ghga-transpiler 2.1.3__py3-none-any.whl → 2.1.4__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.
- ghga_transpiler/__init__.py +1 -1
- ghga_transpiler/configs/0.10.yaml +135 -0
- ghga_transpiler/configs/1.0.yaml +135 -0
- ghga_transpiler/configs/1.1.yaml +135 -0
- {ghga_transpiler-2.1.3.dist-info → ghga_transpiler-2.1.4.dist-info}/METADATA +1 -1
- {ghga_transpiler-2.1.3.dist-info → ghga_transpiler-2.1.4.dist-info}/RECORD +10 -7
- {ghga_transpiler-2.1.3.dist-info → ghga_transpiler-2.1.4.dist-info}/LICENSE +0 -0
- {ghga_transpiler-2.1.3.dist-info → ghga_transpiler-2.1.4.dist-info}/WHEEL +0 -0
- {ghga_transpiler-2.1.3.dist-info → ghga_transpiler-2.1.4.dist-info}/entry_points.txt +0 -0
- {ghga_transpiler-2.1.3.dist-info → ghga_transpiler-2.1.4.dist-info}/top_level.txt +0 -0
ghga_transpiler/__init__.py
CHANGED
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ghga_metadata_version: 0.10.0
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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: !!python/object/apply:ghga_transpiler.transformations.to_attributes []
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format: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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forward_or_reverse: !!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: 6
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name: analyses
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sheet_name: Analysis
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- settings:
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end_column: 8
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name: analysis_process_output_files
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sheet_name: AnalysisProcessOutputFile
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- settings:
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end_column: 5
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name: analysis_processes
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transformations:
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study_input_files: !!python/object/apply:ghga_transpiler.transformations.to_list []
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sample_input_files: !!python/object/apply:ghga_transpiler.transformations.to_list []
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sequencing_process_input_files: !!python/object/apply:ghga_transpiler.transformations.to_list []
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sheet_name: AnalysisProcess
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- settings:
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end_column: 9
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name: biospecimens
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transformations:
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vital_status_at_sampling: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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age_at_sampling: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sheet_name: Biospecimen
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- settings:
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end_column: 9
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name: conditions
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transformations:
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disease_or_healthy: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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case_control_status: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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mutant_or_wildtype: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sheet_name: Condition
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- settings:
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end_column: 3
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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: 8
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name: data_access_policies
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transformations:
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data_use_modifiers: !!python/object/apply:ghga_transpiler.transformations.to_snake_case_list []
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data_use_permission: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sheet_name: DataAccessPolicy
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- settings:
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end_column: 5
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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: 8
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name: individuals
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transformations:
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ancestries: !!python/object/apply:ghga_transpiler.transformations.to_list []
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phenotypic_features: !!python/object/apply:ghga_transpiler.transformations.to_list []
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karyotype: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sex: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sheet_name: Individual
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- settings:
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end_column: 14
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name: library_preparation_protocols
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transformations:
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target_regions: !!python/object/apply:ghga_transpiler.transformations.to_list []
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attributes: !!python/object/apply:ghga_transpiler.transformations.to_attributes []
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library_layout: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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library_type: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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library_selection: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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library_preparation_kit_retail_name: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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rnaseq_strandedness: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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primer: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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end_bias: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sheet_name: LibraryPreparationProtocol
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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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- settings:
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end_column: 8
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name: sample_files
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sheet_name: SampleFile
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- settings:
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end_column: 10
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name: samples
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transformations:
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xref: !!python/object/apply:ghga_transpiler.transformations.to_list []
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type: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sheet_name: Sample
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- settings:
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end_column: 7
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name: sequencing_experiments
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sheet_name: SequencingExperiment
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- settings:
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end_column: 8
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name: sequencing_process_files
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sheet_name: SequencingProcessFile
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- settings:
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end_column: 10
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name: sequencing_processes
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sheet_name: SequencingProcess
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- settings:
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end_column: 20
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name: sequencing_protocols
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transformations:
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instrument_model: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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flow_cell_type: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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umi_barcode_read: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sample_barcode_read: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sheet_name: SequencingProtocol
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- settings:
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end_column: 6
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name: studies
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transformations:
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affiliations: !!python/object/apply:ghga_transpiler.transformations.to_list []
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attributes: !!python/object/apply:ghga_transpiler.transformations.to_attributes []
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type: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sheet_name: Study
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- settings:
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end_column: 8
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name: study_files
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sheet_name: StudyFile
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- settings:
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end_column: 4
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name: trios
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sheet_name: Trio
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@@ -0,0 +1,135 @@
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ghga_metadata_version: 1.0.0
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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: !!python/object/apply:ghga_transpiler.transformations.to_attributes []
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format: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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forward_or_reverse: !!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: 6
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name: analyses
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sheet_name: Analysis
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- settings:
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end_column: 9
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name: analysis_process_output_files
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sheet_name: AnalysisProcessOutputFile
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- settings:
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end_column: 5
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name: analysis_processes
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transformations:
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study_input_files: !!python/object/apply:ghga_transpiler.transformations.to_list []
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sample_input_files: !!python/object/apply:ghga_transpiler.transformations.to_list []
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sequencing_process_input_files: !!python/object/apply:ghga_transpiler.transformations.to_list []
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sheet_name: AnalysisProcess
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- settings:
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end_column: 10
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name: biospecimens
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transformations:
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vital_status_at_sampling: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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age_at_sampling: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sheet_name: Biospecimen
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- settings:
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end_column: 9
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name: conditions
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transformations:
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disease_or_healthy: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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case_control_status: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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mutant_or_wildtype: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sheet_name: Condition
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- settings:
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end_column: 3
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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: 8
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name: data_access_policies
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transformations:
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data_use_modifiers: !!python/object/apply:ghga_transpiler.transformations.to_snake_case_list []
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data_use_permission: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sheet_name: DataAccessPolicy
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- settings:
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end_column: 5
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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: 6
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name: individuals
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transformations:
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ancestries: !!python/object/apply:ghga_transpiler.transformations.to_list []
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phenotypic_features: !!python/object/apply:ghga_transpiler.transformations.to_list []
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karyotype: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sex: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sheet_name: Individual
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- settings:
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end_column: 14
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name: library_preparation_protocols
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transformations:
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target_regions: !!python/object/apply:ghga_transpiler.transformations.to_list []
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attributes: !!python/object/apply:ghga_transpiler.transformations.to_attributes []
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library_layout: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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library_type: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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library_selection: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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library_preparation_kit_retail_name: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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rnaseq_strandedness: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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primer: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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end_bias: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sheet_name: LibraryPreparationProtocol
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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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- settings:
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end_column: 9
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name: sample_files
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sheet_name: SampleFile
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- settings:
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end_column: 10
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name: samples
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transformations:
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xref: !!python/object/apply:ghga_transpiler.transformations.to_list []
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type: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sheet_name: Sample
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- settings:
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end_column: 7
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name: sequencing_experiments
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sheet_name: SequencingExperiment
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- settings:
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end_column: 9
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name: sequencing_process_files
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sheet_name: SequencingProcessFile
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- settings:
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end_column: 12
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name: sequencing_processes
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sheet_name: SequencingProcess
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- settings:
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end_column: 17
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name: sequencing_protocols
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transformations:
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instrument_model: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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flow_cell_type: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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umi_barcode_read: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sample_barcode_read: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sheet_name: SequencingProtocol
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- settings:
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end_column: 6
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name: studies
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transformations:
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affiliations: !!python/object/apply:ghga_transpiler.transformations.to_list []
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attributes: !!python/object/apply:ghga_transpiler.transformations.to_attributes []
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type: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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sheet_name: Study
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- settings:
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end_column: 9
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name: study_files
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sheet_name: StudyFile
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- settings:
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end_column: 4
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name: trios
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sheet_name: Trio
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@@ -0,0 +1,135 @@
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ghga_metadata_version: 1.1.0
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default_settings:
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header_row: 1
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4
|
+
start_row: 7
|
|
5
|
+
start_column: 1
|
|
6
|
+
transformations:
|
|
7
|
+
attributes: !!python/object/apply:ghga_transpiler.transformations.to_attributes []
|
|
8
|
+
format: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
9
|
+
forward_or_reverse: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
10
|
+
worksheets:
|
|
11
|
+
- settings:
|
|
12
|
+
end_column: 6
|
|
13
|
+
name: analyses
|
|
14
|
+
sheet_name: Analysis
|
|
15
|
+
- settings:
|
|
16
|
+
end_column: 9
|
|
17
|
+
name: analysis_process_output_files
|
|
18
|
+
sheet_name: AnalysisProcessOutputFile
|
|
19
|
+
- settings:
|
|
20
|
+
end_column: 5
|
|
21
|
+
name: analysis_processes
|
|
22
|
+
transformations:
|
|
23
|
+
study_input_files: !!python/object/apply:ghga_transpiler.transformations.to_list []
|
|
24
|
+
sample_input_files: !!python/object/apply:ghga_transpiler.transformations.to_list []
|
|
25
|
+
sequencing_process_input_files: !!python/object/apply:ghga_transpiler.transformations.to_list []
|
|
26
|
+
sheet_name: AnalysisProcess
|
|
27
|
+
- settings:
|
|
28
|
+
end_column: 10
|
|
29
|
+
name: biospecimens
|
|
30
|
+
transformations:
|
|
31
|
+
vital_status_at_sampling: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
32
|
+
age_at_sampling: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
33
|
+
sheet_name: Biospecimen
|
|
34
|
+
- settings:
|
|
35
|
+
end_column: 9
|
|
36
|
+
name: conditions
|
|
37
|
+
transformations:
|
|
38
|
+
disease_or_healthy: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
39
|
+
case_control_status: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
40
|
+
mutant_or_wildtype: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
41
|
+
sheet_name: Condition
|
|
42
|
+
- settings:
|
|
43
|
+
end_column: 3
|
|
44
|
+
name: data_access_committees
|
|
45
|
+
sheet_name: DataAccessCommittee
|
|
46
|
+
- settings:
|
|
47
|
+
end_column: 8
|
|
48
|
+
name: data_access_policies
|
|
49
|
+
transformations:
|
|
50
|
+
data_use_modifiers: !!python/object/apply:ghga_transpiler.transformations.to_snake_case_list []
|
|
51
|
+
data_use_permission: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
52
|
+
sheet_name: DataAccessPolicy
|
|
53
|
+
- settings:
|
|
54
|
+
end_column: 5
|
|
55
|
+
name: datasets
|
|
56
|
+
transformations:
|
|
57
|
+
types: !!python/object/apply:ghga_transpiler.transformations.to_list []
|
|
58
|
+
sheet_name: Dataset
|
|
59
|
+
- settings:
|
|
60
|
+
end_column: 6
|
|
61
|
+
name: individuals
|
|
62
|
+
transformations:
|
|
63
|
+
ancestries: !!python/object/apply:ghga_transpiler.transformations.to_list []
|
|
64
|
+
phenotypic_features: !!python/object/apply:ghga_transpiler.transformations.to_list []
|
|
65
|
+
karyotype: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
66
|
+
sex: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
67
|
+
sheet_name: Individual
|
|
68
|
+
- settings:
|
|
69
|
+
end_column: 14
|
|
70
|
+
name: library_preparation_protocols
|
|
71
|
+
transformations:
|
|
72
|
+
target_regions: !!python/object/apply:ghga_transpiler.transformations.to_list []
|
|
73
|
+
attributes: !!python/object/apply:ghga_transpiler.transformations.to_attributes []
|
|
74
|
+
library_layout: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
75
|
+
library_type: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
76
|
+
library_selection: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
77
|
+
library_preparation_kit_retail_name: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
78
|
+
rnaseq_strandedness: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
79
|
+
primer: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
80
|
+
end_bias: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
81
|
+
sheet_name: LibraryPreparationProtocol
|
|
82
|
+
- settings:
|
|
83
|
+
end_column: 9
|
|
84
|
+
name: publications
|
|
85
|
+
transformations:
|
|
86
|
+
xref: !!python/object/apply:ghga_transpiler.transformations.to_list []
|
|
87
|
+
sheet_name: Publication
|
|
88
|
+
- settings:
|
|
89
|
+
end_column: 9
|
|
90
|
+
name: sample_files
|
|
91
|
+
sheet_name: SampleFile
|
|
92
|
+
- settings:
|
|
93
|
+
end_column: 10
|
|
94
|
+
name: samples
|
|
95
|
+
transformations:
|
|
96
|
+
xref: !!python/object/apply:ghga_transpiler.transformations.to_list []
|
|
97
|
+
type: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
98
|
+
sheet_name: Sample
|
|
99
|
+
- settings:
|
|
100
|
+
end_column: 7
|
|
101
|
+
name: sequencing_experiments
|
|
102
|
+
sheet_name: SequencingExperiment
|
|
103
|
+
- settings:
|
|
104
|
+
end_column: 9
|
|
105
|
+
name: sequencing_process_files
|
|
106
|
+
sheet_name: SequencingProcessFile
|
|
107
|
+
- settings:
|
|
108
|
+
end_column: 12
|
|
109
|
+
name: sequencing_processes
|
|
110
|
+
sheet_name: SequencingProcess
|
|
111
|
+
- settings:
|
|
112
|
+
end_column: 17
|
|
113
|
+
name: sequencing_protocols
|
|
114
|
+
transformations:
|
|
115
|
+
instrument_model: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
116
|
+
flow_cell_type: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
117
|
+
umi_barcode_read: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
118
|
+
sample_barcode_read: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
119
|
+
sheet_name: SequencingProtocol
|
|
120
|
+
- settings:
|
|
121
|
+
end_column: 6
|
|
122
|
+
name: studies
|
|
123
|
+
transformations:
|
|
124
|
+
affiliations: !!python/object/apply:ghga_transpiler.transformations.to_list []
|
|
125
|
+
attributes: !!python/object/apply:ghga_transpiler.transformations.to_attributes []
|
|
126
|
+
type: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
|
127
|
+
sheet_name: Study
|
|
128
|
+
- settings:
|
|
129
|
+
end_column: 9
|
|
130
|
+
name: study_files
|
|
131
|
+
sheet_name: StudyFile
|
|
132
|
+
- settings:
|
|
133
|
+
end_column: 4
|
|
134
|
+
name: trios
|
|
135
|
+
sheet_name: Trio
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
ghga_transpiler/__init__.py,sha256=
|
|
1
|
+
ghga_transpiler/__init__.py,sha256=ReD81YbJxri14TnAlARwAfxANDI8nfxLJV961aM-GeY,908
|
|
2
2
|
ghga_transpiler/__main__.py,sha256=EVGi0SsK--oaDF_c6PhVvNyPDnItrJzVapNAsKhgBmM,847
|
|
3
3
|
ghga_transpiler/cli.py,sha256=kw8YMDIs9xxYtAbwU4ovBE5AZnyUxVvL3eB2YZrmcXU,2556
|
|
4
4
|
ghga_transpiler/core.py,sha256=A2MKKNEwxRViCquU0pbuk7KjXCg8y-F_QJpICvSS-IE,5213
|
|
@@ -7,10 +7,13 @@ ghga_transpiler/transformations.py,sha256=o-6qJHB-5ptrnMhi-q-3kXrrVdy_XwqLUjTVIg
|
|
|
7
7
|
ghga_transpiler/config/__init__.py,sha256=f8b3Le48ZrbOwRA5MVf6V6zqKFtxii9SQZMvvx1ulz8,817
|
|
8
8
|
ghga_transpiler/config/config.py,sha256=rDgUR939BCI89QkcqQXeJ1872hkAg1QE4IeGgoijRD0,3787
|
|
9
9
|
ghga_transpiler/config/exceptions.py,sha256=H2xLk9YV3yHuwBDxQDgumbymX_-xSXctlh-rrIxv8Qw,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
|
|
10
13
|
ghga_transpiler/configs/__init__.py,sha256=109RyIL2rxVrEiOS9D0q-PGVqw1_VZblvvFxOh4ZUjU,686
|
|
11
|
-
ghga_transpiler-2.1.
|
|
12
|
-
ghga_transpiler-2.1.
|
|
13
|
-
ghga_transpiler-2.1.
|
|
14
|
-
ghga_transpiler-2.1.
|
|
15
|
-
ghga_transpiler-2.1.
|
|
16
|
-
ghga_transpiler-2.1.
|
|
14
|
+
ghga_transpiler-2.1.4.dist-info/LICENSE,sha256=fBYaxYJmvm_AQEYU4gRvUAWbqhO0bgqPj9Yl6f8RXuU,11452
|
|
15
|
+
ghga_transpiler-2.1.4.dist-info/METADATA,sha256=fdOwjuvvwVrQw4u-93cPVjhTtJ0iCx21RCfMF26QmtA,4407
|
|
16
|
+
ghga_transpiler-2.1.4.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
|
|
17
|
+
ghga_transpiler-2.1.4.dist-info/entry_points.txt,sha256=Fr_VQJynZZl95NXjrQW2gE0bCocgjKVNEZQpaLls8po,65
|
|
18
|
+
ghga_transpiler-2.1.4.dist-info/top_level.txt,sha256=TksRpDO3Y4mvK-B09UhQU3ceZpG19fljNlVDGTfjg8o,16
|
|
19
|
+
ghga_transpiler-2.1.4.dist-info/RECORD,,
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|