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: <[email protected]#> .
+
+<local:C:/Users/Yang Mobei/WorkbenchProjects/Trial/23/script/23_script.sh>
+        a           prov:Entity ;
+        rdfs:label  "script" .
+
+<local:C:/Users/Yang Mobei/WorkbenchProjects/Trial/23/configfiles/23.xml>
+        a                    prov:Entity ;
+        rdfs:label           "simulationConfigurationFile" ;
+        prov:wasGeneratedBy  <local:simulation_input_file_generation> .
+
+<local:upload_SimConfig>
+        a                       prov:Activity ;
+        rdfs:label              "upload" ;
+        prov:endedAtTime        "2023-02-28T08:19:20.003Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:generated          <local:~/WorkbenchSimulations/23/configfiles23.xml> ;
+        prov:startedAtTime      "2023-02-28T08:19:19.454Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:used               <local:C:/Users/Yang Mobei/WorkbenchProjects/Trial/23/configfiles/23.xml> ;
+        prov:wasAssociatedWith  <local:workbench> .
+
+<local:C:/Users/Yang Mobei/WorkbenchProjects/Trial/23/configfiles/NList/ActiveNList.xml>
+        a           prov:Entity ;
+        rdfs:label  "nlist" .
+
+<local:~/WorkbenchSimulations/23/23_script.sh>
+        a                    prov:Entity ;
+        rdfs:label           "script" ;
+        prov:wasDerivedFrom  <local:C:/Users/Yang Mobei/WorkbenchProjects/Trial/23/script/23_script.sh> ;
+        prov:wasGeneratedBy  <local:uploadScript> .
+
+<local:~/WorkbenchSimulations/23/configfiles/NListInhibitoryNList.xml>
+        a                    prov:Entity ;
+        rdfs:label           "nlist" ;
+        prov:wasDerivedFrom  <local:C:/Users/Yang Mobei/WorkbenchProjects/Trial/23/configfiles/NList/InhibitoryNList.xml> ;
+        prov:wasGeneratedBy  <local:upload_INHIBITORY_NList> .
+
+<local:C:/Users/Yang Mobei/WorkbenchProjects/Trial/23/configfiles/NList/probedNList.xml>
+        a           prov:Entity ;
+        rdfs:label  "nlist" .
+
+<local:uploadScript>  a         prov:Activity ;
+        rdfs:label              "upload" ;
+        prov:endedAtTime        "2023-02-28T08:19:17.839Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:generated          <local:~/WorkbenchSimulations/23/23_script.sh> ;
+        prov:startedAtTime      "2023-02-28T08:19:17.285Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:used               <local:C:/Users/Yang Mobei/WorkbenchProjects/Trial/23/script/23_script.sh> ;
+        prov:wasAssociatedWith  <local:workbench> .
+
+<local:workbench>  a  prov:SoftwareAgent .
+
+<local:upload_INHIBITORY_NList>
+        a                       prov:Activity ;
+        rdfs:label              "upload" ;
+        prov:endedAtTime        "2023-02-28T08:19:18.918Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:generated          <local:~/WorkbenchSimulations/23/configfiles/NListInhibitoryNList.xml> ;
+        prov:startedAtTime      "2023-02-28T08:19:18.385Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:used               <local:C:/Users/Yang Mobei/WorkbenchProjects/Trial/23/configfiles/NList/InhibitoryNList.xml> ;
+        prov:wasAssociatedWith  <local:workbench> .
+
+<local:upload_PROBED_NList>
+        a                       prov:Activity ;
+        rdfs:label              "upload" ;
+        prov:endedAtTime        "2023-02-28T08:19:19.454Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:generated          <local:~/WorkbenchSimulations/23/configfiles/NListprobedNList.xml> ;
+        prov:startedAtTime      "2023-02-28T08:19:18.919Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:used               <local:C:/Users/Yang Mobei/WorkbenchProjects/Trial/23/configfiles/NList/probedNList.xml> ;
+        prov:wasAssociatedWith  <local:workbench> .
+
+<local:~/WorkbenchSimulations/23/configfiles23.xml>
+        a                    prov:Entity ;
+        rdfs:label           "simulationConfigurationFile" ;
+        prov:wasDerivedFrom  <local:C:/Users/Yang Mobei/WorkbenchProjects/Trial/23/configfiles/23.xml> ;
+        prov:wasGeneratedBy  <local:upload_SimConfig> .
+
+<local:upload_ACTIVE_NList>
+        a                       prov:Activity ;
+        rdfs:label              "upload" ;
+        prov:endedAtTime        "2023-02-28T08:19:18.385Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:generated          <local:~/WorkbenchSimulations/23/configfiles/NListActiveNList.xml> ;
+        prov:startedAtTime      "2023-02-28T08:19:17.84Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        prov:used               <local:C:/Users/Yang Mobei/WorkbenchProjects/Trial/23/configfiles/NList/ActiveNList.xml> ;
+        prov:wasAssociatedWith  <local:workbench> .
+
+<local:simulation_input_file_generation>
+        a                       prov:Activity ;
+        prov:generated          <local:C:/Users/Yang Mobei/WorkbenchProjects/Trial/23/configfiles/23.xml> ;
+        prov:wasAssociatedWith  <local:workbench> .
+
+<local:~/WorkbenchSimulations/23/configfiles/NListActiveNList.xml>
+        a                    prov:Entity ;
+        rdfs:label           "nlist" ;
+        prov:wasDerivedFrom  <local:C:/Users/Yang Mobei/WorkbenchProjects/Trial/23/configfiles/NList/ActiveNList.xml> ;
+        prov:wasGeneratedBy  <local:upload_ACTIVE_NList> .
+
+<local:C:/Users/Yang Mobei/WorkbenchProjects/Trial/23/configfiles/NList/InhibitoryNList.xml>
+        a           prov:Entity ;
+        rdfs:label  "nlist" .
+
+<local:~/WorkbenchSimulations/23/configfiles/NListprobedNList.xml>
+        a                    prov:Entity ;
+        rdfs:label           "nlist" ;
+        prov:wasDerivedFrom  <local:C:/Users/Yang Mobei/WorkbenchProjects/Trial/23/configfiles/NList/probedNList.xml> ;
+        prov:wasGeneratedBy  <local:upload_PROBED_NList> .

WorkbenchProject/LastSimulation/uri

@@ -0,0 +1,3 @@
+C:\Users\Yang Mobei\WorkbenchProjects\Trial\23\provenance\23.ttl
+[email protected]#
+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());
@@ -71,6 +72,50 @@ public class ProvMgr {
     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.

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

@@ -175,13 +175,22 @@ 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"));
+        return Paths.get(workingDir());
     }
 
     /**

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">
@@ -527,8 +538,17 @@ public boolean runScript() {
                     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();
@@ -537,6 +557,15 @@ public boolean runScript() {
         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.
      *

WorkbenchProject/src/main/java/edu/uwb/braingrid/workbench/comm/SecureFileTransfer.java

@@ -1,19 +1,31 @@
 package edu.uwb.braingrid.workbench.comm;
 
+import com.jcraft.jsch.Channel;
 import com.jcraft.jsch.ChannelExec;
 import com.jcraft.jsch.ChannelSftp;
 import com.jcraft.jsch.JSch;
 import com.jcraft.jsch.JSchException;
 import com.jcraft.jsch.Session;
 import com.jcraft.jsch.SftpException;
 import com.jcraft.jsch.SftpProgressMonitor;
+
+import edu.uwb.braingrid.workbench.WorkbenchManager;
+import edu.uwb.braingrid.workbench.ui.SimulationRuntimeDialog;
+import javafx.scene.control.TextArea;
+import riotcmd.infer;
+
+import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.InputStreamReader;
 import java.util.Date;
 
+import javax.swing.JFrame;
+import javax.swing.JOptionPane;
+
 /**
  * Provides abbreviated SSF/FTP functionality. This includes uploading/downloading files and
  * execution of commands on a remote machine.
@@ -273,4 +285,82 @@ private boolean readInputStream(InputStream in, ChannelExec cExec) {
         return success;
     }
     // </editor-fold>
+
+    /**
+     * Connects to the last simulation.
+     *
+     * @param hostname  The name of the host machine to connect to.
+     * @param username  The user's login username.
+     * @param password  The user's login password.
+     * @param simName  The  last simulation to connect to.
+     * @param manager  The temp place holder.
+     */
+
+  public void checkLastSim(String hostname, String username,
+      String password, String simName, WorkbenchManager manager) {
+    JSch jsch = new JSch();
+    try {
+      session = jsch.getSession(username, hostname, PORT);
+      session.setPassword(password);
+      session.setConfig("StrictHostKeyChecking", "no"); //optional
+      session.connect();
+
+      Channel channel = session.openChannel("exec");
+      ((ChannelExec) channel).setInputStream(null);
+      ((ChannelExec) channel).setCommand("cd WorkbenchSimulations/ && ls");
+      channel.connect();
+
+      InputStream in;
+    try {
+        in = channel.getInputStream();
+        BufferedReader reader = new BufferedReader(new InputStreamReader(in));
+        String files;
+        while ((files = reader.readLine()) != null) {
+          if (files.equals(simName)) {
+              Channel channel2 = session.openChannel("sftp");
+              channel2.connect();
+              //((ChannelSftp) channel2).setInputStream(null);
+              try {
+                ((ChannelSftp) channel2).cd(
+                    "WorkbenchSimulations//" + simName + "//Output//Debug");
+                InputStream workBenchLOG = ((ChannelSftp) channel2).get("workbench.txt");
+                BufferedReader readLOG = new BufferedReader(new InputStreamReader(workBenchLOG));
+                String line;
+                String lastline = "";
+                while ((line = readLOG.readLine()) != null) {
+                    lastline = line;
+                }
+                String completion = "Complete";
+                lastline = lastline.substring(
+                    lastline.length() - completion.length(), lastline.length());
+                if (lastline.equals("Complete")) {
+                  displayDownloadFrame(channel2, manager);
+                  break;
+                }
+            } catch (SftpException e) {
+              e.printStackTrace();
+            }
+          }
+        }
+    } catch (IOException e) {
+      e.printStackTrace();
+    }
+
+    } catch (JSchException e) {
+      e.printStackTrace();
+    }
+  }
+
+  private void displayDownloadFrame(Channel channel, WorkbenchManager manager) {
+    JFrame frame = new JFrame();
+    String[] options = {"Download", "Cancel"};
+    int option = JOptionPane.showOptionDialog(frame,
+        "Last simlation completed, do you want to download?", "Last Simulation Completed",
+        JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE,
+            null, options, options[0]);
+      if (option == JOptionPane.YES_NO_OPTION) {
+        SimulationRuntimeDialog srd = new SimulationRuntimeDialog(
+            new TextArea(manager.getMessages()));
+      }
+  }
 }

WorkbenchProject/src/main/java/edu/uwb/braingrid/workbench/model/ScriptHistory.java

@@ -1,13 +1,15 @@
 package edu.uwb.braingrid.workbench.model;
 
+import java.io.Serializable;
+
 import edu.uwb.braingrid.workbench.utils.DateTime;
 
 /**
  * Represents the history for a script associated with a simulation.
  *
  * @author Aaron Conrad
  */
-public class ScriptHistory {
+public class ScriptHistory implements Serializable {
 
     // <editor-fold defaultstate="collapsed" desc="Members">
     private long startedAt;