datamint 2.4.0__py3-none-any.whl → 2.4.2__py3-none-any.whl

datamint/api/__init__.py

@@ -1,3 +0,0 @@
-from .client import Api
-
-__all__ = ['Api']

datamint/api/endpoints/annotations_api.py

@@ -6,7 +6,6 @@ from ..entity_base_api import ApiConfig, CreatableEntityApi, DeletableEntityApi
 from .models_api import ModelsApi
 from datamint.entities.annotation import Annotation
 from datamint.entities.resource import Resource
-from datamint.entities.project import Project
 from datamint.api.dto import AnnotationType, CreateAnnotationDto, LineGeometry, BoxGeometry, CoordinateSystem, Geometry
 import numpy as np
 import os

datamint/api/endpoints/resources_api.py

@@ -2,9 +2,9 @@ from typing import Any, Optional, Sequence, TypeAlias, Literal, IO
 from ..base_api import ApiConfig, BaseApi
 from ..entity_base_api import CreatableEntityApi, DeletableEntityApi
 from datamint.entities.resource import Resource
-from datamint.entities.project import Project
 from datamint.entities.annotation import Annotation
 from datamint.exceptions import DatamintException, ResourceNotFoundError
+from datamint.api.dto import AnnotationType
 import httpx
 from datetime import date
 import json
@@ -25,6 +25,7 @@ import nest_asyncio  # For running asyncio in jupyter notebooks
 from PIL import Image
 import io
 from datamint.types import ImagingData
+from collections import defaultdict
 
 
 _LOGGER = logging.getLogger(__name__)
@@ -146,7 +147,8 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
 
         return super().get_list(limit=limit, params=payload)
 
-    def get_annotations(self, resource: str | Resource) -> Sequence[Annotation]:
+    def get_annotations(self, resource: str | Resource, 
+                        annotation_type: AnnotationType | str | None = None) -> Sequence[Annotation]:
         """Get annotations for a specific resource.
 
         Args:
@@ -155,7 +157,9 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
         Returns:
             A sequence of Annotation objects associated with the specified resource.
         """
-        return self.annotations_api.get_list(resource=resource)
+        return self.annotations_api.get_list(resource=resource,
+                                             load_ai_segmentations=True,
+                                             annotation_type=annotation_type)
 
     @staticmethod
     def __process_files_parameter(file_path: str | Sequence[str | IO | pydicom.Dataset]
@@ -279,7 +283,6 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
             _LOGGER.warning(msg)
             _USER_LOGGER.warning(msg)
 
-
         mimetype = standardize_mimetype(mimetype)
 
         if is_a_dicom_file == True or is_dicom(file_path):
@@ -440,12 +443,12 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
 
             try:
                 tasks = [__upload_single_resource(f, segfiles, metadata_file)
-                        for f, segfiles, metadata_file in zip(files_path, segmentation_files, metadata_files)]
+                         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 
+                raise
             return await asyncio.gather(*tasks, return_exceptions=on_error == 'skip')
 
     def upload_resources(self,
@@ -996,22 +999,28 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
                     raise
 
     def set_tags(self,
-                 resource: str | Resource,
+                 resource: str | Resource | Sequence[str | Resource],
                  tags: Sequence[str],
                  ):
         """
         Set tags for a resource, IMPORTANT: This replaces all existing tags.
         Args:
-            resource: The resource unique id or Resource object.
+            resource: The resource object or a list of resources.
             tags: The tags to set.
         """
         data = {'tags': tags}
-        resource_id = self._entid(resource)
-
-        response = self._make_entity_request('PUT',
-                                             resource_id,
-                                             add_path='tags',
-                                             json=data)
+        if isinstance(resource, Sequence):
+            resource_ids = [self._entid(res) for res in resource]
+            response = self._make_request('PUT',
+                                          f'{self.endpoint_base}/tags',
+                                          json={'resource_ids': resource_ids,
+                                                'tags': tags})
+        else:
+            resource_id = self._entid(resource)
+            response = self._make_entity_request('PUT',
+                                                 resource_id,
+                                                 add_path='tags',
+                                                 json=data)
         return response
 
     # def get_projects(self, resource: Resource) -> Sequence[Project]:
@@ -1029,7 +1038,7 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
     #     return [proj for proj in self.projects_api.get_all() if proj.id in proj_ids]
 
     def add_tags(self,
-                 resource: str | Resource,
+                 resource: str | Resource | Sequence[str | Resource],
                  tags: Sequence[str],
                  ):
         """
@@ -1040,8 +1049,26 @@ class ResourcesApi(CreatableEntityApi[Resource], DeletableEntityApi[Resource]):
         """
         if isinstance(resource, str):
             resource = self.get_by_id(resource)
+        elif isinstance(resource, Sequence):
+            # Transform every str to Resource first.
+            resources = [self.get_by_id(res) if isinstance(res, str) else res for res in resource]
+
+            # group resource having the exact same tags to minimize requests
+            tag_map: dict[tuple, list[Resource]] = defaultdict(list)
+            for res in resources:
+                old_tags = res.tags if res.tags is not None else []
+                # key = tuple(sorted(old_tags))
+                key = tuple(old_tags)  # keep order, assuming order matters for tags
+                tag_map[key].append(res)
+
+            # finally, set tags for each group
+            for old_tags_tuple, res_group in tag_map.items():
+                old_tags = list(old_tags_tuple)
+                self.set_tags(res_group, old_tags + list(tags))
+            return
+
         old_tags = resource.tags if resource.tags is not None else []
-        return self.set_tags(resource, old_tags + list(tags))
+        self.set_tags(resource, old_tags + list(tags))
 
     def bulk_delete(self, entities: Sequence[str | Resource]) -> None:
         """Delete multiple entities. Faster than deleting them one by one.

datamint/entities/resource.py

@@ -176,11 +176,7 @@ class Resource(BaseEntity):
     ) -> Sequence['Annotation']:
         """Get annotations associated with this resource."""
 
-        annotations = self._api.get_annotations(self)
-
-        if annotation_type:
-            annotation_type = AnnotationType(annotation_type)
-            annotations = [a for a in annotations if a.annotation_type == annotation_type]
+        annotations = self._api.get_annotations(self, annotation_type=annotation_type)
         return annotations
 
     # def get_projects(

{datamint-2.4.0.dist-info → datamint-2.4.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: datamint
-Version: 2.4.0
+Version: 2.4.2
 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

{datamint-2.4.0.dist-info → datamint-2.4.2.dist-info}/RECORD

@@ -1,16 +1,16 @@
 datamint/__init__.py,sha256=ucsnxrYClh6pdy7psRJXWam_9rjAQB4NXzvy7xLovmo,824
-datamint/api/__init__.py,sha256=7QYkmDBXbKh8-zchV7k6Lpolaw6h-IK6ezfXROIWh2A,43
+datamint/api/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 datamint/api/base_api.py,sha256=q-TQKFbupUPCaOTihoFEljxCyTF76ojsDoGkhtIJRPc,20194
 datamint/api/client.py,sha256=x-hkoDoKBWqwVCLbFZjHEWEwfqxo8bwVUSIWB4aebYQ,4018
 datamint/api/dto/__init__.py,sha256=fUi901Zs-q5XHyWwZ4dMi2fEO8-CUEVEdYbpd17lahc,416
 datamint/api/endpoints/__init__.py,sha256=wi4liAb5-wOohwyzKUD6TxHGeZmUPaZerFUGa2IUju4,529
-datamint/api/endpoints/annotations_api.py,sha256=B21oGgNXO7xoir3ynNvhnbo1JyRvWZ9sbsc7VVjghhM,49713
+datamint/api/endpoints/annotations_api.py,sha256=tkYGljljA1mdnLmmtbw6jP1qDowDygvHC1oIzJ9TLoM,49667
 datamint/api/endpoints/annotationsets_api.py,sha256=NIsPIjGGptiUBxHft-EhOMRG-DsQAthheVqd7ph0id4,409
 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=Pfr3fEiMw_aRzoGtcVXHJQ68leVoPAghw23L4ZIglno,8237
-datamint/api/endpoints/resources_api.py,sha256=ZsGy4xTdLHLkM2z8VyRRLEjB0Rv3kTZFQceYkFYpk7A,50601
+datamint/api/endpoints/resources_api.py,sha256=PY3QMF9yPdO07YDMWpGTC7U3GC4H7R_4KfnUSAKuOXg,52177
 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
@@ -35,7 +35,7 @@ datamint/entities/cache_manager.py,sha256=ZN5_HeyM6c0ocWFsJuJEF4CkuOHr6RPErwhZNY
 datamint/entities/channel.py,sha256=9fl22eSx_ng98NosfQGs18cdaRdbeC3wXL61KhSg4Zo,1601
 datamint/entities/datasetinfo.py,sha256=yeGy5CVxqc7h0SFBJROr0UObeIMkOVZKwrOBsZ-iCEg,4151
 datamint/entities/project.py,sha256=QQXBOe6FzupPrCunBcqOlY6d3uqxvnYvGeCq8hZy_U8,4192
-datamint/entities/resource.py,sha256=Ai36-dJ9PhrRYho8QLRnySfsAPWPW8QpKMiVra_jCgA,9316
+datamint/entities/resource.py,sha256=z7W49TyiHXHYLAsijIcPYQfhJcsQDgBzWNAMckAsYFE,9167
 datamint/entities/user.py,sha256=MREHDOsV9NOBEbXqiQ2ww6DmetN07CELId-ZQVpZCb8,620
 datamint/examples/__init__.py,sha256=zcYnd5nLVme9GCTPYH-1JpGo8xXK2WEYvhzcy_2alZc,39
 datamint/examples/example_projects.py,sha256=sU-Gxy7PPqA0WUfN-ZmXV-0YnwrnzpJ79lMXTJp2DzU,2804
@@ -61,7 +61,7 @@ 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-2.4.0.dist-info/METADATA,sha256=g4WkKWDq3mBETvQibcoISGXTtQCRdebfrw4leyurg3E,8974
-datamint-2.4.0.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-datamint-2.4.0.dist-info/entry_points.txt,sha256=wTr9DXteCfAFqLUstN1Qx_SqC_rFLrAUIcDx9q1eXZw,845
-datamint-2.4.0.dist-info/RECORD,,
+datamint-2.4.2.dist-info/METADATA,sha256=GUVaw9czq5utZnZErSe9ohdXB7LROheAwGYkacvX6AY,8974
+datamint-2.4.2.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+datamint-2.4.2.dist-info/entry_points.txt,sha256=wTr9DXteCfAFqLUstN1Qx_SqC_rFLrAUIcDx9q1eXZw,845
+datamint-2.4.2.dist-info/RECORD,,