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AG-1640: deploy to the new dev environment and import dataversion collection #131

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AG-1640: deploy to the new dev environment and import dataversion collection #131

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350a5de
AG-1640: create dataversion collection
hallieswan Jan 29, 2025
6fdfece
AG-1640: generate dataversion if file does not exist in data release
hallieswan Jan 31, 2025
27547a5
AG-1640: update README
hallieswan Jan 31, 2025
ead7cef
AG-1640: fix precommit
hallieswan Jan 31, 2025
7982324
AG-1640: improvement from review
hallieswan Jan 31, 2025
5b7a7c4
AG-1640: handle different data format for manifest vs ADT file
hallieswan Jan 31, 2025
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2 changes: 2 additions & 0 deletions import-data.sh
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Expand Up @@ -69,6 +69,8 @@ mongoimport -h $DB_HOST -d agora -u $DB_USER -p $DB_PASS --authenticationDatabas
mongoimport -h $DB_HOST -d agora -u $DB_USER -p $DB_PASS --authenticationDatabase admin --collection proteomicssrm --jsonArray --drop --file $DATA_DIR/proteomics_srm.json
mongoimport -h $DB_HOST -d agora -u $DB_USER -p $DB_PASS --authenticationDatabase admin --collection genesbiodomains --jsonArray --drop --file $DATA_DIR/genes_biodomains.json
mongoimport -h $DB_HOST -d agora -u $DB_USER -p $DB_PASS --authenticationDatabase admin --collection biodomaininfo --jsonArray --drop --file $DATA_DIR/biodomain_info.json

echo "Importing dataversion from ${DATAVERSION_PATH}"
mongoimport -h $DB_HOST -d agora -u $DB_USER -p $DB_PASS --authenticationDatabase admin --collection dataversion --jsonArray --drop --file $DATAVERSION_PATH
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Note that ADT's generated dataversion.json file is a list of one object (see e.g. https://www.synapse.org/Synapse:syn64713183). If you end up generating dataverison in code, make sure it's also list of one object, or it won't be loadable with the --jsonArray flag.

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Thanks for pointing that out! I didn't realize that ADT's version is a list with one object -- I'll update in the next commit.


mongosh --host $DB_HOST -u $DB_USER -p $DB_PASS --authenticationDatabase admin $WORKING_DIR/create-indexes.js
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