ebi-eva-common-pyutils 0.6.13__tar.gz → 0.6.14__tar.gz

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Files changed (46) hide show
  1. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/CHANGELOG.md +6 -0
  2. {ebi_eva_common_pyutils-0.6.13/ebi_eva_common_pyutils.egg-info → ebi_eva_common_pyutils-0.6.14}/PKG-INFO +1 -1
  3. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14/ebi_eva_common_pyutils.egg-info}/PKG-INFO +1 -1
  4. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils.egg-info/SOURCES.txt +1 -1
  5. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_internal_pyutils/spring_properties.py +3 -1
  6. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/setup.py +1 -1
  7. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/LICENSE +0 -0
  8. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/MANIFEST.in +0 -0
  9. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/README.md +0 -0
  10. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/__init__.py +0 -0
  11. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/assembly/__init__.py +0 -0
  12. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/assembly/assembly.py +0 -0
  13. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/assembly_utils.py +0 -0
  14. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/biosamples_communicators.py +0 -0
  15. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/command_utils.py +0 -0
  16. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/common_utils.py +0 -0
  17. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/config.py +0 -0
  18. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/contig_alias/__init__.py +0 -0
  19. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/contig_alias/contig_alias.py +0 -0
  20. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/ena_utils.py +0 -0
  21. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/file_utils.py +0 -0
  22. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/logger.py +0 -0
  23. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/ncbi_utils.py +0 -0
  24. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/network_utils.py +0 -0
  25. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/reference/__init__.py +0 -0
  26. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/reference/assembly.py +0 -0
  27. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/reference/sequence.py +0 -0
  28. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/taxonomy/__init__.py +0 -0
  29. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/taxonomy/taxonomy.py +0 -0
  30. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/variation/__init__.py +0 -0
  31. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils/variation/contig_utils.py +0 -0
  32. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils.egg-info/dependency_links.txt +0 -0
  33. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils.egg-info/requires.txt +0 -0
  34. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_common_pyutils.egg-info/top_level.txt +0 -0
  35. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_internal_pyutils/__init__.py +0 -0
  36. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_internal_pyutils/archive_directory.py +0 -0
  37. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_internal_pyutils/config_utils.py +0 -0
  38. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_internal_pyutils/metadata_utils.py +0 -0
  39. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_internal_pyutils/mongo_utils.py +0 -0
  40. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_internal_pyutils/mongodb/__init__.py +0 -0
  41. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_internal_pyutils/mongodb/mongo_database.py +0 -0
  42. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_internal_pyutils/nextflow/__init__.py +0 -0
  43. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_internal_pyutils/nextflow/nextflow_pipeline.py +0 -0
  44. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/ebi_eva_internal_pyutils/pg_utils.py +0 -0
  45. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/setup.cfg +0 -0
  46. {ebi_eva_common_pyutils-0.6.13 → ebi_eva_common_pyutils-0.6.14}/tests/test_common.py +0 -0
@@ -2,6 +2,12 @@
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  Changelog for ebi_eva_common_pyutils
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  ===========================
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+ ## 0.6.14 (2025-03-05)
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+ ----------------------
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+
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+ - Bugfix for connection string
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+
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+
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  ## 0.6.13 (2025-03-05)
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  ----------------------
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@@ -1,6 +1,6 @@
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  Metadata-Version: 2.2
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  Name: ebi_eva_common_pyutils
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- Version: 0.6.13
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+ Version: 0.6.14
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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
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.2
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  Name: ebi_eva_common_pyutils
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- Version: 0.6.13
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+ Version: 0.6.14
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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
@@ -4,7 +4,7 @@ MANIFEST.in
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  README.md
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  setup.cfg
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  setup.py
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- /tmp/ebi_eva_common_pyutils-v0.6.13-jtxab0mq/gitclone/ebi_eva_internal_pyutils/archive_directory.py
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+ /tmp/ebi_eva_common_pyutils-v0.6.14-5o4eugy3/gitclone/ebi_eva_internal_pyutils/archive_directory.py
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  ebi_eva_common_pyutils/__init__.py
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  ebi_eva_common_pyutils/assembly_utils.py
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  ebi_eva_common_pyutils/biosamples_communicators.py
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  # See the License for the specific language governing permissions and
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  # limitations under the License.
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  from collections import defaultdict
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+ from urllib.parse import quote_plus
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  from ebi_eva_internal_pyutils.config_utils import get_mongo_creds_for_profile, get_accession_pg_creds_for_profile, \
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  get_count_service_creds_for_profile, get_properties_from_xml_file, get_variant_load_job_tracker_creds_for_profile
@@ -55,7 +56,8 @@ class SpringPropertiesGenerator:
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  def _mongo_properties(self):
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  mongo_host, mongo_user, mongo_pass = get_mongo_creds_for_profile(
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  self.maven_profile, self.private_settings_file)
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- username_with_password = f'{mongo_user}:{mongo_pass}@' if mongo_user is not None and mongo_pass is not None else ''
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+ username_with_password = (f'{quote_plus(mongo_user)}:{quote_plus(mongo_pass)}@'
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+ if mongo_user is not None and mongo_pass is not None else '')
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  return {
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  'spring.data.mongodb.uri': f'mongodb://{username_with_password}{mongo_host}/?retryWrites=true&authSource=admin',
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  }
@@ -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='0.6.13',
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+ version='0.6.14',
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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',