ghga-transpiler 1.2.0__py3-none-any.whl → 2.0.0__py3-none-any.whl

ghga_transpiler/configs/1.1.0.yaml

@@ -1,109 +0,0 @@
-ghga_metadata_version: 1.1.0
-default_settings:
-  header_row: 1
-  start_row: 7
-  start_column: 1
-  transformations:
-    attributes: !!python/object/apply:ghga_transpiler.transformations.to_attributes []
-worksheets:
-  - settings:
-      end_column: 6
-      name: analyses
-    sheet_name: Analysis
-  - settings:
-      end_column: 9
-      name: analysis_process_output_files
-    sheet_name: AnalysisProcessOutputFile
-  - settings:
-      end_column: 5
-      name: analysis_processes
-      transformations:
-        study_input_files: !!python/object/apply:ghga_transpiler.transformations.to_list []
-        sample_input_files: !!python/object/apply:ghga_transpiler.transformations.to_list []
-        sequencing_process_input_files: !!python/object/apply:ghga_transpiler.transformations.to_list []
-    sheet_name: AnalysisProcess
-  - settings:
-      end_column: 10
-      name: biospecimens
-    sheet_name: Biospecimen
-  - settings:
-      end_column: 9
-      name: conditions
-    sheet_name: Condition
-  - settings:
-      end_column: 3
-      name: data_access_committees
-    sheet_name: DataAccessCommittee
-  - settings:
-      end_column: 8
-      name: data_access_policies
-      transformations:
-        data_use_modifiers: !!python/object/apply:ghga_transpiler.transformations.to_list []
-    sheet_name: DataAccessPolicy
-  - settings:
-      end_column: 5
-      name: datasets
-      transformations:
-        types: !!python/object/apply:ghga_transpiler.transformations.to_list []
-    sheet_name: Dataset
-  - settings:
-      end_column: 6
-      name: individuals
-      transformations:
-        ancestries: !!python/object/apply:ghga_transpiler.transformations.to_list []
-        phenotypic_features: !!python/object/apply:ghga_transpiler.transformations.to_list []
-    sheet_name: Individual
-  - settings:
-      end_column: 14
-      name: library_preparation_protocols
-      transformations:
-        target_regions: !!python/object/apply:ghga_transpiler.transformations.to_list []
-        attributes: !!python/object/apply:ghga_transpiler.transformations.to_attributes []
-    sheet_name: LibraryPreparationProtocol
-  - settings:
-      end_column: 9
-      name: publications
-      transformations:
-        xref: !!python/object/apply:ghga_transpiler.transformations.to_list []
-    sheet_name: Publication
-  - settings:
-      end_column: 9
-      name: sample_files
-    sheet_name: SampleFile
-  - settings:
-      end_column: 10
-      name: samples
-      transformations:
-        xref: !!python/object/apply:ghga_transpiler.transformations.to_list []
-    sheet_name: Sample
-  - settings:
-      end_column: 7
-      name: sequencing_experiments
-    sheet_name: SequencingExperiment
-  - settings:
-      end_column: 9
-      name: sequencing_process_files
-    sheet_name: SequencingProcessFile
-  - settings:
-      end_column: 12
-      name: sequencing_processes
-    sheet_name: SequencingProcess
-  - settings:
-      end_column: 17
-      name: sequencing_protocols
-    sheet_name: SequencingProtocol
-  - settings:
-      end_column: 6
-      name: studies
-      transformations:
-        affiliations: !!python/object/apply:ghga_transpiler.transformations.to_list []
-        attributes: !!python/object/apply:ghga_transpiler.transformations.to_attributes []
-    sheet_name: Study
-  - settings:
-      end_column: 9
-      name: study_files
-    sheet_name: StudyFile
-  - settings:
-      end_column: 4
-      name: trios
-    sheet_name: Trio

ghga_transpiler-1.2.0.dist-info/RECORD

@@ -1,34 +0,0 @@
-ghga_transpiler/__init__.py,sha256=Udnso0Hk9DsAOwIF2HgV2ZRm4EosnNMIsUhMwBBLqCk,771
-ghga_transpiler/__main__.py,sha256=NgajDXhJ36WPA6MR5Rb44Qqmogie16_kr0HRL-umGxc,848
-ghga_transpiler/cli.py,sha256=fqZvP1XGwgO5FJ1fV9r8cFDQ_0PtpXld8QXtYipPyiM,2145
-ghga_transpiler/core.py,sha256=7_wtwRBOgPYtt2mI7gW7yBZM8lTdRgrVEx4OG61xmg0,5005
-ghga_transpiler/io.py,sha256=RY_aclqD5eTaASYIEayn8r-KQ9Avh4NJWvicyuhM-rg,1803
-ghga_transpiler/transformations.py,sha256=qI6vKq3gJPPBE2msUm-DMdVNeLrfJIkbga8l45tS7ek,1567
-ghga_transpiler/config/__init__.py,sha256=IKlzAd82ta9a0_aEps3f4I3GLRSJeyV1QImFcHvBLE0,818
-ghga_transpiler/config/config.py,sha256=egao2aF7iD5wAT83UUlek-g3D3R1CIG8tiyLlhcnEAQ,3825
-ghga_transpiler/config/exceptions.py,sha256=_A8wMX9t0YkLw4tk2IhOVdKoGoZxP2pXsEaZwrgkXhw,1091
-ghga_transpiler/configs/0.10.0.yaml,sha256=Z_6oSY9B883bevHb5RaCBToQgp1mP8l-1xXm6tGvUi4,3415
-ghga_transpiler/configs/1.0.0.yaml,sha256=Am6E3pdtwu_prbjSunB-Rps5qPZ722w59MMhyT1r2tg,3415
-ghga_transpiler/configs/1.1.0.yaml,sha256=VTmwAgio8U4eFigj-RJQvd6liojBOtj02M-SSaIXW6c,3415
-ghga_transpiler/configs/__init__.py,sha256=uGpTS9l2diw93p053atk09DuObDZ7eDZJoADCmuYX0g,687
-scripts/__init__.py,sha256=UmLyRp2rXXxZkJJTsuXv3J4LdunfUc-7NEH2eSEYqeE,756
-scripts/get_package_name.py,sha256=Mk3xBFcV-ttLt_61YVsL2_-IfzJrNZSkQ8KnbvbWi3g,1487
-scripts/license_checker.py,sha256=d0BMJyLnu887UIw7BkbpTaEGGgrEmn8lFKltR8b8h-g,18568
-scripts/update_all.py,sha256=C85KFl-P9duV2kTxJCyFvV9NnUGzcus6jEhGyTXLqf4,1461
-scripts/update_config_docs.py,sha256=p2zLkzVP7fb2L3p2_KusajMrBMLWO3_mvhOVF9V3Eek,4972
-scripts/update_readme.py,sha256=2wKLH3JCWwUH1aWKZxC-cFQ9JugzuzWUJ7lEQwqnoME,6789
-scripts/update_template_files.py,sha256=WqbEJlhYVd_PCaX_AJdDTIb54HbKDQkYT_OthrPrM1Q,8499
-scripts/script_utils/__init__.py,sha256=PQXZO-XfoUNet5pRpl2TkWNxiPWNhktX4IPPJcJgTug,737
-scripts/script_utils/cli.py,sha256=aqeY1v0FWwXdpyVSYZSBTbrerCiErlVZ1IfZCP3CR1A,1096
-tests/fixtures/__init__.py,sha256=E9gr4DMX7GAjMI2CGx9jny7essvn07almoATuULdpBU,750
-tests/fixtures/utils.py,sha256=CQ5x_3OFtuIoAQBkz8GaGzKppiqphgbcxh1vUfHbIFQ,1105
-tests/fixtures/configs/0.0.0.yaml,sha256=BvoImVhEQAn8_L6vekhFn3JtxZH37Mn62Ag6_FK9uHs,444
-tests/fixtures/configs/__init__.py,sha256=uGpTS9l2diw93p053atk09DuObDZ7eDZJoADCmuYX0g,687
-tests/fixtures/test_data_objects/__init__.py,sha256=UtnN52xEaTxeSVm2y-Y6LB-tZRAct86NvQgF3hqjhaw,725
-tests/fixtures/test_data_objects/conversion_data.py,sha256=Iw0q4iLFYwwwSbaMHZmN1lF_LtIjGhzsx7Xq5WR2xr4,1429
-ghga_transpiler-1.2.0.dist-info/LICENSE,sha256=a2nPPnhGY9QGdkfGrseHGDVj62fh8o5DoHsUpQp3GzA,11452
-ghga_transpiler-1.2.0.dist-info/METADATA,sha256=RJFbTsINh8zAzjhI_CXWLkxcA1tMiDyWrHUonjD8feM,4321
-ghga_transpiler-1.2.0.dist-info/WHEEL,sha256=AtBG6SXL3KF_v0NxLf0ehyVOh0cold-JbJYXNGorC6Q,92
-ghga_transpiler-1.2.0.dist-info/entry_points.txt,sha256=Fr_VQJynZZl95NXjrQW2gE0bCocgjKVNEZQpaLls8po,65
-ghga_transpiler-1.2.0.dist-info/top_level.txt,sha256=XhvuZqfjvQnMFFAUcwm_x-J9fuHZW7QM_38DclbmV5o,30
-ghga_transpiler-1.2.0.dist-info/RECORD,,

scripts/__init__.py

@@ -1,17 +0,0 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
-# for the German Human Genome-Phenome Archive (GHGA)
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
-"""Scripts and utils used during development or in CI pipelines."""

scripts/get_package_name.py

@@ -1,46 +0,0 @@
-#!/usr/bin/env python3
-
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
-# for the German Human Genome-Phenome Archive (GHGA)
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-"""Extracts the package name from the setup.cfg"""
-
-from pathlib import Path
-
-REPO_ROOT_DIR = Path(__file__).parent.parent.resolve()
-SETUP_CFG_PATH = REPO_ROOT_DIR / "setup.cfg"
-NAME_PREFIX = "name = "
-
-
-def get_package_name() -> str:
-    """Extracts the package name"""
-
-    with open(SETUP_CFG_PATH, "r", encoding="utf8") as setup_cfg:
-        for line in setup_cfg.readlines():
-            line_stripped = line.strip()
-            if line_stripped.startswith(NAME_PREFIX):
-                package_name = line_stripped[len(NAME_PREFIX) :]
-                return package_name
-        raise RuntimeError("Could not find package name.")
-
-
-def run():
-    """Run this script."""
-    package_name = get_package_name()
-    print(package_name)
-
-
-if __name__ == "__main__":
-    run()