ghga-transpiler 2.1.5__py3-none-any.whl → 2.2.0__py3-none-any.whl

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Files changed (8) hide show
  1. ghga_transpiler/__init__.py +1 -1
  2. ghga_transpiler/configs/2.0.yaml +162 -0
  3. {ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.0.dist-info}/METADATA +1 -1
  4. {ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.0.dist-info}/RECORD +8 -7
  5. {ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.0.dist-info}/WHEEL +1 -1
  6. {ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.0.dist-info}/LICENSE +0 -0
  7. {ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.0.dist-info}/entry_points.txt +0 -0
  8. {ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.0.dist-info}/top_level.txt +0 -0
ghga_transpiler/__init__.py CHANGED
@@ -18,7 +18,7 @@
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  from openpyxl.xml import DEFUSEDXML
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- __version__ = "2.1.5"
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+ __version__ = "2.2.0"
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  if not DEFUSEDXML:
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  raise RuntimeError(
ghga_transpiler/configs/2.0.yaml ADDED
@@ -0,0 +1,162 @@
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+ ghga_metadata_version: 2.0.0
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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:
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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: 11
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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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+ 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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+ 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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+ 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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+ 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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+ sheet_name: ResearchDataFile
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+ - settings:
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+ end_column: 7
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+ name: process_data_files
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+ sheet_name: ProcessDataFile
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+ - settings:
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+ end_column: 7
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+ name: datasets
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+ transformations:
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+ types: !!python/object/apply:ghga_transpiler.transformations.to_list []
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+ sheet_name: Dataset
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+ - settings:
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+ end_column: 11
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+ name: data_access_policies
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+ transformations:
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+ data_use_modifier_terms:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case_list []
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+ data_use_permission_term:
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+ !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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+ data_use_modifier_ids:
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+ !!python/object/apply:ghga_transpiler.transformations.to_list []
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+ sheet_name: DataAccessPolicy
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+ - settings:
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+ end_column: 4
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+ name: data_access_committees
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+ sheet_name: DataAccessCommittee
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+ - settings:
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+ end_column: 9
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+ name: publications
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+ transformations:
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+ xref: !!python/object/apply:ghga_transpiler.transformations.to_list []
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+ sheet_name: Publication
{ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.0.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: ghga_transpiler
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- Version: 2.1.5
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+ Version: 2.2.0
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  Summary: GHGA-Transpiler - excel to JSON converter
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  Author-email: "German Human Genome Phenome Archive (GHGA)" <contact@ghga.de>
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  License: Apache 2.0
{ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.0.dist-info}/RECORD RENAMED
@@ -1,4 +1,4 @@
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- ghga_transpiler/__init__.py,sha256=8cxE0fm7rs3CJ91SKgBGROUseHyG3A5655lFtWJX5DU,908
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+ ghga_transpiler/__init__.py,sha256=nLMNY6rki5JHcgg8tcRMgJ41a1C-hiDsdZmAlhx7BV4,908
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  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
@@ -10,10 +10,11 @@ ghga_transpiler/config/exceptions.py,sha256=H2xLk9YV3yHuwBDxQDgumbymX_-xSXctlh-r
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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
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+ ghga_transpiler/configs/2.0.yaml,sha256=ZVHrNqv2MXeY-BWwzvvIHMiEPMa7iAvOyH1teQe7fBg,6237
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  ghga_transpiler/configs/__init__.py,sha256=109RyIL2rxVrEiOS9D0q-PGVqw1_VZblvvFxOh4ZUjU,686
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- ghga_transpiler-2.1.5.dist-info/LICENSE,sha256=fBYaxYJmvm_AQEYU4gRvUAWbqhO0bgqPj9Yl6f8RXuU,11452
15
- ghga_transpiler-2.1.5.dist-info/METADATA,sha256=CpoyraNrzl0jbIW1KuepKDD1Zhajh1UUBni7nc3Kjfw,4595
16
- ghga_transpiler-2.1.5.dist-info/WHEEL,sha256=mguMlWGMX-VHnMpKOjjQidIo1ssRlCFu4a4mBpz1s2M,91
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- ghga_transpiler-2.1.5.dist-info/entry_points.txt,sha256=Fr_VQJynZZl95NXjrQW2gE0bCocgjKVNEZQpaLls8po,65
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- ghga_transpiler-2.1.5.dist-info/top_level.txt,sha256=TksRpDO3Y4mvK-B09UhQU3ceZpG19fljNlVDGTfjg8o,16
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- ghga_transpiler-2.1.5.dist-info/RECORD,,
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+ ghga_transpiler-2.2.0.dist-info/LICENSE,sha256=fBYaxYJmvm_AQEYU4gRvUAWbqhO0bgqPj9Yl6f8RXuU,11452
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+ ghga_transpiler-2.2.0.dist-info/METADATA,sha256=i1w7hL428x58frHNTebUS4mQqwmr5pbknB_KPt1APJ0,4595
17
+ ghga_transpiler-2.2.0.dist-info/WHEEL,sha256=Wyh-_nZ0DJYolHNn1_hMa4lM7uDedD_RGVwbmTjyItk,91
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+ ghga_transpiler-2.2.0.dist-info/entry_points.txt,sha256=Fr_VQJynZZl95NXjrQW2gE0bCocgjKVNEZQpaLls8po,65
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+ ghga_transpiler-2.2.0.dist-info/top_level.txt,sha256=TksRpDO3Y4mvK-B09UhQU3ceZpG19fljNlVDGTfjg8o,16
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+ ghga_transpiler-2.2.0.dist-info/RECORD,,
{ghga_transpiler-2.1.5.dist-info → ghga_transpiler-2.2.0.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
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  Wheel-Version: 1.0
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- Generator: setuptools (70.1.1)
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+ Generator: setuptools (71.1.0)
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  Root-Is-Purelib: true
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  Tag: py3-none-any
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