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Merge pull request #6921 from pkiraly/6920-informative-error-message-…
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…for-custom-metadata-block-definition

#6920 Informative error message for custom metadata block definition.
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@kcondon
kcondon authored May 22, 2020
2 parents 99f4d09 + cfd7974 commit 91ddb11
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Showing 7 changed files with 564 additions and 7 deletions.
85 changes: 78 additions & 7 deletions src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java
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Expand Up @@ -18,6 +18,7 @@
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import javax.ejb.EJB;
import javax.ejb.EJBException;
Expand All @@ -32,10 +33,11 @@
import javax.ws.rs.PathParam;
import javax.ws.rs.core.Response;

import org.apache.commons.io.IOUtils;
import edu.harvard.iq.dataverse.util.BundleUtil;
import org.apache.commons.lang.StringUtils;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.asJsonArray;
import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder;

import java.util.logging.Level;
import java.util.logging.Logger;
import javax.persistence.NoResultException;
Expand Down Expand Up @@ -232,8 +234,7 @@ public Response loadNAControlledVocabularyValue() {
}
}

private enum HeaderType {

public enum HeaderType {
METADATABLOCK, DATASETFIELD, CONTROLLEDVOCABULARY
}

Expand Down Expand Up @@ -298,12 +299,20 @@ public Response loadDatasetFields(File file) {
alr.setActionResult(ActionLogRecord.Result.BadRequest);
alr.setInfo( alr.getInfo() + "// file not found");
return error(Status.EXPECTATION_FAILED, "File not found");


} catch (ArrayIndexOutOfBoundsException e) {
String message = getArrayIndexOutOfBoundMessage(header, lineNumber, e);
logger.log(Level.WARNING, message, e);
alr.setActionResult(ActionLogRecord.Result.InternalError);
alr.setInfo(alr.getInfo() + "// " + message);
return error(Status.INTERNAL_SERVER_ERROR, message);

} catch (Exception e) {
logger.log(Level.WARNING, "Error parsing dataset fields:" + e.getMessage(), e);
String message = getGeneralErrorMessage(header, lineNumber, e.getMessage());
logger.log(Level.WARNING, message, e);
alr.setActionResult(ActionLogRecord.Result.InternalError);
alr.setInfo( alr.getInfo() + "// " + e.getMessage());
return error(Status.INTERNAL_SERVER_ERROR, e.getMessage());
alr.setInfo( alr.getInfo() + "// " + message);
return error(Status.INTERNAL_SERVER_ERROR, message);

} finally {
if (br != null) {
Expand All @@ -319,6 +328,68 @@ public Response loadDatasetFields(File file) {
return ok( Json.createObjectBuilder().add("added", responseArr) );
}

/**
* Provide a general error message including the part and line number
* @param header
* @param lineNumber
* @param message
* @return
*/
public String getGeneralErrorMessage(HeaderType header, int lineNumber, String message) {
List<String> arguments = new ArrayList<>();
arguments.add(header.name());
arguments.add(String.valueOf(lineNumber));
arguments.add(message);
return BundleUtil.getStringFromBundle("api.admin.datasetfield.load.GeneralErrorMessage", arguments);
}

/**
* Turn ArrayIndexOutOfBoundsException into an informative error message
* @param lineNumber
* @param header
* @param e
* @return
*/
public String getArrayIndexOutOfBoundMessage(HeaderType header,
int lineNumber,
ArrayIndexOutOfBoundsException e) {

List<String> columns = getColumnsByHeader(header);
int wrongIndex = Integer.parseInt(e.getMessage());

String column = columns.get(wrongIndex - 1);
List<String> arguments = new ArrayList<>();
arguments.add(header.name());
arguments.add(String.valueOf(lineNumber));
arguments.add(column);
arguments.add(String.valueOf(wrongIndex + 1));
return BundleUtil.getStringFromBundle(
"api.admin.datasetfield.load.ArrayIndexOutOfBoundMessage",
arguments
);
}

/**
* Get the list of columns by the type of header
* @param header
* @return
*/
private List<String> getColumnsByHeader(HeaderType header) {
List<String> columns = null;
if (header.equals(HeaderType.METADATABLOCK)) {
columns = Arrays.asList("name", "dataverseAlias", "displayName");
} else if (header.equals(HeaderType.DATASETFIELD)) {
columns = Arrays.asList("name", "title", "description", "watermark",
"fieldType", "displayOrder", "displayFormat", "advancedSearchField",
"allowControlledVocabulary", "allowmultiples", "facetable",
"displayoncreate", "required", "parent", "metadatablock_id");
} else if (header.equals(HeaderType.CONTROLLEDVOCABULARY)) {
columns = Arrays.asList("DatasetField", "Value", "identifier", "displayOrder");
}

return columns;
}

private String parseMetadataBlock(String[] values) {
//Test to see if it exists by name
MetadataBlock mdb = metadataBlockService.findByName(values[1]);
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4 changes: 4 additions & 0 deletions src/main/java/propertyFiles/Bundle.properties
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Expand Up @@ -2510,3 +2510,7 @@ externaltools.dct.displayname=Data Curation Tool
externaltools.dct.description=Data Curation Tool for curation of variables
externaltools.explorer.displayname=Data Explorer
externaltools.explorer.description=The Data Explorer provides a GUI which lists the variables in a tabular data file allowing searching, charting and cross tabulation analysis.

# api/admin/datasetfield/load
api.admin.datasetfield.load.ArrayIndexOutOfBoundMessage=Error parsing metadata block in {0} part, line #{1}: missing ''{2}'' column (#{3})
api.admin.datasetfield.load.GeneralErrorMessage=Error parsing metadata block in {0} part, line #{1}: {2}
79 changes: 79 additions & 0 deletions src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java
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Expand Up @@ -8,15 +8,24 @@
import edu.harvard.iq.dataverse.authorization.providers.oauth2.impl.GitHubOAuth2AP;
import edu.harvard.iq.dataverse.authorization.providers.oauth2.impl.OrcidOAuth2AP;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;

import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import static javax.ws.rs.core.Response.Status.FORBIDDEN;
import static javax.ws.rs.core.Response.Status.BAD_REQUEST;
import org.junit.Test;
import org.junit.BeforeClass;

import java.util.Map;
import java.util.UUID;
import java.util.logging.Logger;

import static javax.ws.rs.core.Response.Status.CREATED;
import static javax.ws.rs.core.Response.Status.INTERNAL_SERVER_ERROR;
import static javax.ws.rs.core.Response.Status.OK;
import static javax.ws.rs.core.Response.Status.UNAUTHORIZED;
import static junit.framework.Assert.assertEquals;
Expand All @@ -27,6 +36,8 @@

public class AdminIT {

private static final Logger logger = Logger.getLogger(AdminIT.class.getCanonicalName());

@BeforeClass
public static void setUp() {
RestAssured.baseURI = UtilIT.getRestAssuredBaseUri();
Expand Down Expand Up @@ -671,4 +682,72 @@ public void testMigrateHDLToDOI() {
.statusCode(OK.getStatusCode());
}

@Test
public void testLoadMetadataBlock_NoErrorPath() {
Response createUser = UtilIT.createRandomUser();
String apiToken = UtilIT.getApiTokenFromResponse(createUser);

byte[] updatedContent = null;
try {
updatedContent = Files.readAllBytes(Paths.get("src/test/resources/tsv/citation.tsv"));
} catch (IOException e) {
logger.warning(e.getMessage());
assertEquals(0,1);
}
Response response = UtilIT.loadMetadataBlock(apiToken, updatedContent);
assertEquals(200, response.getStatusCode());
response.then().assertThat().statusCode(OK.getStatusCode());

String body = response.getBody().asString();
String status = JsonPath.from(body).getString("status");
assertEquals("OK", status);

Map<String, List<Map<String, String>>> data = JsonPath.from(body).getMap("data");
assertEquals(1, data.size());
List<Map<String, String>> addedElements = data.get("added");
assertEquals(321, addedElements.size());

Map<String, Integer> statistics = new HashMap<>();
for (Map<String, String> unit : addedElements) {
assertEquals(2, unit.size());
assertTrue(unit.containsKey("name"));
assertTrue(unit.containsKey("type"));
String type = unit.get("type");
if (!statistics.containsKey(type))
statistics.put(type, 0);
statistics.put(type, statistics.get(type) + 1);
}

assertEquals(3, statistics.size());
assertEquals(1, (int) statistics.get("MetadataBlock"));
assertEquals(78, (int) statistics.get("DatasetField"));
assertEquals(242, (int) statistics.get("Controlled Vocabulary"));
}

@Test
public void testLoadMetadataBlock_ErrorHandling() {
Response createUser = UtilIT.createRandomUser();
String apiToken = UtilIT.getApiTokenFromResponse(createUser);

byte[] updatedContent = null;
try {
updatedContent = Files.readAllBytes(Paths.get("src/test/resources/tsv/test.tsv"));
} catch (IOException e) {
logger.warning(e.getMessage());
assertEquals(0,1);
}
Response response = UtilIT.loadMetadataBlock(apiToken, updatedContent);
assertEquals(500, response.getStatusCode());
response.then().assertThat().statusCode(INTERNAL_SERVER_ERROR.getStatusCode());

String body = response.getBody().asString();
String status = JsonPath.from(body).getString("status");
assertEquals("ERROR", status);

String message = JsonPath.from(body).getString("message");
assertEquals(
"Error parsing metadata block in DATASETFIELD part, line #5: missing 'watermark' column (#5)",
message
);
}
}
62 changes: 62 additions & 0 deletions src/test/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApiTest.java
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@@ -0,0 +1,62 @@
package edu.harvard.iq.dataverse.api;

import edu.harvard.iq.dataverse.util.BundleUtil;
import org.junit.Test;

import java.util.ArrayList;
import java.util.List;

import static org.junit.Assert.assertEquals;

public class DatasetFieldServiceApiTest {

@Test
public void testArrayIndexOutOfBoundMessageBundle() {
List<String> arguments = new ArrayList<>();
arguments.add("DATASETFIELD");
arguments.add(String.valueOf(5));
arguments.add("watermark");
arguments.add(String.valueOf(4 + 1));

String bundle = "api.admin.datasetfield.load.ArrayIndexOutOfBoundMessage";
String message = BundleUtil.getStringFromBundle(bundle, arguments);
assertEquals(
"Error parsing metadata block in DATASETFIELD part, line #5: missing 'watermark' column (#5)",
message
);
}

@Test
public void testGeneralErrorMessageBundle() {
List<String> arguments = new ArrayList<>();
arguments.add("DATASETFIELD");
arguments.add(String.valueOf(5));
arguments.add("some error message");
String bundle = "api.admin.datasetfield.load.GeneralErrorMessage";
String message = BundleUtil.getStringFromBundle(bundle, arguments);
assertEquals(
"Error parsing metadata block in DATASETFIELD part, line #5: some error message",
message
);
}

@Test
public void testGetArrayIndexOutOfBoundMessage() {
DatasetFieldServiceApi api = new DatasetFieldServiceApi();
String message = api.getArrayIndexOutOfBoundMessage(DatasetFieldServiceApi.HeaderType.DATASETFIELD, 5, new ArrayIndexOutOfBoundsException("4"));
assertEquals(
"Error parsing metadata block in DATASETFIELD part, line #5: missing 'watermark' column (#5)",
message
);
}

@Test
public void testGetGeneralErrorMessage() {
DatasetFieldServiceApi api = new DatasetFieldServiceApi();
String message = api.getGeneralErrorMessage(DatasetFieldServiceApi.HeaderType.DATASETFIELD, 5, "some error");
assertEquals(
"Error parsing metadata block in DATASETFIELD part, line #5: some error",
message
);
}
}
8 changes: 8 additions & 0 deletions src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java
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Expand Up @@ -1368,6 +1368,14 @@ static Response getDatasetThumbnailMetadata(Integer datasetId, String apiToken)
.get("/api/admin/datasets/thumbnailMetadata/" + datasetId);
}

static Response loadMetadataBlock(String apiToken, byte[] body) {
return given()
.header(API_TOKEN_HTTP_HEADER, apiToken)
.contentType("text/tab-separated-values; charset=utf-8")
.body(body)
.post("/api/admin/datasetfield/load");
}

static Response useThumbnailFromDataFile(String datasetPersistentId, long dataFileId1, String apiToken) {
return given()
.header(API_TOKEN_HTTP_HEADER, apiToken)
Expand Down
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