/**
  * 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;
 }
Example #2
0
  /*.................................................................................................................*/
  public String preparePreferencesForXML() {
    StringBuffer buffer = new StringBuffer(200);
    StringUtil.appendXMLTag(buffer, 2, "mxram", mxram);
    StringUtil.appendXMLTag(buffer, 2, "bootStrapReps", bootstrapreps);
    StringUtil.appendXMLTag(buffer, 2, "convertGapsToMissing", convertGapsToMissing);
    StringUtil.appendXMLTag(buffer, 2, "resamplingAllConsensusTrees", resamplingAllConsensusTrees);
    StringUtil.appendXMLTag(buffer, 2, "harvestOnlyStrictConsensus", harvestOnlyStrictConsensus);
    StringUtil.appendXMLTag(buffer, 2, "searchArguments", searchArguments);
    StringUtil.appendXMLTag(buffer, 2, "bootstrapSearchArguments", bootstrapSearchArguments);
    StringUtil.appendXMLTag(buffer, 2, "searchStyle", searchStyle);
    StringUtil.appendXMLTag(buffer, 2, "otherOptions", otherOptions);

    preferencesSet = true;
    return buffer.toString();
  }
  /** The core method that initiates a job on CIPRes. */
  public boolean postJob(
      HttpClient httpclient, MultipartEntityBuilder builder, MesquiteString jobURL) {
    if (builder == null) return false;
    String URL = baseURL + "/job/" + username;
    HttpPost httppost = new HttpPost(URL);
    httppost.addHeader("cipres-appkey", CIPRESkey);

    // some of this from
    // http://stackoverflow.com/questions/18964288/upload-a-file-through-an-http-form-via-multipartentitybuilder-with-a-progress
    HttpEntity cipresEntity = builder.build();

    httppost.setEntity(cipresEntity);

    try {
      HttpResponse response = httpclient.execute(httppost);

      HttpEntity responseEntity = response.getEntity();
      InputStream instream = responseEntity.getContent();
      BufferedReader br = new BufferedReader(new InputStreamReader(instream));
      StringBuffer sb = new StringBuffer();
      String line = "";
      while ((line = br.readLine()) != null) {
        sb.append(line + StringUtil.lineEnding());
      }

      Document cipresResponseDoc = loadXMLFile("jobstatus", sb.toString()); // let's see how it went
      boolean success = false;
      if (cipresResponseDoc != null) {
        processJobSubmissionResponse(cipresResponseDoc, jobURL);
        if (verbose) ownerModule.logln(sb.toString());
        if (jobURL != null) success = StringUtil.notEmpty(jobURL.getValue());
        else success = true;
      } else {
        cipresResponseDoc = loadXMLFile(sb.toString());
        reportError(cipresResponseDoc, "Error with CIPRes run", false);
      }
      EntityUtils.consume(response.getEntity());
      return success;
    } catch (IOException e) {
      Debugg.printStackTrace(e);
    }
    return false;
  }
  /*.................................................................................................................*/
  public void appendToConfigFileGeneral(StringBuffer config) {
    if (config != null) {
      config.append("\ndatafname=" + dataFileName);
      config.append("\nofprefix=" + ofprefix);

      if (useConstraintTree == 0) config.append("\nconstraintfile = none");
      else config.append("\nconstraintfile = constraintTree"); // important to be user-editable

      config.append("\nstreefname = random");

      config.append("\navailablememory = " + availMemory + " \n");
      config.append(" \noutputmostlyuselessfiles = 0");

      config.append("\n\nrandseed = " + randseed); // important to be user-editable

      config.append("\nsearchreps = " + numRuns);

      config.append("\n");
    }
  }
  /*.................................................................................................................*/
  public Object getProgramArguments(String dataFileName, boolean isPreflight) {
    MultipartEntityBuilder arguments = MultipartEntityBuilder.create();
    StringBuffer sb = new StringBuffer();

    if (!isPreflight) {
      getArguments(
          arguments,
          sb,
          dataFileName,
          proteinModel,
          dnaModel,
          otherOptions,
          bootstrapreps,
          bootstrapSeed,
          numRuns,
          outgroupTaxSetString,
          multipleModelFileName,
          false);
      logln("RAxML arguments: \n" + sb.toString() + "\n");
    } else {
      getArguments(
          arguments,
          sb,
          dataFileName,
          proteinModel,
          dnaModel,
          otherOptions,
          bootstrapreps,
          bootstrapSeed,
          numRuns,
          outgroupTaxSetString,
          multipleModelFileName,
          true);
    }
    return arguments;
  }
 /*.................................................................................................................*/
 public String preparePreferencesForXML() {
   StringBuffer buffer = new StringBuffer(200);
   StringUtil.appendXMLTag(buffer, 2, "availMemory", availMemory);
   buffer.append(super.preparePreferencesForXML());
   return buffer.toString();
 }
  /*.................................................................................................................*/
  public Object doCommand(String commandName, String arguments, CommandChecker checker) {
    if (checker.compare(
        this.getClass(), "Returns the matrix source", null, commandName, "getMatrixSource")) {
      return matrixSourceTask;
    } else if (checker.compare(
        this.getClass(), "Copies the data for selected taxon", null, commandName, "copyData")) {
      if (observedStates == null) return null;
      CharacterData data = observedStates.getParentData();
      if (data == null) return null;
      int it = MesquiteInteger.fromString(parser.getFirstToken(arguments));
      if (MesquiteInteger.isCombinable(it)) {
        StringBuffer sb = new StringBuffer();
        data.copyDataFromRowIntoBuffer(it, sb);
        if (StringUtil.notEmpty(sb.toString())) {
          localCopyDataClipboard = sb.toString();
          localCopyData = data;
          localCopyDataTaxon = data.getTaxa().getTaxonName(it);
        } else {
          localCopyDataClipboard = null;
          localCopyData = null;
          localCopyDataTaxon = null;
        }
      }
      return null;
    } else if (checker.compare(
        this.getClass(), "Pastes the data for selected taxon", null, commandName, "pasteData")) {
      if (observedStates == null) return null;
      CharacterData data = observedStates.getParentData();
      if (data == null) return null;
      int it = MesquiteInteger.fromString(parser.getFirstToken(arguments));
      if (MesquiteInteger.isCombinable(it) && StringUtil.notEmpty(localCopyDataClipboard)) {
        data.pasteDataFromStringIntoTaxon(it, localCopyDataClipboard);
      }
      return null;
    } else if (checker.compare(
        this.getClass(),
        "Pastes the data for selected taxon",
        null,
        commandName,
        "deleteDataTouched")) {
      if (observedStates == null) return null;
      CharacterData data = observedStates.getParentData();
      if (data == null) return null;
      int it = MesquiteInteger.fromString(parser.getFirstToken(arguments));
      Debugg.println("prepare to delete row: " + it);
      if (MesquiteInteger.isCombinable(it)) {
        if (!AlertDialog.query(
            containerOfModule(),
            "Delete Data?",
            "Are you sure you want to delete the data for taxon "
                + data.getTaxa().getTaxonName(it)
                + " in the matrix \""
                + data.getName()
                + "\"",
            "No",
            "Yes")) {
          zapData(data, it);
        }
      }
      return null;
    } else if (checker.compare(
        this.getClass(), "Deletes the data for selected taxa", null, commandName, "deleteData")) {
      if (observedStates == null) return null;
      captureCharacterDataFromObservedStates();
      if (data == null) return null;
      if (!AlertDialog.query(
          containerOfModule(),
          "Delete Data?",
          "Are you sure you want to delete the data for these taxa in the matrix \""
              + data.getName()
              + "\"",
          "No",
          "Yes")) zapData(data);
      return null;
    } else if (checker.compare(
        this.getClass(),
        "deleteds () and anything between",
        null,
        commandName,
        "deletePrepended")) {
      if (observedStates == null || taxa == null) return null;
      boolean anySelected = taxa.anySelected();
      int myColumn = -1;
      if (getEmployer() instanceof ListModule) {

        myColumn = ((ListModule) getEmployer()).getMyColumn(this);
        if (table != null)
          anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
      }

      for (int it = 0; it < taxa.getNumTaxa(); it++) {
        if ((!anySelected || selected(taxa, it, myColumn))) {
          String note = getNote(it);
          while (!StringUtil.blank(note) && note.indexOf("(") >= 0) {
            int start = note.indexOf("(");
            int end = note.indexOf(")");
            String firstBit = "";
            if (start > 0) firstBit = note.substring(0, start);
            note = firstBit + note.substring(end + 1, note.length());
          }
          setNote(it, note);
        }
      }
      outputInvalid();
      parametersChanged();
      return null;
    } else if (checker.compare(this.getClass(), "deletes *", null, commandName, "deleteStar")) {
      if (observedStates == null || taxa == null) return null;
      boolean anySelected = taxa.anySelected();
      int myColumn = -1;
      if (getEmployer() instanceof ListModule) {

        myColumn = ((ListModule) getEmployer()).getMyColumn(this);
        if (table != null)
          anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
      }
      for (int it = 0; it < taxa.getNumTaxa(); it++) {
        if ((!anySelected || selected(taxa, it, myColumn))) {
          String note = getNote(it);
          while (!StringUtil.blank(note) && note.indexOf("*") >= 0) {
            int start = note.indexOf("*");
            String firstBit = "";
            if (start > 0) firstBit = note.substring(0, start);
            note = firstBit + note.substring(start + 1, note.length());
          }
          setNote(it, note);
        }
      }
      outputInvalid();
      parametersChanged();
      return null;
    } else if (checker.compare(
        this.getClass(),
        "Prepends to the note the sequence length (including N\'s and ?\'s) for the selected taxa",
        null,
        commandName,
        "prependLength")) {
      if (observedStates == null || taxa == null) return null;
      boolean anySelected = taxa.anySelected();
      int myColumn = -1;
      if (getEmployer() instanceof ListModule) {

        myColumn = ((ListModule) getEmployer()).getMyColumn(this);
        if (table != null)
          anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
      }
      for (int it = 0; it < taxa.getNumTaxa(); it++) {
        if (hasData(it) && (!anySelected || selected(taxa, it, myColumn))) {
          String note = getNote(it);
          if (StringUtil.blank(note)) note = "(" + sequenceLength(it) + ")";
          else note = "(" + sequenceLength(it) + ") " + note;
          setNote(it, note);
        }
      }
      outputInvalid();
      parametersChanged();
      return null;
    } else if (checker.compare(
        this.getClass(),
        "Prepends to the note the number of non-missing sites (not including N\'s and ?\'s) for the selected taxa",
        null,
        commandName,
        "prependNumSites")) {
      if (observedStates == null || taxa == null) return null;
      boolean anySelected = taxa.anySelected();
      int myColumn = -1;
      if (getEmployer() instanceof ListModule) {

        myColumn = ((ListModule) getEmployer()).getMyColumn(this);
        if (table != null)
          anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
      }
      for (int it = 0; it < taxa.getNumTaxa(); it++) {
        if (hasData(it) && (!anySelected || selected(taxa, it, myColumn))) {
          String note = getNote(it);
          if (StringUtil.blank(note)) note = "(" + numSites(it) + ")";
          else note = "(" + numSites(it) + ") " + note;
          setNote(it, note);
        }
      }
      outputInvalid();
      parametersChanged();
      return null;
    } else if (checker.compare(
        this.getClass(),
        "Deletes the notes for the selected taxa",
        null,
        commandName,
        "deleteAnnotation")) {
      if (observedStates == null || taxa == null) return null;
      boolean anySelected = taxa.anySelected();
      int myColumn = -1;
      if (getEmployer() instanceof ListModule) {

        myColumn = ((ListModule) getEmployer()).getMyColumn(this);
        if (table != null)
          anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
      }
      for (int it = 0; it < taxa.getNumTaxa(); it++) {
        if (hasData(it) && (!anySelected || selected(taxa, it, myColumn))) {
          setNote(it, null);
        }
      }
      outputInvalid();
      parametersChanged();
      return null;
    } else return super.doCommand(commandName, arguments, checker);
  }
 /*.................................................................................................................*/
 void addArgument(MultipartEntityBuilder builder, StringBuffer sb, String param, String value) {
   if (builder != null) builder.addTextBody(param, value);
   if (sb != null) sb.append("\n  " + param + " = " + value);
 }
 /*.................................................................................................................*/
 public String preparePreferencesForXML() {
   StringBuffer buffer = new StringBuffer(200);
   StringUtil.appendXMLTag(buffer, 2, "username", username);
   StringUtil.appendXMLTag(buffer, 2, "jobNumber", jobNumber);
   return buffer.toString();
 }