Merge pull request #504 from umccr/update/use-new-metadata-library-en…

…dpoint

Use the new metadata library endpoint for queries

lib/workload/components/python-metadata-tools-layer/metadata_tools_layer/src/metadata_tools/utils/library_helpers.py

@@ -10,7 +10,7 @@ def get_library_from_library_id(library_id: Union[int | str]) -> Dict:
     :param library_id:
     :return:
     """
-    endpoint = "library"
+    endpoint = "api/v1/library"
 
     # Get library id
     if isinstance(library_id, str):
@@ -99,6 +99,6 @@ def get_all_libraries() -> List[Dict]:
     Collect all libraries from the database
     :return:
     """
-    endpoint = "library"
+    endpoint = "api/v1/library"
 
     return get_request_response_results(endpoint)

lib/workload/components/python-metadata-tools-layer/metadata_tools_layer/src/metadata_tools/utils/specimen_helpers.py

@@ -47,7 +47,7 @@ def list_libraries_in_specimen(specimen_id: Union[str, int]) -> List[Dict]:
     # If subject id is a string, we have the internal id (SBJ...)
     specimen = get_specimen_from_specimen_id(specimen_id)
 
-    endpoint = f"library"
+    endpoint = f"api/v1/library"
 
     # Get the subject
     return list(
@@ -63,7 +63,7 @@ def get_all_specimens():
     Get all specimens from the specimen database
     :return:
     """
-    endpoint = "specimen"
+    endpoint = "api/v1/specimen"
 
     return get_request_response_results(endpoint)
 

lib/workload/components/python-metadata-tools-layer/metadata_tools_layer/src/metadata_tools/utils/subject_helpers.py

@@ -18,7 +18,7 @@ def get_subject_from_subject_id(subject_id: Union[str, int]) -> Dict:
     :param subject_id:
     :return:
     """
-    endpoint = "subject"
+    endpoint = "api/v1/subject"
 
     # Get subject id
     if isinstance(subject_id, str):
@@ -80,6 +80,6 @@ def get_all_subjects() -> List[Dict]:
     :return:
     """
 
-    endpoint = "subject"
+    endpoint = "api/v1/subject"
 
     return get_request_response_results(endpoint)