ghga-transpiler 2.1.3__tar.gz → 2.1.5__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-2.1.3/src/ghga_transpiler.egg-info → ghga_transpiler-2.1.5}/PKG-INFO +6 -3
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/pyproject.toml +7 -5
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/src/ghga_transpiler/__init__.py +1 -1
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/src/ghga_transpiler/cli.py +1 -1
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/src/ghga_transpiler/config/config.py +2 -0
- ghga_transpiler-2.1.5/src/ghga_transpiler/configs/0.10.yaml +135 -0
- ghga_transpiler-2.1.5/src/ghga_transpiler/configs/1.0.yaml +135 -0
- ghga_transpiler-2.1.5/src/ghga_transpiler/configs/1.1.yaml +135 -0
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/src/ghga_transpiler/core.py +3 -1
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/src/ghga_transpiler/io.py +2 -0
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/src/ghga_transpiler/transformations.py +1 -1
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5/src/ghga_transpiler.egg-info}/PKG-INFO +6 -3
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/src/ghga_transpiler.egg-info/SOURCES.txt +3 -0
- ghga_transpiler-2.1.5/src/ghga_transpiler.egg-info/requires.txt +13 -0
- ghga_transpiler-2.1.3/src/ghga_transpiler.egg-info/requires.txt +0 -6
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/LICENSE +0 -0
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/README.md +0 -0
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/setup.cfg +0 -0
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/src/ghga_transpiler/__main__.py +0 -0
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/src/ghga_transpiler/config/__init__.py +0 -0
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/src/ghga_transpiler/config/exceptions.py +0 -0
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/src/ghga_transpiler/configs/__init__.py +0 -0
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/src/ghga_transpiler.egg-info/dependency_links.txt +0 -0
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/src/ghga_transpiler.egg-info/entry_points.txt +0 -0
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/src/ghga_transpiler.egg-info/top_level.txt +0 -0
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/tests/test_convert_workbook.py +0 -0
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/tests/test_create_config.py +0 -0
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/tests/test_io.py +0 -0
- {ghga_transpiler-2.1.3 → ghga_transpiler-2.1.5}/tests/test_process_workbook.py +0 -0
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Metadata-Version: 2.1
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Name: ghga_transpiler
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Version: 2.1.
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Version: 2.1.5
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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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Classifier: Topic :: Internet :: WWW/HTTP :: HTTP Servers
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Classifier: Topic :: Software Development :: Libraries
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Classifier: Intended Audience :: Developers
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Requires-Python: >=3.
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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
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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: 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: eval-type-backport==0.2.0; python_version < "3.10"
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[](https://github.com/ghga-de/ghga-transpiler/actions/workflows/unit_and_int_tests.yaml)
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authors = [
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{ name = "German Human Genome Phenome Archive (GHGA)", email = "contact@ghga.de" },
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]
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requires-python = ">=3.
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requires-python = ">=3.9"
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classifiers = [
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"Development Status :: 1 - Planning",
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"Operating System :: POSIX :: Linux",
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"Intended Audience :: Developers",
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]
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name = "ghga_transpiler"
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version = "2.1.
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version = "2.1.5"
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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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"openpyxl >= 3.1.2, == 3.*",
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"defusedxml >= 0.7, == 0.*",
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"pydantic >=2, <3",
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"pydantic >=2.6, <3",
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"PyYAML ~= 6.0",
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"semver == 3.*",
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"exceptiongroup>=1.0.0; python_version < \"3.11\"",
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"tomli>= 2.0.0; python_version < \"3.11\"",
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"eval-type-backport==0.2.0; python_version < \"3.10\"",
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]
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[project.license]
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]
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[tool.setuptools.package-data]
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configs = [
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"ghga_transpiler.configs" = [
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"*.yaml",
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]
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"examples",
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"scripts",
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]
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target-version = "py312"
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[tool.ruff.lint]
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fixable = [
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dir_okay=False,
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readable=True,
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),
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output_file: Optional[Path] = typer.Argument(
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output_file: Optional[Path] = typer.Argument(
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None, help="The path to output file (JSON).", dir_okay=False
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),
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force: bool = typer.Option(
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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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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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case_control_status: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
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name: data_access_committees
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sheet_name: DataAccessCommittee
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name: data_access_policies
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name: datasets
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types: !!python/object/apply:ghga_transpiler.transformations.to_list []
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end_column: 6
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name: individuals
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ancestries: !!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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name: library_preparation_protocols
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target_regions: !!python/object/apply:ghga_transpiler.transformations.to_list []
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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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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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name: publications
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xref: !!python/object/apply:ghga_transpiler.transformations.to_list []
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xref: !!python/object/apply:ghga_transpiler.transformations.to_list []
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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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name: studies
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affiliations: !!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: Study
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end_column: 4
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name: trios
|
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sheet_name: Trio
|
|
@@ -0,0 +1,135 @@
|
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ghga_metadata_version: 1.1.0
|
|
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|
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default_settings:
|
|
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|
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header_row: 1
|
|
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|
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start_row: 7
|
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start_column: 1
|
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|
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transformations:
|
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|
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attributes: !!python/object/apply:ghga_transpiler.transformations.to_attributes []
|
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|
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format: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
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|
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forward_or_reverse: !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
|
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|
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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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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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|
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- settings:
|
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end_column: 3
|
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name: data_access_committees
|
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|
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sheet_name: DataAccessCommittee
|
|
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|
+
- settings:
|
|
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|
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end_column: 8
|
|
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|
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name: data_access_policies
|
|
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|
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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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|
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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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end_column: 12
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name: sequencing_processes
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sheet_name: SequencingProcess
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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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name: studies
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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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name: study_files
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name: trios
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@@ -17,6 +17,8 @@
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"""This module contains functionalities for processing excel sheets into json object."""
|
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from __future__ import annotations
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|
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@@ -97,7 +99,7 @@ def convert_rows(header, rows) -> list[dict]:
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{
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for key, value in zip(header, row
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if value is not None and value != ""
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for row in rows
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@@ -36,7 +36,7 @@ def to_attributes() -> Callable:
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def split_one(value: str) -> dict:
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"""Returns a dictionary with key, value as keys, splitted string as values"""
|
|
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|
splitted = (elem.strip() for elem in value.split("="))
|
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-
return dict(zip(("key", "value"), splitted
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+
return dict(zip(("key", "value"), splitted))
|
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def split_mult(value: str) -> list[dict]:
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"""Converts string to attributes"""
|
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@@ -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.
|
|
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|
+
Version: 2.1.5
|
|
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|
Summary: GHGA-Transpiler - excel to JSON converter
|
|
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5
|
Author-email: "German Human Genome Phenome Archive (GHGA)" <contact@ghga.de>
|
|
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License: Apache 2.0
|
|
@@ -13,15 +13,18 @@ Classifier: License :: OSI Approved :: Apache Software License
|
|
|
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Classifier: Topic :: Internet :: WWW/HTTP :: HTTP Servers
|
|
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Classifier: Topic :: Software Development :: Libraries
|
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Classifier: Intended Audience :: Developers
|
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Requires-Python: >=3.
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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
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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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|
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Requires-Dist: exceptiongroup>=1.0.0; python_version < "3.11"
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