Merge remote-tracking branch 'origin/dev' into galactic-wizardry

.github/workflows/api.yaml

@@ -18,6 +18,7 @@ env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
   GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
   GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
+  GALAXY_TEST_REQUIRE_ALL_NEEDED_TOOLS: '1'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true

.github/workflows/framework_workflows.yaml

@@ -16,6 +16,7 @@ on:
 env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
   GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
+  GALAXY_TEST_WORKFLOW_AFTER_RERUN: '1'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true

client/src/api/schema/schema.ts

@@ -2653,6 +2653,23 @@ export interface paths {
         patch?: never;
         trace?: never;
     };
+    "/api/invocations/{invocation_id}/request": {
+        parameters: {
+            query?: never;
+            header?: never;
+            path?: never;
+            cookie?: never;
+        };
+        /** Get a description modeling an API request to invoke this workflow - this is recreated and will be more specific in some ways than the initial creation request. */
+        get: operations["invocation_as_request_api_invocations__invocation_id__request_get"];
+        put?: never;
+        post?: never;
+        delete?: never;
+        options?: never;
+        head?: never;
+        patch?: never;
+        trace?: never;
+    };
     "/api/invocations/{invocation_id}/step_jobs_summary": {
         parameters: {
             query?: never;
@@ -12399,8 +12416,9 @@ export interface components {
              */
             batch: boolean | null;
             /**
-             * Dataset Map
-             * @description TODO
+             * Legacy Dataset Map
+             * @deprecated
+             * @description An older alternative to specifying inputs using database IDs, do not use this and use inputs instead
              * @default {}
              */
             ds_map: {
@@ -12423,12 +12441,12 @@ export interface components {
             history_id?: string | null;
             /**
              * Inputs
-             * @description TODO
+             * @description Specify values for formal inputs to the workflow
              */
             inputs?: Record<string, never> | null;
             /**
              * Inputs By
-             * @description How inputs maps to inputs (datasets/collections) to workflows steps.
+             * @description How the 'inputs' field maps its inputs (datasets/collections/step parameters) to workflows steps.
              */
             inputs_by?: string | null;
             /**
@@ -12455,35 +12473,35 @@ export interface components {
              */
             no_add_to_history: boolean | null;
             /**
-             * Parameters
-             * @description The raw parameters for the workflow invocation.
+             * Legacy Step Parameters
+             * @description Parameters specified per-step for the workflow invocation, this is legacy and you should generally use inputs and only specify the formal parameters of a workflow instead.
              * @default {}
              */
             parameters: Record<string, never> | null;
             /**
-             * Parameters Normalized
-             * @description Indicates if parameters are already normalized for workflow invocation.
+             * Legacy Step Parameters Normalized
+             * @description Indicates if legacy parameters are already normalized to be indexed by the order_index and are specified as a dictionary per step. Legacy-style parameters could previously be specified as one parameter per step or by tool ID.
              * @default false
              */
             parameters_normalized: boolean | null;
             /**
              * Preferred Intermediate Object Store ID
-             * @description The ID of the ? object store that should be used to store ? datasets in this history.
+             * @description The ID of the object store that should be used to store the intermediate datasets of this workflow -  - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences
              */
             preferred_intermediate_object_store_id?: string | null;
             /**
              * Preferred Object Store ID
-             * @description The ID of the object store that should be used to store new datasets in this history.
+             * @description The ID of the object store that should be used to store all datasets (can instead specify object store IDs for intermediate and outputs datasts separately) -  - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences
              */
             preferred_object_store_id?: string | null;
             /**
              * Preferred Outputs Object Store ID
-             * @description The ID of the object store that should be used to store ? datasets in this history.
+             * @description The ID of the object store that should be used to store the marked output datasets of this workflow - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences.
              */
             preferred_outputs_object_store_id?: string | null;
             /**
              * Replacement Parameters
-             * @description TODO
+             * @description Class of parameters mostly used for string replacement in PJAs. In best practice workflows, these should be replaced with input parameters
              * @default {}
              */
             replacement_params: Record<string, never> | null;
@@ -12495,7 +12513,7 @@ export interface components {
             require_exact_tool_versions: boolean | null;
             /**
              * Resource Parameters
-             * @description TODO
+             * @description If a workflow_resource_params_file file is defined and the target workflow is configured to consumer resource parameters, they can be specified with this parameter. See https://github.com/galaxyproject/galaxy/pull/4830 for more information.
              * @default {}
              */
             resource_params: Record<string, never> | null;
@@ -12504,11 +12522,6 @@ export interface components {
              * @description Scheduler to use for workflow invocation.
              */
             scheduler?: string | null;
-            /**
-             * Step Parameters
-             * @description TODO
-             */
-            step_parameters?: Record<string, never> | null;
             /**
              * Use cached job
              * @description Indicated whether to use a cached job for workflow invocation.
@@ -18202,6 +18215,86 @@ export interface components {
              */
             workflow_id: string;
         };
+        /**
+         * WorkflowInvocationRequestModel
+         * @description Model a workflow invocation request (InvokeWorkflowPayload) for an existing invocation.
+         */
+        WorkflowInvocationRequestModel: {
+            /**
+             * History ID
+             * @description The encoded history id the workflow was run in.
+             */
+            history_id: string;
+            /**
+             * Inputs
+             * @description Values for inputs
+             */
+            inputs: Record<string, never>;
+            /**
+             * Inputs by
+             * @description How the 'inputs' field maps its inputs (datasets/collections/step parameters) to workflows steps.
+             */
+            inputs_by: string;
+            /**
+             * Is instance
+             * @description This API yields a particular workflow instance, newer workflows belonging to the same storedworkflow may have different state.
+             * @default true
+             * @constant
+             * @enum {boolean}
+             */
+            instance: true;
+            /**
+             * Legacy Step Parameters
+             * @description Parameters specified per-step for the workflow invocation, this is legacy and you should generally use inputs and only specify the formal parameters of a workflow instead. If these are set, the workflow was not executed in a best-practice fashion and we the resulting invocation request may not fully reflect the executed workflow state.
+             */
+            parameters?: Record<string, never> | null;
+            /**
+             * Legacy Step Parameters Normalized
+             * @description Indicates if legacy parameters are already normalized to be indexed by the order_index and are specified as a dictionary per step. Legacy-style parameters could previously be specified as one parameter per step or by tool ID.
+             * @default true
+             * @constant
+             * @enum {boolean}
+             */
+            parameters_normalized: true;
+            /**
+             * Preferred Intermediate Object Store ID
+             * @description The ID of the object store that should be used to store the intermediate datasets of this workflow -  - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences
+             */
+            preferred_intermediate_object_store_id?: string | null;
+            /**
+             * Preferred Object Store ID
+             * @description The ID of the object store that should be used to store all datasets (can instead specify object store IDs for intermediate and outputs datasts separately) -  - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences
+             */
+            preferred_object_store_id?: string | null;
+            /**
+             * Preferred Outputs Object Store ID
+             * @description The ID of the object store that should be used to store the marked output datasets of this workflow - Galaxy's job configuration may override this in some cases but this workflow preference will override tool and user preferences.
+             */
+            preferred_outputs_object_store_id?: string | null;
+            /**
+             * Replacement Parameters
+             * @description Class of parameters mostly used for string replacement in PJAs. In best practice workflows, these should be replaced with input parameters
+             * @default {}
+             */
+            replacement_params: Record<string, never> | null;
+            /**
+             * Resource Parameters
+             * @description If a workflow_resource_params_file file is defined and the target workflow is configured to consumer resource parameters, they can be specified with this parameter. See https://github.com/galaxyproject/galaxy/pull/4830 for more information.
+             * @default {}
+             */
+            resource_params: Record<string, never> | null;
+            /**
+             * Use cached job
+             * @description Indicated whether to use a cached job for workflow invocation.
+             * @default false
+             */
+            use_cached_job: boolean;
+            /**
+             * Workflow ID
+             * @description The encoded Workflow ID associated with the invocation.
+             */
+            workflow_id: string;
+        };
         /** WorkflowInvocationResponse */
         WorkflowInvocationResponse:
             | components["schemas"]["WorkflowInvocationElementView"]
@@ -27070,6 +27163,50 @@ export interface operations {
             };
         };
     };
+    invocation_as_request_api_invocations__invocation_id__request_get: {
+        parameters: {
+            query?: never;
+            header?: {
+                /** @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. */
+                "run-as"?: string | null;
+            };
+            path: {
+                /** @description The encoded database identifier of the Invocation. */
+                invocation_id: string;
+            };
+            cookie?: never;
+        };
+        requestBody?: never;
+        responses: {
+            /** @description Successful Response */
+            200: {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["WorkflowInvocationRequestModel"];
+                };
+            };
+            /** @description Request Error */
+            "4XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+            /** @description Server Error */
+            "5XX": {
+                headers: {
+                    [name: string]: unknown;
+                };
+                content: {
+                    "application/json": components["schemas"]["MessageExceptionModel"];
+                };
+            };
+        };
+    };
     invocation_step_jobs_summary_api_invocations__invocation_id__step_jobs_summary_get: {
         parameters: {
             query?: never;

client/src/components/DatasetInformation/DatasetAttributes.vue

@@ -138,7 +138,8 @@ onMounted(async () => {
                     v-if="
                         (!datasetAttributes['conversion_disable'] || !datasetAttributes['datatype_disable']) &&
                         !datasetAttributes['metadata_disable']
-                    ">
+                    "
+                    title-link-class="dataset-edit-datatype-tab">
                     <template v-slot:title>
                         <FontAwesomeIcon :icon="faDatabase" class="mr-1" />
                         {{ localize("Datatypes") }}
@@ -168,7 +169,9 @@ onMounted(async () => {
                                     {{ localize("Save") }}
                                 </BButton>
 
-                                <BButton @click="submit('datatype', 'datatype_detect')">
+                                <BButton
+                                    id="dataset-attributes-autodetect-datatype"
+                                    @click="submit('datatype', 'datatype_detect')">
                                     <FontAwesomeIcon :icon="faRedo" class="mr-1" />
                                     {{ localize("Auto-detect") }}
                                 </BButton>

client/src/components/Help/terms.yml

@@ -106,3 +106,8 @@ galaxy:
       failed: |
         This state indicates there was a problem scheduling the workflow invocation. No additional datasets
         or jobs will be created for this workflow invocation.
+  upload:
+    galaxyUploadUtil: |
+      A utility for uploading files to a Galaxy server from the command line. Use ``galaxy-upload`` to upload
+      file(s) to a Galaxy server, and ``galaxy-history-search``, a helper utility to find Galaxy histories
+      to pass to the ``galaxy-upload`` command.

client/src/components/Upload/UploadModal.vue

@@ -1,4 +1,5 @@
 <script setup>
+import { BModal } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { ref, watch } from "vue";
 
@@ -8,6 +9,8 @@ import { useUserHistories } from "@/composables/userHistories";
 import { useUserStore } from "@/stores/userStore";
 import { wait } from "@/utils/utils";
 
+import ExternalLink from "../ExternalLink.vue";
+import HelpText from "../Help/HelpText.vue";
 import UploadContainer from "./UploadContainer.vue";
 
 const { currentUser } = storeToRefs(useUserStore());
@@ -71,7 +74,7 @@ defineExpose({
 </script>
 
 <template>
-    <b-modal
+    <BModal
         v-model="showModal"
         :static="options.modalStatic"
         header-class="no-separator"
@@ -81,12 +84,20 @@ defineExpose({
         no-enforce-focus
         hide-footer>
         <template v-slot:modal-header>
-            <h2 class="title h-sm" tabindex="0">
-                {{ options.title }}
-                <span v-if="currentHistory">
-                    to <b>{{ currentHistory.name }}</b>
+            <div class="d-flex justify-content-between w-100">
+                <h2 class="title h-sm" tabindex="0">
+                    {{ options.title }}
+                    <span v-if="currentHistory">
+                        to <b>{{ currentHistory.name }}</b>
+                    </span>
+                </h2>
+                <span>
+                    <ExternalLink href="https://galaxy-upload.readthedocs.io/en/latest/"> Click here </ExternalLink>
+                    to check out the
+                    <HelpText uri="galaxy.upload.galaxyUploadUtil" text="galaxy-upload" />
+                    util!
                 </span>
-            </h2>
+            </div>
         </template>
         <UploadContainer
             v-if="currentHistoryId"
@@ -95,7 +106,7 @@ defineExpose({
             :current-history-id="currentHistoryId"
             v-bind="options"
             @dismiss="dismiss" />
-    </b-modal>
+    </BModal>
 </template>
 
 <style>

client/src/utils/navigation/navigation.yml

@@ -349,7 +349,10 @@ edit_dataset_attributes:
     name_input: '[aria-labelledby="dataset-attributes-heading"] input#name'
     info_input: '[aria-labelledby="dataset-attributes-heading"] textarea#info'
     annotation_input: '[aria-labelledby="dataset-attributes-heading"] textarea#annotation'
+    datatypes_tab: '.dataset-edit-datatype-tab'
+    datatype_dropdown: ' #datatype .multiselect'
     save_button: '#dataset-attributes-default-save'
+    auto_detect_datatype_button: '#dataset-attributes-autodetect-datatype'
     alert: '.dataset-attributes-alert'
 
   dbkey_dropdown_results:

client/yarn.lock

@@ -6890,9 +6890,9 @@ http-proxy-agent@^5.0.0:
     debug "4"
 
 http-proxy-middleware@^2.0.3:
-  version "2.0.6"
-  resolved "https://registry.npmjs.org/http-proxy-middleware/-/http-proxy-middleware-2.0.6.tgz"
-  integrity sha512-ya/UeJ6HVBYxrgYotAZo1KvPWlgB48kUJLDePFeneHsVujFaW5WNj2NgWCAE//B1Dl02BIfYlpNgBy8Kf8Rjmw==
+  version "2.0.7"
+  resolved "https://registry.yarnpkg.com/http-proxy-middleware/-/http-proxy-middleware-2.0.7.tgz#915f236d92ae98ef48278a95dedf17e991936ec6"
+  integrity sha512-fgVY8AV7qU7z/MmXJ/rxwbrtQH4jBQ9m7kp3llF0liB7glmFeVZFBepQb32T3y8n8k2+AEYuMPCpinYW+/CuRA==
   dependencies:
     "@types/http-proxy" "^1.17.8"
     http-proxy "^1.18.1"