ebi-eva-common-pyutils 0.6.9__py3-none-any.whl → 0.6.12__py3-none-any.whl

ebi_eva_common_pyutils/biosamples_communicators.py

@@ -103,9 +103,15 @@ class HALCommunicator(AppLogger):
                 url = re.sub('{(' + k + ')(:.*)?}', v, url)
         if join_url:
             url += '/' + join_url
+        text_only = False
+        if 'text_only' in kwargs and kwargs.get('text_only'):
+            text_only = kwargs.pop('text_only')
         # Now query the url
-        json_response = self._req(method, url, **kwargs).json()
+        response = self._req(method, url, **kwargs)
+        if text_only:
+            return response.text
 
+        json_response = response.json()
         # Depaginate the call if requested
         if all_pages is True:
             # This depagination code will iterate over all the pages available until the pages comes back  without a

{ebi_eva_common_pyutils-0.6.9.dist-info → ebi_eva_common_pyutils-0.6.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi-eva-common-pyutils
-Version: 0.6.9
+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-0.6.9.dist-info → ebi_eva_common_pyutils-0.6.12.dist-info}/RECORD

@@ -1,6 +1,6 @@
 ebi_eva_common_pyutils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ebi_eva_common_pyutils/assembly_utils.py,sha256=CklyCGlCjlFp0e9pugg6kSsh5L0xfCe2qPvA2eLVtn0,4187
-ebi_eva_common_pyutils/biosamples_communicators.py,sha256=ngWuSvEYkkttkMnJ9Gjxc5D7ZSi7D3_JX1c8BnEO3os,7596
+ebi_eva_common_pyutils/biosamples_communicators.py,sha256=nyO0E_YpcAeBwbqOfbqe9RDxONq7Oe3NijSTGw7D01I,7815
 ebi_eva_common_pyutils/command_utils.py,sha256=PtelWWqcC0eOwIVesjwBw3F9KaXRzEE_uAUJhQFZ4l8,2340
 ebi_eva_common_pyutils/common_utils.py,sha256=ty_glvfRa3VGhnpAht4qtVkNNmv-IYfVtO958mY-BaA,1192
 ebi_eva_common_pyutils/config.py,sha256=PtD2SgHf96kk21OA9tVIjEgsDXEFuAU-INy_kfQdoPw,4828
@@ -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-0.6.9.data/scripts/archive_directory.py,sha256=0lWJ0ju_AB2ni7lMnJXPFx6U2OdTGbe-WoQs-4BfKOM,4976
+ebi_eva_common_pyutils-0.6.12.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=Ine5O27gu_zQjWt90Euuw1ACyPaqR_DpOpp_zEtSkh8,15494
 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-0.6.9.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-ebi_eva_common_pyutils-0.6.9.dist-info/METADATA,sha256=iEw5N92Ad8rSkru7KNyzfpSgUD0NCpuF4Eu1dPSVp1I,824
-ebi_eva_common_pyutils-0.6.9.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
-ebi_eva_common_pyutils-0.6.9.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
-ebi_eva_common_pyutils-0.6.9.dist-info/RECORD,,
+ebi_eva_common_pyutils-0.6.12.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+ebi_eva_common_pyutils-0.6.12.dist-info/METADATA,sha256=C_HcYzKUZ4y0bpBQGFFx3iUJAxD0JUvUz4UPjmgf8xY,825
+ebi_eva_common_pyutils-0.6.12.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
+ebi_eva_common_pyutils-0.6.12.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
+ebi_eva_common_pyutils-0.6.12.dist-info/RECORD,,

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'):