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package lphystudio.app;
import lphy.core.io.UserDir;
import lphy.core.logger.LoggerUtils;
import lphy.core.model.NarrativeUtils;
import lphystudio.app.graphicalmodelcomponent.GraphicalModelComponent;
import lphystudio.app.graphicalmodelpanel.GraphicalModelPanel;
import lphystudio.app.graphicalmodelpanel.GraphicalModelParserDictionary;
import lphystudio.core.narrative.HTMLNarrative;
import lphystudio.core.narrative.LaTeXNarrative;
import lphystudio.core.narrative.Section;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.nio.file.Path;
import java.nio.file.Paths;
/**
* Create markdown files for Jekyll containing the sections
* (code, data, model, posterior, graphical model)
* to introduce LPhy scripts for the tutorial.
* Input: *.lphy
* Output: narrative.md, references.md
*/
public class NarrativeCreator {
public static final String DIV_BOX_BACKGR_COLOUR =
"
";
HTMLNarrative htmlNarrative;
LaTeXNarrative latexNarrative;
StringBuilder code = new StringBuilder();
StringBuilder narrative = new StringBuilder();
StringBuilder references = new StringBuilder();
// static Preferences preferences = Preferences.userNodeForPackage(NarrativeCreator.class);
public NarrativeCreator(String lphyFileName) throws IOException {
htmlNarrative = new HTMLNarrative();
latexNarrative = new LaTeXNarrative();
Path wd = UserDir.getUserDir(); // working dir
Path imgFile = Paths.get(wd.toString(), "GraphicalModel.png");
// assume file under working dir
Path lphyPath = Paths.get(wd.toString(), lphyFileName);
if (!lphyPath.toFile().exists())
throw new IOException("Cannot find lphy script at " + lphyPath);
try {
GraphicalModelParserDictionary parser = new GraphicalModelParserDictionary();
GraphicalModelPanel panel = new GraphicalModelPanel(parser, null);
panel.getComponent().setShowConstantNodes(false);
// parse and paint
Utils.readFile(lphyPath.toFile(), panel);
createNarrativeExclImg(panel.getParserDictionary(), imgFile);
LoggerUtils.log.warning("Image " + imgFile.getFileName() + " needs to be created separately !");
// TODO The quality of PNG is too low LinguaPhylo/linguaPhylo#130
createImage(imgFile.toFile(), panel.getComponent());
} catch (IOException e) {
e.printStackTrace();
}
try {
writeNarrative(wd);
} catch (IOException e) {
e.printStackTrace();
}
}
// private GraphicalModelContainer getParser(String lphyFileName) throws IOException {
// if (!lphyFileName.endsWith(".lphy"))
// throw new IllegalArgumentException("Invalid LPhy file name " + lphyFileName + " !");
//
// Path path = UserDir.getUserPath(lphyFileName);
// // set user.dir to the folder containing example file,
// // so that the relative path given in readNexus always refers to it
// UserDir.setUserDir(path.getParent().toString());
//
// BufferedReader reader = new BufferedReader(new FileReader(path.toString()));
// LPhyParser parser = new REPL();
// parser.source(reader);
//
// // A wrapper for any implementation of LPhyParser that will be used in the Studio
// return new GraphicalModelContainer(parser);
// }
private void createImage(File imgFile, GraphicalModelComponent component) throws IOException {
Utils.exportToPNG(imgFile, component);
LoggerUtils.log.info("Save " + imgFile.getAbsolutePath());
}
// exclude creating image
private void createNarrativeExclImg(GraphicalModelParserDictionary parserDictionary, final Path imgFile) {
// assume Data, Model, Posterior stay together with this order,
// so wrap them with
for a box with diff background colour.
for (Section section : Section.values()) {
switch (section) {
case Code -> {
code.append(section("Code"));
code.append(htmlNarrative.codeBlock(parserDictionary, 11));
code.append("\n");
}
case GraphicalModel -> {
code.append(section("Graphical Model"));
// create html to load image
code.append("\n\n");
code.append(" \n");
code.append(" \n");
code.append(" \n");
// replace fignum using Liquid in Jekyll MD
code.append(" {{ include.fignum }}: The graphical model\n");
code.append("\n\n");
code.append("\n");
// create image later
}
// move Data, Model, Posterior to the bottom of webpage
case Data -> {
String dataSec = NarrativeUtils.getNarrative(parserDictionary, htmlNarrative, true, false);
// narrative.append("\n\n");
// narrative.append("Click to expand the auto-generated narrative from LPhyStudio ...\n");
narrative.append("\n" + DIV_BOX_BACKGR_COLOUR + "\n");
narrative.append(dataSec);
narrative.append("\n");
}
case Model -> {
String modelSec = NarrativeUtils.getNarrative(parserDictionary, htmlNarrative, false, true);
narrative.append(modelSec);
narrative.append("\n");
}
case Posterior -> {
narrative.append(htmlNarrative.section("Posterior"));
String pos = NarrativeUtils.getInferenceStatement(parserDictionary, latexNarrative);
pos = htmlNarrative.rmLatexEquation(pos);
// replace equation to $$ ... $$
narrative.append("$$\n").append(pos).append("\n$$\n\n");
narrative.append("\n
\n");
// narrative.append("\n\n");
}
case References -> {
String ref = htmlNarrative.referenceSection();
references.append(ref);
}
}
}
// special requirement
// add link
code.append("\nFor the details, please read the auto-generated ")
.append("[narrative](#auto-generated)")
.append(" from LPhyStudio.\n");
}
private void writeNarrative(Path wd) throws IOException {
String lphyStr = replaceEscapeCharInLPhyScript(code.toString());
Path path = Paths.get(wd.toString(), "lphy.md");
writeToFile(lphyStr, path);
// it seems to print as it is if escape chars are inside
String narStr = narrative.toString();
validateTags(narStr, "div");
// validateTags(narStr, "details");
path = Paths.get(wd.toString(), "narrative.md");
writeToFile(narStr, path);
String ref = references.toString();
// convert MD, otherwise will have a gap when add new ref in MD
ref = convertHtmlListToMardown(ref);
// rm all \n, otherwise will have a gap
ref = trimEndNewLine(ref);
path = Paths.get(wd.toString(), "references.md");
writeToFile(ref, path);
}
// case by case to replace escape char in lphy script.
// if * is inside html which is inside a markdown (e.g. jekyll), then use \*,
// also \| to \\|, " to ", and so on
private String replaceEscapeCharInLPhyScript(String old) {
// \| to \\|
String newStr = old.replaceAll("\\\\\\|", "\\\\\\\\|");
// \. to \\.
newStr = newStr.replaceAll("\\\\\\.", "\\\\\\\\.");
// " (must be lphy code, not html) to "
newStr = newStr.replaceAll(">\"", ">"");
newStr = newStr.replaceAll("\"<", ""<");
// ' to '
newStr = newStr.replaceAll(">'", ">'");
newStr = newStr.replaceAll("'<", "'<");
// * to \*
return newStr.replaceAll("\\*", "\\\\*");
}
// if * is inside a jekyll markdown but not inside html tags, use *
// private String replaceAsteriskInMD(String old) {
// return old.replaceAll("\\*", "*");
// }
private void writeToFile(String str, Path path) throws IOException {
PrintWriter writer = new PrintWriter(new FileWriter(path.toString()));
// references do not new line
writer.print(str);
writer.flush();
writer.close();
System.out.println("Write \"" + (str.length() > 20 ? str.substring(0, 20) : str) +
"\" ...\nto " + path.toAbsolutePath());
}
// markdown section
private String section(String header) {
return "## " + header + "\n\n";
}
// convert html list into markdown
private String convertHtmlListToMardown(String ref) {
ref = ref.replace("
", "");
ref = ref.replace("
", "");
ref = ref.replace("
", "* ");
ref = ref.replace("
", "");
return ref;
}
private String trimEndNewLine(String str) {
final int tailIndex = 3;
// a plain-text match, no regex
if (str.endsWith("\n") && str.length() > tailIndex) {
int mark = str.lastIndexOf("\n")-tailIndex;
StringBuilder builder = new StringBuilder(str.substring(0, mark));
String end = str.substring(mark).replace("\n", "");
builder.append(end);
return builder.toString();
}
return str;
}
// check if and
are in correct position
private void validateTags(String narStr, String tagStr) {
int openTag = narStr.toLowerCase().indexOf("<" + tagStr.toLowerCase()); // it may have attrs
int closeTag = narStr.toLowerCase().indexOf("");
if (openTag >= closeTag)
throw new IllegalStateException("Invalid position of <" + tagStr + "> !");
}
private String replaceHTMLSection(String html) {
return html.replaceFirst("<" + HTMLNarrative.SECTION_TAG +
">(.*)", section("$1"));
}
// input: -Duser.dir=/lphy/path/tutorials h3n2.lphy
public static void main(String[] args) {
if (args.length != 1)
throw new IllegalArgumentException("Expecting LPhy file name !");
// always the last arg, such as h5n1.lphy, assuming the file is under user.dir
String lphyFileName = args[args.length - 1];
try {
NarrativeCreator narrativeCreator = new NarrativeCreator(lphyFileName);
} catch (IOException e) {
e.printStackTrace();
}
System.exit(0);
}
}
![\"").append(imgFile.getFileName())](\"").append(imgFile.getFileName()))
\n");
code.append(" \n");
// replace fignum using Liquid in Jekyll MD
code.append("