Merge branch 'chore/rename_rare-with-basket' into 'master'

Rename 'rare-with-basket' in 'brc4env'. GNP-5796.

See merge request urgi-is/data-discovery!314

.gitlab-ci.yml

@@ -205,9 +205,9 @@ build-rare:
   APP_NAME: ${RARE_APP_NAME}
  <<: *build_app           # Merge the contents of the 'build_app' alias
 
-build-rare-with-basket:
+build-brc4env:
  variables:
-  APP_NAME: "rare-with-basket"
+  APP_NAME: "brc4env"
  <<: *build_app           # Merge the contents of the 'build_app' alias
 
 build-wheatis:
@@ -309,11 +309,11 @@ build-data-discovery:
   ES_PORT: ${ES_DEV_PORT} # TODO: TO BE FIXED WHEN PROD CLUSTER AVAILABLE IN OPENSTACK
   APP_CONTEXT: ${APP_NAME}
 
-.variables-rare-with-basket-beta-openstack: &variables-rare-with-basket-beta-openstack
+.variables-brc4env-beta-openstack: &variables-brc4env-beta-openstack
  variables:
   ENV: beta
-  APP_NAME: rare-with-basket
-  APP_PORT: ${BETA_RARE_WITH_BASKET_PORT}
+  APP_NAME: brc4env
+  APP_PORT: ${BETA_BRC4ENV_PORT}
   DATA_DIR: rare
   SERVER_IP: ${SERVER_IP_OPENSTACK}
   SERVER_USER: ${SERVER_USER_OPENSTACK}
@@ -322,11 +322,11 @@ build-data-discovery:
   ES_PORT: ${ES_DEV_PORT}
   APP_CONTEXT: ${APP_NAME}
 
-.variables-rare-with-basket-staging-openstack: &variables-rare-with-basket-staging-openstack
+.variables-brc4env-staging-openstack: &variables-brc4env-staging-openstack
  variables:
   ENV: staging
-  APP_NAME: rare-with-basket
-  APP_PORT: ${STAGING_RARE_WITH_BASKET_PORT}
+  APP_NAME: brc4env
+  APP_PORT: ${STAGING_BRC4ENV_PORT}
   DATA_DIR: rare
   SERVER_IP: ${SERVER_IP_OPENSTACK}
   SERVER_USER: ${SERVER_USER_OPENSTACK}
@@ -336,13 +336,13 @@ build-data-discovery:
   APP_CONTEXT: ${APP_NAME}
 
 # ALPHA
-.variables-rare-with-basket-prod-openstack: &variables-rare-with-basket-prod-openstack
+.variables-brc4env-prod-openstack: &variables-brc4env-prod-openstack
  variables:
   ENV: prod
-  APP_NAME: rare-with-basket
-  APP_PORT: ${PROD_RARE_WITH_BASKET_PORT}
+  APP_NAME: brc4env
+  APP_PORT: ${PROD_BRC4ENV_PORT}
   DATA_DIR: rare
-  SERVER_IP: ${SERVER_IP_OPENSTACK}
+  SERVER_IP: ${SERVER_IP_OPENSTACK_PROD}
   SERVER_USER: ${SERVER_USER_OPENSTACK}
   ES_HOST: ${ES_PROD_HOST_OPENSTACK} # TODO: TO BE FIXED WHEN PROD CLUSTER AVAILABLE IN OPENSTACK
   ES_HOSTS: ${ES_PROD_HOSTS_OPENSTACK} # TODO: TO BE FIXED WHEN PROD CLUSTER AVAILABLE IN OPENSTACK
@@ -516,11 +516,11 @@ deploy-rare-to-prod-openstack:
  when: manual
  allow_failure: false
 
-deploy-rare-with-basket-to-beta-openstack:
+deploy-brc4env-to-beta-openstack:
  stage: deploy-beta
  tags:
   - openstack
- <<: *variables-rare-with-basket-beta-openstack
+ <<: *variables-brc4env-beta-openstack
  <<: *deploy_to_vm_openstack
  only:
   changes:
@@ -533,11 +533,11 @@ deploy-rare-with-basket-to-beta-openstack:
    - master
  allow_failure: false # mandatory to block the execution of the pipeline
 
-deploy-rare-with-basket-to-staging-openstack:
+deploy-brc4env-to-staging-openstack:
  stage: deploy-staging
  tags:
   - openstack
- <<: *variables-rare-with-basket-staging-openstack
+ <<: *variables-brc4env-staging-openstack
  <<: *deploy_to_vm_openstack
  only:
   changes:
@@ -551,11 +551,11 @@ deploy-rare-with-basket-to-staging-openstack:
  when: manual
 
 # ALPHA
-deploy-rare-with-basket-to-prod-openstack:
+deploy-brc4env-to-prod-openstack:
  stage: deploy-production
  tags:
   - openstack
- <<: *variables-rare-with-basket-prod-openstack
+ <<: *variables-brc4env-prod-openstack
  <<: *deploy_to_vm_openstack
  only:
   changes:
@@ -794,16 +794,16 @@ data-integration-rare-prod-openstack:
   refs:
    - master
 
-data-integration-rare-with-basket-beta-openstack:
+data-integration-brc4env-beta-openstack:
  stage: data-integration-beta
  tags:
   - openstack
- <<: *variables-rare-with-basket-beta-openstack
+ <<: *variables-brc4env-beta-openstack
  <<: *data-integration-openstack
  only:
   changes:
    - data/rare/*.json.gz
-   - data/rare/suggestions/rare-with-basket_bulk*.json.gz
+   - data/rare/suggestions/brc4env_bulk*.json.gz
    - scripts/*
   refs:
    - branches
@@ -811,16 +811,16 @@ data-integration-rare-with-basket-beta-openstack:
   refs:
    - master
 
-data-integration-rare-with-basket-staging-openstack:
+data-integration-brc4env-staging-openstack:
  stage: data-integration-staging
  tags:
   - openstack
- <<: *variables-rare-with-basket-staging-openstack
+ <<: *variables-brc4env-staging-openstack
  <<: *data-integration-openstack
  only:
   changes:
    - data/rare/*.json.gz
-   - data/rare/suggestions/rare-with-basket_bulk*.json.gz
+   - data/rare/suggestions/brc4env_bulk*.json.gz
    - scripts/*
   refs:
    - branches
@@ -830,16 +830,16 @@ data-integration-rare-with-basket-staging-openstack:
  when: manual
 
 # ALPHA
-data-integration-rare-with-basket-prod-openstack:
+data-integration-brc4env-prod-openstack:
  stage: data-integration-production
  tags:
   - openstack
- <<: *variables-rare-with-basket-prod-openstack
+ <<: *variables-brc4env-prod-openstack
  <<: *data-integration-openstack
  only:
   changes:
    - data/rare/*.json.gz
-   - data/rare/suggestions/rare-with-basket_bulk*.json.gz
+   - data/rare/suggestions/brc4env_bulk*.json.gz
    - scripts/*
   refs:
    - master

README.md

@@ -102,7 +102,7 @@ Then run `yarn start` to start the app, using the proxy conf to reroute calls to
 The application will be available on:
 
 - <http://localhost:4000/rare-dev> for RARe (runs with: `yarn start:rare` or simply `yarn start`)
-- <http://localhost:4000/rare-dev> for RARe with basket (runs with: `yarn start:rare-with-basket`)
+- <http://localhost:4000/rare-dev> for RARe with basket (runs with: `yarn start:brc4env`)
 - <http://localhost:4100/wheatis-dev> for WheatIS (runs with: `yarn start:wheatis`)
 - <http://localhost:4200/data-discovery-dev> for DataDiscovery (runs with: `yarn start:data-discovery`)
 
@@ -125,14 +125,14 @@ or
 or
 
 ```sh
-./gradlew assemble -Papp=rare-with-basket
+./gradlew assemble -Papp=brc4env
 ```
 
 This will build a standalone jar at `backend/build/libs/`, that you can run with either:
 
 ```sh
 java -jar backend/build/libs/rare.jar
-java -jar backend/build/libs/rare-with-basket.jar
+java -jar backend/build/libs/brc4env.jar
 java -jar backend/build/libs/wheatis.jar
 java -jar backend/build/libs/data-discovery.jar
 ```
@@ -142,7 +142,7 @@ And the full app running on:
 - <http://localhost:8080/rare-dev>
 - <http://localhost:8180/wheatis-dev>
 - <http://localhost:8280/data-discovery-dev>
-- <http://localhost:8580/rare-with-basket-dev>
+- <http://localhost:8580/brc4env-dev>
 
 ## CI
 
@@ -264,20 +264,20 @@ You can also run the backend WheatIS application using
 To assemble the RARe app with support for adding accessions to a basket, run the following command
 
 ```sh
-./gradlew assemble -Papp=rare-with-basket
+./gradlew assemble -Papp=brc4env
 ```
 
 You can also run the backend RARe application with basket support using
 
 ```sh
-./gradlew bootRun -Papp=rare-with-basket
+./gradlew bootRun -Papp=brc4env
 ```
 
 Adding this property has the following consequences:
 
-- the generated jar file (in `backend/build/libs`) is named `wheatis.jar` (resp. `rare-with-basket.jar` instead of `rare.jar`;
-- the Spring active profile in `bootstrap.yml` is `wheatis-app` (resp. `rare-with-basket-app`) instead of `rare-app`;
-- the frontend application built and embedded inside the jar file is the WheatIS frontend application (resp. the RARe application with basket support) instead of the RARe frontend application, i.e. the frontend command `yarn build:wheatis` (resp. `yarn build:rare-with-basket`) is executed instead of the command `yarn:rare`.
+- the generated jar file (in `backend/build/libs`) is named `wheatis.jar` (resp. `brc4env.jar` instead of `rare.jar`;
+- the Spring active profile in `bootstrap.yml` is `wheatis-app` (resp. `brc4env-app`) instead of `rare-app`;
+- the frontend application built and embedded inside the jar file is the WheatIS frontend application (resp. the RARe application with basket support) instead of the RARe frontend application, i.e. the frontend command `yarn build:wheatis` (resp. `yarn build:brc4env`) is executed instead of the command `yarn:rare`.
 
 Since the active Spring profile is different, all the properties specific to this profile
 are applied. In particular:

backend/src/main/java/fr/inra/urgi/datadiscovery/config/AppProfile.java

@@ -9,7 +9,7 @@ package fr.inra.urgi.datadiscovery.config;
 public final class AppProfile {
 
     public static final String RARE = "rare-app";
-    public static final String RARE_WITH_BASKET = "rare-with-basket-app";
+    public static final String BRC4ENV = "brc4env-app";
     public static final String WHEATIS = "wheatis-app";
     public static final String DATADISCOVERY = "data-discovery-app";
 

backend/src/main/java/fr/inra/urgi/datadiscovery/config/RareImplicitRefinementsProperties.java

@@ -8,7 +8,7 @@ import fr.inra.urgi.datadiscovery.dao.rare.RareImplicitAggregation;
 import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.context.annotation.Profile;
 
-@Profile({AppProfile.RARE, AppProfile.RARE_WITH_BASKET})
+@Profile({AppProfile.RARE, AppProfile.BRC4ENV})
 @ConfigurationProperties(prefix = "rare")
 public class RareImplicitRefinementsProperties {
     private Map<RareImplicitAggregation, Set<String>> implicitTerms = new HashMap<>();

backend/src/main/java/fr/inra/urgi/datadiscovery/dao/rare/RareAggregationAnalyzer.java

@@ -17,7 +17,7 @@ import org.springframework.stereotype.Component;
  * @author JB Nizet
  */
 @Component
-@Profile({AppProfile.RARE, AppProfile.RARE_WITH_BASKET})
+@Profile({AppProfile.RARE, AppProfile.BRC4ENV})
 public class RareAggregationAnalyzer implements AggregationAnalyzer {
     private static final List<AppAggregation> AGGREGATIONS =
         Collections.unmodifiableList(Arrays.asList(RareAggregation.values()));

backend/src/main/java/fr/inra/urgi/datadiscovery/dao/rare/RareDocumentDao.java

@@ -9,7 +9,7 @@ import org.springframework.context.annotation.Profile;
 /**
  * DAO for {@link RareDocument}
  */
-@Profile({AppProfile.RARE, AppProfile.RARE_WITH_BASKET})
+@Profile({AppProfile.RARE, AppProfile.BRC4ENV})
 public interface RareDocumentDao
     extends DocumentDao<RareDocument, RareIndexedDocument>, RareDocumentDaoCustom {
 }

backend/src/main/resources/application.yml

@@ -48,7 +48,6 @@ spring:
 
 data-discovery:
   elasticsearch-prefix: 'rare-dev-'
-  resource-dir: /tmp/rare-dev/resources
 
 server:
   port: 8080
@@ -57,28 +56,27 @@ server:
 
 ---
 spring:
-  profiles: rare-with-basket-app
-  cloud.config.name: rare-with-basket
+  profiles: brc4env-app
+  cloud.config.name: brc4env
   security.user:
     name: rare
     password: f01a7031fc17
 
 ## Below properties should not be enabled here because it makes tests failing.
 ## But they may be enabled in cloud-config server if relevant to apply the 
-## filter (for rare-with-basket) or not (for main rare application)
+## filter (for brc4env) or not (for main rare application)
 # rare:
 #   implicit-terms:
 #     PILLAR:
 #       - Pilier Environnement
 
 data-discovery:
-  elasticsearch-prefix: 'rare-with-basket-dev-'
-  resource-dir: /tmp/rare-dev/resources
+  elasticsearch-prefix: 'brc4env-dev-'
 
 server:
   port: 8580
   servlet:
-    context-path: /rare-with-basket-dev
+    context-path: /brc4env-dev
 
 ---
 spring:
@@ -90,7 +88,6 @@ spring:
 
 data-discovery:
   elasticsearch-prefix: 'wheatis-dev-'
-  resource-dir: /tmp/wheatis-dev/resources
 
 server:
   port: 8180
@@ -107,7 +104,6 @@ spring:
 
 data-discovery:
   elasticsearch-prefix: 'data-discovery-dev-'
-  resource-dir: /tmp/data-discovery-dev/resources
 
 server:
   port: 8280

backend/src/test/java/fr/inra/urgi/datadiscovery/RareWithBasketApplicationTest.java

@@ -15,7 +15,7 @@ import org.springframework.test.context.junit.jupiter.SpringExtension;
 @ExtendWith(SpringExtension.class)
 @SpringBootTest
 @TestPropertySource("/test-rare.properties")
-@ActiveProfiles(AppProfile.RARE_WITH_BASKET)
+@ActiveProfiles(AppProfile.BRC4ENV)
 public class RareWithBasketApplicationTest {
     @Test
     public void shouldLoadContext() {}

backend/src/test/java/fr/inra/urgi/datadiscovery/dao/rare/RareDocumentDaoTest.java

@@ -42,7 +42,7 @@ import org.springframework.test.context.junit.jupiter.SpringExtension;
 @Import(ElasticSearchConfig.class)
 @JsonTest
 @TestInstance(TestInstance.Lifecycle.PER_CLASS)
-@ActiveProfiles({AppProfile.RARE, AppProfile.RARE_WITH_BASKET})
+@ActiveProfiles({AppProfile.RARE, AppProfile.BRC4ENV})
 class RareDocumentDaoTest extends DocumentDaoTest {
 
     private static final String PHYSICAL_INDEX = "test-rare-resource-physical-index";

backend/src/test/java/fr/inra/urgi/datadiscovery/dao/rare/RareDocumentDaoWithImplicitTermsTest.java

@@ -39,7 +39,7 @@ import org.springframework.test.context.junit.jupiter.SpringExtension;
 @Import(ElasticSearchConfig.class)
 @JsonTest
 @TestInstance(TestInstance.Lifecycle.PER_CLASS)
-@ActiveProfiles({AppProfile.RARE, AppProfile.RARE_WITH_BASKET})
+@ActiveProfiles({AppProfile.RARE, AppProfile.BRC4ENV})
 class RareDocumentDaoWithImplicitTermsTest extends DocumentDaoTest {
 
     private static final String PHYSICAL_INDEX = "test-rare-resource-physical-index";

buildSrc/src/main/kotlin/app.kt

 import org.gradle.api.*
 
-private val acceptableValues = setOf("rare", "rare-with-basket", "wheatis", "data-discovery")
+private val acceptableValues = setOf("rare", "brc4env", "wheatis", "data-discovery")
 
 val Project.app: String
     get() = findProperty("app")

frontend/angular.json

@@ -112,7 +112,7 @@
                 }
               ]
             },
-            "rare-with-basket": {
+            "brc4env": {
               "budgets": [
                 {
                   "type": "anyComponentStyle",
@@ -122,7 +122,7 @@
               "fileReplacements": [
                 {
                   "replace": "src/environments/environment.ts",
-                  "with": "src/environments/environment.rare-with-basket.ts"
+                  "with": "src/environments/environment.brc4env.ts"
                 },
                 {
                   "replace": "src/assets/rare/band.jpg",
@@ -133,13 +133,13 @@
                   "with": "src/environments/rare-with-basket.ts"
                 }
               ],
-              "baseHref": "/rare-with-basket-dev/"
+              "baseHref": "/brc4env-dev/"
             },
-            "rare-with-basket-production": {
+            "brc4env-production": {
               "fileReplacements": [
                 {
                   "replace": "src/environments/environment.ts",
-                  "with": "src/environments/environment.rare-with-basket.prod.ts"
+                  "with": "src/environments/environment.brc4env.prod.ts"
                 },
                 {
                   "replace": "src/assets/rare/band.jpg",
@@ -319,11 +319,11 @@
             "rare-production": {
               "browserTarget": "data-discovery-frontend:build:rare-production"
             },
-            "rare-with-basket": {
-              "browserTarget": "data-discovery-frontend:build:rare-with-basket"
+            "brc4env": {
+              "browserTarget": "data-discovery-frontend:build:brc4env"
             },
-            "rare-with-basket-production": {
-              "browserTarget": "data-discovery-frontend:build:rare-with-basket-production"
+            "brc4env-production": {
+              "browserTarget": "data-discovery-frontend:build:brc4env-production"
             },
             "wheatis": {
               "browserTarget": "data-discovery-frontend:build:wheatis"

frontend/package.json

@@ -5,13 +5,13 @@
     "ng": "ng",
     "start": "ng serve --configuration=rare --port=4000",
     "start:rare": "ng serve --configuration=rare --port=4000",
-    "start:rare-with-basket": "ng serve --configuration=rare-with-basket --port=4000",
+    "start:brc4env": "ng serve --configuration=brc4env --port=4000",
     "start:wheatis": "ng serve --configuration=wheatis --port=4100",
     "start:wheatis-production": "ng serve --configuration=wheatis-production --port=4101",
     "start:data-discovery": "ng serve --configuration=data-discovery --port=4200",
     "build": "ng build --configuration=rare-production --no-progress",
     "build:rare": "ng build --configuration=rare-production --no-progress",
-    "build:rare-with-basket": "ng build --configuration=rare-with-basket-production --no-progress",
+    "build:brc4env": "ng build --configuration=brc4env-production --no-progress",
     "build:wheatis": "ng build --configuration=wheatis-production --no-progress",
     "build:data-discovery": "ng build --configuration=data-discovery-production --no-progress",
     "test": "ng test --code-coverage --no-progress --no-watch",

frontend/proxy.conf.js

@@ -25,8 +25,8 @@ const PROXY_CONFIG = [
   },
   {
     context: [
-      "/rare-with-basket-dev/api",
-      "/rare-with-basket-dev/actuator"
+      "/brc4env-dev/api",
+      "/brc4env-dev/actuator"
     ],
     target: "http://localhost:8580",
     secure: false

frontend/src/environments/rare-with-basket.prod.ts

@@ -2,10 +2,10 @@
  * Configuration variables for RARe Basket.
  * This contains the configuration for production.
  * This file is only used by the RARe version (without basket) of the application.
- * It replaces rare-with-basket.ts when the application is built with the rare-with-basket + production configuration.
+ * It replaces rare-with-basket.ts when the application is built with the brc4env + production configuration.
  * See angular.json for more details.
  */
 export const rareBasket = {
   isBasketEnabled: true,
-  url: 'https://beta-urgi.versailles.inrae.fr/rare-basket/' // TODO update to proper URL for production
+  url: 'https://urgi.versailles.inrae.fr/rare-basket'
 };

frontend/src/environments/rare-with-basket.ts

@@ -8,5 +8,5 @@
  */
 export const rareBasket = {
   isBasketEnabled: true,
-  url: 'http://localhost:4201/rare-basket' // TODO update to proper URL
+  url: 'http://localhost:4201/rare-basket'
 };

scripts/createIndexAndAliases4CI.sh

@@ -91,7 +91,7 @@ DATE_TMSTP=$(${DATE_CMD} -d @${TIMESTAMP})
 echo "Using timestamp corresponding to date: ${DATE_TMSTP}"
 
 TMP_FILE=$(mktemp)
-if [ "${APP_NAME}" == "rare-with-basket" ]; then
+if [ "${APP_NAME}" == "brc4env" ]; then
     APP_SETTINGS_NAME="rare"
 else
     APP_SETTINGS_NAME="${APP_NAME}"

scripts/createSuggestions.sh

@@ -99,7 +99,7 @@ RARE_FIELDS_TO_EXTRACT=".pillar , .databaseSource , .name , .domain, .taxon, .fa
 
 if [ "${APP_NAME}" == "rare" ] ; then
     FIELDS_TO_EXTRACT="${RARE_FIELDS_TO_EXTRACT}"
-elif [ "${APP_NAME}" == "rare-with-basket" ]; then
+elif [ "${APP_NAME}" == "brc4env" ]; then
     FIELDS_TO_EXTRACT="${RARE_FIELDS_TO_EXTRACT}"
     FILTER_DATA_SCRIPT="${BRC4ENV_FILTER_DATA_SCRIPT}"
     DATADIR=$(readlink -f "$BASEDIR/../data/rare")
@@ -108,7 +108,7 @@ elif [ "${APP_NAME}" == "wheatis" ]; then
 elif [ "${APP_NAME}" == "data-discovery" ]; then
     FIELDS_TO_EXTRACT="${WHEATIS_FIELDS_TO_EXTRACT}"
 else
-    echo -e "${RED_BOLD}ERROR: app value is invalid, please specify one among following: ${GREEN}rare${RED}, ${GREEN}rare-with-basket${RED}, ${GREEN}wheatis${RED}, or ${GREEN}data-discovery${RED}.${NC}" && help && exit 5
+    echo -e "${RED_BOLD}ERROR: app value is invalid, please specify one among following: ${GREEN}rare${RED}, ${GREEN}brc4env${RED}, ${GREEN}wheatis${RED}, or ${GREEN}data-discovery${RED}.${NC}" && help && exit 5
 fi
 
 [ ! -d "${DATADIR}/suggestions" ] && echo "Creating missing directory:" && mkdir -v "${DATADIR}/suggestions"
@@ -116,7 +116,7 @@ fi
 export FILTER_DATA_SCRIPT FIELDS_TO_EXTRACT
 
 extract_suggestions() {
-    bash -c "set -o pipefail; gunzip -c $1 |                                                 # jq below add a filter on some data if needed (noop by default, or only brc4env pillar for rare-with-basket)
+    bash -c "set -o pipefail; gunzip -c $1 |                                                 # jq below add a filter on some data if needed (noop by default, or only brc4env pillar for brc4env)
     jq -rc -f ${FILTER_DATA_SCRIPT} |                               # tee below allows to redirect previous gunzip stdout to several processes using:    >(subprocess)
     tee \
         >(