From 0b877756768ac525d806dfeda05ad3453a067f14 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 14 Jun 2018 09:46:38 +0200
Subject: [PATCH] when hgnc annotator uses element name, only first part before
whitespace is processed as an identifier
---
.../services/annotators/HgncAnnotator.java | 84 +-
.../annotators/HgncAnnotatorTest.java | 1042 +++++++++--------
2 files changed, 576 insertions(+), 550 deletions(-)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
index a8b5d0184f..18f3df2848 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
@@ -237,17 +237,17 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
}
}
- }
- }
- }
- }
- } catch (WrongResponseCodeIOException e) {
- logger.warn(prefix + "Cannot find information for element.");
- } catch (Exception e) {
- throw new AnnotatorException(e);
- }
- }
- }
+ }
+ }
+ }
+ }
+ } catch (WrongResponseCodeIOException e) {
+ logger.warn(prefix + "Cannot find information for element.");
+ } catch (Exception e) {
+ throw new AnnotatorException(e);
+ }
+ }
+ }
/**
* Creates query url for given {@link MiriamType#HGNC} identifier.
@@ -265,10 +265,12 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
*
* @param name
* {@link MiriamType#HGNC_SYMBOL}
- * @return url to restful api webpage for given hgnc symbol
+ * @return url to restful API web page for given HGNC symbol
*/
private String getHgncNameUrl(String name) {
- return REST_API_URL + "symbol/" + name;
+ String hgncSymbol = "" + name;
+ hgncSymbol = hgncSymbol.split("\\s+")[0];
+ return REST_API_URL + "symbol/" + hgncSymbol;
}
/**
@@ -304,34 +306,34 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
} else {
Node entry = getNode("doc", resultNode.getChildNodes());
- NodeList list = entry.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equals("arr")) {
- String type = getNodeAttr("name", node);
- if (type.equals("uniprot_ids")) {
- NodeList uniprotList = node.getChildNodes();
- for (int j = 0; j < uniprotList.getLength(); j++) {
- Node uniprotNode = uniprotList.item(j);
- if (uniprotNode.getNodeType() == Node.ELEMENT_NODE) {
- if (uniprotNode.getNodeName().equals("str")) {
- result.add(createMiriamData(MiriamType.UNIPROT, uniprotNode.getTextContent()));
- }
- }
- }
- }
- }
- }
- }
- }
- return result;
- } catch (WrongResponseCodeIOException e) {
- logger.warn("No HGNC data found for id: "+miriamData);
- return new ArrayList<>();
- } catch (Exception e) {
- throw new AnnotatorException(e);
- }
+ NodeList list = entry.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equals("arr")) {
+ String type = getNodeAttr("name", node);
+ if (type.equals("uniprot_ids")) {
+ NodeList uniprotList = node.getChildNodes();
+ for (int j = 0; j < uniprotList.getLength(); j++) {
+ Node uniprotNode = uniprotList.item(j);
+ if (uniprotNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (uniprotNode.getNodeName().equals("str")) {
+ result.add(createMiriamData(MiriamType.UNIPROT, uniprotNode.getTextContent()));
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ return result;
+ } catch (WrongResponseCodeIOException e) {
+ logger.warn("No HGNC data found for id: " + miriamData);
+ return new ArrayList<>();
+ } catch (Exception e) {
+ throw new AnnotatorException(e);
+ }
}
/**
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
index 71347a9620..5dc32a4bd5 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
@@ -32,514 +32,538 @@ import lcsb.mapviewer.model.map.species.Species;
public class HgncAnnotatorTest extends AnnotationTestFunctions {
- final Logger logger = Logger.getLogger(HgncAnnotatorTest.class);
-
- @Autowired
- private HgncAnnotator hgncAnnotator;
-
- @Before
- public void setUp() {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetAnnotationsForSNCA() throws Exception {
- try {
- MiriamData snca = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
- GenericProtein proteinAlias = new GenericProtein("id");
- proteinAlias.addMiriamData(snca);
- hgncAnnotator.annotateElement(proteinAlias);
- assertNotNull(proteinAlias.getSymbol());
- assertTrue(proteinAlias.getFormerSymbols().size() > 0);
- assertNotNull(proteinAlias.getFullName());
- assertTrue(proteinAlias.getMiriamData().size() > 1);
- assertTrue(proteinAlias.getSynonyms().size() > 0);
-
- boolean ensemble = false;
- boolean hgncId = false;
- boolean hgncSymbol = false;
- boolean refseq = false;
- boolean entrez = false;
- boolean uniprot = false;
- for (MiriamData md : proteinAlias.getMiriamData()) {
- if (MiriamType.ENSEMBL.equals(md.getDataType())) {
- ensemble = true;
- } else if (MiriamType.HGNC.equals(md.getDataType())) {
- assertEquals("Invalid HGNC id", "11138", md.getResource());
- hgncId = true;
- } else if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
- hgncSymbol = true;
- } else if (MiriamType.REFSEQ.equals(md.getDataType())) {
- refseq = true;
- } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
- entrez = true;
- } else if (MiriamType.UNIPROT.equals(md.getDataType())) {
- uniprot = true;
- }
- }
-
- assertTrue("Ensemble symbol cannot be found", ensemble);
- assertTrue("Hgnc id cannot be found", hgncId);
- assertTrue("Hgnc symbol cannot be found", hgncSymbol);
- assertTrue("RefSeq cannot be found", refseq);
- assertTrue("Entrez cannot be found", entrez);
- assertTrue("Uniprot cannot be found", uniprot);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsForElementWithMultiHGNC() throws Exception {
- try {
- MiriamData snca = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
- MiriamData park7 = new MiriamData(MiriamType.HGNC_SYMBOL, "PARK7");
- GenericProtein proteinAlias = new GenericProtein("id");
- proteinAlias.addMiriamData(snca);
- proteinAlias.addMiriamData(park7);
- hgncAnnotator.annotateElement(proteinAlias);
-
- assertEquals(1, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsForHGNC_ID() throws Exception {
- try {
- MiriamData nsmf = new MiriamData(MiriamType.HGNC, "11138");
- GenericProtein proteinAlias = new GenericProtein("id");
- proteinAlias.addMiriamData(nsmf);
- hgncAnnotator.annotateElement(proteinAlias);
- assertNotNull(proteinAlias.getSymbol());
- assertTrue(proteinAlias.getFormerSymbols().size() > 0);
- assertNotNull(proteinAlias.getFullName());
- assertTrue(proteinAlias.getMiriamData().size() > 1);
- assertTrue(proteinAlias.getSynonyms().size() > 0);
-
- boolean ensemble = false;
- boolean hgncId = false;
- boolean hgncSymbol = false;
- boolean refseq = false;
- boolean entrez = false;
- for (MiriamData md : proteinAlias.getMiriamData()) {
- if (MiriamType.ENSEMBL.equals(md.getDataType())) {
- ensemble = true;
- } else if (MiriamType.HGNC.equals(md.getDataType())) {
- hgncId = true;
- } else if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
- hgncSymbol = true;
- } else if (MiriamType.REFSEQ.equals(md.getDataType())) {
- refseq = true;
- } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
- entrez = true;
- }
- }
-
- assertTrue("Ensemble symbol cannot be found", ensemble);
- assertTrue("Hgnc id cannot be found", hgncId);
- assertTrue("Hgnc symbol cannot be found", hgncSymbol);
- assertTrue("RefSeq cannot be found", refseq);
- assertTrue("Entrez cannot be found", entrez);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsForSNCA2() throws Exception {
- try {
- GenericProtein proteinAlias = new GenericProtein("id");
- proteinAlias.setName("SNCA");
- hgncAnnotator.annotateElement(proteinAlias);
- assertNotNull(proteinAlias.getSymbol());
- assertNotNull(proteinAlias.getName());
- assertTrue(proteinAlias.getFormerSymbols().size() > 0);
- assertNotNull(proteinAlias.getFullName());
- assertTrue(proteinAlias.getMiriamData().size() > 1);
- assertTrue(proteinAlias.getSynonyms().size() > 0);
-
- boolean ensemble = false;
- boolean hgncId = false;
- boolean hgncSymbol = false;
- boolean refseq = false;
- boolean entrez = false;
- for (MiriamData md : proteinAlias.getMiriamData()) {
- if (MiriamType.ENSEMBL.equals(md.getDataType())) {
- ensemble = true;
- } else if (MiriamType.HGNC.equals(md.getDataType())) {
- hgncId = true;
- } else if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
- hgncSymbol = true;
- } else if (MiriamType.REFSEQ.equals(md.getDataType())) {
- refseq = true;
- } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
- entrez = true;
- }
- }
-
- assertTrue("Ensemble symbol cannot be found", ensemble);
- assertTrue("Hgnc id cannot be found", hgncId);
- assertTrue("Hgnc symbol cannot be found", hgncSymbol);
- assertTrue("RefSeq cannot be found", refseq);
- assertTrue("Entrez cannot be found", entrez);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsForInvalid() throws Exception {
- try {
- Species proteinAlias = new GenericProtein("id");
- proteinAlias.setName("UNKNNOWNASD asd");
- hgncAnnotator.annotateElement(proteinAlias);
-
- assertEquals(1, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsForInvalid2() throws Exception {
- try {
- Species proteinAlias = new GenericProtein("id");
- proteinAlias.setName("cAMP/cGMP-dependent protein kinase");
- hgncAnnotator.annotateElement(proteinAlias);
-
- assertEquals(1, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testCachableInterfaceInvalidate() throws Exception {
- String query = "http://google.pl/";
- try {
- String newRes = "hello";
-
- waitForRefreshCacheQueueToEmpty();
-
- cache.setCachedQuery(query, hgncAnnotator.getCacheType(), newRes);
- String res = cache.getStringByQuery(query, hgncAnnotator.getCacheType());
- assertEquals(newRes, res);
- cache.invalidateByQuery(query, hgncAnnotator.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- res = cache.getStringByQuery(query, hgncAnnotator.getCacheType());
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testStatus() throws Exception {
- try {
- assertEquals(ExternalServiceStatusType.OK, hgncAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsForInvalidMiriamSet() throws Exception {
- try {
- MiriamData md1 = new MiriamData(MiriamType.HGNC, "11138");
- MiriamData md2 = new MiriamData(MiriamType.HGNC, "111382");
- Species proteinAlias = new GenericProtein("");
- proteinAlias.addMiriamData(md1);
- proteinAlias.addMiriamData(md2);
- hgncAnnotator.annotateElement(proteinAlias);
- assertEquals(1, getWarnings().size());
- assertEquals("SNCA", proteinAlias.getName());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHgncIdToUniprot() throws Exception {
- try {
- List<MiriamData> result = hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.HGNC, "11138"));
- assertEquals(1, result.size());
- assertEquals(new MiriamData(MiriamType.UNIPROT, "P37840", HgncAnnotator.class), result.get(0));
- assertEquals(0, hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.HGNC, "1", HgncAnnotator.class)).size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHgncIdToName() throws Exception {
- try {
- assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "FSD2", HgncAnnotator.class), hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.HGNC, "18024")));
- assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "LMOD1", HgncAnnotator.class), hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.HGNC, "6647")));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUnknownHgncIdToName() throws Exception {
- try {
- assertNull(hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.HGNC, "asd")));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHgncToUniProt1() throws Exception {
- try {
- List<MiriamData> list = hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.HGNC_SYMBOL, "CASP8"));
- assertEquals(1, list.size());
- assertEquals("Q14790", list.get(0).getResource());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHgncToUniProtWithInvalidArg() throws Exception {
- try {
- hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.CAS, "CASP8"));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testHgncToEntrezWithInvalidArg() throws Exception {
- try {
- hgncAnnotator.hgncToEntrez(new MiriamData(MiriamType.CAS, "CASP8"));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIsValidHgnc() throws Exception {
- try {
- assertFalse(hgncAnnotator.isValidHgncMiriam(new MiriamData(MiriamType.CAS, "CASP8")));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIsValidHgnc2() throws Exception {
- try {
- assertTrue(hgncAnnotator.isValidHgncMiriam(new MiriamData(MiriamType.HGNC_SYMBOL, "CASP8")));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testHgncIdToNameWithInvalidArg() throws Exception {
- try {
- hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.CAS, "CASP8"));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHgncToUniProt2() throws Exception {
- try {
-
- MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "CASP8");
- MiriamData data2 = new MiriamData(MiriamType.HGNC_SYMBOL, "CASP10");
-
- List<MiriamData> list = hgncAnnotator.hgncToUniprot(data1);
- assertEquals(1, list.size());
- assertEquals("Q14790", list.get(0).getResource());
-
- list = hgncAnnotator.hgncToUniprot(data2);
- assertEquals(1, list.size());
- assertEquals("Q92851", list.get(0).getResource());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHgncToUniProt3() throws Exception {
- try {
- MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "blablabla invalid name");
- List<MiriamData> list = hgncAnnotator.hgncToUniprot(data1);
- assertNotNull(list);
- assertEquals(0, list.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHgncToEntrez() throws Exception {
- try {
- // check by symbol
- MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "PTGS1");
- MiriamData entrez = hgncAnnotator.hgncToEntrez(data1);
- assertNotNull(entrez);
- assertTrue(new MiriamData(MiriamType.ENTREZ, "5742", HgncAnnotator.class).equals(entrez));
-
- // check by id
- data1 = new MiriamData(MiriamType.HGNC, "11138");
- entrez = hgncAnnotator.hgncToEntrez(data1);
- assertNotNull(entrez);
- assertTrue(new MiriamData(MiriamType.ENTREZ, "6622", HgncAnnotator.class).equals(entrez));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidHgncToEntrez() throws Exception {
- try {
- MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "xxxxxsd");
- MiriamData entrez = hgncAnnotator.hgncToEntrez(data1);
- assertNull(entrez);
-
- data1 = new MiriamData(MiriamType.HGNC, "xxxxxsd");
- entrez = hgncAnnotator.hgncToEntrez(data1);
- assertNull(entrez);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- hgncAnnotator.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 {
- hgncAnnotator.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 testRefreshCacheQueryNotAvailable() throws Exception {
- WebPageDownloader downloader = hgncAnnotator.getWebPageDownloader();
- GeneralCacheInterface originalCache = hgncAnnotator.getCache();
- try {
- // exclude first cached value
- hgncAnnotator.setCache(null);
-
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- hgncAnnotator.setWebPageDownloader(mockDownloader);
- hgncAnnotator.refreshCacheQuery("http://google.pl/");
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- hgncAnnotator.setWebPageDownloader(downloader);
- hgncAnnotator.setCache(originalCache);
- }
- }
-
- @Test
- public void testSimulateDownStatus() throws Exception {
- WebPageDownloader downloader = hgncAnnotator.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- hgncAnnotator.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, hgncAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- hgncAnnotator.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateChangedStatus() throws Exception {
- WebPageDownloader downloader = hgncAnnotator.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<response><result/></response>");
- hgncAnnotator.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, hgncAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- hgncAnnotator.setWebPageDownloader(downloader);
- }
- }
+ final Logger logger = Logger.getLogger(HgncAnnotatorTest.class);
+
+ @Autowired
+ private HgncAnnotator hgncAnnotator;
+
+ @Before
+ public void setUp() {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetAnnotationsForSNCA() throws Exception {
+ try {
+ MiriamData snca = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
+ GenericProtein proteinAlias = new GenericProtein("id");
+ proteinAlias.addMiriamData(snca);
+ hgncAnnotator.annotateElement(proteinAlias);
+ assertNotNull(proteinAlias.getSymbol());
+ assertTrue(proteinAlias.getFormerSymbols().size() > 0);
+ assertNotNull(proteinAlias.getFullName());
+ assertTrue(proteinAlias.getMiriamData().size() > 1);
+ assertTrue(proteinAlias.getSynonyms().size() > 0);
+
+ boolean ensemble = false;
+ boolean hgncId = false;
+ boolean hgncSymbol = false;
+ boolean refseq = false;
+ boolean entrez = false;
+ boolean uniprot = false;
+ for (MiriamData md : proteinAlias.getMiriamData()) {
+ if (MiriamType.ENSEMBL.equals(md.getDataType())) {
+ ensemble = true;
+ } else if (MiriamType.HGNC.equals(md.getDataType())) {
+ assertEquals("Invalid HGNC id", "11138", md.getResource());
+ hgncId = true;
+ } else if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
+ hgncSymbol = true;
+ } else if (MiriamType.REFSEQ.equals(md.getDataType())) {
+ refseq = true;
+ } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
+ entrez = true;
+ } else if (MiriamType.UNIPROT.equals(md.getDataType())) {
+ uniprot = true;
+ }
+ }
+
+ assertTrue("Ensemble symbol cannot be found", ensemble);
+ assertTrue("Hgnc id cannot be found", hgncId);
+ assertTrue("Hgnc symbol cannot be found", hgncSymbol);
+ assertTrue("RefSeq cannot be found", refseq);
+ assertTrue("Entrez cannot be found", entrez);
+ assertTrue("Uniprot cannot be found", uniprot);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForElementWithMultiHGNC() throws Exception {
+ try {
+ MiriamData snca = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
+ MiriamData park7 = new MiriamData(MiriamType.HGNC_SYMBOL, "PARK7");
+ GenericProtein proteinAlias = new GenericProtein("id");
+ proteinAlias.addMiriamData(snca);
+ proteinAlias.addMiriamData(park7);
+ hgncAnnotator.annotateElement(proteinAlias);
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForHGNC_ID() throws Exception {
+ try {
+ MiriamData nsmf = new MiriamData(MiriamType.HGNC, "11138");
+ GenericProtein proteinAlias = new GenericProtein("id");
+ proteinAlias.addMiriamData(nsmf);
+ hgncAnnotator.annotateElement(proteinAlias);
+ assertNotNull(proteinAlias.getSymbol());
+ assertTrue(proteinAlias.getFormerSymbols().size() > 0);
+ assertNotNull(proteinAlias.getFullName());
+ assertTrue(proteinAlias.getMiriamData().size() > 1);
+ assertTrue(proteinAlias.getSynonyms().size() > 0);
+
+ boolean ensemble = false;
+ boolean hgncId = false;
+ boolean hgncSymbol = false;
+ boolean refseq = false;
+ boolean entrez = false;
+ for (MiriamData md : proteinAlias.getMiriamData()) {
+ if (MiriamType.ENSEMBL.equals(md.getDataType())) {
+ ensemble = true;
+ } else if (MiriamType.HGNC.equals(md.getDataType())) {
+ hgncId = true;
+ } else if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
+ hgncSymbol = true;
+ } else if (MiriamType.REFSEQ.equals(md.getDataType())) {
+ refseq = true;
+ } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
+ entrez = true;
+ }
+ }
+
+ assertTrue("Ensemble symbol cannot be found", ensemble);
+ assertTrue("Hgnc id cannot be found", hgncId);
+ assertTrue("Hgnc symbol cannot be found", hgncSymbol);
+ assertTrue("RefSeq cannot be found", refseq);
+ assertTrue("Entrez cannot be found", entrez);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForSNCA2() throws Exception {
+ try {
+ GenericProtein proteinAlias = new GenericProtein("id");
+ proteinAlias.setName("SNCA");
+ hgncAnnotator.annotateElement(proteinAlias);
+ assertNotNull(proteinAlias.getSymbol());
+ assertNotNull(proteinAlias.getName());
+ assertTrue(proteinAlias.getFormerSymbols().size() > 0);
+ assertNotNull(proteinAlias.getFullName());
+ assertTrue(proteinAlias.getMiriamData().size() > 1);
+ assertTrue(proteinAlias.getSynonyms().size() > 0);
+
+ boolean ensemble = false;
+ boolean hgncId = false;
+ boolean hgncSymbol = false;
+ boolean refseq = false;
+ boolean entrez = false;
+ for (MiriamData md : proteinAlias.getMiriamData()) {
+ if (MiriamType.ENSEMBL.equals(md.getDataType())) {
+ ensemble = true;
+ } else if (MiriamType.HGNC.equals(md.getDataType())) {
+ hgncId = true;
+ } else if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
+ hgncSymbol = true;
+ } else if (MiriamType.REFSEQ.equals(md.getDataType())) {
+ refseq = true;
+ } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
+ entrez = true;
+ }
+ }
+
+ assertTrue("Ensemble symbol cannot be found", ensemble);
+ assertTrue("Hgnc id cannot be found", hgncId);
+ assertTrue("Hgnc symbol cannot be found", hgncSymbol);
+ assertTrue("RefSeq cannot be found", refseq);
+ assertTrue("Entrez cannot be found", entrez);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForBID() throws Exception {
+ try {
+ GenericProtein bidProtein = new GenericProtein("id");
+ bidProtein.setName("BID");
+ hgncAnnotator.annotateElement(bidProtein);
+
+ GenericProtein bidMutationProtein = new GenericProtein("id2");
+ bidMutationProtein.setName("BID (p15)");
+ hgncAnnotator.annotateElement(bidMutationProtein);
+
+ assertEquals(bidProtein.getSymbol(),bidMutationProtein.getSymbol());
+ assertEquals(bidProtein.getFormerSymbols(),bidMutationProtein.getFormerSymbols());
+ assertEquals(bidProtein.getFullName(),bidMutationProtein.getFullName());
+ assertEquals(bidProtein.getMiriamData(),bidMutationProtein.getMiriamData());
+ assertEquals(bidProtein.getSynonyms(),bidMutationProtein.getSynonyms());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForInvalid() throws Exception {
+ try {
+ Species proteinAlias = new GenericProtein("id");
+ proteinAlias.setName("UNKNNOWNASD asd");
+ hgncAnnotator.annotateElement(proteinAlias);
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForInvalid2() throws Exception {
+ try {
+ Species proteinAlias = new GenericProtein("id");
+ proteinAlias.setName("cAMP/cGMP-dependent protein kinase");
+ hgncAnnotator.annotateElement(proteinAlias);
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testCachableInterfaceInvalidate() throws Exception {
+ String query = "http://google.pl/";
+ try {
+ String newRes = "hello";
+
+ waitForRefreshCacheQueueToEmpty();
+
+ cache.setCachedQuery(query, hgncAnnotator.getCacheType(), newRes);
+ String res = cache.getStringByQuery(query, hgncAnnotator.getCacheType());
+ assertEquals(newRes, res);
+ cache.invalidateByQuery(query, hgncAnnotator.getCacheType());
+
+ waitForRefreshCacheQueueToEmpty();
+
+ res = cache.getStringByQuery(query, hgncAnnotator.getCacheType());
+
+ assertNotNull(res);
+
+ assertFalse("Value wasn't refreshed from db", newRes.equals(res));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, hgncAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForInvalidMiriamSet() throws Exception {
+ try {
+ MiriamData md1 = new MiriamData(MiriamType.HGNC, "11138");
+ MiriamData md2 = new MiriamData(MiriamType.HGNC, "111382");
+ Species proteinAlias = new GenericProtein("");
+ proteinAlias.addMiriamData(md1);
+ proteinAlias.addMiriamData(md2);
+ hgncAnnotator.annotateElement(proteinAlias);
+ assertEquals(1, getWarnings().size());
+ assertEquals("SNCA", proteinAlias.getName());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncIdToUniprot() throws Exception {
+ try {
+ List<MiriamData> result = hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.HGNC, "11138"));
+ assertEquals(1, result.size());
+ assertEquals(new MiriamData(MiriamType.UNIPROT, "P37840", HgncAnnotator.class), result.get(0));
+ assertEquals(0, hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.HGNC, "1", HgncAnnotator.class)).size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncIdToName() throws Exception {
+ try {
+ assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "FSD2", HgncAnnotator.class),
+ hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.HGNC, "18024")));
+ assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "LMOD1", HgncAnnotator.class),
+ hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.HGNC, "6647")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUnknownHgncIdToName() throws Exception {
+ try {
+ assertNull(hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.HGNC, "asd")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncToUniProt1() throws Exception {
+ try {
+ List<MiriamData> list = hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.HGNC_SYMBOL, "CASP8"));
+ assertEquals(1, list.size());
+ assertEquals("Q14790", list.get(0).getResource());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncToUniProtWithInvalidArg() throws Exception {
+ try {
+ hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.CAS, "CASP8"));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncToEntrezWithInvalidArg() throws Exception {
+ try {
+ hgncAnnotator.hgncToEntrez(new MiriamData(MiriamType.CAS, "CASP8"));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIsValidHgnc() throws Exception {
+ try {
+ assertFalse(hgncAnnotator.isValidHgncMiriam(new MiriamData(MiriamType.CAS, "CASP8")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIsValidHgnc2() throws Exception {
+ try {
+ assertTrue(hgncAnnotator.isValidHgncMiriam(new MiriamData(MiriamType.HGNC_SYMBOL, "CASP8")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncIdToNameWithInvalidArg() throws Exception {
+ try {
+ hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.CAS, "CASP8"));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncToUniProt2() throws Exception {
+ try {
+
+ MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "CASP8");
+ MiriamData data2 = new MiriamData(MiriamType.HGNC_SYMBOL, "CASP10");
+
+ List<MiriamData> list = hgncAnnotator.hgncToUniprot(data1);
+ assertEquals(1, list.size());
+ assertEquals("Q14790", list.get(0).getResource());
+
+ list = hgncAnnotator.hgncToUniprot(data2);
+ assertEquals(1, list.size());
+ assertEquals("Q92851", list.get(0).getResource());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncToUniProt3() throws Exception {
+ try {
+ MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "blablabla invalid name");
+ List<MiriamData> list = hgncAnnotator.hgncToUniprot(data1);
+ assertNotNull(list);
+ assertEquals(0, list.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHgncToEntrez() throws Exception {
+ try {
+ // check by symbol
+ MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "PTGS1");
+ MiriamData entrez = hgncAnnotator.hgncToEntrez(data1);
+ assertNotNull(entrez);
+ assertTrue(new MiriamData(MiriamType.ENTREZ, "5742", HgncAnnotator.class).equals(entrez));
+
+ // check by id
+ data1 = new MiriamData(MiriamType.HGNC, "11138");
+ entrez = hgncAnnotator.hgncToEntrez(data1);
+ assertNotNull(entrez);
+ assertTrue(new MiriamData(MiriamType.ENTREZ, "6622", HgncAnnotator.class).equals(entrez));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidHgncToEntrez() throws Exception {
+ try {
+ MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "xxxxxsd");
+ MiriamData entrez = hgncAnnotator.hgncToEntrez(data1);
+ assertNull(entrez);
+
+ data1 = new MiriamData(MiriamType.HGNC, "xxxxxsd");
+ entrez = hgncAnnotator.hgncToEntrez(data1);
+ assertNull(entrez);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ hgncAnnotator.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 {
+ hgncAnnotator.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 testRefreshCacheQueryNotAvailable() throws Exception {
+ WebPageDownloader downloader = hgncAnnotator.getWebPageDownloader();
+ GeneralCacheInterface originalCache = hgncAnnotator.getCache();
+ try {
+ // exclude first cached value
+ hgncAnnotator.setCache(null);
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ hgncAnnotator.setWebPageDownloader(mockDownloader);
+ hgncAnnotator.refreshCacheQuery("http://google.pl/");
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ hgncAnnotator.setWebPageDownloader(downloader);
+ hgncAnnotator.setCache(originalCache);
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ WebPageDownloader downloader = hgncAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ hgncAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, hgncAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ hgncAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangedStatus() throws Exception {
+ WebPageDownloader downloader = hgncAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
+ .thenReturn("<response><result/></response>");
+ hgncAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, hgncAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ hgncAnnotator.setWebPageDownloader(downloader);
+ }
+ }
}
--
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