Merge branch 'release_25.1' into dev

client/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxyproject/galaxy-client",
-  "version": "24.0.0",
+  "version": "25.0.4",
   "description": "Galaxy client application build system",
   "keywords": [
     "galaxy"

client/src/api/client/index.ts

@@ -1,5 +1,6 @@
 import createClient from "openapi-fetch";
 
+import { createRateLimiterMiddleware } from "@/api/client/rateLimiter";
 import type { GalaxyApiPaths } from "@/api/schema";
 import { getAppRoot } from "@/onload/loadConfig";
 
@@ -9,7 +10,19 @@ function getBaseUrl() {
 }
 
 function apiClientFactory() {
-    return createClient<GalaxyApiPaths>({ baseUrl: getBaseUrl() });
+    const client = createClient<GalaxyApiPaths>({ baseUrl: getBaseUrl() });
+
+    // TODO: Adjust based on server limits (maybe this goes in Galaxy config?)
+    client.use(
+        createRateLimiterMiddleware({
+            maxRequests: 100,
+            windowMs: 3000,
+            retryDelay: 1000,
+            maxRetries: 3,
+        }),
+    );
+
+    return client;
 }
 
 export type GalaxyApiClient = ReturnType<typeof apiClientFactory>;

client/src/api/client/rateLimiter.test.ts

@@ -0,0 +1,139 @@
+import type { MessageException } from "@/api";
+import { GalaxyApi } from "@/api/client";
+import { useServerMock } from "@/api/client/__mocks__";
+
+import { DEFAULT_CONFIG } from "./rateLimiter";
+
+const { server, http } = useServerMock();
+
+/** Spy to count number of times a 429 response is returned */
+const mock429ResponseSpy = jest.fn();
+
+describe("Rate Limiter Middleware", () => {
+    let consoleWarnSpy: jest.SpyInstance;
+    let consoleErrorSpy: jest.SpyInstance;
+
+    /** Helper to verify that there is a 429 response without retries */
+    function ensure429AndNoRetries(response: Response, error: MessageException | undefined) {
+        // Verify the request failed as expected
+        expect(response.status).toBe(429);
+        expect(error).toBeDefined();
+        expect(error?.err_code).toBe(429);
+
+        // Verify no retry behavior occurred by confirming console warns/errors were not called
+        expect(consoleWarnSpy).not.toHaveBeenCalled();
+        expect(consoleErrorSpy).not.toHaveBeenCalled();
+
+        // Verify the mock 429 response was called only once (no retries)
+        expect(mock429ResponseSpy).toHaveBeenCalledTimes(1);
+    }
+
+    beforeEach(() => {
+        consoleWarnSpy = jest.spyOn(console, "warn").mockImplementation();
+        consoleErrorSpy = jest.spyOn(console, "error").mockImplementation();
+    });
+    afterEach(() => {
+        consoleWarnSpy.mockRestore();
+        consoleErrorSpy.mockRestore();
+        mock429ResponseSpy.mockReset();
+    });
+
+    it("should retry 429 GET responses", async () => {
+        // Set up a mock GET endpoint that always returns 429
+        server.use(
+            http.get("/api/histories/{history_id}", ({ response }) => {
+                mock429ResponseSpy();
+                return response("4XX").json({ err_code: 429, err_msg: "Too Many Requests" }, { status: 429 });
+            }),
+        );
+
+        const { error, response } = await GalaxyApi().GET("/api/histories/{history_id}", {
+            params: {
+                path: { history_id: "test" },
+            },
+        });
+
+        // Verify the request failed as expected
+        expect(response.status).toBe(429);
+        expect(error).toBeDefined();
+        expect(error?.err_code).toBe(429);
+
+        // Verify retry behavior occurred by confirming console warns/errors
+        expect(consoleWarnSpy).toHaveBeenCalledWith(
+            expect.stringContaining(`Received 429 from server, waiting ${DEFAULT_CONFIG.retryDelay}ms before retry`),
+        );
+
+        for (let i = 1; i <= DEFAULT_CONFIG.maxRetries; i++) {
+            expect(consoleWarnSpy).toHaveBeenCalledWith(expect.stringContaining(`Retry ${i} also received 429`));
+        }
+
+        expect(consoleErrorSpy).toHaveBeenCalledWith(
+            expect.stringContaining(`Max retries reached for request to ${response.url}`),
+        );
+
+        // Verify the mock 429 response was called the first time and then for each retry
+        expect(mock429ResponseSpy).toHaveBeenCalledTimes(DEFAULT_CONFIG.maxRetries + 1);
+    });
+
+    it("should not retry 429 POST responses", async () => {
+        // Set up a mock POST endpoint that always returns 429
+        server.use(
+            http.post("/api/chat", ({ response }) => {
+                mock429ResponseSpy();
+                return response("4XX").json({ err_code: 429, err_msg: "Too Many Requests" }, { status: 429 });
+            }),
+        );
+
+        const { error, response } = await GalaxyApi().POST("/api/chat", {
+            params: {
+                query: { job_id: "test" },
+            },
+            body: {
+                query: "test message",
+                context: "test",
+            },
+        });
+
+        ensure429AndNoRetries(response, error);
+    });
+
+    it("should not retry 429 DELETE responses", async () => {
+        // Set up a mock DELETE endpoint that always returns 429
+        server.use(
+            http.delete("/api/datasets/{dataset_id}", ({ response }) => {
+                mock429ResponseSpy();
+                return response("4XX").json({ err_code: 429, err_msg: "Too Many Requests" }, { status: 429 });
+            }),
+        );
+
+        const { error, response } = await GalaxyApi().DELETE("/api/datasets/{dataset_id}", {
+            params: {
+                path: { dataset_id: "test_id" },
+                query: { purge: true },
+            },
+        });
+
+        ensure429AndNoRetries(response, error);
+    });
+
+    it("should not retry 429 PUT responses", async () => {
+        // Set up a mock PUT endpoint that always returns 429
+        server.use(
+            http.put("/api/datasets/{dataset_id}", ({ response }) => {
+                mock429ResponseSpy();
+                return response("4XX").json({ err_code: 429, err_msg: "Too Many Requests" }, { status: 429 });
+            }),
+        );
+
+        const { error, response } = await GalaxyApi().PUT("/api/datasets/{dataset_id}", {
+            params: {
+                path: { dataset_id: "test_id" },
+            },
+            body: {
+                deleted: false,
+            },
+        });
+
+        ensure429AndNoRetries(response, error);
+    });
+});

client/src/api/client/rateLimiter.ts

@@ -0,0 +1,94 @@
+import type { Middleware } from "openapi-fetch";
+
+interface RateLimitConfig {
+    /** Maximum requests per window */
+    maxRequests?: number;
+    /** Time the requestwindow lasts in milliseconds */
+    windowMs?: number;
+    /** Delay between retries on 429 */
+    retryDelay?: number;
+    /** Maximum retry attempts */
+    maxRetries?: number;
+}
+
+export const DEFAULT_CONFIG: Required<RateLimitConfig> = {
+    maxRequests: 100,
+    windowMs: 60000,
+    retryDelay: 1000,
+    maxRetries: 3,
+};
+
+/**
+ * Rate limiting middleware to control the rate of API requests.
+ *
+ * Uses a timed window and only allows a maximum number of requests per that window.
+ */
+export function createRateLimiterMiddleware(config: RateLimitConfig = {}): Middleware {
+    const cfg = { ...DEFAULT_CONFIG, ...config };
+
+    let requestCount = 0;
+    let windowStart = Date.now();
+
+    /** Resets the request window if the time has elapsed */
+    function resetWindowIfNeeded() {
+        const now = Date.now();
+        if (now - windowStart >= cfg.windowMs) {
+            requestCount = 0;
+            windowStart = now;
+        }
+    }
+
+    /** Places a request in the rate limiter queue */
+    async function placeRequestInQueue(): Promise<void> {
+        resetWindowIfNeeded();
+
+        if (requestCount < cfg.maxRequests) {
+            requestCount++;
+            return;
+        }
+
+        // Rate limit exceeded, wait for next window
+        const waitTime = cfg.windowMs - (Date.now() - windowStart);
+
+        await new Promise((resolve) => setTimeout(resolve, waitTime));
+
+        // After waiting, try again (this will reset the window)
+        return placeRequestInQueue();
+    }
+
+    const middleware: Middleware = {
+        async onRequest({ request }) {
+            await placeRequestInQueue();
+            return request;
+        },
+
+        async onResponse({ response: res, request }) {
+            // Handle 429 Too Many Requests from server
+            if (res.status === 429 && request.method === "GET") {
+                const retryAfter = res.headers.get("Retry-After");
+                const delay = retryAfter ? parseInt(retryAfter) * 1000 : cfg.retryDelay;
+
+                console.warn(`Received 429 from server, waiting ${delay}ms before retry`);
+
+                let retries = 0;
+                while (retries < cfg.maxRetries) {
+                    retries++;
+                    await new Promise((resolve) => setTimeout(resolve, delay));
+
+                    // A tricky thing here is that we will bypass the middleware chain on retry
+                    const retryResponse = await fetch(request);
+                    if (retryResponse.status !== 429) {
+                        return retryResponse;
+                    }
+                    console.warn(`Retry ${retries} also received 429, retrying...`);
+                }
+
+                console.error(`Max retries reached for request to ${request.url}`);
+            }
+
+            return res;
+        },
+    };
+
+    return middleware;
+}

client/src/components/Workflow/Invocation/InvocationScrollList.vue

@@ -1,4 +1,5 @@
 <script setup lang="ts">
+import { faClock } from "@fortawesome/free-regular-svg-icons";
 import { faHdd, faSitemap } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { storeToRefs } from "pinia";
@@ -123,7 +124,9 @@ function getInvocationBadges(invocation: WorkflowInvocation) {
                 :title-icon="{ icon: faSitemap }"
                 :title-n-lines="2"
                 title-size="text"
-                :update-time="invocation.update_time"
+                :update-time="invocation.create_time"
+                update-time-title="Invoked"
+                :update-time-icon="faClock"
                 @title-click="workflowName(invocation.workflow_id)"
                 @click="() => cardClicked(invocation)">
                 <template v-slot:description>

client/src/components/Workflow/WorkflowAnnotation.test.ts

@@ -93,7 +93,7 @@ async function mountWorkflowAnnotation(version: "run_form" | "invocation", ownsW
         propsData: {
             workflowId: ownsWorkflow ? SAMPLE_WORKFLOW.id : OTHER_USER_WORKFLOW_ID,
             historyId: TEST_HISTORY_ID,
-            invocationUpdateTime: version === "invocation" ? INVOCATION_TIME : undefined,
+            invocationCreateTime: version === "invocation" ? INVOCATION_TIME : undefined,
             showDetails: version === "run_form",
         },
         localVue,
@@ -165,7 +165,7 @@ describe("WorkflowAnnotation renders", () => {
         const { wrapper } = await mountWorkflowAnnotation("invocation");
 
         const timeInfo = wrapper.find(SELECTORS.TIME_INFO);
-        expect(timeInfo.text()).toContain("updated");
+        expect(timeInfo.text()).toContain("invoked");
         expect(timeInfo.find(SELECTORS.DATE).attributes("title")).toBe(INVOCATION_TIME);
     });
 });

client/src/components/Workflow/WorkflowAnnotation.vue

@@ -17,14 +17,14 @@ import WorkflowIndicators from "@/components/Workflow/List/WorkflowIndicators.vu
 
 interface Props {
     workflowId: string;
-    invocationUpdateTime?: string;
+    invocationCreateTime?: string;
     historyId: string;
     showDetails?: boolean;
     hideHr?: boolean;
 }
 
 const props = withDefaults(defineProps<Props>(), {
-    invocationUpdateTime: undefined,
+    invocationCreateTime: undefined,
 });
 
 const { workflow, owned } = useWorkflowInstance(props.workflowId);
@@ -34,7 +34,7 @@ const description = computed(() => {
 });
 
 const timeElapsed = computed(() => {
-    return props.invocationUpdateTime || workflow.value?.update_time;
+    return props.invocationCreateTime || workflow.value?.update_time;
 });
 
 const workflowTags = computed(() => {
@@ -49,11 +49,11 @@ const workflowTags = computed(() => {
                 <i v-if="timeElapsed" data-description="workflow annotation time info">
                     <FontAwesomeIcon :icon="faClock" class="mr-1" />
                     <span v-localize>
-                        {{ props.invocationUpdateTime ? "updated" : "edited" }}
+                        {{ props.invocationCreateTime ? "invoked" : "edited" }}
                     </span>
                     <UtcDate :date="timeElapsed" mode="elapsed" data-description="workflow annotation date" />
                 </i>
-                <span v-if="invocationUpdateTime" class="d-flex flex-gapx-1 align-items-center">
+                <span v-if="invocationCreateTime" class="d-flex flex-gapx-1 align-items-center">
                     <FontAwesomeIcon :icon="faHdd" />History:
 
                     <span class="history-link-wrapper">

client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue

@@ -304,7 +304,7 @@ async function onCancel() {
         <WorkflowAnnotation
             v-if="props.isFullPage"
             :workflow-id="invocation.workflow_id"
-            :invocation-update-time="invocation.update_time"
+            :invocation-create-time="invocation.create_time"
             :history-id="invocation.history_id">
             <template v-slot:middle-content>
                 <div class="progress-bars mx-1">

client/visualizations.yml

@@ -44,7 +44,7 @@ hyphyvision:
     version: 0.0.3
 igv:
     package: "@galaxyproject/igv"
-    version: 0.0.21
+    version: 0.0.23
 jupyterlite:
     package: "@galaxyproject/jupyterlite"
     version: 0.0.17

lib/galaxy/tool_util/deps/mulled/get_tests.py

@@ -108,13 +108,6 @@ def get_anaconda_url(container, anaconda_channel="bioconda"):
     return f"https://anaconda.org/{anaconda_channel}/{name[0]}/{name[1]}/download/linux-64/{'-'.join(name)}.tar.bz2"
 
 
-def prepend_anaconda_url(url):
-    """
-    Take a partial url and prepend 'https://anaconda.org'
-    """
-    return f"https://anaconda.org{url}"
-
-
 def get_test_from_anaconda(url: str) -> Optional[Dict[str, Any]]:
     """
     Given the URL of an anaconda tarball, return tests
@@ -132,20 +125,26 @@ def get_test_from_anaconda(url: str) -> Optional[Dict[str, Any]]:
     return None
 
 
-def find_anaconda_versions(name, anaconda_channel="bioconda"):
+def find_anaconda_download_url(
+    name: str, version: str, build: Optional[str] = None, anaconda_channel: str = "bioconda"
+) -> Optional[str]:
     """
-    Find a list of available anaconda versions for a given container name
+    Find the anaconda download url for a given package.
     """
     r = requests.get(
-        f"https://anaconda.org/{anaconda_channel}/{name}/files",
+        f"https://api.anaconda.org/package/{anaconda_channel}/{name}/files",
         timeout=MULLED_SOCKET_TIMEOUT,
     )
     r.raise_for_status()
-    urls = []
-    for line in r.text.splitlines():
-        if "download/linux" in line:
-            urls.append(line.split('"')[1])
-    return urls
+    package_files = r.json()
+    for package_file in reversed(package_files):
+        if (
+            package_file["version"] == version
+            and (build is None or package_file["attrs"]["build"] == build)
+            and package_file["attrs"]["subdir"] in ["linux-64", "noarch"]
+        ):
+            return f"https:{package_file['download_url']}"
+    return None
 
 
 def open_recipe_file(file, recipes_path=None, github_repo="bioconda/bioconda-recipes"):
@@ -211,50 +210,55 @@ def deep_test_search(
     """
     Look in bioconda-recipes repo as well as anaconda for the tests, checking in multiple possible locations. If no test is found for the specified version, search if other package versions have a test available.
     """
-    name = split_container_name(container)
+    name_tuple = split_container_name(container)
+    assert len(name_tuple) in (2, 3)
+    name = name_tuple[0]
+    version = name_tuple[1]
+    build = name_tuple[2] if len(name_tuple) == 3 else None
     for f in [
         (
             get_commands_from_yaml,
             open_recipe_file,
-            (f"recipes/{name[0]}/{name[1]}/meta.yaml", recipes_path, github_repo),
+            (f"recipes/{name}/{version}/meta.yaml", recipes_path, github_repo),
             container,
         ),
         (
             get_run_test,
             open_recipe_file,
-            (f"recipes/{name[0]}/{name[1]}/run_test.sh", recipes_path, github_repo),
+            (f"recipes/{name}/{version}/run_test.sh", recipes_path, github_repo),
             container,
         ),
         (
             get_commands_from_yaml,
             open_recipe_file,
-            (f"recipes/{name[0]}/meta.yaml", recipes_path, github_repo),
+            (f"recipes/{name}/meta.yaml", recipes_path, github_repo),
             container,
         ),
-        (get_run_test, open_recipe_file, (f"recipes/{name[0]}/run_test.sh", recipes_path, github_repo), container),
+        (get_run_test, open_recipe_file, (f"recipes/{name}/run_test.sh", recipes_path, github_repo), container),
         (get_test_from_anaconda, get_anaconda_url, (container, anaconda_channel), container),
     ]:
         result = try_a_func(*f)
         if result:
             return result
 
-    versions = get_alternative_versions(f"recipes/{name[0]}", "meta.yaml", recipes_path, github_repo)
-    for version in versions:
-        result = try_a_func(get_commands_from_yaml, open_recipe_file, (version, recipes_path, github_repo), container)
+    alt_versions = get_alternative_versions(f"recipes/{name}", "meta.yaml", recipes_path, github_repo)
+    for alt_version in alt_versions:
+        result = try_a_func(
+            get_commands_from_yaml, open_recipe_file, (alt_version, recipes_path, github_repo), container
+        )
         if result:
             return result
 
-    versions = get_alternative_versions(f"recipes/{name[0]}", "run_test.sh", recipes_path, github_repo)
-    for version in versions:
-        result = try_a_func(get_run_test, open_recipe_file, (version, recipes_path, github_repo), container)
+    alt_versions = get_alternative_versions(f"recipes/{name}", "run_test.sh", recipes_path, github_repo)
+    for alt_version in alt_versions:
+        result = try_a_func(get_run_test, open_recipe_file, (alt_version, recipes_path, github_repo), container)
         if result:
             return result
 
-    versions = find_anaconda_versions(name[0], anaconda_channel)
-    for version in versions:
-        result = try_a_func(get_test_from_anaconda, prepend_anaconda_url, (version,), container)
-        if result:
-            return result
+    url = find_anaconda_download_url(name, version, build=build, anaconda_channel=anaconda_channel)
+    result = try_a_func(get_test_from_anaconda, lambda x: x, (url,), container)
+    if result:
+        return result
 
     # if everything fails
     return {"container": container}

package.json

@@ -17,7 +17,7 @@
   },
   "homepage": "https://github.com/galaxyproject/galaxy#readme",
   "dependencies": {
-    "@galaxyproject/galaxy-client": "^24.0.0",
+    "@galaxyproject/galaxy-client": "^25.0.4",
     "cpy-cli": "^5.0.0"
   },
   "packageManager": "yarn@1.22.22+sha512.a6b2f7906b721bba3d67d4aff083df04dad64c399707841b7acf00f6b133b7ac24255f2652fa22ae3534329dc6180534e98d17432037ff6fd140556e2bb3137e"

test/unit/tool_util/mulled/test_get_tests.py

@@ -2,7 +2,7 @@ from unittest import SkipTest
 
 from galaxy.tool_util.deps.mulled.get_tests import (
     deep_test_search,
-    find_anaconda_versions,
+    find_anaconda_download_url,
     get_alternative_versions,
     get_anaconda_url,
     get_commands_from_yaml,
@@ -11,7 +11,6 @@ from galaxy.tool_util.deps.mulled.get_tests import (
     hashed_test_search,
     main_test_search,
     open_recipe_file,
-    prepend_anaconda_url,
 )
 from galaxy.util import smart_str
 from ..util import external_dependency_management
@@ -49,11 +48,6 @@ def test_get_anaconda_url():
     assert url == "https://anaconda.org/bioconda/samtools/1.7/download/linux-64/samtools-1.7-1.tar.bz2"
 
 
-def test_prepend_anaconda_url():
-    url = prepend_anaconda_url("/bioconda/samtools/0.1.12/download/linux-64/samtools-0.1.12-2.tar.bz2")
-    assert url == "https://anaconda.org/bioconda/samtools/0.1.12/download/linux-64/samtools-0.1.12-2.tar.bz2"
-
-
 @external_dependency_management
 def test_get_test_from_anaconda():
     # test old fashion tar.bz2 package
@@ -81,9 +75,20 @@ def test_get_test_from_anaconda():
 
 
 @external_dependency_management
-def test_find_anaconda_versions():
-    versions = find_anaconda_versions("2pg_cartesian")
-    assert "/bioconda/2pg_cartesian/1.0.1/download/linux-64/2pg_cartesian-1.0.1-0.tar.bz2" in versions
+def test_find_anaconda_download_url():
+    download_url = find_anaconda_download_url("2pg_cartesian", "1.0.0")
+    assert download_url is None
+    download_url = find_anaconda_download_url("2pg_cartesian", "1.0.1")
+    assert download_url is not None
+    assert download_url.startswith(
+        "https://api.anaconda.org/download/bioconda/2pg_cartesian/1.0.1/linux-64/2pg_cartesian-1.0.1-"
+    )
+    download_url = find_anaconda_download_url("2pg_cartesian", "1.0.1", "0")
+    assert download_url is not None
+    assert (
+        download_url
+        == "https://api.anaconda.org/download/bioconda/2pg_cartesian/1.0.1/linux-64/2pg_cartesian-1.0.1-0.tar.bz2"
+    )
 
 
 @external_dependency_management