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Code Issues Packages Projects Releases Wiki Activity

DS-3850 Create new submissions from files or identifiers

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This commit is contained in:
Luigi Andrea Pascarelli
2018-08-24 20:22:12 +02:00
committed by Andrea Bollini
parent 66b89a786d
commit c0066d2a2f
32 changed files with 973 additions and 131 deletions
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11
dspace-api/src/main/java/org/dspace/content/WorkspaceItemServiceImpl.java
View File

@@ -147,6 +147,12 @@ public class WorkspaceItemServiceImpl implements WorkspaceItemService {
return workspaceItemDAO.findByEPerson(context, ep);
}
@Override
public List<WorkspaceItem> findByEPerson(Context context, EPerson ep, Integer limit, Integer offset)
throws SQLException {
return workspaceItemDAO.findByEPerson(context, ep, limit, offset);
}
@Override
public List<WorkspaceItem> findByCollection(Context context, Collection collection) throws SQLException {
return workspaceItemDAO.findByCollection(context, collection);
@@ -231,6 +237,11 @@ public class WorkspaceItemServiceImpl implements WorkspaceItemService {
return workspaceItemDAO.countRows(context);
}
@Override
public int countByEPerson(Context context, EPerson ep) throws SQLException {
return workspaceItemDAO.countRows(context, ep);
}
@Override
public List<Map.Entry<Integer, Long>> getStageReachedCounts(Context context) throws SQLException {
return workspaceItemDAO.getStageReachedCounts(context);

6
dspace-api/src/main/java/org/dspace/content/dao/WorkspaceItemDAO.java
View File

@@ -30,6 +30,9 @@ public interface WorkspaceItemDAO extends GenericDAO<WorkspaceItem> {
public List<WorkspaceItem> findByEPerson(Context context, EPerson ep) throws SQLException;
public List<WorkspaceItem> findByEPerson(Context context, EPerson ep, Integer limit, Integer offset)
throws SQLException;
public List<WorkspaceItem> findByCollection(Context context, Collection c) throws SQLException;
public WorkspaceItem findByItem(Context context, Item i) throws SQLException;
@@ -45,4 +48,7 @@ public interface WorkspaceItemDAO extends GenericDAO<WorkspaceItem> {
int countRows(Context context) throws SQLException;
List<Map.Entry<Integer, Long>> getStageReachedCounts(Context context) throws SQLException;
public int countRows(Context context, EPerson ep) throws SQLException;
}

22
dspace-api/src/main/java/org/dspace/content/dao/impl/WorkspaceItemDAOImpl.java
View File

@@ -46,6 +46,20 @@ public class WorkspaceItemDAOImpl extends AbstractHibernateDAO<WorkspaceItem> im
return list(query);
}
@Override
public List<WorkspaceItem> findByEPerson(Context context, EPerson ep, Integer limit, Integer offset)
throws SQLException {
Criteria criteria = createCriteria(context, WorkspaceItem.class, "wi");
criteria.addOrder(Order.asc("workspaceItemId"));
criteria.createAlias("wi.item", "item");
criteria.createAlias("item.submitter", "submitter");
criteria.add(Restrictions.eq("submitter.id", ep.getID()));
criteria.setFirstResult(offset);
criteria.setMaxResults(limit);
return list(criteria);
}
@Override
public List<WorkspaceItem> findByCollection(Context context, Collection c) throws SQLException {
Criteria criteria = createCriteria(context, WorkspaceItem.class);
@@ -99,6 +113,14 @@ public class WorkspaceItemDAOImpl extends AbstractHibernateDAO<WorkspaceItem> im
return count(createQuery(context, "SELECT count(*) from WorkspaceItem"));
}
@Override
public int countRows(Context context, EPerson ep) throws SQLException {
Query query = createQuery(context,
"SELECT count(*) from WorkspaceItem ws where ws.item.submitter = :submitter");
query.setParameter("submitter", ep);
return count(query);
}
@Override
@SuppressWarnings("unchecked")
public List<Map.Entry<Integer, Long>> getStageReachedCounts(Context context) throws SQLException {

19
dspace-api/src/main/java/org/dspace/content/service/WorkspaceItemService.java
View File

@@ -72,6 +72,21 @@ public interface WorkspaceItemService extends InProgressSubmissionService<Worksp
public List<WorkspaceItem> findByEPerson(Context context, EPerson ep)
throws SQLException;
/**
* Get a page of workspace items for a particular e-person. These are ordered by
* workspace item ID, since this should likely keep them in the order in
* which they were created.
*
* @param context the context object
* @param ep the eperson
* @param limit the max number of workspaceitems to return
* @param offset the offset
* @return the corresponding workspace items
* @throws SQLException if database error
*/
public List<WorkspaceItem> findByEPerson(Context context, EPerson ep, Integer limit, Integer offset)
throws SQLException;
/**
* Get all workspace items for a particular collection.
*
@@ -146,4 +161,8 @@ public interface WorkspaceItemService extends InProgressSubmissionService<Worksp
* @throws SQLException if database error
*/
List<Map.Entry<Integer, Long>> getStageReachedCounts(Context context) throws SQLException;
public int countByEPerson(Context context, EPerson ep) throws SQLException;
}

15
dspace-api/src/main/java/org/dspace/submit/AbstractProcessingStep.java
View File

@@ -7,10 +7,12 @@
*/
package org.dspace.submit;
import org.dspace.app.itemimport.BTEBatchImportService;
import org.dspace.authorize.factory.AuthorizeServiceFactory;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.content.InProgressSubmission;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.content.service.BitstreamFormatService;
import org.dspace.content.service.BitstreamService;
import org.dspace.content.service.BundleService;
import org.dspace.content.service.CollectionService;
@@ -20,24 +22,27 @@ import org.dspace.content.service.WorkspaceItemService;
import org.dspace.core.Context;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.dspace.services.model.Request;
/**
* Abstract processing class for DSpace Submission Steps. This defines the base
* methods which are required for any Step processing class.
* Abstract processing class for DSpace Submission Steps. This defines the base methods which are required for any Step
* processing class.
*/
public abstract class AbstractProcessingStep {
protected AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
protected BitstreamService bitstreamService = ContentServiceFactory.getInstance().getBitstreamService();
protected BitstreamFormatService bitstreamFormatService = ContentServiceFactory.getInstance()
.getBitstreamFormatService();
protected BundleService bundleService = ContentServiceFactory.getInstance().getBundleService();
protected CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
protected ItemService itemService = ContentServiceFactory.getInstance().getItemService();
protected MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance().getMetadataFieldService();
protected ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
protected WorkspaceItemService workspaceItemService = ContentServiceFactory.getInstance().getWorkspaceItemService();
protected BTEBatchImportService bteBatchImportService = DSpaceServicesFactory.getInstance().getServiceManager()
.getServiceByName("org.dspace.app.itemimport" + ".BTEBatchImportService", BTEBatchImportService.class);
public abstract void doProcessing(Context context, Request req, InProgressSubmission wsi);
public abstract void doPreProcessing(Context context, InProgressSubmission wsi);
public abstract void doPostProcessing(Context context, Request obj, InProgressSubmission wsi);
public abstract void doPostProcessing(Context context, InProgressSubmission wsi);
}

50
dspace-api/src/main/java/org/dspace/submit/extraction/MetadataExtractor.java Normal file
View File

@@ -0,0 +1,50 @@
/**
* 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.submit.extraction;
import java.util.List;
import gr.ekt.bte.dataloader.FileDataLoader;
import org.dspace.services.ConfigurationService;
/**
* @author Luigi Andrea Pascarelli (luigiandrea.pascarelli at 4science.it)
*/
public class MetadataExtractor {
private List<String> extensions;
private FileDataLoader dataLoader;
private ConfigurationService configurationService;
public List<String> getExtensions() {
return extensions;
}
public void setExtensions(List<String> mime) {
this.extensions = mime;
}
public FileDataLoader getDataLoader() {
return dataLoader;
}
public void setDataLoader(FileDataLoader dataLoader) {
this.dataLoader = dataLoader;
}
public ConfigurationService getConfigurationService() {
return configurationService;
}
public void setConfigurationService(ConfigurationService configurationService) {
this.configurationService = configurationService;
}
}

47
dspace-api/src/main/java/org/dspace/submit/listener/MetadataListener.java Normal file
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@@ -0,0 +1,47 @@
/**
* 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.submit.listener;
import java.util.Map;
import gr.ekt.bte.core.DataLoader;
import org.dspace.services.ConfigurationService;
public class MetadataListener {
private Map<String, String> metadata;
private ConfigurationService configurationService;
private Map<String, DataLoader> dataloadersMap;
public ConfigurationService getConfigurationService() {
return configurationService;
}
public void setConfigurationService(ConfigurationService configurationService) {
this.configurationService = configurationService;
}
public Map<String, String> getMetadata() {
return metadata;
}
public void setMetadata(Map<String, String> metadata) {
this.metadata = metadata;
}
public Map<String, DataLoader> getDataloadersMap() {
return dataloadersMap;
}
public void setDataloadersMap(Map<String, DataLoader> dataloadersMap) {
this.dataloadersMap = dataloadersMap;
}
}

5
dspace-api/src/main/java/org/dspace/submit/step/AccessStep.java
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@@ -10,7 +10,6 @@ package org.dspace.submit.step;
import org.apache.log4j.Logger;
import org.dspace.content.InProgressSubmission;
import org.dspace.core.Context;
import org.dspace.services.model.Request;
import org.dspace.submit.AbstractProcessingStep;
@@ -21,13 +20,13 @@ public class AccessStep extends AbstractProcessingStep {
private static Logger log = Logger.getLogger(AccessStep.class);
@Override
public void doProcessing(Context context, Request req, InProgressSubmission wsi) {
public void doPreProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}
@Override
public void doPostProcessing(Context context, Request obj, InProgressSubmission wsi) {
public void doPostProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}

7
dspace-api/src/main/java/org/dspace/submit/step/CCLicenseStep.java
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@@ -12,7 +12,6 @@ import org.dspace.content.InProgressSubmission;
import org.dspace.core.Context;
import org.dspace.license.factory.LicenseServiceFactory;
import org.dspace.license.service.CreativeCommonsService;
import org.dspace.services.model.Request;
import org.dspace.submit.AbstractProcessingStep;
public class CCLicenseStep extends AbstractProcessingStep {
@@ -25,15 +24,15 @@ public class CCLicenseStep extends AbstractProcessingStep {
.getCreativeCommonsService();
@Override
public void doProcessing(Context context, Request req, InProgressSubmission wsi) {
public void doPreProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}
@Override
public void doPostProcessing(Context context, Request obj, InProgressSubmission wsi) {
public void doPostProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}
}
}

5
dspace-api/src/main/java/org/dspace/submit/step/CompleteStep.java
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@@ -10,7 +10,6 @@ package org.dspace.submit.step;
import org.apache.log4j.Logger;
import org.dspace.content.InProgressSubmission;
import org.dspace.core.Context;
import org.dspace.services.model.Request;
import org.dspace.submit.AbstractProcessingStep;
public class CompleteStep extends AbstractProcessingStep {
@@ -20,13 +19,13 @@ public class CompleteStep extends AbstractProcessingStep {
private static Logger log = Logger.getLogger(CompleteStep.class);
@Override
public void doProcessing(Context context, Request req, InProgressSubmission wsi) {
public void doPreProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}
@Override
public void doPostProcessing(Context context, Request obj, InProgressSubmission wsi) {
public void doPostProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}

24
dspace-api/src/main/java/org/dspace/submit/step/DescribeStep.java
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@@ -8,30 +8,14 @@
package org.dspace.submit.step;
import org.apache.log4j.Logger;
import org.dspace.content.InProgressSubmission;
import org.dspace.core.Context;
import org.dspace.services.model.Request;
import org.dspace.submit.AbstractProcessingStep;
public class DescribeStep extends AbstractProcessingStep {
/**
* @author Luigi Andrea Pascarelli (luigiandrea.pascarelli at 4science.it)
*/
public class DescribeStep extends MetadataStep {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(DescribeStep.class);
@Override
public void doProcessing(Context context, Request req, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}
@Override
public void doPostProcessing(Context context, Request obj, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}
}

22
dspace-api/src/main/java/org/dspace/submit/step/ExtractionStep.java Normal file
View File

@@ -0,0 +1,22 @@
/**
* 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.submit.step;
import org.apache.log4j.Logger;
/**
* @author Luigi Andrea Pascarelli (luigiandrea.pascarelli at 4science.it)
*/
public class ExtractionStep extends MetadataStep {
/**
* log4j logger
*/
private static Logger log = Logger
.getLogger(ExtractionStep.class);
}

5
dspace-api/src/main/java/org/dspace/submit/step/InitialQuestionsStep.java
View File

@@ -9,19 +9,18 @@ package org.dspace.submit.step;
import org.dspace.content.InProgressSubmission;
import org.dspace.core.Context;
import org.dspace.services.model.Request;
import org.dspace.submit.AbstractProcessingStep;
public class InitialQuestionsStep extends AbstractProcessingStep {
@Override
public void doProcessing(Context context, Request req, InProgressSubmission wsi) {
public void doPreProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}
@Override
public void doPostProcessing(Context context, Request obj, InProgressSubmission wsi) {
public void doPostProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}

5
dspace-api/src/main/java/org/dspace/submit/step/LicenseStep.java
View File

@@ -10,7 +10,6 @@ package org.dspace.submit.step;
import org.apache.log4j.Logger;
import org.dspace.content.InProgressSubmission;
import org.dspace.core.Context;
import org.dspace.services.model.Request;
import org.dspace.submit.AbstractProcessingStep;
public class LicenseStep extends AbstractProcessingStep {
@@ -21,13 +20,13 @@ public class LicenseStep extends AbstractProcessingStep {
private static Logger log = Logger.getLogger(LicenseStep.class);
@Override
public void doProcessing(Context context, Request req, InProgressSubmission wsi) {
public void doPreProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}
@Override
public void doPostProcessing(Context context, Request obj, InProgressSubmission wsi) {
public void doPostProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}

196
dspace-api/src/main/java/org/dspace/submit/step/MetadataStep.java Normal file
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@@ -0,0 +1,196 @@
/**
* 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.submit.step;
import java.io.IOException;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import gr.ekt.bte.core.DataLoader;
import gr.ekt.bte.core.Record;
import gr.ekt.bte.core.Value;
import org.apache.commons.lang.StringUtils;
import org.apache.http.HttpException;
import org.apache.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.InProgressSubmission;
import org.dspace.content.Item;
import org.dspace.content.MetadataValue;
import org.dspace.core.Context;
import org.dspace.core.Utils;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.dspace.submit.AbstractProcessingStep;
import org.dspace.submit.listener.MetadataListener;
import org.dspace.submit.lookup.SubmissionLookupDataLoader;
/**
* @author Luigi Andrea Pascarelli (luigiandrea.pascarelli at 4science.it)
*/
public class MetadataStep extends AbstractProcessingStep {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(MetadataStep.class);
protected List<MetadataListener> listeners = DSpaceServicesFactory.getInstance().getServiceManager()
.getServicesByType(MetadataListener.class);
protected Map<String, List<MetadataValue>> metadataMap = new HashMap<String, List<MetadataValue>>();
private Map<String, Set<String>> results = new HashMap<String, Set<String>>();
private Map<String, String> mappingIdentifier = new HashMap<String, String>();
@Override
public void doPreProcessing(Context context, InProgressSubmission wsi) {
for (MetadataListener listener : listeners) {
for (String metadata : listener.getMetadata().keySet()) {
String[] tokenized = Utils.tokenize(metadata);
List<MetadataValue> mm = itemService.getMetadata(wsi.getItem(), tokenized[0], tokenized[1],
tokenized[2], Item.ANY);
if (mm != null && !mm.isEmpty()) {
metadataMap.put(metadata, mm);
} else {
metadataMap.put(metadata, new ArrayList<MetadataValue>());
}
mappingIdentifier.put(metadata, listener.getMetadata().get(metadata));
}
}
}
@Override
public void doPostProcessing(Context context, InProgressSubmission wsi) {
external:
for (String metadata : metadataMap.keySet()) {
String[] tokenized = Utils.tokenize(metadata);
List<MetadataValue> currents = itemService.getMetadata(wsi.getItem(), tokenized[0], tokenized[1],
tokenized[2], Item.ANY);
if (currents != null && !currents.isEmpty()) {
List<MetadataValue> olds = metadataMap.get(metadata);
if (olds.isEmpty()) {
process(context, metadata, currents);
continue external;
}
internal:
for (MetadataValue current : currents) {
boolean found = false;
for (MetadataValue old : olds) {
if (old.getValue().equals(current.getValue())) {
found = true;
}
}
if (!found) {
process(context, metadata, current);
}
}
}
}
if (!results.isEmpty()) {
for (MetadataListener listener : listeners) {
for (DataLoader dataLoader : listener.getDataloadersMap().values()) {
SubmissionLookupDataLoader submissionLookupDataLoader = (SubmissionLookupDataLoader) dataLoader;
try {
List<Record> recordSet = submissionLookupDataLoader.getByIdentifier(context, results);
List<Record> resultSet = convertFields(recordSet, bteBatchImportService.getOutputMap());
enrichItem(context, resultSet, wsi.getItem());
} catch (HttpException | IOException | SQLException | AuthorizeException e) {
log.error(e.getMessage(), e);
}
}
}
}
}
protected void enrichItem(Context context, List<Record> rset, Item item) throws SQLException, AuthorizeException {
for (Record record : rset) {
for (String field : record.getFields()) {
try {
String[] tfield = Utils.tokenize(field);
List<MetadataValue> mdvs = itemService
.getMetadata(item, tfield[0], tfield[1], tfield[2], Item.ANY);
if (mdvs == null || mdvs.isEmpty()) {
for (Value value : record.getValues(field)) {
itemService.addMetadata(context, item, tfield[0], tfield[1], tfield[2], null,
value.getAsString());
}
} else {
external:
for (Value value : record.getValues(field)) {
boolean found = false;
for (MetadataValue mdv : mdvs) {
if (mdv.getValue().equals(value.getAsString())) {
found = true;
continue external;
}
}
if (!found) {
itemService.addMetadata(context, item, tfield[0], tfield[1], tfield[2], null,
value.getAsString());
}
}
}
} catch (SQLException e) {
log.error(e.getMessage(), e);
}
}
}
itemService.update(context, item);
}
private void process(Context context, String metadata, List<MetadataValue> currents) {
for (MetadataValue current : currents) {
process(context, metadata, current);
}
}
private void process(Context context, String metadata, MetadataValue current) {
String key = mappingIdentifier.get(metadata);
Set<String> identifiers = null;
if (!results.containsKey(key)) {
identifiers = new HashSet<String>();
} else {
identifiers = results.get(key);
}
identifiers.add(current.getValue());
results.put(key, identifiers);
}
public List<Record> convertFields(List<Record> recordSet, Map<String, String> fieldMap) {
List<Record> result = new ArrayList<Record>();
for (Record publication : recordSet) {
for (String fieldName : fieldMap.keySet()) {
String md = null;
if (fieldMap != null) {
md = fieldMap.get(fieldName);
}
if (StringUtils.isBlank(md)) {
continue;
} else {
md = md.trim();
}
if (publication.isMutable()) {
List<Value> values = publication.getValues(md);
publication.makeMutable().removeField(md);
publication.makeMutable().addField(fieldName, values);
}
}
result.add(publication);
}
return result;
}
}

5
dspace-api/src/main/java/org/dspace/submit/step/SampleStep.java
View File

@@ -9,19 +9,18 @@ package org.dspace.submit.step;
import org.dspace.content.InProgressSubmission;
import org.dspace.core.Context;
import org.dspace.services.model.Request;
import org.dspace.submit.AbstractProcessingStep;
public class SampleStep extends AbstractProcessingStep {
@Override
public void doProcessing(Context context, Request req, InProgressSubmission wsi) {
public void doPreProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}
@Override
public void doPostProcessing(Context context, Request obj, InProgressSubmission wsi) {
public void doPostProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}

5
dspace-api/src/main/java/org/dspace/submit/step/SelectCollectionStep.java
View File

@@ -10,7 +10,6 @@ package org.dspace.submit.step;
import org.apache.log4j.Logger;
import org.dspace.content.InProgressSubmission;
import org.dspace.core.Context;
import org.dspace.services.model.Request;
import org.dspace.submit.AbstractProcessingStep;
public class SelectCollectionStep extends AbstractProcessingStep {
@@ -18,13 +17,13 @@ public class SelectCollectionStep extends AbstractProcessingStep {
private static final Logger log = Logger.getLogger(SelectCollectionStep.class);
@Override
public void doProcessing(Context context, Request req, InProgressSubmission wsi) {
public void doPreProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}
@Override
public void doPostProcessing(Context context, Request obj, InProgressSubmission wsi) {
public void doPostProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}

7
dspace-api/src/main/java/org/dspace/submit/step/StartSubmissionLookupStep.java
View File

@@ -10,7 +10,6 @@ package org.dspace.submit.step;
import org.apache.log4j.Logger;
import org.dspace.content.InProgressSubmission;
import org.dspace.core.Context;
import org.dspace.services.model.Request;
import org.dspace.submit.AbstractProcessingStep;
public class StartSubmissionLookupStep extends AbstractProcessingStep {
@@ -21,14 +20,14 @@ public class StartSubmissionLookupStep extends AbstractProcessingStep {
.getLogger(StartSubmissionLookupStep.class);
@Override
public void doProcessing(Context context, Request req, InProgressSubmission wsi) {
public void doPreProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}
@Override
public void doPostProcessing(Context context, Request obj, InProgressSubmission wsi) {
public void doPostProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}
}
}

5
dspace-api/src/main/java/org/dspace/submit/step/UploadStep.java
View File

@@ -10,7 +10,6 @@ package org.dspace.submit.step;
import org.apache.log4j.Logger;
import org.dspace.content.InProgressSubmission;
import org.dspace.core.Context;
import org.dspace.services.model.Request;
import org.dspace.submit.AbstractProcessingStep;
public class UploadStep extends AbstractProcessingStep {
@@ -20,13 +19,13 @@ public class UploadStep extends AbstractProcessingStep {
private static final Logger log = Logger.getLogger(UploadStep.class);
@Override
public void doProcessing(Context context, Request req, InProgressSubmission wsi) {
public void doPreProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}
@Override
public void doPostProcessing(Context context, Request obj, InProgressSubmission wsi) {
public void doPostProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}

5
dspace-api/src/main/java/org/dspace/submit/step/VerifyStep.java
View File

@@ -9,19 +9,18 @@ package org.dspace.submit.step;
import org.dspace.content.InProgressSubmission;
import org.dspace.core.Context;
import org.dspace.services.model.Request;
import org.dspace.submit.AbstractProcessingStep;
public class VerifyStep extends AbstractProcessingStep {
@Override
public void doProcessing(Context context, Request req, InProgressSubmission wsi) {
public void doPreProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}
@Override
public void doPostProcessing(Context context, Request obj, InProgressSubmission wsi) {
public void doPostProcessing(Context context, InProgressSubmission wsi) {
// TODO Auto-generated method stub
}

19
dspace-spring-rest/src/main/java/org/dspace/app/rest/converter/WorkspaceItemConverter.java
View File

@@ -24,7 +24,6 @@ import org.dspace.app.util.SubmissionStepConfig;
import org.dspace.content.Collection;
import org.dspace.content.Item;
import org.dspace.eperson.EPerson;
import org.dspace.submit.AbstractProcessingStep;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
@@ -103,22 +102,20 @@ public class WorkspaceItemConverter
Object stepInstance = stepClass.newInstance();
if (stepInstance instanceof AbstractProcessingStep) {
if (stepInstance instanceof AbstractRestProcessingStep) {
// load the interface for this step
AbstractRestProcessingStep stepProcessing = (AbstractRestProcessingStep) stepClass
.newInstance();
AbstractRestProcessingStep stepProcessing =
(AbstractRestProcessingStep) stepClass.newInstance();
for (ErrorRest error : stepProcessing.validate(submissionService, obj, stepConfig)) {
addError(witem.getErrors(), error);
}
witem.getSections()
.put(sections.getId(), stepProcessing.getData(submissionService, obj, stepConfig));
.put(sections.getId(), stepProcessing.getData(submissionService, obj, stepConfig));
} else {
throw new Exception("The submission step class specified by '"
+ stepConfig.getProcessingClassName()
+ "' does not extend the class org.dspace.app.rest.submit" +
".AbstractRestProcessingStep!"
+ " Therefore it cannot be used by the Configurable Submission as the" +
" <processing-class>!");
log.warn("The submission step class specified by '" + stepConfig.getProcessingClassName() +
"' does not extend the class org.dspace.app.rest.submit.AbstractRestProcessingStep!" +
" Therefore it cannot be used by the Configurable Submission as the " +
"<processing-class>!");
}
} catch (Exception e) {

10
dspace-spring-rest/src/main/java/org/dspace/app/rest/model/BaseObjectRest.java
View File

@@ -28,6 +28,13 @@ public abstract class BaseObjectRest<T extends Serializable> implements Identifi
@JsonInclude(Include.NON_EMPTY)
private List<ErrorRest> errors;
private Boolean status;
@JsonInclude(Include.NON_NULL)
public Boolean isStatus() {
return status;
}
@Override
public T getId() {
return id;
@@ -48,4 +55,7 @@ public abstract class BaseObjectRest<T extends Serializable> implements Identifi
this.errors = errors;
}
public void setStatus(Boolean status) {
this.status = status;
}
}

22
dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/DSpaceRestRepository.java
View File

@@ -7,8 +7,11 @@
*/
package org.dspace.app.rest.repository;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.Serializable;
import java.sql.SQLException;
import javax.servlet.http.HttpServletRequest;
import org.apache.log4j.Logger;
@@ -19,7 +22,6 @@ import org.dspace.app.rest.exception.UnprocessableEntityException;
import org.dspace.app.rest.model.RestAddressableModel;
import org.dspace.app.rest.model.hateoas.DSpaceResource;
import org.dspace.app.rest.model.patch.Patch;
import org.dspace.app.rest.model.step.UploadStatusResponse;
import org.dspace.app.util.DCInputsReaderException;
import org.dspace.authorize.AuthorizeException;
import org.dspace.core.Context;
@@ -172,11 +174,12 @@ public abstract class DSpaceRestRepository<T extends RestAddressableModel, ID ex
}
}
protected T createAndReturn(Context context) throws AuthorizeException, RepositoryMethodNotImplementedException {
protected T createAndReturn(Context context)
throws AuthorizeException, SQLException, RepositoryMethodNotImplementedException {
throw new RepositoryMethodNotImplementedException("No implementation found; Method not allowed!", "");
}
public <U extends UploadStatusResponse> U upload(HttpServletRequest request, String apiCategory, String model,
public T upload(HttpServletRequest request, String apiCategory, String model,
ID id, String extraField, MultipartFile file) throws Exception {
throw new RuntimeException("No implementation found; Method not allowed!");
}
@@ -201,4 +204,17 @@ public abstract class DSpaceRestRepository<T extends RestAddressableModel, ID ex
throw new RepositoryMethodNotImplementedException(apiCategory, model);
}
public Iterable<T> upload(HttpServletRequest request, MultipartFile uploadfile)
throws SQLException, FileNotFoundException, IOException, AuthorizeException {
Context context = obtainContext();
Iterable<T> entity = upload(context, request, uploadfile);
context.commit();
return entity;
}
protected Iterable<T> upload(Context context, HttpServletRequest request, MultipartFile uploadfile)
throws SQLException, FileNotFoundException, IOException, AuthorizeException {
throw new RuntimeException("No implementation found; Method not allowed!");
}
}

285
dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/WorkspaceItemRestRepository.java
View File

@@ -7,47 +7,60 @@
*/
package org.dspace.app.rest.repository;
import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.List;
import java.util.UUID;
import javax.servlet.http.HttpServletRequest;
import gr.ekt.bte.core.TransformationEngine;
import gr.ekt.bte.core.TransformationSpec;
import gr.ekt.bte.exceptions.BadTransformationSpec;
import gr.ekt.bte.exceptions.MalformedSourceException;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.dspace.app.rest.Parameter;
import org.dspace.app.rest.SearchRestMethod;
import org.dspace.app.rest.converter.WorkspaceItemConverter;
import org.dspace.app.rest.exception.PatchBadRequestException;
import org.dspace.app.rest.model.ErrorRest;
import org.dspace.app.rest.model.WorkspaceItemRest;
import org.dspace.app.rest.model.hateoas.WorkspaceItemResource;
import org.dspace.app.rest.model.patch.Operation;
import org.dspace.app.rest.model.patch.Patch;
import org.dspace.app.rest.model.step.UploadBitstreamRest;
import org.dspace.app.rest.submit.AbstractRestProcessingStep;
import org.dspace.app.rest.submit.SubmissionService;
import org.dspace.app.rest.submit.UploadableStep;
import org.dspace.app.rest.utils.Utils;
import org.dspace.app.util.SubmissionConfig;
import org.dspace.app.util.SubmissionConfigReader;
import org.dspace.app.util.SubmissionConfigReaderException;
import org.dspace.app.util.SubmissionStepConfig;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Bitstream;
import org.dspace.content.BitstreamFormat;
import org.dspace.content.Bundle;
import org.dspace.content.Item;
import org.dspace.content.Collection;
import org.dspace.content.WorkspaceItem;
import org.dspace.content.service.BitstreamFormatService;
import org.dspace.content.service.BitstreamService;
import org.dspace.content.service.CollectionService;
import org.dspace.content.service.ItemService;
import org.dspace.content.service.WorkspaceItemService;
import org.dspace.core.Constants;
import org.dspace.core.Context;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.EPersonServiceImpl;
import org.dspace.event.Event;
import org.dspace.services.ConfigurationService;
import org.dspace.submit.AbstractProcessingStep;
import org.dspace.submit.lookup.DSpaceWorkspaceItemOutputGenerator;
import org.dspace.submit.lookup.MultipleSubmissionLookupDataLoader;
import org.dspace.submit.lookup.SubmissionItemDataLoader;
import org.dspace.submit.lookup.SubmissionLookupOutputGenerator;
import org.dspace.submit.lookup.SubmissionLookupService;
import org.dspace.submit.util.ItemSubmissionLookupDTO;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageImpl;
@@ -60,7 +73,6 @@ import org.springframework.web.multipart.MultipartFile;
*
* @author Andrea Bollini (andrea.bollini at 4science.it)
*/
@Component(WorkspaceItemRest.CATEGORY + "." + WorkspaceItemRest.NAME)
public class WorkspaceItemRestRepository extends DSpaceRestRepository<WorkspaceItemRest, Integer> {
@@ -87,6 +99,12 @@ public class WorkspaceItemRestRepository extends DSpaceRestRepository<WorkspaceI
@Autowired
EPersonServiceImpl epersonService;
@Autowired
SubmissionLookupService submissionLookupService;
@Autowired
CollectionService collectionService;
private SubmissionConfigReader submissionConfigReader;
public WorkspaceItemRestRepository() throws SubmissionConfigReaderException {
@@ -132,8 +150,8 @@ public class WorkspaceItemRestRepository extends DSpaceRestRepository<WorkspaceI
try {
Context context = obtainContext();
EPerson ep = epersonService.find(context, submitterID);
witems = wis.findByEPerson(context, ep);
total = witems.size();
witems = wis.findByEPerson(context, ep, pageable.getPageSize(), pageable.getOffset());
total = wis.countByEPerson(context, ep);
} catch (SQLException e) {
throw new RuntimeException(e.getMessage(), e);
}
@@ -142,7 +160,7 @@ public class WorkspaceItemRestRepository extends DSpaceRestRepository<WorkspaceI
}
@Override
protected WorkspaceItemRest createAndReturn(Context context) {
protected WorkspaceItemRest createAndReturn(Context context) throws SQLException, AuthorizeException {
WorkspaceItem source = submissionService.createWorkspaceItem(context, getRequestService().getCurrentRequest());
return converter.convert(source);
}
@@ -170,7 +188,7 @@ public class WorkspaceItemRestRepository extends DSpaceRestRepository<WorkspaceI
// load the JSPStep interface for this step
AbstractProcessingStep stepProcessing = (AbstractProcessingStep) stepClass
.newInstance();
stepProcessing.doProcessing(context, getRequestService().getCurrentRequest(), source);
stepProcessing.doPreProcessing(context, source);
} else {
throw new Exception("The submission step class specified by '"
+ stepConfig.getProcessingClassName()
@@ -199,52 +217,55 @@ public class WorkspaceItemRestRepository extends DSpaceRestRepository<WorkspaceI
//TODO @PreAuthorize("hasPermission(#id, 'WORKSPACEITEM', 'WRITE')")
@Override
public UploadBitstreamRest upload(HttpServletRequest request, String apiCategory, String model, Integer id,
String extraField, MultipartFile file) throws Exception {
UploadBitstreamRest result;
Bitstream source = null;
BitstreamFormat bf = null;
public WorkspaceItemRest upload(HttpServletRequest request, String apiCategory, String model, Integer id,
String extraField, MultipartFile file) throws Exception {
Context context = obtainContext();
WorkspaceItem wsi = wis.find(context, id);
Item item = wsi.getItem();
// do we already have a bundle?
List<Bundle> bundles = itemService.getBundles(item, Constants.CONTENT_BUNDLE_NAME);
WorkspaceItemRest wsi = findOne(id);
WorkspaceItem source = wis.find(context, id);
List<ErrorRest> errors = new ArrayList<ErrorRest>();
SubmissionConfig submissionConfig =
submissionConfigReader.getSubmissionConfigByName(wsi.getSubmissionDefinition().getName());
for (int i = 0; i < submissionConfig.getNumberOfSteps(); i++) {
SubmissionStepConfig stepConfig = submissionConfig.getStep(i);
try {
InputStream inputStream = new BufferedInputStream(file.getInputStream());
if (bundles.size() < 1) {
// set bundle's name to ORIGINAL
source = itemService.createSingleBitstream(context, inputStream, item, Constants.CONTENT_BUNDLE_NAME);
} else {
// we have a bundle already, just add bitstream
source = bitstreamService.create(context, bundles.get(0), inputStream);
/*
* First, load the step processing class (using the current
* class loader)
*/
ClassLoader loader = this.getClass().getClassLoader();
Class stepClass;
try {
stepClass = loader.loadClass(stepConfig.getProcessingClassName());
Object stepInstance = stepClass.newInstance();
if (UploadableStep.class.isAssignableFrom(stepClass)) {
UploadableStep uploadableStep = (UploadableStep) stepInstance;
uploadableStep.doPreProcessing(context, source);
ErrorRest err =
uploadableStep.upload(context, submissionService, stepConfig, source, file, extraField);
uploadableStep.doPostProcessing(context, source);
if (err != null) {
errors.add(err);
}
}
} catch (Exception e) {
log.error(e.getMessage(), e);
}
} catch (Exception e) {
log.error(e.getMessage(), e);
result = new UploadBitstreamRest();
result.setMessage(e.getMessage());
result.setStatus(false);
return result;
}
wsi = converter.convert(source);
if (errors.isEmpty()) {
wsi.setStatus(true);
} else {
wsi.setStatus(false);
wsi.getErrors().addAll(errors);
}
source.setName(context, file.getOriginalFilename());
// TODO how retrieve this information?
source.setSource(context, extraField);
// Identify the format
bf = bitstreamFormatService.guessFormat(context, source);
source.setFormat(context, bf);
// Update to DB
bitstreamService.update(context, source);
itemService.update(context, item);
context.commit();
result = submissionService.buildUploadBitstream(configurationService, source);
result.setStatus(true);
return result;
return wsi;
}
//TODO @PreAuthorize("hasPermission(#id, 'WORKSPACEITEM', 'WRITE')")
@@ -290,16 +311,16 @@ public class WorkspaceItemRestRepository extends DSpaceRestRepository<WorkspaceI
if (stepInstance instanceof AbstractRestProcessingStep) {
// load the JSPStep interface for this step
AbstractRestProcessingStep stepProcessing = (AbstractRestProcessingStep) stepClass
.newInstance();
AbstractRestProcessingStep stepProcessing =
(AbstractRestProcessingStep) stepClass.newInstance();
stepProcessing.doPreProcessing(context, source);
stepProcessing.doPatchProcessing(context, getRequestService().getCurrentRequest(), source, op);
stepProcessing.doPostProcessing(context, source);
} else {
throw new PatchBadRequestException("The submission step class specified by '"
+ stepConfig.getProcessingClassName()
+ "' does not extend the class org.dspace.submit" +
".AbstractProcessingStep!"
+ " Therefore it cannot be used by the Configurable " +
"Submission as the <processing-class>!");
throw new PatchBadRequestException(
"The submission step class specified by '" + stepConfig.getProcessingClassName() +
"' does not extend the class org.dspace.submit.AbstractProcessingStep!" +
" Therefore it cannot be used by the Configurable Submission as the <processing-class>!");
}
} catch (Exception e) {
@@ -316,8 +337,154 @@ public class WorkspaceItemRestRepository extends DSpaceRestRepository<WorkspaceI
try {
witem = wis.find(context, id);
wis.deleteAll(context, witem);
context.addEvent(new Event(Event.DELETE, Constants.ITEM, witem.getItem().getID(), null,
itemService.getIdentifiers(context, witem.getItem())));
} catch (SQLException | IOException e) {
log.error(e.getMessage(), e);
}
}
@Override
public Iterable<WorkspaceItemRest> upload(Context context, HttpServletRequest request, MultipartFile uploadfile)
throws SQLException, FileNotFoundException, IOException, AuthorizeException {
File file = Utils.getFile(uploadfile, "upload-loader", "filedataloader");
List<WorkspaceItemRest> results = new ArrayList<>();
try {
String uuid = request.getParameter("collection");
if (StringUtils.isBlank(uuid)) {
uuid = configurationService.getProperty("submission.default.collection");
}
Collection collection = null;
if (StringUtils.isNotBlank(uuid)) {
collection = collectionService.find(context, UUID.fromString(uuid));
} else {
collection = collectionService.findAll(context, 1, 0).get(0);
}
SubmissionConfig submissionConfig =
submissionConfigReader.getSubmissionConfigByCollection(collection.getHandle());
List<ItemSubmissionLookupDTO> tmpResult = new ArrayList<ItemSubmissionLookupDTO>();
TransformationEngine transformationEngine1 = submissionLookupService.getPhase1TransformationEngine();
if (transformationEngine1 != null) {
MultipleSubmissionLookupDataLoader dataLoader =
(MultipleSubmissionLookupDataLoader) transformationEngine1.getDataLoader();
List<String> fileDataLoaders = submissionLookupService.getFileProviders();
for (String fileDataLoader : fileDataLoaders) {
dataLoader.setFile(file.getAbsolutePath(), fileDataLoader);
try {
SubmissionLookupOutputGenerator outputGenerator =
(SubmissionLookupOutputGenerator) transformationEngine1.getOutputGenerator();
outputGenerator.setDtoList(new ArrayList<ItemSubmissionLookupDTO>());
log.debug("BTE transformation is about to start!");
transformationEngine1.transform(new TransformationSpec());
log.debug("BTE transformation finished!");
tmpResult.addAll(outputGenerator.getDtoList());
if (!tmpResult.isEmpty()) {
//exit with the results founded on the first data provided
break;
}
} catch (BadTransformationSpec e1) {
log.error(e1.getMessage(), e1);
} catch (MalformedSourceException e1) {
log.error(e1.getMessage(), e1);
}
}
}
List<WorkspaceItem> result = null;
//try to ingest workspaceitems
if (!tmpResult.isEmpty()) {
TransformationEngine transformationEngine2 = submissionLookupService.getPhase2TransformationEngine();
if (transformationEngine2 != null) {
SubmissionItemDataLoader dataLoader =
(SubmissionItemDataLoader) transformationEngine2.getDataLoader();
dataLoader.setDtoList(tmpResult);
// dataLoader.setProviders()
DSpaceWorkspaceItemOutputGenerator outputGenerator =
(DSpaceWorkspaceItemOutputGenerator) transformationEngine2.getOutputGenerator();
outputGenerator.setCollection(collection);
outputGenerator.setContext(context);
outputGenerator.setFormName(submissionConfig.getSubmissionName());
outputGenerator.setDto(tmpResult.get(0));
try {
transformationEngine2.transform(new TransformationSpec());
result = outputGenerator.getWitems();
} catch (BadTransformationSpec e1) {
e1.printStackTrace();
} catch (MalformedSourceException e1) {
e1.printStackTrace();
}
}
}
//we have to create the workspaceitem to push the file also if nothing found before
if (result == null) {
WorkspaceItem source =
submissionService.createWorkspaceItem(context, getRequestService().getCurrentRequest());
result = new ArrayList<>();
result.add(source);
}
//perform upload of bitstream if there is exact one result and convert workspaceitem to entity rest
if (result != null && !result.isEmpty()) {
for (WorkspaceItem wi : result) {
List<ErrorRest> errors = new ArrayList<ErrorRest>();
//load bitstream into bundle ORIGINAL only if there is one result (approximately this is the
// right behaviour for pdf file but not for other bibliographic format e.g. bibtex)
if (result.size() == 1) {
for (int i = 0; i < submissionConfig.getNumberOfSteps(); i++) {
SubmissionStepConfig stepConfig = submissionConfig.getStep(i);
ClassLoader loader = this.getClass().getClassLoader();
Class stepClass;
try {
stepClass = loader.loadClass(stepConfig.getProcessingClassName());
Object stepInstance = stepClass.newInstance();
if (UploadableStep.class.isAssignableFrom(stepClass)) {
UploadableStep uploadableStep = (UploadableStep) stepInstance;
ErrorRest err = uploadableStep
.upload(context, submissionService, stepConfig, wi, uploadfile,
file.getAbsolutePath());
if (err != null) {
errors.add(err);
}
}
} catch (Exception e) {
log.error(e.getMessage(), e);
}
}
}
WorkspaceItemRest wsi = converter.convert(wi);
if (result.size() == 1) {
if (errors.isEmpty()) {
wsi.setStatus(true);
} else {
wsi.setStatus(false);
wsi.getErrors().addAll(errors);
}
}
results.add(wsi);
}
}
} finally {
file.delete();
}
return results;
}
}

2
dspace-spring-rest/src/main/java/org/dspace/app/rest/submit/AbstractRestProcessingStep.java
View File

@@ -25,7 +25,7 @@ import org.dspace.services.model.Request;
*
* @author Luigi Andrea Pascarelli (luigiandrea.pascarelli at 4science.it)
*/
public interface AbstractRestProcessingStep {
public interface AbstractRestProcessingStep extends ListenerProcessingStep {
public static final String DESCRIBE_STEP_METADATA_OPERATION_ENTRY = "itemmetadata";
public static final String COLLECTION_STEP_OPERATION_ENTRY = "collection";

22
dspace-spring-rest/src/main/java/org/dspace/app/rest/submit/ListenerProcessingStep.java Normal file
View File

@@ -0,0 +1,22 @@
/**
* 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.app.rest.submit;
import org.dspace.content.InProgressSubmission;
import org.dspace.core.Context;
/**
* @author Luigi Andrea Pascarelli (luigiandrea.pascarelli at 4science.it)
*/
public interface ListenerProcessingStep {
public void doPreProcessing(Context context, InProgressSubmission wsi);
public void doPostProcessing(Context context, InProgressSubmission wsi);
}

26
dspace-spring-rest/src/main/java/org/dspace/app/rest/submit/UploadableStep.java Normal file
View File

@@ -0,0 +1,26 @@
/**
* 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.app.rest.submit;
import java.io.IOException;
import org.dspace.app.rest.model.ErrorRest;
import org.dspace.app.util.SubmissionStepConfig;
import org.dspace.content.InProgressSubmission;
import org.dspace.core.Context;
import org.springframework.web.multipart.MultipartFile;
/**
* @author Luigi Andrea Pascarelli (luigiandrea.pascarelli at 4science.it)
*/
public interface UploadableStep extends ListenerProcessingStep {
public ErrorRest upload(Context context, SubmissionService submissionService, SubmissionStepConfig stepConfig,
InProgressSubmission wsi, MultipartFile file, String extraField) throws IOException;
}

110
dspace-spring-rest/src/main/java/org/dspace/app/rest/submit/step/ExtractMetadataStep.java Normal file
View File

@@ -0,0 +1,110 @@
/**
* 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.app.rest.submit.step;
import java.io.File;
import java.io.IOException;
import java.util.List;
import java.util.Map;
import gr.ekt.bte.core.Record;
import gr.ekt.bte.core.RecordSet;
import gr.ekt.bte.core.Value;
import gr.ekt.bte.dataloader.FileDataLoader;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.dspace.app.rest.model.ErrorRest;
import org.dspace.app.rest.repository.WorkspaceItemRestRepository;
import org.dspace.app.rest.submit.SubmissionService;
import org.dspace.app.rest.submit.UploadableStep;
import org.dspace.app.rest.utils.Utils;
import org.dspace.app.util.SubmissionStepConfig;
import org.dspace.content.InProgressSubmission;
import org.dspace.content.Item;
import org.dspace.core.Context;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.dspace.submit.extraction.MetadataExtractor;
import org.dspace.submit.step.ExtractionStep;
import org.springframework.web.multipart.MultipartFile;
/**
* @author Luigi Andrea Pascarelli (luigiandrea.pascarelli at 4science.it)
*/
public class ExtractMetadataStep extends ExtractionStep implements UploadableStep {
private static final Logger log = Logger.getLogger(ExtractMetadataStep.class);
@Override
public ErrorRest upload(Context context, SubmissionService submissionService, SubmissionStepConfig stepConfig,
InProgressSubmission wsi, MultipartFile multipartFile, String extraField)
throws IOException {
Item item = wsi.getItem();
try {
List<MetadataExtractor> extractors =
DSpaceServicesFactory.getInstance().getServiceManager().getServicesByType(MetadataExtractor.class);
File file = null;
for (MetadataExtractor extractor : extractors) {
FileDataLoader dataLoader = extractor.getDataLoader();
RecordSet recordSet = null;
if (extractor.getExtensions()
.contains(FilenameUtils.getExtension(multipartFile.getOriginalFilename()))) {
if (file == null) {
file = Utils.getFile(multipartFile, "submissionlookup-loader", stepConfig.getId());
}
FileDataLoader fdl = (FileDataLoader) dataLoader;
fdl.setFilename(file.getAbsolutePath());
recordSet = convertFields(dataLoader.getRecords(), bteBatchImportService.getOutputMap());
enrichItem(context, recordSet.getRecords(), item);
}
}
} catch (Exception e) {
log.error(e.getMessage(), e);
ErrorRest result = new ErrorRest();
result.setMessage(e.getMessage());
result.getPaths().add("/" + WorkspaceItemRestRepository.OPERATION_PATH_SECTIONS + "/" + stepConfig.getId());
return result;
}
return null;
}
public RecordSet convertFields(RecordSet recordSet, Map<String, String> fieldMap) {
RecordSet result = new RecordSet();
for (Record publication : recordSet.getRecords()) {
for (String fieldName : fieldMap.keySet()) {
String md = null;
if (fieldMap != null) {
md = fieldMap.get(fieldName);
}
if (StringUtils.isBlank(md)) {
continue;
} else {
md = md.trim();
}
if (publication.isMutable()) {
List<Value> values = publication.getValues(md);
publication.makeMutable().removeField(md);
publication.makeMutable().addField(fieldName, values);
}
}
result.addRecord(publication);
}
return result;
}
}

60
dspace-spring-rest/src/main/java/org/dspace/app/rest/submit/step/validation/LicenseValidation.java Normal file
View File

@@ -0,0 +1,60 @@
/**
* 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.app.rest.submit.step.validation;
import java.sql.SQLException;
import java.util.List;
import org.apache.log4j.Logger;
import org.dspace.app.rest.model.ErrorRest;
import org.dspace.app.rest.repository.WorkspaceItemRestRepository;
import org.dspace.app.rest.submit.SubmissionService;
import org.dspace.app.util.DCInputsReaderException;
import org.dspace.app.util.SubmissionStepConfig;
import org.dspace.content.Bitstream;
import org.dspace.content.WorkspaceItem;
import org.dspace.content.service.BitstreamService;
import org.dspace.core.Constants;
import org.springframework.beans.factory.annotation.Autowired;
/**
* Execute check on license bundle
*
* @author Luigi Andrea Pascarelli (luigiandrea.pascarelli at 4science.it)
*/
public class LicenseValidation extends AbstractValidation {
private static final String ERROR_VALIDATION_LICENSEREQUIRED = "error.validation.license.notgranted";
private static final Logger log = Logger.getLogger(LicenseValidation.class);
@Autowired
private BitstreamService bitstreamService;
@Override
public List<ErrorRest> validate(SubmissionService submissionService, WorkspaceItem obj,
SubmissionStepConfig config) throws DCInputsReaderException, SQLException {
Bitstream bitstream = bitstreamService
.getBitstreamByName(obj.getItem(), Constants.LICENSE_BUNDLE_NAME, Constants.LICENSE_BITSTREAM_NAME);
if (bitstream == null) {
addError(ERROR_VALIDATION_LICENSEREQUIRED,
"/" + WorkspaceItemRestRepository.OPERATION_PATH_SECTIONS + "/" + config.getId());
}
return getErrors();
}
public BitstreamService getBitstreamService() {
return bitstreamService;
}
public void setBitstreamService(BitstreamService bitstreamService) {
this.bitstreamService = bitstreamService;
}
}

28
dspace-spring-rest/src/main/java/org/dspace/app/rest/utils/Utils.java
View File

@@ -9,6 +9,13 @@ package org.dspace.app.rest.utils;
import static org.springframework.hateoas.mvc.ControllerLinkBuilder.linkTo;
import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.List;
import org.apache.commons.lang3.StringUtils;
@@ -23,6 +30,7 @@ import org.dspace.app.rest.model.RestAddressableModel;
import org.dspace.app.rest.model.hateoas.DSpaceResource;
import org.dspace.app.rest.repository.DSpaceRestRepository;
import org.dspace.app.rest.repository.LinkRestRepository;
import org.dspace.core.ConfigurationManager;
import org.springframework.beans.factory.NoSuchBeanDefinitionException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
@@ -31,6 +39,7 @@ import org.springframework.data.domain.PageImpl;
import org.springframework.data.domain.Pageable;
import org.springframework.hateoas.Link;
import org.springframework.stereotype.Component;
import org.springframework.web.multipart.MultipartFile;
/**
* Collection of utility methods
@@ -155,4 +164,23 @@ public class Utils {
public String getMetadataKey(String schema, String element, String qualifier) {
return org.dspace.core.Utils.standardize(schema, element, qualifier, ".");
}
public static File getFile(MultipartFile multipartFile, String prefixTempName, String suffixTempName)
throws IOException, FileNotFoundException {
// TODO after change item-submission into
String tempDir = (ConfigurationManager.getProperty("upload.temp.dir") != null)
? ConfigurationManager.getProperty("upload.temp.dir")
: System.getProperty("java.io.tmpdir");
File uploadDir = new File(tempDir);
if (!uploadDir.exists()) {
if (!uploadDir.mkdir()) {
uploadDir = null;
}
}
File file = File.createTempFile(prefixTempName + "-" + suffixTempName, ".temp", uploadDir);
InputStream io = new BufferedInputStream(multipartFile.getInputStream());
BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(file));
org.dspace.core.Utils.bufferedCopy(io, out);
return file;
}
}

30
dspace/config/spring/api/metadata-extractors.xml Normal file
View File

@@ -0,0 +1,30 @@
<?xml version="1.0" encoding="UTF-8"?>
<beans xmlns="http://www.springframework.org/schema/beans"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://www.springframework.org/schema/beans
http://www.springframework.org/schema/beans/spring-beans-2.5.xsd">
<bean id="bibtex" class="org.dspace.submit.extraction.MetadataExtractor">
<property name="dataLoader" ref="bibTeXDataLoader"/>
<property name="configurationService" ref="org.dspace.services.ConfigurationService"/>
<property name="extensions">
<list>
<value>bibtex</value>
<value>bib</value>
</list>
</property>
</bean>
<!-- <bean id="grobid" class="org.dspace.submit.extraction.MetadataExtractor">
<property name="dataLoader" ref="grobidDataLoader"/>
<property name="configurationService" ref="org.dspace.services.ConfigurationService"/>
<property name="extensions">
<list>
<value>pdf</value>
</list>
</property>
</bean>
-->
</beans>

24
dspace/config/spring/api/step-processing-listener.xml Normal file
View File

@@ -0,0 +1,24 @@
<?xml version="1.0" encoding="UTF-8"?>
<beans xmlns="http://www.springframework.org/schema/beans"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://www.springframework.org/schema/beans
http://www.springframework.org/schema/beans/spring-beans-2.5.xsd">
<bean id="lookupListener" class="org.dspace.submit.listener.MetadataListener">
<property name="configurationService" ref="org.dspace.services.ConfigurationService"/>
<property name="metadata">
<map>
<entry key="dc.identifier.doi" value="doi"/>
</map>
</property>
<property name="dataloadersMap">
<map>
<entry key="pubmed" value-ref="pubmedOnlineDataLoader"/>
<entry key="crossref" value-ref="crossRefOnlineDataLoader"/>
<entry key="arxiv" value-ref="arXivOnlineDataLoader"/>
<entry key="cinii" value-ref="ciniiOnlineDataLoader"/>
</map>
</property>
</bean>
</beans>