Changes in [31:9f653697437e:34:8427930c5f88] in AnnotationManagerN4J

Location:

src/main

Files:

• java/de/mpiwg/itgroup/annotations/Person.java (modified) (2 diffs)
• java/de/mpiwg/itgroup/annotations/neo4j/AnnotationStore.java (modified) (21 diffs)
• java/de/mpiwg/itgroup/annotations/restlet/AnnotatorAnnotations.java (modified) (1 diff)
• java/de/mpiwg/itgroup/annotations/restlet/AnnotatorSearch.java (modified) (1 diff)
• java/de/mpiwg/itgroup/annotations/restlet/annotations_ui/AnnotationsUiRestlet.java (modified) (2 diffs)
• java/de/mpiwg/itgroup/annotations/restlet/annotations_ui/GroupResource.java (modified) (4 diffs)
• java/de/mpiwg/itgroup/annotations/restlet/annotations_ui/GroupsResource.java (modified) (4 diffs)
• java/de/mpiwg/itgroup/annotations/restlet/annotations_ui/PersonResource.java (added)
• java/de/mpiwg/itgroup/annotations/restlet/annotations_ui/PersonsResource.java (added)
• webapp/groups/index.html (deleted)
• webapp/groups/new_group.html (deleted)
• webapp/index.html (modified) (1 diff)

src/main/java/de/mpiwg/itgroup/annotations/Person.java

@@ -3 +3 @@
  */
 package de.mpiwg.itgroup.annotations;
+
+import de.mpiwg.itgroup.annotations.restlet.BaseRestlet;
 
 /**
@@ -55 +57 @@
         return null;
     }
+
+    /**
+     * Sets the name from the id using getFullNameFromLdap of the Application.
+     *  
+     * @param application
+     * @return
+     */
+    public String updateName(BaseRestlet application) {
+        if (id != null) {
+            name = application.getFullNameFromLdap(id);
+        }
+        return name;
+    }
 }

src/main/java/de/mpiwg/itgroup/annotations/neo4j/AnnotationStore.java

@@ -5 +5 @@
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Calendar;
 import java.util.HashSet;
@@ -28 +29 @@
 
 /**
+ * Neo4J based Annotation store.
+ * 
  * @author casties
  * 
@@ -40 +43 @@
         ANNOTATION, PERSON, TARGET, GROUP, TAG
     }
+
+    // types of nodes that should not be automatically deleted.
+    public Set<String> permanentNodeTypes = new HashSet<String>(Arrays.asList("PERSON", "GROUP", "TAG"));
 
     protected List<Index<Node>> nodeIndexes;
@@ -85 +91 @@
     }
 
-    
-    
     public List<Actor> getActors(String key, String query, NodeTypes type) {
         ArrayList<Actor> actors = new ArrayList<Actor>();
@@ -124 +128 @@
         return groups;
     }
-    
-    
+
     /**
      * Returns List of Annotations.
@@ -174 +177 @@
     }
 
- 
-   /**
+    /**
      * Returns List of Groups the person is member of.
      * 
@@ -240 +242 @@
         return members;
     }
-    
+
     /**
      * Add Person newMember to Group group.
@@ -257 +259 @@
         return addedMember;
     }
-    
+
     /**
      * Delete Person oldMember from Group group.
@@ -266 +268 @@
     public void deleteGroupMember(Group group, Person member) {
         Node gn = getActorNode(group);
+        Node pn = getActorNode(member);
         Iterable<Relationship> rels = gn.getRelationships(RelationTypes.MEMBER_OF);
         for (Relationship rel : rels) {
             Node mn = rel.getStartNode();
-            if (mn.equals(member)) {
-                rel.delete();
+            if (mn.equals(pn)) {
+                Transaction tx = graphDb.beginTx();
+                try {
+                    rel.delete();
+                    tx.success();
+                } finally {
+                    tx.finish();
+                }
                 // there should be only one
                 break;
             }
-        }        
-    }
-    
+        }
+    }
+
     /**
      * Returns the stored Actor matching the given one.
@@ -284 +293 @@
      */
     public Actor getActor(Actor actor) {
-        Node actorNode = getActorNode(actor);
-        Actor storedActor = createActorFromNode(actorNode);
-        return storedActor;
-    }
-    
-    /**
-     * Stores an Actor (Person or Group). Creates a new actor Node or returns an existing one.
+        Node actorNode = getActorNode(actor);
+        Actor storedActor = createActorFromNode(actorNode);
+        return storedActor;
+    }
+
+    /**
+     * Stores an Actor (Person or Group). Creates a new actor Node or update an
+     * existing one.
      * 
      * @param actor
@@ -296 +306 @@
      */
     public Actor storeActor(Actor actor) {
-        Node actorNode = getOrCreateActorNode(actor);
-        Actor storedActor = createActorFromNode(actorNode);
-        return storedActor;
-    }
-    
+        Node actorNode = getOrCreateActorNode(actor);
+        Transaction tx = graphDb.beginTx();
+        try {
+            // id
+            String id = actor.getId();
+            if (id != null) {
+                actorNode.setProperty("id", id);
+            }
+            // name
+            String name = actor.getName();
+            if (name != null) {
+                actorNode.setProperty("name", name);
+            }
+            // uri
+            String uri = actor.getUri();
+            if (uri != null) {
+                actorNode.setProperty("uri", uri);
+            }
+            tx.success();
+        } finally {
+            tx.finish();
+        }
+        Actor storedActor = createActorFromNode(actorNode);
+        return storedActor;
+    }
+
+    /**
+     * Deletes the given Actor.
+     * 
+     * @param actor
+     */
+    public void deleteActor(Actor actor) {
+        String uri = actor.getUriString();
+        Index<Node> idx;
+        if (actor.isGroup()) {
+            idx = getNodeIndex(NodeTypes.GROUP);
+        } else {
+            idx = getNodeIndex(NodeTypes.PERSON);
+        }
+        Node actorNode = idx.get("uri", uri).getSingle();
+        if (actorNode != null) {
+            // delete relations
+            Transaction tx = graphDb.beginTx();
+            try {
+                for (Relationship rel : actorNode.getRelationships()) {
+                    rel.delete();
+                }
+                if (!actorNode.hasRelationship()) {
+                    // this shouldn't happen
+                    deleteNode(actorNode);
+                } else {
+                    logger.error("deleteActor: unable to delete: Node still has relations.");
+                }
+                tx.success();
+            } finally {
+                tx.finish();
+            }
+        }
+    }
+
     /**
      * Returns the Annotation with the given id.
@@ -403 +468 @@
      */
     protected Actor createActorFromNode(Node actorNode) {
+        if (actorNode == null) return null;
         String id = (String) actorNode.getProperty("id", null);
         String uri = (String) actorNode.getProperty("uri", null);
@@ -414 +480 @@
         return null;
     }
-    
+
     public Tag createTagFromNode(Node tagNode) {
-        String name = (String) tagNode.getProperty("name", null);
-        String uri = (String) tagNode.getProperty("uri", null);
-        String id = (String) tagNode.getProperty("id", null);
-        
-        return new Tag(id, uri, name);
-                
-        }
-
+        if (tagNode == null) return null;
+        String name = (String) tagNode.getProperty("name", null);
+        String uri = (String) tagNode.getProperty("uri", null);
+        String id = (String) tagNode.getProperty("id", null);
+
+        return new Tag(id, uri, name);
+
+    }
 
     /**
@@ -539 +605 @@
                         for (String tag : newTags) {
                             // create new tag
-                            Node tagNode = getOrCreateTagNode(new Tag(null,null,tag));
+                            Node tagNode = getOrCreateTagNode(new Tag(null, null, tag));
                             getOrCreateRelation(annotNode, RelationTypes.HAS_TAG, tagNode);
                         }
@@ -561 +627 @@
      * @param id
      */
-    public void deleteById(String id) {
+    public void deleteAnnotationById(String id) {
         Node annotNode = getNodeIndex(NodeTypes.ANNOTATION).get("id", id).getSingle();
         if (annotNode != null) {
@@ -569 +635 @@
                 for (Relationship rel : annotNode.getRelationships()) {
                     // delete relation and the related node if it has no other
-                    // relations
+                    // relations and is not permanent
                     Node other = rel.getOtherNode(annotNode);
                     rel.delete();
-                    if (!other.hasRelationship()) {
+                    if (!(other.hasRelationship() || permanentNodeTypes.contains(other.getProperty("TYPE", null)))) {
                         deleteNode(other);
                     }
@@ -597 +663 @@
      * @return
      */
-    public List<Annotation> searchByUriUser(String targetUri, String userUri, String limit, String offset) {
+    public List<Annotation> searchAnnotationByUriUser(String targetUri, String userUri, String limit, String offset) {
         List<Annotation> annotations = new ArrayList<Annotation>();
         if (targetUri != null) {
@@ -720 +786 @@
         return person;
     }
-    
+
     protected Node getOrCreateActorNode(Actor actor) {
         // Person/Group is identified by URI or id
@@ -773 +839 @@
                 tag.setProperty("name", tagname);
                 idx.add(tag, "name", tagname);
-                
+
                 tag.setProperty("id", inTag.getId());
                 tag.setProperty("uri", inTag.getUri());
                 idx.add(tag, "uri", inTag.getUri());
-                
+
                 tx.success();
             } finally {
@@ -804 +870 @@
             if (!oldActorNode.equals(newActorNode)) {
                 // new admin is different
-                rel.delete();
+                Transaction tx = graphDb.beginTx();
+                try {
+                    rel.delete();
+                    tx.success();
+                } finally {
+                    tx.finish();
+                }
                 if (newActorNode != null) {
                     rel = getOrCreateRelation(annotNode, type, newActorNode);
@@ -881 +953 @@
     }
 
-        public List<Annotation> getAnnotationsByTag(String tagUri) {
-                
-                ArrayList<Annotation> ret = new  ArrayList<Annotation>();
-                Node tag = getTagNodeByUri(tagUri);
-                
-                
-                Iterable<Relationship> rels = tag.getRelationships(Direction.INCOMING,RelationTypes.HAS_TAG);
-                
-                for (Relationship rel:rels){
-                        Node node = rel.getStartNode();
-                        ret.add(createAnnotationFromNode(node));
-                        
-                }
-                return ret;
-        }
+    public List<Annotation> getAnnotationsByTag(String tagUri) {
+
+        ArrayList<Annotation> ret = new ArrayList<Annotation>();
+        Node tag = getTagNodeByUri(tagUri);
+
+        Iterable<Relationship> rels = tag.getRelationships(Direction.INCOMING, RelationTypes.HAS_TAG);
+
+        for (Relationship rel : rels) {
+            Node node = rel.getStartNode();
+            ret.add(createAnnotationFromNode(node));
+
+        }
+        return ret;
+    }
 
 }

src/main/java/de/mpiwg/itgroup/annotations/restlet/AnnotatorAnnotations.java

@@ -276 +276 @@
         
         // delete annotation
-        store.deleteById(id);
+        store.deleteAnnotationById(id);
         setStatus(Status.SUCCESS_NO_CONTENT);
         return null;

src/main/java/de/mpiwg/itgroup/annotations/restlet/AnnotatorSearch.java

@@ -57 +57 @@
         logger.debug(String.format("searching for uri=%s user=%s", uri, user));
         AnnotationStore store = getAnnotationStore();
-        List<Annotation> annots = store.searchByUriUser(uri, user, limit, offset);
+        List<Annotation> annots = store.searchAnnotationByUriUser(uri, user, limit, offset);
         for (Annotation annot : annots) {
             // check permission

src/main/java/de/mpiwg/itgroup/annotations/restlet/annotations_ui/AnnotationsUiRestlet.java

@@ -17 +17 @@
 public class AnnotationsUiRestlet extends BaseRestlet {
 
-    public final String version = "AnnotationManagerN4J/AnnotationStore 0.1";
+    public final String version = "AnnotationManagerN4J/AnnotationsUI 0.2";
 
     public static Logger logger = Logger.getLogger(AnnotationsUiRestlet.class);
@@ -42 +42 @@
         router.attach("/groups/{id}/", GroupResource.class);
         router.attach("/groups/{id}/members", GroupMembersResource.class);
-              
+        router.attach("/persons", PersonsResource.class);
+        router.attach("/persons/", PersonsResource.class);
+        router.attach("/persons/{id}", PersonResource.class);
+        router.attach("/persons/{id}/", PersonResource.class);
+
         router.attach("/", InfoResource.class);
         // authenticator.setNext(router);

src/main/java/de/mpiwg/itgroup/annotations/restlet/annotations_ui/GroupResource.java

@@ -5 +5 @@
 
 import org.apache.log4j.Logger;
+import org.restlet.data.Form;
 import org.restlet.data.MediaType;
 import org.restlet.data.Reference;
@@ -10 +11 @@
 import org.restlet.representation.Representation;
 import org.restlet.representation.StringRepresentation;
+import org.restlet.resource.Delete;
 import org.restlet.resource.Get;
+import org.restlet.resource.Put;
 import org.restlet.resource.ResourceException;
 import org.restlet.resource.ServerResource;
@@ -29 +32 @@
 
     protected AnnotationStore store;
-    
+
     protected String requestId;
-    
+
     protected Group group;
-    
+
     @Override
     protected void doInit() throws ResourceException {
@@ -58 +61 @@
     @Get("html")
     public Representation doGetHTML(Representation entity) {
-        if (requestId == null || requestId.isEmpty()) {
+        if (group == null) {
+            // invalid id
+            setStatus(Status.CLIENT_ERROR_NOT_FOUND);
+            return null;
+        }
+        String result = null;
+        // get form parameter
+        Form f = this.getQuery();
+        String form = f.getFirstValue("form");
+        if (form != null && form.equals("edit")) {
+            // output edit form
+            result = "<html><body>\n";
+            result += String.format("<h1>Edit group %s</h1>\n", group.getId());
+            result += String.format("<p><a href=\"%s\">All groups</a></p>", this.getReference().getParentRef());
+            // tunnel PUT method through POST
+            result += String.format("<form method=\"post\" action=\"%s?method=PUT\">\n", this.getReference().getHierarchicalPart());
+            result += "<table>";
+            result += String.format("<tr><td><b>name</b></td><td><input type=\"text\" name=\"name\" value=\"%s\"/></td></tr>\n",
+                    group.getName());
+            result += String.format("<tr><td><b>uri</b></td><td><input type=\"text\" name=\"uri\" value=\"%s\"/></td></tr>\n",
+                    group.getUriString());
+            result += "</table>\n";
+            result += "<p><input type=\"submit\"/></p>";
+            result += "</table>\n</form>\n</body>\n</html>";
+        } else {
+            // output group content
+            result = "<html><body>\n<h1>Group</h1>\n";
+            result += String.format("<p><a href=\"%s\">All groups</a></p>", this.getReference().getParentRef());
+            result += "<table>";
+            result += String.format("<tr><td><b>id</b></td><td>%s</td></tr>\n", group.getId());
+            result += String.format("<tr><td><b>name</b></td><td>%s</td></tr>\n", group.getName());
+            result += String.format("<tr><td><b>uri</b></td><td>%s</td></tr>\n", group.getUri());
+            result += String.format("<tr><td><b>members</b></td><td><a href=\"%s\">view members</a></td></tr>\n", this
+                    .getReference().addSegment("members"));
+            result += "</table>\n";
+            result += "<p><a href=\"?form=edit\">Edit group</a></p>\n";
+            // tunnel POST as DELETE
+            result += String.format(
+                    "<form method=\"post\" action=\"%s?method=DELETE\"><input type=\"submit\" value=\"Delete group\"/></form>\n",
+                    this.getReference().getHierarchicalPart());
+            result += "</body>\n</html>";
+        }
+        return new StringRepresentation(result, MediaType.TEXT_HTML);
+    }
+
+    /**
+     * PUT updates the group.
+     * 
+     * @param entity
+     * @return
+     */
+    @Put
+    public Representation doPut(Representation entity) {
+        logger.debug("GroupResource.doPut!");
+        if (group == null) {
             // invalid id
             setStatus(Status.CLIENT_ERROR_BAD_REQUEST);
             return null;
         }
-        String result = null;
-        Reference groupsUrl = this.getReference().getParentRef();
-        result = "<html><body>\n<h1>Group</h1>\n";
-        result += String.format("<p><a href=\"%s\">All groups</a></p>", groupsUrl);
-        result += "<table>";
-        result += String.format("<tr><td><b>id</b></td><td>%s</td></tr>\n", group.getId());
-        result += String.format("<tr><td><b>name</b></td><td>%s</td></tr>\n", group.getName());
-        result += String.format("<tr><td><b>uri</b></td><td>%s</td></tr>\n", group.getUri());
-        result += String.format("<tr><td><b>members</b></td><td><a href=\"%s\">view members</a></td></tr>\n", this.getReference()
-                .addSegment("members"));
-        result += "</table>\n</body>\n</html>";
-
-        logger.debug("sending:");
-        logger.debug(result);
-        return new StringRepresentation(result, MediaType.TEXT_HTML);
+        // TODO: do authentication
+        Form form = new Form(entity);
+        String name = form.getFirstValue("name");
+        String uri = form.getFirstValue("uri");
+        if (name != null && !name.isEmpty()) {
+            group.setName(name);
+        }
+        if (uri != null && !uri.isEmpty()) {
+            group.setUri(uri);
+        }
+        store.storeActor(group);
+        // return 303: see other
+        setStatus(Status.REDIRECTION_SEE_OTHER);
+        // go GET same URL
+        Reference url = this.getReference();
+        this.getResponse().setLocationRef(url);
+        return null;
     }
 
+    /**
+     * DELETE deletes the group.
+     * 
+     * @param entity
+     * @return
+     */
+    @Delete
+    public Representation doDelete(Representation entity) {
+        logger.debug("GroupResource.doDelete!");
+        if (group == null) {
+            // invalid id
+            setStatus(Status.CLIENT_ERROR_BAD_REQUEST);
+            return null;
+        }
+        // TODO: do authentication
+        store.deleteActor(group);
+        // return 303: see other
+        setStatus(Status.REDIRECTION_SEE_OTHER);
+        // go GET parent URL
+        Reference url = this.getReference().getParentRef();
+        this.getResponse().setLocationRef(url);
+        return null;
+    }
 }

src/main/java/de/mpiwg/itgroup/annotations/restlet/annotations_ui/GroupsResource.java

@@ -15 +15 @@
 import org.restlet.resource.Get;
 import org.restlet.resource.Post;
+import org.restlet.resource.ResourceException;
 import org.restlet.resource.ServerResource;
 
@@ -34 +35 @@
     private AnnotationStore store;
 
+    @Override
+    protected void doInit() throws ResourceException {
+        super.doInit();
+        // get store instance
+        if (store == null) {
+            store = ((BaseRestlet) getApplication()).getAnnotationStore();
+        }
+    }
+
     /**
      * GET with HTML content type. Lists all groups.
@@ -43 +53 @@
     public Representation doGetHTML(Representation entity) {
         String result = null;
-        store = getAnnotationStore();
-        // list all groups
-        result = "<html><body>\n<h1>Groups</h1>\n<table>";
-        result += "<tr><th>id</th><th>name</th><th>uri</th></tr>";
-        List<Group> groups = store.getGroups("uri", "*");
-        for (Group group : groups) {
-            Reference groupUrl = this.getReference();
-            groupUrl.addSegment(group.getId());
-            result += String.format("<tr><td><a href=\"%s\">%s</a></td><td>%s</td><td>%s</td></tr>\n", groupUrl, group.getId(),
-                    group.getName(), group.getUri());
+        // get form parameter
+        Form f = this.getQuery();
+        String form = f.getFirstValue("form");
+        if (form != null && form.equals("new_group")) {
+            // output new group form
+            result = "<html><body>\n";
+            result += "<h1>New group</h1>\n";
+            result += String.format("<p><a href=\"%s\">All groups</a></p>", this.getReference());
+            result += String.format("<form method=\"post\" action=\"%s\">\n", this.getReference().getHierarchicalPart());
+            result += "<table>";
+            result += "<tr><td><b>id</b></td><td><input type=\"text\" name=\"id\"/></td></tr>\n";
+            result += "<tr><td><b>name</b></td><td><input type=\"text\" name=\"name\"/></td></tr>\n";
+            result += "</table>\n";
+            result += "<p><input type=\"submit\"/></p>\n";
+            result += "</form>\n</body>\n</html>";
+        } else {
+            // list all groups
+            result = "<html><body>\n<h1>Groups</h1>\n";
+            result += "<table>\n";
+            result += "<tr><th>id</th><th>name</th><th>uri</th></tr>";
+            List<Group> groups = store.getGroups("uri", "*");
+            for (Group group : groups) {
+                Reference groupUrl = this.getReference().clone();
+                groupUrl.addSegment(group.getId());
+                result += String.format("<tr><td><a href=\"%s\">%s</a></td><td>%s</td><td>%s</td></tr>\n", groupUrl, group.getId(),
+                        group.getName(), group.getUri());
+            }
+            result += "</table>\n";
+            result += "<p><a href=\"?form=new_group\">Add new group</a></p>\n";
+            result += "</body>\n</html>";
         }
-        result += "</table>\n</body>\n</html>";
-        logger.debug("sending:");
-        logger.debug(result);
         return new StringRepresentation(result, MediaType.TEXT_HTML);
     }
@@ -79 +106 @@
         String gid = makeGroupId(id);
         Group newGroup = new Group(gid, null, name);
-        store = getAnnotationStore();
         Actor storedGroup = store.storeActor(newGroup);
         gid = storedGroup.getId();

src/main/webapp/index.html

@@ -11 +11 @@
 
 <body>
-        <h1>Annotation Server</h1>
+  <h1>Annotation Server</h1>
+  <h2>View</h2>
+  <ul>
+    <li><a href="tags">View tags</a></li>
+    <li><a href="annotationBrowser">All Annotations</a></li>
+  </ul>
+  <h2>Admin</h2>
         <ul>
-                <li><a href="groups">View and edit groups</a></li>
-                <li><a href="tags">Browse by Tags</a></li>
-                <li><a href="annotationBrowser">All Annotations</a></li>
-                
+                <li><a href="annotations/groups">View and edit groups</a></li>
+    <li><a href="annotations/persons">View and edit persons</a></li>
         </ul>
 </body>