ghga-transpiler 2.2.0__py3-none-any.whl → 2.3.1__py3-none-any.whl

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 (19) hide show
  1. ghga_transpiler/__init__.py +2 -2
  2. ghga_transpiler/__main__.py +1 -1
  3. ghga_transpiler/cli.py +1 -1
  4. ghga_transpiler/config/__init__.py +1 -1
  5. ghga_transpiler/config/config.py +1 -1
  6. ghga_transpiler/config/exceptions.py +1 -1
  7. ghga_transpiler/configs/2.0.yaml +8 -0
  8. ghga_transpiler/configs/2.1.yaml +172 -0
  9. ghga_transpiler/configs/__init__.py +1 -1
  10. ghga_transpiler/core.py +1 -1
  11. ghga_transpiler/io.py +1 -1
  12. ghga_transpiler/transformations.py +1 -1
  13. {ghga_transpiler-2.2.0.dist-info → ghga_transpiler-2.3.1.dist-info}/METADATA +10 -11
  14. ghga_transpiler-2.3.1.dist-info/RECORD +21 -0
  15. {ghga_transpiler-2.2.0.dist-info → ghga_transpiler-2.3.1.dist-info}/WHEEL +1 -1
  16. {ghga_transpiler-2.2.0.dist-info → ghga_transpiler-2.3.1.dist-info/licenses}/LICENSE +1 -1
  17. ghga_transpiler-2.2.0.dist-info/RECORD +0 -20
  18. {ghga_transpiler-2.2.0.dist-info → ghga_transpiler-2.3.1.dist-info}/entry_points.txt +0 -0
  19. {ghga_transpiler-2.2.0.dist-info → ghga_transpiler-2.3.1.dist-info}/top_level.txt +0 -0
ghga_transpiler/__init__.py CHANGED
@@ -1,4 +1,4 @@
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- # Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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+ # Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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  # for the German Human Genome-Phenome Archive (GHGA)
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  # Licensed under the Apache License, Version 2.0 (the "License");
@@ -18,7 +18,7 @@
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  from openpyxl.xml import DEFUSEDXML
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- __version__ = "2.2.0"
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+ __version__ = "2.2.1"
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  if not DEFUSEDXML:
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  raise RuntimeError(
ghga_transpiler/__main__.py CHANGED
@@ -1,4 +1,4 @@
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- # Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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+ # Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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  # for the German Human Genome-Phenome Archive (GHGA)
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  # Licensed under the Apache License, Version 2.0 (the "License");
ghga_transpiler/cli.py CHANGED
@@ -1,4 +1,4 @@
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- # Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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+ # Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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  # for the German Human Genome-Phenome Archive (GHGA)
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  # Licensed under the Apache License, Version 2.0 (the "License");
ghga_transpiler/config/__init__.py CHANGED
@@ -1,4 +1,4 @@
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- # Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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+ # Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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  # for the German Human Genome-Phenome Archive (GHGA)
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  # Licensed under the Apache License, Version 2.0 (the "License");
ghga_transpiler/config/config.py CHANGED
@@ -1,4 +1,4 @@
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- # Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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+ # Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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  # for the German Human Genome-Phenome Archive (GHGA)
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  # Licensed under the Apache License, Version 2.0 (the "License");
ghga_transpiler/config/exceptions.py CHANGED
@@ -1,4 +1,4 @@
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- # Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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+ # Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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  # for the German Human Genome-Phenome Archive (GHGA)
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  # Licensed under the Apache License, Version 2.0 (the "License");
ghga_transpiler/configs/2.0.yaml CHANGED
@@ -39,6 +39,8 @@ worksheets:
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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
@@ -84,6 +86,8 @@ worksheets:
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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
@@ -113,6 +117,8 @@ worksheets:
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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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  sheet_name: ExperimentMethod
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  - settings:
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  end_column: 7
@@ -128,6 +134,8 @@ worksheets:
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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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  sheet_name: ResearchDataFile
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  - settings:
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  end_column: 7
ghga_transpiler/configs/2.1.yaml ADDED
@@ -0,0 +1,172 @@
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+ ghga_metadata_version: 2.1.0
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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: 12
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+ name: analysis_methods
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+ transformations:
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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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+ 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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+ 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/configs/__init__.py CHANGED
@@ -1,4 +1,4 @@
1
- # Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
1
+ # Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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  # for the German Human Genome-Phenome Archive (GHGA)
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3
 
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  # Licensed under the Apache License, Version 2.0 (the "License");
ghga_transpiler/core.py CHANGED
@@ -1,4 +1,4 @@
1
- # Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
1
+ # Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
2
2
  # for the German Human Genome-Phenome Archive (GHGA)
3
3
 
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
ghga_transpiler/io.py CHANGED
@@ -1,4 +1,4 @@
1
- # Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
1
+ # Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
2
2
  # for the German Human Genome-Phenome Archive (GHGA)
3
3
 
4
4
  # Licensed under the Apache License, Version 2.0 (the "License");
ghga_transpiler/transformations.py CHANGED
@@ -1,4 +1,4 @@
1
- # Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
1
+ # Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
2
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  # for the German Human Genome-Phenome Archive (GHGA)
3
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  # Licensed under the Apache License, Version 2.0 (the "License");
{ghga_transpiler-2.2.0.dist-info → ghga_transpiler-2.3.1.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
- Metadata-Version: 2.1
1
+ Metadata-Version: 2.4
2
2
  Name: ghga_transpiler
3
- Version: 2.2.0
3
+ Version: 2.3.1
4
4
  Summary: GHGA-Transpiler - excel to JSON converter
5
5
  Author-email: "German Human Genome Phenome Archive (GHGA)" <contact@ghga.de>
6
6
  License: Apache 2.0
@@ -16,15 +16,14 @@ Classifier: Intended Audience :: Developers
16
16
  Requires-Python: >=3.9
17
17
  Description-Content-Type: text/markdown
18
18
  License-File: LICENSE
19
- Requires-Dist: typer >=0.12
20
- Requires-Dist: openpyxl ==3.*,>=3.1.2
21
- Requires-Dist: defusedxml ==0.*,>=0.7
22
- Requires-Dist: pydantic <3,>=2.6
23
- Requires-Dist: PyYAML ~=6.0
24
- Requires-Dist: semver ==3.*
25
- Requires-Dist: eval-type-backport ==0.2.0 ; python_version < "3.10"
26
- Requires-Dist: exceptiongroup >=1.0.0 ; python_version < "3.11"
27
- Requires-Dist: tomli >=2.0.0 ; python_version < "3.11"
19
+ Requires-Dist: typer>=0.12
20
+ Requires-Dist: openpyxl==3.*,>=3.1.2
21
+ Requires-Dist: defusedxml==0.*,>=0.7
22
+ Requires-Dist: pydantic<3,>=2.6
23
+ Requires-Dist: PyYAML~=6.0
24
+ Requires-Dist: semver==3.*
25
+ Requires-Dist: click==8.1.0
26
+ Dynamic: license-file
28
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  [![tests](https://github.com/ghga-de/ghga-transpiler/actions/workflows/tests.yaml/badge.svg)](https://github.com/ghga-de/ghga-transpiler/actions/workflows/unit_and_int_tests.yaml)
ghga_transpiler-2.3.1.dist-info/RECORD ADDED
@@ -0,0 +1,21 @@
1
+ ghga_transpiler/__init__.py,sha256=b_JlBjNvngOiIolsfKKbwonyfOtS7b5_LJKLuB5LyNQ,908
2
+ ghga_transpiler/__main__.py,sha256=k82ZsGuAOTrbqB4rCNkGOS-AWU8GICtD1_owfiey-Sk,847
3
+ ghga_transpiler/cli.py,sha256=CvRQdiprRj1ZHjXgHpZ7JhDoAum7WB-sdFyMKknjtxk,2522
4
+ ghga_transpiler/core.py,sha256=Fhf5pICDmVPKrUOhQNo6uN-mZB8mA1Vlyq3VGeeVSZ8,5235
5
+ ghga_transpiler/io.py,sha256=e9DT5l5UumX2NcBJOkrR0y7ho_FPvK914WeFRZ4rOjw,1805
6
+ ghga_transpiler/transformations.py,sha256=th320v3teZwjn13T-xS9n2_lCrBo5Wrl9wq0qOnbMEs,2222
7
+ ghga_transpiler/config/__init__.py,sha256=CsnuJcqYMBx5zDcMgAzuKGRs5GQSS9N0evzDZ-T_g7k,817
8
+ ghga_transpiler/config/config.py,sha256=YlIMQwnnpi8BelrdHtbZpJsp9RfwHCDZ56tCvU89wts,3823
9
+ ghga_transpiler/config/exceptions.py,sha256=WB0YM5hJAn7iVGB_SY0p6Q4D0do1ti7AM4pKnMyVfLc,1090
10
+ ghga_transpiler/configs/0.10.yaml,sha256=hsS8xwzJ00SRSb-VIfM-oM8UM0hOdR3xeuflf1fra4Y,5683
11
+ ghga_transpiler/configs/1.0.yaml,sha256=MgSEkDpZjn7I76uLFAfpCfmOqOaCBjEojn6VDX6TnUc,5683
12
+ ghga_transpiler/configs/1.1.yaml,sha256=rgxTV7bEVMwk1UeJ8hAeCZcqTwX10KXQKoaYnpV0bxI,5683
13
+ ghga_transpiler/configs/2.0.yaml,sha256=3lwXFjtbEW-mWGj99d3PaWJflLnuy7WAS5AvNubDJlI,6637
14
+ ghga_transpiler/configs/2.1.yaml,sha256=A-vJbxUcW0yyAKpgz2IkN81n92wxIC2A3sYEq-UZ9d0,6738
15
+ ghga_transpiler/configs/__init__.py,sha256=xL0pfHoTdBh0LhdqA8lpdhp3W68HJVXF7AURhBM7pU4,686
16
+ ghga_transpiler-2.3.1.dist-info/licenses/LICENSE,sha256=nKgIWA3zoWy18_YSW6e9Gd6_p7d7ccwjNZrfJzvKALE,11452
17
+ ghga_transpiler-2.3.1.dist-info/METADATA,sha256=RKXPB_H8N5uLyKugDxk2ptbUG0jxsV4xLaVijDh3C8c,4452
18
+ ghga_transpiler-2.3.1.dist-info/WHEEL,sha256=Nw36Djuh_5VDukK0H78QzOX-_FQEo6V37m3nkm96gtU,91
19
+ ghga_transpiler-2.3.1.dist-info/entry_points.txt,sha256=Fr_VQJynZZl95NXjrQW2gE0bCocgjKVNEZQpaLls8po,65
20
+ ghga_transpiler-2.3.1.dist-info/top_level.txt,sha256=TksRpDO3Y4mvK-B09UhQU3ceZpG19fljNlVDGTfjg8o,16
21
+ ghga_transpiler-2.3.1.dist-info/RECORD,,
{ghga_transpiler-2.2.0.dist-info → ghga_transpiler-2.3.1.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: setuptools (71.1.0)
2
+ Generator: setuptools (80.7.1)
3
3
  Root-Is-Purelib: true
4
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  Tag: py3-none-any
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{ghga_transpiler-2.2.0.dist-info → ghga_transpiler-2.3.1.dist-info/licenses}/LICENSE RENAMED
@@ -186,7 +186,7 @@
186
186
  same "printed page" as the copyright notice for easier
187
187
  identification within third-party archives.
188
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189
- Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
189
+ Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
190
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  for the German Human Genome-Phenome Archive (GHGA)
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  Licensed under the Apache License, Version 2.0 (the "License");
ghga_transpiler-2.2.0.dist-info/RECORD DELETED
@@ -1,20 +0,0 @@
1
- ghga_transpiler/__init__.py,sha256=nLMNY6rki5JHcgg8tcRMgJ41a1C-hiDsdZmAlhx7BV4,908
2
- ghga_transpiler/__main__.py,sha256=EVGi0SsK--oaDF_c6PhVvNyPDnItrJzVapNAsKhgBmM,847
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