From af47306291b713dae159d53bd414d63129ed0991 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 8 Mar 2023 21:02:18 +0100
Subject: [PATCH] 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           | 31 +++++++++++++++++++
 9 files changed, 128 insertions(+), 10 deletions(-)

diff --git a/client/src/components/History/Content/GenericItem.vue b/client/src/components/History/Content/GenericItem.vue
index adda51b27de4..38ae796f2f19 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 1878f3efce9e..1ae30eb94bf8 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 ff1a16d0154e..a584b1300085 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 2893bd0ae698..8f1f59a66415 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 14788e6f688a..8c41f603e6ef 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -903,7 +903,7 @@ def inputs_recursive(input_params, param_values, depth=1, upgrade_messages=None)
                             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 6723e5b69a8d..68cbaa9ea31a 100644
--- a/lib/galaxy/model/security.py
+++ b/lib/galaxy/model/security.py
@@ -4,6 +4,7 @@
     datetime,
     timedelta,
 )
+from typing import List
 
 from sqlalchemy import (
     and_,
@@ -519,6 +520,14 @@ def can_access_datasets(self, user_roles, action_tuples):
 
         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 79818f1ef15a..5e9d61d1a314 100644
--- a/lib/galaxy/webapps/galaxy/api/dataset_collections.py
+++ b/lib/galaxy/webapps/galaxy/api/dataset_collections.py
@@ -13,6 +13,7 @@
     AnyHDCA,
     CreateNewCollectionPayload,
     DatasetCollectionInstanceType,
+    DCESummary,
     HDCADetailed,
 )
 from galaxy.webapps.galaxy.api import (
@@ -36,6 +37,11 @@
     ..., 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 @@ def contents(
         ),
     ) -> 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 17e17fea5a9d..ac313b2fcb1f 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.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 @@ def show(
         )
         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 38db8c02a0c0..b4b73194089b 100644
--- a/lib/galaxy_test/api/test_dataset_collections.py
+++ b/lib/galaxy_test/api/test_dataset_collections.py
@@ -196,6 +196,37 @@ def test_hda_security(self):
                 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']}"
+            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"
+            fist_dataset_element = first_element["object"]["elements"][0]["object"]["elements"][0]
+            assert fist_dataset_element["model_class"] == "DatasetCollectionElement"
+            assert fist_dataset_element["element_type"] == "hda"
+            first_dataset_element_url = f"/api/dataset_collection_element/{fist_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)