ebi-eva-common-pyutils 0.6.10__py3-none-any.whl → 0.6.13__py3-none-any.whl

{ebi_eva_common_pyutils-0.6.10.dist-info → ebi_eva_common_pyutils-0.6.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
-Name: ebi-eva-common-pyutils
-Version: 0.6.10
+Metadata-Version: 2.2
+Name: ebi_eva_common_pyutils
+Version: 0.6.13
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache
@@ -17,7 +17,13 @@ Requires-Dist: pyyaml
 Requires-Dist: cached-property
 Requires-Dist: retry
 Provides-Extra: eva-internal
-Requires-Dist: psycopg2-binary ; extra == 'eva-internal'
-Requires-Dist: pymongo ; extra == 'eva-internal'
-Requires-Dist: networkx (<=2.5) ; extra == 'eva-internal'
-
+Requires-Dist: psycopg2-binary; extra == "eva-internal"
+Requires-Dist: pymongo; extra == "eva-internal"
+Requires-Dist: networkx<=2.5; extra == "eva-internal"
+Dynamic: classifier
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary

{ebi_eva_common_pyutils-0.6.10.dist-info → ebi_eva_common_pyutils-0.6.13.dist-info}/RECORD

@@ -20,20 +20,20 @@ ebi_eva_common_pyutils/taxonomy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm
 ebi_eva_common_pyutils/taxonomy/taxonomy.py,sha256=p3XV4g3y0hEjyeZ4PwgN7Q3Et9G515ctQkSIo1kdDbU,2259
 ebi_eva_common_pyutils/variation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ebi_eva_common_pyutils/variation/contig_utils.py,sha256=kMNEW_P2yPnd8Xx1tep19hy5ee7ojxz6ZOO1grTQsRQ,5230
-ebi_eva_common_pyutils-0.6.10.data/scripts/archive_directory.py,sha256=0lWJ0ju_AB2ni7lMnJXPFx6U2OdTGbe-WoQs-4BfKOM,4976
+ebi_eva_common_pyutils-0.6.13.data/scripts/archive_directory.py,sha256=0lWJ0ju_AB2ni7lMnJXPFx6U2OdTGbe-WoQs-4BfKOM,4976
 ebi_eva_internal_pyutils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ebi_eva_internal_pyutils/archive_directory.py,sha256=IxVEfh_gaCiT652k0Q_-58fonRusy1yzXu7BCO8yVLo,4989
 ebi_eva_internal_pyutils/config_utils.py,sha256=EGRC5rsmU_ug7OY9-t1UW1XZXRsauSyZB9xPcBux8ts,7909
 ebi_eva_internal_pyutils/metadata_utils.py,sha256=t9PcXZdbfjDBP04GJenC4bxm2nOLd8oI_MP9eNe9IBQ,15221
 ebi_eva_internal_pyutils/mongo_utils.py,sha256=YxKHtb5ygDiGLOtEiiAMFCP2ow6FL9Kq0K5R0mWNdXY,3575
 ebi_eva_internal_pyutils/pg_utils.py,sha256=FUQVwiX_7F2-4sSzoaCVX2me0zAqR8nGIj6NW5d304A,4398
-ebi_eva_internal_pyutils/spring_properties.py,sha256=B8TpVKvXUvMilXIv6rJFcHD2kBmaFV_M9R_0doMYNts,15161
+ebi_eva_internal_pyutils/spring_properties.py,sha256=j7_u_2ZVazXK4u5kJrQpJ1fljE0HsC1RbXpmJ7WYh5A,15069
 ebi_eva_internal_pyutils/mongodb/__init__.py,sha256=0oyTlkYZCV7udlPl09Zl-sDyE3c97QZMMTEFIa6uYIw,76
 ebi_eva_internal_pyutils/mongodb/mongo_database.py,sha256=kesaJaaxYFeF_uYZBgL8tbufGKUXll7bXb4WlOS9vKM,9596
 ebi_eva_internal_pyutils/nextflow/__init__.py,sha256=OOiJS8jZOz98q0t77NNog7aI_fFrVxi4kGmiSskuAqM,122
 ebi_eva_internal_pyutils/nextflow/nextflow_pipeline.py,sha256=ew623hhK8jmFLQjJwLZbgBmW9RTiJBEULVqHfIUv_dc,10114
-ebi_eva_common_pyutils-0.6.10.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-ebi_eva_common_pyutils-0.6.10.dist-info/METADATA,sha256=bBaC1wBXTMZ8Sip4qg0Fb9MpapoMsaga7Hh0C8pQBWs,825
-ebi_eva_common_pyutils-0.6.10.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
-ebi_eva_common_pyutils-0.6.10.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
-ebi_eva_common_pyutils-0.6.10.dist-info/RECORD,,
+ebi_eva_common_pyutils-0.6.13.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+ebi_eva_common_pyutils-0.6.13.dist-info/METADATA,sha256=Ogn0HxF_NPkmxL1k4oXhsdYvyWwcflXWGtJGkY-JkTo,956
+ebi_eva_common_pyutils-0.6.13.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
+ebi_eva_common_pyutils-0.6.13.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
+ebi_eva_common_pyutils-0.6.13.dist-info/RECORD,,

{ebi_eva_common_pyutils-0.6.10.dist-info → ebi_eva_common_pyutils-0.6.13.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.38.4)
+Generator: setuptools (75.8.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

ebi_eva_internal_pyutils/spring_properties.py

@@ -55,14 +55,9 @@ class SpringPropertiesGenerator:
     def _mongo_properties(self):
         mongo_host, mongo_user, mongo_pass = get_mongo_creds_for_profile(
             self.maven_profile, self.private_settings_file)
+        username_with_password = f'{mongo_user}:{mongo_pass}@' if mongo_user is not None and mongo_pass is not None else ''
         return {
-            'spring.data.mongodb.host': mongo_host,
-            # Don't specify port if hosts already have the port encoded in them
-            # Also see https://github.com/EBIvariation/variation-commons/blob/329d4fa18da73bdad419ca5456b9897c059e33f0/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/utils/MongoClientURIBuilder.java#L44
-            'spring.data.mongodb.port': '' if ':' in mongo_host else 27017,
-            'spring.data.mongodb.username': '' if mongo_user is None else mongo_user,
-            'spring.data.mongodb.password': '' if mongo_pass is None else mongo_pass,
-            'spring.data.mongodb.authentication-database': 'admin',
+            'spring.data.mongodb.uri': f'mongodb://{username_with_password}{mongo_host}/?retryWrites=true&authSource=admin',
         }
 
     def _variant_load_job_tracker_properties(self):
@@ -83,7 +78,7 @@ 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 +93,7 @@ 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 +136,8 @@ 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 +153,8 @@ 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 +166,8 @@ 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 +261,8 @@ 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'):