From ac432a50233cb4c3dcada2aab513c3855b6acd69 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 8 Mar 2023 21:02:18 +0100
Subject: [PATCH 1/6] Display DCE in job parameter component

Addresses part of #15729
---
 .../History/Content/GenericItem.vue           | 27 ++++++++++-----
 .../JobParameters/JobParametersArrayValue.vue |  2 +-
 .../components/providers/storeProviders.js    | 10 ++++++
 client/src/schema/schema.ts                   | 31 +++++++++++++++++
 lib/galaxy/managers/jobs.py                   |  2 +-
 lib/galaxy/model/security.py                  |  9 +++++
 .../webapps/galaxy/api/dataset_collections.py | 14 ++++++++
 .../galaxy/services/dataset_collections.py    | 12 +++++++
 .../api/test_dataset_collections.py           | 34 +++++++++++++++++++
 9 files changed, 131 insertions(+), 10 deletions(-)

diff --git a/client/src/components/History/Content/GenericItem.vue b/client/src/components/History/Content/GenericItem.vue
index adda51b27de..38ae796f2f1 100644
--- a/client/src/components/History/Content/GenericItem.vue
+++ b/client/src/components/History/Content/GenericItem.vue
@@ -3,19 +3,19 @@
         <loading-span v-if="loading" message="Loading dataset" />
         <div v-else>
             <ContentItem
-                :id="item.hid"
+                :id="item.hid ?? item.element_index + 1"
                 is-history-item
-                :item="item"
-                :name="item.name"
+                :item="item?.object || item"
+                :name="item.name || item.element_identifier"
                 :expand-dataset="expandDataset"
-                :is-dataset="item.history_content_type == 'dataset'"
+                :is-dataset="item.history_content_type == 'dataset' || item.element_type == 'hda'"
                 @update:expand-dataset="expandDataset = $event"
                 @view-collection="viewCollection = !viewCollection"
                 @delete="onDelete(item)"
                 @undelete="onUndelete(item)"
                 @unhide="onUnhide(item)" />
             <div v-if="viewCollection">
-                <GenericElement :dsc="item" />
+                <GenericElement :dsc="item?.object || item" />
             </div>
         </div>
     </component>
@@ -23,13 +23,15 @@
 
 <script>
 import LoadingSpan from "components/LoadingSpan";
-import { DatasetCollectionProvider, DatasetProvider } from "components/providers";
-import { deleteContent, updateContentFields } from "components/History/model/queries";
+import { DatasetCollectionProvider, DatasetProvider } from "@/components/providers";
+import { DatasetCollectionElementProvider } from "@/components/providers/storeProviders";
+import { deleteContent, updateContentFields } from "@/components/History/model/queries";
 import ContentItem from "./ContentItem";
 import GenericElement from "./GenericElement";
 
 export default {
     components: {
+        DatasetCollectionElementProvider,
         ContentItem,
         GenericElement,
         DatasetProvider,
@@ -54,7 +56,16 @@ export default {
     },
     computed: {
         providerComponent() {
-            return this.itemSrc == "hda" ? "DatasetProvider" : "DatasetCollectionProvider";
+            switch (this.itemSrc) {
+                case "hda":
+                    return "DatasetProvider";
+                case "hdca":
+                    return "DatasetCollectionProvider";
+                case "dce":
+                    return "DatasetCollectionElementProvider";
+                default:
+                    throw `Unknown element src ${this.itemSrc}`;
+            }
         },
     },
     methods: {
diff --git a/client/src/components/JobParameters/JobParametersArrayValue.vue b/client/src/components/JobParameters/JobParametersArrayValue.vue
index 1878f3efce9..1ae30eb94bf 100644
--- a/client/src/components/JobParameters/JobParametersArrayValue.vue
+++ b/client/src/components/JobParameters/JobParametersArrayValue.vue
@@ -2,7 +2,7 @@
     <div>
         <div v-for="(elVal, pvIndex) in parameter_value" :key="pvIndex">
             <generic-history-item
-                v-if="['hda', 'hdca'].includes(elVal.src)"
+                v-if="['hda', 'hdca', 'dce'].includes(elVal.src)"
                 :item-id="elVal.id"
                 :item-src="elVal.src" />
             <span v-else> {{ elVal.hid }}: {{ elVal.name }} </span>
diff --git a/client/src/components/providers/storeProviders.js b/client/src/components/providers/storeProviders.js
index ff1a16d0154..a584b130008 100644
--- a/client/src/components/providers/storeProviders.js
+++ b/client/src/components/providers/storeProviders.js
@@ -47,6 +47,7 @@ export const SimpleProviderMixin = {
             loading: this.loading,
             item: this.item,
             save: this.save,
+            result: this.item,
         });
     },
 };
@@ -131,6 +132,15 @@ export const JobProvider = {
     },
 };
 
+export const DatasetCollectionElementProvider = {
+    mixins: [SimpleProviderMixin],
+    computed: {
+        url() {
+            return prependPath(`api/dataset_collection_element/${this.id}`);
+        },
+    },
+};
+
 /**
  * Provider component interface to the actual stores i.e. history items and collection elements stores.
  * @param {String} storeAction The store action is executed when the consuming component e.g. the history panel, changes the provider props.
diff --git a/client/src/schema/schema.ts b/client/src/schema/schema.ts
index 2893bd0ae69..8f1f59a6641 100644
--- a/client/src/schema/schema.ts
+++ b/client/src/schema/schema.ts
@@ -47,6 +47,10 @@ export interface paths {
          */
         put: operations["reload_toolbox_api_configuration_toolbox_put"];
     };
+    "/api/dataset_collection_element/{dce_id}": {
+        /** Content */
+        get: operations["content_api_dataset_collection_element__dce_id__get"];
+    };
     "/api/dataset_collections": {
         /** Create a new dataset collection instance. */
         post: operations["create_api_dataset_collections_post"];
@@ -7544,6 +7548,33 @@ export interface operations {
             };
         };
     };
+    content_api_dataset_collection_element__dce_id__get: {
+        /** Content */
+        parameters: {
+            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            header?: {
+                "run-as"?: string;
+            };
+            /** @description The encoded identifier of the dataset collection element. */
+            path: {
+                dce_id: string;
+            };
+        };
+        responses: {
+            /** @description Successful Response */
+            200: {
+                content: {
+                    "application/json": components["schemas"]["DCESummary"];
+                };
+            };
+            /** @description Validation Error */
+            422: {
+                content: {
+                    "application/json": components["schemas"]["HTTPValidationError"];
+                };
+            };
+        };
+    };
     create_api_dataset_collections_post: {
         /** Create a new dataset collection instance. */
         parameters?: {
diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 14788e6f688..8c41f603e6e 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -903,7 +903,7 @@ def summarize_job_parameters(trans, job):
                             value=f"{len(param_values[input.name])} uploaded datasets",
                         )
                     )
-                elif input.type == "data":
+                elif input.type == "data" or input.type == "data_collection":
                     value = []
                     for element in listify(param_values[input.name]):
                         encoded_id = trans.security.encode_id(element.id)
diff --git a/lib/galaxy/model/security.py b/lib/galaxy/model/security.py
index 6723e5b69a8..68cbaa9ea31 100644
--- a/lib/galaxy/model/security.py
+++ b/lib/galaxy/model/security.py
@@ -4,6 +4,7 @@ from datetime import (
     datetime,
     timedelta,
 )
+from typing import List
 
 from sqlalchemy import (
     and_,
@@ -519,6 +520,14 @@ class GalaxyRBACAgent(RBACAgent):
 
         return True
 
+    def can_access_collection(
+        self, user_roles: List[galaxy.model.Role], collection: galaxy.model.DatasetCollection
+    ):
+        action_tuples = collection.dataset_action_tuples
+        if not self.can_access_datasets(user_roles, action_tuples):
+            return False
+        return True
+
     def can_manage_dataset(self, roles, dataset):
         return self.allow_action(roles, self.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset)
 
diff --git a/lib/galaxy/webapps/galaxy/api/dataset_collections.py b/lib/galaxy/webapps/galaxy/api/dataset_collections.py
index 79818f1ef15..5e9d61d1a31 100644
--- a/lib/galaxy/webapps/galaxy/api/dataset_collections.py
+++ b/lib/galaxy/webapps/galaxy/api/dataset_collections.py
@@ -13,6 +13,7 @@ from galaxy.schema.schema import (
     AnyHDCA,
     CreateNewCollectionPayload,
     DatasetCollectionInstanceType,
+    DCESummary,
     HDCADetailed,
 )
 from galaxy.webapps.galaxy.api import (
@@ -36,6 +37,11 @@ DatasetCollectionIdPathParam: DecodedDatabaseIdField = Path(
     ..., description="The encoded identifier of the dataset collection."
 )
 
+
+DatasetCollectionElementIdPathParam: DecodedDatabaseIdField = Path(
+    ..., description="The encoded identifier of the dataset collection element."
+)
+
 InstanceTypeQueryParam: DatasetCollectionInstanceType = Query(
     default="history",
     description="The type of collection instance. Either `history` (default) or `library`.",
@@ -129,3 +135,11 @@ class FastAPIDatasetCollections:
         ),
     ) -> DatasetCollectionContentElements:
         return self.service.contents(trans, hdca_id, parent_id, instance_type, limit, offset)
+
+    @router.get("/api/dataset_collection_element/{dce_id}")
+    def content(
+        self,
+        trans: ProvidesHistoryContext = DependsOnTrans,
+        dce_id: DecodedDatabaseIdField = DatasetCollectionElementIdPathParam,
+    ) -> DCESummary:
+        return self.service.dce_content(trans, dce_id)
diff --git a/lib/galaxy/webapps/galaxy/services/dataset_collections.py b/lib/galaxy/webapps/galaxy/services/dataset_collections.py
index 17e17fea5a9..ac313b2fcb1 100644
--- a/lib/galaxy/webapps/galaxy/services/dataset_collections.py
+++ b/lib/galaxy/webapps/galaxy/services/dataset_collections.py
@@ -25,6 +25,7 @@ from galaxy.managers.collections_util import (
 from galaxy.managers.context import ProvidesHistoryContext
 from galaxy.managers.hdcas import HDCAManager
 from galaxy.managers.histories import HistoryManager
+from galaxy.model import DatasetCollectionElement
 from galaxy.schema.fields import (
     DecodedDatabaseIdField,
     ModelClassField,
@@ -208,6 +209,17 @@ class DatasetCollectionsService(ServiceBase, UsesLibraryMixinItems):
         )
         return rval
 
+    def dce_content(self, trans: ProvidesHistoryContext, dce_id: DecodedDatabaseIdField) -> DCESummary:
+        dce: Optional[DatasetCollectionElement] = trans.model.session.query(DatasetCollectionElement).get(dce_id)
+        if not dce:
+            raise exceptions.ObjectNotFound("No DatasetCollectionElement found")
+        if not trans.user_is_admin:
+            collection = dce.child_collection or dce.collection
+            if not trans.app.security_agent.can_access_collection(trans.get_current_user_roles(), collection):
+                raise exceptions.ItemAccessibilityException("Collection not accessible by user.")
+        serialized_dce = dictify_element_reference(dce, recursive=False, security=trans.security)
+        return trans.security.encode_all_ids(serialized_dce, recursive=True)
+
     def contents(
         self,
         trans: ProvidesHistoryContext,
diff --git a/lib/galaxy_test/api/test_dataset_collections.py b/lib/galaxy_test/api/test_dataset_collections.py
index 38db8c02a0c..1d2b0d860ed 100644
--- a/lib/galaxy_test/api/test_dataset_collections.py
+++ b/lib/galaxy_test/api/test_dataset_collections.py
@@ -196,6 +196,40 @@ class TestDatasetCollectionsApi(ApiTestCase):
                 create_response = self._post("dataset_collections", payload, json=True)
                 self._assert_status_code_is(create_response, 403)
 
+    def test_dataset_collection_element_security(self):
+        with self.dataset_populator.test_history(require_new=False) as history_id:
+            dataset_collection = self.dataset_collection_populator.create_list_of_list_in_history(
+                history_id,
+                collection_type="list:list:list",
+                wait=True,
+            ).json()
+            first_element = dataset_collection["elements"][0]
+            assert first_element["model_class"] == "DatasetCollectionElement"
+            assert first_element["element_type"] == "dataset_collection"
+            first_element_url = f"/api/dataset_collection_element/{first_element['id']}"
+            # Make one dataset private to check that access permissions are respected
+            first_dataset_element = first_element["object"]["elements"][0]["object"]["elements"][0]
+            self.dataset_populator.make_private(history_id, first_dataset_element["object"]["id"])
+            with self._different_user():
+                assert self._get(first_element_url).status_code == 403
+            collection_dce_response = self._get(first_element_url)
+            collection_dce_response.raise_for_status()
+            collection_dce = collection_dce_response.json()
+            assert collection_dce["model_class"] == "DatasetCollectionElement"
+            assert collection_dce["element_type"] == "dataset_collection"
+            first_dataset_element = first_element["object"]["elements"][0]["object"]["elements"][0]
+            assert first_dataset_element["model_class"] == "DatasetCollectionElement"
+            assert first_dataset_element["element_type"] == "hda"
+            first_dataset_element_url = f"/api/dataset_collection_element/{first_dataset_element['id']}"
+            with self._different_user():
+                assert self._get(first_dataset_element_url).status_code == 403
+            dataset_dce_response = self._get(first_dataset_element_url)
+            dataset_dce_response.raise_for_status()
+            dataset_dce = dataset_dce_response.json()
+            assert dataset_dce["model_class"] == "DatasetCollectionElement"
+            assert dataset_dce["element_type"] == "hda"
+            assert dataset_dce["object"]["model_class"] == "HistoryDatasetAssociation"
+
     def test_enforces_unique_names(self):
         with self.dataset_populator.test_history(require_new=False) as history_id:
             element_identifiers = self.dataset_collection_populator.list_identifiers(history_id)

From 13514a76a6edc6cdfba22df4633b074a63f1226f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 5 May 2023 15:36:04 +0200
Subject: [PATCH 2/6] Wait for tool form data to be set before refreshing tool
 form

If you navigate to a tool re-run url without loading a history first the
tool form would be rebuilt before the tool parameters from the re-run
were actually set, so you would effectively just get the default values
for the tool.
---
 client/src/components/Tool/ToolForm.vue | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index 236abdfc70a..a15fe023361 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/client/src/components/Tool/ToolForm.vue
@@ -155,7 +155,6 @@ export default {
     data() {
         return {
             disabled: false,
-            initialized: false,
             showLoading: true,
             showForm: false,
             showEntryPoints: false,
@@ -163,7 +162,7 @@ export default {
             showError: false,
             showExecuting: false,
             formConfig: {},
-            formData: {},
+            formData: undefined,
             remapAllowed: false,
             errorTitle: null,
             errorContent: null,
@@ -214,6 +213,9 @@ export default {
                 return "The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run.";
             }
         },
+        initialized() {
+            return this.formData !== undefined;
+        },
     },
     watch: {
         currentHistoryId() {
@@ -224,10 +226,7 @@ export default {
         },
     },
     created() {
-        this.requestTool().then(() => {
-            this.initialized = true;
-            console.debug(`ToolForm::created - Started listening to history changes. [${this.id}]`);
-        });
+        this.requestTool();
     },
     methods: {
         ...mapActions(useJobStore, ["saveLatestResponse"]),

From c14db55910411e5e532a3500f87f8f35ad177bbb Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 5 May 2023 15:44:06 +0200
Subject: [PATCH 3/6] Fix re-run with DCE inputs

---
 client/src/mvc/ui/ui-select-content.js | 17 +++++++++-----
 lib/galaxy/model/security.py           |  4 +---
 lib/galaxy/tools/parameters/basic.py   | 32 +++++++++++++++++++++++++-
 3 files changed, 43 insertions(+), 10 deletions(-)

diff --git a/client/src/mvc/ui/ui-select-content.js b/client/src/mvc/ui/ui-select-content.js
index 11de437c075..292d7a32147 100644
--- a/client/src/mvc/ui/ui-select-content.js
+++ b/client/src/mvc/ui/ui-select-content.js
@@ -424,12 +424,12 @@ const View = Backbone.View.extend({
         const select_options = { hda: [], hdca: [] };
         _.each(options, (items, src) => {
             _.each(items, (item) => {
-                self._patchValue(item);
+                self._patchValue(item, src);
                 const current_src = item.src || src;
                 const addOption = !this.model.attributes.tag || item.tags.includes(this.model.attributes.tag);
                 if (addOption) {
                     select_options[current_src].push({
-                        hid: item.hid,
+                        hid: item.hid || Infinity, // if we got no hid we have a "Selected" item
                         keep: item.keep,
                         label: `${item.hid || "Selected"}: ${item.name}`,
                         value: item.id,
@@ -455,7 +455,12 @@ const View = Backbone.View.extend({
                 list.push(value.id);
             });
             // sniff first suitable field type from config list
-            const src = new_value.values[0].src;
+            let src = new_value.values[0].src;
+            if (src === "dce") {
+                src =
+                    this.cache[`dce${new_value.values[0].id}_hda`]?.src ||
+                    this.cache[`dce${new_value.values[0].id}_hdca`]?.src;
+            }
             const multiple = new_value.values.length > 1;
             for (let i = 0; i < this.config.length; i++) {
                 const field = this.fields[i];
@@ -480,11 +485,11 @@ const View = Backbone.View.extend({
 
     /** Library datasets are displayed and selected together with history datasets,
         Dataset collection elements are displayed together with history dataset collections **/
-    _patchValue: function (v) {
-        const patchTo = { ldda: "hda", dce: "hdca" };
+    _patchValue: function (v, src) {
+        const patchTo = { ldda: "hda", dce: src };
         if (v.values) {
             _.each(v.values, (v) => {
-                this._patchValue(v);
+                this._patchValue(v, src);
             });
         } else if (patchTo[v.src]) {
             v.origin = v.src;
diff --git a/lib/galaxy/model/security.py b/lib/galaxy/model/security.py
index 68cbaa9ea31..b92b0014e24 100644
--- a/lib/galaxy/model/security.py
+++ b/lib/galaxy/model/security.py
@@ -520,9 +520,7 @@ class GalaxyRBACAgent(RBACAgent):
 
         return True
 
-    def can_access_collection(
-        self, user_roles: List[galaxy.model.Role], collection: galaxy.model.DatasetCollection
-    ):
+    def can_access_collection(self, user_roles: List[galaxy.model.Role], collection: galaxy.model.DatasetCollection):
         action_tuples = collection.dataset_action_tuples
         if not self.can_access_datasets(user_roles, action_tuples):
             return False
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 15d5df5a6e1..8c5305be6cf 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2092,6 +2092,9 @@ class DataToolParameter(BaseDataToolParameter):
                     elif single_value["src"] == "ldda":
                         decoded_id = trans.security.decode_id(single_value["id"])
                         rval.append(trans.sa_session.query(LibraryDatasetDatasetAssociation).get(decoded_id))
+                    elif single_value["src"] == "dce":
+                        decoded_id = trans.security.decode_id(single_value["id"])
+                        rval.append(trans.sa_session.query(DatasetCollectionElement).get(decoded_id))
                     else:
                         raise ValueError(f"Unknown input source {single_value['src']} passed to job submission API.")
                 elif isinstance(
@@ -2127,6 +2130,9 @@ class DataToolParameter(BaseDataToolParameter):
             elif value["src"] == "hdca":
                 decoded_id = trans.security.decode_id(value["id"])
                 rval.append(trans.sa_session.query(HistoryDatasetCollectionAssociation).get(decoded_id))
+            elif value["src"] == "dce":
+                decoded_id = trans.security.decode_id(value["id"])
+                rval.append(trans.sa_session.query(DatasetCollectionElement).get(decoded_id))
             else:
                 raise ValueError(f"Unknown input source {value['src']} passed to job submission API.")
         elif str(value).startswith("__collection_reduce__|"):
@@ -2280,6 +2286,28 @@ class DataToolParameter(BaseDataToolParameter):
                 value["map_over_type"] = subcollection_type
             return list.append(value)
 
+        def append_dce(dce):
+            if dce.hda:
+                # well this isn't good, but what's the alternative ?
+                # we should be precise about what we're (re-)running here.
+                key = "hda"
+            else:
+                key = "hdca"
+            d["options"][key].append(
+                {
+                    "id": trans.security.encode_id(dce.id),
+                    "name": dce.element_identifier,
+                    "src": "dce",
+                    "tags": [],
+                    "keep": True,
+                }
+            )
+
+        # append DCE
+        if isinstance(other_values.get(self.name), DatasetCollectionElement):
+            dce = other_values[self.name]
+            append_dce(dce)
+
         # add datasets
         hda_list = util.listify(other_values.get(self.name))
         # Prefetch all at once, big list of visible, non-deleted datasets.
@@ -2299,6 +2327,8 @@ class DataToolParameter(BaseDataToolParameter):
                 else:
                     hda_state = "unavailable"
                 append(d["options"]["hda"], hda, f"({hda_state}) {hda.name}", "hda", True)
+            elif isinstance(hda, DatasetCollectionElement):
+                append_dce(hda)
 
         # add dataset collections
         dataset_collection_matcher = dataset_matcher_factory.dataset_collection_matcher(dataset_matcher)
@@ -2460,7 +2490,7 @@ class DataCollectionToolParameter(BaseDataToolParameter):
         # append DCE
         if isinstance(other_values.get(self.name), DatasetCollectionElement):
             dce = other_values[self.name]
-            d["options"]["dce"].append(
+            d["options"]["hdca"].append(
                 {
                     "id": trans.security.encode_id(dce.id),
                     "hid": None,

From 668c2ed08fa17e8acd0acbd6bf43bdf666b2ceaf Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 9 May 2023 12:47:14 +0200
Subject: [PATCH 4/6] Also patch values when setting list of selected datasets

---
 client/src/mvc/ui/ui-select-content.js | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/client/src/mvc/ui/ui-select-content.js b/client/src/mvc/ui/ui-select-content.js
index 292d7a32147..2aa69a0cb45 100644
--- a/client/src/mvc/ui/ui-select-content.js
+++ b/client/src/mvc/ui/ui-select-content.js
@@ -449,11 +449,6 @@ const View = Backbone.View.extend({
     _changeValue: function () {
         const new_value = this.model.get("value");
         if (new_value && new_value.values && new_value.values.length > 0) {
-            // create list with content ids
-            const list = [];
-            _.each(new_value.values, (value) => {
-                list.push(value.id);
-            });
             // sniff first suitable field type from config list
             let src = new_value.values[0].src;
             if (src === "dce") {
@@ -461,6 +456,12 @@ const View = Backbone.View.extend({
                     this.cache[`dce${new_value.values[0].id}_hda`]?.src ||
                     this.cache[`dce${new_value.values[0].id}_hdca`]?.src;
             }
+            this._patchValue(new_value, src);
+            // create list with content ids
+            const list = [];
+            _.each(new_value.values, (value) => {
+                list.push(value.id);
+            });
             const multiple = new_value.values.length > 1;
             for (let i = 0; i < this.config.length; i++) {
                 const field = this.fields[i];

From b9bb92cd1fe3b9533fc3a12ff086ff78f1ec0b7c Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 10 May 2023 12:53:15 +0200
Subject: [PATCH 5/6] Don't build tool state for first param combination

It'll always pull in the first dataset in the `other_values` dict, which
isn'r correct. Tool parameters at this point know how to deal with
collections, so this shouldn't be neceesary.
---
 lib/galaxy/tools/__init__.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index a27c6ea904b..c4b87ff10ba 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2437,12 +2437,6 @@ class Tool(Dictifiable):
         # create parameter object
         params = Params(kwd, sanitize=False)
 
-        # expand incoming parameters (parameters might trigger multiple tool executions,
-        # here we select the first execution only in order to resolve dynamic parameters)
-        expanded_incomings, _ = expand_meta_parameters(trans, self, params.__dict__)
-        if expanded_incomings:
-            params.__dict__ = expanded_incomings[0]
-
         # do param translation here, used by datasource tools
         if self.input_translator:
             self.input_translator.translate(params)

From 3ce0a8dd1c98f998d5d9db5fffdabcb2b76ece4d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 10 May 2023 15:53:10 +0200
Subject: [PATCH 6/6] Selemium test for re-running part of dataset collection
 via DCE

---
 client/src/utils/navigation/navigation.yml |  6 ++++
 lib/galaxy_test/selenium/test_tool_form.py | 32 ++++++++++++++++++++++
 2 files changed, 38 insertions(+)

diff --git a/client/src/utils/navigation/navigation.yml b/client/src/utils/navigation/navigation.yml
index 2b792f2df15..29771100eb8 100644
--- a/client/src/utils/navigation/navigation.yml
+++ b/client/src/utils/navigation/navigation.yml
@@ -242,6 +242,7 @@ history_panel:
       tag_area_button: '.details .stateless-tags .multiselect button'
       tag_area_input: '.details .stateless-tags .multiselect input'
       list_items: '.dataset-collection-panel .listing .content-item'
+      back_to_history: svg[data-description="back to history"]
 
   selectors:
     _: '#current-history-panel'
@@ -492,6 +493,11 @@ tool_form:
     parameter_checkbox: 'div.ui-form-element[id="form-element-${parameter}"] .ui-switch'
     parameter_input: 'div.ui-form-element[id="form-element-${parameter}"] .ui-input'
     parameter_textarea: 'div.ui-form-element[id="form-element-${parameter}"] textarea'
+    parameter_batch_dataset_collection:
+      type: xpath
+      selector: //div[@id='form-element-${parameter}']//i[contains(@class, 'fa-folder-o')]/parent::label
+    data_option_value: option[value="${item_id}"]
+
     repeat_insert: '[data-description="repeat insert"]'
     reference: '.formatted-reference'
     about: '.tool-footer'
diff --git a/lib/galaxy_test/selenium/test_tool_form.py b/lib/galaxy_test/selenium/test_tool_form.py
index d27b36b43e4..768ca62b3e3 100644
--- a/lib/galaxy_test/selenium/test_tool_form.py
+++ b/lib/galaxy_test/selenium/test_tool_form.py
@@ -114,6 +114,38 @@ class TestToolForm(SeleniumTestCase, UsesHistoryItemAssertions):
         self.history_panel_wait_for_hid_ok(2)
         self._check_dataset_details_for_inttest_value(2)
 
+    @selenium_test
+    def test_rerun_dataset_collection_element(self):
+        # upload a first dataset that should not become selected on re-run
+        test_path = self.get_filename("1.fasta")
+        self.perform_upload(test_path)
+        self.history_panel_wait_for_hid_ok(1)
+
+        history_id = self.current_history_id()
+        # upload a nested collection
+        collection_id = self.dataset_collection_populator.create_list_of_list_in_history(
+            history_id,
+            collection_type="list:list",
+            wait=True,
+        ).json()["id"]
+        self.tool_open("identifier_multiple")
+        self.components.tool_form.parameter_batch_dataset_collection(parameter="input1").wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.components.tool_form.data_option_value(item_id=collection_id).wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.tool_form_execute()
+        self.history_panel_wait_for_hid_ok(7)
+        self.history_panel_expand_collection(7)
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.history_panel_click_item_title(1)
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.hda_click_primary_action_button(1, "rerun")
+        self.sleep_for(self.wait_types.UX_RENDER)
+        assert self.driver.find_element(By.CSS_SELECTOR, "option:checked").text == "Selected: test0"
+        self.tool_form_execute()
+        self.components.history_panel.collection_view.back_to_history.wait_for_and_click()
+        self.history_panel_wait_for_hid_ok(9)
+
     @selenium_test
     @flakey
     def test_run_data(self):