/**
* Process the specified HTTP request, and create the corresponding HTTP response (or forward to
* another web component that will create it). Return an <code>ActionForward</code> instance
* describing where and how control should be forwarded, or <code>null</code> if the response has
* already been completed.
*
* @param mapping The ActionMapping used to select this instance
* @param form The optional ActionForm bean for this request (if any)
* @param request The HTTP request we are processing
* @param response The HTTP response we are creating
* @exception Exception if business logic throws an exception
*/
public ActionForward execute(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
// Extract attributes we will need
MessageResources messages = getResources(request);
// save errors
ActionMessages errors = new ActionMessages();
// START check for login (security)
if (!SecurityService.getInstance().checkForLogin(request.getSession(false))) {
return (mapping.findForward("welcome"));
}
// END check for login (security)
// START get id of current project from either request, attribute, or cookie
// id of project from request
String projectId = null;
projectId = request.getParameter("projectViewId");
// check attribute in request
if (projectId == null) {
projectId = (String) request.getAttribute("projectViewId");
}
// id of project from cookie
if (projectId == null) {
projectId = StandardCode.getInstance().getCookie("projectViewId", request.getCookies());
}
// default project to last if not in request or cookie
if (projectId == null) {
java.util.List results = ProjectService.getInstance().getProjectList();
ListIterator iterScroll = null;
for (iterScroll = results.listIterator(); iterScroll.hasNext(); iterScroll.next()) {}
iterScroll.previous();
Project p = (Project) iterScroll.next();
projectId = String.valueOf(p.getProjectId());
}
Integer id = Integer.valueOf(projectId);
// END get id of current project from either request, attribute, or cookie
// get project
Project p = ProjectService.getInstance().getSingleProject(id);
// get user (project manager)
User u =
UserService.getInstance()
.getSingleUserRealName(
StandardCode.getInstance().getFirstName(p.getPm()),
StandardCode.getInstance().getLastName(p.getPm()));
// START process pdf
try {
PdfReader reader = new PdfReader("C://templates/CL01_001.pdf"); // the template
// save the pdf in memory
ByteArrayOutputStream pdfStream = new ByteArrayOutputStream();
// the filled-in pdf
PdfStamper stamp = new PdfStamper(reader, pdfStream);
// stamp.setEncryption(true, "pass", "pass", PdfWriter.AllowCopy | PdfWriter.AllowPrinting);
AcroFields form1 = stamp.getAcroFields();
Date cDate = new Date();
Integer month = cDate.getMonth();
Integer day = cDate.getDate();
Integer year = cDate.getYear() + 1900;
String[] monthName = {
"January",
"February",
"March",
"April",
"May",
"June",
"July",
"August",
"September",
"October",
"November",
"December"
};
// set the field values in the pdf form
// form1.setField("", projectId)
form1.setField("currentdate", monthName[month] + " " + day + ", " + year);
form1.setField(
"firstname", StandardCode.getInstance().noNull(p.getContact().getFirst_name()));
form1.setField("pm", p.getPm());
form1.setField("emailpm", u.getWorkEmail1());
if (u.getWorkPhoneEx() != null && u.getWorkPhoneEx().length() > 0) { // ext present
form1.setField(
"phonepm",
StandardCode.getInstance().noNull(u.getWorkPhone())
+ " ext "
+ StandardCode.getInstance().noNull(u.getWorkPhoneEx()));
} else { // no ext present
form1.setField("phonepm", StandardCode.getInstance().noNull(u.getWorkPhone()));
}
form1.setField("faxpm", StandardCode.getInstance().noNull(u.getLocation().getFax_number()));
form1.setField("postalpm", StandardCode.getInstance().printLocation(u.getLocation()));
// START add images
// if(u.getPicture() != null && u.getPicture().length() > 0) {
// PdfContentByte over;
// Image img = Image.getInstance("C:/Program Files (x86)/Apache Software
// Foundation/Tomcat 7.0/webapps/logo/images/" + u.getPicture());
// img.setAbsolutePosition(200, 200);
// over = stamp.getOverContent(1);
// over.addImage(img, 54, 0,0, 65, 47, 493);
// }
// END add images
form1.setField("productname", StandardCode.getInstance().noNull(p.getProduct()));
form1.setField("project", p.getNumber() + p.getCompany().getCompany_code());
form1.setField("description", StandardCode.getInstance().noNull(p.getProductDescription()));
form1.setField("additional", p.getProjectRequirements());
// get sources and targets
StringBuffer sources = new StringBuffer("");
StringBuffer targets = new StringBuffer("");
if (p.getSourceDocs() != null) {
for (Iterator iterSource = p.getSourceDocs().iterator(); iterSource.hasNext(); ) {
SourceDoc sd = (SourceDoc) iterSource.next();
sources.append(sd.getLanguage() + " ");
if (sd.getTargetDocs() != null) {
for (Iterator iterTarget = sd.getTargetDocs().iterator(); iterTarget.hasNext(); ) {
TargetDoc td = (TargetDoc) iterTarget.next();
if (!td.getLanguage().equals("All")) targets.append(td.getLanguage() + " ");
}
}
}
}
form1.setField("source", sources.toString());
form1.setField("target", targets.toString());
form1.setField(
"start",
(p.getStartDate() != null)
? DateFormat.getDateInstance(DateFormat.SHORT).format(p.getStartDate())
: "");
form1.setField(
"due",
(p.getDueDate() != null)
? DateFormat.getDateInstance(DateFormat.SHORT).format(p.getDueDate())
: "");
if (p.getCompany().getCcurrency().equalsIgnoreCase("USD")) {
form1.setField(
"cost",
(p.getProjectAmount() != null)
? "$ " + StandardCode.getInstance().formatDouble(p.getProjectAmount())
: "");
} else {
form1.setField(
"cost",
(p.getProjectAmount() != null)
? "€ "
+ StandardCode.getInstance()
.formatDouble(p.getProjectAmount() / p.getEuroToUsdExchangeRate())
: "");
}
// stamp.setFormFlattening(true);
stamp.close();
// write to client (web browser)
response.setHeader(
"Content-disposition",
"attachment; filename="
+ p.getNumber()
+ p.getCompany().getCompany_code()
+ "-Order-Confirmation"
+ ".pdf");
OutputStream os = response.getOutputStream();
pdfStream.writeTo(os);
os.flush();
} catch (Exception e) {
System.err.println("PDF Exception:" + e.getMessage());
throw new RuntimeException(e);
}
// END process pdf
// Forward control to the specified success URI
return (mapping.findForward("Success"));
}
/**
* Process the specified HTTP request, and create the corresponding HTTP response (or forward to
* another web component that will create it). Return an <code>ActionForward</code> instance
* describing where and how control should be forwarded, or <code>null</code> if the response has
* already been completed.
*
* @param mapping The ActionMapping used to select this instance
* @param form The optional ActionForm bean for this request (if any)
* @param request The HTTP request we are processing
* @param response The HTTP response we are creating
* @exception Exception if business logic throws an exception
*/
public ActionForward execute(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
// Extract attributes we will need
MessageResources messages = getResources(request);
// save errors
ActionMessages errors = new ActionMessages();
// START check for login (security)
if (!SecurityService.getInstance().checkForLogin(request.getSession(false))) {
return (mapping.findForward("welcome"));
}
// END check for login (security)
// START get id of current project from either request, attribute, or cookie
// id of project from request
String projectId = null;
projectId = request.getParameter("projectViewId");
// check attribute in request
if (projectId == null) {
projectId = (String) request.getAttribute("projectViewId");
}
// id of project from cookie
if (projectId == null) {
projectId = StandardCode.getInstance().getCookie("projectViewId", request.getCookies());
}
// default project to last if not in request or cookie
if (projectId == null) {
List results = ProjectService.getInstance().getProjectList();
ListIterator iterScroll = null;
for (iterScroll = results.listIterator(); iterScroll.hasNext(); iterScroll.next()) {}
iterScroll.previous();
Project p = (Project) iterScroll.next();
projectId = String.valueOf(p.getProjectId());
}
Integer id = Integer.valueOf(projectId);
// END get id of current project from either request, attribute, or cookie
// get project to edit
Project p = ProjectService.getInstance().getSingleProject(id);
// get this project's sources
Set sources = p.getSourceDocs();
// for each source add each sources' Tasks
List totalLinTasks = new ArrayList();
// for each source
for (Iterator sourceIter = sources.iterator(); sourceIter.hasNext(); ) {
SourceDoc sd = (SourceDoc) sourceIter.next();
// for each target of this source
for (Iterator linTargetIter = sd.getTargetDocs().iterator(); linTargetIter.hasNext(); ) {
TargetDoc td = (TargetDoc) linTargetIter.next();
// for each lin Task of this target
for (Iterator linTaskIter = td.getLinTasks().iterator(); linTaskIter.hasNext(); ) {
LinTask lt = (LinTask) linTaskIter.next();
if (lt.getPersonName() != null
&& lt.getDueDateDate() != null
&& (lt.getTaskName().equalsIgnoreCase("Translation")
|| lt.getTaskName().equalsIgnoreCase("Editing")
|| lt.getTaskName().trim().equalsIgnoreCase("Proofreading")
|| lt.getTaskName().equalsIgnoreCase("Proofreading / Linguistic QA"))) {
totalLinTasks.add(lt);
}
System.out.println(
sd.getLanguage() + "--------" + td.getLanguage() + "---------" + lt.getTaskName());
}
}
}
// Sort by task (orderNum), then source (language), then target (language)
Collections.sort(totalLinTasks, CompareTaskLin.getInstance());
Collections.sort(totalLinTasks, CompareTaskLanguages.getInstance());
// array for display in jsp
LinTask[] linTasksArray = (LinTask[]) totalLinTasks.toArray(new LinTask[0]);
for (int i = 0; i < totalLinTasks.size(); i++) {
request.setAttribute(projectId, log);
}
// place all Tasks for this project into the form for display
DynaValidatorForm qvg = (DynaValidatorForm) form;
// HERE down is standard and does not need to change when adding task blocks
// place this project into request for further display in jsp page
request.setAttribute("project", p);
// add this project id to cookies; this will remember the last project
response.addCookie(StandardCode.getInstance().setCookie("projectViewId", projectId));
// add tab location to cookies; this will remember which tab we are at
response.addCookie(StandardCode.getInstance().setCookie("projectViewTab", "Team"));
// an update of totals may be required
// Forward control to the specified success URI
return (mapping.findForward("Success"));
}
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>*/
}