ebi-eva-common-pyutils 0.5.3.dev4__tar.gz → 0.5.3.dev5__tar.gz

{ebi_eva_common_pyutils-0.5.3.dev4 → ebi_eva_common_pyutils-0.5.3.dev5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi_eva_common_pyutils
-Version: 0.5.3.dev4
+Version: 0.5.3.dev5
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache

{ebi_eva_common_pyutils-0.5.3.dev4 → ebi_eva_common_pyutils-0.5.3.dev5}/ebi_eva_common_pyutils/assembly/assembly.py

@@ -21,11 +21,13 @@ logging_config.add_stdout_handler()
 logger = logging_config.get_logger(__name__)
 
 
-def get_supported_asm_from_ensembl(tax_id: int) -> str:
+def get_supported_asm_from_ensembl(tax_id: int) -> str | None:
     logger.info(f'Query Ensembl for species name using taxonomy {tax_id}')
     scientific_name_api_param = get_scientific_name_from_ensembl(tax_id).lower().replace(' ', '_')
     ENSEMBL_REST_API_URL = "http://rest.ensembl.org/info/assembly/{0}?content-type=application/json".format(
         scientific_name_api_param)
     response = json_request(ENSEMBL_REST_API_URL)
-    assembly_accession = str(response.get('assembly_accession'))
-    return assembly_accession
+    assembly_accession_attribute = 'assembly_accession'
+    if assembly_accession_attribute in response:
+        return str(response.get('assembly_accession'))
+    return None

{ebi_eva_common_pyutils-0.5.3.dev4 → ebi_eva_common_pyutils-0.5.3.dev5}/ebi_eva_common_pyutils/metadata_utils.py

@@ -258,19 +258,6 @@ def insert_taxonomy(metadata_connection_handle, taxonomy_id, scientific_name, co
     logger.info('New taxonomy {} added'.format(taxonomy_id))
 
 
-def get_tax_submitted_with_asm_in_eva(metadata_connection_handle, assembly_accession: str) -> list[int]:
-    """
-    :param metadata_connection_handle: Connection handle to the metadata database
-    :param assembly_accession: Assembly accession
-    :return: List of taxonomies submitted to EVA where variants were called with the given assembly accession
-
-    """
-    get_tax_for_asm_query = "select distinct taxonomy_id from {0} where assembly_id = '{1}'".format(
-        SUPPORTED_ASSEMBLY_TRACKER_TABLE, assembly_accession)
-    result = get_all_results_for_query(metadata_connection_handle, get_tax_for_asm_query)
-    return [row[0] for row in result]
-
-
 def add_to_supported_assemblies(metadata_connection_handle, source_of_assembly: str, target_assembly: str,
                                 taxonomy_id: int):
     today = datetime.date.today().strftime('%Y-%m-%d')

{ebi_eva_common_pyutils-0.5.3.dev4 → ebi_eva_common_pyutils-0.5.3.dev5}/ebi_eva_common_pyutils.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi-eva-common-pyutils
-Version: 0.5.3.dev4
+Version: 0.5.3.dev5
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache

{ebi_eva_common_pyutils-0.5.3.dev4 → ebi_eva_common_pyutils-0.5.3.dev5}/setup.py

@@ -7,7 +7,7 @@ setup(
     name='ebi_eva_common_pyutils',
     scripts=[os.path.join(os.path.dirname(__file__), 'ebi_eva_common_pyutils', 'archive_directory.py')],
     packages=find_packages(),
-    version='0.5.3.dev4',
+    version='0.5.3.dev5',
     license='Apache',
     description='EBI EVA - Common Python Utilities',
     url='https://github.com/EBIVariation/eva-common-pyutils',