From version 5/fix issue 769 hg 5463 auto set propertyid

.gitignore

@@ -7,13 +7,30 @@ target/
 .classpath
 .project
 .settings/
+**/.factorypath
 out/
 
+# https://www.jenv.be/
+.java-version
+
 logs/
 
 velocity.log.*
 *.log
 
 dependency-reduced-pom.xml
 
-.protegedata/
+.protegedata/
+
+# Package Files 
+*.jar
+*.war
+*.nar
+*.ear
+*.zip
+*.tar.gz
+*.rar
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+replay_pid*

webprotege-client/src/main/java/edu/stanford/bmir/protege/web/client/projectsettings/ProjectSettingsService.java

@@ -4,6 +4,7 @@
 import com.google.gwt.resources.client.DataResource;
 import edu.stanford.bmir.protege.web.client.dispatch.DispatchServiceManager;
 import edu.stanford.bmir.protege.web.shared.project.ProjectId;
+import edu.stanford.bmir.protege.web.server.util.TypelessJSONSerialization;
 
 import javax.annotation.Nonnull;
 import javax.inject.Inject;
@@ -31,10 +32,12 @@ public ProjectSettingsService(DispatchServiceManager dispatch, ProjectId project
     public void importSettings(@Nonnull String settingsToImportJson,
                                @Nonnull Runnable importSuccessfulHandler,
                                @Nonnull Runnable importErrorHandler) {
+	String settingsJsonWithUpdatedProjectId;
         try {
+            settingsJsonWithUpdatedProjectId = updateInputJSONProjectId(settingsToImportJson);
             RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.POST, "/data/projects/" + projectId.getId() + "/settings");
-
-            requestBuilder.setRequestData(settingsToImportJson);
+            
+            requestBuilder.setRequestData(settingsJsonWithUpdatedProjectId);
             requestBuilder.setHeader("Content-Type", "application/json");
             requestBuilder.setCallback(new RequestCallback() {
                 @Override
@@ -57,5 +60,9 @@ public void onError(Request request, Throwable exception) {
             importErrorHandler.run();
         }
     }
+
+    private String updateInputJSONProjectId(@Nonnull String settingsToImportJson) {
+	return TypelessJSONSerialization.resplaceAllStringValue(settingsToImportJson, "projectId", this.projectId.getId());	
+    }
 
 }

webprotege-server-core/src/main/java/edu/stanford/bmir/protege/web/server/jackson/ObjectMapperProvider.java

@@ -13,10 +13,15 @@
 import org.semanticweb.owlapi.model.*;
 import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
 
+import java.util.concurrent.atomic.AtomicInteger;
+
 import javax.annotation.Nonnull;
 import javax.inject.Inject;
 import javax.inject.Provider;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 /**
  * Matthew Horridge
  * Stanford Center for Biomedical Informatics Research
@@ -26,7 +31,11 @@ public class ObjectMapperProvider implements Provider<ObjectMapper> {
 
     @Nonnull
     private final OWLDataFactory dataFactory;
+
+    private static Logger logger = LoggerFactory.getLogger(ObjectMapperProvider.class);
 
+    private static AtomicInteger mapperInstanceCount = new AtomicInteger();
+
     @Inject
     public ObjectMapperProvider() {
         this.dataFactory = new OWLDataFactoryImpl();
@@ -35,6 +44,9 @@ public ObjectMapperProvider() {
     @Override
     public ObjectMapper get() {
         ObjectMapper mapper = new ObjectMapper();
+        int instanceCount = mapperInstanceCount.incrementAndGet();
+        String msg = String.format("Instantiated another ObjectMappger#%08x, total: %d", mapper.hashCode(), instanceCount);
+        logger.info(msg);
         mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
         mapper.setDefaultPrettyPrinter(new DefaultPrettyPrinter());
         mapper.configure(SerializationFeature.WRITE_DATE_TIMESTAMPS_AS_NANOSECONDS, false);

webprotege-server-core/src/main/java/edu/stanford/bmir/protege/web/server/tag/TagsManager.java

@@ -1,25 +1,41 @@
 package edu.stanford.bmir.protege.web.server.tag;
 
-import com.google.common.collect.Streams;
-import edu.stanford.bmir.protege.web.server.events.HasPostEvents;
-import edu.stanford.bmir.protege.web.shared.event.ProjectEvent;
-import edu.stanford.bmir.protege.web.shared.inject.ProjectSingleton;
-import edu.stanford.bmir.protege.web.shared.project.ProjectId;
-import edu.stanford.bmir.protege.web.shared.tag.*;
-import org.semanticweb.owlapi.model.OWLEntity;
+import static com.google.common.base.Preconditions.checkNotNull;
+import static edu.stanford.bmir.protege.web.shared.tag.TagId.createTagId;
+import static java.util.stream.Collectors.toList;
+import static java.util.stream.Collectors.toMap;
+import static java.util.stream.Collectors.toSet;
 
-import javax.annotation.Nonnull;
-import javax.annotation.Nullable;
-import javax.inject.Inject;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.Set;
 import java.util.concurrent.locks.Lock;
 import java.util.concurrent.locks.ReadWriteLock;
 import java.util.concurrent.locks.ReentrantReadWriteLock;
 import java.util.stream.Stream;
 
-import static com.google.common.base.Preconditions.checkNotNull;
-import static edu.stanford.bmir.protege.web.shared.tag.TagId.createTagId;
-import static java.util.stream.Collectors.*;
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
+import javax.inject.Inject;
+
+import org.semanticweb.owlapi.model.OWLEntity;
+
+import com.google.common.collect.Streams;
+
+import edu.stanford.bmir.protege.web.server.events.HasPostEvents;
+import edu.stanford.bmir.protege.web.shared.event.ProjectEvent;
+import edu.stanford.bmir.protege.web.shared.inject.ProjectSingleton;
+import edu.stanford.bmir.protege.web.shared.project.ProjectId;
+import edu.stanford.bmir.protege.web.shared.tag.EntityTagsChangedEvent;
+import edu.stanford.bmir.protege.web.shared.tag.ProjectTagsChangedEvent;
+import edu.stanford.bmir.protege.web.shared.tag.Tag;
+import edu.stanford.bmir.protege.web.shared.tag.TagData;
+import edu.stanford.bmir.protege.web.shared.tag.TagId;
 
 /**
  * Matthew Horridge
@@ -150,6 +166,8 @@ public Collection<Tag> getProjectTags() {
      */
     public void setProjectTags(@Nonnull Collection<TagData> newProjectTags) {
         checkNotNull(newProjectTags);
+        if (newProjectTags.size() == 0)
+            return;
         Collection<Tag> currentProjectTags = getProjectTags();
         Set<OWLEntity> modifiedEntityTags = new HashSet<>();
         try {

webprotege-server-core/src/main/java/edu/stanford/bmir/protege/web/server/util/JavaUtil.java

@@ -0,0 +1,20 @@
+package edu.stanford.bmir.protege.web.server.util;
+
+public class JavaUtil {
+    /**
+     * The purpose of this cast utility to be able to suppress unchecked
+     * cast in one and only one place so we don't have to pollute the main
+     * application code with @SuppressWarnings and thus be able to flag
+     * places where the type cast warning(s) are/were unexpected.
+     * @param <T>
+     * @param obj
+     * @return
+     *
+     * This great idea came from:
+     * @see http://www.whizu.org/articles/how-to-avoid-unchecked-cast-warnings-with-java-generics.whizu
+     */
+    @SuppressWarnings("unchecked")
+    public static <T> T cast(Object obj) {
+      return (T)obj;
+    }
+}

webprotege-server-core/src/main/java/edu/stanford/bmir/protege/web/server/util/TypelessJSONSerialization.java

@@ -0,0 +1,94 @@
+package edu.stanford.bmir.protege.web.server.util;
+
+import static edu.stanford.bmir.protege.web.server.util.JavaUtil.cast;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.Map;
+
+import javax.annotation.Nonnull;
+
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectReader;
+import com.fasterxml.jackson.databind.ObjectWriter;
+
+/**
+ * These utility methods are for manipulating arbitrary JSON without needing to worry about what
+ * typed entities the JSON should be de/serialized to/from.
+ * 
+ * Initial motivation is to be able to change the value of "projectId" in project settings and 
+ * project forms import JSON.
+ * 
+ * @author Chris Wolf <[email protected]>
+ */
+public class TypelessJSONSerialization {
+
+    // TODO: should probably be injected, but effects the whole upstream DI call chain...
+    // TODO: ...and plus, ObjectMapper very expensive, so should be created only once.
+    private static final ObjectMapper objectMapper = new ObjectMapper();
+
+    public TypelessJSONSerialization() {
+    }
+
+    /**
+     * Accepts any arbitrary JSON and deserializes to nested <code>LinkedHashMap<String, Object></code>
+     * instances.  Note that the <code>Object</code> type parameter could be of type <code>String</code>, 
+     * <code>List</code>, or <code>Map</code> where the latter is for arbitrary nesting levels.
+     * 
+     * <b>N.B.</b> For normal, strongly typed Webprotege serialization, use the <code>ObjectMapper</code> 
+     * obtained from <code>ObjectMapperProvider</code> from <i>webprotege-server-core</i>.
+     * 
+     * @param json
+     * @return
+     * @throws IOException
+     */
+    public static Map<String, Object> deserializeJSON(@Nonnull String json) throws IOException {
+	ObjectReader objectReader = objectMapper.readerFor(new TypeReference<Map<String, Object>>() {
+	});
+	return objectReader.readValue(json);
+    }
+
+    /**
+     * 
+     * @param object
+     * @return
+     * @throws IOException
+     */
+    public static String serializeToJSON(Map<String, Object> object) throws IOException {
+	return serializeToJSON(object, false);
+    }
+
+    public static String serializeToJSON(Map<String, Object> object, boolean prettyPrint) throws IOException {
+	ObjectWriter objectWriter = prettyPrint ? objectMapper.writerWithDefaultPrettyPrinter() : objectMapper.writer();
+	return objectWriter.writeValueAsString(object);
+    }
+
+    public static String resplaceAllStringValue(@Nonnull String json, @Nonnull String keyName,
+	    @Nonnull String replacementValue) throws IOException {
+
+	Map<String, Object> deserialized = deserializeJSON(json);
+
+	walkMapAndDReplace(deserialized, keyName, replacementValue);
+
+	String serialized = serializeToJSON(deserialized);
+
+	return serialized;
+    }
+
+    static void walkMapAndDReplace(Map<String, Object> data, String keyName, String replacementValue) {
+	for (var mapEntry : data.entrySet()) {
+	    if (mapEntry.getValue() instanceof String && mapEntry.getKey().equals(keyName)) {
+		mapEntry.setValue(replacementValue);
+	    } else if (mapEntry.getValue() instanceof List) {
+		List<Object> objlist = cast(mapEntry.getValue());
+		for (Object listEntry : objlist) {
+		    if (listEntry instanceof Map)
+			walkMapAndDReplace(cast(listEntry), keyName, replacementValue);
+		}
+	    } else if (mapEntry.getValue() instanceof Map) {
+		walkMapAndDReplace(cast(mapEntry.getValue()), keyName, replacementValue);
+	    }
+	}
+    }
+}

webprotege-server-core/src/test/java/edu/stanford/bmir/protege/web/TestUtils.java

@@ -0,0 +1,32 @@
+package edu.stanford.bmir.protege.web;
+
+import java.io.IOException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+
+public class TestUtils {
+    /**
+     * Read contents of text file resource from <code>src/test/resources</code>.
+     * Entire content read into memory, so best for small files.
+     * 
+     * @param resourceName
+     * @return text content and assuming UTF-8 encoding
+     * @throws IOException
+     */
+    public static String readResourceTestFile(String resourceName) throws IOException {
+	ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
+	URI resource;
+	try {
+	    resource = classLoader.getResource(resourceName).toURI();
+	} catch (URISyntaxException e) {
+	    String msg = String.format("Can't read '%s'", resourceName);
+	    throw new IOException(msg, e);
+	}
+	byte[] rawContent = Files.readAllBytes(Paths.get(resource));
+
+	return new String(rawContent, StandardCharsets.UTF_8);
+    }
+}

webprotege-server-core/src/test/java/edu/stanford/bmir/protege/web/server/util/TypelessJSONSerialization_TestCase.java

@@ -0,0 +1,56 @@
+package edu.stanford.bmir.protege.web.server.util;
+
+import static edu.stanford.bmir.protege.web.server.util.JavaUtil.cast;
+import static org.junit.Assert.assertEquals;
+
+import java.util.List;
+import java.util.Map;
+
+import org.apache.commons.lang.StringUtils;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mockito.junit.MockitoJUnitRunner.Silent;
+
+import edu.stanford.bmir.protege.web.TestUtils;
+import edu.stanford.bmir.protege.web.shared.project.ProjectId;
+
+@RunWith(Silent.class)
+public class TypelessJSONSerialization_TestCase {
+    private ProjectId projectId = ProjectId.get("c4e39f8f-d2b3-4212-8888-28fabd2aa5ac");
+
+    @Test
+    public void testJSONSerialization() throws Exception {
+	// test basic round-trip deserialize/serialize
+
+	String testSettings = TestUtils
+		.readResourceTestFile("edu/stanford/bmir/protege/web/server/util/project_settings_notags.json");
+	// out.println(testSettings);
+	Map<String, Object> data = TypelessJSONSerialization.deserializeJSON(testSettings);
+
+	String newSettings = TypelessJSONSerialization.serializeToJSON(data, true);
+
+	assertEquals(StringUtils.deleteWhitespace(testSettings), StringUtils.deleteWhitespace(newSettings));
+	// out.println(newSettings);
+    }
+
+    @Test
+    public void testJSONSerializationNameValueReplacement() throws Exception {
+	String testSettings = TestUtils
+		.readResourceTestFile("edu/stanford/bmir/protege/web/server/util/project_settings_notags.json");
+
+	String newSettings = TypelessJSONSerialization.resplaceAllStringValue(testSettings, "projectId",
+		projectId.getId());
+	Map<String, Object> data = TypelessJSONSerialization.deserializeJSON(newSettings);
+
+	String id = projectId.getId();
+	Map<String, Object> projectSettings = cast(data.get("projectSettings"));
+	Map<String, Object> sharingSettings = cast(data.get("sharingSettings"));
+	Map<String, Object> searchSettings = cast(data.get("searchSettings"));
+	List<Map<String, Object>> searchFilters = cast(searchSettings.get("searchFilters"));
+
+	assertEquals(id, projectSettings.get("projectId"));
+	assertEquals(id, sharingSettings.get("projectId"));
+	assertEquals(id, searchSettings.get("projectId"));
+	assertEquals(id, searchFilters.get(0).get("projectId"));
+    }
+}