From fb7c8012f6eb788ad9f7d4c4c206982f83d36a0e Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 14 Jun 2018 11:16:29 +0200
Subject: [PATCH] GO connector uses new API
---
.../services/annotators/GoAnnotator.java | 392 ++++++++---------
.../services/annotators/GoAnnotatorTest.java | 410 +++++++++---------
2 files changed, 403 insertions(+), 399 deletions(-)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
index e4a7a7f4a1..ca0b31d7d3 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
@@ -1,14 +1,15 @@
package lcsb.mapviewer.annotation.services.annotators;
import java.io.IOException;
-
-import javax.xml.xpath.XPath;
-import javax.xml.xpath.XPathExpressionException;
-import javax.xml.xpath.XPathFactory;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
-import org.w3c.dom.Node;
+
+import com.google.gson.Gson;
+import com.google.gson.internal.StringMap;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
@@ -20,14 +21,13 @@ import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.annotation.services.MiriamConnector;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Phenotype;
import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -39,194 +39,194 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*/
public class GoAnnotator extends ElementAnnotator implements IExternalService {
- /**
- * Prefix string used for marking the query in database as query by go term.
- */
- static final String GO_TERM_CACHE_PREFIX = "GO_TERM: ";
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(GoAnnotator.class);
-
- /**
- * Connector used for accessing data from miriam registry.
- */
- @Autowired
- private MiriamConnector mc;
-
- /**
- * Object that allows to serialize {@link Go} elements into xml string and
- * deserialize xml into {@link Go} objects.
- */
- private XmlSerializer<Go> goSerializer;
-
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- try {
- if (query instanceof String) {
- String name = (String) query;
- if (name.startsWith(GO_TERM_CACHE_PREFIX)) {
- String term = name.substring(GO_TERM_CACHE_PREFIX.length());
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, term);
- result = goSerializer.objectToString(getGoElement(md));
- } else if (name.startsWith("http")) {
- result = getWebPageContent(name);
- } else {
- throw new InvalidArgumentException("Don't know what to do with query: " + query);
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- } catch (IOException | GoSearchException e) {
- throw new SourceNotAvailable(e);
- }
- return result;
- }
-
- /**
- * Default constructor. Initializes structures used for transforming
- * {@link Go} from/to xml.
- */
- public GoAnnotator() {
- super(GoAnnotator.class, new Class[] { Phenotype.class, Compartment.class, Complex.class }, true);
- goSerializer = new XmlSerializer<>(Go.class);
- }
-
- @Override
- public void annotateElement(BioEntity object) throws AnnotatorException {
- if (isAnnotatable(object)) {
- MiriamData goTerm = null;
- for (MiriamData md : object.getMiriamData()) {
- if (md.getDataType().equals(MiriamType.GO)) {
- goTerm = md;
- }
- }
- if (goTerm == null) {
- return;
- }
-
- try {
- Go go = getGoElement(goTerm);
-
- String commonName = go.getCommonName();
-
- setFullName((Element) object, commonName, new ElementUtils().getElementTag(object, this));
- String description = go.getDescription();
- setDescription(object, description);
- } catch (GoSearchException e) {
- throw new AnnotatorException(e);
- }
- }
- }
-
- /**
- * Returns go entry from the Gene Ontology database for the goTerm
- * (identifier).
- *
- * @param md
- * {@link MiriamData} object referencing to entry in GO database
- * @return entry in Gene Ontology database
- * @throws GoSearchException
- * thrown when there is a problem with accessing data in go database
- */
- protected Go getGoElement(MiriamData md) throws GoSearchException {
- Go result = goSerializer.xmlToObject(getCacheNode(GO_TERM_CACHE_PREFIX + md.getResource()));
-
- if (result != null) {
- return result;
- } else {
- result = new Go();
- }
-
- String accessUrl = "https://www.ebi.ac.uk/QuickGO-Old/GTerm?id=" + md.getResource() + "&format=oboxml";
- try {
- String tmp = getWebPageContent(accessUrl);
-
- Node xml = getXmlDocumentFromString(tmp.toString());
-
- // XPath is here used to locate parts of an XML document
- XPath xpath = XPathFactory.newInstance().newXPath();
-
- // Locate the term name and print it out
- String commonName = xpath.compile("/obo/term/name").evaluate(xml);
- String description = xpath.compile("/obo/term/def/defstr").evaluate(xml);
- result.setCommonName(commonName);
- result.setDescription(description);
- result.setGoTerm(md.getResource());
-
- setCacheValue(GO_TERM_CACHE_PREFIX + md.getResource(), goSerializer.objectToString(result));
- return result;
- } catch (IOException e) {
- throw new GoSearchException("Problem with accesing go database", e);
- } catch (InvalidXmlSchemaException | XPathExpressionException e) {
- throw new GoSearchException("Data from go db have invalid format", e);
- }
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
-
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- Compartment compartmentAlias = new Compartment("some_id");
- compartmentAlias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, "GO:0046902"));
- annotateElement(compartmentAlias);
-
- if (compartmentAlias.getFullName() == null || compartmentAlias.getFullName().equals("")) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- } else if (compartmentAlias.getNotes() == null || compartmentAlias.getNotes().equals("")) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- } else {
- status.setStatus(ExternalServiceStatusType.OK);
- }
- } catch (Exception e) {
- logger.error("GeneOntology is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- /**
- * @return the mc
- * @see #mc
- */
- public MiriamConnector getMc() {
- return mc;
- }
-
- /**
- * @param mc
- * the mc to set
- * @see #mc
- */
- public void setMc(MiriamConnector mc) {
- this.mc = mc;
- }
-
- @Override
- public String getCommonName() {
- return MiriamType.GO.getCommonName();
- }
-
- @Override
- public String getUrl() {
- return MiriamType.GO.getDbHomepage();
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
+ /**
+ * Prefix string used for marking the query in database as query by go term.
+ */
+ static final String GO_TERM_CACHE_PREFIX = "GO_TERM: ";
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(GoAnnotator.class);
+
+ /**
+ * Connector used for accessing data from miriam registry.
+ */
+ @Autowired
+ private MiriamConnector mc;
+
+ /**
+ * Object that allows to serialize {@link Go} elements into xml string and
+ * deserialize xml into {@link Go} objects.
+ */
+ private XmlSerializer<Go> goSerializer;
+
+ @Override
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ try {
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith(GO_TERM_CACHE_PREFIX)) {
+ String term = name.substring(GO_TERM_CACHE_PREFIX.length());
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, term);
+ result = goSerializer.objectToString(getGoElement(md));
+ } else if (name.startsWith("http")) {
+ result = getWebPageContent(name);
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with query: " + query);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ } catch (IOException | GoSearchException e) {
+ throw new SourceNotAvailable(e);
+ }
+ return result;
+ }
+
+ /**
+ * Default constructor. Initializes structures used for transforming {@link Go}
+ * from/to xml.
+ */
+ public GoAnnotator() {
+ super(GoAnnotator.class, new Class[] { Phenotype.class, Compartment.class, Complex.class }, true);
+ goSerializer = new XmlSerializer<>(Go.class);
+ }
+
+ @Override
+ public void annotateElement(BioEntity object) throws AnnotatorException {
+ if (isAnnotatable(object)) {
+ MiriamData goTerm = null;
+ for (MiriamData md : object.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.GO)) {
+ goTerm = md;
+ }
+ }
+ if (goTerm == null) {
+ return;
+ }
+
+ try {
+ Go go = getGoElement(goTerm);
+ if (go != null) {
+ setFullName((Element) object, go.getCommonName(), new ElementUtils().getElementTag(object, this));
+ setDescription(object, go.getDescription());
+ }
+ } catch (GoSearchException e) {
+ throw new AnnotatorException(e);
+ }
+ }
+ }
+
+ /**
+ * Returns go entry from the Gene Ontology database for the goTerm (identifier).
+ *
+ * @param md
+ * {@link MiriamData} object referencing to entry in GO database
+ * @return entry in Gene Ontology database
+ * @throws GoSearchException
+ * thrown when there is a problem with accessing data in go database
+ */
+ protected Go getGoElement(MiriamData md) throws GoSearchException {
+ Go result = goSerializer.xmlToObject(getCacheNode(GO_TERM_CACHE_PREFIX + md.getResource()));
+
+ if (result != null) {
+ return result;
+ } else {
+ result = new Go();
+ }
+
+ String accessUrl = "https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/" + md.getResource();
+ try {
+ String page = getWebPageContent(accessUrl);
+
+ Gson gson = new Gson();
+
+ Map<?, ?> gsonObject = (Map<?, ?>) gson.fromJson(page, HashMap.class);
+ Double hits = (Double) gsonObject.get("numberOfHits");
+ if (hits < 1) {
+ return null;
+ }
+ List<?> objects = (List<?>) gsonObject.get("results");
+
+ StringMap<?> object = (StringMap<?>) objects.get(0);
+ result.setGoTerm((String) object.get("id"));
+ result.setCommonName((String) object.get("name"));
+
+ StringMap<?> descr = (StringMap<?>) object.get("definition");
+ if (descr != null) {
+ result.setDescription((String) descr.get("text"));
+ }
+
+ return result;
+ } catch (Exception e) {
+ throw new GoSearchException("Problem with accesing go database", e);
+ }
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ Compartment compartment = new Compartment("some_id");
+ compartment.addMiriamData(new MiriamData(MiriamType.GO, "GO:0046902"));
+ annotateElement(compartment);
+
+ if (compartment.getFullName() == null || compartment.getFullName().equals("")) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ } else if (compartment.getNotes() == null || compartment.getNotes().equals("")) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ } else {
+ status.setStatus(ExternalServiceStatusType.OK);
+ }
+ } catch (Exception e) {
+ logger.error("GeneOntology is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ /**
+ * @return the mc
+ * @see #mc
+ */
+ public MiriamConnector getMc() {
+ return mc;
+ }
+
+ /**
+ * @param mc
+ * the mc to set
+ * @see #mc
+ */
+ public void setMc(MiriamConnector mc) {
+ this.mc = mc;
+ }
+
+ @Override
+ public String getCommonName() {
+ return MiriamType.GO.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.GO.getDbHomepage();
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java
index ce4045811d..3f44a98c45 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java
@@ -31,208 +31,212 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.compartment.Compartment;
public class GoAnnotatorTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(GoAnnotatorTest.class);
-
- @Autowired
- GoAnnotator goAnnotator;
-
- @Autowired
- private PermanentDatabaseLevelCacheInterface cache;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testContent() throws Exception {
- try {
- Compartment compartmentAlias = new Compartment("id");
- compartmentAlias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, "GO:0046902"));
- goAnnotator.annotateElement(compartmentAlias);
- assertFalse(compartmentAlias.getFullName().equals(""));
- assertFalse(compartmentAlias.getNotes().equals(""));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotate() throws Exception {
- try {
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, "GO:0042644");
- Go go = goAnnotator.getGoElement(md);
- assertEquals("GO:0042644", go.getGoTerm());
- assertNotNull(go.getCommonName());
- assertNotNull(go.getDescription());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotateWhenProblemWithNetworkResponse() throws Exception {
- try {
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, "GO:0042644");
- GoAnnotator annotator = new GoAnnotator();
- annotator.setMc(goAnnotator.getMc());
- WebPageDownloader downloader = Mockito.mock(WebPageDownloader.class);
- when(downloader.getFromNetwork(anyString())).thenReturn("");
- annotator.setWebPageDownloader(downloader);
- annotator.getGoElement(md);
- fail("Exception expected");
- } catch (GoSearchException e) {
- assertTrue(e.getMessage().contains("Data from go db have invalid format"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testCachableInterface() throws Exception {
- String query = GoAnnotator.GO_TERM_CACHE_PREFIX + "GO:0046902";
- String newRes = "hello";
- try {
- waitForRefreshCacheQueueToEmpty();
-
- cache.setCachedQuery(query, goAnnotator.getCacheType(), newRes);
- cache.invalidateByQuery(query, goAnnotator.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- String res = cache.getStringByQuery(query, goAnnotator.getCacheType());
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQueryNotAvailable() throws Exception {
- WebPageDownloader downloader = goAnnotator.getWebPageDownloader();
- GeneralCacheInterface originalCache = goAnnotator.getCache();
- try {
- // exclude first cached value
- goAnnotator.setCache(null);
-
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
- goAnnotator.setWebPageDownloader(mockDownloader);
- goAnnotator.refreshCacheQuery("http://google.pl/");
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- goAnnotator.setWebPageDownloader(downloader);
- goAnnotator.setCache(originalCache);
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- goAnnotator.refreshCacheQuery("invalid_query");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery2() throws Exception {
- try {
- goAnnotator.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQuery() throws Exception {
- try {
- String res = goAnnotator.refreshCacheQuery("http://google.pl/");
- assertNotNull(res);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testStatus() throws Exception {
- try {
- assertEquals(ExternalServiceStatusType.OK, goAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSimulateDownStatus() throws Exception {
- WebPageDownloader downloader = goAnnotator.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
- goAnnotator.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, goAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- goAnnotator.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateChangedStatus() throws Exception {
- WebPageDownloader downloader = goAnnotator.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("<obo><term><name/><def><defstr/></def></term></obo>");
- goAnnotator.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, goAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- goAnnotator.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateChangedStatus2() throws Exception {
- WebPageDownloader downloader = goAnnotator.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("<obo><term><name>some_name</name><def><defstr/></def></term></obo>");
- goAnnotator.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, goAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- goAnnotator.setWebPageDownloader(downloader);
- }
- }
+ Logger logger = Logger.getLogger(GoAnnotatorTest.class);
+
+ @Autowired
+ GoAnnotator goAnnotator;
+
+ @Autowired
+ private PermanentDatabaseLevelCacheInterface cache;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testContent() throws Exception {
+ try {
+ Compartment compartmentAlias = new Compartment("id");
+ compartmentAlias
+ .addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, "GO:0046902"));
+ goAnnotator.annotateElement(compartmentAlias);
+ assertFalse(compartmentAlias.getFullName().equals(""));
+ assertFalse(compartmentAlias.getNotes().equals(""));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetGoData() throws Exception {
+ try {
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, "GO:0042644");
+ Go go = goAnnotator.getGoElement(md);
+ assertEquals("GO:0042644", go.getGoTerm());
+ assertNotNull(go.getCommonName());
+ assertNotNull(go.getDescription());
+ assertTrue(go.getCommonName().toLowerCase().contains("chloroplast nucleoid"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateWhenProblemWithNetworkResponse() throws Exception {
+ try {
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, "GO:0042644");
+ GoAnnotator annotator = new GoAnnotator();
+ annotator.setMc(goAnnotator.getMc());
+ WebPageDownloader downloader = Mockito.mock(WebPageDownloader.class);
+ when(downloader.getFromNetwork(anyString())).thenReturn("");
+ annotator.setWebPageDownloader(downloader);
+ annotator.getGoElement(md);
+ fail("Exception expected");
+ } catch (GoSearchException e) {
+ assertTrue(e.getMessage().contains("Problem with accesing go database"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testCachableInterface() throws Exception {
+ String query = GoAnnotator.GO_TERM_CACHE_PREFIX + "GO:0046902";
+ String newRes = "hello";
+ try {
+ waitForRefreshCacheQueueToEmpty();
+
+ cache.setCachedQuery(query, goAnnotator.getCacheType(), newRes);
+ cache.invalidateByQuery(query, goAnnotator.getCacheType());
+
+ waitForRefreshCacheQueueToEmpty();
+
+ String res = cache.getStringByQuery(query, goAnnotator.getCacheType());
+
+ assertNotNull(res);
+
+ assertFalse("Value wasn't refreshed from db", newRes.equals(res));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryNotAvailable() throws Exception {
+ WebPageDownloader downloader = goAnnotator.getWebPageDownloader();
+ GeneralCacheInterface originalCache = goAnnotator.getCache();
+ try {
+ // exclude first cached value
+ goAnnotator.setCache(null);
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ goAnnotator.setWebPageDownloader(mockDownloader);
+ goAnnotator.refreshCacheQuery("http://google.pl/");
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ goAnnotator.setWebPageDownloader(downloader);
+ goAnnotator.setCache(originalCache);
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ goAnnotator.refreshCacheQuery("invalid_query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ goAnnotator.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQuery() throws Exception {
+ try {
+ String res = goAnnotator.refreshCacheQuery("http://google.pl/");
+ assertNotNull(res);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, goAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ WebPageDownloader downloader = goAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ goAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, goAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ goAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangedStatus() throws Exception {
+ WebPageDownloader downloader = goAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString()))
+ .thenReturn("{\"numberOfHits\": 1,\"results\": [{\"name\":\"x\"}]}");
+ goAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, goAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ goAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangedStatus2() throws Exception {
+ WebPageDownloader downloader = goAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString()))
+ .thenReturn("{\"numberOfHits\": 1,\"results\": [{}]}");
+ goAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, goAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ goAnnotator.setWebPageDownloader(downloader);
+ }
+ }
}
--
GitLab