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

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Description

  • Updates README to reflect new Agora infra repo
  • Import new dataversion file if it exists, otherwise generate the collection using the data-manifest
  • Updates data-manifest keys to match expected format in dataversion collection

@hallieswan hallieswan marked this pull request as ready for review January 31, 2025 17:20
@hallieswan hallieswan requested review from a team as code owners January 31, 2025 17:20
if [ ! -f "${DATAVERSION_PATH}" ]; then
DATAVERSION_PATH="${WORKING_DIR}/data-manifest.json"
fi

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To help debugging I would print a message with the DATAVERSION_PATH to let you know which one is being used before import happens.

@hallieswan hallieswan requested a review from zaro0508 January 31, 2025 17:55
import-data.sh Outdated
@@ -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.

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lgtm!

@hallieswan hallieswan requested a review from JessterB January 31, 2025 22:00
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3 participants