Fix apptainer workdir metadata

Author: willdunklin

setup.py

@@ -24,10 +24,9 @@ def prerelease_local_scheme(version):
 # perform the install
 setup(
     name='girder-slicer-cli-web',
-    # use_scm_version={
-    #    'local_scheme': prerelease_local_scheme,
-    #    'fallback_version': '0.0.0'},
-    version='1.5.5',
+    use_scm_version={
+       'local_scheme': prerelease_local_scheme,
+       'fallback_version': '0.0.0'},
     setup_requires=[
         'setuptools-scm',
     ],

slicer_cli_web/singularity/slicer_cli_web_singularity/commands.py

@@ -30,13 +30,13 @@ def singularity_pull(name: str, uri: str = 'docker'):
         return ['apptainer', 'pull', '--force', sif_name, f'{uri}://{name}']
 
     @staticmethod
-    def get_entry_path(imageName: str):
+    def get_work_dir(imageName: str):
         switch_to_sif_image_folder()
         sif_name = generate_image_name_for_singularity(imageName)
-        cmd = ['apptainer', 'exec', '--cleanenv', sif_name, 'cat', '/.singularity.d/labels.json']
+        cmd = ['apptainer', 'sif', 'dump', '3', sif_name]
         label_json = run_command(cmd)
         labels = json.loads(label_json)
-        return labels.get('entry_path')
+        return labels.get('WorkingDir')
 
     @staticmethod
     def singualrity_run(imageName: str, run_parameters=None, container_args=None):

slicer_cli_web/singularity/slicer_cli_web_singularity/girder_worker_plugin/direct_singularity_run.py

@@ -27,39 +27,28 @@ def __call__(self, *args, **kwargs):
         super().__call__(*args, **kwargs)
 
 
-def check_local_sif_image(image):
-    """
-    Pulls the specified Plugin image (Ususally a docker image) onto the singularity container
-    if the image is not present
-    """
-    # Image path - Image path has to be present in tmp/images folder
-    if not image:
-        logger.write('Image name cannot be empty')
-        return False
-    # Just for testing. Change it later...
-    return False
-
-
 @app.task(base=DirectSingularityTask, bind=True)
 def run(task, **kwargs):
     """Wraps singularity_run to support running singularity containers"""
     image = kwargs['image']
     kwargs['image'] = generate_image_name_for_singularity(image)
-    try:
-        pwd = SingularityCommands.get_entry_path(image)
-        kwargs['pwd'] = pwd
-    except Exception as e:
-        raise e
+
+    pwd = SingularityCommands.get_work_dir(image)
+    kwargs['pwd'] = pwd
+
     logs_dir = os.getenv('LOGS')
     kwargs['nvidia'] = _is_nvidia_img(image)
+
     # Cahnge to reflect JOBID for logs later
     random_file_name = str(uuid4()) + 'logs.log'
     log_file_name = os.path.join(logs_dir, random_file_name)
     kwargs['log_file'] = log_file_name
+
     # Create file since it doesn't exist
     if not os.path.exists(log_file_name):
         with open(log_file_name, 'x'):
             pass
+
     file_obj = open(log_file_name, 'rb')
     if hasattr(task, 'job_manager'):
         stream_connectors = kwargs.setdefault('stream_connectors', [])

slicer_cli_web/singularity/slicer_cli_web_singularity/job.py

@@ -204,7 +204,7 @@ def get_local_singularity_output(imgName, cmdArg: str):
     function
     """
     try:
-        cwd = SingularityCommands.get_entry_path(imgName)
+        cwd = SingularityCommands.get_work_dir(imgName)
         if not cwd:
             logger.exception('Please set the entry_path env variable on the Docker Image')
             raise Exception('Please set the entry_path env variable on the Docker Image')