[New] Migrate from rdf4j to graphdb + initialize repository

deploy/db-server/Dockerfile

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+FROM ontotext/graphdb:10.6.3
+
+# 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
+### for arm64
+RUN if command -v apt >/dev/null; then \
+    apt update && \
+    apt install -y python3-rdflib && \
+    apt install -y liburi-perl; \
+fi
+
+### for amd64
+RUN if command -v apk >/dev/null; then \
+    apk add py3-rdflib && \
+    apk add perl-uri; \
+fi
+
+# Copy scripts
+COPY bin/* ${GRAPHDB_INSTALL_DIR}/bin/
+
+EXPOSE 7200
+
+# Assuming following input directories:
+#     - /repo-config and data -- configuration ttl files to create repositories
+#     - /root/graphdb-import -- files to import data to specific repositories
+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

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

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+#!/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()
+

deploy/db-server/bin/repo-init.sh

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+#!/bin/sh
+
+#
+# Initializes GraphDB repositories (the repositories are created if they do not exist yet and some of the data are replaced)
+#
+
+SOURCE_DIR=$1
+GRAPHDB_HOME=$2
+
+SCRIPT_DIR="`dirname $0`"
+
+echo "INFO: Running initializer for GraphDB repositories ..."
+
+# Wait for GraphDB to start up
+echo "INFO: Waiting for GraphDB to start up..."
+sleep 15s
+
+ls ${SOURCE_DIR}/*-config.ttl | while read REPO_CONFIG_FILE; do
+
+	REPO_NAME=`$SCRIPT_DIR/get-value-of-rdf-property.py $REPO_CONFIG_FILE 'http://www.openrdf.org/config/repository#repositoryID'`
+
+	if [ -z "$REPO_NAME" ]; then
+    		echo "ERROR: Could not parse repository name from file $REPO_CONFIG_FILE"
+    		exit 1
+	fi
+
+	if [ ! -d ${GRAPHDB_HOME}/data/repositories/${REPO_NAME} ] || [ -z "$(ls -A ${GRAPHDB_HOME})/data/repositories/${REPO_NAME}" ]; then
+		echo "INFO: Initializing repository $REPO_NAME..."
+
+	    # Create repository based on configuration
+	    echo "INFO: Creating repository $REPO_NAME..."
+	    curl -X POST --header "Content-Type: multipart/form-data" -F "config=@${REPO_CONFIG_FILE}" "http://localhost:7200/rest/repositories"
+	    echo "INFO: Repository $REPO_NAME successfully initialized."
+	else
+	    echo "INFO: Repository $REPO_NAME already exists. Skipping initialization..."
+	fi
+done

deploy/db-server/conf/logback.xml

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+<configuration debug="false" scan="true" scanPeriod="30 seconds">
+    <jmxConfigurator />
+
+    <!-- Try to guess the logs destination based on the application server or fallback to a default logs directory(embedded mode)
+    NOTE: We are using a really old version of logback so we have to use p().isEmpty instead of isDefined -->
+
+    <if condition='p("logDestinationDirectory").isEmpty()'>
+        <then>
+            <!-- catalina.base if we are running on tomcat -->
+            <if condition='!p("catalina.base").isEmpty()'>
+                <then>
+                    <property name="logDestinationDirectory" value="${catalina.base}/logs/graphdb"/>
+                </then>
+                <else>
+                    <!-- jetty.base if we are running on tomcat -->
+                    <if condition='!p("jetty.base").isEmpty()'>
+                        <then>
+                            <property name="logDestinationDirectory" value="${jetty.base}/logs/graphdb"/>
+                        </then>
+                        <else>
+                            <!-- we are running in embedded mode -->
+                            <property name="logDestinationDirectory" value="logs"/>
+                        </else>
+                    </if>
+                </else>
+            </if>
+        </then>
+    </if>
+
+    <property name="defaultPattern" value="[%-5p] %d{ISO8601} [%t | %c{5}]%X{headers} %m%n%ex" />
+    <property name="encoding" value="UTF-8" />
+
+    <!-- Audit log. Contains security related things -->
+    <appender name="AuditLog" class="ch.qos.logback.core.rolling.RollingFileAppender">
+        <rollingPolicy class="ch.qos.logback.core.rolling.TimeBasedRollingPolicy">
+            <fileNamePattern>${logDestinationDirectory}/audit-log-%d{yyyy-MM-dd}.log</fileNamePattern>
+        </rollingPolicy>
+        <encoder>
+            <pattern>${defaultPattern}</pattern>
+            <charset>${encoding}</charset>
+        </encoder>
+    </appender>
+
+    <appender name="MainLog" class="ch.qos.logback.core.rolling.RollingFileAppender">
+        <rollingPolicy class="ch.qos.logback.core.rolling.TimeBasedRollingPolicy">
+            <fileNamePattern>${logDestinationDirectory}/main-%d{yyyy-MM-dd}.log</fileNamePattern>
+        </rollingPolicy>
+        <encoder>
+            <pattern>${defaultPattern}</pattern>
+            <charset>${encoding}</charset>
+        </encoder>
+    </appender>
+
+    <appender name="ErrorLog" class="ch.qos.logback.core.rolling.RollingFileAppender">
+        <rollingPolicy class="ch.qos.logback.core.rolling.TimeBasedRollingPolicy">
+            <fileNamePattern>${logDestinationDirectory}/error-%d{yyyy-MM-dd}.log</fileNamePattern>
+        </rollingPolicy>
+        <encoder>
+            <pattern>${defaultPattern}</pattern>
+            <charset>${encoding}</charset>
+        </encoder>
+        <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+            <level>ERROR</level>
+        </filter>
+    </appender>
+
+    <appender name="QueryLog" class="ch.qos.logback.core.rolling.RollingFileAppender">
+        <rollingPolicy class="ch.qos.logback.core.rolling.TimeBasedRollingPolicy">
+            <fileNamePattern>${logDestinationDirectory}/query-log-%d{yyyy-MM-dd}.log</fileNamePattern>
+        </rollingPolicy>
+        <encoder>
+            <pattern>${defaultPattern}</pattern>
+            <charset>${encoding}</charset>
+        </encoder>
+    </appender>
+
+    <appender name="SlowQueryLog" class="ch.qos.logback.core.rolling.RollingFileAppender">
+        <rollingPolicy class="ch.qos.logback.core.rolling.TimeBasedRollingPolicy">
+            <fileNamePattern>${logDestinationDirectory}/slow-query-log-%d{yyyy-MM-dd}.log</fileNamePattern>
+        </rollingPolicy>
+        <encoder>
+            <pattern>${defaultPattern}</pattern>
+            <charset>${encoding}</charset>
+        </encoder>
+    </appender>
+
+    <if condition='!p("graphdb.foreground").isEmpty()'>
+        <then>
+            <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
+                <encoder>
+                    <pattern>${defaultPattern}</pattern>
+                </encoder>
+            </appender>
+        </then>
+    </if>
+
+    <!-- Log all repository, user creations, modifications and deletions. Also logs successful or not attempts to
+    login into system. Updates, queries and imports to repository. Set to "INFO" level for logging all former updates.
+    Will log exceptions on "ERROR" level. Additivity is set to "false" and called first to prevent the messages
+    from cluttering the other logs. -->
+    <logger name="com.ontotext.forest.security.audit.AuditLoggingFilter" level="WARN" additivity="false">
+        <appender-ref ref="AuditLog"/>
+    </logger>
+
+    <!-- Log update operations on workers. Set to "INFO" level by default for logging all updates in workers' QueryLog.
+     Will log exceptions on "ERROR" level. Additivity is set to "false" and called first to prevent the messages
+     from cluttering the other logs.-->
+    <logger name="com.ontotext.trree.monitorRepository.MonitorRepositoryConnection" level="WARN" additivity="false">
+        <appender-ref ref="QueryLog"/>
+    </logger>
+
+    <!-- Log querry operations on the repository. Set to "DEBUG" level for logging all querries. Will log exceptions on "ERROR"
+          level. Additivity is set to "false" to prevent the messages from cluttering the other logs. -->
+    <logger name="com.ontotext.trree.query.LoggingClosableIteration" level="WARN" additivity="false">
+        <appender-ref ref="QueryLog"/>
+    </logger>
+
+    <!-- Log slow queries on "INFO" level. Queries are deemed "slow" if they take more than "SlowOpThresholdMs" from the
+          RepositorySettings property. Set the level to "OFF" to stop this log. Additivity is set to "false" to prevent the messages
+          from cluttering the other logs. -->
+    <logger name="slow-queries" level="ERROR" additivity="false">
+        <appender-ref ref="SlowQueryLog"/>
+    </logger>
+
+    <root>
+        <level value="${graphdb.logger.root.level:-WARN}"/>
+        <appender-ref ref="MainLog"/>
+        <appender-ref ref="ErrorLog" />
+        <if condition='!p("graphdb.foreground").isEmpty()'>
+            <then>
+                <appender-ref ref="STDOUT"/>
+            </then>
+        </if>
+
+    </root>
+
+    <!-- Make some of the more verbose loggers less chatty -->
+    <logger name="org.springframework" level="WARN"/>
+    <logger name="org.apache" level="WARN"/>
+    <logger name="com.github.ziplet" level="WARN"/>
+    <logger name="springfox.documentation" level="WARN"/>
+
+    <!-- OpenRefine loggers be less verbose -->
+    <logger name="CsvExporter" level="WARN"/>
+    <logger name="FileProjectManager" level="WARN"/>
+    <logger name="HistoryEntry" level="WARN"/>
+    <logger name="ImportingParserBase" level="WARN"/>
+    <logger name="JsonParser" level="WARN"/>
+    <logger name="ProjectManager" level="WARN"/>
+    <logger name="RecordModel" level="WARN"/>
+    <logger name="TreeImportUtilities" level="WARN"/>
+    <logger name="velocity" level="WARN"/>
+    <logger name="Velocity.*" level="WARN"/>
+    <logger name="XmlImportUtilities" level="WARN"/>
+    <logger name="binning_clusterer" level="WARN"/>
+    <logger name="butterfly" level="WARN"/>
+    <logger name="butterfly.*" level="WARN"/>
+    <logger name="command" level="WARN"/>
+    <logger name="compute-clusters_command" level="WARN"/>
+    <logger name="create-import-job_command" level="WARN"/>
+    <logger name="create-project_command" level="WARN"/>
+    <logger name="get-scatterplot_command" level="WARN"/>
+    <logger name="import-project_command" level="WARN"/>
+    <logger name="importing" level="WARN"/>
+    <logger name="importing-controller_command" level="WARN"/>
+    <logger name="importing-utilities" level="WARN"/>
+    <logger name="javascript" level="WARN"/>
+    <logger name="kNN_clusterer" level="WARN"/>
+    <logger name="open" level="WARN"/>
+    <logger name="office" level="WARN"/>
+    <logger name="project" level="WARN"/>
+    <logger name="project_metadata" level="WARN"/>
+    <logger name="project_metadata_utilities" level="WARN"/>
+    <logger name="project_utilities" level="WARN"/>
+    <logger name="recon-config" level="WARN"/>
+    <logger name="recon-operation" level="WARN"/>
+    <logger name="refine" level="WARN"/>
+    <logger name="refine-standard-recon" level="WARN"/>
+    <logger name="refine_clientSideResourceManager" level="WARN"/>
+    <logger name="scatterplot_facet" level="WARN"/>
+
+    <!-- GeoSPAQRL related deps be less verbose -->
+    <logger name="hsqldb.*" level="WARN"/>
+    <logger name="org.geotoolkit.*" level="WARN"/>
+
+    <!-- SemanticVectors related logger be less verbose -->
+    <logger name="pitt.search.semanticvectors.DocVectors" level="WARN"/>
+</configuration>

deploy/db-server/init-config/s-pipes-hello-world-config.ttl

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+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix rep: <http://www.openrdf.org/config/repository#> .
+@prefix sail: <http://www.openrdf.org/config/sail#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix graphdb: <http://www.ontotext.com/config/graphdb#>.
+
+<#s-pipes-hello-world> a rep:Repository;
+  rep:repositoryID "s-pipes-hello-world";
+  rep:repositoryImpl [
+      rep:repositoryType "graphdb:SailRepository";
+      <http://www.openrdf.org/config/repository/sail#sailImpl> [
+          graphdb:base-URL "http://example.org/owlim#";
+          graphdb:check-for-inconsistencies "false";
+          graphdb:defaultNS "";
+          graphdb:disable-sameAs "true";
+          graphdb:enable-context-index "true";
+          graphdb:enable-literal-index "true";
+          graphdb:enablePredicateList "true";
+          graphdb:entity-id-size "32";
+          graphdb:entity-index-size "10000000";
+          graphdb:imports "";
+          graphdb:in-memory-literal-properties "true";
+          graphdb:owlim-license "";
+          graphdb:query-limit-results "0";
+          graphdb:query-timeout "0";
+          graphdb:read-only "false";
+          graphdb:repository-type "file-repository";
+          graphdb:storage-folder "storage";
+          graphdb:throw-QueryEvaluationException-on-timeout "false";
+          sail:sailType "graphdb:Sail"
+        ]
+    ];
+  rdfs:label "SPipes Hello World repository" .