ebi-eva-common-pyutils 0.6.3__tar.gz → 0.6.4__tar.gz

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Files changed (44) hide show
  1. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/CHANGELOG.md +5 -0
  2. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/PKG-INFO +1 -1
  3. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils.egg-info/PKG-INFO +1 -1
  4. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_internal_pyutils/mongodb/mongo_database.py +1 -3
  5. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/setup.py +1 -1
  6. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/LICENSE +0 -0
  7. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/MANIFEST.in +0 -0
  8. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/README.md +0 -0
  9. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/__init__.py +0 -0
  10. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/assembly/__init__.py +0 -0
  11. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/assembly/assembly.py +0 -0
  12. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/assembly_utils.py +0 -0
  13. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/command_utils.py +0 -0
  14. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/common_utils.py +0 -0
  15. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/config.py +0 -0
  16. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/contig_alias/__init__.py +0 -0
  17. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/contig_alias/contig_alias.py +0 -0
  18. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/ena_utils.py +0 -0
  19. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/file_utils.py +0 -0
  20. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/logger.py +0 -0
  21. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/ncbi_utils.py +0 -0
  22. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/network_utils.py +0 -0
  23. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/reference/__init__.py +0 -0
  24. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/reference/assembly.py +0 -0
  25. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/reference/sequence.py +0 -0
  26. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/taxonomy/__init__.py +0 -0
  27. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/taxonomy/taxonomy.py +0 -0
  28. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/variation/__init__.py +0 -0
  29. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils/variation/contig_utils.py +0 -0
  30. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils.egg-info/SOURCES.txt +0 -0
  31. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils.egg-info/dependency_links.txt +0 -0
  32. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils.egg-info/requires.txt +0 -0
  33. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils.egg-info/top_level.txt +0 -0
  34. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_internal_pyutils/__init__.py +0 -0
  35. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_internal_pyutils/archive_directory.py +0 -0
  36. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_internal_pyutils/config_utils.py +0 -0
  37. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_internal_pyutils/metadata_utils.py +0 -0
  38. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_internal_pyutils/mongo_utils.py +0 -0
  39. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_internal_pyutils/mongodb/__init__.py +0 -0
  40. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_internal_pyutils/nextflow/__init__.py +0 -0
  41. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_internal_pyutils/nextflow/nextflow_pipeline.py +0 -0
  42. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_internal_pyutils/pg_utils.py +0 -0
  43. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_internal_pyutils/spring_properties.py +0 -0
  44. {ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/setup.cfg +0 -0
{ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/CHANGELOG.md RENAMED
@@ -2,6 +2,11 @@
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  Changelog for ebi_eva_common_pyutils
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  ===========================
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+ ## 0.6.4 (2024-03-21)
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+ ---------------------
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+
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+ - Update Mongodb client to use mongosh instead of the legacy mongo.
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+
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  ## 0.6.3 (2024-02-22)
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  ---------------------
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{ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/PKG-INFO RENAMED
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  Metadata-Version: 2.1
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  Name: ebi_eva_common_pyutils
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- Version: 0.6.3
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+ Version: 0.6.4
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  Summary: EBI EVA - Common Python Utilities
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  Home-page: https://github.com/EBIVariation/eva-common-pyutils
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  License: Apache
{ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_common_pyutils.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: ebi-eva-common-pyutils
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- Version: 0.6.3
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+ Version: 0.6.4
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  Summary: EBI EVA - Common Python Utilities
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  Home-page: https://github.com/EBIVariation/eva-common-pyutils
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  License: Apache
{ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/ebi_eva_internal_pyutils/mongodb/mongo_database.py RENAMED
@@ -111,9 +111,7 @@ class MongoDatabase(AppLogger):
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  shard_collection_command = f'sh.shardCollection(' \
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  f'"{self.db_name}.{collection_name}", ' \
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  f'{shard_key_repr}, {str(shard_key_uniqueness_flag).lower()})'
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- sharding_command = f"mongo --host {self.uri} " \
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- f"--eval " \
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- f"'{shard_collection_command}' "
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+ sharding_command = f"mongosh --eval '{shard_collection_command}' {self.uri} "
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  sharding_command += self._get_optional_secrets_file_stdin()
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  run_command_with_output(f"Sharding collection {collection_name} in the database {self.uri_with_db_name} "
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  f"with key {shard_key_repr}...", sharding_command,
{ebi_eva_common_pyutils-0.6.3 → ebi_eva_common_pyutils-0.6.4}/setup.py RENAMED
@@ -7,7 +7,7 @@ setup(
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  name='ebi_eva_common_pyutils',
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  scripts=[os.path.join(os.path.dirname(__file__), 'ebi_eva_internal_pyutils', 'archive_directory.py')],
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  packages=find_packages(),
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- version='0.6.3',
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+ version='0.6.4',
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  license='Apache',
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  description='EBI EVA - Common Python Utilities',
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  url='https://github.com/EBIVariation/eva-common-pyutils',