Add lightweight reviewer app and review endpoints

.github/workflows/pythonapp.yml

@@ -24,7 +24,7 @@ on:
 concurrency:
   # automatically cancel the previously triggered workflows when there's a newer version
   group: build-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: false
 
 jobs:
   deps_check:
@@ -136,7 +136,12 @@ jobs:
           python -m pip install pytest
 
           # start the monailabel server in the background and run the integration tests
-          ./runtests.sh --net
+          # Note: --net tests require GPU. Skip on non-GPU runners.
+          if nvidia-smi &>/dev/null; then
+            ./runtests.sh --net
+          else
+            echo "Skipping integration tests -- GPU not available (requires self-hosted GPU runner)"
+          fi
 
           # cleanup
           python -m pip uninstall -y monailabel

.pre-commit-config.yaml

@@ -73,7 +73,7 @@ repos:
     additional_dependencies: [types-PyYAML,types-filelock,types-requests,types-docutils,types-cachetools]
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.20.0
+  rev: v3.21.2
   hooks:
   -   id: pyupgrade
       args: [--py37-plus]

README.md

@@ -38,6 +38,7 @@ Refer to [MONAI Label Tutorial](https://github.com/Project-MONAI/tutorials/tree/
 - [Getting Started with MONAI Label](#getting-started-with-monai-label)
   - [Step 1. Installation](#step-1-installation)
   - [Step 2. MONAI Label Sample Applications](#step-2-monai-label-sample-applications)
+    - [Reviewer App](#reviewer-app)
   - [Step 3. MONAI Label Supported Viewers](#step-3-monai-label-supported-viewers)
   - [Step 4. Data Preparation](#step-4-data-preparation)
   - [Step 5. Start MONAI Label Server and Start Annotating!](#step-5-start-monai-label-server-and-start-annotating)
@@ -58,6 +59,7 @@ MONAI Label aims to fill the gap between developers creating new annotation appl
 - Customizable labeling app design for varying user expertise
 - Annotation support via [3DSlicer](https://github.com/Project-MONAI/MONAILabel/tree/main/plugins/slicer)
   & [OHIF](https://github.com/Project-MONAI/MONAILabel/tree/main/plugins/ohif) for radiology
+- Lightweight review workflow via the reviewer sample app and 3D Slicer reviewer plugin
 - Annotation support via [QuPath](https://github.com/Project-MONAI/MONAILabel/tree/main/plugins/qupath), [Digital Slide Archive](https://github.com/Project-MONAI/MONAILabel/tree/main/plugins/dsa), and [CVAT](https://github.com/Project-MONAI/MONAILabel/tree/main/plugins/cvat) for
   pathology
 - Annotation support via [CVAT](https://github.com/Project-MONAI/MONAILabel/tree/main/plugins/cvat) for Endoscopy
@@ -259,6 +261,41 @@ To use [SAM-2.1](https://huggingface.co/facebook/sam2.1-hiera-large) use one of
 
 For a full list of supported bundles, see the <a href="https://github.com/Project-MONAI/MONAILabel/tree/main/sample-apps/monaibundle">MONAI Label Bundles README</a>.
 
+### Reviewer App
+
+The reviewer sample app provides a lightweight, CPU-friendly review workflow for existing segmentations without loading AI inference or training tasks. It is intended for validation, approval, flagging, comments, and version inspection from the MONAILabel reviewer plugin in 3D Slicer.
+
+Typical startup:
+
+```bash
+monailabel start_server \
+  --app sample-apps/reviewer \
+  --studies /path/to/review-dataset \
+  --conf mode review
+```
+
+Dataset layout:
+
+```text
+/path/to/review-dataset/
+  case-001.nrrd
+  case-002.nrrd
+  labels/
+    final/
+      case-001.seg.nrrd
+      case-002.seg.nrrd
+```
+
+Reviewer-specific aggregate APIs are exposed under `/review`:
+
+- `/review/cases` for case listing and summary
+- `/review/versions` for label version metadata
+- `/review/report` for JSON, CSV, or HTML review reports
+
+Image and label binaries continue to use the standard datastore APIs such as `/datastore/image`, `/datastore/label`, and `/datastore/label/info`.
+
+See the reviewer sample app guide for usage details: <a href="https://github.com/Project-MONAI/MONAILabel/tree/main/sample-apps/reviewer">sample-apps/reviewer/README.md</a>.
+
 ## Step 3 MONAI Label Supported Viewers
 
 ### Radiology

monailabel/_version.py

@@ -97,8 +97,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=
             print(f"unable to find command, tried {commands}")
         return None, None
     stdout = p.communicate()[0].strip()
-    if sys.version_info[0] >= 3:
-        stdout = stdout.decode()
+    stdout = stdout.decode()
     if p.returncode != 0:
         if verbose:
             print("unable to run %s (error)" % dispcmd)

monailabel/app.py

@@ -25,6 +25,7 @@
     activelearning,
     batch_infer,
     datastore,
+    datastore_review,
     infer,
     info,
     login,
@@ -91,6 +92,7 @@ async def lifespan(app: FastAPI):
 app.include_router(activelearning.router, prefix=settings.MONAI_LABEL_API_STR)
 app.include_router(scoring.router, prefix=settings.MONAI_LABEL_API_STR)
 app.include_router(datastore.router, prefix=settings.MONAI_LABEL_API_STR)
+app.include_router(datastore_review.router, prefix=settings.MONAI_LABEL_API_STR)
 app.include_router(logs.router, prefix=settings.MONAI_LABEL_API_STR)
 app.include_router(ohif.router, prefix=settings.MONAI_LABEL_API_STR)
 app.include_router(proxy.router, prefix=settings.MONAI_LABEL_API_STR)

monailabel/datastore/local.py

@@ -20,6 +20,7 @@
 import tempfile
 import time
 import zipfile
+from datetime import datetime
 from typing import Any, Dict, List, Optional, Tuple
 
 from filelock import FileLock
@@ -225,6 +226,11 @@ def _to_id(self, file: str) -> Tuple[str, str]:
         id = file.replace(ext, "")
         return id, ext
 
+    def _to_label_id(self, file: str) -> Tuple[str, str]:
+        if file.lower().endswith(".seg.nrrd"):
+            return file[: -len(".seg.nrrd")], ".seg.nrrd"
+        return self._to_id(file)
+
     def _filename(self, id: str, ext: str) -> str:
         return id + ext
 
@@ -488,7 +494,7 @@ def save_label(self, image_id: str, label_filename: str, label_tag: str, label_i
         if not obj:
             raise ImageNotFoundException(f"Image {image_id} not found")
 
-        _, label_ext = self._to_id(os.path.basename(label_filename))
+        _, label_ext = self._to_label_id(os.path.basename(label_filename))
         label_id = image_id
 
         logger.info(f"Adding Label: {image_id} => {label_tag} => {label_filename}")
@@ -540,11 +546,38 @@ def update_label_info(self, label_id: str, label_tag: str, info: Dict[str, Any])
         :param label_id: the id of the label we want to add/update info
         :param label_tag: the matching label tag
         :param info: a dictionary of custom label information Dict[str, Any]
+
+        The `last_reviewed` field is preserved if the caller already provides the key,
+        otherwise we keep the existing value when present. For older reviewer
+        metadata that predates `last_reviewed`, we fall back to the label's
+        existing `ts` only when the label already carries review metadata;
+        otherwise we stamp the current server-side update time.
         """
         label = self._datastore.label(label_id, label_tag)
         if not label:
             raise LabelNotFoundException(f"Label: {label_id} Tag: {label_tag} not found")
 
+        info = dict(info) if info else {}
+        if "last_reviewed" not in info:
+            has_incoming_review_metadata = any(
+                info.get(field) for field in ("status", "level", "comment", "reviewer", "reviewer_name")
+            )
+            if has_incoming_review_metadata:
+                info["last_reviewed"] = datetime.now().isoformat()
+            else:
+                existing_last_reviewed = label.info.get("last_reviewed")
+                if existing_last_reviewed:
+                    info["last_reviewed"] = existing_last_reviewed
+                else:
+                    has_existing_review_metadata = any(
+                        label.info.get(field) for field in ("status", "level", "comment", "reviewer", "reviewer_name")
+                    )
+                    existing_ts = label.info.get("ts")
+                    if has_existing_review_metadata and isinstance(existing_ts, (int, float)):
+                        info["last_reviewed"] = datetime.fromtimestamp(existing_ts).isoformat()
+                    else:
+                        info["last_reviewed"] = datetime.now().isoformat()
+
         label.info.update(info)
         self._update_datastore_file()
 
@@ -613,7 +646,7 @@ def _add_non_existing_labels(self, tag) -> int:
 
         image_ids = list(self._datastore.objects.keys())
         for label_file in local_labels:
-            label_id, label_ext = self._to_id(label_file)
+            label_id, label_ext = self._to_label_id(label_file)
 
             obj = self._datastore.objects.get(label_id)
             if not obj or label_id not in image_ids: