Merge remote-tracking branch 'origin/rsd-v2-release' into 923-add-sup…

…port-for-categories-for-software-and-projects
research-software-directory · Aug 28, 2023 · c6d28b1 · c6d28b1
2 parents 7439667 + ab1edac
commit c6d28b1
Show file tree

Hide file tree

Showing 643 changed files with 27,477 additions and 10,800 deletions.
diff --git a/.env.example b/.env.example
@@ -61,7 +61,7 @@ RSD_AUTH_URL=http://auth:7000
 # Allowed values are: SURFCONEXT, HELMHOLTZAAI, ORCID or LOCAL
 # if env value is not provided default provider is set to be SURFCONEXT
 # if you add the value "LOCAL", then local accounts are enabled, USE THIS FOR TESTING PURPOSES ONLY
-RSD_AUTH_PROVIDERS=SURFCONEXT;ORCID;LOCAL
+RSD_AUTH_PROVIDERS=SURFCONEXT;ORCID;AZURE;LOCAL
 
 # Define a semicolon-separated list of user email addresses (exact match incl. the letter casing) of RSD admins.
 # When someome authenticates with an email address in this list,
@@ -120,6 +120,27 @@ ORCID_SCOPES=openid
 # consumed by: frontend/utils/loginHelpers
 ORCID_RESPONSE_MODE=query
 
+# AZURE ACTIVE DIRECTORY
+# consumed by: authentication, frontend/utils/loginHelpers
+AZURE_CLIENT_ID=
+# consumed by: authentication, frontend/utils/loginHelpers
+AZURE_REDIRECT=http://localhost/auth/login/azure
+# consumed by: authentication, frontend/utils/loginHelpers
+AZURE_WELL_KNOWN_URL=
+# consumed by: authentication, frontend/utils/loginHelpers
+AZURE_SCOPES=openid+email+profile
+# consumed by: authentication, frontend/utils/loginHelpers
+AZURE_LOGIN_PROMPT=select_account
+# consumed by: frontend
+# the name displayed to users when multiple providers are configured
+AZURE_DISPLAY_NAME="Imperial College Login"
+# consumed by: frontend
+# the description text displayed to users when multiple providers are configured
+AZURE_DESCRIPTION_HTML="Sign in with your institutional credentials"
+# consumed by: authentication
+# the organisation recorded for users logged in via this provider
+AZURE_ORGANISATION=
+
 # max requests to the GitHub API per run, runs 10 times per hour
 # optional, comment out if not available, a default of 6 will be used
 # consumed by: scrapers
@@ -164,6 +185,10 @@ AUTH_HELMHOLTZAAI_CLIENT_SECRET=
 # obtain the secret from the project team
 AUTH_ORCID_CLIENT_SECRET=
 
+# Azure Active Directory
+# consumed by services: authentication
+AUTH_AZURE_CLIENT_SECRET=
+
 # POSTGREST JWT SECRET
 # consumed by services: authentication, frontend (auth-node), auth-tests, scrapers
 # generate random/strong password with at least 32 characters

diff --git a/.github/workflows/authentication_tests.yml b/.github/workflows/authentication_tests.yml
@@ -0,0 +1,49 @@
+# SPDX-FileCopyrightText: 2022 - 2023 Ewan Cahen (Netherlands eScience Center) <[email protected]>
+# SPDX-FileCopyrightText: 2022 - 2023 Netherlands eScience Center
+# SPDX-FileCopyrightText: 2022 Dusan Mijatovic (dv4all)
+# SPDX-FileCopyrightText: 2022 dv4all
+#
+# SPDX-License-Identifier: Apache-2.0
+
+name: authentication tests
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+    paths:
+      - "authentication/**"
+  pull_request:
+    paths:
+      - "authentication/**"
+
+jobs:
+  authentication-tests:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
+      - name: Cache SonarCloud packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.sonar/cache
+          key: ${{ runner.os }}-sonar
+          restore-keys: ${{ runner.os }}-sonar
+      - name: Cache Maven packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.m2
+          key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
+          restore-keys: ${{ runner.os }}-m2
+      - name: "Maven JUnit tests and JaCoCo test report"
+        working-directory: authentication
+        run: |
+          JAVA_HOME=$JAVA_HOME_17_X64 mvn verify
+      - name: SonarCloud Scan authentication
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        working-directory: authentication
+        run: JAVA_HOME=$JAVA_HOME_17_X64 mvn -B verify org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=nl.research-software:authentication -Pcoverage
diff --git a/.github/workflows/database_scan.yml b/.github/workflows/database_scan.yml
@@ -0,0 +1,39 @@
+# SPDX-FileCopyrightText: 2023 Ewan Cahen (Netherlands eScience Center) <[email protected]>
+# SPDX-FileCopyrightText: 2023 Netherlands eScience Center
+#
+# SPDX-License-Identifier: Apache-2.0
+
+name: database scan
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+    paths:
+      - "database/**"
+  pull_request:
+    paths:
+      - "database/**"
+
+jobs:
+  build:
+    name: Build and analyse with SonarCloud
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
+      - name: Cache SonarCloud packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.sonar/cache
+          key: ${{ runner.os }}-sonar
+          restore-keys: ${{ runner.os }}-sonar
+      - name: SonarCloud Scan database
+        uses: sonarsource/sonarcloud-github-action@master
+        with:
+          projectBaseDir: database
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
diff --git a/.github/workflows/frontend_tests.yml b/.github/workflows/frontend_tests.yml
@@ -1,5 +1,8 @@
 # SPDX-FileCopyrightText: 2022 - 2023 Dusan Mijatovic (dv4all)
 # SPDX-FileCopyrightText: 2022 - 2023 dv4all
+# SPDX-FileCopyrightText: 2023 Dusan Mijatovic (Netherlands eScience Center)
+# SPDX-FileCopyrightText: 2023 Ewan Cahen (Netherlands eScience Center) <[email protected]>
+# SPDX-FileCopyrightText: 2023 Netherlands eScience Center
 #
 # SPDX-License-Identifier: Apache-2.0
 
@@ -21,6 +24,8 @@ jobs:
     runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
       - name: "install node v18.5 and cash yarn"
         uses: actions/setup-node@v3
         with:
@@ -30,9 +35,25 @@ jobs:
       - name: "install dependencies"
         working-directory: frontend
         run: yarn install --frozen-lockfile
+      - name: "run eslint check"
+        working-directory: frontend
+        run: yarn lint
       - name: "run unit test"
         working-directory: frontend
         run: yarn test:coverage
+      - name: Cache SonarCloud packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.sonar/cache
+          key: ${{ runner.os }}-sonar
+          restore-keys: ${{ runner.os }}-sonar
+      - name: SonarCloud Scan frontend
+        uses: sonarsource/sonarcloud-github-action@master
+        with:
+          projectBaseDir: frontend
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
       - name: "run build test"
         working-directory: frontend
         run: yarn build
diff --git a/.github/workflows/scrapers_tests.yml b/.github/workflows/scrapers_tests.yml
@@ -1,13 +1,19 @@
+# SPDX-FileCopyrightText: 2022 - 2023 Ewan Cahen (Netherlands eScience Center) <[email protected]>
+# SPDX-FileCopyrightText: 2022 - 2023 Netherlands eScience Center
 # SPDX-FileCopyrightText: 2022 Dusan Mijatovic (dv4all)
-# SPDX-FileCopyrightText: 2022 Ewan Cahen (Netherlands eScience Center) <[email protected]>
-# SPDX-FileCopyrightText: 2022 Netherlands eScience Center
 # SPDX-FileCopyrightText: 2022 dv4all
 #
 # SPDX-License-Identifier: Apache-2.0
 
 name: scrapers tests
 
 on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+    paths:
+      - "scrapers/**"
   pull_request:
     paths:
       - "scrapers/**"
@@ -17,8 +23,27 @@ jobs:
     runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v3
-      - name: "Maven JUnit tests"
+        with:
+          fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
+      - name: Cache SonarCloud packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.sonar/cache
+          key: ${{ runner.os }}-sonar
+          restore-keys: ${{ runner.os }}-sonar
+      - name: Cache Maven packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.m2
+          key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
+          restore-keys: ${{ runner.os }}-m2
+      - name: "Maven JUnit tests and JaCoCo test report"
         working-directory: scrapers
         run: |
-          JAVA_HOME=$JAVA_HOME_17_X64 mvn test
-
+          JAVA_HOME=$JAVA_HOME_17_X64 mvn verify
+      - name: SonarCloud Scan scrapers
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        working-directory: scrapers
+        run: JAVA_HOME=$JAVA_HOME_17_X64 mvn -B verify org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=nl.research-software:scrapers -Pcoverage
diff --git a/.gitignore b/.gitignore
@@ -1,7 +1,8 @@
 # SPDX-FileCopyrightText: 2021 - 2022 Dusan Mijatovic (dv4all)
 # SPDX-FileCopyrightText: 2021 - 2022 Ewan Cahen (Netherlands eScience Center) <[email protected]>
-# SPDX-FileCopyrightText: 2021 - 2022 Netherlands eScience Center
 # SPDX-FileCopyrightText: 2021 - 2022 dv4all
+# SPDX-FileCopyrightText: 2021 - 2023 Netherlands eScience Center
+# SPDX-FileCopyrightText: 2023 Dusan Mijatovic (Netherlands eScience Center)
 #
 # SPDX-License-Identifier: Apache-2.0
 
@@ -52,3 +53,4 @@ yarn-error.log*
 
 # typescript
 *.tsbuildinfo
+.history
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -23,7 +23,7 @@
   "editor.quickSuggestions": {
     "strings": true
   },
-  "tailwindCSS.includeLanguages":{
+  "tailwindCSS.includeLanguages": {
     "plaintext": "html"
   },
   "[java]": {
@@ -39,5 +39,13 @@
     "editor.tabSize": 2,
     "editor.insertSpaces": true,
     "editor.detectIndentation": false
-  }
-}
+  },
+  "[typescriptreact]": {
+    "editor.formatOnSave": true,
+    "editor.defaultFormatter": "dbaeumer.vscode-eslint"
+  },
+  "[javascript]": {
+    "editor.formatOnSave": true,
+    "editor.defaultFormatter": "dbaeumer.vscode-eslint"
+  },
+}
diff --git a/.vscode/settings.json.license b/.vscode/settings.json.license
@@ -1,3 +1,7 @@
-SPDX-FileCopyrightText: 2022 Netherlands eScience Center
+SPDX-FileCopyrightText: 2022 - 2023 Netherlands eScience Center
+SPDX-FileCopyrightText: 2023 Dusan Mijatovic (Netherlands eScience Center)
+SPDX-FileCopyrightText: 2023 Dusan Mijatovic (dv4all)
+SPDX-FileCopyrightText: 2023 dv4all
 
+SPDX-License-Identifier: Apache-2.0
 SPDX-License-Identifier: CC0-1.0
diff --git a/Makefile b/Makefile
@@ -5,6 +5,7 @@
 # SPDX-FileCopyrightText: 2022 - 2023 Netherlands eScience Center
 # SPDX-FileCopyrightText: 2022 - 2023 dv4all
 # SPDX-FileCopyrightText: 2022 Jesús García Gonzalez (Netherlands eScience Center) <[email protected]>
+# SPDX-FileCopyrightText: 2023 Dusan Mijatovic (Netherlands eScience Center)
 #
 # SPDX-License-Identifier: Apache-2.0
 
@@ -45,11 +46,6 @@ install: clean
 clean:
 	docker compose down --volumes
 
-
-dev:
-	docker compose up --scale scrapers=0 --detach
-	make -j 2 dev-docs dev-frontend # Run concurrently
-
 stop:
 	docker compose down
 
@@ -73,7 +69,10 @@ frontend/.env.local: .env
 	sed -i 's/POSTGREST_URL=http:\/\/backend:3500/POSTGREST_URL=http:\/\/localhost\/api\/v1/g' frontend/.env.local
 	sed -i 's/RSD_AUTH_URL=http:\/\/auth:7000/RSD_AUTH_URL=http:\/\/localhost\/auth/g' frontend/.env.local
 
-dev-frontend: frontend/.env.local
+dev: frontend/.env.local
+	docker compose build # build all services
+	docker compose up --scale data-generation=1 --scale scrapers=0 --scale frontend=0 --detach
+	# open http://localhost:3000 to see the application running
 	cd frontend && yarn dev
 
 # run end-to-end test locally

diff --git a/authentication/pom.xml b/authentication/pom.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
 <!--
-SPDX-FileCopyrightText: 2021 - 2022 Ewan Cahen (Netherlands eScience Center) <[email protected]>
-SPDX-FileCopyrightText: 2021 - 2022 Netherlands eScience Center
+SPDX-FileCopyrightText: 2021 - 2023 Ewan Cahen (Netherlands eScience Center) <[email protected]>
+SPDX-FileCopyrightText: 2021 - 2023 Netherlands eScience Center
 SPDX-FileCopyrightText: 2022 Helmholtz Centre Potsdam - GFZ German Research Centre for Geosciences
 SPDX-FileCopyrightText: 2022 Matthias Rüster (GFZ) <[email protected]>
 
@@ -22,6 +22,8 @@ SPDX-License-Identifier: Apache-2.0
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<maven.compiler.source>17</maven.compiler.source>
 		<maven.compiler.target>17</maven.compiler.target>
+		<sonar.organization>research-software-directory</sonar.organization>
+		<sonar.host.url>https://sonarcloud.io</sonar.host.url>
 	</properties>
 
 	<build>
@@ -61,6 +63,32 @@ SPDX-License-Identifier: Apache-2.0
 				<artifactId>maven-surefire-plugin</artifactId>
 				<version>3.0.0-M6</version>
 			</plugin>
+
+			<!-- https://docs.sonarcloud.io/enriching/test-coverage/java-test-coverage/ -->
+			<plugin>
+				<groupId>org.jacoco</groupId>
+				<artifactId>jacoco-maven-plugin</artifactId>
+				<version>0.8.10</version>
+				<executions>
+					<execution>
+						<id>prepare-agent</id>
+						<goals>
+							<goal>prepare-agent</goal>
+						</goals>
+					</execution>
+					<execution>
+						<id>report</id>
+						<goals>
+							<goal>report</goal>
+						</goals>
+						<configuration>
+							<formats>
+								<format>XML</format>
+							</formats>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
 		</plugins>
 	</build>