Isochrones for credo

Agents/IsochroneAgent/Dockerfile

@@ -1,6 +1,6 @@
 # First stage: build war file
 #==================================================================================================
-FROM maven:3.6-openjdk-11-slim as builder
+FROM maven:3.6-openjdk-11-slim AS builder
 
 # Copy all files into root's home, including the source, pom file, ./m2 directory and credentials
 ADD . /root
@@ -17,10 +17,9 @@ WORKDIR /root/isochroneagent
 RUN --mount=type=cache,target=/root/.m2/repository mvn package
 
 #==================================================================================================
-
 # Second stage: copy the downloaded dependency into a new image and build into an app
 #==================================================================================================
-FROM tomcat:9.0 as agent
+FROM tomcat:9.0 AS agent
 
 WORKDIR /root/isochroneagent
 

Agents/IsochroneAgent/docker-compose-debug.yml

@@ -0,0 +1,7 @@
+version: '3.8'
+services:
+  stack-manager:
+    environment:
+      - "JAVA_OPTS=-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=*:5005"
+    ports:
+      - "${DEBUG_PORT}:5005"

Agents/IsochroneAgent/docker-compose-stack.yml

@@ -1,4 +1,3 @@
-version: '3.8'
 services:
   isochroneagent:
     deploy:

Agents/IsochroneAgent/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.8"
 
 services:
   isochroneagent:
-    image: ghcr.io/cambridge-cares/isochroneagent:1.5.0
+    image: ghcr.io/cambridge-cares/isochroneagent:1.5.0-op-SNAPSHOT
     build: .
     ports:
       - "10105:8080"

Agents/IsochroneAgent/inputs/config.properties

@@ -1,5 +1,5 @@
 #DbName
-db.name=postgres
+db.name=credo_roads
 
 #Segmentization length
 segmentization_length= 0.000045

Agents/IsochroneAgent/inputs/credo/POIqueries/primarySubstation.sparql

@@ -0,0 +1,22 @@
+PREFIX obe:       <https://www.theworldavatar.com/kg/ontobuiltenv/>
+PREFIX rdf:       <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX geo:       <http://www.opengis.net/ont/geosparql#>
+PREFIX geof:      <http://www.opengis.net/def/function/geosparql/>
+PREFIX uom:       <http://www.opengis.net/def/uom/OGC/1.0/>
+PREFIX ukpn:      <http://theworldavatar.com/ontology/ontocredo/ontoukpn.owl#>
+
+SELECT DISTINCT ?poi_iri ?poi_type ?geometry
+WHERE {
+        {
+          SERVICE [ONTOP] {
+            SELECT DISTINCT * WHERE {
+              ?sub a ukpn:PrimarySubStation ;
+              geo:hasDefaultGeometry/geo:asWKT ?geometry
+
+              BIND(?sub AS ?poi_iri)
+              BIND(ukpn:PrimarySubStation AS ?poi_type)
+            }
+            LIMIT 10
+          }
+        }
+}

Agents/IsochroneAgent/inputs/credo/edgesSQLTable/Drive_Normal.sql

@@ -0,0 +1 @@
+SELECT gid as id, source, target, cost_s as cost FROM routing_ways_segment WHERE tag_id IN (100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 121, 123, 124, 125, 401)

Agents/IsochroneAgent/isochroneagent/pom.xml

@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <project xmlns="http://maven.apache.org/POM/4.0.0"
-         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <groupId>uk.ac.cam.cares.jps</groupId>
     <artifactId>isochroneagent</artifactId>
-    <version>1.5.0</version>
+    <version>1.5.0-op-SNAPSHOT</version>
     <packaging>war</packaging>
 
     <properties>
@@ -45,14 +45,12 @@
             <id>prod-profile</id>
             <properties>
                 <!-- Set property to download production logging config -->
-                <log.artifact>java-logging-prod</log.artifact>
             </properties>
         </profile>
     </profiles>
 
     <!-- Build settings -->
     <build>
-
         <plugins>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
@@ -64,7 +62,7 @@
                 </configuration>
             </plugin>
 
-                        <!-- Allows maven executions -->
+            <!-- Allows maven executions -->
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>exec-maven-plugin</artifactId>
@@ -122,7 +120,7 @@
         <dependency>
             <groupId>org.json</groupId>
             <artifactId>json</artifactId>
-            <version>20180813</version>
+            <version>20240303</version>
             <type>jar</type>
         </dependency>
         <!-- Logging, versions pulled from parent -->
@@ -162,7 +160,6 @@
         <dependency>
             <groupId>org.postgresql</groupId>
             <artifactId>postgresql</artifactId>
-            <version>42.5.4</version>
         </dependency>
         <!-- for interacting with the stack -->
         <dependency>

Agents/IsochroneAgent/isochroneagent/src/main/java/uk/ac/cam/cares/jps/agent/isochroneagent/EndpointConfig.java

@@ -6,12 +6,9 @@
 
 public class EndpointConfig {
     private PostGISEndpointConfig postGISEndpointConfig;
-    private String dburl;
     private String dbUser;
     private String dbPassword;
     private String kgurl;
-    private String kguser;
-    private String kgpassword;
 
 
     public EndpointConfig() {
@@ -23,10 +20,6 @@ public EndpointConfig() {
         BlazegraphEndpointConfig blazegraphEndpointConfig = containerClient.readEndpointConfig("blazegraph",
                 BlazegraphEndpointConfig.class);
         this.kgurl = blazegraphEndpointConfig.getUrl("kb");
-        this.kguser = blazegraphEndpointConfig.getUsername();
-        this.kgpassword = blazegraphEndpointConfig.getPassword();
-
-
     }
 
     public String getDbUrl(String dbName) {

Agents/IsochroneAgent/isochroneagent/src/main/java/uk/ac/cam/cares/jps/agent/isochroneagent/FileReader.java

@@ -16,8 +16,14 @@
 
 public class FileReader {
 
+    // Private constructor to hide the implicit public one
+    private FileReader() {
+        throw new UnsupportedOperationException("This is a utility class and cannot be instantiated");
+    }
+
     /**
      * Read input files
+     * 
      * @param path
      * @return
      * @throws FileNotFoundException
@@ -26,14 +32,15 @@ public static InputStream getStream(String path) throws FileNotFoundException {
         return new FileInputStream(path);
     }
 
-
     /**
-     * Read Point of Interest (POI) files from directory and parse into Map, allows multiple SPARQL files.
-     * @param POI_PATH Path for directory containing POI SPARQL queries
+     * Read Point of Interest (POI) files from directory and parse into Map, allows
+     * multiple SPARQL files.
+     * 
+     * @param poiPath Path for directory containing POI SPARQL queries
      * @return
      */
-    public static Map readPOIsparql(Path POI_PATH) {
-        try (Stream<Path> files = Files.list(POI_PATH)) {
+    public static Map<String, String> readPOIsparql(Path poiPath) {
+        try (Stream<Path> files = Files.list(poiPath)) {
             // Find all available SPARQL files
             Map<String, String> sparqlFiles = files
                     .filter(Files::isRegularFile)
@@ -50,24 +57,25 @@ public static Map readPOIsparql(Path POI_PATH) {
                             }));
 
             // Process each SPARQL file
-            sparqlFiles.forEach((fileName, filePath) -> {
-                // Process the SPARQL file here
-                // You can replace the following line with your processing logic
-                System.out.println("Processing SPARQL file: " + filePath);
-            });
+            sparqlFiles.forEach((fileName, filePath) ->
+            // Process the SPARQL file here
+            // You can replace the following line with your processing logic
+            System.out.println("Processing SPARQL file: " + filePath));
             return sparqlFiles;
         } catch (IOException ex) {
-            throw new RuntimeException("Failed to read files from the directory.", ex);
+            throw new RuntimeException("Failed to read SPARQL files from" + poiPath, ex);
         }
     }
 
     /**
-     * Read EDGESTABLE SQL files from directory and parse into Map, allows multiple .SQL files.
-     * @param EDGESTABLESQL_PATH Path for directory containing .SQL
+     * Read EDGESTABLE SQL files from directory and parse into Map, allows multiple
+     * .SQL files.
+     * 
+     * @param edgesTableSQLPath Path for directory containing .SQL
      * @return
      */
-    public static Map readEdgesTableSQL(Path EDGESTABLESQL_PATH) {
-        try (Stream<Path> files = Files.list(EDGESTABLESQL_PATH)) {
+    public static Map<String, String> readEdgesTableSQL(Path edgesTableSQLPath) {
+        try (Stream<Path> files = Files.list(edgesTableSQLPath)) {
             // Find all available EdgesTableSQL files
             Map<String, String> edgesTableSQLFiles = files
                     .filter(Files::isRegularFile)
@@ -84,33 +92,36 @@ public static Map readEdgesTableSQL(Path EDGESTABLESQL_PATH) {
                             }));
 
             // Process each EdgesTableSQL file
-            edgesTableSQLFiles.forEach((fileName, filePath) -> {
+            edgesTableSQLFiles.forEach((fileName, filePath) -> 
                 // Process the EdgesTableSQL file here
                 // You can replace the following line with your processing logic
-                System.out.println("Processing EdgesTableSQL file: " + filePath);
-            });
+                System.out.println("Processing EdgesTableSQL file: " + filePath)
+            );
 
             return edgesTableSQLFiles;
         } catch (IOException ex) {
-            throw new RuntimeException("Failed to read files from the directory.", ex);
+            throw new RuntimeException("Failed to read SQL files from" + edgesTableSQLPath, ex);
         }
     }
 
-    /** Retrieve POI locations from knowledge graph by executing the input SPARQL queries.
+    /**
+     * Retrieve POI locations from knowledge graph by executing the input SPARQL
+     * queries.
+     * 
      * @param storeClient
-     * @param POImap
+     * @param poiMap
      * @return
      */
-    public static JSONArray getPOILocation(RemoteStoreClient storeClient, Map<String, String> POImap)
-    {            
+    public static JSONArray getPOILocation(RemoteStoreClient storeClient, Map<String, String> poiMap) {
         JSONArray cumulativePOI = new JSONArray();
-        for (Map.Entry<String, String> entry : POImap.entrySet()) {
+        for (Map.Entry<String, String> entry : poiMap.entrySet()) {
             String value = entry.getValue();
-            JSONArray POI = storeClient.executeQuery(value);
+            JSONArray poi = storeClient.executeQuery(value);
 
-            // Iterate through the POIs in this iteration and add them to the cumulative array
-            for (int i = 0; i < POI.length(); i++) {
-                cumulativePOI.put(POI.get(i));
+            // Iterate through the POIs in this iteration and add them to the cumulative
+            // array
+            for (int i = 0; i < poi.length(); i++) {
+                cumulativePOI.put(poi.get(i));
             }
         }
         return cumulativePOI;

Agents/IsochroneAgent/isochroneagent/src/main/java/uk/ac/cam/cares/jps/agent/isochroneagent/IsochroneAgent.java

@@ -1,9 +1,5 @@
 package uk.ac.cam.cares.jps.agent.isochroneagent;
 
-import javax.servlet.annotation.WebServlet;
-import javax.ws.rs.BadRequestException;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
@@ -18,15 +14,17 @@
 
 import org.json.JSONArray;
 import org.json.JSONObject;
-import uk.ac.cam.cares.jps.base.agent.JPSAgent;
-import uk.ac.cam.cares.jps.base.exception.JPSRuntimeException;
-import uk.ac.cam.cares.jps.base.query.RemoteRDBStoreClient;
-import uk.ac.cam.cares.jps.base.query.RemoteStoreClient;
+
 import com.cmclinnovations.stack.clients.geoserver.GeoServerClient;
 import com.cmclinnovations.stack.clients.geoserver.GeoServerVectorSettings;
 import com.cmclinnovations.stack.clients.geoserver.UpdatedGSVirtualTableEncoder;
 import com.cmclinnovations.stack.clients.ontop.OntopClient;
 
+import uk.ac.cam.cares.jps.base.agent.JPSAgent;
+import uk.ac.cam.cares.jps.base.exception.JPSRuntimeException;
+import uk.ac.cam.cares.jps.base.query.RemoteRDBStoreClient;
+import uk.ac.cam.cares.jps.base.query.RemoteStoreClient;
+
 @WebServlet(urlPatterns = "/update")
 
 public class IsochroneAgent extends JPSAgent {
@@ -36,15 +34,15 @@ public class IsochroneAgent extends JPSAgent {
     private static int timeInterval;
     private static final String PROPETIES_PATH = "/inputs/config.properties";
     private static final Path obdaFile = Path.of("/inputs/isochrone.obda");
-    private final String FUNCTION_KEY = "function";
-    private final String TIMETHRESHOLD_KEY = "timethreshold";
-    private final String TIMEINTERVAL_KEY = "timeinterval";
+    private static final String FUNCTION_KEY = "function";
+    private static final String TIMETHRESHOLD_KEY = "timethreshold";
+    private static final String TIMEINTERVAL_KEY = "timeinterval";
 
     private static final Logger LOGGER = LogManager.getLogger(IsochroneAgent.class);
 
-    private EndpointConfig endpointConfig = new EndpointConfig();
+    private final EndpointConfig endpointConfig = new EndpointConfig();
     private String dbName;
-    private static String populationTables;
+    private String populationTables;
     private String kgEndpoint;
     private RemoteStoreClient storeClient;
     private RemoteRDBStoreClient remoteRDBStoreClient;
@@ -63,6 +61,7 @@ public class IsochroneAgent extends JPSAgent {
     /**
      * Initialise agent
      */
+    @Override
     public void init() {
         readConfig();
 
@@ -84,7 +83,7 @@ public void init() {
      * Read configuration settings from config.properties
      */
     public void readConfig() {
-        try (InputStream input = FileReader.getStream(PROPETIES_PATH)) {
+        try (InputStream input = FileReader.getStream(PROPERTIES_PATH)) {
             Properties prop = new Properties();
             prop.load(input);
             this.dbName = prop.getProperty("db.name");
@@ -148,6 +147,9 @@ public void readConfig() {
      */
     @Override
     public JSONObject processRequestParameters(JSONObject requestParams) {
+        int timeInterval;
+        int timeThreshold;
+        String isochroneFunction = null;
 
         if (!validateInput(requestParams)) {
             throw new JPSRuntimeException("Unable to validate request sent to the agent.");
@@ -257,6 +259,15 @@ public JSONObject processRequestParameters(JSONObject requestParams) {
         return response;
     }
 
+    private void tryToUpdateMapping() {
+        try {
+            OntopClient ontopClient = OntopClient.getInstance();
+            ontopClient.updateOBDA(obdaFile);
+        } catch (Exception e) {
+            System.out.println("Could not retrieve isochrone .obda file.");
+        }
+    }
+
     /**
      * Check if the JSONObject in the processRequestParameters inputs are correct or
      * missing.