public static Document getDocument(final URLConnection request_con)
throws ParserConfigurationException, SAXException, IOException {
InputStream result_stream = null;
Document doc = null;
try {
result_stream = new BufferedInputStream(request_con.getInputStream());
doc = getDocument(result_stream);
} finally {
GeneralUtils.safeClose(result_stream);
}
return doc;
}
/**
* Computes metrics
*
* @param tune is a boolean
* @param supervised is a boolean
*/
@SuppressWarnings("unchecked")
public void computeMetrics(boolean tune, boolean supervised) {
if (supervised) {
if (!(goldVector != null)) log.error("Supervised data not available");
assert goldVector != null : "Supervised data not available";
}
metrics = new Metrics(this.getCategories());
if (supervised) {
log.info("Computing Metrics -- supervised");
GeneralUtils.computeMetrics(resultVector, metrics, groundTruthVector, goldVector);
log.info("Updated metrics");
} else if (!tune) {
log.info("Computing Metrics -- unsupervised");
GeneralUtils.computeMetrics(resultVector, metrics, groundTruthVector);
log.info("Updated metrics");
} else if (tune) {
log.info("Computing Metrics -- tune");
GeneralUtils.computeMetrics(resultVector, metrics, tuneVector);
log.info("Updated metrics");
}
}
private static void runWithUserParmValues() {
Izhikevich9pModelMC model = getRightInstanceForModel();
double k0, k1, k2;
double a0, a1, a2;
double b0, b1, b2;
double d0, d1, d2;
double C0, C1, C2;
double vR0;
double vT0, vT1, vT2;
double vPeak0, vPeak1, vPeak2;
double c0, c1, c2;
double Gt_1, P_1, Gt_2, P_2;
double[] newCurrents = new double[] {408}; // , currents[1]};
k0 = 1.029252f;
a0 = 0.0015812784f;
b0 = 2.3435593f;
d0 = 3.0f;
C0 = 85.0f;
vR0 = -60.772045f;
vT0 = -30.712957f;
vPeak0 = 19.3511f;
c0 = -53.59736f;
model.setK(getDouble1dArray(k0));
model.setA(getDouble1dArray(a0));
model.setB(getDouble1dArray(b0));
model.setD(getDouble1dArray(d0));
model.setcM(getDouble1dArray(C0));
model.setvR(vR0);
model.setvT(getDouble1dArray(vT0));
model.setvMin(getDouble1dArray(c0));
model.setvPeak(getDouble1dArray(vPeak0));
model.setG(getDouble1dArray(0));
model.setP(getDouble1dArray(0));
double[] weights = new double[] {};
ModelEvaluatorMC evaluator =
new ModelEvaluatorMC(
model,
ModelEvaluatorWrapper.INPUT_SPIKE_PATTERN_CONS,
ModelEvaluatorWrapper.INPUT_PHENOTYPE_CONSTRAINT,
ModelEvaluatorWrapper.INPUT_PAT_REP_WEIGHTS,
ModelEvaluatorWrapper.INPUT_MC_CONS,
newCurrents,
weights);
evaluator.setDisplayAll(true);
evaluator.getFitness();
System.out.println("\nSpike Times: ");
GeneralUtils.displayArray(evaluator.getModelSomaSpikePatternHolder().getSpikeTimes());
}
public String details(boolean html) {
StringBuilder sb = new StringBuilder();
sb.append(
"Network contains "
+ GeneralUtils.getBold(this.getNumberSingleInputs(), html)
+ " inputs in total"
+ GeneralUtils.getEndLine(html)
+ GeneralUtils.getEndLine(html));
Enumeration keys = this.myElecInputs.keys();
String indent = " ";
if (html) indent = " ";
while (keys.hasMoreElements()) {
String input = (String) keys.nextElement();
ArrayList<SingleElectricalInput> singleInputList = myElecInputs.get(input);
sb.append(
"Input: "
+ GeneralUtils.getBold(input, html)
+ " has "
+ GeneralUtils.getBold(singleInputList.size(), html)
+ " entries"
+ GeneralUtils.getEndLine(html));
for (int i = 0; (i < singleInputList.size()); i++) {
sb.append(
"Input "
+ i
+ ": "
+ singleInputList.get(i).details(html)
+ GeneralUtils.getEndLine(html));
if (singleInputList.get(i).getInstanceProps() != null) {
sb.append(
indent
+ "Input specific properties: "
+ singleInputList.get(i).getInstanceProps().details(html)
+ GeneralUtils.getEndLine(html));
}
}
sb.append(GeneralUtils.getEndLine(html));
}
return sb.toString();
}
public static final String get32MD5Str(String str) {
if (GeneralUtils.isNullOrZeroLenght(str)) {
return str;
}
MessageDigest messageDigest = null;
try {
messageDigest = MessageDigest.getInstance("MD5");
messageDigest.reset();
messageDigest.update(str.getBytes("UTF-8"));
} catch (NoSuchAlgorithmException e) {
System.out.println("NoSuchAlgorithmException caught!");
System.exit(-1);
} catch (UnsupportedEncodingException e) {
e.printStackTrace();
}
byte[] byteArray = messageDigest.digest();
StringBuffer md5StrBuff = new StringBuffer();
for (int i = 0; i < byteArray.length; i++) {
if (Integer.toHexString(0xFF & byteArray[i]).length() == 1)
md5StrBuff.append("0").append(Integer.toHexString(0xFF & byteArray[i]));
else md5StrBuff.append(Integer.toHexString(0xFF & byteArray[i]));
}
return md5StrBuff.toString();
}
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. "
+ "<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(" ");
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(" ");
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>*/
}
public static String handleWhitespaces(String text) {
return GeneralUtils.replaceAllTokens(text, "\n", "<br/>");
}
private static void runPrimary(
double[] parms,
String opFolder,
boolean displayParms,
boolean displayErrors,
boolean drawPlots) {
Izhikevich9pModelMC model = getRightInstanceForModel();
EAGenes genes = new EAGenes(parms, iso_comp);
model.setK(genes.getK());
model.setA(genes.getA());
model.setB(genes.getB());
model.setD(genes.getD());
model.setcM(genes.getCM());
model.setvR(genes.getVR());
model.setvT(genes.getVT());
model.setvMin(genes.getVMIN());
model.setvPeak(genes.getVPEAK());
model.setG(genes.getG());
model.setP(genes.getP());
double[] currents = genes.getI();
// float[] newCurrents = new float[currents.length];
// for(int i=0;i<newCurrents.length;i++)
// newCurrents[i] = currents[i];
double[] weights = new double[model.getNCompartments() - 1]; // genes.getW();
for (int wi = 0; wi < weights.length; wi++) {
weights[wi] = 1;
}
ModelEvaluatorMC evaluator =
new ModelEvaluatorMC(
model,
ModelEvaluatorWrapper.INPUT_SPIKE_PATTERN_CONS,
ModelEvaluatorWrapper.INPUT_PHENOTYPE_CONSTRAINT,
ModelEvaluatorWrapper.INPUT_PAT_REP_WEIGHTS,
ModelEvaluatorWrapper.INPUT_MC_CONS,
currents,
weights);
evaluator.setRampRheo(false);
if (displayErrors || displayOnlyFitness) {
if (displayOnlyFitness) {
evaluator.setDisplayAll(false);
evaluator.setDisplayOnlyClass(true);
} else {
evaluator.setDisplayAll(true);
}
// evaluator.setDisplayForPlotIdx(0);
float f = evaluator.getFitness();
if (displayOnlyFitness) {
System.out.print("\t" + f + "\t");
}
// System.out.println();
// evaluator.get
double[] spikeTimes = evaluator.getModelSomaSpikePatternHolder().getSpikeTimes();
spikeTimes = GeneralUtils.roundOff(spikeTimes);
// GeneralUtils.displayArray(spikeTimes);
}
if (displayParms) {
for (int idx = 0; idx < model.getNCompartments(); idx++) {
displayForBrian(model, idx);
}
for (int idx = 0; idx < model.getNCompartments() - 1; idx++) {
System.out.println("Gt_" + (idx + 1) + "=" + model.getG()[idx] + "/ms");
System.out.println("P_" + (idx + 1) + "=" + model.getP()[idx]);
System.out.println("W" + idx + "=" + weights[idx]);
}
// System.out.println();
GeneralUtils.displayArrayUnformatWithSpace(parms, 1, 3);
}
if (drawPlots) {
// float I = currents[0];
double[][] Is = null;
double[] Idurs = null;
if (model.getNCompartments() > 1) {
Idurs =
new double
[ModelEvaluatorWrapper.INPUT_SPIKE_PATTERN_CONS.length + 4]; // exc., ir., sp., EPSP
int i;
for (i = 0; i < ModelEvaluatorWrapper.INPUT_SPIKE_PATTERN_CONS.length; i++) {
Idurs[i] = (float) ModelEvaluatorWrapper.INPUT_SPIKE_PATTERN_CONS[i].getCurrentDuration();
}
if (!ModelEvaluatorWrapper.ISO_COMPS) {
Idurs[i++] =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[0].getAttribute(
MCConstraintAttributeID.current_duration); // exc.
Idurs[i++] =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[1].getAttribute(
MCConstraintAttributeID.current_duration); // ir.
Idurs[i++] =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[2].getAttribute(
MCConstraintAttributeID.dend_current_duration); // sp.
Idurs[i++] =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[3].getAttribute(
MCConstraintAttributeID.sim_duration); // epsp.
}
// *** similarly additional mc currents
double[] somaCurrents = new double[currents.length + 4];
double[] dend1Currents = new double[currents.length + 4];
for (i = 0; i < currents.length; i++) {
somaCurrents[i] = currents[i]; // somatic scenarios
dend1Currents[i] = 0; // no dend current for somatic scenarios
}
double[] rheoComp = model.getRheoBases();
somaCurrents[i] = rheoComp[0]; // exc.
dend1Currents[i++] = rheoComp[1]; // exc.
if (!ModelEvaluatorWrapper.ISO_COMPS) {
somaCurrents[i] =
(double)
ModelEvaluatorWrapper.INPUT_MC_CONS[1].getAttribute(
MCConstraintAttributeID.current); // ir
dend1Currents[i++] =
(double)
ModelEvaluatorWrapper.INPUT_MC_CONS[1].getAttribute(
MCConstraintAttributeID.current); // ir
somaCurrents[i] =
0; // indirectly get the I required for single spike prop as below: (have to go
// through unnecessary steps?!)
float dend_curr_min =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[2].getAttribute(
MCConstraintAttributeID.dend_current_min);
float dend_curr_max =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[2].getAttribute(
MCConstraintAttributeID.dend_current_max);
float dend_current_time_min =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[2].getAttribute(
MCConstraintAttributeID.dend_current_time_min);
float dend_current_duration =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[2].getAttribute(
MCConstraintAttributeID.dend_current_duration);
float dend_current_step =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[2].getAttribute(
MCConstraintAttributeID.dend_current_step);
float dend_target_spike_freq =
(float)
ModelEvaluatorWrapper.INPUT_MC_CONS[2].getAttribute(
MCConstraintAttributeID.dend_target_spike_freq);
for (int c = 1; c < model.getNCompartments(); c++) {
float[] spikeCounts =
evaluator
.getMcEvalholder()
.propagatedSpikeCounts(
c,
MultiCompConstraintEvaluator.forwardConnectionIdcs[c],
dend_curr_min,
dend_curr_max,
dend_current_time_min,
dend_current_duration,
dend_current_step,
dend_target_spike_freq);
dend1Currents[i++] =
spikeCounts[2]; // MUST HAVE 2D ARRAY for dend currents for more than 2 comps!!!!
}
}
somaCurrents[i] = 0; // epsp; syn simulation
dend1Currents[i++] = 0; // epsp; syn simulation
Is = new double[model.getNCompartments()][];
Is[0] = somaCurrents;
Is[1] = dend1Currents;
} else {
Is = new double[1][];
Idurs = new double[ModelEvaluatorWrapper.INPUT_SPIKE_PATTERN_CONS.length];
for (int i = 0; i < ModelEvaluatorWrapper.INPUT_SPIKE_PATTERN_CONS.length; i++) {
Idurs[i] = (float) ModelEvaluatorWrapper.INPUT_SPIKE_PATTERN_CONS[i].getCurrentDuration();
}
Is[0] = currents;
}
BrianInvoker invoker = new BrianInvoker(opFolder, Is, Idurs);
invoker.setDisplayErrorStream(true);
invoker.invoke(model);
}
}
public static boolean transform(
File origXmlFileOrDir, File xslFile, File targetDir, String extension) {
logger.logComment(
"Going to transform " + origXmlFileOrDir + " into dir " + targetDir + " using: " + xslFile,
true);
if (!origXmlFileOrDir.exists()) {
GuiUtils.showErrorMessage(
logger,
"Warning, XML file/directory: " + origXmlFileOrDir + " doesn't exist",
null,
null);
return false;
}
if (!xslFile.exists()) {
GuiUtils.showErrorMessage(
logger, "Warning, XSL file: " + xslFile + " doesn't exist", null, null);
return false;
}
if (!targetDir.exists()) {
GuiUtils.showErrorMessage(
logger, "Warning, target directory: " + targetDir + " doesn't exist", null, null);
return false;
}
if (origXmlFileOrDir.isDirectory()) {
logger.logComment("That file is a directory. Converting all of the XML files in it");
File[] files = origXmlFileOrDir.listFiles();
boolean totalSuccess = true;
for (int i = 0; i < files.length; i++) {
if (!files[i].isDirectory()
&& (files[i].getName().endsWith(".xml") || files[i].getName().endsWith(".XML"))) {
boolean partialSuccess = transform(files[i], xslFile, targetDir, extension);
totalSuccess = totalSuccess || partialSuccess;
} else if (files[i].isDirectory() && !GeneralUtils.isVersionControlDir(files[i])) {
File newFolder = new File(targetDir, files[i].getName());
newFolder.mkdir();
logger.logComment(
"Found a sub folder. Going to convert all there into: " + newFolder + "...");
transform(files[i], xslFile, newFolder, extension);
}
}
return totalSuccess;
}
String result = transform(origXmlFileOrDir, xslFile);
String newName = origXmlFileOrDir.getName();
if (newName.endsWith(".xml") || newName.endsWith(".XML")) {
newName = newName.substring(0, newName.length() - 4) + extension;
}
File targetFile = new File(targetDir, newName);
try {
FileWriter fw = new FileWriter(targetFile);
fw.write(result);
fw.close();
} catch (IOException ex) {
GuiUtils.showErrorMessage(logger, "Exception writing to file: " + targetFile, ex, null);
return false;
}
logger.logComment("The result is in " + targetFile + " *************");
return result != null;
}
