Merge 23.0 into dev

client/src/components/Workflow/Editor/Draggable.vue

@@ -28,6 +28,7 @@ const props = defineProps({
 
 const emit = defineEmits(["mousedown", "mouseup", "move", "dragstart", "start", "stop"]);
 
+let dragImg: HTMLImageElement | undefined;
 const draggable = ref();
 const size = reactive(useAnimationFrameSize(draggable));
 const transform: Ref<ZoomTransform> | undefined = inject("transform");
@@ -40,8 +41,16 @@ const onStart = (position: Position, event: DragEvent) => {
     emit("start");
     emit("mousedown", event);
     if (event.type == "dragstart") {
+        dragImg = document.createElement("img");
+        dragImg.src = "data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7";
+        document.body.appendChild(dragImg);
         // I guess better than copy ?
         event.dataTransfer!.effectAllowed = "link";
+        try {
+            event.dataTransfer!.setDragImage(dragImg, 0, 0);
+        } catch (e) {
+            console.error(e);
+        }
         if (props.dragData) {
             event.dataTransfer!.setData("text/plain", JSON.stringify(props.dragData));
         }
@@ -66,6 +75,9 @@ const onMove = (position: Position, event: DragEvent) => {
 };
 
 const onEnd = (position: Position, event: DragEvent) => {
+    if (dragImg) {
+        document.body.removeChild(dragImg);
+    }
     emit("stop");
     emit("mouseup");
 };

client/src/components/Workflow/Editor/Node.vue

@@ -49,11 +49,13 @@
                     triggers="hover"
                     placement="bottom"
                     :show.sync="popoverShow">
-                    <Recommendations
-                        v-if="popoverShow"
-                        :step-id="id"
-                        :datatypes-mapper="datatypesMapper"
-                        @onCreate="onCreate" />
+                    <div>
+                        <Recommendations
+                            v-if="popoverShow"
+                            :step-id="id"
+                            :datatypes-mapper="datatypesMapper"
+                            @onCreate="onCreate" />
+                    </div>
                 </b-popover>
             </b-button-group>
             <i :class="iconClass" />
@@ -232,13 +234,7 @@ const invalidOutputs = computed(() => {
     });
 });
 const outputs = computed(() => {
-    let stepOutputs = props.step.outputs;
-    if (props.step.when) {
-        stepOutputs = stepOutputs.map((output) => {
-            return { ...output, optional: true };
-        });
-    }
-    return [...stepOutputs, ...invalidOutputs.value];
+    return [...props.step.outputs, ...invalidOutputs.value];
 });
 
 function onDragConnector(dragPosition: TerminalPosition, terminal: OutputTerminals) {

client/src/components/Workflow/Editor/NodeOutput.vue

@@ -15,6 +15,7 @@ import {
 } from "@/stores/workflowStepStore";
 import { assertDefined, ensureDefined } from "@/utils/assertions";
 import type { UseScrollReturn } from "@vueuse/core";
+import { NULL_COLLECTION_TYPE_DESCRIPTION, type CollectionTypeDescriptor } from "./modules/collectionTypeDescription";
 
 const props = defineProps<{
     output: OutputTerminalSource;
@@ -204,6 +205,50 @@ const terminalClass = computed(() => {
     return cls;
 });
 
+function collectionTypeToDescription(collectionTypeDescription: CollectionTypeDescriptor) {
+    let collectionDescription = collectionTypeDescription.collectionType;
+    if (
+        collectionTypeDescription &&
+        collectionTypeDescription.isCollection &&
+        collectionTypeDescription.collectionType
+    ) {
+        // we'll give a prettier label to the must common nested lists
+        switch (collectionTypeDescription.collectionType) {
+            case "list:paired": {
+                collectionDescription = "list of pairs dataset collection";
+                break;
+            }
+            case "list:list": {
+                collectionDescription = "list of lists dataset collection";
+                break;
+            }
+            default: {
+                if (collectionTypeDescription.rank > 1) {
+                    collectionDescription = `dataset collection with ${collectionTypeDescription.rank} levels of nesting`;
+                }
+                break;
+            }
+        }
+    }
+    return collectionDescription;
+}
+
+const outputDetails = computed(() => {
+    let collectionType = "collectionType" in terminal.value && terminal.value.collectionType;
+    const outputType =
+        collectionType && collectionType.isCollection && collectionType.collectionType
+            ? `output is ${collectionTypeToDescription(collectionType)}`
+            : `output is dataset`;
+    if (isMultiple.value) {
+        if (!collectionType) {
+            collectionType = NULL_COLLECTION_TYPE_DESCRIPTION;
+        }
+        const effectiveOutputType = terminal.value.mapOver.append(collectionType);
+        return `${outputType} and mapped-over to produce a ${collectionTypeToDescription(effectiveOutputType)} `;
+    }
+    return outputType;
+});
+
 onBeforeUnmount(() => {
     stateStore.deleteOutputTerminalPosition(props.stepId, props.output.name);
 });
@@ -245,6 +290,7 @@ onBeforeUnmount(() => {
             @move="onMove">
             <div
                 ref="icon"
+                v-b-tooltip.hover="outputDetails"
                 class="icon prevent-zoom"
                 tabindex="0"
                 :aria-label="`Connect output ${output.name} to input. Press space to see a list of available inputs`"

client/src/components/Workflow/Editor/composables/useTerminal.ts

@@ -11,10 +11,11 @@ export function useTerminal(
 ) {
     const terminal: Ref<ReturnType<typeof terminalFactory> | null> = ref(null);
     const stepStore = useWorkflowStepStore();
+    const step = computed(() => stepStore.getStep(stepId.value));
     const isMappedOver = computed(() => stepStore.stepMapOver[stepId.value]?.isCollection ?? false);
 
     watch(
-        [stepId, terminalSource, datatypesMapper],
+        [step, terminalSource, datatypesMapper],
         () => {
             // rebuild terminal if any of the tracked dependencies change
             const newTerminal = terminalFactory(stepId.value, terminalSource.value, datatypesMapper.value);

client/src/components/Workflow/Editor/modules/terminals.test.ts

@@ -380,6 +380,18 @@ describe("canAccept", () => {
         dataInTwo.disconnect(dataOut);
         expect(dataIn.mapOver).toEqual(NULL_COLLECTION_TYPE_DESCRIPTION);
     });
+    it("maintains step map over state when disconnecting output", () => {
+        const listListOut = terminals["list:list input"]?.["output"] as OutputCollectionTerminal;
+        const filterFailedInput = terminals["filter_failed"]?.["input"] as InputCollectionTerminal;
+        const filterFailedOutput = terminals["filter_failed"]?.["output"] as OutputCollectionTerminal;
+        const dataIn = terminals["simple data"]?.["input"] as InputTerminal;
+        filterFailedInput.connect(listListOut);
+        dataIn.connect(filterFailedOutput);
+        expect(filterFailedInput.isMappedOver()).toBe(true);
+        expect(stepStore.stepMapOver[filterFailedOutput.stepId]?.isCollection).toBe(true);
+        dataIn.disconnect(filterFailedOutput);
+        expect(stepStore.stepMapOver[filterFailedOutput.stepId]?.isCollection).toBe(true);
+    });
     it("rejects connecting incompatible connection types", () => {
         const pairedOut = terminals["paired input"]!["output"] as OutputCollectionTerminal;
         const collectionIn = terminals["list collection input"]!["input1"] as InputCollectionTerminal;

client/src/components/Workflow/Editor/modules/terminals.ts

@@ -239,7 +239,12 @@ class BaseInputTerminal extends Terminal {
                 const terminalSource = step.outputs[0];
                 if (terminalSource) {
                     const terminal = terminalFactory(step.id, terminalSource, this.datatypesMapper);
+                    // drop mapping restrictions
                     terminal.resetMappingIfNeeded();
+                    // re-establish map over through inputs
+                    step.inputs.forEach((input) => {
+                        terminalFactory(step.id, input, this.datatypesMapper).getStepMapOver();
+                    });
                 }
             } else {
                 console.error(`Invalid step. Could not fine step with id ${stepId} in store.`);
@@ -359,9 +364,6 @@ class BaseInputTerminal extends Terminal {
                 });
             }
             const postJobActionKey = `ChangeDatatypeAction${connection.output.name}`;
-            if (outputStep.when) {
-                terminalSource = { ...terminalSource, optional: true };
-            }
             if (
                 "extensions" in terminalSource &&
                 outputStep.post_job_actions &&
@@ -626,7 +628,7 @@ class BaseOutputTerminal extends Terminal {
     constructor(attr: BaseOutputTerminalArgs) {
         super(attr);
         this.datatypes = attr.datatypes;
-        this.optional = attr.optional;
+        this.optional = attr.optional || Boolean(this.stepStore.getStep(this.stepId)?.when);
         this.terminalType = "output";
     }
     getConnectedTerminals(): InputTerminalsAndInvalid[] {
@@ -743,7 +745,15 @@ export class OutputCollectionTerminal extends BaseOutputTerminal {
                                 otherCollectionType.canMapOver(collectionType)
                         );
                         if (connectedCollectionType) {
-                            return connectedCollectionType;
+                            if (connectedCollectionType.collectionType === "any") {
+                                // if the input collection type is "any" this output's collection type
+                                // is exactly the same as the connected output
+                                return otherCollectionType;
+                            } else {
+                                // else we pick the matching input collection type
+                                // so that the map over logic applies correctly
+                                return connectedCollectionType;
+                            }
                         }
                     }
                 }

client/src/schema/schema.ts

@@ -3767,6 +3767,8 @@ export interface components {
              * @description The current state of this dataset.
              */
             state: components["schemas"]["galaxy__model__Dataset__states"];
+            /** Tags */
+            tags: string[];
         };
         /**
          * HDASummary

client/src/utils/navigation/navigation.yml

@@ -11,6 +11,7 @@ _:  # global stuff
   selectors:
     editable_text: '.editable-text'
     tooltip_balloon: '.tooltip'
+    tooltip_inner: .tooltip-inner
     left_panel_drag: '#left > .unified-panel-footer > .drag'
     left_panel_collapse: '#left > .unified-panel-footer > .panel-collapse'
     right_panel_drag: '#right > .unified-panel-footer > .drag'

config/plugins/webhooks/demo/search/styles.css

@@ -4,7 +4,7 @@
 
 .search-screen {
     position: fixed;
-    z-index: 202;
+    z-index: 5100;
     width:100%;
     height:100%;
     display:none;
@@ -15,7 +15,7 @@
     top:0;
     left:0;
     background: rgba(224, 224, 224, 0.75);
-    z-index: 201;
+    z-index: 5000;
     width:100%;
     height:100%;
     display:none;
@@ -64,7 +64,7 @@
     position: fixed;
     top: 34px;
     width: 100%;
-    z-index: 203;
+    z-index: 5200;
 }
 
 .txtbx-search-data {

config/plugins/webhooks/gtn/styles.css

@@ -1,6 +1,6 @@
 #gtn-screen {
 	position: fixed;
-	z-index: 202;
+	z-index: 5100;
 	width:100%;
 	height:100%;
 }
@@ -10,7 +10,7 @@
 	top:0;
 	left:0;
 	background: rgba(224, 224, 224, 0.75);
-	z-index: 201;
+	z-index: 5000;
 	width:100%;
 	height:100%;
 	opacity: 2;
@@ -20,7 +20,7 @@
 	position: fixed;
 	height: 100%;
 	width: 100%;
-	z-index: 203;
+	z-index: 5200;
 	display: flex;
 	justify-content: center;
 	flex-direction: column;

config/plugins/webhooks/news/styles.css

@@ -1,6 +1,6 @@
 #news-screen {
 	position: fixed;
-	z-index: 202;
+	z-index: 5100;
 	width:100%;
 	height:100%;
 }
@@ -10,7 +10,7 @@
 	top:0;
 	left:0;
 	background: rgba(224, 224, 224, 0.75);
-	z-index: 201;
+	z-index: 5000;
 	width:100%;
 	height:100%;
 	opacity: 2;
@@ -20,7 +20,7 @@
 	position: fixed;
 	height: 100%;
 	width: 100%;
-	z-index: 203;
+	z-index: 5200;
 	display: flex;
 	justify-content: center;
 	flex-direction: column;

lib/galaxy/dependencies/pinned-requirements.txt

@@ -73,7 +73,7 @@ fsspec==2023.1.0 ; python_version >= "3.7" and python_version < "3.12"
 future==0.18.3 ; python_version >= "3.7" and python_version < "3.12"
 galaxy-sequence-utils==1.1.5 ; python_version >= "3.7" and python_version < "3.12"
 galaxy2cwl==0.1.4 ; python_version >= "3.7" and python_version < "3.12"
-gravity==1.0.1 ; python_version >= "3.7" and python_version < "3.12"
+gravity==1.0.2 ; python_version >= "3.7" and python_version < "3.12"
 greenlet==2.0.2 ; python_version >= "3.7" and platform_machine == "aarch64" and python_version < "3.12" or python_version >= "3.7" and platform_machine == "ppc64le" and python_version < "3.12" or python_version >= "3.7" and platform_machine == "x86_64" and python_version < "3.12" or python_version >= "3.7" and platform_machine == "amd64" and python_version < "3.12" or python_version >= "3.7" and platform_machine == "AMD64" and python_version < "3.12" or python_version >= "3.7" and platform_machine == "win32" and python_version < "3.12" or python_version >= "3.7" and platform_machine == "WIN32" and python_version < "3.12"
 gunicorn==20.1.0 ; python_version >= "3.7" and python_version < "3.12"
 gxformat2==0.17.0 ; python_version >= "3.7" and python_version < "3.12"

lib/galaxy/jobs/runners/aws.py

@@ -597,6 +597,7 @@ def write_command(self, job_wrapper: "MinimalJobWrapper") -> str:
             "exit_code_path": exit_code_path,
             "working_directory": job_wrapper.working_directory,
             "shell": job_wrapper.shell,
+            "galaxy_virtual_env": None,
         }
         job_file_contents = self.get_job_file(job_wrapper, **job_script_props)
         self.write_executable_script(job_file, job_file_contents, job_io=job_wrapper.job_io)

lib/galaxy/managers/cloud.py

@@ -293,7 +293,7 @@ def get(self, trans, history_id, bucket_name, objects, authz_id, input_args=None
             incoming = params.__dict__
             history = trans.sa_session.query(trans.app.model.History).get(history_id)
             if not history:
-                raise ObjectNotFound(f"History with ID `{trans.app.security.encode_id(history_id)}` not found.")
+                raise ObjectNotFound("History with the ID provided was not found.")
             output = trans.app.toolbox.get_tool("upload1").handle_input(trans, incoming, history=history)
 
             job_errors = output.get("job_errors", [])
@@ -360,7 +360,7 @@ def send(self, trans, history_id, bucket_name, authz_id, dataset_ids=None, overw
 
         history = trans.sa_session.query(trans.app.model.History).get(history_id)
         if not history:
-            raise ObjectNotFound(f"History with ID `{trans.app.security.encode_id(history_id)}` not found.")
+            raise ObjectNotFound("History with the provided ID not found.")
 
         sent = []
         failed = []

lib/galaxy/managers/collections.py

@@ -786,7 +786,7 @@ def __get_history_collection_instance(
             instance_id
         )
         if not collection_instance:
-            raise RequestParameterInvalidException(f"History dataset collection association {id} not found")
+            raise RequestParameterInvalidException("History dataset collection association not found")
         history = getattr(trans, "history", collection_instance.history)
         if check_ownership:
             self.history_manager.error_unless_owner(collection_instance.history, trans.user, current_history=history)
@@ -808,7 +808,7 @@ def __get_library_collection_instance(
             instance_id
         )
         if not collection_instance:
-            raise RequestParameterInvalidException(f"Library dataset collection association {id} not found")
+            raise RequestParameterInvalidException("Library dataset collection association not found")
         if check_accessible:
             if not trans.app.security_agent.can_access_library_item(
                 trans.get_current_user_roles(), collection_instance, trans.user

lib/galaxy/managers/collections_util.py

@@ -178,6 +178,7 @@ def dictify_element_reference(element, rank_fuzzy_counts=None, recursive=True, s
             object_details["state"] = element_object.state
             object_details["hda_ldda"] = "hda"
             object_details["history_id"] = element_object.history_id
+            object_details["tags"] = element_object.make_tag_string_list()
 
         dictified["object"] = object_details
     else:

lib/galaxy/managers/group_roles.py

@@ -7,7 +7,6 @@
 from galaxy import model
 from galaxy.exceptions import ObjectNotFound
 from galaxy.managers.context import ProvidesAppContext
-from galaxy.schema.fields import DecodedDatabaseIdField
 from galaxy.structured_app import MinimalManagerApp
 
 log = logging.getLogger(__name__)
@@ -63,13 +62,13 @@ def delete(self, trans: ProvidesAppContext, role_id: int, group_id: int) -> mode
     def _get_group(self, trans: ProvidesAppContext, group_id: int) -> model.Group:
         group = trans.sa_session.query(model.Group).get(group_id)
         if not group:
-            raise ObjectNotFound(f"Group with id {DecodedDatabaseIdField.encode(group_id)} was not found.")
+            raise ObjectNotFound("Group with the id provided was not found.")
         return group
 
     def _get_role(self, trans: ProvidesAppContext, role_id: int) -> model.Role:
         role = trans.sa_session.query(model.Role).get(role_id)
         if not role:
-            raise ObjectNotFound(f"Role with id {DecodedDatabaseIdField.encode(role_id)} was not found.")
+            raise ObjectNotFound("Role with the id provided was not found.")
         return role
 
     def _get_group_role(