datamint 2.2.0__py3-none-any.whl → 2.2.1__py3-none-any.whl

datamint/api/endpoints/resources_api.py

@@ -85,8 +85,8 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
 
         Args:
             status: The resource status. Possible values: 'inbox', 'published', 'archived' or None. If None, it will return all resources.
-            from_date : The start date.
-            to_date: The end date.
+            from_date : The start date (inclusive).
+            to_date: The end date (exclusive).
             tags: The tags to filter the resources.
             modality: The modality of the resources.
             mimetype: The mimetype of the resources.
@@ -235,30 +235,26 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
                                             metadata_file: Optional[str | dict] = None,
                                             ) -> str:
         if is_io_object(file_path):
-            name = file_path.name
+            source_filepath = os.path.abspath(os.path.expanduser(file_path.name))
+            filename = os.path.basename(source_filepath)
         else:
-            name = file_path
+            source_filepath = os.path.abspath(os.path.expanduser(file_path))
+            filename = os.path.basename(source_filepath)
 
         if session is not None and not isinstance(session, aiohttp.ClientSession):
             raise ValueError("session must be an aiohttp.ClientSession object.")
 
-        name = os.path.expanduser(os.path.normpath(name))
-        if len(Path(name).parts) == 0:
-            raise ValueError(f"File path '{name}' is not valid.")
-        name = os.path.join(*[x if x != '..' else '_' for x in Path(name).parts])
-
         if mung_filename is not None:
-            file_parts = Path(name).parts
+            file_parts = Path(source_filepath).parts
             if file_parts[0] == os.path.sep:
                 file_parts = file_parts[1:]
             if mung_filename == 'all':
-                new_file_path = '_'.join(file_parts)
+                new_filename = '_'.join(file_parts)
             else:
                 folder_parts = file_parts[:-1]
-                new_file_path = '_'.join([folder_parts[i-1] for i in mung_filename if i <= len(folder_parts)])
-                new_file_path += '_' + file_parts[-1]
-            name = new_file_path
-            _LOGGER.debug(f"New file path: {name}")
+                new_filename = '_'.join([folder_parts[i-1] for i in mung_filename if i <= len(folder_parts)])
+                new_filename += '_' + file_parts[-1]
+            filename = new_filename
 
         is_a_dicom_file = None
         if mimetype is None:
@@ -268,14 +264,12 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
                     mimetype = DEFAULT_NIFTI_MIME
                     break
             else:
-                if ext == '.nii.gz' or name.lower().endswith('nii.gz'):
+                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 = standardize_mimetype(mimetype)
-        filename = os.path.basename(name)
-        _LOGGER.debug(f"File name '{filename}' mimetype: {mimetype}")
 
         if is_a_dicom_file == True or is_dicom(file_path):
             if tags is None:
@@ -292,7 +286,7 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
             elif lat == 'R':
                 tags.append("right")
             # make the dicom `ds` object a file-like object in order to avoid unnecessary disk writes
-            f = to_bytesio(ds, name)
+            f = to_bytesio(ds, filename)
         else:
             f = _open_io(file_path)
 
@@ -329,7 +323,7 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
             form.add_field('source', 'api')
 
             form.add_field(file_key, f, filename=filename, content_type=mimetype)
-            form.add_field('source_filepath', name)  # full path to the file
+            form.add_field('source_filepath', source_filepath)  # full path to the file
             if mimetype is not None:
                 form.add_field('mimetype', mimetype)
             if channel is not None:
@@ -354,11 +348,11 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
                                                             data=form)
             if 'error' in resp_data:
                 raise DatamintException(resp_data['error'])
-            _LOGGER.debug(f"Response on uploading {name}: {resp_data}")
+            _LOGGER.debug(f"Response on uploading {filename}: {resp_data}")
             return resp_data['id']
         except Exception as e:
-            if 'name' in locals():
-                _LOGGER.error(f"Error uploading {name}: {e}")
+            if 'filename' in locals():
+                _LOGGER.error(f"Error uploading {filename}: {e}")
             else:
                 _LOGGER.error(f"Error uploading {file_path}: {e}")
             raise
@@ -676,7 +670,7 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
                     channel='study_channel',
                     segmentation_files={
                         'files': ['path/to/segmentation.nii.gz'],
-                        'names': {1: 'Bone', 2: 'Tissue'}
+                        'names': {1: 'Brain', 2: 'Lung'}
                     },
                     metadata={'patient_age': 45, 'modality': 'CT'}
                 )

datamint/client_cmd_tools/datamint_upload.py

@@ -492,7 +492,7 @@ def _get_files_from_path(path: str | Path,
     Returns:
         List of file paths as strings
     """
-    path = Path(path)
+    path = Path(path).resolve()
 
     if path.is_file():
         return [str(path)]
@@ -507,7 +507,7 @@ def _get_files_from_path(path: str | Path,
 
         file_paths = walk_to_depth(path, recursive_depth, exclude_pattern)
         filtered_files = filter_files(file_paths, include_extensions, exclude_extensions)
-        return [str(f) for f in filtered_files]
+        return [str(f.resolve()) for f in filtered_files]
 
     except Exception as e:
         _LOGGER.error(f'Error in recursive search: {e}')
@@ -786,7 +786,6 @@ def main():
             _USER_LOGGER.error(f'❌ Connection failed: {e}')
             return
         try:
-            print('>>>', segfiles)
             results = api.resources.upload_resources(channel=args.channel,
                                                      files_path=files_path,
                                                      tags=args.tag,

{datamint-2.2.0.dist-info → datamint-2.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: datamint
-Version: 2.2.0
+Version: 2.2.1
 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
@@ -21,7 +21,7 @@ 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 (>=0.7.0)
+Requires-Dist: medimgkit (>=0.7.2)
 Requires-Dist: nest-asyncio (>=1.0.0,<2.0.0)
 Requires-Dist: nibabel (>=4.0.0)
 Requires-Dist: numpy

{datamint-2.2.0.dist-info → datamint-2.2.1.dist-info}/RECORD

@@ -8,7 +8,7 @@ datamint/api/endpoints/annotations_api.py,sha256=zzCiL2z7czB1ojU3CCM5QgeOuDoNB_2
 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/projects_api.py,sha256=9tYIQsnMFOGTXrsoizweoWNqNue5907nbI6G9PAcYcA,7784
-datamint/api/endpoints/resources_api.py,sha256=jlap40_wpzz8L8a-sX9tNGxsgPgP2_hv8kdb3g75-NU,48455
+datamint/api/endpoints/resources_api.py,sha256=Hd8sObIarvAdATS6qmAvT9EdXzPfruyMHnlGXcYkeMg,48320
 datamint/api/endpoints/users_api.py,sha256=pnkuTZ1B9Y0FtwwvXO8J64e02RSkRxnBmTl9UGSuC5I,1186
 datamint/api/entity_base_api.py,sha256=gPE28bwv7B6JngMk9szD2XwaVhB8OwB1HJjaMYD354k,12935
 datamint/apihandler/annotation_api_handler.py,sha256=W3vV4z3BqX1OQe1r7zr8dI-IVu4zUDxED4QttdiWV-E,57098
@@ -20,7 +20,7 @@ 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=jPzvlNeBZfOOxuG6ryswJ8OG4jXuTrPtArUetoKVGj0,36073
+datamint/client_cmd_tools/datamint_upload.py,sha256=rZEqBRZZDBFSlwMvIg_DbipqgBtQD31v7DC1C6tysqA,36058
 datamint/configs.py,sha256=Bdp6NydYwyCJ2dk19_gf_o3M2ZyQOmMHpLi8wEWNHUk,1426
 datamint/dataset/__init__.py,sha256=4PlUKSvVhdfQvvuq8jQXrkdqnot-iTTizM3aM1vgSwg,47
 datamint/dataset/annotation.py,sha256=qN1IMjdfLD2ceQ6va3l76jOXA8Vb_c-eBk1oWQu6hW0,7994
@@ -44,7 +44,7 @@ datamint/logging.yaml,sha256=tOMxtc2UmwlIMTK6ljtnBwTco1PNrPeq3mx2iMuSbiw,482
 datamint/utils/logging_utils.py,sha256=9pRoaPrWu2jOdDCiAoUsjEdP5ZwaealWL3hjUqFvx9g,4022
 datamint/utils/torchmetrics.py,sha256=lwU0nOtsSWfebyp7dvjlAggaqXtj5ohSEUXOg3L0hJE,2837
 datamint/utils/visualization.py,sha256=yaUVAOHar59VrGUjpAWv5eVvQSfztFG0eP9p5Vt3l-M,4470
-datamint-2.2.0.dist-info/METADATA,sha256=mjsQSKJrpkEtWe_BodST4fYWWoQ49k7fUFbjt55KHAA,4203
-datamint-2.2.0.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-datamint-2.2.0.dist-info/entry_points.txt,sha256=mn5H6jPjO-rY0W0CAZ6Z_KKWhMLvyVaSpoqk77jlTI4,145
-datamint-2.2.0.dist-info/RECORD,,
+datamint-2.2.1.dist-info/METADATA,sha256=Pk5Mf1hH3s4M6sIBr1F77V0l76toCcWoGblTb_Ms5tQ,4203
+datamint-2.2.1.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+datamint-2.2.1.dist-info/entry_points.txt,sha256=mn5H6jPjO-rY0W0CAZ6Z_KKWhMLvyVaSpoqk77jlTI4,145
+datamint-2.2.1.dist-info/RECORD,,