Merge branch 'release_24.1' into dev

.github/codeql/codeql-config.yml

@@ -0,0 +1,2 @@
+paths-ignore:
+  - 'lib/galaxy/datatypes/test/*.bcsl.ts'

.github/labeler.yml

@@ -1,73 +1,129 @@
 ---
 area/admin:
-  - client/src/components/admin/**/*
-  - doc/source/admin/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - client/src/components/admin/**/*
+      - doc/source/admin/**/*
 area/API:
-  - lib/galaxy/webapps/galaxy/api/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/webapps/galaxy/api/**/*
 area/auth:
-  - lib/galaxy/auth/**/*
-  - lib/galaxy/authnz/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/auth/**/*
+      - lib/galaxy/authnz/**/*
 area/client:
-  - client/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - client/*
 area/database:
-  - lib/galaxy/model/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/model/**/*
 area/datatypes:
-  - lib/galaxy/datatypes/**/*
-  - lib/galaxy/config/sample/datatypes_conf.xml.sample
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/datatypes/**/*
+      - lib/galaxy/config/sample/datatypes_conf.xml.sample
 area/dependencies:
-  - lib/galaxy/dependencies/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/dependencies/**/*
 area/documentation:
-  - doc/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - doc/**/*
 area/jobs:
-  - lib/galaxy/jobs/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/jobs/**/*
 area/libraries:
-  - client/src/components/LibraryFolder/**/*
-  - lib/galaxy/webapps/galaxy/api/libraries.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - client/src/components/LibraryFolder/**/*
+      - lib/galaxy/webapps/galaxy/api/libraries.py
 area/objectstore:
-  - lib/galaxy/objectstore/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/objectstore/**/*
 area/packaging:
-  - packages/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - packages/**/*
 area/reports:
-  - client/src/reports/**/*
-  - lib/galaxy/webapps/reports/**/*
-  - templates/webapps/reports/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - client/src/reports/**/*
+      - lib/galaxy/webapps/reports/**/*
+      - templates/webapps/reports/**/*
 area/scripts:
-  - scripts/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - scripts/**/*
 area/security:
-  - lib/galaxy/security/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/security/**/*
 area/testing:
-  - lib/galaxy_test/**/*
-  - run_tests.sh
-  - test/**/*
-  - test-data/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy_test/**/*
+      - run_tests.sh
+      - test/**/*
+      - test-data/**/*
 area/testing/api:
-  - lib/galaxy_test/api/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy_test/api/**/*
 area/testing/integration:
-  - test/integration/**/*
-  - test/integration_selenium/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - test/integration/**/*
+      - test/integration_selenium/**/*
 area/testing/selenium:
-  - lib/galaxy/selenium/**/*
-  - lib/galaxy_test/selenium/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/selenium/**/*
+      - lib/galaxy_test/selenium/**/*
 area/tool-dependencies:
-  - lib/galaxy/tool_util/deps/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/tool_util/deps/**/*
 area/tool-framework:
-  - lib/galaxy/tools/**/*
-  - lib/galaxy/tool_util/**/*
-  - lib/galaxy/webapps/galaxy/api/tools.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/tools/**/*
+      - lib/galaxy/tool_util/**/*
+      - lib/galaxy/webapps/galaxy/api/tools.py
 area/tools:
-  - tools/**/*
-  - tool-data/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - tools/**/*
+      - tool-data/**/*
 area/toolshed:
-  - client/src/toolshed/**/*
-  - lib/galaxy/webapps/galaxy/api/toolshed.py
-  - lib/toolshed/**/*
-  - templates/webapps/tool_shed/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - client/src/toolshed/**/*
+      - lib/galaxy/webapps/galaxy/api/toolshed.py
+      - lib/toolshed/**/*
+      - templates/webapps/tool_shed/**/*
 area/UI-UX:
-  - all: ["client/src/**/*", "!client/src/api/schema/schema.ts"]
-    any: ["templates/**/*"]
+  - changed-files:
+    - any-glob-to-any-file:
+      - client/src/**/*
+      - templates/**/*
+    - all-globs-to-all-files:
+      - '!client/src/api/schema/schema.ts'
 area/util:
-  - lib/galaxy/util/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/util/**/*
 area/visualizations:
-  - config/plugins/visualizations/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - config/plugins/visualizations/**/*
 area/workflows:
-  - lib/galaxy/workflow/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/workflow/**/*

.github/workflows/codeql-analysis.yml

@@ -54,6 +54,9 @@ jobs:
           # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
           # queries: security-extended,security-and-quality
 
+          config-file: ./.github/codeql/codeql-config.yml
+
+
       # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
       # If this step fails, then you should remove it and run the build manually (see below)
       - name: Autobuild

client/openapi_to_schema.mjs

@@ -7,11 +7,15 @@ const inputFilePath = process.argv[2];
 const localPath = new URL(inputFilePath, import.meta.url);
 openapiTS(localPath, {
     transform(schemaObject, metadata) {
-        if (
-            "const" in schemaObject &&
-            (typeof schemaObject.const === "string" || schemaObject.const instanceof String)
-        ) {
-            return `"${schemaObject.const}"`;
+        if ("const" in schemaObject) {
+            const constType = typeof schemaObject.const;
+            switch (constType) {
+                case "number":
+                case "boolean":
+                    return `${schemaObject.const}`;
+                default:
+                    return `"${schemaObject.const}"`;
+            }
         }
     },
 }).then((output) => console.log(output));

client/src/api/index.ts

@@ -94,6 +94,11 @@ export type HDADetailed = components["schemas"]["HDADetailed"];
  */
 export type HistoryItemSummary = HDASummary | HDCASummary;
 
+/**
+ * Represents a HistoryDatasetAssociation that is inaccessible to the user.
+ */
+export type HDAInaccessible = components["schemas"]["HDAInaccessible"];
+
 /**
  * Contains storage (object store, quota, etc..) details for a dataset.
  */
@@ -102,7 +107,7 @@ export type DatasetStorageDetails = components["schemas"]["DatasetStorageDetails
 /**
  * Represents a HistoryDatasetAssociation with either summary or detailed information.
  */
-export type DatasetEntry = HDASummary | HDADetailed;
+export type DatasetEntry = HDASummary | HDADetailed | HDAInaccessible;
 
 /**
  * Contains summary information about a DCE (DatasetCollectionElement).
@@ -188,6 +193,10 @@ export function hasDetails(entry: DatasetEntry): entry is HDADetailed {
     return "peek" in entry;
 }
 
+export function isInaccessible(entry: DatasetEntry): entry is HDAInaccessible {
+    return "accessible" in entry && !entry.accessible;
+}
+
 /**
  * Contains dataset metadata information.
  */

client/src/api/remoteFiles.ts

@@ -46,16 +46,42 @@ export async function fetchFileSources(options: FilterFileSourcesOptions = {}):
 
 export const remoteFilesFetcher = fetcher.path("/api/remote_files").method("get").create();
 
+export interface BrowseRemoteFilesResult {
+    entries: RemoteEntry[];
+    totalMatches: number;
+}
+
 /**
  * Get the list of files and directories from the server for the given file source URI.
  * @param uri The file source URI to browse.
  * @param isRecursive Whether to recursively retrieve all files inside subdirectories.
  * @param writeable Whether to return only entries that can be written to.
+ * @param limit The maximum number of entries to return.
+ * @param offset The number of entries to skip before returning the rest.
+ * @param query The query string to filter the entries.
+ * @param sortBy The field to sort the entries by.
  * @returns The list of files and directories from the server for the given URI.
  */
-export async function browseRemoteFiles(uri: string, isRecursive = false, writeable = false): Promise<RemoteEntry[]> {
-    const { data } = await remoteFilesFetcher({ target: uri, recursive: isRecursive, writeable });
-    return data as RemoteEntry[];
+export async function browseRemoteFiles(
+    uri: string,
+    isRecursive = false,
+    writeable = false,
+    limit?: number,
+    offset?: number,
+    query?: string,
+    sortBy?: string
+): Promise<BrowseRemoteFilesResult> {
+    const { data, headers } = await remoteFilesFetcher({
+        target: uri,
+        recursive: isRecursive,
+        writeable,
+        limit,
+        offset,
+        query,
+        sort_by: sortBy,
+    });
+    const totalMatches = parseInt(headers.get("total_matches") ?? "0");
+    return { entries: data as RemoteEntry[], totalMatches };
 }
 
 const createEntry = fetcher.path("/api/remote_files").method("post").create();