Rename indexing repository. GNP-5861

scripts/harvest.sh

@@ -52,7 +52,7 @@ check_acknowledgment() {
 	local MSG=$2
 	echo $LOG | jq '.acknowledged? == true' | grep 'true' >/dev/null || {
 		echo -e "${RED}ERROR: a problem occurred when trying to ${MSG}.${NC}"
-		echo -e "${ORANGE}$(echo ${LOG})${NC}"
+		echo -e "${ORANGE}$(echo "${LOG}")${NC}"
 		exit 1;
 	}
 }
@@ -61,7 +61,7 @@ check_acknowledgment() {
 MISSING_COUNT=0
 PROGRAMS="gzip parallel jq"
 for PROGRAM in ${PROGRAMS}; do
-	command -v ${PROGRAM} >/dev/null || {
+	command -v "${PROGRAM}" >/dev/null || {
 		echo -e "${ORANGE}Program ${PROGRAM} is missing, cannot continue...${NC}"
 		((MISSING_COUNT += 1))
 	}
@@ -102,24 +102,24 @@ if [ ! -d "${DATA_DIR}" ]; then
 	echo -e "${RED}ERROR: Mandatory parameter 'jsonDir' is missing!${NC}"
 	echo && help
 fi
-if [ $(find ${DATA_DIR} -name "*.json" | wc -l) -le 0 ] && [ $(find ${DATA_DIR} -name "*.json.gz" | wc -l) -le 0 ]; then
+if [ $(find "${DATA_DIR}" -name "*.json" | wc -l) -le 0 ] && [ $(find "${DATA_DIR}" -name "*.json.gz" | wc -l) -le 0 ]; then
 	echo -e "${RED}ERROR: The JSON directory ${DATA_DIR} contains no JSON files!${NC}"
 	echo && help
 fi
 [ "${DOCUMENT_TYPES}" == "all" ] && DOCUMENT_TYPES="${ALL_DOCUMENT_TYPES}"
 for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
-	if [ $(find ${DATA_DIR} -name "${DOCUMENT_TYPE}*.json" | wc -l) -le 0 ] && [ $(find ${DATA_DIR} -name "${DOCUMENT_TYPE}*.json.gz" | wc -l) -le 0 ]; then
+	if [ $(find "${DATA_DIR}" -name "${DOCUMENT_TYPE}*.json" | wc -l) -le 0 ] && [ $(find ${DATA_DIR} -name "${DOCUMENT_TYPE}*.json.gz" | wc -l) -le 0 ]; then
 		echo -e "${ORANGE}WARNING: The JSON directory ${DATA_DIR} contains no ${DOCUMENT_TYPE} document. Type will be ignored!${NC}"
 		DOCUMENT_TYPES=$(echo "${DOCUMENT_TYPES}" | sed "s/ *${DOCUMENT_TYPE} */ /g")
 	fi
 done
 
 # Compress JSON files
-for FILE in $(find ${DATA_DIR} -name "*.json"); do
-	gzip $FILE
+for FILE in $(find "${DATA_DIR}" -name "*.json"); do
+	gzip "$FILE"
 done
 
-LOG_DIR="${DATA_DIR%/}/log"
+LOG_DIR="${DATA_DIR%/}/indexing-log"
 
 if [[ -d ${LOG_DIR} ]]
 then
@@ -155,8 +155,8 @@ for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
 	\"index_patterns\": [\"${INDEX_PATTERN}-*\"],
 	\"order\": 101,
 	\"mappings\":
-		$(cat ${BASEDIR}/../backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/${DOCUMENT_TYPE}_mapping.json),
-	\"settings\": $(cat ${BASEDIR}/../backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/settings.json)
+		$(cat "${BASEDIR}"/../backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/${DOCUMENT_TYPE}_mapping.json),
+	\"settings\": $(cat "${BASEDIR}"/../backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/settings.json)
 }")
 	check_acknowledgment "${LOG}" "create template"
 
@@ -170,7 +170,7 @@ for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
 		echo -e "${RED}ERROR: a problem occurred when trying to index data with parallel program.${NC}"
 		exit $code
 	}
-	parallel "gunzip -c {} | jq '.errors' | grep -q true && echo -e '${ORANGE}ERROR found in {}${NC}' >> ${TMP_FILE} ;" ::: $(find ${DATA_DIR} -name "${DOCUMENT_TYPE}-*.log.gz")
+	parallel "gunzip -c {} | jq '.errors' | grep -q true && echo -e '${ORANGE}ERROR found in {}${NC}' >> ${TMP_FILE} ;" ::: $(find "${DATA_DIR}" -name "${DOCUMENT_TYPE}-*.log.gz")
 	if [ -f "${TMP_FILE}" ] && [ -s "${TMP_FILE}" ]; then
 		echo -e "${RED}ERROR: a problem occurred when trying to index data into ${ES_HOST}:${ES_PORT}/${INDEX_NAME} indice.${NC}"
 		echo -e "${ORANGE}$(cat ${TMP_FILE})${NC}"