feat: mount local DLS-filesystem mirror into dev backend for image serving

The backend image endpoints read atlas/grid-square files off disk using the
absolute /dls/... paths stored in the DB, but a DB dump has no files. Mount a
local mirror of Diamond's /dls filesystem into the dev API pod so those
endpoints resolve.

- smartem-workspace scaffolds testdata/dls-filesystem/ as the convention dir
  (a local mirror of /dls; populated by hand with imagery). Bump 0.6.1 -> 0.7.0.
- dev-k8s.sh ensure_image_mount patches smartem-http-api with a hostPath
  <workspace>/testdata/dls-filesystem -> /dls (readOnly), overridable via
  SMARTEM_DLS_FILESYSTEM_DIR, skipped when absent. hostPath must be absolute and
  kustomize can't template, so this mirrors the existing ensure_* post-apply
  patch pattern. API service only: the worker never reads image files from disk.

Author: vredchenko

packages/smartem-workspace/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "smartem-workspace"
-version = "0.6.1"
+version = "0.7.0"
 description = "CLI tool to automate SmartEM multi-repo workspace setup"
 readme = "README.md"
 license = "Apache-2.0"

packages/smartem-workspace/smartem_workspace/__init__.py

@@ -1,3 +1,3 @@
 """SmartEM workspace setup CLI tool."""
 
-__version__ = "0.6.1"
+__version__ = "0.7.0"

packages/smartem-workspace/smartem_workspace/setup/workspace.py

@@ -15,6 +15,9 @@ def setup_workspace_structure(workspace_path: Path) -> bool:
     - repos/
     - tmp/
     - testdata/
+    - testdata/dls-filesystem/  (local mirror of Diamond's /dls shared filesystem;
+      populated by hand with microscopy imagery and mounted into the dev backend
+      pod at /dls so image-serving endpoints can resolve DB /dls/... paths)
 
     Returns:
         True if successful
@@ -26,6 +29,8 @@ def setup_workspace_structure(workspace_path: Path) -> bool:
         "repos",
         "tmp",
         "testdata",
+        # Mirrors Diamond's /dls DFS root; mounted into the dev backend at /dls.
+        "testdata/dls-filesystem",
     ]
 
     for dir_name in directories:

scripts/k8s/dev-k8s.sh

@@ -419,6 +419,46 @@ ensure_local_image() {
     fi
 }
 
+# Mount the local DLS-filesystem mirror into the API pod so image-serving endpoints can
+# read atlas/grid-square files that the DB references by absolute /dls/... paths. hostPath
+# must be absolute and kustomize can't template, so (like the configmap/secret steps) we
+# patch the live deployment here. API service only: the worker never reads image files.
+# The mirror lives at <workspace>/testdata/dls-filesystem by convention; override with
+# SMARTEM_DLS_FILESYSTEM_DIR. Skipped silently when absent (images show placeholders).
+ensure_image_mount() {
+    local workspace_root dls_dir
+    workspace_root="$(cd "$PROJECT_ROOT/../../.." 2>/dev/null && pwd)"
+    dls_dir="${SMARTEM_DLS_FILESYSTEM_DIR:-$workspace_root/testdata/dls-filesystem}"
+
+    if [[ ! -d "$dls_dir" ]]; then
+        log_info "No DLS-filesystem mirror at $dls_dir - skipping image mount (atlas/grid-square images will show placeholders)"
+        return 0
+    fi
+
+    log_info "Mounting DLS-filesystem mirror into smartem-http-api: $dls_dir -> /dls"
+    if kubectl patch deployment smartem-http-api -n "$NAMESPACE" --type strategic --patch "$(cat <<PATCH
+spec:
+  template:
+    spec:
+      containers:
+        - name: smartem-http-api
+          volumeMounts:
+            - name: dls-filesystem
+              mountPath: /dls
+              readOnly: true
+      volumes:
+        - name: dls-filesystem
+          hostPath:
+            path: $dls_dir
+            type: Directory
+PATCH
+)" &> /dev/null; then
+        log_success "DLS-filesystem mount applied to smartem-http-api"
+    else
+        log_warning "Could not apply DLS-filesystem mount (non-fatal; images will show placeholders)"
+    fi
+}
+
 # Deploy the environment
 deploy_environment() {
     log_info "Deploying development environment..."
@@ -440,6 +480,9 @@ deploy_environment() {
     # Ensure local image is built and available for development
     ensure_local_image
 
+    # Mount the local DLS-filesystem mirror so the API can serve atlas/grid-square images
+    ensure_image_mount
+
     log_success "Deployment initiated"
 }