ebi-eva-common-pyutils 0.6.10__tar.gz → 0.6.12__tar.gz

{ebi_eva_common_pyutils-0.6.10 → ebi_eva_common_pyutils-0.6.12}/CHANGELOG.md

@@ -2,6 +2,18 @@
 Changelog for ebi_eva_common_pyutils
 ===========================
 
+## 0.6.12 (2025-01-21)
+----------------------
+
+- Added new properties in clustering job to run clustering qc duplicate rs accession job
+
+
+## 0.6.11 (2024-11-15)
+----------------------
+
+- Added hikari max-pool-size connection property to the method that generate property for spring jobs
+
+
 ## 0.6.10 (2024-08-06)
 ----------------------
 

{ebi_eva_common_pyutils-0.6.10 → ebi_eva_common_pyutils-0.6.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi_eva_common_pyutils
-Version: 0.6.10
+Version: 0.6.12
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache

{ebi_eva_common_pyutils-0.6.10 → ebi_eva_common_pyutils-0.6.12}/ebi_eva_common_pyutils.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi-eva-common-pyutils
-Version: 0.6.10
+Version: 0.6.12
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache

{ebi_eva_common_pyutils-0.6.10 → ebi_eva_common_pyutils-0.6.12}/ebi_eva_internal_pyutils/spring_properties.py

@@ -83,7 +83,7 @@ class SpringPropertiesGenerator:
             'eva.count-stats.password': counts_password
         }
 
-    def _common_properties(self, *, read_preference='primary', chunk_size=100):
+    def _common_properties(self, *, read_preference='primary', chunk_size=100, max_pool_size=2):
         """Properties common to all Spring pipelines"""
         props = {
             'spring.datasource.driver-class-name': 'org.postgresql.Driver',
@@ -98,6 +98,7 @@ class SpringPropertiesGenerator:
             'spring.jpa.properties.hibernate.temp.use_jdbc_metadata_defaults': 'false',
             'spring.jpa.database-platform': 'org.hibernate.dialect.PostgreSQL9Dialect',
             'parameters.chunkSize': chunk_size,
+            'spring.datasource.hikari.maximum-pool-size': max_pool_size
         }
         merge = {**self._mongo_properties(), **self._count_stats_properties(), **props}
         return merge
@@ -140,7 +141,8 @@ class SpringPropertiesGenerator:
         """Properties for accessioning pipeline."""
         return self._format(
             self._common_accessioning_clustering_properties(assembly_accession=target_assembly,
-                                                            read_preference='secondaryPreferred', chunk_size=chunk_size),
+                                                            read_preference='secondaryPreferred',
+                                                            chunk_size=chunk_size),
             {
                 'spring.batch.job.names': 'CREATE_SUBSNP_ACCESSION_JOB',
                 'parameters.assemblyReportUrl': self._format_str('file:{0}', assembly_report),
@@ -156,8 +158,8 @@ class SpringPropertiesGenerator:
         )
 
     def get_clustering_properties(self, *, read_preference='primary', job_name=None, source_assembly='',
-                                  target_assembly='', rs_report_path='', projects='',
-                                  project_accession='', vcf=''):
+                                  target_assembly='', rs_report_path='', rs_acc_file='', duplicate_rs_acc_file='',
+                                  projects='', project_accession='', vcf=''):
         """Properties common to all clustering pipelines, though not all are always used."""
         return self._format(
             self._common_accessioning_clustering_properties(assembly_accession=target_assembly,
@@ -169,6 +171,8 @@ class SpringPropertiesGenerator:
                 'parameters.projectAccession': project_accession,
                 'parameters.vcf': vcf,
                 'parameters.rsReportPath': rs_report_path,
+                'parameters.rsAccFile': rs_acc_file,
+                'parameters.duplicateRSAccFile': duplicate_rs_acc_file,
             }
         )
 
@@ -262,7 +266,8 @@ class SpringPropertiesGenerator:
             'logging.level.org.springframework': 'INFO',
         }
 
-        merge = {**self._common_properties(read_preference=read_preference, chunk_size=100), **props, **job_tracker_properties}
+        merge = {**self._common_properties(read_preference=read_preference, chunk_size=100), **props,
+                 **job_tracker_properties}
         return merge
 
     def get_accession_import_properties(self, opencga_path, read_preference='secondaryPreferred'):

{ebi_eva_common_pyutils-0.6.10 → ebi_eva_common_pyutils-0.6.12}/setup.py

@@ -7,7 +7,7 @@ setup(
     name='ebi_eva_common_pyutils',
     scripts=[os.path.join(os.path.dirname(__file__), 'ebi_eva_internal_pyutils', 'archive_directory.py')],
     packages=find_packages(),
-    version='0.6.10',
+    version='0.6.12',
     license='Apache',
     description='EBI EVA - Common Python Utilities',
     url='https://github.com/EBIVariation/eva-common-pyutils',