public static void main(String[] args) { try { Project p = Project.loadProject( new File(ProjectStructure.getnCExamplesDir(), "Ex5_Networks/Ex5_Networks.ncx"), null); GeneratedElecInputs gei = new GeneratedElecInputs(p); System.out.println("Internal info: \n" + gei.toString()); // IClamp ic = new IClamp(2,3,4, true); gei.addSingleInput("Input_0", "IClamp", "cg1", 3, 3, 3, null); gei.addSingleInput("Input_0", "IClamp", "cg1", 38, 3, 3, null); gei.addSingleInput("Input_2", "IClamp", "cg3", 3, 38, 39, null); System.out.println("Internal info: \n" + gei.toString()); File f = new File("../temp/tempp.txt"); gei.saveToFile(f); GeneratedElecInputs cpr2 = new GeneratedElecInputs(null); System.out.println( "---- v1.8.1: \n" + gei.getNetworkMLElement(UnitConverter.GENESIS_SI_UNITS) .getXMLString(" ", false)); ArrayList<SimpleXMLEntity> els = gei.getNetworkMLEntities( UnitConverter.GENESIS_SI_UNITS, NeuroMLConstants.NeuroMLVersion.NEUROML_VERSION_2_ALPHA, null); System.out.println("---- v2.0 alpha: "); for (SimpleXMLEntity el : els) System.out.println(el.getXMLString(" ", false)); els = gei.getNetworkMLEntities( UnitConverter.GENESIS_SI_UNITS, NeuroMLConstants.NeuroMLVersion.getLatestVersion(), null); System.out.println("---- v2.0 beta: "); for (SimpleXMLEntity el : els) System.out.println(el.getXMLString(" ", false)); System.out.println("-------------- "); } catch (Exception ex) { ex.printStackTrace(); } }
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>*/ }