feat(breadbox): Added support for associations to breadbox client and…

… other associations small fixes (#164)

breadbox-client/breadbox_facade/client.py

@@ -31,28 +31,28 @@
 from breadbox_client.api.groups import remove_group_access as remove_group_access_client
 from breadbox_client.api.groups import get_groups as get_groups_client
 from breadbox_client.api.types import add_dimension_type as add_dimension_type_client
-from breadbox_client.api.types import add_feature_type as add_feature_type_client
-from breadbox_client.api.types import add_sample_type as add_sample_type_client
 from breadbox_client.api.types import get_dimension_type as get_dimension_type_client
 from breadbox_client.api.types import get_dimension_types as get_dimension_types_client
 from breadbox_client.api.types import get_feature_types as get_feature_types_client
 from breadbox_client.api.types import get_sample_types as get_sample_types_client
 from breadbox_client.api.types import remove_dimension_type as remove_dimension_type_client
 from breadbox_client.api.types import update_dimension_type as update_dimension_type_client
-from breadbox_client.api.types import update_feature_type_metadata as update_feature_type_metadata_client
-from breadbox_client.api.types import update_sample_type_metadata as update_sample_type_metadata_client
+from breadbox_client.api.temp import get_associations as get_associations_client
+from breadbox_client.api.temp import add_associations as add_associations_client
+from breadbox_client.api.temp import get_associations_for_slice as get_associations_for_slice_client
+#
+
 from breadbox_client.models import (
     AccessType,
     AddDatasetResponse,
     AddDimensionType,
+    Associations,
+    AssociationTable,
+    AssociationsIn,
+    AssociationsInAxis,
     AddDimensionTypeAxis,
-    AnnotationTypeMap,
     BodyAddDataType,
-    BodyAddFeatureType,
-    BodyAddSampleType,
     BodyGetDatasetData,
-    BodyUpdateFeatureTypeMetadata,
-    BodyUpdateSampleTypeMetadata,
     BodyUploadFile,
     ColumnMetadata,
     ComputeParams,
@@ -66,12 +66,13 @@
     GroupEntry,
     GroupEntryIn,
     GroupOut,
-    IdMapping,
     MatrixDatasetParams,
     MatrixDatasetParamsDatasetMetadataType0,
     MatrixDatasetParamsFormat,
     MatrixDatasetResponse,
     SampleTypeOut,
+    SliceQuery,
+    SliceQueryIdentifierType,
     TableDatasetParams,
     TableDatasetParamsColumnsMetadata,
     TableDatasetParamsDatasetMetadataType0,
@@ -472,6 +473,24 @@ def remove_group_access(self, group_entry_id: str) -> str:
         breadbox_response = remove_group_access_client.sync_detailed(client=self.client, group_entry_id=group_entry_id)
         return self._parse_client_response(breadbox_response)
 
+    # ASSOCIATIONS
+    def get_associations(self) -> List[AssociationTable]:
+        breadbox_response = get_associations_client.sync_detailed(client=self.client)
+        return self._parse_client_response(breadbox_response)
+
+    def add_associations(self, dataset_1_id:str, dataset_2_id: str, axis :str, associations_table_filename : str) -> AssociationTable:
+        with open(associations_table_filename, "rb") as fd:
+            uploaded_file = self.upload_file(fd)
+
+        associations_in = AssociationsIn(axis = AssociationsInAxis(axis), dataset_1_id=dataset_1_id, dataset_2_id=dataset_2_id, file_ids=uploaded_file.file_ids, md5=uploaded_file.md5)
+        breadbox_response = add_associations_client.sync_detailed(client=self.client, body=associations_in)
+
+        return self._parse_client_response(breadbox_response)
+
+    def get_associations_for_slice(self, dataset_id: str, identifier: str, identifier_type: str) -> Associations:
+        breadbox_response = get_associations_for_slice_client.sync_detailed(client=self.client, body=SliceQuery(dataset_id=dataset_id, identifier=identifier,
+                                                                                    identifier_type=SliceQueryIdentifierType(identifier_type)))
+        return self._parse_client_response(breadbox_response)
 
     # API
 

breadbox/breadbox/api/temp/associations.py

@@ -16,6 +16,7 @@
 from breadbox.crud import associations as associations_crud
 import uuid
 from breadbox.db.util import transaction
+from typing import cast, Literal
 
 from .router import router
 
@@ -46,7 +47,12 @@ def query_associations_for_slice(
 def get_associations(db: Annotated[SessionWithUser, Depends(get_db_with_user)]):
     return [
         AssociationTable(
-            id=a.id, dataset_1_id=a.dataset_1_id, dataset_2_id=a.dataset_2_id
+            id=a.id,
+            dataset_1_id=a.dataset_1_id,
+            dataset_2_id=a.dataset_2_id,
+            dataset_1_name=a.dataset_1.name,
+            dataset_2_name=a.dataset_2.name,
+            axis=a.axis,
         )
         for a in associations_crud.get_association_tables(db, None)
     ]
@@ -117,4 +123,7 @@ def add_associations(
         id=assoc_table.id,
         dataset_1_id=assoc_table.dataset_1_id,
         dataset_2_id=assoc_table.dataset_2_id,
+        dataset_1_name=assoc_table.dataset_1.name,
+        dataset_2_name=assoc_table.dataset_2.name,
+        axis=cast(Literal["sample", "feature"], assoc_table.axis),
     )

breadbox/breadbox/crud/dataset.py

@@ -18,6 +18,7 @@
     ColumnMetadata,
     UpdateDatasetParams,
 )
+
 from ..schemas.custom_http_exception import (
     DatasetAccessError,
     ResourceNotFoundError,
@@ -39,6 +40,7 @@
     PropertyToIndex,
     ValueType,
     DimensionType,
+    PrecomputedAssociation,
 )
 from breadbox.crud.group import (
     get_group,
@@ -1202,9 +1204,24 @@ def update_dataset(
 def delete_dataset(
     db: SessionWithUser, user: str, dataset: Dataset, filestore_location: str
 ):
+    from .associations import delete_association_table
+
     if not user_has_access_to_group(dataset.group, user, write_access=True):
         return False
 
+    log.info("delete any referenced precomputed associations")
+    for associations in (
+        db.query(PrecomputedAssociation)
+        .filter(
+            or_(
+                PrecomputedAssociation.dataset_1_id == dataset.id,
+                PrecomputedAssociation.dataset_2_id == dataset.id,
+            )
+        )
+        .all()
+    ):
+        delete_association_table(db, associations.id, filestore_location)
+
     log.info("delete Dimension")
     db.query(Dimension).filter(Dimension.dataset_id == dataset.id).delete()
     log.info("delete_dataset %s delete dataset itself", dataset.id)

breadbox/breadbox/schemas/associations.py

@@ -36,5 +36,8 @@ class AssociationsIn(BaseModel):
 
 class AssociationTable(BaseModel):
     id: str
+    dataset_1_name: str
+    dataset_2_name: str
+    axis: Literal["sample", "feature"]
     dataset_1_id: str
     dataset_2_id: str