Remember last sim

WorkbenchProject/LastSimulation/model.ttl

@@ -0,0 +1,108 @@
+@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix xsd:   <http://www.w3.org/2000/10/XMLSchema#> .
+@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix remote: <otachi.uwb.edu#> .
+@prefix prov:  <http://www.w3.org/ns/prov#> .
+@prefix local: <DESKTOP-3N8B16A@205.175.118.10#> .
+
+<local:~/WorkbenchSimulations/trial404/configfilestrial404.xml>
+        a                    prov:Entity ;
+        rdfs:label           "simulationConfigurationFile" ;
+        prov:wasDerivedFrom  <local:C:/Users/Administrator/WorkbenchProjects/Default/trial404/configfiles/trial404.xml> ;
+        prov:wasGeneratedBy  <local:upload_SimConfig> .
+
+<local:~/WorkbenchSimulations/trial404/configfiles/NListActiveNList.xml>
+        a                    prov:Entity ;
+        rdfs:label           "nlist" ;
+        prov:wasDerivedFrom  <local:C:/Users/Administrator/WorkbenchProjects/Default/trial404/configfiles/NList/ActiveNList.xml> ;
+        prov:wasGeneratedBy  <local:upload_ACTIVE_NList> .
+
+<local:upload_SimConfig>
+        a                       prov:Activity ;
+        rdfs:label              "upload" ;
+        prov:endedAtTime        "2023-03-01T00:04:26.626Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:generated          <local:~/WorkbenchSimulations/trial404/configfilestrial404.xml> ;
+        prov:startedAtTime      "2023-03-01T00:04:26.298Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:used               <local:C:/Users/Administrator/WorkbenchProjects/Default/trial404/configfiles/trial404.xml> ;
+        prov:wasAssociatedWith  <local:workbench> .
+
+<local:C:/Users/Administrator/WorkbenchProjects/Default/trial404/configfiles/NList/ActiveNList.xml>
+        a           prov:Entity ;
+        rdfs:label  "nlist" .
+
+<local:~/WorkbenchSimulations/trial404/configfiles/NListprobedNList.xml>
+        a                    prov:Entity ;
+        rdfs:label           "nlist" ;
+        prov:wasDerivedFrom  <local:C:/Users/Administrator/WorkbenchProjects/Default/trial404/configfiles/NList/probedNList.xml> ;
+        prov:wasGeneratedBy  <local:upload_PROBED_NList> .
+
+<local:C:/Users/Administrator/WorkbenchProjects/Default/trial404/configfiles/NList/probedNList.xml>
+        a           prov:Entity ;
+        rdfs:label  "nlist" .
+
+<local:uploadScript>  a         prov:Activity ;
+        rdfs:label              "upload" ;
+        prov:endedAtTime        "2023-03-01T00:04:25.333Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:generated          <local:~/WorkbenchSimulations/trial404/trial404_script.sh> ;
+        prov:startedAtTime      "2023-03-01T00:04:25.026Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:used               <local:C:/Users/Administrator/WorkbenchProjects/Default/trial404/script/trial404_script.sh> ;
+        prov:wasAssociatedWith  <local:workbench> .
+
+<local:workbench>  a  prov:SoftwareAgent .
+
+<local:upload_INHIBITORY_NList>
+        a                       prov:Activity ;
+        rdfs:label              "upload" ;
+        prov:endedAtTime        "2023-03-01T00:04:25.99Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:generated          <local:~/WorkbenchSimulations/trial404/configfiles/NListInhibitoryNList.xml> ;
+        prov:startedAtTime      "2023-03-01T00:04:25.682Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:used               <local:C:/Users/Administrator/WorkbenchProjects/Default/trial404/configfiles/NList/InhibitoryNList.xml> ;
+        prov:wasAssociatedWith  <local:workbench> .
+
+<local:upload_PROBED_NList>
+        a                       prov:Activity ;
+        rdfs:label              "upload" ;
+        prov:endedAtTime        "2023-03-01T00:04:26.298Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:generated          <local:~/WorkbenchSimulations/trial404/configfiles/NListprobedNList.xml> ;
+        prov:startedAtTime      "2023-03-01T00:04:25.991Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:used               <local:C:/Users/Administrator/WorkbenchProjects/Default/trial404/configfiles/NList/probedNList.xml> ;
+        prov:wasAssociatedWith  <local:workbench> .
+
+<local:C:/Users/Administrator/WorkbenchProjects/Default/trial404/configfiles/NList/InhibitoryNList.xml>
+        a           prov:Entity ;
+        rdfs:label  "nlist" .
+
+<local:upload_ACTIVE_NList>
+        a                       prov:Activity ;
+        rdfs:label              "upload" ;
+        prov:endedAtTime        "2023-03-01T00:04:25.682Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:generated          <local:~/WorkbenchSimulations/trial404/configfiles/NListActiveNList.xml> ;
+        prov:startedAtTime      "2023-03-01T00:04:25.333Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:used               <local:C:/Users/Administrator/WorkbenchProjects/Default/trial404/configfiles/NList/ActiveNList.xml> ;
+        prov:wasAssociatedWith  <local:workbench> .
+
+<local:simulation_input_file_generation>
+        a                       prov:Activity ;
+        prov:generated          <local:C:/Users/Administrator/WorkbenchProjects/Default/trial404/configfiles/trial404.xml> ;
+        prov:wasAssociatedWith  <local:workbench> .
+
+<local:C:/Users/Administrator/WorkbenchProjects/Default/trial404/configfiles/trial404.xml>
+        a                    prov:Entity ;
+        rdfs:label           "simulationConfigurationFile" ;
+        prov:wasGeneratedBy  <local:simulation_input_file_generation> .
+
+<local:~/WorkbenchSimulations/trial404/configfiles/NListInhibitoryNList.xml>
+        a                    prov:Entity ;
+        rdfs:label           "nlist" ;
+        prov:wasDerivedFrom  <local:C:/Users/Administrator/WorkbenchProjects/Default/trial404/configfiles/NList/InhibitoryNList.xml> ;
+        prov:wasGeneratedBy  <local:upload_INHIBITORY_NList> .
+
+<local:C:/Users/Administrator/WorkbenchProjects/Default/trial404/script/trial404_script.sh>
+        a           prov:Entity ;
+        rdfs:label  "script" .
+
+<local:~/WorkbenchSimulations/trial404/trial404_script.sh>
+        a                    prov:Entity ;
+        rdfs:label           "script" ;
+        prov:wasDerivedFrom  <local:C:/Users/Administrator/WorkbenchProjects/Default/trial404/script/trial404_script.sh> ;
+        prov:wasGeneratedBy  <local:uploadScript> .

WorkbenchProject/LastSimulation/uri

@@ -0,0 +1,3 @@
+C:\Users\Administrator\WorkbenchProjects\Default\trial404\provenance\trial404.ttl
+DESKTOP-3N8B16A@205.175.118.10#
+null

WorkbenchProject/src/main/java/edu/uwb/braingrid/provenance/ProvMgr.java

@@ -6,6 +6,7 @@
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.PrintStream;
+import java.io.Serializable;
 import java.net.InetAddress;
 import java.net.URL;
 import java.net.URLConnection;
@@ -50,7 +51,7 @@
  * @author Del Davis, Extended by Joseph Conquest
  * @version 1.2
  */
-public class ProvMgr {
+public class ProvMgr implements Serializable {
 
     // <editor-fold defaultstate="collapsed" desc="Members">
     private static final Logger LOG = Logger.getLogger(ProvMgr.class.getName());
@@ -63,14 +64,58 @@ public class ProvMgr {
     public static final String LOCAL_NS_PREFIX = "local";
 
     /* URIs used to describe the provenance */
-    private String provOutputFileURI;
-    private String localNameSpaceURI;
-    private String remoteNameSpaceURI;
+    private String provOutputFileUri;
+    private String localNameSpaceUri;
+    private String remoteNameSpaceUri;
 
     /* RDF in-memory representation of the provenance */
     private Model model;
     // </editor-fold>
 
+  /**
+   * The getter for provURI.
+   *
+   *  @return return the provURI.
+   *
+   */
+  public String getProvUri() {
+      return provOutputFileUri;
+  }
+
+  /**
+   * The getter for LocalURI.
+   *
+   *  @return return the LocalURI.
+   *
+   */
+  public String getLocalUri() {
+    return localNameSpaceUri;
+  }
+
+    /**
+     * The getter for RemoteURI.
+     *
+     *  @return return the RemoteURI.
+     *
+     */
+  public String getRemoteUri() {
+    return remoteNameSpaceUri;
+    }
+  /**
+   * The constructor used by resume Lastsimulation.
+   *
+   *  @param provURI the provURI
+   *  @param localURI the localURI
+   *  @param remoteURI the remoteURI
+   *  @param model the model
+   */
+  public ProvMgr(String provURI, String localURI, String remoteURI, Model model) {
+    this.provOutputFileUri = provURI;
+    this.localNameSpaceUri = localURI;
+    this.remoteNameSpaceUri = remoteURI;
+    this.model = model;
+    }
+
     // <editor-fold defaultstate="collapsed" desc="Construction">
     /**
      * Constructs the Provenance Constructor object from a previously recorded provenance file.
@@ -97,7 +142,7 @@ public ProvMgr(Simulation simulation, boolean load) throws IOException, RiotNotF
     private void init(Simulation simulation) {
         // create RDF model
         model = ModelFactory.createDefaultModel();
-        provOutputFileURI = simulation.getProvLocation()
+        provOutputFileUri = simulation.getProvLocation()
                 .resolve(simulation.getName() + ".ttl").toString();
         // set prefixes for...
         // RDF syntax
@@ -108,9 +153,9 @@ private void init(Simulation simulation) {
         model.setNsPrefix("prov", ProvOntology.getPROVNameSpaceURI());
         // XML schema
         model.setNsPrefix("xsd", ProvOntology.getXSDNameSpaceURI());
-        localNameSpaceURI = getLocalNameSpaceURI();
+        localNameSpaceUri = getLocalNameSpaceURI();
         // Graphitti Prov
-        model.setNsPrefix(LOCAL_NS_PREFIX, localNameSpaceURI);
+        model.setNsPrefix(LOCAL_NS_PREFIX, localNameSpaceUri);
     }
 
     /**
@@ -120,10 +165,10 @@ private void init(Simulation simulation) {
      */
     private void load(Simulation simulation) throws RiotNotFoundException {
         String name = simulation.getName();
-        provOutputFileURI = simulation.getProvLocation().resolve(name + ".ttl").toString();
-        model = RDFDataMgr.loadModel(provOutputFileURI);
-        localNameSpaceURI = getLocalNameSpaceURI();
-        model.setNsPrefix(LOCAL_NS_PREFIX, localNameSpaceURI);
+        provOutputFileUri = simulation.getProvLocation().resolve(name + ".ttl").toString();
+        model = RDFDataMgr.loadModel(provOutputFileUri);
+        localNameSpaceUri = getLocalNameSpaceURI();
+        model.setNsPrefix(LOCAL_NS_PREFIX, localNameSpaceUri);
         trimRemoteNS();
     }
 
@@ -137,8 +182,8 @@ private void trimRemoteNS() {
             String nameSpace = entry.getKey();
             String uri = entry.getValue();
             if (nameSpace.startsWith(REMOTE_NS_PREFIX)) {
-                remoteNameSpaceURI = uri.substring(uri.lastIndexOf('/') + 1);
-                model.setNsPrefix(nameSpace, remoteNameSpaceURI);
+                remoteNameSpaceUri = uri.substring(uri.lastIndexOf('/') + 1);
+                model.setNsPrefix(nameSpace, remoteNameSpaceUri);
             }
         }
     }
@@ -166,8 +211,8 @@ public void setNsPrefix(String prefix, String uri) {
      *
      * @return The URI of the provenance output file
      */
-    public String getProvFileURI() {
-        return provOutputFileURI;
+    public String getProvFileUri() {
+        return provOutputFileUri;
     }
 
     /**

WorkbenchProject/src/main/java/edu/uwb/braingrid/workbench/FileManager.java

@@ -175,14 +175,23 @@ public static Path getCurrentProjectDirectory() {
         return getProjectsDirectory().resolve(WorkbenchManager.getInstance().getProjectName());
     }
 
+  private static String workingDir() {
+    String dir = System.getProperty("user.dir");
+    String target = "\\target";
+    if (dir.endsWith(target)) {
+      dir = dir.substring(0, dir.length() - target.length());
+    }
+    return dir;
+  }
+
     /**
      * Provides the working directory of the current user.
      *
      * @return The working directory of the current user
      */
-    public static Path getUserDir() {
-        return Paths.get(System.getProperty("user.dir"));
-    }
+  public static Path getUserDir() {
+    return Paths.get(workingDir());
+  }
 
     /**
      * Provides the home directory of the current user.

WorkbenchProject/src/main/java/edu/uwb/braingrid/workbench/WorkbenchManager.java

@@ -4,7 +4,10 @@
 import com.jcraft.jsch.JSchException;
 import com.jcraft.jsch.SftpException;
 import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.ObjectOutputStream;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.HashMap;
@@ -56,6 +59,14 @@ public final class WorkbenchManager {
     private Project project;
     private Simulation simulation;
     private ProvMgr prov;
+
+  public void simulationSetter(Simulation inputSimulation) {
+    this.simulation = inputSimulation;
+  }
+
+  public void provMgrSetter(ProvMgr inputProv) {
+    this.prov = inputProv;
+  }
     // </editor-fold>
 
     // <editor-fold defaultstate="collapsed" desc="Construction">
@@ -516,26 +527,44 @@ public boolean generateScript() {
      * @return True if all files were uploaded/copied successfully and the script was started,
      *         otherwise false
      */
-    public boolean runScript() {
-        boolean success = false;
-        ScriptManager sm = new ScriptManager();
-        try {
-            String simulationName = simulation.getName();
-            String scriptPath = simulation.getScriptFilePath();
-            String[] neuronLists = FileManager.getNeuronListFilenames(simulationName);
-            success = sm.runScript(prov, simulation.getSimSpec(), simulationName, scriptPath,
-                    neuronLists, simulation.getSimConfigFilename());
-            simulation.setScriptRan(success);
-            simulation.setScriptStartedAt();
-            messageAccumulator += sm.getOutstandingMessages();
-        } catch (JSchException | SftpException | IOException | NullPointerException e) {
-            messageAccumulator += "\n" + "Script did not run do to "
-                    + e.getClass() + "...\n";
-            messageAccumulator += "Exception message: " + e.getMessage();
-        }
-
-        return success;
-    }
+  public boolean runScript() {
+    boolean success = false;
+    ScriptManager sm = new ScriptManager();
+    try {
+      String simulationName = simulation.getName();
+      String scriptPath = simulation.getScriptFilePath();
+      String[] neuronLists = FileManager.getNeuronListFilenames(simulationName);
+      success = sm.runScript(prov, simulation.getSimSpec(), simulationName, scriptPath,
+          neuronLists, simulation.getSimConfigFilename());
+      simulation.setScriptRan(success);
+      simulation.setScriptStartedAt();
+      if (success) {
+        File simulationFile = new File(workingDir() + "\\LastSimulation\\simulation");
+        FileOutputStream simOut = new FileOutputStream(simulationFile);
+        ObjectOutputStream simObjOut = new ObjectOutputStream(simOut);
+        simObjOut.writeObject(simulation);
+      }
+
+       //save the simulation here
+      messageAccumulator += sm.getOutstandingMessages();
+    } catch (JSchException | SftpException | IOException | NullPointerException e) {
+      e.printStackTrace();
+      messageAccumulator += "\n" + "Script did not run do to "
+          + e.getClass() + "...\n";
+      messageAccumulator += "Exception message: " + e.getMessage();
+    }
+
+    return success;
+  }
+
+  private static String workingDir() {
+    String dir = System.getProperty("user.dir");
+    String target = "\\target";
+    if (dir.endsWith(target)) {
+      dir = dir.substring(0, dir.length() - target.length());
+    }
+    return dir;
+  }
 
     /**
      * Analyzes the redirected provenance output from an executed script.
@@ -611,7 +640,7 @@ private void persistProvenance() {
                 prov.persist(simulation);
                 messageAccumulator += "\n"
                         + "Provenance persisted to: "
-                        + prov.getProvFileURI() + "\n";
+                        + prov.getProvFileUri() + "\n";
             } catch (IOException e) {
                 messageAccumulator += "\n"
                         + "Unable to persist provenance\n"
@@ -735,6 +764,15 @@ public String getMessages() {
         return messageAccumulator;
     }
 
+    /**
+     * Set the message for message Accumulator, used for remember last simulation.
+     *
+     *  @param msg msg to set
+     */
+  public void setMessages(String msg) {
+    messageAccumulator = msg;
+  }
+
     /**
      * Clears the accumulated messages for this manager.
      */