Commit c2dc40ac authored by Piotr Gawron's avatar Piotr Gawron
Browse files

unused method removed

parent ecc31fd7
package lcsb.mapviewer.annotation.services;
import java.io.IOException;
import java.util.*;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import org.apache.commons.lang3.SerializationException;
import org.apache.http.HttpStatus;
......@@ -12,7 +16,11 @@ import org.w3c.dom.Node;
import com.google.gson.Gson;
import lcsb.mapviewer.annotation.cache.*;
import lcsb.mapviewer.annotation.cache.CachableInterface;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.cache.XmlSerializer;
import lcsb.mapviewer.annotation.data.MeSH;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
......@@ -60,7 +68,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
}
@Override
public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
public Object refreshCacheQuery(final Object query) throws SourceNotAvailable {
Object result = null;
try {
if (query instanceof String) {
......@@ -92,7 +100,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
}
@Override
protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
protected void setWebPageDownloader(final WebPageDownloader webPageDownloader) {
super.setWebPageDownloader(webPageDownloader);
}
......@@ -103,7 +111,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
* @throws AnnotatorException
* thrown when there is a problem with accessing mesh database
*/
public MeSH getMeSH(MiriamData meshID) throws AnnotatorException {
public MeSH getMeSH(final MiriamData meshID) throws AnnotatorException {
if (meshID == null || meshID.getResource() == null) {
throw new InvalidArgumentException("mesh cannot be null ");
}
......@@ -142,7 +150,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
* id as miriam data.
* @return return the object.
*/
public String getIdentifier(MiriamData meshID) {
public String getIdentifier(final MiriamData meshID) {
return MESH_PREFIX + meshID.getResource();
}
......@@ -155,7 +163,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
* @throws AnnotatorException
* thrown when there is a problem with accessing mesh db
*/
private MeSH getMeSHByIdFromDB(MiriamData meshID) throws IOException {
private MeSH getMeSHByIdFromDB(final MiriamData meshID) throws IOException {
try {
MeSH result = new MeSH();
String page = getWebPageContent(URL_MESH_DATABASE + meshID.getResource());
......@@ -163,7 +171,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
Gson gson = new Gson();
Map<?, ?> gsonObject = new HashMap<String, Object>();
gsonObject = (Map<?, ?>) gson.fromJson(page, gsonObject.getClass());
gsonObject = gson.fromJson(page, gsonObject.getClass());
Set<String> synonyms = getSynonyms(gsonObject);
String name = getName(gsonObject);
String description = getDescription(gsonObject);
......@@ -191,7 +199,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
* gson to process
* @return name of {@link MeSH} entry
*/
private String getName(Map<?, ?> gsonObject) {
private String getName(final Map<?, ?> gsonObject) {
Map<?, ?> descriptorTag = (Map<?, ?>) gsonObject.get("DescriptorName");
if (descriptorTag == null) {
descriptorTag = (Map<?, ?>) gsonObject.get("SupplementalRecordName");
......@@ -206,7 +214,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
* gson to process
* @return id of {@link MeSH} entry
*/
private String getId(Map<?, ?> gsonObject) {
private String getId(final Map<?, ?> gsonObject) {
Map<?, ?> descriptorTag = (Map<?, ?>) gsonObject.get("DescriptorUI");
if (descriptorTag == null) {
descriptorTag = (Map<?, ?>) gsonObject.get("SupplementalRecordUI");
......@@ -221,7 +229,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
* gson to process
* @return description of {@link MeSH} entry
*/
private String getDescription(Map<?, ?> gsonObject) {
private String getDescription(final Map<?, ?> gsonObject) {
Map<?, ?> concepts = (Map<?, ?>) gsonObject.get("_generated");
return (String) concepts.get("PreferredConceptScopeNote");
}
......@@ -233,7 +241,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
* gson to process
* @return synonyms of {@link MeSH} entry
*/
private Set<String> getSynonyms(Map<?, ?> gsonObject) {
private Set<String> getSynonyms(final Map<?, ?> gsonObject) {
Set<String> synonyms = new HashSet<>();
Map<?, ?> concepts = (Map<?, ?>) gsonObject.get("ConceptList");
ArrayList<?> conceptList = (ArrayList<?>) concepts.get("Concept");
......@@ -280,33 +288,14 @@ public class MeSHParser extends CachableInterface implements IExternalService {
* @throws AnnotatorException
* thrown when there is problem with accessing mesh db
*/
public boolean isValidMeshId(MiriamData meshId) throws AnnotatorException {
public boolean isValidMeshId(final MiriamData meshId) throws AnnotatorException {
if (meshId == null) {
return false;
}
return getMeSH(meshId) != null;
}
public List<MeSH> getMeshBySynonym(String synonym) throws AnnotatorException {
try {
List<MeSH> result = new ArrayList<>();
String page = getWebPageContent(URL_SEARCH_BY_SYNONYM + synonym);
Gson gson = new Gson();
Map<?, ?> gsonObject = new HashMap<String, Object>();
gsonObject = (Map<?, ?>) gson.fromJson(page, gsonObject.getClass());
Set<MiriamData> synonyms = getIdsBySynonymQuery(gsonObject);
for (MiriamData meshID : synonyms) {
result.add(getMeSH(meshID));
}
return result;
} catch (IOException e) {
throw new AnnotatorException(e);
}
}
private Set<MiriamData> getIdsBySynonymQuery(Map<?, ?> gsonObject) {
private Set<MiriamData> getIdsBySynonymQuery(final Map<?, ?> gsonObject) {
Set<MiriamData> result = new HashSet<>();
Map<?, ?> hits = (Map<?, ?>) gsonObject.get("hits");
ArrayList<?> hitsList = (ArrayList<?>) hits.get("hits");
......
package lcsb.mapviewer.annotation.services;
import static org.junit.Assert.*;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.nullable;
import static org.mockito.Mockito.when;
import java.io.IOException;
import java.util.List;
import org.apache.http.HttpStatus;
import org.apache.logging.log4j.LogManager;
......@@ -16,7 +19,9 @@ import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.*;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.data.MeSH;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
......@@ -42,15 +47,6 @@ public class MeSHParserTest extends AnnotationTestFunctions {
assertTrue(mesh.getSynonyms().size() > 0);
}
@Test
public void testGetMeshBySynonym() throws Exception {
String synonym = "MPTP";
List<MeSH> result = meshParser.getMeshBySynonym(synonym);
assertEquals(1, result.size());
MeSH mesh = result.get(0);
assertTrue(mesh.getSynonyms().contains(synonym));
}
@Test
public void testIsValidMesh() throws Exception {
MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D004298");
......
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