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Data Capture Module: add dataType to citation IQSS#3145
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pdurbin committed May 31, 2016
1 parent 2935cde commit c717523
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2 changes: 2 additions & 0 deletions conf/solr/4.6.0/schema.xml
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Expand Up @@ -389,6 +389,7 @@
<field name="dataCollectionSituation" type="text_en" multiValued="false" stored="true" indexed="true"/>
<field name="dataCollector" type="text_en" multiValued="false" stored="true" indexed="true"/>
<field name="dataSources" type="text_en" multiValued="true" stored="true" indexed="true"/>
<field name="dataType" type="text_en" multiValued="false" stored="true" indexed="true"/>
<field name="datadePublicao" type="text_en" multiValued="false" stored="true" indexed="true"/>
<field name="datasetContact" type="text_en" multiValued="true" stored="true" indexed="true"/>
<field name="datasetContactAffiliation" type="text_en" multiValued="true" stored="true" indexed="true"/>
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<copyField source="dataCollectionSituation" dest="text" maxChars="3000"/>
<copyField source="dataCollector" dest="text" maxChars="3000"/>
<copyField source="dataSources" dest="text" maxChars="3000"/>
<copyField source="dataType" dest="text" maxChars="3000"/>
<copyField source="datadePublicao" dest="text" maxChars="3000"/>
<copyField source="datasetContact" dest="text" maxChars="3000"/>
<copyField source="datasetContactAffiliation" dest="text" maxChars="3000"/>
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7 changes: 6 additions & 1 deletion scripts/api/data/metadatablocks/citation.tsv
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Expand Up @@ -78,6 +78,7 @@
originOfSources Origin of Sources For historical materials, information about the origin of the sources and the rules followed in establishing the sources should be specified. textbox 74 FALSE FALSE FALSE FALSE FALSE FALSE citation
characteristicOfSources Characteristic of Sources Noted Assessment of characteristics and source material. textbox 75 FALSE FALSE FALSE FALSE FALSE FALSE citation
accessToSources Documentation and Access to Sources Level of documentation of the original sources. textbox 76 FALSE FALSE FALSE FALSE FALSE FALSE citation
dataType Data Type We currently support X-ray diffraction datasets. If you would like to deposit any other dataset type please contact us first at help@sbgrid.org. text 1 TRUE TRUE FALSE TRUE FALSE FALSE citation

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pdurbin May 31, 2016

Author Owner

Whoops, we can't leave the SBGrid email address in here.
#controlledVocabulary DatasetField Value identifier displayOrder
subject Agricultural Sciences D01 0
subject Arts and Humanities D0 1
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language Yoruba 181
language Zhuang, Chuang 182
language Zulu 183
language Not applicable 184
language Not applicable 184
dataType X-Ray Diffraction xray 0
dataType Structural Model sm 1

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pdurbin Jun 9, 2016

Author Owner

The "Structural Model" dataType may have data that changes: http://irclog.iq.harvard.edu/dataverse/2016-06-09#i_36529
dataType Micro-Electron Diffraction me 2
dataType Lattice Light-Sheet Microscopy llsm 3
52 changes: 52 additions & 0 deletions src/test/java/edu/harvard/iq/dataverse/api/DatasetsIT.java
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Expand Up @@ -8,6 +8,12 @@
import org.junit.AfterClass;
import static com.jayway.restassured.RestAssured.given;
import static junit.framework.Assert.assertEquals;
import com.jayway.restassured.path.json.JsonPath;
import java.util.List;
import java.util.Map;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;

public class DatasetsIT {

Expand Down Expand Up @@ -40,6 +46,52 @@ public void testCreateDataset() {

}

@Test
public void testCreateDatasetWithDcmDependency() {

Response createUser = UtilIT.createRandomUser();
createUser.prettyPrint();
String username = UtilIT.getUsernameFromResponse(createUser);
String apiToken = UtilIT.getApiTokenFromResponse(createUser);

Response createDataverseResponse = UtilIT.createRandomDataverse(apiToken);
createDataverseResponse.prettyPrint();
String dataverseAlias = UtilIT.getAliasFromResponse(createDataverseResponse);

Response createDatasetResponse = UtilIT.createDatasetWithDcmDependency(dataverseAlias, apiToken);
createDatasetResponse.prettyPrint();
Integer datasetId = UtilIT.getDatasetIdFromResponse(createDatasetResponse);

Response getDatasetResponse = given()
.header(UtilIT.API_TOKEN_HTTP_HEADER, apiToken)
.get("/api/datasets/" + datasetId);
getDatasetResponse.prettyPrint();
getDatasetResponse.then().assertThat()
.statusCode(200);

final List<Map<String, ?>> dataTypeField = JsonPath.with(getDatasetResponse.body().asString())
.get("data.latestVersion.metadataBlocks.citation.fields.findAll { it.typeName == 'dataType' }");
logger.fine("dataTypeField: " + dataTypeField);
assertThat(dataTypeField.size(), equalTo(1));
assertEquals("dataType", dataTypeField.get(0).get("typeName"));
assertEquals("controlledVocabulary", dataTypeField.get(0).get("typeClass"));
assertEquals("X-Ray Diffraction", dataTypeField.get(0).get("value"));
assertTrue(dataTypeField.get(0).get("multiple").equals(false));

Response deleteDatasetResponse = UtilIT.deleteDatasetViaNativeApi(datasetId, apiToken);
deleteDatasetResponse.prettyPrint();
assertEquals(200, deleteDatasetResponse.getStatusCode());

Response deleteDataverseResponse = UtilIT.deleteDataverse(dataverseAlias, apiToken);
deleteDataverseResponse.prettyPrint();
assertEquals(200, deleteDataverseResponse.getStatusCode());

Response deleteUserResponse = UtilIT.deleteUser(username);
deleteUserResponse.prettyPrint();
assertEquals(200, deleteUserResponse.getStatusCode());

}

@Test
public void testGetDdi() {
String persistentIdentifier = "FIXME";
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21 changes: 21 additions & 0 deletions src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java
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Expand Up @@ -175,6 +175,27 @@ private static String getDatasetJson() {
}
}

static Response createDatasetWithDcmDependency(String dataverseAlias, String apiToken) {
String jsonIn = getDatasetJsonWithDcmDependency();
Response createDatasetResponse = given()
.header(API_TOKEN_HTTP_HEADER, apiToken)
.body(jsonIn)
.contentType("application/json")
.post("/api/dataverses/" + dataverseAlias + "/datasets");
return createDatasetResponse;
}

private static String getDatasetJsonWithDcmDependency() {
File datasetVersionJson = new File("src/test/java/edu/harvard/iq/dataverse/api/x-ray-diffraction.json");
try {
String datasetVersionAsJson = new String(Files.readAllBytes(Paths.get(datasetVersionJson.getAbsolutePath())));
return datasetVersionAsJson;
} catch (IOException ex) {
Logger.getLogger(UtilIT.class.getName()).log(Level.SEVERE, null, ex);
return null;
}
}

static Response createRandomDatasetViaSwordApi(String dataverseToCreateDatasetIn, String apiToken) {
String xmlIn = getDatasetXml(getRandomIdentifier(), getRandomIdentifier(), getRandomIdentifier());
return createDatasetViaSwordApiFromXML(dataverseToCreateDatasetIn, xmlIn, apiToken);
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173 changes: 173 additions & 0 deletions src/test/java/edu/harvard/iq/dataverse/api/x-ray-diffraction.json
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{
"datasetVersion": {
"metadataBlocks": {
"citation": {
"displayName": "Citation Metadata",
"fields": [
{
"typeName": "title",
"multiple": false,
"typeClass": "primitive",
"value": "X-Ray Diffraction data from Lin28A/let-7g microRNA complex, source of 3TS2 structure"
},
{
"typeName": "dataType",
"multiple": false,
"typeClass": "controlledVocabulary",
"value": "X-Ray Diffraction"
},
{
"typeName": "author",
"multiple": true,
"typeClass": "compound",
"value": [
{
"authorName": {
"typeName": "authorName",
"multiple": false,
"typeClass": "primitive",
"value": "Sliz, Piotr"
},
"authorAffiliation": {
"typeName": "authorAffiliation",
"multiple": false,
"typeClass": "primitive",
"value": "Harvard Medical School"
},
"authorIdentifierScheme": {
"typeName": "authorIdentifierScheme",
"multiple": false,
"typeClass": "controlledVocabulary",
"value": "ORCID"
},
"authorIdentifier": {
"typeName": "authorIdentifier",
"multiple": false,
"typeClass": "primitive",
"value": "0000-0002-6522-0835"
}
}
]
},
{
"typeName": "datasetContact",
"multiple": true,
"typeClass": "compound",
"value": [
{
"datasetContactName": {
"typeName": "datasetContactName",
"multiple": false,
"typeClass": "primitive",
"value": "Admin, Dataverse"
},
"datasetContactAffiliation": {
"typeName": "datasetContactAffiliation",
"multiple": false,
"typeClass": "primitive",
"value": "sbgrid.org / SBDG"
},
"datasetContactEmail": {
"typeName": "datasetContactEmail",
"multiple": false,
"typeClass": "primitive",
"value": "generic@mailinator.com"
}
}
]
},
{
"typeName": "dsDescription",
"multiple": true,
"typeClass": "compound",
"value": [
{
"dsDescriptionValue": {
"typeName": "dsDescriptionValue",
"multiple": false,
"typeClass": "primitive",
"value": "Native Dataset"
}
}
]
},
{
"typeName": "subject",
"multiple": true,
"typeClass": "controlledVocabulary",
"value": [
"Medicine, Health and Life Sciences"
]
},
{
"typeName": "publication",
"multiple": true,
"typeClass": "compound",
"value": [
{
"publicationCitation": {
"typeName": "publicationCitation",
"multiple": false,
"typeClass": "primitive",
"value": "Nam Y, Chen C, Gregory RI, Chou JJ, Sliz P. Molecular Basis for Interaction of let-7 MicroRNAs with Lin28. Cell 2011; 147:1080–1091."
},
"publicationIDType": {
"typeName": "publicationIDType",
"multiple": false,
"typeClass": "controlledVocabulary",
"value": "doi"
},
"publicationIDNumber": {
"typeName": "publicationIDNumber",
"multiple": false,
"typeClass": "primitive",
"value": "10.1016/j.cell.2011.10.020"
},
"publicationURL": {
"typeName": "publicationURL",
"multiple": false,
"typeClass": "primitive",
"value": "http://dx.doi.org/10.1016/j.cell.2011.10.020"
}
}
]
},
{
"typeName": "contributor",
"multiple": true,
"typeClass": "compound",
"value": [
{
"contributorType": {
"typeName": "contributorType",
"multiple": false,
"typeClass": "controlledVocabulary",
"value": "Data Collector"
},
"contributorName": {
"typeName": "contributorName",
"multiple": false,
"typeClass": "primitive",
"value": "Nam, Yunsun"
}
}
]
},
{
"typeName": "depositor",
"multiple": false,
"typeClass": "primitive",
"value": "Sliz, Piotr"
},
{
"typeName": "dateOfDeposit",
"multiple": false,
"typeClass": "primitive",
"value": "2015-04-10T14:45:03Z"
}
]
}
},
"files": []
}
}

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