コード例 #1
0
 /*.................................................................................................................*/
 boolean checkUsernamePassword(boolean tellUserAboutCipres) {
   if (StringUtil.blank(username) || StringUtil.blank(password)) {
     MesquiteBoolean answer = new MesquiteBoolean(false);
     MesquiteString usernameString = new MesquiteString();
     if (username != null) usernameString.setValue(username);
     MesquiteString passwordString = new MesquiteString();
     if (password != null) passwordString.setValue(password);
     String help =
         "You will need an account on the CIPRes REST system to use this service.  To register, go to https://www.phylo.org/restusers/register.action";
     new UserNamePasswordDialog(
         ownerModule.containerOfModule(),
         "Sign in to CIPRes",
         help,
         "",
         "Username",
         "Password",
         answer,
         usernameString,
         passwordString);
     if (answer.getValue()) {
       username = usernameString.getValue();
       password = passwordString.getValue();
     }
     ownerModule.storePreferences();
   }
   boolean success = StringUtil.notEmpty(username) && StringUtil.notEmpty(password);
   if (!success && tellUserAboutCipres) {
     MesquiteMessage.discreetNotifyUser(
         "Use of the CIPRes service requires an account with CIPRes's REST service.  Go to https://www.phylo.org/restusers/register.action to register for an account");
   }
   return success;
 }
コード例 #2
0
 /** This method simply lists the tools available */
 public void listTools(HttpClient httpclient) {
   Document cipresResponseDoc = cipresQuery(httpclient, baseURL + "/tool", "tools");
   if (cipresResponseDoc != null) {
     String elementName = "tool";
     List tools = cipresResponseDoc.getRootElement().elements(elementName);
     int count = 0;
     for (Iterator iter = tools.iterator();
         iter.hasNext(); ) { // let's get a count as to how many tools there are.
       Element nextTool = (Element) iter.next();
       count++;
     }
     String[] toolName = new String[count];
     count = 0;
     for (Iterator iter = tools.iterator(); iter.hasNext(); ) {
       Element nextTool = (Element) iter.next();
       String name = nextTool.elementText("toolId");
       if (!StringUtil.blank(name) && count < toolName.length) {
         ownerModule.logln(name);
       }
       name = nextTool.elementText("toolName");
       if (!StringUtil.blank(name) && count < toolName.length) {
         ownerModule.logln("   " + name);
       }
       count++;
     }
   }
 }
コード例 #3
0
 public String[] getJobURLs(Document cipresResponseDoc) {
   String elementName = "jobstatus";
   Element jobs = cipresResponseDoc.getRootElement().element("jobs");
   if (jobs == null) return null;
   List tools = jobs.elements("jobstatus");
   int count = 0;
   for (Iterator iter = tools.iterator(); iter.hasNext(); ) {
     Element nextTool = (Element) iter.next();
     count++;
   }
   String[] url = new String[count];
   count = 0;
   for (Iterator iter = tools.iterator(); iter.hasNext(); ) {
     Element nextJob = (Element) iter.next();
     if (nextJob != null) {
       Element selfUriElement = nextJob.element("selfUri");
       if (selfUriElement != null) {
         String jobURL = selfUriElement.elementText("url");
         if (!StringUtil.blank(jobURL) && count < url.length) {
           url[count] = jobURL;
         }
       }
       count++;
     }
   }
   return url;
 }
コード例 #4
0
 /*.................................................................................................................*/
 public boolean downloadWorkingResults(
     HttpClient httpclient,
     String jobURL,
     String rootDir,
     String fileName,
     boolean onlyNewOrModified) {
   if (StringUtil.blank(fileName)) return false;
   String workingUri = getWorkingDirectory(jobURL);
   if (StringUtil.notEmpty(workingUri)) {
     Document cipresResponseDoc = cipresQuery(httpclient, workingUri, "workingdir");
     if (cipresResponseDoc != null) {
       CipresJobFile[] cipresJobFiles = processFilesDocument(cipresResponseDoc);
       if (cipresJobFiles == null || cipresJobFiles.length == 0) {
         return false;
       }
       for (int job = 0; job < cipresJobFiles.length; job++) {
         if (fileName.equalsIgnoreCase(cipresJobFiles[job].getFileName())
             && (!onlyNewOrModified
                 || fileNewOrModified(previousCipresJobFiles, cipresJobFiles, job)))
           cipresDownload(
               httpclient,
               cipresJobFiles[job].getDownloadURL(),
               rootDir + cipresJobFiles[job].getFileName());
       }
       previousCipresJobFiles = cipresJobFiles.clone();
       return true;
     }
   }
   return false;
 }
コード例 #5
0
 /**
  * this is the primary method that sends a query to the CIPRes REST service. It expects to receive
  * an XML file, which it returns in Document if the root tag matc hes xmlRootTag
  */
 public Document cipresQuery(HttpClient httpclient, String URL, String xmlRootTag) {
   if (StringUtil.blank(URL)) return null;
   try {
     HttpGet httpget = new HttpGet(URL);
     httpget.addHeader("cipres-appkey", CIPRESkey);
     try {
       HttpResponse response = httpclient.execute(httpget);
       HttpEntity responseEntity = response.getEntity();
       InputStream instream = responseEntity.getContent();
       BufferedReader br = new BufferedReader(new InputStreamReader(instream));
       String line = "";
       StringBuffer sb = new StringBuffer();
       while ((line = br.readLine()) != null) {
         sb.append(line + StringUtil.lineEnding());
       }
       Document cipresResponseDoc = loadXMLFile(xmlRootTag, sb.toString());
       if (cipresResponseDoc != null && verbose) {
         ownerModule.logln(sb.toString());
       }
       if (cipresResponseDoc == null) {
         Document errorDoc = loadXMLFile(sb.toString());
         if (errorDoc != null) reportError(errorDoc, "Error in communicating with CIPRes", true);
       }
       EntityUtils.consume(response.getEntity());
       return cipresResponseDoc;
     } catch (IOException e) {
       Debugg.printStackTrace(e);
     } catch (Exception e) {
       Debugg.printStackTrace(e);
     }
   } catch (Exception e) {
     Debugg.printStackTrace(e);
   }
   return null;
 }
コード例 #6
0
 /**
  * This method returns a Document from the contents of the XML file as contained in the String
  * xmlFile, with no restriction as to the root element.
  */
 public Document loadXMLFile(String xmlFile) {
   if (!StringUtil.blank(xmlFile)) {
     Document CipresDoc = XMLUtil.getDocumentFromString(xmlFile);
     return CipresDoc;
   }
   return null;
 }
コード例 #7
0
  /**
   * This processes information about the files contained in either the results or working directory
   * of a job.
   */
  public CipresJobFile[] processFilesDocument(Document cipresResponseDoc) {
    Element jobfiles = cipresResponseDoc.getRootElement().element("jobfiles");
    if (jobfiles == null) return null;
    List tools = jobfiles.elements("jobfile");
    int count = 0;
    for (Iterator iter = tools.iterator(); iter.hasNext(); ) {
      Element nextTool = (Element) iter.next();
      count++;
    }
    if (count == 0) return null;
    CipresJobFile[] cipresJobFile = new CipresJobFile[count];
    count = 0;
    for (Iterator iter = tools.iterator(); iter.hasNext(); ) {
      Element nextJob = (Element) iter.next();
      if (nextJob != null) {
        if (cipresJobFile[count] == null) cipresJobFile[count] = new CipresJobFile();
        Element jobFileElement = nextJob.element("downloadUri");
        String fileInfo = null;
        if (jobFileElement != null) {
          fileInfo = jobFileElement.elementText("url");
          if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
            cipresJobFile[count].setDownloadURL(fileInfo);
          }
          fileInfo = jobFileElement.elementText("title");
          if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
            cipresJobFile[count].setDownloadTitle(fileInfo);
          }
        }
        fileInfo = nextJob.elementText("dateModified");
        if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
          cipresJobFile[count].setLastModified(fileInfo);
        }
        fileInfo = nextJob.elementText("filename");
        if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
          cipresJobFile[count].setFileName(fileInfo);
        }
        fileInfo = nextJob.elementText("length");
        if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
          cipresJobFile[count].setLength(MesquiteLong.fromString(fileInfo));
        }

        count++;
      }
    }
    return cipresJobFile;
  }
コード例 #8
0
  /*.................................................................................................................*/
  public boolean monitorAndCleanUpShell(String jobURL) {
    boolean stillGoing = true;

    if (!checkUsernamePassword(true)) {
      return false;
    }
    lastModified = null;
    if (outputFilePaths != null) {
      lastModified = new long[outputFilePaths.length];
      LongArray.deassignArray(lastModified);
    }
    String status = "";
    while (!jobCompleted(jobURL) && stillGoing) {
      if (StringUtil.blank(status))
        ownerModule.logln(
            "CIPRes Job Status: " + getJobStatus(jobURL) + "  (" + StringUtil.getDateTime() + ")");

      //	if (jobSubmitted(jobURL))
      //		processOutputFiles();
      try {
        Thread.sleep(minPollIntervalSeconds * 1000);
      } catch (InterruptedException e) {
        MesquiteMessage.notifyProgrammer("InterruptedException in CIPRes monitoring");
        return false;
      }

      stillGoing = watcher == null || watcher.continueShellProcess(null);
      String newStatus = getJobStatus(jobURL);
      if (newStatus != null && !newStatus.equalsIgnoreCase(status)) {
        ownerModule.logln(
            "CIPRes Job Status: " + newStatus + "  (" + StringUtil.getDateTime() + ")");
        status = newStatus;
      } else ownerModule.log(".");
      if (newStatus != null && newStatus.equalsIgnoreCase("SUBMITTED")) { // job is running
        processOutputFiles(jobURL);
      }
    }
    ownerModule.logln("CIPRes job completed.");
    if (outputFileProcessor != null) {
      if (rootDir != null) {
        ownerModule.logln("About to download results from CIPRes.");
        if (downloadResults(jobURL, rootDir, false))
          outputFileProcessor.processCompletedOutputFiles(outputFilePaths);
        else return false;
      }
    }

    return true;
  }