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adressing helix' comments to the DS-2659 PR

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This commit is contained in:
Ondřej Košarko
2015-07-30 16:48:02 +02:00
parent d2f9fb5104
commit aed0741fec
10 changed files with 85 additions and 66 deletions
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3
dspace-api/src/main/java/org/dspace/health/Check.java
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@@ -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 {

8
dspace-api/src/main/java/org/dspace/health/ChecksumCheck.java
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@@ -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();

89
dspace-api/src/main/java/org/dspace/health/Core.java
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@@ -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.content.Item;
import org.dspace.content.ItemIterator;
import org.dspace.content.Metadatum;
import org.dspace.app.util.CollectionDropDown;
import org.dspace.content.*;
import org.dspace.content.Collection;
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.HashMap;
import java.util.List;
import java.util.Map;
import java.util.*;
/**
* @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 text_value FROM metadatavalue "
+ "WHERE metadata_field_id=64 AND resource_type_id=3 AND resource_id=col.collection_id) AS name, "
+ "SUM(bit.size_bytes) AS sum "
+ "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;");
"SELECT" +
"(SELECT text_value FROM metadatavalue NATURAL JOIN metadatafieldregistry " +
"NATURAL JOIN metadataschemaregistry WHERE element='title' AND qualifier IS NULL AND short_id='dc'" +
" AND resource_type_id=3 AND resource_id=col.collection_id) AS name," +
"SUM(bit.size_bytes) AS sum," +
" 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(
"\t%s: %s\n", row.getStringColumn("name"), FileUtils.byteCountToDisplaySize((long)size));
Collection col = Collection.find(context, row.getIntColumn("collection_id"));
ret.append(String.format(
"\t%s: %s\n", CollectionDropDown.collectionPath(col), FileUtils.byteCountToDisplaySize((long) size)));
}
ret += String.format(
"Total size: %s\n", FileUtils.byteCountToDisplaySize(total_size));
context.abort();
ret.append(String.format(
"Total size: %s\n", FileUtils.byteCountToDisplaySize(total_size)));
ret += String.format(
"Resource without policy: %d\n", getBitstreamsWithoutPolicyCount());
ret.append(String.format(
"Resource without policy: %d\n", getBitstreamsWithoutPolicyCount()));
ret += String.format(
"Deleted bitstreams: %d\n", getBitstreamsDeletedCount());
ret.append(String.format(
"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(
"Orphan bitstreams: %d [%s]\n", rows.size(), list_str);
ret.append(String.format(
"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 text_value FROM metadatavalue "
+ "WHERE metadata_field_id=64 AND resource_type_id=6 AND resource_id=eperson_group_id) AS name "
+ "FROM epersongroup "
+ "WHERE eperson_group_id NOT IN (SELECT eperson_group_id FROM epersongroup2eperson)");
"SELECT eperson_group_id," +
"(SELECT text_value FROM metadatavalue NATURAL JOIN metadatafieldregistry" +
" NATURAL JOIN metadataschemaregistry WHERE element='title'" +
" AND qualifier IS NULL AND short_id='dc' AND resource_type_id=6 AND resource_id=eperson_group_id) AS name "+
"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;

5
dspace-api/src/main/java/org/dspace/health/EmbargoCheck.java
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@@ -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();

9
dspace-api/src/main/java/org/dspace/health/InfoCheck.java
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@@ -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(

7
dspace-api/src/main/java/org/dspace/health/ItemCheck.java
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@@ -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();
}

7
dspace-api/src/main/java/org/dspace/health/LogAnalyserCheck.java
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@@ -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();

15
dspace-api/src/main/java/org/dspace/health/Report.java
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@@ -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.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.PosixParser;
import org.apache.commons.cli.*;
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);
}
}

3
dspace-api/src/main/java/org/dspace/health/ReportInfo.java
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@@ -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 {

5
dspace-api/src/main/java/org/dspace/health/UserCheck.java
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@@ -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