ebi-eva-common-pyutils 0.5.3.dev3__tar.gz → 0.5.3.dev5__tar.gz

{ebi_eva_common_pyutils-0.5.3.dev3 → 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.dev3
+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.dev3 → 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.dev3 → ebi_eva_common_pyutils-0.5.3.dev5}/ebi_eva_common_pyutils/metadata_utils.py

@@ -11,6 +11,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+import datetime
 import re
 from urllib.parse import urlsplit
 
@@ -20,10 +21,11 @@ from ebi_eva_common_pyutils.config_utils import get_metadata_creds_for_profile
 from ebi_eva_common_pyutils.ena_utils import get_scientific_name_and_common_name
 from ebi_eva_common_pyutils.logger import logging_config
 from ebi_eva_common_pyutils.ncbi_utils import get_ncbi_assembly_name_from_term
-from ebi_eva_common_pyutils.pg_utils import get_result_cursor, get_all_results_for_query
+from ebi_eva_common_pyutils.pg_utils import get_result_cursor, get_all_results_for_query, execute_query
 from ebi_eva_common_pyutils.taxonomy.taxonomy import get_scientific_name_from_ensembl
 
 logger = logging_config.get_logger(__name__)
+SUPPORTED_ASSEMBLY_TRACKER_TABLE = "evapro.supported_assembly_tracker"
 
 
 def get_metadata_connection_handle(profile, settings_xml_file):
@@ -254,3 +256,33 @@ def insert_taxonomy(metadata_connection_handle, taxonomy_id, scientific_name, co
                 'VALUES (%s, %s, %s, %s, %s)',
                 (taxonomy_id, common_name, scientific_name, taxonomy_code, eva_species_name))
     logger.info('New taxonomy {} added'.format(taxonomy_id))
+
+
+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')
+    # First check if the current assembly is already target - if so don't do anything
+    current_query = (
+        f"SELECT assembly_id FROM evapro.supported_assembly_tracker "
+        f"WHERE taxonomy_id={taxonomy_id} AND current=true;"
+    )
+    results = get_all_results_for_query(metadata_connection_handle, current_query)
+    if len(results) > 0 and results[0][0] == target_assembly:
+        logger.warning(f'Current assembly for taxonomy {taxonomy_id} is already {target_assembly}!')
+        return
+
+    # Deprecate the last current assembly
+    update_query = (
+        f"UPDATE evapro.supported_assembly_tracker "
+        f"SET current=false, end_date='{today}' "
+        f"WHERE taxonomy_id={taxonomy_id} AND current=true;"
+    )
+    execute_query(metadata_connection_handle, update_query)
+
+    # Then insert the new assembly
+    insert_query = (
+        f"INSERT INTO evapro.supported_assembly_tracker "
+        f"(taxonomy_id, source, assembly_id, current, start_date) "
+        f"VALUES({taxonomy_id}, '{source_of_assembly}', '{target_assembly}', true, '{today}');"
+    )
+    execute_query(metadata_connection_handle, insert_query)

{ebi_eva_common_pyutils-0.5.3.dev3 → 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.dev3
+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.dev3 → 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.dev3',
+    version='0.5.3.dev5',
     license='Apache',
     description='EBI EVA - Common Python Utilities',
     url='https://github.com/EBIVariation/eva-common-pyutils',