53 lines
1.5 KiB
Bash
53 lines
1.5 KiB
Bash
#!/bin/bash
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excelFile="../../orig/drug_bank_database/Publication_citations_in_Drug_Bank_database.xlsx"
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workdir=/tmp/drugbank
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rm -rf "$workdir" && mkdir "$workdir"
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echo
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echo "Links from drugbank db Import:"
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#--------------------------------
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echo " - Generating csv file"
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csv="$workdir/drugbank.csv"
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xlsx2csv -c UTF-8 "$excelFile" > $csv
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#--------------------------------
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echo " - Recreating the drugbank database"
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dbname=drugbank
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dropdb $dbname --if-exists;
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createdb $dbname;
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psql $dbname -f schema.sql
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if [[ -f "$csv" ]]; then
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echo " - Importing data: $csv"
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psql $dbname -c "COPY data(id,d_b_id,doi,pmcid,pmid,drug_substance,funder,section_of_drug_bank_entry_where_citation_occured) FROM '$csv' CSV HEADER;"
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else
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echo " - Invalid file: $csv"
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fi
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echo " - Fix funder names"
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psql $dbname -c "UPDATE data SET funder='EC' WHERE funder = 'European Research Council'"
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psql $dbname -c "UPDATE data SET funder='Austrian Science Fund FWF' WHERE funder = 'FWF'"
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psql $dbname -c "UPDATE data SET funder='Swiss National Science Foundation SNSF' WHERE funder = 'Swiss National Science Foundation'"
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#--------------------------------
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echo " - Generating json files"
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rm -f ../../jsonfiles/drug_bank_database/*.json
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psql $dbname -f projects2json.sql | sed 's/\\\\/\\/g' > ../../jsonfiles/drug_bank_database/project.json
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psql $dbname -f docOtherId2json.sql | sed 's/\\\\/\\/g' > ../../jsonfiles/drug_bank_database/docotherid.json
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psql $dbname -f projDocOtherIds2json.sql | sed 's/\\\\/\\/g' > ../../jsonfiles/drug_bank_database/projectdocotherid.json
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echo "Done."
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echo
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