ghga-transpiler 2.2.1__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 (18) hide show
  1. ghga_transpiler/__init__.py +1 -1
  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/2.1.yaml +172 -0
  8. ghga_transpiler/configs/__init__.py +1 -1
  9. ghga_transpiler/core.py +1 -1
  10. ghga_transpiler/io.py +1 -1
  11. ghga_transpiler/transformations.py +1 -1
  12. {ghga_transpiler-2.2.1.dist-info → ghga_transpiler-2.3.1.dist-info}/METADATA +10 -11
  13. ghga_transpiler-2.3.1.dist-info/RECORD +21 -0
  14. {ghga_transpiler-2.2.1.dist-info → ghga_transpiler-2.3.1.dist-info}/WHEEL +1 -1
  15. {ghga_transpiler-2.2.1.dist-info → ghga_transpiler-2.3.1.dist-info/licenses}/LICENSE +1 -1
  16. ghga_transpiler-2.2.1.dist-info/RECORD +0 -20
  17. {ghga_transpiler-2.2.1.dist-info → ghga_transpiler-2.3.1.dist-info}/entry_points.txt +0 -0
  18. {ghga_transpiler-2.2.1.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");
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/2.1.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 @@
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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/core.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/io.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/transformations.py CHANGED
@@ -1,4 +1,4 @@
1
- # 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-2.2.1.dist-info → ghga_transpiler-2.3.1.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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- Metadata-Version: 2.1
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+ Metadata-Version: 2.4
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  Name: ghga_transpiler
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- Version: 2.2.1
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+ Version: 2.3.1
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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
@@ -16,15 +16,14 @@ Classifier: Intended Audience :: Developers
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  Requires-Python: >=3.9
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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- Requires-Dist: typer >=0.12
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- Requires-Dist: openpyxl ==3.*,>=3.1.2
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- 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: eval-type-backport ==0.2.0 ; python_version < "3.10"
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- Requires-Dist: exceptiongroup >=1.0.0 ; python_version < "3.11"
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- Requires-Dist: tomli >=2.0.0 ; python_version < "3.11"
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+ Requires-Dist: typer>=0.12
20
+ Requires-Dist: openpyxl==3.*,>=3.1.2
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+ Requires-Dist: defusedxml==0.*,>=0.7
22
+ Requires-Dist: pydantic<3,>=2.6
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+ Requires-Dist: PyYAML~=6.0
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+ Requires-Dist: semver==3.*
25
+ Requires-Dist: click==8.1.0
26
+ Dynamic: license-file
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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
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+ ghga_transpiler/__main__.py,sha256=k82ZsGuAOTrbqB4rCNkGOS-AWU8GICtD1_owfiey-Sk,847
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+ ghga_transpiler/cli.py,sha256=CvRQdiprRj1ZHjXgHpZ7JhDoAum7WB-sdFyMKknjtxk,2522
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+ ghga_transpiler/core.py,sha256=Fhf5pICDmVPKrUOhQNo6uN-mZB8mA1Vlyq3VGeeVSZ8,5235
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+ ghga_transpiler/io.py,sha256=e9DT5l5UumX2NcBJOkrR0y7ho_FPvK914WeFRZ4rOjw,1805
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+ ghga_transpiler/transformations.py,sha256=th320v3teZwjn13T-xS9n2_lCrBo5Wrl9wq0qOnbMEs,2222
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+ ghga_transpiler/config/__init__.py,sha256=CsnuJcqYMBx5zDcMgAzuKGRs5GQSS9N0evzDZ-T_g7k,817
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+ ghga_transpiler/config/config.py,sha256=YlIMQwnnpi8BelrdHtbZpJsp9RfwHCDZ56tCvU89wts,3823
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+ ghga_transpiler/config/exceptions.py,sha256=WB0YM5hJAn7iVGB_SY0p6Q4D0do1ti7AM4pKnMyVfLc,1090
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+ ghga_transpiler/configs/0.10.yaml,sha256=hsS8xwzJ00SRSb-VIfM-oM8UM0hOdR3xeuflf1fra4Y,5683
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+ 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
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+ 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
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+ 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-2.2.1.dist-info → ghga_transpiler-2.3.1.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: setuptools (72.0.0)
2
+ Generator: setuptools (80.7.1)
3
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  Root-Is-Purelib: true
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  Tag: py3-none-any
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{ghga_transpiler-2.2.1.dist-info → ghga_transpiler-2.3.1.dist-info/licenses}/LICENSE RENAMED
@@ -186,7 +186,7 @@
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  same "printed page" as the copyright notice for easier
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187
  identification within third-party archives.
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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
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190
  for the German Human Genome-Phenome Archive (GHGA)
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  Licensed under the Apache License, Version 2.0 (the "License");
ghga_transpiler-2.2.1.dist-info/RECORD DELETED
@@ -1,20 +0,0 @@
1
- ghga_transpiler/__init__.py,sha256=58eVmIOrztgGdUW8SxujAGlzfj0Rg4iMwp4RiXldbcU,908
2
- ghga_transpiler/__main__.py,sha256=EVGi0SsK--oaDF_c6PhVvNyPDnItrJzVapNAsKhgBmM,847
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- ghga_transpiler/cli.py,sha256=76TEXMPUCVnFqoQQWDvLBNw2iNjv3LgXAkJK-qjJNrE,2522
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- ghga_transpiler/core.py,sha256=i3JIaqWNsHryEphEHWOlLUI0BRUkTHGdphCs4KvMawY,5235
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- ghga_transpiler/io.py,sha256=T0P4BHCxIDny58v7H8B27eNEBnwghEp_OhYOOqpfTVw,1805
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- ghga_transpiler/transformations.py,sha256=Ii1CMBo9Ng43zZDfpHjOLaZ-9rCKFAvU42qBew6O2A0,2222
7
- ghga_transpiler/config/__init__.py,sha256=f8b3Le48ZrbOwRA5MVf6V6zqKFtxii9SQZMvvx1ulz8,817
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- ghga_transpiler/config/config.py,sha256=k4LC_7-9kBLqWC2oahuZDOFpJpeOSoI4vhuhOi4f8kQ,3823
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- ghga_transpiler/config/exceptions.py,sha256=H2xLk9YV3yHuwBDxQDgumbymX_-xSXctlh-rrIxv8Qw,1090
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- ghga_transpiler/configs/0.10.yaml,sha256=hsS8xwzJ00SRSb-VIfM-oM8UM0hOdR3xeuflf1fra4Y,5683
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- ghga_transpiler/configs/1.0.yaml,sha256=MgSEkDpZjn7I76uLFAfpCfmOqOaCBjEojn6VDX6TnUc,5683
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- ghga_transpiler/configs/1.1.yaml,sha256=rgxTV7bEVMwk1UeJ8hAeCZcqTwX10KXQKoaYnpV0bxI,5683
13
- ghga_transpiler/configs/2.0.yaml,sha256=3lwXFjtbEW-mWGj99d3PaWJflLnuy7WAS5AvNubDJlI,6637
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- ghga_transpiler/configs/__init__.py,sha256=109RyIL2rxVrEiOS9D0q-PGVqw1_VZblvvFxOh4ZUjU,686
15
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