/*.................................................................................................................*/
public Object getProgramArguments(
String dataFileName, String configFileName, boolean isPreflight) {
MesquiteString arguments = new MesquiteString();
if (externalProcRunner.isWindows()) arguments.setValue(" --batch " + configFileName);
else
arguments.setValue(
""); // GARLI command is very simple as all of the arguments are in the config file
return arguments;
}
/** Called to alter data in all cells */
public boolean operateOnData(CharacterData data) {
if (!(data instanceof ContinuousData)) return false;
ContinuousData cData = (ContinuousData) data;
int numItems = cData.getNumItems();
String[] items = new String[numItems];
for (int i = 0; i < items.length; i++) {
if (StringUtil.blank(cData.getItemName(i))) items[i] = "(unnamed)";
else items[i] = cData.getItemName(i);
}
int d =
ListDialog.queryList(
containerOfModule(),
"Rename item",
"Rename item:",
MesquiteString.helpString,
items,
0);
if (!MesquiteInteger.isCombinable(d) || d < 0 || d >= numItems) return false;
else {
String s =
MesquiteString.queryString(
containerOfModule(), "Rename Item", "New name for " + items[d], items[d]);
if (StringUtil.blank(s)) return false;
cData.setItemReference(d, NameReference.getNameReference(s));
return true;
}
}
/*.................................................................................................................*/
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;
}
/*.................................................................................................................*/
public void calculateNumber(
Tree tree1, Tree tree2, MesquiteNumber result, MesquiteString resultString) {
if (result == null) return;
clearResultAndLastResult(result);
if (tree1 == null) return;
if (tree2 == null) return;
int numTaxa = tree1.getTaxa().getNumTaxa();
double[][] patristic1 = null;
patristic1 =
p1.calculatePatristic(
tree1,
numTaxa,
patristic1); // for this tree calculate patristic distances (number of nodes separating
// terminals; no branch lengths)
double[][] patristic2 = null;
patristic2 =
p2.calculatePatristic(
tree2,
numTaxa,
patristic2); // for this tree calculate patristic distances (number of nodes separating
// terminals; no branch lengths)
double correl = offDiagonalPMCorrelationFILTERED(patristic1, patristic2);
if (isDistance && (MesquiteDouble.isCombinable(correl)))
correl = -correl + 1.0; // shifting 1 to -1 to be 0 to 2 to act as distance
result.setValue(correl);
if (resultString != null) {
if (isDistance)
resultString.setValue(
"Patristic correlation (converted to distance): " + result.toString());
else resultString.setValue("Patristic correlation: " + result.toString());
}
saveLastResult(result);
saveLastResultString(resultString);
}
/*.................................................................................................................*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(
this.getClass(),
"Sets module supplying characters",
"[name of module]",
commandName,
"setCharacterSource")) {
CharacterObedSource newCharacterSourceTask;
if (hiringCondition != null)
newCharacterSourceTask =
(CharacterObedSource)
replaceCompatibleEmployee(
CharacterObedSource.class,
arguments,
characterSourceTask,
hiringCondition); // , "Source of characters"
else
newCharacterSourceTask =
(CharacterObedSource)
replaceEmployee(
CharacterObedSource.class,
arguments,
"Source of characters",
characterSourceTask);
if (newCharacterSourceTask != null) {
characterSourceTask = newCharacterSourceTask;
characterSourceTask.setHiringCommand(cstC);
charSourceName.setValue(characterSourceTask.getName());
resetContainingMenuBar();
parametersChanged();
return characterSourceTask;
} else {
discreetAlert(
"Unable to activate character source \""
+ arguments
+ "\" for use by "
+ employer.getName());
}
} else if (characterSourceTask != null) { // todo: temporary, for snapshot conversions
return characterSourceTask.doCommand(commandName, arguments, checker);
} else return super.doCommand(commandName, arguments, checker);
return null;
}
public void calculateNumber(Taxon taxon, MesquiteNumber result, MesquiteString resultString) {
if (result == null) return;
clearResultAndLastResult(result);
Taxa taxa = taxon.getTaxa();
int it = taxa.whichTaxonNumber(taxon);
if (taxa != currentTaxa || observedStates == null) {
observedStates = matrixSourceTask.getCurrentMatrix(taxa);
currentTaxa = taxa;
}
if (observedStates == null || !(observedStates.getParentData() instanceof DNAData)) return;
DNAData data = (DNAData) observedStates.getParentData();
int count = data.getAminoAcidNumbers(it, ProteinData.TER, countEvenIfOthers.getValue());
if (result != null) result.setValue(count);
if (resultString != null)
resultString.setValue(
"Number of stop codons in taxon " + observedStates.getName() + ": " + count);
saveLastResult(result);
saveLastResultString(resultString);
}
/** 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 processJobSubmissionResponse(Document cipresResponseDoc, MesquiteString jobURL) {
Element element = cipresResponseDoc.getRootElement().element("selfUri");
Element subelement = null;
if (element != null) subelement = element.element("url");
if ("false".equals(cipresResponseDoc.getRootElement().elementText("failed"))) {
element = cipresResponseDoc.getRootElement().element("metadata");
List entries = element.elements("entry");
String reportedJobID = "";
for (Iterator iter = entries.iterator(); iter.hasNext(); ) {
Element nextEntry = (Element) iter.next();
if ("clientJobId".equals(nextEntry.elementText("key")))
reportedJobID = nextEntry.elementText("value");
}
ownerModule.logln("\nJob successfully submitted to CIPRes.");
ownerModule.logln(" Job URL: " + subelement.getText());
ownerModule.logln(" Job ID: " + reportedJobID + "\n");
if (jobURL != null) jobURL.setValue(subelement.getText());
}
}
/*.................................................................................................................*/
public Tree getTrees(
TreeVector trees,
Taxa taxa,
MCharactersDistribution matrix,
long seed,
MesquiteDouble finalScore) {
if (!initializeGetTrees(CategoricalData.class, taxa, matrix)) return null;
setTNTSeed(seed);
isProtein = data instanceof ProteinData;
// David: if isDoomed() then module is closing down; abort somehow
// write data file
String tempDir =
MesquiteFileUtil.createDirectoryForFiles(
this, MesquiteFileUtil.IN_SUPPORT_DIR, "TNT", "-Run.");
if (tempDir == null) return null;
String dataFileName = "data.ss"; // replace this with actual file name?
String dataFilePath = tempDir + dataFileName;
FileInterpreterI exporter = ZephyrUtil.getFileInterpreter(this, "#InterpretTNT");
if (exporter == null) return null;
boolean fileSaved = false;
String translationTable = namer.getTranslationTable(taxa);
((InterpretHennig86Base) exporter).setTaxonNamer(namer);
fileSaved = ZephyrUtil.saveExportFile(this, exporter, dataFilePath, data, selectedTaxaOnly);
if (!fileSaved) return null;
String translationFileName = IOUtil.translationTableFileName;
setTaxonTranslation(taxa);
taxonNumberTranslation = getTaxonNumberTranslation(taxa);
namer.setNumberTranslationTable(taxonNumberTranslation);
setFileNames();
TaxaSelectionSet outgroupSet =
(TaxaSelectionSet) taxa.getSpecsSet(outgroupTaxSetString, TaxaSelectionSet.class);
int firstOutgroup = MesquiteInteger.unassigned;
if (outgroupSet != null) firstOutgroup = outgroupSet.firstBitOn();
formCommandFile(dataFileName, firstOutgroup);
logln("\n\nCommands given to TNT:");
logln(commands);
logln("");
MesquiteString arguments = new MesquiteString();
arguments.setValue(" proc " + commandsFileName);
String programCommand = externalProcRunner.getExecutableCommand();
int numInputFiles = 3;
String[] fileContents = new String[numInputFiles];
String[] fileNames = new String[numInputFiles];
for (int i = 0; i < numInputFiles; i++) {
fileContents[i] = "";
fileNames[i] = "";
}
fileContents[0] = MesquiteFile.getFileContentsAsString(dataFilePath);
fileNames[0] = dataFileName;
fileContents[1] = commands;
fileNames[1] = commandsFileName;
fileContents[2] = translationTable;
fileNames[2] = translationFileName;
// ----------//
boolean success =
runProgramOnExternalProcess(
programCommand, arguments, fileContents, fileNames, ownerModule.getName());
if (!isDoomed()) {
if (success) {
desuppressProjectPanelReset();
return retrieveTreeBlock(trees, finalScore); // here's where we actually process everything.
} else {
if (!beanWritten) postBean("unsuccessful [1]", false);
beanWritten = true;
}
}
desuppressProjectPanelReset();
if (data == null) data.decrementEditInhibition();
externalProcRunner.finalCleanup();
return null;
}