diff options
Diffstat (limited to 'genenetwork-local-container.sh')
| -rwxr-xr-x | genenetwork-local-container.sh | 34 |
1 files changed, 23 insertions, 11 deletions
diff --git a/genenetwork-local-container.sh b/genenetwork-local-container.sh index 5a81e61..0108390 100755 --- a/genenetwork-local-container.sh +++ b/genenetwork-local-container.sh @@ -33,6 +33,8 @@ SYSTEM_DIRECTORIES=( "$BASE_DIR/var/lib/redis" "$BASE_DIR/var/lib/virtuoso" "$BASE_DIR/var/lib/data" + "$BASE_DIR/var/lib/gn-uploader/data" + "$BASE_DIR/var/lib/gn-uploader/sessions" "$BASE_DIR/var/lib/xapian" "$BASE_DIR/var/genenetwork/genotype-files/genotype/json" "$BASE_DIR/var/lib/genenetwork-sqlite" @@ -46,15 +48,18 @@ GN_PROJECTS=( "gn-transform-databases:https://git.genenetwork.org/gn-transform-databases/" "gn-auth:https://git.genenetwork.org/gn-auth" "gn-docs:https://git.genenetwork.org/gn-docs" + "gn-uploader:https://git.genenetwork.org/gn-uploader" ) # File mappings: source -> destination declare -A FILE_MAPPINGS=( ["etc/auth.db"]="$BASE_DIR/var/genenetwork/auth.db" + ["etc/gn-uploader.db"]="$BASE_DIR/var/genenetwork/gn-uploader.db" ["etc/llm.db"]="$BASE_DIR/var/lib/genenetwork-sqlite/llm.db" ["etc/gn2-secrets.py"]="$BASE_DIR/etc/genenetwork/conf/gn2/secrets.py" ["etc/gn3-secrets.py"]="$BASE_DIR/etc/genenetwork/conf/gn3/secrets.py" ["etc/gn-auth-secrets.py"]="$BASE_DIR/etc/genenetwork/conf/gn-auth/secrets.py" + ["etc/gn-uploader-secrets.py"]="$BASE_DIR/etc/genenetwork/conf/gn-uploader/secrets.py" ) CONTAINER_SCM="genenetwork-local-container.scm" @@ -197,18 +202,22 @@ if [ "$1" = "--init-container" ]; then fi done - FLASK_SESSION="$BASE_DIR/genenetwork2/flask_session" - log "INFO" "Checking FLASK_SESSION directory: $FLASK_SESSION" - if [ ! -d "$FLASK_SESSION" ]; then - log "INFO" "Creating FLASK_SESSION directory: $FLASK_SESSION" - if ! mkdir -p "$FLASK_SESSION"; then - log "ERROR" "Failed to create FLASK_SESSION directory: $FLASK_SESSION" - exit 1 + FLASK_SESSIONS=( + "gn-uploader:$BASE_DIR/gn-uploader/flask_session" + "genenetwork2:$BASE_DIR/genenetwork2/flask_session" + ) + for flask_session in "${FLASK_SESSIONS[@]}"; do + IFS=':' read -r project session_dir <<< "$flask_session" + if [ ! -d "$session_dir" ]; then + log "INFO" "Creating FLASK_SESSION directory: $session_dir" + if ! mkdir -p "$session_dir"; then + log "ERROR" "Failed to create FLASK_SESSION directory: $session_dir" + exit 1 + fi + else + log "DEBUG" "FLASK_SESSION directory already exists: $session_dir" fi - else - log "DEBUG" "FLASK_SESSION directory already exists: $FLASK_SESSION" - fi - + done # Verify container SCM file exists if [ ! -f "$CONTAINER_SCM" ]; then @@ -226,8 +235,11 @@ if [ "$1" = "--init-container" ]; then "--share=$BASE_DIR/var/lib/redis=/var/lib/redis" "--share=$BASE_DIR/var/lib/virtuoso=/var/lib/virtuoso" "--share=$BASE_DIR/var/lib/data=/var/lib/data" + "--share=$BASE_DIR/var/lib/gn-uploader/data=/var/lib/gn-uploader/data" + "--share=$BASE_DIR/var/lib/gn-uploader/sessions=/var/lib/gn-uploader/sessions" "--share=$BASE_DIR/genenetwork2=/genenetwork2" "--share=$BASE_DIR/genenetwork3=/genenetwork3" + "--share=$BASE_DIR/gn-uploader=/gn-uploader" "--share=$BASE_DIR/gn-auth=/gn-auth" "--share=$BASE_DIR/var/lib/xapian=/var/lib/xapian" "--share=$BASE_DIR/var/lib/genenetwork-sqlite=/var/lib/genenetwork-sqlite" |