ghga-transpiler 2.2.1__tar.gz → 2.3.2__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.
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/LICENSE +1 -1
- {ghga_transpiler-2.2.1/src/ghga_transpiler.egg-info → ghga_transpiler-2.3.2}/PKG-INFO +4 -5
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/pyproject.toml +2 -4
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler/__init__.py +1 -1
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler/__main__.py +1 -1
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler/cli.py +1 -1
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler/config/__init__.py +1 -1
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler/config/config.py +1 -1
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler/config/exceptions.py +1 -1
- ghga_transpiler-2.3.2/src/ghga_transpiler/configs/2.1.yaml +172 -0
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler/configs/__init__.py +1 -1
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler/core.py +1 -1
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler/io.py +1 -1
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler/transformations.py +1 -1
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2/src/ghga_transpiler.egg-info}/PKG-INFO +4 -5
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler.egg-info/SOURCES.txt +1 -0
- ghga_transpiler-2.3.2/src/ghga_transpiler.egg-info/requires.txt +7 -0
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/tests/test_convert_workbook.py +1 -1
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/tests/test_create_config.py +1 -1
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/tests/test_io.py +1 -1
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/tests/test_process_workbook.py +1 -1
- ghga_transpiler-2.2.1/src/ghga_transpiler.egg-info/requires.txt +0 -13
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/README.md +0 -0
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/setup.cfg +0 -0
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler/configs/0.10.yaml +0 -0
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler/configs/1.0.yaml +0 -0
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler/configs/1.1.yaml +0 -0
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler/configs/2.0.yaml +0 -0
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler.egg-info/dependency_links.txt +0 -0
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler.egg-info/entry_points.txt +0 -0
- {ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler.egg-info/top_level.txt +0 -0
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same "printed page" as the copyright notice for easier
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identification within third-party archives.
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Copyright 2021 -
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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");
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Metadata-Version: 2.
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Metadata-Version: 2.4
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Name: ghga_transpiler
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Version: 2.2
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Version: 2.3.2
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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
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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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Dynamic: license-file
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[](https://github.com/ghga-de/ghga-transpiler/actions/workflows/unit_and_int_tests.yaml)
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"Intended Audience :: Developers",
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name = "ghga_transpiler"
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version = "2.2
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version = "2.3.2"
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description = "GHGA-Transpiler - excel to JSON converter"
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dependencies = [
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"typer >= 0.12",
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"
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"tomli>= 2.0.0; python_version < \"3.11\"",
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[project.license]
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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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# Copyright 2021 -
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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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# Copyright 2021 -
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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");
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# Copyright 2021 -
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# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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# Copyright 2021 -
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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");
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# Copyright 2021 -
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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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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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diagnosis_terms:
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sex:
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ancestry_terms:
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ancestry_ids:
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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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storage:
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disease_or_healthy:
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case_control_status:
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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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biospecimen_vital_status_at_sampling:
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biospecimen_isolation:
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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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library_preparation_kit_retail_name:
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primer:
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end_bias:
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target_regions:
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rnaseq_strandedness:
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instrument_model:
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sequencing_layout:
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flow_cell_type:
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sample_barcode_read:
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sequencing_layout:
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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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format:
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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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data_use_permission_term:
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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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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
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# Copyright 2021 -
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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");
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# Copyright 2021 -
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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");
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# Copyright 2021 -
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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");
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# Copyright 2021 -
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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");
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@@ -1,6 +1,6 @@
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1
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-
Metadata-Version: 2.
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Metadata-Version: 2.4
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Name: ghga_transpiler
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Version: 2.2
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Version: 2.3.2
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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
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@@ -22,9 +22,8 @@ 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:
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Requires-Dist: eval-type-backport==0.2.0; python_version < "3.10"
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Requires-Dist: click~=8.1.0
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Dynamic: license-file
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[](https://github.com/ghga-de/ghga-transpiler/actions/workflows/unit_and_int_tests.yaml)
|
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@@ -20,6 +20,7 @@ src/ghga_transpiler/configs/0.10.yaml
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src/ghga_transpiler/configs/1.0.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/__init__.py
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tests/test_convert_workbook.py
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tests/test_create_config.py
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# Copyright 2021 -
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# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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# Copyright 2021 -
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# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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# Licensed under the Apache License, Version 2.0 (the "License");
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# Copyright 2021 -
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# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
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# Licensed under the Apache License, Version 2.0 (the "License");
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@@ -1,4 +1,4 @@
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# Copyright 2021 -
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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");
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|
{ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler.egg-info/dependency_links.txt
RENAMED
|
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|
{ghga_transpiler-2.2.1 → ghga_transpiler-2.3.2}/src/ghga_transpiler.egg-info/entry_points.txt
RENAMED
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File without changes
|