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add option to run import metadata graphs using docker for testing
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@@ -31,3 +31,9 @@ logs/ | |
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| # Ignore jEnv files | ||
| .java-version | ||
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| processed_files/ | ||
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| queries.txt | ||
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| graph_comparison.csv | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,85 @@ | ||
| #!/usr/bin/env bash | ||
| profile=$1 | ||
| acronym=$2 | ||
| set -e | ||
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| if [ -z "$profile" ]; then | ||
| echo "Usage: $0 <acronym> <profile>" | ||
| exit 1 | ||
| fi | ||
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| BACKEND_TYPE=$profile | ||
| if [ "$BACKEND_TYPE" == "ag" ]; then | ||
| # AllegroGraph backend | ||
| export GOO_BACKEND_NAME="allegrograph" | ||
| export GOO_PORT="10035" | ||
| export GOO_PATH_QUERY="/repositories/ontoportal_test" | ||
| export GOO_PATH_DATA="/repositories/ontoportal_test/statements" | ||
| export GOO_PATH_UPDATE="/repositories/ontoportal_test/statements" | ||
| export COMPOSE_PROFILES="ag" | ||
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| elif [ "$BACKEND_TYPE" == "fs" ]; then | ||
| # 4store backend | ||
| export GOO_PORT="9000" | ||
| export COMPOSE_PROFILES="fs" | ||
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| elif [ "$BACKEND_TYPE" == "vo" ]; then | ||
| # Virtuoso backend | ||
| export GOO_BACKEND_NAME="virtuoso" | ||
| export GOO_PORT="8890" | ||
| export GOO_PATH_QUERY="/sparql" | ||
| export GOO_PATH_DATA="/sparql" | ||
| export GOO_PATH_UPDATE="/sparql" | ||
| export COMPOSE_PROFILES="vo" | ||
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| elif [ "$BACKEND_TYPE" == "gb" ]; then | ||
| # Graphdb backend | ||
| export GOO_BACKEND_NAME="graphdb" | ||
| export GOO_PORT="7200" | ||
| export GOO_PATH_QUERY="/repositories/ontoportal" | ||
| export GOO_PATH_DATA="/repositories/ontoportal/statements" | ||
| export GOO_PATH_UPDATE="/repositories/ontoportal/statements" | ||
| else | ||
| echo "Error: Unknown backend type. Please set BACKEND_TYPE to 'ag', 'fs', or 'vo'." | ||
| fi | ||
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| echo "###########################################################################" | ||
| echo "Stop and remove all containers, networks, and volumes and start fresh" | ||
| docker compose --profile fs --profile vo --profile gb --profile ag down --volumes --remove-orphans && docker compose --profile "$profile" up -d | ||
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| echo "Waiting for all Docker services to start..." | ||
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| while true; do | ||
| # Get the status of all containers | ||
| container_status=$(docker compose --profile "$profile" ps -a --format '{{.Names}} {{.State}}') | ||
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| all_running=true | ||
| while read -r container state; do | ||
| if [ "$state" != "running" ] && [ "$state" != "exited" ]; then | ||
| all_running=false | ||
| break | ||
| fi | ||
| done <<< "$container_status" | ||
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| # If all containers are running, exit the loop | ||
| if [ "$all_running" = true ]; then | ||
| echo "All containers are running!" | ||
| break | ||
| fi | ||
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| # Wait before checking again | ||
| sleep 2 | ||
| done | ||
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| if [ -z "$acronym" ]; then | ||
| exit 0 | ||
| fi | ||
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| echo "###########################################################################" | ||
| echo "Create a new user and make it an admin" | ||
| bundle exec rake user:create[admin,[email protected],password] | ||
| bundle exec rake user:adminify[admin] | ||
| echo "###########################################################################" | ||
| echo "Create a new ontology $acronym and import it from a remote server" | ||
| bin/ncbo_ontology_import --admin-user admin -o "$acronym" --from https://data.stageportal.lirmm.fr --from-apikey 82602563-4750-41be-9654-36f46056a0db |