Merge pull request #762 from hubmapconsortium/yuanzhou/remove-assaytype

Yuanzhou/remove assaytype

Author: yuanzhou

VERSION

@@ -1 +1 @@
-2.3.27
+2.3.28

src/app.py

@@ -3338,13 +3338,6 @@ def get_prov_info():
     if user_in_hubmap_read_group(request):
         published_only = False
 
-    # Parsing the organ types yaml has to be done here rather than calling schema.schema_triggers.get_organ_description
-    # because that would require using a urllib request for each dataset
-
-    # As above, we parse te assay type yaml here rather than calling the special method for it because this avoids
-    # having to access the resource for every dataset.
-    assay_types_dict = schema_manager.get_assay_types()
-    
     # Processing and validating query parameters
     accepted_arguments = ['format', 'organ', 'has_rui_info', 'dataset_status', 'group_uuid']
     return_json = False
@@ -3705,13 +3698,6 @@ def get_prov_info_for_dataset(id):
         HEADER_PROCESSED_DATASET_STATUS, HEADER_PROCESSED_DATASET_PORTAL_URL, HEADER_DATASET_SAMPLES
     ]
 
-    # Parsing the organ types yaml has to be done here rather than calling schema.schema_triggers.get_organ_description
-    # because that would require using a urllib request for each dataset
-
-    # As above, we parse te assay type yaml here rather than calling the special method for it because this avoids
-    # having to access the resource for every dataset.
-    assay_types_dict = schema_manager.get_assay_types()
-
     hubmap_ids = schema_manager.get_hubmap_ids(id)
 
     # Get the target uuid if all good
@@ -3942,10 +3928,6 @@ def sankey_data():
     # because that would require using a urllib request for each dataset
     organ_types_dict = schema_manager.get_organ_types()
 
-    # As above, we parse te assay type yaml here rather than calling the special method for it because this avoids
-    # having to access the resource for every dataset.
-    assay_types_dict = schema_manager.get_assay_types()
-
     # Instantiation of the list dataset_sankey_list
     dataset_sankey_list = []
 

src/schema/schema_constants.py

@@ -18,7 +18,6 @@ class SchemaConstants(object):
     UUID_API_ID_ENDPOINT = '/uuid'
     INGEST_API_FILE_COMMIT_ENDPOINT = '/file-commit'
     INGEST_API_FILE_REMOVE_ENDPOINT = '/file-remove'
-    ONTOLOGY_API_ASSAY_TYPES_ENDPOINT = '/assaytype?application_context=HUBMAP'
     ONTOLOGY_API_ORGAN_TYPES_ENDPOINT = '/organs/by-code?application_context=HUBMAP'
 
     DOI_BASE_URL = 'https://doi.org/'

src/schema/schema_manager.py

@@ -2248,69 +2248,6 @@ def get_organ_types():
         return _organ_types
 
 
-"""
-Retrive the assay types from ontology-api
-
-Returns
--------
-dict
-    The available assay types by name in the following format:
-
-    {
-        "10x-multiome": {
-            "contains_pii": true,
-            "description": "10x Multiome",
-            "name": "10x-multiome",
-            "primary": true,
-            "vis_only": false,
-            "vitessce_hints": []
-        },
-        "AF": {
-            "contains_pii": false,
-            "description": "Autofluorescence Microscopy",
-            "name": "AF",
-            "primary": true,
-            "vis_only": false,
-            "vitessce_hints": []
-        },
-        ...
-    }
-"""
-def get_assay_types():
-    global _ontology_api_url
-
-    target_url = _ontology_api_url + SchemaConstants.ONTOLOGY_API_ASSAY_TYPES_ENDPOINT
-
-    # Use Memcached to improve performance
-    response = make_request_get(target_url, internal_token_used = True)
-
-    # Invoke .raise_for_status(), an HTTPError will be raised with certain status codes
-    response.raise_for_status()
-
-    if response.status_code == 200:
-        assay_types_by_name = {}
-        result_dict = response.json()
-
-        # Due to the json envelop being used int the json result
-        assay_types_list = result_dict['result']
-        for assay_type_dict in assay_types_list:
-            assay_types_by_name[assay_type_dict['name']] = assay_type_dict
-
-        return assay_types_by_name
-    else:
-        # Log the full stack trace, prepend a line with our message
-        logger.exception("Unable to make a request to query the assay types via ontology-api")
-
-        logger.debug("======get_assay_types() status code from ontology-api======")
-        logger.debug(response.status_code)
-
-        logger.debug("======get_assay_types() response text from ontology-api======")
-        logger.debug(response.text)
-
-        # Also bubble up the error message from ontology-api
-        raise requests.exceptions.RequestException(response.text)
-
-
 ####################################################################################################
 ## Internal functions
 ####################################################################################################

src/schema/schema_triggers.py

@@ -2204,61 +2204,3 @@ def _delete_files(target_property_key, property_key, normalized_type, user_token
 
     return generated_dict
 
-
-"""
-Get the assay type description based on the given assay type
-
-Parameters
-----------
-assay_type : str
-    The assay type name
-
-Returns
--------
-str: The corresponding assay type description
-"""
-def _get_assay_type_description(assay_type):
-    assay_types_dict = schema_manager.get_assay_types()
-
-    if assay_type in assay_types_dict:
-        return assay_types_dict[assay_type]['description'].lower()
-
-
-"""
-Compose the assay type description based on the given assay types
-
-Parameters
-----------
-data_types : list
-    A list of dataset data types
-
-Returns
--------
-str: The combined and formatted assay type description
-"""
-def _get_combined_assay_type_description(data_types):
-    assay_types = []
-    assay_type_desc = ''
-
-    for data_type in data_types:
-        assay_types.append(_get_assay_type_description(data_type))
-
-    # Formatting based on the number of items in the list
-    if assay_types:
-        if len(assay_types) == 1:
-            assay_type_desc = assay_types[0]
-        elif len(assay_types) == 2:
-            # <assay_type1> and <assay_type2>
-            assay_type_desc = ' and '.join(assay_types)
-        else:
-            # <assay_type1>, <assay_type2>, and <assay_type3>
-            assay_type_desc = f"{', '.join(assay_types[:-1])}, and {assay_types[-1]}"
-    else:
-        msg = "Empty list of assay_types"
-
-        logger.error(msg)
-
-        raise ValueError(msg)
-
-    return assay_type_desc
-