Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev

.ci/jenkins/api-py3

@@ -0,0 +1 @@
+api

.ci/jenkins/api-py3/run_tests.sh

@@ -1,3 +0,0 @@
-#!/bin/bash
-
-./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --skip_flakey_fails -api "$@"

.ci/jenkins/framework-py3

@@ -0,0 +1 @@
+framework

.ci/jenkins/framework-py3/run_tests.sh

@@ -1,3 +0,0 @@
-#!/bin/bash
-
-./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --framework "$@"

.ci/jenkins/integration-py3

@@ -0,0 +1 @@
+integration

.ci/jenkins/integration-py3/run_tests.sh

@@ -1,3 +0,0 @@
-#!/bin/bash
-
-DOCKER_RUN_EXTRA_ARGS="--privileged" ./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --integration "$@"

.ci/jenkins/main-tools-py3

@@ -0,0 +1 @@
+main-tools

.ci/jenkins/main-tools-py3/run_tests.sh

@@ -1,3 +0,0 @@
-#!/bin/bash
-
-./run_tests.sh --dockerize --python3 --db postgres --clean_pyc -main "$@"

.ci/jenkins/selenium-compose/run_galaxy.bash

@@ -20,8 +20,7 @@ virtualenv "$GALAXY_VIRTUAL_ENV"
 chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" "$GALAXY_VIRTUAL_ENV"
 
 cd /galaxy
-HOME=/galaxy
-sudo -E -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }
+sudo -E -H -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }
 
 echo "Waiting for postgres to become available"
 while ! nc -z postgres 5432;
@@ -34,7 +33,7 @@ echo "Creating postgres database for Galaxy"
 createdb -w -U postgres -h postgres galaxy
 
 echo "Starting and waiting for Galaxy daemon(s)"
-sudo -E -u "#${GALAXY_TEST_UID}" GALAXY_RUN_ALL=1 bash "$GALAXY_ROOT/run.sh" --daemon --wait
+sudo -E -H -u "#${GALAXY_TEST_UID}" GALAXY_RUN_ALL=1 bash "$GALAXY_ROOT/run.sh" --daemon --wait
 
 echo "Galaxy daemon ready, monitoring Galaxy logs"
 tail -f "$GALAXY_ROOT/main.log"

.ci/jenkins/selenium-py3

@@ -0,0 +1 @@
+selenium

.ci/jenkins/selenium-py3/run_tests.sh

@@ -1,26 +0,0 @@
-#!/bin/bash
-
-# Enable retries on tests to reduce chances of transient failures.
-: ${GALAXY_TEST_SELENIUM_RETRIES:=1}
-
-# If in Jenkins environment, use it for artifacts.
-if [ -n "$BUILD_NUMBER" ];
-then
-    : ${GALAXY_TEST_ERRORS_DIRECTORY:=${BUILD_NUMBER}-test-errors}
-    : ${GALAXY_TEST_SCREENSHOTS_DIRECTORY:=${BUILD_NUMBER}-test-screenshots}
-else
-    : ${GALAXY_TEST_ERRORS_DIRECTORY:=database/test-errors}
-    : ${GALAXY_TEST_SCREENSHOTS_DIRECTORY:=database/test-screenshots}
-fi
-
-mkdir -p "$GALAXY_TEST_ERRORS_DIRECTORY"
-mkdir -p "$GALAXY_TEST_SCREENSHOTS_DIRECTORY"
-
-mkdir -p ~/.jenkins-yarn-cache
-YARN_CACHE_FOLDER=~/.jenkins-yarn-cache
-
-# Start Selenium server in the test Docker container.
-DOCKER_RUN_EXTRA_ARGS="${DOCKER_RUN_EXTRA_ARGS} --shm-size=2g -v $YARN_CACHE_FOLDER:$YARN_CACHE_FOLDER -e YARN_CACHE_FOLDER=$YARN_CACHE_FOLDER -e USE_SELENIUM=1 -e GALAXY_TEST_SELENIUM_RETRIES=${GALAXY_TEST_SELENIUM_RETRIES} -e GALAXY_TEST_ERRORS_DIRECTORY=${GALAXY_TEST_ERRORS_DIRECTORY} -e GALAXY_TEST_SCREENSHOTS_DIRECTORY=${GALAXY_TEST_SCREENSHOTS_DIRECTORY}"
-export DOCKER_RUN_EXTRA_ARGS
-
-./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --skip_flakey_fails --selenium "$@"

.circleci/config.yml

@@ -81,23 +81,6 @@ jobs:
           key: v1-repo-{{ .Environment.CIRCLE_SHA1 }}
           paths:
             - ~/repo
-  py27_lint:
-    docker:
-      - image: circleci/python:2.7
-    <<: *set_workdir
-    steps:
-      - *restore_repo_cache
-      - *install_tox
-      - run: tox -e py27-lint
-  py27_unit:
-    docker:
-      - image: circleci/python:2.7
-    <<: *set_workdir
-    steps:
-      - *restore_repo_cache
-      # Ensure minimum virtualenv version due to https://github.com/pypa/virtualenv/issues/1670
-      - run: sudo pip install tox 'virtualenv>=20.0.8'
-      - run: tox -e py27-unit
   py35_docstring:
     docker:
       - image: circleci/python:3.5
@@ -106,14 +89,6 @@ jobs:
       - *restore_repo_cache
       - *install_tox
       - run: tox -e py35-lint_docstring_include_list
-  py27_first_startup:
-    docker:
-      - image: circleci/python:2.7
-    <<: *set_workdir
-    steps:
-      - *restore_repo_cache
-      - *install_tox
-      - run: tox -e py27-first_startup
   py35_lint:
     docker:
       - image: circleci/python:3.5
@@ -136,10 +111,9 @@ jobs:
     <<: *set_workdir
     steps:
       - *restore_repo_cache
-      - run: sh scripts/common_startup.sh
-      - run: wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite
-      - run: mv db_gx_rev_0127.sqlite database/universe.sqlite
-      - run: sh manage_db.sh -c ./config/galaxy.yml.sample upgrade
+      # Use this job to test the latest migrations
+      - run: wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0141.sqlite
+      - run: mv db_gx_rev_0141.sqlite database/universe.sqlite
       - *install_tox
       - run: tox -e py35-first_startup
   validate_test_tools:
@@ -195,12 +169,6 @@ workflows:
   get_code_and_test:
     jobs:
       - get_code
-      - py27_lint:
-          <<: *requires_get_code
-      - py27_unit:
-          <<: *requires_get_code
-      - py27_first_startup:
-          <<: *requires_get_code
       - py35_docstring:
           <<: *requires_get_code
       - py35_lint:

.github/workflows/integration_selenium.yaml

@@ -0,0 +1,45 @@
+name: Integration Selenium
+on: [push, pull_request]
+env:
+  GALAXY_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+  GALAXY_TEST_SELENIUM_REMOTE: '1'
+  GALAXY_TEST_SELENIUM_REMOTE_PORT: "4444"
+  GALAXY_SKIP_CLIENT_BUILD: '0'
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        python-version: [3.7]
+    services:
+      postgres:
+        image: postgres:11
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+      selenium:
+        image: selenium/standalone-chrome:3.141.59
+        ports:
+          - 4444:4444
+    steps:
+    - name: Prune unused docker image, volumes and containers
+      run: docker system prune -a -f
+    - uses: actions/checkout@v2
+      with:
+        path: 'galaxy root'
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache pip dir
+      uses: actions/cache@v1
+      id: pip-cache
+      with:
+        path: ~/.cache/pip
+        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+    - name: Run tests
+      run: './run_tests.sh -integration test/integration_selenium'
+      working-directory: 'galaxy root'

.gitignore

@@ -178,3 +178,4 @@ packages/*/*.egg-info
 config/plugins/visualizations/**/static/script.js
 # TODO: Really need to follow up on this and make it standard.
 config/plugins/visualizations/**/static/main.css
+config/plugins/visualizations/**/static/plugin_build_hash.txt

README.rst

@@ -5,14 +5,14 @@ The latest information about Galaxy can be found on the `Galaxy Community Hub <h
 
 Community support is available at `Galaxy Help <https://help.galaxyproject.org/>`__.
 
-.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
-    :target: https://webchat.freenode.net/?channels=galaxyproject
-    :alt: Chat on irc
-
 .. image:: https://img.shields.io/badge/chat-gitter-blue.svg
     :target: https://gitter.im/galaxyproject/Lobby
     :alt: Chat on gitter
 
+.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
+    :target: https://webchat.freenode.net/?channels=galaxyproject
+    :alt: Chat on irc
+
 .. image:: https://img.shields.io/badge/release-documentation-blue.svg
     :target: https://docs.galaxyproject.org/en/master/
     :alt: Release Documentation
@@ -24,12 +24,12 @@ Community support is available at `Galaxy Help <https://help.galaxyproject.org/>
 Galaxy Quickstart
 =================
 
-Galaxy requires Python 2.7 To check your python version, run:
+Galaxy requires Python 3.5 or 3.6 . To check your Python version, run:
 
 .. code:: console
 
     $ python -V
-    Python 2.7.3
+    Python 3.6.10
 
 Start Galaxy:
 
@@ -38,18 +38,19 @@ Start Galaxy:
     $ sh run.sh
 
 Once Galaxy completes startup, you should be able to view Galaxy in your
-browser at:
+browser at: http://localhost:8080
 
-http://localhost:8080
+For more installation details please see: https://getgalaxy.org/
 
-Configuration & Tools
-=====================
+Documentation is available at: https://docs.galaxyproject.org/
 
-You may wish to make changes from the default configuration. This can be
-done in the ``config/galaxy.ini`` file.
+Tutorials on how to use Galaxy, perform scientific analyses with it, develop Galaxy and its tools, and admin a Galaxy server are at: https://training.galaxyproject.org/
+
+Tools
+=====
 
 Tools can be either installed from the Tool Shed or added manually.
- For details please see the `tutorial <https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/>`__.
+For details please see the `tutorial <https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/>`__.
 Note that not all dependencies for the tools provided in the
 ``tool_conf.xml.sample`` are included. To install them please visit
 "Manage dependencies" in the admin interface.
@@ -58,8 +59,3 @@ Issues and Galaxy Development
 =============================
 
 Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ .
-
-Roadmap
-=============================
-
-Interested in the next steps for Galaxy? Take a look at the `roadmap <https://github.com/galaxyproject/galaxy/projects/8>`__.

client/galaxy/scripts/bundleEntries.js

@@ -95,6 +95,7 @@ export { mountJobMetrics } from "components/JobMetrics";
 export { mountJobParameters } from "components/JobParameters";
 export { mountWorkflowEditor } from "components/Workflow/Editor/mount";
 export { mountPageDisplay } from "components/PageDisplay";
+export { mountDestinationParams } from "components/JobDestinationParams";
 
 // Used in common.mako
 export { default as store } from "storemodern";

client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.test.js

@@ -0,0 +1,67 @@
+import Vuex from "vuex";
+import axios from "axios";
+import MockAdapter from "axios-mock-adapter";
+import { mount, createLocalVue } from "@vue/test-utils";
+import { createStore } from "../../store";
+import flushPromises from "flush-promises";
+import JobDestinationParams from "./JobDestinationParams";
+import jobDestinationResponse from "./testData/jobDestinationResponse";
+
+const JOB_ID = "foo_job_id";
+
+describe("JobDestinationParams/JobDestinationParams.vue", () => {
+    const localVue = createLocalVue();
+    localVue.use(Vuex);
+
+    const responseKeys = Object.keys(jobDestinationResponse);
+
+    let testStore, axiosMock, wrapper;
+
+    beforeEach(async () => {
+        axiosMock = new MockAdapter(axios);
+        testStore = createStore();
+        const propsData = {
+            jobId: JOB_ID,
+        };
+        axiosMock.onGet(`/api/jobs/${JOB_ID}/destination_params`).reply(200, jobDestinationResponse);
+        wrapper = mount(JobDestinationParams, {
+            store: testStore,
+            propsData,
+            localVue,
+        });
+        await flushPromises();
+        assert(responseKeys.length > 0, "test data is invalid!");
+    });
+
+    afterEach(() => {
+        axiosMock.restore();
+    });
+
+    it("destination parameters should exist", async () => {
+        expect(Object.keys(wrapper.vm.jobDestinationParams).length).to.equals(responseKeys.length);
+        expect(wrapper.vm.jobId).to.equals(JOB_ID);
+        expect(wrapper.vm.jobDestinationParams["docker_net"]).to.equals("bridge");
+        expect(wrapper.vm.jobDestinationParams["docker_set_user"]).to.equals(null);
+    });
+
+    it("destination parameters should be rendered", async () => {
+        console.log(wrapper.html());
+        const paramsTable = wrapper.find("#destination_parameters");
+        expect(paramsTable.isVisible()).to.equals(true);
+        const params = paramsTable.findAll("tbody > tr");
+        expect(params.length).to.equals(responseKeys.length);
+
+        for (let counter = 0; counter < responseKeys.length - 1; counter++) {
+            const parameter = params.at(counter).findAll("td");
+            const parameterTitle = parameter.at(0).text();
+            const parameterValue = parameter.at(1).text();
+
+            assert(responseKeys.includes(parameterTitle), "rendered parameter should exist in test data!");
+            // since we render null as an empty string, rendered empty string should always equal null in test data
+            assert(
+                jobDestinationResponse[parameterTitle] === (parameterValue === "" ? null : parameterValue),
+                "parameter value is not equal to test data!"
+            );
+        }
+    });
+});

client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue

@@ -0,0 +1,36 @@
+<template>
+    <div>
+        <table id="destination_parameters" class="tabletip info_data_table">
+            <tbody>
+                <tr v-for="(value, title) in jobDestinationParams" :key="title">
+                    <td>{{ title }}</td>
+                    <td>{{ value }}</td>
+                </tr>
+            </tbody>
+        </table>
+    </div>
+</template>
+
+<script>
+import { mapCacheActions } from "vuex-cache";
+
+export default {
+    props: {
+        jobId: {
+            type: String,
+            required: true,
+        },
+    },
+    created: function () {
+        this.fetchJobDestinationParams(this.jobId);
+    },
+    computed: {
+        jobDestinationParams: function () {
+            return this.$store.getters.jobDestinationParams(this.jobId);
+        },
+    },
+    methods: {
+        ...mapCacheActions(["fetchJobDestinationParams"]),
+    },
+};
+</script>

client/galaxy/scripts/components/JobDestinationParams/index.js

@@ -0,0 +1,3 @@
+export { default as JobDestinationParams } from "./JobDestinationParams";
+
+export { mountDestinationParams } from "./mount";

client/galaxy/scripts/components/JobDestinationParams/mount.js

@@ -0,0 +1,13 @@
+/**
+ * Endpoint for mounting job metrics from non-Vue environment.
+ */
+import $ from "jquery";
+import JobDestinationParams from "./JobDestinationParams.vue";
+import { mountVueComponent } from "utils/mountVueComponent";
+
+export const mountDestinationParams = (propsData = {}) => {
+    $(".job-destination-parameters").each((index, el) => {
+        propsData.jobId = $(el).attr("job_id");
+        mountVueComponent(JobDestinationParams)(propsData, el);
+    });
+};

client/galaxy/scripts/components/JobDestinationParams/testData/jobDestinationResponse.json

@@ -0,0 +1,12 @@
+{
+  "Runner": "local",
+  "Runner Job ID": "23027",
+  "Handler": "main.web.1",
+  "docker_auto_rm": "true",
+  "docker_enabled": "true",
+  "docker_net": "bridge",
+  "docker_set_user": null,
+  "docker_sudo": "false",
+  "docker_volumes": "$galaxy_root:ro,$tool_directory:ro,$job_directory:rw,$working_directory:rw,$default_file_path:ro",
+  "require_container": "true"
+}

client/galaxy/scripts/components/JobMetrics/JobMetrics.test.js

@@ -5,6 +5,7 @@ import { mount, createLocalVue } from "@vue/test-utils";
 import { createStore } from "../../store";
 import flushPromises from "flush-promises";
 import JobMetrics from "./JobMetrics";
+import ec2 from "./ec2.json";
 
 const JOB_ID = "moo";
 
@@ -65,4 +66,63 @@ describe("JobMetrics/JobMetrics.vue", () => {
         expect(metricsTables.at(1).find(".metrics_plugin_title").text()).to.equals("extended");
         expect(metricsTables.at(1).findAll("tr").length).to.equals(1);
     });
+
+    it("should render correct AWS Estimates", async () => {
+        let deriveRenderedAwsEstimate = async (cores, seconds, memory) => {
+            const JOB_ID = Math.random().toString(36).substring(2);
+            const propsData = {
+                jobId: JOB_ID,
+                aws_estimate: "True",
+            };
+            const metricsResponse = [
+                { plugin: "core", name: "galaxy_slots", raw_value: cores },
+                { plugin: "core", name: "runtime_seconds", raw_value: seconds },
+                { plugin: "core", name: "galaxy_memory_mb", raw_value: memory },
+            ];
+            axiosMock.onGet(`/api/jobs/${JOB_ID}/metrics`).reply(200, metricsResponse);
+            const wrapper = mount(JobMetrics, {
+                store: testStore,
+                propsData,
+                localVue,
+            });
+            // Wait for axios and rendering.
+            await flushPromises();
+
+            const estimates = {};
+
+            if (!wrapper.find("#aws-estimate").exists()) return false;
+
+            estimates.cost = wrapper.find("#aws-estimate > b").text();
+            estimates.vcpus = wrapper.find("#aws_vcpus").text();
+            estimates.cpu = wrapper.find("#aws_cpu").text();
+            estimates.mem = wrapper.find("#aws_mem").text();
+            estimates.name = wrapper.find("#aws_name").text();
+
+            return estimates;
+        };
+        let assertAwsInstance = (estimates) => {
+            const instance = ec2.find((instance) => estimates.name === instance.name);
+            expect(estimates.mem).to.equals(instance.mem.toString());
+            expect(estimates.vcpus).to.equals(instance.vcpus.toString());
+            expect(estimates.cpu).to.equals(instance.cpu.toString());
+        };
+
+        let estimates_small = await deriveRenderedAwsEstimate("1.0000000", "9.0000000", "2048.0000000");
+
+        expect(estimates_small.name).to.equals("t2.small");
+        expect(estimates_small.cost).to.equals("0.00 USD");
+        assertAwsInstance(estimates_small);
+
+        let estimates_large = await deriveRenderedAwsEstimate("40.0000000", "18000.0000000", "194560.0000000");
+        expect(estimates_large.name).to.equals("m5d.12xlarge");
+        expect(estimates_large.cost).to.equals("16.32 USD");
+        assertAwsInstance(estimates_large);
+
+        let estimates_not_available = await deriveRenderedAwsEstimate(
+            "99999.0000000",
+            "18000.0000000",
+            "99999.0000000"
+        );
+        expect(estimates_not_available).to.equals(false);
+    });
 });

client/galaxy/scripts/components/JobMetrics/JobMetrics.vue

@@ -12,12 +12,27 @@
                 </tbody>
             </table>
         </div>
+
+        <div id="aws-estimate" v-if="isAwsEstimate && awsEstimate">
+            <h3>AWS estimate</h3>
+            <b>{{ awsEstimate.price }} USD</b><br />
+            This job requested {{ awsEstimate.vcpus }} cores and {{ awsEstimate.memory }} Gb. Given this, the smallest
+            EC2 machine we could find is <span id="aws_name">{{ awsEstimate.instance.name }}</span> (<span
+                id="aws_mem"
+                >{{ awsEstimate.instance.mem }}</span
+            >
+            GB / <span id="aws_vcpus">{{ awsEstimate.instance.vcpus }}</span> vCPUs /
+            <span id="aws_cpu">{{ awsEstimate.instance.cpu }}</span
+            >). That instance is priced at {{ awsEstimate.instance.price }} USD/hour.<br />
+            Please note, that those numbers are only estimates, all jobs are always free of charge for all users.
+        </div>
     </div>
 </template>
 
 <script>
 import { mapCacheActions } from "vuex-cache";
 import { mapGetters } from "vuex";
+import ec2 from "./ec2.json";
 
 export default {
     props: {
@@ -27,6 +42,9 @@ export default {
         datasetId: {
             type: String,
         },
+        aws_estimate: {
+            type: String,
+        },
         datasetType: {
             type: String,
             default: "hda",
@@ -48,6 +66,40 @@ export default {
     },
     computed: {
         ...mapGetters(["getJobMetricsByDatasetId", "getJobMetricsByJobId"]),
+        isAwsEstimate: function () {
+            return this.aws_estimate && this.aws_estimate.toUpperCase() === "true".toUpperCase();
+        },
+        awsEstimate: function () {
+            if (!this.isAwsEstimate) return;
+
+            const aws = {};
+            this.jobMetrics.forEach((metric) => {
+                switch (metric.name) {
+                    case "galaxy_memory_mb":
+                        aws.memory = parseInt(metric.raw_value);
+                        break;
+                    case "galaxy_slots":
+                        aws.vcpus = parseInt(metric.raw_value);
+                        break;
+                    case "runtime_seconds":
+                        aws.seconds = parseInt(metric.raw_value);
+                        break;
+                    default:
+                }
+            });
+
+            if (aws.memory) aws.memory /= 1024;
+            // if memory was not specified, assign the smallest amount (we judge based on CPU-count only)
+            else aws.memory = 0.5;
+
+            // ec2 is already pre-sorted
+            aws.instance = ec2.find((ec) => {
+                return ec.mem >= aws.memory && ec.vcpus >= aws.vcpus;
+            });
+            if (aws.instance === undefined) return;
+            aws.price = ((aws.seconds * aws.instance.price) / 3600).toFixed(2);
+            return aws;
+        },
         jobMetrics: function () {
             if (this.jobId) {
                 return this.getJobMetricsByJobId(this.jobId);

client/galaxy/scripts/components/JobMetrics/ec2.json

@@ -0,0 +1,306 @@
+[
+  {
+    "name": "t2.nano",
+    "mem": 0.5,
+    "price": 0.0067,
+    "priceunit": "Hrs",
+    "vcpus": 1,
+    "cpu": "Intel Xeon Family"
+  },
+  {
+    "name": "t3.nano",
+    "mem": 0.5,
+    "price": 0.006,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Skylake E5 2686 v5 (2.5 GHz)"
+  },
+  {
+    "name": "t2.micro",
+    "mem": 1,
+    "price": 0.0134,
+    "priceunit": "Hrs",
+    "vcpus": 1,
+    "cpu": "Intel Xeon Family"
+  },
+  {
+    "name": "t3.micro",
+    "mem": 1,
+    "price": 0.012,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Skylake E5 2686 v5 (2.5 GHz)"
+  },
+  {
+    "name": "t2.small",
+    "mem": 2,
+    "price": 0.0268,
+    "priceunit": "Hrs",
+    "vcpus": 1,
+    "cpu": "Intel Xeon Family"
+  },
+  {
+    "name": "t3.small",
+    "mem": 2,
+    "price": 0.024,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Skylake E5 2686 v5 (2.5 GHz)"
+  },
+  {
+    "name": "m3.medium",
+    "mem": 3.75,
+    "price": 0.079,
+    "priceunit": "Hrs",
+    "vcpus": 1,
+    "cpu": "Intel Xeon E5-2670 v2 (Ivy Bridge/Sandy Bridge)"
+  },
+  {
+    "name": "t2.medium",
+    "mem": 4,
+    "price": 0.0536,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Xeon Family"
+  },
+  {
+    "name": "t3.medium",
+    "mem": 4,
+    "price": 0.048,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Skylake E5 2686 v5 (2.5 GHz)"
+  },
+  {
+    "name": "m3.large",
+    "mem": 7.5,
+    "price": 0.158,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Xeon E5-2670 v2 (Ivy Bridge/Sandy Bridge)"
+  },
+  {
+    "name": "t2.large",
+    "mem": 8,
+    "price": 0.1072,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Xeon Family"
+  },
+  {
+    "name": "t3.large",
+    "mem": 8,
+    "price": 0.096,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Skylake E5 2686 v5 (2.5 GHz)"
+  },
+  {
+    "name": "m5.large",
+    "mem": 8,
+    "price": 0.115,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m5d.large",
+    "mem": 8,
+    "price": 0.136,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m4.large",
+    "mem": 8,
+    "price": 0.12,
+    "priceunit": "Hrs",
+    "vcpus": 2,
+    "cpu": "Intel Xeon E5-2676 v3 (Haswell)"
+  },
+  {
+    "name": "m3.xlarge",
+    "mem": 15,
+    "price": 0.315,
+    "priceunit": "Hrs",
+    "vcpus": 4,
+    "cpu": "Intel Xeon E5-2670 v2 (Ivy Bridge/Sandy Bridge)"
+  },
+  {
+    "name": "m5.xlarge",
+    "mem": 16,
+    "price": 0.23,
+    "priceunit": "Hrs",
+    "vcpus": 4,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m4.xlarge",
+    "mem": 16,
+    "price": 0.24,
+    "priceunit": "Hrs",
+    "vcpus": 4,
+    "cpu": "Intel Xeon E5-2676 v3 (Haswell)"
+  },
+  {
+    "name": "t3.xlarge",
+    "mem": 16,
+    "price": 0.192,
+    "priceunit": "Hrs",
+    "vcpus": 4,
+    "cpu": "Intel Skylake E5 2686 v5 (2.5 GHz)"
+  },
+  {
+    "name": "t2.xlarge",
+    "mem": 16,
+    "price": 0.2144,
+    "priceunit": "Hrs",
+    "vcpus": 4,
+    "cpu": "Intel Xeon Family"
+  },
+  {
+    "name": "m5d.xlarge",
+    "mem": 16,
+    "price": 0.272,
+    "priceunit": "Hrs",
+    "vcpus": 4,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m3.2xlarge",
+    "mem": 30,
+    "price": 0.632,
+    "priceunit": "Hrs",
+    "vcpus": 8,
+    "cpu": "Intel Xeon E5-2670 v2 (Ivy Bridge/Sandy Bridge)"
+  },
+  {
+    "name": "m5d.2xlarge",
+    "mem": 32,
+    "price": 0.544,
+    "priceunit": "Hrs",
+    "vcpus": 8,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m5.2xlarge",
+    "mem": 32,
+    "price": 0.46,
+    "priceunit": "Hrs",
+    "vcpus": 8,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m4.2xlarge",
+    "mem": 32,
+    "price": 0.48,
+    "priceunit": "Hrs",
+    "vcpus": 8,
+    "cpu": "Intel Xeon E5-2676 v3 (Haswell)"
+  },
+  {
+    "name": "t3.2xlarge",
+    "mem": 32,
+    "price": 0.384,
+    "priceunit": "Hrs",
+    "vcpus": 8,
+    "cpu": "Intel Skylake E5 2686 v5 (2.5 GHz)"
+  },
+  {
+    "name": "t2.2xlarge",
+    "mem": 32,
+    "price": 0.4288,
+    "priceunit": "Hrs",
+    "vcpus": 8,
+    "cpu": "Intel Xeon Family"
+  },
+  {
+    "name": "m5d.4xlarge",
+    "mem": 64,
+    "price": 1.088,
+    "priceunit": "Hrs",
+    "vcpus": 16,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m4.4xlarge",
+    "mem": 64,
+    "price": 0.96,
+    "priceunit": "Hrs",
+    "vcpus": 16,
+    "cpu": "Intel Xeon E5-2676 v3 (Haswell)"
+  },
+  {
+    "name": "m5.4xlarge",
+    "mem": 64,
+    "price": 0.92,
+    "priceunit": "Hrs",
+    "vcpus": 16,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m4.10xlarge",
+    "mem": 160,
+    "price": 2.4,
+    "priceunit": "Hrs",
+    "vcpus": 40,
+    "cpu": "Intel Xeon E5-2676 v3 (Haswell)"
+  },
+  {
+    "name": "m5d.12xlarge",
+    "mem": 192,
+    "price": 3.264,
+    "priceunit": "Hrs",
+    "vcpus": 48,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m5.12xlarge",
+    "mem": 192,
+    "price": 2.76,
+    "priceunit": "Hrs",
+    "vcpus": 48,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m4.16xlarge",
+    "mem": 256,
+    "price": 3.84,
+    "priceunit": "Hrs",
+    "vcpus": 64,
+    "cpu": "Intel Xeon E5-2686 v4 (Broadwell)"
+  },
+  {
+    "name": "m5d.metal",
+    "mem": 384,
+    "price": 6.528,
+    "priceunit": "Hrs",
+    "vcpus": 96,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m5.metal",
+    "mem": 384,
+    "price": 5.52,
+    "priceunit": "Hrs",
+    "vcpus": 96,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m5d.24xlarge",
+    "mem": 384,
+    "price": 6.528,
+    "priceunit": "Hrs",
+    "vcpus": 96,
+    "cpu": "Intel Xeon Platinum 8175"
+  },
+  {
+    "name": "m5.24xlarge",
+    "mem": 384,
+    "price": 5.52,
+    "priceunit": "Hrs",
+    "vcpus": 96,
+    "cpu": "Intel Xeon Platinum 8175"
+  }
+]

client/galaxy/scripts/components/JobMetrics/mount.js

@@ -8,11 +8,13 @@ import { mountVueComponent } from "utils/mountVueComponent";
 export const mountJobMetrics = (propsData = {}) => {
     $(".job-metrics").each((index, el) => {
         const jobId = $(el).attr("job_id");
+        const aws_estimate = $(el).attr("aws_estimate");
         const datasetId = $(el).attr("dataset_id");
         const datasetType = $(el).attr("dataset_type") || "hda";
         propsData.jobId = jobId;
         propsData.datasetId = datasetId;
         propsData.datasetType = datasetType;
+        propsData.aws_estimate = aws_estimate;
         mountVueComponent(JobMetrics)(propsData, el);
     });
 };

client/galaxy/scripts/components/RuleBuilder/ColumnSelector.vue

@@ -0,0 +1,138 @@
+<template>
+    <div class="rule-column-selector" v-if="!multiple || !ordered">
+        <label class="d-flex justify-content-end align-items-center">
+            <span class="mr-auto" v-b-tooltip.hover :title="help">{{ label }}</span>
+            <div class="mr-1" v-b-tooltip.hover :title="title">
+                <select2 :value="target" @input="handleInput" :multiple="multiple">
+                    <option v-for="(col, index) in colHeaders" :value="index" :key="col">{{ col }}</option>
+                </select2>
+            </div>
+            <slot></slot>
+        </label>
+    </div>
+    <div class="rule-column-selector" v-else>
+        <span>{{ label }}</span>
+        <slot></slot>
+        <ol>
+            <li v-for="(targetEl, index) in target" :index="index" :key="targetEl" class="rule-column-selector-target">
+                {{ colHeaders[targetEl] }}
+                <span class="fa fa-times rule-column-selector-target-remove" @click="handleRemove(index)"></span>
+                <span class="fa fa-arrow-up rule-column-selector-up" v-if="index !== 0" @click="moveUp(index)"></span>
+                <span
+                    class="fa fa-arrow-down rule-column-selector-down"
+                    v-if="index < target.length - 1"
+                    @click="moveUp(index + 1)"
+                ></span>
+            </li>
+            <li v-if="this.target.length < this.colHeaders.length">
+                <span class="rule-column-selector-target-add" v-if="!orderedEdit">
+                    <i @click="$emit('update:orderedEdit', true)">... {{ l("Assign Another Column") }}</i>
+                </span>
+                <span class="rule-column-selector-target-select" v-else>
+                    <select2 @input="handleAdd" placeholder="Select a column">
+                        <option /><!-- empty option selection for placeholder -->
+                        <option v-for="(col, index) in remainingHeaders" :value="index" :key="col">{{ col }}</option>
+                    </select2>
+                </span>
+            </li>
+        </ol>
+    </div>
+</template>
+
+<script>
+import Vue from "vue";
+import _l from "utils/localization";
+import Select2 from "components/Select2";
+export default {
+    components: {
+        Select2,
+    },
+    data: function () {
+        return {
+            l: _l,
+        };
+    },
+    props: {
+        target: {
+            required: true,
+        },
+        label: {
+            required: false,
+            type: String,
+            default: _l("From Column"),
+        },
+        help: {
+            required: false,
+        },
+        colHeaders: {
+            type: Array,
+            required: true,
+        },
+        multiple: {
+            type: Boolean,
+            required: false,
+            default: false,
+        },
+        ordered: {
+            type: Boolean,
+            required: false,
+            default: false,
+        },
+        valueAsList: {
+            type: Boolean,
+            required: false,
+            default: false,
+        },
+        orderedEdit: {
+            type: Boolean,
+            required: false,
+            default: false,
+        },
+    },
+    computed: {
+        remainingHeaders() {
+            const colHeaders = this.colHeaders;
+            if (!this.multiple) {
+                return colHeaders;
+            }
+            const remaining = {};
+            for (const key in colHeaders) {
+                if (this.target.indexOf(parseInt(key)) === -1) {
+                    remaining[key] = colHeaders[key];
+                }
+            }
+            return remaining;
+        },
+        title() {
+            return _l("Select a column");
+        },
+    },
+    methods: {
+        handleInput(value) {
+            if (this.multiple) {
+                // https://stackoverflow.com/questions/262427/why-does-parseint-yield-nan-with-arraymap
+                const val = value.map((idx) => parseInt(idx));
+                this.$emit("update:target", val);
+            } else {
+                let val = parseInt(value);
+                if (this.valueAsList) {
+                    val = [val];
+                }
+                this.$emit("update:target", val);
+            }
+        },
+        handleAdd(value) {
+            this.target.push(parseInt(value));
+            this.$emit("update:orderedEdit", false);
+        },
+        handleRemove(index) {
+            this.target.splice(index, 1);
+        },
+        moveUp(value) {
+            const swapVal = this.target[value - 1];
+            Vue.set(this.target, value - 1, this.target[value]);
+            Vue.set(this.target, value, swapVal);
+        },
+    },
+};
+</script>

client/galaxy/scripts/components/RuleBuilder/IdentifierDisplay.vue

@@ -0,0 +1,54 @@
+<template>
+    <li class="rule">
+        <span v-b-tooltip.hover :title="help">Set {{ columnsLabel }} as {{ typeDisplay }}</span>
+        <span v-b-tooltip.hover :title="titleEdit" class="fa fa-edit" @click="edit"></span>
+        <span v-b-tooltip.hover :title="titleRemove" class="fa fa-times" @click="remove"></span>
+    </li>
+</template>
+
+<script>
+import _l from "utils/localization";
+import RuleDefs from "mvc/rules/rule-definitions";
+const MAPPING_TARGETS = RuleDefs.MAPPING_TARGETS;
+
+export default {
+    props: {
+        type: {
+            type: String,
+            required: true,
+        },
+        columns: {
+            required: true,
+        },
+        colHeaders: {
+            type: Array,
+            required: true,
+        },
+    },
+    methods: {
+        remove() {
+            this.$emit("remove");
+        },
+        edit() {
+            this.$emit("edit");
+        },
+    },
+    computed: {
+        typeDisplay() {
+            return MAPPING_TARGETS[this.type].label;
+        },
+        help() {
+            return MAPPING_TARGETS[this.type].help || "";
+        },
+        titleEdit() {
+            return _l("Edit column definition");
+        },
+        titleRemove() {
+            return _l("Remove this column definition");
+        },
+        columnsLabel() {
+            return RuleDefs.columnDisplay(this.columns, this.colHeaders);
+        },
+    },
+};
+</script>

client/galaxy/scripts/components/RuleBuilder/RegularExpressionInput.vue

@@ -0,0 +1,43 @@
+<template>
+    <div>
+        <label for="regular_expression" v-b-tooltip.hover :title="title">{{ label }}</label>
+        <span v-b-popover.html="popoverContent" :title="popoverTitle" class="fa fa-question"></span>
+        <input
+            v-b-tooltip.hover.left
+            :title="title"
+            name="regular_expression"
+            class="rule-regular-expression"
+            type="text"
+            :value="target"
+            @input="$emit('update:target', $event.target.value)"
+        />
+    </div>
+</template>
+
+<script>
+import _l from "utils/localization";
+
+export default {
+    props: {
+        target: {
+            required: true,
+        },
+    },
+    computed: {
+        label() {
+            return _l("Regular Expression");
+        },
+        title() {
+            return _l("Enter a regular expression.");
+        },
+        popoverTitle() {
+            return _l("Regular Expressions");
+        },
+        popoverContent() {
+            return _l(
+                `Regular expressions are patterns used to match character combinations in strings. This input accepts Python-style regular expressions, find more information about these in <a href="https://pythonforbiologists.com/regular-expressions/">this Python for Biologists tutorial</a>.`
+            );
+        },
+    },
+};
+</script>

client/galaxy/scripts/components/RuleBuilder/RuleComponent.vue

@@ -0,0 +1,48 @@
+<template>
+    <div v-if="ruleType == displayRuleType" class="rule-editor" :class="typeToClass">
+        <slot></slot>
+        <div class="buttons rule-edit-buttons d-flex justify-content-end">
+            <button type="button" class="btn rule-editor-cancel mr-1" @click="cancel">{{ cancelLabel }}</button>
+            <button type="button" class="btn btn-primary rule-editor-ok" @click="okay">{{ applyLabel }}</button>
+        </div>
+    </div>
+</template>
+
+<script>
+import _l from "utils/localization";
+
+export default {
+    data: function () {
+        return {
+            applyLabel: _l("Apply"),
+            cancelLabel: _l("Cancel"),
+        };
+    },
+    props: {
+        ruleType: {
+            type: String,
+            required: true,
+        },
+        displayRuleType: {
+            required: true,
+        },
+        builder: {
+            required: true,
+        },
+    },
+    methods: {
+        cancel() {
+            this.builder.displayRuleType = null;
+        },
+        okay() {
+            this.builder.handleRuleSave(this.ruleType);
+            this.cancel();
+        },
+    },
+    computed: {
+        typeToClass() {
+            return "rule-edit-" + this.ruleType.replace(/_/g, "-");
+        },
+    },
+};
+</script>

client/galaxy/scripts/components/RuleBuilder/RuleDisplay.vue

@@ -0,0 +1,54 @@
+<template>
+    <li class="rule">
+        <span class="rule-display">
+            <span class="mr-1">{{ title }}</span>
+            <span v-b-tooltip.hover :title="editTitle" class="fa fa-edit mr-1" @click="edit"></span>
+            <span v-b-tooltip.hover :title="removeTitle" class="fa fa-times map" @click="remove"></span>
+        </span>
+        <span class="rule-warning" v-if="rule.warn">
+            {{ rule.warn }}
+        </span>
+        <span class="rule-error" v-if="rule.error">
+            <span class="alert-message">{{ rule.error }}</span>
+        </span>
+    </li>
+</template>
+
+<script>
+import _l from "utils/localization";
+import RuleDefs from "mvc/rules/rule-definitions";
+const RULES = RuleDefs.RULES;
+
+export default {
+    props: {
+        rule: {
+            required: true,
+            type: Object,
+        },
+        colHeaders: {
+            type: Array,
+            required: true,
+        },
+    },
+    computed: {
+        title() {
+            const ruleType = this.rule.type;
+            return RULES[ruleType].display(this.rule, this.colHeaders);
+        },
+        editTitle() {
+            return _l("Edit this rule.");
+        },
+        removeTitle() {
+            return _l("Remove this rule.");
+        },
+    },
+    methods: {
+        edit() {
+            this.$emit("edit");
+        },
+        remove() {
+            this.$emit("remove");
+        },
+    },
+};
+</script>

client/galaxy/scripts/components/RuleBuilder/RuleModalFooter.vue

@@ -0,0 +1,10 @@
+<template>
+    <div class="rule-footer footer flex-row no-flex">
+        <slot name="inputs"></slot>
+        <div class="actions clear vertically-spaced">
+            <div class="main-options float-right">
+                <slot></slot>
+            </div>
+        </div>
+    </div>
+</template>

client/galaxy/scripts/components/RuleBuilder/RuleModalHeader.vue

@@ -0,0 +1,3 @@
+<template>
+    <div class="header flex-row no-flex"><slot></slot></div>
+</template>

client/galaxy/scripts/components/RuleBuilder/RuleModalMiddle.vue

@@ -0,0 +1,3 @@
+<template>
+    <div class="middle flex-row flex-row-container"><slot></slot></div>
+</template>

client/galaxy/scripts/components/RuleBuilder/RuleTargetComponent.vue

@@ -0,0 +1,34 @@
+<template>
+    <a
+        class="rule-link dropdown-item"
+        href="javascript:void(0)"
+        :class="linkClassName"
+        @click="builder.addNewRule(ruleType)"
+        >{{ title }}</a
+    >
+</template>
+
+<script>
+import RuleDefs from "mvc/rules/rule-definitions";
+const RULES = RuleDefs.RULES;
+
+export default {
+    props: {
+        ruleType: {
+            type: String,
+            required: true,
+        },
+        builder: {
+            required: true,
+        },
+    },
+    computed: {
+        linkClassName() {
+            return "rule-link-" + this.ruleType.replace(/_/g, "-");
+        },
+        title() {
+            return RULES[this.ruleType].title;
+        },
+    },
+};
+</script>

client/galaxy/scripts/components/RuleBuilder/StateDiv.vue

@@ -0,0 +1,5 @@
+<template>
+    <div class="rule-collection-creator collection-creator flex-row-container">
+        <slot></slot>
+    </div>
+</template>

client/galaxy/scripts/components/RuleCollectionBuilder.vue

@@ -576,360 +576,22 @@ import RuleDefs from "mvc/rules/rule-definitions";
 import Vue from "vue";
 import BootstrapVue from "bootstrap-vue";
 import Select2 from "components/Select2";
+import ColumnSelector from "components/RuleBuilder/ColumnSelector";
+import RegularExpressionInput from "components/RuleBuilder/RegularExpressionInput";
+import RuleDisplay from "components/RuleBuilder/RuleDisplay";
+import IdentifierDisplay from "components/RuleBuilder/IdentifierDisplay";
+import RuleTargetComponent from "components/RuleBuilder/RuleTargetComponent";
+import RuleComponent from "components/RuleBuilder/RuleComponent";
+import RuleModalHeader from "components/RuleBuilder/RuleModalHeader";
+import RuleModalMiddle from "components/RuleBuilder/RuleModalMiddle";
+import RuleModalFooter from "components/RuleBuilder/RuleModalFooter";
+import StateDiv from "components/RuleBuilder/StateDiv";
 
 Vue.use(BootstrapVue);
 
 const RULES = RuleDefs.RULES;
 const MAPPING_TARGETS = RuleDefs.MAPPING_TARGETS;
 
-const ColumnSelector = {
-    template: `
-        <div class="rule-column-selector" v-if="!multiple || !ordered">
-            <label class="d-flex justify-content-end align-items-center">
-                <span class="mr-auto" v-b-tooltip.hover :title="help">{{ label }}</span>
-                <div class="mr-1" v-b-tooltip.hover :title="title"><select2 :value="target" @input="handleInput" :multiple="multiple">
-                    <option v-for="(col, index) in colHeaders" :value="index">{{ col }}</option>
-                </select2></div>
-                <slot></slot>
-            </label>
-        </div>
-        <div class="rule-column-selector" v-else>
-            <span>{{ label }}</span>
-            <slot></slot>
-            <ol>
-                <li v-for="(targetEl, index) in target"
-                    v-bind:index="index"
-                    v-bind:key="targetEl"
-                    class="rule-column-selector-target">
-                    {{ colHeaders[targetEl] }}
-                    <span class="fa fa-times rule-column-selector-target-remove" @click="handleRemove(index)"></span>
-                    <span class="fa fa-arrow-up rule-column-selector-up" v-if="index !== 0" @click="moveUp(index)"></span>
-                    <span class="fa fa-arrow-down rule-column-selector-down" v-if="index < target.length - 1" @click="moveUp(index + 1)"></span>
-                </li>
-                <li v-if="this.target.length < this.colHeaders.length">
-                    <span class="rule-column-selector-target-add" v-if="!orderedEdit">
-                        <i @click="$emit('update:orderedEdit', true)">... {{ l("Assign Another Column") }}</i>
-                    </span>
-                    <span class="rule-column-selector-target-select" v-else>
-                        <select2 @input="handleAdd" placeholder="Select a column">
-                            <option /><!-- empty option selection for placeholder -->
-                            <option v-for="(col, index) in remainingHeaders" :value="index">{{ col }}</option>
-                        </select2>
-                    </span>
-                </li>
-            </ol>
-        </div>
-    `,
-    data: function () {
-        return {
-            l: _l,
-        };
-    },
-    props: {
-        target: {
-            required: true,
-        },
-        label: {
-            required: false,
-            type: String,
-            default: _l("From Column"),
-        },
-        help: {
-            required: false,
-        },
-        colHeaders: {
-            type: Array,
-            required: true,
-        },
-        multiple: {
-            type: Boolean,
-            required: false,
-            default: false,
-        },
-        ordered: {
-            type: Boolean,
-            required: false,
-            default: false,
-        },
-        valueAsList: {
-            type: Boolean,
-            required: false,
-            default: false,
-        },
-        orderedEdit: {
-            type: Boolean,
-            required: false,
-            default: false,
-        },
-    },
-    computed: {
-        remainingHeaders() {
-            const colHeaders = this.colHeaders;
-            if (!this.multiple) {
-                return colHeaders;
-            }
-            const remaining = {};
-            for (const key in colHeaders) {
-                if (this.target.indexOf(parseInt(key)) === -1) {
-                    remaining[key] = colHeaders[key];
-                }
-            }
-            return remaining;
-        },
-        title() {
-            return _l("Select a column");
-        },
-    },
-    methods: {
-        handleInput(value) {
-            if (this.multiple) {
-                // https://stackoverflow.com/questions/262427/why-does-parseint-yield-nan-with-arraymap
-                const val = value.map((idx) => parseInt(idx));
-                this.$emit("update:target", val);
-            } else {
-                let val = parseInt(value);
-                if (this.valueAsList) {
-                    val = [val];
-                }
-                this.$emit("update:target", val);
-            }
-        },
-        handleAdd(value) {
-            this.target.push(parseInt(value));
-            this.$emit("update:orderedEdit", false);
-        },
-        handleRemove(index) {
-            this.target.splice(index, 1);
-        },
-        moveUp(value) {
-            const swapVal = this.target[value - 1];
-            Vue.set(this.target, value - 1, this.target[value]);
-            Vue.set(this.target, value, swapVal);
-        },
-    },
-    components: {
-        Select2,
-    },
-};
-
-const RegularExpressionInput = {
-    template: `
-        <div>
-            <label for="regular_expression" v-b-tooltip.hover :title="title">{{ label }}</label>
-            <span v-b-popover.html="popoverContent" :title="popoverTitle" class="fa fa-question"></span>
-            <input v-b-tooltip.hover.left :title="title" name="regular_expression" class="rule-regular-expression" type="text" :value="target" @input="$emit('update:target', $event.target.value)" />
-        </div>
-    `,
-    props: {
-        target: {
-            required: true,
-        },
-    },
-    computed: {
-        label() {
-            return _l("Regular Expression");
-        },
-        title() {
-            return _l("Enter a regular expression.");
-        },
-        popoverTitle() {
-            return _l("Regular Expressions");
-        },
-        popoverContent() {
-            return _l(
-                `Regular expressions are patterns used to match character combinations in strings. This input accepts Python-style regular expressions, find more information about these in <a href="https://pythonforbiologists.com/regular-expressions/">this Python for Biologists tutorial</a>.`
-            );
-        },
-    },
-};
-
-const RuleDisplay = {
-    template: `
-        <li class="rule">
-            <span class="rule-display">
-                <span class="mr-1">{{ title }}</span>
-                <span v-b-tooltip.hover :title="editTitle" class="fa fa-edit mr-1" @click="edit"></span>
-                <span v-b-tooltip.hover :title="removeTitle" class="fa fa-times map" @click="remove"></span>
-            </span>
-            <span class="rule-warning" v-if="rule.warn">
-                {{ rule.warn }}
-            </span>
-            <span class="rule-error" v-if="rule.error">
-                <span class="alert-message">{{ rule.error }}</span>
-            </span>
-        </li>
-    `,
-    props: {
-        rule: {
-            required: true,
-            type: Object,
-        },
-        colHeaders: {
-            type: Array,
-            required: true,
-        },
-    },
-    computed: {
-        title() {
-            const ruleType = this.rule.type;
-            return RULES[ruleType].display(this.rule, this.colHeaders);
-        },
-        editTitle() {
-            return _l("Edit this rule.");
-        },
-        removeTitle() {
-            return _l("Remove this rule.");
-        },
-    },
-    methods: {
-        edit() {
-            this.$emit("edit");
-        },
-        remove() {
-            this.$emit("remove");
-        },
-    },
-};
-
-const IdentifierDisplay = {
-    template: `
-      <li class="rule">
-        <span v-b-tooltip.hover :title="help">Set {{ columnsLabel }} as {{ typeDisplay }}</span>
-        <span v-b-tooltip.hover :title="titleEdit" class="fa fa-edit" @click="edit"></span>
-        <span v-b-tooltip.hover :title="titleRemove" class="fa fa-times" @click="remove"></span>
-      </li>
-    `,
-    props: {
-        type: {
-            type: String,
-            required: true,
-        },
-        columns: {
-            required: true,
-        },
-        colHeaders: {
-            type: Array,
-            required: true,
-        },
-    },
-    methods: {
-        remove() {
-            this.$emit("remove");
-        },
-        edit() {
-            this.$emit("edit");
-        },
-    },
-    computed: {
-        typeDisplay() {
-            return MAPPING_TARGETS[this.type].label;
-        },
-        help() {
-            return MAPPING_TARGETS[this.type].help || "";
-        },
-        titleEdit() {
-            return _l("Edit column definition");
-        },
-        titleRemove() {
-            return _l("Remove this column definition");
-        },
-        columnsLabel() {
-            return RuleDefs.columnDisplay(this.columns, this.colHeaders);
-        },
-    },
-};
-
-const RuleTargetComponent = {
-    template: `<a class="rule-link dropdown-item" href="javascript:void(0)" :class="linkClassName" @click="builder.addNewRule(ruleType)">{{title}}</a>`,
-    props: {
-        ruleType: {
-            type: String,
-            required: true,
-        },
-        builder: {
-            required: true,
-        },
-    },
-    computed: {
-        linkClassName() {
-            return "rule-link-" + this.ruleType.replace(/_/g, "-");
-        },
-        title() {
-            return RULES[this.ruleType].title;
-        },
-    },
-};
-
-const RuleComponent = {
-    template: `
-    <div v-if="ruleType == displayRuleType" class="rule-editor" :class="typeToClass">
-        <slot></slot>
-        <div class="buttons rule-edit-buttons d-flex justify-content-end">
-           <button type="button" class="btn rule-editor-cancel mr-1" @click="cancel">{{ cancelLabel }}</button>
-           <button type="button" class="btn btn-primary rule-editor-ok" @click="okay">{{ applyLabel }}</button>
-        </div>
-    </div>`,
-    data: function () {
-        return {
-            applyLabel: _l("Apply"),
-            cancelLabel: _l("Cancel"),
-        };
-    },
-    props: {
-        ruleType: {
-            type: String,
-            required: true,
-        },
-        displayRuleType: {
-            required: true,
-        },
-        builder: {
-            required: true,
-        },
-    },
-    methods: {
-        cancel() {
-            this.builder.displayRuleType = null;
-        },
-        okay() {
-            this.builder.handleRuleSave(this.ruleType);
-            this.cancel();
-        },
-    },
-    computed: {
-        typeToClass() {
-            return "rule-edit-" + this.ruleType.replace(/_/g, "-");
-        },
-    },
-};
-
-const StateDiv = {
-    template: `
-        <div class="rule-collection-creator collection-creator flex-row-container">
-            <slot></slot>
-        </div>`,
-};
-
-const RuleModalHeader = {
-    template: `<div class="header flex-row no-flex"><slot></slot></div>`,
-};
-
-const RuleModalMiddle = {
-    template: `<div class="middle flex-row flex-row-container"><slot></slot></div>`,
-};
-
-const RuleModalFooter = {
-    template: `
-        <div class="rule-footer footer flex-row no-flex">
-            <slot name="inputs"></slot>
-            <div class="actions clear vertically-spaced">
-                <div class="main-options float-right">
-                    <slot></slot>
-                </div>
-            </div>
-        </div>`,
-};
-
 export default {
     data: function () {
         let orientation = "vertical";
@@ -1977,19 +1639,19 @@ export default {
 <style>
 .table-column {
     width: 100%;
-    /* overflow: scroll; */
+    overflow: hidden;
 }
 .select2-container {
     min-width: 60px;
 }
 .vertical #hot-table {
     width: 100%;
-    overflow: scroll;
+    overflow: hidden;
     height: 400px;
 }
 .horizontal #hot-table {
     width: 100%;
-    overflow: scroll;
+    overflow: hidden;
     height: 250px;
 }
 .rule-builder-body {

client/galaxy/scripts/components/ToolRecommendation.vue

@@ -1,6 +1,6 @@
 <template>
-    <div id="tool-recommendation" class="tool-recommendation-view">
-        <div v-if="!deprecated" class="infomessagelarge">
+    <div>
+        <div v-if="!deprecated && showMessage" class="infomessagelarge">
             <h4>Tool recommendation</h4>
             You have used {{ getToolId }} tool. For further analysis, you could try using the following/recommended
             tools. The recommended tools are shown in the decreasing order of their scores predicted using machine
@@ -8,14 +8,17 @@
             tool than a tool with a lower score. Please click on one of the following/recommended tools to open its
             definition.
         </div>
-        <div v-else class="warningmessagelarge">You have used {{ getToolId }} tool. {{ deprecatedMessage }}</div>
+        <div v-else-if="deprecated" class="warningmessagelarge">
+            You have used {{ getToolId }} tool. {{ deprecatedMessage }}
+        </div>
+        <div id="tool-recommendation" class="tool-recommendation-view"></div>
     </div>
 </template>
 
 <script>
 import * as d3 from "d3";
 import { getAppRoot } from "onload/loadConfig";
-import axios from "axios";
+import { getDatatypeMapping, getToolPredictions } from "components/Workflow/Editor/services";
 
 export default {
     props: {
@@ -26,8 +29,9 @@ export default {
     },
     data() {
         return {
-            deprecated: null,
+            deprecated: false,
             deprecatedMessage: "",
+            showMessage: false,
         };
     },
     created() {
@@ -46,86 +50,75 @@ export default {
     methods: {
         loadRecommendations() {
             const toolId = this.getToolId;
-            const url = `${getAppRoot()}api/workflows/get_tool_predictions`;
-            axios
-                .post(url, {
-                    tool_sequence: toolId,
-                })
-                .then((response) => {
-                    axios.get(`${getAppRoot()}api/datatypes/mapping`).then((responseMapping) => {
-                        const predData = response.data.predicted_data;
-                        const datatypesMapping = responseMapping.data;
-                        const extToType = datatypesMapping.ext_to_class_name;
-                        const typeToType = datatypesMapping.class_to_classes;
-                        this.deprecated = predData.is_deprecated;
-
-                        if (response.data !== null && predData.children.length > 0) {
-                            const filteredData = {};
-                            const compatibleTools = {};
-                            const filteredChildren = [];
-                            const outputDatatypes = predData.o_extensions;
-                            const children = predData.children;
-                            for (const nameObj of children.entries()) {
-                                const inputDatatypes = nameObj[1].i_extensions;
-                                for (const out_t of outputDatatypes.entries()) {
-                                    for (const in_t of inputDatatypes.entries()) {
-                                        const child = extToType[out_t[1]];
-                                        const parent = extToType[in_t[1]];
-                                        if (
-                                            (typeToType[child] && parent in typeToType[child]) === true ||
-                                            out_t[1] === "input" ||
-                                            out_t[1] === "_sniff_" ||
-                                            out_t[1] === "input_collection"
-                                        ) {
-                                            compatibleTools[nameObj[1].tool_id] = nameObj[1].name;
-                                            break;
-                                        }
-                                    }
-                                }
-                            }
-                            for (const id in compatibleTools) {
-                                for (const nameObj of children.entries()) {
-                                    if (nameObj[1].tool_id === id) {
-                                        filteredChildren.push(nameObj[1]);
+            const requestData = {
+                tool_sequence: toolId,
+            };
+            getToolPredictions(requestData).then((responsePred) => {
+                getDatatypeMapping().then((datatypesMapping) => {
+                    const predData = responsePred.predicted_data;
+                    const extToType = datatypesMapping.ext_to_class_name;
+                    const typeToType = datatypesMapping.class_to_classes;
+                    this.deprecated = predData.is_deprecated;
+                    this.deprecatedMessage = predData.message;
+                    if (responsePred !== null && predData.children.length > 0) {
+                        const filteredData = {};
+                        const compatibleTools = {};
+                        const filteredChildren = [];
+                        const outputDatatypes = predData.o_extensions;
+                        const children = predData.children;
+                        for (const nameObj of children.entries()) {
+                            const inputDatatypes = nameObj[1].i_extensions;
+                            for (const outT of outputDatatypes.entries()) {
+                                for (const inTool of inputDatatypes.entries()) {
+                                    const child = extToType[outT[1]];
+                                    const parent = extToType[inTool[1]];
+                                    if (
+                                        (typeToType[child] && parent in typeToType[child]) === true ||
+                                        outT[1] === "input" ||
+                                        outT[1] === "_sniff_" ||
+                                        outT[1] === "input_collection"
+                                    ) {
+                                        compatibleTools[nameObj[1].tool_id] = nameObj[1].name;
                                         break;
                                     }
                                 }
                             }
-                            filteredData.o_extensions = predData.o_extensions;
-                            filteredData.name = predData.name;
-                            filteredData.children = filteredChildren;
-                            if (filteredChildren.length > 0 && this.deprecated === false) {
-                                this.renderD3Tree(filteredData);
-                            } else if (this.deprecated === true) {
-                                this.deprecatedMessage = predData.message;
+                        }
+                        for (const id in compatibleTools) {
+                            for (const nameObj of children.entries()) {
+                                if (nameObj[1].tool_id === id) {
+                                    filteredChildren.push(nameObj[1]);
+                                    break;
+                                }
                             }
                         }
-                    });
+                        filteredData.o_extensions = predData.o_extensions;
+                        filteredData.name = predData.name;
+                        filteredData.children = filteredChildren;
+                        if (filteredChildren.length > 0 && this.deprecated === false) {
+                            this.showMessage = true;
+                            this.renderD3Tree(filteredData);
+                        }
+                    }
                 });
+            });
         },
         renderD3Tree(predictedTools) {
-            const duration = 750;
-            const svg = d3.select("#tool-recommendation").append("svg").attr("class", "tree-size").append("g");
             let i = 0;
             let root = null;
-            let x = 0;
-            let y = 0;
-            let translateX = 0;
-
+            const duration = 750;
+            const maxTextLength = 20;
+            const svg = d3.select("#tool-recommendation").append("svg").attr("class", "tree-size").append("g");
             const gElem = svg[0][0];
             const svgElem = gElem.parentNode;
             const clientH = svgElem.clientHeight;
             const clientW = svgElem.clientWidth;
-            y = parseInt(clientH * 0.9);
-            x = parseInt(clientW * 0.6);
-            translateX = parseInt(clientW * 0.15);
+            const translateX = parseInt(clientW * 0.15);
 
-            svgElem.setAttribute("viewBox", "0 0 " + x + " " + clientH);
-            svgElem.setAttribute("preserveAspectRatio", "xMinYMin");
-            gElem.setAttribute("transform", "translate(" + translateX + ", 5)");
-
-            const tree = d3.layout.tree().size([y, x]);
+            svgElem.setAttribute("viewBox", -translateX + " 0 " + 0.5 * clientW + " " + clientH);
+            svgElem.setAttribute("preserveAspectRatio", "xMidYMid meet");
 
+            const tree = d3.layout.tree().size([clientH, clientW]);
             const diagonal = d3.svg.diagonal().projection((d) => {
                 return [d.y, d.x];
             });
@@ -135,9 +128,9 @@ export default {
                 const links = tree.links(nodes);
                 // Normalize for fixed-depth.
                 nodes.forEach((d) => {
-                    d.y = d.depth * 180;
+                    d.y = d.depth * (clientW / 10);
                 });
-                // Update the nodes…
+                // Update the nodes
                 const node = svg.selectAll("g.node").data(nodes, (d) => {
                     return d.id || (d.id = ++i);
                 });
@@ -161,11 +154,14 @@ export default {
                         return d.children || d._children ? "end" : "start";
                     })
                     .text((d) => {
+                        const tName = d.name;
+                        if (tName.length > maxTextLength) {
+                            return tName.slice(0, maxTextLength) + "...";
+                        }
                         return d.name;
-                    })
-                    .attr("class", "node-enter");
+                    });
                 nodeEnter.append("title").text((d) => {
-                    return d.children || d._children ? "Click to collapse" : "Click to open tool definition";
+                    return d.children || d._children ? d.name : "Open tool - " + d.name;
                 });
                 // Transition nodes to their new position.
                 const nodeUpdate = node
@@ -174,19 +170,15 @@ export default {
                     .attr("transform", (d) => {
                         return "translate(" + d.y + "," + d.x + ")";
                     });
-                nodeUpdate.select("circle").attr("r", 4.5);
-                nodeUpdate.select("text").attr("class", "node-update");
+                nodeUpdate.select("circle").attr("r", 2.5);
                 // Transition exiting nodes to the parent's new position.
-                const nodeExit = node
-                    .exit()
+                node.exit()
                     .transition()
                     .duration(duration)
                     .attr("transform", (d) => {
                         return "translate(" + source.y + "," + source.x + ")";
                     })
                     .remove();
-                nodeExit.select("circle").attr("r", 1e-6);
-                nodeExit.select("text").attr("class", "node-enter");
                 // Update the links
                 const link = svg.selectAll("path.link").data(links, (d) => {
                     return d.target.id;
@@ -239,7 +231,7 @@ export default {
                 }
             };
             root = predictedTools;
-            root.x0 = y / 2;
+            root.x0 = parseInt(clientH / 2);
             root.y0 = 0;
             root.children.forEach(collapse);
             update(root);

client/galaxy/scripts/components/Toolshed/Index.vue

@@ -4,6 +4,7 @@
         <div v-else>
             <b-input-group class="mb-3">
                 <b-input
+                    id="toolshed-repo-search"
                     placeholder="Search Repositories"
                     v-model="queryInput"
                     @input="delayQuery"

client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationSettings.vue

@@ -1,5 +1,5 @@
 <template>
-    <b-modal :static="modalStatic" v-model="modalShow" @ok="onOk" @hide="onHide">
+    <b-modal id="repo-install-settings" :static="modalStatic" v-model="modalShow" @ok="onOk" @hide="onHide">
         <template v-slot:modal-header>
             <h4 class="title m-0">
                 {{ modalTitle }}

client/galaxy/scripts/components/Toolshed/SearchList/Repositories.vue

@@ -1,6 +1,6 @@
 <template>
     <div>
-        <b-table striped :items="repositories" :fields="fields">
+        <b-table striped id="shed-search-results" :items="repositories" :fields="fields">
             <template v-slot:cell(name)="row">
                 <b-link href="javascript:void(0)" role="button" class="font-weight-bold" @click="row.toggleDetails">
                     {{ row.item.name }}

client/galaxy/scripts/components/Upload/UploadBoxMixin.js

@@ -260,6 +260,7 @@ export default {
             // add ftp file viewer
             this.ftp = new Popover({
                 title: _l("FTP files"),
+                class: "ftp-upload",
                 container: $(this.$refs.btnFtp),
             });
         },

client/galaxy/scripts/components/User/UserPreferencesModel.js

@@ -83,7 +83,7 @@ export const getUserPreferencesModel = () => {
         },
         logout: {
             title: _l("Sign Out"),
-            id: "edit-preferences-custom-builds",
+            id: "edit-preferences-sign-out",
             description: _l("Click here to sign out of all sessions."),
             icon: "fa-sign-out",
             shouldRender: !!Galaxy.session_csrf_token,

client/galaxy/scripts/components/Workflow/Editor/Node.vue

@@ -10,6 +10,19 @@
             >
                 <i class="fa fa-times" />
             </b-button>
+            <b-button
+                :id="popoverId"
+                v-if="isEnabled"
+                class="node-recommendations py-0 float-right"
+                variant="primary"
+                size="sm"
+                aria-label="tool recommendations"
+            >
+                <i class="fa fa-arrow-right" />
+            </b-button>
+            <b-popover :target="popoverId" triggers="hover" placement="bottom" :show.sync="popoverShow">
+                <WorkflowRecommendations :node="node" @onCreate="onCreate" />
+            </b-popover>
             <b-button
                 v-if="canClone"
                 class="node-clone py-0 float-right"
@@ -35,13 +48,22 @@
 import Vue from "vue";
 import BootstrapVue from "bootstrap-vue";
 import WorkflowIcons from "components/Workflow/icons";
+import { getModule } from "./services";
 import LoadingSpan from "components/LoadingSpan";
+import { getGalaxyInstance } from "app";
+import WorkflowRecommendations from "components/Workflow/Editor/Recommendations";
 
 Vue.use(BootstrapVue);
 
 export default {
     components: {
         LoadingSpan,
+        WorkflowRecommendations,
+    },
+    data() {
+        return {
+            popoverShow: false,
+        };
     },
     props: {
         id: {
@@ -60,6 +82,10 @@ export default {
             type: Object,
             default: null,
         },
+        nodeId: {
+            type: String,
+            default: "",
+        },
     },
     computed: {
         iconClass() {
@@ -69,9 +95,15 @@ export default {
             }
             return null;
         },
+        popoverId() {
+            return `popover-${this.nodeId}`;
+        },
         canClone() {
             return this.type != "subworkflow";
         },
+        isEnabled() {
+            return getGalaxyInstance().config.enable_tool_recommendations;
+        },
     },
     methods: {
         onDestroy() {
@@ -80,6 +112,18 @@ export default {
         onClone() {
             this.node.clone();
         },
+        onCreate(toolId, event) {
+            const requestData = {
+                tool_id: toolId,
+                type: "tool",
+                _: "true",
+            };
+            getModule(requestData).then((response) => {
+                var node = this.node.app.create_node("tool", response.name, toolId);
+                this.node.app.set_node(node, response);
+                this.popoverShow = false;
+            });
+        },
     },
 };
 </script>

client/galaxy/scripts/components/Workflow/Editor/Recommendations.vue

@@ -0,0 +1,145 @@
+<template>
+    <div class="workflow-recommendations">
+        <div class="header-background">
+            <h4>{{ popoverHeaderText }}</h4>
+        </div>
+        <LoadingSpan v-if="showLoading" message="Loading recommendations" />
+        <div v-if="compatibleTools.length > 0 && !isDeprecated">
+            <div v-for="tool in compatibleTools" :key="tool.id">
+                <i class="fa mr-1 fa-wrench"></i>
+                <a href="#" title="Open tool" :id="tool.id" @click="$emit('onCreate', tool.id, $event)">
+                    {{ tool.name }}
+                </a>
+            </div>
+        </div>
+        <div v-else-if="isDeprecated">
+            {{ deprecatedMessage }}
+        </div>
+        <div v-if="compatibleTools.length === 0 && !showLoading">
+            {{ noRecommendationsMessage }}
+        </div>
+    </div>
+</template>
+
+<script>
+import { getToolPredictions } from "./services";
+import LoadingSpan from "components/LoadingSpan";
+import _l from "utils/localization";
+
+export default {
+    components: {
+        LoadingSpan,
+    },
+    props: {
+        node: {
+            type: Object,
+            required: true,
+        },
+    },
+    data() {
+        return {
+            compatibleTools: [],
+            isDeprecated: false,
+            popoverHeaderText: _l("Tool recommendations"),
+            noRecommendationsMessage: _l("No tool recommendations"),
+            deprecatedMessage: "",
+            showLoading: true,
+        };
+    },
+    created() {
+        this.loadRecommendations();
+    },
+    methods: {
+        getToolId(toolId) {
+            if (toolId !== undefined && toolId !== null && toolId.indexOf("/") > -1) {
+                const toolIdSlash = toolId.split("/");
+                toolId = toolIdSlash[toolIdSlash.length - 2];
+            }
+            return toolId;
+        },
+        getWorkflowPath(wfSteps, currentNodeId) {
+            const steps = {};
+            const stepNames = {};
+            for (const stpIdx in wfSteps.steps) {
+                const step = wfSteps.steps[stpIdx];
+                const inputConnections = step.input_connections;
+                stepNames[step.id] = this.getToolId(step.content_id);
+                for (const icIdx in inputConnections) {
+                    const ic = inputConnections[icIdx];
+                    if (ic !== null && ic !== undefined) {
+                        const prevConn = [];
+                        for (const conn of ic) {
+                            prevConn.push(conn.id.toString());
+                        }
+                        steps[step.id.toString()] = prevConn;
+                    }
+                }
+            }
+            // recursive call to determine path
+            function readPaths(nodeId, ph) {
+                for (const st in steps) {
+                    if (parseInt(st) === parseInt(nodeId)) {
+                        const parentId = parseInt(steps[st][0]);
+                        if (parentId !== undefined && parentId !== null) {
+                            ph.push(parentId);
+                            if (steps[parentId] !== undefined && steps[parentId] !== null) {
+                                readPaths(parentId, ph);
+                            }
+                        }
+                    }
+                }
+                return ph;
+            }
+            let ph = [];
+            const stepNameList = [];
+            ph.push(currentNodeId);
+            ph = readPaths(currentNodeId, ph);
+            for (const sIdx of ph) {
+                const sName = stepNames[sIdx.toString()];
+                if (sName !== undefined && sName !== null) {
+                    stepNameList.push(sName);
+                }
+            }
+            return stepNameList.join(",");
+        },
+        loadRecommendations() {
+            const workflowSimple = this.node.app.to_simple();
+            const node = this.node;
+            const toolSequence = this.getWorkflowPath(workflowSimple, node.id);
+            const requestData = { tool_sequence: toolSequence };
+            getToolPredictions(requestData).then((responsePred) => {
+                const predictedData = responsePred.predicted_data;
+                const outputDatatypes = predictedData.o_extensions;
+                const predictedDataChildren = predictedData.children;
+                const app = this.node.app;
+                this.isDeprecated = predictedData.is_deprecated;
+                this.deprecatedMessage = predictedData.message;
+                if (predictedDataChildren.length > 0) {
+                    const cTools = [];
+                    for (const nameObj of predictedDataChildren.entries()) {
+                        const t = {};
+                        const inputDatatypes = nameObj[1].i_extensions;
+                        for (const outT of outputDatatypes.entries()) {
+                            for (const inTool of inputDatatypes.entries()) {
+                                if (
+                                    app.isSubType(outT[1], inTool[1]) === true ||
+                                    outT[1] === "input" ||
+                                    outT[1] === "_sniff_" ||
+                                    outT[1] === "input_collection"
+                                ) {
+                                    t.id = nameObj[1].tool_id;
+                                    t.name = nameObj[1].name;
+                                    cTools.push(t);
+                                    break;
+                                }
+                            }
+                        }
+                    }
+                    this.compatibleTools = cTools;
+                }
+                this.showLoading = false;
+            });
+        },
+    },
+};
+</script>

client/galaxy/scripts/components/Workflow/Editor/services.js

@@ -67,3 +67,21 @@ export async function saveWorkflow(workflow, id) {
     }
     return {};
 }
+
+export async function getDatatypeMapping() {
+    try {
+        const mappingRequest = await axios.get(`${getAppRoot()}api/datatypes/mapping`);
+        return mappingRequest.data;
+    } catch (e) {
+        rethrowSimple(e);
+    }
+}
+
+export async function getToolPredictions(requestData) {
+    try {
+        const response = await axios.post(`${getAppRoot()}api/workflows/get_tool_predictions`, requestData);
+        return response.data;
+    } catch (e) {
+        rethrowSimple(e);
+    }
+}

client/galaxy/scripts/components/login/Login.vue

@@ -84,6 +84,7 @@ export default {
         const oidc_idps_icons = {
             google: "https://developers.google.com/identity/images/btn_google_signin_light_normal_web.png",
             elixir: "https://elixir-europe.org/sites/default/files/images/login-button-orange.png",
+            okta: "https://www.okta.com/sites/all/themes/Okta/images/blog/Logos/Okta_Logo_BrightBlue_Medium.png",
         };
         return {
             login: null,

client/galaxy/scripts/entry/analysis/AnalysisRouter.js

@@ -321,10 +321,7 @@ export const getAnalysisRouter = (Galaxy) =>
         },
 
         show_workflows: function () {
-            const workflowListInstance = Vue.extend(WorkflowList);
-            const vm = document.createElement("div");
-            this.page.display(vm);
-            new workflowListInstance().$mount(vm);
+            this._display_vue_helper(WorkflowList);
         },
 
         show_workflows_create: function () {

client/galaxy/scripts/entry/panels/admin-panel.js

@@ -87,6 +87,7 @@ const AdminPanel = Backbone.View.extend({
                         title: _l("Forms"),
                         url: "admin/forms",
                         target: "__use_router__",
+                        id: "admin-link-forms",
                     },
                 ],
             },
@@ -97,17 +98,20 @@ const AdminPanel = Backbone.View.extend({
                         title: _l("Install and Uninstall"),
                         url: "admin/toolshed",
                         target: "__use_router__",
+                        id: "admin-link-toolshed",
                         enabled: this.settings.is_tool_shed_installed,
                     },
                     {
                         title: _l("Manage Metadata"),
                         url: "admin/reset_metadata",
+                        id: "admin-link-metadata",
                         enabled: this.settings.is_repo_installed,
                         target: "__use_router__",
                     },
                     {
                         title: _l("Manage Whitelist"),
                         url: "admin/sanitize_whitelist",
+                        id: "admin-link-whitelist",
                     },
                     {
                         title: _l("Manage Dependencies"),
@@ -123,14 +127,17 @@ const AdminPanel = Backbone.View.extend({
                         title: _l("View Lineage"),
                         url: "admin/tool_versions",
                         target: "__use_router__",
+                        id: "admin-link-tool-versions",
                     },
                     {
                         title: _l("View Migration Stages"),
                         url: "admin/review_tool_migration_stages",
+                        id: "admin-link-migrations",
                     },
                     {
                         title: _l("View Error Logs"),
                         url: "admin/error_stack",
+                        id: "admin-link-error-stack",
                         target: "__use_router__",
                     },
                 ],

client/galaxy/scripts/mvc/ui/ui-popover.js

@@ -21,7 +21,7 @@ export default Backbone.View.extend({
      * Show popover
      */
     show: function ($content) {
-        const btn = "<i class='fa fa-times-circle'/>";
+        const btn = "<i class='popover-close fa fa-times-circle'/>";
         $(this.$target).popover({
             title: `${this.options.title} ${btn}`,
             placement: this.options.placement,
@@ -29,6 +29,9 @@ export default Backbone.View.extend({
             html: true,
             trigger: "manual",
         });
+        if (this.options.class) {
+            $(this.$target).addClass(this.options.class);
+        }
         $(this.$target).popover("show");
 
         // add event to hide if click is outside of popup and not on container

client/galaxy/scripts/mvc/workflow/workflow-manager.js

@@ -18,6 +18,7 @@ class Workflow extends EventEmitter {
         this.has_changes = false;
         this.workflowOutputLabels = {};
         this.workflow_version = 0;
+        this.popover_counter = 0;
 
         // Canvas overview management
         this.canvas_manager = new WorkflowCanvas(this, $("#canvas-viewport"), $("#overview-container"));
@@ -142,8 +143,10 @@ class Workflow extends EventEmitter {
             type: type,
             title: title_text,
             node: node,
+            nodeId: this.popover_counter,
         });
 
+        this.popover_counter++;
         // Set initial scroll position
         $f.css("left", $(window).scrollLeft() + 20);
         $f.css("top", $(window).scrollTop() + 20);

client/galaxy/scripts/store/index.js

@@ -9,6 +9,7 @@ import createCache from "vuex-cache";
 import { gridSearchStore } from "./gridSearchStore";
 import { tagStore } from "./tagStore";
 import { jobMetricsStore } from "./jobMetricsStore";
+import { jobDestinationParametersStore } from "./jobDestinationParametersStore";
 import { invocationStore } from "./invocationStore";
 import { historyStore } from "./historyStore";
 import { userStore } from "./userStore";
@@ -31,6 +32,7 @@ export function createStore() {
             histories: historyStore,
             tags: tagStore,
             jobMetrics: jobMetricsStore,
+            destinationParameters: jobDestinationParametersStore,
             invocations: invocationStore,
             user: userStore,
             config: configStore,

client/galaxy/scripts/store/jobDestinationParametersStore.js

@@ -0,0 +1,33 @@
+export const state = {
+    jobDestinationParametersByJobId: {},
+};
+
+import Vue from "vue";
+import { getAppRoot } from "onload/loadConfig";
+import axios from "axios";
+
+const getters = {
+    jobDestinationParams: (state) => (jobId) => {
+        return state.jobDestinationParametersByJobId[jobId] || [];
+    },
+};
+
+const actions = {
+    fetchJobDestinationParams: async ({ commit }, jobId) => {
+        const { data } = await axios.get(`${getAppRoot()}api/jobs/${jobId}/destination_params`);
+        commit("saveJobDestinationParamsForJobId", { jobId, jobDestinationParams: data });
+    },
+};
+
+const mutations = {
+    saveJobDestinationParamsForJobId: (state, { jobId, jobDestinationParams }) => {
+        Vue.set(state.jobDestinationParametersByJobId, jobId, jobDestinationParams);
+    },
+};
+
+export const jobDestinationParametersStore = {
+    state,
+    getters,
+    actions,
+    mutations,
+};

client/galaxy/style/scss/base.scss

@@ -1656,31 +1656,29 @@ body.reports {
     .node {
         cursor: pointer;
         circle {
-            fill: lighten($brand-primary, 20%);
-            stroke: lighten($brand-primary, 20%);
-            stroke-width: 0.1rem;
+            fill: $brand-primary;
+            stroke: $brand-primary;
         }
         text {
-            font: 0.4rem sans-serif;
+            font-size: 0.4rem;
         }
     }
 
-    .node-enter {
-        fill-opacity: 1e-6;
-    }
-
-    .node-update {
-        fill-opacity: 1;
-    }
-
     .tree-size {
         width: 100%;
-        height: 50%;
     }
 
     .link {
         fill: none;
-        stroke: lighten($brand-primary, 20%);
-        stroke-width: 0.2rem;
+        stroke: $brand-primary;
+        stroke-width: 1;
+    }
+}
+
+.workflow-recommendations {
+    display: block;
+    .header-background {
+        border-bottom: solid 1px $brand-primary;
+        margin-bottom: 0.5rem;
     }
 }

client/galaxy/style/scss/workflow.scss

@@ -7,6 +7,9 @@
         display: flex;
         flex-direction: column;
         flex-grow: 1;
+        .workflow-recommendations {
+            height: 30rem;
+        }
         .workflow-node {
             @extend .card;
             @extend .position-absolute;

client/gulpfile.js

@@ -2,14 +2,14 @@ const path = require("path");
 const fs = require("fs");
 const del = require("del");
 const { src, dest, series, parallel } = require("gulp");
-const spawn = require("child_process").spawnSync;
+const child_process = require("child_process");
 const glob = require("glob");
 
 const paths = {
     node_modules: "./node_modules",
     plugin_dirs: [
         "../config/plugins/{visualizations,interactive_environments}/*/static/**/*",
-        "../config/plugins/{visualizations,interactive_environments}/*/*/static/**/*"
+        "../config/plugins/{visualizations,interactive_environments}/*/*/static/**/*",
     ],
     /*
      * We'll want a flexible glob down the road, but for now there are no
@@ -20,9 +20,7 @@ const paths = {
     //    "../config/plugins/{visualizations,interactive_environments}/*/package.json",
     //    "../config/plugins/{visualizations,interactive_environments}/*/*/package.json"
     //],
-    plugin_build_dirs: [
-        "../config/plugins/visualizations/{annotate_image,hyphyvision,openlayers,editor}/package.json",
-    ],
+    plugin_build_dirs: ["../config/plugins/visualizations/{annotate_image,hyphyvision,openlayers,editor}/package.json"],
     lib_locs: {
         // This is a stepping stone towards having all this staged
         // automatically.  Eventually, this dictionary and staging step will
@@ -37,13 +35,13 @@ const paths = {
         "jquery-mousewheel": ["jquery.mousewheel.js", "jquery/jquery.mousewheel.js"],
         "raven-js": ["dist/raven.js", "raven.js"],
         requirejs: ["require.js", "require.js"],
-        underscore: ["underscore.js", "underscore.js"]
+        underscore: ["underscore.js", "underscore.js"],
     },
-    libs: ["galaxy/scripts/libs/**/*.js"]
+    libs: ["galaxy/scripts/libs/**/*.js"],
 };
 
 function stageLibs(callback) {
-    Object.keys(paths.lib_locs).forEach(lib => {
+    Object.keys(paths.lib_locs).forEach((lib) => {
         var p1 = path.resolve(path.join(paths.node_modules, lib, paths.lib_locs[lib][0]));
         var p2 = path.resolve(path.join("galaxy", "scripts", "libs", paths.lib_locs[lib][1]));
         if (fs.existsSync(p1)) {
@@ -69,18 +67,45 @@ function stagePlugins() {
     return src(paths.plugin_dirs).pipe(dest("../static/plugins/"));
 }
 
-function buildPlugins(callback){
+function buildPlugins(callback) {
     /*
-     * Walk plugin build glob and attempt to build anything with a package.json 
+     * Walk plugin_build_dirs glob and attempt to build modules.
      * */
-    paths.plugin_build_dirs.map( build_dir => {
+    paths.plugin_build_dirs.map((build_dir) => {
         glob(build_dir, {}, (er, files) => {
-            files.map( file => {
+            files.map((file) => {
+                let skip_build = false;
                 const f = path.join(process.cwd(), file).slice(0, -12);
-                console.log("Installing Dependencies for", f);
-                spawn('yarn', ['install', '--production=false', '--network-timeout=300000', '--check-files'], { cwd: f, stdio: 'inherit', shell: true });
-                console.log("Building ", f);
-                spawn('yarn', ['build'], { cwd: f, stdio: 'inherit', shell: true });
+                const plugin_name = path.dirname(file).split(path.sep).pop();
+                const hash_file_path = path.join(f, "static", "plugin_build_hash.txt");
+
+                if (fs.existsSync(hash_file_path)) {
+                    skip_build =
+                        child_process.spawnSync("git", ["diff", "--quiet", `$(cat ${hash_file_path})`, "--", f], {
+                            stdio: "inherit",
+                            shell: true,
+                        }).status === 0;
+                } else {
+                    console.log(`No build hashfile detected for ${plugin_name}, generating now.`);
+                }
+
+                if (skip_build) {
+                    console.log(`No changes detected for ${plugin_name}`);
+                } else {
+                    console.log(`Installing Dependencies for ${plugin_name}`);
+                    child_process.spawnSync(
+                        "yarn",
+                        ["install", "--production=false", "--network-timeout=300000", "--check-files"],
+                        {
+                            cwd: f,
+                            stdio: "inherit",
+                            shell: true,
+                        }
+                    );
+                    console.log(`Building ${plugin_name}`);
+                    child_process.spawnSync("yarn", ["build"], { cwd: f, stdio: "inherit", shell: true });
+                    child_process.exec(`"(git rev-parse HEAD 2>/dev/null || echo \`\`) > ${hash_file_path} "`);
+                }
             });
         });
     });
@@ -92,7 +117,7 @@ function cleanPlugins() {
 }
 
 client = parallel(fonts, stageLibs);
-plugins = series(cleanPlugins, buildPlugins, stagePlugins);
+plugins = series(buildPlugins, cleanPlugins, stagePlugins);
 
 module.exports.client = client;
 module.exports.plugins = plugins;

display_applications/igv/vcf.xml

@@ -12,8 +12,8 @@
         <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter>
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
         <url>${redirect_url}</url>
-        <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" />
-        <param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" />
+        <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" allow_cors="true" mimetype="application/octet-stream"/>
+        <param type="data" name="tabix_file" metadata="tabix_index" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" allow_cors="true" mimetype="application/octet-stream"/>
         <param type="template" name="site_organism" strip="True" >
             #if ($dataset.dbkey in $site_dbkeys)
                 $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ]
@@ -94,8 +94,8 @@
         <filter>${ $dataset.dbkey == $value }</filter>
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
         <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bgzip_file.qp}&amp;genome=${qp($bgzip_file.dbkey)}&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
-        <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" />
-        <param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" />
+        <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" mimetype="application/octet-stream"/>
+        <param type="data" name="tabix_file" metadata="tabix_index" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="vcf_bgzip" mimetype="application/octet-stream"/>
     </dynamic_links>
 </display>
 <!-- Dan Blankenberg -->

doc/source/admin/authentication.md

@@ -18,7 +18,7 @@ If deploying Galaxy using the default authentication option, user activation can
 ## OIDC and OAuth2.0
 Leveraging OpenID Connect (OIDC) protocol, we enable login to Galaxy without explicitly creating a Galaxy user. This feature is disabled by default. In short, to enable this feature, a Galaxy server admin has to take the following two steps: 
 
-1. Define the Galaxy instance on an OIDC identity provider. At the moment, we support Google. To set a Galaxy instance on Google, go to _credentials_ section at [developers console](https://console.developers.google.com/), and configure the instance. At the end, you'll receive _client ID_ and _client secret_ take a note of these two tokens. 
+1. Define the Galaxy instance on an OIDC identity provider. At the moment, we support Google and Okta. To set a Galaxy instance on Google, go to _credentials_ section at [developers console](https://console.developers.google.com/), and configure the instance. At the end, you'll receive _client ID_ and _client secret_ take a note of these two tokens. For Okta, create a new application in Okta, type _web_. At the end you should take note of the _client ID_ and _client secret_ tokens.
 
 2. Configure Galaxy. In the `galaxy.yml` file enable the OIDC service using the `enable_oidc` key and set the two configuration files (i.e., `oidc_config_file` and `oidc_backends_config_file`), based on the IdP information. 
 

doc/source/admin/galaxy_options.rst

@@ -1376,6 +1376,19 @@
 :Type: bool
 
 
+~~~~~~~~~~~~~~~~
+``aws_estimate``
+~~~~~~~~~~~~~~~~
+
+:Description:
+    This flag enables an AWS cost estimate for every job based on
+    their runtime matrices. CPU, RAM and runtime usage is mapped
+    against AWS pricing table. Please note, that those numbers are
+    only estimates.
+:Default: ``false``
+:Type: bool
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``interactivetools_proxy_host``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -2317,8 +2330,7 @@
 :Description:
     Heartbeat log filename. Can accept the template variables
     {server_name} and {pid}
-    Sample default 'heartbeat_{server_name}.log'
-:Default: ``None``
+:Default: ``heartbeat_{server_name}.log``
 :Type: str
 
 
@@ -3836,11 +3848,13 @@
     from workflow_resource_params_file). If this this is a function
     reference it will be passed various inputs (workflow model object
     and user) and it should produce a list of input IDs. If it is a
-    path it is expected to an XML or YAML file describing how to map
-    group names to parameter descriptions (additional types of
+    path it is expected to be an XML or YAML file describing how to
+    map group names to parameter descriptions (additional types of
     mappings via these files could be implemented but haven't yet -
     for instance using workflow tags to do the mapping).
-:Default: ``config/workflow_resource_mapper_conf.yml``
+    Sample default path
+    'config/workflow_resource_mapper_conf.yml.sample'
+:Default: ``None``
 :Type: str
 
 

lib/galaxy/authnz/managers.py

@@ -121,6 +121,11 @@ class AuthnzManager(object):
             'enable_idp_logout': asbool(config_xml.findtext('enable_idp_logout', 'false'))}
         if config_xml.find('prompt') is not None:
             rtv['prompt'] = config_xml.find('prompt').text
+        if config_xml.find('api_url') is not None:
+            rtv['api_url'] = config_xml.find('api_url').text
+        if config_xml.find('url') is not None:
+            rtv['url'] = config_xml.find('url').text
+
         return rtv
 
     def _parse_custos_config(self, config_xml):

lib/galaxy/authnz/psa_authnz.py

@@ -22,14 +22,16 @@ DEFAULTS = {
 
 BACKENDS = {
     'google': 'social_core.backends.google_openidconnect.GoogleOpenIdConnect',
-    "globus": "social_core.backends.globus.GlobusOpenIdConnect",
-    'elixir': 'social_core.backends.elixir.ElixirOpenIdConnect'
+    'globus': 'social_core.backends.globus.GlobusOpenIdConnect',
+    'elixir': 'social_core.backends.elixir.ElixirOpenIdConnect',
+    'okta': 'social_core.backends.okta_openidconnect.OktaOpenIdConnect'
 }
 
 BACKENDS_NAME = {
     'google': 'google-openidconnect',
-    "globus": "globus",
-    'elixir': 'elixir'
+    'globus': 'globus',
+    'elixir': 'elixir',
+    'okta': 'okta-openidconnect'
 }
 
 AUTH_PIPELINE = (
@@ -114,8 +116,10 @@ class PSAAuthnz(IdentityProvider):
 
         # Secondary AuthZ with Google identities is currently supported
         if provider != "google":
-            del self.config["SOCIAL_AUTH_SECONDARY_AUTH_PROVIDER"]
-            del self.config["SOCIAL_AUTH_SECONDARY_AUTH_ENDPOINT"]
+            if 'SOCIAL_AUTH_SECONDARY_AUTH_PROVIDER' in self.config:
+                del self.config["SOCIAL_AUTH_SECONDARY_AUTH_PROVIDER"]
+            if 'SOCIAL_AUTH_SECONDARY_AUTH_ENDPOINT' in self.config:
+                del self.config["SOCIAL_AUTH_SECONDARY_AUTH_ENDPOINT"]
 
     def _setup_idp(self, oidc_backend_config):
         self.config[setting_name('AUTH_EXTRA_ARGUMENTS')] = {'access_type': 'offline'}
@@ -124,6 +128,10 @@ class PSAAuthnz(IdentityProvider):
         self.config['redirect_uri'] = oidc_backend_config.get('redirect_uri')
         if oidc_backend_config.get('prompt') is not None:
             self.config[setting_name('AUTH_EXTRA_ARGUMENTS')]['prompt'] = oidc_backend_config.get('prompt')
+        if oidc_backend_config.get('api_url') is not None:
+            self.config[setting_name('API_URL')] = oidc_backend_config.get('api_url')
+        if oidc_backend_config.get('url') is not None:
+            self.config[setting_name('URL')] = oidc_backend_config.get('url')
 
     def _get_helper(self, name, do_import=False):
         this_config = self.config.get(setting_name(name), DEFAULTS.get(name, None))

lib/galaxy/config/__init__.py

@@ -340,6 +340,13 @@ class CommonConfigurationMixin(object):
         # Warning: the value of self.config_dict['foo'] may be different from self.foo
         return self.config_dict.get(key, default)
 
+    def _ensure_directory(self, path):
+        if path not in [None, False] and not os.path.isdir(path):
+            try:
+                os.makedirs(path)
+            except Exception as e:
+                raise ConfigurationError("Unable to create missing directory: %s\n%s" % (path, unicodify(e)))
+
 
 class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
     deprecated_options = ('database_file', 'track_jobs_in_database')
@@ -348,11 +355,16 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
 
     def __init__(self, **kwargs):
         super(GalaxyAppConfiguration, self).__init__(**kwargs)
+        self._override_tempdir(kwargs)
         self._process_config(kwargs)
 
     def _load_schema(self):
         return AppSchema(GALAXY_CONFIG_SCHEMA_PATH, GALAXY_APP_NAME)
 
+    def _override_tempdir(self, kwargs):
+        if string_as_bool(kwargs.get("override_tempdir", "True")):
+            tempfile.tempdir = self.new_file_path
+
     def _process_config(self, kwargs):
         # Resolve paths of other config files
         self.parse_config_file_options(kwargs)
@@ -377,10 +389,6 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
             self.thread_local_log = threading.local()
         # Install database related configuration (if different)
         self.install_database_engine_options = get_database_engine_options(kwargs, model_prefix="install_")
-
-        override_tempdir = string_as_bool(kwargs.get("override_tempdir", "True"))
-        if override_tempdir:
-            tempfile.tempdir = self.new_file_path
         self.shared_home_dir = kwargs.get("shared_home_dir")
         self.cookie_path = kwargs.get("cookie_path")
         self.tool_path = self._in_root_dir(self.tool_path)
@@ -493,14 +501,9 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         # you want yours tools to be broken in the future.
         self.enable_beta_tool_formats = string_as_bool(kwargs.get('enable_beta_tool_formats', 'False'))
 
-        workflow_resource_params_mapper = kwargs.get("workflow_resource_params_mapper")
-        if not workflow_resource_params_mapper:
-            workflow_resource_params_mapper = None
-        elif ":" not in workflow_resource_params_mapper:
-            # Assume it is not a Python function, so a file
-            workflow_resource_params_mapper = self._in_root_dir(workflow_resource_params_mapper)
-        # else: a Python a function!
-        self.workflow_resource_params_mapper = workflow_resource_params_mapper
+        if self.workflow_resource_params_mapper and ':' not in self.workflow_resource_params_mapper:
+            # Assume it is not a Python function, so a file; else: a Python function
+            self.workflow_resource_params_mapper = self._in_root_dir(self.workflow_resource_params_mapper)
 
         self.pbs_application_server = kwargs.get('pbs_application_server', "")
         self.pbs_dataset_server = kwargs.get('pbs_dataset_server', "")
@@ -600,8 +603,6 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         # Heartbeat log file name override
         if self.global_conf is not None and 'heartbeat_log' in self.global_conf:
             self.heartbeat_log = self.global_conf['heartbeat_log']
-        if self.heartbeat_log is None:
-            self.heartbeat_log = 'heartbeat_{server_name}.log'
         # Determine which 'server:' this is
         self.server_name = 'main'
         for arg in sys.argv:
@@ -670,8 +671,8 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
 
         # InteractiveTools propagator mapping file
         self.interactivetools_map = self._in_root_dir(kwargs.get("interactivetools_map", self._in_data_dir("interactivetools_map.sqlite")))
-        self.interactivetool_prefix = kwargs.get("interactivetools_prefix", "interactivetool")
-        self.interactivetool_proxy_host = kwargs.get("interactivetool_proxy_host", None)
+        self.interactivetools_prefix = kwargs.get("interactivetools_prefix", "interactivetool")
+        self.interactivetools_proxy_host = kwargs.get("interactivetool_proxy_host", None)
 
         self.containers_conf = parse_containers_config(self.containers_config_file)
 
@@ -810,26 +811,21 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
     def ensure_tempdir(self):
         self._ensure_directory(self.new_file_path)
 
-    def _ensure_directory(self, path):
-        if path not in [None, False] and not os.path.isdir(path):
-            try:
-                os.makedirs(path)
-            except Exception as e:
-                raise ConfigurationError("Unable to create missing directory: %s\n%s" % (path, unicodify(e)))
-
     def check(self):
-        paths_to_check = [self.tool_data_path, self.data_dir, self.managed_config_dir]
-        # Check that required directories exist
+        # Check that required directories exist; attempt to create otherwise
+        paths_to_check = [
+            self.data_dir,
+            self.ftp_upload_dir,
+            self.library_import_dir,
+            self.managed_config_dir,
+            self.new_file_path,
+            self.nginx_upload_store,
+            self.object_store_cache_path,
+            self.template_cache_path,
+            self.tool_data_path,
+            self.user_library_import_dir,
+        ]
         for path in paths_to_check:
-            if path not in [None, False] and not os.path.isdir(path):
-                try:
-                    os.makedirs(path)
-                except Exception as e:
-                    raise ConfigurationError("Unable to create missing directory: %s\n%s" % (path, unicodify(e)))
-        # Create the directories that it makes sense to create
-        for path in (self.new_file_path, self.template_cache_path, self.ftp_upload_dir,
-                     self.library_import_dir, self.user_library_import_dir,
-                     self.nginx_upload_store, self.object_store_cache_path):
             self._ensure_directory(path)
         # Check that required files exist
         tool_configs = self.tool_configs

lib/galaxy/config/sample/datatypes_conf.xml.sample

@@ -230,19 +230,27 @@
     <datatype extension="directory" type="galaxy.datatypes.data:Directory">
     </datatype>
     <!-- Proteomics Datatypes -->
+    <datatype extension="mrm" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" subclass="true"/>
+    <datatype extension="dta" type="galaxy.datatypes.proteomics:Dta" display_in_upload="true" />
+    <datatype extension="dta2d" type="galaxy.datatypes.proteomics:Dta2d" display_in_upload="true" />
+    <datatype extension="edta" type="galaxy.datatypes.proteomics:Edta" display_in_upload="true" />
     <datatype extension="pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="raw_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
     <datatype extension="peptideprophet_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
     <datatype extension="interprophet_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
     <datatype extension="protxml" type="galaxy.datatypes.proteomics:ProtXML" mimetype="application/xml" display_in_upload="true"/>
-    <datatype extension="trafoxml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" subclass="true" display_in_upload="true" description="Transformation of retention times"/>
+    <datatype extension="paramxml" type="galaxy.datatypes.proteomics:ParamXml" mimetype="application/xml" subclass="true" display_in_upload="true" />
     <datatype extension="qcml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" subclass="true" display_in_upload="true" description="Quality control data in XML format (https://code.google.com/p/qcml/)."/>
+    <datatype extension="kroenik" type="galaxy.datatypes.proteomics:Kroenik" display_in_upload="true"/>
+    <datatype extension="peplist" type="galaxy.datatypes.proteomics:PepList" display_in_upload="true"/>
+    <datatype extension="psms" type="galaxy.datatypes.proteomics:PSMS" display_in_upload="true"/>
     <datatype extension="pepxml.tsv" type="galaxy.datatypes.proteomics:PepXmlReport" display_in_upload="true"/>
     <datatype extension="protxml.tsv" type="galaxy.datatypes.proteomics:ProtXmlReport" display_in_upload="true"/>
     <datatype extension="mascotdat" type="galaxy.datatypes.proteomics:MascotDat" display_in_upload="false"/>
     <datatype extension="mzid" type="galaxy.datatypes.proteomics:MzIdentML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="idxml" type="galaxy.datatypes.proteomics:IdXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="tandem" type="galaxy.datatypes.proteomics:TandemXML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="sirius.ms" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="false"/>
     <datatype extension="thermo.raw" type="galaxy.datatypes.proteomics:ThermoRAW" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="brukerbaf.d.tar" type="galaxy.datatypes.binary:BafTar" display_in_upload="true"/>
     <datatype extension="agilentbrukeryep.d.tar" type="galaxy.datatypes.binary:YepTar" display_in_upload="true"/>
@@ -250,6 +258,9 @@
     <datatype extension="agilentmasshunter.d.tar" type="galaxy.datatypes.binary:MassHunterTar" display_in_upload="true"/>
     <datatype extension="watersmasslynx.raw.tar" type="galaxy.datatypes.binary:MassLynxTar" display_in_upload="true"/>
     <datatype extension="wiff.tar" type="galaxy.datatypes.binary:WiffTar" display_in_upload="true"/>
+    <datatype extension="mascotxml" type="galaxy.datatypes.proteomics:MascotXML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="mztab" type="galaxy.datatypes.proteomics:MzTab" display_in_upload="true"/>
+    <datatype extension="mztab2" type="galaxy.datatypes.proteomics:MzTab2" display_in_upload="true"/>
     <datatype extension="mzml" type="galaxy.datatypes.proteomics:MzML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="nmrml" type="galaxy.datatypes.proteomics:NmrML" mimetype="application/xml" display_in_upload="true" description="nmrML is an open mark-up language for NMR data." description_url="http://nmrml.org/schema/"/>
     <datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf" display_in_upload="true"/>
@@ -258,11 +269,18 @@
     <datatype extension="mzdata" type="galaxy.datatypes.proteomics:MzData" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="ms2" type="galaxy.datatypes.proteomics:Ms2" display_in_upload="true"/>
     <datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="mz.sqlite" type="galaxy.datatypes.binary:MzSQlite" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="osw" type="galaxy.datatypes.binary:OSW" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="pqp" type="galaxy.datatypes.binary:PQP" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="trafoxml" type="galaxy.datatypes.proteomics:TrafoXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="uniprotxml" type="galaxy.datatypes.proteomics:UniProtXML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="xquest.xml" type="galaxy.datatypes.proteomics:XquestXML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="spec.xml" type="galaxy.datatypes.proteomics:XquestSpecXML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="qcml" type="galaxy.datatypes.proteomics:QCML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="msp" type="galaxy.datatypes.proteomics:Msp" display_in_upload="true"/>
     <datatype extension="splib_noindex" type="galaxy.datatypes.proteomics:SPLibNoIndex" display_in_upload="true"/>
     <datatype extension="splib" type="galaxy.datatypes.proteomics:SPLib" display_in_upload="true"/>
@@ -286,6 +304,7 @@
     <datatype extension="kronik" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
     <datatype extension="imzml" type="galaxy.datatypes.proteomics:ImzML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="analyze75" type="galaxy.datatypes.proteomics:Analyze75" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="peff" type="galaxy.datatypes.proteomics:PEFF" display_in_upload="true"/>
     <!-- End Proteomics Datatypes -->
     <datatype extension="deeptools_compute_matrix_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
     <datatype extension="deeptools_coverage_matrix" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
@@ -343,9 +362,7 @@
       <converter file="tabular_to_csv.xml" target_datatype="csv"/>
     </datatype>
     <datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
-    <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/>
-    <datatype extension="pqp" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true" subclass="true"/>
-    <datatype extension="osw" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true" subclass="true"/>
+    <datatype extension="sqmass" type="galaxy.datatypes.binary:SQmass" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="gemini.sqlite" type="galaxy.datatypes.binary:GeminiSQLite" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="cuffdiff.sqlite" type="galaxy.datatypes.binary:CuffDiffSQlite" display_in_upload="true"/>
     <datatype extension="gafa.sqlite" type="galaxy.datatypes.binary:GAFASQLite" mimetype="application/octet-stream" display_in_upload="true"/>
@@ -381,7 +398,11 @@
       <display file="igb/wig.xml"/>
     </datatype>
     <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="true"/>
-    <datatype extension="odgi" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs self index used by odgi."/>
+    <datatype extension="odgi" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs self index used by odgi." display_in_upload="true"/>
+    <datatype extension="vg" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs." display_in_upload="true"/>
+    <datatype extension="xg" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs with vg index." display_in_upload="true"/>
+    <datatype extension="protobuf2" type="galaxy.datatypes.binary:Binary" subclass="true" description="Protocol Buffers (Protobuf) is data format for serializing structured data."/>
+    <datatype extension="protobuf3" type="galaxy.datatypes.binary:Binary" subclass="true" description="Protocol Buffers (Protobuf) is data format for serializing structured data."/>
     <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="true"/>
     <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="true"/>
     <datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" display_in_upload="true">
@@ -801,7 +822,10 @@
     <sniffer type="galaxy.datatypes.tabular:Vcf"/>
     <sniffer type="galaxy.datatypes.binary:TwoBit"/>
     <sniffer type="galaxy.datatypes.binary:GeminiSQLite"/>
+    <sniffer type="galaxy.datatypes.binary:SQmass"/>
     <sniffer type="galaxy.datatypes.binary:MzSQlite"/>
+    <sniffer type="galaxy.datatypes.binary:OSW"/>
+    <sniffer type="galaxy.datatypes.binary:PQP"/>
     <sniffer type="galaxy.datatypes.binary:IdpDB"/>
     <sniffer type="galaxy.datatypes.binary:ElibSQlite"/>
     <sniffer type="galaxy.datatypes.binary:DlibSQlite"/>
@@ -851,21 +875,40 @@
     <sniffer type="galaxy.datatypes.xml:Phyloxml"/>
     <sniffer type="galaxy.datatypes.xml:Owl"/>
     <sniffer type="galaxy.datatypes.xml:Sbml"/>
-    <sniffer type="galaxy.datatypes.proteomics:MzML"/>
-    <sniffer type="galaxy.datatypes.proteomics:NmrML"/>
-    <sniffer type="galaxy.datatypes.proteomics:TandemXML"/>
-    <sniffer type="galaxy.datatypes.proteomics:PepXml"/>
+    <sniffer type="galaxy.datatypes.proteomics:Dta2d"/>
+    <sniffer type="galaxy.datatypes.proteomics:Edta"/>
+    <sniffer type="galaxy.datatypes.proteomics:ConsensusXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:IdXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:FeatureXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:MascotXML"/>
     <sniffer type="galaxy.datatypes.proteomics:Mgf"/>
-    <sniffer type="galaxy.datatypes.proteomics:ProtXML"/>
-    <sniffer type="galaxy.datatypes.proteomics:MzXML"/>
-    <sniffer type="galaxy.datatypes.proteomics:MzData"/>
-    <sniffer type="galaxy.datatypes.proteomics:TraML"/>
-    <sniffer type="galaxy.datatypes.proteomics:MzIdentML"/>
-    <sniffer type="galaxy.datatypes.proteomics:MzQuantML"/>
-    <sniffer type="galaxy.datatypes.proteomics:UniProtXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:Ms2"/>
     <sniffer type="galaxy.datatypes.proteomics:Msp"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzData"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzIdentML"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzML"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzQuantML"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzTab"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzTab2"/>
+    <sniffer type="galaxy.datatypes.proteomics:ParamXml"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:NmrML"/>
+    <sniffer type="galaxy.datatypes.proteomics:Kroenik"/>
+    <sniffer type="galaxy.datatypes.proteomics:PepList"/>
+    <sniffer type="galaxy.datatypes.proteomics:PSMS"/>
+    <sniffer type="galaxy.datatypes.proteomics:PepXml"/>
+    <sniffer type="galaxy.datatypes.proteomics:ProtXML"/>
     <sniffer type="galaxy.datatypes.proteomics:SPLib"/>
+    <sniffer type="galaxy.datatypes.proteomics:TandemXML"/>
     <sniffer type="galaxy.datatypes.proteomics:ThermoRAW"/>
+    <sniffer type="galaxy.datatypes.proteomics:TraML"/>
+    <sniffer type="galaxy.datatypes.proteomics:TrafoXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:UniProtXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:XquestXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:XquestSpecXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:QCML"/>
+    <sniffer type="galaxy.datatypes.proteomics:Wiff"/>
+    <sniffer type="galaxy.datatypes.proteomics:PEFF"/>
     <sniffer type="galaxy.datatypes.molecules:CML"/>
     <sniffer type="galaxy.datatypes.xml:GenericXml"/>
     <sniffer type="galaxy.datatypes.triples:HDT"/>

lib/galaxy/config/sample/galaxy.yml.sample

@@ -761,6 +761,11 @@ galaxy:
   # Enable InteractiveTools.
   #interactivetools_enable: false
 
+  # This flag enables an AWS cost estimate for every job based on their
+  # runtime matrices. CPU, RAM and runtime usage is mapped against AWS
+  # pricing table. Please note, that those numbers are only estimates.
+  #aws_estimate: false
+
   # Proxy host - assumed to just be hosted on the same hostname and port
   # as Galaxy by default.
   #interactivetools_proxy_host: null
@@ -1161,8 +1166,7 @@ galaxy:
 
   # Heartbeat log filename. Can accept the template variables
   # {server_name} and {pid}
-  # Sample default 'heartbeat_{server_name}.log'
-  #heartbeat_log: null
+  #heartbeat_log: heartbeat_{server_name}.log
 
   # Log to Sentry Sentry is an open source logging and error aggregation
   # platform.  Setting sentry_dsn will enable the Sentry middleware and
@@ -1881,11 +1885,13 @@ galaxy:
   # workflow_resource_params_file). If this this is a function reference
   # it will be passed various inputs (workflow model object and user)
   # and it should produce a list of input IDs. If it is a path it is
-  # expected to an XML or YAML file describing how to map group names to
-  # parameter descriptions (additional types of mappings via these files
-  # could be implemented but haven't yet - for instance using workflow
-  # tags to do the mapping).
-  #workflow_resource_params_mapper: config/workflow_resource_mapper_conf.yml
+  # expected to be an XML or YAML file describing how to map group names
+  # to parameter descriptions (additional types of mappings via these
+  # files could be implemented but haven't yet - for instance using
+  # workflow tags to do the mapping).
+  # Sample default path
+  # 'config/workflow_resource_mapper_conf.yml.sample'
+  #workflow_resource_params_mapper: null
 
   # Optional configuration file similar to `job_config_file` to specify
   # which Galaxy processes should schedule workflows.

lib/galaxy/config/sample/oidc_backends_config.xml.sample

@@ -110,4 +110,25 @@ Please mind `http` and `https`.
         <prompt>consent</prompt>
     </provider>
 
+    <provider name="Okta">
+        <client_id> ... </client_id>
+        <client_secret> ... </client_secret>
+        <redirect_uri>http://localhost:8080/authnz/okta/callback</redirect_uri>
+        <!-- Okta API URL, based on 'Single Sign-On to Okta' URL here: https://developer.okta.com/docs/api/resources/oidc#2-okta-as-the-identity-platform-for-your-app-or-api
+        This has subsequently had the '/v1/authorize' removed. In productive deployments, this will likely resemble:
+        https://${company}.okta.com/oauth2/${authServerId}/
+
+        To get the URL, you have to create an application in Okta. The following settings serve as example as of the time of writing:
+        - Page 1 - Platform
+          - Platform: Web
+        - Page 2 - Settings
+          - Name: (Decide yourself)
+          - Base URIs: http://localhost:8080/
+          - Login redirect URIs: http://localhost:8080/authnz/okta/callback
+          - Grant type allowed: Authorization code
+
+        You should subsequently be able to get the client ID and the client secret from the Okta website.
+         -->
+        <api_url> ... </api_url>
+    </provider>
 </OIDC>

lib/galaxy/config/sample/tool_conf.xml.sample

@@ -5,6 +5,7 @@
     <tool file="data_source/ucsc_tablebrowser.xml" />
     <!-- <tool file="data_source/ucsc_tablebrowser_test.xml" /> -->
     <tool file="data_source/ucsc_tablebrowser_archaea.xml" />
+    <tool file="data_source/sra.xml" />
     <tool file="data_source/ebi_sra.xml" />
     <tool file="data_source/fly_modencode.xml" />
     <tool file="data_source/intermine.xml" />

lib/galaxy/config/sample/tool_shed.yml.sample

@@ -246,10 +246,12 @@ tool_shed:
   #allow_user_deletion: false
 
   # For use by email messages sent from the Tool Shed.
-  #smtp_server: smtp.your_tool_shed_server
+  # (smtp.your_tool_shed_server)
+  #smtp_server: null
 
   # For use by email messages sent from the Tool Shed.
-  #email_from: your_tool_shed_email@server
+  # (your_tool_shed_email@server)
+  #email_from: null
 
   # If your SMTP server requires a username and password, you can
   # provide them here (password in cleartext here, but if your server
@@ -377,7 +379,7 @@ tool_shed:
   # logged are grid views, tool searches, and use of "recently" used
   # tools menu.  The log_events and log_actions functionality will
   # eventually be merged.
-  #log_actions: true
+  #log_actions: false
 
   # Password expiration period (in days). Users are required to change
   # their password every x days. Users will be redirected to the change

lib/galaxy/datatypes/binary.py

@@ -1581,6 +1581,91 @@ class MzSQlite(SQlite):
         return False
 
 
+class PQP(SQlite):
+    """
+    Class describing a Peptide query parameters file
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.pqp')
+    >>> PQP().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.osw')
+    >>> PQP().sniff(fname)
+    False
+    """
+    file_ext = "pqp"
+
+    def set_meta(self, dataset, overwrite=True, **kwd):
+        super(PQP, self).set_meta(dataset, overwrite=overwrite, **kwd)
+
+    def sniff(self, filename):
+        """
+        table definition according to https://github.com/grosenberger/OpenMS/blob/develop/src/openms/source/ANALYSIS/OPENSWATH/TransitionPQPFile.cpp#L264
+        for now VERSION GENE PEPTIDE_GENE_MAPPING are excluded, since
+        there is test data wo these tables, see also here https://github.com/OpenMS/OpenMS/issues/4365
+        """
+        if not super(PQP, self).sniff(filename):
+            return False
+        table_names = ['COMPOUND', 'PEPTIDE', 'PEPTIDE_PROTEIN_MAPPING', 'PRECURSOR',
+                       'PRECURSOR_COMPOUND_MAPPING', 'PRECURSOR_PEPTIDE_MAPPING', 'PROTEIN',
+                       'TRANSITION', 'TRANSITION_PEPTIDE_MAPPING', 'TRANSITION_PRECURSOR_MAPPING']
+        osw_table_names = ['FEATURE', 'FEATURE_MS1', 'FEATURE_MS2', 'FEATURE_TRANSITION', 'RUN']
+        return self.sniff_table_names(filename, table_names) and not self.sniff_table_names(filename, osw_table_names)
+
+
+class OSW(SQlite):
+    """
+    Class describing OpenSwath output
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.osw')
+    >>> OSW().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.sqmass')
+    >>> OSW().sniff(fname)
+    False
+    """
+    file_ext = "osw"
+
+    def set_meta(self, dataset, overwrite=True, **kwd):
+        super(OSW, self).set_meta(dataset, overwrite=overwrite, **kwd)
+
+    def sniff(self, filename):
+        # osw seems to be an extension of pqp (few tables are added)
+        # see also here https://github.com/OpenMS/OpenMS/issues/4365
+        if not super(OSW, self).sniff(filename):
+            return False
+        table_names = ['COMPOUND', 'PEPTIDE', 'PEPTIDE_PROTEIN_MAPPING', 'PRECURSOR',
+                       'PRECURSOR_COMPOUND_MAPPING', 'PRECURSOR_PEPTIDE_MAPPING', 'PROTEIN',
+                       'TRANSITION', 'TRANSITION_PEPTIDE_MAPPING', 'TRANSITION_PRECURSOR_MAPPING',
+                       'FEATURE', 'FEATURE_MS1', 'FEATURE_MS2', 'FEATURE_TRANSITION', 'RUN']
+        return self.sniff_table_names(filename, table_names)
+
+
+class SQmass(SQlite):
+    """
+    Class describing a Sqmass database
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.sqmass')
+    >>> SQmass().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.pqp')
+    >>> SQmass().sniff(fname)
+    False
+    """
+    file_ext = "sqmass"
+
+    def set_meta(self, dataset, overwrite=True, **kwd):
+        super(SQmass, self).set_meta(dataset, overwrite=overwrite, **kwd)
+
+    def sniff(self, filename):
+        if super(SQmass, self).sniff(filename):
+            table_names = ["CHROMATOGRAM", "PRECURSOR", "RUN", "SPECTRUM", "DATA", "PRODUCT", "RUN_EXTRA"]
+            return self.sniff_table_names(filename, table_names)
+        return False
+
+
 class BlibSQlite(SQlite):
     """Class describing a Proteomics Spectral Library Sqlite database """
     MetadataElement(name="blib_version", default='1.8', param=MetadataParameter, desc="Blib Version",

lib/galaxy/datatypes/proteomics.py

@@ -7,8 +7,9 @@ import re
 from galaxy.datatypes import data
 from galaxy.datatypes.binary import Binary
 from galaxy.datatypes.data import Text
+from galaxy.datatypes.sequence import Sequence
 from galaxy.datatypes.sniff import build_sniff_from_prefix
-from galaxy.datatypes.tabular import Tabular
+from galaxy.datatypes.tabular import Tabular, TabularData
 from galaxy.datatypes.xml import GenericXml
 from galaxy.util import nice_size
 
@@ -53,6 +54,221 @@ class Wiff(Binary):
         return "\n".join(rval)
 
 
+@build_sniff_from_prefix
+class MzTab(Text):
+    """
+    exchange format for proteomics and metabolomics results
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.mztab')
+    >>> MzTab().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.mztab2')
+    >>> MzTab().sniff(fname)
+    False
+    """
+    edam_data = "data_3681"
+    file_ext = "mztab"
+    # section names (except MTD)
+    _sections = ["PRH", "PRT", "PEH", "PEP", "PSH", "PSM", "SMH", "SML", "COM"]
+    # mandatory metadata fields and list of allowed entries (in lower case)
+    # (or None if everything is allowed)
+    _man_mtd = {"mzTab-mode": ["complete", "summary"],
+                "mzTab-type": ['quantification', 'identification'],
+                "description": None}
+    _version_re = r"(1)(\.[0-9])?(\.[0-9])?"
+
+    def __init__(self, **kwd):
+        super(MzTab, self).__init__(**kwd)
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek(dataset.file_name)
+            dataset.blurb = 'mzTab Format'
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def sniff_prefix(self, file_prefix):
+        """ Determines whether the file is the correct type. """
+        has_version = False
+        found_man_mtd = set()
+        contents = file_prefix.string_io()
+        for line in contents:
+            if re.match(r"^\s*$", line):
+                continue
+            line = line.strip("\r\n").split("\t")
+            if line[0] == "MTD":
+                if line[1] == "mzTab-version" and re.match(self._version_re, line[2]) is not None:
+                    has_version = True
+                elif line[1] in self._man_mtd and (self._man_mtd[line[1]] is None or line[2].lower() in self._man_mtd[line[1]]):
+                    found_man_mtd.add(line[1])
+            elif not line[0] in self._sections:
+                return False
+        return has_version and found_man_mtd == set(self._man_mtd.keys())
+
+
+class MzTab2(MzTab):
+    """
+    exchange format for proteomics and metabolomics results
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.mztab2')
+    >>> MzTab2().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.mztab')
+    >>> MzTab2().sniff(fname)
+    False
+    """
+    file_ext = "mztab2"
+    _sections = ["SMH", "SML", "SFH", "SMF", "SEH", "SME", "COM"]
+    _version_re = r"(2)(\.[0-9])?(\.[0-9])?-M$"
+    _man_mtd = {"mzTab-ID": None}
+
+    def __init__(self, **kwd):
+        super(MzTab2, self).__init__(**kwd)
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek(dataset.file_name)
+            dataset.blurb = 'mzTab2 Format'
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+
+@build_sniff_from_prefix
+class Kroenik(Tabular):
+    """
+    Kroenik (HardKloer sibling) files
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.kroenik')
+    >>> Kroenik().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.peplist')
+    >>> Kroenik().sniff(fname)
+    False
+    """
+    file_ext = "kroenik"
+
+    def __init__(self, **kwd):
+        super(Kroenik, self).__init__(**kwd)
+        self.column_names = ["File", "First Scan", "Last Scan", "Num of Scans", "Charge", "Monoisotopic Mass", "Base Isotope Peak", "Best Intensity", "Summed Intensity", "First RTime", "Last RTime", "Best RTime", "Best Correlation", "Modifications"]
+
+    def display_peek(self, dataset):
+        """Returns formated html of peek"""
+        return self.make_html_table(dataset, column_names=self.column_names)
+
+    def sniff_prefix(self, file_prefix):
+        fh = file_prefix.string_io()
+        line = [_.strip() for _ in fh.readline().split("\t")]
+        if line != self.column_names:
+            return False
+        line = fh.readline().split("\t")
+        try:
+            [int(_) for _ in line[1:5]]
+            [float(_) for _ in line[5:13]]
+        except ValueError:
+            return False
+        return True
+
+
+@build_sniff_from_prefix
+class PepList(Tabular):
+    """
+    Peplist file as used in OpenMS
+    https://github.com/OpenMS/OpenMS/blob/0fc8765670a0ad625c883f328de60f738f7325a4/src/openms/source/FORMAT/FileHandler.cpp#L432
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.peplist')
+    >>> PepList().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.psms')
+    >>> PepList().sniff(fname)
+    False
+    """
+    file_ext = "peplist"
+
+    def __init__(self, **kwd):
+        super(PepList, self).__init__(**kwd)
+        self.column_names = ["m/z", "rt(min)", "snr", "charge", "intensity"]
+
+    def display_peek(self, dataset):
+        """Returns formated html of peek"""
+        return self.make_html_table(dataset, column_names=self.column_names)
+
+    def sniff_prefix(self, file_prefix):
+        fh = file_prefix.string_io()
+        line = [_.strip() for _ in fh.readline().split("\t")]
+        if line == self.column_names:
+            return True
+        return False
+
+
+@build_sniff_from_prefix
+class PSMS(Tabular):
+    """
+    Percolator tab-delimited output (PSM level, .psms) as used in OpenMS
+    https://github.com/OpenMS/OpenMS/blob/0fc8765670a0ad625c883f328de60f738f7325a4/src/openms/source/FORMAT/FileHandler.cpp#L453
+    see also http://www.kojak-ms.org/docs/percresults.html
+
+    Note that the data rows can have more columns than the header line
+    since ProteinIds are listed tab-separated.
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.psms')
+    >>> PSMS().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.kroenik')
+    >>> PSMS().sniff(fname)
+    False
+    """
+    file_ext = "psms"
+
+    def __init__(self, **kwd):
+        super(PSMS, self).__init__(**kwd)
+        self.column_names = ["PSMId", "score", "q-value", "posterior_error_prob", "peptide", "proteinIds"]
+
+    def display_peek(self, dataset):
+        """Returns formated html of peek"""
+        return self.make_html_table(dataset, column_names=self.column_names)
+
+    def sniff_prefix(self, file_prefix):
+        fh = file_prefix.string_io()
+        line = [_.strip() for _ in fh.readline().split("\t")]
+        if line == self.column_names:
+            return True
+        return False
+
+
+@build_sniff_from_prefix
+class PEFF(Sequence):
+    """
+    PSI Extended FASTA Format
+    https://github.com/HUPO-PSI/PEFF
+    """
+    file_ext = "peff"
+
+    def sniff_prefix(self, file_prefix):
+        """
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname( 'test.peff' )
+        >>> PEFF().sniff( fname )
+        True
+        >>> fname = get_test_fname( 'sequence.fasta' )
+        >>> PEFF().sniff( fname )
+        False
+        """
+        fh = file_prefix.string_io()
+        if re.match(r"# PEFF \d+.\d+", fh.readline()):
+            return True
+        else:
+            return False
+
+
 class PepXmlReport(Tabular):
     """pepxml converted to tabular report"""
     edam_data = "data_2536"
@@ -92,6 +308,277 @@ class ProtXmlReport(Tabular):
         return self.make_html_table(dataset, column_names=self.column_names)
 
 
+class Dta(TabularData):
+    """dta
+    The first line contains the singly protonated peptide mass (MH+) and the
+    peptide charge state separated by a space. Subsequent lines contain space
+    separated pairs of fragment ion m/z and intensity values.
+    """
+    file_ext = "dta"
+    comment_lines = 0
+
+    def set_meta(self, dataset, **kwd):
+        column_types = []
+        data_row = []
+        data_lines = 0
+        if dataset.has_data():
+            with open(dataset.file_name, 'r') as dtafile:
+                for line in dtafile:
+                    data_lines += 1
+
+        # Guess column types
+        for cell in data_row:
+            column_types.append(self.guess_type(cell))
+
+        # Set metadata
+        dataset.metadata.data_lines = data_lines
+        dataset.metadata.comment_lines = 0
+        dataset.metadata.column_types = ['float', 'float']
+        dataset.metadata.columns = 2
+        dataset.metadata.column_names = ['m/z', 'intensity']
+        dataset.metadata.delimiter = " "
+
+
+@build_sniff_from_prefix
+class Dta2d(TabularData):
+    """
+    dta2d: files with three tab/space-separated columns.
+    The default format is: retention time (seconds) , m/z , intensity.
+    If the first line starts with '#', a different order is defined by the the
+    order of the keywords 'MIN' (retention time in minutes) or 'SEC' (retention
+    time in seconds), 'MZ', and 'INT'.
+    Example: '#MZ MIN INT'
+    The peaks of one retention time have to be in subsequent lines.
+
+    Note: sniffer detects (tab or space separated) dta2d files with correct
+    header, wo header seems to generic
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.dta2d')
+    >>> Dta2d().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.edta')
+    >>> Dta2d().sniff(fname)
+    False
+    """
+    file_ext = "dta2d"
+    comment_lines = 0
+
+    def _parse_header(self, line):
+        if len(line) != 3 or len(line[0]) < 3 or not line[0].startswith("#"):
+            return None
+        line[0] = line[0].lstrip("#")
+        line = [_.strip() for _ in line]
+        if 'MZ' not in line or 'INT' not in line or ('MIN' not in line and 'SEC' not in line):
+            return None
+        return line
+
+    def _parse_delimiter(self, line):
+        if len(line.split(" ")) == 3:
+            return " "
+        elif len(line.split("\t")) == 3:
+            return "\t"
+        return None
+
+    def _parse_dataline(self, line):
+        try:
+            line = [float(_) for _ in line]
+        except ValueError:
+            return False
+        if not all(_ >= 0 for _ in line):
+            return False
+        return True
+
+    def set_meta(self, dataset, **kwd):
+        data_lines = 0
+        delim = None
+        if dataset.has_data():
+            with open(dataset.file_name, 'r') as dtafile:
+                for line in dtafile:
+                    if delim is None:
+                        delim = self._parse_delimiter(line)
+                        dataset.metadata.column_names = self._parse_header(line.split(delim))
+                    data_lines += 1
+
+        # Set metadata
+        if delim is not None:
+            dataset.metadata.delimiter = delim
+
+        dataset.metadata.data_lines = data_lines
+        dataset.metadata.comment_lines = 0
+        dataset.metadata.column_types = ['float', 'float', 'float']
+        dataset.metadata.columns = 3
+        if dataset.metadata.column_names is None or dataset.metadata.column_names == []:
+            dataset.metadata.comment_lines += 1
+            dataset.metadata.data_lines -= 1
+            dataset.metadata.column_names = ['SEC', 'MZ', 'INT']
+
+    def sniff_prefix(self, file_prefix):
+        sep = None
+        header = None
+        for idx, line in enumerate(file_prefix.line_iterator()):
+            line = line.strip()
+            if sep is None:
+                sep = self._parse_delimiter(line)
+                if sep is None:
+                    return False
+            line = line.split(sep)
+            if len(line) != 3:
+                return False
+            if idx == 0:
+                header = self._parse_header(line)
+                if (header is None) and not self._parse_dataline(line):
+                    return False
+            elif not self._parse_dataline(line):
+                return False
+        if sep is None or header is None:
+            return False
+        return True
+
+
+@build_sniff_from_prefix
+class Edta(TabularData):
+    """
+    Input text file containing tab, space or comma separated columns.
+    The separator between columns is checked in the first line in this order.
+
+    It supports three variants of this format.
+
+    1. Columns are: RT, MZ, Intensity A header is optional.
+    2. Columns are: RT, MZ, Intensity, Charge, <Meta-Data> columns{0,} A header is mandatory.
+    3. Columns are: (RT, MZ, Intensity, Charge){1,}, <Meta-Data> columns{0,}
+       Header is mandatory. First quadruplet is the consensus. All following
+       quadruplets describe the sub-features. This variant is discerned from
+       variant #2 by the name of the fifth column, which is required to be RT1
+       (or rt1). All other column names for sub-features are faithfully ignored.
+
+    Note the sniffer only detects files with header.
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.edta')
+    >>> Edta().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.dta2d')
+    >>> Edta().sniff(fname)
+    False
+    """
+    file_ext = "edta"
+    comment_lines = 0
+
+    def _parse_delimiter(self, line):
+        if len(line.split(" ")) >= 3:
+            return " "
+        elif len(line.split("\t")) >= 3:
+            return "\t"
+        elif len(line.split(",")) >= 3:
+            return "\t"
+        return None
+
+    def _parse_type(self, line):
+        """
+        parse the type from the header line
+        types 1-3 as in the class docs, 0: type 1 wo/wrong header
+        """
+        if len(line) < 3:
+            return None
+        line = [_.lower().replace("/", "") for _ in line]
+        if len(line) == 3:
+            if line[0] == "rt" and line[1] == "mz" and (line[2] == "int" or line[2] == "intensity"):
+                return 1
+            else:
+                return None
+        if line[0] != "rt" or line[1] != "mz" or (line[2] != "int" and line[2] != "intensity") or line[3] != "charge":
+            return None
+        if not line[4].startswith("rt"):
+            return 2
+        else:
+            return 3
+
+    def _parse_dataline(self, line, tpe):
+        if tpe == 2 or tpe == 3:
+            idx = 4
+        else:
+            idx = 3
+        try:
+            line = [float(_) for _ in line[:idx]]
+        except ValueError:
+            return False
+        if not all(_ >= 0 for _ in line[:idx]):
+            return False
+        return True
+
+    def _clean_header(self, line):
+        for idx, el in enumerate(line):
+            el = el.lower()
+            if el.startswith("rt"):
+                line[idx] = "RT"
+            elif el.startswith("int"):
+                line[idx] = "intensity"
+            elif el.startswith("mz"):
+                line[idx] = "m/z"
+            elif el.startswith("charge"):
+                line[idx] = "charge"
+            else:
+                break
+            if idx // 4 > 0:
+                line[idx] += str(idx // 4)
+        return line
+
+    def set_meta(self, dataset, **kwd):
+        data_lines = 0
+        delim = None
+        if dataset.has_data():
+            with open(dataset.file_name, 'r') as dtafile:
+                for idx, line in enumerate(dtafile):
+                    if idx == 0:
+                        delim = self._parse_delimiter(line)
+                        tpe = self._parse_type(line.split(delim))
+                        if tpe == 0:
+                            dataset.metadata.column_names = ["RT", "m/z", "intensity"]
+                        else:
+                            dataset.metadata.column_names = self._clean_header(line.split(delim))
+                    data_lines += 1
+
+        # Set metadata
+        if delim is not None:
+            dataset.metadata.delimiter = delim
+        for c in dataset.metadata.column_names:
+            if any(c.startswith(_) for _ in ["RT", "m/z", "intensity", "charge"]):
+                dataset.metadata.column_types.append("float")
+            else:
+                dataset.metadata.column_types.append("str")
+
+        dataset.metadata.data_lines = data_lines
+        dataset.metadata.comment_lines = 0
+        dataset.metadata.columns = len(dataset.metadata.column_names)
+        if tpe > 0:
+            dataset.metadata.comment_lines += 1
+            dataset.metadata.data_lines -= 1
+
+    def sniff_prefix(self, file_prefix):
+        sep = None
+        tpe = None
+        for idx, line in enumerate(file_prefix.line_iterator()):
+            line = line.strip("\r\n")
+            if sep is None:
+                sep = self._parse_delimiter(line)
+                if sep is None:
+                    return False
+            line = line.split(sep)
+
+            if idx == 0:
+                tpe = self._parse_type(line)
+                if tpe is None:
+                    return False
+                elif tpe == 0 and not self._parse_dataline(line, tpe):
+                    return False
+            elif not self._parse_dataline(line, tpe):
+                return False
+        if tpe is None:
+            return False
+        return True
+
+
 class ProteomicsXml(GenericXml):
     """ An enhanced XML datatype used to reuse code across several
     proteomic/mass-spec datatypes. """
@@ -102,12 +589,12 @@ class ProteomicsXml(GenericXml):
         """ Determines whether the file is the correct XML type. """
         contents = file_prefix.string_io()
         while True:
-            line = contents.readline()
+            line = contents.readline().strip()
             if line is None or not line.startswith('<?'):
                 break
         # pattern match <root or <ns:root for any ns string
-        pattern = r'^<(\w*:)?%s' % self.root
-        return line is not None and re.match(pattern, line) is not None
+        pattern = r'<(\w*:)?%s' % self.root
+        return line is not None and re.search(pattern, line) is not None
 
     def set_peek(self, dataset, is_multi_byte=False):
         """Set the peek and blurb text"""
@@ -119,6 +606,13 @@ class ProteomicsXml(GenericXml):
             dataset.blurb = 'file purged from disk'
 
 
+class ParamXml(ProteomicsXml):
+    """store Parameters in XML formal"""
+    file_ext = "paramxml"
+    blurb = "parameters in xmls"
+    root = "parameters|PARAMETERS"
+
+
 class PepXml(ProteomicsXml):
     """pepXML data"""
     edam_format = "format_3655"
@@ -127,6 +621,13 @@ class PepXml(ProteomicsXml):
     root = "msms_pipeline_analysis"
 
 
+class MascotXML(ProteomicsXml):
+    """mzXML data"""
+    file_ext = "mascotxml"
+    blurb = "mascot Mass Spectrometry data"
+    root = "mascot_search_results"
+
+
 class MzML(ProteomicsXml):
     """mzML data"""
     edam_format = "format_3244"
@@ -180,6 +681,12 @@ class TraML(ProteomicsXml):
     root = "TraML"
 
 
+class TrafoXML(ProteomicsXml):
+    file_ext = "trafoxml"
+    blurb = "RT alignment tranformation"
+    root = "TrafoXML"
+
+
 class MzQuantML(ProteomicsXml):
     edam_format = "format_3248"
     file_ext = "mzq"
@@ -218,6 +725,29 @@ class UniProtXML(ProteomicsXml):
     root = "uniprot"
 
 
+class XquestXML(ProteomicsXml):
+    file_ext = "xquest.xml"
+    blurb = "XQuest XML file"
+    root = "xquest_results"
+
+
+class XquestSpecXML(ProteomicsXml):
+    """spec.xml"""
+    file_ext = "spec.xml"
+    blurb = 'xquest_spectra'
+    root = "xquest_spectra"
+
+
+class QCML(ProteomicsXml):
+    """qcml
+    https://github.com/OpenMS/OpenMS/blob/113c49d01677f7f03343ce7cd542d83c99b351ee/share/OpenMS/SCHEMAS/mzQCML_0_0_5.xsd
+    https://github.com/OpenMS/OpenMS/blob/3cfc57ad1788e7ab2bd6dd9862818b2855234c3f/share/OpenMS/SCHEMAS/qcML_0.0.7.xsd
+    """
+    file_ext = "qcml"
+    blurb = 'QualityAssessments to runs'
+    root = "qcML|MzQualityML)"
+
+
 class Mgf(Text):
     """Mascot Generic Format data"""
     edam_data = "data_2536"
@@ -278,7 +808,7 @@ class ThermoRAW(Binary):
     """Class describing a Thermo Finnigan binary RAW file"""
     edam_data = "data_2536"
     edam_format = "format_3712"
-    file_ext = "raw"
+    file_ext = "thermo.raw"
 
     def sniff(self, filename):
         # Thermo Finnigan RAW format is proprietary and hence not well documented.

lib/galaxy/datatypes/registry.py

@@ -765,23 +765,19 @@ class Registry(object):
                 'coverage'      : coverage.LastzCoverage(),
                 'customtrack'   : interval.CustomTrack(),
                 'csfasta'       : sequence.csFasta(),
-                'db3'           : binary.SQlite(),
                 'fasta'         : sequence.Fasta(),
                 'eland'         : tabular.Eland(),
                 'fastq'         : sequence.Fastq(),
                 'fastqsanger'   : sequence.FastqSanger(),
-                'gemini.sqlite' : binary.GeminiSQLite(),
                 'gtf'           : interval.Gtf(),
                 'gff'           : interval.Gff(),
                 'gff3'          : interval.Gff3(),
                 'genetrack'     : tracks.GeneTrack(),
                 'h5'            : binary.H5(),
-                'idpdb'         : binary.IdpDB(),
                 'interval'      : interval.Interval(),
                 'laj'           : images.Laj(),
                 'lav'           : sequence.Lav(),
                 'maf'           : sequence.Maf(),
-                'mz.sqlite'     : binary.MzSQlite(),
                 'pileup'        : tabular.Pileup(),
                 'qualsolid'     : qualityscore.QualityScoreSOLiD(),
                 'qualsolexa'    : qualityscore.QualityScoreSolexa(),
@@ -801,26 +797,21 @@ class Registry(object):
                 'axt'           : 'text/plain',
                 'bam'           : 'application/octet-stream',
                 'bed'           : 'text/plain',
-                'blib'          : 'application/octet-stream',
                 'customtrack'   : 'text/plain',
                 'csfasta'       : 'text/plain',
-                'db3'           : 'application/octet-stream',
                 'eland'         : 'application/octet-stream',
                 'fasta'         : 'text/plain',
                 'fastq'         : 'text/plain',
                 'fastqsanger'   : 'text/plain',
-                'gemini.sqlite' : 'application/octet-stream',
                 'gtf'           : 'text/plain',
                 'gff'           : 'text/plain',
                 'gff3'          : 'text/plain',
                 'h5'            : 'application/octet-stream',
-                'idpdb'         : 'application/octet-stream',
                 'interval'      : 'text/plain',
                 'laj'           : 'text/plain',
                 'lav'           : 'text/plain',
                 'maf'           : 'text/plain',
                 'memexml'       : 'application/xml',
-                'mz.sqlite'     : 'application/octet-stream',
                 'pileup'        : 'text/plain',
                 'qualsolid'     : 'text/plain',
                 'qualsolexa'    : 'text/plain',
@@ -846,10 +837,6 @@ class Registry(object):
                 binary.Bam(),
                 binary.Sff(),
                 binary.H5(),
-                binary.GeminiSQLite(),
-                binary.MzSQlite(),
-                binary.IdpDB(),
-                binary.SQlite(),
                 xml.GenericXml(),
                 sequence.Maf(),
                 sequence.Lav(),

lib/galaxy/datatypes/test/test.dta2d

@@ -0,0 +1,9 @@
+#MZ	SEC	INT
+500.0	0	50
+600.0	1	100
+700.0	2	200
+800.0	3	400
+900.0	4	200
+1000.0	5	100
+1100.0	6	50
+900.0	2	200

lib/galaxy/datatypes/test/test.edta

@@ -0,0 +1,7 @@
+RT	mz	Int	charge	Meta2
+10	114	2342	1
+10	115	232	2
+10	116	523	2
+14	220	343	1	value
+14	431.1	343	2
+15	543.2393	343	3	b

lib/galaxy/datatypes/test/test.kroenik

@@ -0,0 +1,23 @@
+File	First Scan	Last Scan	Num of Scans	Charge	Monoisotopic Mass	Base Isotope Peak	Best Intensity	Summed Intensity	First RTime	Last RTime	Best RTime	Best Correlation	Modifications
+20060502data08_exc_RTf.mzXML	1480	1578	15	3	1345.607960	449.543300	60834.925781	506348.656250	521.106018	553.833008	533.018982	0.991700	_
+20060502data08_exc_RTf.mzXML	1487	1557	11	2	1345.608400	673.811500	26904.589844	199969.046875	523.559998	546.731018	533.018982	0.995300	_
+20060502data08_exc_RTf.mzXML	1557	1620	10	3	2002.810800	668.945100	38904.792969	217929.312500	546.731018	567.784973	553.833008	0.986300	_
+20060502data08_exc_RTf.mzXML	1571	1592	4	2	2002.811525	1002.913800	4603.663086	14353.689453	551.427979	558.577026	556.184998	0.978400	_
+20060502data08_exc_RTf.mzXML	1592	1690	15	3	1772.892100	591.971200	91715.507813	502103.500000	558.577026	590.963013	567.784973	0.986900	_
+20060502data08_exc_RTf.mzXML	1599	1683	13	4	1772.891285	444.230100	72974.398438	417335.125000	560.914001	588.521973	570.002014	0.974700	_
+20060502data08_exc_RTf.mzXML	1599	1676	11	2	1772.889336	887.452600	22342.041016	122096.265625	560.914001	586.155029	567.784973	0.994600	_
+20060502data08_exc_RTf.mzXML	1690	1774	13	2	1401.655615	701.834900	37010.062500	262936.343750	590.963013	619.705017	605.291992	0.995500	_
+20060502data08_exc_RTf.mzXML	1746	1816	11	2	1065.545100	533.779800	48403.296875	347601.562500	610.046997	634.202026	622.135986	0.979800	_
+20060502data08_exc_RTf.mzXML	1816	1851	6	4	2095.873767	525.226300	17985.734375	73192.179688	634.202026	646.385986	641.471008	0.986700	_
+20060502data08_exc_RTf.mzXML	1858	1879	4	4	1904.987400	477.504500	7037.772461	16893.957031	648.786011	656.114014	656.114014	0.962100	_
+20060502data08_exc_RTf.mzXML	1879	1907	4	2	994.581075	498.297700	28557.644531	92082.468750	656.114014	665.525024	660.861023	0.996100	_
+20060502data08_exc_RTf.mzXML	1886	1994	15	3	1506.688193	503.236500	223091.640625	1329185.625000	658.479980	693.369995	670.021973	0.989100	_
+20060502data08_exc_RTf.mzXML	1893	1955	10	2	1506.689740	754.352500	49197.664063	307397.281250	660.861023	680.966003	672.174988	0.990500	_
+20060502data08_exc_RTf.mzXML	1907	2056	23	4	2239.081209	561.027900	189284.390625	1359320.875000	665.525024	713.080994	685.143005	0.973600	_
+20060502data08_exc_RTf.mzXML	1914	1994	13	2	1336.644692	669.329400	174888.703125	994234.375000	667.744019	693.369995	676.612000	0.990700	_
+20060502data08_exc_RTf.mzXML	1921	1988	10	2	1478.675160	740.344800	119720.226563	577115.250000	670.021973	691.309998	678.859985	0.985600	_
+20060502data08_exc_RTf.mzXML	1928	1948	3	2	1697.803500	849.907800	3211.451660	7545.761719	672.174988	678.859985	672.174988	0.927400	_
+20060502data08_exc_RTf.mzXML	1935	1955	4	2	1127.618850	564.816500	67462.703125	183348.593750	674.471985	680.966003	680.966003	0.950400	_
+20060502data08_exc_RTf.mzXML	1941	2021	12	3	2239.081067	747.701800	67137.210938	463090.031250	676.612000	701.872009	683.143982	0.991200	_
+20060502data08_exc_RTf.mzXML	1948	2028	13	2	1583.758454	792.886000	36854.781250	262471.843750	678.859985	704.109009	691.309998	0.993400	_
+20060502data08_exc_RTf.mzXML	1955	2021	11	3	1583.757945	528.926500	128648.492188	829892.062500	680.966003	701.872009	691.309998	0.990400	_

lib/galaxy/datatypes/test/test.mztab

@@ -0,0 +1,28 @@
+MTD	mzTab-version	1.0 rc5
+MTD	mzTab-mode	Summary
+MTD	mzTab-type	Identification
+MTD	mzTab-ID	Cytidine
+MTD	description	LC-MS/MS Reference Standard
+MTD	sample_processing[1]	[MS, MS:1000544, Conversion to mzML, ]|[MS, MS:1000035, Peak picking, ]|[MS, MS:1001994, Top Hat baseline reduction, ]|[MS, MS:1000782, Savitzky-Golay smoothing, ]|[MS, MS:1000594, Low intensity data point removal, ]
+MTD	instrument[1]-name	[MS, MS:1000483, Thermo Fisher Scientific instrument model, LTQ Orbitrap Velos]
+MTD	instrument[1]-source	[MS, MS:1000008, Ionization Type, ESI]
+MTD	instrument[1]-analyzer[1]	[MS, MS:1000443, Mass Analyzer Type, Orbitrap]
+MTD	instrument[1]-detector	[MS, MS:1000453, Detector, Dynode Detector]
+MTD	software[1]	[MS, MS:1002205, ProteoWizard msconvert, ]
+MTD	software[1]-setting[1]	Peak Picking MS1
+MTD	software[1]	[MS, MS:1001457, data processing software, MassCascade-KNIME]
+MTD	smallmolecule_search_engine_score[1]	[MS, MS:1001153, search engine specific score,]
+MTD	contact[1]-name	Stephan Beisken
+MTD	contact[1]-affiliation	European Bioinformatics Institute (EMBL-EBI)
+MTD	contact[1]-email	beiken@ebi.ac.uk
+MTD	uri[1]	http://www.ebi.ac.uk/metabolights/MTBLS38
+MTD	fixed_mod[1]	[MS, MS:1002453, No fixed modifications searched, ]
+MTD	variable_mod[1]	[ , , CHEMMOD:2M+H, ]
+MTD	variable_mod[2]	[ , , CHEMMOD:M-C5H8O4, ]
+MTD	ms_run[1]-format	[MS, MS:1000584, Proteomics Standards Inititative mzML file format, mzML file]
+MTD	ms_run[1]-location	ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS38/cytidine.mzML
+MTD	ms_run[1]-id_format	[MS, MS:1000767, Native spectrum identifier format, ]
+MTD	ms_run[1]-fragmentation_method	[MS, MS:1000133, Collision-induced dissociation, ]
+
+SMH	identifier	chemical_formula	smiles	inchi_key	description	exp_mass_to_charge	calc_mass_to_charge	charge	retention_time	taxid	species	database	database_version	spectra_ref	search_engine	best_search_engine_score[1]	modifications
+SML	CHEBI:17562	C9H13N3O5	Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=O)n1	UHDGCWIWMRVCDJ-XVFCMESISA-N	Cytidine	244.0928	null	1	193.25	null	null	ChEBI	109	null	[MS, MS:1001083, ms-ms search, MassBank]	977	CHEMMOD:2M+H,CHEMMOD:M-C5H8O4

lib/galaxy/datatypes/test/test.mztab2

@@ -0,0 +1,92 @@
+COM	Meta data section																		
+MTD	mzTab-version	2.0.0-M																	
+MTD	mzTab-ID	mzTab-GCxGC-MS																	
+MTD	description	Minimal sample file for GCxGC-MS quantification of small molecules between two experiments																	
+MTD	instrument[1]-name	[MS, MS:1001945, Pegasus 4D, ]																	
+MTD	instrument[1]-source	[MS, MS:1000389, electron Ionization, ]																	
+MTD	instrument[1]-analyzer[1]	[MS, MS:1000084, time-of-flight, ]																	
+MTD	instrument[1]-detector	[MS, MS:1000114, microchannel plate detector, ]																	
+MTD	software[1]	[MS, MS:1001799, ChromaTOF software, 3.21]
+MTD	software[1]-setting[1]	baseline=0.2
+MTD	software[1]-setting[2]	dbMatchTreshold=900
+MTD	sample[1]-species[1]	[NCBITaxon, NCBITaxon:9606, Homo sapiens, ]																	
+MTD	sample[1]-cell_type[1]	[CL, CL:0000233, platelet, ]																	
+MTD	sample[1]-description	Unstimulated human blood platelets																	
+MTD	sample[2]-species[1]	[NCBITaxon, NCBITaxon:9606, Homo sapiens, ]																	
+MTD	sample[2]-cell_type[1]	[CL, CL:0000233, platelet, ]																	
+MTD	sample[2]-description	Unstimulated human blood platelets																	
+MTD	ms_run[1]-location	file://c:/data/control.mzML																	
+MTD	ms_run[1]-format	[MS, MS:1000584, mzML file, ]																	
+MTD	ms_run[1]-id_format	[MS, MS:1000776, scan number only nativeID format, ]
+MTD	ms_run[1]-scan_polarity[1]	[MS, MS:1000130, positive scan, ]																	
+MTD	ms_run[2]-location	file://c:/data/treatment.mzML																	
+MTD	ms_run[2]-format	[MS, MS:1000584, mzML file, ]																	
+MTD	ms_run[2]-id_format	[MS, MS:1000776, scan number only nativeID format, ]
+MTD	ms_run[2]-scan_polarity[1]	[MS, MS:1000130, positive scan, ]																	
+MTD	assay[1]-sample_ref	sample[1]																	
+MTD	assay[1]-ms_run_ref	ms_run[1]																	
+MTD	assay[2]-sample_ref	sample[2]																	
+MTD	assay[2]-ms_run_ref	ms_run[2]																	
+MTD	study_variable[1]	Untreated																	
+MTD	study_variable[1]-assay_refs	assay[1]																	
+MTD	study_variable[1]-description	drug response control																	
+MTD	study_variable[1]-average_function	[MS, MS:1002962, mean, ]																	
+MTD	study_variable[1]-variation_function	[MS, MS:1002885, standard error, ]																	
+MTD	study_variable[2]	Treated																	
+MTD	study_variable[2]-assay_refs	assay[2]																	
+MTD	study_variable[2]-description	drug response treatment																	
+MTD	study_variable[2]-average_function	[MS, MS:1002962, mean, ]																	
+MTD	study_variable[2]-variation_function	[MS, MS:1002885, standard error, ]																	
+MTD	cv[1]-label	MS																	
+MTD	cv[1]-full_name	PSI-MS controlled vocabulary																	
+MTD	cv[1]-version	20-06-2018																	
+MTD	cv[1]-uri	https://www.ebi.ac.uk/ols/ontologies/ms																	
+MTD	cv[2]-label	NCBITaxon																	
+MTD	cv[2]-full_name	An ontology representation of the NCBI organismal taxonomy Ontology																	
+MTD	cv[2]-version	2018-03-02																	
+MTD	cv[2]-uri	https://www.ebi.ac.uk/ols/ontologies/ncbitaxon																	
+MTD	cv[3]-label	CL																	
+MTD	cv[3]-full_name	The Cell Ontology is a structured controlled vocabulary for cell types in animals.																	
+MTD	cv[3]-version	2017-12-11																	
+MTD	cv[3]-uri	https://www.ebi.ac.uk/ols/ontologies/cl																	
+MTD	cv[4]-label	PRIDE																	
+MTD	cv[4]-full_name	PRIDE PRoteomics IDEntifications (PRIDE) database controlled vocabulary																	
+MTD	cv[4]-version	14-06-2018																	
+MTD	cv[4]-uri	https://www.ebi.ac.uk/ols/ontologies/pride																	
+MTD	cv[5]-label	CHEBI																	
+MTD	cv[5]-full_name	Chemical Entities of Biological Interest
+MTD	cv[5]-version	08-02-2019																	
+MTD	cv[5]-uri	https://www.ebi.ac.uk/ols/ontologies/chebi
+MTD	database[1]	[, ,Golm Metabolite Database, ]																	
+MTD	database[1]-prefix	GMD																	
+MTD	database[1]-version	2.3																	
+MTD	database[1]-uri	http://gmd.mpimp-golm.mpg.de/																	
+MTD	database[2]	[, , no database, null]																	
+MTD	database[2]-prefix	null																	
+MTD	database[2]-uri	null																	
+MTD	database[2]-version	Unknown																	
+MTD	derivatization_agent[1]	[,,Methoxylamine hydrochloride,]																	
+MTD	derivatization_agent[2]	[CHEBI, CHEBI:85064, N-methyl-N-(trimethylsilyl)trifluoroacetamide,]																	
+MTD	small_molecule-identification_reliability	[MS, MS:1002896, compound identification confidence level, ]																	
+MTD	id_confidence_measure[1]	[MS, MS:1002890, fragmentation score, ]																	
+MTD	small_molecule-quantification_unit	[PRIDE, PRIDE:0000330, Arbitrary quantification unit, ]																	
+MTD	small_molecule_feature-quantification_unit	[PRIDE, PRIDE:0000330, Arbitrary quantification unit, ]																	
+MTD	quantification_method	[,,baseline-corrected intensity quantification,]																	
+MTD	custom[1]	[MS, MS:1000901, retention time normalization standard, n-alkanes C10–C36]																	
+																			
+COM	Small molecule summary rows (similar to Protein section). 																		
+COM	Evidences (e.g. multiple modifications, adducts incl. charge variants are summarized). 																		
+COM	For most use cases this summary lines might be sufficient.																		
+SMH	SML_ID	SMF_ID_REFS	database_identifier	chemical_formula	smiles	inchi	chemical_name	uri	theoretical_neutral_mass	adduct_ions	reliability	best_id_confidence_measure	best_id_confidence_value	abundance_assay[1]	abundance_study_variable[1]	abundance_variation_study_variable[1]	abundance_assay[2]	abundance_study_variable[2]	abundance_variation_study_variable[2]
+SML	1	1 | 2	GMD:cd7993ea-ad14-452a-a907-33376cc98790	C18H36O2	CCCCCCCCCCCCCCCCCC(O)=O	InChI=1S/C18H36O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h2-17H2,1H3,(H,19,20)	Octadecanoic acid	http://identifiers.org/gmd/cd7993ea-ad14-452a-a907-33376cc98790	284.478	[M+H]1+	2	[MS, MS:1002890, fragmentation score, ]	978	805.16	805.16	0	589.9	589.9	0
+																			
+COM	Small molecule feature rows (only reported in Complete Quantification files and if feature information like e.g. mass traces are important)																		
+SFH	SMF_ID	SME_ID_REFS	SME_ID_REF_ambiguity_code	adduct_ion	isotopomer	exp_mass_to_charge	charge	retention_time_in_seconds	retention_time_in_seconds_start	retention_time_in_seconds_end	abundance_assay[1]	abundance_assay[2]	opt_global_retention_time_nd	opt_global_retention_time_nd_window_start	opt_global_retention_time_nd_window_end				
+SMF	1	1	null	[M+H]1+	null	285.484	1	1564.47	1559.45	1564.48	805.16	805.16	1562 | 2.47 	1557 | 2.45 	1562 | 2.48				
+SMF	2	2	null	[M+H]1+	null	285.484	1	1564.48	1554.45	1569.47	589.9	589.9	1562 | 2.48	1552 | 2.45	1567| 2.47				
+																			
+COM	Small molecule evidence rows for parent ions. Analog to PSM. 																		
+COM	Primary use case: report single hits from spectral library or accurate mass searches without quantification.																		
+SEH	SME_ID	evidence_input_id	database_identifier	chemical_formula	smiles	inchi	chemical_name	uri	derivatized_form	adduct_ion	exp_mass_to_charge	charge	theoretical_mass_to_charge	spectra_ref	identification_method	ms_level	id_confidence_measure[1]	rank	
+SME	1	ms_run[1]:scan=8	GMD:f634c736-39e8-4323-8155-fa3cc26ac9e3	C18H36O2	CCCCCCCCCCCCCCCCCC(O)=O	InChI=1S/C18H36O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h2-17H2,1H3,(H,19,20)	Octadecanoic acid (1TMS)	http://identifiers.org/gmd.analyte/f634c736-39e8-4323-8155-fa3cc26ac9e3	[CHEBI, CHEBI:51088, trimethylsilyl group, 1]	[M+H]+	356.6588	1	356.659	ms_run[1]:scan=8	[,, ChromaTOF database search,]	[MS, MS:1000511, ms level, 1]	957	1	
+SME	2	ms_run[2]:scan=23	GMD:f634c736-39e8-4323-8155-fa3cc26ac9e3	C18H36O2	CCCCCCCCCCCCCCCCCC(O)=O	InChI=1S/C18H36O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h2-17H2,1H3,(H,19,20)	Octadecanoic acid (1TMS)	http://identifiers.org/gmd.analyte/f634c736-39e8-4323-8155-fa3cc26ac9e3	[CHEBI, CHEBI:51088, trimethylsilyl group, 1]	[M+H]+	356.6589	1	356.659	ms_run[2]:scan=23	[,, ChromaTOF database search,]	[MS, MS:1000511, ms level, 1]	972	1	

lib/galaxy/datatypes/test/test.peff

@@ -0,0 +1,11 @@
+# PEFF 1.0
+# //
+# DbName=Minimal Test example PEFF_Minimal_Valid.peff
+# Prefix=sp
+# DbSource=http://www.peptideatlas.org/formats/PEFF/PEFF_Minimal_Valid.peff
+# DbVersion=1
+# SequenceType=AA
+# NumberOfEntries=1
+# //
+>sp:Q9Y2X3 \Length=1
+M

lib/galaxy/datatypes/test/test.peplist

@@ -0,0 +1,36 @@
+       m/z	     rt(min)	       snr	      charge	   intensity
+  706.0656	     47.997	     70.443	          3	   3709.630
+  740.4292	     60.127	     28.895	          4	   2153.832
+  708.7055	     63.321	     28.970	          3	   2377.576
+  728.7255	     56.390	     28.530	          3	   1820.929
+  721.3855	     57.410	     25.965	          3	   1332.942
+  740.4400	     64.272	     16.639	          2	   1024.329
+  707.3855	     63.423	     20.248	          3	   1495.899
+  735.7055	     50.275	     29.838	          3	    804.873
+  726.7255	     63.966	     13.282	          3	   1364.349
+  723.4000	     57.647	     13.069	          2	    713.563
+  700.4400	     61.588	     11.435	          2	    579.007
+  736.3400	     61.113	      9.765	          2	    464.364
+  705.4000	     54.454	     12.855	          2	    457.507
+  709.0056	     57.104	     12.614	          3	    454.622
+  710.3000	     49.459	     18.364	          2	    534.519
+  719.4000	     64.714	      7.860	          3	    447.372
+  742.4400	     64.170	      6.799	          2	    357.583
+  752.4000	     55.983	      7.138	          2	    290.348
+  714.1492	     47.114	     22.442	          4	    576.568
+  753.4256	     61.486	      7.788	          3	    318.019
+  730.3800	     53.536	      8.914	          2	    284.038
+  708.8400	     58.836	      6.272	          2	    246.319
+  737.0400	     50.207	     12.257	          3	    309.824
+  716.9200	     58.123	      6.188	          2	    283.297
+  729.7456	     50.308	      9.760	          3	    428.650
+  712.3200	     49.391	      8.749	          2	    235.981
+  748.9400	     51.294	      9.114	          2	    250.202
+  712.8800	     53.672	      6.466	          2	    160.206
+  714.9000	     53.604	      6.417	          2	    202.450
+  716.8800	     54.080	      6.920	          2	    225.521
+  715.7055	     49.017	     10.866	          3	    198.560
+  728.3600	     53.299	      6.913	          3	    156.242
+  753.8800	     49.527	      6.406	          2	    113.352
+  724.0400	     47.997	      6.559	          3	    281.194
+  745.9200	     47.521	      6.732	          2	     87.974

lib/galaxy/datatypes/test/test.psms

@@ -0,0 +1,122 @@
+PSMId	score	q-value	posterior_error_prob	peptide	proteinIds
+query:161610;rank:1;spectrum:1093.0258_2187.96_spectrum=40633_uteruspremenopause;rt:2187.96;mz:1093.0258;charge:2	11.0472	0	1.48741e-12	X.SLAGSSGPGASSGTSGDHGELVVR.X	UniProt_E9PI39	UniProt_E9PIZ1	UniProt_E9PK01	UniProt_E9PL12	UniProt_E9PMW7	UniProt_E9PPR1	UniProt_E9PQ49	UniProt_E9PRY8	UniProt_H0YCK7	UniProt_P29692	UniProt_P29692-2	genCDS_ENST00000317198_8_143579792-143586845_-1	genCDS_ENST00000395119_8_143579792-143586845_-1	genCDS_ENST00000419152_8_143579792-143586845_-1	genCDS_ENST00000423316_8_143579792-143590081_-1	genCDS_ENST00000442189_8_143579792-143590081_-1	genCDS_ENST00000524397_8_143580630-143586845_-1	genCDS_ENST00000529007_8_143580630-143586845_-1	genCDS_ENST00000529272_8_143579792-143586845_-1	genCDS_ENST00000530191_8_143580506-143586845_-1	genCDS_ENST00000530445_8_143580620-143586845_-1	genCDS_ENST00000530616_8_143580630-143589222_-1	genCDS_ENST00000531218_8_143580522-143586845_-1	genCDS_ENST00000532741_8_143579792-143590231_-1	genCDS_ENST00000533204_8_143580506-143586845_-1	genCDS_ENST00000533494_8_143580613-143586845_-1	genCDS_ENST00000533749_8_143581079-143599321_-1	genCDS_ENST00000534380_8_143580034-143586845_-1	genCDS_ENST00000618139_8_143580019-143590081_-1
+query:132093;rank:1;spectrum:832.40479_2605.29_spectrum=72602_uteruspremenopause;rt:2605.29;mz:832.40479;charge:2	9.36298	0	7.2763e-11	X.AAAFEEQENETVVVK.X	UniProt_Q5TCU6	UniProt_Q9Y490	genCDS_ENST00000314888_9_35697791-35725694_-1
+query:119552;rank:1;spectrum:769.39142_3320.48_spectrum=167622_uteruspremenopause;rt:3320.48;mz:769.39142;charge:2	8.72204	0	3.19783e-10	X.FALQDLSVEETSAK.X	UniProt_B2RCS5	UniProt_G3V2E8	UniProt_G3V2N5	UniProt_G3V2W4	UniProt_G3V2X9	UniProt_G3V5M4	UniProt_H9KV75	UniProt_O43707	UniProt_P12814	UniProt_P12814-2	UniProt_P12814-3	UniProt_P12814-4	UniProt_P35609	UniProt_Q08043	genCDS_ENST00000193403_14_68874859-68979056_-1	genCDS_ENST00000252699_19_38647746-38729432_1	genCDS_ENST00000366578_1_236686674-236762619_1	genCDS_ENST00000376839_14_68874859-68925582_-1	genCDS_ENST00000394419_14_68874859-68979056_-1	genCDS_ENST00000438964_14_68874859-68979056_-1	genCDS_ENST00000502692_11_66546511-66563193_1	genCDS_ENST00000513398_11_66546938-66563193_1	genCDS_ENST00000538545_14_68874859-68979056_-1	genCDS_ENST00000542672_1_236686674-236762619_1	genCDS_ENST00000553370_14_68904702-68925582_-1	genCDS_ENST00000553779_14_68910020-68925582_-1	genCDS_ENST00000555616_14_68892228-68925582_-1	genCDS_ENST00000556433_14_68893665-68978258_-1	genCDS_ENST00000556571_14_68910022-68978051_-1
+query:105717;rank:1;spectrum:715.89587_3127.2_spectrum=82140_uteruspremenopause;rt:3127.2;mz:715.89587;charge:2	8.58807	0	4.35755e-10	X.LDSLSAQLSQLQK.X	UniProt_P02545	UniProt_P02545-2	UniProt_P02545-3	UniProt_P02545-4	UniProt_P02545-5	UniProt_P02545-6	UniProt_Q5TCI8	genCDS_ENST00000347559_1_156114919-156139106_1	genCDS_ENST00000361308_1_156114919-156137764_1	genCDS_ENST00000368297_1_156126803-156137764_1	genCDS_ENST00000368299_1_156114919-156139106_1	genCDS_ENST00000368300_1_156114919-156139106_1	genCDS_ENST00000368301_1_156114919-156137764_1	genCDS_ENST00000448611_1_156126204-156139839_1	genCDS_ENST00000473598_1_156129850-156139106_1
+query:121144;rank:1;spectrum:776.86639_1943.52_spectrum=62937_uteruspremenopause;rt:1943.52;mz:776.86639;charge:2	8.31993	0	8.09508e-10	X.TSTTSSMVASAEQPR.X	UniProt_E7EMN6	UniProt_E7EUI7	UniProt_P41236	UniProt_Q6NXS1	genCDS_ENST00000413183_3_195527890-195543025_-1	genCDS_ENST00000438848_3_195516925-195543025_-1	genCDS_ENST00000618156_3_195516896-195543025_-1
+query:91084;rank:1;spectrum:661.3443_2685.51_spectrum=127861_uteruspremenopause;rt:2685.51;mz:661.3443;charge:2	7.84396	0	2.43037e-09	X.STSGGTAALGCLVK.X	UniProt_P01857	UniProt_P01860	genCDS_ENST00000390542_14_105741473-105743071_-1	genCDS_ENST00000390548_14_105737762-105743071_-1	genCDS_ENST00000390549_14_105741473-105743071_-1	genCDS_ENST00000390551_14_105769237-105771405_-1	genCDS_ENST00000612473_14_105741473-106005532_-1	genCDS_ENST00000613152_14_105741473-106211391_-1	genCDS_ENST00000615822_14_105741473-106062604_-1	genCDS_ENST00000616127_14_105769237-106038345_-1	genCDS_ENST00000618145_14_105741473-106012356_-1	genCDS_ENST00000618756_14_105668245-106538265_-1	genCDS_ENST00000619212_14_105741473-106211391_-1	genCDS_ENST00000621473_14_105769237-106005532_-1
+query:128131;rank:1;spectrum:813.40948_2244.71_spectrum=40773_uteruspremenopause;rt:2244.71;mz:813.40948;charge:2	7.38397	0	7.03248e-09	X.DALQNPNDLQLQEK.X	UniProt_C9IYV6	UniProt_C9JPE5	UniProt_Q9H0Q0	genCDS_ENST00000381323_2_16552936-16588119_-1	genCDS_ENST00000406434_2_16552936-16588119_-1	genCDS_ENST00000445605_2_16564005-16588119_-1	genCDS_ENST00000451689_2_16564024-16588119_-1
+query:141775;rank:1;spectrum:893.9129_2874.06_spectrum=158864_uteruspremenopause;rt:2874.06;mz:893.9129;charge:2	7.1148	0	1.30952e-08	X.NKDQGTYEDYVEGLR.X	Augustus2_AUGUSTUS00000061902_12_56160654-56153919_1	UniProt_B7Z6Z4	UniProt_F8VPF3	UniProt_F8VZU9	UniProt_F8W180	UniProt_F8W1R7	UniProt_G3V1V0	UniProt_G3V1Y7	UniProt_G8JLA2	UniProt_J3KND3	UniProt_P60660	UniProt_P60660-2	genCDS_ENST00000293422_12_56158402-56161415_1	genCDS_ENST00000348108_12_56158402-56160654_1	genCDS_ENST00000536128_12_56158402-56160331_1	genCDS_ENST00000547408_12_56158402-56162322_1	genCDS_ENST00000547649_12_56158402-56161415_1	genCDS_ENST00000548293_12_56158402-56160654_1	genCDS_ENST00000548400_12_56158402-56160654_1	genCDS_ENST00000548580_12_56158402-56161415_1	genCDS_ENST00000549392_12_56158402-56160320_1	genCDS_ENST00000549566_12_56158402-56161415_1	genCDS_ENST00000550697_12_56158402-56160654_1	genCDS_ENST00000551589_12_56158402-56160331_1
+query:71406;rank:1;spectrum:404.21942_2506.81_spectrum=119549_uteruspremenopause;rt:2506.81;mz:404.21942;charge:3	7.03952	0	1.55822e-08	X.TANDAVELHLK.X	UniProt_Q9P2B2	genCDS_ENST00000393203_1_116910204-116986967_1
+query:129027;rank:1;spectrum:817.40759_3010.12_spectrum=35161_uteruspremenopause;rt:3010.12;mz:817.40759;charge:2	7.02828	0	1.5992e-08	X.EGCTVSPETLSLNVK.X	UniProt_E5KLJ5	UniProt_E5KLJ6	UniProt_E5KLJ9	UniProt_E5KLK1	UniProt_O60313	UniProt_O60313-2	genCDS_ENST00000361150_3_193593378-193692127_1	genCDS_ENST00000361510_3_193593378-193692127_1	genCDS_ENST00000361715_3_193593378-193692127_1	genCDS_ENST00000361828_3_193593378-193692127_1	genCDS_ENST00000361908_3_193593378-193692127_1	genCDS_ENST00000392438_3_193593378-193692127_1
+query:79758;rank:1;spectrum:627.82471_1646.41_spectrum=69987_uteruspremenopause;rt:1646.41;mz:627.82471;charge:2	6.79995	0	2.70985e-08	X.LEPGGGAEAQAVR.X	UniProt_Q14315	UniProt_Q14315-2	genCDS_ENST00000325888_7_128830638-128858523_1	genCDS_ENST00000346177_7_128830638-128858523_1
+query:107233;rank:1;spectrum:721.87775_2878.99_spectrum=96857_uteruspremenopause;rt:2878.99;mz:721.87775;charge:2	6.53355	0	5.01392e-08	X.EAGAGGLSLAVEGPSK.X	UniProt_E7EN95	UniProt_O75369	UniProt_O75369-2	UniProt_O75369-3	UniProt_O75369-6	UniProt_O75369-7	UniProt_O75369-8	UniProt_O75369-9	UniProt_Q14315	UniProt_Q14315-2	genCDS_ENST00000295956_3_58008565-58170762_1	genCDS_ENST00000325888_7_128830638-128858523_1	genCDS_ENST00000346177_7_128830638-128858523_1	genCDS_ENST00000358537_3_58008565-58170762_1	genCDS_ENST00000429972_3_58008565-58170762_1	genCDS_ENST00000490882_3_58008565-58170762_1	genCDS_ENST00000493452_3_58078486-58170762_1
+query:146872;rank:1;spectrum:619.28918_2152.13_spectrum=141583_uteruspremenopause;rt:2152.13;mz:619.28918;charge:3	6.13383	0	1.26226e-07	X.SEETKENEGFTVTAEGK.X	UniProt_M0QYC8	UniProt_P01024	genCDS_ENST00000245907_19_6677882-6720589_-1	genCDS_ENST00000596548_19_6680159-6685038_-1
+query:172404;rank:1;spectrum:871.76086_2726.33_spectrum=42005_uteruspremenopause;rt:2726.33;mz:871.76086;charge:3	5.99128	0	1.75446e-07	X.SEAEEALTSFN(Deamidated)GHKPPGSSEPLTVK.X	UniProt_B4DVB8	UniProt_Q15717	genCDS_ENST00000351593_19_7963483-7991815_-1	genCDS_ENST00000407627_19_7963483-7991815_-1	genCDS_ENST00000596459_19_7963483-7991815_-1
+query:105836;rank:1;spectrum:716.36646_2072.32_spectrum=141400_uteruspremenopause;rt:2072.32;mz:716.36646;charge:2	5.83486	0	2.51791e-07	X.VASSPVM(Oxidation)VSNPATR.X	UniProt_A6NEM2	UniProt_P51610	UniProt_P51610-2	UniProt_P51610-4	genCDS_ENST00000310441_X_153949347-153970840_-1	genCDS_ENST00000369984_X_153949347-153970840_-1
+query:89905;rank:1;spectrum:657.87396_3407.52_spectrum=152816_uteruspremenopause;rt:3407.52;mz:657.87396;charge:2	5.75831	0	3.00493e-07	X.EHALLAYTLGVK.X	Augustus2_AUGUSTUS00000028250_3_184026960-184027756_-1	UniProt_P68104	UniProt_Q05639	UniProt_Q5VTE0	calCuffs_CUFF.68550.1_19_35873852-35875252_1_1_ORF2	ensBodymap_RNASEQT00000006703_5_14651962-14653630_-1	ensBodymap_RNASEQT00000053260_5_14650973-14653630_-1	ensBodymap_RNASEQT00000095825_9_135894020-135896638_1	ensBodymap_RNASEQT00000213862_9_135894020-135896638_1	genCDS_ENST00000217182_20_63488298-63497763_-1	genCDS_ENST00000298049_20_63488298-63497763_-1	genCDS_ENST00000309268_6_73517810-73520026_-1	genCDS_ENST00000316292_6_73517810-73520026_-1	genCDS_ENST00000331523_6_73517810-73520026_-1	genCDS_ENST00000615060_6_73517916-73520026_-1	genpseudogene_ENST00000415278_1_96446930-96448318_1_1_ORF2	genpseudogene_ENST00000419025_3_184026369-184027756_-1_2_ORF4	genpseudogene_ENST00000436459_9_133019486-133020874_1_1_ORF1	genpseudogene_ENST00000514975_4_105484698-105486080_1_1_ORF1	genpseudogene_ENST00000596811_19_35382172-35384052_1_1_ORF5	yalePseudo_PGOHUM00000234671_19_35873074-35874951_1_2_ORF13	yalePseudo_PGOHUM00000237893_3_183744160-183745544_-1_2_ORF4	yalePseudo_PGOHUM00000244804_1_96912486-96913871_1_1_ORF2	yalePseudo_PGOHUM00000246017_4_106405855-106407234_1_1_ORF1
+query:120224;rank:1;spectrum:772.3432_1845.25_spectrum=39781_uteruspremenopause;rt:1845.25;mz:772.3432;charge:2	5.59137	0	4.41859e-07	X.FYEQM(Oxidation)N(Deamidated)GPVAGASR.X	UniProt_E9PI39	UniProt_E9PIZ1	UniProt_E9PK01	UniProt_E9PK06	UniProt_E9PK72	UniProt_E9PKK3	UniProt_E9PL12	UniProt_E9PL71	UniProt_E9PMW7	UniProt_E9PN91	UniProt_E9PPR1	UniProt_E9PQ49	UniProt_E9PQZ1	UniProt_E9PRY8	UniProt_H0YCK7	UniProt_P29692	UniProt_P29692-2	UniProt_P29692-3	UniProt_P29692-4	genCDS_ENST00000317198_8_143579792-143586845_-1	genCDS_ENST00000395119_8_143579792-143586845_-1	genCDS_ENST00000419152_8_143579792-143586845_-1	genCDS_ENST00000423316_8_143579792-143590081_-1	genCDS_ENST00000442189_8_143579792-143590081_-1	genCDS_ENST00000524397_8_143580630-143586845_-1	genCDS_ENST00000524624_8_143579792-143586845_-1	genCDS_ENST00000525223_8_143586729-143586845_-1	genCDS_ENST00000526340_8_143586219-143586845_-1	genCDS_ENST00000526838_8_143579792-143586845_-1	genCDS_ENST00000528610_8_143579792-143586845_-1	genCDS_ENST00000529007_8_143580630-143586845_-1	genCDS_ENST00000529272_8_143579792-143586845_-1	genCDS_ENST00000529516_8_143580642-143586845_-1	genCDS_ENST00000530191_8_143580506-143586845_-1	genCDS_ENST00000530445_8_143580620-143586845_-1	genCDS_ENST00000530616_8_143580630-143589222_-1	genCDS_ENST00000531218_8_143580522-143586845_-1	genCDS_ENST00000531621_8_143579792-143586845_-1	genCDS_ENST00000532543_8_143586729-143586845_-1	genCDS_ENST00000532741_8_143579792-143590231_-1	genCDS_ENST00000533204_8_143580506-143586845_-1	genCDS_ENST00000533494_8_143580613-143586845_-1	genCDS_ENST00000533749_8_143581079-143599321_-1	genCDS_ENST00000533833_8_143580630-143586845_-1	genCDS_ENST00000534377_8_143580186-143586845_-1	genCDS_ENST00000534380_8_143580034-143586845_-1	genCDS_ENST00000618139_8_143580019-143590081_-1	genpseudogene_ENST00000433698_9_92836826-92837668_-1_1_ORF1	yalePseudo_PGOHUM00000236264_9_95599111-95599989_-1_1_ORF1
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+query:36143;rank:1;spectrum:504.74222_1377.49_spectrum=31223_uteruspremenopause;rt:1377.49;mz:504.74222;charge:2	2.02503	0.000173319	0.00125862	X.SLM(Oxidation)SADNVR.X	UniProt_O43143	genCDS_ENST00000336812_4_24527924-24584393_-1
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lib/galaxy/dependencies/conditional-requirements.txt

@@ -31,4 +31,4 @@ influxdb
 
 # Deep learning packages for tool recommendation
 keras==2.2.4
-tensorflow==1.12.2
+tensorflow==1.15.2

lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt

@@ -4,20 +4,20 @@ alabaster==0.7.12
 atomicwrites==1.3.0
 attrs==19.3.0
 babel==2.8.0
-certifi==2019.11.28
+certifi==2020.4.5.1
 chardet==3.0.4
 commonmark==0.9.1
 configparser==4.0.2 ; python_version < '3.2'
 contextlib2==0.6.0.post1 ; python_version < '3.5'
-coverage==5.0.3
-deprecated==1.2.7
+coverage==5.0.4
+deprecated==1.2.9
 docutils==0.15.2
 funcsigs==1.0.2 ; python_version < '3.3'
 future==0.18.2
 gunicorn==19.10.0
 idna==2.9
 imagesize==1.2.0
-importlib-metadata==1.5.0 ; python_version < '3.8'
+importlib-metadata==1.6.0 ; python_version < '3.8'
 jinja2==2.11.1
 lxml==4.5.0
 markdown==3.1.1
@@ -27,17 +27,18 @@ mock==3.0.5
 more-itertools==5.0.0
 nose==1.3.7
 nosehtml==0.4.5
-packaging==20.1
+packaging==20.3
 pathlib2==2.3.5 ; python_version < '3.6'
 pathtools==0.1.2
 pluggy==0.13.1
 port-for==0.4
+prettytable==0.7.2
 psutil==5.7.0
 py==1.8.1
 pygithub==1.45
 pygments==2.5.2
 pyjwt==1.7.1
-pyparsing==2.4.6
+pyparsing==2.4.7
 pytest-cov==2.8.1
 pytest-html==1.22.1
 pytest-metadata==1.8.0
@@ -61,6 +62,7 @@ twill==2.0
 typing==3.7.4.1 ; python_version < '3.5'
 urllib3==1.25.8
 watchdog==0.10.2
-wcwidth==0.1.8
-wrapt==1.12.0
+wcwidth==0.1.9
+wrapt==1.12.1
+xmlrunner==1.7.7
 zipp==1.2.0

lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

@@ -23,8 +23,8 @@ bcrypt==3.1.7
 bdbag==1.5.6
 beaker==1.11.0
 bioblend==0.13.0
-bleach==3.1.1
-boltons==20.0.0
+bleach==3.1.4
+boltons==20.1.0
 boto3==1.9.114
 boto==2.49.0
 botocore==1.12.253
@@ -32,7 +32,7 @@ bx-python==0.8.8
 bz2file==0.98 ; python_version < '3.3'
 cachecontrol==0.11.7
 cachetools==3.1.1
-certifi==2019.11.28
+certifi==2020.4.5.1
 cffi==1.14.0
 chardet==3.0.4
 cheetah3==3.2.4
@@ -43,18 +43,18 @@ cmd2==0.8.9
 coloredlogs==14.0
 configparser==4.0.2 ; python_version < '3.2'
 contextlib2==0.6.0.post1 ; python_version < '3.5'
-cryptography==2.8
+cryptography==2.9
 cwltool==1.0.20191225192155
 debtcollector==1.22.0
 decorator==4.4.2
-deprecated==1.2.7
+deprecated==1.2.9
 deprecation==2.0.7
 dictobj==0.4
 docopt==0.6.2
 docutils==0.15.2
 dogpile.cache==0.9.0
 ecdsa==0.15
-enum34==1.1.9 ; python_version < '3.4'
+enum34==1.1.10 ; python_version < '3.4'
 fabric3==1.14.post1
 funcsigs==1.0.2 ; python_version < '3.3'
 functools32==3.2.3.post2 ; python_version < '3.2'
@@ -63,13 +63,13 @@ futures==3.3.0 ; python_version == '2.6' or python_version == '2.7'
 galaxy-sequence-utils==1.1.5
 google-api-python-client==1.7.8
 google-auth-httplib2==0.0.3
-google-auth==1.11.2
-gxformat2==0.10.1
+google-auth==1.13.1
+gxformat2==0.11.1
 h5py==2.10.0
-httplib2==0.17.0
-humanfriendly==7.1.1
+httplib2==0.17.2
+humanfriendly==8.1
 idna==2.9
-importlib-metadata==1.5.0 ; python_version < '3.8'
+importlib-metadata==1.6.0 ; python_version < '3.8'
 ipaddress==1.0.23 ; python_version < '3.3'
 isa-rwval==0.10.7
 iso8601==0.1.12
@@ -78,14 +78,14 @@ jmespath==0.9.5
 jsonpatch==1.25
 jsonpointer==2.0
 jsonschema==3.2.0
-keystoneauth1==3.18.0
-kombu==4.6.7
+keystoneauth1==4.0.0
+kombu==4.6.8
 lockfile==0.12.2
 lxml==4.5.0
-mako==1.1.1
+mako==1.1.2
 markdown==3.1.1
 markupsafe==1.1.1
-mercurial==5.3
+mercurial==5.3.2
 mistune==0.8.4
 monotonic==1.5
 msgpack==1.0.0
@@ -102,7 +102,7 @@ numpy==1.16.6
 oauth2client==4.1.3
 oauthlib==3.1.0
 openstacksdk==0.17.0
-os-client-config==2.0.0
+os-client-config==2.1.0
 os-service-types==1.7.0
 osc-lib==2.0.0
 oslo.config==7.0.0
@@ -111,21 +111,21 @@ oslo.i18n==3.25.1
 oslo.log==3.45.2
 oslo.serialization==2.29.2
 oslo.utils==3.42.1
-packaging==20.1
+packaging==20.3
 paramiko==2.7.1
 parsley==1.3
 paste==3.4.0
 pastedeploy==2.1.0
 pastescript==3.2.0
 pathlib2==2.3.5 ; python_version < '3.6'
-pbr==5.4.4
+pbr==5.4.5
 prettytable==0.7.2
 prov==1.5.1
 psutil==5.7.0
-pulsar-galaxy-lib==0.14.0.dev1
+pulsar-galaxy-lib==0.14.0.dev3
 pyasn1-modules==0.2.8
 pyasn1==0.4.8
-pycparser==2.19
+pycparser==2.20
 pycryptodome==3.9.7
 pyeventsystem==0.1.0
 pyinotify==0.9.6 ; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5'
@@ -133,9 +133,9 @@ pyjwt==1.7.1
 pykwalify==1.7.0
 pynacl==1.3.0
 pyopenssl==19.1.0
-pyparsing==2.4.6
-pyperclip==1.7.0
-pyrsistent==0.15.7
+pyparsing==2.4.7
+pyperclip==1.8.0
+pyrsistent==0.16.0
 pysam==0.15.2
 pysftp==0.2.9
 python-cinderclient==4.0.0
@@ -149,7 +149,7 @@ python-openid==2.2.5 ; python_version < '3.0'
 python-swiftclient==3.6.0
 pytz==2019.3
 pyuwsgi==2.0.18.post0
-pyyaml==5.3
+pyyaml==5.3.1
 rdflib-jsonld==0.4.0
 rdflib==4.2.2
 repoze.lru==0.7
@@ -157,7 +157,7 @@ requests-oauthlib==1.3.0
 requests-toolbelt==0.9.1
 requests==2.23.0
 requestsexceptions==1.4.0
-rfc3986==1.3.2
+rfc3986==1.4.0
 routes==2.4.1
 rsa==4.0
 ruamel.ordereddict==0.4.14 ; platform_python_implementation == 'CPython' and python_version <= '2.7'
@@ -170,17 +170,17 @@ setuptools-scm==3.5.0
 shellescape==3.4.1
 simplejson==3.17.0
 six==1.11.0
-social-auth-core[openidconnect]==3.1.0+gx0
+social-auth-core[openidconnect]==3.3.0
 sqlalchemy-migrate==0.13.0
-sqlalchemy-utils==0.36.1
-sqlalchemy==1.3.13
+sqlalchemy-utils==0.36.3
+sqlalchemy==1.3.16
 sqlparse==0.3.1
 stevedore==1.32.0
 subprocess32==3.5.4 ; python_version < '3.0'
 svgwrite==1.3.1
 tempita==0.5.2
 tenacity==4.12.0
-typing-extensions==3.7.4.1
+typing-extensions==3.7.4.2
 typing==3.7.4.1 ; python_version < '3.5'
 tzlocal==2.0.0
 unicodecsv==0.14.1 ; python_version < '3.0'
@@ -188,9 +188,9 @@ uritemplate==3.0.1
 urllib3==1.25.8
 vine==1.3.0
 warlock==1.3.3
-wcwidth==0.1.8
+wcwidth==0.1.9
 webencodings==0.5.1
 webob==1.8.6
 whoosh==2.7.4
-wrapt==1.12.0
+wrapt==1.12.1
 zipp==1.2.0

lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt

@@ -1,7 +1,7 @@
 -i https://pypi.python.org/simple
 configparser==4.0.2 ; python_version < '3.2'
 entrypoints==0.3
-enum34==1.1.9 ; python_version < '3.4'
+enum34==1.1.10 ; python_version < '3.4'
 flake8-import-order==0.18.1
 flake8==3.7.9
 functools32==3.2.3.post2 ; python_version < '3.2'

lib/galaxy/jobs/__init__.py

@@ -1141,6 +1141,14 @@ class JobWrapper(HasResourceParameters):
             raise Exception('(%s) Unable to create job working directory',
                             job.id)
 
+    @property
+    def guest_ports(self):
+        if hasattr(self, "interactivetools"):
+            guest_ports = [ep.get('port') for ep in self.interactivetools]
+            return guest_ports
+        else:
+            return []
+
     @property
     def working_directory(self):
         if self.__working_directory is None:

lib/galaxy/jobs/runners/__init__.py

@@ -425,7 +425,7 @@ class BaseJobRunner(object):
             compute_tmp_directory = job_wrapper.tmp_directory()
 
         tool = job_wrapper.tool
-        guest_ports = [ep.get('port') for ep in getattr(job_wrapper, 'interactivetools', [])]
+        guest_ports = job_wrapper.guest_ports
         tool_info = ToolInfo(
             tool.containers,
             tool.requirements,

lib/galaxy/jobs/runners/kubernetes.py

@@ -19,12 +19,15 @@ from galaxy.jobs.runners import (
 from galaxy.jobs.runners.util.pykube_util import (
     DEFAULT_JOB_API_VERSION,
     ensure_pykube,
+    find_job_object_by_name,
+    galaxy_instance_id,
     Job,
     job_object_dict,
     Pod,
     produce_unique_k8s_job_name,
     pull_policy,
     pykube_client_from_dict,
+    stop_job,
 )
 from galaxy.util.bytesize import ByteSize
 
@@ -201,25 +204,8 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         return None
 
     def __get_galaxy_instance_id(self):
-        """
-        Gets the id of the Galaxy instance. This will be added to Jobs and Pods names, so it needs to be DNS friendly,
-        this means: `The Internet standards (Requests for Comments) for protocols mandate that component hostname labels
-        may contain only the ASCII letters 'a' through 'z' (in a case-insensitive manner), the digits '0' through '9',
-        and the minus sign ('-').`
-
-        It looks for the value set on self.runner_params['k8s_galaxy_instance_id'], which might or not be set. The
-        idea behind this is to allow the Galaxy instance to trust (or not) existing k8s Jobs and Pods that match the
-        setup of a Job that is being recovered or restarted after a downtime/reboot.
-        :return:
-        :rtype:
-        """
-        if "k8s_galaxy_instance_id" in self.runner_params:
-            if re.match(r"(?!-)[a-z\d-]{1,20}(?<!-)$", self.runner_params['k8s_galaxy_instance_id']):
-                return self.runner_params['k8s_galaxy_instance_id']
-            else:
-                log.error("Galaxy instance '" + self.runner_params['k8s_galaxy_instance_id'] + "' is either too long "
-                          + '(>20 characters) or it includes non DNS acceptable characters, ignoring it.')
-        return None
+        """Parse the ID of the Galaxy instance from runner params."""
+        return galaxy_instance_id(self.runner_params)
 
     def __produce_unique_k8s_job_name(self, galaxy_internal_job_id):
         # wrapper.get_id_tag() instead of job_id for compatibility with TaskWrappers.
@@ -509,19 +495,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
 
     def __cleanup_k8s_job(self, job):
         k8s_cleanup_job = self.runner_params['k8s_cleanup_job']
-        job_failed = (job.obj['status']['failed'] > 0
-                      if 'failed' in job.obj['status'] else False)
-        # Scale down the job just in case even if cleanup is never
-        job.scale(replicas=0)
-        if (k8s_cleanup_job == "always" or
-                (k8s_cleanup_job == "onsuccess" and not job_failed)):
-            delete_options = {
-                "apiVersion": "v1",
-                "kind": "DeleteOptions",
-                "propagationPolicy": "Background"
-            }
-            r = job.api.delete(json=delete_options, **job.api_kwargs())
-            job.api.raise_for_status(r)
+        stop_job(job, k8s_cleanup_job)
 
     def __job_failed_due_to_walltime_limit(self, job):
         conditions = job.obj['status'].get('conditions') or []
@@ -550,11 +524,10 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         """Attempts to delete a dispatched job to the k8s cluster"""
         job = job_wrapper.get_job()
         try:
-            jobs = Job.objects(self._pykube_api).filter(
-                selector="app=" + self.__produce_unique_k8s_job_name(job.get_id_tag()),
-                namespace=self.runner_params['k8s_namespace'])
-            if len(jobs.response['items']) > 0:
-                job_to_delete = Job(self._pykube_api, jobs.response['items'][0])
+            name = self.__produce_unique_k8s_job_name(job.get_id_tag())
+            namespace = self.runner_params['k8s_namespace']
+            job_to_delete = find_job_object_by_name(self._pykube_api, name, namespace)
+            if job_to_delete:
                 self.__cleanup_k8s_job(job_to_delete)
             # TODO assert whether job parallelism == 0
             # assert not job_to_delete.exists(), "Could not delete job,"+job.job_runner_external_id+" it still exists"

lib/galaxy/jobs/runners/pulsar.py

@@ -189,6 +189,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
     runner_name = "PulsarJobRunner"
     default_build_pulsar_app = False
     use_mq = False
+    poll = True
 
     def __init__(self, app, nworkers, **kwds):
         """Start the job runner."""
@@ -207,12 +208,13 @@ class PulsarJobRunner(AsynchronousJobRunner):
         if self.use_mq:
             # This is a message queue driven runner, don't monitor
             # just setup required callback.
-            self._init_noop_monitor()
-
             self.client_manager.ensure_has_status_update_callback(self.__async_update)
             self.client_manager.ensure_has_ack_consumers()
-        else:
+
+        if self.poll:
             self._init_monitor_thread()
+        else:
+            self._init_noop_monitor()
 
     def __init_client_manager(self):
         pulsar_conf = self.runner_params.get('pulsar_app_config', None)
@@ -262,6 +264,23 @@ class PulsarJobRunner(AsynchronousJobRunner):
         return JobDestination(runner="pulsar", params=url_to_destination_params(url))
 
     def check_watched_item(self, job_state):
+        if self.use_mq:
+            # Might still need to check pod IPs.
+            job_wrapper = job_state.job_wrapper
+            guest_ports = job_wrapper.guest_ports
+            if len(guest_ports) > 0:
+                client = self.get_client_from_state(job_state)
+                job_ip = client.job_ip()
+                if job_ip:
+                    ports_dict = {}
+                    for guest_port in guest_ports:
+                        ports_dict[str(guest_port)] = dict(host=job_ip, port=guest_port, protocol="http")
+                    self.app.interactivetool_manager.configure_entry_points(job_wrapper.get_job(), ports_dict)
+            return job_state
+        else:
+            return self.check_watched_item_state(job_state)
+
+    def check_watched_item_state(self, job_state):
         try:
             client = self.get_client_from_state(job_state)
             status = client.get_status()
@@ -366,6 +385,7 @@ class PulsarJobRunner(AsynchronousJobRunner):
                 remote_pulsar_app_config=remote_pulsar_app_config,
                 job_directory_files=job_directory_files,
                 container=None if not remote_container else remote_container.container_id,
+                guest_ports=job_wrapper.guest_ports,
             )
             job_id = pulsar_submit_job(client, client_job_description, remote_job_config)
             log.info("Pulsar job submitted with job_id %s" % job_id)
@@ -853,6 +873,7 @@ class PulsarLegacyJobRunner(PulsarJobRunner):
 class PulsarMQJobRunner(PulsarJobRunner):
     """Flavor of Pulsar job runner with sensible defaults for message queue communication."""
     use_mq = True
+    poll = False
 
     destination_defaults = dict(
         default_file_action="remote_transfer",
@@ -868,7 +889,7 @@ KUBERNETES_DESTINATION_DEFAULTS = {
     "default_file_action": "remote_transfer",
     "rewrite_parameters": "true",
     "jobs_directory": "/pulsar_staging",
-    "pulsar_container_image": "galaxy/pulsar-pod-staging:0.13.0",
+    "pulsar_container_image": "galaxy/pulsar-pod-staging:0.14.0",
     "remote_container_handling": True,
     "k8s_enabled": True,
     "url": PARAMETER_SPECIFICATION_IGNORED,
@@ -878,6 +899,7 @@ KUBERNETES_DESTINATION_DEFAULTS = {
 
 class PulsarKubernetesJobRunner(PulsarMQJobRunner):
     destination_defaults = KUBERNETES_DESTINATION_DEFAULTS
+    poll = True  # Poll so we can check API for pod IP for ITs.
 
     def _populate_parameter_defaults(self, job_destination):
         super(PulsarKubernetesJobRunner, self)._populate_parameter_defaults(job_destination)

lib/galaxy/jobs/runners/util/pykube_util.py

@@ -1,5 +1,7 @@
 """Interface layer for pykube library shared between Galaxy and Pulsar."""
+import logging
 import os
+import re
 import uuid
 
 try:
@@ -17,8 +19,13 @@ except ImportError as exc:
                           'this feature, please install it or correct the '
                           'following error:\nImportError %s' % str(exc))
 
+log = logging.getLogger(__name__)
+
 DEFAULT_JOB_API_VERSION = "batch/v1"
 DEFAULT_NAMESPACE = "default"
+INSTANCE_ID_INVALID_MESSAGE = ("Galaxy instance [%s] is either too long "
+                               "(>20 characters) or it includes non DNS "
+                               "acceptable characters, ignoring it.")
 
 
 def ensure_pykube():
@@ -61,6 +68,44 @@ def pull_policy(params):
     return None
 
 
+def find_job_object_by_name(pykube_api, job_name, namespace=None):
+    return _find_object_by_name(Job, pykube_api, job_name, namespace=namespace)
+
+
+def find_pod_object_by_name(pykube_api, pod_name, namespace=None):
+    return _find_object_by_name(Pod, pykube_api, pod_name, namespace=namespace)
+
+
+def _find_object_by_name(clazz, pykube_api, object_name, namespace=None):
+    filter_kwd = dict(selector="app=%s" % object_name)
+    if namespace is not None:
+        filter_kwd["namespace"] = namespace
+
+    objs = clazz.objects(pykube_api).filter(**filter_kwd)
+    obj = None
+    if len(objs.response['items']) > 0:
+        obj = clazz(pykube_api, objs.response['items'][0])
+    return obj
+
+
+def stop_job(job, cleanup="always"):
+    job_failed = (job.obj['status']['failed'] > 0
+                  if 'failed' in job.obj['status'] else False)
+    # Scale down the job just in case even if cleanup is never
+    job.scale(replicas=0)
+    api_delete = cleanup == "always"
+    if not api_delete and cleanup == "onsuccess" and not job_failed:
+        api_delete = True
+    if api_delete:
+        delete_options = {
+            "apiVersion": "v1",
+            "kind": "DeleteOptions",
+            "propagationPolicy": "Background"
+        }
+        r = job.api.delete(json=delete_options, **job.api_kwargs())
+        job.api.raise_for_status(r)
+
+
 def job_object_dict(params, job_name, spec):
     k8s_job_obj = {
         "apiVersion": params.get('k8s_job_api_version', DEFAULT_JOB_API_VERSION),
@@ -77,13 +122,38 @@ def job_object_dict(params, job_name, spec):
     return k8s_job_obj
 
 
+def galaxy_instance_id(params):
+    """Parse and validate the id of the Galaxy instance from supplied dict.
+
+    This will be added to Jobs and Pods names, so it needs to be DNS friendly,
+    this means: `The Internet standards (Requests for Comments) for protocols mandate that component hostname labels
+    may contain only the ASCII letters 'a' through 'z' (in a case-insensitive manner), the digits '0' through '9',
+    and the minus sign ('-').`
+
+    It looks for the value set on params['k8s_galaxy_instance_id'], which might or not be set. The
+    idea behind this is to allow the Galaxy instance to trust (or not) existing k8s Jobs and Pods that match the
+    setup of a Job that is being recovered or restarted after a downtime/reboot.
+    """
+    if "k8s_galaxy_instance_id" in params:
+        raw_value = params['k8s_galaxy_instance_id']
+        if re.match(r"(?!-)[a-z\d-]{1,20}(?<!-)$", raw_value):
+            return raw_value
+        else:
+            log.error(INSTANCE_ID_INVALID_MESSAGE % raw_value)
+    return None
+
+
 __all__ = (
     "DEFAULT_JOB_API_VERSION",
     "ensure_pykube",
+    "find_job_object_by_name",
+    "find_pod_object_by_name",
+    "galaxy_instance_id",
     "Job",
     "job_object_dict",
     "Pod",
     "produce_unique_k8s_job_name",
     "pull_policy",
     "pykube_client_from_dict",
+    "stop_job",
 )

lib/galaxy/managers/configuration.py

@@ -91,6 +91,7 @@ class ConfigSerializer(base.ModelSerializer):
             '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,

lib/galaxy/managers/interactivetool.py

@@ -263,10 +263,10 @@ class InteractiveToolManager(object):
             protocol = trans.request.host_url.split('//', 1)[0]
             entry_point_encoded_id = trans.security.encode_id(entry_point.id)
             entry_point_class = entry_point.__class__.__name__.lower()
-            entry_point_prefix = self.app.config.interactivetool_prefix
-            interactivetool_proxy_host = self.app.config.interactivetool_proxy_host or request_host
+            entry_point_prefix = self.app.config.interactivetools_prefix
+            interactivetools_proxy_host = self.app.config.interactivetools_proxy_host or request_host
             rval = '%s//%s-%s.%s.%s.%s/' % (protocol, entry_point_encoded_id,
-                    entry_point.token, entry_point_class, entry_point_prefix, interactivetool_proxy_host)
+                    entry_point.token, entry_point_class, entry_point_prefix, interactivetools_proxy_host)
             if entry_point.entry_url:
                 rval = '%s/%s' % (rval.rstrip('/'), entry_point.entry_url.lstrip('/'))
             return rval

lib/galaxy/managers/jobs.py

@@ -498,6 +498,20 @@ def summarize_job_metrics(trans, job):
     return list(map(metric_to_dict, metrics))
 
 
+def summarize_destination_params(trans, job):
+    """Produce a dict-ified version of job destination parameters ready for tabular rendering.
+
+    Precondition: the caller has verified the job is accessible to the user
+    represented by the trans parameter.
+    """
+
+    destination_params = {'Runner': job.job_runner_name,
+                          'Runner Job ID': job.job_runner_external_id,
+                          'Handler': job.handler}
+    destination_params.update(job.destination_params)
+    return destination_params
+
+
 def summarize_job_parameters(trans, job):
     """Produce a dict-ified version of job parameters ready for tabular rendering.
 

lib/galaxy/objectstore/__init__.py

@@ -5,6 +5,7 @@ all providers ensure that data can be accessed on the filesystem for running
 tools
 """
 
+import abc
 import logging
 import os
 import random
@@ -39,8 +40,9 @@ log = logging.getLogger(__name__)
 
 
 class ObjectStore(object):
+    __metaclass__ = abc.ABCMeta
 
-    """ObjectStore abstract interface.
+    """ObjectStore interface.
 
     FIELD DESCRIPTIONS (these apply to all the methods in this class):
 
@@ -82,6 +84,120 @@ class ObjectStore(object):
         000/obj.id)
     """
 
+    @abc.abstractmethod
+    def exists(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+        """Return True if the object identified by `obj` exists, False otherwise."""
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def create(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+        """
+        Mark the object (`obj`) as existing in the store, but with no content.
+
+        This method will create a proper directory structure for
+        the file if the directory does not already exist.
+        """
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def empty(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+        """
+        Test if the object identified by `obj` has content.
+
+        If the object does not exist raises `ObjectNotFound`.
+        """
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def size(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+        """
+        Return size of the object identified by `obj`.
+
+        If the object does not exist, return 0.
+        """
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def delete(self, obj, entire_dir=False, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+        """
+        Delete the object identified by `obj`.
+
+        :type entire_dir: boolean
+        :param entire_dir: If True, delete the entire directory pointed to by
+                           extra_dir. For safety reasons, this option applies
+                           only for and in conjunction with the extra_dir or
+                           obj_dir options.
+        """
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def get_data(self, obj, start=0, count=-1, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+        """
+        Fetch `count` bytes of data offset by `start` bytes using `obj.id`.
+
+        If the object does not exist raises `ObjectNotFound`.
+
+        :type start: int
+        :param start: Set the position to start reading the dataset file
+
+        :type count: int
+        :param count: Read at most `count` bytes from the dataset
+        """
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+        """
+        Get the expected filename with absolute path for object with id `obj.id`.
+
+        This can be used to access the contents of the object.
+        """
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def update_from_file(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, file_name=None, create=False):
+        """
+        Inform the store that the file associated with `obj.id` has been updated.
+
+        If `file_name` is provided, update from that file instead of the
+        default.
+        If the object does not exist raises `ObjectNotFound`.
+
+        :type file_name: string
+        :param file_name: Use file pointed to by `file_name` as the source for
+                          updating the dataset identified by `obj`
+
+        :type create: boolean
+        :param create: If True and the default dataset does not exist, create
+            it first.
+        """
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+        """
+        Return the URL for direct acces if supported, otherwise return None.
+
+        Note: need to be careful to not bypass dataset security with this.
+        """
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def get_store_usage_percent(self):
+        """Return the percentage indicating how full the store is."""
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def get_store_by(self, obj):
+        """Return how object is stored (by 'uuid', 'id', or None if not yet saved).
+
+        Certain Galaxy remote data features aren't available if objects are stored by 'id'.
+        """
+        raise NotImplementedError()
+
+
+class BaseObjectStore(ObjectStore):
+
     def __init__(self, config, config_dict=None, **kwargs):
         """
         :type config: object
@@ -111,10 +227,6 @@ class ObjectStore(object):
         """Close any connections for this ObjectStore."""
         self.running = False
 
-    def exists(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
-        """Return True if the object identified by `obj` exists, False otherwise."""
-        raise NotImplementedError()
-
     def file_ready(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
         """
         Check if a file corresponding to a dataset is ready to be used.
@@ -123,102 +235,6 @@ class ObjectStore(object):
         """
         return True
 
-    def create(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
-        """
-        Mark the object (`obj`) as existing in the store, but with no content.
-
-        This method will create a proper directory structure for
-        the file if the directory does not already exist.
-        """
-        raise NotImplementedError()
-
-    def empty(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
-        """
-        Test if the object identified by `obj` has content.
-
-        If the object does not exist raises `ObjectNotFound`.
-        """
-        raise NotImplementedError()
-
-    def size(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
-        """
-        Return size of the object identified by `obj`.
-
-        If the object does not exist, return 0.
-        """
-        raise NotImplementedError()
-
-    def delete(self, obj, entire_dir=False, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
-        """
-        Delete the object identified by `obj`.
-
-        :type entire_dir: boolean
-        :param entire_dir: If True, delete the entire directory pointed to by
-                           extra_dir. For safety reasons, this option applies
-                           only for and in conjunction with the extra_dir or
-                           obj_dir options.
-        """
-        raise NotImplementedError()
-
-    def get_data(self, obj, start=0, count=-1, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
-        """
-        Fetch `count` bytes of data offset by `start` bytes using `obj.id`.
-
-        If the object does not exist raises `ObjectNotFound`.
-
-        :type start: int
-        :param start: Set the position to start reading the dataset file
-
-        :type count: int
-        :param count: Read at most `count` bytes from the dataset
-        """
-        raise NotImplementedError()
-
-    def get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
-        """
-        Get the expected filename with absolute path for object with id `obj.id`.
-
-        This can be used to access the contents of the object.
-        """
-        raise NotImplementedError()
-
-    def update_from_file(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, file_name=None, create=False):
-        """
-        Inform the store that the file associated with `obj.id` has been updated.
-
-        If `file_name` is provided, update from that file instead of the
-        default.
-        If the object does not exist raises `ObjectNotFound`.
-
-        :type file_name: string
-        :param file_name: Use file pointed to by `file_name` as the source for
-                          updating the dataset identified by `obj`
-
-        :type create: boolean
-        :param create: If True and the default dataset does not exist, create
-            it first.
-        """
-        raise NotImplementedError()
-
-    def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
-        """
-        Return the URL for direct acces if supported, otherwise return None.
-
-        Note: need to be careful to not bypass dataset security with this.
-        """
-        raise NotImplementedError()
-
-    def get_store_usage_percent(self):
-        """Return the percentage indicating how full the store is."""
-        raise NotImplementedError()
-
-    def get_store_by(self, obj):
-        """Return how object is stored (by 'uuid', 'id', or None if not yet saved).
-
-        Certain Galaxy remote data features aren't available if objects are stored by 'id'.
-        """
-        raise NotImplementedError()
-
     @classmethod
     def parse_xml(clazz, config_xml):
         """Parse an XML description of a configuration for this object store.
@@ -251,8 +267,44 @@ class ObjectStore(object):
             # job working directories.
             return obj.id
 
+    def _invoke(self, delegate, obj=None, **kwargs):
+        return self.__getattribute__("_" + delegate)(obj=obj, **kwargs)
 
-class ConcreteObjectStore(ObjectStore):
+    def exists(self, obj, **kwargs):
+        return self._invoke('exists', obj, **kwargs)
+
+    def create(self, obj, **kwargs):
+        return self._invoke('create', obj, **kwargs)
+
+    def empty(self, obj, **kwargs):
+        return self._invoke('empty', obj, **kwargs)
+
+    def size(self, obj, **kwargs):
+        return self._invoke('size', obj, **kwargs)
+
+    def delete(self, obj, **kwargs):
+        return self._invoke('delete', obj, **kwargs)
+
+    def get_data(self, obj, **kwargs):
+        return self._invoke('get_data', obj, **kwargs)
+
+    def get_filename(self, obj, **kwargs):
+        return self._invoke('get_filename', obj, **kwargs)
+
+    def update_from_file(self, obj, **kwargs):
+        return self._invoke('update_from_file', obj, **kwargs)
+
+    def get_object_url(self, obj, **kwargs):
+        return self._invoke('get_object_url', obj, **kwargs)
+
+    def get_store_usage_percent(self):
+        return self._invoke('get_store_usage_percent')
+
+    def get_store_by(self, obj, **kwargs):
+        return self._invoke('get_store_by', obj, **kwargs)
+
+
+class ConcreteObjectStore(BaseObjectStore):
     """Subclass of ObjectStore for stores that don't delegate (non-nested).
 
     Currently only adds store_by functionality. Which doesn't make
@@ -280,7 +332,7 @@ class ConcreteObjectStore(ObjectStore):
         rval["store_by"] = self.store_by
         return rval
 
-    def get_store_by(self, obj):
+    def _get_store_by(self, obj):
         return self.store_by
 
 
@@ -343,7 +395,7 @@ class DiskObjectStore(ConcreteObjectStore):
         as_dict["files_dir"] = self.file_path
         return as_dict
 
-    def _get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+    def __get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
         """
         Return the absolute path for the file corresponding to the `obj.id`.
 
@@ -425,7 +477,7 @@ class DiskObjectStore(ConcreteObjectStore):
             path = os.path.join(path, alt_name if alt_name else "dataset_%s.dat" % obj_id)
         return os.path.abspath(path)
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         """Override `ObjectStore`'s stub and check on disk."""
         if self.check_old_style:
             path = self._construct_path(obj, old_style=True, **kwargs)
@@ -435,9 +487,9 @@ class DiskObjectStore(ConcreteObjectStore):
                 return True
         return os.path.exists(self._construct_path(obj, **kwargs))
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
         """Override `ObjectStore`'s stub by creating any files and folders on disk."""
-        if not self.exists(obj, **kwargs):
+        if not self._exists(obj, **kwargs):
             path = self._construct_path(obj, **kwargs)
             dir_only = kwargs.get('dir_only', False)
             # Create directory if it does not exist
@@ -448,18 +500,18 @@ class DiskObjectStore(ConcreteObjectStore):
                 open(path, 'w').close()  # Should be rb?
                 umask_fix_perms(path, self.config.umask, 0o666)
 
-    def empty(self, obj, **kwargs):
+    def _empty(self, obj, **kwargs):
         """Override `ObjectStore`'s stub by checking file size on disk."""
         return self.size(obj, **kwargs) == 0
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         """Override `ObjectStore`'s stub by return file size on disk.
 
         Returns 0 if the object doesn't exist yet or other error.
         """
-        if self.exists(obj, **kwargs):
+        if self._exists(obj, **kwargs):
             try:
-                filepath = self.get_filename(obj, **kwargs)
+                filepath = self._get_filename(obj, **kwargs)
                 for _ in range(0, 2):
                     size = os.path.getsize(filepath)
                     if size != 0:
@@ -472,31 +524,31 @@ class DiskObjectStore(ConcreteObjectStore):
         else:
             return 0
 
-    def delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir=False, **kwargs):
         """Override `ObjectStore`'s stub; delete the file or folder on disk."""
-        path = self.get_filename(obj, **kwargs)
+        path = self._get_filename(obj, **kwargs)
         extra_dir = kwargs.get('extra_dir', None)
         obj_dir = kwargs.get('obj_dir', False)
         try:
             if entire_dir and (extra_dir or obj_dir):
                 shutil.rmtree(path)
                 return True
-            if self.exists(obj, **kwargs):
+            if self._exists(obj, **kwargs):
                 os.remove(path)
                 return True
         except OSError as ex:
-            log.critical('%s delete error %s' % (self._get_filename(obj, **kwargs), ex))
+            log.critical('%s delete error %s' % (self.__get_filename(obj, **kwargs), ex))
         return False
 
-    def get_data(self, obj, start=0, count=-1, **kwargs):
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
         """Override `ObjectStore`'s stub; retrieve data directly from disk."""
-        data_file = open(self.get_filename(obj, **kwargs), 'r')  # Should be rb?
+        data_file = open(self._get_filename(obj, **kwargs), 'r')  # Should be rb?
         data_file.seek(start)
         content = data_file.read(count)
         data_file.close()
         return content
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         """
         Override `ObjectStore`'s stub.
 
@@ -514,27 +566,27 @@ class DiskObjectStore(ConcreteObjectStore):
             raise ObjectNotFound
         return path
 
-    def update_from_file(self, obj, file_name=None, create=False, **kwargs):
+    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
         """`create` parameter is not used in this implementation."""
         preserve_symlinks = kwargs.pop('preserve_symlinks', False)
         # FIXME: symlinks and the object store model may not play well together
         # these should be handled better, e.g. registering the symlink'd file
         # as an object
         if create:
-            self.create(obj, **kwargs)
-        if file_name and self.exists(obj, **kwargs):
+            self._create(obj, **kwargs)
+        if file_name and self._exists(obj, **kwargs):
             try:
                 if preserve_symlinks and os.path.islink(file_name):
-                    force_symlink(os.readlink(file_name), self.get_filename(obj, **kwargs))
+                    force_symlink(os.readlink(file_name), self._get_filename(obj, **kwargs))
                 else:
-                    path = self.get_filename(obj, **kwargs)
+                    path = self._get_filename(obj, **kwargs)
                     shutil.copy(file_name, path)
                     umask_fix_perms(path, self.config.umask, 0o666)
             except IOError as ex:
-                log.critical('Error copying %s to %s: %s' % (file_name, self._get_filename(obj, **kwargs), ex))
+                log.critical('Error copying %s to %s: %s' % (file_name, self.__get_filename(obj, **kwargs), ex))
                 raise ex
 
-    def get_object_url(self, obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
         """
         Override `ObjectStore`'s stub.
 
@@ -542,13 +594,13 @@ class DiskObjectStore(ConcreteObjectStore):
         """
         return None
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self, **kwargs):
         """Override `ObjectStore`'s stub by return percent storage used."""
         st = os.statvfs(self.file_path)
         return (float(st.f_blocks - st.f_bavail) / st.f_blocks) * 100
 
 
-class NestedObjectStore(ObjectStore):
+class NestedObjectStore(BaseObjectStore):
 
     """
     Base for ObjectStores that use other ObjectStores.
@@ -567,51 +619,51 @@ class NestedObjectStore(ObjectStore):
             store.shutdown()
         super(NestedObjectStore, self).shutdown()
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         """Determine if the `obj` exists in any of the backends."""
-        return self._call_method('exists', obj, False, False, **kwargs)
+        return self._call_method('_exists', obj, False, False, **kwargs)
 
     def file_ready(self, obj, **kwargs):
         """Determine if the file for `obj` is ready to be used by any of the backends."""
         return self._call_method('file_ready', obj, False, False, **kwargs)
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
         """Create a backing file in a random backend."""
         random.choice(list(self.backends.values())).create(obj, **kwargs)
 
-    def empty(self, obj, **kwargs):
+    def _empty(self, obj, **kwargs):
         """For the first backend that has this `obj`, determine if it is empty."""
-        return self._call_method('empty', obj, True, False, **kwargs)
+        return self._call_method('_empty', obj, True, False, **kwargs)
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         """For the first backend that has this `obj`, return its size."""
-        return self._call_method('size', obj, 0, False, **kwargs)
+        return self._call_method('_size', obj, 0, False, **kwargs)
 
-    def delete(self, obj, **kwargs):
+    def _delete(self, obj, **kwargs):
         """For the first backend that has this `obj`, delete it."""
-        return self._call_method('delete', obj, False, False, **kwargs)
+        return self._call_method('_delete', obj, False, False, **kwargs)
 
-    def get_data(self, obj, **kwargs):
+    def _get_data(self, obj, **kwargs):
         """For the first backend that has this `obj`, get data from it."""
-        return self._call_method('get_data', obj, ObjectNotFound, True, **kwargs)
+        return self._call_method('_get_data', obj, ObjectNotFound, True, **kwargs)
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         """For the first backend that has this `obj`, get its filename."""
-        return self._call_method('get_filename', obj, ObjectNotFound, True, **kwargs)
+        return self._call_method('_get_filename', obj, ObjectNotFound, True, **kwargs)
 
-    def update_from_file(self, obj, **kwargs):
+    def _update_from_file(self, obj, **kwargs):
         """For the first backend that has this `obj`, update it from the given file."""
         if kwargs.get('create', False):
-            self.create(obj, **kwargs)
+            self._create(obj, **kwargs)
             kwargs['create'] = False
-        return self._call_method('update_from_file', obj, ObjectNotFound, True, **kwargs)
+        return self._call_method('_update_from_file', obj, ObjectNotFound, True, **kwargs)
 
-    def get_object_url(self, obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
         """For the first backend that has this `obj`, get its URL."""
-        return self._call_method('get_object_url', obj, None, False, **kwargs)
+        return self._call_method('_get_object_url', obj, None, False, **kwargs)
 
-    def get_store_by(self, obj):
-        return self._call_method('get_store_by', obj, None, False)
+    def _get_store_by(self, obj):
+        return self._call_method('_get_store_by', obj, None, False)
 
     def _repr_object_for_exception(self, obj):
         try:
@@ -776,9 +828,9 @@ class DistributedObjectStore(NestedObjectStore):
             self.weighted_backend_ids = new_weighted_backend_ids
             self.sleeper.sleep(120)  # Test free space every 2 minutes
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
         """The only method in which obj.object_store_id may be None."""
-        if obj.object_store_id is None or not self.exists(obj, **kwargs):
+        if obj.object_store_id is None or not self._exists(obj, **kwargs):
             if obj.object_store_id is None or obj.object_store_id not in self.backends:
                 try:
                     obj.object_store_id = random.choice(self.weighted_backend_ids)
@@ -865,14 +917,14 @@ class HierarchicalObjectStore(NestedObjectStore):
         as_dict["backends"] = backends
         return as_dict
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         """Check all child object stores."""
         for store in self.backends.values():
             if store.exists(obj, **kwargs):
                 return True
         return False
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
         """Call the primary object store."""
         self.backends[0].create(obj, **kwargs)
 

lib/galaxy/objectstore/azure_blob.py

@@ -310,7 +310,7 @@ class AzureBlobObjectStore(ConcreteObjectStore):
     # Public Methods #
     ##################
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         in_cache = in_azure = False
         rel_path = self._construct_path(obj, **kwargs)
 
@@ -357,9 +357,9 @@ class AzureBlobObjectStore(ConcreteObjectStore):
 
         return False
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
 
-        if not self.exists(obj, **kwargs):
+        if not self._exists(obj, **kwargs):
 
             # Pull out locally used fields
             extra_dir = kwargs.get('extra_dir', None)
@@ -393,25 +393,25 @@ class AzureBlobObjectStore(ConcreteObjectStore):
                 open(os.path.join(self.staging_path, rel_path), 'w').close()
                 self._push_to_os(rel_path, from_string='')
 
-    def empty(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
-            return bool(self.size(obj, **kwargs) > 0)
+    def _empty(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
+            return bool(self._size(obj, **kwargs) > 0)
         else:
             raise ObjectNotFound('objectstore.empty, object does not exist: %s, kwargs: %s' % (str(obj), str(kwargs)))
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         if self._in_cache(rel_path):
             try:
                 return os.path.getsize(self._get_cache_path(rel_path))
             except OSError as ex:
                 log.info("Could not get size of file '%s' in local cache, will try Azure. Error: %s", rel_path, ex)
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             return self._get_size_in_azure(rel_path)
         log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
         return 0
 
-    def delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir=False, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         extra_dir = kwargs.get('extra_dir', None)
         base_dir = kwargs.get('base_dir', None)
@@ -445,10 +445,10 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         except AzureHttpError:
             log.exception("Could not delete blob '%s' from Azure", rel_path)
         except OSError:
-            log.exception('%s delete error', self.get_filename(obj, **kwargs))
+            log.exception('%s delete error', self._get_filename(obj, **kwargs))
         return False
 
-    def get_data(self, obj, start=0, count=-1, **kwargs):
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         # Check cache first and get file if not there
         if not self._in_cache(rel_path):
@@ -460,7 +460,7 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         data_file.close()
         return content
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         base_dir = kwargs.get('base_dir', None)
         dir_only = kwargs.get('dir_only', False)
@@ -483,7 +483,7 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         if self._in_cache(rel_path):
             return cache_path
         # Check if the file exists in persistent storage and, if it does, pull it into cache
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             if dir_only:  # Directories do not get pulled into cache
                 return cache_path
             else:
@@ -495,10 +495,10 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         #     return cache_path
         raise ObjectNotFound('objectstore.get_filename, no cache_path: %s, kwargs: %s' % (str(obj), str(kwargs)))
 
-    def update_from_file(self, obj, file_name=None, create=False, **kwargs):
+    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
         if create is True:
-            self.create(obj, **kwargs)
-        elif self.exists(obj, **kwargs):
+            self._create(obj, **kwargs)
+        elif self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             # Chose whether to use the dataset file itself or an alternate file
             if file_name:
@@ -520,8 +520,8 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         else:
             raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s' % (str(obj), str(kwargs)))
 
-    def get_object_url(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             try:
                 url = self.service.make_blob_url(container_name=self.container_name, blob_name=rel_path)
@@ -530,7 +530,7 @@ class AzureBlobObjectStore(ConcreteObjectStore):
                 log.exception("Trouble generating URL for dataset '%s'", rel_path)
         return None
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         return 0.0
 
     ##################

lib/galaxy/objectstore/cloud.py

@@ -510,7 +510,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
                       os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_cloud(rel_path))
         return False
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         in_cache = False
         rel_path = self._construct_path(obj, **kwargs)
 
@@ -543,8 +543,8 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         else:
             return False
 
-    def create(self, obj, **kwargs):
-        if not self.exists(obj, **kwargs):
+    def _create(self, obj, **kwargs):
+        if not self._exists(obj, **kwargs):
 
             # Pull out locally used fields
             extra_dir = kwargs.get('extra_dir', None)
@@ -572,26 +572,26 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
                 open(os.path.join(self.staging_path, rel_path), 'w').close()
                 self._push_to_os(rel_path, from_string='')
 
-    def empty(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
-            return bool(self.size(obj, **kwargs) > 0)
+    def _empty(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
+            return bool(self._size(obj, **kwargs) > 0)
         else:
             raise ObjectNotFound('objectstore.empty, object does not exist: %s, kwargs: %s'
                                  % (str(obj), str(kwargs)))
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         if self._in_cache(rel_path):
             try:
                 return os.path.getsize(self._get_cache_path(rel_path))
             except OSError as ex:
                 log.info("Could not get size of file '%s' in local cache, will try cloud. Error: %s", rel_path, ex)
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             return self._get_size_in_cloud(rel_path)
         log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
         return 0
 
-    def delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir=False, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         extra_dir = kwargs.get('extra_dir', None)
         base_dir = kwargs.get('base_dir', None)
@@ -626,10 +626,10 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         except Exception:
             log.exception("Could not delete key '%s' from cloud", rel_path)
         except OSError:
-            log.exception('%s delete error', self.get_filename(obj, **kwargs))
+            log.exception('%s delete error', self._get_filename(obj, **kwargs))
         return False
 
-    def get_data(self, obj, start=0, count=-1, **kwargs):
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         # Check cache first and get file if not there
         if not self._in_cache(rel_path):
@@ -641,7 +641,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         data_file.close()
         return content
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         base_dir = kwargs.get('base_dir', None)
         dir_only = kwargs.get('dir_only', False)
         obj_dir = kwargs.get('obj_dir', False)
@@ -664,7 +664,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         if self._in_cache(rel_path):
             return cache_path
         # Check if the file exists in persistent storage and, if it does, pull it into cache
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             if dir_only:  # Directories do not get pulled into cache
                 return cache_path
             else:
@@ -678,10 +678,10 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
                              % (str(obj), str(kwargs)))
         # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
-    def update_from_file(self, obj, file_name=None, create=False, **kwargs):
+    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
         if create:
-            self.create(obj, **kwargs)
-        if self.exists(obj, **kwargs):
+            self._create(obj, **kwargs)
+        if self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             # Chose whether to use the dataset file itself or an alternate file
             if file_name:
@@ -703,8 +703,8 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
             raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
                                  % (str(obj), str(kwargs)))
 
-    def get_object_url(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             try:
                 key = self.bucket.objects.get(rel_path)
@@ -713,5 +713,5 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
                 log.exception("Trouble generating URL for dataset '%s'", rel_path)
         return None
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         return 0.0

lib/galaxy/objectstore/irods.py

@@ -420,7 +420,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
                       os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_irods(rel_path))
         return False
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         in_cache = in_irods = False
         rel_path = self._construct_path(obj, **kwargs)
 
@@ -451,8 +451,8 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
         else:
             return False
 
-    def create(self, obj, **kwargs):
-        if not self.exists(obj, **kwargs):
+    def _create(self, obj, **kwargs):
+        if not self._exists(obj, **kwargs):
             # Pull out locally used fields
             extra_dir = kwargs.get('extra_dir', None)
             extra_dir_at_root = kwargs.get('extra_dir_at_root', False)
@@ -479,26 +479,26 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
                 open(os.path.join(self.staging_path, rel_path), 'w').close()
                 self._push_to_irods(rel_path, from_string='')
 
-    def empty(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
-            return bool(self.size(obj, **kwargs) > 0)
+    def _empty(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
+            return bool(self._size(obj, **kwargs) > 0)
         else:
             raise ObjectNotFound('objectstore.empty, object does not exist: %s, kwargs: %s'
                                  % (str(obj), str(kwargs)))
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         if self._in_cache(rel_path):
             try:
                 return os.path.getsize(self._get_cache_path(rel_path))
             except OSError as ex:
                 log.info("Could not get size of file '%s' in local cache, will try S3. Error: %s", rel_path, ex)
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             return self._get_size_in_irods(rel_path)
         log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
         return 0
 
-    def delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir=False, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         extra_dir = kwargs.get('extra_dir', None)
         base_dir = kwargs.get('base_dir', None)
@@ -558,10 +558,10 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
                     return True
 
         except OSError:
-            log.exception('%s delete error', self.get_filename(obj, **kwargs))
+            log.exception('%s delete error', self._get_filename(obj, **kwargs))
         return False
 
-    def get_data(self, obj, start=0, count=-1, **kwargs):
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         # Check cache first and get file if not there
         if not self._in_cache(rel_path):
@@ -573,7 +573,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
         data_file.close()
         return content
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         base_dir = kwargs.get('base_dir', None)
         dir_only = kwargs.get('dir_only', False)
         obj_dir = kwargs.get('obj_dir', False)
@@ -596,7 +596,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
         if self._in_cache(rel_path):
             return cache_path
         # Check if the file exists in persistent storage and, if it does, pull it into cache
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             if dir_only:  # Directories do not get pulled into cache
                 return cache_path
             else:
@@ -610,10 +610,10 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
                              % (str(obj), str(kwargs)))
         # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
-    def update_from_file(self, obj, file_name=None, create=False, **kwargs):
+    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
         if create:
-            self.create(obj, **kwargs)
-        if self.exists(obj, **kwargs):
+            self._create(obj, **kwargs)
+        if self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             # Chose whether to use the dataset file itself or an alternate file
             if file_name:
@@ -636,8 +636,8 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
                                  % (str(obj), str(kwargs)))
 
     # Unlike S3, url is not really applicable to iRODS
-    def get_object_url(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
 
             p = Path(rel_path)
@@ -649,5 +649,5 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
 
             return data_object_path
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         return 0.0

lib/galaxy/objectstore/pithos.py

@@ -221,7 +221,7 @@ class PithosObjectStore(ConcreteObjectStore):
 
     # No need to overwrite "shutdown"
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         """Check if file exists, fix if file in cache and not on Pithos+
         :returns: weather the file exists remotely or in cache
         """
@@ -253,9 +253,9 @@ class PithosObjectStore(ConcreteObjectStore):
             return True
         return False
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
         """Touch a file (aka create empty), if it doesn't exist"""
-        if not self.exists(obj, **kwargs):
+        if not self._exists(obj, **kwargs):
             # Pull out locally used fields
             extra_dir = kwargs.get('extra_dir', None)
             extra_dir_at_root = kwargs.get('extra_dir_at_root', False)
@@ -288,18 +288,18 @@ class PithosObjectStore(ConcreteObjectStore):
                 open(new_file, 'w').close()
                 self.pithos.upload_from_string(rel_path, '')
 
-    def empty(self, obj, **kwargs):
+    def _empty(self, obj, **kwargs):
         """
         :returns: weather the object has content
         :raises ObjectNotFound:
         """
-        if not self.exists(obj, **kwargs):
+        if not self._exists(obj, **kwargs):
             raise ObjectNotFound(
                 'objectstore.empty, object does not exist: {obj}, '
                 'kwargs: {kwargs}'.format(obj=obj, kwargs=kwargs))
-        return bool(self.size(obj, **kwargs))
+        return bool(self._size(obj, **kwargs))
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         """
         :returns: The size of the object, or 0 if it doesn't exist (sorry for
             that, not our fault, the ObjectStore interface is like that some
@@ -321,7 +321,7 @@ class PithosObjectStore(ConcreteObjectStore):
             return 0
         return int(file['content-length'])
 
-    def delete(self, obj, **kwargs):
+    def _delete(self, obj, **kwargs):
         """Delete the object
         :returns: weather the object was deleted
         """
@@ -347,13 +347,13 @@ class PithosObjectStore(ConcreteObjectStore):
                 self.pithos.del_object(path)
         except OSError:
             log.exception(
-                '{0} delete error'.format(self.get_filename(obj, **kwargs)))
+                '{0} delete error'.format(self._get_filename(obj, **kwargs)))
         except ClientError as ce:
             log.exception('Could not delete {path} from Pithos, {err}'.format(
                 path=path, err=ce))
         return False
 
-    def get_data(self, obj, start=0, count=-1, **kwargs):
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
         """Fetch (e.g., download) data
         :param start: Chunk of data starts here
         :param count: Fetch at most as many data, fetch all if negative
@@ -369,7 +369,7 @@ class PithosObjectStore(ConcreteObjectStore):
         data_file.close()
         return content
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         """Get the expected filename with absolute path"""
         base_dir = kwargs.get('base_dir', None)
         dir_only = kwargs.get('dir_only', False)
@@ -386,7 +386,7 @@ class PithosObjectStore(ConcreteObjectStore):
             return cache_path
         if self._in_cache(path):
             return cache_path
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             if not dir_only:
                 self._pull_into_cache(path)
                 return cache_path
@@ -394,11 +394,11 @@ class PithosObjectStore(ConcreteObjectStore):
             'objectstore.get_filename, no cache_path: {obj}, '
             'kwargs: {kwargs}'.format(obj, kwargs))
 
-    def update_from_file(self, obj, **kwargs):
+    def _update_from_file(self, obj, **kwargs):
         """Update the store when a file is updated"""
         if kwargs.get('create'):
-            self.create(obj, **kwargs)
-        if not self.exists(obj, **kwargs):
+            self._create(obj, **kwargs)
+        if not self._exists(obj, **kwargs):
             raise ObjectNotFound(
                 'objectstore.update_from_file, object does not exist: {obj}, '
                 'kwargs: {kwargs}'.format(obj, kwargs))
@@ -420,11 +420,11 @@ class PithosObjectStore(ConcreteObjectStore):
             with open(cache_path) as f:
                 self.pithos.upload_object(obj, f)
 
-    def get_object_url(self, obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
         """
         :returns: URL for direct access, None if no object
         """
-        if self.exists(obj, **kwargs):
+        if self._exists(obj, **kwargs):
             path = self._construct_path(obj, **kwargs)
             try:
                 return self.pithos.publish_object(path)
@@ -434,7 +434,7 @@ class PithosObjectStore(ConcreteObjectStore):
                 log.exception('Kamaki: {0}'.format(ce))
         return None
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         """
         :returns: percentage indicating how full the store is
         """

lib/galaxy/objectstore/pulsar.py

@@ -1,6 +1,6 @@
 from __future__ import absolute_import  # Need to import pulsar_client absolutely.
 
-from ..objectstore import ObjectStore
+from ..objectstore import BaseObjectStore
 
 try:
     from pulsar.client.manager import ObjectStoreClientManager
@@ -8,7 +8,7 @@ except ImportError:
     ObjectStoreClientManager = None
 
 
-class PulsarObjectStore(ObjectStore):
+class PulsarObjectStore(BaseObjectStore):
     """
     Object store implementation that delegates to a remote Pulsar server.
 
@@ -26,38 +26,38 @@ class PulsarObjectStore(ObjectStore):
     def __init__(self, config, config_xml):
         self.pulsar_client = self.__build_pulsar_client(config_xml)
 
-    def exists(self, obj, **kwds):
+    def _exists(self, obj, **kwds):
         return self.pulsar_client.exists(**self.__build_kwds(obj, **kwds))
 
     def file_ready(self, obj, **kwds):
         return self.pulsar_client.file_ready(**self.__build_kwds(obj, **kwds))
 
-    def create(self, obj, **kwds):
+    def _create(self, obj, **kwds):
         return self.pulsar_client.create(**self.__build_kwds(obj, **kwds))
 
-    def empty(self, obj, **kwds):
+    def _empty(self, obj, **kwds):
         return self.pulsar_client.empty(**self.__build_kwds(obj, **kwds))
 
-    def size(self, obj, **kwds):
+    def _size(self, obj, **kwds):
         return self.pulsar_client.size(**self.__build_kwds(obj, **kwds))
 
-    def delete(self, obj, **kwds):
+    def _delete(self, obj, **kwds):
         return self.pulsar_client.delete(**self.__build_kwds(obj, **kwds))
 
     # TODO: Optimize get_data.
-    def get_data(self, obj, **kwds):
+    def _get_data(self, obj, **kwds):
         return self.pulsar_client.get_data(**self.__build_kwds(obj, **kwds))
 
-    def get_filename(self, obj, **kwds):
+    def _get_filename(self, obj, **kwds):
         return self.pulsar_client.get_filename(**self.__build_kwds(obj, **kwds))
 
-    def update_from_file(self, obj, **kwds):
+    def _update_from_file(self, obj, **kwds):
         return self.pulsar_client.update_from_file(**self.__build_kwds(obj, **kwds))
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         return self.pulsar_client.get_store_usage_percent()
 
-    def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+    def _get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None):
         return None
 
     def __build_kwds(self, obj, **kwds):

lib/galaxy/objectstore/s3.py

@@ -504,7 +504,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
                       os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_s3(rel_path))
         return False
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         in_cache = in_s3 = False
         rel_path = self._construct_path(obj, **kwargs)
 
@@ -537,8 +537,8 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         else:
             return False
 
-    def create(self, obj, **kwargs):
-        if not self.exists(obj, **kwargs):
+    def _create(self, obj, **kwargs):
+        if not self._exists(obj, **kwargs):
 
             # Pull out locally used fields
             extra_dir = kwargs.get('extra_dir', None)
@@ -572,26 +572,26 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
                 open(os.path.join(self.staging_path, rel_path), 'w').close()
                 self._push_to_os(rel_path, from_string='')
 
-    def empty(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
-            return bool(self.size(obj, **kwargs) > 0)
+    def _empty(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
+            return bool(self._size(obj, **kwargs) > 0)
         else:
             raise ObjectNotFound('objectstore.empty, object does not exist: %s, kwargs: %s'
                                  % (str(obj), str(kwargs)))
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         if self._in_cache(rel_path):
             try:
                 return os.path.getsize(self._get_cache_path(rel_path))
             except OSError as ex:
                 log.info("Could not get size of file '%s' in local cache, will try S3. Error: %s", rel_path, ex)
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             return self._get_size_in_s3(rel_path)
         log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
         return 0
 
-    def delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir=False, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         extra_dir = kwargs.get('extra_dir', None)
         base_dir = kwargs.get('base_dir', None)
@@ -626,10 +626,10 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         except S3ResponseError:
             log.exception("Could not delete key '%s' from S3", rel_path)
         except OSError:
-            log.exception('%s delete error', self.get_filename(obj, **kwargs))
+            log.exception('%s delete error', self._get_filename(obj, **kwargs))
         return False
 
-    def get_data(self, obj, start=0, count=-1, **kwargs):
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         # Check cache first and get file if not there
         if not self._in_cache(rel_path):
@@ -641,7 +641,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         data_file.close()
         return content
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         base_dir = kwargs.get('base_dir', None)
         dir_only = kwargs.get('dir_only', False)
         obj_dir = kwargs.get('obj_dir', False)
@@ -664,7 +664,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         if self._in_cache(rel_path):
             return cache_path
         # Check if the file exists in persistent storage and, if it does, pull it into cache
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             if dir_only:  # Directories do not get pulled into cache
                 return cache_path
             else:
@@ -678,10 +678,10 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
                              % (str(obj), str(kwargs)))
         # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
-    def update_from_file(self, obj, file_name=None, create=False, **kwargs):
+    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
         if create:
-            self.create(obj, **kwargs)
-        if self.exists(obj, **kwargs):
+            self._create(obj, **kwargs)
+        if self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             # Chose whether to use the dataset file itself or an alternate file
             if file_name:
@@ -703,8 +703,8 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
             raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
                                  % (str(obj), str(kwargs)))
 
-    def get_object_url(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             try:
                 key = Key(self._bucket, rel_path)
@@ -713,7 +713,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
                 log.exception("Trouble generating URL for dataset '%s'", rel_path)
         return None
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         return 0.0
 
     def shutdown(self):

lib/galaxy/security/passwords.py

@@ -1,12 +1,6 @@
 import hashlib
-import hmac
 from base64 import b64encode
-from itertools import starmap
-from operator import xor
 from os import urandom
-from struct import Struct
-
-import six
 
 from galaxy.util import (
     safe_str_cmp,
@@ -17,7 +11,7 @@ from galaxy.util import (
 SALT_LENGTH = 12
 KEY_LENGTH = 24
 HASH_FUNCTION = 'sha256'
-COST_FACTOR = 10000
+COST_FACTOR = 100000
 
 
 def hash_password(password):
@@ -47,7 +41,7 @@ def hash_password_PBKDF2(password):
     # Generate a random salt
     salt = b64encode(urandom(SALT_LENGTH))
     # Apply the pbkdf2 encoding
-    hashed_password = pbkdf2_bin(password, salt, COST_FACTOR, KEY_LENGTH, getattr(hashlib, HASH_FUNCTION))
+    hashed_password = pbkdf2_bin(password, salt, COST_FACTOR, KEY_LENGTH, HASH_FUNCTION)
     encoded_password = unicodify(b64encode(hashed_password))
     # Format
     return 'PBKDF2${0}${1}${2}${3}'.format(HASH_FUNCTION, COST_FACTOR, unicodify(salt), encoded_password)
@@ -57,39 +51,18 @@ def check_password_PBKDF2(guess, hashed):
     # Split the database representation to extract cost_factor and salt
     name, hash_function, cost_factor, salt, encoded_original = hashed.split('$', 5)
     # Hash the guess using the same parameters
-    hashed_guess = pbkdf2_bin(guess, salt, int(cost_factor), KEY_LENGTH, getattr(hashlib, hash_function))
+    hashed_guess = pbkdf2_bin(guess, salt, int(cost_factor), KEY_LENGTH, hash_function)
     encoded_guess = unicodify(b64encode(hashed_guess))
     return safe_str_cmp(encoded_original, encoded_guess)
 
 
-# Taken from https://github.com/mitsuhiko/python-pbkdf2/blob/master/pbkdf2.py
-# (c) Copyright 2011 by Armin Ronacher, BSD LICENSE
-_pack_int = Struct('>I').pack
-
-
-def pbkdf2_bin(data, salt, iterations=1000, keylen=24, hashfunc=None):
+def pbkdf2_bin(data, salt, iterations=COST_FACTOR, keylen=KEY_LENGTH, hashfunc=HASH_FUNCTION):
     """Returns a binary digest for the PBKDF2 hash algorithm of `data`
     with the given `salt`.  It iterates `iterations` time and produces a
-    key of `keylen` bytes.  By default SHA-1 is used as hash function,
+    key of `keylen` bytes.  By default SHA-256 is used as hash function,
     a different hashlib `hashfunc` can be provided.
     """
-    hashfunc = hashfunc or hashlib.sha1
-    mac = hmac.new(smart_str(data), None, hashfunc)
-
-    def _pseudorandom(x, mac=mac):
-        h = mac.copy()
-        h.update(x)
-        digest = h.digest()
-        if six.PY2:
-            return digest, [ord(_) for _ in digest]
-        return digest, digest
-
-    buf = []
+    data = smart_str(data)
     salt = smart_str(salt)
-    for block in range(1, -(-keylen // mac.digest_size) + 1):
-        digest, rv = _pseudorandom(salt + _pack_int(block))
-        for _ in range(iterations - 1):
-            digest, u = _pseudorandom(digest)
-            rv = starmap(xor, zip(rv, u))
-        buf.extend(rv)
-    return bytes(bytearray(buf))[:keylen]
+
+    return hashlib.pbkdf2_hmac(hashfunc, data, salt, iterations, keylen)