://trec.nist.gov/pubs/trec13/papers/microsoft-cambridge.web.hard.pdf
                 # http://en.wikipedia.org/wiki/Okapi_BM25
                 # __Basically__ the higher number the bigger weight.
-                repo_weighting = RepoWeighting(field_B={'name_B' : boosts.repo_name_boost,
-                                                        'description_B' : boosts.repo_description_boost,
-                                                        'long_description_B' : boosts.repo_long_description_boost,
-                                                        'homepage_url_B' : boosts.repo_homepage_url_boost,
-                                                        'remote_repository_url_B' : boosts.repo_remote_repository_url_boost,
-                                                        'repo_owner_username_B' : boosts.repo_owner_username_boost,
-                                                        'categories_B' : boosts.categories_boost})
+                repo_weighting = RepoWeighting(field_B={'name_B': boosts.repo_name_boost,
+                                                        'description_B': boosts.repo_description_boost,
+                                                        'long_description_B': boosts.repo_long_description_boost,
+                                                        'homepage_url_B': boosts.repo_homepage_url_boost,
+                                                        'remote_repository_url_B': boosts.repo_remote_repository_url_boost,
+                                                        'repo_owner_username_B': boosts.repo_owner_username_boost,
+                                                        'categories_B': boosts.categories_boost})
                 searcher = index.searcher(weighting=repo_weighting)
                 parser = MultifieldParser([
                     'name',
diff --git a/lib/tool_shed/webapp/search/tool_search.py b/lib/tool_shed/webapp/search/tool_search.py
index 2f5935e1366..97b3dafacc8 100644
--- a/lib/tool_shed/webapp/search/tool_search.py
+++ b/lib/tool_shed/webapp/search/tool_search.py
@@ -48,10 +48,10 @@ class ToolSearch:
                 # http://en.wikipedia.org/wiki/Okapi_BM25
                 # __Basically__ the higher number the bigger weight.
                 tool_weighting = scoring.BM25F(field_B={
-                                               'name_B' : boosts.tool_name_boost,
-                                               'description_B' : boosts.tool_description_boost,
-                                               'help_B' : boosts.tool_help_boost,
-                                               'repo_owner_username_B' : boosts.tool_repo_owner_username_boost})
+                                               'name_B': boosts.tool_name_boost,
+                                               'description_B': boosts.tool_description_boost,
+                                               'help_B': boosts.tool_help_boost,
+                                               'repo_owner_username_B': boosts.tool_repo_owner_username_boost})
                 searcher = index.searcher(weighting=tool_weighting)
 
                 parser = MultifieldParser([
diff --git a/packages/app/galaxy/main_config.py b/packages/app/galaxy/main_config.py
new file mode 120000
index 00000000000..f26b2577893
--- /dev/null
+++ b/packages/app/galaxy/main_config.py
@@ -0,0 +1 @@
+../../../lib/galaxy/main_config.py
\ No newline at end of file
diff --git a/packages/app/galaxy/structured_app.py b/packages/app/galaxy/structured_app.py
new file mode 120000
index 00000000000..883e27f471a
--- /dev/null
+++ b/packages/app/galaxy/structured_app.py
@@ -0,0 +1 @@
+../../../lib/galaxy/structured_app.py
\ No newline at end of file
diff --git a/packages/data/requirements.txt b/packages/data/requirements.txt
index 98424dcbef5..ae42366d5fe 100644
--- a/packages/data/requirements.txt
+++ b/packages/data/requirements.txt
@@ -1,15 +1,16 @@
 galaxy-objectstore
-galaxy-sequence-utils==1.1.3
+galaxy-sequence-utils
 galaxy-util[template]
 bdbag
 bx-python
 h5py
 isa-rwval
 parsley
-numpy<=1.16
+numpy
 pycryptodome
+pydantic
 pysam
-social_auth_core
+social-auth-core[openidconnect]==3.3.0
 SQLAlchemy
 sqlalchemy-migrate
 sqlalchemy-utils
diff --git a/packages/tool_util/test-requirements.txt b/packages/tool_util/test-requirements.txt
index e079f8a6038..12136494321 100644
--- a/packages/tool_util/test-requirements.txt
+++ b/packages/tool_util/test-requirements.txt
@@ -1 +1,2 @@
 pytest
+pytest-mock
diff --git a/scripts/api/copy_hda_to_library_folder.py b/scripts/api/copy_hda_to_library_folder.py
index dd9ceb7c342..722e078f2f2 100755
--- a/scripts/api/copy_hda_to_library_folder.py
+++ b/scripts/api/copy_hda_to_library_folder.py
@@ -10,9 +10,9 @@ usage = "USAGE: copy_hda_to_library_folder.py <base url> <api key> <hda id> <lib
 def copy_hda_to_library_folder(base_url, key, hda_id, library_id, folder_id, message=''):
     url = f'http://{base_url}/api/libraries/{library_id}/contents'
     payload = {
-        'folder_id'     : folder_id,
-        'create_type'   : 'file',
-        'from_hda_id'   : hda_id,
+        'folder_id': folder_id,
+        'create_type': 'file',
+        'from_hda_id': hda_id,
     }
     if message:
         payload.update(dict(ldda_message=message))
diff --git a/scripts/api/example_watch_folder.py b/scripts/api/example_watch_folder.py
index 8ca8d980aae..152443aae82 100755
--- a/scripts/api/example_watch_folder.py
+++ b/scripts/api/example_watch_folder.py
@@ -66,7 +66,7 @@ def main(api_key, api_url, in_folder, out_folder, data_library, workflow):
                         wf_data['workflow_id'] = workflow['id']
                         wf_data['history'] = "{} - {}".format(fname, workflow['name'])
                         wf_data['ds_map'] = {}
-                        for step_id, ds_in in workflow['inputs'].items():
+                        for step_id in workflow['inputs'].keys():
                             wf_data['ds_map'][step_id] = {'src': 'ld', 'id': ds['id']}
                         res = submit(api_key, api_url + 'workflows', wf_data, return_formatted=False)
                         if res:
diff --git a/scripts/api/upload_to_history.py b/scripts/api/upload_to_history.py
index 3f071105577..0c073644810 100755
--- a/scripts/api/upload_to_history.py
+++ b/scripts/api/upload_to_history.py
@@ -10,8 +10,8 @@ import sys
 try:
     import requests
 except ImportError:
-    print("Could not import the requests module. See http://docs.python-requests.org/en/latest/" +
-          " or install with 'pip install requests'")
+    print("Could not import the requests module. See http://docs.python-requests.org/en/latest/"
+          + " or install with 'pip install requests'")
     raise
 
 
@@ -19,17 +19,17 @@ def upload_file(base_url, api_key, history_id, filepath, **kwargs):
     full_url = base_url + '/api/tools'
 
     payload = {
-        'key'           : api_key,
-        'tool_id'       : 'upload1',
-        'history_id'    : history_id,
+        'key': api_key,
+        'tool_id': 'upload1',
+        'history_id': history_id,
     }
     inputs = {
-        'files_0|NAME'  : kwargs.get('filename', os.path.basename(filepath)),
-        'files_0|type'  : 'upload_dataset',
+        'files_0|NAME': kwargs.get('filename', os.path.basename(filepath)),
+        'files_0|type': 'upload_dataset',
         # TODO: the following doesn't work with tools.py
-        'dbkey'         : '?',
-        'file_type'     : kwargs.get('file_type', 'auto'),
-        'ajax_upload'   : 'true',
+        'dbkey': '?',
+        'file_type': kwargs.get('file_type', 'auto'),
+        'ajax_upload': 'true',
     }
     payload['inputs'] = json.dumps(inputs)
 
@@ -42,8 +42,8 @@ def upload_file(base_url, api_key, history_id, filepath, **kwargs):
 
 if __name__ == '__main__':
     if len(sys.argv) < 5:
-        print("history_upload.py <api key> <galaxy base url> <history id> <filepath to upload>\n" +
-              "  (where galaxy base url is just the root url where your Galaxy is served; e.g. 'localhost:8080')")
+        print("history_upload.py <api key> <galaxy base url> <history id> <filepath to upload>\n"
+              + "  (where galaxy base url is just the root url where your Galaxy is served; e.g. 'localhost:8080')")
         sys.exit(1)
 
     api_key, base_url, history_id, filepath = sys.argv[1:5]
diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py
index 78a0968214c..2db6c16f93e 100644
--- a/scripts/bootstrap_history.py
+++ b/scripts/bootstrap_history.py
@@ -172,6 +172,8 @@ Please see the `full release notes <${release}_announce.html>`_ for more details
 """)
 
 NEXT_TEMPLATE = string.Template("""
+:orphan:
+
 ===========================================================
 ${month_name} 20${year} Galaxy Release (v ${version})
 ===========================================================
@@ -640,7 +642,7 @@ def _text_target(pull_request, labels=None):
         try:
             github = _github_client()
             labels = github.issues.labels.list_by_issue(int(pr_number), user=PROJECT_OWNER, repo=PROJECT_NAME)
-            labels = [l.name.lower() for l in labels]
+            labels = [label.name.lower() for label in labels]
         except Exception as e:
             print(e)
     is_bug = is_enhancement = is_feature = is_minor = is_major = is_merge = is_small_enhancement = False
@@ -706,7 +708,7 @@ def _text_target(pull_request, labels=None):
 
 
 def _pr_to_labels(pr):
-    labels = [l.name.lower() for l in pr.labels]
+    labels = [label.name.lower() for label in pr.labels]
     return labels
 
 
diff --git a/scripts/build_toolbox.py b/scripts/build_toolbox.py
index 6938f60ef2e..6309f4d85df 100644
--- a/scripts/build_toolbox.py
+++ b/scripts/build_toolbox.py
@@ -1,9 +1,10 @@
 import os
+from collections import defaultdict
+from xml.dom import minidom
 from xml.etree import ElementTree as ET
 
 
 def prettify(elem):
-    from xml.dom import minidom
     rough_string = ET.tostring(elem, 'utf-8')
     repaired = minidom.parseString(rough_string)
     return repaired.toprettyxml(indent='  ')
@@ -12,7 +13,7 @@ def prettify(elem):
 # Build a list of all toolconf xml files in the tools directory
 def getfilenamelist(startdir):
     filenamelist = []
-    for root, dirs, files in os.walk(startdir):
+    for root, _dirs, files in os.walk(startdir):
         for fn in files:
             fullfn = os.path.join(root, fn)
             if fn.endswith('toolconf.xml'):
@@ -36,7 +37,6 @@ def getfilenamelist(startdir):
 
 class ToolBox:
     def __init__(self):
-        from collections import defaultdict
         self.tools = defaultdict(list)
         self.sectionorders = {}
 
@@ -155,7 +155,7 @@ def scanfiles(filenamelist):
 def assemble():
     filenamelist = []
     for directorytree in ['tools']:
-        filenamelist.extend(getfilenamelist('tools'))
+        filenamelist.extend(getfilenamelist(directorytree))
     filenamelist.sort()
 
     toolbox = scanfiles(filenamelist)
diff --git a/scripts/cleanup_datasets/admin_cleanup_datasets.py b/scripts/cleanup_datasets/admin_cleanup_datasets.py
index 947175f61b6..4cce0df77ec 100755
--- a/scripts/cleanup_datasets/admin_cleanup_datasets.py
+++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py
@@ -263,8 +263,8 @@ def _get_tool_id_for_hda(app, hda_id):
         return None
     job = app.sa_session.query(app.model.Job).\
         join(app.model.JobToOutputDatasetAssociation).\
-        filter(app.model.JobToOutputDatasetAssociation.table.c.dataset_id ==
-               hda_id).first()
+        filter(app.model.JobToOutputDatasetAssociation.table.c.dataset_id
+               == hda_id).first()
     if job is not None:
         return job.tool_id
     else:
diff --git a/scripts/cleanup_datasets/cleanup_datasets.py b/scripts/cleanup_datasets/cleanup_datasets.py
index a9ab1a175e9..9934b5c297b 100755
--- a/scripts/cleanup_datasets/cleanup_datasets.py
+++ b/scripts/cleanup_datasets/cleanup_datasets.py
@@ -89,9 +89,9 @@ def main():
     if args.legacy_config:
         config_override = args.legacy_config
 
-    if not (args.purge_folders ^ args.delete_userless_histories ^
-            args.purge_libraries ^ args.purge_histories ^
-            args.purge_datasets ^ args.delete_datasets):
+    if not (args.purge_folders ^ args.delete_userless_histories
+            ^ args.purge_libraries ^ args.purge_histories
+            ^ args.purge_datasets ^ args.delete_datasets):
         parser.print_help()
         sys.exit(0)
 
diff --git a/scripts/cleanup_datasets/pgcleanup.py b/scripts/cleanup_datasets/pgcleanup.py
index 2fbb92fb755..21cb488e5b1 100755
--- a/scripts/cleanup_datasets/pgcleanup.py
+++ b/scripts/cleanup_datasets/pgcleanup.py
@@ -136,12 +136,11 @@ class Action:
             h = set_log_handler(filename=logf)
         h.setLevel(logging.DEBUG if self._debug else logging.INFO)
         h.setFormatter(LevelFormatter())
-        l = logging.getLogger(self.name)
-        l.addHandler(h)
-        l.propagate = False
+        self.__log = logging.getLogger(self.name)
+        self.__log.addHandler(h)
+        self.__log.propagate = False
         m = ('==== Log opened: %s ' % datetime.datetime.now().isoformat()).ljust(72, '=')
-        l.info(m)
-        self.__log = l
+        self.__log.info(m)
 
     def __close_log(self):
         m = ('==== Log closed: %s ' % datetime.datetime.now().isoformat()).ljust(72, '=')
@@ -274,9 +273,9 @@ class RemovesObjects:
                 if not self._dry_run:
                     self.object_store.delete(object_to_remove, entire_dir=entire_dir, **object_store_kwargs)
         except ObjectNotFound as e:
-            [l.warning('object store failure: %s: %s', object_to_remove, e) for l in loggers]
+            [log_.warning('object store failure: %s: %s', object_to_remove, e) for log_ in loggers]
         except Exception as e:
-            [l.error('delete failure: %s: %s', object_to_remove, e) for l in loggers]
+            [log_.error('delete failure: %s: %s', object_to_remove, e) for log_ in loggers]
 
     def remove_object(self, object_to_remove):
         raise NotImplementedError()
diff --git a/scripts/docker_swarm_manager.py b/scripts/docker_swarm_manager.py
index a03de7876be..ffd5392cfdb 100644
--- a/scripts/docker_swarm_manager.py
+++ b/scripts/docker_swarm_manager.py
@@ -362,8 +362,8 @@ class SwarmState:
             total += node.cpus / self._cpus
         # need at least this many slots
         needed = used + self.get_limit(constraints, 'slots_min_spare')
-        if (len(services) > self._conf.service_wait_count_limit and
-                time.time() - self._waiting_since.get(constraints, time.time()) > self._conf.service_wait_time_limit):
+        if (len(services) > self._conf.service_wait_count_limit
+                and time.time() - self._waiting_since.get(constraints, time.time()) > self._conf.service_wait_time_limit):
             # add slots for waiting services that have exceeded limits
             needed += sum([s.cpus for s in services]) / self._cpus
         # subtract slots for spawning nodes
diff --git a/scripts/extract_toolbox_sections.py b/scripts/extract_toolbox_sections.py
index 0efd285ff09..b7f7b67b2f4 100644
--- a/scripts/extract_toolbox_sections.py
+++ b/scripts/extract_toolbox_sections.py
@@ -88,8 +88,8 @@ def main():
                 # create empty tags element
                 newelements.append("<tags/>\n  ")
 
-            contents = (contents[0:addelementsatposition] + newelements +
-                        contents[addelementsatposition:])
+            contents = (contents[0:addelementsatposition] + newelements
+                        + contents[addelementsatposition:])
 
             # add .new for testing/safety purposes :P
             newtoolconffile = open(toolconffile, 'w')
@@ -117,7 +117,7 @@ def addToToolDict(tool, sectionname, sectionindex, toolindex, currentlabel):
 # Build a list of all toolconf xml files in the tools directory
 def getfnl(startdir):
     filenamelist = []
-    for root, dirs, files in os.walk(startdir):
+    for root, _dirs, files in os.walk(startdir):
         for fn in files:
             fullfn = os.path.join(root, fn)
             if fn.endswith('.xml'):
diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py
index 6fb9a7f09de..18ad65c8ff6 100644
--- a/scripts/functional_tests.py
+++ b/scripts/functional_tests.py
@@ -13,7 +13,7 @@ galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pa
 sys.path[1:1] = [os.path.join(galaxy_root, "lib"), os.path.join(galaxy_root, "test")]
 
 from galaxy.util import classproperty
-from galaxy_test.base.api_util import get_master_api_key, get_user_api_key
+from galaxy_test.base.api_util import get_admin_api_key, get_user_api_key
 from galaxy_test.driver import driver_util
 
 log = driver_util.build_logger()
@@ -86,7 +86,7 @@ class DataManagersGalaxyTestDriver(driver_util.GalaxyTestDriver):
         functional.test_data_managers.build_tests(
             tmp_dir=self.galaxy_test_tmp_dir,
             testing_shed_tools=self.testing_shed_tools,
-            master_api_key=get_master_api_key(),
+            master_api_key=get_admin_api_key(),
             user_api_key=get_user_api_key(),
             user_email=self.app.config.admin_users_list[0],
             create_admin=True,
diff --git a/scripts/galaxy_main.py b/scripts/galaxy_main.py
index cc4cdea7374..c6a49f20bcc 100755
--- a/scripts/galaxy_main.py
+++ b/scripts/galaxy_main.py
@@ -57,15 +57,18 @@ else:
     except Exception:
         log.exception("Failed to add Galaxy to sys.path")
         raise
+from galaxy.main_config import (
+    absolute_config_path,
+    config_is_ini,
+    DEFAULT_CONFIG_SECTION,
+    DEFAULT_INI_APP,
+    find_config,
+)
 from galaxy.util import unicodify
 from galaxy.web_stack import get_app_kwds
 
 REQUIRES_DAEMONIZE_MESSAGE = "Attempted to use Galaxy in daemon mode, but daemonize is unavailable."
 
-DEFAULT_INI_APP = "main"
-DEFAULT_CONFIG_SECTION = "galaxy"
-DEFAULT_INIS = ["config/galaxy.yml", "config/galaxy.ini", "universe_wsgi.ini", "config/galaxy.yml.sample"]
-
 DEFAULT_PID = "galaxy.pid"
 DEFAULT_VERBOSE = True
 DESCRIPTION = "Daemonized entry point for Galaxy."
@@ -156,29 +159,6 @@ def app_loop(args, log):
         raise
 
 
-def absolute_config_path(path, galaxy_root):
-    if path and not os.path.isabs(path):
-        path = os.path.join(galaxy_root, path)
-    return path
-
-
-def find_config(supplied_config, galaxy_root):
-    if supplied_config:
-        return supplied_config
-
-    if galaxy_root is None:
-        return os.path.abspath('galaxy.yml')
-
-    # If not explicitly supplied an config, check galaxy.ini and then
-    # just resort to sample if that has not been configured.
-    for guess in DEFAULT_INIS:
-        config_path = os.path.join(galaxy_root, guess)
-        if os.path.exists(config_path):
-            return config_path
-
-    return guess
-
-
 class GalaxyConfigBuilder:
     """ Generate paste-like configuration from supplied command-line arguments.
     """
@@ -218,7 +198,7 @@ class GalaxyConfigBuilder:
 
     @property
     def config_is_ini(self):
-        return self.config_file.endswith('.ini') or self.config_file.endswith('.ini.sample')
+        return config_is_ini(self.config_file)
 
     def app_kwds(self):
         kwds = get_app_kwds(self.app_name, app_name=self.app_name)
diff --git a/scripts/interactivetools/key_type_token_mapping.py b/scripts/interactivetools/key_type_token_mapping.py
index df6dff6506a..0a236c4f8f6 100644
--- a/scripts/interactivetools/key_type_token_mapping.py
+++ b/scripts/interactivetools/key_type_token_mapping.py
@@ -77,8 +77,8 @@ def key_type_token_mapper(key, key_type, token, route_extra, url):
     # print 'key %s key_type %s token %s route_extra %s url %s\n' % (key, key_type, token, route_extra, url)
     if key and key_type and token:
         # sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id x and this is thread id y.
-        # So try upto 2 times
-        for i in range(2):
+        # So try up to 2 times
+        for _ in range(2):
             # Order by rowid gives us the last row added
             try:
                 row = db_conn.execute("SELECT host, port FROM %s WHERE key=? AND key_type=? AND token=? ORDER BY rowid DESC LIMIT 1" % (DATABASE_TABLE_NAME), (key, key_type, token)).fetchone()
diff --git a/scripts/loc_files/create_all_fasta_loc.py b/scripts/loc_files/create_all_fasta_loc.py
index 00a2c3b335e..9c6387de2f7 100644
--- a/scripts/loc_files/create_all_fasta_loc.py
+++ b/scripts/loc_files/create_all_fasta_loc.py
@@ -227,7 +227,7 @@ def __main__():
         possible_names.extend([f'{genome_subdir}{_}' for _ in variants])
         # get paths to all fasta files
         for path_to_look_in in paths_to_look_in:
-            for dirpath, dirnames, filenames in os.walk(path_to_look_in % genome_subdir):
+            for dirpath, _dirnames, filenames in os.walk(path_to_look_in % genome_subdir):
                 for fn in filenames:
                     ext = os.path.splitext(fn)[-1]
                     fasta_base = os.path.splitext(fn)[0]
diff --git a/scripts/metagenomics/convert_title.py b/scripts/metagenomics/convert_title.py
index cf1152c3594..58f203290e3 100644
--- a/scripts/metagenomics/convert_title.py
+++ b/scripts/metagenomics/convert_title.py
@@ -12,7 +12,7 @@ if __name__ == '__main__':
     invalid_lines = 0
     gi = None
 
-    for i, line in enumerate(sys.stdin):
+    for line in sys.stdin:
         line = line.rstrip('\r\n')
         if line.startswith('>'):
             if len_seq > 0:
diff --git a/scripts/microbes/util.py b/scripts/microbes/util.py
index 5bc88bc5a61..b0e664f65e5 100644
--- a/scripts/microbes/util.py
+++ b/scripts/microbes/util.py
@@ -39,7 +39,7 @@ class Region:
 
 class GenBankFeatureParser:
     """Parses Features from Single Locus GenBank file"""
-    def __init__(self, fh, features_list=[]):
+    def __init__(self, fh):
         self.fh = fh
         self.features = {}
         fh.seek(0)
@@ -63,12 +63,11 @@ class GenBankFeatureParser:
                     last_attr_name = None
                     fields = lstrip.split(None, 1)
                     last_feature_name = fields[0].strip()
-                    if not features_list or (features_list and last_feature_name in features_list):
-                        if last_feature_name not in self.features:
-                            self.features[last_feature_name] = []
-                        region = Region()
-                        region.set_coordinates_by_location(fields[1])
-                        self.features[last_feature_name].append(region)
+                    if last_feature_name not in self.features:
+                        self.features[last_feature_name] = []
+                    region = Region()
+                    region.set_coordinates_by_location(fields[1])
+                    self.features[last_feature_name].append(region)
                 else:
                     # add info to last known feature
                     line = line.strip()
diff --git a/scripts/objectstore/copy_files_to_irods.py b/scripts/objectstore/copy_files_to_irods.py
index 299b201de62..50b393ebecb 100644
--- a/scripts/objectstore/copy_files_to_irods.py
+++ b/scripts/objectstore/copy_files_to_irods.py
@@ -127,7 +127,7 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
         args = ('ok', start_dataset_id, end_dataset_id, osi_keys)
         read_cursor.execute(read_sql_statement, args)
         rows = read_cursor.fetchall()
-        for num, row in enumerate(rows):
+        for row in rows:
             objectid = row[0]
             object_store_id = row[1]
             uuid_without_dash = row[2]
@@ -153,7 +153,7 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
                 session.collections.create(irods_file_collection_path)
 
                 # Add disk file to collection
-                options = {kw.REG_CHKSUM_KW : '', kw.RESC_NAME_KW: irods_resc}
+                options = {kw.REG_CHKSUM_KW: '', kw.RESC_NAME_KW: irods_resc}
                 session.data_objects.put(disk_file_path, irods_file_path, **options)
                 print(f"Copied disk file {disk_file_path} to irods {irods_file_path}")
 
@@ -189,7 +189,7 @@ def copy_files_to_irods(start_dataset_id, end_dataset_id, object_store_info_file
                 # Recursively verify that the checksum of all files in this folder matches that in irods
                 if os.path.isdir(disk_folder_path):
                     # Recursively traverse the files in this folder
-                    for root, dirs, files in os.walk(disk_folder_path):
+                    for root, _dirs, files in os.walk(disk_folder_path):
                         for file_name in files:
                             a_disk_file_path = os.path.join(root, file_name)
                             # Get checksum for disk file
diff --git a/setup.cfg b/setup.cfg
index 29200c5b5bb..7cb609b3060 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -2,15 +2,14 @@
 universal = 1
 
 [flake8]
-# These are exceptions allowed by Galaxy style guidelines.
+# These are exceptions allowed by Galaxy style guidelines:
+# B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body)
 # E128 continuation line under-indented for visual indent
-# E203 whitespace before ':'
 # E402 module level import not at top of file # TODO, we would like to improve this.
 # E501 is line length
-# E741 do not use variables named 'l', 'O' or 'I'
 # W503 is line breaks before binary operators, which has been reversed in PEP 8.
 # D** are docstring linting - which we mostly ignore except D302. (Hopefully we will solve more over time).
-ignore = E128,E203,E501,E402,E741,W503,W504,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
+ignore = B008,E128,E501,E402,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
 exclude = lib/galaxy/util/jstree.py
 # For flake8-import-order
 # https://github.com/PyCQA/flake8-import-order/blob/master/tests/test_cases/complete_smarkets.py
diff --git a/test-data/2.tabular b/test-data/2.tabular
index c1e73a28a26..52834cc059f 100644
--- a/test-data/2.tabular
+++ b/test-data/2.tabular
@@ -5,6 +5,6 @@
 5	58	3.2
 6	60	3.1
 7	67	3.8
-8	68	4.1
-9	71	4.3
+8	168	4.1
+9	171	4.3
 10	69	3.7
diff --git a/test/functional/test_toolbox_pytest.py b/test/functional/test_toolbox_pytest.py
index 88cdfe56d8f..0b31344c99a 100644
--- a/test/functional/test_toolbox_pytest.py
+++ b/test/functional/test_toolbox_pytest.py
@@ -28,7 +28,7 @@ class DefaultGalaxyTestDriver(driver_util.GalaxyTestDriver):
 
 def get_skiplist():
     with open(SKIPTEST) as skiptest:
-        skiplist = [l.strip() for l in skiptest if l.strip() and not l.startswith('#')]
+        skiplist = [line.strip() for line in skiptest if line.strip() and not line.startswith('#')]
         return skiplist
 
 
@@ -54,7 +54,7 @@ def get_cases():
     cases = []
     for test_name, test_class in tests.items():
         if test_name.startswith(TEST_PREFIX):
-            test_class.runTest = lambda : None
+            test_class.runTest = lambda: None
             test_instance = test_class()
             cases.append(test_instance)
     return cases
diff --git a/test/functional/tool-data/fasta_indexes.loc b/test/functional/tool-data/fasta_indexes.loc
index 3383ed89752..57f11daa9a9 100644
--- a/test/functional/tool-data/fasta_indexes.loc
+++ b/test/functional/tool-data/fasta_indexes.loc
@@ -1,2 +1,2 @@
-hg19	hg19	hg19	hg19
-hg18	hg18	hg18	hg18
\ No newline at end of file
+hg19_value	hg19	hg19_name	hg19_path
+hg18_value	hg18	hg18_name	hg18_path
diff --git a/test/functional/tools/dbkey_filter_collection.xml b/test/functional/tools/dbkey_filter_collection.xml
index eeb5937336e..ed8b5a13d8f 100644
--- a/test/functional/tools/dbkey_filter_collection.xml
+++ b/test/functional/tools/dbkey_filter_collection.xml
@@ -31,9 +31,9 @@
                     <element name="e2" value="simple_line_alternative.txt" dbkey="hg19"/>
                 </collection>
             </param>
-            <param name="index" value="hg19" />
+            <param name="index" value="hg19_value" />
             <output name="output">
-                <assert_contents><has_text text="hg19" /></assert_contents>
+                <assert_contents><has_text text="hg19_value" /></assert_contents>
             </output>
         </test>
         <!-- can choose any dbkey if none specified in reference -->
@@ -44,10 +44,10 @@
                     <element name="e2" value="simple_line_alternative.txt"/>
                 </collection>
             </param>
-            <param name="index" value="hg18" />
+            <param name="index" value="hg18_value" />
             <output name="output">
                 <assert_contents>
-                    <has_text text="hg18" /></assert_contents>
+                    <has_text text="hg18_value" /></assert_contents>
             </output>
         </test>
         <!-- can choose any dbkey specified in reference -->
@@ -58,9 +58,9 @@
                     <element name="e2" value="simple_line_alternative.txt" dbkey="hg18"/>
                 </collection>
             </param>
-            <param name="index" value="hg18" />
+            <param name="index" value="hg18_value" />
             <output name="output">
-                <assert_contents><has_text text="hg18" /></assert_contents>
+                <assert_contents><has_text text="hg18_value" /></assert_contents>
             </output>
         </test>
         <!-- cant choose a dkkey different from reference -->
@@ -71,9 +71,9 @@
                     <element name="e2" value="simple_line_alternative.txt" dbkey="hg19"/>
                 </collection>
             </param>
-            <param name="index" value="hg18" />
+            <param name="index" value="hg18_value" />
             <output name="output">
-                <assert_contents><not_has_text text="hg18" /></assert_contents>
+                <assert_contents><not_has_text text="hg18_value" /></assert_contents>
             </output>
         </test>
     </tests>
diff --git a/test/functional/tools/dbkey_filter_input.xml b/test/functional/tools/dbkey_filter_input.xml
index ae04f6fc58f..15daef6f8b2 100644
--- a/test/functional/tools/dbkey_filter_input.xml
+++ b/test/functional/tools/dbkey_filter_input.xml
@@ -1,7 +1,8 @@
 <tool id="dbkey_filter_input" name="dbkey_filter_input" version="0.1.0">
     <description>Filter (single) input on a dbkey</description>
     <command><![CDATA[
-cat '$inputs' > '$output'
+       cat '$inputs' > '$output' &&
+       echo $index
     ]]></command>
     <inputs>
         <param name="inputs" type="data" format="txt" label="Inputs" help="" />
@@ -21,21 +22,36 @@ cat '$inputs' > '$output'
         <!-- can choose a dbkey if it matches input -->
         <test>
             <param name="inputs" value="simple_line.txt" dbkey="hg19" />
-            <param name="index" value="hg19" />
+            <param name="index" value="hg19_value" />
             <output name="output" file="simple_line.txt" />
+            <assert_stdout>
+                <has_text text="hg19_value"/>
+            </assert_stdout>
         </test>
         <!-- choose any dbkey if not specified in reference -->
         <test>
             <param name="inputs" value="simple_line.txt" />
-            <param name="index" value="hg19" />
+            <param name="index" value="hg19_value" />
             <output name="output" file="simple_line.txt" />
+            <assert_stdout>
+                <has_text text="hg19_value"/>
+            </assert_stdout>
         </test>
         <!-- cant choose a dkkey different from reference -->
         <test expect_failure="true">
             <param name="inputs" value="simple_line.txt" dbkey="hg18" />
-            <param name="index" value="hg19" />
+            <param name="index" value="hg19_value" />
             <output name="output" file="simple_line.txt" />
         </test>
+        <!-- demonstrate that dynamic selects can be chosen by name -->
+        <test>
+            <param name="inputs" value="simple_line.txt" />
+            <param name="index" value="hg19_name" />
+            <output name="output" file="simple_line.txt" />
+            <assert_stdout>
+                <has_text text="hg19_value"/>
+            </assert_stdout>
+        </test>
     </tests>
     <help>
     </help>
diff --git a/test/functional/tools/dbkey_filter_multi_input.xml b/test/functional/tools/dbkey_filter_multi_input.xml
index df04926938d..9463440c2af 100644
--- a/test/functional/tools/dbkey_filter_multi_input.xml
+++ b/test/functional/tools/dbkey_filter_multi_input.xml
@@ -23,19 +23,19 @@
         <!-- can choose a dbkey if it matches input -->
         <test>
             <param name="inputs" value="simple_line.txt,simple_line.txt" dbkey="hg19" />
-            <param name="index" value="hg19" />
+            <param name="index" value="hg19_value" />
             <output name="output" file="simple_line_x2.txt"/>
         </test>
         <!-- can choose any dbkey if none specified in reference -->
         <test>
             <param name="inputs" value="simple_line.txt,simple_line.txt" />
-            <param name="index" value="hg19" />
+            <param name="index" value="hg19_value" />
             <output name="output" file="simple_line_x2.txt"/>
         </test>
         <!-- can choose any dbkey none specified in reference -->
         <test expect_failure="true">
             <param name="inputs" value="simple_line.txt,simple_line.txt" dbkey="hg19"/>
-            <param name="index" value="hg18" />
+            <param name="index" value="hg18_value" />
             <output name="output" file="simple_line_x2.txt"/>
         </test>
     </tests>
diff --git a/test/functional/tools/dbkey_output_action.xml b/test/functional/tools/dbkey_output_action.xml
index 128e43d721f..1d29a0b4e65 100644
--- a/test/functional/tools/dbkey_output_action.xml
+++ b/test/functional/tools/dbkey_output_action.xml
@@ -26,7 +26,7 @@ echo foo > '$mapped_reads'
     <tests>
         <test>
             <param name="input" value="simple_line.txt" dbkey="hg18" />
-            <param name="index" value="hg18"/>
+            <param name="index" value="hg18_value"/>
             <output name="mapped_reads">
                 <metadata name="dbkey" value="hg18" />
                 <assert_contents>
diff --git a/test/functional/tools/filter_static_regexp.xml b/test/functional/tools/filter_static_regexp.xml
index ebfcd0756e8..090f8835e8d 100644
--- a/test/functional/tools/filter_static_regexp.xml
+++ b/test/functional/tools/filter_static_regexp.xml
@@ -45,10 +45,10 @@ echo $index_regexp_keep >> '$output' &&
     <tests>
         <!-- can choose a dbkey if it matches input -->
         <test>
-            <param name="index_static" value="hg19" />
-            <param name="index_static_keep" value="hg19" />
-            <param name="index_regexp" value="hg19" />
-            <param name="index_regexp_keep" value="hg19" />
+            <param name="index_static" value="hg19_value" />
+            <param name="index_static_keep" value="hg19_value" />
+            <param name="index_regexp" value="hg19_value" />
+            <param name="index_regexp_keep" value="hg19_value" />
             <output name="output">
                 <assert_contents>
                     <has_text text="hg19" />    
@@ -60,24 +60,24 @@ echo $index_regexp_keep >> '$output' &&
         <!-- Does this make sense - if no dbkey is defined there is no option
              available? -->
         <test expect_failure="true">
-            <param name="index_static" value="hg18" />
-            <param name="index_static_keep" value="hg19" />
-            <param name="index_regexp" value="hg19" />
-            <param name="index_regexp_keep" value="hg19" />
+            <param name="index_static" value="hg18_value" />
+            <param name="index_static_keep" value="hg19_value" />
+            <param name="index_regexp" value="hg19_value" />
+            <param name="index_regexp_keep" value="hg19_value" />
             <output name="output"/>
         </test>
         <test expect_failure="true">
-            <param name="index_static" value="hg19" />
-            <param name="index_static_keep" value="hg18" />
-            <param name="index_regexp" value="hg19" />
-            <param name="index_regexp_keep" value="hg19" />
+            <param name="index_static" value="hg19_value" />
+            <param name="index_static_keep" value="hg18_value" />
+            <param name="index_regexp" value="hg19_value" />
+            <param name="index_regexp_keep" value="hg19_value" />
             <output name="output"/>
         </test>
         <test expect_failure="true">
-            <param name="index_static" value="hg19" />
-            <param name="index_static_keep" value="hg19" />
-            <param name="index_regexp" value="hg18" />
-            <param name="index_regexp_keep" value="hg19" />
+            <param name="index_static" value="hg19_value" />
+            <param name="index_static_keep" value="hg19_value" />
+            <param name="index_regexp" value="hg18_value" />
+            <param name="index_regexp_keep" value="hg19_value" />
             <output name="output"/>
         </test>
         <test expect_failure="true">
diff --git a/test/functional/tools/remove_value.xml b/test/functional/tools/remove_value.xml
index 5671e27e278..b01e01a24f5 100644
--- a/test/functional/tools/remove_value.xml
+++ b/test/functional/tools/remove_value.xml
@@ -6,8 +6,8 @@ echo $choose_value > '$out_file'
         <param name="choose_value" type="select">
             <options from_data_table="test_fasta_indexes">
                 <!-- contains hg18 and hg19 -->
-                <filter type="remove_value" value="hg18"/>
-                <filter type="remove_value" value="hg20"/>
+                <filter type="remove_value" value="hg18_value"/>
+                <filter type="remove_value" value="hg20_value"/>
                 <!-- This doesn't work as we don't have the remaining values like name and path
                 <filter type="add_value" value="hg20"/>
                 -->
@@ -21,12 +21,12 @@ echo $choose_value > '$out_file'
         <test>
             <output name="out_file">
                 <assert_contents>
-                    <has_line line="hg19" />
+                    <has_line line="hg19_value" />
                 </assert_contents>
             </output>
         </test>
         <test expect_failure="true">
-            <param name="choose_value" value="hg18"/>
+            <param name="choose_value" value="hg18_value"/>
         </test>
     </tests>
 </tool>
diff --git a/test/functional/tools/select_from_dataset.xml b/test/functional/tools/select_from_dataset.xml
index 3a67ac01db8..b5e949025cb 100644
--- a/test/functional/tools/select_from_dataset.xml
+++ b/test/functional/tools/select_from_dataset.xml
@@ -5,11 +5,11 @@ echo select_single '$select_single' > '$output' &&
 echo select_multiple '$select_multiple' >> '$output' &&
 echo select_collection '$select_collection' >> '$output'
     ]]></command>
-	<inputs>
+    <inputs>
         <param name="single" type="data" format="tabular" label="single"/>
         <param name="select_single" type="select" label="select_single">
             <options from_dataset="single">
-                <column name="name" index="0"/>
+                <column name="name" index="1"/>
                 <column name="value" index="0"/>
                 <validator type="no_options" message="No data is available in single" />
             </options>
@@ -17,19 +17,19 @@ echo select_collection '$select_collection' >> '$output'
         <param name="multiple" type="data" format="tabular" multiple="true" label="multiple"/>
         <param name="select_multiple" type="select" multiple="true" label="select_multiple">
             <options from_dataset="multiple">
-                <column name="name" index="0"/>
+                <column name="name" index="1"/>
                 <column name="value" index="0"/>
                 <validator type="no_options" message="No data is available in single" />
             </options>
         </param>
-		<param name="collection" type="data_collection" format="tabular" collection_type="list" label="collection"/>
+        <param name="collection" type="data_collection" format="tabular" collection_type="list" label="collection"/>
         <param name="select_collection" type="select" multiple="true" label="select_collection">
             <options from_dataset="collection">
-                <column name="name" index="0"/>
+                <column name="name" index="1"/>
                 <column name="value" index="0"/>
                 <validator type="no_options" message="No data is available in single" />
             </options>
-		</param>
+        </param>
     </inputs>
 
     <outputs>
@@ -39,16 +39,16 @@ echo select_collection '$select_collection' >> '$output'
     <tests>
         <test>
             <param name="single" value="1.tabular" />
-			<param name="select_single" value="chr10" />
+            <param name="select_single" value="chr10" />
             <param name="multiple" value="1.tabular,2.tabular" />
             <param name="select_multiple" value="chr10,7" />
-			<param name="collection">
-			    <collection type="list">
-					<element name="1" value="1.tabular" />
-					<element name="2" value="2.tabular" />
+            <param name="collection">
+                <collection type="list">
+                    <element name="1" value="1.tabular" />
+                    <element name="2" value="2.tabular" />
                 </collection>
-	        </param>
-			<param name="select_collection" value="chr10,7" />
+            </param>
+            <param name="select_collection" value="chr10,7" />
             <output name="output">
                 <assert_contents>
                     <has_text text="select_single chr10" />    
@@ -57,6 +57,26 @@ echo select_collection '$select_collection' >> '$output'
                 </assert_contents>
             </output>
         </test>
+        <!-- test that dynamic selects can be chosen by name -->
+        <test>
+            <param name="single" value="2.tabular" />
+            <param name="select_single" value="68" />
+            <param name="multiple" value="2.tabular" />
+            <param name="select_multiple" value="71,62" />
+            <param name="collection">
+                <collection type="list">
+                    <element name="2" value="2.tabular" />
+                </collection>
+            </param>
+            <param name="select_collection" value="75,58" />
+            <output name="output">
+                <assert_contents>
+                    <has_text text="select_single 1" />    
+                    <has_text text="select_multiple 2,3" />    
+                    <has_text text="select_collection 4,5" />    
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
     </help>
diff --git a/test/integration/test_local_job_cancellation.py b/test/integration/test_local_job_cancellation.py
index 75b866c2551..632269e1439 100644
--- a/test/integration/test_local_job_cancellation.py
+++ b/test/integration/test_local_job_cancellation.py
@@ -91,7 +91,7 @@ class LocalJobCancellationTestCase(CancelsJob, integration_util.IntegrationTestC
 
             state = None
             # Now make sure the job becomes complete.
-            for i in range(100):
+            for _ in range(100):
                 sa_session.refresh(job)
                 state = job.state
                 if state == app.model.Job.states.DELETED:
@@ -99,7 +99,7 @@ class LocalJobCancellationTestCase(CancelsJob, integration_util.IntegrationTestC
                 time.sleep(.1)
 
             # Now make sure the pid is actually killed.
-            for i in range(100):
+            for _ in range(100):
                 if not pid_exists:
                     break
                 pid_exists = psutil.pid_exists(external_id)
diff --git a/test/integration/test_tool_data_delete.py b/test/integration/test_tool_data_delete.py
new file mode 100644
index 00000000000..0b883178c48
--- /dev/null
+++ b/test/integration/test_tool_data_delete.py
@@ -0,0 +1,70 @@
+"""Integration tests for tool data tables that require special configuration.
+
+This file checks API endpoints that require different non-default Galaxy
+configuration options, in particular the DELETE endpoint.
+To avoid altering the '.loc' files in test/functional/tool-data, these files are
+copied to a temp directory and then used by the integration test.
+"""
+
+import json
+import os
+import shutil
+import time
+
+from requests import delete
+
+
+from galaxy_test.base.populators import DatasetPopulator
+from galaxy_test.driver import integration_util
+
+
+THIS_DIR = os.path.dirname(__file__)
+SOURCE_TOOL_DATA_DIRECTORY = os.path.join(THIS_DIR, os.pardir, "functional", "tool-data")
+
+
+class AdminToolDataIntegrationTestCase(integration_util.IntegrationTestCase):
+    require_admin_user = True
+
+    def setUp(self):
+        super().setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+
+    @classmethod
+    def configure_temp_tool_data_dir(cls):
+        cls.temp_tool_data_dir = cls.temp_config_dir("tool-data")
+        cls.temp_tool_data_tables_file = os.path.join(cls.temp_tool_data_dir, "sample_tool_data_tables.xml")
+        shutil.copytree(SOURCE_TOOL_DATA_DIRECTORY, cls.temp_tool_data_dir)
+        cls._test_driver.temp_directories.append(cls.temp_tool_data_dir)
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        cls.configure_temp_tool_data_dir()
+        config["tool_data_path"] = cls.temp_tool_data_dir
+        config["tool_data_table_config_path"] = cls.temp_tool_data_tables_file
+
+    def test_admin_delete_data_table_entry(self):
+        show_response = self._get("tool_data/testbeta")
+        original_count = len(show_response.json()["fields"])
+
+        history_id = self.dataset_populator.new_history()
+        payload = self.dataset_populator.run_tool_payload(
+            tool_id="data_manager",
+            inputs={"ignored_value": "moo"},
+            history_id=history_id,
+        )
+        create_response = self._post("tools", data=payload)
+        create_response.raise_for_status()
+        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+        time.sleep(2)
+        show_response = self._get("tool_data/testbeta")
+        updated_fields = show_response.json()["fields"]
+        self.assertEquals(len(updated_fields), original_count + 1)
+        new_field = updated_fields[-1]
+        url = self._api_url(f"tool_data/testbeta?key={self.galaxy_interactor.api_key}")
+        delete_response = delete(url, data=json.dumps({"values": "\t".join(new_field)}))
+        delete_response.raise_for_status()
+        time.sleep(2)
+        show_response = self._get("tool_data/testbeta")
+        show_response.raise_for_status()
+        updated_fields = show_response.json()["fields"]
+        assert len(updated_fields) == original_count
diff --git a/test/integration/test_upload_configuration_options.py b/test/integration/test_upload_configuration_options.py
index c25e4e08c23..7f1d9feaf3b 100644
--- a/test/integration/test_upload_configuration_options.py
+++ b/test/integration/test_upload_configuration_options.py
@@ -876,7 +876,7 @@ class FetchByPathTestCase(BaseUploadContentConfigurationTestCase):
         }
         self.dataset_populator.fetch(payload)
         libraries = self.library_populator.get_libraries()
-        matching = [l for l in libraries if l["name"] == "My Cool Library"]
+        matching = [library for library in libraries if library["name"] == "My Cool Library"]
         assert len(matching) == 1
         library = matching[0]
         dataset = self.library_populator.get_library_contents_with_path(library["id"], "/file1")
diff --git a/test/integration/test_workflow_handler_configuration.py b/test/integration/test_workflow_handler_configuration.py
index 4b59d625841..42c80cff24b 100644
--- a/test/integration/test_workflow_handler_configuration.py
+++ b/test/integration/test_workflow_handler_configuration.py
@@ -115,7 +115,7 @@ class BaseWorkflowHandlerConfigurationTestCase(integration_util.IntegrationTestC
         request["inputs"] = dumps(index_map)
         request["inputs_by"] = 'step_index'
         url = "workflows/%s/invocations" % (workflow_id)
-        for i in range(n):
+        for _ in range(n):
             self._post(url, data=request)
 
     def _get_workflow_invocations(self):
diff --git a/test/integration/test_workflow_refactoring.py b/test/integration/test_workflow_refactoring.py
index 852484cf8d4..d842e738b94 100644
--- a/test/integration/test_workflow_refactoring.py
+++ b/test/integration/test_workflow_refactoring.py
@@ -826,10 +826,10 @@ def _step_with_label(native_dict, label):
 class MockTrans(ProvidesAppContext):
 
     def __init__(self, app, user):
-        self.app = app
+        self._app = app
         self.user = user
         self.history = None
 
     @property
-    def security(self):
-        return self.app.security
+    def app(self):
+        return self._app
diff --git a/test/integration_selenium/test_history_import_export_ftp.py b/test/integration_selenium/test_history_import_export_ftp.py
new file mode 100644
index 00000000000..faa82462f8c
--- /dev/null
+++ b/test/integration_selenium/test_history_import_export_ftp.py
@@ -0,0 +1,65 @@
+import os
+
+from .framework import (
+    selenium_test,
+    SeleniumIntegrationTestCase
+)
+
+
+class HistoryImportExportFtpSeleniumIntegrationTestCase(SeleniumIntegrationTestCase):
+    ensure_registered = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        ftp_dir = cls.ftp_dir()
+        os.makedirs(ftp_dir)
+        config["ftp_upload_dir"] = ftp_dir
+        config["ftp_upload_site"] = "ftp://ftp.galaxyproject.com"
+
+    @classmethod
+    def ftp_dir(cls):
+        return cls.temp_config_dir("ftp")
+
+    @selenium_test
+    def test_history_import_export(self):
+        email = self.get_logged_in_user()["email"]
+        user_ftp_dir = os.path.join(self.ftp_dir(), email)
+        os.makedirs(user_ftp_dir)
+
+        gx_selenium_context = self
+        gx_selenium_context.perform_upload_of_pasted_content("my cool content")
+        gx_selenium_context.history_panel_wait_for_hid_ok(1)
+        gx_selenium_context.click_history_options()
+        gx_selenium_context.components.history_panel.options_show_export_history_to_file.wait_for_and_click()
+        history_export = gx_selenium_context.components.history_export
+        files_dialog = gx_selenium_context.components.files_dialog
+
+        # we land on link version, but go to export to file
+        history_export.export_link.wait_for_visible()
+        history_export.tab_export_to_file.wait_for_and_click()
+        history_export.export_link.wait_for_absent_or_hidden()
+        history_export.directory_input.wait_for_and_click()
+        files_dialog.ftp_row.wait_for_and_click()
+        history_export.name_input.wait_for_and_send_keys("my_export.tar.gz")
+        history_export.export_button.wait_for_and_click()
+
+        history_export.running.wait_for_visible()
+        history_export.running.wait_for_absent(wait_type=gx_selenium_context.wait_types.JOB_COMPLETION)
+        history_export.success_message.wait_for_visible()
+
+        gx_selenium_context.navigate_to_histories_page()
+        gx_selenium_context.components.histories.import_button.wait_for_and_click()
+        history_import = gx_selenium_context.components.history_import
+        history_import.radio_button_remote_files.wait_for_and_click()
+        files_dialog.ftp_row.wait_for_and_click()
+        files_dialog.row(uri="gxftp://my_export.tar.gz").wait_for_and_click()
+
+        history_import.import_button.wait_for_and_click()
+
+        history_import.running.wait_for_visible()
+        history_import.running.wait_for_absent(wait_type=gx_selenium_context.wait_types.JOB_COMPLETION)
+        history_import.success_message.wait_for_visible()
+
+        gx_selenium_context.navigate_to_histories_page()
+        newest_history_name = gx_selenium_context.histories_get_history_names()[0]
+        assert newest_history_name.startswith("imported from archive")
diff --git a/test/manual/workflows_scaling.py b/test/manual/workflows_scaling.py
index 6c9c49e173c..36faad66669 100644
--- a/test/manual/workflows_scaling.py
+++ b/test/manual/workflows_scaling.py
@@ -63,7 +63,7 @@ def main(argv=None):
 
     target = functools.partial(_run, args, gi, workflow_id, uuid)
     threads = []
-    for i in range(args.workflow_count):
+    for _ in range(args.workflow_count):
         t = Thread(target=target)
         t.daemon = True
         t.start()
diff --git a/test/unit/data/security/test_id_encode_decode.py b/test/unit/data/security/test_id_encode_decode.py
index 00693f5d062..55422c28aac 100644
--- a/test/unit/data/security/test_id_encode_decode.py
+++ b/test/unit/data/security/test_id_encode_decode.py
@@ -119,7 +119,7 @@ def test_encode_dict():
 
 def test_guid_generation():
     guids = set()
-    for i in range(100):
+    for _ in range(100):
         guids.add(test_helper_1.get_new_guid())
     assert len(guids) == 100  # Not duplicate guids generated.
 
diff --git a/test/unit/data/test_galaxy_mapping.py b/test/unit/data/test_galaxy_mapping.py
index 2b0b5ecc301..1299a6e48cd 100644
--- a/test/unit/data/test_galaxy_mapping.py
+++ b/test/unit/data/test_galaxy_mapping.py
@@ -302,7 +302,7 @@ class MappingTests(BaseModelTestCase):
 
         u = model.User(email="mary2@example.com", password="password")
         lf = model.LibraryFolder(name="RootFolder")
-        l = model.Library(name="Library1", root_folder=lf)
+        library = model.Library(name="Library1", root_folder=lf)
         ld1 = model.LibraryDataset()
         ld2 = model.LibraryDataset()
 
@@ -312,7 +312,7 @@ class MappingTests(BaseModelTestCase):
         c1 = model.DatasetCollection(collection_type="pair")
         dce1 = model.DatasetCollectionElement(collection=c1, element=ldda1)
         dce2 = model.DatasetCollectionElement(collection=c1, element=ldda2)
-        self.persist(u, l, lf, ld1, ld2, c1, ldda1, ldda2, dce1, dce2)
+        self.persist(u, library, lf, ld1, ld2, c1, ldda1, ldda2, dce1, dce2)
 
         # TODO:
         # loaded_dataset_collection = self.query( model.DatasetCollection ).filter( model.DatasetCollection.name == "LibraryCollectionTest1" ).first()
diff --git a/test/unit/data/test_model_copy.py b/test/unit/data/test_model_copy.py
index be76adcb3b1..6ac92cc66ac 100644
--- a/test/unit/data/test_model_copy.py
+++ b/test/unit/data/test_model_copy.py
@@ -34,7 +34,7 @@ def test_history_dataset_copy(num_datasets=NUM_DATASETS, include_metadata_file=I
         print("history copied %s" % history_copy_timer)
         assert new_history.name == "HistoryCopyHistory1"
         assert new_history.user == old_history.user
-        for i, hda in enumerate(new_history.active_datasets):
+        for hda in new_history.active_datasets:
             assert hda.get_size() == 3
             if include_metadata_file:
                 _check_metadata_file(hda)
@@ -84,7 +84,7 @@ def test_history_collection_copy(list_size=NUM_DATASETS):
         new_history = old_history.copy(target_user=old_history.user)
         print("history copied %s" % history_copy_timer)
 
-        for i, hda in enumerate(new_history.active_datasets):
+        for hda in new_history.active_datasets:
             assert hda.get_size() == 3
             annotation_str = hda.get_item_annotation_str(model.context, old_history.user, hda)
             assert annotation_str == "annotation #%d" % hda.hid, annotation_str
diff --git a/test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py b/test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
index bee466b8796..4cea416e3ce 100644
--- a/test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
+++ b/test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
@@ -94,10 +94,10 @@ class TestDynamicToolDestination(unittest.TestCase):
     # =======================map_tool_to_destination()================================
 
     @log_capture()
-    def test_brokenDestYML(self, l):
+    def test_brokenDestYML(self, lc):
         self.assertRaises(JobMappingException, map_tool_to_destination, runJob, theApp, vanillaTool, "user@email.com", True, broken_default_dest_path, job_conf_path)
 
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
@@ -106,11 +106,11 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_filesize_empty(self, l):
+    def test_filesize_empty(self, lc):
         self.assertRaises(JobMappingException, map_tool_to_destination, emptyJob, theApp, vanillaTool, "user@email.com", True, path, job_conf_path)
         self.assertRaises(JobMappingException, map_tool_to_destination, emptyJob, theApp, vanillaTool, "user@email.com", True, priority_path, job_conf_path)
 
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.empty'),
@@ -125,11 +125,11 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_filesize_zero(self, l):
+    def test_filesize_zero(self, lc):
         self.assertRaises(JobMappingException, map_tool_to_destination, zeroJob, theApp, vanillaTool, "user@email.com", True, path, job_conf_path)
         self.assertRaises(JobMappingException, map_tool_to_destination, zeroJob, theApp, vanillaTool, "user@email.com", True, priority_path, job_conf_path)
 
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Total size: 0.00 B'),
@@ -142,11 +142,11 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_filesize_fail(self, l):
+    def test_filesize_fail(self, lc):
         self.assertRaises(JobMappingException, map_tool_to_destination, failJob, theApp, vanillaTool, "user@email.com", True, path, job_conf_path)
         self.assertRaises(JobMappingException, map_tool_to_destination, failJob, theApp, vanillaTool, "user@email.com", True, priority_path, job_conf_path)
 
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test1.full'),
@@ -161,13 +161,13 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_filesize_run(self, l):
+    def test_filesize_run(self, lc):
         job = map_tool_to_destination(runJob, theApp, vanillaTool, "user@email.com", True, path, job_conf_path)
         self.assertEqual(job, 'Destination1')
         priority_job = map_tool_to_destination(runJob, theApp, vanillaTool, "user@email.com", True, priority_path, job_conf_path)
         self.assertEqual(priority_job, 'Destination1_high')
 
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test3.full'),
@@ -184,13 +184,13 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_default_tool(self, l):
+    def test_default_tool(self, lc):
         job = map_tool_to_destination(runJob, theApp, defaultTool, "user@email.com", True, path, job_conf_path)
         self.assertEqual(job, 'cluster_default')
         priority_job = map_tool_to_destination(runJob, theApp, defaultTool, "user@email.com", True, priority_path, job_conf_path)
         self.assertEqual(priority_job, 'cluster_default_high')
 
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'test_tooldefault' not specified in config. Using default destination."),
@@ -203,13 +203,13 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_arguments_tool(self, l):
+    def test_arguments_tool(self, lc):
         job = map_tool_to_destination(argJob, theApp, argTool, "user@email.com", True, path, job_conf_path)
         self.assertEqual(job, 'Destination6')
         priority_job = map_tool_to_destination(argJob, theApp, argTool, "user@email.com", True, priority_path, job_conf_path)
         self.assertEqual(priority_job, 'Destination6_med')
 
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_arguments' with 'Destination6'."),
@@ -220,13 +220,13 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_arguments_arg_not_found(self, l):
+    def test_arguments_arg_not_found(self, lc):
         job = map_tool_to_destination(argNotFoundJob, theApp, argTool, "user@email.com", True, path, job_conf_path)
         self.assertEqual(job, 'cluster_default')
         priority_job = map_tool_to_destination(argNotFoundJob, theApp, argTool, "user@email.com", True, priority_path, job_conf_path)
         self.assertEqual(priority_job, 'cluster_default_high')
 
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_arguments' with 'cluster_default'."),
@@ -237,13 +237,13 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_tool_not_found(self, l):
+    def test_tool_not_found(self, lc):
         job = map_tool_to_destination(runJob, theApp, unTool, "user@email.com", True, path, job_conf_path)
         self.assertEqual(job, 'cluster_default')
         priority_job = map_tool_to_destination(runJob, theApp, unTool, "user@email.com", True, priority_path, job_conf_path)
         self.assertEqual(priority_job, 'cluster_default_high')
 
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'unregistered' not specified in config. Using default destination."),
@@ -256,13 +256,13 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_fasta(self, l):
+    def test_fasta(self, lc):
         job = map_tool_to_destination(dbJob, theApp, dbTool, "user@email.com", True, path, job_conf_path)
         self.assertEqual(job, 'Destination4')
         priority_job = map_tool_to_destination(dbJob, theApp, dbTool, "user@email.com", True, priority_path, job_conf_path)
         self.assertEqual(priority_job, 'Destination4_high')
 
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.fasta'),
@@ -277,13 +277,13 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_fasta_count(self, l):
+    def test_fasta_count(self, lc):
         job = map_tool_to_destination(dbcountJob, theApp, dbTool, "user@email.com", True, path, job_conf_path)
         self.assertEqual(job, 'Destination4')
         priority_job = map_tool_to_destination(dbcountJob, theApp, dbTool, "user@email.com", True, priority_path, job_conf_path)
         self.assertEqual(priority_job, 'Destination4_high')
 
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Loading file: input1' + script_dir + '/data/test.fasta'),
@@ -298,42 +298,42 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_no_verbose(self, l):
+    def test_no_verbose(self, lc):
         job = map_tool_to_destination(runJob, theApp, noVBTool, "user@email.com", True, no_verbose_path, job_conf_path)
         self.assertEqual(job, 'Destination1')
 
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_no_verbose' with 'Destination1'.")
         )
 
     @log_capture()
-    def test_authorized_user(self, l):
+    def test_authorized_user(self, lc):
         job = map_tool_to_destination(runJob, theApp, usersTool, "user@email.com", True, users_test_path, job_conf_path)
         self.assertEqual(job, 'special_cluster')
 
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_users' with 'special_cluster'."),
         )
 
     @log_capture()
-    def test_unauthorized_user(self, l):
+    def test_unauthorized_user(self, lc):
         job = map_tool_to_destination(runJob, theApp, usersTool, "userblah@email.com", True, users_test_path, job_conf_path)
         self.assertEqual(job, 'lame_cluster')
 
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Running 'test_users' with 'lame_cluster'.")
         )
 
 # ================================Invalid yaml files==============================
     @log_capture()
-    def test_no_file(self, l):
+    def test_no_file(self, lc):
         self.assertRaises(IOError, dt.parse_yaml, path="")
-        l.check_present()
+        lc.check_present()
 
     @log_capture()
-    def test_bad_nice(self, l):
+    def test_bad_nice(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest11, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
              "Running config validation..."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
@@ -342,67 +342,67 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_empty_file(self, l):
+    def test_empty_file(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest2, job_conf_path=job_conf_path, test=True), {})
 
     @log_capture()
-    def test_no_tool_name(self, l):
+    def test_no_tool_name(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest3, job_conf_path=job_conf_path, test=True), yt.iv3dict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Malformed YML; expected job name, but found a list instead!'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_no_rule_type(self, l):
+    def test_no_rule_type(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest4, job_conf_path=job_conf_path, test=True), yt.ivDict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No rule_type found for rule 1 in 'spades'."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_no_rule_lower_bound(self, l):
+    def test_no_rule_lower_bound(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest51, job_conf_path=job_conf_path, test=True), yt.ivDict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing bounds for rule 1 in 'spades'. Ignoring rule."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_no_rule_upper_bound(self, l):
+    def test_no_rule_upper_bound(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest52, job_conf_path=job_conf_path, test=True), yt.ivDict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing bounds for rule 1 in 'spades'. Ignoring rule."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_no_rule_arg(self, l):
+    def test_no_rule_arg(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest53, job_conf_path=job_conf_path, test=True), yt.ivDict53)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Found a fail_message for rule 1 in 'spades', but destination is not 'fail'! Setting destination to 'fail'."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_bad_rule_type(self, l):
+    def test_bad_rule_type(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest6, job_conf_path=job_conf_path, test=True), yt.ivDict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Unrecognized rule_type 'iencs' found in 'spades'. Ignoring..."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_no_err_msg(self, l):
+    def test_no_err_msg(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest91, job_conf_path=job_conf_path, test=True), yt.iv91dict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No nice_value found for rule 1 in 'spades'. Setting nice_value to 0."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'spades'. Adding generic fail_message."),
@@ -410,18 +410,18 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_no_default_dest(self, l):
+    def test_no_default_dest(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest7, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_invalid_category(self, l):
+    def test_invalid_category(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest8, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Unrecognized category 'ice_cream' found in config file!"),
@@ -429,9 +429,9 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_arguments_no_err_msg(self, l):
+    def test_arguments_no_err_msg(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest12, job_conf_path=job_conf_path, test=True), yt.iv12dict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
              "Missing a fail_message for rule 1 in 'spades'. Adding generic fail_message."),
@@ -439,9 +439,9 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_arguments_no_args(self, l):
+    def test_arguments_no_args(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest131, job_conf_path=job_conf_path, test=True), yt.iv131dict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
              "No arguments found for rule 1 in 'spades' despite being of type arguments. Ignoring rule."),
@@ -449,99 +449,99 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_arguments_no_arg(self, l):
+    def test_arguments_no_arg(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest132, job_conf_path=job_conf_path, test=True), yt.iv132dict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Found a fail_message for rule 1 in 'spades', but destination is not 'fail'! Setting destination to 'fail'."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_return_bool_for_multiple_jobs(self, l):
+    def test_return_bool_for_multiple_jobs(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest133, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'smalt'.")
         )
 
     @log_capture()
-    def test_return_rule_for_multiple_jobs(self, l):
+    def test_return_rule_for_multiple_jobs(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest133, job_conf_path=job_conf_path, test=True), yt.iv133dict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'smalt'. Adding generic fail_message."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_return_bool_for_no_destination(self, l):
+    def test_return_bool_for_no_destination(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest134, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No destination specified for rule 1 in 'spades'.")
         )
 
     @log_capture()
-    def test_return_rule_for_no_destination(self, l):
+    def test_return_rule_for_no_destination(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest134, job_conf_path=job_conf_path, test=True), yt.iv134dict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No destination specified for rule 1 in 'spades'. Ignoring..."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_return_rule_for_reversed_bounds(self, l):
+    def test_return_rule_for_reversed_bounds(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest135, job_conf_path=job_conf_path, test=True), yt.iv135dict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "lower_bound exceeds upper_bound for rule 1 in 'spades'. Reversing bounds."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_return_bool_for_missing_tool_fields(self, l):
+    def test_return_bool_for_missing_tool_fields(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest136, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'spades' does not have rules nor a default_destination!")
         )
 
     @log_capture()
-    def test_return_rule_for_missing_tool_fields(self, l):
+    def test_return_rule_for_missing_tool_fields(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest136, job_conf_path=job_conf_path, test=True), yt.iv136dict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'spades' does not have rules nor a default_destination!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_return_bool_for_blank_tool(self, l):
+    def test_return_bool_for_blank_tool(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest137, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Config section for tool 'spades' is blank!")
         )
 
     @log_capture()
-    def test_return_rule_for_blank_tool(self, l):
+    def test_return_rule_for_blank_tool(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest137, job_conf_path=job_conf_path, test=True), yt.iv137dict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Config section for tool 'spades' is blank!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_return_bool_for_malformed_users(self, l):
+    def test_return_bool_for_malformed_users(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest138, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry '123' in users for rule 1 in tool 'spades' is in an invalid format!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invaliduser.email@com' for rule 1 in tool 'spades' is in an invalid format!")
         )
 
     @log_capture()
-    def test_return_rule_for_malformed_users(self, l):
+    def test_return_rule_for_malformed_users(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest138, job_conf_path=job_conf_path, test=True), yt.iv138dict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry '123' in users for rule 1 in tool 'spades' is in an invalid format! Ignoring entry."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invaliduser.email@com' for rule 1 in tool 'spades' is in an invalid format! Ignoring email."),
@@ -549,34 +549,34 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_return_bool_for_no_users(self, l):
+    def test_return_bool_for_no_users(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest139, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Couldn't find a list under 'users:'!")
         )
 
     @log_capture()
-    def test_return_rule_for_no_users(self, l):
+    def test_return_rule_for_no_users(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest139, job_conf_path=job_conf_path, test=True), yt.iv139dict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Couldn't find a list under 'users:'! Ignoring rule."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_return_bool_for_malformed_user_email(self, l):
+    def test_return_bool_for_malformed_user_email(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest140, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user2@com' for rule 2 in tool 'spades' is in an invalid format!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user1@com' for rule 2 in tool 'spades' is in an invalid format!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'!")
         )
 
     @log_capture()
-    def test_return_rule_for_malformed_user_email(self, l):
+    def test_return_rule_for_malformed_user_email(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest140, job_conf_path=job_conf_path, test=True), yt.iv140dict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user2@com' for rule 2 in tool 'spades' is in an invalid format! Ignoring email."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user1@com' for rule 2 in tool 'spades' is in an invalid format! Ignoring email."),
@@ -585,18 +585,18 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_return_bool_for_empty_users(self, l):
+    def test_return_bool_for_empty_users(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest141, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'!")
         )
 
     @log_capture()
-    def test_return_rule_for_empty_users(self, l):
+    def test_return_rule_for_empty_users(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest141, job_conf_path=job_conf_path, test=True), yt.iv141dict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format! Ignoring entry."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format! Ignoring entry."),
@@ -605,42 +605,42 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_return_bool_for_bad_num_input_datasets_bounds(self, l):
+    def test_return_bool_for_bad_num_input_datasets_bounds(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest142, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "lower_bound exceeds upper_bound for rule 1 in 'smalt'.")
         )
 
     @log_capture()
-    def test_return_rule_for_bad_num_input_datasets_bound(self, l):
+    def test_return_rule_for_bad_num_input_datasets_bound(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest142, job_conf_path=job_conf_path, test=True), yt.iv142dict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound! Setting lower_bound to 0!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_return_bool_for_worse_num_input_datasets_bounds(self, l):
+    def test_return_bool_for_worse_num_input_datasets_bounds(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest143, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound!")
         )
 
     @log_capture()
-    def test_return_rule_for_worse_num_input_datasets_bound(self, l):
+    def test_return_rule_for_worse_num_input_datasets_bound(self, lc):
         self.assertEqual(dt.parse_yaml(path=yt.ivYMLTest143, job_conf_path=job_conf_path, test=True), yt.iv143dict)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound! Setting lower_bound to 0!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_tool_without_low_default_destination(self, l):
+    def test_tool_without_low_default_destination(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest146, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid priority 'low' for rule 1 in 'smalt'. Ignoring..."),
@@ -648,9 +648,9 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_tool_with_invalid_priority_destination(self, l):
+    def test_tool_with_invalid_priority_destination(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest147, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid priority 'mine' for rule 1 in 'smalt'. Ignoring..."),
@@ -658,18 +658,18 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_not_all_priorities_in_tool(self, l):
+    def test_not_all_priorities_in_tool(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest149, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_rule_destination_not_in_job_conf(self, l):
+    def test_rule_destination_not_in_job_conf(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest150, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Destination for 'blegh', rule 1: 'fake_destination' does not exist in job configuration. Ignoring..."),
@@ -677,9 +677,9 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_tool_default_destination_not_in_job_conf_with_no_rules(self, l):
+    def test_tool_default_destination_not_in_job_conf_with_no_rules(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest151, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'not_true_destination' does not appear in the job configuration."),
@@ -688,9 +688,9 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_default_destination_not_in_job_conf(self, l):
+    def test_default_destination_not_in_job_conf(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest152, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'no_such_dest' does not appear in the job configuration."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
@@ -698,9 +698,9 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_rule_destination_without_priority_not_in_job_conf(self, l):
+    def test_rule_destination_without_priority_not_in_job_conf(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest153, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Destination for 'blegh', rule 1: 'fake_destination' does not exist in job configuration. Ignoring..."),
@@ -708,9 +708,9 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_tool_default_destination_without_priority_not_in_job_conf_with_no_rules(self, l):
+    def test_tool_default_destination_without_priority_not_in_job_conf_with_no_rules(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest154, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'not_true_destination' does not appear in the job configuration."),
@@ -719,18 +719,18 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_default_destination_without_priority_not_in_job_conf(self, l):
+    def test_default_destination_without_priority_not_in_job_conf(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest155, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'no_such_dest' does not appear in the job configuration."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_tool_rule_priority_does_not_exist(self, l):
+    def test_tool_rule_priority_does_not_exist(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest156, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid priority 'notAPriority' for rule 1 in 'aTool'. Ignoring..."),
@@ -738,9 +738,9 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_tool_default_destination_priority_does_not_exist(self, l):
+    def test_tool_default_destination_priority_does_not_exist(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest157, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid default destination priority 'notAPriority' for 'aTool'."),
@@ -748,9 +748,9 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_tool_default_destination_not_in_job_conf(self, l):
+    def test_tool_default_destination_not_in_job_conf(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest158, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default_priority section found in config. Setting 'med' as default priority."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'not_true_destination' does not appear in the job configuration."),
@@ -758,131 +758,131 @@ class TestDynamicToolDestination(unittest.TestCase):
         )
 
     @log_capture()
-    def test_tool_default_destination_without_priority_not_in_job_conf(self, l):
+    def test_tool_default_destination_without_priority_not_in_job_conf(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest159, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'not_true_destination' does not appear in the job configuration."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_empty_priority_dict(self, l):
+    def test_empty_priority_dict(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest163, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No global default destinations specified in config!"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_default_dest_is_string_but_priorities_used_in_rule(self, l):
+    def test_default_dest_is_string_but_priorities_used_in_rule(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest161, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid priority 'med' for rule 1 in 'blah'. Ignoring..."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_default_dest_is_string_but_priorities_used_in_tool_default_dest(self, l):
+    def test_default_dest_is_string_but_priorities_used_in_tool_default_dest(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest162, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid default destination priority 'med' for 'blah'."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_typo_in_str_default_dest(self, l):
+    def test_typo_in_str_default_dest(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest164, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'cluster-kow' does not appear in the job configuration. Did you mean 'cluster_low'?"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_typo_in_dict_default_dest(self, l):
+    def test_typo_in_dict_default_dest(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest165, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'cluster_kow' does not appear in the job configuration. Did you mean 'cluster_low'?"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_typo_in_dict_tool_default_dest(self, l):
+    def test_typo_in_dict_tool_default_dest(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest166, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'cluster_defaut' does not appear in the job configuration. Did you mean 'cluster_default'?"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_typo_in_str_tool_default_dest(self, l):
+    def test_typo_in_str_tool_default_dest(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest167, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'Destination_3_med' does not appear in the job configuration. Did you mean 'Destination3_med'?"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_typo_in_str_tool_rule_dest(self, l):
+    def test_typo_in_str_tool_rule_dest(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest168, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Destination for 'blah', rule 1: 'thig' does not exist in job configuration. Did you mean 'things'? Ignoring..."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_typo_in_dict_tool_rule_dest(self, l):
+    def test_typo_in_dict_tool_rule_dest(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest169, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Destination for 'blah', rule 1: 'even_lamerr_cluster' does not exist in job configuration. Did you mean 'even_lamer_cluster'? Ignoring..."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_typo_in_case(self, l):
+    def test_typo_in_case(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest170, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'destinationf' does not appear in the job configuration. Did you mean 'DestinationF'?"),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_invalid_verbose_value(self, l):
+    def test_invalid_verbose_value(self, lc):
         dt.parse_yaml(path=yt.ivYMLTest171, job_conf_path=job_conf_path, test=True)
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Verbose value 'notavalue' is not True or False! Falling back to verbose..."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
         )
 
     @log_capture()
-    def test_invalid_default_dest_valid_tool_default_dest_bool(self, l):
+    def test_invalid_default_dest_valid_tool_default_dest_bool(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest172, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination 'fake_destination' does not appear in the job configuration."),
         )
 
     @log_capture()
-    def test_valid_default_dest_invalid_tool_default_dest_bool(self, l):
+    def test_valid_default_dest_invalid_tool_default_dest_bool(self, lc):
         self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest173, job_conf_path=job_conf_path, test=True, return_bool=True))
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Default destination for 'blah': 'fake_destination' does not appear in the job configuration."),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'blah' does not have rules nor a default_destination!"),
         )
 
 # ================================Valid yaml files==============================
     @log_capture()
-    def test_parse_valid_yml(self, l):
+    def test_parse_valid_yml(self, lc):
         self.assertEqual(dt.parse_yaml(yt.vYMLTest1, job_conf_path=job_conf_path, test=True), yt.vdictTest1_yml)
         self.assertEqual(dt.parse_yaml(yt.vYMLTest2, job_conf_path=job_conf_path, test=True), yt.vdictTest2_yml)
         self.assertEqual(dt.parse_yaml(yt.vYMLTest3, job_conf_path=job_conf_path, test=True), yt.vdictTest3_yml)
@@ -899,7 +899,7 @@ class TestDynamicToolDestination(unittest.TestCase):
         self.assertTrue(dt.parse_yaml(yt.vYMLTest164, job_conf_path=job_conf_path, test=True, return_bool=True))
         self.assertEqual(dt.parse_yaml(yt.vYMLTest164, job_conf_path=job_conf_path, test=True), yt.vdictTest164_yml)
 
-        l.check_present(
+        lc.check_present(
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
             ('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
@@ -942,8 +942,7 @@ class TestDynamicToolDestination(unittest.TestCase):
         self.assertEqual(dt.str_to_bytes("1 YB"), valueY)
 
 # ==============================Testing bytes_to_str=============================
-    @log_capture()
-    def test_bytes_to_str_invalid(self, l):
+    def test_bytes_to_str_invalid(self):
         testValue = ""
         self.assertRaises(ValueError, dt.bytes_to_str, testValue)
         testValue = "5564fads"
diff --git a/test/unit/jobs/test_rule_helper.py b/test/unit/jobs/test_rule_helper.py
index aedf595947a..82b51c30304 100644
--- a/test/unit/jobs/test_rule_helper.py
+++ b/test/unit/jobs/test_rule_helper.py
@@ -102,7 +102,7 @@ def test_job_hash_unique_by_default():
     rule_helper = __rule_helper()
     job1, job2 = __two_jobs_in_a_history()
 
-    rule_helper.job_hash(job1) != rule_helper.job_hash(job2)
+    assert rule_helper.job_hash(job1) != rule_helper.job_hash(job2)
 
 
 def test_job_hash_history():
@@ -163,7 +163,7 @@ def __two_jobs():
 
 
 def __do_a_bunch(work):
-    for i in range(20):
+    for _ in range(20):
         work()
 
 
diff --git a/test/unit/jobs/test_runner_local.py b/test/unit/jobs/test_runner_local.py
index ab37d781be6..59d2bdff99c 100644
--- a/test/unit/jobs/test_runner_local.py
+++ b/test/unit/jobs/test_runner_local.py
@@ -161,7 +161,7 @@ class MockJobWrapper:
     def wait_for_external_id(self):
         """Test method for waiting until an external id has been registered."""
         external_id = None
-        for i in range(50):
+        for _ in range(50):
             external_id = self.job.job_runner_external_id
             if external_id:
                 break
diff --git a/test/unit/managers/test_DatasetManager.py b/test/unit/managers/test_DatasetManager.py
index f8b5a039fc9..3e00699f568 100644
--- a/test/unit/managers/test_DatasetManager.py
+++ b/test/unit/managers/test_DatasetManager.py
@@ -233,8 +233,8 @@ class DatasetSerializerTestCase(BaseTestCase):
         self.log('should have a serializer for all serializable keys')
         for key in self.dataset_serializer.serializable_keyset:
             instantiated_attribute = getattr(dataset, key, None)
-            if not ((key in self.dataset_serializer.serializers) or
-                    (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))):
+            if not ((key in self.dataset_serializer.serializers)
+                    or (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))):
                 self.fail(f'no serializer for: {key} ({instantiated_attribute})')
         else:
             self.assertTrue(True, 'all serializable keys have a serializer')
diff --git a/test/unit/managers/test_HDAManager.py b/test/unit/managers/test_HDAManager.py
index 113c45bddc0..a4068918957 100644
--- a/test/unit/managers/test_HDAManager.py
+++ b/test/unit/managers/test_HDAManager.py
@@ -238,13 +238,13 @@ class HDAManagerTestCase(HDATestCase):
         accessible = self.hda_manager.get_accessible(item1.id, owner, current_history=self.trans.history)
         self.assertEqual(accessible, item1)
 
-        self.log("after setting a dataset to private (one user) permissions, " +
-            "access should be not allowed for other users")
+        self.log("after setting a dataset to private (one user) permissions, "
+            + "access should be not allowed for other users")
         self.assertRaises(exceptions.ItemAccessibilityException,
             self.hda_manager.get_accessible, item1.id, non_owner, current_history=self.trans.history)
 
-        self.log("a copy of a restricted dataset in another users history should be inaccessible even to " +
-            "the histories owner")
+        self.log("a copy of a restricted dataset in another users history should be inaccessible even to "
+            + "the histories owner")
         history2 = self.history_manager.create(name='history2', user=non_owner)
         self.trans.set_history(history2)
         item2 = self.hda_manager.copy(item1, history=history2)
@@ -300,14 +300,14 @@ class HDAManagerTestCase(HDATestCase):
         dataset_owner = self.user_manager.create(**user3_data)
         self.dataset_manager.permissions.set_private_to_one_user(dataset1, dataset_owner)
 
-        self.log("anonymous users should not be able to access datasets within their own histories if " +
-            "permissions do not allow")
+        self.log("anonymous users should not be able to access datasets within their own histories if "
+            + "permissions do not allow")
         self.assertFalse(self.hda_manager.is_accessible(item1, anon_user))
         self.assertRaises(exceptions.ItemAccessibilityException,
             self.hda_manager.error_unless_accessible, item1, anon_user)
 
-        self.log("those users with access permissions should still be allowed access to datasets " +
-            "within anon users' histories")
+        self.log("those users with access permissions should still be allowed access to datasets "
+            + "within anon users' histories")
         self.assertTrue(self.hda_manager.is_accessible(item1, dataset_owner))
 
     def test_error_if_uploading(self):
@@ -380,15 +380,15 @@ class HDASerializerTestCase(HDATestCase):
 
         # skip metadata for this test
         def is_metadata(key):
-            return (key == 'metadata' or
-                key.startswith('metadata_'))
+            return (key == 'metadata'
+                or key.startswith('metadata_'))
 
         self.log('should have a serializer for all serializable keys')
         for key in self.hda_serializer.serializable_keyset:
             instantiated_attribute = getattr(hda, key, None)
-            if not ((key in self.hda_serializer.serializers) or
-                   (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS)) or
-                   (is_metadata(key))):
+            if not ((key in self.hda_serializer.serializers)
+                   or (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))
+                   or (is_metadata(key))):
                 self.fail(f'no serializer for: {key} ({instantiated_attribute})')
         else:
             self.assertTrue(True, 'all serializable keys have a serializer')
diff --git a/test/unit/managers/test_HDCAManager.py b/test/unit/managers/test_HDCAManager.py
index a5d2ca632a0..7ac099f0466 100644
--- a/test/unit/managers/test_HDCAManager.py
+++ b/test/unit/managers/test_HDCAManager.py
@@ -87,8 +87,8 @@ class HDCASerializerTestCase(HDCATestCase):
         self.log('should have a serializer for all serializable keys')
         for key in serializer.serializable_keyset:
             instantiated_attribute = getattr(item, key, None)
-            if not ((key in serializer.serializers) or
-                   (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))):
+            if not ((key in serializer.serializers)
+                   or (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))):
                 self.fail(f'no serializer for: {key} ({instantiated_attribute})')
         else:
             self.assertTrue(True, 'all serializable keys have a serializer')
diff --git a/test/unit/managers/test_HistoryManager.py b/test/unit/managers/test_HistoryManager.py
index 3558d99c5d9..d4c22d25bbf 100644
--- a/test/unit/managers/test_HistoryManager.py
+++ b/test/unit/managers/test_HistoryManager.py
@@ -422,8 +422,8 @@ class HistorySerializerTestCase(BaseTestCase):
         self.log('should have a serializer for all serializable keys')
         for key in self.history_serializer.serializable_keyset:
             instantiated_attribute = getattr(history1, key, None)
-            if not ((key in self.history_serializer.serializers) or
-                    (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))):
+            if not ((key in self.history_serializer.serializers)
+                    or (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))):
                 self.fail(f'no serializer for: {key} ({instantiated_attribute})')
         else:
             self.assertTrue(True, 'all serializable keys have a serializer')
diff --git a/test/unit/managers/test_UserManager.py b/test/unit/managers/test_UserManager.py
index f79274ca0c9..bf2f48a7e76 100644
--- a/test/unit/managers/test_UserManager.py
+++ b/test/unit/managers/test_UserManager.py
@@ -241,8 +241,8 @@ class UserSerializerTestCase(BaseTestCase):
         self.log('should have a serializer for all serializable keys')
         for key in self.user_serializer.serializable_keyset:
             instantiated_attribute = getattr(user, key, None)
-            if not ((key in self.user_serializer.serializers) or
-                    (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))):
+            if not ((key in self.user_serializer.serializers)
+                    or (isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))):
                 self.fail(f'no serializer for: {key} ({instantiated_attribute})')
         else:
             self.assertTrue(True, 'all serializable keys have a serializer')
diff --git a/test/unit/queue_worker/test_database_heartbeat.py b/test/unit/queue_worker/test_database_heartbeat.py
index 38d2447e4c7..43b2c9bb7fb 100644
--- a/test/unit/queue_worker/test_database_heartbeat.py
+++ b/test/unit/queue_worker/test_database_heartbeat.py
@@ -59,7 +59,7 @@ def test_database_heartbeat(heartbeat_app):
 
 def wait_for_assertion(assert_f):
     assertion_error = None
-    for i in range(10):
+    for _ in range(10):
         try:
             v = assert_f()
             return v
diff --git a/test/unit/shed_unit/test_tool_panel_manager.py b/test/unit/shed_unit/test_tool_panel_manager.py
index cb379d666da..7c31c3ad6f7 100644
--- a/test/unit/shed_unit/test_tool_panel_manager.py
+++ b/test/unit/shed_unit/test_tool_panel_manager.py
@@ -135,15 +135,10 @@ class ToolPanelManagerTestCase(BaseToolBoxTestCase):
         all_versions = new_toolbox.get_tool("test_tool", get_all_versions=True)
         assert not all_versions
 
-        # Check that tool panel has reverted to old value...
-        section = new_toolbox._tool_panel["tid"]
-        assert len(section.elems) == 0
-
     def _setup_two_versions_remove_one(self, section, uninstall):
         self._init_tool()
-        self._setup_two_versions_in_config(section=True)
+        self._setup_two_versions_in_config(section=section)
         self._setup_two_versions()
-        self.toolbox
         self._remove_repository_contents("github.com/galaxyproject/example/test_tool/0.2", uninstall=uninstall)
 
     def _verify_version_2_removed_from_panel(self, section=True):
@@ -161,7 +156,7 @@ class ToolPanelManagerTestCase(BaseToolBoxTestCase):
 
             assert "github.com/galaxyproject/example/test_tool/0.2" not in new_toolbox._integrated_tool_panel["tid"].elems
         else:
-            next(iter(self.toolbox._tool_panel.values())).id == "github.com/galaxyproject/example/test_tool/0.1"
+            assert next(iter(new_toolbox._tool_panel.values())).id == "github.com/galaxyproject/example/test_tool/0.1"
             assert "github.com/galaxyproject/example/test_tool/0.2" not in new_toolbox._integrated_tool_panel
 
     def _remove_repository_contents(self, guid, uninstall, shed_tool_conf="tool_conf.xml"):
diff --git a/test/unit/test_galaxy_transactions.py b/test/unit/test_galaxy_transactions.py
index 3ab458980ee..d3214ff8b52 100644
--- a/test/unit/test_galaxy_transactions.py
+++ b/test/unit/test_galaxy_transactions.py
@@ -7,7 +7,11 @@ from galaxy.util import bunch
 class TestTransaction(context.ProvidesAppContext):
 
     def __init__(self):
-        self.app = TestApp()
+        self._app = TestApp()
+
+    @property
+    def app(self):
+        return self._app
 
 
 def test_logging_events_off():
diff --git a/test/unit/test_model_store.py b/test/unit/test_model_store.py
index e230b043d45..d180fe71176 100644
--- a/test/unit/test_model_store.py
+++ b/test/unit/test_model_store.py
@@ -140,7 +140,7 @@ def test_import_export_library():
     all_lddas = sa_session.query(model.LibraryDatasetDatasetAssociation).all()
     assert len(all_lddas) == 2, len(all_lddas)
 
-    new_library = [l for l in all_libraries if l.id != library.id][0]
+    new_library = [lib for lib in all_libraries if lib.id != library.id][0]
     assert new_library.name == "my library 1"
     assert new_library.description == "my library description"
     assert new_library.synopsis == "my synopsis"
diff --git a/test/unit/tool_util/test_container_resolution.py b/test/unit/tool_util/test_container_resolution.py
new file mode 100644
index 00000000000..7b079497b61
--- /dev/null
+++ b/test/unit/tool_util/test_container_resolution.py
@@ -0,0 +1,53 @@
+from subprocess import CalledProcessError
+
+from galaxy.tool_util.deps.container_resolvers.mulled import (
+    CachedMulledDockerContainerResolver,
+    MulledDockerContainerResolver,
+)
+from galaxy.tool_util.deps.dependencies import ToolInfo
+from galaxy.tool_util.deps.requirements import ToolRequirement
+
+
+def test_docker_container_resolver_detects_docker_cli_absent(mocker):
+    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.which', return_value=None)
+    resolver = CachedMulledDockerContainerResolver()
+    assert resolver._cli_available is False
+
+
+def test_docker_container_resolver_detects_docker_cli(mocker):
+    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled', return_value='/bin/docker')
+    resolver = CachedMulledDockerContainerResolver()
+    assert resolver.cli_available
+
+
+def test_cached_docker_container_docker_cli_absent_resolve(mocker):
+    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.which', return_value=None)
+    resolver = CachedMulledDockerContainerResolver()
+    assert resolver.cli_available is False
+    assert resolver.resolve(enabled_container_types=[], tool_info={}) is None
+
+
+def test_docker_container_docker_cli_absent_resolve(mocker):
+    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.which', return_value=None)
+    resolver = MulledDockerContainerResolver()
+    assert resolver.cli_available is False
+    requirement = ToolRequirement(name="samtools", version="1.10", type="package")
+    tool_info = ToolInfo(requirements=[requirement])
+    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.targets_to_mulled_name', return_value='samtools:1.10--h2e538c0_3')
+    container_description = resolver.resolve(enabled_container_types=['docker'], tool_info=tool_info)
+    assert container_description.type == 'docker'
+    assert container_description.identifier == 'quay.io/biocontainers/samtools:1.10--h2e538c0_3'
+
+
+def test_docker_container_docker_cli_exception_resolve(mocker):
+    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.which', return_value='/bin/docker')
+    resolver = MulledDockerContainerResolver()
+    assert resolver.cli_available is True
+    requirement = ToolRequirement(name="samtools", version="1.10", type="package")
+    tool_info = ToolInfo(requirements=[requirement])
+    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.targets_to_mulled_name', return_value='samtools:1.10--h2e538c0_3')
+    mocker.patch('galaxy.tool_util.deps.container_resolvers.mulled.docker_cached_container_description', side_effect=CalledProcessError(1, 'bla'))
+    container_description = resolver.resolve(enabled_container_types=['docker'], tool_info=tool_info, install=True)
+    assert resolver.cli_available is True
+    assert container_description.type == 'docker'
+    assert container_description.identifier == 'quay.io/biocontainers/samtools:1.10--h2e538c0_3'
diff --git a/test/unit/tool_util/test_verify_script.py b/test/unit/tool_util/test_verify_script.py
index a8f5ced2ef0..0253e190c38 100644
--- a/test/unit/tool_util/test_verify_script.py
+++ b/test/unit/tool_util/test_verify_script.py
@@ -294,7 +294,7 @@ class MockGalaxyInteractor:
                 continue
 
             count = version_defs['count']
-            for i in range(count):
+            for _ in range(count):
                 test_def = {
                     'tool_id': tool_id,
                     'tool_version': this_tool_version or '0.1.1-default',
diff --git a/test/unit/tool_util/test_wait.py b/test/unit/tool_util/test_wait.py
index a946051a18f..14f69ed4fcd 100644
--- a/test/unit/tool_util/test_wait.py
+++ b/test/unit/tool_util/test_wait.py
@@ -42,7 +42,7 @@ def test_timeout_first_call():
         wait_on(condition, "never met condition", 1, delta=2, sleep_=sleeper.sleep)
     except TimeoutAssertionError as e:
         assert "never met condition" in str(e)
-        assert "after 2 seconds" in str(e)
+        assert "after 2.0 seconds" in str(e)
         exception_called = True
     assert len(sleeper.sleeps) == 1
     assert sleeper.sleeps[0] == 2  # delta of 2
diff --git a/test/unit/tools/test_data_parameters.py b/test/unit/tools/test_data_parameters.py
index a328fb218de..dfa93fbbf19 100644
--- a/test/unit/tools/test_data_parameters.py
+++ b/test/unit/tools/test_data_parameters.py
@@ -50,7 +50,7 @@ class DataToolParameterTestCase(BaseParameterTestCase):
         hda1.visible = False
         hda2.visible = False
         self.stub_active_datasets(hda1, hda2)
-        field = self._simple_field(other_values={"data2" : hda2})
+        field = self._simple_field(other_values={"data2": hda2})
         assert len(field['options']['hda']) == 1  # hda1 not an option, not visible or selected
         assert field['options']['hda'][0]['name'] == "(hidden) hda2"
 
@@ -60,7 +60,7 @@ class DataToolParameterTestCase(BaseParameterTestCase):
         hda1.visible = False
         hda2.deleted = True
         self.stub_active_datasets(hda1, hda2)
-        field = self._simple_field(other_values={"data2" : hda2})
+        field = self._simple_field(other_values={"data2": hda2})
         assert len(field['options']['hda']) == 1  # hda1 not an option, not visible or selected
         assert field['options']['hda'][0]['name'] == "(deleted) hda2"
 
diff --git a/test/unit/tools/test_history_imp_exp.py b/test/unit/tools/test_history_imp_exp.py
index fe3e8cd4967..8f1d34c5908 100644
--- a/test/unit/tools/test_history_imp_exp.py
+++ b/test/unit/tools/test_history_imp_exp.py
@@ -597,8 +597,8 @@ def _hid_dict(history):
     return hids
 
 
-def _assert_distinct(l):
-    assert len(l) == len(set(l))
+def _assert_distinct(list_):
+    assert len(list_) == len(set(list_))
 
 
 def _create_datasets(sa_session, history, n, extension="txt"):
diff --git a/test/unit/tools/test_select_parameters.py b/test/unit/tools/test_select_parameters.py
index 21cae260370..d80533a5582 100644
--- a/test/unit/tools/test_select_parameters.py
+++ b/test/unit/tools/test_select_parameters.py
@@ -1,3 +1,5 @@
+import pytest
+
 from galaxy import model
 from galaxy.tools.parameters import basic
 from galaxy.util import bunch
@@ -8,21 +10,15 @@ class SelectToolParameterTestCase(BaseParameterTestCase):
 
     def test_validated_values(self):
         self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
-        try:
+        with pytest.raises(ValueError) as exc_info:
             self.param.from_json("42", self.trans, {"input_bam": model.HistoryDatasetAssociation()})
-        except ValueError as err:
-            assert str(err) == "parameter 'my_name': requires a value, but no legal values defined"
-            return
-        assert False
+            assert str(exc_info.value) == "parameter 'my_name': requires a value, but no legal values defined"
 
     def test_validated_values_missing_dependency(self):
         self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
-        try:
+        with pytest.raises(ValueError) as exc_info:
             self.param.from_json("42", self.trans)
-        except ValueError as err:
-            assert str(err) == "parameter 'my_name': requires a value, but no legal values defined"
-            return
-        assert False
+            assert str(exc_info.value) == "parameter 'my_name': requires a value, but no legal values defined"
 
     def test_unvalidated_values(self):
         self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
@@ -31,12 +27,9 @@ class SelectToolParameterTestCase(BaseParameterTestCase):
 
     def test_validated_datasets(self):
         self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
-        try:
+        with pytest.raises(ValueError) as exc_info:
             self.param.from_json(model.HistoryDatasetAssociation(), self.trans, {"input_bam": None})
-        except ValueError as err:
-            assert str(err) == "parameter 'my_name': requires a value, but no legal values defined"
-            return
-        assert False
+            assert str(exc_info.value) == "parameter 'my_name': requires a value, but no legal values defined"
 
     def test_unvalidated_datasets(self):
         self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
diff --git a/test/unit/tools/test_watcher.py b/test/unit/tools/test_watcher.py
index e31aeb8d714..be74e071bdf 100644
--- a/test/unit/tools/test_watcher.py
+++ b/test/unit/tools/test_watcher.py
@@ -52,7 +52,7 @@ def test_tool_conf_watcher():
 
 def wait_for_reload(check):
     reloaded = False
-    for i in range(10):
+    for _ in range(10):
         reloaded = check()
         if reloaded:
             break
diff --git a/test/unit/unittest_utils/galaxy_mock.py b/test/unit/unittest_utils/galaxy_mock.py
index 3b258b9c60d..fe16971e2e4 100644
--- a/test/unit/unittest_utils/galaxy_mock.py
+++ b/test/unit/unittest_utils/galaxy_mock.py
@@ -170,6 +170,7 @@ class MockAppConfig(Bunch):
 
         # set by MockDir
         self.root = root
+        self.enable_tool_document_cache = False
         self.tool_cache_data_dir = os.path.join(root, 'tool_cache')
         self.delay_tool_initialization = True
         self.external_chown_script = None
@@ -220,7 +221,7 @@ class MockTrans:
         self.history = history
 
         self.request = Bunch(headers={}, body=None)
-        self.response = Bunch(headers={}, set_content_type=lambda i : None)
+        self.response = Bunch(headers={}, set_content_type=lambda i: None)
 
     def check_csrf_token(self, payload):
         pass
diff --git a/test/unit/util/test_lazy_process.py b/test/unit/util/test_lazy_process.py
index 4200ec29166..c81dc76e867 100644
--- a/test/unit/util/test_lazy_process.py
+++ b/test/unit/util/test_lazy_process.py
@@ -18,7 +18,7 @@ def test_lazy_process():
     assert lazy_process.process.poll() is None
     lazy_process.shutdown()
     ret_val = None
-    for i in range(10):
+    for _ in range(10):
         ret_val = lazy_process.process.poll()
         if ret_val is not None:
             break
diff --git a/test/unit/util/test_sqlite_utils.py b/test/unit/util/test_sqlite_utils.py
index 9f051794eae..8e627614316 100644
--- a/test/unit/util/test_sqlite_utils.py
+++ b/test/unit/util/test_sqlite_utils.py
@@ -1,3 +1,5 @@
+import pytest
+
 from galaxy.util import sqlite
 
 
@@ -37,19 +39,14 @@ def test_sqlite_exploits():
 
 def __assert_has_n_rows(connection, query, n):
     count = 0
-    for row in connection.cursor().execute(query):
+    for _ in connection.cursor().execute(query):
         count += 1
     assert count == n
 
 
 def __assert_query_errors(connection, query):
-    exception = False
-    try:
-        for row in connection.cursor().execute(query):
-            pass
-    except Exception:
-        exception = True
-    assert exception
+    with pytest.raises(Exception):
+        connection.cursor().execute(query)
 
 
 def __assert_allowed(query):
diff --git a/test/unit/util/test_utils.py b/test/unit/util/test_utils.py
index 08ffd0fc04a..f0048b968a3 100644
--- a/test/unit/util/test_utils.py
+++ b/test/unit/util/test_utils.py
@@ -24,10 +24,10 @@ def test_strip_control_characters():
 def test_strip_control_characters_nested():
     s = '\x00bla'
     stripped_s = 'bla'
-    l = [s]
+    list_ = [s]
     t = (s, 'blub')
     d = {42: s}
-    assert util.strip_control_characters_nested(l)[0] == stripped_s
+    assert util.strip_control_characters_nested(list_)[0] == stripped_s
     assert util.strip_control_characters_nested(t)[0] == stripped_s
     assert util.strip_control_characters_nested(d)[42] == stripped_s
 
diff --git a/test/unit/workflows/test_extract_summary.py b/test/unit/workflows/test_extract_summary.py
index 4b437269421..18be155c675 100644
--- a/test/unit/workflows/test_extract_summary.py
+++ b/test/unit/workflows/test_extract_summary.py
@@ -110,6 +110,7 @@ class MockTrans:
 class MockHda:
 
     def __init__(self, state='ok', output_name='out1', job=None):
+        self.hid = 1
         self.id = 123
         self.state = state
         self.copied_from_history_dataset_association = None
diff --git a/tools/data_source/import.py b/tools/data_source/import.py
index f522abf1051..4f89d4f68d0 100644
--- a/tools/data_source/import.py
+++ b/tools/data_source/import.py
@@ -17,21 +17,21 @@ out_name = sys.argv[2]
 
 
 id2name = {
-    'eryth'         : 'ErythPreCRMmm3_cusTrk.txt',
-    'cishg16'       : 'ReglRegHBBhg16CusTrk.txt',
-    'cishg17'       : 'ReglRegHBBhg17CusTrk.txt',
-    'exons'         : 'ExonsKnownGenes_mm3.txt',
-    'krhg16'        : 'known_regulatory_hg16.bed',
-    'krhg17'        : 'known_regulatory_hg17.bed',
-    'tARhg16mmc'    : 'hg16.mouse.t_AR.cold.bed',
-    'tARhg16mmm'    : 'hg16.mouse.t_AR.medium.bed',
-    'tARhg16mmh'    : 'hg16.mouse.t_AR.hot.bed',
-    'tARhg16rnc'    : 'hg16.rat.t_AR.cold.bed',
-    'tARhg16rnm'    : 'hg16.rat.t_AR.medium.bed',
-    'tARhg16rnh'    : 'hg16.rat.t_AR.hot.bed',
-    'phastConsHg16' : 'phastConsMost_hg16.bed',
-    'omimhg16'      : 'omimDisorders_hg16.tab',
-    'omimhg17'      : 'omimDisorders_hg17.tab',
+    'eryth': 'ErythPreCRMmm3_cusTrk.txt',
+    'cishg16': 'ReglRegHBBhg16CusTrk.txt',
+    'cishg17': 'ReglRegHBBhg17CusTrk.txt',
+    'exons': 'ExonsKnownGenes_mm3.txt',
+    'krhg16': 'known_regulatory_hg16.bed',
+    'krhg17': 'known_regulatory_hg17.bed',
+    'tARhg16mmc': 'hg16.mouse.t_AR.cold.bed',
+    'tARhg16mmm': 'hg16.mouse.t_AR.medium.bed',
+    'tARhg16mmh': 'hg16.mouse.t_AR.hot.bed',
+    'tARhg16rnc': 'hg16.rat.t_AR.cold.bed',
+    'tARhg16rnm': 'hg16.rat.t_AR.medium.bed',
+    'tARhg16rnh': 'hg16.rat.t_AR.hot.bed',
+    'phastConsHg16': 'phastConsMost_hg16.bed',
+    'omimhg16': 'omimDisorders_hg16.tab',
+    'omimhg17': 'omimDisorders_hg17.tab',
 }
 
 fname = id2name.get(dataid, '')
diff --git a/tools/data_source/microbial_import.py b/tools/data_source/microbial_import.py
index ce9c10d999c..38a72e36636 100644
--- a/tools/data_source/microbial_import.py
+++ b/tools/data_source/microbial_import.py
@@ -28,7 +28,7 @@ while have_none:
 available_files = {}
 try:
     filename = sys.argv[-1]
-    for i, line in enumerate(open(filename)):
+    for line in open(filename):
         if not line or line[0:1] == "#":
             continue
         fields = line.split('\t')
diff --git a/tools/data_source/microbial_import_code.py b/tools/data_source/microbial_import_code.py
index 9466f25f9d1..b8186b060d0 100644
--- a/tools/data_source/microbial_import_code.py
+++ b/tools/data_source/microbial_import_code.py
@@ -10,7 +10,7 @@ def load_microbial_data(GALAXY_DATA_INDEX_DIR, sep='\t'):
     orgs = {}
 
     filename = "%s/microbial_data.loc" % GALAXY_DATA_INDEX_DIR
-    for i, line in enumerate(open(filename)):
+    for line in open(filename):
         line = line.rstrip('\r\n')
         if line and not line.startswith('#'):
             fields = line.split(sep)
diff --git a/tools/data_source/upload.py b/tools/data_source/upload.py
index 8f99bded139..d7568a28f8c 100644
--- a/tools/data_source/upload.py
+++ b/tools/data_source/upload.py
@@ -108,7 +108,7 @@ def add_file(dataset, registry, output_path):
 
     # Base on the check_upload_content Galaxy config option and on by default, this enables some
     # security related checks on the uploaded content, but can prevent uploads from working in some cases.
-    check_content = dataset.get('check_content' , True)
+    check_content = dataset.get('check_content', True)
 
     # auto_decompress is a request flag that can be swapped off to prevent Galaxy from automatically
     # decompressing archive files before sniffing.
diff --git a/tools/extract/extract_genomic_dna.py b/tools/extract/extract_genomic_dna.py
index 9c13b9a5ac3..643dc4ffc15 100755
--- a/tools/extract/extract_genomic_dna.py
+++ b/tools/extract/extract_genomic_dna.py
@@ -260,7 +260,7 @@ def __main__():
             sequence = reverse_complement(sequence)
 
         if output_format == "fasta":
-            l = len(sequence)
+            len_sequence = len(sequence)
             c = 0
             if gff_format:
                 start, end = gff_util.convert_bed_coords_to_gff([start, end])
@@ -270,8 +270,8 @@ def __main__():
                 fout.write(">%s %s\n" % (meta_data, name))
             else:
                 fout.write(">%s\n" % meta_data)
-            while c < l:
-                b = min(c + 50, l)
+            while c < len_sequence:
+                b = min(c + 50, len_sequence)
                 fout.write("%s\n" % str(sequence[c:b]))
                 c = b
         else:  # output_format == "interval"
diff --git a/tools/filters/gff/extract_GFF_Features.py b/tools/filters/gff/extract_GFF_Features.py
index ba93fafcc3f..321814c0f28 100644
--- a/tools/filters/gff/extract_GFF_Features.py
+++ b/tools/filters/gff/extract_GFF_Features.py
@@ -34,7 +34,7 @@ def main():
         stop_err("Column %d has no features to display, select another column." % (column + 1))
 
     fo = open(out_file, 'w')
-    for i, line in enumerate(open(inp_file)):
+    for line in open(inp_file):
         line = line.rstrip('\r\n')
         if line and line.startswith('#'):
             # Keep valid comment lines in the output
diff --git a/tools/filters/gff/gff_filter_by_attribute.py b/tools/filters/gff/gff_filter_by_attribute.py
index d498056e29a..e8216ebd9e3 100644
--- a/tools/filters/gff/gff_filter_by_attribute.py
+++ b/tools/filters/gff/gff_filter_by_attribute.py
@@ -231,7 +231,7 @@ if not check_expression(cond_text):
 # Prepare the column variable names and wrappers for column data types. Only
 # prepare columns up to largest column in condition.
 attrs, type_casts = [], []
-for name, attr_type in attribute_types.items():
+for name in attribute_types.keys():
     attrs.append(name)
     type_cast = "get_value('%(name)s', attribute_types['%(name)s'], attribute_values)" % ({'name': name})
     type_casts.append(type_cast)
diff --git a/tools/filters/gff/gff_filter_by_feature_count.py b/tools/filters/gff/gff_filter_by_feature_count.py
index 08f3cec6117..7a32432b6a8 100644
--- a/tools/filters/gff/gff_filter_by_feature_count.py
+++ b/tools/filters/gff/gff_filter_by_feature_count.py
@@ -148,7 +148,7 @@ def __main__():
     skipped_lines = 0
     first_skipped_line = 0
     out = open(output_name, 'w')
-    for i, feature in enumerate(GFFReaderWrapper(open(input_name))):
+    for i, feature in enumerate(GFFReaderWrapper(open(input_name))):  # noqa: B007
         if not isinstance(feature, GenomicInterval):
             continue
         count = 0
diff --git a/tools/filters/grep.py b/tools/filters/grep.py
index 2cd8e0c4d3d..fad39281aac 100644
--- a/tools/filters/grep.py
+++ b/tools/filters/grep.py
@@ -70,14 +70,14 @@ def main():
 
     # replace if input has been escaped, remove sq
     # characters that are allowed but need to be escaped
-    mapped_chars = {'>' : '__gt__',
-                    '<' : '__lt__',
+    mapped_chars = {'>': '__gt__',
+                    '<': '__lt__',
                     '\'': '__sq__',
-                    '"' : '__dq__',
-                    '[' : '__ob__',
-                    ']' : '__cb__',
-                    '{' : '__oc__',
-                    '}' : '__cc__'}
+                    '"': '__dq__',
+                    '[': '__ob__',
+                    ']': '__cb__',
+                    '{': '__oc__',
+                    '}': '__cc__'}
 
     # with new sanitizing we only need to replace for single quote,
     # but this needs to remain for backwards compatibility
diff --git a/tools/filters/sff_extract.py b/tools/filters/sff_extract.py
index 06850e899ff..5c179f3ba53 100644
--- a/tools/filters/sff_extract.py
+++ b/tools/filters/sff_extract.py
@@ -94,12 +94,8 @@ def check_magic(magic):
 
 def check_version(version):
     '''It checks that the version is supported, otherwise it raises an error.'''
-    supported = ('\x00', '\x00', '\x00', '\x01')
-    i = 0
-    for item in version:
-        if version[i] != supported[i]:
-            raise RuntimeError('SFF version not supported. Please contact the author of the software.')
-        i += 1
+    if version != ('\x00', '\x00', '\x00', '\x01'):
+        raise RuntimeError('SFF version not supported. Please contact the author of the software.')
 
 
 def read_header(fileh):
@@ -322,8 +318,8 @@ def create_basic_xml_info(readname, fname):
     # we print the info that we have
     if info:
         for key in info:
-            to_print.append('        <' + key + '>' + info[key] +
-                            '</' + key + '>\n')
+            to_print.append('        <' + key + '>' + info[key]
+                            + '</' + key + '>\n')
 
     return ''.join(to_print)
 
@@ -1326,7 +1322,7 @@ def main():
         if len(args) == 0:
             raise RuntimeError("No SFF file given?")
         extract_reads_from_sff(config, args)
-    except (OSError, IOError, RuntimeError) as errval:
+    except (OSError, IOError, RuntimeError) as errval:  # noqa: B014 Python 2.7
         print(errval)
         return 1
 
diff --git a/tools/maf/interval2maf.py b/tools/maf/interval2maf.py
index 5ea52316184..e96a6136372 100755
--- a/tools/maf/interval2maf.py
+++ b/tools/maf/interval2maf.py
@@ -109,7 +109,7 @@ def __main__():
     # Iterate over input regions
     num_blocks = 0
     num_regions = None
-    for num_regions, region in enumerate(bx.intervals.io.NiceReaderWrapper(open(interval_file), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False)):
+    for num_regions, region in enumerate(bx.intervals.io.NiceReaderWrapper(open(interval_file), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False)):  # noqa: B007
         src = maf_utilities.src_merge(dbkey, region.chrom)
         for block in index.get_as_iterator(src, region.start, region.end):
             if split_blocks_by_species:
diff --git a/tools/maf/maf_filter.py b/tools/maf/maf_filter.py
index 500c3e652da..f2134f9398d 100644
--- a/tools/maf/maf_filter.py
+++ b/tools/maf/maf_filter.py
@@ -51,7 +51,7 @@ def main():
     # 'ret_val' should be set to True if the block is to be kept
     i = 0
     blocks_kept = 0
-    for i, maf_block in enumerate(maf_reader):
+    for i, maf_block in enumerate(maf_reader):  # noqa: B007
         if min_size <= maf_block.text_size <= max_size:
             local = {'maf_block': maf_block, 'ret_val': False}
             exec(compile(open(script_file).read(), script_file, 'exec'), {}, local)
diff --git a/tools/maf/maf_limit_size.py b/tools/maf/maf_limit_size.py
index a616e3e6e15..62982397562 100644
--- a/tools/maf/maf_limit_size.py
+++ b/tools/maf/maf_limit_size.py
@@ -26,7 +26,7 @@ def __main__():
 
     blocks_kept = 0
     i = 0
-    for i, m in enumerate(maf_reader):
+    for i, m in enumerate(maf_reader):  # noqa: B007
         if min_size <= m.text_size <= max_size:
             maf_writer.write(m)
             blocks_kept += 1
diff --git a/tools/maf/maf_reverse_complement.py b/tools/maf/maf_reverse_complement.py
index e8543d62a6f..958fa81b9ee 100644
--- a/tools/maf/maf_reverse_complement.py
+++ b/tools/maf/maf_reverse_complement.py
@@ -28,7 +28,7 @@ def __main__():
         sys.exit()
     try:
         count = 0
-        for count, maf in enumerate(bx.align.maf.Reader(open(input_file))):
+        for count, maf in enumerate(bx.align.maf.Reader(open(input_file))):  # noqa: B007
             maf = maf.reverse_complement()
             if species:
                 maf = maf.limit_to_species(species)
diff --git a/tools/maf/maf_split_by_species.py b/tools/maf/maf_split_by_species.py
index f148064f18b..eeb6f36ad98 100644
--- a/tools/maf/maf_split_by_species.py
+++ b/tools/maf/maf_split_by_species.py
@@ -28,7 +28,7 @@ def __main__():
 
     start_count = 0
     end_count = 0
-    for start_count, start_block in enumerate(maf_reader):
+    for start_count, start_block in enumerate(maf_reader):  # noqa: B007
         for block in maf_utilities.iter_blocks_split_by_species(start_block):
             if collapse_columns:
                 block.remove_all_gap_columns()
diff --git a/tools/maf/maf_stats.py b/tools/maf/maf_stats.py
index d1b66e74492..5f1f2760c16 100644
--- a/tools/maf/maf_stats.py
+++ b/tools/maf/maf_stats.py
@@ -61,7 +61,7 @@ def __main__():
     species_summary = {}
     total_length = 0
     # loop through interval file
-    for num_region, region in enumerate(bx.intervals.io.NiceReaderWrapper(open(input_interval_filename, 'r'), chrom_col=chr_col, start_col=start_col, end_col=end_col, fix_strand=True, return_header=False, return_comments=False)):
+    for num_region, region in enumerate(bx.intervals.io.NiceReaderWrapper(open(input_interval_filename, 'r'), chrom_col=chr_col, start_col=start_col, end_col=end_col, fix_strand=True, return_header=False, return_comments=False)):  # noqa: B007
         src = "%s.%s" % (dbkey, region.chrom)
         region_length = region.end - region.start
         if region_length < 1:
diff --git a/tools/maf/maf_to_bed.py b/tools/maf/maf_to_bed.py
index 4387d111c4a..6e0be5d3aec 100644
--- a/tools/maf/maf_to_bed.py
+++ b/tools/maf/maf_to_bed.py
@@ -27,7 +27,7 @@ def __main__():
     if "None" in species:
         species = OrderedDict()
         try:
-            for i, m in enumerate(maf.Reader(open(input_filename))):
+            for m in maf.Reader(open(input_filename)):
                 for c in m.components:
                     spec, chrom = src_split(c.src)
                     if not spec or not chrom:
@@ -57,14 +57,14 @@ def __main__():
 
         block_num = -1
 
-        for i, m in enumerate(maf_reader):
+        for m in maf_reader:
             block_num += 1
             if "None" not in species:
                 m = m.limit_to_species(species)
-            l = m.components
-            if len(l) < num_species and partial == "partial_disallowed":
+            components = m.components
+            if len(components) < num_species and partial == "partial_disallowed":
                 continue
-            for c in l:
+            for c in components:
                 spec, chrom = src_split(c.src)
                 if not spec or not chrom:
                     spec = chrom = c.src
diff --git a/tools/maf/vcf_to_maf_customtrack.py b/tools/maf/vcf_to_maf_customtrack.py
index 5b89907c5e1..da67ad75ea4 100644
--- a/tools/maf/vcf_to_maf_customtrack.py
+++ b/tools/maf/vcf_to_maf_customtrack.py
@@ -96,7 +96,7 @@ def main():
         for vc, variants in vcf_file:
             num_ins = 0
             num_dels = 0
-            for variant_name, variant_text in variants:
+            for _variant_name, variant_text in variants:
                 if 'D' in variant_text:
                     num_dels = max(num_dels, int(variant_text[1:]))
                 elif 'I' in variant_text:
diff --git a/tools/metag_tools/blat_wrapper.py b/tools/metag_tools/blat_wrapper.py
index b815e6dcf55..6360b9b1bcb 100644
--- a/tools/metag_tools/blat_wrapper.py
+++ b/tools/metag_tools/blat_wrapper.py
@@ -16,7 +16,7 @@ def check_nib_file(dbkey, GALAXY_DATA_INDEX_DIR):
     nib_file = "%s/alignseq.loc" % GALAXY_DATA_INDEX_DIR
     nib_path = ''
     nibs = {}
-    for i, line in enumerate(open(nib_file)):
+    for line in open(nib_file):
         line = line.rstrip('\r\n')
         if line and not line.startswith("#"):
             fields = line.split('\t')
@@ -33,7 +33,7 @@ def check_twobit_file(dbkey, GALAXY_DATA_INDEX_DIR):
     twobit_file = "%s/twobit.loc" % GALAXY_DATA_INDEX_DIR
     twobit_path = ''
     twobits = {}
-    for i, line in enumerate(open(twobit_file)):
+    for line in open(twobit_file):
         line = line.rstrip('\r\n')
         if line and not line.startswith("#"):
             fields = line.split('\t')
diff --git a/tools/metag_tools/shrimp_color_wrapper.py b/tools/metag_tools/shrimp_color_wrapper.py
index fc0b27d1e4d..275b4b786a0 100644
--- a/tools/metag_tools/shrimp_color_wrapper.py
+++ b/tools/metag_tools/shrimp_color_wrapper.py
@@ -86,7 +86,7 @@ def __main__():
     # check SHRiMP output: count number of lines
     num_hits = 0
     if shrimp_outfile:
-        for i, line in enumerate(open(shrimp_outfile)):
+        for line in open(shrimp_outfile):
             line = line.rstrip('\r\n')
             if not line or line.startswith('#'):
                 continue
@@ -99,7 +99,7 @@ def __main__():
     if num_hits == 0:   # no hits generated
         err_msg = ''
         if shrimp_log:
-            for i, line in enumerate(open(shrimp_log)):
+            for line in open(shrimp_log):
                 if line.startswith('error'):            # deal with memory error:
                     err_msg += line                     # error: realloc failed: Cannot allocate memory
                 if re.search('Reads Matched', line):    # deal with zero hits
diff --git a/tools/metag_tools/shrimp_wrapper.py b/tools/metag_tools/shrimp_wrapper.py
index 5ad3dc839fe..ea8cdcaf4a8 100644
--- a/tools/metag_tools/shrimp_wrapper.py
+++ b/tools/metag_tools/shrimp_wrapper.py
@@ -85,7 +85,7 @@ def generate_sub_table(result_file, ref_file, score_files, table_outfile, hit_pe
     seq = ''
     title = None
 
-    for i, line in enumerate(open(ref_file)):
+    for line in open(ref_file):
         line = line.rstrip()
         if not line or line.startswith('#'):
             continue
@@ -108,7 +108,7 @@ def generate_sub_table(result_file, ref_file, score_files, table_outfile, hit_pe
 
     # find hits: one end and/or the other
     hits = {}
-    for i, line in enumerate(open(result_file)):
+    for line in open(result_file):
         line = line.rstrip()
         if not line or line.startswith('#'):
             continue
@@ -144,7 +144,7 @@ def generate_sub_table(result_file, ref_file, score_files, table_outfile, hit_pe
     score = ''
     for num_score_file in range(len(all_score_file)):
         score_file = all_score_file[num_score_file]
-        for i, line in enumerate(open(score_file)):
+        for line in open(score_file):
             line = line.rstrip()
             if not line or line.startswith('#'):
                 continue
@@ -198,14 +198,14 @@ def generate_sub_table(result_file, ref_file, score_files, table_outfile, hit_pe
             end1_data = hits[readkey]['1']
             end2_data = hits[readkey]['2']
 
-            for i, end1_hit in enumerate(end1_data):
+            for end1_hit in end1_data:
                 crin_strand = {'+': False, '-': False}
                 crin_insertSize = {'+': False, '-': False}
 
                 crin_strand[end1_hit[0]] = True
                 crin_insertSize[end1_hit[0]] = int(end1_hit[2])
 
-                for j, end2_hit in enumerate(end2_data):
+                for end2_hit in end2_data:
                     crin_strand[end2_hit[0]] = True
                     crin_insertSize[end2_hit[0]] = int(end2_hit[2])
 
@@ -350,7 +350,7 @@ def generate_sub_table(result_file, ref_file, score_files, table_outfile, hit_pe
     temp_table.close()
 
     # chrom-wide coverage
-    for i, line in enumerate(open(temp_table_name)):
+    for line in open(temp_table_name):
         line = line.rstrip()
         if not line or line.startswith('#'):
             continue
@@ -463,7 +463,7 @@ def convert_fastqsolexa_to_fasta_qual(infile_name, query_fasta, query_qual):
                 else:
                     stop_err('Invalid fastqsolexa format at line %d: the number of quality scores ( %d ) is not the same as bases ( %d ).' % (i + 1, quality_score_length, read_length))
 
-                for j, char in enumerate(line):
+                for char in line:
                     score = ord(char) - qual_score_startswith    # 64
                     qual = "%s%s " % (qual, str(score))
 
@@ -591,7 +591,7 @@ def __main__():
     # check SHRiMP output: count number of lines
     num_hits = 0
     if shrimp_outfile:
-        for i, line in enumerate(open(shrimp_outfile)):
+        for line in open(shrimp_outfile):
             line = line.rstrip('\r\n')
             if not line or line.startswith('#'):
                 continue
@@ -604,7 +604,7 @@ def __main__():
     if num_hits == 0:   # no hits generated
         err_msg = ''
         if shrimp_log:
-            for i, line in enumerate(open(shrimp_log)):
+            for line in open(shrimp_log):
                 if line.startswith('error'):            # deal with memory error:
                     err_msg += line                     # error: realloc failed: Cannot allocate memory
                 if re.search('Reads Matched', line):    # deal with zero hits
diff --git a/tools/next_gen_conversion/fastq_gen_conv.py b/tools/next_gen_conversion/fastq_gen_conv.py
index 68a72e5a1f7..aad04791c51 100644
--- a/tools/next_gen_conversion/fastq_gen_conv.py
+++ b/tools/next_gen_conversion/fastq_gen_conv.py
@@ -85,8 +85,8 @@ def __main__():
                         # make sure we haven't lost any quality values
                         if len(phred_list) == base_len:
                             # print first three lines
-                            for l in lines:
-                                fout.write(l)
+                            for line_to_write in lines:
+                                fout.write(line_to_write)
                             # print converted quality line
                             fout.write(''.join(phred_list))
                             # reset
@@ -147,8 +147,8 @@ def __main__():
                         # make sure we don't have bad qualities
                         if len(quals) == base_len:
                             # print first three lines
-                            for l in lines:
-                                fout.write(l)
+                            for line_to_write in lines:
+                                fout.write(line_to_write)
                             # print out quality line
                             fout.write(quals + '\n')
                         # reset
diff --git a/tools/phenotype_association/pagetag.py b/tools/phenotype_association/pagetag.py
index 42cdd71cf26..1b558d7b293 100755
--- a/tools/phenotype_association/pagetag.py
+++ b/tools/phenotype_association/pagetag.py
@@ -296,7 +296,7 @@ if __name__ == "__main__":
         elif o in ("-s", "--sample"):
             samples = read_list(a)
         else:
-            assert False, "unhandled option"
+            raise AssertionError("unhandled option")
 
     if rsquare < 0.00 or rsquare > 1.00:
         print("input value of rsquare should be in [0.00, 1.00]", file=stderr)
diff --git a/tools/phenotype_association/senatag.py b/tools/phenotype_association/senatag.py
index 2140396a182..04834b29277 100755
--- a/tools/phenotype_association/senatag.py
+++ b/tools/phenotype_association/senatag.py
@@ -253,7 +253,7 @@ if __name__ == "__main__":
         elif o in ("-e", "--excluded"):
             excluded = read_list(a)
         else:
-            assert False, "unhandled option"
+            raise AssertionError("unhandled option")
 
     if len(args) != 2:
         usage()
diff --git a/tools/solid_tools/maq_cs_wrapper.py b/tools/solid_tools/maq_cs_wrapper.py
index 9e5dd35db17..5405bb84d32 100644
--- a/tools/solid_tools/maq_cs_wrapper.py
+++ b/tools/solid_tools/maq_cs_wrapper.py
@@ -83,7 +83,7 @@ def __main__():
                 ii += 1
             while True:
                 all_done = True
-                for j, k in enumerate(subprocess_dict.keys()):
+                for j in range(len(subprocess_dict)):
                     if subprocess_dict['sp' + str(j + 1)].wait() != 0:
                         err = subprocess_dict['sp' + str(j + 1)].communicate()[1]
                         if err is not None:
@@ -158,7 +158,7 @@ def __main__():
 
             while True:
                 all_done = True
-                for j, k in enumerate(subprocess_dict.keys()):
+                for j in range(len(subprocess_dict)):
                     if subprocess_dict['sp' + str(j + 1)].wait() != 0:
                         err = subprocess_dict['sp' + str(j + 1)].communicate()[1]
                         if err is not None:
diff --git a/tools/solid_tools/solid_qual_stats.py b/tools/solid_tools/solid_qual_stats.py
index 4dd0e992644..30239ccb979 100644
--- a/tools/solid_tools/solid_qual_stats.py
+++ b/tools/solid_tools/solid_qual_stats.py
@@ -57,7 +57,7 @@ def __main__():
 
             position_dict = {}
             print("column\tcount\tmin\tmax\tsum\tmean\tQ1\tmed\tQ3\tIQR\tlW\trW", file=fout)
-            for k, line in enumerate(open(infile_name)):
+            for line in open(infile_name):
                 line = line.strip()
                 if not(line) or line.startswith("#") or line.startswith(">"):
                     continue