ebi-eva-common-pyutils 0.6.6__py3-none-any.whl → 0.6.7__py3-none-any.whl

{ebi_eva_common_pyutils-0.6.6.dist-info → ebi_eva_common_pyutils-0.6.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi-eva-common-pyutils
-Version: 0.6.6
+Version: 0.6.7
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache

{ebi_eva_common_pyutils-0.6.6.dist-info → ebi_eva_common_pyutils-0.6.7.dist-info}/RECORD

@@ -19,20 +19,20 @@ 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-0.6.6.data/scripts/archive_directory.py,sha256=0lWJ0ju_AB2ni7lMnJXPFx6U2OdTGbe-WoQs-4BfKOM,4976
+ebi_eva_common_pyutils-0.6.7.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=WjPozWtXbAZGNqlgvY6GHps2KFB1rY9OaTs46obW3pM,15265
+ebi_eva_internal_pyutils/spring_properties.py,sha256=B8TpVKvXUvMilXIv6rJFcHD2kBmaFV_M9R_0doMYNts,15161
 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-0.6.6.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-ebi_eva_common_pyutils-0.6.6.dist-info/METADATA,sha256=w_We0B6eam8FRWLiTjedqj7rCvQCSf8w16KsC45XMlI,824
-ebi_eva_common_pyutils-0.6.6.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
-ebi_eva_common_pyutils-0.6.6.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
-ebi_eva_common_pyutils-0.6.6.dist-info/RECORD,,
+ebi_eva_common_pyutils-0.6.7.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+ebi_eva_common_pyutils-0.6.7.dist-info/METADATA,sha256=CkS0gM_NHH4fr1TBxoXn6FTnZ4vfT4fS41ReZCKAy0U,824
+ebi_eva_common_pyutils-0.6.7.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
+ebi_eva_common_pyutils-0.6.7.dist-info/top_level.txt,sha256=sXoiqiGU8vlMQpFWDlKrekxhlusk06AhkOH3kSvDT6c,48
+ebi_eva_common_pyutils-0.6.7.dist-info/RECORD,,

ebi_eva_internal_pyutils/spring_properties.py

@@ -117,10 +117,9 @@ class SpringPropertiesGenerator:
         merge = {**self._common_properties(read_preference=read_preference, chunk_size=chunk_size), **props}
         return merge
 
-    def _common_accessioning_clustering_properties(self, *, instance='', assembly_accession, read_preference, chunk_size):
+    def _common_accessioning_clustering_properties(self, *, assembly_accession, read_preference, chunk_size):
         """Properties common to accessioning and clustering pipelines."""
         props = {
-            'accessioning.instanceId': self._format_str('instance-{0}', instance),
             'accessioning.submitted.categoryId': 'ss',
             'accessioning.clustered.categoryId': 'rs',
             'accessioning.monotonic.ss.blockSize': 100000,
@@ -129,16 +128,18 @@ class SpringPropertiesGenerator:
             'accessioning.monotonic.rs.blockSize': 100000,
             'accessioning.monotonic.rs.blockStartValue': 3000000000,
             'accessioning.monotonic.rs.nextBlockInterval': 1000000000,
+            # This value is not used but is required to create beans in Java
+            'recovery.cutoff.days': 9999999
         }
         merge = {**self._common_accessioning_properties(assembly_accession, read_preference, chunk_size), **props}
         return merge
 
-    def get_accessioning_properties(self, *, instance=None, target_assembly=None, fasta=None, assembly_report=None,
+    def get_accessioning_properties(self, *, target_assembly=None, fasta=None, assembly_report=None,
                                     project_accession=None, aggregation='BASIC', taxonomy_accession=None,
                                     vcf_file='', output_vcf='', chunk_size=100):
         """Properties for accessioning pipeline."""
         return self._format(
-            self._common_accessioning_clustering_properties(instance=instance, assembly_accession=target_assembly,
+            self._common_accessioning_clustering_properties(assembly_accession=target_assembly,
                                                             read_preference='secondaryPreferred', chunk_size=chunk_size),
             {
                 'spring.batch.job.names': 'CREATE_SUBSNP_ACCESSION_JOB',
@@ -154,21 +155,20 @@ class SpringPropertiesGenerator:
             },
         )
 
-    def get_clustering_properties(self, *, instance=None, read_preference='primary',
-                                  job_name=None, source_assembly='', target_assembly='', rs_report_path='', projects='',
+    def get_clustering_properties(self, *, read_preference='primary', job_name=None, source_assembly='',
+                                  target_assembly='', rs_report_path='', projects='',
                                   project_accession='', vcf=''):
         """Properties common to all clustering pipelines, though not all are always used."""
         return self._format(
-            self._common_accessioning_clustering_properties(instance=instance, assembly_accession=target_assembly,
-                                                            read_preference=read_preference, chunk_size=100,
-                                                            ),
+            self._common_accessioning_clustering_properties(assembly_accession=target_assembly,
+                                                            read_preference=read_preference, chunk_size=100),
             {
                 'spring.batch.job.names': job_name,
                 'parameters.remappedFrom': source_assembly,
                 'parameters.projects': projects,
                 'parameters.projectAccession': project_accession,
                 'parameters.vcf': vcf,
-                'parameters.rsReportPath': rs_report_path
+                'parameters.rsReportPath': rs_report_path,
             }
         )