ghga-transpiler 2.3.1__tar.gz → 2.4.0__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (31) hide show
  1. {ghga_transpiler-2.3.1/src/ghga_transpiler.egg-info → ghga_transpiler-2.4.0}/PKG-INFO +2 -2
  2. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/pyproject.toml +2 -2
  3. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/configs/2.0.yaml +4 -0
  4. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/configs/2.1.yaml +4 -0
  5. ghga_transpiler-2.4.0/src/ghga_transpiler/configs/2.2.yaml +178 -0
  6. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/transformations.py +5 -0
  7. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0/src/ghga_transpiler.egg-info}/PKG-INFO +2 -2
  8. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler.egg-info/SOURCES.txt +1 -0
  9. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler.egg-info/requires.txt +1 -1
  10. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/LICENSE +0 -0
  11. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/README.md +0 -0
  12. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/setup.cfg +0 -0
  13. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/__init__.py +0 -0
  14. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/__main__.py +0 -0
  15. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/cli.py +0 -0
  16. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/config/__init__.py +0 -0
  17. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/config/config.py +0 -0
  18. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/config/exceptions.py +0 -0
  19. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/configs/0.10.yaml +0 -0
  20. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/configs/1.0.yaml +0 -0
  21. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/configs/1.1.yaml +0 -0
  22. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/configs/__init__.py +0 -0
  23. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/core.py +0 -0
  24. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/io.py +0 -0
  25. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler.egg-info/dependency_links.txt +0 -0
  26. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler.egg-info/entry_points.txt +0 -0
  27. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler.egg-info/top_level.txt +0 -0
  28. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/tests/test_convert_workbook.py +0 -0
  29. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/tests/test_create_config.py +0 -0
  30. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/tests/test_io.py +0 -0
  31. {ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/tests/test_process_workbook.py +0 -0
{ghga_transpiler-2.3.1/src/ghga_transpiler.egg-info → ghga_transpiler-2.4.0}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: ghga_transpiler
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- Version: 2.3.1
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+ Version: 2.4.0
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  Summary: GHGA-Transpiler - excel to JSON converter
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  Author-email: "German Human Genome Phenome Archive (GHGA)" <contact@ghga.de>
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  License: Apache 2.0
@@ -22,7 +22,7 @@ Requires-Dist: defusedxml==0.*,>=0.7
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  Requires-Dist: pydantic<3,>=2.6
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  Requires-Dist: PyYAML~=6.0
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  Requires-Dist: semver==3.*
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- Requires-Dist: click==8.1.0
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+ Requires-Dist: click~=8.1.0
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  Dynamic: license-file
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{ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/pyproject.toml RENAMED
@@ -21,7 +21,7 @@ classifiers = [
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  "Intended Audience :: Developers",
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  ]
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  name = "ghga_transpiler"
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- version = "2.3.1"
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+ version = "2.4.0"
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  description = "GHGA-Transpiler - excel to JSON converter"
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  dependencies = [
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  "typer >= 0.12",
@@ -30,7 +30,7 @@ dependencies = [
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  "pydantic >=2.6, <3",
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  "PyYAML ~= 6.0",
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  "semver == 3.*",
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- "click==8.1.0",
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+ "click ~= 8.1.0",
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  ]
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  [project.license]
{ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/configs/2.0.yaml RENAMED
@@ -119,6 +119,8 @@ worksheets:
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  !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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  attributes:
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  !!python/object/apply:ghga_transpiler.transformations.to_attributes []
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+ sequencing_read_length:
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+ !!python/name:ghga_transpiler.transformations.to_string
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  sheet_name: ExperimentMethod
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  - settings:
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  end_column: 7
@@ -136,6 +138,8 @@ worksheets:
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  !!python/object/apply:ghga_transpiler.transformations.to_list []
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  format:
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  !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ sequencing_lane_id:
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+ !!python/name:ghga_transpiler.transformations.to_string
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  sheet_name: ResearchDataFile
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  - settings:
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  end_column: 7
{ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/configs/2.1.yaml RENAMED
@@ -121,6 +121,8 @@ worksheets:
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  !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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  attributes:
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  !!python/object/apply:ghga_transpiler.transformations.to_attributes []
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+ sequencing_read_length:
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+ !!python/name:ghga_transpiler.transformations.to_string
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  sheet_name: ExperimentMethod
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  - settings:
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  end_column: 7
@@ -138,6 +140,8 @@ worksheets:
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  !!python/object/apply:ghga_transpiler.transformations.to_list []
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  format:
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  !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ sequencing_lane_id:
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+ !!python/name:ghga_transpiler.transformations.to_string
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  sheet_name: ResearchDataFile
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  - settings:
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  end_column: 7
ghga_transpiler-2.4.0/src/ghga_transpiler/configs/2.2.yaml ADDED
@@ -0,0 +1,178 @@
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+ ghga_metadata_version: 2.2.0
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+ default_settings:
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+ header_row: 1
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+ start_row: 7
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+ start_column: 1
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+ transformations:
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+ attributes:
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+ !!python/object/apply:ghga_transpiler.transformations.to_attributes []
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+ format:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ worksheets:
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+ - settings:
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+ end_column: 7
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+ name: analyses
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+ transformations:
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+ research_data_files:
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+ !!python/object/apply:ghga_transpiler.transformations.to_list []
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+ sheet_name: Analysis
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+ - settings:
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+ end_column: 17
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+ name: analysis_methods
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+ transformations:
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+ reference_type:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ parameters:
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+ !!python/object/apply:ghga_transpiler.transformations.to_attributes []
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+ software_versions:
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+ !!python/object/apply:ghga_transpiler.transformations.to_attributes []
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+ attributes:
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+ !!python/object/apply:ghga_transpiler.transformations.to_attributes []
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+ sheet_name: AnalysisMethod
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+ - settings:
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+ end_column: 7
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+ name: analysis_method_supporting_files
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+ sheet_name: AnalysisMethodSupportingFile
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+ - settings:
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+ end_column: 7
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+ name: studies
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+ transformations:
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+ affiliations:
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+ !!python/object/apply:ghga_transpiler.transformations.to_list []
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+ attributes:
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+ !!python/object/apply:ghga_transpiler.transformations.to_attributes []
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+ types:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case_list []
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+ attributes:
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+ !!python/object/apply:ghga_transpiler.transformations.to_attributes []
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+ sheet_name: Study
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+ - settings:
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+ end_column: 10
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+ name: individuals
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+ transformations:
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+ phenotypic_features_terms:
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+ !!python/object/apply:ghga_transpiler.transformations.to_list []
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+ phenotypic_features_ids:
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+ !!python/object/apply:ghga_transpiler.transformations.to_list []
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+ diagnosis_ids:
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+ !!python/object/apply:ghga_transpiler.transformations.to_list []
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+ diagnosis_terms:
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+ !!python/object/apply:ghga_transpiler.transformations.to_list []
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+ sex:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ ancestry_terms:
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+ !!python/object/apply:ghga_transpiler.transformations.to_list []
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+ ancestry_ids:
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+ !!python/object/apply:ghga_transpiler.transformations.to_list []
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+ sheet_name: Individual
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+ - settings:
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+ end_column: 7
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+ name: individual_supporting_files
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+ sheet_name: IndividualSupportingFile
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+ - settings:
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+ end_column: 21
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+ name: samples
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+ transformations:
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+ type:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ storage:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ disease_or_healthy:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ case_control_status:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ xref: !!python/object/apply:ghga_transpiler.transformations.to_list []
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+ biospecimen_age_at_sampling:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ biospecimen_vital_status_at_sampling:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ biospecimen_isolation:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ biospecimen_storage:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ attributes:
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+ !!python/object/apply:ghga_transpiler.transformations.to_attributes []
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+ sheet_name: Sample
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+ - settings:
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+ end_column: 23
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+ name: experiment_methods
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+ transformations:
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+ library_type:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ library_selection_methods:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case_list []
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+ library_preparation_kit_retail_name:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ primer:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ end_bias:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ target_regions:
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+ !!python/object/apply:ghga_transpiler.transformations.to_list []
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+ rnaseq_strandedness:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ instrument_model:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ sequencing_layout:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ flow_cell_type:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ sample_barcode_read:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ sequencing_layout:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ attributes:
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+ !!python/object/apply:ghga_transpiler.transformations.to_attributes []
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+ sequencing_read_length:
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+ !!python/name:ghga_transpiler.transformations.to_string
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+ sheet_name: ExperimentMethod
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+ - settings:
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+ end_column: 7
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+ name: experiment_method_supporting_files
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+ sheet_name: ExperimentMethodSupportingFile
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+ - settings:
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+ end_column: 8
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+ name: experiments
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+ sheet_name: Experiment
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+ - settings:
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+ end_column: 9
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+ name: research_data_files
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+ transformations:
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+ experiments:
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+ !!python/object/apply:ghga_transpiler.transformations.to_list []
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+ format:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ sequencing_lane_id:
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+ !!python/name:ghga_transpiler.transformations.to_string
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+ sheet_name: ResearchDataFile
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+ - settings:
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+ end_column: 7
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+ name: process_data_files
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+ sheet_name: ProcessDataFile
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+ - settings:
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+ end_column: 7
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+ name: datasets
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+ transformations:
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+ types: !!python/object/apply:ghga_transpiler.transformations.to_list []
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+ sheet_name: Dataset
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+ - settings:
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+ end_column: 11
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+ name: data_access_policies
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+ transformations:
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+ data_use_modifier_terms:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case_list []
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+ data_use_permission_term:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ data_use_modifier_ids:
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+ !!python/object/apply:ghga_transpiler.transformations.to_list []
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+ sheet_name: DataAccessPolicy
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+ - settings:
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+ end_column: 4
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+ name: data_access_committees
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+ sheet_name: DataAccessCommittee
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+ - settings:
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+ end_column: 9
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+ name: publications
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+ transformations:
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+ xref: !!python/object/apply:ghga_transpiler.transformations.to_list []
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+ sheet_name: Publication
{ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler/transformations.py RENAMED
@@ -20,6 +20,11 @@
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  from collections.abc import Callable
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+ def to_string(value: int | str) -> str:
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+ """Converts a value to string"""
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+ return str(value)
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+
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+
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  def split_by_semicolon(value: str) -> list[str]:
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  """Splits a string by semicolon"""
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  return [elem.strip() for elem in value.split(";")]
{ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0/src/ghga_transpiler.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: ghga_transpiler
3
- Version: 2.3.1
3
+ Version: 2.4.0
4
4
  Summary: GHGA-Transpiler - excel to JSON converter
5
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  Author-email: "German Human Genome Phenome Archive (GHGA)" <contact@ghga.de>
6
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  License: Apache 2.0
@@ -22,7 +22,7 @@ Requires-Dist: defusedxml==0.*,>=0.7
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  Requires-Dist: pydantic<3,>=2.6
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  Requires-Dist: PyYAML~=6.0
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  Requires-Dist: semver==3.*
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- Requires-Dist: click==8.1.0
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+ Requires-Dist: click~=8.1.0
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  Dynamic: license-file
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{ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler.egg-info/SOURCES.txt RENAMED
@@ -21,6 +21,7 @@ src/ghga_transpiler/configs/1.0.yaml
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  src/ghga_transpiler/configs/1.1.yaml
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  src/ghga_transpiler/configs/2.0.yaml
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  src/ghga_transpiler/configs/2.1.yaml
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+ src/ghga_transpiler/configs/2.2.yaml
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  src/ghga_transpiler/configs/__init__.py
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  tests/test_convert_workbook.py
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  tests/test_create_config.py
{ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/src/ghga_transpiler.egg-info/requires.txt RENAMED
@@ -4,4 +4,4 @@ defusedxml==0.*,>=0.7
4
4
  pydantic<3,>=2.6
5
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  PyYAML~=6.0
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  semver==3.*
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- click==8.1.0
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+ click~=8.1.0
{ghga_transpiler-2.3.1 → ghga_transpiler-2.4.0}/LICENSE RENAMED
File without changes