Update to use new version of ebi_eva_common_pyutils

eva-accession-release-automation/gather_clustering_counts/gather_clustering_counts_from_mongo.py

@@ -8,10 +8,10 @@
 from datetime import datetime
 
 from ebi_eva_common_pyutils.logger import logging_config
-from ebi_eva_common_pyutils.mongodb import MongoDatabase
-from ebi_eva_common_pyutils.config_utils import get_accession_pg_creds_for_profile
-from ebi_eva_common_pyutils.pg_utils import execute_query, get_all_results_for_query
-from ebi_eva_common_pyutils.metadata_utils import get_metadata_connection_handle
+from ebi_eva_internal_pyutils.mongodb import MongoDatabase
+from ebi_eva_internal_pyutils.config_utils import get_accession_pg_creds_for_profile
+from ebi_eva_internal_pyutils.pg_utils import execute_query, get_all_results_for_query
+from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle
 from gather_clustering_counts.gather_per_species_clustering_counts import assembly_table_name, tracker_table_name
 from urllib.parse import urlsplit
 

eva-accession-release-automation/gather_clustering_counts/gather_per_species_clustering_counts.py

@@ -2,9 +2,9 @@
 import os
 
 from ebi_eva_common_pyutils.logger import logging_config
-from ebi_eva_common_pyutils.metadata_utils import get_metadata_connection_handle
+from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle
 from ebi_eva_common_pyutils.command_utils import run_command_with_output
-from ebi_eva_common_pyutils.pg_utils import get_all_results_for_query, execute_query
+from ebi_eva_internal_pyutils.pg_utils import get_all_results_for_query, execute_query
 
 logger = logging_config.get_logger(__name__)
 logging_config.add_stdout_handler()

eva-accession-release-automation/gather_clustering_counts/gather_release_counts.py

@@ -8,10 +8,10 @@
 
 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_utils import get_metadata_creds_for_profile
 from ebi_eva_common_pyutils.logger import logging_config, 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.config_utils import get_metadata_creds_for_profile
+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 sqlalchemy import select
 from sqlalchemy.orm import Session

eva-accession-release-automation/gather_clustering_counts/load_additional_counts_from_tsv.py

@@ -1,9 +1,9 @@
 import argparse
 import csv
 
-from ebi_eva_common_pyutils.metadata_utils import get_metadata_connection_handle
+from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle
 from ebi_eva_common_pyutils.logger import logging_config
-from ebi_eva_common_pyutils.pg_utils import execute_query
+from ebi_eva_internal_pyutils.pg_utils import execute_query
 
 from gather_clustering_counts.gather_per_species_clustering_counts import assembly_table_name
 

eva-accession-release-automation/gather_clustering_counts/qc_release_counts.py

@@ -7,8 +7,8 @@
 
 from ebi_eva_common_pyutils.common_utils import pretty_print
 from ebi_eva_common_pyutils.logger import logging_config
-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, execute_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, execute_query
 
 from gather_clustering_counts.gather_per_species_clustering_counts import get_taxonomy_and_scientific_name, \
     assembly_table_name, id_to_column

eva-accession-release-automation/publish_release_to_ftp/publish_release_files_to_ftp.py

@@ -23,8 +23,8 @@
 from publish_release_to_ftp.create_assembly_name_symlinks import create_assembly_name_symlinks
 from ebi_eva_common_pyutils.command_utils import run_command_with_output
 from ebi_eva_common_pyutils.logger import logging_config
-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 run_release_in_embassy.run_release_for_species import get_common_release_properties
 from run_release_in_embassy.release_metadata import release_vcf_file_categories, release_text_file_categories
 

eva-accession-release-automation/run_release_in_embassy/copy_accessioning_collections_to_embassy.py

@@ -19,9 +19,9 @@
 import traceback
 
 from ebi_eva_common_pyutils.command_utils import run_command_with_output
-from ebi_eva_common_pyutils.config_utils import get_mongo_uri_for_eva_profile
-from ebi_eva_common_pyutils.metadata_utils import get_metadata_connection_handle
-from ebi_eva_common_pyutils.mongo_utils import copy_db
+from ebi_eva_internal_pyutils.config_utils import get_mongo_uri_for_eva_profile
+from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle
+from ebi_eva_internal_pyutils.mongo_utils import copy_db
 from pymongo import MongoClient
 from pymongo.uri_parser import parse_uri
 from run_release_in_embassy.release_common_utils import open_mongo_port_to_tempmongo, close_mongo_port_to_tempmongo, \

eva-accession-release-automation/run_release_in_embassy/create_release_properties_file.py

@@ -14,8 +14,8 @@
 import os
 
 import click
-from ebi_eva_common_pyutils.metadata_utils import get_metadata_connection_handle
-from ebi_eva_common_pyutils.spring_properties import SpringPropertiesGenerator
+from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle
+from ebi_eva_internal_pyutils.spring_properties import SpringPropertiesGenerator
 
 from run_release_in_embassy.release_common_utils import get_release_db_name_in_tempmongo_instance
 from run_release_in_embassy.release_metadata import get_release_inventory_info_for_assembly

eva-accession-release-automation/run_release_in_embassy/create_release_tracking_table.py

@@ -18,11 +18,11 @@
 from itertools import cycle
 
 from ebi_eva_common_pyutils.assembly import NCBIAssembly
-from ebi_eva_common_pyutils.config_utils import get_mongo_uri_for_eva_profile
+from ebi_eva_internal_pyutils.config_utils import get_mongo_uri_for_eva_profile
 from ebi_eva_common_pyutils.logger import logging_config, AppLogger
-from ebi_eva_common_pyutils.metadata_utils import get_metadata_connection_handle
-from ebi_eva_common_pyutils.mongodb import MongoDatabase
-from ebi_eva_common_pyutils.pg_utils import get_all_results_for_query, execute_query
+from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle
+from ebi_eva_internal_pyutils.mongodb import MongoDatabase
+from ebi_eva_internal_pyutils.pg_utils import get_all_results_for_query, execute_query
 from ebi_eva_common_pyutils.taxonomy.taxonomy import normalise_taxon_scientific_name, get_scientific_name_from_ensembl
 
 

eva-accession-release-automation/run_release_in_embassy/create_table_for_multimap_snps.py

@@ -19,7 +19,7 @@
 from include_mapping_weight_from_dbsnp.snpmapinfo_metadata import \
     get_snpmapinfo_tables_with_overweight_snps_for_dbsnp_species, get_snpmapinfo_asm_columns
 from include_mapping_weight_from_dbsnp.dbsnp_mirror_metadata import get_db_conn_for_species, get_species_info
-from ebi_eva_common_pyutils.pg_utils import get_pg_connection_handle, execute_query, create_index_on_table, \
+from ebi_eva_internal_pyutils.pg_utils import get_pg_connection_handle, execute_query, create_index_on_table, \
     vacuum_analyze_table
 
 

eva-accession-release-automation/run_release_in_embassy/initiate_release_status_for_assembly.py

@@ -17,7 +17,7 @@
 
 
 from run_release_in_embassy.release_metadata import update_release_progress_status
-from ebi_eva_common_pyutils.metadata_utils import get_metadata_connection_handle
+from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle
 
 
 logger = logging.getLogger(__name__)

eva-accession-release-automation/run_release_in_embassy/merge_dbsnp_eva_release_files.py

@@ -18,7 +18,7 @@
 import os
 
 from ebi_eva_common_pyutils.command_utils import run_command_with_output
-from ebi_eva_common_pyutils.metadata_utils import get_metadata_connection_handle
+from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle
 from run_release_in_embassy.release_metadata import release_vcf_file_categories, release_text_file_categories, \
     get_release_inventory_info_for_assembly
 from run_release_in_embassy.release_common_utils import get_bgzip_bcftools_index_commands_for_file, \

eva-accession-release-automation/run_release_in_embassy/release_common_utils.py

@@ -18,7 +18,7 @@
 import traceback
 
 from run_release_in_embassy.release_metadata import get_target_mongo_instance_for_assembly
-from ebi_eva_common_pyutils.metadata_utils import get_metadata_connection_handle
+from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle
 from ebi_eva_common_pyutils.network_utils import get_available_local_port, forward_remote_port_to_local_port
 from ebi_eva_common_pyutils.taxonomy import taxonomy
 

eva-accession-release-automation/run_release_in_embassy/release_metadata.py

@@ -13,7 +13,7 @@
 # limitations under the License.
 import datetime
 
-from ebi_eva_common_pyutils.pg_utils import get_all_results_for_query
+from ebi_eva_internal_pyutils.pg_utils import get_all_results_for_query
 
 release_vcf_file_categories = ["current_ids", "merged_ids"]
 release_text_file_categories = ["deprecated_ids", "merged_deprecated_ids"]

eva-accession-release-automation/run_release_in_embassy/run_release_for_species.py

@@ -21,7 +21,7 @@
 import yaml
 
 from ebi_eva_common_pyutils.common_utils import merge_two_dicts
-from ebi_eva_common_pyutils.metadata_utils import get_metadata_connection_handle
+from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle
 from run_release_in_embassy.release_metadata import get_release_assemblies_for_taxonomy
 from run_release_in_embassy.release_common_utils import get_release_folder_name
 

eva-accession-release-automation/run_release_in_embassy/update_release_status_for_assembly.py

@@ -17,7 +17,7 @@
 
 
 from run_release_in_embassy.release_metadata import update_release_progress_status
-from ebi_eva_common_pyutils.metadata_utils import get_metadata_connection_handle
+from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle
 
 
 logger = logging.getLogger(__name__)

eva-accession-release-automation/run_release_in_embassy/validate_release_vcf_files.py

@@ -19,7 +19,7 @@
 from run_release_in_embassy.release_metadata import get_release_inventory_info_for_assembly, \
     release_vcf_file_categories, vcf_validation_output_file_pattern, asm_report_output_file_pattern
 from ebi_eva_common_pyutils.command_utils import run_command_with_output
-from ebi_eva_common_pyutils.metadata_utils import get_metadata_connection_handle
+from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle
 
 
 def remove_index_if_outdated(fasta_path):