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Merge branch 'master' into DS-3908_Metadata_patch_support

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This commit is contained in:
Chris Wilper
2019-03-07 08:32:57 -05:00
parent 185766d8d2 d7ec9e537a
commit 229b9f1039
21 changed files with 630 additions and 259 deletions
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39
dspace-api/src/main/java/org/dspace/ctask/test/WorkflowReportTest.java Normal file
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@@ -0,0 +1,39 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.ctask.test;
import java.io.IOException;
import org.dspace.content.DSpaceObject;
import org.dspace.curate.AbstractCurationTask;
import org.dspace.curate.Curator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Curation task which simply reports its invocation without changing anything.
* Meant for testing.
*
* @author mhwood
*/
public class WorkflowReportTest
extends AbstractCurationTask {
private static final Logger LOG = LoggerFactory.getLogger(WorkflowReportTest.class);
@Override
public int perform(DSpaceObject dso)
throws IOException {
LOG.info("Class {} as task {} received 'perform' for object {}",
WorkflowReportTest.class.getSimpleName(), taskId, dso);
curator.report(String.format(
"Class %s as task %s received 'perform' for object %s%n",
WorkflowReportTest.class.getSimpleName(), taskId, dso));
return Curator.CURATE_SUCCESS;
}
}

21
dspace-api/src/main/java/org/dspace/curate/CurationCli.java
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@@ -9,6 +9,10 @@ package org.dspace.curate;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.PrintStream;
import java.io.Writer;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
@@ -18,6 +22,7 @@ import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.PosixParser;
import org.apache.commons.io.output.NullOutputStream;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.core.Context;
import org.dspace.core.factory.CoreServiceFactory;
@@ -57,7 +62,9 @@ public class CurationCli {
options.addOption("e", "eperson", true,
"email address of curating eperson");
options.addOption("r", "reporter", true,
"reporter to manage results - use '-' to report to console. If absent, no reporting");
"relative or absolute path to the desired report file. "
+ "Use '-' to report to console. "
+ "If absent, no reporting");
options.addOption("s", "scope", true,
"transaction scope to impose: use 'object', 'curation', or 'open'. If absent, 'open' " +
"applies");
@@ -165,9 +172,17 @@ public class CurationCli {
}
Curator curator = new Curator();
if (reporterName != null) {
curator.setReporter(reporterName);
OutputStream reporter;
if (null == reporterName) {
reporter = new NullOutputStream();
} else if ("-".equals(reporterName)) {
reporter = System.out;
} else {
reporter = new PrintStream(reporterName);
}
Writer reportWriter = new OutputStreamWriter(reporter);
curator.setReporter(reportWriter);
if (scope != null) {
Curator.TxScope txScope = Curator.TxScope.valueOf(scope.toUpperCase());
curator.setTransactionScope(txScope);

18
dspace-api/src/main/java/org/dspace/curate/Curator.java
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@@ -15,6 +15,7 @@ import java.util.Iterator;
import java.util.List;
import java.util.Map;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Collection;
import org.dspace.content.Community;
@@ -69,16 +70,12 @@ public class Curator {
INTERACTIVE, BATCH, ANY
}
;
// transaction scopes
public static enum TxScope {
OBJECT, CURATION, OPEN
}
;
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(Curator.class);
private static final Logger log = LogManager.getLogger();
protected static final ThreadLocal<Context> curationCtx = new ThreadLocal<>();
@@ -86,7 +83,7 @@ public class Curator {
protected Map<String, TaskRunner> trMap = new HashMap<>();
protected List<String> perfList = new ArrayList<>();
protected TaskQueue taskQ = null;
protected String reporter = null;
protected Appendable reporter = null;
protected Invoked iMode = null;
protected TaskResolver resolver = new TaskResolver();
protected TxScope txScope = TxScope.OPEN;
@@ -193,7 +190,7 @@ public class Curator {
* causes reporting to standard out.
* @return return self (Curator instance) with reporter set
*/
public Curator setReporter(String reporter) {
public Curator setReporter(Appendable reporter) {
this.reporter = reporter;
return this;
}
@@ -346,9 +343,10 @@ public class Curator {
* @param message the message to output to the reporting stream.
*/
public void report(String message) {
// Stub for now
if ("-".equals(reporter)) {
System.out.println(message);
try {
reporter.append(message);
} catch (IOException ex) {
log.error("Task reporting failure", ex);
}
}

88
dspace-api/src/main/java/org/dspace/curate/FileReporter.java Normal file
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@@ -0,0 +1,88 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.curate;
import java.io.FileWriter;
import java.io.IOException;
import java.io.Writer;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.GregorianCalendar;
import org.dspace.services.ConfigurationService;
import org.dspace.utils.DSpace;
/**
* Save a curation report to a unique file in the reports directory.
* Reports are named by the date and time of day, for example:
* "curation-20180916T113903045.report".
*
* @author mhwood
*/
public class FileReporter
implements Reporter {
private final Writer writer;
/**
* Open a writer to a file in a directory named by the configuration
* property {@code report.dir}, or in {@code [DSpace]/reports} if not
* configured.
*
* @throws IOException if there is a problem with the file path.
*/
public FileReporter()
throws IOException {
// Calculate a unique(?) file name.
Date now = GregorianCalendar.getInstance().getTime();
SimpleDateFormat sdf = new SimpleDateFormat("yyyyMMdd'T'hhmmssSSS");
String filename = String.format("curation-%s.report", sdf.format(now));
// Build a path to the directory which is to receive the file.
ConfigurationService cfg = new DSpace().getConfigurationService();
String reportDir = cfg.getProperty("report.dir");
Path reportPath;
if (null == reportDir) {
reportPath = Paths.get(cfg.getProperty("dspace.dir"),
"reports",
filename);
} else {
reportPath = Paths.get(reportDir, filename);
}
// Open the file.
writer = new FileWriter(reportPath.toFile());
}
@Override
public Appendable append(CharSequence cs)
throws IOException {
writer.append(cs);
return this;
}
@Override
public Appendable append(CharSequence cs, int i, int i1)
throws IOException {
writer.append(cs, i, i1);
return this;
}
@Override
public Appendable append(char c) throws IOException {
writer.append(c);
return this;
}
@Override
public void close() throws Exception {
writer.close();
}
}

62
dspace-api/src/main/java/org/dspace/curate/LogReporter.java Normal file
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@@ -0,0 +1,62 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.curate;
import java.io.IOException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Write curation report records through the logging framework.
* Whole lines (strings ending in '\n') are written to the log category "curation".
* Any partial line is flushed when the reporter is {@code close()}d.
*
* @author mhwood
*/
public class LogReporter
implements Reporter {
private static final Logger LOG = LoggerFactory.getLogger("curation");
private final StringBuilder buffer = new StringBuilder();
@Override
public Appendable append(CharSequence cs)
throws IOException {
for (int pos = 0; pos < cs.length(); pos++) {
char c = cs.charAt(pos);
if (c == '\n') {
LOG.info(buffer.toString());
buffer.delete(0, buffer.length()); // Clear the buffer
} else {
buffer.append(c);
}
}
return this;
}
@Override
public Appendable append(CharSequence cs, int i, int i1)
throws IOException {
return append(cs.subSequence(i, i1));
}
@Override
public Appendable append(char c)
throws IOException {
return append(String.valueOf(c));
}
@Override
public void close()
throws Exception {
if (buffer.length() > 0) {
LOG.info(buffer.toString());
}
}
}

18
dspace-api/src/main/java/org/dspace/curate/Reporter.java Normal file
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@@ -0,0 +1,18 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.curate;
/**
* A marker interface needed to make curation reporter classes into plugins.
*
* @author mhwood
*/
public interface Reporter
extends Appendable, AutoCloseable {
}

21
dspace-api/src/main/java/org/dspace/curate/WorkflowCuratorServiceImpl.java
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@@ -30,6 +30,8 @@ import org.dspace.content.Item;
import org.dspace.content.service.CollectionService;
import org.dspace.core.Context;
import org.dspace.core.LogManager;
import org.dspace.core.factory.CoreServiceFactory;
import org.dspace.core.service.PluginService;
import org.dspace.curate.service.WorkflowCuratorService;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.Group;
@@ -56,9 +58,10 @@ import org.springframework.beans.factory.annotation.Autowired;
public class WorkflowCuratorServiceImpl implements WorkflowCuratorService {
/**
* log4j logger
* Logging category
*/
private Logger log = org.apache.logging.log4j.LogManager.getLogger(WorkflowCuratorServiceImpl.class);
private static final Logger log
= org.apache.logging.log4j.LogManager.getLogger();
protected Map<String, TaskSet> tsMap = new HashMap<String, TaskSet>();
@@ -118,6 +121,7 @@ public class WorkflowCuratorServiceImpl implements WorkflowCuratorService {
Curator curator = new Curator();
// are we going to perform, or just put on queue?
if (step.queue != null) {
// The queue runner will call setReporter
for (Task task : step.tasks) {
curator.addTask(task.name);
}
@@ -125,7 +129,18 @@ public class WorkflowCuratorServiceImpl implements WorkflowCuratorService {
basicWorkflowItemService.update(c, wfi);
return false;
} else {
return curate(curator, c, wfi);
PluginService plugins = CoreServiceFactory.getInstance()
.getPluginService();
try (Reporter reporter
= (Reporter) plugins
.getSinglePlugin(Reporter.class);) {
curator.setReporter(reporter);
boolean status = curate(curator, c, wfi);
reporter.close();
return status;
} catch (Exception e) {
log.error("Failed to close report", e);
}
}
}
return true;

52
dspace-api/src/main/java/org/dspace/storage/rdbms/DatabaseUtils.java
View File

@@ -10,6 +10,7 @@ package org.dspace.storage.rdbms;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.sql.Connection;
import java.sql.DatabaseMetaData;
@@ -23,6 +24,7 @@ import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.sql.DataSource;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.core.Context;
@@ -88,7 +90,8 @@ public class DatabaseUtils {
// Usage checks
if (argv.length < 1) {
System.out.println("\nDatabase action argument is missing.");
System.out.println("Valid actions: 'test', 'info', 'migrate', 'repair', 'validate' or 'clean'");
System.out.println("Valid actions: 'test', 'info', 'migrate', 'repair', 'validate', " +
"'update-sequences' or 'clean'");
System.out.println("\nOr, type 'database help' for more information.\n");
System.exit(1);
}
@@ -328,24 +331,49 @@ public class DatabaseUtils {
e.printStackTrace();
System.exit(1);
}
} else if (argv[0].equalsIgnoreCase("update-sequences")) {
try (Connection connection = dataSource.getConnection()) {
String dbType = getDbType(connection);
String sqlfile = "org/dspace/storage/rdbms/sqlmigration/" + dbType +
"/update-sequences.sql";
InputStream sqlstream = DatabaseUtils.class.getClassLoader().getResourceAsStream(sqlfile);
if (sqlstream != null) {
String s = IOUtils.toString(sqlstream, "UTF-8");
if (!s.isEmpty()) {
System.out.println("Running " + sqlfile);
connection.createStatement().execute(s);
System.out.println("update-sequences complete");
} else {
System.err.println(sqlfile + " contains no SQL to execute");
}
} else {
System.err.println(sqlfile + " not found");
}
}
} else {
System.out.println("\nUsage: database [action]");
System.out.println("Valid actions: 'test', 'info', 'migrate', 'repair' or 'clean'");
System.out.println("Valid actions: 'test', 'info', 'migrate', 'repair', " +
"'update-sequences' or 'clean'");
System.out.println(
" - test = Performs a test connection to database to validate connection settings");
" - test = Performs a test connection to database to " +
"validate connection settings");
System.out.println(
" - info / status = Describe basic info/status about database, including validating the " +
"compatibility of this database");
System.out.println(" - migrate = Migrate the database to the latest version");
" - info / status = Describe basic info/status about database, including validating the " +
"compatibility of this database");
System.out.println(
" - repair = Attempt to repair any previously failed database migrations or checksum " +
"mismatches (via Flyway repair)");
" - migrate = Migrate the database to the latest version");
System.out.println(
" - validate = Validate current database's migration status (via Flyway validate), " +
"validating all migration checksums.");
" - repair = Attempt to repair any previously failed database " +
"migrations or checksum mismatches (via Flyway repair)");
System.out.println(
" - clean = DESTROY all data and tables in database (WARNING there is no going back!). " +
"Requires 'db.cleanDisabled=false' setting in config.");
" - validate = Validate current database's migration status (via Flyway validate), " +
"validating all migration checksums.");
System.out.println(
" - update-sequences = Update database sequences after running AIP ingest.");
System.out.println(
" - clean = DESTROY all data and tables in database " +
"(WARNING there is no going back!). " +
"Requires 'db.cleanDisabled=false' setting in config.");
System.out.println("");
System.exit(0);
}

79
dspace-api/src/main/resources/org/dspace/storage/rdbms/sqlmigration/oracle/update-sequences.sql Normal file
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@@ -0,0 +1,79 @@
--
-- The contents of this file are subject to the license and copyright
-- detailed in the LICENSE and NOTICE files at the root of the source
-- tree and available online at
--
-- http://www.dspace.org/license/
--
-- SQL code to update the ID (primary key) generating sequences, if some
-- import operation has set explicit IDs.
--
-- Sequences are used to generate IDs for new rows in the database. If a
-- bulk import operation, such as an SQL dump, specifies primary keys for
-- imported data explicitly, the sequences are out of sync and need updating.
-- This SQL code does just that.
--
-- This should rarely be needed; any bulk import should be performed using the
-- org.dspace.content API which is safe to use concurrently and in multiple
-- JVMs. The SQL code below will typically only be required after a direct
-- SQL data dump from a backup or somesuch.
-- The 'updateseq' procedure was derived from incseq.sql found at:
-- http://www.akadia.com/services/scripts/incseq.sql
DECLARE
PROCEDURE updateseq ( seq IN VARCHAR,
tbl IN VARCHAR,
attr IN VARCHAR,
cond IN VARCHAR DEFAULT '' ) IS
curr NUMBER := 0;
BEGIN
EXECUTE IMMEDIATE 'SELECT max(' || attr
|| ') FROM ' || tbl
|| ' ' || cond
INTO curr;
curr := curr + 1;
EXECUTE IMMEDIATE 'DROP SEQUENCE ' || seq;
EXECUTE IMMEDIATE 'CREATE SEQUENCE '
|| seq
|| ' START WITH '
|| NVL(curr, 1);
END updateseq;
BEGIN
updateseq('bitstreamformatregistry_seq', 'bitstreamformatregistry',
'bitstream_format_id');
updateseq('fileextension_seq', 'fileextension', 'file_extension_id');
updateseq('resourcepolicy_seq', 'resourcepolicy', 'policy_id');
updateseq('workspaceitem_seq', 'workspaceitem', 'workspace_item_id');
updateseq('workflowitem_seq', 'workflowitem', 'workflow_id');
updateseq('tasklistitem_seq', 'tasklistitem', 'tasklist_id');
updateseq('registrationdata_seq', 'registrationdata',
'registrationdata_id');
updateseq('subscription_seq', 'subscription', 'subscription_id');
updateseq('metadatafieldregistry_seq', 'metadatafieldregistry',
'metadata_field_id');
updateseq('metadatavalue_seq', 'metadatavalue', 'metadata_value_id');
updateseq('metadataschemaregistry_seq', 'metadataschemaregistry',
'metadata_schema_id');
updateseq('harvested_collection_seq', 'harvested_collection', 'id');
updateseq('harvested_item_seq', 'harvested_item', 'id');
updateseq('webapp_seq', 'webapp', 'webapp_id');
updateseq('requestitem_seq', 'requestitem', 'requestitem_id');
updateseq('handle_id_seq', 'handle', 'handle_id');
-- Handle Sequence is a special case. Since Handles minted by DSpace
-- use the 'handle_seq', we need to ensure the next assigned handle
-- will *always* be unique. So, 'handle_seq' always needs to be set
-- to the value of the *largest* handle suffix. That way when the
-- next handle is assigned, it will use the next largest number. This
-- query does the following:
-- For all 'handle' values which have a number in their suffix
-- (after '/'), find the maximum suffix value, convert it to a
-- number, and set the 'handle_seq' to start at the next value (see
-- updateseq above for more).
updateseq('handle_seq', 'handle',
q'{to_number(regexp_replace(handle, '.*/', ''), '999999999999')}',
q'{WHERE REGEXP_LIKE(handle, '^.*/[0123456789]*$')}');
END;

12
dspace-api/src/main/resources/org/dspace/storage/rdbms/sqlmigration/postgres/README.md
View File

@@ -17,4 +17,16 @@ not realize you manually ran one or more scripts.
Please see the Flyway Documentation for more information: http://flywaydb.org/
## Using the update-sequences.sql script
The `update-sequences.sql` script in this directory may still be used to update
your internal database counts if you feel they have gotten out of "sync". This
may sometimes occur after large restores of content (e.g. when using the DSpace
[AIP Backup and Restore](https://wiki.duraspace.org/display/DSDOC5x/AIP+Backup+and+Restore)
feature).
This `update-sequences.sql` script can be executed by running
"dspace database update-sequences". It will not harm your
database (or its contents) in any way. It just ensures all database counts (i.e.
sequences) are properly set to the next available value.

35
dspace/etc/postgres/update-sequences.sql → dspace-api/src/main/resources/org/dspace/storage/rdbms/sqlmigration/postgres/update-sequences.sql
View File

@@ -1,35 +1,10 @@
--
-- update-sequences.sql
-- The contents of this file are subject to the license and copyright
-- detailed in the LICENSE and NOTICE files at the root of the source
-- tree and available online at
--
-- http://www.dspace.org/license/
--
-- Copyright (c) 2002-2016, The DSpace Foundation. All rights reserved.
--
-- Redistribution and use in source and binary forms, with or without
-- modification, are permitted provided that the following conditions are
-- met:
--
-- - Redistributions of source code must retain the above copyright
-- notice, this list of conditions and the following disclaimer.
--
-- - Redistributions in binary form must reproduce the above copyright
-- notice, this list of conditions and the following disclaimer in the
-- documentation and/or other materials provided with the distribution.
--
-- Neither the name of the DSpace Foundation nor the names of its
-- contributors may be used to endorse or promote products derived from
-- this software without specific prior written permission.
--
-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-- ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-- A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-- HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
-- INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
-- BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
-- OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-- ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
-- TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
-- USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-- DAMAGE.
-- SQL code to update the ID (primary key) generating sequences, if some
-- import operation has set explicit IDs.

2
dspace-api/src/test/java/org/dspace/curate/CuratorTest.java
View File

@@ -58,7 +58,7 @@ public class CuratorTest
// Get and configure a Curator.
Curator instance = new Curator();
instance.setReporter("-"); // Send any report to standard out. FIXME when DS-3989 is merged
instance.setReporter(System.out); // Send any report to standard out.
instance.addTask(TASK_NAME);
// Configure the run.

202
dspace-api/src/test/java/org/dspace/curate/ITCurator.java Normal file
View File

@@ -0,0 +1,202 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.curate;
import java.io.IOException;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Pattern;
import org.dspace.AbstractUnitTest;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Community;
import org.dspace.content.DSpaceObject;
import org.dspace.content.Site;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.services.ConfigurationService;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Assert;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Drive the Curator and check results.
*
* @author mhwood
*/
public class ITCurator
extends AbstractUnitTest {
Logger LOG = LoggerFactory.getLogger(ITCurator.class);
public ITCurator() {
}
@BeforeClass
public static void setUpClass() {
}
@AfterClass
public static void tearDownClass() {
}
@Before
public void setUp() {
}
@After
public void tearDown() {
}
/**
* The report should contain contributions from all tasks and all curated objects.
*
* @throws SQLException passed through.
* @throws IOException passed through.
* @throws AuthorizeException passed through.
*/
@Test
public void testCurate_Reporting()
throws SQLException, IOException, AuthorizeException {
// Configure for testing.
ConfigurationService cfg = kernelImpl.getConfigurationService();
cfg.setProperty("plugin.named.org.dspace.curate.CurationTask",
Task1.class.getName() + " = task1");
cfg.addPropertyValue("plugin.named.org.dspace.curate.CurationTask",
Task2.class.getName() + " = task2");
// Create some structure.
context.turnOffAuthorisationSystem();
Site site = ContentServiceFactory.getInstance()
.getSiteService()
.findSite(context);
Community community = ContentServiceFactory.getInstance()
.getCommunityService()
.create(null, context);
// Run some tasks.
ListReporter reporter = new ListReporter();
Curator curator = new Curator();
curator.setReporter(reporter);
curator.addTask("task1");
curator.addTask("task2");
curator.curate(context, site);
// Validate the results.
List<String> report = reporter.getReport();
for (String aReport : report) {
LOG.info("Report: {}", aReport);
}
Pattern pattern;
pattern = Pattern.compile(String.format("task1.*%s", site.getHandle()));
Assert.assertTrue("A report should mention 'task1' and site's handle",
reportMatcher(report, pattern));
pattern = Pattern.compile(String.format("task1.*%s", community.getHandle()));
Assert.assertTrue("A report should mention 'task1' and the community's handle",
reportMatcher(report, pattern));
pattern = Pattern.compile(String.format("task2.*%s", site.getHandle()));
Assert.assertTrue("A report should mention 'task2' and the Site's handle",
reportMatcher(report, pattern));
pattern = Pattern.compile(String.format("task2.*%s", community.getHandle()));
Assert.assertTrue("A report should mention 'task2' and the community's handle",
reportMatcher(report, pattern));
}
/**
* Match a collection of strings against a regular expression.\
*
* @param reports strings to be searched.
* @param pattern expression to be matched.
* @return true if at least one string matches the expression.
*/
private boolean reportMatcher(List<String> reports, Pattern pattern) {
for (String aReport : reports) {
if (pattern.matcher(aReport).find()) {
return true;
}
}
return false;
}
/**
* Dummy curation task for testing. Reports how it was invoked.
*
* @author mhwood
*/
public static class Task1 extends AbstractCurationTask {
public Task1() {
}
@Override
public int perform(DSpaceObject dso)
throws IOException {
curator.report(String.format(
"Task1 received 'perform' on taskId '%s' for object '%s'%n",
taskId, dso.getHandle()));
return Curator.CURATE_SUCCESS;
}
}
/**
* Dummy curation task for testing. Reports how it was invoked.
*
* @author mhwood
*/
public static class Task2 extends AbstractCurationTask {
public Task2() {
}
@Override
public int perform(DSpaceObject dso) throws IOException {
curator.report(String.format(
"Task2 received 'perform' on taskId '%s' for object '%s'%n",
taskId, dso.getHandle()));
return Curator.CURATE_SUCCESS;
}
}
/**
* Absorb report strings into a sequential collection.
*/
class ListReporter
implements Appendable {
private final List<String> report = new ArrayList<>();
/**
* Get the content of the report accumulator.
* @return accumulated reports.
*/
List<String> getReport() {
return report;
}
@Override
public Appendable append(CharSequence cs)
throws IOException {
report.add(cs.toString());
return this;
}
@Override
public Appendable append(CharSequence cs, int i, int i1)
throws IOException {
throw new UnsupportedOperationException("Not supported yet.");
}
@Override
public Appendable append(char c)
throws IOException {
throw new UnsupportedOperationException("Not supported yet.");
}
}
}

20
dspace-services/src/main/java/org/dspace/servicemanager/config/DSpaceConfigurationService.java
View File

@@ -346,6 +346,26 @@ public final class DSpaceConfigurationService implements ConfigurationService {
}
}
@Override
public synchronized boolean addPropertyValue(String name, Object value) {
if (name == null) {
throw new IllegalArgumentException("name cannot be null for setting configuration");
}
if (value == null) {
throw new IllegalArgumentException("configuration value may not be null");
}
// If the value is a type of String, trim any leading/trailing spaces before saving it.
if (String.class.isInstance(value)) {
value = ((String) value).trim();
}
Configuration configuration = getConfiguration();
boolean isNew = !configuration.containsKey(name);
configuration.addProperty(name, value);
return isNew;
}
/* (non-Javadoc)
* @see org.dspace.services.ConfigurationService#setProperty(java.lang.String, java.lang.Object)
*/

10
dspace-services/src/main/java/org/dspace/services/ConfigurationService.java
View File

@@ -237,6 +237,16 @@ public interface ConfigurationService {
*/
public boolean hasProperty(String name);
/**
* Add a value to a configuration property.
*
* @param name the property name. May not be null.
* @param value the property value. May not be null.
* @return true if a new property was created.
* @throws IllegalArgumentException if the name or value is null.
*/
public boolean addPropertyValue(String name, Object value);
/**
* Set a configuration property (setting) in the system.
* Type is not important here since conversion happens automatically

12
dspace/config/modules/submission-curation.cfg
View File

@@ -2,7 +2,15 @@
#------------SUBMISSION CURATION CONFIGURATIONS-----------------#
#---------------------------------------------------------------#
# This file contains configuration properties solely relating #
# to the scheduling of curation tasks during submission. #
# to the scheduling of curation tasks during submission -- that #
# is: when tasks are attached to a workflow. #
#---------------------------------------------------------------#
# Scan for viruses
submission-curation.virus-scan = false
submission-curation.virus-scan = false
# Report serializer plugin, to capture submission task reports.
# Uncomment exactly one, or configure your own.
# FileReporter writes reports to ${report.dir}/curation-yyyyMMddThhmmssSSS.report
plugin.single.org.dspace.curate.Reporter = org.dspace.curate.FileReporter
# LogReporter writes report lines to the DSpace log.
#plugin.single.org.dspace.curate.Reporter = org.dspace.curate.LogReporter

33
dspace/etc/oracle/README.md
View File

@@ -1,33 +0,0 @@
# DSpace Database Now Upgrades Automatically
AS OF DSPACE 5, the DSpace database now upgrades itself AUTOMATICALLY.
Therefore, all `database_schema*.sql` files have been removed. Starting
with DSpace 4.x -> 5.0 upgrade, you will no longer need to manually run any
SQL scripts to upgrade your database.
Please see the [5.0 Upgrade Instructions](https://wiki.duraspace.org/display/DSDOC5x/Upgrading+DSpace)
for more information on upgrading to DSpace 5.
## More info on automatic database upgrades
As of DSpace 5.0, we now use [Flyway DB](http://flywaydb.org/) along with the
SQL scripts embedded in the `dspace-api.jar` to automatically keep your DSpace
database up-to-date. These scripts are now located in the source code at:
`[dspace-src]/dspace-api/src/main/resources/org/dspace/storage/rdbms/sqlmigration/oracle`
As Flyway automates the upgrade process, you should NEVER run these SQL scripts
manually. For more information, please see the `README.md` in the scripts directory.
## Using the update-sequences.sql script
The `update-sequences.sql` script in this directory may still be used to update
your internal database counts if you feel they have gotten out of "sync". This
may sometimes occur after large restores of content (e.g. when using the DSpace
[AIP Backup and Restore](https://wiki.duraspace.org/display/DSDOC5x/AIP+Backup+and+Restore)
feature).
This `update-sequences.sql` script can be run manually. It will not harm your
database (or its contents) in any way. It just ensures all database counts (i.e.
sequences) are properly set to the next available value.

75
dspace/etc/oracle/update-sequences.sql
View File

@@ -1,75 +0,0 @@
--
-- update-sequences.sql
--
-- Copyright (c) 2002-2016, The DSpace Foundation. All rights reserved.
--
-- Redistribution and use in source and binary forms, with or without
-- modification, are permitted provided that the following conditions are
-- met:
--
-- - Redistributions of source code must retain the above copyright
-- notice, this list of conditions and the following disclaimer.
--
-- - Redistributions in binary form must reproduce the above copyright
-- notice, this list of conditions and the following disclaimer in the
-- documentation and/or other materials provided with the distribution.
--
-- - Neither the name of the DSpace Foundation nor the names of its
-- contributors may be used to endorse or promote products derived from
-- this software without specific prior written permission.
--
-- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-- ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-- A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-- HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
-- INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
-- BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
-- OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-- ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
-- TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
-- USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-- DAMAGE.
-- SQL code to update the ID (primary key) generating sequences, if some
-- import operation has set explicit IDs.
--
-- Sequences are used to generate IDs for new rows in the database. If a
-- bulk import operation, such as an SQL dump, specifies primary keys for
-- imported data explicitly, the sequences are out of sync and need updating.
-- This SQL code does just that.
--
-- This should rarely be needed; any bulk import should be performed using the
-- org.dspace.content API which is safe to use concurrently and in multiple
-- JVMs. The SQL code below will typically only be required after a direct
-- SQL data dump from a backup or somesuch.
-- Depends on being run from sqlplus with incseq.sql in the current path
-- you can find incseq.sql at: http://www.akadia.com/services/scripts/incseq.sql
-- Here that script was renamed to updateseq.sql.
@updateseq.sql bitstreamformatregistry_seq bitstreamformatregistry bitstream_format_id ""
@updateseq.sql fileextension_seq fileextension file_extension_id ""
@updateseq.sql resourcepolicy_seq resourcepolicy policy_id ""
@updateseq.sql workspaceitem_seq workspaceitem workspace_item_id ""
@updateseq.sql workflowitem_seq workflowitem workflow_id ""
@updateseq.sql tasklistitem_seq tasklistitem tasklist_id ""
@updateseq.sql registrationdata_seq registrationdata registrationdata_id ""
@updateseq.sql subscription_seq subscription subscription_id ""
@updateseq.sql metadatafieldregistry_seq metadatafieldregistry metadata_field_id ""
@updateseq.sql metadatavalue_seq metadatavalue metadata_value_id ""
@updateseq.sql metadataschemaregistry_seq metadataschemaregistry metadata_schema_id ""
@updateseq.sql harvested_collection_seq harvested_collection id ""
@updateseq.sql harvested_item_seq harvested_item id ""
@updateseq.sql webapp_seq webapp webapp_id ""
@updateseq.sql requestitem_seq requestitem requestitem_id ""
@updateseq.sql handle_id_seq handle handle_id ""
-- Handle Sequence is a special case. Since Handles minted by DSpace use the 'handle_seq',
-- we need to ensure the next assigned handle will *always* be unique. So, 'handle_seq'
-- always needs to be set to the value of the *largest* handle suffix. That way when the
-- next handle is assigned, it will use the next largest number. This query does the following:
-- For all 'handle' values which have a number in their suffix (after '/'), find the maximum
-- suffix value, convert it to a number, and set the 'handle_seq' to start at the next value
-- (see updateseq.sql script for more)
@updateseq.sql handle_seq handle "to_number(regexp_replace(handle, '.*/', ''), '999999999999')" "WHERE REGEXP_LIKE(handle, '^.*/[0123456789]*$')"

30
dspace/etc/oracle/updateseq.sql
View File

@@ -1,30 +0,0 @@
-- #############################################################################################
--
-- %Purpose: Set a sequence to the max value of a given attribute
--
-- #############################################################################################
--
-- Paramters:
-- 1: sequence name
-- 2: table name
-- 3: attribute name
--
-- Sample usage:
-- @updateseq.sql my_sequence my_table my_attribute where-clause
--
--------------------------------------------------------------------------------
--
SET SERVEROUTPUT ON SIZE 1000000;
--
DECLARE
curr NUMBER := 0;
BEGIN
SELECT max(&3) INTO curr FROM &2 &4;
curr := curr + 1;
EXECUTE IMMEDIATE 'DROP SEQUENCE &1';
EXECUTE IMMEDIATE 'CREATE SEQUENCE &1 START WITH ' || NVL(curr,1);
END;
/

33
dspace/etc/postgres/README.md
View File

@@ -1,33 +0,0 @@
# DSpace Database Now Upgrades Automatically
AS OF DSPACE 5, the DSpace database now upgrades itself AUTOMATICALLY.
Therefore, all `database_schema*.sql` files have been removed. Starting
with DSpace 4.x -> 5.0 upgrade, you will no longer need to manually run any
SQL scripts to upgrade your database.
Please see the [5.0 Upgrade Instructions](https://wiki.duraspace.org/display/DSDOC5x/Upgrading+DSpace)
for more information on upgrading to DSpace 5.
## More info on automatic database upgrades
As of DSpace 5.0, we now use [Flyway DB](http://flywaydb.org/) along with the
SQL scripts embedded in the `dspace-api.jar` to automatically keep your DSpace
database up-to-date. These scripts are now located in the source code at:
`[dspace-src]/dspace-api/src/main/resources/org/dspace/storage/rdbms/sqlmigration/postgres`
As Flyway automates the upgrade process, you should NEVER run these SQL scripts
manually. For more information, please see the `README.md` in the scripts directory.
## Using the update-sequences.sql script
The `update-sequences.sql` script in this directory may still be used to update
your internal database counts if you feel they have gotten out of "sync". This
may sometimes occur after large restores of content (e.g. when using the DSpace
[AIP Backup and Restore](https://wiki.duraspace.org/display/DSDOC5x/AIP+Backup+and+Restore)
feature).
This `update-sequences.sql` script can be run manually. It will not harm your
database (or its contents) in any way. It just ensures all database counts (i.e.
sequences) are properly set to the next available value.

27
dspace/src/main/config/build.xml
View File

@@ -569,16 +569,6 @@ Common usage:
<fileset dir="lib" />
</copy>
<move todir="${dspace.dir}/etc.bak-${build.date}" failonerror="no">
<fileset dir="${dspace.dir}/etc">
<include name="**/*" />
</fileset>
</move>
<copy todir="${dspace.dir}/etc" preservelastmodified="true">
<fileset dir="etc" />
</copy>
<copy todir="${dspace.dir}/solr" preservelastmodified="true">
<fileset dir="solr"/>
</copy>
@@ -593,10 +583,6 @@ Common usage:
${dspace.dir}/lib.bak-${build.date}
${dspace.dir}/etc was backed up to
${dspace.dir}/etc.bak-${build.date}
Please review these directories and delete if no longer needed.
====================================================================
</echo>
@@ -728,8 +714,6 @@ Common usage:
<mkdir dir="${dspace.dir}/lib" />
<mkdir dir="${dspace.dir}/etc" />
<mkdir dir="${dspace.dir}/webapps" />
<mkdir dir="${dspace.dir}/triplestore" />
@@ -821,17 +805,6 @@ Common usage:
<fileset dir="lib" />
</copy>
<!-- NB: no regular use is made of etc/ files in an installed
- system, so this step is 'deprecated', and will eventually
- be removed. -->
<delete failonerror="no">
<fileset dir="${dspace.dir}/etc" includes="**/*" />
</delete>
<copy todir="${dspace.dir}/etc" preservelastmodified="true">
<fileset dir="etc" />
</copy>
<copy todir="${dspace.dir}/solr" preservelastmodified="true">
<fileset dir="solr" />
</copy>