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Merge pull request #9 from monarch-initiative/robot-template
Robot template
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|---|---|---|
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@@ -4,9 +4,9 @@ | |
| name: Build and release | ||
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| on: | ||
| # schedule: | ||
| # - cron: "0 0 * * 0" # weekly on Sunday at midnight | ||
| workflow_dispatch: | ||
| schedule: | ||
| - cron: "0 0 * * 0" # weekly on Sunday at midnight | ||
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| jobs: | ||
| build_and_release: | ||
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@@ -15,7 +15,9 @@ jobs: | |
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: build | ||
| run: make all | ||
| # todo: reactivate `make all`, pending pending https://github.com/monarch-initiative/medgen/issues/11 | ||
| # run: make all | ||
| run: make minimal | ||
| - name: Get current time | ||
| uses: josStorer/[email protected] | ||
| id: current-time | ||
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@@ -29,7 +31,11 @@ jobs: | |
| automatic_release_tag: "${{ steps.current-time.outputs.formattedTime }}" | ||
| title: "${{ steps.current-time.outputs.formattedTime }}" | ||
| prerelease: false | ||
| # todo: add back `release/medgen-disease-extract.owl`, pending https://github.com/monarch-initiative/medgen/issues/11 | ||
| # todo: add `medgen.sssom.tsv`, pending https://github.com/monarch-initiative/medgen/issues/6 | ||
| # output/release/medgen-disease-extract.owl | ||
| # output/release/medgen.sssom.tsv | ||
| files: | | ||
| release/medgen.obo | ||
| release/medgen-disease-extract.obo | ||
| release/medgen-disease-extract.owl | ||
| output/release/medgen.obo | ||
| output/release/medgen-disease-extract.obo | ||
| output/release/medgen-xrefs.robot.template.tsv | ||
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| """Medgen->Mondo robot template | ||
| Create a robot template to be used by Mondo to add MedGen xrefs curated by MedGen. | ||
| See also: | ||
| - PR: https://github.com/monarch-initiative/medgen/pull/9 | ||
| - Used here: https://github.com/monarch-initiative/mondo/pull/6560 | ||
| """ | ||
| from argparse import ArgumentParser | ||
| from copy import copy | ||
| from pathlib import Path | ||
| from typing import Dict, List | ||
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| import pandas as pd | ||
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| SRC_DIR = Path(__file__).parent | ||
| PROJECT_DIR = SRC_DIR.parent | ||
| FTP_DIR = PROJECT_DIR / "ftp.ncbi.nlm.nih.gov" / "pub" / "medgen" | ||
| INPUT_FILE = str(FTP_DIR / "MedGenIDMappings.txt") | ||
| OUTPUT_FILE = str(PROJECT_DIR / "medgen-xrefs.robot.template.tsv") | ||
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| def _prefixed_id_rows_from_common_df(source_df: pd.DataFrame, mondo_col='mondo_id', xref_col='xref_id') -> List[Dict]: | ||
| """From worksheets having same common format, get prefixed xrefs for the namespaces we're looking to cover | ||
| Note: This same exact function is used in: | ||
| - mondo repo: medgen_conflicts_add_xrefs.py | ||
| - medgen repo: mondo_robot_template.py""" | ||
| df = copy(source_df) | ||
| df[xref_col] = df[xref_col].apply( | ||
| lambda x: f'MEDGENCUI:{x}' if x.startswith('CN') # "CUI Novel" | ||
| else f'UMLS:{x}' if x.startswith('C') # CUI: will be created twice: one for MEDGENCUI, one for UMLS | ||
| else f'MEDGEN:{x}') # UID | ||
| rows = df.to_dict('records') | ||
| rows2 = [{mondo_col: x[mondo_col], xref_col: x[xref_col].replace('UMLS', 'MEDGENCUI')} for x in rows if | ||
| x[xref_col].startswith('UMLS')] | ||
| return rows + rows2 | ||
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| def run(input_file: str = INPUT_FILE, output_file: str = OUTPUT_FILE): | ||
| """Create robot template""" | ||
| # Read input | ||
| df = pd.read_csv(input_file, sep='|').rename(columns={'#CUI': 'xref_id'}) | ||
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| # Get explicit Medgen (CUI, CN) -> Mondo mappings | ||
| df_medgen_mondo = df[df['source'] == 'MONDO'][['source_id', 'xref_id']].rename(columns={'source_id': 'mondo_id'}) | ||
| out_df_cui_cn = pd.DataFrame(_prefixed_id_rows_from_common_df(df_medgen_mondo)) | ||
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| # Get Medgen (UID) -> Mondo mappings | ||
| # - Done by proxy: UID <-> CUI <-> MONDO | ||
| df_medgen_medgenuid = df[df['source'] == 'MedGen'][['source_id', 'xref_id']].rename( | ||
| columns={'source_id': 'medgen_uid'}) | ||
| out_df_uid = pd.merge(df_medgen_mondo, df_medgen_medgenuid, on='xref_id')[['mondo_id', 'medgen_uid']]\ | ||
| .rename(columns={'medgen_uid': 'xref_id'}) | ||
| out_df_uid['xref_id'] = out_df_uid['xref_id'].apply(lambda x: f'MEDGEN:{x}') | ||
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| # Save | ||
| out_df = pd.concat([out_df_cui_cn, out_df_uid]).sort_values(['xref_id', 'mondo_id']).drop_duplicates() | ||
| out_df = pd.concat([pd.DataFrame([{'mondo_id': 'ID', 'xref_id': 'A oboInOwl:hasDbXref'}]), out_df]) | ||
| out_df.to_csv(output_file, index=False, sep='\t') | ||
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| def cli(): | ||
| """Command line interface.""" | ||
| parser = ArgumentParser( | ||
| prog='"Medgen->Mondo robot template', | ||
| description='Create a robot template to be used by Mondo to add MedGen xrefs curated by MedGen.') | ||
| parser.add_argument( | ||
| '-i', '--input-file', default=INPUT_FILE, help='Mapping file sourced from MedGen') | ||
| parser.add_argument( | ||
| '-o', '--output-file', default=OUTPUT_FILE, help='ROBOT template to be used to add xrefs') | ||
| run(**vars(parser.parse_args())) | ||
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| if __name__ == '__main__': | ||
| cli() |