Merge branch 'release_25.1' into dev

Author: mvdbeek

client/src/components/User/Credentials/ServiceCredentialsGroupsList.vue

@@ -18,7 +18,7 @@
  * <ServiceCredentialsGroupsList :service-groups="groups" />
  */
 
-import { faKey, faPencilAlt, faTrash, faWrench } from "@fortawesome/free-solid-svg-icons";
+import { faExclamationTriangle, faKey, faPencilAlt, faTrash, faWrench } from "@fortawesome/free-solid-svg-icons";
 import { BModal } from "bootstrap-vue";
 import { faCheck } from "font-awesome-6";
 import { storeToRefs } from "pinia";
@@ -71,7 +71,7 @@ const props = defineProps<Props>();
 
 const { confirm } = useConfirmDialog();
 
-const { getToolNameById } = useToolStore();
+const { getToolForId, getToolNameById } = useToolStore();
 
 const userToolsServiceCredentialsStore = useUserToolsServiceCredentialsStore();
 const { userToolsServicesCurrentGroupIds } = storeToRefs(userToolsServiceCredentialsStore);
@@ -95,12 +95,25 @@ const cardTitle = computed(() => (group: ServiceCredentialsGroupDetails) => {
     return `${group.serviceDefinition.name} (v${group.serviceDefinition.version}) - ${group.name}`;
 });
 
+/**
+ * Checks if the source tool for a credential group is missing/deleted.
+ * @param {ServiceCredentialsGroupDetails} group - The credential group to check.
+ * @returns {boolean} True if the tool is no longer available.
+ */
+const isToolMissing = computed(() => (group: ServiceCredentialsGroupDetails) => {
+    return !getToolForId(group.sourceId);
+});
+
 /**
  * Checks if a credential group is currently in use by any tool.
  * @param {ServiceCredentialsGroupDetails} group - The credential group to check.
  * @returns {boolean} True if the group is in use.
  */
 const isGroupInUse = computed(() => (group: ServiceCredentialsGroupDetails) => {
+    if (isToolMissing.value(group)) {
+        return false;
+    }
+
     const userToolKey = userToolsServiceCredentialsStore.getUserToolKey(group.sourceId, group.sourceVersion);
     const userToolService = userToolsServicesCurrentGroupIds.value[userToolKey];
     for (const groupId of Object.values(userToolService || {})) {
@@ -111,6 +124,18 @@ const isGroupInUse = computed(() => (group: ServiceCredentialsGroupDetails) => {
     return false;
 });
 
+/**
+ * Gets the display name for a tool, with a fallback for missing/deleted tools.
+ * @param {ServiceCredentialsGroupDetails} group - The credential group.
+ * @returns {string} The tool name or a fallback indicator.
+ */
+const getToolDisplayName = computed(() => (group: ServiceCredentialsGroupDetails) => {
+    if (isToolMissing.value(group)) {
+        return `${group.sourceId} (deleted)`;
+    }
+    return getToolNameById(group.sourceId);
+});
+
 /**
  * Deletes a credential group after user confirmation.
  * @param {ServiceCredentialsGroupDetails} groupToDelete - The group to delete.
@@ -120,7 +145,9 @@ const isGroupInUse = computed(() => (group: ServiceCredentialsGroupDetails) => {
 async function deleteGroup(groupToDelete: ServiceCredentialsGroupDetails): Promise<void> {
     let message = `Are you sure you want to delete the credentials group "${groupToDelete.name}"?`;
 
-    if (isGroupInUse.value(groupToDelete)) {
+    if (isToolMissing.value(groupToDelete)) {
+        message = message.concat(` The associated tool is no longer available.`);
+    } else if (isGroupInUse.value(groupToDelete)) {
         message = message.concat(` This group is currently in use by '${getToolNameById(groupToDelete.sourceId)}'.`);
     }
 
@@ -221,23 +248,40 @@ async function onSaveChanges(): Promise<void> {
  * @returns {CardBadge[]} Array of badge configurations.
  */
 function getBadgesFor(group: ServiceCredentialsGroupDetails): CardBadge[] {
-    const badges: CardBadge[] = [
-        {
-            id: `tool-${group.sourceId}`,
-            icon: faWrench,
-            title: "This tool is using this credentials group. Click to view.",
-            label: getToolNameById(group.sourceId),
-            to: `/root?tool_id=${group.sourceId}&tool_version=${group.sourceVersion}`,
-        },
-        {
+    const toolMissing = isToolMissing.value(group);
+    const badges: CardBadge[] = [];
+
+    if (toolMissing) {
+        badges.push({
+            id: `tool-missing-${group.id}`,
+            icon: faExclamationTriangle,
+            title: "The tool associated with these credentials is no longer available. You cannot edit or use this group.",
+            label: "Tool Unavailable",
+            variant: "warning",
+        });
+    }
+
+    badges.push({
+        id: `tool-${group.sourceId}`,
+        icon: faWrench,
+        title: toolMissing
+            ? "This tool is no longer available."
+            : "This tool is using this credentials group. Click to view.",
+        label: getToolDisplayName.value(group),
+        to: toolMissing ? undefined : `/root?tool_id=${group.sourceId}&tool_version=${group.sourceVersion}`,
+    });
+
+    if (!toolMissing) {
+        badges.push({
             id: `in-use-${group.id}`,
             icon: faCheck,
             title: "This group is currently in use.",
             label: "In Use",
             variant: "success",
             visible: isGroupInUse.value(group),
-        },
-    ];
+        });
+    }
+
     return badges;
 }
 
@@ -247,6 +291,7 @@ function getBadgesFor(group: ServiceCredentialsGroupDetails): CardBadge[] {
  * @returns {CardAction[]} Array of action configurations
  */
 function getPrimaryActions(group: ServiceCredentialsGroupDetails): CardAction[] {
+    const toolMissing = isToolMissing.value(group);
     const primaryActions: CardAction[] = [
         {
             id: `delete-${group.id}`,
@@ -259,10 +304,11 @@ function getPrimaryActions(group: ServiceCredentialsGroupDetails): CardAction[]
         {
             id: `edit-${group.id}`,
             label: "Edit",
-            title: "Edit this group",
+            title: !toolMissing ? "Cannot edit - tool definition not available" : "Edit this group",
             icon: faPencilAlt,
             variant: "outline-info",
             handler: () => editGroup(group),
+            disabled: toolMissing,
         },
     ];
     return primaryActions;

lib/galaxy/config/sample/tool_conf.xml.sample

@@ -53,6 +53,7 @@
     <tool file="${model_tools_path}/build_list.xml" />
     <tool file="${model_tools_path}/build_list_1.2.0.xml" />
     <tool file="${model_tools_path}/sample_sheet_to_tabular.xml" />
+    <tool file="${model_tools_path}/convert_sample_sheet.xml" />
     <tool file="${model_tools_path}/extract_dataset.xml" />
     <tool file="${model_tools_path}/duplicate_file_to_collection.xml" />
   </section>

lib/galaxy/files/sources/_rdm.py

@@ -23,13 +23,13 @@
 
 
 class RDMFileSourceTemplateConfiguration(BaseFileSourceTemplateConfiguration):
-    token: Union[str, TemplateExpansion]
-    public_name: Union[str, TemplateExpansion]
+    token: Optional[Union[str, TemplateExpansion]] = None
+    public_name: Optional[Union[str, TemplateExpansion]] = None
 
 
 class RDMFileSourceConfiguration(BaseFileSourceConfiguration):
-    token: str
-    public_name: str
+    token: Optional[str] = None
+    public_name: Optional[str] = None
 
 
 class ContainerAndFileIdentifier(NamedTuple):
@@ -51,7 +51,7 @@ class RDMRepositoryInteractor:
     """
 
     def __init__(self, repository_url: str, plugin: "RDMFilesSource"):
-        self._repository_url = repository_url
+        self._repository_url = self._strip_last_slash(repository_url)
         self._plugin = plugin
 
     @property
@@ -138,6 +138,12 @@ def download_file_from_container(
         """
         raise NotImplementedError()
 
+    def _strip_last_slash(self, url: str) -> str:
+        """Utility method to strip the last slash from a URL if present."""
+        if url.endswith("/"):
+            return url[:-1]
+        return url
+
 
 class RDMFilesSource(BaseFilesSource[RDMFileSourceTemplateConfiguration, RDMFileSourceConfiguration]):
     """Base class for Research Data Management (RDM) file sources.

lib/galaxy/files/sources/dataverse.py

@@ -13,6 +13,7 @@
 
 from galaxy.exceptions import (
     AuthenticationRequired,
+    MessageException,
     ObjectNotFound,
 )
 from galaxy.files.models import (
@@ -105,6 +106,7 @@ def parse_path(self, source_path: str, container_id_only: bool = False) -> Conta
         - doi:10.70122/FK2/AVNCLL (persistent ID)
         - doi:10.70122/FK2/DIG2DG/AVNCLL (persistent ID)
         - doi:10.70122/FK2/DIG2DG/id:12345 (database ID)
+        - doi:10.5072/FK2/doi:10.70122/AVNCLL (persistent ID)
         - perma:BSC/3ST00L/id:9056 (database ID)
         """
         if not source_path.startswith("/"):
@@ -125,20 +127,54 @@ def parse_path(self, source_path: str, container_id_only: bool = False) -> Conta
                 f"Invalid source path: '{source_path}'. Expected format: '/<dataset_id>/<file_identifier>'."
             )
 
-        file_id_part = parts[-1]
-        dataset_id = "/".join(parts[:-1])
+        dataset_id, file_id_part = self._split_dataset_and_file_pid(parts)
 
         # The file identifier can be either:
         # - A persistent ID suffix (e.g., 'AVNCLL' -> full ID is 'doi:10.70122/FK2/DIG2DG/AVNCLL')
         # - A database ID with 'id:' prefix (e.g., 'id:12345' -> file_identifier is 'id:12345')
         if file_id_part.startswith("id:"):
             # Database ID format - keep the 'id:' prefix as the file identifier
             file_id = file_id_part
+        elif re.match(r"^[a-zA-Z][a-zA-Z0-9+.-]*:.*", file_id_part):
+            # Full persistent identifier (e.g. doi:, hdl:, ark:, or custom PID providers).
+            # Files in Dataverse may have their own independent persistent IDs that are
+            # not hierarchically related to the dataset persistent ID.
+            file_id = file_id_part
         else:
-            # Persistent ID format - construct full persistent ID
+            # Dataset-scoped persistent ID suffix - construct full persistent ID
             file_id = f"{dataset_id}/{file_id_part}"
         return ContainerAndFileIdentifier(container_id=dataset_id, file_identifier=file_id)
 
+    @staticmethod
+    def _split_dataset_and_file_pid(parts: list[str]) -> tuple[str, str]:
+        """
+        Split a Dataverse source path into dataset ID and file identifier parts.
+
+        Dataverse file-level persistent IDs may themselves contain slashes and are not
+        necessarily hierarchically related to the dataset persistent ID. For example:
+
+            /doi:10.57745/I8EUTL/doi:10.57745/L7SOAJ
+
+        In this case:
+            dataset_id = doi:10.57745/I8EUTL
+            file_id     = doi:10.57745/L7SOAJ
+
+        This helper detects such cases by recognizing URI-scheme prefixes in path segments
+        and grouping them accordingly.
+        """
+        # Default: last segment is the file identifier
+        file_id_part = parts[-1]
+        dataset_id = "/".join(parts[:-1])
+
+        # Heuristic: if the penultimate segment starts a URI scheme (e.g. doi:, hdl:, ark:),
+        # then the file persistent ID spans the last two segments.
+        pid_scheme_re = re.compile(r"^[a-zA-Z][a-zA-Z0-9+.-]*:")
+        if len(parts) >= 3 and pid_scheme_re.match(parts[-2]):
+            file_id_part = f"{parts[-2]}/{parts[-1]}"
+            dataset_id = "/".join(parts[:-2])
+
+        return dataset_id, file_id_part
+
     def get_container_id_from_path(self, source_path: str) -> str:
         return self.parse_path(source_path, container_id_only=True).container_id
 
@@ -336,14 +372,14 @@ def create_draft_file_container(
         collection_payload = self._prepare_collection_data(title, public_name, user_email)
         collection = self._create_collection(":root", collection_payload, context)
         if not collection or "data" not in collection or "alias" not in collection["data"]:
-            raise Exception("Could not create collection in Dataverse or response has an unexpected format.")
+            raise MessageException("Could not create collection in Dataverse or response has an unexpected format.")
         collection_alias = collection["data"]["alias"]
 
         # Prepare and create the dataset
         dataset_payload = self._prepare_dataset_data(title, public_name, user_email)
         dataset = self._create_dataset(collection_alias, dataset_payload, context)
         if not dataset or "data" not in dataset:
-            raise Exception("Could not create dataset in Dataverse or response has an unexpected format.")
+            raise MessageException("Could not create dataset in Dataverse or response has an unexpected format.")
 
         dataset["data"]["name"] = title
         return dataset["data"]
@@ -421,14 +457,18 @@ def _download_file(
                     f"Authentication required to download file from '{download_file_content_url}'. "
                     f"Please provide a valid API token in your user preferences."
                 )
-            # TODO: We can only download files from published datasets for now
-            if e.code in [403, 404]:
+            if e.code == 403:
+                # Permission denied: dataset may be unpublished or user lacks access rights
+                raise ObjectNotFound(
+                    f"Access forbidden when downloading file from '{download_file_content_url}'. "
+                    f"You may not have permission to access this file, or the dataset is not published."
+                )
+            if e.code == 404:
                 raise ObjectNotFound(
                     f"File not found at '{download_file_content_url}'. "
                     f"Please make sure the dataset and file exist and are published."
                 )
-            else:
-                raise
+            raise
 
     def _get_datasets_from_response(self, response: dict) -> list[RemoteDirectory]:
         rval: list[RemoteDirectory] = []
@@ -494,7 +534,7 @@ def _ensure_response_has_expected_status_code(self, response, expected_status_co
             error_message = self._get_response_error_message(response)
             if response.status_code == 403:
                 self._raise_auth_required(error_message)
-            raise Exception(
+            raise MessageException(
                 f"Request to {response.url} failed with status code {response.status_code}: {error_message}"
             )
 

lib/galaxy/model/dataset_collections/types/sample_sheet_workbook.py

@@ -618,5 +618,24 @@ def _list_to_sample_sheet_collection_type(input_collection_type: str) -> SampleS
         )
 
 
+def _sample_sheet_to_list_collection_type(input_collection_type: str) -> str:
+    """Convert sample_sheet collection types to corresponding list collection types.
+
+    Converts sample_sheet types to list types (e.g., sample_sheet:paired -> list:paired).
+    """
+    if input_collection_type == "sample_sheet":
+        return "list"
+    elif input_collection_type == "sample_sheet:paired":
+        return "list:paired"
+    elif input_collection_type == "sample_sheet:paired_or_unpaired":
+        return "list:paired_or_unpaired"
+    elif input_collection_type == "sample_sheet:record":
+        return "list:record"
+    else:
+        raise RequestParameterInvalidException(
+            f"Invalid collection type for sample sheet conversion: {input_collection_type}"
+        )
+
+
 def _prefix_column_to_column_target(column_header: FetchPrefixColumn) -> ColumnTarget:
     return target_model_by_type(column_header.type)