Revision 8190
Added by ben leinfelder over 11 years ago
| src/edu/ucsb/nceas/metacat/dataone/MNodeService.java | ||
|---|---|---|
| 30 | 30 |
import java.io.FileOutputStream; |
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import java.io.IOException; |
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import java.io.InputStream; |
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import java.io.InputStreamReader; |
|
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import java.io.OutputStreamWriter; |
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import java.io.UnsupportedEncodingException; |
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import java.io.Writer; |
| ... | ... | |
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import org.apache.commons.beanutils.BeanUtils; |
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import org.apache.commons.io.IOUtils; |
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import org.apache.log4j.Logger; |
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import org.apache.wicket.protocol.http.mock.MockHttpServletRequest; |
|
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import org.dataone.client.CNode; |
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import org.dataone.client.D1Client; |
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import org.dataone.client.MNode; |
| ... | ... | |
| 137 | 139 |
import edu.ucsb.nceas.metacat.util.DocumentUtil; |
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import edu.ucsb.nceas.metacat.util.SystemUtil; |
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import edu.ucsb.nceas.utilities.PropertyNotFoundException; |
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import edu.ucsb.nceas.utilities.XMLUtilities; |
|
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import gov.loc.repository.bagit.Bag; |
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import gov.loc.repository.bagit.BagFactory; |
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import gov.loc.repository.bagit.writer.impl.ZipWriter; |
| ... | ... | |
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this.update(session, originalIdentifier, inputStream, newIdentifier, sysmeta); |
| 1606 | 1609 |
|
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// update ORE that references the scimeta |
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// TODO: better ORE location algorithm -- this is just convention for generated resource maps and is fragile
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// first try the naive method, then check the SOLR index
|
|
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try {
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String localId = IdentifierManager.getInstance().getLocalId(originalIdentifier.getValue()); |
| 1611 | 1614 |
|
| ... | ... | |
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} catch (NotFound nf) {
|
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// this is probably okay for many sci meta data docs |
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logMetacat.warn("No potential ORE map found for: " + potentialOreIdentifier.getValue());
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// try the SOLR index |
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List<Identifier> potentialOreIdentifiers = this.lookupOreFor(originalIdentifier); |
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if (potentialOreIdentifiers != null) {
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potentialOreIdentifier = potentialOreIdentifiers.get(0); |
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try {
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oreInputStream = this.get(session, potentialOreIdentifier); |
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} catch (NotFound nf2) {
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// this is probably okay for many sci meta data docs |
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logMetacat.warn("No potential ORE map found for: " + potentialOreIdentifier.getValue());
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} |
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} |
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} |
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if (oreInputStream != null) {
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Identifier newOreIdentifier = MNodeService.getInstance(request).generateIdentifier(session, MNodeService.UUID_SCHEME, null); |
| ... | ... | |
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} |
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|
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/** |
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* Determines if we already have registered an ORE map for this package |
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* NOTE: uses a solr query to locate OREs for the object |
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* @param guid of the EML/packaging object |
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* @return list of resource map identifiers for the given pid |
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*/ |
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public List<Identifier> lookupOreFor(Identifier guid) {
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// Search for the ORE if we can find it |
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String pid = guid.getValue(); |
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List<Identifier> retList = null; |
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try {
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MockHttpServletRequest request = new MockHttpServletRequest(null, null, null); |
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String query = "fl=id,resourceMap&wt=xml&q=formatType:METADATA+-obsoletedBy:*+resourceMap:*+id:\"" + pid + "\""; |
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InputStream results = this.query("solr", query);
|
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org.w3c.dom.Node rootNode = XMLUtilities.getXMLReaderAsDOMTreeRootNode(new InputStreamReader(results, "UTF-8")); |
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//String resultString = XMLUtilities.getDOMTreeAsString(rootNode); |
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org.w3c.dom.NodeList nodeList = XMLUtilities.getNodeListWithXPath(rootNode, "//arr[@name=\"resourceMap\"]/str"); |
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if (nodeList != null && nodeList.getLength() > 0) {
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retList = new ArrayList<Identifier>(); |
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for (int i = 0; i < nodeList.getLength(); i++) {
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String found = nodeList.item(i).getFirstChild().getNodeValue(); |
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Identifier oreId = new Identifier(); |
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oreId.setValue(found); |
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retList.add(oreId); |
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} |
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} |
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} catch (Exception e) {
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logMetacat.error("Error checking for resourceMap[s] on pid " + pid + ". " + e.getMessage(), e);
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} |
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|
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return retList; |
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} |
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|
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/** |
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* Packages the given package in a Bagit collection for download |
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* @param pid |
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* @throws NotImplemented |
| src/edu/ucsb/nceas/metacat/dataone/SystemMetadataFactory.java | ||
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| 28 | 28 |
import java.io.File; |
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import java.io.IOException; |
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import java.io.InputStream; |
| 31 |
import java.io.InputStreamReader; |
|
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import java.math.BigInteger; |
| 33 | 32 |
import java.net.URL; |
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import java.net.URLConnection; |
| ... | ... | |
| 71 | 70 |
import org.dataone.service.util.DateTimeMarshaller; |
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import org.dspace.foresite.ResourceMap; |
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import org.jibx.runtime.JiBXException; |
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import org.w3c.dom.Node; |
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import org.w3c.dom.NodeList; |
|
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import org.xml.sax.SAXException; |
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|
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import java.util.Calendar; |
| ... | ... | |
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import edu.ucsb.nceas.metacat.util.DocumentUtil; |
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import edu.ucsb.nceas.utilities.ParseLSIDException; |
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import edu.ucsb.nceas.utilities.PropertyNotFoundException; |
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import edu.ucsb.nceas.utilities.XMLUtilities; |
|
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|
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public class SystemMetadataFactory {
|
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|
| ... | ... | |
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return sysMeta; |
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} |
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|
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/** |
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/** |
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* Checks for potential ORE object existence |
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* @param identifier |
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* @return |
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*/ |
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public static boolean oreExistsFor(Identifier identifier) {
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MockHttpServletRequest request = new MockHttpServletRequest(null, null, null); |
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List<Identifier> ids = MNodeService.getInstance(request).lookupOreFor(identifier); |
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return (ids != null && ids.size() > 0); |
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} |
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|
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/** |
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* Generate SystemMetadata for any object in the object store that does |
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* not already have it. SystemMetadata documents themselves, are, of course, |
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* exempt. This is a utility method for migration of existing object |
| ... | ... | |
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} |
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logMetacat.info("done generating system metadata for given list");
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} |
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|
|
| 665 |
/** |
|
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* Determines if we already have registered an ORE map for this package |
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* NOTE: uses a solr query to locate OREs for the object |
|
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* @param guid of the EML/packaging object |
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* @return true if there is an ORE map for the given package |
|
| 670 |
*/ |
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| 671 |
public static boolean oreExistsFor(Identifier guid) {
|
|
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// Search for the ORE if we can find it |
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String pid = guid.getValue(); |
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MockHttpServletRequest request = new MockHttpServletRequest(null, null, null); |
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String query = "fl=id,resourceMap&wt=xml&q=formatType:METADATA+-obsoletedBy:*+resourceMap:*+id:\"" + pid + "\""; |
|
| 676 |
try {
|
|
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InputStream results = MNodeService.getInstance(request).query("solr", query);
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|
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Node rootNode = XMLUtilities.getXMLReaderAsDOMTreeRootNode(new InputStreamReader(results, "UTF-8")); |
|
| 679 |
//String resultString = XMLUtilities.getDOMTreeAsString(rootNode); |
|
| 680 |
NodeList nodeList = XMLUtilities.getNodeListWithXPath(rootNode, "//arr[@name=\"resourceMap\"]/str"); |
|
| 681 |
if (nodeList != null && nodeList.getLength() > 0) {
|
|
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//String found = nodeList.item(0).getFirstChild().getNodeValue(); |
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| 683 |
return true; |
|
| 684 |
} |
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| 685 |
} catch (Exception e) {
|
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| 686 |
logMetacat.error("Error checking for resourceMap[s] on pid " + pid + ". " + e.getMessage(), e);
|
|
| 687 |
} |
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| 688 |
|
|
| 689 |
return false; |
|
| 690 |
} |
|
| 691 | 671 |
|
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/** |
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* Find the size (in bytes) of a stream. Note: This needs to refactored out |
Also available in: Unified diff
better checking for ORE maps when publishing DOIs (need to update the packages that contain sci meta). https://projects.ecoinformatics.org/ecoinfo/issues/6061