private void deflate(String tmpDir, String path) {
String tmpFile = "tmp-" + Utils.timestamp() + ".zip";
try {
ZipFile zipFile = new ZipFile(tmpFile);
ZipParameters parameters = new ZipParameters();
parameters.setCompressionMethod(Zip4jConstants.COMP_DEFLATE);
parameters.setCompressionLevel(Zip4jConstants.DEFLATE_LEVEL_NORMAL);
parameters.setIncludeRootFolder(false);
zipFile.addFolder(tmpDir, parameters);
} catch (Exception e) {
e.printStackTrace();
return;
}
File from = null;
File to = null;
try {
File target = new File(path);
if (target.exists()) FileUtils.forceDelete(target);
from = new File(tmpFile);
to = new File(path);
FileUtils.moveFile(from, to);
} catch (IOException e) {
Utils.onError(new Error.FileMove(tmpFile, path));
}
try {
FileUtils.deleteDirectory(new File(tmpDir));
} catch (IOException e) {
Utils.log("can't delete temporary folder");
}
}
/**
* Transforms the given XML file using the specified XSL file.
*
* @param origXmlFile The file containg the XML to transform
* @param xslFile The XML Stylesheet conntaining the transform instructions
* @return String representation of the transformation
*/
public static String transform(File origXmlFile, File xslFile) {
if (!origXmlFile.exists()) {
GuiUtils.showErrorMessage(
logger, "Warning, XML file: " + origXmlFile + " doesn't exist", null, null);
return null;
}
if (!xslFile.exists()) {
GuiUtils.showErrorMessage(
logger, "Warning, XSL file: " + xslFile + " doesn't exist", null, null);
return null;
}
try {
logger.logComment("The xslFile is " + xslFile + " *************");
TransformerFactory tFactory = TransformerFactory.newInstance();
StreamSource xslFileSource = new StreamSource(xslFile);
Transformer transformer = tFactory.newTransformer(xslFileSource);
StringWriter writer = new StringWriter();
transformer.transform(new StreamSource(origXmlFile), new StreamResult(writer));
return writer.toString();
} catch (Exception e) {
GuiUtils.showErrorMessage(logger, "Error when loading the XML file: " + origXmlFile, e, null);
return null;
}
}
public void apply(String path, String[] scripts)
throws ParserConfigurationException, TransformerConfigurationException {
File target = new File(path);
if (target.isDirectory()) {
String callerDir = this.targetDir;
this.targetDir = path;
for (String script : scripts) call(script);
this.targetDir = callerDir;
} else {
String tmpDir = inflate(path);
if (tmpDir == null) return;
apply(tmpDir, scripts);
deflate(tmpDir, path);
}
}
private static void validateXMLWithURL(File nmlFile, String schemaUrl) {
try {
Source schemaFileSource = new StreamSource(schemaUrl);
SchemaFactory factory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
Schema schema = factory.newSchema(schemaFileSource);
Validator validator = schema.newValidator();
Source xmlFileSource = new StreamSource(nmlFile);
validator.validate(xmlFileSource);
System.out.println(
"**** File: " + nmlFile + " is VALID according to " + schemaUrl + "!!! ****");
} catch (Exception ex) {
System.err.println(
"Problem validating xml file: "
+ nmlFile.getAbsolutePath()
+ " according to "
+ schemaUrl
+ "!!!");
ex.printStackTrace();
System.exit(1);
}
}
private void processDelete(Node operation) {
String path = absolutePath(operation.getTextContent());
File target = new File(path);
if (!target.exists()) {
Utils.onError(new Error.FileNotFound(target.getPath()));
return;
}
try {
if (target.isDirectory()) {
FileUtils.deleteDirectory(target);
} else {
FileUtils.forceDelete(target);
}
} catch (IOException ex) {
Utils.onError(new Error.FileDelete(target.getPath()));
}
}
public void apply(String path, NodeList[] operations)
throws ParserConfigurationException, TransformerConfigurationException {
File target = new File(path);
if (target.isDirectory()) {
String callerDir = this.targetDir;
this.targetDir = path;
for (NodeList ops : operations) {
for (int i = 0; i < ops.getLength(); i++) call(ops.item(i));
}
this.targetDir = callerDir;
} else {
String tmpDir = inflate(path);
if (tmpDir == null) return;
apply(tmpDir, operations);
deflate(tmpDir, path);
}
}
private void processXml(Node operation)
throws ParserConfigurationException, TransformerConfigurationException {
List<Node> targets = getChildNodes(operation, "target");
List<Node> appendOpNodes = getChildNodes(operation, "append");
List<Node> setOpNodes = getChildNodes(operation, "set");
List<Node> replaceOpNodes = getChildNodes(operation, "replace");
List<Node> removeOpNodes = getChildNodes(operation, "remove");
if (targets.isEmpty()) {
return;
}
for (int t = 0; t < targets.size(); t++) {
File target = new File(absolutePath(targets.get(t).getTextContent()));
if (!target.exists()) {
Utils.onError(new Error.FileNotFound(target.getPath()));
return;
}
DocumentBuilder db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
Document doc = null;
try {
doc = db.parse(target);
} catch (Exception ex) {
Utils.onError(new Error.FileParse(target.getPath()));
return;
}
for (int i = 0; i < removeOpNodes.size(); i++) removeXmlEntry(doc, removeOpNodes.get(i));
for (int i = 0; i < replaceOpNodes.size(); i++) replaceXmlEntry(doc, replaceOpNodes.get(i));
for (int i = 0; i < setOpNodes.size(); i++) setXmlEntry(doc, setOpNodes.get(i));
for (int i = 0; i < appendOpNodes.size(); i++) appendXmlEntry(doc, appendOpNodes.get(i));
try {
OutputFormat format = new OutputFormat(doc);
format.setOmitXMLDeclaration(true);
format.setLineWidth(65);
format.setIndenting(true);
format.setIndent(4);
Writer out = new FileWriter(target);
XMLSerializer serializer = new XMLSerializer(out, format);
serializer.serialize(doc);
} catch (IOException e) {
Utils.onError(new Error.WriteXmlConfig(target.getPath()));
}
}
}
private Transformer buildTransformer(String name, File xslDir, TransformerFactory tf)
throws Exception {
Transformer tr =
tf.newTransformer(
new StreamSource(
new FileReader(xslDir.getAbsolutePath() + File.separatorChar + name + ".xsl")));
tr.setOutputProperty(OutputKeys.INDENT, "yes");
tr.setOutputProperty(OutputKeys.METHOD, "html");
tr.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
return tr;
}
// ## operation Chemkin(double,double,String)
public Chemkin(double p_rtol, double p_atol, String p_reactorType) {
// #[ operation Chemkin(double,double,String)
if (p_rtol < 0 || p_atol < 0)
throw new InvalidChemkinParameterException("Negative rtol or atol!");
if (p_reactorType == null) throw new NullPointerException();
String dir = System.getProperty("RMG.workingDirectory");
// create the documentTypesDefinitions
File docFile = new File("chemkin/documentTypeDefinitions");
docFile.mkdir();
copyFiles(
dir + "/software/reactorModel/documentTypeDefinitions/reactorInput.dtd",
"chemkin/documentTypeDefinitions/reactorInput.dtd");
copyFiles(
dir + "/software/reactorModel/documentTypeDefinitions/reactorOutput.dtd",
"chemkin/documentTypeDefinitions/reactorOutput.dtd");
rtol = p_rtol;
atol = p_atol;
reactorType = p_reactorType;
}
/**
* Transforms the given XML string using the specified XSL file.
*
* @param xmlString The String containg the XML to transform
* @param xslFile The XML Stylesheet conntaining the transform instructions
* @return String representation of the transformation
*/
public static String transform(String xmlString, File xslFile) {
if (!xslFile.exists()) {
GuiUtils.showErrorMessage(
logger, "Warning, XSL file: " + xslFile + " doesn't exist", null, null);
return null;
}
String shortString = new String(xmlString);
if (shortString.length() > 100) shortString = shortString.substring(0, 100) + "...";
try {
logger.logComment("The xslFile is " + xslFile.getAbsolutePath() + " *************");
TransformerFactory tFactory = TransformerFactory.newInstance();
logger.logComment("Transforming string: " + shortString);
StreamSource xslFileSource = new StreamSource(xslFile);
Transformer transformer = tFactory.newTransformer(xslFileSource);
StringWriter writer = new StringWriter();
transformer.transform(
new StreamSource(new StringReader(xmlString)), new StreamResult(writer));
String shortResult = writer.toString();
if (shortResult.length() > 100) shortResult = shortResult.substring(0, 100) + "...";
logger.logComment("Result: " + shortResult);
return writer.toString();
} catch (TransformerException e) {
GuiUtils.showErrorMessage(logger, "Error when transforming the XML: " + shortString, e, null);
return null;
}
}
/**
* opens existing file
*
* @param a_file
*/
public GlyphFile(File a_file) {
super();
m_fileName = a_file;
URL url = null;
try {
url = a_file.toURI().toURL();
} catch (MalformedURLException e) {
e.printStackTrace();
}
init(url);
}
private void processCopy(Node operation) {
List<Node> fromNode = getChildNodes(operation, "from");
List<Node> toNode = getChildNodes(operation, "to");
if (fromNode.isEmpty() || toNode.isEmpty()) {
return;
}
String path = fromNode.get(0).getTextContent();
String fromPath = (new File(path).isAbsolute()) ? path : absolutePath(path);
String toPath = absolutePath(toNode.get(0).getTextContent());
Boolean copyContents = fromPath.endsWith(File.separator + "*");
File from = new File((copyContents) ? fromPath.substring(0, fromPath.length() - 2) : fromPath);
File to = new File(toPath);
if (!from.exists()) {
Utils.onError(new Error.FileNotFound(from.getPath()));
return;
}
try {
if (copyContents) {
FileUtils.forceMkdir(to);
FileUtils.copyDirectory(from, to);
} else if (from.isDirectory()) {
FileUtils.forceMkdir(to);
FileUtils.copyDirectoryToDirectory(from, to);
} else {
if (to.isDirectory()) {
FileUtils.forceMkdir(to);
FileUtils.copyFileToDirectory(from, to);
} else {
File toDir = new File(Utils.getParentDir(to));
FileUtils.forceMkdir(toDir);
FileUtils.copyFile(from, to);
}
}
} catch (IOException ex) {
Utils.onError(new Error.FileCopy(from.getPath(), to.getPath()));
}
}
/**
* XML Circuit constructor
*
* @param file the file that contains the XML description of the circuit
* @param g the graphics that will paint the node
* @throws CircuitLoadingException if the internal circuit can not be loaded
*/
public CircuitUI(File file, Graphics g) throws CircuitLoadingException {
this("");
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder;
Document doc;
Element root;
Hashtable<Integer, Link> linkstable = new Hashtable<Integer, Link>();
try {
builder = factory.newDocumentBuilder();
doc = builder.parse(file);
} catch (SAXException sxe) {
throw new CircuitLoadingException("SAX exception raised, invalid XML file.");
} catch (ParserConfigurationException pce) {
throw new CircuitLoadingException(
"Parser exception raised, parser configuration is invalid.");
} catch (IOException ioe) {
throw new CircuitLoadingException("I/O exception, file cannot be loaded.");
}
root = (Element) doc.getElementsByTagName("Circuit").item(0);
this.setName(root.getAttribute("name"));
NodeList nl = root.getElementsByTagName("Node");
Element e;
Node n;
Class cl;
for (int i = 0; i < nl.getLength(); ++i) {
e = (Element) nl.item(i);
try {
cl = Class.forName(e.getAttribute("class"));
} catch (Exception exc) {
System.err.println(exc.getMessage());
throw new RuntimeException("Circuit creation from xml.");
}
try {
n = ((Node) cl.newInstance());
} catch (Exception exc) {
System.err.println(exc.getMessage());
throw new RuntimeException("Circuit creation from xml.");
}
this.nodes.add(n);
n.setLocation(new Integer(e.getAttribute("x")), new Integer(e.getAttribute("y")));
if (n instanceof giraffe.ui.Nameable) ((Nameable) n).setNodeName(e.getAttribute("node_name"));
if (n instanceof giraffe.ui.CompositeNode) {
try {
((CompositeNode) n)
.load(new File(file.getParent() + "/" + e.getAttribute("file_name")), g);
} catch (Exception exc) {
/* try to load from the lib */
((CompositeNode) n)
.load(new File(giraffe.Giraffe.PATH + "/lib/" + e.getAttribute("file_name")), g);
}
}
NodeList nlist = e.getElementsByTagName("Anchor");
Element el;
for (int j = 0; j < nlist.getLength(); ++j) {
el = (Element) nlist.item(j);
Anchor a = n.getAnchor(new Integer(el.getAttribute("id")));
NodeList linklist = el.getElementsByTagName("Link");
Element link;
Link l;
for (int k = 0; k < linklist.getLength(); ++k) {
link = (Element) linklist.item(k);
int id = new Integer(link.getAttribute("id"));
int index = new Integer(link.getAttribute("index"));
if (id >= this.linkID) linkID = id + 1;
if (linkstable.containsKey(id)) {
l = linkstable.get(id);
l.addLinkedAnchorAt(a, index);
a.addLink(l);
} else {
l = new Link(id);
l.addLinkedAnchorAt(a, index);
this.links.add(l);
linkstable.put(id, l);
a.addLink(l);
}
}
}
}
}
public void init(ServletConfig config) throws ServletException {
super.init(config);
context = config.getServletContext();
TextProcessor tp = new CaseFolder();
try {
wikipedia =
new Wikipedia(
context.getInitParameter("mysql_server"),
context.getInitParameter("mysql_database"),
context.getInitParameter("mysql_user"),
context.getInitParameter("mysql_password"));
} catch (Exception e) {
throw new ServletException("Could not connect to wikipedia database.");
}
// Escaper escaper = new Escaper() ;
definer = new Definer(this);
comparer = new Comparer(this);
searcher = new Searcher(this);
try {
wikifier = new Wikifier(this, tp);
} catch (Exception e) {
System.err.println("Could not initialize wikifier");
}
try {
File dataDirectory = new File(context.getInitParameter("data_directory"));
if (!dataDirectory.exists() || !dataDirectory.isDirectory()) {
throw new Exception();
}
cachingThread = new CacherThread(dataDirectory, tp);
cachingThread.start();
} catch (Exception e) {
throw new ServletException("Could not locate wikipedia data directory.");
}
try {
TransformerFactory tf = TransformerFactory.newInstance();
transformersByName = new HashMap<String, Transformer>();
transformersByName.put(
"help", buildTransformer("help", new File("/research/wikipediaminer/web/xsl"), tf));
transformersByName.put(
"loading", buildTransformer("loading", new File("/research/wikipediaminer/web/xsl"), tf));
transformersByName.put(
"search", buildTransformer("search", new File("/research/wikipediaminer/web/xsl"), tf));
transformersByName.put(
"compare", buildTransformer("compare", new File("/research/wikipediaminer/web/xsl"), tf));
transformersByName.put(
"wikify", buildTransformer("wikify", new File("/research/wikipediaminer/web/xsl"), tf));
Transformer serializer = TransformerFactory.newInstance().newTransformer();
serializer.setOutputProperty(OutputKeys.INDENT, "yes");
serializer.setOutputProperty(OutputKeys.METHOD, "xml");
serializer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
transformersByName.put("serializer", serializer);
} catch (Exception e) {
throw new ServletException("Could not load xslt library.");
}
}
public void run() {
// String a =
// "http://neuromorpho.org/neuroMorpho/dableFiles/borst/CNG%20version/dCH-cobalt.CNG.swc"; //
// For developer use
if (myArgs.length == 0) {
String usage =
"\nError, missing SWC file containing morphology!\n\nUsage: \n java -cp build cvapp.main swc_file [-test]"
+ "\n or:\n ./run.sh swc_file ["
+ TEST_FLAG
+ "|"
+ TEST_NOGUI_FLAG
+ "|"
+ NEUROML1_EXPORT_FLAG
+ "|"
+ NEUROML2_EXPORT_FLAG
+ "]\n\n"
+ "where swc_file is the file name or URL of the SWC morphology file\n";
System.out.println(usage);
System.exit(0);
}
String a = myArgs[0];
File baseDir = new File(".");
if ((new File(a)).exists()) {
baseDir = (new File(a)).getParentFile();
}
try {
File root =
new File(main.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath())
.getParentFile();
if (!a.startsWith("http://") && !a.startsWith("file://")) {
a = "file://" + (new File(a)).getCanonicalPath();
}
boolean supressGui = false;
if (myArgs.length == 2
&& (myArgs[1].equals(TEST_NOGUI_FLAG)
|| myArgs[1].equals(NEUROML1_EXPORT_FLAG)
|| myArgs[1].equals(NEUROML2_EXPORT_FLAG))) {
supressGui = true;
}
neuronEditorFrame nef = null;
nef = new neuronEditorFrame(700, 600, supressGui);
// nef.validate();
nef.pack();
centerWindow(nef);
nef.setVisible(!supressGui);
nef.setReadWrite(true, true);
int indexof = a.lastIndexOf('/') + 1;
String directory = a.substring(0, indexof);
String fileName = a.substring(indexof, a.length());
URL u = new URL(a);
String sdata[] = readStringArrayFromURL(u);
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + fileName);
nef.loadFile(sdata, directory, fileName);
System.out.println("Loaded: " + fileName);
if (myArgs.length == 2 && myArgs[1].equals(TEST_ONE_FLAG)) {
// Thread.sleep(1000);
doTests(nef, fileName);
} else if (myArgs.length == 2 && myArgs[1].equals(NEUROML1_EXPORT_FLAG)) {
File rootFile = (new File(baseDir, fileName)).getAbsoluteFile();
String nml1FileName =
rootFile.getName().endsWith(".swc")
? rootFile.getName().substring(0, rootFile.getName().length() - 4) + ".xml"
: rootFile.getName() + ".xml";
File nml1File = new File(rootFile.getParentFile(), nml1FileName);
neuronEditorPanel nep = nef.getNeuronEditorPanel();
nep.writeStringToFile(nep.getCell().writeNeuroML_v1_8_1(), nml1File.getAbsolutePath());
System.out.println(
"Saved NeuroML representation of the file to: "
+ nml1File.getAbsolutePath()
+ ": "
+ nml1File.exists());
File v1schemaFile = new File(root, "Schemas/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd");
validateXML(nml1File, v1schemaFile);
System.exit(0);
} else if (myArgs.length == 2 && myArgs[1].equals(NEUROML2_EXPORT_FLAG)) {
File rootFile = (new File(baseDir, fileName)).getAbsoluteFile();
String nml2FileName =
rootFile.getName().endsWith(".swc")
? rootFile.getName().substring(0, rootFile.getName().length() - 4) + ".cell.nml"
: rootFile.getName() + ".cell.nml";
if (Character.isDigit(nml2FileName.charAt(0))) {
nml2FileName = "Cell_" + nml2FileName;
}
File nml2File = new File(rootFile.getParentFile(), nml2FileName);
neuronEditorPanel nep = nef.getNeuronEditorPanel();
nep.writeStringToFile(nep.getCell().writeNeuroML_v2beta(), nml2File.getAbsolutePath());
System.out.println(
"Saved the NeuroML representation of the file to: "
+ nml2File.getAbsolutePath()
+ ": "
+ nml2File.exists());
validateXML(nml2File, new File(root, "Schemas/v2/NeuroML_v2beta4.xsd"));
System.exit(0);
} else if (myArgs.length == 2
&& (myArgs[1].equals(TEST_FLAG) || (myArgs[1].equals(TEST_NOGUI_FLAG)))) {
// Thread.sleep(1000);
doTests(nef, fileName);
File exampleDir = new File("twoCylSwc");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
exampleDir = new File("spherSomaSwc");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
exampleDir = new File("caseExamples");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
if (supressGui) System.exit(0);
}
} catch (Exception exception) {
System.err.println("Error while handling SWC file (" + a + ")");
exception.printStackTrace();
}
}
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;
}
/*
* Carries out a number of tests, generates NEURON, GENESIS and NeuroML code etc.
*/
private static void doTests(neuronEditorFrame nef, String fileName) {
System.out.println(
"Testing Cvapp/NeuroMorpho.Org by generating NEURON, GENESIS and NeuroML files for "
+ fileName);
File tempDir = new File("temp");
if (!tempDir.exists()) tempDir.mkdir();
neuronEditorPanel nep = nef.getNeuronEditorPanel();
String rootFileName = fileName;
if (rootFileName.toLowerCase().endsWith(".swc")) {
rootFileName = rootFileName.substring(0, rootFileName.length() - 4);
}
if (rootFileName.lastIndexOf(System.getProperty("file.separator")) > 0) {
rootFileName =
rootFileName.substring(
rootFileName.lastIndexOf(System.getProperty("file.separator")) + 1);
}
// NEURON save...
String neuronFileName = rootFileName + ".hoc";
File neuronFile = new File(tempDir, neuronFileName);
File neuronTestFile = new File(tempDir, rootFileName + "_test.hoc");
nep.writeStringToFile(nep.getCell().HOCwriteNS(), neuronFile.getAbsolutePath());
StringBuilder sbNeuTest = new StringBuilder();
sbNeuTest.append("load_file(\"nrngui.hoc\")\n");
sbNeuTest.append("load_file(\"../neuronUtils/nCtools.hoc\")\n");
sbNeuTest.append("load_file(\"../neuronUtils/cellCheck.hoc\")\n");
sbNeuTest.append("load_file(\"nrngui.hoc\")\n");
sbNeuTest.append("load_file(\"" + neuronFileName + "\")\n\n");
sbNeuTest.append("forall morph()\n");
System.out.println("--------------------------------------------------------------");
nep.writeStringToFile(sbNeuTest.toString(), neuronTestFile.getAbsolutePath());
System.out.println(
"Saved NEURON representation of the file to: "
+ neuronFile.getAbsolutePath()
+ ": "
+ neuronFile.exists());
System.out.println("--------------------------------------------------------------");
// GENESIS save...
String genesisFileName = rootFileName + ".p";
File genesisFile = new File(tempDir, genesisFileName);
File genesisTestFile = new File(tempDir, rootFileName + "_test.g");
nep.writeStringToFile(nep.getCell().GENESISwriteHR(), genesisFile.getAbsolutePath());
StringBuilder sbGenTest = new StringBuilder();
sbGenTest.append("include compartments \n");
sbGenTest.append("create neutral /library\n");
sbGenTest.append("disable /library\n");
sbGenTest.append("ce /library\n");
sbGenTest.append("make_cylind_compartment\n");
sbGenTest.append("make_cylind_symcompartment\n");
sbGenTest.append("make_sphere_compartment\n");
sbGenTest.append("ce /\n");
sbGenTest.append(
"echo \"Prototype compartments created, reading cell from " + genesisFileName + "\"\n");
sbGenTest.append("readcell " + genesisFileName + " /mycell\n\n");
sbGenTest.append("create xform /form [0,0,400,400] -nolabel\n");
sbGenTest.append(
"create xdraw /form/draw [0,0,100%,100%] -wx 0.002 -wy 0.002 -transform ortho3d -bg white\n");
sbGenTest.append(
"setfield /form/draw xmin -3.0E-4 xmax 3.0E-4 ymin -3.0E-4 ymax 3.0E-4 vx 0.0 vy 0.0 vz -0.002\n");
sbGenTest.append(
"create xcell /form/draw/cell -path \"/mycell/##[][TYPE=compartment],/mycell/##[][TYPE=symcompartment]\" -colfield Vm -colmin -0.07 -colmax 0.03 -diarange -5\n");
sbGenTest.append("xcolorscale hot\n");
sbGenTest.append("xshow /form\n\n");
sbGenTest.append("showfield /mycell/##[][TYPE=compartment] **\n\n");
nep.writeStringToFile(sbGenTest.toString(), genesisTestFile.getAbsolutePath());
System.out.println(
"Saved GENESIS representation of the file to: "
+ genesisFile.getAbsolutePath()
+ ": "
+ genesisFile.exists());
System.out.println("--------------------------------------------------------------");
// NeuroML save...
String nml1FileName = rootFileName + ".xml";
File nml1File = new File(tempDir, nml1FileName);
nep.writeStringToFile(nep.getCell().writeNeuroML_v1_8_1(), nml1File.getAbsolutePath());
System.out.println(
"Saved NeuroML representation of the file to: "
+ nml1File.getAbsolutePath()
+ ": "
+ nml1File.exists());
File v1schemaFile = new File("Schemas/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd");
validateXML(nml1File, v1schemaFile);
String nml2FileName = rootFileName + ".cell.nml";
if (Character.isDigit(nml2FileName.charAt(0))) {
nml2FileName = "Cell_" + nml2FileName;
}
File nml2File = new File(tempDir, nml2FileName);
nep.writeStringToFile(nep.getCell().writeNeuroML_v2beta(), nml2File.getAbsolutePath());
System.out.println(
"Saved NeuroML representation of the file to: "
+ nml2File.getAbsolutePath()
+ ": "
+ nml2File.exists());
validateXMLWithURL(nml2File, "Schemas/v2/NeuroML_v2beta4.xsd");
}
public String getShortFileName() {
return m_fileName.getName();
}
private void processTxt(Node operation) {
List<Node> targets = getChildNodes(operation, "target");
List<Node> optionNodes = getChildNodes(operation, "opt");
List<Node> separatorNode = getChildNodes(operation, "separator");
if (targets.isEmpty() || optionNodes.isEmpty()) {
return;
}
String defaultSeparator = "=";
String globalSeparator = defaultSeparator;
if (!separatorNode.isEmpty()) {
globalSeparator = separatorNode.get(0).getTextContent();
if (globalSeparator.length() != 1) {
globalSeparator = defaultSeparator;
}
}
Map<String, String> options = new HashMap<String, String>();
Map<String, String> processedOptions = new HashMap<String, String>();
for (int i = 0; i < optionNodes.size(); i++) {
Node option = optionNodes.get(i);
String name = option.getAttributes().getNamedItem("name").getNodeValue();
String value = option.getTextContent();
if (options.containsKey(name)) {
options.remove(name);
}
options.put(name, value);
}
for (int t = 0; t < targets.size(); t++) {
File target = new File(absolutePath(targets.get(t).getTextContent()));
File tmpFile = new File(Utils.timestamp());
BufferedWriter bw = null;
BufferedReader br = null;
try {
Node separatorAttr = targets.get(t).getAttributes().getNamedItem("separator");
String separator = (separatorAttr == null) ? globalSeparator : separatorAttr.getNodeValue();
if (separator.length() != 1) {
separator = globalSeparator;
}
bw = new BufferedWriter(new FileWriter(tmpFile));
if (target.exists()) {
br = new BufferedReader(new FileReader(target));
for (String line; (line = br.readLine()) != null; ) {
String[] parts = line.split(separator);
if (parts.length < 2) {
bw.write(line);
bw.newLine();
continue;
}
String optName = parts[0].trim();
if (options.containsKey(optName)) {
String optValue = options.get(optName);
bw.write(optName + " " + separator + " " + optValue);
bw.newLine();
processedOptions.put(optName, optValue);
options.remove(optName);
} else if (processedOptions.containsKey(optName)) {
bw.write(optName + " " + separator + " " + processedOptions.get(optName));
bw.newLine();
} else {
bw.write(line);
bw.newLine();
}
}
br.close();
}
for (Map.Entry<String, String> entry : options.entrySet()) {
bw.write(entry.getKey() + " " + separator + " " + entry.getValue());
bw.newLine();
}
bw.close();
FileUtils.copyFile(tmpFile, target);
FileUtils.forceDelete(tmpFile);
} catch (IOException ex) {
Utils.onError(new Error.WriteTxtConfig(target.getPath()));
}
}
}