fix: handle triples

docs/configuration.md

@@ -87,6 +87,41 @@ execution =
 
 The publisher section of the configuration file describes how the Wings system shares data, execution, and provenance. The following properties are available:
 
-| Name           | Description                                      | Default Value |
-| -------------- | ------------------------------------------------ | ------------- |
-| publisher.data | Location and URI of the WINGS ontology data file | /data         |
+```
+    publisher =
+    {
+        file-store=
+        {
+            url = "https://publisher.mint.isi.edu";
+            type = "FILE_SYSTEM";
+        }
+        triple-store = {
+            export-name = "exportTest";
+            export-url = "https://opmw.org/";
+            publish = https://endpoint.mint.isi.edu/provenance/data;
+            query = https://endpoint.mint.isi.edu/provenance/query;
+            domains-directory = /opt/wings/storage/default;
+        }
+    }
+```
+
+### File store
+
+The file store section of the configuration file describes how the Wings system shares data. The following properties are available:
+
+| Name                      | Description                       | Default Value |
+| ------------------------- | --------------------------------- | ------------- |
+| publisher.file-store.url  | URI where the files are published |               |
+| publisher.file-store.type | Type of file store (FILE_SYSTEM)  | FILE_SYSTEM   |
+
+### Triple store
+
+The triple store section of the configuration file describes how the Wings system shares execution and provenance. The following properties are available:
+
+| Name                                     | Description                            | Default Value                                  |
+| ---------------------------------------- | -------------------------------------- | ---------------------------------------------- |
+| publisher.triple-store.export-name       | Name of the export (exportTest)        | exportTest                                     |
+| publisher.triple-store.export-url        | URI where the files are published      | https://opmw.org/                              |
+| publisher.triple-store.publish           | URI where the provenance is published  | https://endpoint.mint.isi.edu/provenance/data  |
+| publisher.triple-store.query             | URI where the provenance is queried    | https://endpoint.mint.isi.edu/provenance/query |
+| publisher.triple-store.domains-directory | Directory where the domains are stored | /opt/wings/storage/default                     |

portal.properties

@@ -41,9 +41,10 @@
             type = "FILE_SYSTEM";
         }
         triple-store = {
-            graph-name = "exportTest"
-            publish = http://ontosoft.isi.edu:3030/provenance/data;
-            query = http://ontosoft.isi.edu:3030/provenance/sparql;
+            export-name = "exportTest";
+            export-url = "https://opmw.org/";
+            publish = https://endpoint.mint.isi.edu/provenance/data;
+            query = https://endpoint.mint.isi.edu/provenance/query;
             domains-directory = /opt/wings/storage/default;
         }
     }

portal/pom.xml

@@ -17,7 +17,7 @@
 
 	<properties>
 		<!-- rewrite.version>2.0.12.Final</rewrite.version -->
-		<wings-opmm.version>2.0.0</wings-opmm.version>
+		<wings-opmm.version>2.0.1</wings-opmm.version>
 		<servlet-api.version>2.5</servlet-api.version>
 		<httpclient.version>4.5.2</httpclient.version>
 		<jersey.version>2.27</jersey.version>

portal/src/main/java/edu/isi/wings/portal/classes/config/FileStore.java

@@ -24,6 +24,22 @@ public static enum Type {
   SecureShell ssh;
   Http http;
 
+  public FileStore.Type getType() {
+    return type;
+  }
+
+  public FileSystem getFileSystem() {
+    return fileSystem;
+  }
+
+  public SecureShell getSsh() {
+    return ssh;
+  }
+
+  public Http getHttp() {
+    return http;
+  }
+
   public FileStore(PropertyListConfiguration serverConfig) {
     this.type = FileStore.Type.valueOf(serverConfig.getString(PUBLISHER_FILE_STORE_TYPE));
     switch (this.type) {

portal/src/main/java/edu/isi/wings/portal/classes/config/FileStoreHandler/FileSystem.java

@@ -12,6 +12,14 @@ public class FileSystem {
   private static final String PUBLISHER_FILE_STORE_FILE_SYSTEM_DIRECTORY = "publisher.file-store.file-system.directory";
   private String directory;
 
+  public static String getPublisherFileStoreFileSystemDirectory() {
+    return PUBLISHER_FILE_STORE_FILE_SYSTEM_DIRECTORY;
+  }
+
+  public String getDirectory() {
+    return directory;
+  }
+
   public FileSystem(PropertyListConfiguration serverConfig) {
     this.directory = serverConfig.getString(PUBLISHER_FILE_STORE_FILE_SYSTEM_DIRECTORY);
   }

portal/src/main/java/edu/isi/wings/portal/classes/config/TripleStoreConfig.java

@@ -15,17 +15,21 @@ public class TripleStoreConfig {
   private static final String PUBLISHER_SPARQL_DOMAINS_DIRECTORY_KEY = "publisher.triple-store.domains-directory";
   private static final String PUBLISHER_ENDPOINT_QUERY_KEY = "publisher.triple-store.query";
   private static final String PUBLISHER_ENDPOINT_POST_KEY = "publisher.triple-store.publish";
-  private static final String PUBLISHER_GRAPH_NAME = "publisher.triple-store.graph-name";
+  private static final String PUBLISHER_EXPORT_URL = "publisher.triple-store.export-url";
+  private static final String PUBLISHER_EXPORT_NAME = "publisher.triple-store.export-name";
 
   String publishUrl;
   String queryUrl;
-  String graphName;
+  String exportName;
+  String exportUrl;
+
   String domainsDir;
 
   public TripleStoreConfig(PropertyListConfiguration serverConfig) {
     this.publishUrl = serverConfig.getString(PUBLISHER_ENDPOINT_POST_KEY);
     this.queryUrl = serverConfig.getString(PUBLISHER_ENDPOINT_QUERY_KEY);
-    this.graphName = serverConfig.getString(PUBLISHER_GRAPH_NAME);
+    this.exportName = serverConfig.getString(PUBLISHER_EXPORT_NAME);
+    this.exportUrl = serverConfig.getString(PUBLISHER_EXPORT_URL);
     this.domainsDir = serverConfig.getString(PUBLISHER_SPARQL_DOMAINS_DIRECTORY_KEY);
   }
 
@@ -37,11 +41,16 @@ public String getQueryUrl() {
     return queryUrl;
   }
 
-  public String getGraphName() {
-    return graphName;
+  public String getExportPath() {
+    return exportName;
   }
 
   public String getDomainsDir() {
     return domainsDir;
   }
+
+  public String getExportUrl() {
+    return exportUrl;
+  }
+
 }

portal/src/main/java/edu/isi/wings/portal/controllers/RunController.java

@@ -78,6 +78,7 @@
 import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClients;
 import org.apache.jena.base.Sys;
+import org.apache.jena.riot.Lang;
 
 public class RunController {
 
@@ -631,8 +632,6 @@ public ProvenanceResponseSchema publishRun(String runid) throws Exception {
             webServerDomain);
         String domain = config.getDomainId();
         String catalogRepositoryDirectory = "domains";
-        String endpointQueryURI = "https://endpoint.mint.isi.edu/provenance/query";
-        String endpointPostURI = "https://endpoint.mint.isi.edu/provenance/query";
         PublisherConfig publisher = config.portalConfig.getPublisher();
 
         String runName = runid.substring(runid.indexOf('#') + 1);
@@ -731,9 +730,11 @@ public ProvenanceResponseSchema publishRun(String runid) throws Exception {
         /**
          * Publisher configuration
          */
-        String serialization = "turtle";
-        String exportUrl = "https://opmw.org/";
-        String exportPath = "exportTest";
+        Lang serialization = Lang.TURTLE;
+        String exportUrl = config.portalConfig.getPublisher().getTripleStore().getExportUrl();
+        String exportPath = config.portalConfig.getPublisher().getTripleStore().getExportPath();
+        String endpointQueryURI = config.portalConfig.getPublisher().getTripleStore().getQueryUrl();
+        String endpointPostURI = config.portalConfig.getPublisher().getTripleStore().getPublishUrl();
         TriplesPublisher executionPublisher = new TriplesPublisher(
             endpointQueryURI,
             endpointPostURI,