datamint 2.3.3__tar.gz → 2.3.5__tar.gz

{datamint-2.3.3 → datamint-2.3.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: datamint
-Version: 2.3.3
+Version: 2.3.5
 Summary: A library for interacting with the Datamint API, designed for efficient data management, processing and Deep Learning workflows.
 Requires-Python: >=3.10
 Classifier: Programming Language :: Python :: 3
@@ -22,7 +22,7 @@ Requires-Dist: humanize (>=4.0.0,<5.0.0)
 Requires-Dist: lazy-loader (>=0.3.0)
 Requires-Dist: lightning
 Requires-Dist: matplotlib
-Requires-Dist: medimgkit (>=0.7.2)
+Requires-Dist: medimgkit (>=0.7.3)
 Requires-Dist: nest-asyncio (>=1.0.0,<2.0.0)
 Requires-Dist: nibabel (>=4.0.0)
 Requires-Dist: numpy

{datamint-2.3.3 → datamint-2.3.5}/datamint/api/base_api.py

@@ -121,11 +121,12 @@ class BaseApi:
         url = endpoint.lstrip('/')  # Remove leading slash for httpx
 
         try:
-            curl_command = self._generate_curl_command({"method": method,
-                                                        "url": url,
-                                                        "headers": self.client.headers,
-                                                        **kwargs}, fail_silently=True)
-            logger.debug(f'Equivalent curl command: "{curl_command}"')
+            if logger.isEnabledFor(logging.DEBUG):
+                curl_command = self._generate_curl_command({"method": method,
+                                                            "url": url,
+                                                            "headers": self.client.headers,
+                                                            **kwargs}, fail_silently=True)
+                logger.debug(f'Equivalent curl command: "{curl_command}"')
             response = self.client.request(method, url, **kwargs)
             response.raise_for_status()
             return response

{datamint-2.3.3 → datamint-2.3.5}/datamint/api/endpoints/projects_api.py

@@ -1,8 +1,10 @@
-from typing import Sequence, Literal
+from typing import Sequence, Literal, TYPE_CHECKING
 from ..entity_base_api import ApiConfig, CRUDEntityApi
 from datamint.entities.project import Project
-from datamint.entities.resource import Resource
 import httpx
+from datamint.entities.resource import Resource
+if TYPE_CHECKING:
+    from .resources_api import ResourcesApi
 
 
 class ProjectsApi(CRUDEntityApi[Project]):
@@ -10,14 +12,17 @@ class ProjectsApi(CRUDEntityApi[Project]):
 
     def __init__(self,
                  config: ApiConfig,
-                 client: httpx.Client | None = None) -> None:
+                 client: httpx.Client | None = None,
+                 resources_api: 'ResourcesApi | None' = None) -> None:
         """Initialize the projects API handler.
 
         Args:
             config: API configuration containing base URL, API key, etc.
             client: Optional HTTP client instance. If None, a new one will be created.
         """
+        from .resources_api import ResourcesApi
         super().__init__(config, Project, 'projects', client)
+        self.resources_api = resources_api or ResourcesApi(config, client, projects_api=self)
 
     def get_project_resources(self, project: Project | str) -> list[Resource]:
         """Get resources associated with a specific project.
@@ -30,7 +35,7 @@ class ProjectsApi(CRUDEntityApi[Project]):
         """
         response = self._get_child_entities(project, 'resources')
         resources_data = response.json()
-        resources = [Resource(**item) for item in resources_data]
+        resources = [self.resources_api._init_entity_obj(**item) for item in resources_data]
         return resources
 
     def create(self,

{datamint-2.3.3 → datamint-2.3.5}/datamint/api/endpoints/resources_api.py

@@ -70,7 +70,7 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
         nest_asyncio.apply()
         self.annotations_api = AnnotationsApi(
             config, client, resources_api=self) if annotations_api is None else annotations_api
-        self.projects_api = ProjectsApi(config, client) if projects_api is None else projects_api
+        self.projects_api = projects_api or ProjectsApi(config, client, resources_api=self)
 
     def get_list(self,
                  status: Optional[ResourceStatus] = None,
@@ -263,8 +263,8 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
             filename = new_filename
 
         is_a_dicom_file = None
-        if mimetype is None:
-            mimetype_list, ext = guess_typez(file_path, use_magic=True)
+        if not mimetype:
+            mimetype_list, ext = guess_typez(file_path, use_magic=False)
             for mime in mimetype_list:
                 if mime in NIFTI_MIMES:
                     mimetype = DEFAULT_NIFTI_MIME
@@ -273,7 +273,12 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
                 if ext == '.nii.gz' or filename.lower().endswith('nii.gz'):
                     mimetype = DEFAULT_NIFTI_MIME
                 else:
-                    mimetype = mimetype_list[-1] if mimetype_list else DEFAULT_MIME_TYPE
+                    mimetype = mimetype_list[-1] if mimetype_list and mimetype_list[-1] else DEFAULT_MIME_TYPE
+        if (not mimetype) or mimetype == DEFAULT_MIME_TYPE:
+            msg = f"Could not determine mimetype for file {source_filepath}."
+            _LOGGER.warning(msg)
+            _USER_LOGGER.warning(msg)
+
 
         mimetype = standardize_mimetype(mimetype)
 
@@ -433,8 +438,14 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
                             )
                 return rid
 
-            tasks = [__upload_single_resource(f, segfiles, metadata_file)
-                     for f, segfiles, metadata_file in zip(files_path, segmentation_files, metadata_files)]
+            try:
+                tasks = [__upload_single_resource(f, segfiles, metadata_file)
+                        for f, segfiles, metadata_file in zip(files_path, segmentation_files, metadata_files)]
+            except ValueError:
+                msg = f"Error preparing upload tasks. Try `assemble_dicom=False`."
+                _LOGGER.error(msg)
+                _USER_LOGGER.error(msg)
+                raise 
             return await asyncio.gather(*tasks, return_exceptions=on_error == 'skip')
 
     def upload_resources(self,

{datamint-2.3.3 → datamint-2.3.5}/datamint/client_cmd_tools/datamint_upload.py

@@ -574,6 +574,8 @@ def _parse_args() -> tuple[Any, list[str], Optional[list[dict]], Optional[list[s
                         help='Automatically detect and include JSON metadata files with the same base name as NIFTI files')
     parser.add_argument('--no-auto-detect-json', dest='auto_detect_json', action='store_false',
                         help='Disable automatic detection of JSON metadata files (default behavior)')
+    parser.add_argument('--no-assemble-dicoms', dest='assemble_dicoms', action='store_false', default=True,
+                        help='Do not assemble DICOM files into series (default: assemble them)')
     parser.add_argument('--version', action='version', version=f'%(prog)s {datamint_version}')
     parser.add_argument('--verbose', action='store_true', help='Print debug messages', default=False)
     args = parser.parse_args()
@@ -797,7 +799,7 @@ def main():
                                                      publish_to=args.project,
                                                      segmentation_files=segfiles,
                                                      transpose_segmentation=args.transpose_segmentation,
-                                                     assemble_dicoms=True,
+                                                     assemble_dicoms=args.assemble_dicoms,
                                                      metadata=metadata_files,
                                                      progress_bar=True
                                                      )

{datamint-2.3.3 → datamint-2.3.5}/pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "datamint"
 description = "A library for interacting with the Datamint API, designed for efficient data management, processing and Deep Learning workflows."
-version = "2.3.3"
+version = "2.3.5"
 dynamic = ["dependencies"]
 requires-python = ">=3.10"
 readme = "README.md"
@@ -40,7 +40,7 @@ matplotlib = "*"
 lightning = "*"
 albumentations = ">=2.0.0"
 lazy-loader = ">=0.3.0"
-medimgkit = ">=0.7.2"
+medimgkit = ">=0.7.3"
 typing_extensions = ">=4.0.0"
 pydantic = ">=2.6.4"
 httpx = "*"