Esempio n. 1
0
 public void updateJob(ApplicationInfo appInfo, CIJob job) throws PhrescoException {
   if (debugEnabled) {
     S_LOGGER.debug(
         "Entering Method ProjectAdministratorImpl.updateJob(Project project, CIJob job)");
   }
   FileWriter writer = null;
   try {
     CIJobStatus jobStatus = configureJob(job, FrameworkConstants.CI_UPDATE_JOB_COMMAND);
     if (jobStatus.getCode() == -1) {
       throw new PhrescoException(jobStatus.getMessage());
     }
     if (debugEnabled) {
       S_LOGGER.debug("getCustomModules() ProjectInfo = " + appInfo);
     }
     updateJsonJob(appInfo, job);
   } catch (ClientHandlerException ex) {
     if (debugEnabled) {
       S_LOGGER.error(ex.getLocalizedMessage());
     }
     throw new PhrescoException(ex);
   } finally {
     if (writer != null) {
       try {
         writer.close();
       } catch (IOException e) {
         if (debugEnabled) {
           S_LOGGER.error(e.getLocalizedMessage());
         }
       }
     }
   }
 }
 /**
  * Create an Internet shortcut
  *
  * @param name name of the shortcut
  * @param where location of the shortcut
  * @param target URL
  * @param icon URL (ex. http://www.server.com/favicon.ico)
  */
 public static void createInternetShortcut(String name, String where, String target, String icon) {
   try (FileWriter fw = new FileWriter(where)) {
     fw.write("[InternetShortcut]\n");
     fw.write("URL=" + target + '\n');
     if (!icon.isEmpty()) fw.write("IconFile=" + icon + '\n');
   } catch (IOException iox) {
     /**/
   }
 }
  public static void main(String[] args) {
    try {
      BufferedReader br = new BufferedReader(new FileReader(args[0]));
      int tIndex = 0;
      int pIndex = 0;

      // This will probably change soon (name and implementation)
      NgramParser tnp = new NgramParser(args[1]);

      ArrayList<String> triplet = tnp.getTriplet();
      ArrayList<String> polarity = tnp.getPolarity();

      FileWriter sw = new FileWriter(args[2]);
      String line = null;

      while (((line = br.readLine()) != null)
          && (tIndex < triplet.size())
          && (pIndex < polarity.size())) {
        if (line.matches("^[\\d]*:")) {
          // System.out.println(line);
          sw.write(line + "\n");
        } else {
          Scanner sc = new Scanner(line);
          String trip = sc.findInLine(Pattern.compile("[a-zA-Z]+#[a-z]+[#]?[0-9]*"));
          // if (trip != null && trip.equals(triplet.get(tIndex))) {
          System.out.println(trip);
          if (trip != null && !trip.toLowerCase().contains("no#cl")) {
            // System.out.println(triplet.get(tIndex) + ":" +polarity.get(pIndex));
            String pol = polarity.get(pIndex);
            sw.write(line + " " + pol + "\n");
            sc.close();
            tIndex++;
            pIndex++;
          } else {
            String pol = "neg";
            sw.write("no#a#1" + " " + pol + "\n");
            sc.close();
          }
        }

        // sw.flush();
      }

      sw.close();

    } catch (IOException e) {
      e.printStackTrace();
    }
  }
 // write a single line in a FileWriter writer for given String line
 static void writeLine(FileWriter writer, String line) {
   try {
     writer.append(line + '\n');
   } catch (IOException e) {
     e.printStackTrace();
   }
 }
Esempio n. 5
0
 private void writeJsonJobs(ApplicationInfo appInfo, List<CIJob> jobs, String status)
     throws PhrescoException {
   try {
     if (jobs == null) {
       return;
     }
     Gson gson = new Gson();
     List<CIJob> existingJobs = getJobs(appInfo);
     if (CI_CREATE_NEW_JOBS.equals(status) || existingJobs == null) {
       existingJobs = new ArrayList<CIJob>();
     }
     existingJobs.addAll(jobs);
     FileWriter writer = null;
     File ciJobFile = new File(getCIJobPath(appInfo));
     String jobJson = gson.toJson(existingJobs);
     writer = new FileWriter(ciJobFile);
     writer.write(jobJson);
     writer.flush();
   } catch (Exception e) {
     throw new PhrescoException(e);
   }
 }
  static void writeUsersToFile() {
    userWriter = createCSVFile("Users.dat");
    // write the list of users to file
    System.out.println("Users that are both seller and buyer BUT different ratings: ");
    Enumeration<String> keys = userList.keys();
    while (keys.hasMoreElements()) {
      String curUserID = keys.nextElement();
      String curUser[] = userList.get(curUserID);
      String userRow =
          wrapQuotations(curUser[0])
              + ","
              + curUser[1]
              + ","
              + curUser[2]
              + ","
              + wrapQuotations(curUser[3])
              + ","
              + wrapQuotations(curUser[4]);
      writeLine(userWriter, userRow);
      // if(curUser[1] != null && curUser[2] != null && !curUser[1].equals(curUser[2]))
      //    System.out.println(curUser[0]);
    }
    System.out.println("----end different ratings----");

    // System.out.println("The users that are both seller and buyer: ");
    // Enumeration<String> both = bothSellerAndBuyer.elements();
    // while(both.hasMoreElements()) {
    //    System.out.println(both.nextElement());
    // }
    // System.out.println("----end both----");

    try {
      userWriter.flush();
      userWriter.close();
    } catch (IOException e) {
      e.printStackTrace();
    }
  }
Esempio n. 7
0
 private boolean adaptExistingJobs(ApplicationInfo appInfo) {
   try {
     CIJob existJob = getJob(appInfo);
     S_LOGGER.debug("Going to get existing jobs to relocate!!!!!");
     if (existJob != null) {
       S_LOGGER.debug("Existing job found " + existJob.getName());
       boolean deleteExistJob = deleteCIJobFile(appInfo);
       Gson gson = new Gson();
       List<CIJob> existingJobs = new ArrayList<CIJob>();
       existingJobs.addAll(Arrays.asList(existJob));
       FileWriter writer = null;
       File ciJobFile = new File(getCIJobPath(appInfo));
       String jobJson = gson.toJson(existingJobs);
       writer = new FileWriter(ciJobFile);
       writer.write(jobJson);
       writer.flush();
       S_LOGGER.debug("Existing job moved to new type of project!!");
     }
     return true;
   } catch (Exception e) {
     S_LOGGER.debug("It is already adapted !!!!! ");
   }
   return false;
 }
  /* Process one items-???.xml file.
   */
  static void processFile(File xmlFile) {
    Document doc = null;
    try {
      doc = builder.parse(xmlFile);
    } catch (IOException e) {
      e.printStackTrace();
      System.exit(3);
    } catch (SAXException e) {
      System.out.println("Parsing error on file " + xmlFile);
      System.out.println("  (not supposed to happen with supplied XML files)");
      e.printStackTrace();
      System.exit(3);
    }

    /* At this point 'doc' contains a DOM representation of an 'Items' XML
     * file. Use doc.getDocumentElement() to get the root Element. */
    System.out.println("Successfully parsed - " + xmlFile);

    /* Fill in code here (you will probably need to write auxiliary
    methods). */

    // open each CSV file (creates it if it doesn't exist)
    System.out.println("creating dat file");
    itemWriter = createCSVFile("Items.dat");
    itemCategoriesWriter = createCSVFile("ItemCategories.dat");
    bidWriter = createCSVFile("Bids.dat");

    Element itemsElem = doc.getDocumentElement();
    Element[] itemList = getElementsByTagNameNR(itemsElem, "Item");
    System.out.println("There are " + itemList.length + " <item> tags");

    for (Element curItem : itemList) {
      processItem(curItem);
    }

    // close the dat files
    try {
      itemWriter.flush();
      itemWriter.close();

      itemCategoriesWriter.flush();
      itemCategoriesWriter.close();

      bidWriter.flush();
      bidWriter.close();
    } catch (IOException e) {
      e.printStackTrace();
    }
    /** *********************************************************** */
  }
Esempio n. 9
0
 /**
  * This function writes the generated relative overview to a file.
  *
  * @param f The file to write to.
  * @throws IOException Thrown if unable to open or write to the file.
  * @throws InsufficientDataException Thrown if unable to generate the overview.
  */
 public void writeToFile(File f) throws IOException, InsufficientDataException {
   f.createNewFile();
   FileWriter fw = new FileWriter(f);
   fw.write(generateOverviewText());
   fw.close();
 }
Esempio n. 10
0
  public static void generateMainPage(File mainFile, File sourceProjDir)
      throws IOException, ProjectFileParsingException, NeuroMLException {
    SimpleXMLElement root = new SimpleXMLElement("document");
    SimpleXMLElement header = new SimpleXMLElement("header");
    root.addChildElement(header);

    SimpleXMLElement title = new SimpleXMLElement("title");
    header.addChildElement(title);

    SimpleXMLElement body = new SimpleXMLElement("body");
    root.addChildElement(body);
    SimpleXMLElement intro = new SimpleXMLElement("p");
    body.addChildElement(intro);

    if (!mainFile.getParentFile().exists()) mainFile.getParentFile().mkdir();

    File targetDownloadDir = new File(mainFile.getParentFile(), "downloads");
    if (!targetDownloadDir.exists()) targetDownloadDir.mkdir();

    if (sourceProjDir.getName().indexOf("examples") >= 0) {
      title.addContent("neuroConstruct example projects");

      intro.addContent(
          "Downloadable neuroConstruct example projects. These <strong>illustrate the core "
              + "functionality of neuroConstruct</strong>, as opposed to providing electrophysiologically accurate "
              + "models. Projects based on published conductance based models can be found <a href=\"../models/index.html\">here</a>");
    }
    if (sourceProjDir.getName().indexOf("models") >= 0) {
      title.addContent("neuroConstruct projects based on published neuronal and network models");

      intro.addContent(
          "Downloadable neuroConstruct projects <strong>based on published conductance based models</strong>. "
              + "Some examples to illustrate the core functionality of neuroConstruct, as opposed to "
              + "providing electrophysiologically accurate models can be found <a href=\"../samples/index.html\">here</a>."
              + "<p>Note: These models are currently being moved to a repository to allow open source, collaborative development of NeuroML models.</p>"
              + "<p>See the <a href=\"http://www.opensourcebrain.org\">Open Source Brain</a> website for full details.&nbsp;&nbsp;&nbsp;&nbsp;"
              + "<img alt=\"Open Source Brain\" src=\"http://www.opensourcebrain.org/images/logo.png\"/></p>");
    }
    File[] fileArray = sourceProjDir.listFiles();

    fileArray = GeneralUtils.reorderAlphabetically(fileArray, true);

    ArrayList<File> files = GeneralUtils.toArrayList(fileArray);
    // if (files.contains(""))

    ArrayList<String> toIgnore = new ArrayList<String>();
    // toIgnore.add("Thalamocortical"); // temporarily
    // toIgnore.add("CA1PyramidalCell"); // temporarily
    // toIgnore.add("SolinasEtAl-GolgiCell"); // temporarily

    for (File exProjDir : files) {
      File morphDir = new File(exProjDir, "cellMechanisms");

      if (morphDir.isDirectory() && !toIgnore.contains(exProjDir.getName())) {
        String projName = exProjDir.getName();
        SimpleXMLElement section = new SimpleXMLElement("section");
        body.addChildElement(section);

        SimpleXMLElement secTitle = new SimpleXMLElement("title");
        section.addChildElement(secTitle);
        secTitle.addContent(projName);

        SimpleXMLElement anchor = new SimpleXMLElement("anchor");
        section.addChildElement(anchor);
        anchor.addAttribute("id", projName);

        SimpleXMLElement table = new SimpleXMLElement("table");

        section.addChildElement(table);

        SimpleXMLElement row = new SimpleXMLElement("tr");
        table.addChildElement(row);

        String largeImg = "large.png";
        String smallImg = "small.png";

        File targetImageDir = new File(mainFile.getParentFile(), "images");
        if (!targetImageDir.exists()) targetImageDir.mkdir();

        File targetProjImageDir = new File(targetImageDir, projName);

        if (!targetProjImageDir.exists()) targetProjImageDir.mkdir();

        File smallImgFile = new File(exProjDir, "images/" + smallImg);
        File largeImgFile = new File(exProjDir, "images/" + largeImg);

        if (smallImgFile.exists()) {
          GeneralUtils.copyFileIntoDir(smallImgFile, targetProjImageDir);

          SimpleXMLElement col2 = new SimpleXMLElement("td");
          row.addChildElement(col2);
          col2.addAttribute("width", "120");

          SimpleXMLElement secImg = new SimpleXMLElement("p");
          col2.addChildElement(secImg);

          SimpleXMLElement img = new SimpleXMLElement("img");
          img.addAttribute("src", "images/" + projName + "/small.png");
          img.addAttribute("alt", "Screenshot of " + projName);

          if (largeImgFile.exists()) {
            GeneralUtils.copyFileIntoDir(largeImgFile, targetProjImageDir);

            SimpleXMLElement imgRef = new SimpleXMLElement("a");
            img.addAttribute("title", "Click to enlarge");
            imgRef.addAttribute("href", "images/" + projName + "/" + largeImg);
            imgRef.addChildElement(img);
            secImg.addChildElement(imgRef);
          } else {
            secImg.addChildElement(img);
          }
        }

        SimpleXMLElement secIntro = new SimpleXMLElement("p");
        SimpleXMLElement colMid = new SimpleXMLElement("td");
        SimpleXMLElement colRight = new SimpleXMLElement("td");
        row.addChildElement(colMid);
        row.addChildElement(colRight);
        colRight.addAttribute("width", "150");
        colMid.addChildElement(secIntro);
        secIntro.addContent("Project name: <strong>" + projName + "</strong>");

        File projFile = ProjectStructure.findProjectFile(exProjDir);

        Project project = Project.loadProject(projFile, null);
        String descFull = project.getProjectDescription();
        String breakpoint = "\n\n";
        String descShort = new String(descFull);

        if (descFull.indexOf(breakpoint) > 0) {
          descShort = descFull.substring(0, descFull.indexOf(breakpoint));
        }

        SimpleXMLElement desc = new SimpleXMLElement("p");
        colMid.addChildElement(desc);
        desc.addContent(GeneralUtils.parseForHyperlinks(descShort));

        SimpleXMLElement modified = new SimpleXMLElement("p");
        colMid.addChildElement(modified);

        SimpleDateFormat formatter = new SimpleDateFormat("EEEE MMMM d, yyyy");

        java.util.Date date = new java.util.Date(projFile.lastModified());

        modified.addContent("Project last modified: " + formatter.format(date));

        File zipFile = null;
        String zipFileName =
            targetDownloadDir.getAbsolutePath()
                + "/"
                + projName
                + ProjectStructure.getNewProjectZipFileExtension();

        ArrayList<String> ignore = new ArrayList<String>();
        ArrayList<String> ignoreNone = new ArrayList<String>();
        ArrayList<String> ignoreExtns = new ArrayList<String>();

        ignore.add("i686");
        ignore.add("x86_64");
        ignore.add(".svn");
        ignore.add("simulations");
        ignore.add("generatedNEURON");
        ignore.add("generatedNeuroML");
        ignore.add("generatedGENESIS");
        ignore.add("generatedMOOSE");
        ignore.add("generatedPyNN");
        ignore.add("generatedPSICS");
        ignore.add("dataSets");
        ignoreExtns.add("bak");

        zipFile = ZipUtils.zipUp(exProjDir, zipFileName, ignore, ignoreExtns);

        logger.logComment(
            "The zip file: "
                + zipFile.getAbsolutePath()
                + " ("
                + zipFile.length()
                + " bytes)  contains all of the project files");

        SimpleXMLElement downloads = new SimpleXMLElement("p");
        colRight.addChildElement(downloads);
        downloads.addContent("Downloads<a href=\"#downloadInfo\">*</a>:");

        SimpleXMLElement downloadProj = new SimpleXMLElement("p");
        colRight.addChildElement(downloadProj);

        SimpleXMLElement link = new SimpleXMLElement("a");
        link.addAttribute("href", "downloads/" + zipFile.getName());
        link.addContent("neuroConstruct project");
        link.addAttribute("title", "Download full project for loading into neuroConstruct");
        downloadProj.addChildElement(link);

        ArrayList<String> noNeuroML = new ArrayList<String>();
        noNeuroML.add("Ex3_Morphology");
        noNeuroML.add("DentateGyrus");
        noNeuroML.add("RothmanEtAl_KoleEtAl_PyrCell");

        if (!noNeuroML.contains(projName)) {
          project.neuromlFileManager.generateNeuroMLFiles(
              null, new OriginalCompartmentalisation(), 1234, false);

          File neuroMLDir = ProjectStructure.getNeuroML1Dir(project.getProjectMainDirectory());

          String nmlZipFileName =
              targetDownloadDir.getAbsolutePath() + "/" + projName + "_NeuroML.zip";

          zipFile = ZipUtils.zipUp(neuroMLDir, nmlZipFileName, ignoreNone, ignoreNone);

          SimpleXMLElement downloadNml = new SimpleXMLElement("p");
          colRight.addChildElement(downloadNml);
          // downloadNml.addContent("Download project as pure NeuroML: ");

          SimpleXMLElement img = new SimpleXMLElement("img");
          img.addAttribute("src", "../images/NeuroMLSmall.png");
          String info = "Download core project elements in NeuroML format";
          img.addAttribute("alt", info);

          SimpleXMLElement imgRef = new SimpleXMLElement("a");
          img.addAttribute("title", info);
          imgRef.addAttribute("href", "downloads/" + zipFile.getName());
          imgRef.addChildElement(img);

          downloadNml.addChildElement(imgRef);
        }
      }
    }

    SimpleXMLElement end = new SimpleXMLElement("p");
    body.addChildElement(end);
    end.addContent("&nbsp;");

    SimpleXMLElement infoDlanchor = new SimpleXMLElement("anchor");
    body.addChildElement(infoDlanchor);
    end.addAttribute("id", "downloadInfo");

    SimpleXMLElement infoDl = new SimpleXMLElement("p");
    body.addChildElement(infoDl);
    end.addContent(
        "* Note: neuroConstruct project downloads (most of which are included with the standard software distribution) "
            + "can be loaded directly into neuroConstruct to generate cell and network scripts for NEURON, GENESIS, etc.,"
            + " but NeuroML downloads just consist of the core elements of the project"
            + " (morphologies, channels, etc.) which have been exported in NeuroML format. The latter can be useful for testing NeuroML compliant applications. "
            + "If no NeuroML download link is present, this usually indicates that the model is mainly implemented using channel/synapse mechanisms in a simulator's "
            + "native language (e.g. mod files) which have not fully been converted to ChannelML yet.");

    SimpleXMLElement end2 = new SimpleXMLElement("p");
    body.addChildElement(end2);
    end2.addContent("&nbsp;");

    FileWriter fw = null;
    try {

      fw = new FileWriter(mainFile);
      fw.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"); // quick hack, todo: add to
      // SimpleXMLDoc...

      fw.write(
          "<!DOCTYPE document PUBLIC \"-//APACHE//DTD Documentation V2.0//EN\" \"http://forrest.apache.org/dtd/document-v20.dtd\">\n\n");
      fw.write(root.getXMLString("", false));

      fw.flush();
      fw.close();

    } catch (IOException ex) {
      logger.logError("Problem: ", ex);
      fw.close();
    }

    /*
             <header>
      <title>Examples of neuroConstruct in use</title>
    </header>
    <body>
        <p>Some screenshots of neuroConstruct in action are given below.
        Click on the thumbnails to see a full size version of the screenshots</p>

      <section>
        <title>Examples included with distribution</title>*/

  }