send relatedIdentifier to DataCite #4782 #4795

pdurbin · 2018-06-28T20:37:57Z

connects to #4782

coveralls · 2018-06-28T20:48:09Z

Coverage decreased (-0.01%) to 15.531% when pulling 7d3e216 on 4782-datacite into 8cfca31 on develop.

oscardssmith · 2018-06-29T19:56:44Z

workingDataCiteMetadataTemplate-Files.xml

@@ -1,20 +0,0 @@
-<resource xsi:schemaLocation="http://datacite.org/schema/kernel-3 http://schema.datacite.org/meta/kernel-3/metadata.xsd"


Why isn't this necessary anymore?

Different DataCite schema version maybe (but I'd expect that to be a version change, rather than deletion)?

I removed workingDataCiteMetadataTemplate-Files.xml because it's not used and is sitting in the root of the repo. The file that actually is being used is src/main/resources/edu/harvard/iq/dataverse/datacite_metadata_template.xml but I'm grumpy that it's in the main "dataverse" package, which is a dumping ground, rather than being in a package such as "templates" to help keep the code organized.

… save them before I switched over to develop. #4782

This a topic branch and should be merged to 4782-DataCite

…ry comments #4782

Conflicts: src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java src/main/java/edu/harvard/iq/dataverse/DOIDataCiteServiceBean.java src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java

matthew-a-dunlap · 2018-07-25T20:58:30Z

src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java

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


Kinda picky, but some of the indentation and whitespace in this file could be cleaned up. Other ones seem ok though.

fyi, alt shift f does this for a full file.

matthew-a-dunlap · 2018-07-25T21:02:30Z

src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java

@@ -144,8 +147,17 @@ private String getMetadataFromDvObject(String identifier, Map<String, String> me
        }
        metadataTemplate.setPublisher(producerString);
        metadataTemplate.setPublisherYear(metadata.get("datacite.publicationyear"));
-        String xmlMetadata = metadataTemplate.generateXML();
-        logger.log(Level.FINE, "XML to send to DataCite: {0}", xmlMetadata);
+        if (dvObject.isInstanceofDataFile()) {


We do a check for isInstanceofDataFile() a few lines up, can we collapse these two bits of logic together?

matthew-a-dunlap · 2018-07-25T21:07:05Z

src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java

@@ -211,6 +223,26 @@ public String modifyIdentifier(String identifier, HashMap<String, String> metada
        }
        return retString;
    }
+
+    public String setUpFileIdentifiers(DvObject dvObject)


Is this used? I tried searching it in the project and don't see it.

matthew-a-dunlap · 2018-07-25T21:12:00Z

src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java

+                    sb.append("</relatedIdentifiers>");
+                }
+            }
+        } else if (dvObject.isInstanceofDataFile()){


Is there ever a case where we have a data file but for some reason it doesn't know its owner?

I'm pretty sure the answer to that is no. Data files will have an owner if they are in a dataset.

matthew-a-dunlap · 2018-07-25T21:13:24Z

src/main/java/edu/harvard/iq/dataverse/DataFile.java

@@ -405,7 +405,7 @@ public void setOwner(Dataset dataset) {
 //        return this.fileSystemName;
 //    }
 //
-//    public void setStorageIdentifier(String storageIdentifier) {
+//    public void setStorageIdentifier(String storageifier) {


I think this was an accident.

matthew-a-dunlap · 2018-07-25T21:13:51Z

src/main/java/edu/harvard/iq/dataverse/DatasetPage.java

@@ -1378,7 +1378,7 @@ private String init(boolean initFull) {
                // Set Working Version and Dataset by PersistentID
                dataset = datasetService.findByGlobalId(persistentId);
                if (dataset == null) {
-                    logger.warning("No such dataset: "+persistentId);
+                    logger.warning("++++No such dataset: "+persistentId);


Is this and the one below also an accident? Looks weird.

If you want to keep these warning messages in for production, its good to have a bit more description about where the error is happening so its easier to debug from the log files.

@matthew-a-dunlap

…eft by @matthew-a-dunlap #4782

matthew-a-dunlap

Looks good!

oscardssmith · 2018-07-26T13:57:45Z

src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java

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


fyi, alt shift f does this for a full file.

oscardssmith · 2018-07-26T18:27:10Z

src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java

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


this should probably be back to fine

oscardssmith · 2018-07-26T18:29:13Z

src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java

+
+                datafileIdentifiers = new ArrayList<>();
+                for (DataFile dataFile : dataset.getFiles()) {
+                    String add = "";


Should this use a stringbuilder for performance?

…nerateRelatedIdentifiers method so it used only a StringBuilder instead of strings and StringBuilder

…atacite

send relatedIdentifier to DataCite #4782

ac5a485

pdurbin mentioned this pull request Jun 28, 2018

Add RelatedIdentifier of Dataset to File Metadata sent to DataCite #4782

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oscardssmith reviewed Jun 29, 2018

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benjamin-martinez and others added 6 commits July 13, 2018 12:06

In the process of testing. This work isn't finished, I just needed to…

e883110

… save them before I switched over to develop. #4782

Some changes to how Dataset XML will be sent to DataCite. #4782

fa08107

This a topic branch and should be merged to 4782-DataCite

#4782 related identifier metadata

f436817

Generates File DOIs prior to dataset publication #4782

ca8e332

Closing changes. I basically just removed extra loggers and unnecessa…

91abbc5

…ry comments #4782

matthew-a-dunlap suggested changes Jul 25, 2018

View reviewed changes

Some minor formatting and refactoring changes based on the comments l…

eeea6f8

…eft by @matthew-a-dunlap #4782

matthew-a-dunlap approved these changes Jul 26, 2018

View reviewed changes

oscardssmith reviewed Jul 26, 2018

View reviewed changes

Changed a logger message from INFO to FINE and then refactored the ge…

995902b

…nerateRelatedIdentifiers method so it used only a StringBuilder instead of strings and StringBuilder

oscardssmith approved these changes Jul 26, 2018

View reviewed changes

benjamin-martinez and others added 3 commits July 26, 2018 17:08

Merge branch 'develop' into 4782-datacite #4782

0343d1f

Merge branch 'develop' into 4782-datacite

fe9a22e

Merge branch '4782-datacite' of github.com:IQSS/dataverse into 4782-d…

7d3e216

…atacite

kcondon merged commit 8c82278 into develop Jul 27, 2018

kcondon deleted the 4782-datacite branch July 27, 2018 21:22

pdurbin added this to the 4.9.2 - Stata Upgrades, etc. milestone Aug 9, 2018

philippconzett mentioned this pull request Sep 24, 2018

resourceType for dataset files #5086

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send relatedIdentifier to DataCite #4782 #4795

send relatedIdentifier to DataCite #4782 #4795

pdurbin commented Jun 28, 2018

coveralls commented Jun 28, 2018 •

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oscardssmith Jul 26, 2018

oscardssmith Jul 26, 2018

		@@ -1,20 +0,0 @@
		<resource xsi:schemaLocation="http://datacite.org/schema/kernel-3 http://schema.datacite.org/meta/kernel-3/metadata.xsd"



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

send relatedIdentifier to DataCite #4782 #4795

send relatedIdentifier to DataCite #4782 #4795

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coveralls commented Jun 28, 2018 •

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