public void updateJob(ApplicationInfo appInfo, CIJob job) throws PhrescoException {
if (debugEnabled) {
S_LOGGER.debug(
"Entering Method ProjectAdministratorImpl.updateJob(Project project, CIJob job)");
}
FileWriter writer = null;
try {
CIJobStatus jobStatus = configureJob(job, FrameworkConstants.CI_UPDATE_JOB_COMMAND);
if (jobStatus.getCode() == -1) {
throw new PhrescoException(jobStatus.getMessage());
}
if (debugEnabled) {
S_LOGGER.debug("getCustomModules() ProjectInfo = " + appInfo);
}
updateJsonJob(appInfo, job);
} catch (ClientHandlerException ex) {
if (debugEnabled) {
S_LOGGER.error(ex.getLocalizedMessage());
}
throw new PhrescoException(ex);
} finally {
if (writer != null) {
try {
writer.close();
} catch (IOException e) {
if (debugEnabled) {
S_LOGGER.error(e.getLocalizedMessage());
}
}
}
}
}
/**
* Create an Internet shortcut
*
* @param name name of the shortcut
* @param where location of the shortcut
* @param target URL
* @param icon URL (ex. http://www.server.com/favicon.ico)
*/
public static void createInternetShortcut(String name, String where, String target, String icon) {
try (FileWriter fw = new FileWriter(where)) {
fw.write("[InternetShortcut]\n");
fw.write("URL=" + target + '\n');
if (!icon.isEmpty()) fw.write("IconFile=" + icon + '\n');
} catch (IOException iox) {
/**/
}
}
public static void main(String[] args) {
try {
BufferedReader br = new BufferedReader(new FileReader(args[0]));
int tIndex = 0;
int pIndex = 0;
// This will probably change soon (name and implementation)
NgramParser tnp = new NgramParser(args[1]);
ArrayList<String> triplet = tnp.getTriplet();
ArrayList<String> polarity = tnp.getPolarity();
FileWriter sw = new FileWriter(args[2]);
String line = null;
while (((line = br.readLine()) != null)
&& (tIndex < triplet.size())
&& (pIndex < polarity.size())) {
if (line.matches("^[\\d]*:")) {
// System.out.println(line);
sw.write(line + "\n");
} else {
Scanner sc = new Scanner(line);
String trip = sc.findInLine(Pattern.compile("[a-zA-Z]+#[a-z]+[#]?[0-9]*"));
// if (trip != null && trip.equals(triplet.get(tIndex))) {
System.out.println(trip);
if (trip != null && !trip.toLowerCase().contains("no#cl")) {
// System.out.println(triplet.get(tIndex) + ":" +polarity.get(pIndex));
String pol = polarity.get(pIndex);
sw.write(line + " " + pol + "\n");
sc.close();
tIndex++;
pIndex++;
} else {
String pol = "neg";
sw.write("no#a#1" + " " + pol + "\n");
sc.close();
}
}
// sw.flush();
}
sw.close();
} catch (IOException e) {
e.printStackTrace();
}
}
// write a single line in a FileWriter writer for given String line
static void writeLine(FileWriter writer, String line) {
try {
writer.append(line + '\n');
} catch (IOException e) {
e.printStackTrace();
}
}
private void writeJsonJobs(ApplicationInfo appInfo, List<CIJob> jobs, String status)
throws PhrescoException {
try {
if (jobs == null) {
return;
}
Gson gson = new Gson();
List<CIJob> existingJobs = getJobs(appInfo);
if (CI_CREATE_NEW_JOBS.equals(status) || existingJobs == null) {
existingJobs = new ArrayList<CIJob>();
}
existingJobs.addAll(jobs);
FileWriter writer = null;
File ciJobFile = new File(getCIJobPath(appInfo));
String jobJson = gson.toJson(existingJobs);
writer = new FileWriter(ciJobFile);
writer.write(jobJson);
writer.flush();
} catch (Exception e) {
throw new PhrescoException(e);
}
}
static void writeUsersToFile() {
userWriter = createCSVFile("Users.dat");
// write the list of users to file
System.out.println("Users that are both seller and buyer BUT different ratings: ");
Enumeration<String> keys = userList.keys();
while (keys.hasMoreElements()) {
String curUserID = keys.nextElement();
String curUser[] = userList.get(curUserID);
String userRow =
wrapQuotations(curUser[0])
+ ","
+ curUser[1]
+ ","
+ curUser[2]
+ ","
+ wrapQuotations(curUser[3])
+ ","
+ wrapQuotations(curUser[4]);
writeLine(userWriter, userRow);
// if(curUser[1] != null && curUser[2] != null && !curUser[1].equals(curUser[2]))
// System.out.println(curUser[0]);
}
System.out.println("----end different ratings----");
// System.out.println("The users that are both seller and buyer: ");
// Enumeration<String> both = bothSellerAndBuyer.elements();
// while(both.hasMoreElements()) {
// System.out.println(both.nextElement());
// }
// System.out.println("----end both----");
try {
userWriter.flush();
userWriter.close();
} catch (IOException e) {
e.printStackTrace();
}
}
private boolean adaptExistingJobs(ApplicationInfo appInfo) {
try {
CIJob existJob = getJob(appInfo);
S_LOGGER.debug("Going to get existing jobs to relocate!!!!!");
if (existJob != null) {
S_LOGGER.debug("Existing job found " + existJob.getName());
boolean deleteExistJob = deleteCIJobFile(appInfo);
Gson gson = new Gson();
List<CIJob> existingJobs = new ArrayList<CIJob>();
existingJobs.addAll(Arrays.asList(existJob));
FileWriter writer = null;
File ciJobFile = new File(getCIJobPath(appInfo));
String jobJson = gson.toJson(existingJobs);
writer = new FileWriter(ciJobFile);
writer.write(jobJson);
writer.flush();
S_LOGGER.debug("Existing job moved to new type of project!!");
}
return true;
} catch (Exception e) {
S_LOGGER.debug("It is already adapted !!!!! ");
}
return false;
}
/* Process one items-???.xml file.
*/
static void processFile(File xmlFile) {
Document doc = null;
try {
doc = builder.parse(xmlFile);
} catch (IOException e) {
e.printStackTrace();
System.exit(3);
} catch (SAXException e) {
System.out.println("Parsing error on file " + xmlFile);
System.out.println(" (not supposed to happen with supplied XML files)");
e.printStackTrace();
System.exit(3);
}
/* At this point 'doc' contains a DOM representation of an 'Items' XML
* file. Use doc.getDocumentElement() to get the root Element. */
System.out.println("Successfully parsed - " + xmlFile);
/* Fill in code here (you will probably need to write auxiliary
methods). */
// open each CSV file (creates it if it doesn't exist)
System.out.println("creating dat file");
itemWriter = createCSVFile("Items.dat");
itemCategoriesWriter = createCSVFile("ItemCategories.dat");
bidWriter = createCSVFile("Bids.dat");
Element itemsElem = doc.getDocumentElement();
Element[] itemList = getElementsByTagNameNR(itemsElem, "Item");
System.out.println("There are " + itemList.length + " <item> tags");
for (Element curItem : itemList) {
processItem(curItem);
}
// close the dat files
try {
itemWriter.flush();
itemWriter.close();
itemCategoriesWriter.flush();
itemCategoriesWriter.close();
bidWriter.flush();
bidWriter.close();
} catch (IOException e) {
e.printStackTrace();
}
/** *********************************************************** */
}
/**
* This function writes the generated relative overview to a file.
*
* @param f The file to write to.
* @throws IOException Thrown if unable to open or write to the file.
* @throws InsufficientDataException Thrown if unable to generate the overview.
*/
public void writeToFile(File f) throws IOException, InsufficientDataException {
f.createNewFile();
FileWriter fw = new FileWriter(f);
fw.write(generateOverviewText());
fw.close();
}
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>*/
}