ebi-eva-common-pyutils 0.6.11__tar.gz → 0.6.12__tar.gz

{ebi_eva_common_pyutils-0.6.11 → ebi_eva_common_pyutils-0.6.12}/CHANGELOG.md

@@ -2,6 +2,12 @@
 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)
 ----------------------
 

{ebi_eva_common_pyutils-0.6.11 → ebi_eva_common_pyutils-0.6.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi_eva_common_pyutils
-Version: 0.6.11
+Version: 0.6.12
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache
@@ -10,13 +10,5 @@ Classifier: Intended Audience :: Developers
 Classifier: Topic :: Software Development :: Build Tools
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python :: 3
-License-File: LICENSE
-Requires-Dist: requests
-Requires-Dist: lxml
-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"
+License-File: LICENSE

{ebi_eva_common_pyutils-0.6.11 → 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: 0.6.11
+Version: 0.6.12
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache
@@ -10,13 +10,5 @@ Classifier: Intended Audience :: Developers
 Classifier: Topic :: Software Development :: Build Tools
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python :: 3
-License-File: LICENSE
-Requires-Dist: requests
-Requires-Dist: lxml
-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"
+License-File: LICENSE

{ebi_eva_common_pyutils-0.6.11 → ebi_eva_common_pyutils-0.6.12}/ebi_eva_common_pyutils.egg-info/SOURCES.txt

@@ -4,7 +4,6 @@ MANIFEST.in
 README.md
 setup.cfg
 setup.py
-/home/nkumar2/PycharmProjects/eva-common-pyutils/ebi_eva_internal_pyutils/archive_directory.py
 ebi_eva_common_pyutils/__init__.py
 ebi_eva_common_pyutils/assembly_utils.py
 ebi_eva_common_pyutils/biosamples_communicators.py
@@ -42,5 +41,4 @@ ebi_eva_internal_pyutils/spring_properties.py
 ebi_eva_internal_pyutils/mongodb/__init__.py
 ebi_eva_internal_pyutils/mongodb/mongo_database.py
 ebi_eva_internal_pyutils/nextflow/__init__.py
-ebi_eva_internal_pyutils/nextflow/nextflow_pipeline.py
-tests/test_common.py
+ebi_eva_internal_pyutils/nextflow/nextflow_pipeline.py

{ebi_eva_common_pyutils-0.6.11 → ebi_eva_common_pyutils-0.6.12}/ebi_eva_internal_pyutils/spring_properties.py

@@ -141,7 +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),
@@ -157,8 +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,
@@ -170,6 +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,
             }
         )
 
@@ -263,7 +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-0.6.11 → 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='0.6.11',
+    version='0.6.12',
     license='Apache',
     description='EBI EVA - Common Python Utilities',
     url='https://github.com/EBIVariation/eva-common-pyutils',

ebi_eva_common_pyutils-0.6.11/tests/test_common.py

@@ -1,22 +0,0 @@
-import os
-from unittest import TestCase
-
-from ebi_eva_common_pyutils.common_utils import merge_two_dicts, pretty_print
-
-
-class TestCommon(TestCase):
-
-    resources_folder = os.path.join(os.path.dirname(__file__), 'resources')
-
-
-class TestCommonUtils(TestCase):
-
-    def test_merge_two_dicts(self):
-        d1 = {'a': 1, 'b': 2, 'c': 3}
-        d2 = {'d': 4, 'a': 5, 'e': 6}
-        assert merge_two_dicts(d1, d2) == {'a': 5, 'b': 2, 'c': 3, 'd': 4, 'e': 6}
-        assert merge_two_dicts(d2, d1) == {'a': 1, 'b': 2, 'c': 3, 'd': 4, 'e': 6}
-
-    def test_pretty_print(self):
-        pretty_print(['Header 1', 'Long Header 2'],
-                     [['row1 cell 1', 'row1 cell 2'], ['row2 cell 1', 'Super long row2 cell 2']])