Merge branch 'release_24.1' into dev

client/src/components/DatasetInformation/DatasetDetails.vue

@@ -33,7 +33,6 @@ const userStore = useUserStore();
 const { currentUser } = storeToRefs(userStore);
 
 const loading = ref(false);
-const jobLoading = ref(true);
 const jobTimeOut = ref<any>(null);
 const jobDetails = ref<JobDetails>();
 const dataset = ref<HDADetailed | null>(null);
@@ -57,8 +56,6 @@ async function getDatasetDetails() {
 }
 
 async function loadJobDetails() {
-    jobLoading.value = true;
-
     try {
         const { data } = await fetchJobDetails({ job_id: dataset.value?.creating_job as string, full: true });
 
@@ -73,8 +70,6 @@ async function loadJobDetails() {
         const error = e as AxiosError<{ err_msg?: string }>;
 
         jobLoadingError.value = error.response?.data?.err_msg || "Unable to fetch available dataset details.";
-    } finally {
-        jobLoading.value = false;
     }
 }
 
@@ -102,7 +97,7 @@ onUnmounted(() => {
             {{ datasetLoadingError }}
         </BAlert>
         <div v-else-if="dataset">
-            <div v-if="dataset.creating_job && !jobLoading" class="details">
+            <div v-if="dataset.creating_job" class="details">
                 <DatasetInformation :dataset="dataset" />
 
                 <JobParameters dataset_type="hda" :dataset-id="datasetId" />
@@ -124,7 +119,7 @@ onUnmounted(() => {
 
                 <JobDestinationParams v-if="currentUser?.is_admin" :job-id="dataset.creating_job" />
 
-                <JobDependencies v-if="jobDetails.dependencies" :dependencies="jobDetails.dependencies" />
+                <JobDependencies v-if="jobDetails?.dependencies" :dependencies="jobDetails.dependencies" />
 
                 <div v-if="dataset.peek">
                     <h2 class="h-md">Dataset Peek</h2>

client/src/components/FilesDialog/FilesDialog.vue

@@ -272,7 +272,11 @@ function load(record?: SelectionItem) {
         }
 
         if (shouldUseItemsProvider()) {
-            itemsProvider.value = provideItems;
+            itemsProvider.value = (ctx) => provideItems(ctx, currentDirectory.value?.url);
+            optionsShow.value = true;
+            showTime.value = true;
+            showDetails.value = false;
+            return;
         }
 
         browseRemoteFiles(currentDirectory.value?.url, false, props.requireWritable)
@@ -295,31 +299,27 @@ function load(record?: SelectionItem) {
  * If it does, we will use the items provider to fetch items.
  */
 function shouldUseItemsProvider(): boolean {
-    const fileSource = filesSources.getFileSourceById(currentDirectory.value?.id!);
+    if (!currentDirectory.value) {
+        return false;
+    }
+    const fileSource = filesSources.getFileSourceByUri(currentDirectory.value.url);
     const supportsPagination = fileSource?.supports?.pagination;
     return Boolean(supportsPagination);
 }
 
 /**
  *  Fetches items from the server using server-side pagination and filtering.
  **/
-async function provideItems(ctx: ItemsProviderContext): Promise<SelectionItem[]> {
+async function provideItems(ctx: ItemsProviderContext, url?: string): Promise<SelectionItem[]> {
     isBusy.value = true;
     try {
-        if (!currentDirectory.value) {
+        if (!url) {
             return [];
         }
         const limit = ctx.perPage;
         const offset = (ctx.currentPage - 1) * ctx.perPage;
         const query = ctx.filter;
-        const response = await browseRemoteFiles(
-            currentDirectory.value?.url,
-            false,
-            props.requireWritable,
-            limit,
-            offset,
-            query
-        );
+        const response = await browseRemoteFiles(url, false, props.requireWritable, limit, offset, query);
         const result = response.entries.map(entryToRecord);
         totalItems.value = response.totalMatches;
         items.value = result;

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

@@ -98,7 +98,7 @@
                             @onUpgrade="onUpgrade" />
                     </div>
                 </div>
-                <div ref="right-panel" class="unified-panel-body workflow-right p-2">
+                <div ref="rightPanelElement" class="unified-panel-body workflow-right p-2">
                     <div v-if="!initialLoading">
                         <FormTool
                             v-if="hasActiveNodeTool"
@@ -184,7 +184,7 @@ import { useMagicKeys, whenever } from "@vueuse/core";
 import { logicAnd, logicNot, logicOr } from "@vueuse/math";
 import { Toast } from "composables/toast";
 import { storeToRefs } from "pinia";
-import Vue, { computed, nextTick, onUnmounted, ref, unref } from "vue";
+import Vue, { computed, nextTick, onUnmounted, ref, unref, watch } from "vue";
 
 import { getUntypedWorkflowParameters } from "@/components/Workflow/Editor/modules/parameters";
 import { ConfirmDialog } from "@/composables/confirmDialog";
@@ -366,6 +366,22 @@ export default {
             setTagsHandler.set(tags.value, newTags);
         }
 
+        watch(
+            () => stateStore.activeNodeId,
+            () => {
+                scrollToTop();
+            }
+        );
+
+        const rightPanelElement = ref(null);
+
+        function scrollToTop() {
+            rightPanelElement.value?.scrollTo({
+                top: 0,
+                behavior: "instant",
+            });
+        }
+
         const { comments } = storeToRefs(commentStore);
         const { getStepIndex, steps } = storeToRefs(stepStore);
         const { activeNodeId } = storeToRefs(stateStore);
@@ -427,6 +443,8 @@ export default {
             setAnnotation,
             tags,
             setTags,
+            rightPanelElement,
+            scrollToTop,
             connectionStore,
             hasChanges,
             hasInvalidConnections,
@@ -914,9 +932,6 @@ export default {
                 this.setCreator(creator);
             }
         },
-        onActiveNode(nodeId) {
-            this.$refs["right-panel"].scrollTop = 0;
-        },
         onInsertedStateMessages(insertedStateMessages) {
             this.insertedStateMessages = insertedStateMessages;
             this.hideModal();

lib/galaxy/config/sample/object_store_conf.sample.yml

@@ -223,9 +223,9 @@ auth:
   # an access token suitable for data access (allowing calls to the Oneprovider REST API).
   access_token: ...
 connection:
-  # the domain of the Onezone service (e.g. "demo.onedata.org"), or its IP address for
+  # the domain of the Onezone service (e.g. datahub.egi.eu), or its IP address for
   # devel instances (see above).
-  onezone_domain: demo.onedata.org
+  onezone_domain: datahub.egi.eu
   # Allows connection to Onedata servers that do not present trusted SSL certificates. 
   # SHOULD NOT be used unless you really know what you are doing.
   disable_tls_certificate_validation: false

lib/galaxy/config/sample/object_store_conf.xml.sample

@@ -165,7 +165,7 @@
         an access token suitable for data access (allowing calls to the Oneprovider REST API).
 
     //connection/@onezone_domain -
-        the domain of the Onezone service (e.g. "demo.onedata.org"), or its IP address for
+        the domain of the Onezone service (e.g. datahub.egi.eu), or its IP address for
         devel instances (see above).
 
     //connection/@disable_tls_certificate_validation - 
@@ -182,7 +182,7 @@
 <!--
 <object_store type="onedata">
     <auth access_token="..." />
-    <connection onezone_domain="demo.onedata.org" disable_tls_certificate_validation="False"/>
+    <connection onezone_domain="datahub.egi.eu" disable_tls_certificate_validation="False"/>
     <space name="demo-space" path="galaxy-data" />
     <cache path="database/object_store_cache" size="1000" cache_updated_data="True" />
     <extra_dir type="job_work" path="database/job_working_directory_onedata"/>

lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample

@@ -141,7 +141,7 @@ preferences:
         description: Your Onedata account
         inputs:
             - name: onezone_domain
-              label: Domain of the Onezone service (e.g. "demo.onedata.org")
+              label: Domain of the Onezone service (e.g. datahub.egi.eu)
               type: text
               required: False
             - name: access_token

lib/galaxy/dependencies/conditional-requirements.txt

@@ -24,7 +24,7 @@ fs.googledrivefs # type: googledrive
 fs-gcsfs # type: googlecloudstorage
 # fs-gcsfs doesn't pin google-cloud-storage, and old versions log noisy exceptions and break test discovery
 google-cloud-storage>=2.8.0  # type: googlecloudstorage
-fs.onedatarestfs # type: onedata, depends on onedatafilerestclient
+fs.onedatarestfs==21.2.5.1 # type: onedata, depends on onedatafilerestclient
 fs-basespace # type: basespace
 fs-azureblob # type: azure
 

lib/galaxy/dependencies/dev-requirements.txt

@@ -79,7 +79,7 @@ myst-parser==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
 nh3==0.2.17 ; python_version >= "3.8" and python_version < "3.13"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
 numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
-onedatafilerestclient==21.2.5rc1 ; python_version >= "3.8" and python_version < "3.13"
+onedatafilerestclient==21.2.5.1 ; python_version >= "3.8" and python_version < "3.13"
 outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13"
 packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
 pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"

lib/galaxy/files/sources/_pyfilesystem2.py

@@ -85,22 +85,7 @@ def _list(
             raise MessageException(f"Problem listing file source path {path}. Reason: {e}") from e
 
     def _get_total_matches_count(self, fs: FS, path: str, filter: Optional[List[str]] = None) -> int:
-        # For some reason, using "*" as glob does not return all files and directories, only files.
-        # So we need to count files and directories "*/" separately.
-        # Also, some filesystems do not properly support directories count (like Google Cloud Storage),
-        # so we need to catch TypeError exceptions and fallback to 0.
-        files_glob_pattern = f"{path}/{filter[0] if filter else '*'}"
-        try:
-            files_count = fs.glob(files_glob_pattern).count().files
-        except TypeError:
-            files_count = 0
-
-        directory_glob_pattern = f"{files_glob_pattern}/"
-        try:
-            directories_count = fs.glob(directory_glob_pattern).count().directories
-        except TypeError:
-            directories_count = 0
-        return files_count + directories_count
+        return sum(1 for _ in fs.filterdir(path, namespaces=["basic"], files=filter, dirs=filter))
 
     def _to_page(self, limit: Optional[int] = None, offset: Optional[int] = None) -> Optional[Tuple[int, int]]:
         if limit is None and offset is None: