Merge branch 'release_25.1' into forward_merge_10_11_25

Author: mvdbeek

client/src/components/History/useHistoryCardActions.ts

@@ -247,25 +247,6 @@ export function useHistoryCardActions(
                 handler: onRestore,
                 visible: history.value.deleted && !history.value.purged && isMyHistory(history.value),
             },
-            {
-                id: "switch",
-                title: localize("Set as current history"),
-                label: localize("Set as Current"),
-                variant: "outline-primary",
-                icon: faExchangeAlt,
-                handler: () => historyStore.setCurrentHistory(String(history.value.id)),
-                visible:
-                    (isMyHistory(history.value) || archivedView) && historyStore.currentHistoryId !== history.value.id,
-            },
-            {
-                title: "current history",
-                id: "current",
-                label: "Current",
-                variant: "outline-primary",
-                disabled: true,
-                visible:
-                    (isMyHistory(history.value) || archivedView) && historyStore.currentHistoryId === history.value.id,
-            },
             {
                 id: "import-copy",
                 label: localize("Import Copy"),
@@ -291,9 +272,28 @@ export function useHistoryCardActions(
                 label: localize("View"),
                 title: localize("View this history"),
                 icon: faEye,
-                variant: "primary",
+                variant: "outline-primary",
                 to: `/histories/view?id=${history.value.id}`,
             },
+            {
+                id: "switch",
+                title: localize("Set as current history"),
+                label: localize("Set as Current"),
+                variant: "primary",
+                icon: faExchangeAlt,
+                handler: () => historyStore.setCurrentHistory(String(history.value.id)),
+                visible:
+                    (isMyHistory(history.value) || archivedView) && historyStore.currentHistoryId !== history.value.id,
+            },
+            {
+                title: "current history",
+                id: "current",
+                label: "Current",
+                variant: "outline-primary",
+                disabled: true,
+                visible:
+                    (isMyHistory(history.value) || archivedView) && historyStore.currentHistoryId === history.value.id,
+            },
         ];
     });
 

client/src/components/Panels/Common/Tool.test.js

@@ -1,3 +1,4 @@
+import { createTestingPinia } from "@pinia/testing";
 import { mount } from "@vue/test-utils";
 import { getLocalVue } from "tests/jest/helpers";
 
@@ -7,11 +8,15 @@ const localVue = getLocalVue();
 
 describe("Tool", () => {
     test("test tool", () => {
+        const pinia = createTestingPinia();
         const wrapper = mount(Tool, {
             propsData: {
-                tool: {},
+                tool: {
+                    id: "test_tool",
+                },
             },
             localVue,
+            pinia,
         });
         const nameElement = wrapper.findAll(".name");
         expect(nameElement.at(0).text()).toBe("");
@@ -25,15 +30,18 @@ describe("Tool", () => {
         expect(wrapper.emitted().onOperation).toBeDefined();
     });
     test("test tool operation", () => {
+        const pinia = createTestingPinia();
         const wrapper = mount(Tool, {
             propsData: {
                 tool: {
+                    id: "test_tool",
                     name: "name",
                 },
                 operationIcon: "operationIconClass",
                 operationTitle: "operationTitle",
             },
             localVue,
+            pinia,
         });
         const nameElement = wrapper.findAll(".name");
         expect(nameElement.at(0).text()).toBe("name");
@@ -43,15 +51,18 @@ describe("Tool", () => {
         expect(title).toBe("operationTitle");
     });
     test("test tool hide name, test description", () => {
+        const pinia = createTestingPinia();
         const wrapper = mount(Tool, {
             propsData: {
                 tool: {
+                    id: "test_tool",
                     name: "name",
                     description: "description",
                 },
                 hideName: true,
             },
             localVue,
+            pinia,
         });
         const nameElement = wrapper.findAll(".name");
         expect(nameElement.length).toBe(0);

client/src/components/Panels/Common/Tool.vue

@@ -8,8 +8,8 @@
             v-else
             :class="targetClass"
             :data-tool-id="tool.id"
-            :href="tool.link"
-            :target="tool.target"
+            :href="toolLink"
+            :target="toolTarget"
             :title="tool.help"
             @click="onClick">
             <span class="labels">
@@ -35,6 +35,7 @@
 import BootstrapVue from "bootstrap-vue";
 import Vue from "vue";
 
+import { useToolStore } from "@/stores/toolStore";
 import ariaAlert from "@/utils/ariaAlert";
 
 Vue.use(BootstrapVue);
@@ -67,7 +68,20 @@ export default {
             default: false,
         },
     },
+    setup() {
+        const toolStore = useToolStore();
+        return {
+            getLinkById: toolStore.getLinkById,
+            getTargetById: toolStore.getTargetById,
+        };
+    },
     computed: {
+        toolLink() {
+            return this.getLinkById(this.tool.id);
+        },
+        toolTarget() {
+            return this.getTargetById(this.tool.id);
+        },
         targetClass() {
             if (this.toolKey) {
                 return `tool-menu-item-${this.tool[this.toolKey]} title-link cursor-pointer`;

client/src/stores/toolStore.ts

@@ -103,6 +103,28 @@ export const useToolStore = defineStore("toolStore", () => {
         return toolSections.value[effectiveView] || {};
     });
 
+    const getLinkById = computed(() => {
+        return (toolId: string) => {
+            const tool = toolsById.value[toolId];
+            const appRoot = getAppRoot();
+            if (tool && tool.model_class === "DataSourceTool") {
+                return `${appRoot}tool_runner/data_source_redirect?tool_id=${encodeURIComponent(toolId)}`;
+            } else if (tool?.model_class) {
+                return `${appRoot}?tool_id=${encodeURIComponent(toolId)}&version=latest`;
+            } else {
+                // accommodates hacky toolbox markdown directive overload
+                return undefined;
+            }
+        };
+    });
+
+    const getTargetById = computed(() => {
+        return (toolId: string) => {
+            const tool = toolsById.value[toolId];
+            return tool?.model_class === "DataSourceTool" ? "_top" : "galaxy_main";
+        };
+    });
+
     const getToolsById = computed(() => {
         return (q?: string) => {
             if (!q?.trim()) {
@@ -299,6 +321,8 @@ export const useToolStore = defineStore("toolStore", () => {
         fetchPanels,
         fetchToolForId,
         fetchTools,
+        getLinkById,
+        getTargetById,
         helpDataCached,
         initializePanel,
         isPanelPopulated,

client/src/utils/navigation/navigation.yml

@@ -408,8 +408,8 @@ tool_panel:
   selectors:
     edam_link: 'a[href^="https://edamontology.github.io/edam-browser"]'
     tool_box: '[data-description="panel toolbox"]'
-    tool_link: 'a[href$$="tool_runner?tool_id=${tool_id}"]'
-    outer_tool_link: '.toolTitle a[href$$="tool_runner?tool_id=${tool_id}"]'
+    tool_link: 'a[href$$="/?tool_id=${tool_id}&version=latest"]'
+    outer_tool_link: '.toolTitle a[href$$="/?tool_id=${tool_id}&version=latest"]'
     data_source_tool_link: 'a[href$$="tool_runner/data_source_redirect?tool_id=${tool_id}"]'
     search: '.search-query'
     toolbox: '[data-description="panel toolbox"]'

lib/galaxy/model/__init__.py

@@ -1664,7 +1664,17 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
         back_populates="job"
     )
 
-    dict_collection_visible_keys = ["id", "state", "exit_code", "update_time", "create_time", "galaxy_version"]
+    dict_collection_visible_keys = [
+        "id",
+        "state",
+        "exit_code",
+        "update_time",
+        "create_time",
+        "galaxy_version",
+        "tool_id",
+        "tool_version",
+        "history_id",
+    ]
     dict_element_visible_keys = [
         "id",
         "state",
@@ -1675,6 +1685,9 @@ class Job(Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable):
         "command_version",
         "copied_from_job_id",
         "user_id",
+        "tool_id",
+        "tool_version",
+        "history_id",
     ]
 
     _numeric_metric = JobMetricNumeric
@@ -2210,9 +2223,6 @@ def to_dict(self, view="collection", system_details=False):
             rval = super().to_dict(view="collection")
         else:
             rval = super().to_dict(view=view)
-        rval["tool_id"] = self.tool_id
-        rval["tool_version"] = self.tool_version
-        rval["history_id"] = self.history_id
         if system_details or view == "admin_job_list":
             # System level details that only admins should have.
             rval["external_id"] = self.job_runner_external_id
@@ -2848,6 +2858,17 @@ def job_list(self):
             .all()
         )
 
+    def get_job_attributes(self, attributes: list[str]):
+        session = required_object_session(self)
+        targets = [getattr(Job.table.columns, attr) for attr in attributes]
+        stmt = (
+            select(*targets)
+            .select_from(Job)
+            .join(ImplicitCollectionJobsJobAssociation, Job.id == ImplicitCollectionJobsJobAssociation.job_id)
+            .where(ImplicitCollectionJobsJobAssociation.implicit_collection_jobs_id == self.id)
+        )
+        return session.execute(stmt)
+
     def _serialize(self, id_encoder, serialization_options):
         rval = dict_for(
             self,
@@ -10169,6 +10190,15 @@ def _serialize(self, id_encoder, serialization_options):
 
         return step_attrs
 
+    def get_jobs_dict(self):
+        if self.implicit_collection_jobs:
+            result = self.implicit_collection_jobs.get_job_attributes(Job.dict_collection_visible_keys)
+            return [{"model_class": "Job", **row._mapping} for row in result]
+        elif self.job:
+            return [self.job.to_dict()]
+        else:
+            return []
+
     def to_dict(self, view="collection", value_mapper=None):
         rval = super().to_dict(view=view, value_mapper=value_mapper)
         rval["order_index"] = self.workflow_step.order_index
@@ -10177,9 +10207,7 @@ def to_dict(self, view="collection", value_mapper=None):
         # Following no longer makes sense...
         # rval['state'] = self.job.state if self.job is not None else None
         if view == "element":
-            jobs = []
-            for job in self.jobs:
-                jobs.append(job.to_dict())
+            jobs = self.get_jobs_dict()
 
             outputs = {}
             for output_assoc in self.output_datasets:

lib/galaxy/tool_util/verify/interactor.py

@@ -332,7 +332,6 @@ def verify_output(self, history_id, jobs, output_data, output_testdef, tool_id,
         attributes = output_testdef.attributes
         name = output_testdef.name
         expected_count = attributes.get("count")
-        self.wait_for_jobs(history_id, jobs, maxseconds)
         hid = self.__output_id(output_data)
         # TODO: Twill version verifies dataset is 'ok' in here.
         try:

lib/galaxy/tools/execute.py

@@ -659,7 +659,10 @@ def finalize_dataset_collections(self, trans):
                 # We mark this here so that the job cache query in subsequent
                 # jobs considers this to be a valid cached input.
                 completed_job_ids = {job.id for job in self.completed_jobs.values() if job}
-                if all(job.copied_from_job_id in completed_job_ids for job in self.implicit_collection_jobs.job_list):
+                completed_implicit_jobs_copied_from = set(
+                    self.implicit_collection_jobs.get_job_attributes(["copied_from_job_id"]).all()
+                )
+                if completed_implicit_jobs_copied_from <= completed_job_ids:
                     completed_collections = {
                         jtodca.name: jtodca.dataset_collection_instance
                         for jtodca in self.completed_jobs[0].output_dataset_collection_instances