bump pyutils version and fix imports

bin/add_target_assembly.py

@@ -13,7 +13,7 @@
 # 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.
-from argparse import ArgumentParser, ArgumentError
+from argparse import ArgumentParser
 
 from ebi_eva_common_pyutils.logger import logging_config
 

bin/genome_target_tracker.py

@@ -17,9 +17,9 @@
 
 import requests
 from ebi_eva_common_pyutils.logger import logging_config
-from ebi_eva_common_pyutils.metadata_utils import get_metadata_connection_handle, insert_new_assembly_and_taxonomy
-from ebi_eva_common_pyutils.pg_utils import get_all_results_for_query
 from ebi_eva_common_pyutils.taxonomy.taxonomy import get_scientific_name_from_ensembl
+from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle, insert_new_assembly_and_taxonomy
+from ebi_eva_internal_pyutils.pg_utils import get_all_results_for_query
 
 logger = logging_config.get_logger(__name__)
 logging_config.add_stdout_handler()

eva_assembly_ingestion/assembly_ingestion_job.py

@@ -21,14 +21,14 @@
 from ebi_eva_common_pyutils.command_utils import run_command_with_output
 from ebi_eva_common_pyutils.common_utils import pretty_print
 from ebi_eva_common_pyutils.config import cfg
-from ebi_eva_common_pyutils.config_utils import get_contig_alias_db_creds_for_profile
 from ebi_eva_common_pyutils.contig_alias.contig_alias import ContigAliasClient
 from ebi_eva_common_pyutils.logger import AppLogger
-from ebi_eva_common_pyutils.metadata_utils import get_metadata_connection_handle, insert_new_assembly_and_taxonomy, \
-    add_to_supported_assemblies
-from ebi_eva_common_pyutils.pg_utils import execute_query, get_all_results_for_query
-from ebi_eva_common_pyutils.spring_properties import SpringPropertiesGenerator
 from ebi_eva_common_pyutils.taxonomy.taxonomy import get_scientific_name_from_taxonomy
+from ebi_eva_internal_pyutils.config_utils import get_contig_alias_db_creds_for_profile
+from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle, insert_new_assembly_and_taxonomy, \
+    add_to_supported_assemblies
+from ebi_eva_internal_pyutils.pg_utils import execute_query, get_all_results_for_query
+from ebi_eva_internal_pyutils.spring_properties import SpringPropertiesGenerator
 from psycopg2.extras import execute_values
 
 from eva_assembly_ingestion.config import get_nextflow_config_flag
@@ -37,6 +37,7 @@
 
 SUPPORTED_ASSEMBLY_TRACKER_TABLE = "evapro.supported_assembly_tracker"
 
+
 class AssemblyIngestionJob(AppLogger):
     all_tasks = ['load_tracker', 'remap_cluster', 'update_dbs']
     tracking_table = 'eva_progress_tracker.remapping_tracker'

eva_assembly_ingestion/custom_assembly.py

@@ -22,8 +22,8 @@
 from cached_property import cached_property
 from ebi_eva_common_pyutils.config import cfg
 from ebi_eva_common_pyutils.logger import AppLogger
-from ebi_eva_common_pyutils.metadata_utils import get_metadata_connection_handle
-from ebi_eva_common_pyutils.pg_utils import get_all_results_for_query
+from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle
+from ebi_eva_internal_pyutils.pg_utils import get_all_results_for_query
 from retry import retry
 
 

requirements.txt

@@ -1,4 +1,4 @@
-ebi-eva-common-pyutils==0.5.5
+ebi-eva-common-pyutils[internal]==0.6.7
 pyyaml
 requests
 retry