From db7ffa81fbf0d0f2a53618a06d8ae2b6591bdf21 Mon Sep 17 00:00:00 2001
From: Celia Michotey <celia.michotey@inra.fr>
Date: Fri, 4 Oct 2019 17:59:49 +0200
Subject: [PATCH 01/11] Create script to index data in FAIDARE. Update program
mapping file.
---
.../es/setup/index/program_mapping.json | 94 +++++---
scripts/harvest.sh | 221 ++++++++++++++++++
2 files changed, 283 insertions(+), 32 deletions(-)
create mode 100755 scripts/harvest.sh
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/program_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/program_mapping.json
index b556355a..aef2ae37 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/program_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/program_mapping.json
@@ -1,34 +1,64 @@
{
- "program": {
- "dynamic": false,
- "properties": {
- "programDbId": {
- "type": "keyword"
- },
- "programName": {
- "type": "keyword"
- },
- "abbreviation": {
- "type": "keyword"
- },
- "groupId": {
- "type": "long"
- },
- "leadPerson": {
- "type": "keyword"
- },
- "objective": {
- "type": "keyword"
- },
- "source": {
- "type": "keyword"
- },
- "speciesGroup": {
- "type": "integer"
- },
- "documentationURL": {
- "type": "keyword"
- }
- }
- }
+ "program": {
+ "dynamic": "strict",
+ "properties": {
+ "programDbId": {
+ "type": "keyword"
+ },
+ "name": {
+ "type": "keyword"
+ },
+ "programName": {
+ "type": "keyword"
+ },
+ "abbreviation": {
+ "type": "keyword"
+ },
+ "objective": {
+ "type": "keyword"
+ },
+ "leadPerson": {
+ "type": "keyword"
+ },
+ "source": {
+ "type": "keyword"
+ },
+ "studyDbIds": {
+ "type": "keyword"
+ },
+ "trialDbIds": {
+ "type": "keyword"
+ },
+ "documentationURL": {
+ "type": "keyword"
+ },
+ "programURI": {
+ "type": "keyword"
+ },
+ "studyURIs": {
+ "type": "keyword"
+ },
+ "trialURIs": {
+ "type": "keyword"
+ },
+ "groupId": {
+ "type": "long"
+ },
+ "@type": {
+ "type": "keyword"
+ },
+ "@id": {
+ "type": "keyword"
+ },
+ "schema:includedInDataCatalog": {
+ "type": "keyword"
+ },
+ "schema:identifier": {
+ "type": "keyword"
+ },
+ "schema:name": {
+ "type": "keyword"
+ }
+ }
+ }
}
diff --git a/scripts/harvest.sh b/scripts/harvest.sh
new file mode 100755
index 00000000..bacc1e63
--- /dev/null
+++ b/scripts/harvest.sh
@@ -0,0 +1,221 @@
+#!/bin/bash
+
+DATA_DIR=""
+ES_HOST="localhost"
+ES_PORT="9200"
+ENV="dev"
+DOCUMENT_TYPES="all"
+
+ALL_DOCUMENT_TYPES="germplasm germplasmAttribute germplasmPedigree germplasmProgeny location program study trial observationUnit datadiscovery"
+ALL_ENVS="dev beta staging int prod test"
+BASEDIR=$(dirname "$0")
+
+RED='\033[0;31m'
+GREEN='\033[0;32m'
+ORANGE='\033[0;33m'
+BOLD='\033[1m'
+NC='\033[0m' # No format
+
+
+help() {
+ cat <<EOF
+DESCRIPTION:
+ Script used to index data in FAIDARE
+
+USAGE:
+ ${SCRIPT} -jsonDir <JSON directory> -es_host <Elasticsearch node host> -es_port <Elasticsearch node port> -env <application environment name> -type <document type(s) to index> [-h|--help]
+
+PARAMS:
+ -jsonDir The directory where JSON bulk files to index are
+ -es_host The hostname or IP of Elasticsearch node (local, dev or prod cluster). Default: $ES_HOST
+ -es_port The port of Elasticsearch node (local, dev or prod cluster). Default: $ES_PORT
+ -env The environment name of the targeted FAIDARE application ($(echo $ALL_ENVS | tr ' ' ', ')). Default: $ENV
+ -type The document type(s) to index, separated by a comma ($(echo $ALL_DOCUMENT_TYPES | tr ' ' ', ')). Default: $DOCUMENT_TYPES
+ -h|--help Display this message
+ -v|--verbose Verbose mode
+ --debug Debug mode (same as set -x)
+
+DEPENDENCIES:
+ - jq 1.6+: https://github.com/stedolan/jq/releases/tag/jq-1.6
+ - GNU parallel: https://www.gnu.org/software/parallel/
+ - gzip: http://www.gzip.org/
+
+EOF
+ exit 1
+}
+
+check_acknowledgment() {
+ local LOG=$1
+ 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}"
+ exit 1;
+ }
+}
+
+# Check programs
+MISSING_COUNT=0
+PROGRAMS="gzip parallel jq"
+for PROGRAM in ${PROGRAMS}; do
+ command -v ${PROGRAM} >/dev/null || {
+ echo -e "${ORANGE}Program ${PROGRAM} is missing, cannot continue...${NC}"
+ ((MISSING_COUNT += 1))
+ }
+done
+if [ $MISSING_COUNT -ne 0 ]; then
+ echo -e "${RED}ERROR: You must install the $MISSING_COUNT missing program(s).${NC}"
+ exit $MISSING_COUNT
+fi
+
+# Get and Check parameters
+# any params
+[ -z "$1" ] && echo && help
+# get params
+while [ -n "$1" ]; do
+ case "$1" in
+ -h|--help) help;;
+ -v|--verbose) VERBOSE=1;shift 1;;
+ --debug) set -x;shift 1;;
+ -jsonDir) DATA_DIR="$2"; shift 2;;
+ -es_host) ES_HOST="$2"; shift 2;;
+ -es_port) ES_PORT="$2"; shift 2;;
+ -env) ENV="$2"; shift 2;;
+ -type) DOCUMENT_TYPES=$(echo "$2" | tr ',' ' '); shift 2;;
+ -*) echo -e "${RED}Unknown option: $1 ${NC}\n" echo && help;;
+ *) break;;
+ esac
+done
+
+if [ -z "$ES_HOST" ] || [ -z "$ES_PORT" ]; then
+ echo -e "${RED}ERROR: 'es_host' and 'es_port' parameters are mandatory!${NC}"
+ echo && help
+fi
+if [[ "$ALL_ENVS" != *"$ENV"* ]]; then
+ echo -e "${RED}ERROR: The value of parameter 'env' must be one of the following: ${ALL_ENVS}.${NC}"
+ echo && help
+fi
+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 ${DATA_DIR} -name *.json.gz | wc -l) -le 0 ]; then
+ echo -e "${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}*.json | wc -l) -le 0 ] && [ $(find ${DATA_DIR} -name ${DOCUMENT}*.json.gz | wc -l) -le 0 ]; then
+ echo -e "${ORANGE}WARNING: The JSON directory ${DATA_DIR} contains no ${DOCUMENT} document, so it will be ignored!${NC}"
+ fi
+done
+
+# Compress JSON files
+for FILE in $(find ${DATA_DIR} -name *.json); do
+ gzip $FILE
+done
+
+for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
+ echo -e "${BOLD}Manage ${DOCUMENT_TYPE} documents...${NC}"
+ INDEX_PATTERN="faidare_${DOCUMENT_TYPE}_${ENV}"
+
+ # Create template
+ TEMPLATE_NAME="${INDEX_PATTERN}_template"
+ echo -e "Create setting/mapping template ${TEMPLATE_NAME}..."
+ LOG=$(curl -s -H 'Content-Type: application/json' -XPUT "${ES_HOST}:${ES_PORT}/_template/${TEMPLATE_NAME}" -d"
+{
+ \"index_patterns\": [\"${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 ${BASEDIR}/../backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/settings.json)
+}")
+ check_acknowledgment "${LOG}" "create template"
+
+ # Index JSON Bulk
+ INDEX_NAME="${INDEX_PATTERN}-d"$(date +%s)
+ echo -e "Index documents into ${ES_HOST}:${ES_PORT}/${INDEX_NAME} indice..."
+ {
+ time parallel --bar "
+ curl -s -H 'Content-Type: application/x-ndjson' -H 'Content-Encoding: gzip' -H 'Accept-Encoding: gzip' -XPOST ${ES_HOST}:${ES_PORT}/${INDEX_NAME}/_bulk --data-binary '@{}' > {.}.log.gz" \
+ ::: $(find ${DATA_DIR} -name ${DOCUMENT_TYPE}*.json.gz)
+ } || {
+ code=$?
+ echo -e "${RED}ERROR: a problem occurred when trying to index data with parallel program.${NC}"
+ exit $code
+ }
+ #echo -e "${RED}ERROR: a problem occurred when trying to index data into ${ES_HOST}:${ES_PORT}/${INDEX_NAME} indice.${NC}"
+ parallel "gunzip -c {} | jq '.errors' | grep -q true && echo -e '${ORANGE}ERROR found in {}${NC}' ;" ::: $(find ${DATA_DIR} -name ${DOCUMENT_TYPE}*.log.gz)
+
+ # Check indexed data
+ echo -e "Check data indexed from ${DATA_DIR} into ${INDEX_NAME}..."
+ # skip some documents because they contain nested objects that distort the count
+ if [[ "${DOCUMENT_TYPE}" != "germplasmAttribute" && "${DOCUMENT_TYPE}" != "observationUnit" && "${DOCUMENT_TYPE}" != "datadiscovery" ]]; then
+ COUNT_EXTRACTED_DOCS=0
+ for FILE in $(find ${DATA_DIR} -name ${DOCUMENT_TYPE}*.json.gz); do
+ echo $FILE
+ COUNT_FILE_DOCS=$(zcat ${FILE} | grep "\"_id\"" | sort | uniq | wc -l)
+ COUNT_EXTRACTED_DOCS=$((COUNT_EXTRACTED_DOCS+COUNT_FILE_DOCS))
+ done
+ COUNT_INDEXED_DOCS=$(curl -s -XGET "${ES_HOST}:${ES_PORT}/_cat/indices/${INDEX_NAME}?h=docs.count" | tr -d ' ')
+ fi
+ if [ "$COUNT_INDEXED_DOCS" != "$COUNT_EXTRACTED_DOCS" ]; then
+ echo -e "${RED}ERROR: a problem occurred when indexing data from ${DATA_DIR} on FAIDARE ${ENV}.${NC}"
+ echo -e "${ORANGE}Expected ${COUNT_EXTRACTED_DOCS} documents but got ${COUNT_INDEXED_DOCS} indexed documents.${NC}"
+ exit 1;
+ fi
+
+ # Add aliases
+ ALIAS_PATTERN="${INDEX_PATTERN}-group*"
+ echo -e "Delete aliases ${ALIAS_PATTERN}..."
+ echo "curl -s -XGET '${ES_HOST}:${ES_PORT}/_aliases/${ALIAS_PATTERN}'"
+ LOG=$(curl -s -XDELETE "${ES_HOST}:${ES_PORT}/*/_aliases/${ALIAS_PATTERN}")
+ check_acknowledgment "${LOG}" "delete aliases"
+
+ echo -e "List groupId from ${INDEX_NAME} (to create filtered aliases)..."
+ GROUP_IDS=$(curl -s -H 'Content-Type: application/json' -XGET "${ES_HOST}:${ES_PORT}/${INDEX_NAME}/_search" -d'
+{
+ "size":"0",
+ "aggs" : {
+ "uniq_group" : {
+ "terms" : { "field" : "groupId" }
+ }
+ }
+}' | jq -cr '.aggregations.uniq_group.buckets[].key') # Extract ES aggregation bucket keys
+ [ -z "$GROUP_IDS" ] && {
+ echo -e "${RED}ERROR: could not list 'groupId' values from index.${NC}"
+ exit 1;
+ }
+ echo -e "Create aliases:"
+ for GROUP_ID in ${GROUP_IDS}; do
+ ALIAS_NAME="${INDEX_PATTERN}-group${GROUP_ID}"
+ FILTER=""
+ if [[ "$GROUP_ID" = "0" || "${GROUP_ID}" = "null" ]]; then
+ FILTER="{ \"bool\" : { \"must_not\" : { \"exists\" : { \"field\" : \"groupId\" } } } }"
+ else
+ FILTER="{ \"term\" : { \"groupId\" : \"${GROUP_ID}\" } }"
+ fi
+ echo -e "\t${ALIAS_NAME}..."
+ LOG=$(curl -s -H 'Content-Type: application/json' -XPOST "${ES_HOST}:${ES_PORT}/_aliases" -d "
+{
+ \"actions\" : [
+ {
+ \"add\" : {
+ \"index\" : \"${INDEX_NAME}\",
+ \"alias\" : \"${ALIAS_NAME}\",
+ \"filter\" : ${FILTER}
+ }
+ }
+ ]
+}")
+ check_acknowledgment "${LOG}" "create aliase"
+ done
+
+ # Delete all but last created indices (thanks to the timestamp suffix)
+ echo -e "Delete old indices ${INDEX_PATTERN} (to avoid accumulation over time)..."
+ OLD_INDICES=$(curl -sf -XGET "${ES_HOST}:${ES_PORT}/_cat/indices/${INDEX_PATTERN}?h=index" | sort | head -n -1)
+ for OLD_INDEX in ${OLD_INDICES}; do
+ LOG=$(curl -s -XDELETE "${ES_HOST}:${ES_PORT}/${OLD_INDEX}")
+ check_acknowledgment "${LOG}" "delete index ${OLD_INDEX}"
+ done
+done
--
GitLab
From 3fa2cc6a64fe5b17a2501d5529405dc84eec1893 Mon Sep 17 00:00:00 2001
From: Celia Michotey <celia.michotey@inra.fr>
Date: Tue, 8 Oct 2019 11:15:35 +0200
Subject: [PATCH 02/11] Correct bugs in indexation script.
---
scripts/harvest.sh | 39 +++++++++++++++++++++------------------
1 file changed, 21 insertions(+), 18 deletions(-)
diff --git a/scripts/harvest.sh b/scripts/harvest.sh
index bacc1e63..d91297e8 100755
--- a/scripts/harvest.sh
+++ b/scripts/harvest.sh
@@ -1,12 +1,13 @@
#!/bin/bash
+
DATA_DIR=""
ES_HOST="localhost"
ES_PORT="9200"
ENV="dev"
DOCUMENT_TYPES="all"
-ALL_DOCUMENT_TYPES="germplasm germplasmAttribute germplasmPedigree germplasmProgeny location program study trial observationUnit datadiscovery"
+ALL_DOCUMENT_TYPES="germplasm germplasm-mcpd germplasmAttribute germplasmPedigree germplasmProgeny location program study trial observationUnit datadiscovery"
ALL_ENVS="dev beta staging int prod test"
BASEDIR=$(dirname "$0")
@@ -106,7 +107,7 @@ fi
[ "${DOCUMENT_TYPES}" == "all" ] && DOCUMENT_TYPES = "${ALL_DOCUMENT_TYPES}"
for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
if [ $(find ${DATA_DIR} -name ${DOCUMENT}*.json | wc -l) -le 0 ] && [ $(find ${DATA_DIR} -name ${DOCUMENT}*.json.gz | wc -l) -le 0 ]; then
- echo -e "${ORANGE}WARNING: The JSON directory ${DATA_DIR} contains no ${DOCUMENT} document, so it will be ignored!${NC}"
+ echo -e "${ORANGE}WARNING: The JSON directory ${DATA_DIR} contains no ${DOCUMENT} document!${NC}"
fi
done
@@ -116,12 +117,12 @@ for FILE in $(find ${DATA_DIR} -name *.json); do
done
for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
- echo -e "${BOLD}Manage ${DOCUMENT_TYPE} documents...${NC}"
+ echo && echo -e "${BOLD}Manage ${DOCUMENT_TYPE} documents...${NC}"
INDEX_PATTERN="faidare_${DOCUMENT_TYPE}_${ENV}"
# Create template
TEMPLATE_NAME="${INDEX_PATTERN}_template"
- echo -e "Create setting/mapping template ${TEMPLATE_NAME}..."
+ echo -e "* Create setting/mapping template ${TEMPLATE_NAME}..."
LOG=$(curl -s -H 'Content-Type: application/json' -XPUT "${ES_HOST}:${ES_PORT}/_template/${TEMPLATE_NAME}" -d"
{
\"index_patterns\": [\"${INDEX_PATTERN}-*\"],
@@ -134,9 +135,9 @@ for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
# Index JSON Bulk
INDEX_NAME="${INDEX_PATTERN}-d"$(date +%s)
- echo -e "Index documents into ${ES_HOST}:${ES_PORT}/${INDEX_NAME} indice..."
+ echo -e "* Index documents into ${ES_HOST}:${ES_PORT}/${INDEX_NAME} indice..."
{
- time parallel --bar "
+ parallel --bar "
curl -s -H 'Content-Type: application/x-ndjson' -H 'Content-Encoding: gzip' -H 'Accept-Encoding: gzip' -XPOST ${ES_HOST}:${ES_PORT}/${INDEX_NAME}/_bulk --data-binary '@{}' > {.}.log.gz" \
::: $(find ${DATA_DIR} -name ${DOCUMENT_TYPE}*.json.gz)
} || {
@@ -148,16 +149,16 @@ for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
parallel "gunzip -c {} | jq '.errors' | grep -q true && echo -e '${ORANGE}ERROR found in {}${NC}' ;" ::: $(find ${DATA_DIR} -name ${DOCUMENT_TYPE}*.log.gz)
# Check indexed data
- echo -e "Check data indexed from ${DATA_DIR} into ${INDEX_NAME}..."
+ echo -e "* Check data indexed from ${DATA_DIR} into ${INDEX_NAME}..."
# skip some documents because they contain nested objects that distort the count
if [[ "${DOCUMENT_TYPE}" != "germplasmAttribute" && "${DOCUMENT_TYPE}" != "observationUnit" && "${DOCUMENT_TYPE}" != "datadiscovery" ]]; then
COUNT_EXTRACTED_DOCS=0
- for FILE in $(find ${DATA_DIR} -name ${DOCUMENT_TYPE}*.json.gz); do
- echo $FILE
+ for FILE in $(find ${DATA_DIR} -name ${DOCUMENT_TYPE}*.json.gz); do
COUNT_FILE_DOCS=$(zcat ${FILE} | grep "\"_id\"" | sort | uniq | wc -l)
COUNT_EXTRACTED_DOCS=$((COUNT_EXTRACTED_DOCS+COUNT_FILE_DOCS))
- done
- COUNT_INDEXED_DOCS=$(curl -s -XGET "${ES_HOST}:${ES_PORT}/_cat/indices/${INDEX_NAME}?h=docs.count" | tr -d ' ')
+ done
+ curl -s -XGET "${ES_HOST}:${ES_PORT}/${INDEX_NAME}/_refresh" >/dev/null
+ COUNT_INDEXED_DOCS=$(curl -s -XGET "${ES_HOST}:${ES_PORT}/_cat/indices/${INDEX_NAME}?h=docs.count")
fi
if [ "$COUNT_INDEXED_DOCS" != "$COUNT_EXTRACTED_DOCS" ]; then
echo -e "${RED}ERROR: a problem occurred when indexing data from ${DATA_DIR} on FAIDARE ${ENV}.${NC}"
@@ -167,12 +168,14 @@ for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
# Add aliases
ALIAS_PATTERN="${INDEX_PATTERN}-group*"
- echo -e "Delete aliases ${ALIAS_PATTERN}..."
- echo "curl -s -XGET '${ES_HOST}:${ES_PORT}/_aliases/${ALIAS_PATTERN}'"
- LOG=$(curl -s -XDELETE "${ES_HOST}:${ES_PORT}/*/_aliases/${ALIAS_PATTERN}")
- check_acknowledgment "${LOG}" "delete aliases"
+ ALIAS_EXIST=$(curl -s -XGET "${ES_HOST}:${ES_PORT}/_alias/${ALIAS_PATTERN}" | jq '.status' | grep -q "404" && echo "false" || echo "true")
+ if [ "${ALIAS_EXIST}" == "true" ]; then
+ echo -e "* Delete aliases ${ALIAS_PATTERN}..."
+ LOG=$(curl -s -XDELETE "${ES_HOST}:${ES_PORT}/*/_aliases/${ALIAS_PATTERN}")
+ check_acknowledgment "${LOG}" "delete aliases"
+ fi
- echo -e "List groupId from ${INDEX_NAME} (to create filtered aliases)..."
+ echo -e "* List groupId from ${INDEX_NAME} (to create filtered aliases)..."
GROUP_IDS=$(curl -s -H 'Content-Type: application/json' -XGET "${ES_HOST}:${ES_PORT}/${INDEX_NAME}/_search" -d'
{
"size":"0",
@@ -186,7 +189,7 @@ for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
echo -e "${RED}ERROR: could not list 'groupId' values from index.${NC}"
exit 1;
}
- echo -e "Create aliases:"
+ echo -e "* Create aliases:"
for GROUP_ID in ${GROUP_IDS}; do
ALIAS_NAME="${INDEX_PATTERN}-group${GROUP_ID}"
FILTER=""
@@ -212,7 +215,7 @@ for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
done
# Delete all but last created indices (thanks to the timestamp suffix)
- echo -e "Delete old indices ${INDEX_PATTERN} (to avoid accumulation over time)..."
+ echo -e "* Delete old indices ${INDEX_PATTERN} (to avoid accumulation over time)..."
OLD_INDICES=$(curl -sf -XGET "${ES_HOST}:${ES_PORT}/_cat/indices/${INDEX_PATTERN}?h=index" | sort | head -n -1)
for OLD_INDEX in ${OLD_INDICES}; do
LOG=$(curl -s -XDELETE "${ES_HOST}:${ES_PORT}/${OLD_INDEX}")
--
GitLab
From 5dad7bafbe8d536e35f10069b3552dcd5da51f0a Mon Sep 17 00:00:00 2001
From: Celia Michotey <celia.michotey@inra.fr>
Date: Tue, 8 Oct 2019 13:14:24 +0200
Subject: [PATCH 03/11] Update mappings to be coherent with generated JSON
format.
---
.../repository/es/setup/index/README.md | 2 -
.../es/setup/index/datadiscovery_mapping.json | 151 ++-
.../index/germplasmAttribute_mapping.json | 98 +-
.../index/germplasmPedigree_mapping.json | 136 +-
.../setup/index/germplasmProgeny_mapping.json | 82 +-
.../es/setup/index/germplasm_mapping.json | 1103 +++++++++--------
.../es/setup/index/location_mapping.json | 128 +-
.../setup/index/observationUnit_mapping.json | 451 +++----
.../es/setup/index/program_mapping.json | 20 +-
.../repository/es/setup/index/settings.json | 80 +-
.../es/setup/index/study_mapping.json | 273 ++--
.../es/setup/index/transplant_mapping.json | 22 +-
.../es/setup/index/trial_mapping.json | 246 ++--
13 files changed, 1510 insertions(+), 1282 deletions(-)
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/README.md b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/README.md
index f5a7b39f..2f959242 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/README.md
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/README.md
@@ -1,7 +1,5 @@
This directory contains document mappings and index settings for FAIDARE Elasticsearch documents.
-This directory is a copy of the directory from the GnpIS `database` git repository with the path: `GnpIS/elasticsearch/template/gnpis`.
-
# Custom analyzers
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/datadiscovery_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/datadiscovery_mapping.json
index eb223e17..331335a1 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/datadiscovery_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/datadiscovery_mapping.json
@@ -1,80 +1,79 @@
{
- "datadiscovery": {
- "dynamic": false,
- "_source": {
- "includes": ["@id", "@type", "schema:*", "groupId"]
- },
- "properties": {
- "groupId": {
- "type": "long"
- },
+ "datadiscovery": {
+ "dynamic": "strict",
+ "_source": {
+ "includes": ["@id", "@type", "schema:*", "groupId"]
+ },
+ "properties": {
+ "groupId": {
+ "type": "long"
+ },
+ "@type": {
+ "type": "keyword"
+ },
+ "@id": {
+ "type": "keyword"
+ },
+ "schema:includedInDataCatalog": {
+ "type": "keyword"
+ },
+ "schema:identifier": {
+ "type": "keyword"
+ },
+ "schema:name": {
+ "type": "keyword"
+ },
+ "schema:url": {
+ "type": "keyword"
+ },
+ "schema:description": {
+ "type": "keyword"
+ },
- "@type": {
- "type": "keyword"
- },
- "@id": {
- "type": "keyword"
- },
- "schema:includedInDataCatalog": {
- "type": "keyword"
- },
- "schema:identifier": {
- "type": "keyword"
- },
- "schema:name": {
- "type": "keyword"
- },
- "schema:url": {
- "type": "keyword"
- },
- "schema:description": {
- "type": "keyword"
- },
+ "germplasm": {
+ "type": "object",
+ "properties": {
+ "cropName": {
+ "type": "keyword",
+ "fields": {
+ "suggest": {
+ "type": "text",
+ "search_analyzer": "search_suggester",
+ "analyzer": "index_suggester"
+ }
+ }
+ },
+ "germplasmList": {
+ "type": "keyword",
+ "fields": {
+ "suggest": {
+ "type": "text",
+ "search_analyzer": "search_suggester",
+ "analyzer": "index_suggester"
+ }
+ }
+ },
+ "accession": {
+ "type": "keyword",
+ "fields": {
+ "suggest": {
+ "type": "text",
+ "search_analyzer": "search_suggester",
+ "analyzer": "index_suggester"
+ }
+ }
+ }
+ }
+ },
- "germplasm": {
- "type": "object",
- "properties": {
- "cropName": {
- "type": "keyword",
- "fields": {
- "suggest": {
- "type": "text",
- "search_analyzer": "search_suggester",
- "analyzer": "index_suggester"
- }
- }
- },
- "germplasmList": {
- "type": "keyword",
- "fields": {
- "suggest": {
- "type": "text",
- "search_analyzer": "search_suggester",
- "analyzer": "index_suggester"
- }
- }
- },
- "accession": {
- "type": "keyword",
- "fields": {
- "suggest": {
- "type": "text",
- "search_analyzer": "search_suggester",
- "analyzer": "index_suggester"
- }
- }
- }
- }
- },
-
- "trait": {
- "type": "object",
- "properties": {
- "observationVariableIds": {
- "type": "keyword"
- }
- }
- }
- }
- }
+ "trait": {
+ "type": "object",
+ "properties": {
+ "observationVariableIds": {
+ "type": "keyword"
+ }
+ }
+ }
+ }
+ }
}
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmAttribute_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmAttribute_mapping.json
index cfb34f97..6a7c900b 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmAttribute_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmAttribute_mapping.json
@@ -1,40 +1,60 @@
{
- "germplasmAttribute": {
- "dynamic": false,
- "properties": {
- "groupId": {
- "type": "long"
- },
- "source": {
- "type": "keyword"
- },
- "speciesGroup": {
- "type": "long"
- },
- "germplasmDbId": {
- "type": "keyword"
- },
- "data": {
- "type": "nested",
- "properties": {
- "attributeDbId": {
- "type": "keyword"
- },
- "attributeName": {
- "type": "keyword"
- },
- "attributeCode": {
- "type": "keyword"
- },
- "value": {
- "type": "keyword"
- },
- "determinedDate": {
- "type": "date",
- "format": "YYYY-MM-dd"
- }
- }
- }
- }
- }
-}
+ "germplasmAttribute": {
+ "dynamic": "strict",
+ "properties": {
+ "germplasmDbId": {
+ "type": "keyword"
+ },
+ "data": {
+ "type": "nested",
+ "properties": {
+ "attributeDbId": {
+ "type": "keyword"
+ },
+ "attributeName": {
+ "type": "keyword"
+ },
+ "attributeCode": {
+ "type": "keyword"
+ },
+ "value": {
+ "type": "keyword"
+ },
+ "determinedDate": {
+ "type": "date",
+ "format": "YYYY-MM-dd"
+ }
+ }
+ },
+
+ "documentationURL": {
+ "type": "keyword"
+ },
+ "source": {
+ "type": "keyword"
+ },
+
+ "groupId": {
+ "type": "long"
+ },
+ "@type": {
+ "type": "keyword"
+ },
+ "@id": {
+ "type": "keyword"
+ },
+ "schema:includedInDataCatalog": {
+ "type": "keyword"
+ },
+ "schema:identifier": {
+ "type": "keyword"
+ },
+ "schema:name": {
+ "type": "keyword"
+ },
+ "schema:url": {
+ "type": "keyword"
+ }
+ }
+ }
+}
\ No newline at end of file
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmPedigree_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmPedigree_mapping.json
index 2952343f..ad7070d9 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmPedigree_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmPedigree_mapping.json
@@ -1,58 +1,82 @@
{
- "germplasmPedigree": {
- "properties": {
- "docId": {
- "type": "keyword"
- },
- "groupId": {
- "type": "long"
- },
- "siblings": {
- "properties": {
- "defaultDisplayName": {
- "type": "keyword"
- },
- "germplasmDbId": {
- "type": "keyword"
- }
- }
- },
- "parent1DbId": {
- "type": "keyword"
- },
- "parent2Name": {
- "type": "keyword"
- },
- "familyCode": {
- "type": "keyword"
- },
- "germplasmDbId": {
- "type": "keyword"
- },
- "parent1Type": {
- "type": "keyword"
- },
- "pedigree": {
- "type": "keyword"
- },
- "parent2DbId": {
- "type": "keyword"
- },
- "defaultDisplayName": {
- "type": "keyword"
- },
- "crossingPlan": {
- "type": "keyword"
- },
- "parent2Type": {
- "type": "keyword"
- },
- "parent1Name": {
- "type": "keyword"
- },
- "crossingYear": {
- "type": "keyword"
- }
- }
- }
+ "germplasmPedigree": {
+ "dynamic": "strict",
+ "properties": {
+ "germplasmDbId": {
+ "type": "keyword"
+ },
+ "defaultDisplayName": {
+ "type": "keyword"
+ },
+ "pedigree": {
+ "type": "keyword"
+ },
+ "crossingPlan": {
+ "type": "keyword"
+ },
+ "crossingYear": {
+ "type": "keyword"
+ },
+ "familyCode": {
+ "type": "keyword"
+ },
+ "parent1DbId": {
+ "type": "keyword"
+ },
+ "parent1Name": {
+ "type": "keyword"
+ },
+ "parent1Type": {
+ "type": "keyword"
+ },
+ "parent2DbId": {
+ "type": "keyword"
+ },
+ "parent2Name": {
+ "type": "keyword"
+ },
+ "parent2Type": {
+ "type": "keyword"
+ },
+ "siblings": {
+ "properties": {
+ "germplasmDbId": {
+ "type": "keyword"
+ },
+ "defaultDisplayName": {
+ "type": "keyword"
+ }
+ }
+ },
+
+ "documentationURL": {
+ "type": "keyword"
+ },
+ "source": {
+ "type": "keyword"
+ },
+
+ "groupId": {
+ "type": "long"
+ },
+ "@type": {
+ "type": "keyword"
+ },
+ "@id": {
+ "type": "keyword"
+ },
+ "schema:includedInDataCatalog": {
+ "type": "keyword"
+ },
+ "schema:identifier": {
+ "type": "keyword"
+ },
+ "schema:name": {
+ "type": "keyword"
+ },
+ "schema:url": {
+ "type": "keyword"
+ }
+ }
+ }
}
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmProgeny_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmProgeny_mapping.json
index c47f5c46..cdfe1cc4 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmProgeny_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmProgeny_mapping.json
@@ -1,31 +1,55 @@
{
- "germplasmProgeny": {
- "properties": {
- "docId": {
- "type": "keyword"
- },
- "groupId": {
- "type": "long"
- },
- "germplasmDbId": {
- "type": "keyword"
- },
- "defaultDisplayName": {
- "type": "keyword"
- },
- "progeny": {
- "properties": {
- "defaultDisplayName": {
- "type": "keyword"
- },
- "germplasmDbId": {
- "type": "keyword"
- },
- "parentType": {
- "type": "keyword"
- }
- }
- }
- }
- }
+ "germplasmProgeny": {
+ "dynamic": "strict",
+ "properties": {
+ "germplasmDbId": {
+ "type": "keyword"
+ },
+ "defaultDisplayName": {
+ "type": "keyword"
+ },
+ "progeny": {
+ "properties": {
+ "germplasmDbId": {
+ "type": "keyword"
+ },
+ "defaultDisplayName": {
+ "type": "keyword"
+ },
+ "parentType": {
+ "type": "keyword"
+ }
+ }
+ },
+
+ "documentationURL": {
+ "type": "keyword"
+ },
+ "source": {
+ "type": "keyword"
+ },
+
+ "groupId": {
+ "type": "long"
+ },
+ "@type": {
+ "type": "keyword"
+ },
+ "@id": {
+ "type": "keyword"
+ },
+ "schema:includedInDataCatalog": {
+ "type": "keyword"
+ },
+ "schema:identifier": {
+ "type": "keyword"
+ },
+ "schema:name": {
+ "type": "keyword"
+ },
+ "schema:url": {
+ "type": "keyword"
+ }
+ }
+ }
}
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json
index 8f7ca21e..2c5cd2b5 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json
@@ -1,539 +1,568 @@
{
- "germplasm": {
- "dynamic": false,
- "properties": {
- "groupId": {
- "type": "long"
- },
- "source": {
- "type": "keyword"
- },
- "documentationURL": {
- "type": "keyword"
- },
- "germplasmDbId": {
- "type": "keyword"
- },
- "defaultDisplayName": {
- "type": "keyword"
- },
- "accessionNumber": {
- "type": "keyword",
- "doc_values": true
- },
- "germplasmName": {
- "type": "keyword",
- "doc_values": true
- },
- "germplasmPUI": {
- "type": "keyword"
- },
- "pedigree": {
- "type": "keyword"
- },
- "seedSource": {
- "type": "keyword"
- },
- "synonyms": {
- "type": "keyword",
- "doc_values": true
- },
- "commonCropName": {
- "type": "keyword",
- "doc_values": true
- },
- "instituteCode": {
- "type": "keyword"
- },
- "instituteName": {
- "type": "keyword"
- },
- "biologicalStatusOfAccessionCode": {
- "type": "keyword"
- },
- "countryOfOriginCode": {
- "type": "keyword"
- },
- "typeOfGermplasmStorageCode": {
- "type": "keyword"
- },
- "taxonIds": {
- "properties": {
- "sourceName": {
- "type": "keyword"
- },
- "taxonId": {
- "type": "keyword"
- }
- }
- },
- "genus": {
- "type": "keyword",
- "doc_values": true
- },
- "species": {
- "type": "keyword"
- },
- "speciesAuthority": {
- "type": "keyword"
- },
- "subtaxa": {
- "type": "keyword"
- },
- "subtaxaAuthority": {
- "type": "keyword"
- },
- "donors": {
- "properties": {
- "donorInstituteCode": {
- "type": "keyword"
- },
- "donorGermplasmPUI": {
- "type": "keyword"
- },
- "donorAccessionNumber": {
- "type": "keyword"
- },
- "donorInstitute": {
- "properties": {
- "instituteName": {
- "type": "keyword"
- },
- "instituteCode": {
- "type": "keyword"
- },
- "acronym": {
- "type": "keyword"
- },
- "organisation": {
- "type": "keyword"
- },
- "instituteType": {
- "type": "keyword"
- },
- "webSite": {
- "type": "keyword"
- },
- "address": {
- "type": "keyword"
- },
- "logo": {
- "type": "keyword"
- }
- }
- },
- "donationDate": {
- "type": "integer"
- }
- }
- },
- "acquisitionDate": {
- "type": "keyword"
- },
- "genusSpecies": {
- "type": "keyword",
- "doc_values": true
- },
- "genusSpeciesSubtaxa": {
- "type": "keyword",
- "doc_values": true
- },
- "taxonSynonyms": {
- "type": "keyword",
- "doc_values": true
- },
- "taxonCommonNames": {
- "type": "keyword",
- "doc_values": true
- },
- "geneticNature": {
- "type": "keyword"
- },
- "comment": {
- "type": "keyword"
- },
- "photo": {
- "properties": {
- "fileName": {
- "type": "keyword"
- },
- "thumbnailFileName": {
- "type": "keyword"
- },
- "photoName": {
- "type": "keyword"
- },
- "description": {
- "type": "keyword"
- },
- "copyright": {
- "type": "keyword"
- }
- }
- },
- "holdingInstitute": {
- "properties": {
- "instituteName": {
- "type": "keyword"
- },
- "instituteCode": {
- "type": "keyword"
- },
- "acronym": {
- "type": "keyword"
- },
- "organisation": {
- "type": "keyword"
- },
- "instituteType": {
- "type": "keyword"
- },
- "webSite": {
- "type": "keyword"
- },
- "address": {
- "type": "keyword"
- },
- "logo": {
- "type": "keyword"
- }
- }
- },
- "holdingGenbank": {
- "properties": {
- "instituteName": {
- "type": "keyword",
- "doc_values": true
- },
- "instituteCode": {
- "type": "keyword"
- },
- "webSite": {
- "type": "keyword"
- }
- }
- },
- "presenceStatus": {
- "type": "keyword"
- },
- "genealogy": {
- "properties": {
- "crossingPlan": {
- "type": "keyword"
- },
- "crossingYear": {
- "type": "keyword"
- },
- "familyCode": {
- "type": "keyword"
- },
- "firstParentName": {
- "type": "keyword"
- },
- "firstParentPUI": {
- "type": "keyword"
- },
- "firstParentType": {
- "type": "keyword"
- },
- "secondParentName": {
- "type": "keyword"
- },
- "secondParentPUI": {
- "type": "keyword"
- },
- "secondParentType": {
- "type": "keyword"
- },
- "sibblings": {
- "properties": {
- "pui": {
- "type": "keyword"
- },
- "name": {
- "type": "keyword"
- }
- }
- }
- }
- },
- "children": {
- "properties": {
- "firstParentName": {
- "type": "keyword"
- },
- "firstParentPUI": {
- "type": "keyword"
- },
- "secondParentName": {
- "type": "keyword"
- },
- "secondParentPUI": {
- "type": "keyword"
- },
- "sibblings": {
- "properties": {
- "pui": {
- "type": "keyword"
- },
- "name": {
- "type": "keyword"
- }
- }
- }
- }
- },
- "descriptors": {
- "properties": {
- "name": {
- "type": "keyword"
- },
- "value": {
- "type": "keyword"
- }
- }
- },
- "originSite": {
- "properties": {
- "siteId": {
- "type": "long"
- },
- "siteName": {
- "type": "keyword"
- },
- "latitude": {
- "type": "float"
- },
- "longitude": {
- "type": "float"
- },
- "siteType": {
- "type": "keyword"
- }
- }
- },
- "collectingSite": {
- "properties": {
- "siteId": {
- "type": "long"
- },
- "siteName": {
- "type": "keyword"
- },
- "latitude": {
- "type": "float"
- },
- "longitude": {
- "type": "float"
- },
- "siteType": {
- "type": "keyword"
- }
- }
- },
- "evaluationSites": {
- "properties": {
- "siteId": {
- "type": "long"
- },
- "siteName": {
- "type": "keyword"
- },
- "latitude": {
- "type": "float"
- },
- "longitude": {
- "type": "float"
- },
- "siteType": {
- "type": "keyword"
- }
- }
- },
- "collector": {
- "properties": {
- "institute": {
- "properties": {
- "instituteName": {
- "type": "keyword"
- },
- "instituteCode": {
- "type": "keyword"
- },
- "acronym": {
- "type": "keyword"
- },
- "organisation": {
- "type": "keyword"
- },
- "instituteType": {
- "type": "keyword"
- },
- "webSite": {
- "type": "keyword"
- },
- "address": {
- "type": "keyword"
- },
- "logo": {
- "type": "keyword"
- }
- }
- },
- "accessionNumber": {
- "type": "keyword"
- },
- "accessionCreationDate": {
- "type": "integer"
- },
- "materialType": {
- "type": "keyword"
- },
- "collectors": {
- "type": "keyword"
- }
- }
- },
- "breeder": {
- "properties": {
- "institute": {
- "properties": {
- "instituteName": {
- "type": "keyword"
- },
- "instituteCode": {
- "type": "keyword"
- },
- "acronym": {
- "type": "keyword"
- },
- "organisation": {
- "type": "keyword"
- },
- "instituteType": {
- "type": "keyword"
- },
- "webSite": {
- "type": "keyword"
- },
- "address": {
- "type": "keyword"
- },
- "logo": {
- "type": "keyword"
- }
- }
- },
- "accessionNumber": {
- "type": "keyword"
- },
- "accessionCreationDate": {
- "type": "integer"
- },
- "registrationYear": {
- "type": "integer"
- },
- "deregistrationYear": {
- "type": "integer"
- }
- }
- },
- "distributors": {
- "properties": {
- "institute": {
- "properties": {
- "instituteName": {
- "type": "keyword"
- },
- "instituteCode": {
- "type": "keyword"
- },
- "acronym": {
- "type": "keyword"
- },
- "organisation": {
- "type": "keyword"
- },
- "instituteType": {
- "type": "keyword"
- },
- "webSite": {
- "type": "keyword"
- },
- "address": {
- "type": "keyword"
- },
- "logo": {
- "type": "keyword"
- }
- }
- },
- "accessionNumber": {
- "type": "keyword"
- },
- "distributionStatus": {
- "type": "keyword"
- }
- }
- },
- "panel": {
- "properties": {
- "id": {
- "type": "long"
- },
- "name": {
- "type": "keyword",
- "doc_values": true
- },
- "germplasmCount": {
- "type": "integer"
- }
- }
- },
- "collection": {
- "properties": {
- "id": {
- "type": "long"
- },
- "name": {
- "type": "keyword",
- "doc_values": true
- },
- "type": {
- "type": "keyword"
- },
- "germplasmCount": {
- "type": "integer"
- }
- }
- },
- "population": {
- "properties": {
- "id": {
- "type": "long"
- },
- "name": {
- "type": "keyword",
- "doc_values": true
- },
- "type": {
- "type": "keyword"
- },
- "germplasmRef": {
- "properties": {
- "pui": {
- "type": "keyword"
- },
- "name": {
- "type": "keyword"
- }
- }
- },
- "germplasmCount": {
- "type": "integer"
- }
- }
- }
- }
- }
+ "germplasm": {
+ "dynamic": "strict",
+ "properties": {
+ "germplasmDbId": {
+ "type": "keyword"
+ },
+ "defaultDisplayName": {
+ "type": "keyword"
+ },
+ "accessionNumber": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "germplasmName": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "germplasmPUI": {
+ "type": "keyword"
+ },
+ "pedigree": {
+ "type": "keyword"
+ },
+ "seedSource": {
+ "type": "keyword"
+ },
+ "synonyms": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "commonCropName": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "instituteCode": {
+ "type": "keyword"
+ },
+ "instituteName": {
+ "type": "keyword"
+ },
+ "biologicalStatusOfAccessionCode": {
+ "type": "keyword"
+ },
+ "countryOfOriginCode": {
+ "type": "keyword"
+ },
+ "typeOfGermplasmStorageCode": {
+ "type": "keyword"
+ },
+ "taxonIds": {
+ "properties": {
+ "sourceName": {
+ "type": "keyword"
+ },
+ "taxonId": {
+ "type": "keyword"
+ }
+ }
+ },
+ "genus": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "species": {
+ "type": "keyword"
+ },
+ "speciesAuthority": {
+ "type": "keyword"
+ },
+ "subtaxa": {
+ "type": "keyword"
+ },
+ "subtaxaAuthority": {
+ "type": "keyword"
+ },
+ "donors": {
+ "properties": {
+ "donorInstituteCode": {
+ "type": "keyword"
+ },
+ "donorGermplasmPUI": {
+ "type": "keyword"
+ },
+ "donorAccessionNumber": {
+ "type": "keyword"
+ },
+ "donorInstitute": {
+ "properties": {
+ "instituteName": {
+ "type": "keyword"
+ },
+ "instituteCode": {
+ "type": "keyword"
+ },
+ "acronym": {
+ "type": "keyword"
+ },
+ "organisation": {
+ "type": "keyword"
+ },
+ "instituteType": {
+ "type": "keyword"
+ },
+ "webSite": {
+ "type": "keyword"
+ },
+ "address": {
+ "type": "keyword"
+ },
+ "logo": {
+ "type": "keyword"
+ }
+ }
+ },
+ "donationDate": {
+ "type": "integer"
+ }
+ }
+ },
+ "acquisitionDate": {
+ "type": "keyword"
+ },
+ "genusSpecies": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "genusSpeciesSubtaxa": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "taxonSynonyms": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "taxonCommonNames": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "taxonComment": {
+ "type": "keyword"
+ },
+ "geneticNature": {
+ "type": "keyword"
+ },
+ "comment": {
+ "type": "keyword"
+ },
+ "photo": {
+ "properties": {
+ "file": {
+ "type": "keyword"
+ },
+ "thumbnailFile": {
+ "type": "keyword"
+ },
+ "photoName": {
+ "type": "keyword"
+ },
+ "description": {
+ "type": "keyword"
+ },
+ "copyright": {
+ "type": "keyword"
+ }
+ }
+ },
+ "holdingInstitute": {
+ "properties": {
+ "instituteName": {
+ "type": "keyword"
+ },
+ "instituteCode": {
+ "type": "keyword"
+ },
+ "acronym": {
+ "type": "keyword"
+ },
+ "organisation": {
+ "type": "keyword"
+ },
+ "instituteType": {
+ "type": "keyword"
+ },
+ "webSite": {
+ "type": "keyword"
+ },
+ "address": {
+ "type": "keyword"
+ },
+ "logo": {
+ "type": "keyword"
+ }
+ }
+ },
+ "holdingGenbank": {
+ "properties": {
+ "instituteName": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "instituteCode": {
+ "type": "keyword"
+ },
+ "webSite": {
+ "type": "keyword"
+ },
+ "logo": {
+ "type": "keyword"
+ }
+ }
+ },
+ "presenceStatus": {
+ "type": "keyword"
+ },
+ "genealogy": {
+ "properties": {
+ "crossingPlan": {
+ "type": "keyword"
+ },
+ "crossingYear": {
+ "type": "keyword"
+ },
+ "familyCode": {
+ "type": "keyword"
+ },
+ "firstParentName": {
+ "type": "keyword"
+ },
+ "firstParentPUI": {
+ "type": "keyword"
+ },
+ "firstParentType": {
+ "type": "keyword"
+ },
+ "secondParentName": {
+ "type": "keyword"
+ },
+ "secondParentPUI": {
+ "type": "keyword"
+ },
+ "secondParentType": {
+ "type": "keyword"
+ },
+ "sibblings": {
+ "properties": {
+ "pui": {
+ "type": "keyword"
+ },
+ "name": {
+ "type": "keyword"
+ }
+ }
+ }
+ }
+ },
+ "children": {
+ "properties": {
+ "firstParentName": {
+ "type": "keyword"
+ },
+ "firstParentPUI": {
+ "type": "keyword"
+ },
+ "secondParentName": {
+ "type": "keyword"
+ },
+ "secondParentPUI": {
+ "type": "keyword"
+ },
+ "sibblings": {
+ "properties": {
+ "pui": {
+ "type": "keyword"
+ },
+ "name": {
+ "type": "keyword"
+ }
+ }
+ }
+ }
+ },
+ "descriptors": {
+ "properties": {
+ "name": {
+ "type": "keyword"
+ },
+ "value": {
+ "type": "keyword"
+ }
+ }
+ },
+ "originSite": {
+ "properties": {
+ "siteId": {
+ "type": "long"
+ },
+ "siteName": {
+ "type": "keyword"
+ },
+ "latitude": {
+ "type": "float"
+ },
+ "longitude": {
+ "type": "float"
+ },
+ "siteType": {
+ "type": "keyword"
+ }
+ }
+ },
+ "collectingSite": {
+ "properties": {
+ "siteId": {
+ "type": "long"
+ },
+ "siteName": {
+ "type": "keyword"
+ },
+ "latitude": {
+ "type": "float"
+ },
+ "longitude": {
+ "type": "float"
+ },
+ "siteType": {
+ "type": "keyword"
+ }
+ }
+ },
+ "evaluationSites": {
+ "properties": {
+ "siteId": {
+ "type": "long"
+ },
+ "siteName": {
+ "type": "keyword"
+ },
+ "latitude": {
+ "type": "float"
+ },
+ "longitude": {
+ "type": "float"
+ },
+ "siteType": {
+ "type": "keyword"
+ }
+ }
+ },
+ "collector": {
+ "properties": {
+ "institute": {
+ "properties": {
+ "instituteName": {
+ "type": "keyword"
+ },
+ "instituteCode": {
+ "type": "keyword"
+ },
+ "acronym": {
+ "type": "keyword"
+ },
+ "organisation": {
+ "type": "keyword"
+ },
+ "instituteType": {
+ "type": "keyword"
+ },
+ "webSite": {
+ "type": "keyword"
+ },
+ "address": {
+ "type": "keyword"
+ },
+ "logo": {
+ "type": "keyword"
+ }
+ }
+ },
+ "accessionNumber": {
+ "type": "keyword"
+ },
+ "accessionCreationDate": {
+ "type": "integer"
+ },
+ "materialType": {
+ "type": "keyword"
+ },
+ "collectors": {
+ "type": "keyword"
+ }
+ }
+ },
+ "breeder": {
+ "properties": {
+ "institute": {
+ "properties": {
+ "instituteName": {
+ "type": "keyword"
+ },
+ "instituteCode": {
+ "type": "keyword"
+ },
+ "acronym": {
+ "type": "keyword"
+ },
+ "organisation": {
+ "type": "keyword"
+ },
+ "instituteType": {
+ "type": "keyword"
+ },
+ "webSite": {
+ "type": "keyword"
+ },
+ "address": {
+ "type": "keyword"
+ },
+ "logo": {
+ "type": "keyword"
+ }
+ }
+ },
+ "accessionNumber": {
+ "type": "keyword"
+ },
+ "accessionCreationDate": {
+ "type": "integer"
+ },
+ "registrationYear": {
+ "type": "integer"
+ },
+ "deregistrationYear": {
+ "type": "integer"
+ }
+ }
+ },
+ "distributors": {
+ "properties": {
+ "institute": {
+ "properties": {
+ "instituteName": {
+ "type": "keyword"
+ },
+ "instituteCode": {
+ "type": "keyword"
+ },
+ "acronym": {
+ "type": "keyword"
+ },
+ "organisation": {
+ "type": "keyword"
+ },
+ "instituteType": {
+ "type": "keyword"
+ },
+ "webSite": {
+ "type": "keyword"
+ },
+ "address": {
+ "type": "keyword"
+ },
+ "logo": {
+ "type": "keyword"
+ }
+ }
+ },
+ "accessionNumber": {
+ "type": "keyword"
+ },
+ "distributionStatus": {
+ "type": "keyword"
+ }
+ }
+ },
+ "panel": {
+ "properties": {
+ "id": {
+ "type": "long"
+ },
+ "name": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "germplasmCount": {
+ "type": "integer"
+ }
+ }
+ },
+ "collection": {
+ "properties": {
+ "id": {
+ "type": "long"
+ },
+ "name": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "type": {
+ "type": "keyword"
+ },
+ "germplasmCount": {
+ "type": "integer"
+ }
+ }
+ },
+ "population": {
+ "properties": {
+ "id": {
+ "type": "long"
+ },
+ "name": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "type": {
+ "type": "keyword"
+ },
+ "germplasmRef": {
+ "properties": {
+ "pui": {
+ "type": "keyword"
+ },
+ "name": {
+ "type": "keyword"
+ }
+ }
+ },
+ "germplasmCount": {
+ "type": "integer"
+ }
+ }
+ },
+ "studyDbIds": {
+ "type": "keyword"
+ },
+
+ "documentationURL": {
+ "type": "keyword"
+ },
+ "source": {
+ "type": "keyword"
+ },
+
+ "groupId": {
+ "type": "long"
+ },
+ "@type": {
+ "type": "keyword"
+ },
+ "@id": {
+ "type": "keyword"
+ },
+ "schema:includedInDataCatalog": {
+ "type": "keyword"
+ },
+ "schema:identifier": {
+ "type": "keyword"
+ },
+ "schema:name": {
+ "type": "keyword"
+ },
+ "schema:url": {
+ "type": "keyword"
+ }
+ }
+ }
}
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/location_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/location_mapping.json
index 1955fe94..498fb319 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/location_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/location_mapping.json
@@ -1,56 +1,76 @@
{
- "location": {
- "dynamic": false,
- "properties": {
- "locationDbId": {
- "type": "keyword"
- },
- "locationName": {
- "type": "keyword"
- },
- "locationType": {
- "type": "keyword"
- },
- "abbreviation": {
- "type": "keyword"
- },
- "additionalInfo": {
- "dynamic": "true",
- "properties": {}
- },
- "altitude": {
- "type": "double"
- },
- "countryCode": {
- "type": "keyword"
- },
- "countryName": {
- "type": "keyword"
- },
- "groupId": {
- "type": "long"
- },
- "institutionAdress": {
- "type": "keyword"
- },
- "institutionName": {
- "type": "keyword"
- },
- "latitude": {
- "type": "double"
- },
- "longitude": {
- "type": "double"
- },
- "source": {
- "type": "keyword"
- },
- "speciesGroup": {
- "type": "long"
- },
- "documentationURL": {
- "type": "keyword"
- }
- }
- }
+ "location": {
+ "dynamic": "strict",
+ "properties": {
+ "locationDbId": {
+ "type": "keyword"
+ },
+ "locationName": {
+ "type": "keyword"
+ },
+ "name": {
+ "type": "keyword"
+ },
+ "locationType": {
+ "type": "keyword"
+ },
+ "abbreviation": {
+ "type": "keyword"
+ },
+ "countryCode": {
+ "type": "keyword"
+ },
+ "countryName": {
+ "type": "keyword"
+ },
+ "institutionName": {
+ "type": "keyword"
+ },
+ "institutionAdress": {
+ "type": "keyword"
+ },
+ "latitude": {
+ "type": "double"
+ },
+ "longitude": {
+ "type": "double"
+ },
+ "altitude": {
+ "type": "double"
+ },
+ "additionalInfo": {
+ "dynamic": "true",
+ "properties": {}
+ },
+
+ "documentationURL": {
+ "type": "keyword"
+ },
+ "source": {
+ "type": "keyword"
+ },
+
+ "groupId": {
+ "type": "long"
+ },
+ "@type": {
+ "type": "keyword"
+ },
+ "@id": {
+ "type": "keyword"
+ },
+ "schema:includedInDataCatalog": {
+ "type": "keyword"
+ },
+ "schema:identifier": {
+ "type": "keyword"
+ },
+ "schema:name": {
+ "type": "keyword"
+ },
+ "schema:url": {
+ "type": "keyword"
+ }
+ }
+ }
}
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/observationUnit_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/observationUnit_mapping.json
index c7280ebb..ca56d679 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/observationUnit_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/observationUnit_mapping.json
@@ -1,216 +1,239 @@
{
- "observationUnit": {
- "dynamic": false,
- "properties": {
- "groupId": {
- "type": "long"
- },
- "speciesGroup": {
- "type": "integer"
- },
- "source": {
- "type": "keyword"
- },
- "observationUnitDbId": {
- "type": "keyword"
- },
- "observationLevel": {
- "type": "keyword"
- },
- "observationLevels": {
- "type": "keyword"
- },
- "observationLevelDetails": {
- "properties": {
- "type": {
- "type": "keyword"
- },
- "name": {
- "type": "keyword"
- },
- "value": {
- "type": "keyword"
- }
- }
- },
- "plotNumber": {
- "type": "keyword",
- "index": false
- },
- "plantNumber": {
- "type": "keyword",
- "index": false
- },
- "blockNumber": {
- "type": "keyword",
- "index": false
- },
- "replicate": {
- "type": "keyword",
- "index": false
- },
- "observationUnitName": {
- "type": "keyword"
- },
- "germplasmId": {
- "type": "long"
- },
- "germplasmDbId": {
- "type": "keyword"
- },
- "germplasmName": {
- "type": "keyword"
- },
- "observationUnitXref": {
- "properties": {
- "id": {
- "type": "keyword"
- },
- "source": {
- "type": "keyword"
- }
- }
- },
- "studyDbId": {
- "type": "keyword"
- },
- "studyName": {
- "type": "keyword"
- },
- "studyLocationDbId": {
- "type": "keyword"
- },
- "studyLocation": {
- "type": "keyword"
- },
- "programDbId": {
- "type": "keyword"
- },
- "programName": {
- "type": "keyword"
- },
- "X": {
- "type": "keyword"
- },
- "Y": {
- "type": "keyword"
- },
- "Xname": {
- "type": "keyword"
- },
- "Yname": {
- "type": "keyword"
- },
- "Xm": {
- "type": "keyword"
- },
- "Ym": {
- "type": "keyword"
- },
- "entryType": {
- "type": "keyword",
- "index": false
- },
- "entryNumber": {
- "type": "keyword",
- "index": false
- },
- "treatments": {
- "properties": {
- "factor": {
- "type": "keyword"
- },
- "modality": {
- "type": "keyword"
- }
- }
- },
- "observations": {
- "type": "nested",
- "properties": {
- "observationDbId": {
- "type": "keyword"
- },
- "observationVariableDbId": {
- "type": "keyword"
- },
- "observationVariableName": {
- "type": "keyword"
- },
- "observationTimeStamp": {
- "type": "date",
- "format": "yyyy-MM-dd'T'HH:mm:ss'Z'"
- },
- "season": {
- "type": "keyword"
- },
- "collector": {
- "type": "keyword",
- "index": false
- },
- "value": {
- "type": "keyword"
- },
- "specificName": {
- "type": "keyword"
- },
- "observationVariableId": {
- "type": "long"
- },
- "isDataFile": {
- "type": "boolean",
- "index": false
- },
- "gdd": {
- "type": "float"
- }
- }
- },
- "studyId": {
- "type": "long"
- },
- "trials": {
- "properties": {
- "id": {
- "type": "long"
- },
- "name": {
- "type": "keyword"
- }
- }
- },
- "accessionNumber": {
- "type": "keyword"
- },
- "taxonId": {
- "type": "long"
- },
- "taxonScientificName": {
- "type": "keyword"
- },
- "germplasmGenus": {
- "type": "keyword"
- },
- "germplasmCollections": {
- "properties": {
- "id": {
- "type": "long"
- },
- "name": {
- "type": "keyword"
- }
- }
- },
- "germplasmPanels": {
- "properties": {
- "id": {
- "type": "long"
- },
- "name": {
- "type": "keyword"
- }
- }
- }
- }
- }
+ "observationUnit": {
+ "dynamic": "strict",
+ "properties": {
+ "observationUnitDbId": {
+ "type": "keyword"
+ },
+ "observationUnitName": {
+ "type": "keyword"
+ },
+ "observationLevel": {
+ "type": "keyword"
+ },
+ "observationLevels": {
+ "type": "keyword"
+ },
+ "observationLevelDetails": {
+ "properties": {
+ "type": {
+ "type": "keyword"
+ },
+ "name": {
+ "type": "keyword"
+ },
+ "value": {
+ "type": "keyword"
+ }
+ }
+ },
+ "plotNumber": {
+ "type": "keyword",
+ "index": false
+ },
+ "plantNumber": {
+ "type": "keyword",
+ "index": false
+ },
+ "blockNumber": {
+ "type": "keyword",
+ "index": false
+ },
+ "replicate": {
+ "type": "keyword",
+ "index": false
+ },
+ "X": {
+ "type": "keyword"
+ },
+ "Y": {
+ "type": "keyword"
+ },
+ "Xname": {
+ "type": "keyword"
+ },
+ "Yname": {
+ "type": "keyword"
+ },
+ "Xm": {
+ "type": "keyword"
+ },
+ "Ym": {
+ "type": "keyword"
+ },
+ "germplasmDbId": {
+ "type": "keyword"
+ },
+ "germplasmId": {
+ "type": "long"
+ },
+ "germplasmPUI": {
+ "type": "long"
+ },
+ "germplasmName": {
+ "type": "keyword"
+ },
+ "observationUnitXref": {
+ "properties": {
+ "id": {
+ "type": "keyword"
+ },
+ "source": {
+ "type": "keyword"
+ }
+ }
+ },
+ "studyDbId": {
+ "type": "keyword"
+ },
+ "studyName": {
+ "type": "keyword"
+ },
+ "studyLocationDbId": {
+ "type": "keyword"
+ },
+ "studyLocation": {
+ "type": "keyword"
+ },
+ "programDbId": {
+ "type": "keyword"
+ },
+ "programName": {
+ "type": "keyword"
+ },
+ "treatments": {
+ "properties": {
+ "factor": {
+ "type": "keyword"
+ },
+ "modality": {
+ "type": "keyword"
+ }
+ }
+ },
+ "observations": {
+ "type": "nested",
+ "properties": {
+ "observationDbId": {
+ "type": "keyword"
+ },
+ "observationVariableDbId": {
+ "type": "keyword"
+ },
+ "observationVariableName": {
+ "type": "keyword"
+ },
+ "observationTimeStamp": {
+ "type": "date",
+ "format": "yyyy-MM-dd'T'HH:mm:ss'Z'"
+ },
+ "season": {
+ "type": "keyword"
+ },
+ "collector": {
+ "type": "keyword",
+ "index": false
+ },
+ "value": {
+ "type": "keyword"
+ },
+ "specificName": {
+ "type": "keyword"
+ },
+ "observationVariableId": {
+ "type": "long"
+ },
+ "isDataFile": {
+ "type": "boolean",
+ "index": false
+ },
+ "gdd": {
+ "type": "float"
+ }
+ }
+ },
+ "entryType": {
+ "type": "keyword",
+ "index": false
+ },
+ "entryNumber": {
+ "type": "keyword",
+ "index": false
+ },
+ "studyId": {
+ "type": "long"
+ },
+ "trials": {
+ "properties": {
+ "id": {
+ "type": "long"
+ },
+ "name": {
+ "type": "keyword"
+ }
+ }
+ },
+ "accessionNumber": {
+ "type": "keyword"
+ },
+ "taxonId": {
+ "type": "long"
+ },
+ "taxonScientificName": {
+ "type": "keyword"
+ },
+ "germplasmGenus": {
+ "type": "keyword"
+ },
+ "germplasmCollections": {
+ "properties": {
+ "id": {
+ "type": "long"
+ },
+ "name": {
+ "type": "keyword"
+ }
+ }
+ },
+ "germplasmPanels": {
+ "properties": {
+ "id": {
+ "type": "long"
+ },
+ "name": {
+ "type": "keyword"
+ }
+ }
+ },
+
+ "documentationURL": {
+ "type": "keyword"
+ },
+ "source": {
+ "type": "keyword"
+ },
+
+ "groupId": {
+ "type": "long"
+ },
+ "@type": {
+ "type": "keyword"
+ },
+ "@id": {
+ "type": "keyword"
+ },
+ "schema:includedInDataCatalog": {
+ "type": "keyword"
+ },
+ "schema:identifier": {
+ "type": "keyword"
+ },
+ "schema:name": {
+ "type": "keyword"
+ },
+ "schema:url": {
+ "type": "keyword"
+ }
+ }
+ }
}
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/program_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/program_mapping.json
index aef2ae37..ea591f7a 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/program_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/program_mapping.json
@@ -1,6 +1,6 @@
{
"program": {
- "dynamic": "strict",
+ "dynamic": "strict",
"properties": {
"programDbId": {
"type": "keyword"
@@ -20,18 +20,13 @@
"leadPerson": {
"type": "keyword"
},
- "source": {
- "type": "keyword"
- },
+
"studyDbIds": {
"type": "keyword"
},
"trialDbIds": {
"type": "keyword"
},
- "documentationURL": {
- "type": "keyword"
- },
"programURI": {
"type": "keyword"
},
@@ -41,6 +36,14 @@
"trialURIs": {
"type": "keyword"
},
+
+ "documentationURL": {
+ "type": "keyword"
+ },
+ "source": {
+ "type": "keyword"
+ },
+
"groupId": {
"type": "long"
},
@@ -58,6 +61,9 @@
},
"schema:name": {
"type": "keyword"
+ },
+ "schema:url": {
+ "type": "keyword"
}
}
}
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/settings.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/settings.json
index acad8ff5..db9668c8 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/settings.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/settings.json
@@ -1,42 +1,42 @@
{
- "index" : {
- "max_inner_result_window": 10000
- },
- "analysis": {
- "filter": {
- "1-20-edgeNGram": {
- "type": "edgeNGram",
- "side": "front",
- "min_gram": 1,
- "max_gram": 20
- }
- },
- "tokenizer": {
- "special_tokenizer": {
- "type": "pattern",
- "pattern": "\\s|,|-|\\(|\\)|\\[|\\]|\\{|\\}|_"
- }
- },
- "analyzer": {
- "search_suggester": {
- "type": "custom",
- "tokenizer": "special_tokenizer",
- "filter": [
- "standard",
- "lowercase",
- "asciifolding"
- ]
- },
- "index_suggester": {
- "type": "custom",
- "tokenizer": "special_tokenizer",
- "filter": [
- "standard",
- "lowercase",
- "asciifolding",
- "1-20-edgeNGram"
- ]
- }
- }
- }
+ "index" : {
+ "max_inner_result_window": 10000
+ },
+ "analysis": {
+ "filter": {
+ "1-20-edgeNGram": {
+ "type": "edgeNGram",
+ "side": "front",
+ "min_gram": 1,
+ "max_gram": 20
+ }
+ },
+ "tokenizer": {
+ "special_tokenizer": {
+ "type": "pattern",
+ "pattern": "\\s|,|-|\\(|\\)|\\[|\\]|\\{|\\}|_"
+ }
+ },
+ "analyzer": {
+ "search_suggester": {
+ "type": "custom",
+ "tokenizer": "special_tokenizer",
+ "filter": [
+ "standard",
+ "lowercase",
+ "asciifolding"
+ ]
+ },
+ "index_suggester": {
+ "type": "custom",
+ "tokenizer": "special_tokenizer",
+ "filter": [
+ "standard",
+ "lowercase",
+ "asciifolding",
+ "1-20-edgeNGram"
+ ]
+ }
+ }
+ }
}
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/study_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/study_mapping.json
index a254ceff..d8e3e07d 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/study_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/study_mapping.json
@@ -1,127 +1,150 @@
{
- "study": {
- "dynamic": false,
- "properties": {
- "studyName": {
- "type": "keyword"
- },
- "studyDbId": {
- "type": "keyword"
- },
- "studyType": {
- "type": "keyword"
- },
- "active": {
- "type": "boolean"
- },
- "additionalInfo": {
- "type": "object",
- "properties": {}
- },
- "contacts": {
- "properties": {
- "contactDbId": {
- "type": "keyword"
- },
- "email": {
- "type": "keyword"
- },
- "institutionName": {
- "type": "keyword"
- },
- "name": {
- "type": "keyword"
- },
- "orcid": {
- "type": "keyword"
- },
- "type": {
- "type": "keyword"
- }
- }
- },
- "dataLinks": {
- "properties": {
- "name": {
- "type": "keyword"
- },
- "type": {
- "type": "keyword"
- },
- "url": {
- "type": "keyword"
- }
- }
- },
- "endDate": {
- "type": "date",
- "format": "YYYY-MM-dd"
- },
- "germplasmDbIds": {
- "type": "keyword"
- },
- "groupId": {
- "type": "long"
- },
- "lastUpdate": {
- "properties": {
- "version": {
- "type": "keyword"
- },
- "timestamp": {
- "type": "date",
- "format": "yyyy-MM-dd||yyyy-MM-dd'T'HH:mm:ss'Z'"
- }
- }
- },
- "locationDbId": {
- "type": "keyword"
- },
- "locationName": {
- "type": "keyword"
- },
- "location": {
- "dynamic": "true",
- "properties": {
- "locationDbId": {
- "type": "keyword"
- }
- }
- },
- "observationVariableDbIds": {
- "type": "keyword"
- },
- "programDbId": {
- "type": "keyword"
- },
- "programName": {
- "type": "keyword"
- },
- "seasons": {
- "type": "keyword"
- },
- "source": {
- "type": "keyword"
- },
- "speciesGroup": {
- "type": "integer"
- },
- "startDate": {
- "type": "date",
- "format": "YYYY-MM-dd"
- },
- "trialName": {
- "type": "keyword"
- },
- "trialDbId": {
- "type": "keyword"
- },
- "trialDbIds": {
- "type": "keyword"
- },
- "documentationURL": {
- "type": "keyword"
- }
- }
- }
+ "study": {
+ "dynamic": "strict",
+ "properties": {
+ "studyDbId": {
+ "type": "keyword"
+ },
+ "studyName": {
+ "type": "keyword"
+ },
+ "name": {
+ "type": "keyword"
+ },
+ "startDate": {
+ "type": "date",
+ "format": "YYYY-MM-dd"
+ },
+ "endDate": {
+ "type": "date",
+ "format": "YYYY-MM-dd"
+ },
+ "active": {
+ "type": "boolean"
+ },
+ "studyType": {
+ "type": "keyword"
+ },
+
+ "lastUpdate": {
+ "properties": {
+ "version": {
+ "type": "keyword"
+ },
+ "timestamp": {
+ "type": "date",
+ "format": "yyyy-MM-dd||yyyy-MM-dd'T'HH:mm:ss'Z'"
+ }
+ }
+ },
+ "trialDbId": {
+ "type": "keyword"
+ },
+ "trialName": {
+ "type": "keyword"
+ },
+ "trialDbIds": {
+ "type": "keyword"
+ },
+ "programDbId": {
+ "type": "keyword"
+ },
+ "programName": {
+ "type": "keyword"
+ },
+
+ "seasons": {
+ "type": "keyword"
+ },
+ "locationDbId": {
+ "type": "keyword"
+ },
+ "locationName": {
+ "type": "keyword"
+ },
+ "location": {
+ "dynamic": "true",
+ "properties": {
+ "locationDbId": {
+ "type": "keyword"
+ }
+ }
+ },
+ "dataLinks": {
+ "properties": {
+ "name": {
+ "type": "keyword"
+ },
+ "type": {
+ "type": "keyword"
+ },
+ "url": {
+ "type": "keyword"
+ }
+ }
+ },
+ "contacts": {
+ "properties": {
+ "contactDbId": {
+ "type": "keyword"
+ },
+ "name": {
+ "type": "keyword"
+ },
+ "institutionName": {
+ "type": "keyword"
+ },
+ "email": {
+ "type": "keyword"
+ },
+ "type": {
+ "type": "keyword"
+ },
+ "orcid": {
+ "type": "keyword"
+ }
+ }
+ },
+ "observationVariableDbIds": {
+ "type": "keyword"
+ },
+ "germplasmDbIds": {
+ "type": "keyword"
+ },
+ "additionalInfo": {
+ "dynamic": "true",
+ "type": "object",
+ "properties": {}
+ },
+
+ "documentationURL": {
+ "type": "keyword"
+ },
+ "source": {
+ "type": "keyword"
+ },
+
+ "groupId": {
+ "type": "long"
+ },
+ "@type": {
+ "type": "keyword"
+ },
+ "@id": {
+ "type": "keyword"
+ },
+ "schema:includedInDataCatalog": {
+ "type": "keyword"
+ },
+ "schema:identifier": {
+ "type": "keyword"
+ },
+ "schema:name": {
+ "type": "keyword"
+ },
+ "schema:url": {
+ "type": "keyword"
+ }
+ }
+ }
}
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/transplant_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/transplant_mapping.json
index f470dc9d..5aec114c 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/transplant_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/transplant_mapping.json
@@ -1,13 +1,13 @@
{
- "transplant": {
- "dynamic": "true",
- "properties": {
- "entry_type": {
- "type": "keyword"
- },
- "linkedRessourcesID": {
- "type": "keyword"
- }
- }
- }
+ "transplant": {
+ "dynamic": "true",
+ "properties": {
+ "entry_type": {
+ "type": "keyword"
+ },
+ "linkedRessourcesID": {
+ "type": "keyword"
+ }
+ }
+ }
}
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/trial_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/trial_mapping.json
index fcc2adf3..4ce25a38 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/trial_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/trial_mapping.json
@@ -1,94 +1,156 @@
{
- "trial": {
- "dynamic": false,
- "properties": {
- "active": {
- "type": "boolean"
- },
- "additionalInfo": {
- "type": "object",
- "properties": {}
- },
- "contacts": {
- "properties": {
- "contactDbId": {
- "type": "keyword"
- },
- "email": {
- "type": "keyword"
- },
- "institutionName": {
- "type": "keyword"
- },
- "name": {
- "type": "keyword"
- },
- "orcid": {
- "type": "keyword"
- },
- "type": {
- "type": "keyword"
- }
- }
- },
- "datasetAuthorship": {
- "properties": {
- "license": {
- "type": "keyword"
- },
- "datasetPUI": {
- "type": "keyword"
- }
- }
- },
- "docId": {
- "type": "keyword"
- },
- "endDate": {
- "type": "date",
- "format": "YYYY-MM-dd"
- },
- "groupId": {
- "type": "long"
- },
- "source": {
- "type": "keyword"
- },
- "speciesGroup": {
- "type": "integer"
- },
- "startDate": {
- "type": "date",
- "format": "YYYY-MM-dd"
- },
- "studies": {
- "properties": {
- "locationName": {
- "type": "keyword"
- },
- "locationDbId": {
- "type": "keyword"
- },
- "studyDbId": {
- "type": "keyword"
- },
- "studyName": {
- "type": "keyword"
- }
- }
- },
- "trialDbId": {
- "type": "keyword"
- },
- "trialName": {
- "type": "keyword"
- },
- "trialType": {
- "type": "keyword"
- },
- "documentationURL": {
- "type": "keyword"
- }
- }
- }
+ "trial": {
+ "dynamic": "strict",
+ "properties": {
+ "docId": {
+ "type": "keyword"
+ },
+ "trialDbId": {
+ "type": "keyword"
+ },
+ "trialPUI": {
+ "type": "keyword"
+ },
+ "trialName": {
+ "type": "keyword"
+ },
+ "trialType": {
+ "type": "keyword"
+ },
+ "startDate": {
+ "type": "date",
+ "format": "YYYY-MM-dd"
+ },
+ "endDate": {
+ "type": "date",
+ "format": "YYYY-MM-dd"
+ },
+ "active": {
+ "type": "boolean"
+ },
+ "datasetAuthorship": {
+ "properties": {
+ "license": {
+ "type": "keyword"
+ },
+ "datasetPUI": {
+ "type": "keyword"
+ }
+ }
+ },
+ "datasetAuthorships": {
+ "properties": {
+ "license": {
+ "type": "keyword"
+ },
+ "datasetPUI": {
+ "type": "keyword"
+ }
+ }
+ },
+ "contacts": {
+ "properties": {
+ "contactDbId": {
+ "type": "keyword"
+ },
+ "name": {
+ "type": "keyword"
+ },
+ "institutionName": {
+ "type": "keyword"
+ },
+ "email": {
+ "type": "keyword"
+ },
+ "type": {
+ "type": "keyword"
+ },
+ "contactURI": {
+ "type": "keyword"
+ },
+ "orcid": {
+ "type": "keyword"
+ }
+ }
+ },
+ "studies": {
+ "properties": {
+ "studyDbId": {
+ "type": "keyword"
+ },
+ "studyName": {
+ "type": "keyword"
+ },
+ "name": {
+ "type": "keyword"
+ },
+ "locationDbId": {
+ "type": "keyword"
+ },
+ "locationName": {
+ "type": "keyword"
+ },
+ "studyURI": {
+ "type": "keyword"
+ },
+ "locationURI": {
+ "type": "keyword"
+ }
+ }
+ },
+ "commonCropName": {
+ "type": "keyword"
+ },
+ "additionalInfo": {
+ "dynamic": "true",
+ "type": "object",
+ "properties": {}
+ },
+ "programDbId": {
+ "type": "keyword"
+ },
+ "programName": {
+ "type": "keyword"
+ },
+ "studyDbIds": {
+ "type": "keyword"
+ },
+ "contactDbIds": {
+ "type": "keyword"
+ },
+
+ "trialURI": {
+ "type": "keyword"
+ },
+
+ "documentationURL": {
+ "type": "keyword"
+ },
+ "source": {
+ "type": "keyword"
+ },
+
+ "groupId": {
+ "type": "long"
+ },
+ "@type": {
+ "type": "keyword"
+ },
+ "@id": {
+ "type": "keyword"
+ },
+ "schema:includedInDataCatalog": {
+ "type": "keyword"
+ },
+ "schema:identifier": {
+ "type": "keyword"
+ },
+ "schema:name": {
+ "type": "keyword"
+ },
+ "schema:url": {
+ "type": "keyword"
+ }
+ }
+ }
}
--
GitLab
From 2190f7acf9640235086b3877a1e183654c90493d Mon Sep 17 00:00:00 2001
From: Celia Michotey <celia.michotey@inra.fr>
Date: Wed, 23 Oct 2019 14:28:10 +0200
Subject: [PATCH 04/11] Finish indexation script and update mappings.
---
.gitignore | 3 +
.../es/setup/index/datadiscovery_mapping.json | 15 +-
.../index/germplasmAttribute_mapping.json | 24 +-
.../index/germplasmPedigree_mapping.json | 28 +-
.../setup/index/germplasmProgeny_mapping.json | 16 +-
.../es/setup/index/germplasm_mapping.json | 125 +++++----
.../es/setup/index/location_mapping.json | 33 ++-
.../setup/index/observationUnit_mapping.json | 181 ++++++------
.../es/setup/index/program_mapping.json | 30 +-
.../es/setup/index/study_mapping.json | 195 ++++++++++---
.../es/setup/index/trial_mapping.json | 260 +++++++++++++++---
scripts/harvest.sh | 18 +-
12 files changed, 664 insertions(+), 264 deletions(-)
diff --git a/.gitignore b/.gitignore
index fc67b540..c456a808 100644
--- a/.gitignore
+++ b/.gitignore
@@ -91,6 +91,9 @@ local.properties
# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and WebStorm
# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+*.iml
+*.ipr
+
# User-specific stuff
.idea/*
.idea/**/workspace.xml
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/datadiscovery_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/datadiscovery_mapping.json
index 331335a1..076ea76a 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/datadiscovery_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/datadiscovery_mapping.json
@@ -1,6 +1,6 @@
{
"datadiscovery": {
- "dynamic": "strict",
+ "dynamic": "false",
"_source": {
"includes": ["@id", "@type", "schema:*", "groupId"]
},
@@ -30,6 +30,19 @@
"type": "keyword"
},
+ "germplasmURI": {
+ "type": "keyword"
+ },
+ "germplasmDbId": {
+ "type": "keyword"
+ },
+ "studyURIs": {
+ "type": "keyword"
+ },
+ "studyDbIds": {
+ "type": "keyword"
+ },
+
"germplasm": {
"type": "object",
"properties": {
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmAttribute_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmAttribute_mapping.json
index 6a7c900b..d0133c0b 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmAttribute_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmAttribute_mapping.json
@@ -2,38 +2,46 @@
"germplasmAttribute": {
"dynamic": "strict",
"properties": {
+ "germplasmAttributeURI": {
+ "type": "keyword"
+ },
+ "germplasmAttributeDbId": {
+ "type": "keyword"
+ },
+ "germplasmURI": {
+ "type": "keyword"
+ },
"germplasmDbId": {
"type": "keyword"
},
"data": {
"type": "nested",
"properties": {
- "attributeDbId": {
+ "attributeURI": {
"type": "keyword"
},
- "attributeName": {
+ "attributeDbId": {
"type": "keyword"
},
"attributeCode": {
"type": "keyword"
},
- "value": {
+ "attributeName": {
"type": "keyword"
},
"determinedDate": {
"type": "date",
"format": "YYYY-MM-dd"
+ },
+ "value": {
+ "type": "keyword"
}
}
},
- "documentationURL": {
- "type": "keyword"
- },
"source": {
"type": "keyword"
},
-
"groupId": {
"type": "long"
},
@@ -57,4 +65,4 @@
}
}
}
-}
\ No newline at end of file
+}
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmPedigree_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmPedigree_mapping.json
index ad7070d9..79986a17 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmPedigree_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmPedigree_mapping.json
@@ -2,13 +2,19 @@
"germplasmPedigree": {
"dynamic": "strict",
"properties": {
- "germplasmDbId": {
+ "germplasmPedigreeURI": {
"type": "keyword"
},
- "defaultDisplayName": {
+ "germplasmPedigreeDbId": {
"type": "keyword"
},
- "pedigree": {
+ "germplasmURI": {
+ "type": "keyword"
+ },
+ "germplasmDbId": {
+ "type": "keyword"
+ },
+ "defaultDisplayName": {
"type": "keyword"
},
"crossingPlan": {
@@ -20,6 +26,9 @@
"familyCode": {
"type": "keyword"
},
+ "parent1URI": {
+ "type": "keyword"
+ },
"parent1DbId": {
"type": "keyword"
},
@@ -29,6 +38,9 @@
"parent1Type": {
"type": "keyword"
},
+ "parent2URI": {
+ "type": "keyword"
+ },
"parent2DbId": {
"type": "keyword"
},
@@ -38,8 +50,14 @@
"parent2Type": {
"type": "keyword"
},
+ "pedigree": {
+ "type": "keyword"
+ },
"siblings": {
"properties": {
+ "germplasmURI": {
+ "type": "keyword"
+ },
"germplasmDbId": {
"type": "keyword"
},
@@ -49,13 +67,9 @@
}
},
- "documentationURL": {
- "type": "keyword"
- },
"source": {
"type": "keyword"
},
-
"groupId": {
"type": "long"
},
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmProgeny_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmProgeny_mapping.json
index cdfe1cc4..58eb7a9b 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmProgeny_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmProgeny_mapping.json
@@ -2,6 +2,15 @@
"germplasmProgeny": {
"dynamic": "strict",
"properties": {
+ "germplasmProgenyURI": {
+ "type": "keyword"
+ },
+ "germplasmProgenyDbId": {
+ "type": "keyword"
+ },
+ "germplasmURI": {
+ "type": "keyword"
+ },
"germplasmDbId": {
"type": "keyword"
},
@@ -10,6 +19,9 @@
},
"progeny": {
"properties": {
+ "germplasmURI": {
+ "type": "keyword"
+ },
"germplasmDbId": {
"type": "keyword"
},
@@ -22,13 +34,9 @@
}
},
- "documentationURL": {
- "type": "keyword"
- },
"source": {
"type": "keyword"
},
-
"groupId": {
"type": "long"
},
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json
index 2c5cd2b5..3298d98a 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json
@@ -2,76 +2,43 @@
"germplasm": {
"dynamic": "strict",
"properties": {
- "germplasmDbId": {
+ "germplasmURI": {
"type": "keyword"
},
- "defaultDisplayName": {
+ "germplasmDbId": {
"type": "keyword"
},
- "accessionNumber": {
- "type": "keyword",
- "doc_values": true
- },
- "germplasmName": {
- "type": "keyword",
- "doc_values": true
- },
"germplasmPUI": {
"type": "keyword"
},
- "pedigree": {
- "type": "keyword"
- },
- "seedSource": {
- "type": "keyword"
- },
- "synonyms": {
+ "germplasmName": {
"type": "keyword",
"doc_values": true
},
- "commonCropName": {
+ "accessionNumber": {
"type": "keyword",
"doc_values": true
},
- "instituteCode": {
- "type": "keyword"
- },
- "instituteName": {
+ "acquisitionDate": {
"type": "keyword"
},
"biologicalStatusOfAccessionCode": {
"type": "keyword"
},
- "countryOfOriginCode": {
+ "breedingMethodDbId": {
"type": "keyword"
},
- "typeOfGermplasmStorageCode": {
- "type": "keyword"
- },
- "taxonIds": {
- "properties": {
- "sourceName": {
- "type": "keyword"
- },
- "taxonId": {
- "type": "keyword"
- }
- }
- },
- "genus": {
+ "commonCropName": {
"type": "keyword",
"doc_values": true
},
- "species": {
- "type": "keyword"
- },
- "speciesAuthority": {
+ "countryOfOriginCode": {
"type": "keyword"
},
- "subtaxa": {
+ "defaultDisplayName": {
"type": "keyword"
},
- "subtaxaAuthority": {
+ "documentationURL": {
"type": "keyword"
},
"donors": {
@@ -82,6 +49,9 @@
"donorGermplasmPUI": {
"type": "keyword"
},
+ "germplasmPUI": {
+ "type": "keyword"
+ },
"donorAccessionNumber": {
"type": "keyword"
},
@@ -118,17 +88,70 @@
}
}
},
- "acquisitionDate": {
+ "genus": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "germplasmGenus": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "species": {
"type": "keyword"
},
+ "germplasmSpecies": {
+ "type": "keyword",
+ "doc_values": true
+ },
"genusSpecies": {
"type": "keyword",
"doc_values": true
},
+ "speciesAuthority": {
+ "type": "keyword"
+ },
+ "subtaxa": {
+ "type": "keyword"
+ },
+ "subTaxa": {
+ "type": "keyword"
+ },
"genusSpeciesSubtaxa": {
"type": "keyword",
"doc_values": true
},
+ "subtaxaAuthority": {
+ "type": "keyword"
+ },
+ "instituteCode": {
+ "type": "keyword"
+ },
+ "instituteName": {
+ "type": "keyword"
+ },
+ "pedigree": {
+ "type": "keyword"
+ },
+ "seedSource": {
+ "type": "keyword"
+ },
+ "SeedSource": {
+ "type": "keyword"
+ },
+ "synonyms": {
+ "type": "keyword",
+ "doc_values": true
+ },
+ "taxonIds": {
+ "properties": {
+ "sourceName": {
+ "type": "keyword"
+ },
+ "taxonId": {
+ "type": "keyword"
+ }
+ }
+ },
"taxonSynonyms": {
"type": "keyword",
"doc_values": true
@@ -140,6 +163,9 @@
"taxonComment": {
"type": "keyword"
},
+ "typeOfGermplasmStorageCode": {
+ "type": "keyword"
+ },
"geneticNature": {
"type": "keyword"
},
@@ -531,17 +557,22 @@
}
}
},
+ "studyURIs": {
+ "type": "keyword"
+ },
"studyDbIds": {
"type": "keyword"
},
-
- "documentationURL": {
+ "studyURI": {
"type": "keyword"
},
- "source": {
+ "studyDbId": {
"type": "keyword"
},
+ "source": {
+ "type": "keyword"
+ },
"groupId": {
"type": "long"
},
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/location_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/location_mapping.json
index 498fb319..8ab41d2a 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/location_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/location_mapping.json
@@ -2,6 +2,9 @@
"location": {
"dynamic": "strict",
"properties": {
+ "locationURI": {
+ "type": "keyword"
+ },
"locationDbId": {
"type": "keyword"
},
@@ -11,10 +14,13 @@
"name": {
"type": "keyword"
},
- "locationType": {
+ "abbreviation": {
"type": "keyword"
},
- "abbreviation": {
+ "abreviation": {
+ "type": "keyword"
+ },
+ "locationType": {
"type": "keyword"
},
"countryCode": {
@@ -23,19 +29,25 @@
"countryName": {
"type": "keyword"
},
- "institutionName": {
+ "documentationURL": {
+ "type": "keyword"
+ },
+ "instituteName": {
"type": "keyword"
},
- "institutionAdress": {
+ "instituteAddress": {
"type": "keyword"
},
- "latitude": {
+ "instituteAdress": {
+ "type": "keyword"
+ },
+ "altitude": {
"type": "double"
},
- "longitude": {
+ "latitude": {
"type": "double"
},
- "altitude": {
+ "longitude": {
"type": "double"
},
"additionalInfo": {
@@ -43,13 +55,16 @@
"properties": {}
},
- "documentationURL": {
+ "studyDbIds": {
"type": "keyword"
},
- "source": {
+ "studyURIs": {
"type": "keyword"
},
+ "source": {
+ "type": "keyword"
+ },
"groupId": {
"type": "long"
},
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/observationUnit_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/observationUnit_mapping.json
index ca56d679..5bce2cd4 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/observationUnit_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/observationUnit_mapping.json
@@ -2,111 +2,85 @@
"observationUnit": {
"dynamic": "strict",
"properties": {
+ "observationUnitURI": {
+ "type": "keyword"
+ },
"observationUnitDbId": {
"type": "keyword"
},
"observationUnitName": {
"type": "keyword"
},
- "observationLevel": {
+ "X": {
"type": "keyword"
},
- "observationLevels": {
+ "Y": {
"type": "keyword"
},
- "observationLevelDetails": {
- "properties": {
- "type": {
- "type": "keyword"
- },
- "name": {
- "type": "keyword"
- },
- "value": {
- "type": "keyword"
- }
- }
+ "Xname": {
+ "type": "keyword"
},
- "plotNumber": {
- "type": "keyword",
- "index": false
+ "Yname": {
+ "type": "keyword"
},
- "plantNumber": {
- "type": "keyword",
- "index": false
+ "Xm": {
+ "type": "keyword"
+ },
+ "Ym": {
+ "type": "keyword"
},
"blockNumber": {
"type": "keyword",
"index": false
},
- "replicate": {
+ "entryNumber": {
"type": "keyword",
"index": false
},
- "X": {
- "type": "keyword"
+ "entryType": {
+ "type": "keyword",
+ "index": false
},
- "Y": {
+ "germplasmURI": {
"type": "keyword"
},
- "Xname": {
+ "germplasmDbId": {
"type": "keyword"
},
- "Yname": {
+ "germplasmPUI": {
"type": "keyword"
},
- "Xm": {
+ "germplasmName": {
"type": "keyword"
},
- "Ym": {
+ "accessionNumber": {
"type": "keyword"
},
- "germplasmDbId": {
+ "observationLevel": {
"type": "keyword"
},
- "germplasmId": {
- "type": "long"
- },
- "germplasmPUI": {
- "type": "long"
- },
- "germplasmName": {
+ "observationLevels": {
"type": "keyword"
},
- "observationUnitXref": {
+ "observationLevelDetails": {
"properties": {
- "id": {
+ "type": {
"type": "keyword"
},
- "source": {
+ "name": {
+ "type": "keyword"
+ },
+ "value": {
"type": "keyword"
}
}
},
- "studyDbId": {
- "type": "keyword"
- },
- "studyName": {
- "type": "keyword"
- },
- "studyLocationDbId": {
- "type": "keyword"
- },
- "studyLocation": {
- "type": "keyword"
- },
- "programDbId": {
- "type": "keyword"
- },
- "programName": {
- "type": "keyword"
- },
- "treatments": {
+ "observationUnitXref": {
"properties": {
- "factor": {
+ "id": {
"type": "keyword"
},
- "modality": {
+ "source": {
"type": "keyword"
}
}
@@ -114,54 +88,95 @@
"observations": {
"type": "nested",
"properties": {
- "observationDbId": {
+ "observationURI": {
"type": "keyword"
},
- "observationVariableDbId": {
+ "observationDbId": {
"type": "keyword"
},
- "observationVariableName": {
- "type": "keyword"
+ "collector": {
+ "type": "keyword",
+ "index": false
},
"observationTimeStamp": {
"type": "date",
"format": "yyyy-MM-dd'T'HH:mm:ss'Z'"
},
- "season": {
+ "gdd": {
+ "type": "float"
+ },
+ "observationVariableURI": {
"type": "keyword"
},
- "collector": {
- "type": "keyword",
- "index": false
+ "observationVariableDbId": {
+ "type": "keyword"
},
- "value": {
+ "observationVariableName": {
"type": "keyword"
},
"specificName": {
"type": "keyword"
},
- "observationVariableId": {
- "type": "long"
+ "season": {
+ "type": "keyword"
+ },
+ "value": {
+ "type": "keyword"
},
"isDataFile": {
"type": "boolean",
"index": false
- },
- "gdd": {
- "type": "float"
}
}
},
- "entryType": {
+ "plantNumber": {
"type": "keyword",
"index": false
},
- "entryNumber": {
+ "plotNumber": {
"type": "keyword",
"index": false
},
- "studyId": {
- "type": "long"
+ "programURI": {
+ "type": "keyword"
+ },
+ "programDbId": {
+ "type": "keyword"
+ },
+ "programName": {
+ "type": "keyword"
+ },
+ "replicate": {
+ "type": "keyword",
+ "index": false
+ },
+ "studyURI": {
+ "type": "keyword"
+ },
+ "studyDbId": {
+ "type": "keyword"
+ },
+ "studyName": {
+ "type": "keyword"
+ },
+ "studyLocationURI": {
+ "type": "keyword"
+ },
+ "studyLocationDbId": {
+ "type": "keyword"
+ },
+ "studyLocation": {
+ "type": "keyword"
+ },
+ "treatments": {
+ "properties": {
+ "factor": {
+ "type": "keyword"
+ },
+ "modality": {
+ "type": "keyword"
+ }
+ }
},
"trials": {
"properties": {
@@ -173,12 +188,6 @@
}
}
},
- "accessionNumber": {
- "type": "keyword"
- },
- "taxonId": {
- "type": "long"
- },
"taxonScientificName": {
"type": "keyword"
},
@@ -206,13 +215,9 @@
}
},
- "documentationURL": {
- "type": "keyword"
- },
"source": {
"type": "keyword"
},
-
"groupId": {
"type": "long"
},
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/program_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/program_mapping.json
index ea591f7a..abd710be 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/program_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/program_mapping.json
@@ -2,48 +2,56 @@
"program": {
"dynamic": "strict",
"properties": {
- "programDbId": {
+ "programURI": {
"type": "keyword"
},
- "name": {
+ "programDbId": {
"type": "keyword"
},
"programName": {
"type": "keyword"
},
+ "name": {
+ "type": "keyword"
+ },
"abbreviation": {
"type": "keyword"
},
- "objective": {
+ "commonCropName": {
+ "type": "keyword"
+ },
+ "documentationURL": {
"type": "keyword"
},
"leadPerson": {
"type": "keyword"
},
-
- "studyDbIds": {
+ "leadPersonDbId": {
"type": "keyword"
},
- "trialDbIds": {
+ "leadPersonName": {
"type": "keyword"
},
- "programURI": {
+ "objective": {
"type": "keyword"
},
- "studyURIs": {
+
+ "trialDbIds": {
"type": "keyword"
},
"trialURIs": {
"type": "keyword"
},
-
- "documentationURL": {
+ "studyDbIds": {
"type": "keyword"
},
- "source": {
+ "studyURIs": {
"type": "keyword"
},
+ "source": {
+ "type": "keyword"
+ },
"groupId": {
"type": "long"
},
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/study_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/study_mapping.json
index d8e3e07d..d1f7286d 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/study_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/study_mapping.json
@@ -2,6 +2,9 @@
"study": {
"dynamic": "strict",
"properties": {
+ "studyURI": {
+ "type": "keyword"
+ },
"studyDbId": {
"type": "keyword"
},
@@ -11,6 +14,65 @@
"name": {
"type": "keyword"
},
+ "active": {
+ "type": "boolean"
+ },
+ "commonCropName": {
+ "type": "keyword"
+ },
+ "organism": {
+ "type": "keyword"
+ },
+ "contactURIs": {
+ "type": "keyword"
+ },
+ "contactDbIds": {
+ "type": "keyword"
+ },
+ "contacts": {
+ "properties": {
+ "contactURI": {
+ "type": "keyword"
+ },
+ "contactDbId": {
+ "type": "keyword"
+ },
+ "name": {
+ "type": "keyword"
+ },
+ "instituteName": {
+ "type": "keyword"
+ },
+ "email": {
+ "type": "keyword"
+ },
+ "type": {
+ "type": "keyword"
+ },
+ "orcid": {
+ "type": "keyword"
+ }
+ }
+ },
+ "dataLinks": {
+ "properties": {
+ "dataLinkName": {
+ "type": "keyword"
+ },
+ "name": {
+ "type": "keyword"
+ },
+ "type": {
+ "type": "keyword"
+ },
+ "url": {
+ "type": "keyword"
+ }
+ }
+ },
+ "documentationURL": {
+ "type": "keyword"
+ },
"startDate": {
"type": "date",
"format": "YYYY-MM-dd"
@@ -19,13 +81,9 @@
"type": "date",
"format": "YYYY-MM-dd"
},
- "active": {
- "type": "boolean"
- },
- "studyType": {
+ "year": {
"type": "keyword"
},
-
"lastUpdate": {
"properties": {
"version": {
@@ -37,23 +95,16 @@
}
}
},
- "trialDbId": {
- "type": "keyword"
- },
- "trialName": {
- "type": "keyword"
- },
- "trialDbIds": {
+ "license": {
"type": "keyword"
},
- "programDbId": {
+ "locationURIs": {
"type": "keyword"
},
- "programName": {
+ "locationDbIds": {
"type": "keyword"
},
-
- "seasons": {
+ "locationURI": {
"type": "keyword"
},
"locationDbId": {
@@ -63,67 +114,131 @@
"type": "keyword"
},
"location": {
- "dynamic": "true",
"properties": {
+ "locationURI": {
+ "type": "keyword"
+ },
"locationDbId": {
"type": "keyword"
- }
- }
- },
- "dataLinks": {
- "properties": {
+ },
+ "locationName": {
+ "type": "keyword"
+ },
"name": {
"type": "keyword"
},
- "type": {
+ "abbreviation": {
"type": "keyword"
},
- "url": {
+ "abreviation": {
"type": "keyword"
- }
- }
- },
- "contacts": {
- "properties": {
- "contactDbId": {
+ },
+ "locationType": {
"type": "keyword"
},
- "name": {
+ "countryCode": {
"type": "keyword"
},
- "institutionName": {
+ "countryName": {
"type": "keyword"
},
- "email": {
+ "documentationURL": {
"type": "keyword"
},
- "type": {
+ "instituteName": {
"type": "keyword"
},
- "orcid": {
+ "instituteAddress": {
"type": "keyword"
+ },
+ "instituteAdress": {
+ "type": "keyword"
+ },
+ "altitude": {
+ "type": "double"
+ },
+ "latitude": {
+ "type": "double"
+ },
+ "longitude": {
+ "type": "double"
+ },
+ "additionalInfo": {
+ "dynamic": "true",
+ "type": "object",
+ "properties": {}
}
}
},
- "observationVariableDbIds": {
+ "programURIs": {
+ "type": "keyword"
+ },
+ "programDbIds": {
+ "type": "keyword"
+ },
+ "programURI": {
+ "type": "keyword"
+ },
+ "programDbId": {
+ "type": "keyword"
+ },
+ "programName": {
+ "type": "keyword"
+ },
+ "seasons": {
+ "type": "keyword"
+ },
+ "studyDescription": {
+ "type": "keyword"
+ },
+ "studyTypeURI": {
+ "type": "keyword"
+ },
+ "studyTypeDbId": {
+ "type": "keyword"
+ },
+ "studyType": {
+ "type": "keyword"
+ },
+ "studyTypeName": {
+ "type": "keyword"
+ },
+ "trialURIs": {
+ "type": "keyword"
+ },
+ "trialDbIds": {
+ "type": "keyword"
+ },
+ "trialURI": {
+ "type": "keyword"
+ },
+ "trialDbId": {
+ "type": "keyword"
+ },
+ "trialName": {
+ "type": "keyword"
+ },
+ "germplasmURIs": {
"type": "keyword"
},
"germplasmDbIds": {
"type": "keyword"
},
+ "observationVariableURIs": {
+ "type": "keyword"
+ },
+ "observationVariableDbIds": {
+ "type": "keyword"
+ },
"additionalInfo": {
"dynamic": "true",
"type": "object",
"properties": {}
},
- "documentationURL": {
- "type": "keyword"
- },
"source": {
"type": "keyword"
},
-
"groupId": {
"type": "long"
},
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/trial_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/trial_mapping.json
index 4ce25a38..4bde6c12 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/trial_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/trial_mapping.json
@@ -2,21 +2,30 @@
"trial": {
"dynamic": "strict",
"properties": {
- "docId": {
+ "trialURI": {
"type": "keyword"
},
"trialDbId": {
"type": "keyword"
},
- "trialPUI": {
+ "trialName": {
"type": "keyword"
},
- "trialName": {
+ "trialPUI": {
"type": "keyword"
},
"trialType": {
"type": "keyword"
},
+ "active": {
+ "type": "boolean"
+ },
+ "commonCropName": {
+ "type": "keyword"
+ },
+ "documentationURL": {
+ "type": "keyword"
+ },
"startDate": {
"type": "date",
"format": "YYYY-MM-dd"
@@ -25,9 +34,179 @@
"type": "date",
"format": "YYYY-MM-dd"
},
- "active": {
- "type": "boolean"
+ "programURIs": {
+ "type": "keyword"
},
+ "programDbIds": {
+ "type": "keyword"
+ },
+ "programURI": {
+ "type": "keyword"
+ },
+ "programDbId": {
+ "type": "keyword"
+ },
+ "programName": {
+ "type": "keyword"
+ },
+ "studyURIs": {
+ "type": "keyword"
+ },
+ "studyDbIds": {
+ "type": "keyword"
+ },
+ "studies": {
+ "properties": {
+ "studyURI": {
+ "type": "keyword"
+ },
+ "studyDbId": {
+ "type": "keyword"
+ },
+ "studyName": {
+ "type": "keyword"
+ },
+ "name": {
+ "type": "keyword"
+ },
+ "locationURI": {
+ "type": "keyword"
+ },
+ "locationDbId": {
+ "type": "keyword"
+ },
+ "locationName": {
+ "type": "keyword"
+ },
+ "active": {
+ "type": "boolean"
+ },
+ "commonCropName": {
+ "type": "keyword"
+ },
+ "contactURIs": {
+ "type": "keyword"
+ },
+ "contactDbIds": {
+ "type": "keyword"
+ },
+ "dataLinks": {
+ "properties": {
+ "name": {
+ "type": "keyword"
+ },
+ "type": {
+ "type": "keyword"
+ },
+ "url": {
+ "type": "keyword"
+ }
+ }
+ },
+ "documentationURL": {
+ "type": "keyword"
+ },
+ "startDate": {
+ "type": "date",
+ "format": "YYYY-MM-dd"
+ },
+ "endDate": {
+ "type": "date",
+ "format": "YYYY-MM-dd"
+ },
+ "license": {
+ "type": "keyword"
+ },
+ "programURIs": {
+ "type": "keyword"
+ },
+ "programDbIds": {
+ "type": "keyword"
+ },
+ "programURI": {
+ "type": "keyword"
+ },
+ "programDbId": {
+ "type": "keyword"
+ },
+ "programName": {
+ "type": "keyword"
+ },
+ "seasons": {
+ "dynamic": "true",
+ "properties": {}
+ },
+ "studyType": {
+ "type": "keyword"
+ },
+ "studyTypeName": {
+ "type": "keyword"
+ },
+ "trialURIs": {
+ "type": "keyword"
+ },
+ "trialDbIds": {
+ "type": "keyword"
+ },
+ "trialURI": {
+ "type": "keyword"
+ },
+ "trialDbId": {
+ "type": "keyword"
+ },
+ "trialName": {
+ "type": "keyword"
+ },
+ "germplasmURIs": {
+ "type": "keyword"
+ },
+ "germplasmDbIds": {
+ "type": "keyword"
+ },
+ "observationVariableURIs": {
+ "type": "keyword"
+ },
+ "observationVariableDbIds": {
+ "type": "keyword"
+ },
+ "locationURIs": {
+ "type": "keyword"
+ },
+ "locationDbIds": {
+ "type": "keyword"
+ },
+ "additionalInfo": {
+ "dynamic": "true",
+ "type": "object",
+ "properties": {}
+ },
+
+ "source": {
+ "type": "keyword"
+ },
+ "groupId": {
+ "type": "long"
+ },
+ "@type": {
+ "type": "keyword"
+ },
+ "@id": {
+ "type": "keyword"
+ },
+ "schema:includedInDataCatalog": {
+ "type": "keyword"
+ },
+ "schema:identifier": {
+ "type": "keyword"
+ },
+ "schema:name": {
+ "type": "keyword"
+ },
+ "schema:url": {
+ "type": "keyword"
+ }
+ }
+ },
"datasetAuthorship": {
"properties": {
"license": {
@@ -48,15 +227,24 @@
}
}
},
+ "contactURIs": {
+ "type": "keyword"
+ },
+ "contactDbIds": {
+ "type": "keyword"
+ },
"contacts": {
"properties": {
+ "contactURI": {
+ "type": "keyword"
+ },
"contactDbId": {
"type": "keyword"
},
"name": {
"type": "keyword"
},
- "institutionName": {
+ "instituteName": {
"type": "keyword"
},
"email": {
@@ -65,71 +253,57 @@
"type": {
"type": "keyword"
},
- "contactURI": {
+ "orcid": {
"type": "keyword"
},
- "orcid": {
+ "studyURIs": {
"type": "keyword"
- }
- }
- },
- "studies": {
- "properties": {
- "studyDbId": {
+ },
+ "studyDbIds": {
"type": "keyword"
},
- "studyName": {
+ "trialURIs": {
"type": "keyword"
},
- "name": {
+ "trialDbIds": {
"type": "keyword"
},
- "locationDbId": {
+
+ "source": {
"type": "keyword"
},
- "locationName": {
+ "groupId": {
+ "type": "long"
+ },
+ "@type": {
"type": "keyword"
},
- "studyURI": {
+ "@id": {
"type": "keyword"
},
- "locationURI": {
+ "schema:includedInDataCatalog": {
+ "type": "keyword"
+ },
+ "schema:identifier": {
+ "type": "keyword"
+ },
+ "schema:name": {
+ "type": "keyword"
+ },
+ "schema:url": {
"type": "keyword"
}
}
},
- "commonCropName": {
- "type": "keyword"
- },
"additionalInfo": {
"dynamic": "true",
"type": "object",
"properties": {}
},
- "programDbId": {
- "type": "keyword"
- },
- "programName": {
- "type": "keyword"
- },
- "studyDbIds": {
- "type": "keyword"
- },
- "contactDbIds": {
- "type": "keyword"
- },
- "trialURI": {
- "type": "keyword"
- },
-
- "documentationURL": {
- "type": "keyword"
- },
"source": {
"type": "keyword"
},
-
"groupId": {
"type": "long"
},
diff --git a/scripts/harvest.sh b/scripts/harvest.sh
index d91297e8..9b397ef9 100755
--- a/scripts/harvest.sh
+++ b/scripts/harvest.sh
@@ -7,9 +7,10 @@ ES_PORT="9200"
ENV="dev"
DOCUMENT_TYPES="all"
-ALL_DOCUMENT_TYPES="germplasm germplasm-mcpd germplasmAttribute germplasmPedigree germplasmProgeny location program study trial observationUnit datadiscovery"
+ALL_DOCUMENT_TYPES="germplasm germplasmMcpd germplasmAttribute germplasmPedigree germplasmProgeny location program study trial observationUnit datadiscovery"
ALL_ENVS="dev beta staging int prod test"
BASEDIR=$(dirname "$0")
+TMP_FILE="log.tmp"
RED='\033[0;31m'
GREEN='\033[0;32m'
@@ -118,7 +119,7 @@ done
for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
echo && echo -e "${BOLD}Manage ${DOCUMENT_TYPE} documents...${NC}"
- INDEX_PATTERN="faidare_${DOCUMENT_TYPE}_${ENV}"
+ INDEX_PATTERN=$(echo "faidare_${DOCUMENT_TYPE}_${ENV}" | sed -E "s/([a-z])([A-Z])/\1-\2/" | tr '[:upper:]' '[:lower:]')
# Create template
TEMPLATE_NAME="${INDEX_PATTERN}_template"
@@ -139,21 +140,26 @@ for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
{
parallel --bar "
curl -s -H 'Content-Type: application/x-ndjson' -H 'Content-Encoding: gzip' -H 'Accept-Encoding: gzip' -XPOST ${ES_HOST}:${ES_PORT}/${INDEX_NAME}/_bulk --data-binary '@{}' > {.}.log.gz" \
- ::: $(find ${DATA_DIR} -name ${DOCUMENT_TYPE}*.json.gz)
+ ::: $(find ${DATA_DIR} -name ${DOCUMENT_TYPE}-*.json.gz)
} || {
code=$?
echo -e "${RED}ERROR: a problem occurred when trying to index data with parallel program.${NC}"
exit $code
}
- #echo -e "${RED}ERROR: a problem occurred when trying to index data into ${ES_HOST}:${ES_PORT}/${INDEX_NAME} indice.${NC}"
- parallel "gunzip -c {} | jq '.errors' | grep -q true && echo -e '${ORANGE}ERROR found in {}${NC}' ;" ::: $(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}"
+ rm "${TMP_FILE}"
+ exit 1;
+ fi
# Check indexed data
echo -e "* Check data indexed from ${DATA_DIR} into ${INDEX_NAME}..."
# skip some documents because they contain nested objects that distort the count
if [[ "${DOCUMENT_TYPE}" != "germplasmAttribute" && "${DOCUMENT_TYPE}" != "observationUnit" && "${DOCUMENT_TYPE}" != "datadiscovery" ]]; then
COUNT_EXTRACTED_DOCS=0
- for FILE in $(find ${DATA_DIR} -name ${DOCUMENT_TYPE}*.json.gz); do
+ for FILE in $(find ${DATA_DIR} -name ${DOCUMENT_TYPE}-*.json.gz); do
COUNT_FILE_DOCS=$(zcat ${FILE} | grep "\"_id\"" | sort | uniq | wc -l)
COUNT_EXTRACTED_DOCS=$((COUNT_EXTRACTED_DOCS+COUNT_FILE_DOCS))
done
--
GitLab
From dcd0a6eedf554ade6ae5aa4dac9c55292f348d4d Mon Sep 17 00:00:00 2001
From: jdestin <jeremy.destin@inra.fr>
Date: Thu, 28 Nov 2019 18:30:01 +0100
Subject: [PATCH 05/11] fix: Add missing fields in trial mapping
---
.../es/setup/index/trial_mapping.json | 25 ++++++++++++++++---
1 file changed, 22 insertions(+), 3 deletions(-)
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/trial_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/trial_mapping.json
index 4bde6c12..d03aed99 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/trial_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/trial_mapping.json
@@ -23,6 +23,9 @@
"commonCropName": {
"type": "keyword"
},
+ "trialDescription": {
+ "type": "keyword"
+ },
"documentationURL": {
"type": "keyword"
},
@@ -34,6 +37,16 @@
"type": "date",
"format": "YYYY-MM-dd"
},
+ "publications": {
+ "properties": {
+ "publicationReference": {
+ "type": "keyword"
+ },
+ "publicationPUI": {
+ "type": "keyword"
+ }
+ }
+ },
"programURIs": {
"type": "keyword"
},
@@ -69,6 +82,9 @@
"name": {
"type": "keyword"
},
+ "studyDescription": {
+ "type": "keyword"
+ },
"locationURI": {
"type": "keyword"
},
@@ -180,7 +196,7 @@
"type": "object",
"properties": {}
},
-
+
"source": {
"type": "keyword"
},
@@ -206,7 +222,7 @@
"type": "keyword"
}
}
- },
+ },
"datasetAuthorship": {
"properties": {
"license": {
@@ -247,6 +263,9 @@
"instituteName": {
"type": "keyword"
},
+ "institutionName": {
+ "type": "keyword"
+ },
"email": {
"type": "keyword"
},
@@ -268,7 +287,7 @@
"trialDbIds": {
"type": "keyword"
},
-
+
"source": {
"type": "keyword"
},
--
GitLab
From d225c3e5d910da56f6c6dc731f588af3c3623ca5 Mon Sep 17 00:00:00 2001
From: Celia Michotey <celia.michotey@inra.fr>
Date: Sun, 1 Dec 2019 16:28:34 +0100
Subject: [PATCH 06/11] Correct bugs.
---
scripts/harvest.sh | 17 ++++++++++-------
1 file changed, 10 insertions(+), 7 deletions(-)
diff --git a/scripts/harvest.sh b/scripts/harvest.sh
index 9b397ef9..a68dcdab 100755
--- a/scripts/harvest.sh
+++ b/scripts/harvest.sh
@@ -7,7 +7,8 @@ ES_PORT="9200"
ENV="dev"
DOCUMENT_TYPES="all"
-ALL_DOCUMENT_TYPES="germplasm germplasmMcpd germplasmAttribute germplasmPedigree germplasmProgeny location program study trial observationUnit datadiscovery"
+#ALL_DOCUMENT_TYPES="germplasm germplasmMcpd germplasmAttribute germplasmPedigree germplasmProgeny location program study trial observationUnit datadiscovery"
+ALL_DOCUMENT_TYPES="germplasm germplasmAttribute germplasmPedigree germplasmProgeny location program study trial observationUnit datadiscovery"
ALL_ENVS="dev beta staging int prod test"
BASEDIR=$(dirname "$0")
TMP_FILE="log.tmp"
@@ -25,7 +26,7 @@ DESCRIPTION:
Script used to index data in FAIDARE
USAGE:
- ${SCRIPT} -jsonDir <JSON directory> -es_host <Elasticsearch node host> -es_port <Elasticsearch node port> -env <application environment name> -type <document type(s) to index> [-h|--help]
+ ${SCRIPT} -jsonDir <JSON directory> -es_host <Elasticsearch node host> -es_port <Elasticsearch node port> -env <application environment name> -type <document type(s) to index> [-v|--verbose] [-h|--help]
PARAMS:
-jsonDir The directory where JSON bulk files to index are
@@ -105,10 +106,11 @@ if [ $(find ${DATA_DIR} -name *.json | wc -l) -le 0 ] && [ $(find ${DATA_DIR} -n
echo -e "${RED}ERROR: The JSON directory ${DATA_DIR} contains no JSON files!${NC}"
echo && help
fi
-[ "${DOCUMENT_TYPES}" == "all" ] && DOCUMENT_TYPES = "${ALL_DOCUMENT_TYPES}"
+[ "${DOCUMENT_TYPES}" == "all" ] && DOCUMENT_TYPES="${ALL_DOCUMENT_TYPES}"
for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
- if [ $(find ${DATA_DIR} -name ${DOCUMENT}*.json | wc -l) -le 0 ] && [ $(find ${DATA_DIR} -name ${DOCUMENT}*.json.gz | wc -l) -le 0 ]; then
- echo -e "${ORANGE}WARNING: The JSON directory ${DATA_DIR} contains no ${DOCUMENT} document!${NC}"
+ 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
@@ -221,9 +223,10 @@ for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
done
# Delete all but last created indices (thanks to the timestamp suffix)
- echo -e "* Delete old indices ${INDEX_PATTERN} (to avoid accumulation over time)..."
- OLD_INDICES=$(curl -sf -XGET "${ES_HOST}:${ES_PORT}/_cat/indices/${INDEX_PATTERN}?h=index" | sort | head -n -1)
+ echo -e "* Delete old indices ${INDEX_PATTERN} (to avoid accumulation over time):"
+ OLD_INDICES=$(curl -sf -XGET "${ES_HOST}:${ES_PORT}/_cat/indices/${INDEX_PATTERN}*?h=index" | sort | head -n -1)
for OLD_INDEX in ${OLD_INDICES}; do
+ echo -e "\t${OLD_INDEX}..."
LOG=$(curl -s -XDELETE "${ES_HOST}:${ES_PORT}/${OLD_INDEX}")
check_acknowledgment "${LOG}" "delete index ${OLD_INDEX}"
done
--
GitLab
From c066e35b55d302cf44deb54a9647beeaaad44e66 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rapha=C3=ABl=20Flores?= <raphael.flores@inra.fr>
Date: Thu, 6 Feb 2020 19:02:54 +0100
Subject: [PATCH 07/11] Increase the agg bucket size to fetch all existing
groupdId, allowing to create aliases for all of them, not only 10 by default.
---
scripts/harvest.sh | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/scripts/harvest.sh b/scripts/harvest.sh
index a68dcdab..24d877ea 100755
--- a/scripts/harvest.sh
+++ b/scripts/harvest.sh
@@ -189,7 +189,10 @@ for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
"size":"0",
"aggs" : {
"uniq_group" : {
- "terms" : { "field" : "groupId" }
+ "terms" : {
+ "field" : "groupId",
+ "size": 99999
+ }
}
}
}' | jq -cr '.aggregations.uniq_group.buckets[].key') # Extract ES aggregation bucket keys
--
GitLab
From e6b2ab1aeb2883826abcdbc0552cfc3c63b364b1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rapha=C3=ABl=20Flores?= <raphael.flores@inra.fr>
Date: Thu, 6 Feb 2020 19:04:10 +0100
Subject: [PATCH 08/11] Fixes quotes.
---
scripts/harvest.sh | 22 +++++++++++-----------
1 file changed, 11 insertions(+), 11 deletions(-)
diff --git a/scripts/harvest.sh b/scripts/harvest.sh
index 24d877ea..6949773f 100755
--- a/scripts/harvest.sh
+++ b/scripts/harvest.sh
@@ -22,7 +22,7 @@ NC='\033[0m' # No format
help() {
cat <<EOF
-DESCRIPTION:
+DESCRIPTION:
Script used to index data in FAIDARE
USAGE:
@@ -66,7 +66,7 @@ for PROGRAM in ${PROGRAMS}; do
((MISSING_COUNT += 1))
}
done
-if [ $MISSING_COUNT -ne 0 ]; then
+if [ $MISSING_COUNT -ne 0 ]; then
echo -e "${RED}ERROR: You must install the $MISSING_COUNT missing program(s).${NC}"
exit $MISSING_COUNT
fi
@@ -102,7 +102,7 @@ if [ ! -d "${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
@@ -115,7 +115,7 @@ for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
done
# Compress JSON files
-for FILE in $(find ${DATA_DIR} -name *.json); do
+for FILE in $(find ${DATA_DIR} -name "*.json"); do
gzip $FILE
done
@@ -130,38 +130,38 @@ for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
{
\"index_patterns\": [\"${INDEX_PATTERN}-*\"],
\"order\": 101,
- \"mappings\":
+ \"mappings\":
$(cat ${BASEDIR}/../backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/${DOCUMENT_TYPE}_mapping.json),
\"settings\": $(cat ${BASEDIR}/../backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/settings.json)
}")
check_acknowledgment "${LOG}" "create template"
-
+
# Index JSON Bulk
INDEX_NAME="${INDEX_PATTERN}-d"$(date +%s)
echo -e "* Index documents into ${ES_HOST}:${ES_PORT}/${INDEX_NAME} indice..."
{
parallel --bar "
curl -s -H 'Content-Type: application/x-ndjson' -H 'Content-Encoding: gzip' -H 'Accept-Encoding: gzip' -XPOST ${ES_HOST}:${ES_PORT}/${INDEX_NAME}/_bulk --data-binary '@{}' > {.}.log.gz" \
- ::: $(find ${DATA_DIR} -name ${DOCUMENT_TYPE}-*.json.gz)
+ ::: $(find ${DATA_DIR} -name "${DOCUMENT_TYPE}-*.json.gz")
} || {
code=$?
echo -e "${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}"
rm "${TMP_FILE}"
exit 1;
fi
-
+
# Check indexed data
echo -e "* Check data indexed from ${DATA_DIR} into ${INDEX_NAME}..."
# skip some documents because they contain nested objects that distort the count
if [[ "${DOCUMENT_TYPE}" != "germplasmAttribute" && "${DOCUMENT_TYPE}" != "observationUnit" && "${DOCUMENT_TYPE}" != "datadiscovery" ]]; then
COUNT_EXTRACTED_DOCS=0
- for FILE in $(find ${DATA_DIR} -name ${DOCUMENT_TYPE}-*.json.gz); do
+ for FILE in $(find ${DATA_DIR} -name "${DOCUMENT_TYPE}-*.json.gz"); do
COUNT_FILE_DOCS=$(zcat ${FILE} | grep "\"_id\"" | sort | uniq | wc -l)
COUNT_EXTRACTED_DOCS=$((COUNT_EXTRACTED_DOCS+COUNT_FILE_DOCS))
done
@@ -200,7 +200,7 @@ for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
echo -e "${RED}ERROR: could not list 'groupId' values from index.${NC}"
exit 1;
}
- echo -e "* Create aliases:"
+ echo -e "* Create aliases:"
for GROUP_ID in ${GROUP_IDS}; do
ALIAS_NAME="${INDEX_PATTERN}-group${GROUP_ID}"
FILTER=""
--
GitLab
From 62e1b4f43148e416bf8f7bd554d85d6516a3a615 Mon Sep 17 00:00:00 2001
From: Celia Michotey <celia.michotey@inra.fr>
Date: Wed, 19 Feb 2020 16:30:14 +0100
Subject: [PATCH 09/11] Update mappings to match the new sources JSON schemas.
---
.../es/setup/index/germplasm_mapping.json | 18 +++++++++
.../es/setup/index/location_mapping.json | 3 ++
.../es/setup/index/study_mapping.json | 10 +++++
.../es/setup/index/trial_mapping.json | 37 +++++++++++++------
4 files changed, 56 insertions(+), 12 deletions(-)
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json
index 3298d98a..cb66adb0 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json
@@ -35,6 +35,9 @@
"countryOfOriginCode": {
"type": "keyword"
},
+ "countryOfOrigin": {
+ "type": "keyword"
+ },
"defaultDisplayName": {
"type": "keyword"
},
@@ -557,6 +560,21 @@
}
}
},
+ "xref": {
+ "properties": {
+ "id": {
+ "type": "keyword"
+ },
+ "source": {
+ "type": "keyword"
+ }
+ }
+ },
+ "additionalInfo": {
+ "dynamic": "true",
+ "properties": {}
+ },
+
"studyURIs": {
"type": "keyword"
},
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/location_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/location_mapping.json
index 8ab41d2a..57c7ade3 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/location_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/location_mapping.json
@@ -23,6 +23,9 @@
"locationType": {
"type": "keyword"
},
+ "type": {
+ "type": "keyword"
+ },
"countryCode": {
"type": "keyword"
},
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/study_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/study_mapping.json
index d1f7286d..ea2a7e22 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/study_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/study_mapping.json
@@ -20,6 +20,16 @@
"commonCropName": {
"type": "keyword"
},
+ "cropDbId": {
+ "type": "keyword"
+ },
+ "statisticalDesign": {
+ "dynamic": "true",
+ "properties": {}
+ },
+ "description": {
+ "type": "keyword"
+ },
"organism": {
"type": "keyword"
},
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/trial_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/trial_mapping.json
index d03aed99..3793e3f8 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/trial_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/trial_mapping.json
@@ -23,7 +23,10 @@
"commonCropName": {
"type": "keyword"
},
- "trialDescription": {
+ "cropDbId": {
+ "type": "keyword"
+ },
+ "trialDescription": {
"type": "keyword"
},
"documentationURL": {
@@ -37,16 +40,16 @@
"type": "date",
"format": "YYYY-MM-dd"
},
- "publications": {
- "properties": {
- "publicationReference": {
- "type": "keyword"
- },
- "publicationPUI": {
- "type": "keyword"
- }
- }
- },
+ "publications": {
+ "properties": {
+ "publicationReference": {
+ "type": "keyword"
+ },
+ "publicationPUI": {
+ "type": "keyword"
+ }
+ }
+ },
"programURIs": {
"type": "keyword"
},
@@ -82,9 +85,12 @@
"name": {
"type": "keyword"
},
- "studyDescription": {
+ "studyDescription": {
"type": "keyword"
},
+ "description": {
+ "type": "keyword"
+ },
"locationURI": {
"type": "keyword"
},
@@ -100,6 +106,9 @@
"commonCropName": {
"type": "keyword"
},
+ "cropDbId": {
+ "type": "keyword"
+ },
"contactURIs": {
"type": "keyword"
},
@@ -130,6 +139,10 @@
"type": "date",
"format": "YYYY-MM-dd"
},
+ "lastUpdate": {
+ "dynamic": "true",
+ "properties": {}
+ },
"license": {
"type": "keyword"
},
--
GitLab
From 64a46400140d8d2a1cfb4443bc91c1307b25421d Mon Sep 17 00:00:00 2001
From: Celia Michotey <celia.michotey@inra.fr>
Date: Wed, 19 Feb 2020 16:31:40 +0100
Subject: [PATCH 10/11] Update filter request to correctly create group 0
aliases.
---
backend/src/main/resources/application.yml | 1 +
scripts/harvest.sh | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/backend/src/main/resources/application.yml b/backend/src/main/resources/application.yml
index 8f989fcc..28fa23c5 100644
--- a/backend/src/main/resources/application.yml
+++ b/backend/src/main/resources/application.yml
@@ -81,6 +81,7 @@ faidare:
url: https://terraref.org
name: TERRA-REF
image: https://urgi.versailles.inra.fr/files/faidare/logo/TERRAREF.png
+
server:
compression:
enabled: true
diff --git a/scripts/harvest.sh b/scripts/harvest.sh
index 6949773f..3d5504d1 100755
--- a/scripts/harvest.sh
+++ b/scripts/harvest.sh
@@ -205,7 +205,7 @@ for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
ALIAS_NAME="${INDEX_PATTERN}-group${GROUP_ID}"
FILTER=""
if [[ "$GROUP_ID" = "0" || "${GROUP_ID}" = "null" ]]; then
- FILTER="{ \"bool\" : { \"must_not\" : { \"exists\" : { \"field\" : \"groupId\" } } } }"
+ FILTER="{ \"bool\": { \"should\": [ { \"bool\": { \"must_not\": { \"exists\": { \"field\": \"groupId\" } } } }, { \"term\": { \"groupId\": 0 } } ] } }"
else
FILTER="{ \"term\" : { \"groupId\" : \"${GROUP_ID}\" } }"
fi
--
GitLab
From 21918f97a3063a120c82a1c1c3155026a8b28501 Mon Sep 17 00:00:00 2001
From: Celia Michotey <celia.michotey@inra.fr>
Date: Thu, 20 Feb 2020 14:38:39 +0100
Subject: [PATCH 11/11] Update tests to match mapping modifications.
---
.secrets.baseline | 271 ++++++++++++++----
.../domain/brapi/v1/data/BrapiLocation.java | 6 +-
.../urgi/faidare/domain/data/LocationVO.java | 28 +-
backend/src/main/resources/application.yml | 7 +-
.../repository/es/LocationRepositoryTest.java | 6 +-
.../es/setup/fixture/germplasm0.json | 2 +-
.../es/setup/fixture/location0.json | 4 +-
.../es/setup/index/germplasm_mapping.json | 4 +-
.../es/setup/index/location_mapping.json | 4 +-
frontend/src/app/brapi.service.spec.ts | 4 +-
frontend/src/app/map/map.component.spec.ts | 4 +-
frontend/src/app/models/brapi.model.ts | 4 +-
.../app/site-card/site-card.component.html | 4 +-
.../app/site-card/site-card.component.spec.ts | 4 +-
.../study-card/study-card.component.spec.ts | 8 +-
15 files changed, 259 insertions(+), 101 deletions(-)
diff --git a/.secrets.baseline b/.secrets.baseline
index e1fe1bd5..dc028389 100644
--- a/.secrets.baseline
+++ b/.secrets.baseline
@@ -1049,11 +1049,18 @@
}
],
"backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/datadiscovery_mapping.json": [
+ {
+ "hashed_secret": "344a627efbdf17dfc804f04e2eb1626843c0e825",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 36,
+ "type": "Base64 High Entropy String"
+ },
{
"hashed_secret": "d0346392c0a55403e2f845c277b44f3c2dd75356",
"is_secret": false,
"is_verified": false,
- "line_number": 73,
+ "line_number": 85,
"type": "Base64 High Entropy String"
}
],
@@ -1065,6 +1072,20 @@
"line_number": 2,
"type": "Base64 High Entropy String"
},
+ {
+ "hashed_secret": "33eaf59bec55989c018c03e0c08e7c84468d0989",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 5,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "00151beea622cd89dd76a49f565c0e0fedfda196",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 8,
+ "type": "Base64 High Entropy String"
+ },
{
"hashed_secret": "344a627efbdf17dfc804f04e2eb1626843c0e825",
"is_secret": false,
@@ -1074,134 +1095,169 @@
}
],
"backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmPedigree_mapping.json": [
+ {
+ "hashed_secret": "4e6b74a5f8dcffcf88aa65d37b9cc39350417075",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 5,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "7b498d397c91a97424810ee96fdedea25cd57ba1",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 8,
+ "type": "Base64 High Entropy String"
+ },
{
"hashed_secret": "344a627efbdf17dfc804f04e2eb1626843c0e825",
"is_secret": false,
"is_verified": false,
- "line_number": 29,
+ "line_number": 61,
"type": "Base64 High Entropy String"
},
{
"hashed_secret": "8aeabf21d3d9e270937890493769a88db1669c1c",
"is_secret": false,
"is_verified": false,
- "line_number": 41,
+ "line_number": 64,
"type": "Base64 High Entropy String"
}
],
"backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasmProgeny_mapping.json": [
{
- "hashed_secret": "8aeabf21d3d9e270937890493769a88db1669c1c",
+ "hashed_secret": "98a0735d3da290e8f12cccded043a0c03230aaa4",
"is_secret": false,
"is_verified": false,
- "line_number": 18,
+ "line_number": 5,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "58784c2b5d9df6ac722be78940aea4a78e53db6e",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 8,
"type": "Base64 High Entropy String"
},
{
"hashed_secret": "344a627efbdf17dfc804f04e2eb1626843c0e825",
"is_secret": false,
"is_verified": false,
- "line_number": 21,
+ "line_number": 25,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "8aeabf21d3d9e270937890493769a88db1669c1c",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 28,
"type": "Base64 High Entropy String"
}
],
"backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json": [
{
- "hashed_secret": "e74767ee7e0c0605639855344de4098474d6a035",
+ "hashed_secret": "344a627efbdf17dfc804f04e2eb1626843c0e825",
"is_secret": false,
"is_verified": false,
- "line_number": 11,
+ "line_number": 8,
"type": "Base64 High Entropy String"
},
{
- "hashed_secret": "344a627efbdf17dfc804f04e2eb1626843c0e825",
+ "hashed_secret": "ce74e278f4bd61efdd35fcdce522284654db7762",
"is_secret": false,
"is_verified": false,
- "line_number": 14,
+ "line_number": 25,
"type": "Base64 High Entropy String"
},
{
- "hashed_secret": "8aeabf21d3d9e270937890493769a88db1669c1c",
+ "hashed_secret": "012998a2c2a373295a416186fadd47092b8b6a18",
"is_secret": false,
"is_verified": false,
- "line_number": 17,
+ "line_number": 28,
"type": "Base64 High Entropy String"
},
{
- "hashed_secret": "ce74e278f4bd61efdd35fcdce522284654db7762",
+ "hashed_secret": "a577a4f5f8dab94eff3f257aec15319f14a8037a",
"is_secret": false,
"is_verified": false,
- "line_number": 51,
+ "line_number": 35,
"type": "Base64 High Entropy String"
},
{
- "hashed_secret": "a577a4f5f8dab94eff3f257aec15319f14a8037a",
+ "hashed_secret": "8aeabf21d3d9e270937890493769a88db1669c1c",
"is_secret": false,
"is_verified": false,
- "line_number": 54,
+ "line_number": 41,
"type": "Base64 High Entropy String"
},
{
- "hashed_secret": "8bc4d3d053073fb0ca1be835e7df704f5e9e59c8",
+ "hashed_secret": "e74767ee7e0c0605639855344de4098474d6a035",
"is_secret": false,
"is_verified": false,
- "line_number": 57,
+ "line_number": 44,
"type": "Base64 High Entropy String"
},
{
"hashed_secret": "d040d54181adb8004eb93b9aa8d524a9f9fd15e0",
"is_secret": false,
"is_verified": false,
- "line_number": 91,
+ "line_number": 52,
"type": "Base64 High Entropy String"
},
{
"hashed_secret": "bdc2a9b3bb8f37f0e0878203c438c5532311e456",
"is_secret": false,
"is_verified": false,
- "line_number": 94,
+ "line_number": 58,
"type": "Base64 High Entropy String"
},
{
"hashed_secret": "084c833a01fb1d770f994aaec6a07f282e41827a",
"is_secret": false,
"is_verified": false,
- "line_number": 137,
+ "line_number": 122,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "8bc4d3d053073fb0ca1be835e7df704f5e9e59c8",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 169,
"type": "Base64 High Entropy String"
},
{
"hashed_secret": "2a69cd41c702095b3a691f8af030a26c01c56f94",
"is_secret": false,
"is_verified": false,
- "line_number": 236,
+ "line_number": 262,
"type": "Base64 High Entropy String"
},
{
"hashed_secret": "a1a3ca02f085d8764199a02ec874180bc531044b",
"is_secret": false,
"is_verified": false,
- "line_number": 245,
+ "line_number": 271,
"type": "Base64 High Entropy String"
},
{
"hashed_secret": "52358cbf3e977b038f019edc3b5bbef04f6a8c32",
"is_secret": false,
"is_verified": false,
- "line_number": 271,
+ "line_number": 297,
"type": "Base64 High Entropy String"
},
{
"hashed_secret": "38d9070c435d5fc2e1186bf2c4ff4ddd39dc60c7",
"is_secret": false,
"is_verified": false,
- "line_number": 471,
+ "line_number": 497,
"type": "Base64 High Entropy String"
},
{
"hashed_secret": "78b81b0db9858bec686e7f868c87b47a49b94c8c",
"is_secret": false,
"is_verified": false,
- "line_number": 532,
+ "line_number": 558,
"type": "Base64 High Entropy String"
}
],
@@ -1210,100 +1266,121 @@
"hashed_secret": "e74767ee7e0c0605639855344de4098474d6a035",
"is_secret": false,
"is_verified": false,
- "line_number": 51,
+ "line_number": 35,
"type": "Base64 High Entropy String"
}
],
"backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/observationUnit_mapping.json": [
{
- "hashed_secret": "2551dc9d8bf4d26a73430ce6b030ed92e8d16c0e",
+ "hashed_secret": "0c0602d57a515d6428cbf114b34d7a22137d0021",
"is_secret": false,
"is_verified": false,
- "line_number": 14,
+ "line_number": 5,
"type": "Base64 High Entropy String"
},
{
- "hashed_secret": "2402e29f071d5850104e80f675c9cb1cc4667dc5",
+ "hashed_secret": "2551dc9d8bf4d26a73430ce6b030ed92e8d16c0e",
"is_secret": false,
"is_verified": false,
- "line_number": 23,
+ "line_number": 8,
"type": "Base64 High Entropy String"
},
{
"hashed_secret": "6002039add8a7885d38a6542bdce3acdaf936fb4",
"is_secret": false,
"is_verified": false,
- "line_number": 52,
+ "line_number": 11,
"type": "Base64 High Entropy String"
},
{
"hashed_secret": "344a627efbdf17dfc804f04e2eb1626843c0e825",
"is_secret": false,
"is_verified": false,
- "line_number": 58,
+ "line_number": 47,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "38d9070c435d5fc2e1186bf2c4ff4ddd39dc60c7",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 56,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "2402e29f071d5850104e80f675c9cb1cc4667dc5",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 65,
"type": "Base64 High Entropy String"
},
{
"hashed_secret": "2df7d10363b2ada000a8cc031ec38febf4b15876",
"is_secret": false,
"is_verified": false,
- "line_number": 64,
+ "line_number": 78,
"type": "Base64 High Entropy String"
},
{
- "hashed_secret": "921bd972137666fa4e9467b44243e0d5d3cee1fd",
+ "hashed_secret": "205078c35ddce349e66a7812e9eb6a964b7b2f0f",
"is_secret": false,
"is_verified": false,
- "line_number": 80,
+ "line_number": 91,
"type": "Base64 High Entropy String"
},
{
"hashed_secret": "aacf4ca2a9ef5d886765677f925013e7e90365f3",
"is_secret": false,
"is_verified": false,
- "line_number": 131,
+ "line_number": 94,
"type": "Base64 High Entropy String"
},
{
- "hashed_secret": "16446a8fe4999a2dc3381b100b249a63e8bc82af",
+ "hashed_secret": "fe4bdf7ff8c0bde6ff4a5fe73c3df64686b59da0",
"is_secret": false,
"is_verified": false,
- "line_number": 134,
+ "line_number": 101,
"type": "Base64 High Entropy String"
},
{
- "hashed_secret": "4b7ddad028dd65bc04a04513b452aa2075b986c7",
+ "hashed_secret": "41eb5625f5040c318ff364b48309d86d434f0309",
"is_secret": false,
"is_verified": false,
- "line_number": 137,
+ "line_number": 108,
"type": "Base64 High Entropy String"
},
{
- "hashed_secret": "fe4bdf7ff8c0bde6ff4a5fe73c3df64686b59da0",
+ "hashed_secret": "16446a8fe4999a2dc3381b100b249a63e8bc82af",
"is_secret": false,
"is_verified": false,
- "line_number": 140,
+ "line_number": 111,
"type": "Base64 High Entropy String"
},
{
- "hashed_secret": "abf79a44146478a20f13f902ae2a558dddba9840",
+ "hashed_secret": "4b7ddad028dd65bc04a04513b452aa2075b986c7",
"is_secret": false,
"is_verified": false,
- "line_number": 157,
+ "line_number": 114,
"type": "Base64 High Entropy String"
},
{
- "hashed_secret": "38d9070c435d5fc2e1186bf2c4ff4ddd39dc60c7",
+ "hashed_secret": "6337ad4b23e55afd26f8740749e57303c1eec31c",
"is_secret": false,
"is_verified": false,
- "line_number": 182,
+ "line_number": 162,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "921bd972137666fa4e9467b44243e0d5d3cee1fd",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 165,
"type": "Base64 High Entropy String"
},
{
"hashed_secret": "93e1c42e7930d5dbc24a9fec0d4f0f21a08c007b",
"is_secret": false,
"is_verified": false,
- "line_number": 194,
+ "line_number": 197,
"type": "Base64 High Entropy String"
}
],
@@ -1312,6 +1389,13 @@
"hashed_secret": "e74767ee7e0c0605639855344de4098474d6a035",
"is_secret": false,
"is_verified": false,
+ "line_number": 23,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "468ee5a5c55cfbe1809ed69e8f70cc085acb5df2",
+ "is_secret": false,
+ "is_verified": false,
"line_number": 29,
"type": "Base64 High Entropy String"
}
@@ -1340,25 +1424,46 @@
}
],
"backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/study_mapping.json": [
+ {
+ "hashed_secret": "21dd317a0556efd2b68ba31da5abdf544617c8a4",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 114,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "e74767ee7e0c0605639855344de4098474d6a035",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 155,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "c662a29dce3c6c5bea525be1a7fd7956ac1fae3b",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 201,
+ "type": "Base64 High Entropy String"
+ },
{
"hashed_secret": "e02307234404d08f6346900b32b17ca90f9c4ed8",
"is_secret": false,
"is_verified": false,
- "line_number": 60,
+ "line_number": 234,
"type": "Base64 High Entropy String"
},
{
- "hashed_secret": "f98c96dfd0a6ae593449b5dd101af7838d2e4837",
+ "hashed_secret": "dc30764ce81629f15d8423d97f5eaac8f86817bb",
"is_secret": false,
"is_verified": false,
- "line_number": 91,
+ "line_number": 237,
"type": "Base64 High Entropy String"
},
{
- "hashed_secret": "e74767ee7e0c0605639855344de4098474d6a035",
+ "hashed_secret": "f98c96dfd0a6ae593449b5dd101af7838d2e4837",
"is_secret": false,
"is_verified": false,
- "line_number": 122,
+ "line_number": 240,
"type": "Base64 High Entropy String"
}
],
@@ -1372,11 +1477,60 @@
}
],
"backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/trial_mapping.json": [
+ {
+ "hashed_secret": "c11c73c2efefc4ce6b873bb87ec5ef956b649367",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 45,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "278de07e8dd2362e5535d3d99fd2ed2120a59014",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 48,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "c662a29dce3c6c5bea525be1a7fd7956ac1fae3b",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 88,
+ "type": "Base64 High Entropy String"
+ },
{
"hashed_secret": "e74767ee7e0c0605639855344de4098474d6a035",
"is_secret": false,
"is_verified": false,
- "line_number": 89,
+ "line_number": 131,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "e02307234404d08f6346900b32b17ca90f9c4ed8",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 192,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "dc30764ce81629f15d8423d97f5eaac8f86817bb",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 195,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "f98c96dfd0a6ae593449b5dd101af7838d2e4837",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 198,
+ "type": "Base64 High Entropy String"
+ },
+ {
+ "hashed_secret": "21dd317a0556efd2b68ba31da5abdf544617c8a4",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 204,
"type": "Base64 High Entropy String"
}
],
@@ -2178,6 +2332,15 @@
"line_number": 170,
"type": "Base64 High Entropy String"
}
+ ],
+ "scripts/harvest.sh": [
+ {
+ "hashed_secret": "9b4ea0964706f977148ec989e7373d9622613547",
+ "is_secret": false,
+ "is_verified": false,
+ "line_number": 162,
+ "type": "Base64 High Entropy String"
+ }
]
},
"version": "0.13.0",
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiLocation.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiLocation.java
index 9a1a35a7..81ffd3a9 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiLocation.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/brapi/v1/data/BrapiLocation.java
@@ -51,15 +51,15 @@ public interface BrapiLocation extends HasBrapiDocumentationURL {
// Institution
@JsonView(JSONView.BrapiFields.class)
- String getInstitutionAddress();
+ String getInstituteAddress();
// For backward compatibility with brapi v1
@JsonView(JSONView.BrapiFields.class)
@Deprecated
- String getInstitutionAdress();
+ String getInstituteAdress();
@JsonView(JSONView.BrapiFields.class)
- String getInstitutionName();
+ String getInstituteName();
// Additional info
@JsonView(JSONView.BrapiFields.class)
diff --git a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/LocationVO.java b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/LocationVO.java
index f8dea56d..f22c2bf5 100644
--- a/backend/src/main/java/fr/inra/urgi/faidare/domain/data/LocationVO.java
+++ b/backend/src/main/java/fr/inra/urgi/faidare/domain/data/LocationVO.java
@@ -29,8 +29,8 @@ public class LocationVO implements GnpISInternal, BrapiLocation, HasURI, HasURL,
private String countryCode;
private String countryName;
- private String institutionAddress;
- private String institutionName;
+ private String instituteAddress;
+ private String instituteName;
private Double altitude;
private Double latitude;
@@ -111,19 +111,19 @@ public class LocationVO implements GnpISInternal, BrapiLocation, HasURI, HasURL,
}
@Override
- public String getInstitutionAddress() {
- return institutionAddress;
+ public String getInstituteAddress() {
+ return instituteAddress;
}
@Deprecated
@Override
- public String getInstitutionAdress() {
- return institutionAddress;
+ public String getInstituteAdress() {
+ return instituteAddress;
}
@Override
- public String getInstitutionName() {
- return institutionName;
+ public String getInstituteName() {
+ return instituteName;
}
@Override
@@ -184,16 +184,16 @@ public class LocationVO implements GnpISInternal, BrapiLocation, HasURI, HasURL,
this.countryName = countryName;
}
- public void setInstitutionAddress(String institutionAddress) {
- this.institutionAddress = institutionAddress;
+ public void setInstituteAddress(String instituteAddress) {
+ this.instituteAddress = instituteAddress;
}
- public void setInstitutionAdress(String institutionAdress) {
- this.institutionAddress = institutionAdress;
+ public void setInstituteAdress(String instituteAdress) {
+ this.instituteAddress = instituteAdress;
}
- public void setInstitutionName(String institutionName) {
- this.institutionName = institutionName;
+ public void setInstituteName(String instituteName) {
+ this.instituteName = instituteName;
}
public void setAltitude(Double altitude) {
diff --git a/backend/src/main/resources/application.yml b/backend/src/main/resources/application.yml
index 28fa23c5..d84119e5 100644
--- a/backend/src/main/resources/application.yml
+++ b/backend/src/main/resources/application.yml
@@ -66,12 +66,7 @@ faidare:
url: http://tropgenedb.cirad.fr
name: CIRAD TropGENE
image: https://urgi.versailles.inra.fr/files/faidare/logo/CIRAD.jpg
- # EVA
- - uri: https://www.ebi.ac.uk/eva
- url: https://www.ebi.ac.uk/eva
- name: EVA
- image: https://urgi.versailles.inra.fr/files/faidare/logo/EVA.png
- # ENA
+ # EVA/ENA
- uri: https://www.ebi.ac.uk/eva
url: https://www.ebi.ac.uk/eva
name: EBI European Nucleotide Archive
diff --git a/backend/src/test/java/fr/inra/urgi/faidare/repository/es/LocationRepositoryTest.java b/backend/src/test/java/fr/inra/urgi/faidare/repository/es/LocationRepositoryTest.java
index 879ce410..88bcef7e 100644
--- a/backend/src/test/java/fr/inra/urgi/faidare/repository/es/LocationRepositoryTest.java
+++ b/backend/src/test/java/fr/inra/urgi/faidare/repository/es/LocationRepositoryTest.java
@@ -75,16 +75,16 @@ class LocationRepositoryTest {
@SuppressWarnings("deprecation")
@Test
- void should_Have_Same_InstitutionAddress_And_InstitutionAdress() {
+ void should_Have_Same_InstituteAddress_And_InstituteAdress() {
// 805
LocationVO result = repository.getById("805");
assertThat(result).isNotNull();
- assertThat(result.getInstitutionAddress()).isNotBlank().isEqualTo(result.getInstitutionAdress());
+ assertThat(result.getInstituteAddress()).isNotBlank().isEqualTo(result.getInstituteAdress());
// 806
result = repository.getById("806");
assertThat(result).isNotNull();
- assertThat(result.getInstitutionAddress()).isNotBlank().isEqualTo(result.getInstitutionAdress());
+ assertThat(result.getInstituteAddress()).isNotBlank().isEqualTo(result.getInstituteAdress());
}
@Test
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/fixture/germplasm0.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/fixture/germplasm0.json
index 041375e5..6d275e99 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/fixture/germplasm0.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/fixture/germplasm0.json
@@ -26,7 +26,7 @@
"species": "melongena"
},
{
- "docId": "ZG9pOjEwLjE1NDU0LzEuNDkyMTc4NjY1NTk0NDEwNkUxMg==",
+ "germplasmDbId": "ZG9pOjEwLjE1NDU0LzEuNDkyMTc4NjY1NTk0NDEwNkUxMg==",
"accessionNumber": "A0336",
"genus": "Solanum",
"species": "melongena"
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/fixture/location0.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/fixture/location0.json
index 3fa15aeb..97e29895 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/fixture/location0.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/fixture/location0.json
@@ -3,14 +3,14 @@
"locationDbId": "805",
"name": "L805",
"locationType": "Breeding and Evaluation site",
- "institutionAdress": "Add 805",
+ "instituteAdress": "Add 805",
"abbreviation": "AL805"
},
{
"locationDbId": "806",
"locationName": "L806",
"locationType": "Breeding and Evaluation site",
- "institutionAddress": "Add 806",
+ "instituteAddress": "Add 806",
"abreviation": "AL806"
},
{
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json
index cb66adb0..359f0616 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/germplasm_mapping.json
@@ -36,8 +36,8 @@
"type": "keyword"
},
"countryOfOrigin": {
- "type": "keyword"
- },
+ "type": "keyword"
+ },
"defaultDisplayName": {
"type": "keyword"
},
diff --git a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/location_mapping.json b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/location_mapping.json
index 57c7ade3..06aad559 100644
--- a/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/location_mapping.json
+++ b/backend/src/test/resources/fr/inra/urgi/faidare/repository/es/setup/index/location_mapping.json
@@ -24,8 +24,8 @@
"type": "keyword"
},
"type": {
- "type": "keyword"
- },
+ "type": "keyword"
+ },
"countryCode": {
"type": "keyword"
},
diff --git a/frontend/src/app/brapi.service.spec.ts b/frontend/src/app/brapi.service.spec.ts
index 58330188..5466b472 100644
--- a/frontend/src/app/brapi.service.spec.ts
+++ b/frontend/src/app/brapi.service.spec.ts
@@ -27,8 +27,8 @@ describe('BrapiService', () => {
abbreviation: null,
countryCode: 'Fr',
countryName: 'France',
- institutionAddress: null,
- institutionName: 'Insti',
+ instituteAddress: null,
+ instituteName: 'Insti',
altitude: null,
latitude: null,
longitude: null,
diff --git a/frontend/src/app/map/map.component.spec.ts b/frontend/src/app/map/map.component.spec.ts
index 275f0291..7a0b4df3 100644
--- a/frontend/src/app/map/map.component.spec.ts
+++ b/frontend/src/app/map/map.component.spec.ts
@@ -11,8 +11,8 @@ describe('MapComponent', () => {
latitude: 1,
longitude: 1,
altitude: 1,
- institutionName: '',
- institutionAddress: '',
+ instituteName: '',
+ instituteAddress: '',
countryName: '',
countryCode: '',
locationType: '',
diff --git a/frontend/src/app/models/brapi.model.ts b/frontend/src/app/models/brapi.model.ts
index 7b28c9c5..c758338c 100644
--- a/frontend/src/app/models/brapi.model.ts
+++ b/frontend/src/app/models/brapi.model.ts
@@ -70,8 +70,8 @@ export interface BrapiLocation extends BrapiHasDocumentationURL, schema.Dataset
abbreviation?: string;
countryCode?: string;
countryName?: string;
- institutionAddress?: string;
- institutionName?: string;
+ instituteAddress?: string;
+ instituteName?: string;
altitude?: number;
latitude: number;
longitude: number;
diff --git a/frontend/src/app/site-card/site-card.component.html b/frontend/src/app/site-card/site-card.component.html
index 89712a2f..928a341b 100644
--- a/frontend/src/app/site-card/site-card.component.html
+++ b/frontend/src/app/site-card/site-card.component.html
@@ -42,12 +42,12 @@
<faidare-card-row
label="Institution/Landowner"
- [value]="location.institutionName">
+ [value]="location.instituteName">
</faidare-card-row>
<faidare-card-row
label="Institution address"
- [value]="location.institutionAddress">
+ [value]="location.instituteAddress">
</faidare-card-row>
<faidare-card-row
diff --git a/frontend/src/app/site-card/site-card.component.spec.ts b/frontend/src/app/site-card/site-card.component.spec.ts
index fdf9e83b..a739104e 100644
--- a/frontend/src/app/site-card/site-card.component.spec.ts
+++ b/frontend/src/app/site-card/site-card.component.spec.ts
@@ -36,8 +36,8 @@ describe('SiteCardComponent', () => {
latitude: 1,
longitude: 1,
altitude: 1,
- institutionName: '',
- institutionAddress: '',
+ instituteName: '',
+ instituteAddress: '',
countryName: '',
countryCode: '',
locationType: '',
diff --git a/frontend/src/app/study-card/study-card.component.spec.ts b/frontend/src/app/study-card/study-card.component.spec.ts
index 0761e873..22eb6e08 100644
--- a/frontend/src/app/study-card/study-card.component.spec.ts
+++ b/frontend/src/app/study-card/study-card.component.spec.ts
@@ -73,8 +73,8 @@ describe('StudyCardComponent', () => {
abbreviation: null,
countryCode: 'Fr',
countryName: 'France',
- institutionAddress: null,
- institutionName: 'Insti',
+ instituteAddress: null,
+ instituteName: 'Insti',
altitude: null,
latitude: null,
longitude: null,
@@ -90,8 +90,8 @@ describe('StudyCardComponent', () => {
abbreviation: null,
countryCode: 'Fr',
countryName: 'France',
- institutionAddress: null,
- institutionName: 'Insti',
+ instituteAddress: null,
+ instituteName: 'Insti',
altitude: null,
latitude: 48.8534,
longitude: 2.3488,
--
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