datamint 2.3.3__py3-none-any.whl → 2.3.5__py3-none-any.whl

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/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/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/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.dist-info → datamint-2.3.5.dist-info}/METADATA

@@ -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.dist-info → datamint-2.3.5.dist-info}/RECORD

@@ -1,6 +1,6 @@
 datamint/__init__.py,sha256=ucsnxrYClh6pdy7psRJXWam_9rjAQB4NXzvy7xLovmo,824
 datamint/api/__init__.py,sha256=7QYkmDBXbKh8-zchV7k6Lpolaw6h-IK6ezfXROIWh2A,43
-datamint/api/base_api.py,sha256=UmNEgcFt1czkqyVCM3t5P9UvA1F9AEZITPqdakojvJs,18810
+datamint/api/base_api.py,sha256=RUtiTMy0h6LV-nXKfRdQ9FDJzwLf6k2RCCMytacB2AU,18881
 datamint/api/client.py,sha256=ndKSj2QnveRNOtaQhE9qM4tCGtgrTxfInDy9FhdReCo,3922
 datamint/api/dto/__init__.py,sha256=fUi901Zs-q5XHyWwZ4dMi2fEO8-CUEVEdYbpd17lahc,416
 datamint/api/endpoints/__init__.py,sha256=wi4liAb5-wOohwyzKUD6TxHGeZmUPaZerFUGa2IUju4,529
@@ -9,8 +9,8 @@ datamint/api/endpoints/annotationsets_api.py,sha256=NIsPIjGGptiUBxHft-EhOMRG-DsQ
 datamint/api/endpoints/channels_api.py,sha256=oQqxSw9DJzAqtVQI7-tc1llTdnsm-URx8jwtXNXnhio,867
 datamint/api/endpoints/datasetsinfo_api.py,sha256=WdzrUzK63w9gvAP6U--P65FbD-3X-jm9TPCcYnRNjas,597
 datamint/api/endpoints/models_api.py,sha256=tbVuajc-mCsIp5AKSCoq3uQRDWgKnJaIA6tf_ck8-XY,1502
-datamint/api/endpoints/projects_api.py,sha256=C5IqKXaYRrg5LDBjIRSo4NBCvbN2619X3SSgKqGe8pc,7929
-datamint/api/endpoints/resources_api.py,sha256=Ez-mGYElCpwHZ8T8NlqXH188mCFBZGfs8b320xa43tc,50142
+datamint/api/endpoints/projects_api.py,sha256=Pfr3fEiMw_aRzoGtcVXHJQ68leVoPAghw23L4ZIglno,8237
+datamint/api/endpoints/resources_api.py,sha256=ZsGy4xTdLHLkM2z8VyRRLEjB0Rv3kTZFQceYkFYpk7A,50601
 datamint/api/endpoints/users_api.py,sha256=pnkuTZ1B9Y0FtwwvXO8J64e02RSkRxnBmTl9UGSuC5I,1186
 datamint/api/entity_base_api.py,sha256=-8SIt4M8P9G2b8SQznuWpFuFE8zEQjQxkRkw0s_w0Y4,11692
 datamint/apihandler/annotation_api_handler.py,sha256=W3vV4z3BqX1OQe1r7zr8dI-IVu4zUDxED4QttdiWV-E,57098
@@ -22,7 +22,7 @@ datamint/apihandler/exp_api_handler.py,sha256=hFUgUgBc5rL7odK7gTW3MnrvMY1pVfJUpU
 datamint/apihandler/root_api_handler.py,sha256=jBof_XPTeq4o41CW-l-I5GHQKVa76kaX75RovS_qAM4,63384
 datamint/client_cmd_tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 datamint/client_cmd_tools/datamint_config.py,sha256=MpR5UHv_xpElOOYyEESBkDg2n3JjP_PNLI2jqmZgYQ8,16222
-datamint/client_cmd_tools/datamint_upload.py,sha256=rZEqBRZZDBFSlwMvIg_DbipqgBtQD31v7DC1C6tysqA,36058
+datamint/client_cmd_tools/datamint_upload.py,sha256=zGNEylfS2P5XUyzBz44ruHjoyAoKZFwZbw4wRVANEL8,36279
 datamint/configs.py,sha256=ArVD5QxuohLcM6NB0dMxcEfrD1-x5lPRDLcBdY8jhMU,1625
 datamint/dataset/__init__.py,sha256=4PlUKSvVhdfQvvuq8jQXrkdqnot-iTTizM3aM1vgSwg,47
 datamint/dataset/annotation.py,sha256=qN1IMjdfLD2ceQ6va3l76jOXA8Vb_c-eBk1oWQu6hW0,7994
@@ -48,7 +48,7 @@ datamint/types.py,sha256=2OaY5QJvQIJKxyMNJYzxBksKCa9ZS2gb_ayJrByvu2Y,410
 datamint/utils/logging_utils.py,sha256=9pRoaPrWu2jOdDCiAoUsjEdP5ZwaealWL3hjUqFvx9g,4022
 datamint/utils/torchmetrics.py,sha256=lwU0nOtsSWfebyp7dvjlAggaqXtj5ohSEUXOg3L0hJE,2837
 datamint/utils/visualization.py,sha256=yaUVAOHar59VrGUjpAWv5eVvQSfztFG0eP9p5Vt3l-M,4470
-datamint-2.3.3.dist-info/METADATA,sha256=Cl4QTN2lWp65r0Sot2NP-n5h0A-1B-PqH0l_gT94XUY,4262
-datamint-2.3.3.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-datamint-2.3.3.dist-info/entry_points.txt,sha256=mn5H6jPjO-rY0W0CAZ6Z_KKWhMLvyVaSpoqk77jlTI4,145
-datamint-2.3.3.dist-info/RECORD,,
+datamint-2.3.5.dist-info/METADATA,sha256=Iu3geKgUkPz0cGntOO4i1Kdvf4i0UhAJeoxrNhKbuHs,4262
+datamint-2.3.5.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+datamint-2.3.5.dist-info/entry_points.txt,sha256=mn5H6jPjO-rY0W0CAZ6Z_KKWhMLvyVaSpoqk77jlTI4,145
+datamint-2.3.5.dist-info/RECORD,,