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formatting after review dog notice
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@qqmyers
qqmyers committed Oct 16, 2024
1 parent 330462e commit 816b704
Showing 1 changed file with 63 additions and 50 deletions.
113 changes: 63 additions & 50 deletions ...test/java/edu/harvard/iq/dataverse/pidproviders/doi/datacite/XmlMetadataTemplateTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,9 @@ public static void setupMocks() {

}

/** A minimal example to assure that the XMLMetadataTemplate generates output consistent with the DataCite XML v4.5 schema.
/**
* A minimal example to assure that the XMLMetadataTemplate generates output
* consistent with the DataCite XML v4.5 schema.
*/
@Test
public void testDataCiteXMLCreation() throws IOException {
Expand Down Expand Up @@ -126,7 +128,7 @@ public void testDataCiteXMLCreation() throws IOException {
doiMetadata.setAuthors(authors);
doiMetadata.setPublisher("Dataverse");
XmlMetadataTemplate template = new XmlMetadataTemplate(doiMetadata);

Dataset d = new Dataset();
GlobalId doi = new GlobalId("doi", "10.5072", "FK2/ABCDEF", null, null, null);
d.setGlobalId(doi);
Expand Down Expand Up @@ -159,11 +161,12 @@ public void testDataCiteXMLCreation() throws IOException {
try {
StreamSource source = new StreamSource(new StringReader(xml));
source.setSystemId("DataCite XML for test dataset");
assertTrue(XmlValidator.validateXmlSchema(source, new URL("https://schema.datacite.org/meta/kernel-4/metadata.xsd")));
assertTrue(XmlValidator.validateXmlSchema(source,
new URL("https://schema.datacite.org/meta/kernel-4/metadata.xsd")));
} catch (SAXException e) {
System.out.println("Invalid schema: " + e.getMessage());
}

}

/**
Expand All @@ -189,38 +192,39 @@ public void testDataCiteXMLCreationAllFields() throws IOException {
dv.setVersionState(VersionState.DRAFT);

testDatasetField.setDatasetVersion(dv);

File datasetVersionJson = new File("src/test/java/edu/harvard/iq/dataverse/export/dataset-all-defaults.txt");
String datasetVersionAsJson = new String(Files.readAllBytes(Paths.get(datasetVersionJson.getAbsolutePath())));
JsonObject datasetJson = JsonUtil.getJsonObject(datasetVersionAsJson);

GlobalId doi = new GlobalId("doi", datasetJson.getString("authority"), datasetJson.getString("identifier"), null, null, null);

GlobalId doi = new GlobalId("doi", datasetJson.getString("authority"), datasetJson.getString("identifier"),
null, null, null);
d.setGlobalId(doi);


List<DatasetField> fields = assertDoesNotThrow(() -> XmlMetadataTemplateTest.parseMetadataBlocks(datasetJson.getJsonObject("datasetVersion").getJsonObject("metadataBlocks")));
List<DatasetField> fields = assertDoesNotThrow(() -> XmlMetadataTemplateTest
.parseMetadataBlocks(datasetJson.getJsonObject("datasetVersion").getJsonObject("metadataBlocks")));
dv.setDatasetFields(fields);

ArrayList<DatasetVersion> dsvs = new ArrayList<>();
dsvs.add(0, dv);
d.setVersions(dsvs);
DatasetType dType = new DatasetType();
dType.setName(DatasetType.DATASET_TYPE_DATASET);
d.setDatasetType(dType);
String xml = DOIDataCiteRegisterService.getMetadataFromDvObject(
dv.getDataset().getGlobalId().asString(), new DataCitation(dv).getDataCiteMetadata(), dv.getDataset());
String xml = DOIDataCiteRegisterService.getMetadataFromDvObject(dv.getDataset().getGlobalId().asString(),
new DataCitation(dv).getDataCiteMetadata(), dv.getDataset());
System.out.println("Output from dataset-all-defaults is " + xml);
try {
StreamSource source = new StreamSource(new StringReader(xml));
source.setSystemId("DataCite XML for test dataset");
assertTrue(XmlValidator.validateXmlSchema(source, new URL("https://schema.datacite.org/meta/kernel-4/metadata.xsd")));
assertTrue(XmlValidator.validateXmlSchema(source,
new URL("https://schema.datacite.org/meta/kernel-4/metadata.xsd")));
} catch (SAXException e) {
System.out.println("Invalid schema: " + e.getMessage());
}

}


/**
* Mock Utility Methods - These methods support importing DatasetFields from the
* Dataverse JSON export format. They assume that any DatasetFieldType
Expand All @@ -230,9 +234,9 @@ public void testDataCiteXMLCreationAllFields() throws IOException {
* references and DatasetFieldType-related error checking removed.
*/
public static List<DatasetField> parseMetadataBlocks(JsonObject json) throws JsonParseException {

Map<String, DatasetFieldType> existingTypes = new HashMap<>();

Set<String> keys = json.keySet();
List<DatasetField> fields = new LinkedList<>();

Expand All @@ -259,18 +263,18 @@ private static List<DatasetField> parseFieldsFromArray(JsonArray fieldsArray, Bo
}
return fields;

}
}


public static DatasetField parseField(JsonObject json, Boolean testType, MetadataBlock block, Map<String, DatasetFieldType> existingTypes) throws JsonParseException {
public static DatasetField parseField(JsonObject json, Boolean testType, MetadataBlock block,
Map<String, DatasetFieldType> existingTypes) throws JsonParseException {
if (json == null) {
return null;
}

DatasetField ret = new DatasetField();
String fieldName = json.getString("typeName", "");
String typeClass = json.getString("typeClass", "");
if(!existingTypes.containsKey(fieldName)) {
if (!existingTypes.containsKey(fieldName)) {
boolean multiple = json.getBoolean("multiple");
DatasetFieldType fieldType = new DatasetFieldType();
fieldType.setName(fieldName);
Expand All @@ -294,32 +298,35 @@ public static DatasetField parseField(JsonObject json, Boolean testType, Metad

return ret;
}

public static void parseCompoundValue(DatasetField dsf, DatasetFieldType compoundType, JsonObject json, Boolean testType, MetadataBlock block, Map<String, DatasetFieldType> existingTypes) throws JsonParseException {

public static void parseCompoundValue(DatasetField dsf, DatasetFieldType compoundType, JsonObject json,
Boolean testType, MetadataBlock block, Map<String, DatasetFieldType> existingTypes)
throws JsonParseException {
List<ControlledVocabularyException> vocabExceptions = new ArrayList<>();
List<DatasetFieldCompoundValue> vals = new LinkedList<>();
if (compoundType.isAllowMultiples()) {
int order = 0;
try {
json.getJsonArray("value").getValuesAs(JsonObject.class);
} catch (ClassCastException cce) {
throw new JsonParseException("Invalid values submitted for " + compoundType.getName() + ". It should be an array of values.");
throw new JsonParseException("Invalid values submitted for " + compoundType.getName()
+ ". It should be an array of values.");
}
for (JsonObject obj : json.getJsonArray("value").getValuesAs(JsonObject.class)) {
DatasetFieldCompoundValue cv = new DatasetFieldCompoundValue();
List<DatasetField> fields = new LinkedList<>();
for (String fieldName : obj.keySet()) {
JsonObject childFieldJson = obj.getJsonObject(fieldName);
DatasetField f=null;
DatasetField f = null;
try {
f = parseField(childFieldJson, testType, block, existingTypes);
} catch(ControlledVocabularyException ex) {
} catch (ControlledVocabularyException ex) {
vocabExceptions.add(ex);
}
if (f!=null) {

if (f != null) {
f.setParentDatasetFieldCompoundValue(cv);
fields.add(f);
fields.add(f);
}
}
if (!fields.isEmpty()) {
Expand All @@ -330,22 +337,20 @@ public static void parseCompoundValue(DatasetField dsf, DatasetFieldType compoun
order++;
}



} else {

DatasetFieldCompoundValue cv = new DatasetFieldCompoundValue();
List<DatasetField> fields = new LinkedList<>();
JsonObject value = json.getJsonObject("value");
for (String key : value.keySet()) {
JsonObject childFieldJson = value.getJsonObject(key);
DatasetField f = null;
try {
f=parseField(childFieldJson, testType, block, existingTypes);
} catch(ControlledVocabularyException ex ) {
f = parseField(childFieldJson, testType, block, existingTypes);
} catch (ControlledVocabularyException ex) {
vocabExceptions.add(ex);
}
if (f!=null) {
if (f != null) {
f.setParentDatasetFieldCompoundValue(cv);
fields.add(f);
}
Expand All @@ -354,10 +359,11 @@ public static void parseCompoundValue(DatasetField dsf, DatasetFieldType compoun
cv.setChildDatasetFields(fields);
vals.add(cv);
}
}

}
if (!vocabExceptions.isEmpty()) {
throw new CompoundVocabularyException( "Invalid controlled vocabulary in compound field ", vocabExceptions, vals);
throw new CompoundVocabularyException("Invalid controlled vocabulary in compound field ", vocabExceptions,
vals);
}

for (DatasetFieldCompoundValue dsfcv : vals) {
Expand All @@ -366,13 +372,15 @@ public static void parseCompoundValue(DatasetField dsf, DatasetFieldType compoun
dsf.setDatasetFieldCompoundValues(vals);
}

public static void parsePrimitiveValue(DatasetField dsf, DatasetFieldType dft , JsonObject json) throws JsonParseException {
public static void parsePrimitiveValue(DatasetField dsf, DatasetFieldType dft, JsonObject json)
throws JsonParseException {
List<DatasetFieldValue> vals = new LinkedList<>();
if (dft.isAllowMultiples()) {
try {
json.getJsonArray("value").getValuesAs(JsonObject.class);
try {
json.getJsonArray("value").getValuesAs(JsonObject.class);
} catch (ClassCastException cce) {
throw new JsonParseException("Invalid values submitted for " + dft.getName() + ". It should be an array of values.");
throw new JsonParseException(
"Invalid values submitted for " + dft.getName() + ". It should be an array of values.");
}
for (JsonString val : json.getJsonArray("value").getValuesAs(JsonString.class)) {
DatasetFieldValue datasetFieldValue = new DatasetFieldValue(dsf);
Expand All @@ -382,10 +390,12 @@ public static void parsePrimitiveValue(DatasetField dsf, DatasetFieldType dft ,
}

} else {
try {json.getString("value");}
catch (ClassCastException cce) {
throw new JsonParseException("Invalid value submitted for " + dft.getName() + ". It should be a single value.");
}
try {
json.getString("value");
} catch (ClassCastException cce) {
throw new JsonParseException(
"Invalid value submitted for " + dft.getName() + ". It should be a single value.");
}
DatasetFieldValue datasetFieldValue = new DatasetFieldValue();
datasetFieldValue.setValue(json.getString("value", "").trim());
datasetFieldValue.setDatasetField(dsf);
Expand All @@ -394,15 +404,17 @@ public static void parsePrimitiveValue(DatasetField dsf, DatasetFieldType dft ,

dsf.setDatasetFieldValues(vals);
}

public static void parseControlledVocabularyValue(DatasetField dsf, DatasetFieldType cvvType, JsonObject json) throws JsonParseException {

public static void parseControlledVocabularyValue(DatasetField dsf, DatasetFieldType cvvType, JsonObject json)
throws JsonParseException {
List<ControlledVocabularyValue> vals = new LinkedList<>();
try {
if (cvvType.isAllowMultiples()) {
try {
json.getJsonArray("value").getValuesAs(JsonObject.class);
} catch (ClassCastException cce) {
throw new JsonParseException("Invalid values submitted for " + cvvType.getName() + ". It should be an array of values.");
throw new JsonParseException(
"Invalid values submitted for " + cvvType.getName() + ". It should be an array of values.");
}
for (JsonString strVal : json.getJsonArray("value").getValuesAs(JsonString.class)) {
String strValue = strVal.getString();
Expand All @@ -416,7 +428,8 @@ public static void parseControlledVocabularyValue(DatasetField dsf, DatasetField
try {
json.getString("value");
} catch (ClassCastException cce) {
throw new JsonParseException("Invalid value submitted for " + cvvType.getName() + ". It should be a single value.");
throw new JsonParseException(
"Invalid value submitted for " + cvvType.getName() + ". It should be a single value.");
}
String strValue = json.getString("value", "");
ControlledVocabularyValue cvv = new ControlledVocabularyValue();
Expand Down

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