Fix for protegeproject#769 - IllegalArgumentException: state should b…

…e: writes is not an empty list upon savings Tags and Sharing Settings - also workaround for com.mongodb.DuplicateKeyException: Write failed with error code 11000 and error message 'E11000 duplicate key error collection: webprotege.RoleAssignments index: userName_1_projectId_1 version-5/fix_issue_769-HG-5463 - upgrade dependency-plugin for https://issues.apache.org/jira/browse/MDEP-613
wolfch-elsevier · Jun 7, 2022 · b216c1c · b216c1c
1 parent 2500943
commit b216c1c
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Showing 9 changed files with 104 additions and 30 deletions.
diff --git a/.gitignore b/.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*
diff --git a/pom.xml b/pom.xml
@@ -273,8 +273,9 @@
                     </executions>
                 </plugin>
                 <plugin>
+                    <!-- need 3.1.2: https://issues.apache.org/jira/browse/MDEP-613 -->
                     <artifactId>maven-dependency-plugin</artifactId>
-                    <version>3.1.1</version>
+                    <version>3.1.2</version>
                 </plugin>
 
                 <plugin>

diff --git a/...tege-server-api/src/main/java/edu/stanford/bmir/protege/web/server/tag/TagRepository.java b/...tege-server-api/src/main/java/edu/stanford/bmir/protege/web/server/tag/TagRepository.java
@@ -16,7 +16,7 @@ public interface TagRepository {
 
     void saveTag(@Nonnull Tag tag);
 
-    void saveTags(@Nonnull Iterable<Tag> tags);
+    void saveTags(@Nonnull List<Tag> tags);
 
     void deleteTag(@Nonnull TagId tagId);
 

diff --git a/...core/src/main/java/edu/stanford/bmir/protege/web/server/jackson/ObjectMapperProvider.java b/...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
@@ -27,6 +32,10 @@ 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);

diff --git a/...in/java/edu/stanford/bmir/protege/web/server/search/EntitySearchFilterRepositoryImpl.java b/...in/java/edu/stanford/bmir/protege/web/server/search/EntitySearchFilterRepositoryImpl.java
@@ -94,6 +94,8 @@ public ImmutableList<EntitySearchFilter> getSearchFilters(@Nonnull ProjectId pro
     public void saveSearchFilters(@Nonnull ImmutableList<EntitySearchFilter> filters) {
         try {
             writeLock.lock();
+            if (filters.size() < 1)
+        	return;
             var writes = filters.stream()
                                 .map(this::toMongoDocument)
                                 .map(this::toReplaceOne)

diff --git a/.../java/edu/stanford/bmir/protege/web/server/sharing/ProjectSharingSettingsManagerImpl.java b/.../java/edu/stanford/bmir/protege/web/server/sharing/ProjectSharingSettingsManagerImpl.java
@@ -1,6 +1,25 @@
 package edu.stanford.bmir.protege.web.server.sharing;
 
+import static edu.stanford.bmir.protege.web.server.access.Subject.forAnySignedInUser;
+import static edu.stanford.bmir.protege.web.server.access.Subject.forUser;
+import static java.util.Collections.emptySet;
+import static java.util.stream.Collectors.toMap;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+
+import javax.inject.Inject;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import com.google.common.collect.ImmutableSet;
+import com.mongodb.DuplicateKeyException;
+
 import edu.stanford.bmir.protege.web.server.access.AccessManager;
 import edu.stanford.bmir.protege.web.server.access.ProjectResource;
 import edu.stanford.bmir.protege.web.server.access.Subject;
@@ -12,16 +31,6 @@
 import edu.stanford.bmir.protege.web.shared.sharing.SharingPermission;
 import edu.stanford.bmir.protege.web.shared.sharing.SharingSetting;
 import edu.stanford.bmir.protege.web.shared.user.UserId;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import javax.inject.Inject;
-import java.util.*;
-
-import static edu.stanford.bmir.protege.web.server.access.Subject.forAnySignedInUser;
-import static edu.stanford.bmir.protege.web.server.access.Subject.forUser;
-import static java.util.Collections.emptySet;
-import static java.util.stream.Collectors.toMap;
 
 /**
  * Matthew Horridge
@@ -66,12 +75,24 @@ public ProjectSharingSettings getProjectSharingSettings(ProjectId projectId) {
 
     @Override
     public void setProjectSharingSettings(ProjectSharingSettings settings) {
-        ProjectId projectId = settings.getProjectId();
-        ProjectResource projectResource = new ProjectResource(projectId);
+	ProjectId projectId = settings.getProjectId();
+	ProjectResource projectResource = new ProjectResource(projectId);
 
-        // Remove existing assignments
-        accessManager.getSubjectsWithAccessToResource(projectResource)
-                .forEach(subject -> accessManager.setAssignedRoles(subject, projectResource, Collections.emptySet()));
+	// Overwrite existing assignments with blank assignment
+	for (Subject subject : accessManager.getSubjectsWithAccessToResource(projectResource)) {
+	    try {
+		logger.info("Subject: {}, resource: {}", subject, projectResource);
+		accessManager.setAssignedRoles(subject, projectResource, Collections.emptySet());
+	    } catch (DuplicateKeyException e) {
+		// TODO: fix for intermittent 'E11000 duplicate key error collection:
+		// webprotege.RoleAssignments
+		// index: userName_1_projectId_1
+		// dup key: { userName: null, projectId: "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx"
+		// }'
+		String msg = String.format("Subject: %s, resource: %s", subject, projectResource);
+		logger.warn(msg, e);
+	    }
+	}
 
         Map<PersonId, SharingSetting> map = settings.getSharingSettings().stream()
                                                     .collect(toMap(SharingSetting::getPersonId, s -> s, (s1, s2) -> s1));
@@ -93,7 +114,7 @@ public void setProjectSharingSettings(ProjectSharingSettings settings) {
                                                roles);
             }
             else {
-                logger.info("User in sharing setting not found.  An email invitation needs to be sent");
+                logger.warn("User in sharing setting not found.  An email invitation needs to be sent");
                 // TODO
                 // We need to send the user an email invitation
             }

diff --git a/...core/src/main/java/edu/stanford/bmir/protege/web/server/tag/TagRepositoryCachingImpl.java b/...core/src/main/java/edu/stanford/bmir/protege/web/server/tag/TagRepositoryCachingImpl.java
@@ -53,7 +53,7 @@ public synchronized void saveTag(@Nonnull Tag tag) {
     }
 
     @Override
-    public synchronized void saveTags(@Nonnull Iterable<Tag> tags) {
+    public synchronized void saveTags(@Nonnull List<Tag> tags) {
         delegate.saveTags(tags);
         invalidate();
     }

diff --git a/...server-core/src/main/java/edu/stanford/bmir/protege/web/server/tag/TagRepositoryImpl.java b/...server-core/src/main/java/edu/stanford/bmir/protege/web/server/tag/TagRepositoryImpl.java
@@ -105,8 +105,10 @@ private Document toDocument(@Nonnull Tag tag) {
         return objectMapper.convertValue(tag, Document.class);
     }
 
-    public void saveTags(@Nonnull Iterable<Tag> tags) {
+    public void saveTags(@Nonnull List<Tag> tags) {
         writeLock.lock();
+        if (tags.size() < 1)
+            return;
         try {
             checkNotNull(tags);
             Spliterator<Tag> spliterator = tags.spliterator();

diff --git a/...main/java/edu/stanford/bmir/protege/web/server/api/resources/ProjectSettingsResource.java b/...main/java/edu/stanford/bmir/protege/web/server/api/resources/ProjectSettingsResource.java
@@ -1,8 +1,24 @@
 package edu.stanford.bmir.protege.web.server.api.resources;
 
+import static com.google.common.base.Preconditions.checkNotNull;
+import static com.google.common.collect.ImmutableList.toImmutableList;
+import static javax.ws.rs.core.MediaType.APPLICATION_JSON;
+
+import javax.annotation.Nonnull;
+import javax.ws.rs.Consumes;
+import javax.ws.rs.GET;
+import javax.ws.rs.POST;
+import javax.ws.rs.Path;
+import javax.ws.rs.Produces;
+import javax.ws.rs.core.Context;
+import javax.ws.rs.core.Response;
+
 import com.google.auto.factory.AutoFactory;
 import com.google.auto.factory.Provided;
 import com.google.common.collect.ImmutableList;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import edu.stanford.bmir.protege.web.server.api.ActionExecutor;
 import edu.stanford.bmir.protege.web.shared.crud.GetEntityCrudKitSettingsAction;
 import edu.stanford.bmir.protege.web.shared.crud.IRIPrefixUpdateStrategy;
@@ -23,21 +39,14 @@
 import edu.stanford.bmir.protege.web.shared.tag.TagData;
 import edu.stanford.bmir.protege.web.shared.user.UserId;
 
-import javax.annotation.Nonnull;
-import javax.ws.rs.*;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
-
-import static com.google.common.base.Preconditions.checkNotNull;
-import static com.google.common.collect.ImmutableList.toImmutableList;
-import static javax.ws.rs.core.MediaType.APPLICATION_JSON;
-
 /**
  * Matthew Horridge
  * Stanford Center for Biomedical Informatics Research
  * 2020-08-24
  */
 public class ProjectSettingsResource {
+
+    protected static Logger logger = LoggerFactory.getLogger(ProjectSettingsResource.class);
 
     @Nonnull
     private final ProjectId projectId;
@@ -78,6 +87,16 @@ public Response getProjectSettings(@Context UserId userId) {
     @POST
     @Consumes(APPLICATION_JSON)
     public Response setProjectSettings(@Context UserId userId, AllProjectSettings allProjectSettings) {
+	logger.info("Called setProjectSettings for projectId '{}'", this.projectId.getId());
+	try {
+	    return _setProjectSettings(userId, allProjectSettings);
+	} catch (Exception e) {
+	    logger.error("setProjectSettings failed", e);
+	    throw e;	    
+	}
+    }
+
+    private Response _setProjectSettings(@Context UserId userId, AllProjectSettings allProjectSettings) {
         var projectSettings = allProjectSettings.getProjectSettings().withProjectId(projectId);
         actionExecutor.execute(new SetProjectSettingsAction(projectSettings), userId);