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2471 destroy command should unregister doi #6060

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merged 4 commits into from
Aug 5, 2019
Merged

2471 destroy command should unregister doi #6060

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46e19f5
#2471 add generic metadata for destroyed datasets and files
sekmiller Jul 26, 2019
990fc28
Merge branch 'develop' into 2471-destroy-command-should-unregister-doi
sekmiller Jul 26, 2019
bd9491f
#2471 implement changes suggested in code review
sekmiller Aug 2, 2019
4cd5863
Merge branch 'develop' into 2471-destroy-command-should-unregister-doi
sekmiller Aug 2, 2019
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15 changes: 14 additions & 1 deletion src/main/java/edu/harvard/iq/dataverse/AbstractGlobalIdServiceBean.java
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,20 @@ protected Map<String, String> addBasicMetadata(DvObject dvObjectIn, Map<String,
metadata.put("datacite.publisher", producerString);
metadata.put("datacite.publicationyear", generateYear(dvObjectIn));
return metadata;
}
}

protected HashMap<String, String> addMetadataForDestroyedDataset(DvObject dvObjectIn) {
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Should the return type be Map instead of the more specific HashMap?

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Sure. Will change.

HashMap<String, String> metadata = new HashMap<>();
String authorString = ":unav";
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Where is this special string from?

String producerString = ":unav";
String titleString = "This item has been removed from publication";

metadata.put("datacite.creator", authorString);
metadata.put("datacite.title", titleString);
metadata.put("datacite.publisher", producerString);
metadata.put("datacite.publicationyear", "9999");
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@landreev landreev Aug 2, 2019 •
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I agree with @bencomp, that special strings should generally be defined as constants somewhere.
Also, I find this a little confusing that this method is in AbstractGlobalIdServiceBean - but it does something that's very specific to the Datacite metadata. I understand you are modeling this method after the already existing method above (addBasicMetadata()) that does the same thing... I'm assuming we do this in the "abstract" bean because this datacite metadata format is used by both the Datacite and EZID DOI implementations. I still feel this could be confusing for the next person working with this code; could you rename these methods, to somehow indicate that they are specific to the DOI implementations - but not to Handles (that extends the same Abstract service class); something like addDOIMetadataForDestroyedDataset() etc.?

return metadata;
}

protected String getTargetUrl(DvObject dvObjectIn) {
logger.log(Level.FINE,"getTargetUrl");
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71 changes: 52 additions & 19 deletions src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java
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Expand Up @@ -118,20 +118,19 @@ public String registerIdentifier(String identifier, Map<String, String> metadata

public String deactivateIdentifier(String identifier, HashMap<String, String> metadata, DvObject dvObject) {
String retString = "";
DOIDataCiteRegisterCache rc = findByDOI(identifier);

try {
DataCiteRESTfullClient client = getClient();
if (rc != null) {
rc.setStatus("unavailable");
retString = client.inactiveDataset(identifier.substring(identifier.indexOf(":") + 1));
}
String metadataString = getMetadataForDeactivateIdentifier(identifier, metadata, dvObject);
retString = client.postMetadata(metadataString);
retString = client.inactiveDataset(identifier.substring(identifier.indexOf(":") + 1));
} catch (IOException io) {

}
return retString;
}

public static String getMetadataFromDvObject(String identifier, Map<String, String> metadata, DvObject dvObject) {
public static String getMetadataFromDvObject(String identifier, Map<String, String> metadata, DvObject dvObject) {

Dataset dataset = null;

Expand Down Expand Up @@ -189,6 +188,32 @@ public static String getMetadataFromDvObject(String identifier, Map<String, Stri
return xmlMetadata;
}

public static String getMetadataForDeactivateIdentifier(String identifier, Map<String, String> metadata, DvObject dvObject) {

System.out.print("Start of getMetadataForDeactivateIdentifier: ");
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Why would you not use logging?

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This is debug code that should have been removed altogether. I will delete it.

DataCiteMetadataTemplate metadataTemplate = new DataCiteMetadataTemplate();
metadataTemplate.setIdentifier(identifier.substring(identifier.indexOf(':') + 1));
metadataTemplate.setCreators(Util.getListFromStr(metadata.get("datacite.creator")));

metadataTemplate.setDescription(":unav");
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Where does this special value come from?

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The special values here come from the DataCite Metadata schema https://support.datacite.org/docs/schema-values-unknown-information-v41

My intent for this is to mask any identifying information since the Dataset in question has been destroyed by Dataverse and in the opinion of the Dataverse admin should never have been created/published.


String title =metadata.get("datacite.title");

System.out.print("Map metadata title: "+ metadata.get("datacite.title"));

metadataTemplate.setAuthors(null);

metadataTemplate.setTitle(title);
String producerString = ":unav";

metadataTemplate.setPublisher(producerString);
metadataTemplate.setPublisherYear(metadata.get("datacite.publicationyear"));

String xmlMetadata = metadataTemplate.generateXML(dvObject);
logger.log(Level.FINE, "XML to send to DataCite: {0}", xmlMetadata);
return xmlMetadata;
}

public String modifyIdentifier(String identifier, HashMap<String, String> metadata, DvObject dvObject) throws IOException {

String xmlMetadata = getMetadataFromDvObject(identifier, metadata, dvObject);
Expand Down Expand Up @@ -279,6 +304,8 @@ public HashMap<String, String> getMetadata(String identifier) throws IOException
DOIDataCiteRegisterCache rc = findByDOI(identifier);
if (rc != null) {
metadata.put("_status", rc.getStatus());
} else {
metadata.put("_status", "public");
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Should this public be a constant?

}
} catch (RuntimeException e) {
logger.log(Level.INFO, identifier, e);
Expand Down Expand Up @@ -418,8 +445,9 @@ public String generateXML(DvObject dvObject) {
.replace("${publisher}", this.publisher)
.replace("${publisherYear}", publisherYearFinal)
.replace("${description}", this.description);

StringBuilder creatorsElement = new StringBuilder();
if (!authors.isEmpty()) {
if (authors!= null && !authors.isEmpty()) {
for (DatasetAuthor author : authors) {
creatorsElement.append("<creator><creatorName>");
creatorsElement.append(author.getName().getDisplayValue());
Expand Down Expand Up @@ -450,21 +478,26 @@ public String generateXML(DvObject dvObject) {
xmlMetadata = xmlMetadata.replace("${creators}", creatorsElement.toString());

StringBuilder contributorsElement = new StringBuilder();
for (String[] contact : this.getContacts()) {
if (!contact[0].isEmpty()) {
contributorsElement.append("<contributor contributorType=\"ContactPerson\"><contributorName>" + contact[0] + "</contributorName>");
if (!contact[1].isEmpty()) {
contributorsElement.append("<affiliation>" + contact[1] + "</affiliation>");
if (this.getContacts() != null) {
for (String[] contact : this.getContacts()) {
if (!contact[0].isEmpty()) {
contributorsElement.append("<contributor contributorType=\"ContactPerson\"><contributorName>" + contact[0] + "</contributorName>");
if (!contact[1].isEmpty()) {
contributorsElement.append("<affiliation>" + contact[1] + "</affiliation>");
}
contributorsElement.append("</contributor>");
}
contributorsElement.append("</contributor>");
}
}
for (String[] producer : this.getProducers()) {
contributorsElement.append("<contributor contributorType=\"Producer\"><contributorName>" + producer[0] + "</contributorName>");
if (!producer[1].isEmpty()) {
contributorsElement.append("<affiliation>" + producer[1] + "</affiliation>");

if (this.getProducers() != null) {
for (String[] producer : this.getProducers()) {
contributorsElement.append("<contributor contributorType=\"Producer\"><contributorName>" + producer[0] + "</contributorName>");
if (!producer[1].isEmpty()) {
contributorsElement.append("<affiliation>" + producer[1] + "</affiliation>");
}
contributorsElement.append("</contributor>");
}
contributorsElement.append("</contributor>");
}

String relIdentifiers = generateRelatedIdentifiers(dvObject);
Expand Down
14 changes: 7 additions & 7 deletions src/main/java/edu/harvard/iq/dataverse/DOIDataCiteServiceBean.java
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Expand Up @@ -176,10 +176,10 @@ public void deleteIdentifier(DvObject dvObject) throws Exception {
}

String idStatus = doiMetadata.get("_status");

if ( idStatus != null ) {
switch ( idStatus ) {
case "reserved":
case "draft":
logger.log(Level.INFO, "Delete status is reserved..");
try {
doiDataCiteRegisterService.deleteIdentifier(identifier);
Expand All @@ -189,15 +189,15 @@ public void deleteIdentifier(DvObject dvObject) throws Exception {
break;

case "public":
case "findable":
//if public then it has been released set to unavailable and reset target to n2t url
updateIdentifierStatus(dvObject, "unavailable");
HashMap<String, String> metadata = addMetadataForDestroyedDataset(dvObject);
metadata.put("_status", "registered");
metadata.put("_target", getTargetUrl(dvObject));
doiDataCiteRegisterService.modifyIdentifier(identifier, metadata, dvObject);
doiDataCiteRegisterService.deactivateIdentifier(identifier, metadata, dvObject);
break;
}
return;
}
if (idStatus != null && idStatus.equals("public")) {
//if public then it has been released set to unavailable and reset target to n2t url
doiDataCiteRegisterService.deactivateIdentifier(identifier, doiMetadata, dvObject);
}
}

Expand Down