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Merge pull request #285 from helxplatform/add-bdc-dbgap-ids
This PR adds the list of dbGaP identifiers that should be loaded into BDC Dug (https://renci.atlassian.net/browse/DUG-223?focusedCommentId=10809) to this repository, as well as a Bash script that can be used to download all these files. I kept running into errors with the FTP download command, but luckily dbGaP is simultaneously available over HTTPS, so this script now uses FTP to list all the data dictionaries in an FTP folder, and then uses HTTPS (via the Requests library) to actually download the files.
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#!/bin/bash | ||
# | ||
# Download the data dictionaries from dbGaP as listed in bdc_dbgap_ids.csv | ||
# into the bdc_dbgap/ directory. | ||
# | ||
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CSV_FILE=bdc_dbgap_ids.csv | ||
OUTPUT_DIR=bdc_dbgap_data_dicts | ||
SCRIPT=../bin/get_dbgap_data_dicts.py | ||
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mkdir -p $OUTPUT_DIR | ||
python $SCRIPT $CSV_FILE --format CSV --field Accession --outdir $OUTPUT_DIR --skip phs000571.v6.p2 |
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