diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 55cc1ad5826136eeb8c81fdacaf86e62fae8453d..a7f52743f98cccd1c355fd7a5ea54c602a16924f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -8,7 +8,7 @@ stages:
- deploy-production
-image: registry.forgemia.inra.fr/urgi-is/docker-rare/docker-browsers:latest
+image: circleci/openjdk:11-jdk-browsers
# Disable the Gradle daemon for Continuous Integration servers as correctness
@@ -26,10 +26,10 @@ variables:
DOCKER_OPTS: "--mtu=1450"
# Gradle cache for all jobs
-cache:
- key: "$CI_COMMIT_REF_NAME"
- paths:
- - ".gradle"
+# cache:
+# key: "$CI_COMMIT_REF_NAME"
+# paths:
+# - ".gradle"
# PRE-BUILD
@@ -60,6 +60,7 @@ build-loader-docker-image:
# TESTS
test-and-sonarqube:
+ # image: circleci/openjdk:11-jdk-browsers
stage: test
tags:
- openstack
@@ -79,18 +80,20 @@ test-and-sonarqube:
# `max virtual memory areas vm.max_map_count [65530] is too low, increase to at least [262144]`
command: ["bin/elasticsearch", "-Ediscovery.type=single-node"]
variables:
- GRADLE_OPTS: "-Xms512m -Xmx8192m -XX:MaxMetaspaceSize=8192m -Dorg.gradle.daemon=false"
- SONAR_USER_HOME: "${CI_PROJECT_DIR}/.sonar" # Defines the location of the analysis task cache
- GIT_DEPTH: "0" # Tells git to fetch all the branches of the project, required by the analysis task
+ # GRADLE_OPTS: "-Xms512m -Xmx8192m -XX:MaxMetaspaceSize=8192m -Dorg.gradle.daemon=false"
+ # SONAR_USER_HOME: "${CI_PROJECT_DIR}/.sonar" # Defines the location of the analysis task cache
+ # GIT_DEPTH: "0" # Tells git to fetch all the branches of the project, required by the analysis task
ES_JAVA_OPTS: "-Xms2g -Xmx2g"
- cache:
- key: "${CI_COMMIT_REF_NAME}"
- policy: pull-push
- paths:
- - ".gradle"
- - .sonar/cache
+ # cache:
+ # key: "${CI_COMMIT_REF_NAME}"
+ # policy: pull-push
+ # paths:
+ # # - ".gradle"
+ # - .sonar/cache
script:
- - ./gradlew test jacocoTestReport -s sonarqube
+ # - ls -lshR /builds/urgi-is/faidare/.gradle/wrapper/dists/gradle-7.4.1-bin/58kw26xllvsiedyf3nujyarhn
+ - ./gradlew clean test
+ # jacocoTestReport -s sonarqube
artifacts:
reports:
junit:
@@ -98,6 +101,7 @@ test-and-sonarqube:
rules:
- if: $CI_PIPELINE_SOURCE == "merge_request_event" || $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
interruptible: true
+ allow_failure: false
# BUILD
build:
@@ -106,11 +110,11 @@ build:
stage: build
script:
- ./gradlew assemble
- cache:
- key: "${CI_COMMIT_REF_NAME}"
- policy: pull
- paths:
- - ".gradle"
+ # cache:
+ # key: "${CI_COMMIT_REF_NAME}"
+ # policy: pull
+ # paths:
+ # - ".gradle"
artifacts:
paths:
- "$JAR_PATH"
diff --git a/ABOUT.md b/ABOUT.md
index 3153002be6f3231e3423893f3d91c88ef332e8a1..74858069932c922249f65bffdb74b741bf5c2e57 100644
--- a/ABOUT.md
+++ b/ABOUT.md
@@ -8,6 +8,6 @@ It also provides a standard interface that can be accessed programatically throu
It is an extension of the generic [Data-Discovery portal](https://forgemia.inra.fr/urgi-is/data-discovery), a web portal that allows finding any type of data across several databases through a lightweight keyword based search.
FAIDARE offers more detailed search and data retrieval capabilities and it takes advantage of the growing adoption of the BrAPI.
-It has been developed by [INRAE-URGI](http://urgi.versailles.inrae.fr/) in collaboration with [**Elixir Plant**](https://elixir-europe.org/communities/plant-sciences), [**Phenome-Emphasis.fr**](https://www.phenome-emphasis.fr/phenome_eng/Methodological-projects/MCP2-Distributed-Information-system) and [**Elixir-fr/IFB**](https://www.france-bioinformatique.fr).
+It has been developed by [INRAE-URGI](https://urgi.versailles.inrae.fr/) in collaboration with [**Elixir Plant**](https://elixir-europe.org/communities/plant-sciences), [**Phenome-Emphasis.fr**](https://www.phenome-emphasis.fr/phenome_eng/Methodological-projects/MCP2-Distributed-Information-system) and [**Elixir-fr/IFB**](https://www.france-bioinformatique.fr).
If you want to join the FAIDARE federation, please read the "Join us" section and [contact us](mailto:urgi-contact@inrae.fr?subject=%5BFAIDARE%5D).
diff --git a/backend/src/main/resources/application.yml b/backend/src/main/resources/application.yml
index 9cce0f6a869386f51c7b4fd726c61079791de4ba..c5810a44a99aeebe5dd0d5b489edacc8d4a33d9d 100644
--- a/backend/src/main/resources/application.yml
+++ b/backend/src/main/resources/application.yml
@@ -90,6 +90,12 @@ faidare:
url: https://terraref.org
name: TERRA-REF
image: https://urgi.versailles.inrae.fr/files/faidare/logo/TERRAREF.png
+ # DDBJ
+ - uri: https://ddbj.nig.ac.jp
+ url: https://ddbj.nig.ac.jp
+ name: DDBJ
+ image: https://www.ddbj.nig.ac.jp/../images/logotype.svg
+
server:
compression:
diff --git a/scripts/harvest.sh b/scripts/harvest.sh
index 183f9f479e7fe8995dac56da85997a470c4dcc37..0bd5f7f5c8233b4f587ad309e334bc210eceafe9 100755
--- a/scripts/harvest.sh
+++ b/scripts/harvest.sh
@@ -159,12 +159,23 @@ for DOCUMENT_TYPE in ${DOCUMENT_TYPES}; do
check_acknowledgment "${LOG}" "create template"
# Index JSON Bulk
- INDEX_NAME="${INDEX_PATTERN}-d"$(date +%s)
+ TIMESTAMP=$(date +%s)
+ export TIMESTAMP
+ INDEX_NAME="${INDEX_PATTERN}-d"${TIMESTAMP}
echo -e "* Index documents into ${ES_HOST}:${ES_PORT}/${INDEX_NAME} indice..."
{
parallel -j 4 --bar index_resources {1} {1/.} ::: "$(find "${DATA_DIR}" -name "${DOCUMENT_TYPE}-*.json.gz")"
}
+ log_actions() {
+ if [ -n "$LOGIN" ]; then
+ echo "Indexed $INDEX_PATTERN on: $(date -d @$TIMESTAMP +%Y-%m-%d_%Hh-%Mm-%Ss) (TIMESTAMP=$TIMESTAMP) by: $LOGIN ; used data from $DATA_DIR which last commit was: $(cd "$DATA_DIR" || exit 1 ; git log --oneline|head -1)" >> ~/last_index.log
+ else
+ echo "WARN: no LOGIN variable found. Logging actions is not possible. If you are not launching the scripts from the ETL VM, you can safely ignore this message."
+ fi
+ }
+log_actions
+
# check all JQ err files...
FILES_IN_ERROR=$(find "${OUTDIR}" -size "+0" -name "*${DOCUMENT_TYPE}*jq.err")
[ -n "${FILES_IN_ERROR}" ] && { echo -e "${RED}ERROR: some problems occured with JQ processing, look at files:${ORANGE} ${FILES_IN_ERROR}${NC}" ; exit 4 ; }