/** * 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; }
/*.................................................................................................................*/ 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(); }