/**
* Get a list of all communities in the system. These are alphabetically sorted by community name.
*
* @param context DSpace context object
* @return the communities in the system
*/
@Override
public List<Community> findAll(Context context, MetadataField sortField) throws SQLException {
StringBuilder queryBuilder = new StringBuilder();
queryBuilder.append("SELECT community FROM Community as community ");
addMetadataLeftJoin(
queryBuilder, Community.class.getSimpleName().toLowerCase(), Arrays.asList(sortField));
addMetadataSortQuery(queryBuilder, Arrays.asList(sortField), ListUtils.EMPTY_LIST);
Query query = createQuery(context, queryBuilder.toString());
query.setParameter(sortField.toString(), sortField.getFieldID());
return list(query);
}
/**
* Serialize a single metadata field registry entry to xml
*
* @param context DSpace context
* @param xmlSerializer xml serializer
* @param mdField DSpace metadata field
* @throws SAXException if XML error
* @throws RegistryExportException if export error
* @throws SQLException if database error
* @throws IOException if IO error
*/
private static void saveType(Context context, XMLSerializer xmlSerializer, MetadataField mdField)
throws SAXException, RegistryExportException, SQLException, IOException {
// If we haven't been given a field, it's an error
if (mdField == null) {
throw new RegistryExportException("no field to export");
}
// Get the data from the metadata field
String schemaName = getSchemaName(context, mdField);
String element = mdField.getElement();
String qualifier = mdField.getQualifier();
String scopeNote = mdField.getScopeNote();
// We must have a schema and element
if (schemaName == null || element == null) {
throw new RegistryExportException("incomplete field information");
}
// Output the parent tag
xmlSerializer.startElement("dc-type", null);
// Output the schema name
xmlSerializer.startElement("schema", null);
xmlSerializer.characters(schemaName.toCharArray(), 0, schemaName.length());
xmlSerializer.endElement("schema");
// Output the element
xmlSerializer.startElement("element", null);
xmlSerializer.characters(element.toCharArray(), 0, element.length());
xmlSerializer.endElement("element");
// Output the qualifier, if present
if (qualifier != null) {
xmlSerializer.startElement("qualifier", null);
xmlSerializer.characters(qualifier.toCharArray(), 0, qualifier.length());
xmlSerializer.endElement("qualifier");
} else {
xmlSerializer.comment("unqualified");
}
// Output the scope note, if present
if (scopeNote != null) {
xmlSerializer.startElement("scope_note", null);
xmlSerializer.characters(scopeNote.toCharArray(), 0, scopeNote.length());
xmlSerializer.endElement("scope_note");
} else {
xmlSerializer.comment("no scope note");
}
xmlSerializer.endElement("dc-type");
}
/**
* Utility method for pattern-matching metadata elements. This method will return <code>true
* </code> if the given schema, element, qualifier and language match the schema, element,
* qualifier and language of the <code>DCValue</code> object passed in. Any or all of the element,
* qualifier and language passed in can be the <code>Item.ANY</code> wildcard.
*
* @param schema the schema for the metadata field. <em>Must</em> match the <code>name</code> of
* an existing metadata schema.
* @param element the element to match, or <code>Item.ANY</code>
* @param qualifier the qualifier to match, or <code>Item.ANY</code>
* @param language the language to match, or <code>Item.ANY</code>
* @param metadataValue the Dublin Core value
* @return <code>true</code> if there is a match
*/
protected boolean match(
String schema,
String element,
String qualifier,
String language,
MetadataValue metadataValue) {
MetadataField metadataField = metadataValue.getMetadataField();
MetadataSchema metadataSchema = metadataField.getMetadataSchema();
// We will attempt to disprove a match - if we can't we have a match
if (!element.equals(Item.ANY) && !element.equals(metadataField.getElement())) {
// Elements do not match, no wildcard
return false;
}
if (qualifier == null) {
// Value must be unqualified
if (metadataField.getQualifier() != null) {
// Value is qualified, so no match
return false;
}
} else if (!qualifier.equals(Item.ANY)) {
// Not a wildcard, so qualifier must match exactly
if (!qualifier.equals(metadataField.getQualifier())) {
return false;
}
}
if (language == null) {
// Value must be null language to match
if (metadataValue.getLanguage() != null) {
// Value is qualified, so no match
return false;
}
} else if (!language.equals(Item.ANY)) {
// Not a wildcard, so language must match exactly
if (!language.equals(metadataValue.getLanguage())) {
return false;
}
}
if (!schema.equals(Item.ANY)) {
if (metadataSchema != null && !metadataSchema.getName().equals(schema)) {
// The namespace doesn't match
return false;
}
}
// If we get this far, we have a match
return true;
}
public void addBody(Body body) throws WingException, SQLException, AuthorizeException {
// Get all our parameters
MetadataSchema[] schemas = MetadataSchema.findAll(context);
String idsString = parameters.getParameter("fieldIDs", null);
ArrayList<MetadataField> fields = new ArrayList<MetadataField>();
for (String id : idsString.split(",")) {
MetadataField field = MetadataField.find(context, Integer.valueOf(id));
fields.add(field);
}
// DIVISION: metadata-field-move
Division moved =
body.addInteractiveDivision(
"metadata-field-move",
contextPath + "/admin/metadata-registry",
Division.METHOD_POST,
"primary administrative metadata-registry");
moved.setHead(T_head1);
moved.addPara(T_para1);
Table table = moved.addTable("metadata-field-move", fields.size() + 1, 3);
Row header = table.addRow(Row.ROLE_HEADER);
header.addCell().addContent(T_column1);
header.addCell().addContent(T_column2);
header.addCell().addContent(T_column3);
for (MetadataField field : fields) {
String fieldID = String.valueOf(field.getID());
String fieldEelement = field.getElement();
String fieldQualifier = field.getQualifier();
MetadataSchema schema = MetadataSchema.find(context, field.getSchemaID());
String schemaName = schema.getName();
String fieldName = schemaName + "." + fieldEelement;
if (fieldQualifier != null && fieldQualifier.length() > 0) fieldName += "." + fieldQualifier;
String fieldScopeNote = field.getScopeNote();
Row row = table.addRow();
row.addCell().addContent(fieldID);
row.addCell().addContent(fieldName);
row.addCell().addContent(fieldScopeNote);
}
Row row = table.addRow();
Cell cell = row.addCell(1, 3);
cell.addContent(T_para2);
Select toSchema = cell.addSelect("to_schema");
for (MetadataSchema schema : schemas) {
toSchema.addOption(schema.getID(), schema.getNamespace());
}
Para buttons = moved.addPara();
buttons.addButton("submit_move").setValue(T_submit_move);
buttons.addButton("submit_cancel").setValue(T_submit_cancel);
moved.addHidden("administrative-continue").setValue(knot.getId());
}
@Override
public void loadMetadata(Item item) {
MetadataFieldDAO mfDAO = MetadataFieldDAOFactory.getInstance(context);
MetadataSchemaDAO msDAO = MetadataSchemaDAOFactory.getInstance(context);
try {
TableRowIterator tri =
DatabaseManager.queryTable(
context,
"metadatavalue",
"SELECT * FROM MetadataValue "
+ "WHERE item_id = ? "
+ "ORDER BY metadata_field_id, place",
item.getID());
List<DCValue> metadata = new ArrayList<DCValue>();
for (TableRow row : tri.toList()) {
// Get the associated metadata field and schema information
int fieldID = row.getIntColumn("metadata_field_id");
MetadataField field = mfDAO.retrieve(fieldID);
if (field == null) {
log.error("Loading item - cannot find metadata field " + fieldID);
} else {
MetadataSchema schema = msDAO.retrieve(field.getSchemaID());
// Make a DCValue object
DCValue dcv = new DCValue();
dcv.schema = schema.getName();
dcv.element = field.getElement();
dcv.qualifier = field.getQualifier();
dcv.language = row.getStringColumn("text_lang");
dcv.value = row.getStringColumn("text_value");
// Add it to the item
metadata.add(dcv);
}
}
item.setMetadata(metadata);
} catch (SQLException sqle) {
throw new RuntimeException(sqle);
}
}
protected MetadataField getMetadataField(DCValue dcv) throws SQLException, AuthorizeException {
if (allMetadataFields == null) {
allMetadataFields = MetadataField.findAll(ourContext);
}
if (allMetadataFields != null) {
int schemaID = getMetadataSchemaID(dcv);
for (MetadataField field : allMetadataFields) {
if (field.getSchemaID() == schemaID
&& StringUtils.equals(field.getElement(), dcv.element)
&& StringUtils.equals(field.getQualifier(), dcv.qualifier)) {
return field;
}
}
}
return null;
}
@Override
public Iterator<Item> findBySubmitter(
Context context, EPerson eperson, MetadataField metadataField, int limit)
throws SQLException {
StringBuilder query = new StringBuilder();
query.append("SELECT item FROM Item as item ");
addMetadataLeftJoin(
query, Item.class.getSimpleName().toLowerCase(), Collections.singletonList(metadataField));
query.append(" WHERE item.inArchive = :in_archive");
query.append(" AND item.submitter =:submitter");
addMetadataSortQuery(query, Collections.singletonList(metadataField), null);
Query hibernateQuery = createQuery(context, query.toString());
hibernateQuery.setParameter(metadataField.toString(), metadataField.getFieldID());
hibernateQuery.setParameter("in_archive", true);
hibernateQuery.setParameter("submitter", eperson);
hibernateQuery.setMaxResults(limit);
return iterate(hibernateQuery);
}
/**
* Helper method to retrieve a schema name for the field. Caches the name after looking up the id.
*
* @param context DSpace Context
* @param mdField DSpace metadata field
* @return name of schema
* @throws SQLException if database error
* @throws RegistryExportException if export error
*/
private static String getSchemaName(Context context, MetadataField mdField)
throws SQLException, RegistryExportException {
// Get name from cache
String name = schemaMap.get(mdField.getMetadataSchema().getSchemaID());
if (name == null) {
// Name not retrieved before, so get the schema now
MetadataSchema mdSchema =
metadataSchemaService.find(context, mdField.getMetadataSchema().getSchemaID());
if (mdSchema != null) {
name = mdSchema.getName();
schemaMap.put(mdSchema.getSchemaID(), name);
} else {
// Can't find the schema
throw new RegistryExportException("Can't get schema name for field");
}
}
return name;
}
@Override
public void update(Context context, MetadataField metadataField)
throws SQLException, AuthorizeException, NonUniqueMetadataException, IOException {
// Check authorisation: Only admins may update the metadata registry
if (!authorizeService.isAdmin(context)) {
throw new AuthorizeException("Only administrators may modiffy the Dublin Core registry");
}
// Ensure the element and qualifier are unique within a given schema.
if (hasElement(
context,
metadataField.getFieldID(),
metadataField.getMetadataSchema(),
metadataField.getElement(),
metadataField.getQualifier())) {
throw new NonUniqueMetadataException(
"Please make "
+ metadataField.getMetadataSchema().getName()
+ "."
+ metadataField.getElement()
+ "."
+ metadataField.getQualifier());
}
metadataFieldDAO.save(context, metadataField);
log.info(
LogManager.getHeader(
context,
"update_metadatafieldregistry",
"metadata_field_id="
+ metadataField.getFieldID()
+ "element="
+ metadataField.getElement()
+ "qualifier="
+ metadataField.getQualifier()));
}
@Override
public void delete(Context context, MetadataField metadataField)
throws SQLException, AuthorizeException {
// Check authorisation: Only admins may create DC types
if (!authorizeService.isAdmin(context)) {
throw new AuthorizeException("Only administrators may modify the metadata registry");
}
log.info(
LogManager.getHeader(
context, "delete_metadata_field", "metadata_field_id=" + metadataField.getFieldID()));
metadataValueService.deleteByMetadataField(context, metadataField);
metadataFieldDAO.delete(context, metadataField);
}
List<DCValue> get(Context c, int resourceId, int resourceTypeId, Logger log)
throws SQLException {
if (metadata == null) {
metadata = new ArrayList<DCValue>();
// Get Dublin Core metadata
TableRowIterator tri = retrieveMetadata(resourceId, resourceTypeId);
if (tri != null) {
try {
while (tri.hasNext()) {
TableRow resultRow = tri.next();
// Get the associated metadata field and schema information
int fieldID = resultRow.getIntColumn("metadata_field_id");
MetadataField field = MetadataField.find(c, fieldID);
if (field == null) {
log.error("Loading item - cannot find metadata field " + fieldID);
} else {
MetadataSchema schema = MetadataSchema.find(c, field.getSchemaID());
if (schema == null) {
log.error(
"Loading item - cannot find metadata schema "
+ field.getSchemaID()
+ ", field "
+ fieldID);
} else {
// Make a DCValue object
DCValue dcv = new DCValue();
dcv.element = field.getElement();
dcv.qualifier = field.getQualifier();
dcv.value = resultRow.getStringColumn("text_value");
dcv.language = resultRow.getStringColumn("text_lang");
// dcv.namespace = schema.getNamespace();
dcv.schema = schema.getName();
dcv.authority = resultRow.getStringColumn("authority");
dcv.confidence = resultRow.getIntColumn("confidence");
// Add it to the list
metadata.add(dcv);
}
}
}
} finally {
// close the TableRowIterator to free up resources
if (tri != null) {
tri.close();
}
}
}
}
return metadata;
}
/**
* Update the metadata field in the database.
*
* @param context dspace context
* @throws SQLException
* @throws AuthorizeException
* @throws NonUniqueMetadataException
* @throws IOException
*/
public void update(Context context)
throws SQLException, AuthorizeException, NonUniqueMetadataException, IOException {
// Check authorisation: Only admins may update the metadata registry
if (!AuthorizeManager.isAdmin(context)) {
throw new AuthorizeException("Only administrators may modiffy the Dublin Core registry");
}
// Check to see if the schema ID was altered. If is was then we will
// query to ensure that there is not already a duplicate name field.
if (row.getIntColumn("metadata_schema_id") != schemaID) {
if (MetadataField.hasElement(context, schemaID, element, qualifier)) {
throw new NonUniqueMetadataException("Duplcate field name found in target schema");
}
}
// Ensure the element and qualifier are unique within a given schema.
if (!unique(context, schemaID, element, qualifier)) {
throw new NonUniqueMetadataException("Please make " + element + "." + qualifier);
}
row.setColumn("metadata_schema_id", schemaID);
row.setColumn("element", element);
row.setColumn("qualifier", qualifier);
row.setColumn("scope_note", scopeNote);
DatabaseManager.update(context, row);
decache();
log.info(
LogManager.getHeader(
context,
"update_metadatafieldregistry",
"metadata_field_id="
+ getFieldID()
+ "element="
+ getElement()
+ "qualifier="
+ getQualifier()));
}
@Override
public MetadataField create(
Context context,
MetadataSchema metadataSchema,
String element,
String qualifier,
String scopeNote)
throws AuthorizeException, SQLException, NonUniqueMetadataException {
// Check authorisation: Only admins may create DC types
if (!authorizeService.isAdmin(context)) {
throw new AuthorizeException("Only administrators may modify the metadata registry");
}
// Ensure the element and qualifier are unique within a given schema.
if (hasElement(context, -1, metadataSchema, element, qualifier)) {
throw new NonUniqueMetadataException(
"Please make "
+ element
+ "."
+ qualifier
+ " unique within schema #"
+ metadataSchema.getSchemaID());
}
// Create a table row and update it with the values
MetadataField metadataField = new MetadataField();
metadataField.setElement(element);
metadataField.setQualifier(qualifier);
metadataField.setScopeNote(scopeNote);
metadataField.setMetadataSchema(metadataSchema);
metadataField = metadataFieldDAO.create(context, metadataField);
metadataFieldDAO.save(context, metadataField);
log.info(
LogManager.getHeader(
context, "create_metadata_field", "metadata_field_id=" + metadataField.getFieldID()));
return metadataField;
}
/**
* Simple command-line rig for testing the DIM output of a stylesheet. Usage: java
* XSLTIngestionCrosswalk <crosswalk-name> <input-file>
*/
public static void main(String[] argv) throws Exception {
if (argv.length < 2) {
System.err.println("Usage: java XSLTIngestionCrosswalk [-l] <crosswalk-name> <input-file>");
System.exit(1);
}
int i = 0;
boolean list = false;
// skip first arg if it's the list option
if (argv.length > 2 && argv[0].equals("-l")) {
++i;
list = true;
}
IngestionCrosswalk xwalk =
(IngestionCrosswalk) PluginManager.getNamedPlugin(IngestionCrosswalk.class, argv[i]);
if (xwalk == null) {
System.err.println(
"Error, cannot find an IngestionCrosswalk plugin for: \"" + argv[i] + "\"");
System.exit(1);
}
XSLTransformer xform = ((XSLTIngestionCrosswalk) xwalk).getTransformer(DIRECTION);
if (xform == null)
throw new CrosswalkInternalException(
"Failed to initialize transformer, probably error loading stylesheet.");
SAXBuilder builder = new SAXBuilder();
Document inDoc = builder.build(new FileInputStream(argv[i + 1]));
XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat());
Document dimDoc = null;
List dimList = null;
if (list) {
dimList = xform.transform(inDoc.getRootElement().getChildren());
outputter.output(dimList, System.out);
} else {
dimDoc = xform.transform(inDoc);
outputter.output(dimDoc, System.out);
dimList = dimDoc.getRootElement().getChildren();
}
// Sanity-check the generated DIM, make sure it would load.
Context context = new Context();
Iterator di = dimList.iterator();
while (di.hasNext()) {
// skip over comment, text and other trash some XSLs generate..
Object o = di.next();
if (!(o instanceof Element)) continue;
Element elt = (Element) o;
if (elt.getName().equals("field") && elt.getNamespace().equals(DIM_NS)) {
String schema = elt.getAttributeValue("mdschema");
String element = elt.getAttributeValue("element");
String qualifier = elt.getAttributeValue("qualifier");
MetadataSchema ms = MetadataSchema.find(context, schema);
if (ms == null) {
System.err.println(
"DIM Error, Cannot find metadata schema for: schema=\""
+ schema
+ "\" (... element=\""
+ element
+ "\", qualifier=\""
+ qualifier
+ "\")");
} else {
if (qualifier != null && qualifier.equals("")) {
System.err.println(
"DIM Warning, qualifier is empty string: "
+ " schema=\""
+ schema
+ "\", element=\""
+ element
+ "\", qualifier=\""
+ qualifier
+ "\"");
qualifier = null;
}
MetadataField mf =
MetadataField.findByElement(context, ms.getSchemaID(), element, qualifier);
if (mf == null)
System.err.println(
"DIM Error, Cannot find metadata field for: schema=\""
+ schema
+ "\", element=\""
+ element
+ "\", qualifier=\""
+ qualifier
+ "\"");
}
} else {
// ("Got unexpected element in DIM list: "+elt.toString());
throw new MetadataValidationException(
"Got unexpected element in DIM list: " + elt.toString());
}
}
}
private void addDCValue(Context c, Item i, String schema, Node n)
throws TransformerException, SQLException, AuthorizeException {
String value = getStringValue(n); // n.getNodeValue();
// compensate for empty value getting read as "null", which won't display
if (value == null) {
value = "";
}
// //getElementData(n, "element");
String element = getAttributeValue(n, "element");
String qualifier = getAttributeValue(n, "qualifier"); // NodeValue();
// //getElementData(n,
// "qualifier");
String language = getAttributeValue(n, "language");
if (language != null) {
language = language.trim();
}
if (!isQuiet) {
System.out.println(
"\tSchema: "
+ schema
+ " Element: "
+ element
+ " Qualifier: "
+ qualifier
+ " Value: "
+ value);
}
if ("none".equals(qualifier) || "".equals(qualifier)) {
qualifier = null;
}
// if language isn't set, use the system's default value
if (StringUtils.isEmpty(language)) {
language = ConfigurationManager.getProperty("default.language");
}
// a goofy default, but there it is
if (language == null) {
language = "en";
}
if (!isTest) {
i.addMetadata(schema, element, qualifier, language, value);
} else {
// If we're just test the import, let's check that the actual metadata field exists.
MetadataSchema foundSchema = MetadataSchema.find(c, schema);
if (foundSchema == null) {
System.out.println("ERROR: schema '" + schema + "' was not found in the registry.");
return;
}
int schemaID = foundSchema.getSchemaID();
MetadataField foundField = MetadataField.findByElement(c, schemaID, element, qualifier);
if (foundField == null) {
System.out.println(
"ERROR: Metadata field: '"
+ schema
+ "."
+ element
+ "."
+ qualifier
+ "' was not found in the registry.");
return;
}
}
}
@Override
public void addMetadata(
Context context,
T dso,
MetadataField metadataField,
String lang,
List<String> values,
List<String> authorities,
List<Integer> confidences)
throws SQLException {
boolean authorityControlled = metadataAuthorityService.isAuthorityControlled(metadataField);
boolean authorityRequired = metadataAuthorityService.isAuthorityRequired(metadataField);
// We will not verify that they are valid entries in the registry
// until update() is called.
for (int i = 0; i < values.size(); i++) {
MetadataValue metadataValue = metadataValueService.create(context, dso, metadataField);
metadataValue.setLanguage(lang == null ? null : lang.trim());
// Logic to set Authority and Confidence:
// - normalize an empty string for authority to NULL.
// - if authority key is present, use given confidence or NOVALUE if not given
// - otherwise, preserve confidence if meaningful value was given since it may document a
// failed authority lookup
// - CF_UNSET signifies no authority nor meaningful confidence.
// - it's possible to have empty authority & CF_ACCEPTED if e.g. user deletes authority key
if (authorityControlled) {
if (authorities != null && authorities.get(i) != null && authorities.get(i).length() > 0) {
metadataValue.setAuthority(authorities.get(i));
metadataValue.setConfidence(
confidences == null ? Choices.CF_NOVALUE : confidences.get(i));
} else {
metadataValue.setAuthority(null);
metadataValue.setConfidence(confidences == null ? Choices.CF_UNSET : confidences.get(i));
}
// authority sanity check: if authority is required, was it supplied?
// XXX FIXME? can't throw a "real" exception here without changing all the callers to expect
// it, so use a runtime exception
if (authorityRequired
&& (metadataValue.getAuthority() == null
|| metadataValue.getAuthority().length() == 0)) {
throw new IllegalArgumentException(
"The metadata field \""
+ metadataField.toString()
+ "\" requires an authority key but none was provided. Value=\""
+ values.get(i)
+ "\"");
}
}
if (values.get(i) != null) {
// remove control unicode char
String temp = values.get(i).trim();
char[] dcvalue = temp.toCharArray();
for (int charPos = 0; charPos < dcvalue.length; charPos++) {
if (Character.isISOControl(dcvalue[charPos])
&& !String.valueOf(dcvalue[charPos]).equals("\u0009")
&& !String.valueOf(dcvalue[charPos]).equals("\n")
&& !String.valueOf(dcvalue[charPos]).equals("\r")) {
dcvalue[charPos] = ' ';
}
}
metadataValue.setValue(String.valueOf(dcvalue));
;
} else {
metadataValue.setValue(null);
}
// An update here isn't needed, this is persited upon the merge of the owning object
// metadataValueService.update(context, metadataValue);
dso.addDetails(metadataField.toString());
}
}
/**
* Return true if and only if the schema has a field with the given element and qualifier pair.
*
* @param context dspace context
* @param schemaID schema by ID
* @param element element name
* @param qualifier qualifier name
* @return true if the field exists
* @throws SQLException
* @throws AuthorizeException
*/
private static boolean hasElement(Context context, int schemaID, String element, String qualifier)
throws SQLException, AuthorizeException {
return MetadataField.findByElement(context, schemaID, element, qualifier) != null;
}