Dev bilayers

.gitignore

@@ -4,4 +4,5 @@ node_modules
 omero_biomero/group_mappings.json
 /venv
 omero_biomero/_version.py
-file.db
+file.db
+/.idea

omero-init.sh

@@ -8,7 +8,7 @@ CONTAINER_NAME="nl-biomero-omeroweb-1"
 # COMMAND1="/usr/local/bin/entrypoint.sh"
 COMMAND0="chmod a+w /opt/omero/web/OMERO.web/var/static"
 
-COMMAND1="/opt/omero/web/venv3/bin/python -m pip install -e /opt/omero/web/OMERO.biomero"
+COMMAND1="/opt/omero/web/venv3/bin/python -m pip install --no-cache-dir -e /opt/omero/web/OMERO.biomero --force-reinstall --no-deps ; /opt/omero/web/venv3/bin/python -m pip install --no-cache-dir --force-reinstall 'biomero-schema @ git+https://github.com/BioImageTools/biomero-schema.git@dev-bilayers' 'biomero @ git+https://github.com/NL-BioImaging/biomero.git@dev-bilayers'"
 COMMAND2="/opt/omero/web/venv3/bin/omero-biomero-setup"
 
 COMMAND3="/opt/omero/web/venv3/bin/omero web stop || true; rm -f /opt/omero/web/OMERO.web/var/django.pid"

omero_biomero/static/omero_biomero/assets/asset-manifest.json

@@ -1,5 +1,5 @@
 {
-  "main.js": "/omero_biomero/assets/main.699499eae873f02794cc.js",
+  "main.js": "/omero_biomero/assets/main.bc363aff9500f001994b.js",
   "blueprint-icons-all-paths-loader.js": "/omero_biomero/assets/main.842384bb9fbdafbc9d23.js",
   "blueprint-icons-split-paths-by-size-loader.js": "/omero_biomero/assets/main.2402bf9c06063ed4b903.js",
   "blueprint-icons-all-paths.js": "/omero_biomero/assets/main.14619d69ed529fa1589a.js",

omero_biomero/tests/test_analyzer_views.py

@@ -31,7 +31,7 @@ def __enter__(self):
         def __exit__(self, exc_type, exc, tb):
             return False
 
-        def pull_descriptor_from_github(self, name):
+        def generic_descriptor_from_github(self, name):
             return self._metadata.get(name, {})
 
         @classmethod
@@ -164,7 +164,7 @@ def __enter__(self):
     # --- get_workflow_metadata ---
     def test_get_workflow_metadata_missing(self):
         view = _raw("get_workflow_metadata")
-        request = SimpleNamespace(method="GET")
+        request = SimpleNamespace(method="GET", GET={}, headers={})
         resp = view(request)
         self.assertEqual(resp.status_code, 400)
 
@@ -174,7 +174,7 @@ class StubSlurm(self._StubSlurmBase):
 
         with patch("omero_biomero.analyzer_views.SlurmClient", StubSlurm):
             view = _raw("get_workflow_metadata")
-            request = SimpleNamespace(method="GET")
+            request = SimpleNamespace(method="GET", GET={}, headers={})
             resp = view(request, name="wfA")
         self.assertEqual(resp.status_code, 404)
 
@@ -187,7 +187,7 @@ class StubSlurm(self._StubSlurmBase):
 
         with patch("omero_biomero.analyzer_views.SlurmClient", StubSlurm):
             view = _raw("get_workflow_metadata")
-            request = SimpleNamespace(method="GET")
+            request = SimpleNamespace(method="GET", GET={}, headers={})
             resp = view(request, name="wfA")
         self.assertEqual(resp.status_code, 200)
         data = json.loads(resp.content)

omero_biomero/urls.py

@@ -27,7 +27,7 @@
     # Analyzer API under /api/analyzer/
     path(
         "api/analyzer/workflows/",
-        analyzer_views.list_workflows,  # GET
+        analyzer_views.list_workflows,  # GET: returns {"workflows": [name, ...]}
         name="analyzer_workflows_list",
     ),
     path(
@@ -50,6 +50,16 @@
         analyzer_views.get_slurm_status,  # GET: SLURM cluster status
         name="analyzer_slurm_status",
     ),
+    path(
+        "api/analyzer/attachments/",
+        analyzer_views.get_attachments,  # GET: browse OMERO file annotations
+        name="analyzer_attachments",
+    ),
+    path(
+        "api/analyzer/object-annotations/",
+        analyzer_views.get_object_annotations,  # GET: file annotations for one OMERO object
+        name="analyzer_object_annotations",
+    ),
     # Main Biomero URL
     path(
         "biomero/",

setup.py

@@ -52,7 +52,7 @@ def read(fname):
     install_requires=[
         "omero-web>=5.31.0,<6",
         "pyjwt>=2.12.1,<3",
-        "biomero>=2.6,<3",
+        "biomero @ git+https://github.com/NL-BioImaging/biomero.git@dev-bilayers",
         "configupdater>=3.2,<4",
         "biomero-importer>=1.2.1,<2",
     ],

webapp/src/AppContext.js

@@ -37,7 +37,10 @@ const INFRA_PARAMS = new Set([
 
 const MAX_INPUT_IDS_SHOWN = 20;
 
-const WorkflowSubmitToast = ({ workflowName, startedAt, params }) => {
+// File-type param types (mirrors WorkflowFileInputStep)
+const FILE_INPUT_TYPES_SET = new Set(["file", "array", "measurement", "executable"]);
+
+const WorkflowSubmitToast = ({ workflowName, startedAt, params, metadata }) => {
   const [openSection, setOpenSection] = React.useState(null);
   const toggle = (key) => setOpenSection((prev) => (prev === key ? null : key));
 
@@ -54,9 +57,35 @@ const WorkflowSubmitToast = ({ workflowName, startedAt, params }) => {
   if (params.attachToOriginalImages) outputLines.push("Attached to input images");
   if (params.receiveEmail) outputLines.push("E-mail on completion");
 
-  const wfParams = Object.entries(params).filter(([k]) => !INFRA_PARAMS.has(k));
+  // Build lookup from descriptor so we can classify each param
+  const inputById = {};
+  (metadata?.inputs || []).forEach((inp) => { inputById[inp.id] = inp; });
+
+  // File attachment params (set-by-server + file type) → shown in Input section
+  const fileAttachmentEntries = Object.entries(params).filter(([k]) => {
+    const inp = inputById[k];
+    return inp && inp["set-by-server"] && FILE_INPUT_TYPES_SET.has(inp.type);
+  });
+
+  // True workflow params: not infra, not set-by-server, not output-dir-set.
+  // Falls back to old behaviour (show everything non-infra) when metadata is absent.
+  const wfParams = Object.entries(params).filter(([k]) => {
+    if (INFRA_PARAMS.has(k)) return false;
+    if (!metadata) return true;
+    const inp = inputById[k];
+    if (!inp) return false;            // not in descriptor — skip
+    if (inp["set-by-server"]) return false;  // handled elsewhere
+    if (inp["output-dir-set"]) return false; // internal dir — not user-facing
+    return true;
+  });
+
   const inputCount = params.IDs?.length || 0;
   const dataType = params.Data_Type || "Image";
+  // Count non-empty file attachment slots for the Input section label
+  const attachmentCount = fileAttachmentEntries.reduce((sum, [, v]) => {
+    const ids = Array.isArray(v) ? v.filter((x) => x != null && x !== "") : (v != null && v !== "" ? [v] : []);
+    return sum + ids.length;
+  }, 0);
   const batchInfo = params.batchEnabled
     ? `${params.batchCount} jobs × ${params.batchSize} ${dataType}s`
     : null;
@@ -87,15 +116,21 @@ const WorkflowSubmitToast = ({ workflowName, startedAt, params }) => {
         </SectionRow>
       )}
 
-      <SectionRow label={`Input: ${inputCount} ${dataType}${inputCount !== 1 ? "s" : ""}`} sectionKey="input">
+      <SectionRow label={`Input: ${inputCount} ${dataType}${inputCount !== 1 ? "s" : ""}${attachmentCount > 0 ? ` + ${attachmentCount} file${attachmentCount !== 1 ? "s" : ""}` : ""}`} sectionKey="input">
         {params.IDs?.slice(0, MAX_INPUT_IDS_SHOWN).map((id) => <div key={id}>• {dataType} #{id}</div>)}
         {inputCount > MAX_INPUT_IDS_SHOWN && <div className="opacity-60">…and {inputCount - MAX_INPUT_IDS_SHOWN} more</div>}
         {params.useZarrFormat && <div>• Format: ZARR</div>}
         {batchInfo && <div>• Batch: {batchInfo}</div>}
+        {fileAttachmentEntries.flatMap(([k, v]) => {
+          const ids = Array.isArray(v) ? v.filter((x) => x != null && x !== "") : (v != null && v !== "" ? [v] : []);
+          if (!ids.length) return [];
+          const label = inputById[k]?.name || k;
+          return ids.map((id) => <div key={`${k}-${id}`}>• {label}: Attachment #{id}</div>);
+        })}
       </SectionRow>
 
-      {wfParams.length > 0 && (
-        <SectionRow label={`Parameters (${wfParams.length})`} sectionKey="params">
+      {(wfParams.length > 0 || params.version) && (
+        <SectionRow label={`Parameters (${wfParams.length + (params.version ? 1 : 0)})`} sectionKey="params">
           {params.version && <div>• version: <strong>{params.version}</strong></div>}
           {wfParams.map(([k, v]) => (
             <div key={k}>• {k}: <strong>{String(v)}</strong></div>
@@ -215,7 +250,6 @@ export const AppProvider = ({ children }) => {
   }, []);
 
   const loadThumbnails = async (imageIds) => {
-    setLoading(true);
     setError(null);
 
     try {
@@ -236,8 +270,6 @@ export const AppProvider = ({ children }) => {
       }));
     } catch (err) {
       setError(err.message);
-    } finally {
-      setLoading(false);
     }
   };
 
@@ -279,6 +311,24 @@ export const AppProvider = ({ children }) => {
           if (images.length > 0) {
             allImages = [...allImages, ...imagesWithSource];
 
+            // Flush each page into state immediately so thumbnails can start loading
+            // for the first page while remaining pages are still in flight.
+            setState(prev => ({
+              ...prev,
+              omeroFileTreeData: {
+                ...prev.omeroFileTreeData,
+                [index]: {
+                  ...dataset,
+                  children: allImages,
+                },
+              },
+              images: [
+                ...new Map(
+                  [...(prev.images || []), ...allImages].map((img) => [img.id, img])
+                ).values(),
+              ],
+            }));
+
             // Check if we have fetched enough images
             if (allImages.length >= childCount) {
               keepFetching = false; // We fetched enough images
@@ -289,24 +339,6 @@ export const AppProvider = ({ children }) => {
             keepFetching = false; // No more images to fetch
           }
         }
-
-        // Store images in the parent structure in state.omeroFileTreeData
-        // Use functional setState to avoid race condition when loading multiple datasets concurrently
-        setState(prev => ({
-          ...prev,
-          omeroFileTreeData: {
-            ...prev.omeroFileTreeData,
-            [index]: {
-              ...dataset,
-              children: allImages,
-            },
-          },
-          images: [
-            ...new Map(
-              [...(prev.images || []), ...allImages].map((img) => [img.id, img])
-            ).values(),
-          ],
-        }));
       } else if (type === "plate") {
         const plateId = parseInt(id, 10);
         // Use our existing API service functions
@@ -368,7 +400,7 @@ export const AppProvider = ({ children }) => {
       toaster.show({
         intent: "success",
         icon: "tick-circle",
-        message: <WorkflowSubmitToast workflowName={workflowName} startedAt={startedAt} params={params} />,
+        message: <WorkflowSubmitToast workflowName={workflowName} startedAt={startedAt} params={params} metadata={state.selectedWorkflow?.metadata} />,
         timeout: 0,
       });
     } catch (err) {

webapp/src/apiService.js

@@ -103,11 +103,75 @@ export const fetchSlurmStatus = async () => {
   return apiRequest(urls.api_slurm_status, "GET");
 };
 
-// Fetch metadata for a specific workflow
-export const fetchWorkflowMetadata = async (workflow) => {
+/**
+ * Fetch OMERO file annotations (attachments) accessible to the current user.
+ * @param {string[]} formats - Optional list of file extensions to filter by (e.g. ["csv", "parquet"])
+ * @param {string}   search  - Optional substring to filter by filename
+ * @param {number}   groupId - Optional OMERO group ID to scope the query
+ * @returns {Promise<{attachments: Array}>}
+ */
+
+// Module-level cache so multiple OmeroAttachmentBrowser instances that render
+// at the same time (one per file-type param) share a single HTTP request.
+// Keyed by group ID, expires after 60 s.
+const _attachmentsCache = {}; // { [groupKey]: { ts, promise } }
+const ATTACHMENTS_TTL_MS = 60_000;
+
+export const fetchAttachments = (groupId = null) => {
+  const { urls, user } = getDjangoConstants();
+  const resolvedGroup = groupId !== null ? groupId : user.active_group_id;
+  const key = String(resolvedGroup);
+  const now = Date.now();
+  const cached = _attachmentsCache[key];
+  if (cached && now - cached.ts < ATTACHMENTS_TTL_MS) {
+    return cached.promise;
+  }
+  const promise = apiRequest(
+    `${urls.api_attachments}?group=${resolvedGroup}&_=${now}`,
+    "GET"
+  );
+  _attachmentsCache[key] = { ts: now, promise };
+  return promise;
+};
+
+/** Invalidate the attachment cache (call when user manually refreshes). */
+export const invalidateAttachmentsCache = (groupId = null) => {
+  if (groupId !== null) {
+    delete _attachmentsCache[String(groupId)];
+  } else {
+    Object.keys(_attachmentsCache).forEach((k) => delete _attachmentsCache[k]);
+  }
+};
+
+/**
+ * Fetch file annotations attached to a single OMERO object.
+ * Used by the By-Parent tree browser to lazily load attachments per node.
+ *
+ * @param {string} objectType - "Project" | "Dataset" | "Image" | "Plate" | "Screen"
+ * @param {number} objectId
+ * @returns {Promise<{annotations: Array}>}
+ */
+export const fetchObjectAnnotations = async (objectType, objectId) => {
   const { urls } = getDjangoConstants();
-  const workflowMetadataUrl = `${urls.workflows}${workflow}/`; // analyzer detail includes metadata
-  return apiRequest(workflowMetadataUrl, "GET");
+  return apiRequest(
+    `${urls.api_object_annotations}?object_type=${encodeURIComponent(objectType)}&object_id=${objectId}`,
+    "GET"
+  );
+};
+
+// Fetch metadata for a specific workflow, or descriptor info for an unsaved repo URL.
+// - fetchWorkflowMetadata(workflowName)  → GET /api/analyzer/workflows/<name>/
+// - fetchWorkflowMetadata(null, repoUrl) → GET /api/analyzer/workflows/_/?repo=<url>  (urls.workflow_metadata)
+//   Returns the full biomero-schema descriptor dict including 'requires-zarr',
+//   'requires-plate', and 'name' (tool name from descriptor).
+export const fetchWorkflowMetadata = async (workflow, repoUrl = null) => {
+  const { urls } = getDjangoConstants();
+  if (repoUrl) {
+    return apiRequest(
+      `${urls.workflow_metadata}?repo=${encodeURIComponent(repoUrl)}`, "GET"
+    );
+  }
+  return apiRequest(`${urls.workflows}${workflow}/`, "GET");
 };
 
 // GitHub URL is included in fetchWorkflowMetadata().githubUrl
@@ -412,26 +476,27 @@ export const extractGitHubInfo = (repoUrl) => {
   };
 };
 
-/**
- * Fetches the name field from a descriptor.json in a GitHub repository.
- * Uses raw.githubusercontent.com (no API rate limits).
- * @param {string} repoUrl - GitHub repository URL (e.g., https://github.com/owner/repo/tree/v1.0.0)
- * @returns {Promise<string|null>} The name field from descriptor.json, lowercased and slugified, or null
- */
-export const fetchDescriptorName = async (repoUrl) => {
-  const info = extractGitHubInfo(repoUrl);
-  if (!info?.owner || !info?.repo) return null;
+export const slugify = (name) => name.toLowerCase().replace(/[\s-]+/g, '_').replace(/[^a-z0-9_]/g, '');
+
+// In-memory cache for workflow metadata (session-scoped, keyed by repo URL).
+const _metadataCache = new Map();
 
-  const ref = info.currentVersion || 'main';
-  const rawUrl = `https://raw.githubusercontent.com/${info.owner}/${info.repo}/${ref}/descriptor.json`;
+export const fetchWorkflowMetadataCached = async (repoUrl) => {
+  if (_metadataCache.has(repoUrl)) return _metadataCache.get(repoUrl);
+  const result = await fetchWorkflowMetadata(null, repoUrl);
+  _metadataCache.set(repoUrl, result);
+  return result;
+};
 
+/**
+ * Fetches the container image reference via the backend (cached).
+ * Returns the full image string e.g. "cellularimagingcf/w_cellpose:v1.0.0", or null.
+ */
+export const fetchContainerImage = async (repoUrl) => {
+  if (!repoUrl) return null;
   try {
-    const response = await fetch(rawUrl);
-    if (!response.ok) return null;
-    const descriptor = await response.json();
-    if (!descriptor?.name) return null;
-    // Slugify: lowercase, spaces/hyphens → underscores, strip non-alphanumeric except _
-    return descriptor.name.toLowerCase().replace(/[\s-]+/g, '_').replace(/[^a-z0-9_]/g, '');
+    const metadata = await fetchWorkflowMetadataCached(repoUrl);
+    return metadata?.['container-image']?.image ?? null;
   } catch {
     return null;
   }

webapp/src/biomero/components/CollapsibleSection.js

@@ -1,7 +1,7 @@
 import React, { useState } from "react";
 import { Collapse, Button, H5, Icon, Tag, Tooltip } from "@blueprintjs/core";
 
-const CollapsibleSection = ({ title, children, versionSummary, versionCheckLoading, onRefresh }) => {
+const CollapsibleSection = ({ title, children, versionSummary, versionCheckLoading, onRefresh, errorCount }) => {
   const [isOpen, setIsOpen] = useState(false);
 
   return (
@@ -13,6 +13,14 @@ const CollapsibleSection = ({ title, children, versionSummary, versionCheckLoadi
             className="mr-2" 
           />
           <span>{title}</span>
+          {/* Validation error count tag — same style as version warning tags */}
+          {errorCount > 0 && (
+            <Tooltip content="Expand this section to see and fix the validation errors">
+              <Tag minimal intent="danger" className="ml-2">
+                {errorCount} validation error{errorCount !== 1 ? 's' : ''}
+              </Tag>
+            </Tooltip>
+          )}
           {/* Version summary for Models Settings */}
           {versionSummary && (
             <span className="ml-2 flex items-center">