Merge branch '32-rest-additions' into 'develop'

REST access for corrupt collections + files

Closes #32

See merge request !5

ace-am/src/main/java/edu/umiacs/ace/monitor/core/MonitoredItemManager.java

@@ -34,6 +34,11 @@ package edu.umiacs.ace.monitor.core;
 import edu.umiacs.ace.monitor.log.LogEnum;
 import edu.umiacs.ace.monitor.log.LogEventManager;
 import edu.umiacs.ace.util.PersistUtil;
+import org.apache.log4j.Logger;
+
+import javax.persistence.EntityManager;
+import javax.persistence.EntityTransaction;
+import javax.persistence.Query;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.Date;
@@ -42,10 +47,6 @@ import java.util.List;
 import java.util.Set;
 import java.util.concurrent.locks.Lock;
 import java.util.concurrent.locks.ReentrantLock;
-import javax.persistence.EntityManager;
-import javax.persistence.EntityTransaction;
-import javax.persistence.Query;
-import org.apache.log4j.Logger;
 
 /**
  *
@@ -58,13 +59,13 @@ public class MonitoredItemManager {
             MonitoredItemManager.class);
     EntityManager em;
     // TODO: This may leak...
-    private Set<String> existingParents = new HashSet<String>();
+    private Set<String> existingParents = new HashSet<>();
 
     public MonitoredItemManager( EntityManager em ) {
         this.em = em;
     }
 
-    public List<MonitoredItem> listItemsBefore( Collection c, Date d ) {
+    public Iterable<MonitoredItem> listItemsBefore( Collection c, Date d ) {
         lock.lock();
         try {
 

ace-am/src/main/java/edu/umiacs/ace/monitor/reporting/SummaryGenerator.java

@@ -31,12 +31,17 @@
 
 package edu.umiacs.ace.monitor.reporting;
 
-import edu.umiacs.ace.monitor.log.*;
-import edu.umiacs.ace.util.PersistUtil;
 import edu.umiacs.ace.monitor.core.Collection;
+import edu.umiacs.ace.monitor.log.LogEnum;
+import edu.umiacs.ace.util.PersistUtil;
 import edu.umiacs.sql.SQL;
 import edu.umiacs.util.Argument;
 import edu.umiacs.util.Strings;
+import org.apache.log4j.Logger;
+
+import javax.persistence.EntityManager;
+import javax.persistence.EntityTransaction;
+import javax.sql.DataSource;
 import java.sql.Connection;
 import java.sql.PreparedStatement;
 import java.sql.ResultSet;
@@ -45,10 +50,6 @@ import java.sql.Timestamp;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
-import javax.persistence.EntityManager;
-import javax.persistence.EntityTransaction;
-import javax.sql.DataSource;
-import org.apache.log4j.Logger;
 
 /**
  * Log summary generator, this will generate a report summarizing all log entries
@@ -168,7 +169,7 @@ public class SummaryGenerator extends ReportItemTypes {
                         + "MIN(logevent.ID), logevent.LOGTYPE, count(logevent.LOGTYPE)"
                         + "FROM logevent WHERE logevent.COLLECTION_ID = ? "
                         + "GROUP BY logevent.LOGTYPE");
-                ps.setLong(2, collection.getId());
+                ps.setLong(1, collection.getId());
             }
 
             // create entries for each result, for start date and session id

ace-am/src/main/java/edu/umiacs/ace/rest/ListController.java

 package edu.umiacs.ace.rest;
 
 import edu.umiacs.ace.monitor.core.Collection;
+import edu.umiacs.ace.monitor.core.MonitoredItem;
 import edu.umiacs.ace.util.PersistUtil;
+import org.apache.log4j.Logger;
 
 import javax.persistence.EntityManager;
 import javax.persistence.Query;
+import javax.persistence.criteria.CriteriaBuilder;
+import javax.persistence.criteria.CriteriaQuery;
+import javax.persistence.criteria.Root;
 import javax.ws.rs.GET;
 import javax.ws.rs.Path;
 import javax.ws.rs.PathParam;
 import javax.ws.rs.Produces;
+import javax.ws.rs.QueryParam;
 import javax.ws.rs.core.MediaType;
 import java.util.ArrayList;
 import java.util.List;
 
 /**
+ * Get a listing of groups/collections in ACE
+ *
  * Created by shake on 10/22/14.
  */
 @Path("/")
 public class ListController {
+    private static final Logger LOG = Logger.getLogger(ListController.class);
 
     /**
      * Get a list of all the groups registered in ACE
@@ -64,7 +73,7 @@ public class ListController {
         // Get all
         Query q = em.createNamedQuery("Collection.listAllCollections");
         List<Collection> results = q.getResultList();
-        List<Collection> groupless = new ArrayList<Collection>();
+        List<Collection> groupless = new ArrayList<>();
 
         // Filter if the group == null
         for (Collection result : results) {
@@ -75,4 +84,65 @@ public class ListController {
         return groupless;
     }
 
+    /**
+     * New API method to get all collections with query parameters
+     *
+     * @return
+     */
+    @GET
+    @Path("collections")
+    @Produces(MediaType.APPLICATION_JSON)
+    public List<Collection> getCollections(@QueryParam("group") String group,
+                                           @QueryParam("active") Boolean active,
+                                           @QueryParam("corrupt") Boolean corrupt) {
+        EntityManager entityManager = PersistUtil.getEntityManager();
+        CriteriaBuilder cb = entityManager.getCriteriaBuilder();
+        CriteriaQuery<Collection> cq = cb.createQuery(Collection.class);
+        Root<Collection> coll = cq.from(Collection.class);
+        cq.select(coll);
+        if (active != null && active) {
+            cq.where(cb.equal(coll.get("state"), 'A'));
+        }
+
+        if (corrupt != null && corrupt) {
+            cq.where(cb.equal(coll.get("state"), 'E'));
+        }
+
+        return entityManager.createQuery(cq).getResultList();
+    }
+
+    /**
+     * API for getting items in a collection. We can offer more query parameters (path, last seen, etc),
+     * but for now just query based on state
+     *
+     * @param id The id of the collection
+     * @param state The state of the monitored items
+     * @return a list of monitored items for the collection
+     */
+    @GET
+    @Path("collections/{id}/items")
+    @Produces(MediaType.APPLICATION_JSON)
+    public List<MonitoredItemBean> getCollectionItems(@PathParam("id") Long id,
+                                                      @QueryParam("state") String state) {
+        EntityManager entityManager = PersistUtil.getEntityManager();
+        Collection c = entityManager.find(Collection.class, id);
+
+        CriteriaBuilder cb = entityManager.getCriteriaBuilder();
+        CriteriaQuery<MonitoredItemBean> cq = cb.createQuery(MonitoredItemBean.class);
+        Root<MonitoredItem> mi = cq.from(MonitoredItem.class);
+
+        cq.select(cb.construct(MonitoredItemBean.class,
+                mi.get("id"), mi.get("path"),
+                mi.get("state"), mi.get("fileDigest"),
+                mi.get("size"), mi.get("lastSeen"),
+                mi.get("stateChange"), mi.get("lastVisited")));
+
+        cq.where(cb.equal(mi.get("parentCollection"), c));
+        if (state != null && !state.isEmpty()) {
+            cq.where(cb.equal(mi.get("state"), state));
+        }
+
+        return entityManager.createQuery(cq).getResultList();
+    }
+
 }

ace-am/src/main/java/edu/umiacs/ace/rest/MonitoredItemBean.java

+package edu.umiacs.ace.rest;
+
+import java.util.Date;
+
+/**
+ * Bean for displaying certain MonitoredItem properties in our api
+ *
+ * Created by shake on 11/14/16.
+ */
+public class MonitoredItemBean {
+
+    private Long id;
+    private String path;
+    private String state;
+    private String fileDigest;
+    private Long size;
+    private Date lastSeen;
+    private Date stateChange;
+    private Date lastVisited;
+
+    public MonitoredItemBean() {
+    }
+
+    public MonitoredItemBean(Long id, String path, char state, String fileDigest, Long size , Date lastSeen, Date stateChange, Date lastVisited) {
+        this.id = id;
+        this.path = path;
+        this.state = String.valueOf(state);
+        this.fileDigest = fileDigest;
+        this.size = size;
+        this.lastSeen = lastSeen;
+        this.stateChange = stateChange;
+        this.lastVisited = lastVisited;
+    }
+
+
+    public Long getId() {
+        return id;
+    }
+
+    public MonitoredItemBean setId(Long id) {
+        this.id = id;
+        return this;
+    }
+
+    public String getPath() {
+        return path;
+    }
+
+    public MonitoredItemBean setPath(String path) {
+        this.path = path;
+        return this;
+    }
+
+    public String getState() {
+        return state;
+    }
+
+    public MonitoredItemBean setState(String state) {
+        this.state = state;
+        return this;
+    }
+
+    public String getFileDigest() {
+        return fileDigest;
+    }
+
+    public MonitoredItemBean setFileDigest(String fileDigest) {
+        this.fileDigest = fileDigest;
+        return this;
+    }
+
+    public Long getSize() {
+        return size;
+    }
+
+    public MonitoredItemBean setSize(Long size) {
+        this.size = size;
+        return this;
+    }
+
+    public Date getLastSeen() {
+        return lastSeen;
+    }
+
+    public MonitoredItemBean setLastSeen(Date lastSeen) {
+        this.lastSeen = lastSeen;
+        return this;
+    }
+
+    public Date getStateChange() {
+        return stateChange;
+    }
+
+    public MonitoredItemBean setStateChange(Date stateChange) {
+        this.stateChange = stateChange;
+        return this;
+    }
+
+    public Date getLastVisited() {
+        return lastVisited;
+    }
+
+    public MonitoredItemBean setLastVisited(Date lastVisited) {
+        this.lastVisited = lastVisited;
+        return this;
+    }
+}

ace-am/src/main/java/edu/umiacs/ace/rest/SettingsManagement.java

@@ -4,10 +4,11 @@
  */
 package edu.umiacs.ace.rest;
 
-import com.sun.istack.logging.Logger;
 import edu.umiacs.ace.driver.irods.IrodsSetting;
 import edu.umiacs.ace.monitor.core.Collection;
 import edu.umiacs.ace.util.PersistUtil;
+import org.apache.log4j.Logger;
+
 import javax.persistence.EntityManager;
 import javax.persistence.EntityTransaction;
 import javax.persistence.NoResultException;

ace-am/src/main/java/edu/umiacs/ace/util/KSFuture.java

@@ -49,6 +49,7 @@ public class KSFuture<V extends Runnable> extends KnownFuture<Submittable<V>> {
         Submittable<V> result = getKnownResult();
         beforeExecute(result);
         super.run();
+        // TODO: Check exception and print if true?
         afterExecute(result);
     }
 

ace-am/src/main/resources/META-INF/persistence.xml

@@ -23,6 +23,9 @@
     <exclude-unlisted-classes>true</exclude-unlisted-classes>
     <properties>
       <!-- <property name="toplink.logging.level" value="FINE"/> -->
+      <!-- <property name="eclipselink.logging.file" value="/tmp/eclipselink.log"/> -->
+      <!-- <property name="eclipselink.logging.level" value="FINE"/> -->
+      <!-- <property name="eclipselink.logging.level.sql" value="FINE"/> -->
       <property name="eclipselink.session.customizer" value="edu.umiacs.ace.util.DataSourceSessionCustomizer"/>
       <!-- <property name="eclipselink.create-ddl-jdbc-file-name" value="create.sql"/>
       <property name="eclipselink.ddl-generation.output-mode" value="sql-script"/>

ace-common/src/main/java/edu/umiacs/ace/hashtree/HashTreeBuilder.java

@@ -254,7 +254,7 @@ public final class HashTreeBuilder {
         // Find out how many nodes are going to be in the parent level
         int parentNodeCount = size / order;
         List<HashTree.Node> parentLevel =
-                new ArrayList<HashTree.Node>(parentNodeCount);
+                new ArrayList<>(parentNodeCount);
 
         // Index for iterating through the nodes in this level
         int iterIndex = 0;
@@ -290,7 +290,7 @@ public final class HashTreeBuilder {
 
             // Construct the parent node
             List<HashTree.Node> childrenNodes =
-                    new ArrayList<HashTree.Node>(childrenNodeCount);
+                    new ArrayList<>(childrenNodeCount);
             HashTree.Node parentNode = new HashTree.Node();
 
             for ( int i = iterIndex, childIndex = 0;