Time series for ontop

stack-clients/docker-compose.yml

@@ -1,6 +1,6 @@
 services:
   stack-client:
-    image: ghcr.io/theworldavatar/stack-client${IMAGE_SUFFIX}:1.54.1
+    image: ghcr.io/theworldavatar/stack-client${IMAGE_SUFFIX}:1.55.0
     secrets:
       - blazegraph_password
       - postgis_password

stack-clients/pom.xml

@@ -7,7 +7,7 @@
 
     <groupId>com.cmclinnovations</groupId>
     <artifactId>stack-clients</artifactId>
-    <version>1.54.1</version>
+    <version>1.55.0</version>
 
     <name>Stack Clients</name>
     <url>https://theworldavatar.io</url>
@@ -116,7 +116,7 @@
         <dependency>
             <groupId>uk.ac.cam.cares.jps</groupId>
             <artifactId>jps-base-lib</artifactId>
-            <version>1.48.0</version>
+            <version>1.49.0</version>
         </dependency>
 
         <!-- https://mvnrepository.com/artifact/io.swagger.core.v3/swagger-annotations -->

stack-clients/src/main/java/com/cmclinnovations/stack/clients/timeseries/TimeSeriesRDBClient.java

@@ -0,0 +1,131 @@
+package com.cmclinnovations.stack.clients.timeseries;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URI;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.sql.Connection;
+import java.time.Instant;
+import java.util.List;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import com.cmclinnovations.stack.clients.core.EndpointNames;
+import com.cmclinnovations.stack.clients.ontop.OntopClient;
+import com.cmclinnovations.stack.clients.utils.LocalTempDir;
+import com.cmclinnovations.stack.services.OntopService;
+import com.cmclinnovations.stack.services.ServiceManager;
+import com.cmclinnovations.stack.services.config.ServiceConfig;
+
+import uk.ac.cam.cares.jps.base.exception.JPSRuntimeException;
+import uk.ac.cam.cares.jps.base.timeseries.TimeSeriesRDBClientOntop;
+
+public class TimeSeriesRDBClient<T> extends TimeSeriesRDBClientOntop<T> {
+
+    private static final String UNIX_TRS = "http://dbpedia.org/resource/Unix_time";
+    private static final String GENERIC_TRS = "http://example.org/TRS_placeholder";
+
+    /**
+     * Logger for error output.
+     */
+    private static final Logger LOGGER = LogManager.getLogger(TimeSeriesRDBClient.class);
+
+    // IRI of temporal reference system, used in ontop mapping to indicate reference
+    // of time, e.g. Unix
+    private final String trsIri;
+
+    // name of ontop container
+    private String ontopName = "ontop-timeseries";
+
+    public TimeSeriesRDBClient(Class<T> timeClass) {
+        this(timeClass, null);
+    }
+
+    public TimeSeriesRDBClient(Class<T> timeClass, String trsIri) {
+        super(timeClass);
+        if (null != trsIri) {
+            this.trsIri = trsIri;
+            LOGGER.info("TRS is set to {}", trsIri);
+        } else {
+            if (Instant.class == timeClass) {
+                this.trsIri = UNIX_TRS;
+                LOGGER.info("Time class is Instant, TRS is set to {}", UNIX_TRS);
+            } else {
+                this.trsIri = GENERIC_TRS;
+                LOGGER.info("Time class is not Instant, TRS is set to {}", GENERIC_TRS);
+            }
+        }
+    }
+
+    public void setOntopName(String ontopName) {
+        this.ontopName = ontopName;
+    }
+
+    @Override
+    public List<Integer> bulkInitTimeSeriesTable(List<List<String>> dataIRIs, List<List<Class<?>>> dataClasses,
+            List<String> tsIRIs, Integer srid, Connection conn) {
+        List<Integer> result = super.bulkInitTimeSeriesTable(dataIRIs, dataClasses, tsIRIs, srid, conn);
+
+        // spin up a new ontop container if it does not exist
+        configureOntop();
+
+        return result;
+    }
+
+    public void configureOntop() {
+        String stackName = System.getenv("STACK_NAME");
+        if (stackName == null) {
+            LOGGER.warn("STACK_NAME not detected, skipping Ontop intialisation");
+            return;
+        }
+
+        ServiceManager serviceManager = new ServiceManager(false);
+
+        ServiceConfig newOntopServiceConfig = serviceManager.duplicateServiceConfig(EndpointNames.ONTOP, ontopName);
+        newOntopServiceConfig.setEnvironmentVariable(OntopService.ONTOP_DB_NAME, "postgres");
+
+        newOntopServiceConfig.getEndpoints()
+                .replaceAll((endpointName, connection) -> new com.cmclinnovations.stack.services.config.Connection(
+                        connection.getUrl(),
+                        connection.getUri(),
+                        URI.create(connection.getExternalPath().toString()
+                                .replace(EndpointNames.ONTOP, ontopName))));
+        serviceManager.initialiseService(stackName, ontopName);
+
+        OntopClient ontopClient = OntopClient.getInstance(ontopName);
+
+        // create temporary file for ontop mapping
+        try (LocalTempDir tempDir = new LocalTempDir()) {
+
+            String obda = prepareMapping();
+
+            Path filePath = tempDir.getPath().resolve("ontop.obda");
+            Files.write(filePath, obda.getBytes());
+
+            // sends obda to container
+            ontopClient.updateOBDA(filePath);
+        } catch (IOException e) {
+            throw new JPSRuntimeException("Failed to write ontop mapping into temporary folder", e);
+        }
+    }
+
+    /**
+     * set TRS in Ontop mapping
+     * 
+     * @return
+     */
+    private String prepareMapping() {
+        // read template from resources folder
+        try (InputStream is = TimeSeriesRDBClient.class.getResourceAsStream("timeseries_ontop_template.obda")) {
+            return IOUtils.toString(is, StandardCharsets.UTF_8)
+                    .replace("[TRS_REPLACE]", trsIri).replace("[SCHEMA]", getSchema());
+        } catch (IOException e) {
+            throw new JPSRuntimeException("Error while reading timeseries_ontop_template.obda", e);
+        }
+    }
+
+}

stack-clients/src/main/resources/com/cmclinnovations/stack/clients/timeseries/timeseries_ontop_template.obda

@@ -0,0 +1,29 @@
+[PrefixDeclaration]
+obda:		https://w3id.org/obda/vocabulary#
+geo:		http://www.opengis.net/ont/geosparql#
+timeprefix:	http://www.w3.org/2006/time#
+timeseries:	https://www.theworldavatar.com/kg/ontotimeseries/
+
+[MappingDeclaration] @collection [[
+mappingId	time_series_data_[SCHEMA]
+target		timeseries:data/[SCHEMA]/{data_iri_index} timeseries:hasObservation timeseries:observation/[SCHEMA]/{id} .
+            timeseries:observation/[SCHEMA]/{id} a timeseries:Observation ; 
+                timeseries:observationOf timeseries:data/[SCHEMA]/{data_iri_index} ; 
+                timeseries:hasResult timeseries:result/[SCHEMA]/{id} ; 
+                timeprefix:hasTime timeseries:time/[SCHEMA]/{id} . 
+            timeseries:time/[SCHEMA]/{id} a timeprefix:Instant ;
+                timeprefix:inXSDDateTime {time_as_timestamp} ;
+                timeprefix:inTimePosition timeseries:timePosition/[SCHEMA]/{id}.
+            timeseries:timePosition/[SCHEMA]/{id} a timeprefix:TimePosition ;
+                timeprefix:numericPosition {time_as_number} ;
+                timeprefix:unitType timeprefix:unitSecond ;
+                timeprefix:hasTRS <[TRS_REPLACE]> .
+            timeseries:result/[SCHEMA]/{id} a timeseries:Result ; 
+                timeseries:hasValue {"double precision"}, {wkt}^^geo:wktLiteral, {int};
+                timeseries:hasUnit {unit} . 
+source		SELECT id, time_as_number, time_as_timestamp, data_iri_index, "double precision", ST_AsText("geometry(Point,4326)") AS wkt, int, unit FROM "[SCHEMA]".time_series_data
+
+mappingId	equivalent_iri_[SCHEMA]
+target		<{data_iri}> obda:isCanonicalIRIOf timeseries:data/[SCHEMA]/{data_iri_index} . 
+source		SELECT data_iri, data_iri_index from "[SCHEMA]".time_series_data_iri
+]]

stack-data-uploader/docker-compose.yml

@@ -1,6 +1,6 @@
 services:
   stack-data-uploader:
-    image: ghcr.io/theworldavatar/stack-data-uploader${IMAGE_SUFFIX}:1.54.1
+    image: ghcr.io/theworldavatar/stack-data-uploader${IMAGE_SUFFIX}:1.55.0
     secrets:
       - blazegraph_password
       - postgis_password

stack-data-uploader/pom.xml

@@ -7,7 +7,7 @@
 
     <groupId>com.cmclinnovations</groupId>
     <artifactId>stack-data-uploader</artifactId>
-    <version>1.54.1</version>
+    <version>1.55.0</version>
 
     <name>Stack Data Uploader</name>
     <url>https://theworldavatar.io</url>
@@ -38,7 +38,7 @@
         <dependency>
             <groupId>com.cmclinnovations</groupId>
             <artifactId>stack-clients</artifactId>
-            <version>1.54.1</version>
+            <version>1.55.0</version>
         </dependency>
 
         <dependency>

stack-manager/docker-compose.yml

@@ -1,6 +1,6 @@
 services:
   stack-manager:
-    image: ghcr.io/theworldavatar/stack-manager${IMAGE_SUFFIX}:1.54.1
+    image: ghcr.io/theworldavatar/stack-manager${IMAGE_SUFFIX}:1.55.0
     environment:
       EXTERNAL_PORT: "${EXTERNAL_PORT-3838}"
       STACK_BASE_DIR: "${STACK_BASE_DIR}"

stack-manager/pom.xml

@@ -7,7 +7,7 @@
 
     <groupId>com.cmclinnovations</groupId>
     <artifactId>stack-manager</artifactId>
-    <version>1.54.1</version>
+    <version>1.55.0</version>
 
     <name>Stack Manager</name>
     <url>https://theworldavatar.io</url>
@@ -38,7 +38,7 @@
         <dependency>
             <groupId>com.cmclinnovations</groupId>
             <artifactId>stack-clients</artifactId>
-            <version>1.54.1</version>
+            <version>1.55.0</version>
         </dependency>
 
         <dependency>