Merge pull request #18360 from jmchilton/merge_to_dev_0

Merge latest 24.1 into dev.
galaxyproject · Jun 10, 2024 · 1cab2ba · 1cab2ba
2 parents 81a00cb + 659d505
commit 1cab2ba
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Showing 33 changed files with 75 additions and 166 deletions.
diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
@@ -12651,8 +12651,6 @@ export interface components {
             device?: string | null;
             /** Hidden */
             hidden: boolean;
-            /** Id */
-            id: number | string;
             /** Name */
             name?: string | null;
             /** Object Store Id */
@@ -12730,8 +12728,6 @@ export interface components {
             description: string | null;
             /** Hidden */
             hidden: boolean;
-            /** Id */
-            id: string | number;
             /** Name */
             name: string;
             /** Purged */
@@ -14972,7 +14968,7 @@ export interface operations {
             header?: {
                 "run-as"?: string | null;
             };
-            /** @description The index for a persisted UserFileSourceStore object. */
+            /** @description The UUID index for a persisted UserFileSourceStore object. */
             path: {
                 user_file_source_id: string;
             };
@@ -14999,7 +14995,7 @@ export interface operations {
             header?: {
                 "run-as"?: string | null;
             };
-            /** @description The index for a persisted UserFileSourceStore object. */
+            /** @description The UUID index for a persisted UserFileSourceStore object. */
             path: {
                 user_file_source_id: string;
             };
@@ -15034,7 +15030,7 @@ export interface operations {
             header?: {
                 "run-as"?: string | null;
             };
-            /** @description The index for a persisted UserFileSourceStore object. */
+            /** @description The UUID index for a persisted UserFileSourceStore object. */
             path: {
                 user_file_source_id: string;
             };
@@ -20896,7 +20892,7 @@ export interface operations {
             header?: {
                 "run-as"?: string | null;
             };
-            /** @description The identifier used to index a persisted UserObjectStore object. */
+            /** @description The UUID used to identify a persisted UserObjectStore object. */
             path: {
                 user_object_store_id: string;
             };
@@ -20923,7 +20919,7 @@ export interface operations {
             header?: {
                 "run-as"?: string | null;
             };
-            /** @description The identifier used to index a persisted UserObjectStore object. */
+            /** @description The UUID used to identify a persisted UserObjectStore object. */
             path: {
                 user_object_store_id: string;
             };
@@ -20958,7 +20954,7 @@ export interface operations {
             header?: {
                 "run-as"?: string | null;
             };
-            /** @description The identifier used to index a persisted UserObjectStore object. */
+            /** @description The UUID used to identify a persisted UserObjectStore object. */
             path: {
                 user_object_store_id: string;
             };

diff --git a/client/src/components/ConfigTemplates/test_fixtures.ts b/client/src/components/ConfigTemplates/test_fixtures.ts
@@ -114,7 +114,6 @@ export const OBJECT_STORE_INSTANCE: UserConcreteObjectStore = {
     secrets: ["oldsecret", "droppedsecret"],
     quota: { enabled: false },
     private: false,
-    id: 4,
     uuid: "112f889f-72d7-4619-a8e8-510a8c685aa7",
     active: true,
     hidden: false,

diff --git a/client/src/components/FileSources/Instances/EditInstance.vue b/client/src/components/FileSources/Instances/EditInstance.vue
@@ -13,7 +13,7 @@ import EditSecrets from "./EditSecrets.vue";
 import InstanceForm from "@/components/ConfigTemplates/InstanceForm.vue";
 
 interface Props {
-    instanceId: number | string;
+    instanceId: string;
 }
 
 const props = defineProps<Props>();
@@ -36,7 +36,7 @@ const loadingMessage = "Loading file source template and instance information";
 async function onSubmit(formData: any) {
     if (template.value) {
         const payload = editFormDataToPayload(template.value, formData);
-        const args = { user_file_source_id: String(instance?.value?.id) };
+        const args = { user_file_source_id: String(instance?.value?.uuid) };
         const { data: fileSource } = await update({ ...args, ...payload });
         await onUpdate(fileSource);
     }

diff --git a/client/src/components/FileSources/Instances/EditSecrets.vue b/client/src/components/FileSources/Instances/EditSecrets.vue
@@ -19,7 +19,7 @@ async function onUpdate(secretName: string, secretValue: string) {
         secret_name: secretName,
         secret_value: secretValue,
     };
-    const args = { user_file_source_id: String(props.fileSource.id) };
+    const args = { user_file_source_id: String(props.fileSource.uuid) };
     await update({ ...args, ...payload });
 }
 </script>

diff --git a/client/src/components/FileSources/Instances/InstanceDropdown.vue b/client/src/components/FileSources/Instances/InstanceDropdown.vue
@@ -15,8 +15,8 @@ interface Props {
 }
 
 const props = defineProps<Props>();
-const routeEdit = computed(() => `/file_source_instances/${props.fileSource.id}/edit`);
-const routeUpgrade = computed(() => `/file_source_instances/${props.fileSource.id}/upgrade`);
+const routeEdit = computed(() => `/file_source_instances/${props.fileSource.uuid}/edit`);
+const routeUpgrade = computed(() => `/file_source_instances/${props.fileSource.uuid}/upgrade`);
 const isUpgradable = computed(() =>
     fileSourceTemplatesStore.canUpgrade(props.fileSource.template_id, props.fileSource.template_version)
 );

diff --git a/client/src/components/FileSources/Instances/UpgradeForm.vue b/client/src/components/FileSources/Instances/UpgradeForm.vue
@@ -31,7 +31,7 @@ const loadingMessage = "Loading file source template and instance information";
 
 async function onSubmit(formData: any) {
     const payload = upgradeFormDataToPayload(props.latestTemplate, formData);
-    const args = { user_file_source_id: String(props.instance.id) };
+    const args = { user_file_source_id: String(props.instance.uuid) };
     try {
         const { data: fileSource } = await update({ ...args, ...payload });
         await onUpgrade(fileSource);

diff --git a/client/src/components/FileSources/Instances/UpgradeInstance.vue b/client/src/components/FileSources/Instances/UpgradeInstance.vue
@@ -9,7 +9,7 @@ import UpgradeForm from "./UpgradeForm.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
 
 interface Props {
-    instanceId: number | string;
+    instanceId: string;
 }
 
 const props = defineProps<Props>();

diff --git a/client/src/components/FileSources/Instances/instance.ts b/client/src/components/FileSources/Instances/instance.ts
@@ -4,7 +4,7 @@ import type { FileSourceTemplateSummary, UserFileSourceModel } from "@/api/fileS
 import { useFileSourceInstancesStore } from "@/stores/fileSourceInstancesStore";
 import { useFileSourceTemplatesStore } from "@/stores/fileSourceTemplatesStore";
 
-export function useInstanceAndTemplate(instanceIdRef: Ref<string | number>) {
+export function useInstanceAndTemplate(instanceIdRef: Ref<string>) {
     const fileSourceTemplatesStore = useFileSourceTemplatesStore();
     const fileSourceInstancesStore = useFileSourceInstancesStore();
     fileSourceInstancesStore.fetchInstances();

diff --git a/client/src/components/FileSources/Instances/services.ts b/client/src/components/FileSources/Instances/services.ts
@@ -7,7 +7,7 @@ export const update = fetcher.path("/api/file_source_instances/{user_file_source
 
 export async function hide(instance: UserFileSourceModel) {
     const payload = { hidden: true };
-    const args = { user_file_source_id: String(instance?.id) };
+    const args = { user_file_source_id: String(instance?.uuid) };
     const { data: fileSource } = await update({ ...args, ...payload });
     return fileSource;
 }
diff --git a/client/src/components/ObjectStore/Instances/EditInstance.vue b/client/src/components/ObjectStore/Instances/EditInstance.vue
@@ -13,7 +13,7 @@ import EditSecrets from "./EditSecrets.vue";
 import InstanceForm from "@/components/ConfigTemplates/InstanceForm.vue";
 
 interface Props {
-    instanceId: number | string;
+    instanceId: string;
 }
 
 const props = defineProps<Props>();
@@ -36,7 +36,7 @@ const loadingMessage = "Loading storage location template and instance informati
 async function onSubmit(formData: any) {
     if (template.value) {
         const payload = editFormDataToPayload(template.value, formData);
-        const args = { user_object_store_id: String(instance?.value?.id) };
+        const args = { user_object_store_id: String(instance?.value?.uuid) };
         const { data: objectStore } = await update({ ...args, ...payload });
         await onUpdate(objectStore);
     }

diff --git a/client/src/components/ObjectStore/Instances/EditSecrets.vue b/client/src/components/ObjectStore/Instances/EditSecrets.vue
@@ -20,7 +20,7 @@ async function onUpdate(secretName: string, secretValue: string) {
         secret_name: secretName,
         secret_value: secretValue,
     };
-    const args = { user_object_store_id: String(props.objectStore.id) };
+    const args = { user_object_store_id: String(props.objectStore.uuid) };
     await update({ ...args, ...payload });
 }
 </script>

diff --git a/client/src/components/ObjectStore/Instances/InstanceDropdown.vue b/client/src/components/ObjectStore/Instances/InstanceDropdown.vue
@@ -15,8 +15,8 @@ interface Props {
 }
 
 const props = defineProps<Props>();
-const routeEdit = computed(() => `/object_store_instances/${props.objectStore.id}/edit`);
-const routeUpgrade = computed(() => `/object_store_instances/${props.objectStore.id}/upgrade`);
+const routeEdit = computed(() => `/object_store_instances/${props.objectStore.uuid}/edit`);
+const routeUpgrade = computed(() => `/object_store_instances/${props.objectStore.uuid}/upgrade`);
 const isUpgradable = computed(() =>
     objectStoreTemplatesStore.canUpgrade(props.objectStore.template_id, props.objectStore.template_version)
 );

diff --git a/client/src/components/ObjectStore/Instances/UpgradeForm.test.ts b/client/src/components/ObjectStore/Instances/UpgradeForm.test.ts
@@ -59,7 +59,6 @@ const INSTANCE: UserConcreteObjectStore = {
     secrets: ["oldsecret", "droppedsecret"],
     quota: { enabled: false },
     private: false,
-    id: 4,
     uuid: "112f889f-72d7-4619-a8e8-510a8c685aa7",
     active: true,
     hidden: false,

diff --git a/client/src/components/ObjectStore/Instances/UpgradeForm.vue b/client/src/components/ObjectStore/Instances/UpgradeForm.vue
@@ -32,7 +32,7 @@ const loadingMessage = "Loading storage location template and instance informati
 
 async function onSubmit(formData: any) {
     const payload = upgradeFormDataToPayload(props.latestTemplate, formData);
-    const args = { user_object_store_id: String(props.instance.id) };
+    const args = { user_object_store_id: String(props.instance.uuid) };
     try {
         const { data: objectStore } = await update({ ...args, ...payload });
         await onUpgrade(objectStore);

diff --git a/client/src/components/ObjectStore/Instances/UpgradeInstance.vue b/client/src/components/ObjectStore/Instances/UpgradeInstance.vue
@@ -9,7 +9,7 @@ import UpgradeForm from "./UpgradeForm.vue";
 import LoadingSpan from "@/components/LoadingSpan.vue";
 
 interface Props {
-    instanceId: number | string;
+    instanceId: string;
 }
 
 const props = defineProps<Props>();

diff --git a/client/src/components/ObjectStore/Instances/instance.ts b/client/src/components/ObjectStore/Instances/instance.ts
@@ -6,7 +6,7 @@ import { useObjectStoreTemplatesStore } from "@/stores/objectStoreTemplatesStore
 
 import type { UserConcreteObjectStore } from "./types";
 
-export function useInstanceAndTemplate(instanceIdRef: Ref<string | number>) {
+export function useInstanceAndTemplate(instanceIdRef: Ref<string>) {
     const objectStoreTemplatesStore = useObjectStoreTemplatesStore();
     const objectStoreInstancesStore = useObjectStoreInstancesStore();
     objectStoreInstancesStore.fetchInstances();

diff --git a/client/src/components/ObjectStore/Instances/services.ts b/client/src/components/ObjectStore/Instances/services.ts
@@ -8,7 +8,7 @@ export const update = fetcher.path("/api/object_store_instances/{user_object_sto
 
 export async function hide(instance: UserConcreteObjectStore) {
     const payload = { hidden: true };
-    const args = { user_object_store_id: String(instance?.id) };
+    const args = { user_object_store_id: String(instance?.uuid) };
     const { data: objectStore } = await update({ ...args, ...payload });
     return objectStore;
 }
diff --git a/client/src/stores/fileSourceInstancesStore.ts b/client/src/stores/fileSourceInstancesStore.ts
@@ -22,7 +22,7 @@ export const useFileSourceInstancesStore = defineStore("fileSourceInstances", {
             return !state.fetched;
         },
         getInstance: (state) => {
-            return (id: number | string) => state.instances.find((i) => i.id.toString() == id.toString());
+            return (uuid: string) => state.instances.find((i) => i.uuid == uuid);
         },
     },
     actions: {

diff --git a/client/src/stores/objectStoreInstancesStore.test.ts b/client/src/stores/objectStoreInstancesStore.test.ts
@@ -4,6 +4,7 @@ import { useObjectStoreInstancesStore } from "@/stores/objectStoreInstancesStore
 import { setupTestPinia } from "./testUtils";
 
 const type = "aws_s3" as ObjectStoreTemplateType;
+const UUID = "112f889f-72d7-4619-a8e8-510a8c685aa7";
 const TEST_INSTANCE = {
     type: type,
     name: "moo",
@@ -15,8 +16,7 @@ const TEST_INSTANCE = {
     secrets: [],
     quota: { enabled: false },
     private: false,
-    id: 4,
-    uuid: "112f889f-72d7-4619-a8e8-510a8c685aa7",
+    uuid: UUID,
     active: true,
     hidden: false,
     purged: false,
@@ -45,13 +45,7 @@ describe("Object Store Instances Store", () => {
     it("should allow finding an instance by instance id", () => {
         const objectStoreInstancesStore = useObjectStoreInstancesStore();
         objectStoreInstancesStore.handleInit([TEST_INSTANCE]);
-        expect(objectStoreInstancesStore.getInstance(4)?.name).toBe("moo");
-    });
-
-    it("should allow finding an instance by instance id as string (for props)", () => {
-        const objectStoreInstancesStore = useObjectStoreInstancesStore();
-        objectStoreInstancesStore.handleInit([TEST_INSTANCE]);
-        expect(objectStoreInstancesStore.getInstance("4")?.name).toBe("moo");
+        expect(objectStoreInstancesStore.getInstance(UUID)?.name).toBe("moo");
     });
 
     it("should populate an error with handleError", () => {

diff --git a/client/src/stores/objectStoreInstancesStore.ts b/client/src/stores/objectStoreInstancesStore.ts
@@ -22,7 +22,7 @@ export const useObjectStoreInstancesStore = defineStore("objectStoreInstances",
             return !state.fetched;
         },
         getInstance: (state) => {
-            return (id: number | string) => state.instances.find((i) => i.id.toString() == id.toString());
+            return (uuid: string) => state.instances.find((i) => i.uuid == uuid);
         },
     },
     actions: {

diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
@@ -435,7 +435,6 @@ def _configure_object_store(self, **kwds):
             gid=self.config.gid,
             object_store_cache_size=self.config.object_store_cache_size,
             object_store_cache_path=self.config.object_store_cache_path,
-            user_config_templates_index_by=self.config.user_config_templates_index_by,
             user_config_templates_use_saved_configuration=self.config.user_config_templates_use_saved_configuration,
         )
         self._register_singleton(UserObjectStoresAppConfig, app_config)

diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
@@ -581,19 +581,6 @@ mapping:
         desc: |
           Configured user file source templates embedded into Galaxy's config.
 
-      user_config_templates_index_by:
-        type: str
-        default: 'uuid'
-        required: false
-        enum: ['uuid', 'id']
-        desc: |
-          Configure URIs for user object stores to use either the object ID ('id')
-          or UUIDs ('uuid'). Either is fine really, Galaxy doesn't typically expose
-          database objects by 'id' but there isn't any obvious disadvantage to doing
-          it in this case and it keeps user exposed URIs much smaller. The default of
-          UUID feels a little more like a typical way to do this within Galaxy though.
-          Do not change this value once user object stores have been created.
-
       user_config_templates_use_saved_configuration:
         type: str
         default: 'fallback'