adressing helix' comments to the DS-2659 PR

dspace-api/src/main/java/org/dspace/health/Check.java

@@ -4,8 +4,6 @@
  * tree and available online at
  *
  * http://www.dspace.org/license/
- *
- * by lindat-dev team
  */
 package org.dspace.health;
 
@@ -13,6 +11,7 @@ import org.apache.log4j.Logger;
 
 /**
  * Abstract check interface.
+ * @author LINDAT/CLARIN dev team
  */
 
 public abstract class Check {

dspace-api/src/main/java/org/dspace/health/ChecksumCheck.java

@@ -4,8 +4,6 @@
  * tree and available online at
  *
  * http://www.dspace.org/license/
- *
- * by lindat-dev team
  */
 package org.dspace.health;
 
@@ -18,6 +16,9 @@ import java.util.Calendar;
 import java.util.Date;
 import java.util.List;
 
+/**
+ * @author LINDAT/CLARIN dev team
+ */
 public class ChecksumCheck extends Check {
 
     @Override
@@ -27,9 +28,6 @@ public class ChecksumCheck extends Check {
         Date process_start = Calendar.getInstance().getTime();
         checker.setProcessStartDate(process_start);
         checker.setDispatcher(
-            // new LimitedCountDispatcher(new SimpleDispatcher(new
-            // BitstreamInfoDAO(), null, false), 1)
-            // loop through all files
             new SimpleDispatcher(new BitstreamInfoDAO(), process_start, false));
 
         md5_collector collector = new md5_collector();

dspace-api/src/main/java/org/dspace/health/Core.java

@@ -4,66 +4,82 @@
  * tree and available online at
  *
  * http://www.dspace.org/license/
- *
- * by lindat-dev team
  */
 package org.dspace.health;
 
 import org.apache.commons.io.FileUtils;
-import org.dspace.content.Community;
+import org.dspace.app.util.CollectionDropDown;
-import org.dspace.content.Item;
+import org.dspace.content.*;
-import org.dspace.content.ItemIterator;
+import org.dspace.content.Collection;
-import org.dspace.content.Metadatum;
 import org.dspace.core.Context;
 import org.dspace.storage.rdbms.DatabaseManager;
 import org.dspace.storage.rdbms.TableRow;
 import org.dspace.storage.rdbms.TableRowIterator;
 
 import java.sql.SQLException;
-import java.util.ArrayList;
+import java.util.*;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
 
+/**
+ * @author LINDAT/CLARIN dev team
+ */
 public class Core {
 
     // get info
     //
     public static String getCollectionSizesInfo() throws SQLException {
-        String ret = "";
+        final StringBuffer ret = new StringBuffer();
         List<TableRow> rows = sql(
-            "SELECT "
+                "SELECT" +
-                + "(SELECT text_value FROM metadatavalue "
+                        "(SELECT text_value FROM metadatavalue NATURAL JOIN metadatafieldregistry " +
-                + "WHERE metadata_field_id=64 AND resource_type_id=3 AND resource_id=col.collection_id) AS name, "
+                            "NATURAL JOIN metadataschemaregistry WHERE element='title' AND qualifier IS NULL AND short_id='dc'" +
-                + "SUM(bit.size_bytes) AS sum "
+                            " AND resource_type_id=3 AND resource_id=col.collection_id) AS name," +
-                + "FROM collection2item col, item2bundle item, bundle2bitstream bun, bitstream bit "
+                        "SUM(bit.size_bytes) AS sum," +
-                + "WHERE col.item_id=item.item_id AND item.bundle_id=bun.bundle_id AND bun.bitstream_id=bit.bitstream_id "
+                        " collection_id" +
-                + "GROUP BY col.collection_id;");
+                        " FROM collection2item col, item2bundle item, bundle2bitstream bun, bitstream bit" +
+                            " WHERE col.item_id=item.item_id AND item.bundle_id=bun.bundle_id AND bun.bitstream_id=bit.bitstream_id " +
+                        "GROUP BY col.collection_id;"
+        );
         long total_size = 0;
+        final Context context = new Context();
+        Collections.sort(rows, new Comparator<TableRow>() {
+            @Override
+            public int compare(TableRow o1, TableRow o2) {
+                try {
+                    return CollectionDropDown.collectionPath(Collection.find(context, o1.getIntColumn("collection_id"))).compareTo(
+                        CollectionDropDown.collectionPath(Collection.find(context, o2.getIntColumn("collection_id")))
+                    );
+                } catch (Exception e) {
+                    ret.append(e.getMessage());
+                }
+                return 0;
+            }
+        });
         for (TableRow row : rows) {
-            double size = row.getLongColumn("sum") / (1024. * 1024.);
+            double size = row.getLongColumn("sum");
             total_size += size;
-            ret += String.format(
+            Collection col = Collection.find(context, row.getIntColumn("collection_id"));
-                "\t%s:  %s\n", row.getStringColumn("name"), FileUtils.byteCountToDisplaySize((long)size));
+            ret.append(String.format(
+                    "\t%s:  %s\n", CollectionDropDown.collectionPath(col), FileUtils.byteCountToDisplaySize((long) size)));
         }
-        ret += String.format(
+	context.abort();
-            "Total size:              %s\n", FileUtils.byteCountToDisplaySize(total_size));
+        ret.append(String.format(
+                "Total size:              %s\n", FileUtils.byteCountToDisplaySize(total_size)));
 
-        ret += String.format(
+        ret.append(String.format(
-            "Resource without policy: %d\n", getBitstreamsWithoutPolicyCount());
+                "Resource without policy: %d\n", getBitstreamsWithoutPolicyCount()));
 
-        ret += String.format(
+        ret.append(String.format(
-            "Deleted bitstreams:      %d\n", getBitstreamsDeletedCount());
+                "Deleted bitstreams:      %d\n", getBitstreamsDeletedCount()));
 
         rows = getBitstreamOrphansRows();
         String list_str = "";
         for (TableRow row : rows) {
             list_str += String.format("%d, ", row.getIntColumn("bitstream_id"));
         }
-        ret += String.format(
+        ret.append(String.format(
-            "Orphan bitstreams:       %d [%s]\n", rows.size(), list_str);
+                "Orphan bitstreams:       %d [%s]\n", rows.size(), list_str));
 
-        return ret;
+        return ret.toString();
     }
 
     public static String getObjectSizesInfo() throws SQLException {
@@ -183,13 +199,14 @@ public class Core {
         Context c = new Context();
         TableRowIterator irows = DatabaseManager
             .query(c,
-                "SELECT eperson_group_id, "
+                "SELECT eperson_group_id," +
-                    + "(SELECT text_value FROM metadatavalue "
+                        "(SELECT text_value FROM metadatavalue NATURAL JOIN metadatafieldregistry" +
-                    + "WHERE metadata_field_id=64 AND resource_type_id=6 AND resource_id=eperson_group_id) AS name "
+                            " NATURAL JOIN metadataschemaregistry WHERE element='title'" +
-                    + "FROM epersongroup "
+                                " AND qualifier IS NULL AND short_id='dc' AND resource_type_id=6 AND resource_id=eperson_group_id) AS name "+
-                    + "WHERE eperson_group_id NOT IN (SELECT eperson_group_id FROM epersongroup2eperson)");
+                        "FROM epersongroup " +
+                        "WHERE eperson_group_id NOT IN (SELECT eperson_group_id FROM epersongroup2eperson)");
         for (TableRow row : irows.toList()) {
-            ret.add( row.getStringColumn("name") );
+            ret.add(String.format("id=%s;name=%s", row.getIntColumn("eperson_group_id"), row.getStringColumn("name") ));
         }
         c.complete();
         return ret;

dspace-api/src/main/java/org/dspace/health/EmbargoCheck.java

@@ -4,8 +4,6 @@
  * tree and available online at
  *
  * http://www.dspace.org/license/
- *
- * by lindat-dev team
  */
 package org.dspace.health;
 
@@ -19,6 +17,9 @@ import org.dspace.embargo.service.EmbargoService;
 import java.sql.SQLException;
 import java.util.Iterator;
 
+/**
+ * @author LINDAT/CLARIN dev team
+ */
 public class EmbargoCheck extends Check {
 
     private static final EmbargoService embargoService = EmbargoServiceFactory.getInstance().getEmbargoService();

dspace-api/src/main/java/org/dspace/health/InfoCheck.java

@@ -4,8 +4,6 @@
  * tree and available online at
  *
  * http://www.dspace.org/license/
- *
- * by lindat-dev team
  */
 package org.dspace.health;
 
@@ -16,6 +14,9 @@ import org.dspace.core.ConfigurationManager;
 import java.io.File;
 import java.util.Date;
 
+/**
+ * @author LINDAT/CLARIN dev team
+ */
 public class InfoCheck extends Check {
 
     @Override
@@ -27,9 +28,9 @@ public class InfoCheck extends Check {
         ).append("\n");
 
         sb.append("From - Till: ").append(
-            new SimpleDateFormat("MM/dd/yyyy").format(ri.from().getTime())
+            new SimpleDateFormat("yyyy-MM-dd").format(ri.from().getTime())
         ).append(" - ").append(
-            new SimpleDateFormat("MM/dd/yyyy").format(ri.till().getTime())
+            new SimpleDateFormat("yyyy-MM-dd").format(ri.till().getTime())
         ).append("\n");
 
         sb.append("Url: ").append(

dspace-api/src/main/java/org/dspace/health/ItemCheck.java

@@ -4,8 +4,6 @@
  * tree and available online at
  *
  * http://www.dspace.org/license/
- *
- * by lindat-dev team
  */
 package org.dspace.health;
 
@@ -15,6 +13,9 @@ import org.dspace.storage.rdbms.TableRow;
 import java.sql.SQLException;
 import java.util.Map;
 
+/**
+ * @author LINDAT/CLARIN dev team
+ */
 public class ItemCheck extends Check {
 
     @Override
@@ -23,7 +24,7 @@ public class ItemCheck extends Check {
         int tot_cnt = 0;
         try {
             for (Map.Entry<String, Integer> name_count : Core.getCommunities()) {
-                ret += String.format("Collection [%s]: %d\n",
+                ret += String.format("Community [%s]: %d\n",
                     name_count.getKey(), name_count.getValue());
                 tot_cnt += name_count.getValue();
             }

dspace-api/src/main/java/org/dspace/health/LogAnalyserCheck.java

@@ -4,8 +4,6 @@
  * tree and available online at
  *
  * http://www.dspace.org/license/
- *
- * by lindat-dev team
  */
 package org.dspace.health;
 
@@ -17,6 +15,9 @@ import java.text.SimpleDateFormat;
 import java.util.HashMap;
 import java.util.Map;
 
+/**
+ * @author LINDAT/CLARIN dev team
+ */
 public class LogAnalyserCheck extends Check {
 
     final static private String[][] interesting_fields = new String[][] {
@@ -56,7 +57,7 @@ public class LogAnalyserCheck extends Check {
                 sb.append( String.format("%-17s: %s\n", info[1], info_map.get(info[0])) );
             }
             sb.append( String.format("Items added since [%s] (db): %s\n",
-                new SimpleDateFormat("MM/dd/yyyy").format(ri.from().getTime()),
+                new SimpleDateFormat("yyyy-MM-dd").format(ri.from().getTime()),
                 LogAnalyser.getNumItems(c)));
 
             c.complete();

dspace-api/src/main/java/org/dspace/health/Report.java

@@ -4,15 +4,10 @@
  * tree and available online at
  *
  * http://www.dspace.org/license/
- *
- * by lindat-dev team
  */
 package org.dspace.health;
 
-import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.*;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
 import org.apache.commons.lang.exception.ExceptionUtils;
 import org.apache.log4j.Logger;
 import org.dspace.core.ConfigurationManager;
@@ -23,6 +18,9 @@ import java.text.SimpleDateFormat;
 import java.util.*;
 import java.util.Map.Entry;
 
+/**
+ * @author LINDAT/CLARIN dev team
+ */
 public class Report {
 
     private static Logger log = Logger.getLogger(Report.class);
@@ -147,7 +145,9 @@ public class Report {
             for (String check_name: checks().keySet()) {
                 checks_summary += String.format( "%d. %s\n", pos++, check_name );
             }
-            System.out.println( "Available checks:\n" + checks_summary );
+            HelpFormatter formatter = new HelpFormatter();
+            formatter.printHelp("dspace healthcheck", options);
+            System.out.println( "\nAvailable checks:\n" + checks_summary );
             return;
         }
 
@@ -198,6 +198,7 @@ public class Report {
                     email.send();
                 } catch (Exception e) {
                     log.fatal("Error sending email:", e);
+                    System.err.println("Error sending email:\n" + e.getMessage());
                     System.exit(1);
                 }
             }

dspace-api/src/main/java/org/dspace/health/ReportInfo.java

@@ -4,8 +4,6 @@
  * tree and available online at
  *
  * http://www.dspace.org/license/
- *
- * by lindat-dev team
  */
 package org.dspace.health;
 
@@ -18,6 +16,7 @@ import static java.util.Calendar.YEAR;
 
 /**
  * Information about a report run accessible by each check.
+ * @author LINDAT/CLARIN dev team
  */
 public class ReportInfo {
 

dspace-api/src/main/java/org/dspace/health/UserCheck.java

@@ -4,8 +4,6 @@
  * tree and available online at
  *
  * http://www.dspace.org/license/
- *
- * by lindat-dev team
  */
 package org.dspace.health;
 
@@ -19,6 +17,9 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
+/**
+ * @author LINDAT/CLARIN dev team
+ */
 public class UserCheck extends Check {
 
     @Override