Merge branch 'master' into proposalGroup-update-permission

.env.example

@@ -34,7 +34,48 @@ SMTP_HOST=<SMTP_HOST>
 SMTP_MESSAGE_FROM=<SMTP_MESSAGE_FROM>
 SMTP_PORT=<SMTP_PORT>
 SMTP_SECURE=<SMTP_SECURE>
+
+DATASET_CREATION_VALIDATION_ENABLED=true
+DATASET_CREATION_VALIDATION_REGEX="^[0-9A-F]{8}-[0-9A-F]{4}-4[0-9A-F]{3}-[89AB][0-9A-F]{3}-[0-9A-F]{12}$"
+
+ADMIN_GROUPS=""
+DELETE_GROUPS=""
 CREATE_DATASET_GROUPS="all"
 CREATE_DATASET_WITH_PID_GROUPS=""
-DATASET_CREATION_VALIDATION_ENABLED=true
-DATASET_CREATION_VALIDATION_REGEX="^[0-9A-F]{8}-[0-9A-F]{4}-4[0-9A-F]{3}-[89AB][0-9A-F]{3}-[0-9A-F]{12}$"
+CREATE_DATASET_PRIVILEGED_GROUPS=""
+CREATE_JOB_GROUPS=""
+UPDATE_JOB_GROUPS=""
+SAMPLE_PRIVILEGED_GROUPS="sampleingestor"
+SAMPLE_GROUPS="group1"
+PROPOSAL_GROUPS=""
+
+ACCESS_GROUPS_GRAPHQL_ENABLED=true
+ACCESS_GROUP_SERVICE_TOKEN=""
+ACCESS_GROUP_SERVICE_API_URL=""
+ACCESS_GROUP_SERVICE_HANDLER=""
+ACCESS_GROUPS_STATIC_ENABLED=true
+ACCESS_GROUPS_OIDCPAYLOAD_ENABLED=true
+
+OIDC_USERINFO_MAPPING_FIELD_USERNAME="iss, sub"
+OIDC_USERINFO_MAPPING_FIELD_DISPLAYNAME="preferred_username"
+OIDC_USERINFO_MAPPING_FIELD_EMAIL="email"
+OIDC_USERINFO_MAPPING_FIELD_GROUP="groups"
+OIDC_USERQUERY_OPERATOR=<"or"|"and">
+OIDC_USERQUERY_FILTER="username:username, email:email"
+
+ELASTICSEARCH_ENABLED=<"yes"|"no">
+APP_PORT=3003
+STACK_VERSION="8.8.2"
+CLUSTER_NAME="es-cluster"
+MEM_LIMIT="4G"
+MONGODB_COLLECTION="Dataset"
+ES_MAX_RESULT=100000
+ES_FIELDS_LIMIT=400000
+ES_INDEX="dataset"
+ES_PORT=9200
+ES_HOST="https://localhost:9200"
+ES_USERNAME="elastic"
+ES_PASSWORD="duo-password"
+ES_REFRESH=<"wait_for"|"false">
+
+LOGGERS_CONFIG_FILE="loggers.json"

.github/workflows/auto-merge-dependabot.yaml

@@ -15,7 +15,7 @@ jobs:
       ## Extract information about the dependencies being updated by a Dependabot-generated PR
       - name: Dependabot metadata
         id: dependabot-metadata
-        uses: dependabot/fetch-metadata@v1.6.0
+        uses: dependabot/fetch-metadata@v2.0.0
         with:
           github-token: "${{ secrets.GITHUB_TOKEN }}"
 

CI/E2E/config.e2e.json

@@ -7,7 +7,7 @@
   "editDatasetSampleEnabled": true,
   "editMetadataEnabled": true,
   "editPublishedData": false,
-  "editSampleEnabled": true,
+  "addSampleEnabled": true,
   "externalAuthEndpoint": "/api/v3/auth/msad",
   "facility": "ESS",
   "loginFacilityLabel": "ESS",
@@ -119,4 +119,4 @@
   "shoppingCartEnabled": true,
   "shoppingCartOnHeader": true,
   "tableSciDataEnabled": true
-}
+}

CI/E2E/frontend.config.json

@@ -6,7 +6,7 @@
   "editDatasetSampleEnabled": true,
   "editMetadataEnabled": true,
   "editPublishedData": false,
-  "editSampleEnabled": true,
+  "addSampleEnabled": true,
   "externalAuthEndpoint": "/api/v3/auth/msad",
   "facility": "ESS",
   "loginFacilityLabel": "ESS",
@@ -36,7 +36,7 @@
       "order": 1,
       "type": "standard",
       "enabled": true
-    },    
+    },
     {
       "name": "datasetName",
       "order": 2,

CI/MLZ/frontend.config.json

@@ -12,7 +12,7 @@
   ],
   "externalAuthEndpoint": "/auth/ldap",
   "editMetadataEnabled": true,
-  "editSampleEnabled": true,
+  "addSampleEnabled": true,
   "editPublishedData": true,
   "scienceSearchEnabled": true,
   "facility": "MLZ",
@@ -118,7 +118,5 @@
   "scienceSearchUnitsEnabled": false,
   "metadataStructure": "",
   "loginFormEnabled": true,
-  "oAuth2Endpoints": [
-	  {"displayText": "MLZ", "authURL":"api/v3/auth/oidc"}
-  ]
+  "oAuth2Endpoints": [{ "displayText": "MLZ", "authURL": "api/v3/auth/oidc" }]
 }

CI/MLZ/frontend.config.ts

@@ -4,17 +4,17 @@ export default {
   retrieveDestinations: [
     {
       option: "MLZ",
-      location: "/home/out"
+      location: "/home/out",
     },
     {
-      option: "MLZ S3 (Testphase)"
-    }
+      option: "MLZ S3 (Testphase)",
+    },
   ],
   accessTokenPrefix: "Bearer ",
   lbTokenPrefix: "Bearer ",
   externalAuthEndpoint: "",
   editMetadataEnabled: true,
-  editSampleEnabled: true,
+  addSampleEnabled: true,
   editPublishedData: true,
   scienceSearchEnabled: true,
   facility: "MLZ",
@@ -33,74 +33,74 @@ export default {
       name: "select",
       order: 0,
       type: "standard",
-      enabled: true
+      enabled: true,
     },
     {
       name: "datasetName",
       order: 1,
       type: "standard",
-      enabled: true
+      enabled: true,
     },
     {
       name: "runNumber",
       order: 2,
       type: "standard",
-      enabled: true
+      enabled: true,
     },
     {
       name: "sourceFolder",
       order: 3,
       type: "standard",
-      enabled: true
+      enabled: true,
     },
     {
       name: "size",
       order: 4,
       type: "standard",
-      enabled: true
+      enabled: true,
     },
     {
       name: "creationTime",
       order: 5,
       type: "standard",
-      enabled: true
+      enabled: true,
     },
     {
       name: "type",
       order: 6,
       type: "standard",
-      enabled: true
+      enabled: true,
     },
     {
       name: "image",
       order: 7,
       type: "standard",
-      enabled: true
+      enabled: true,
     },
     {
       name: "metadata",
       order: 8,
       type: "standard",
-      enabled: true
+      enabled: true,
     },
     {
       name: "proposalId",
       order: 9,
       type: "standard",
-      enabled: true
+      enabled: true,
     },
     {
       name: "ownerGroup",
       order: 10,
       type: "standard",
-      enabled: true
+      enabled: true,
     },
     {
       name: "dataStatus",
       order: 11,
       type: "standard",
-      enabled: true
-    }
+      enabled: true,
+    },
   ],
   logbookEnabled: true,
   metadataPreviewEnabled: true,
@@ -121,8 +121,9 @@ export default {
   metadataStructure: "",
   loginFormEnabled: true,
   oAuth2Endpoints: [
-	  {
-		  displayText: "MLZ",
-		  authURL: "api/v3/auth/oidc"}
-  ]
+    {
+      displayText: "MLZ",
+      authURL: "api/v3/auth/oidc",
+    },
+  ],
 };

README.md

@@ -28,19 +28,21 @@ or the SciCat team at ESS.
 2. `npm install`
 3. Add _.env_ file to project root folder. See [Environment variables](#environment-variables).
 4. _Optional_ Add [functionalAccounts.json](#local-user-accounts) file to project root folder to create local users.
-5. `npm run start:dev`
-6. Go to http://localhost:3000/explorer to get an overview of available endpoints and database schemas.
-7. To be able to run the e2e tests with the same setup as in the Github actions you will need to run `npm run  prepare:local` and after that run `npm run start:dev`. This will start all needed containers and copy some configuration to the right place.
+5. _Optional_ Add [loggers.json](#loggers-configuration) file to the root folder and configure multiple loggers.
+6. `npm run start:dev`
+7. Go to http://localhost:3000/explorer to get an overview of available endpoints and database schemas.
+8. To be able to run the e2e tests with the same setup as in the Github actions you will need to run `npm run  prepare:local` and after that run `npm run start:dev`. This will start all needed containers and copy some configuration to the right place.
 
 ## Develop in a container using the docker-compose.dev file
 
 1. `git clone https://github.com/SciCatProject/scicat-backend-next.git`
 2. docker-compose -f docker-compose.dev.yaml up -d
 3. _Optional_ Mount [functionalAccounts.json](#local-user-accounts) file to a volume in the container to create local users.
-4. _Optional_ change the container env variables
-5. Attach to the container
-6. `npm run start:dev`
-7. Go to http://localhost:3000/explorer to get an overview of available endpoints and database schemas.
+4. _Optional_ Mount [loggers.json](#loggers-configuration) file to a volume in the container to configure multiple loggers.
+5. _Optional_ change the container env variables
+6. Attach to the container
+7. `npm run start:dev`
+8. Go to http://localhost:3000/explorer to get an overview of available endpoints and database schemas.
 
 ## Test the app
 
@@ -77,6 +79,12 @@ automatically create the specified accounts on startup. If this file is not prov
 Follow the structure of [functionalAccounts.json.minimal.example](/functionalAccounts.json.minimal.example) to create
 your own _functionalAccounts.json_ file.
 
+### Loggers configuration
+
+Providing a file called _loggers.json_ at the root of the project, locally or in the container, and create an external logger class in the `src/loggers/loggingProviders/`directory will automatically create specified one or multiple loggers instances.
+
+The `loggers.json.example` file in the root directory showcases the example of configuration structure for the one or multiple loggers. `logger.service.ts` file contains the configuration handling process logic, and `src/loggers/loggingProviders/grayLogger.ts` includes actual usecase of grayLogger.
+
 ## Environment variables
 
 Valid environment variables for the .env file. See [.env.example](/.env.example) for examples value formats.
@@ -161,6 +169,8 @@ Valid environment variables for the .env file. See [.env.example](/.env.example)
 - `ES_FIELDS_LIMIT` [number] The total number of fields in an index. Default value: 1000
 - `ES_REFRESH` [string] If set to `wait_for` Elasticsearch will wait till data is insereted to specificied index then return response. Unless you have a good reason to wait for the change to become visible, always use `false` (the default setting).
 
+- `LOGGERS_CONFIG_FILE` [string] The file name for loggers configuration which needs to be located in the project root directory. Default value: "loggers.json"
+
 ## Migrating from the old SciCat Backend
 
 Where the [current SciCat Backend](https://github.com/SciCatProject/backend) accepts id fields in the database named `pid`, `doi`, or similar, this implementation requires there to be an id field of the form `_id` on every document. It is therefore necessary to run a database migration script towards MongoDB instance from a place where you have access to it and can install `migrate-mongo` package.