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DS-2330 bug fix: lost authors when using ORCID column

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This commit is contained in:
Antoine Snyers
2014-12-11 13:39:03 +01:00
parent 8ab085e3f0
commit 53d387fed2
3 changed files with 66 additions and 34 deletions
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13
dspace-api/src/main/java/org/dspace/app/bulkedit/DSpaceCSV.java
View File

@@ -7,6 +7,7 @@
*/
package org.dspace.app.bulkedit;
import org.apache.commons.lang3.StringUtils;
import org.dspace.authority.AuthorityValue;
import org.dspace.app.bulkedit.DSpaceCSVLine;
import org.dspace.app.bulkedit.MetadataImport;
@@ -14,6 +15,7 @@ import org.dspace.app.bulkedit.MetadataImportInvalidHeadingException;
import org.dspace.content.Collection;
import org.dspace.content.*;
import org.dspace.content.Collection;
import org.dspace.content.authority.Choices;
import org.dspace.core.ConfigurationManager;
import org.dspace.core.Context;
@@ -185,7 +187,7 @@ public class DSpaceCSV implements Serializable
StringBuilder lineBuilder = new StringBuilder();
String lineRead;
while ((lineRead = input.readLine()) != null)
while (StringUtils.isNotBlank(lineRead = input.readLine()))
{
if (lineBuilder.length() > 0) {
// Already have a previously read value - add this line
@@ -449,7 +451,7 @@ public class DSpaceCSV implements Serializable
String mdValue = value.value;
if (value.authority != null && !"".equals(value.authority))
{
mdValue += authoritySeparator + value.authority + authoritySeparator + value.confidence;
mdValue += authoritySeparator + value.authority + authoritySeparator + (value.confidence != -1 ? value.confidence : Choices.CF_ACCEPTED);
}
line.add(key, mdValue);
if (!headings.contains(key))
@@ -610,8 +612,9 @@ public class DSpaceCSV implements Serializable
// Create the headings line
String[] csvLines = new String[counter + 1];
csvLines[0] = "id" + fieldSeparator + "collection";
Collections.sort(headings);
for (String value : headings)
List<String> headingsCopy = new ArrayList<String>(headings);
Collections.sort(headingsCopy);
for (String value : headingsCopy)
{
csvLines[0] = csvLines[0] + fieldSeparator + value;
}
@@ -620,7 +623,7 @@ public class DSpaceCSV implements Serializable
int c = 1;
while (i.hasNext())
{
csvLines[c++] = i.next().toCSV(headings);
csvLines[c++] = i.next().toCSV(headingsCopy);
}
return csvLines;

37
dspace-api/src/main/java/org/dspace/app/bulkedit/DSpaceCSVLine.java
View File

@@ -7,12 +7,10 @@
*/
package org.dspace.app.bulkedit;
import org.dspace.authority.AuthorityValue;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.*;
/**
* Utility class to store a line from a CSV file
@@ -21,12 +19,35 @@ import java.util.Set;
*/
public class DSpaceCSVLine implements Serializable
{
/** The item id of the item represented by this line. -1 is for a new item */
private int id;
/** The elements in this line in a hashtable, keyed by the metadata type */
private Map<String, ArrayList> items;
/** ensuring that the order-sensible columns of the csv are processed in the correct order */
private final Comparator<? super String> headerComparator = new Comparator<String>() {
@Override
public int compare(String md1, String md2) {
// The metadata coming from an external source should be processed after the others
AuthorityValue source1 = MetadataImport.getAuthorityValueType(md1);
AuthorityValue source2 = MetadataImport.getAuthorityValueType(md2);
int compare;
if (source1 == null && source2 != null) {
compare = -1;
}
else if (source1 != null && source2 == null) {
compare = 1;
} else {
// the order of the rest does not matter
compare = md1.compareTo(md2);
}
return compare;
}
};
/**
* Create a new CSV line
*
@@ -36,7 +57,8 @@ public class DSpaceCSVLine implements Serializable
{
// Store the ID + separator, and initialise the hashtable
this.id = itemId;
items = new HashMap<String, ArrayList>();
items = new TreeMap<String, ArrayList>(headerComparator);
// this.items = new HashMap<String, ArrayList>();
}
/**
@@ -46,7 +68,8 @@ public class DSpaceCSVLine implements Serializable
{
// Set the ID to be -1, and initialise the hashtable
this.id = -1;
this.items = new HashMap<String, ArrayList>();
this.items = new TreeMap<String, ArrayList>(headerComparator);
// this.items = new HashMap<String, ArrayList>();
}
/**

50
dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImport.java
View File

@@ -166,7 +166,7 @@ public class MetadataImport
}
// Compare
compare(item, fromCSV, change, md, whatHasChanged);
compare(item, fromCSV, change, md, whatHasChanged, line);
}
}
@@ -412,11 +412,12 @@ public class MetadataImport
* @param md The element to compare
* @param changes The changes object to populate
*
* @param line
* @throws SQLException if there is a problem accessing a Collection from the database, from its handle
* @throws AuthorizeException if there is an authorization problem with permissions
*/
private void compare(Item item, String[] fromCSV, boolean change,
String md, BulkEditChange changes) throws SQLException, AuthorizeException
String md, BulkEditChange changes, DSpaceCSVLine line) throws SQLException, AuthorizeException
{
// Log what metadata element we're looking at
String all = "";
@@ -473,25 +474,25 @@ public class MetadataImport
",looking_for_element=" + element +
",looking_for_qualifier=" + qualifier +
",looking_for_language=" + language));
Metadatum[] current = item.getMetadata(schema, element, qualifier, language);
String[] dcvalues = new String[current.length];
int i = 0;
for (Metadatum dcv : current)
{
if (dcv.authority == null || !isAuthorityControlledField(md))
{
dcvalues[i] = dcv.value;
String[] dcvalues = new String[0];
if(fromAuthority==null) {
Metadatum[] current = item.getMetadata(schema, element, qualifier, language);
dcvalues = new String[current.length];
int i = 0;
for (Metadatum dcv : current) {
if (dcv.authority == null || !isAuthorityControlledField(md)) {
dcvalues[i] = dcv.value;
} else {
dcvalues[i] = dcv.value + DSpaceCSV.authoritySeparator + dcv.authority;
dcvalues[i] += DSpaceCSV.authoritySeparator + (dcv.confidence != -1 ? dcv.confidence : Choices.CF_ACCEPTED);
}
i++;
log.debug(LogManager.getHeader(c, "metadata_import",
"item_id=" + item.getID() + ",fromCSV=" + all +
",found=" + dcv.value));
}
else
{
dcvalues[i] = dcv.value + DSpaceCSV.authoritySeparator + dcv.authority;
dcvalues[i] += DSpaceCSV.authoritySeparator + (dcv.confidence != -1 ? dcv.confidence : Choices.CF_ACCEPTED);
}
i++;
log.debug(LogManager.getHeader(c, "metadata_import",
"item_id=" + item.getID() + ",fromCSV=" + all +
",found=" + dcv.value));
}else{
dcvalues = line.get(md).toArray(new String[line.get(md).size()]);
}
// Compare from current->csv
@@ -530,7 +531,9 @@ public class MetadataImport
dcv.confidence = (parts.length > 2 ? Integer.valueOf(parts[2]) : Choices.CF_ACCEPTED);
}
if ((value != null) && (!"".equals(value)) && (!contains(value, fromCSV)))
if ((value != null) && (!"".equals(value)) && (!contains(value, fromCSV)) && fromAuthority==null)
// fromAuthority==null: with the current implementation metadata values from external authority sources can only be used to add metadata, not to change or remove them
// because e.g. an author that is not in the column "ORCID:dc.contributor.author" could still be in the column "dc.contributor.author" so don't remove it
{
// Remove it
log.debug(LogManager.getHeader(c, "metadata_import",
@@ -862,7 +865,8 @@ public class MetadataImport
}
// look up the value and authority in solr
List<AuthorityValue> byValue = authorityValueFinder.findByValue(c, schema, element, qualifier, value);
AuthorityValue example = fromAuthority.newInstance(value);
List<AuthorityValue> byValue = authorityValueFinder.findByValue(c, schema, element, qualifier, example.getValue());
AuthorityValue authorityValue = null;
if (byValue.isEmpty()) {
String toGenerate = fromAuthority.generateString() + value;
@@ -1167,6 +1171,8 @@ public class MetadataImport
{
int pos = md.indexOf("[");
String mdf = (pos > -1 ? md.substring(0, pos) : md);
pos = md.indexOf(":");
mdf = (pos > -1 ? md.substring(pos+1) : md);
return authorityControlled.contains(mdf);
}