Create SciJava Discoverer Therapi

Author: gselzer

scijava/scijava-discovery-therapi/src/main/java/org/scijava/discovery/therapi/TherapiDiscoverer.java

@@ -11,6 +11,11 @@
 import java.lang.reflect.AnnotatedElement;
 import java.lang.reflect.Field;
 import java.lang.reflect.Method;
+import java.net.URI;
+import java.nio.file.FileSystem;
+import java.nio.file.FileSystems;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -215,7 +220,9 @@ public static List<File> getJavadocedFiles(String path) {
 		else if (file.getPath().endsWith(".jar")) {
 			try {
 				for (String s : getJarContent(path))
-					if (s.endsWith("__Javadoc.json")) filesList.add(file);
+					if (s.endsWith("__Javadoc.json")) {
+						filesList.add(new File(s));
+					}
 			}
 			catch (IOException exc) {
 				// TODO Auto-generated catch block
@@ -241,8 +248,12 @@ private static void recurse(List<File> filesList, File f) {
 	}
 
 	private static String getFullyQualifiedName(File f, String path) {
+		if (f.getPath().contains(path)) {
 		return f.getPath().substring(path.length() + 1, f.getPath().indexOf(
 			"__Javadoc.json")).replace(System.getProperty("file.separator"), ".");
+		}
+		return f.getPath().substring(0, f.getPath().indexOf(
+			"__Javadoc.json")).replace(System.getProperty("file.separator"), ".");
 	}
 
 	/**

scijava/scijava-discovery-therapi/src/test/java/module-info.java

@@ -1,4 +1,4 @@
-package org.scijava.discovery.therapi.test;
+package org.scijava.discovery.therapi;
 
 import java.lang.reflect.AnnotatedElement;
 import java.util.List;
@@ -14,8 +14,6 @@ public class TherapiDiscovererTest extends TherapiDiscoverer {
 
 	@Test
 	public void discoverClass() {
-		System.out.println("CLASS PATH: " + System.getProperty("java.class.path") + "\n");
-		System.out.println("MODULE PATH: " + System.getProperty("jdk.module.path"));
 		List<Discovery<AnnotatedElement>> list = new TherapiDiscoverer().elementsTaggedWith("test");
 		List<AnnotatedElement> elements = list.stream().map(d -> d.discovery()).collect(Collectors.toList());
 		Assert.assertTrue(elements.contains(ClassTest.class));

scijava/scijava-discovery-therapi/src/test/java/org/scijava/discovery/therapi/test/TherapiDiscovererTest.java renamed to scijava/scijava-discovery-therapi/src/test/java/org/scijava/discovery/therapi/TherapiDiscovererTest.java

@@ -35,6 +35,7 @@
 
 	requires org.scijava;
 	requires org.scijava.discovery;
+	requires org.scijava.discovery.therapi;
 	requires org.scijava.function;
 	requires org.scijava.progress;
 	requires org.scijava.struct;

scijava/scijava-ops-engine/src/main/java/module-info.java

@@ -38,6 +38,7 @@
 import org.scijava.InstantiableException;
 import org.scijava.discovery.Discoverer;
 import org.scijava.discovery.Discovery;
+import org.scijava.discovery.therapi.TherapiDiscoverer;
 import org.scijava.log.LogService;
 import org.scijava.ops.api.OpBuilder;
 import org.scijava.ops.api.OpEnvironment;
@@ -109,7 +110,7 @@ private synchronized void initEnv() {
 			new OpClassBasedClassOpInfoGenerator(d1, d2),
 			new OpCollectionInfoGenerator(d1, d2),
 			new TagBasedOpInfoGenerator(d3));
-		env = new DefaultOpEnvironment(types, log, history, infoGenerators, d1, d2);
+		env = new DefaultOpEnvironment(types, log, history, infoGenerators, d1, d2, d3);
 	}
 
 	private synchronized void initHistory() {