build_db_all

#!/bin/bash


if [[ -z $1 || -z $2 ]]
then 
	echo Please run with via the following: $0 postgres_host postgres_user
	exit
fi

echo "Starting Alliancemine DB Build: Host: $1 User: $2"
date

fasta_sources=(alliance-wb-fasta alliance-fb-fasta alliance-zfin-fasta alliance-mgi-fasta alliance-rgd-fasta)
ontology_sources=(do go eco mmo emapa zfa wbbt fbbt so psi-mi-ontology go-slim)
sgd_sources=(sgd sgd-gff sgd-gff-utr sgd-db-utr fungi-homologs cgob-homologs cglabrata-homologs pombe-homologs homolog-genes sgd-complementation-db sgd-complexes sgd-protein-properties sgd-protein-ntermini)
alliance_sources=(alliance-genes go-annotation alliance-disease alliance-orthologs alliance-alleles alliance-expression entrez-organism)
postprocess_sources=(create-references do-sources transfer-sequences create-attribute-indexes summarise-objectstore)
solr_indexes=(create-autocomplete-index create-search-index)

echo createdb -U $2 -h $1 alliancemine || true
createdb -U $2 -h $1 alliancemine || true
echo createdb -U $2 -h $1 items-alliancemine || true
createdb -U $2 -h $1 items-alliancemine || true
echo ./gradlew --no-daemon builddb
./gradlew --no-daemon builddb
date

for i in "${fasta_sources[@]}"
do
	echo "./gradlew --no-daemon integrate -Psource=$i"
	./gradlew --no-daemon --stacktrace integrate -Psource=$i
	date
done

for i in "${ontology_sources[@]}"
do
	echo "./gradlew --no-daemon integrate -Psource=$i"
	./gradlew --no-daemon --stacktrace integrate -Psource=$i
	date
done

for i in "${sgd_sources[@]}"
do
	echo "./gradlew --no-daemon integrate -Psource=$i"
	./gradlew --no-daemon --stacktrace integrate -Psource=$i
	date
done

for i in "${alliance_sources[@]}"
do
	echo "./gradlew --no-daemon integrate -Psource=$i"
	./gradlew --no-daemon --stacktrace integrate -Psource=$i
	date
done

for i in "${postprocess_sources[@]}"
do
	echo "./gradlew --no-daemon postprocess -Pprocess=$i"
	./gradlew --no-daemon --stacktrace postprocess -Pprocess=$i
	date
done

echo pg_dump -F c -U $2 -h $1 -f /root/data/alliancemine.dump alliancemine
pg_dump -F c -U $2 -h $1 -f /root/data/alliancemine.dump alliancemine

date

echo "Backup DB File to S3: aws s3 cp /root/data/alliancemine.dump s3://agr-db-backups/alliancemine/stage/`date "+%Y-%m-%d_%H:%M:%S".dump`"
aws s3 cp /root/data/alliancemine.dump s3://agr-db-backups/alliancemine/stage/`date "+%Y-%m-%d_%H:%M:%S".dump`

echo "Finished Alliancemine DB Build"
date