Merge branch 'master' into 'release-1.4.4'

Master

See merge request !288

dbrepo-ui/components/identifier/Citation.vue

@@ -63,8 +63,11 @@ export default {
       identifierService.findOne(this.identifier.id, accept)
         .then((citation) => {
           this.citation = citation
+          this.loading = false
         })
-        .finally(() => {
+        .error(({code, message}) => {
+          const toast = useToastInstance()
+          toast.error(this.$t(`${code}: ${message}`))
           this.loading = false
         })
     }

dbrepo-ui/locales/en-US.json

@@ -35,6 +35,9 @@
   "pages": {
     "identifier": {
       "title": "Identifier",
+      "export": {
+        "text": "Metadata Export"
+      },
       "pid": {
         "title": "Persistent Identifier"
       },
@@ -1209,10 +1212,6 @@
       "created": "Successfully created table",
       "semantics": "Successfully assigned semantic instance"
     },
-    "schema": {
-      "tables": "Successfully refreshed database tables metadata",
-      "views": "Successfully refreshed database views metadata"
-    },
     "schema": {
       "tables": "Successfully refreshed database tables metadata.",
       "views": "Successfully refreshed database views metadata."

docker-compose.yml

@@ -14,13 +14,11 @@ services:
     restart: "no"
     container_name: dbrepo-metadata-db
     hostname: metadata-db
-    image: dbrepo-metadata-db:latest
-    build:
-      context: ./dbrepo-metadata-db
-      network: host
+    image: docker.io/bitnami/mariadb:11.1.3-debian-11-r6
     volumes:
       - metadata-db-data:/bitnami/mariadb
-      - ./dbrepo-metadata-db/setup-data.sql:/docker-entrypoint-initdb.d/setup-schema_local.sql
+      - ./dbrepo-metadata-db/setup-schema.sql:/docker-entrypoint-initdb.d/1_setup-schema.sql
+      - ./dbrepo-metadata-db/setup-data.sql:/docker-entrypoint-initdb.d/2_setup-data.sql
     ports:
       - "3306:3306"
     environment:
@@ -38,7 +36,7 @@ services:
     restart: "no"
     container_name: dbrepo-data-db
     hostname: data-db
-    image: docker.io/bitnami/mariadb-galera:11.2.2-debian-11-r0
+    image: docker.io/bitnami/mariadb:11.1.3-debian-11-r6
     volumes:
       - data-db-data:/bitnami/mariadb
       - "${SHARED_VOLUME:-/tmp}:/tmp"
@@ -46,7 +44,6 @@ services:
       - "3307:3306"
     environment:
       MARIADB_ROOT_PASSWORD: "${USER_DB_PASSWORD:-dbrepo}"
-      MARIADB_GALERA_MARIABACKUP_PASSWORD: "${USER_DB_BACKUP_PASSWORD:-dbrepo}"
     healthcheck:
       test: mysqladmin ping --user="${USER_DB_USERNAME:-root}" --password="${USER_DB_PASSWORD:-dbrepo}" --silent
       interval: 10s
@@ -59,7 +56,7 @@ services:
     restart: "no"
     container_name: dbrepo-auth-db
     hostname: auth-db
-    image: docker.io/bitnami/mariadb:11.2.2-debian-11-r0
+    image: docker.io/bitnami/mariadb:11.1.3-debian-11-r6
     volumes:
       - auth-db-data:/bitnami/mariadb
     ports:
@@ -331,7 +328,7 @@ services:
     restart: "no"
     container_name: dbrepo-gateway-service
     hostname: gateway-service
-    image: docker.io/nginx:1.25-alpine-slim
+    image: docker.io/nginx:1.27.0-alpine3.19-slim
     ports:
       - "80:80"
       - "443:443"

helm/dbrepo/Chart.lock

 dependencies:
 - name: opensearch
-  repository: https://opensearch-project.github.io/helm-charts/
-  version: 2.15.0
+  repository: https://charts.bitnami.com/bitnami
+  version: 1.2.2
 - name: keycloak
   repository: https://charts.bitnami.com/bitnami
   version: 17.3.3
-- name: mariadb-galera
+- name: mariadb
   repository: https://charts.bitnami.com/bitnami
-  version: 11.0.1
-- name: mariadb-galera
+  version: 14.1.4
+- name: mariadb
   repository: https://charts.bitnami.com/bitnami
-  version: 11.0.1
+  version: 14.1.4
 - name: rabbitmq
   repository: https://charts.bitnami.com/bitnami
   version: 14.0.0
@@ -20,5 +20,5 @@ dependencies:
 - name: tusd
   repository: https://charts.sagikazarmark.dev
   version: 0.1.2
-digest: sha256:f724e33944ae5284b9417a3424a4af9cd67eb8bea0baa0ebeddc76f4c0c9c63a
-generated: "2024-05-17T21:25:35.919266246+02:00"
+digest: sha256:867a4a60bbccfaeb880d000eeb634db20554ef91523aa3b1331c53bdf48e8db4
+generated: "2024-06-14T15:12:25.44560113+02:00"

helm/dbrepo/Chart.yaml

@@ -10,28 +10,28 @@ keywords:
   - dbrepo
 maintainers:
   - name: Martin Weise
-    email: martin.weise@tuwien.ac.at
+    email: martin.weise@tuwien.ac.a
 home: https://www.ifs.tuwien.ac.at/infrastructures/dbrepo/
 icon: https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/master/dbrepo-ui/public/favicon.png
 dependencies:
   - name: opensearch
     alias: searchdb
-    version: 2.15.0
-    repository: https://opensearch-project.github.io/helm-charts/
+    version: 1.2.2
+    repository: https://charts.bitnami.com/bitnami
     condition: searchdb.enabled
   - name: keycloak
     alias: authservice
     version: 17.3.3
     repository: https://charts.bitnami.com/bitnami
     condition: authservice.enabled
-  - name: mariadb-galera
+  - name: mariadb
     alias: datadb
-    version: 11.0.1
+    version: 14.1.4
     repository: https://charts.bitnami.com/bitnami
     condition: datadb.enabled
-  - name: mariadb-galera
+  - name: mariadb
     alias: metadatadb
-    version: 11.0.1
+    version: 14.1.4
     repository: https://charts.bitnami.com/bitnami
     condition: metadatadb.enabled
   - name: rabbitmq

helm/dbrepo/hack/generate-rabbitmq-pw.sh

+#!/bin/bash
+# https://stackoverflow.com/a/53175209/2634294
+# THIS SCRIPT REQUIRES xxd TO BE INSTALLED:
+#     DEBIAN: apt install xxd
+#     MACOS: brew install coreutils
+function encode_password()
+{
+    SALT=$(od -A n -t x -N 4 /dev/urandom)
+    PASS=$SALT$(echo -n $1 | xxd -ps | tr -d '\n' | tr -d ' ')
+    PASS=$(echo -n $PASS | xxd -r -p | sha256sum | head -c 128)
+    PASS=$(echo -n $SALT$PASS | xxd -r -p | base64 | tr -d '\n')
+    echo $PASS
+}
+encode_password $1
\ No newline at end of file

helm/dbrepo/templates/broker-secret.yaml

@@ -34,7 +34,7 @@ stringData:
         {
           "configure": ".*",
           "read": ".*",
-          "user": "broker",
+          "user": "{{ .Values.brokerservice.auth.username }}",
           "vhost": "dbrepo",
           "write": ".*"
         }
@@ -60,8 +60,8 @@ stringData:
         {
           "hashing_algorithm": "rabbit_password_hashing_sha256",
           "limits": {},
-          "name": "broker",
-          "password_hash": "Sek6WxpX2L6UhxlwRkD0cnYAH5GbtTcCFq1yY/SCc1mAa0gB",
+          "name": "{{ .Values.brokerservice.auth.username }}",
+          "password_hash": "{{ .Values.brokerservice.auth.passwordHash }}",
           "tags": [
             "administrator"
           ]

helm/dbrepo/templates/metadata-configmap.yaml

@@ -12,7 +12,7 @@ data:
   02-setup-data.sql: |
     BEGIN;
     INSERT INTO `mdb_containers` (name, internal_name, image_id, host, port, sidecar_host, sidecar_port, privileged_username, privileged_password)
-      VALUES ('MariaDB Galera 11.1.3', 'mariadb_11_1_3', 1, 'data-db', 3306, 'data-db', 80, 'root', 'dbrepo');
+      VALUES ('MariaDB 11.1.3', 'mariadb_11_1_3', 1, 'data-db', 3306, 'data-db', 80, 'root', 'dbrepo');
     COMMIT;
   01-setup-schema.sql: |
     BEGIN;

helm/dbrepo/templates/metadata-secret.yaml

@@ -15,7 +15,7 @@ stringData:
   AUTH_SERVICE_CLIENT: "{{ .Values.authservice.client.id }}"
   AUTH_SERVICE_CLIENT_SECRET: "{{ .Values.authservice.client.secret }}"
   AUTH_SERVICE_ENDPOINT: "{{ .Values.authservice.endpoint }}"
-  BASE_URL: "{{ .Values.hostname }}"
+  BASE_URL: "{{ .Values.gateway }}"
   BROKER_EXCHANGE_NAME: "{{ .Values.brokerservice.exchangeName }}"
   BROKER_HOST: "{{ .Values.brokerservice.host }}"
   BROKER_QUEUE_NAME: "{{ .Values.brokerservice.queueName }}"
@@ -33,11 +33,11 @@ stringData:
   GRANULARITY: "{{ .Values.metadataservice.granularity }}"
   JWT_PUBKEY: "{{ .Values.authservice.jwt.pubkey }}"
   LOG_LEVEL: "{{ ternary "trace" "info" .Values.metadataservice.image.debug }}"
-  METADATA_DB: "{{ .Values.metadatadb.db.name }}"
+  METADATA_DB: "{{ .Values.metadatadb.auth.database }}"
   METADATA_HOST: "{{ .Values.metadatadb.host }}"
   METADATA_JDBC_EXTRA_ARGS: "{{ .Values.metadatadb.jdbcExtraArgs }}"
-  METADATA_USERNAME: "{{ .Values.metadatadb.rootUser.user }}"
-  METADATA_PASSWORD: "{{ .Values.metadatadb.rootUser.password }}"
+  METADATA_USERNAME: "{{ .Values.metadatadb.auth.root }}"
+  METADATA_PASSWORD: "{{ .Values.metadatadb.auth.rootPassword }}"
   PID_BASE: "{{ $pidBase }}"
   REPOSITORY_NAME: "{{ .Values.metadataservice.repositoryName }}"
   SEARCH_SERVICE_ENDPOINT: "{{ .Values.searchservice.endpoint }}"

install.sh

 #!/bin/bash
 
 # preset
-VERSION="latest"
+VERSION="1.4.4"
 MIN_CPU=8
 MIN_RAM=8
 MIN_MAP_COUNT=262144
@@ -59,7 +59,8 @@ fi
 echo "[🚀] Gathering environment ..."
 mkdir -p ./dist
 curl -sSL -o ./docker-compose.yml "https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-${VERSION}/.docker/docker-compose.yml"
-curl -sSL -o ./dist/2_setup-data.sql "https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-${VERSION}/dbrepo-metadata-db/2_setup-data.sql"
+curl -sSL -o ./dist/1_setup-schema.sql "https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-${VERSION}/dbrepo-metadata-db/setup-schema.sql"
+curl -sSL -o ./dist/2_setup-data.sql "https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-${VERSION}/dbrepo-metadata-db/setup-data.sql"
 curl -sSL -o ./dist/rabbitmq.conf "https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-${VERSION}/dbrepo-broker-service/rabbitmq.conf"
 curl -sSL -o ./dist/enabled_plugins "https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-${VERSION}/dbrepo-broker-service/enabled_plugins"
 curl -sSL -o ./dist/cert.pem "https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-${VERSION}/dbrepo-broker-service/cert.pem"

lib/python/dbrepo/RestClient.py

@@ -1543,8 +1543,7 @@ class RestClient:
         raise ResponseCodeError(f'Failed to delete database access: response code: {response.status_code} is not '
                                 f'201 (CREATED): {response.text}')
 
-    def create_subset(self, database_id: int, query: str, page: int = 0, size: int = 10,
-                      timestamp: datetime.datetime = datetime.datetime.now()) -> Result:
+    def create_subset(self, database_id: int, query: str, page: int = 0, size: int = 10) -> Result:
         """
         Executes a SQL query in a database where the current user has at least read access with given database id. The
         result set can be paginated with setting page and size (both). Historic data can be queried by setting
@@ -1554,7 +1553,6 @@ class RestClient:
         :param query: The query statement.
         :param page: The result pagination number. Optional. Default: 0.
         :param size: The result pagination size. Optional. Default: 10.
-        :param timestamp: The query execution time. Optional. Default: now.
 
         :returns: The result set, if successful.
 
@@ -1569,8 +1567,8 @@ class RestClient:
         url = f'/api/database/{database_id}/subset'
         if page is not None and size is not None:
             url += f'?page={page}&size={size}'
-        response = self._wrapper(method="post", url=url, force_auth=True,
-                                 payload=ExecuteQuery(statement=query, timestamp=timestamp))
+        response = self._wrapper(method="post", url=url, force_auth=True, headers={"Accept": "application/json"},
+                                 payload=ExecuteQuery(statement=query))
         if response.status_code == 201:
             body = response.json()
             return Result.model_validate(body)

lib/python/dbrepo/api/dto.py

@@ -720,7 +720,6 @@ class Unit(BaseModel):
 
 class ExecuteQuery(BaseModel):
     statement: str
-    timestamp: Timestamp
 
 
 class TitleType(str, Enum):