202 fine grained

.github/workflows/build-server-docker.yml → .github/workflows/docker-image.yml

@@ -1,43 +1,42 @@
-name: Build server docker
+name: Publish Docker Image
 
 on:
   push:
-    branches: [ master ]
+    branches: [ main ]
   pull_request:
-    branches: [ master ]
+    branches: [ main ]
   workflow_dispatch:
 env:
-  IMAGE_NAME: record-manager-server
-  MVN_PROFILE: production-docker
-  MAIN_BRANCH_NAME: master
+  # The last two fragments of the identifier of the docker image
+  IMAGE_NAME: ${{ github.repository }}
+  MAIN_BRANCH_NAME: main
+  REGISTRY: ghcr.io
+
 jobs:
-
   build-and-publish:
-
+    # Skip if PR is from a fork
+    if: github.event_name != 'pull_request' || github.event.repository.full_name == github.event.pull_request.head.repo.full_name
     runs-on: ubuntu-latest
-    
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - name: Build application archive
-        run: mvn clean package -B -P $MVN_PROFILE
-
       - name: Build docker image
         run: docker build . --file Dockerfile --tag $IMAGE_NAME
 
       - name: Log in to the Container registry
-        run: echo "${{ github.token }}" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin
+        run: echo "${{ github.token }}" | docker login ${{ env.REGISTRY }} -u ${{ github.actor }} --password-stdin
 
       - name: Push image
         run: |
-          IMAGE_ID=docker.pkg.github.com/${{ github.repository }}/$IMAGE_NAME
+          IMAGE_ID=${{ env.REGISTRY }}/$IMAGE_NAME
           # Change all uppercase to lowercase
           IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
           # Get branch name if merge to a branch
           GIT_BRANCH_NAME=$(echo "${{ github.ref }}" | grep 'refs/heads/.*' | cut -d"/" -f 3)
           # Get pull request id (e.g. "pr-123" from "/pulls/123")
           PULL_REQUEST_ID=$(echo "${{ github.event.pull_request.number }}" | grep -v "^$" | sed 's/^/pr-/')
-          # Get tag id while strip "v" prefix (e.g. "1.2" from "v1.2")
+          # Get tag id while stripping "v" prefix (e.g. "1.2" from "v1.2")
           TAG_ID=$(echo "${{ github.ref }}" | grep 'refs/tags/.*' | cut -d"/" -f 3 | sed -e 's/^v//')
           # Version is either "git branch name"/"pull request id"/"tag id"                    
           VERSION=${GIT_BRANCH_NAME:-${PULL_REQUEST_ID:-${TAG_ID}}}

.github/workflows/protect-master.yml → .github/workflows/protect-main.yml

@@ -6,9 +6,9 @@ name: CI
 # events but only for the master branch
 on:
   push:
-    branches: [ master ]
+    branches: [ main ]
   pull_request:
-    branches: [ master ]
+    branches: [ main ]
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
@@ -20,12 +20,12 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-    - uses: actions/checkout@v2
-
-    # Runs a single command using the runners shell
-#    - name: Compile
-#      run: mvn compile
+    - uses: actions/checkout@v3
+    - uses: actions/setup-java@v3
+      with:
+        java-version: '17'
+        distribution: 'adopt'
 
     # Runs a set of commands using the runners shell
-#    - name: Test
-#      run: mvn test
+    - name: Test
+      run: mvn -B test

.gitignore

@@ -3,6 +3,7 @@
 target
 node_modules
 build
+logs
 **/generated-sources
 **/npm-debug.log
 .DS_store

Dockerfile

@@ -1,7 +1,18 @@
-FROM tomcat:9.0-jdk8-slim
+FROM maven:3-eclipse-temurin-17 as build
 
-EXPOSE 8080
+WORKDIR /record-manager
+
+COPY pom.xml pom.xml
+
+RUN mvn -B de.qaware.maven:go-offline-maven-plugin:resolve-dependencies
+
+COPY src src
 
-COPY /target/record-manager-0.*.war /usr/local/tomcat/webapps/record-manager.war
+RUN mvn package -B -DskipTests=true
+
+FROM eclipse-temurin:17-jdk-alpine as runtime
+COPY --from=build  /record-manager/target/record-manager.jar record-manager.jar
+
+EXPOSE 8080
 
-CMD ["catalina.sh","run"]
+ENTRYPOINT ["java","-jar","/record-manager.jar"]

README.md

@@ -1,12 +1,11 @@
 # OFN Record Manager
 
-Manager of records based on OFN (https://opendata.gov.cz/otevřené-formální-normy:start).
+Manager of records based on OFN (https://data.gov.cz/ofn/).
 
 ## Required Technologies
 
-- JDK 8 (preferably Oracle)
-- Apache Maven 3.5.x
-- Apache Tomcat 9 or newer (required by Servlet API 4)
+- JDK 17
+- Apache Maven 3.5.x or later
 
 ## System Architecture
 

db-server/Dockerfile

@@ -0,0 +1,22 @@
+FROM ontotext/graphdb:10.2.0
+
+# Override parent entrypoint
+ENTRYPOINT []
+
+ENV GRAPHDB_HOME=/opt/graphdb/home
+ENV GRAPHDB_INSTALL_DIR=/opt/graphdb/dist
+
+WORKDIR ${GRAPHDB_HOME}
+
+# Install libs related to RDF processing
+RUN apk add py3-rdflib
+RUN apk add perl-uri
+
+# Copy initialization data and repository config
+COPY init-data /root/graphdb-import
+COPY init-config /repo-config
+COPY bin/* ${GRAPHDB_INSTALL_DIR}/bin/
+
+EXPOSE 7200
+
+CMD ${GRAPHDB_INSTALL_DIR}/bin/repo-init.sh /repo-config ${GRAPHDB_HOME} & ${GRAPHDB_INSTALL_DIR}/bin/graphdb -Dgraphdb.home=${GRAPHDB_HOME} -Dgraphdb.logback=${GRAPHDB_INSTALL_DIR}/conf/logback.xml

db-server/bin/get-rdf-subject-by-type.py

@@ -0,0 +1,75 @@
+#!/usr/bin/python3
+
+import sys
+from rdflib import Graph, URIRef
+
+def log(message):
+    print("ERROR: " + message, file=sys.stderr)
+
+def check_params():
+    if len(sys.argv) != 3:
+        log(f"""Illegal number of parameters.
+
+Script returns single subject of triple matching the pattern '?result a <type-uri>' 
+from the file specified by <rdf-file-path>.
+
+Usage: {sys.argv[0]} <rdf-file-path> <type-uri>
+
+Example: {sys.argv[0]} "./init-data/forms/example-1.ttl" "http://onto.fel.cvut.cz/ontologies/form/form-template"
+""")
+        sys.exit(1)
+
+def check_only_one_instance(results, rdf_type):
+    if len(results) == 0:
+        log(f"No instance found for the specified {rdf_type}.")
+        sys.exit(2)
+    elif len(results) > 1:
+        error_message = f"Multiple instances found for the type {rdf_type}. Triple that match pattern '?s a <{rdf_type}>' are:\n"
+        for row in results:
+            subject = row[0]
+            error_message += f"  {subject.n3()} a <{rdf_type}> .\n"
+        log(error_message)
+        sys.exit(3)
+
+
+def load_rdf_graph(file_path):
+    # Load RDF file into an RDFLib graph
+    g = Graph()
+
+    # Explicitly specify the format based on the file extension
+    if file_path.endswith(".ttl"):
+        g.parse(file_path, format="turtle")
+    elif file_path.endswith(".rdf"):
+        g.parse(file_path, format="xml")
+    else:
+        log(f"Unsupported RDF file format of {file_path}.")
+        sys.exit(1)
+
+    return g
+
+def main():
+    check_params()
+
+    file_path = sys.argv[1]
+    rdf_type = URIRef(sys.argv[2])
+
+    g = load_rdf_graph(file_path)
+
+    # Query for subjects with the specified RDF type
+    query = f"""
+        SELECT ?subject
+        WHERE {{
+            ?subject a <{rdf_type}>.
+        }}
+    """
+
+    results = g.query(query)
+
+    check_only_one_instance(results, rdf_type)
+
+    for row in results:
+        subject = row[0]
+        print(subject.n3())
+
+if __name__ == "__main__":
+    main()

db-server/bin/get-value-of-rdf-property.py

@@ -0,0 +1,73 @@
+#!/usr/bin/python3
+
+import sys
+from rdflib import Graph, URIRef
+
+def log(message):
+    print("ERROR: " + message, file=sys.stderr)
+
+def check_params():
+    if len(sys.argv) != 3:
+        log(f"""Illegal number of parameters.
+
+Script returns single value of <rdf-property-uri> from file specified by <rdf-file-path>.
+
+Usage: {sys.argv[0]} <rdf-file-path> <rdf-property-uri>
+
+Example: {sys.argv[0]} "./init-config/repo-config.ttl" "http://www.openrdf.org/config/repository#repositoryID"
+""")
+        sys.exit(1)
+
+
+def check_property_has_single_value(results, rdf_property):
+    if len(results) == 0:
+        log(f"No values found for the specified property {rdf_property}.")
+        sys.exit(2)
+    elif len(results) > 1:
+        error_message = f"Multiple values found for the property {rdf_property}. Triple that match pattern '?s <{rdf_property}> ?o' are:\n"
+        for row in results:
+            subject, value = row
+            error_message += f"  {subject} {rdf_property} {value} .\n"
+        log(error_message)
+        sys.exit(3)
+
+def load_rdf_graph(file_path):
+    # Load RDF file into an RDFLib graph
+    g = Graph()
+
+    # Explicitly specify the format based on the file extension
+    if file_path.endswith(".ttl"):
+        g.parse(file_path, format="turtle")
+    elif file_path.endswith(".rdf"):
+        g.parse(file_path, format="xml")
+    else:
+        log(f"Unsupported RDF file format of {file_path}.")
+        sys.exit(1)
+    return g
+
+def main():
+    check_params()
+
+    file_path = sys.argv[1]
+    rdf_property = URIRef(sys.argv[2])
+
+    g = load_rdf_graph(file_path)
+
+    # Query for subjects with the specified property
+    query = f"""
+        SELECT ?subject ?value
+        WHERE {{
+            ?subject <{rdf_property}> ?value.
+        }}
+    """
+    results = g.query(query)
+
+    check_property_has_single_value(results, rdf_property)
+
+    for row in results:
+        subject, value = row
+        print(f"{value}")
+
+if __name__ == "__main__":
+    main()
+