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lphystudio.app.docgenerator.GeneratorMarkdown Maven / Gradle / Ivy
package lphystudio.app.docgenerator;
import lphy.core.model.Generator;
import lphy.core.model.GeneratorUtils;
import lphy.core.model.NarrativeUtils;
import lphy.core.model.annotation.*;
import net.steppschuh.markdowngenerator.link.Link;
import net.steppschuh.markdowngenerator.list.UnorderedList;
import net.steppschuh.markdowngenerator.text.Text;
import net.steppschuh.markdowngenerator.text.emphasis.BoldText;
import net.steppschuh.markdowngenerator.text.heading.Heading;
import java.lang.reflect.Method;
import java.util.*;
/**
* A util class to create lphy doc in markdown.
* @author Alexei Drummond
* @author Walter Xie
*/
public class GeneratorMarkdown {
// this is in JEBL lib
public static final String SEQU_TYPE = "SequenceType";
static String getGeneratorMarkdown(Class generatorClass, final String typesDir) {
GeneratorInfo generatorInfo = GeneratorUtils.getGeneratorInfo(generatorClass);
List pInfo = GeneratorUtils.getParameterInfo(generatorClass, 0);
Class[] types = NarrativeUtils.getParameterTypes(generatorClass, 0);
StringBuilder md = new StringBuilder();
StringBuilder signature = new StringBuilder();
signature.append(GeneratorUtils.getGeneratorName(generatorClass)).append("(");
int count = 0;
for (int i = 0; i < pInfo.size(); i++) {
ParameterInfo pi = pInfo.get(i);
if (count > 0) signature.append(", ");
String typeName = types[i].getSimpleName();
Link typeLink = new Link(typeName, getTypeURL(typesDir, typeName));
signature.append(typeLink).append(" ").append(new BoldText(pi.name()));
count += 1;
}
signature.append(")");
md.append(new Heading(signature.toString(), 2)).append("\n\n");
if (generatorInfo != null) md.append(generatorInfo.description()).append("\n\n");
if (pInfo.size() > 0) {
md.append(new Heading("Parameters", 3)).append("\n\n");
List paramText = new ArrayList<>();
for (int i = 0; i < pInfo.size(); i++) {
ParameterInfo pi = pInfo.get(i);
String typeName = types[i].getSimpleName();
Link typeLink = new Link(typeName,getTypeURL(typesDir, typeName));
boolean isOptional = pi.optional();
paramText.add(new Text(typeLink + " " + new BoldText(pi.name()) + " - " +
(isOptional ? "(optional) " : "") + pi.description()));
}
md.append(new UnorderedList<>(paramText));
}
md.append("\n\n");
md.append(new Heading("Return type", 3)).append("\n\n");
String returnTypeName = GeneratorUtils.getReturnType(generatorClass).getSimpleName();
Link returnTypeLink = new Link(returnTypeName,getTypeURL(typesDir, returnTypeName));
md.append(returnTypeLink).append("\n\n");
if (generatorInfo != null){
String[] examples = generatorInfo.examples();
if (examples.length > 0) {
md.append("\n").append(new Heading("Examples",3)).append("\n\n");
md.append(new UnorderedList<>(Arrays.stream(examples).toList())).append("\n\n");
}
}
Citation citation = CitationUtils.getCitation(generatorClass);
if (citation != null) {
md.append(new Heading("Reference", 3)).append("\n\n");
md.append(citation.value());
if (citation.DOI().length() > 0) {
String url = citation.DOI();
if (!url.startsWith("http")) {
url = "http://doi.org/" + url;
}
md.append(new Link(url, url));
}
}
return md.toString();
}
/**
* @param typesDir the dir name where all types are
* @param name type md file name without .md
* @return the link to this type md file.
*/
private static String getTypeURL(final String typesDir, final String name) {
// the working dir should be where index.md is
return "../" + typesDir + "/" + name + ".md";
}
// private static String getTypeURL(final String typesDir, final String name) {
// // the working dir should be where index.md is
// String url = typesDir + "/" + name + ".md";
// // check if file exists, if no then add repo link
// File md = new File(url);
// if (!md.exists())
// url = "https://github.com/LinguaPhylo/linguaPhylo/blob/master/lphy/doc/types/" + name + ".md";
// else url = "../" + url; // otherwise, add ../ because the link is based on where the $name.md file is.
// return url;
// }
static String generateTypeMarkdown(Class type) {
StringBuilder builder = new StringBuilder();
String typeName = type.getSimpleName();
builder.append(new Heading(typeName,2)).append("\n");
// from TypeInfo
TypeInfo typeInfo = type.getAnnotation(TypeInfo.class);
String desc;
String[] examples = new String[0];
if (typeInfo == null) {
desc = getTypeDescription(typeName);
} else {
desc = typeInfo.description();
examples = typeInfo.examples();
}
if (!desc.isEmpty())
builder.append("\n").append(new Text(desc)).append("\n\n");
TreeMap methodInfoTreeMap = new TreeMap<>();
for (Method method : type.getMethods()) {
MethodInfo methodInfo = method.getAnnotation(MethodInfo.class);
if (methodInfo != null) {
methodInfoTreeMap.put(method.getName(), methodInfo);
}
}
if (methodInfoTreeMap.size() > 0) {
builder.append(new Heading("Methods",3)).append("\n\n");
List methodText = new ArrayList<>();
for (Map.Entry methodInfoEntry : methodInfoTreeMap.entrySet()) {
methodText.add(new BoldText(methodInfoEntry.getKey()) + "\n - " + methodInfoEntry.getValue().description());
}
builder.append(new UnorderedList<>(methodText));
}
// Examples
if (examples.length > 0) {
builder.append("\n").append(new Heading("Examples",3)).append("\n\n");
builder.append(new UnorderedList<>(Arrays.stream(examples).toList())).append("\n\n");
}
return builder.toString();
}
static String generateSequenceTypeMarkdown() {
StringBuilder builder = new StringBuilder();
builder.append(new Heading(SEQU_TYPE,2)).append("\n");
final String desc = "Sequences data types, such as nucleotide, amino acid, binary, " +
"standard type (e.g. morphology, locations, traits, ...), etc.";
builder.append("\n").append(new Text(desc)).append("\n\n");
final String seealso = "https://github.com/LinguaPhylo/linguaPhylo/tree/master/lphy/doc/sequence-type";
builder.append("\n").append(new Text("See also: " + seealso)).append("\n\n");
return builder.toString();
}
private static String getTypeDescription(String name) {
return switch (name) {
case "Boolean" -> "The [Boolean](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/Boolean.html) data type wraps a boolean value, such as true or false.";
case "Boolean[]" -> "The [Boolean](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/Boolean.html) array.";
case "Double" -> "The [Double](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/Double.html) data type wraps a real number, such as 0.1.";
case "Double[]" -> "The [Double](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/Double.html) data type array.";
case "Double[][]" -> "The [Double](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/Double.html) data type 2-d array.";
case "Integer" -> "The [Integer](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/Integer.html) data type wraps an integer number, such as 1.";
case "Integer[]" -> "The [Integer](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/Integer.html) data type array.";
case "Integer[][]" -> "The [Integer](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/Integer.html) data type 2-d array.";
case "Number" -> "The [Number](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/Number.html) is the superclass of data type wrapping numeric values, such as Double or Integer.";
case "Number[]" -> "The [Number](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/Number.html) data type array.";
case "Number[][]" -> "The [Number](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/Number.html) data type 2-d array.";
case "Object" -> "It could be any data type or class.";
case "Object[]" -> "The Object array.";
case "Object[][]" -> "The Object 2-d array.";
case "String" -> "The [String](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/String.html) data type represents character strings, such as \"lphy\".";
case "String[]" -> "The [String](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/String.html) data type array.";
case "String[][]" -> "The [String](https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/String.html) data type 2-d array.";
default -> "";
};
}
}
