diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/CachableInterface.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/CachableInterface.java
index f271d6c39a716f6bbbce53cbd7bd77af10fc50ff..f2401af95111187f5dd2b868db1468029141856b 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/CachableInterface.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/CachableInterface.java
@@ -161,9 +161,9 @@ public abstract class CachableInterface extends XmlParser {
public final void setCache(GeneralCacheInterface cache) {
this.cache = cache;
}
-
+
/**
- * Returns a content of the webpage for a given url.
+ * Returns a content of the webpage for a given url using GET request.
*
* @param accessUrl
* webpage url address
@@ -172,13 +172,36 @@ public abstract class CachableInterface extends XmlParser {
* thrown when there are problems with connection to ChEMBL database
*/
protected final String getWebPageContent(String accessUrl) throws IOException {
+ return getWebPageContent(accessUrl, "GET", null);
+ }
+
+ /**
+ * Returns a content of the webpage for a given url. If postData is not null,
+ * the page will be accessed using POST request. Otherwise GET will be used.
+ *
+ * @param accessUrl
+ * webpage url address
+ * @param httpRequestMethod
+ * type of HTTP request (GET, POST, PUT, PATCH, DELETE, ...)
+ * @param postData
+ * string to be sent in the body of the request
+ * @return content of the webpage
+ * @throws IOException
+ * thrown when there are problems with connection to ChEMBL database
+ */
+ protected final String getWebPageContent(String accessUrl, String httpRequestMethod, String data) throws IOException {
// check if we have the page in our internal cache
+
+ String cacheKey = accessUrl;
+ if (data != null) {
+ cacheKey += data;
+ }
- String result = getCacheValue(accessUrl);
+ String result = getCacheValue(cacheKey);
if (result == null) {
- result = webPageDownloader.getFromNetwork(accessUrl);
+ result = webPageDownloader.getFromNetwork(accessUrl, httpRequestMethod, data);
if (result != null) {
- setCacheValue(accessUrl, result);
+ setCacheValue(cacheKey, result);
}
}
return result;
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
index 80d2c2f7a7d76259ebfd9e032514fb1d70abf7be..c03944fd8fb1507836139a32d05ffcde9b3864d3 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
@@ -4,6 +4,7 @@ import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
+import java.io.DataOutputStream;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
@@ -26,6 +27,10 @@ import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
* @author Piotr Gawron
*
*/
+/**
+ * @author Piotr Gawron
+ *
+ */
public class WebPageDownloader {
/**
@@ -50,17 +55,39 @@ public class WebPageDownloader {
* receiving INTERNAL SERVER ERROR http response.
*/
private static final int HTTP_INTERNAL_ERROR_RECONNECT_TIMES = 2;
-
+
+
+
/**
- * Returns content of the webpage identified by url.
+ * Returns content of the webpage identified by url using GET.
*
* @param accessUrl
* url of a webpage
* @return content of the webpage identified by url
* @throws IOException
- * thrown when there is any problem with accesing webpage
+ * thrown when there is any problem with accessing webpage
*/
public String getFromNetwork(String accessUrl) throws IOException {
+ return getFromNetwork(accessUrl, "GET", null);
+ }
+
+
+ /**
+ * Returns content of the webpage identified by url. The HTTP query is done
+ * using the provided POST if postData is not null.
+ *
+ *
+ * @param accessUrl
+ * url of a webpage
+ * @param httpRequestMethod
+ * type of HTTP request (GET, POST, PUT, PATCH, DELETE, ...)
+ * @param data
+ * string to be sent in the body of the
+ * @return content of the webpage identified by url
+ * @throws IOException
+ * thrown when there is any problem with accessing webpage
+ */
+ public String getFromNetwork(String accessUrl, String httpRequestMethod, String data) throws IOException {
/**
* Tasks that retrieves content from webpage
@@ -77,12 +104,20 @@ public class WebPageDownloader {
int code = HttpURLConnection.HTTP_INTERNAL_ERROR;
HttpURLConnection urlConn = null;
- // connect to the server, if HTTP_INTERNAL_ERROR occurres then try to
+ // connect to the server, if HTTP_INTERNAL_ERROR occurred then try to
// reconnect HTTP_INTERNAL_ERROR_RECONNECT_TIMES times
while (code == HttpURLConnection.HTTP_INTERNAL_ERROR || code == HttpURLConnection.HTTP_NOT_FOUND) {
- urlConn = openConnection(accessUrl);
- urlConn.setRequestMethod("GET");
+ urlConn = openConnection(accessUrl);
urlConn.addRequestProperty("User-Agent", "minerva-framework");
+
+ urlConn.setRequestMethod(httpRequestMethod);
+ if (data != null) {
+ urlConn.setDoOutput(true);
+ DataOutputStream wr = new DataOutputStream(urlConn.getOutputStream());
+ wr.writeBytes(data);
+ wr.close();
+ }
+
try {
urlConn.connect();
code = urlConn.getResponseCode();
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceTest.java
index f8b08ad58c37f168150c19efb19203eae0e5f954..d7f21ed334e040a47f925c142d6161b0465a08ef 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceTest.java
@@ -50,6 +50,27 @@ public class CachableInterfaceTest extends AnnotationTestFunctions {
throw e;
}
}
+
+ @Test
+ public void testGetWebPageGetCache() throws Exception {
+ try {
+ CachableInterfaceMock ci = new CachableInterfaceMock(CachableInterface.class);
+
+ CacheTypeDao mock = Mockito.mock(CacheTypeDao.class);
+ when(mock.getByClassName(anyString())).thenReturn(new CacheType());
+ ci.setCacheTypeDao(mock);
+ ci.setCache(new GeneralCache());
+
+ String cacheKey = "https://www.google.com/";
+ String result = ci.getWebPageContent(cacheKey);
+ assertNotNull(result);
+ String cacheValue = ci.getCacheValue(cacheKey);
+ assertTrue(result.equals(cacheValue));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
@Test
public void testSetNode() throws Exception {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/WebPageDownloaderTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/WebPageDownloaderTest.java
index 8f58a75c427fea9dabc00e2b224d6452b310b9d3..d548f06e95733454bbf64761aa45f161f0d6c95d 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/WebPageDownloaderTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/WebPageDownloaderTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.annotation.cache;
import static org.junit.Assert.fail;
+import static org.junit.Assert.assertNotNull;
import java.io.IOException;
import java.net.HttpURLConnection;
@@ -61,5 +62,37 @@ public class WebPageDownloaderTest {
} catch (IOException e) {
}
}
+
+ @Test
+ public void testSend1() {
+ WebPageDownloader downloader = new WebPageDownloader();
+ try {
+ String result = downloader.getFromNetwork("https://www.google.com/");
+ assertNotNull("GET request to Google should return non-null result", result);
+ } catch (IOException e) {
+ }
+ }
+
+ @Test
+ public void testPost1() {
+ WebPageDownloader downloader = new WebPageDownloader();
+ try {
+ String result = downloader.getFromNetwork("https://www.ebi.ac.uk/pdbe/api/mappings/best_structures/", "POST", "P29373");
+ assertNotNull("POST request to Uniprot should return non-null result", result);
+ } catch (IOException e) {
+ }
+
+ }
+
+ @Test
+ public void testInvalidHttpRequestType() {
+ WebPageDownloader downloader = new WebPageDownloader();
+ try {
+ String result = downloader.getFromNetwork("https://www.ebi.ac.uk/pdbe/api/mappings/best_structures/", "XXX", "P29373");
+ fail("Invalid request exception expected");
+ } catch (IOException e) {
+ }
+
+ }
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
index 8a2ccae9ca521c17970dc194fe339b1ff1308628..90b26f72ff4c3f6524a35975e7ed10abda0e9bde 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
@@ -297,7 +297,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("invalid xml");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "water"));
fail("Exception expected");
@@ -319,7 +319,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("invalid xml");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.findDrug("test");
fail("Exception expected");
@@ -341,7 +341,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "water"));
fail("Exception expected");
@@ -403,7 +403,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("<target><unk/></target>");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<target><unk/></target>");
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "water"));
assertEquals(1, getWarnings().size());
@@ -422,7 +422,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("<target><target_components><target_component/></target_components></target>");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<target><target_components><target_component/></target_components></target>");
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "water"));
assertEquals(1, getWarnings().size());
@@ -441,7 +441,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("<target><target_chembl_id>inv id</target_chembl_id></target>");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<target><target_chembl_id>inv id</target_chembl_id></target>");
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "water"));
assertEquals(1, getWarnings().size());
@@ -836,7 +836,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
// simulate problem with downloading
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.refreshCacheQuery("http://google.pl/");
fail("Exception expected");
@@ -860,7 +860,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
// simulate problem with downloading
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getDrugsByChemblTarget(new MiriamData());
@@ -886,7 +886,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
// simulate problem with downloading
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getDrugsByChemblTarget(new MiriamData());
@@ -914,7 +914,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
// simulate problem with downloading
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.refreshCacheQuery(query);
fail("Exception expected");
@@ -943,7 +943,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
WebPageDownloader downloader = chemblParser.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, chemblParser.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -959,7 +959,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
WebPageDownloader downloader = chemblParser.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("<response><molecules/></response>");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<response><molecules/></response>");
chemblParser.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.CHANGED, chemblParser.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -977,7 +977,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
// valid xml but with empty data
- when(mockDownloader.getFromNetwork(anyString())).thenReturn(
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn(
"<response><molecules>" + "<molecule><pref_name/><max_phase/><molecule_chembl_id/><molecule_synonyms/></molecule>"
+ "</molecules><mechanisms/><molecule_forms/></response>");
chemblParser.setWebPageDownloader(mockDownloader);
@@ -1016,7 +1016,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("invalid xml");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getTargetsByDrugId(new MiriamData(MiriamType.CHEMBL_COMPOUND, "123"));
fail("Exception expected");
@@ -1036,7 +1036,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getTargetsByDrugId(new MiriamData(MiriamType.CHEMBL_COMPOUND, "123"));
fail("Exception expected");
@@ -1056,7 +1056,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getDrugListByTarget(new MiriamData(MiriamType.UNIPROT, "O60391"));
fail("Exception expected");
@@ -1077,7 +1077,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("invalid xml");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getDrugListByTarget(new MiriamData(MiriamType.UNIPROT, "O60391"));
fail("Exception expected");
@@ -1140,7 +1140,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("invalid xml");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getDrugById(new MiriamData(MiriamType.CHEMBL_COMPOUND, ""));
fail("Exception expected");
@@ -1160,7 +1160,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getDrugById(new MiriamData(MiriamType.CHEMBL_COMPOUND, ""));
fail("Exception expected");
@@ -1193,7 +1193,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getTargetsForChildElements(new MiriamData());
fail("Exception expected");
@@ -1213,7 +1213,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("invalid xml");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getTargetsForChildElements(new MiriamData());
fail("Exception expected");
@@ -1233,7 +1233,7 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
try {
chemblParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("<response><molecule_forms><node/></molecule_forms></response>");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<response><molecule_forms><node/></molecule_forms></response>");
chemblParser.setWebPageDownloader(mockDownloader);
chemblParser.getTargetsForChildElements(new MiriamData());
assertEquals(1, getWarnings().size());
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
index f03eb92e179fd32c00e3ac5686e069374d0d8a32..8fc7c418987177d2d153cd58ca73816a35ef8517 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
@@ -77,7 +77,7 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
// skip first call to cache, so we will have to at least parse the data
chemicalParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
chemicalParser.setWebPageDownloader(mockDownloader);
// Parkinson disease
MiriamData diseaseID = new MiriamData(MiriamType.MESH_2012, "D010300");
@@ -431,7 +431,7 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
// simulate problem with downloading
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
chemicalParser.setWebPageDownloader(mockDownloader);
chemicalParser.refreshCacheQuery(query);
fail("Exception expected");
@@ -460,7 +460,7 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
WebPageDownloader downloader = chemicalParser.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
chemicalParser.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, chemicalParser.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -476,7 +476,7 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
WebPageDownloader downloader = chemicalParser.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
chemicalParser.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.CHANGED, chemicalParser.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -559,7 +559,7 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
chemicalParser.setCache(new GeneralCacheWithExclusion(chemicalParser.getCache(), 1));
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
chemicalParser.setWebPageDownloader(mockDownloader);
try {
chemicalParser.getChemicals(diseaseID, idsList);
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
index 98ad19ad4dc01856566b7fefaa0ad30befe659ba..92e47385e96e2b236654cd938046a279d230d407 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
@@ -597,7 +597,7 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
WebPageDownloader downloader = drugBankHTMLParser.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
drugBankHTMLParser.setWebPageDownloader(mockDownloader);
drugBankHTMLParser.refreshCacheQuery("http://google.pl/");
fail("Exception expected");
@@ -616,7 +616,7 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
GeneralCacheInterface cache = drugBankHTMLParser.getCache();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
drugBankHTMLParser.setWebPageDownloader(mockDownloader);
drugBankHTMLParser.setCache(null);
@@ -709,7 +709,7 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
WebPageDownloader downloader = drugBankHTMLParser.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
drugBankHTMLParser.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, drugBankHTMLParser.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -725,7 +725,7 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
WebPageDownloader downloader = drugBankHTMLParser.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
drugBankHTMLParser.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.CHANGED, drugBankHTMLParser.getServiceStatus().getStatus());
} catch (Exception e) {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
index b0812d94b85ce8118767e20e84aa733981a39179..dad33fc058968a8dbf3b8cb930a39d050941904f 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
@@ -169,7 +169,7 @@ public class MeSHParserTest extends AnnotationTestFunctions {
MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D004298");
MeSHParser parserUnderTest = new MeSHParser();
WebPageDownloader webPageDownloader = Mockito.mock(WebPageDownloader.class);
- when(webPageDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(webPageDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
parserUnderTest.setWebPageDownloader(webPageDownloader);
parserUnderTest.getMeSH(meshID);
@@ -276,7 +276,7 @@ public class MeSHParserTest extends AnnotationTestFunctions {
try {
meshParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
meshParser.setWebPageDownloader(mockDownloader);
MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D010300");
@@ -299,7 +299,7 @@ public class MeSHParserTest extends AnnotationTestFunctions {
WebPageDownloader downloader = meshParser.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
meshParser.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, meshParser.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -315,7 +315,7 @@ public class MeSHParserTest extends AnnotationTestFunctions {
WebPageDownloader downloader = meshParser.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new WrongResponseCodeIOException(null, HttpStatus.SC_NOT_FOUND));
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new WrongResponseCodeIOException(null, HttpStatus.SC_NOT_FOUND));
meshParser.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.CHANGED, meshParser.getServiceStatus().getStatus());
} catch (Exception e) {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
index 8814930e8ddd1ff50b723d84098f482f71d18d8c..86d950eeae2c6e0e99f4326ae8a688b830a49046 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
@@ -227,7 +227,7 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
// exclude first cached value
miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
miriamConnector.setWebPageDownloader(mockDownloader);
miriamConnector.getUrlString2(TaxonomyBackend.HUMAN_TAXONOMY);
@@ -251,7 +251,7 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
// exclude first cached value
miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
miriamConnector.setWebPageDownloader(mockDownloader);
miriamConnector.getUrlString2(TaxonomyBackend.HUMAN_TAXONOMY);
@@ -273,7 +273,7 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = miriamConnector.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
miriamConnector.setWebPageDownloader(mockDownloader);
miriamConnector.refreshCacheQuery("http://google.pl/");
fail("Exception expected");
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java
index 06f813e37e4ee83f231db96b20f68b234ec2f513..bb4b0b68f3e02fc3f3aab621247718b1753bf037 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java
@@ -232,7 +232,7 @@ public class PubmedParserTest extends AnnotationTestFunctions {
try {
pubmedParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
pubmedParser.setWebPageDownloader(mockDownloader);
String query = PubmedParser.PUBMED_PREFIX + PubmedParser.SERVICE_STATUS_PUBMED_ID;
@@ -289,7 +289,7 @@ public class PubmedParserTest extends AnnotationTestFunctions {
WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
pubmedParser.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, pubmedParser.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -305,7 +305,7 @@ public class PubmedParserTest extends AnnotationTestFunctions {
WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString()))
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
.thenReturn("<responseWrapper><version>" + PubmedParser.SUPPORTED_VERSION + "</version></responseWrapper>");
pubmedParser.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, pubmedParser.getServiceStatus().getStatus());
@@ -322,7 +322,7 @@ public class PubmedParserTest extends AnnotationTestFunctions {
WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString()))
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
.thenReturn("<responseWrapper><version>" + PubmedParser.SUPPORTED_VERSION + "blabla</version></responseWrapper>");
pubmedParser.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.CHANGED, pubmedParser.getServiceStatus().getStatus());
@@ -350,7 +350,7 @@ public class PubmedParserTest extends AnnotationTestFunctions {
pubmedParser.setCache(null);
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("unknown response");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("unknown response");
pubmedParser.setWebPageDownloader(mockDownloader);
pubmedParser.getApiVersion();
fail("Exception expected");
@@ -370,7 +370,7 @@ public class PubmedParserTest extends AnnotationTestFunctions {
pubmedParser.setCache(null);
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("<xml/>");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<xml/>");
pubmedParser.setWebPageDownloader(mockDownloader);
assertNull(pubmedParser.getApiVersion());
} catch (Exception e) {
@@ -388,7 +388,7 @@ public class PubmedParserTest extends AnnotationTestFunctions {
pubmedParser.setCache(null);
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
pubmedParser.setWebPageDownloader(mockDownloader);
pubmedParser.getApiVersion();
fail("Exception expected");
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java
index 611295b0f3c183697a2e537b1b67b8394ce04ddd..3c8b521e144a99725ba4a3d7910c72872828b5dc 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java
@@ -123,7 +123,7 @@ public class TaxonomyBackendTest extends AnnotationTestFunctions {
WebPageDownloader downloader = taxonomyBackend.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
taxonomyBackend.setWebPageDownloader(mockDownloader);
taxonomyBackend.setCache(null);
taxonomyBackend.getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, "9606"));
@@ -265,7 +265,7 @@ public class TaxonomyBackendTest extends AnnotationTestFunctions {
WebPageDownloader downloader = taxonomyBackend.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
taxonomyBackend.setWebPageDownloader(mockDownloader);
taxonomyBackend.refreshCacheQuery("http://google.pl/");
fail("Exception expected");
@@ -293,7 +293,7 @@ public class TaxonomyBackendTest extends AnnotationTestFunctions {
WebPageDownloader downloader = taxonomyBackend.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
taxonomyBackend.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, taxonomyBackend.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -309,7 +309,7 @@ public class TaxonomyBackendTest extends AnnotationTestFunctions {
WebPageDownloader downloader = taxonomyBackend.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
taxonomyBackend.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.CHANGED, taxonomyBackend.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -325,7 +325,7 @@ public class TaxonomyBackendTest extends AnnotationTestFunctions {
WebPageDownloader downloader = taxonomyBackend.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("<em>Taxonomy ID: </em>1234");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<em>Taxonomy ID: </em>1234");
taxonomyBackend.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.CHANGED, taxonomyBackend.getServiceStatus().getStatus());
} catch (Exception e) {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
index ffcbd0d3d44f0042f0f4bac79ccfc14e74b6908f..8366b4f6c7766a789235186030f86aa89f126138 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
@@ -177,7 +177,7 @@ public class EnsemblAnnotatorTest extends AnnotationTestFunctions {
ensemblAnnotator.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
ensemblAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, ensemblAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -200,7 +200,7 @@ public class EnsemblAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
String dataXml = "<opt></opt>";
String versionXml = "<opt><data release=\"" + EnsemblAnnotator.SUPPORTED_VERSION + "\"/></opt>";
- when(mockDownloader.getFromNetwork(anyString())).thenReturn(dataXml).thenReturn(versionXml);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn(dataXml).thenReturn(versionXml);
ensemblAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.CHANGED, ensemblAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -223,7 +223,7 @@ public class EnsemblAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
String dataXml = "<opt></opt>";
String versionXml = "<opt><data release=\"blablabla\"/></opt>";
- when(mockDownloader.getFromNetwork(anyString())).thenReturn(dataXml).thenReturn(versionXml);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn(dataXml).thenReturn(versionXml);
ensemblAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.CHANGED, ensemblAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -279,7 +279,7 @@ public class EnsemblAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = ensemblAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new WrongResponseCodeIOException(null, 0));
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new WrongResponseCodeIOException(null, 0));
ensemblAnnotator.setWebPageDownloader(mockDownloader);
Species proteinAlias = new GenericProtein("id");
proteinAlias.addMiriamData(new MiriamData(MiriamType.ENSEMBL, "1234"));
@@ -302,7 +302,7 @@ public class EnsemblAnnotatorTest extends AnnotationTestFunctions {
ensemblAnnotator.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
ensemblAnnotator.setWebPageDownloader(mockDownloader);
ensemblAnnotator.refreshCacheQuery("http://google.pl/");
fail("Exception expected");
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java
index 40b24bc0e229e5a026e377b048fb0cbd2b9c649a..be988ab5020c6a4ae950d3184a2d05e82f1693e6 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java
@@ -141,7 +141,7 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = entrezAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
entrezAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, entrezAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -270,7 +270,7 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
entrezAnnotator.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
entrezAnnotator.setWebPageDownloader(mockDownloader);
entrezAnnotator.refreshCacheQuery("http://google.pl/");
fail("Exception expected");
@@ -293,7 +293,7 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
entrezAnnotator.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
entrezAnnotator.setWebPageDownloader(mockDownloader);
entrezAnnotator.refreshCacheQuery(EntrezAnnotator.ENTREZ_DATA_PREFIX + "6647");
fail("Exception expected");
@@ -359,7 +359,7 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
entrezAnnotator.setCache(null);
String response = super.readFile("testFiles/annotation/entrezResponse.xml");
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn(response);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn(response);
entrezAnnotator.setWebPageDownloader(mockDownloader);
EntrezData data = entrezAnnotator.getEntrezForMiriamData(new MiriamData(), "");
boolean ensembl = false;
@@ -394,7 +394,7 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
entrezAnnotator.setCache(null);
String response = "";
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn(response);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn(response);
entrezAnnotator.setWebPageDownloader(mockDownloader);
entrezAnnotator.getEntrezForMiriamData(new MiriamData(), "");
fail("Exception expected");
@@ -416,7 +416,7 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
try {
entrezAnnotator.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new WrongResponseCodeIOException(null, 404));
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new WrongResponseCodeIOException(null, 404));
entrezAnnotator.setWebPageDownloader(mockDownloader);
entrezAnnotator.getEntrezForMiriamData(new MiriamData(), "");
fail("Exception expected");
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 ce4045811d0c0d2e4de8c34a71092946ed8d1e00..3f410c345bc04e18408c2bb29af39dab5dbc908f 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
@@ -82,7 +82,7 @@ public class GoAnnotatorTest extends AnnotationTestFunctions {
GoAnnotator annotator = new GoAnnotator();
annotator.setMc(goAnnotator.getMc());
WebPageDownloader downloader = Mockito.mock(WebPageDownloader.class);
- when(downloader.getFromNetwork(anyString())).thenReturn("");
+ when(downloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
annotator.setWebPageDownloader(downloader);
annotator.getGoElement(md);
fail("Exception expected");
@@ -126,7 +126,7 @@ public class GoAnnotatorTest extends AnnotationTestFunctions {
goAnnotator.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
goAnnotator.setWebPageDownloader(mockDownloader);
goAnnotator.refreshCacheQuery("http://google.pl/");
fail("Exception expected");
@@ -192,7 +192,7 @@ public class GoAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = goAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
goAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, goAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -208,7 +208,7 @@ public class GoAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = goAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("<obo><term><name/><def><defstr/></def></term></obo>");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<obo><term><name/><def><defstr/></def></term></obo>");
goAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.CHANGED, goAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -224,7 +224,7 @@ public class GoAnnotatorTest extends AnnotationTestFunctions {
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>");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), 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) {
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 d9c60e80eadcfb8f3a1707c8b434bbbf7a13d6d9..2a286755299c830ffaa48e1c6a8ba7157c467f2c 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
@@ -496,7 +496,7 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
hgncAnnotator.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
hgncAnnotator.setWebPageDownloader(mockDownloader);
hgncAnnotator.refreshCacheQuery("http://google.pl/");
fail("Exception expected");
@@ -515,7 +515,7 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = hgncAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
hgncAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, hgncAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -531,7 +531,7 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = hgncAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("<response><result/></response>");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<response><result/></response>");
hgncAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.CHANGED, hgncAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
index 78fe4d4a99c7f8b02e0467cf0fdd345543fc140e..b70fe82bdfabbcbfa40783db536a92d0c659e17f 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
@@ -83,7 +83,7 @@ public class ReconAnnotatorTest extends AnnotationTestFunctions {
reconAnnotator.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
reconAnnotator.setWebPageDownloader(mockDownloader);
reconAnnotator.annotateElement(ion);
@@ -112,7 +112,7 @@ public class ReconAnnotatorTest extends AnnotationTestFunctions {
String response = super.readFile("testFiles/annotation/recon_reaction_response.json");
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn(response);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn(response);
reconAnnotator.setWebPageDownloader(mockDownloader);
reconAnnotator.annotateElement(ion);
@@ -142,7 +142,7 @@ public class ReconAnnotatorTest extends AnnotationTestFunctions {
String response = super.readFile("testFiles/annotation/recon_chemical_response.json");
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn(response);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn(response);
reconAnnotator.setWebPageDownloader(mockDownloader);
reconAnnotator.annotateElement(reaction);
@@ -282,7 +282,7 @@ public class ReconAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = reconAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
reconAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, reconAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -298,7 +298,7 @@ public class ReconAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = reconAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("{\"results\":[{}]}");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("{\"results\":[{}]}");
reconAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.CHANGED, reconAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -314,7 +314,7 @@ public class ReconAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = reconAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("{\"results\":[{\"keggId\":\"C00001\",\"xxx\":\"yyy\"}]}");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("{\"results\":[{\"keggId\":\"C00001\",\"xxx\":\"yyy\"}]}");
reconAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.CHANGED, reconAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -334,7 +334,7 @@ public class ReconAnnotatorTest extends AnnotationTestFunctions {
reconAnnotator.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
reconAnnotator.setWebPageDownloader(mockDownloader);
reconAnnotator.refreshCacheQuery("http://google.pl/");
fail("Exception expected");
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java
index 8f7b2edc3bde536c68846e5529e046a16038b830..c27be152ae03470035eab296978d066bcdcd7488 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java
@@ -240,7 +240,7 @@ public class UniprotAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = uniprotAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
uniprotAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, uniprotAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -258,7 +258,7 @@ public class UniprotAnnotatorTest extends AnnotationTestFunctions {
uniprotAnnotator.setCache(new GeneralCacheWithExclusion(cache, 1));
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
uniprotAnnotator.setWebPageDownloader(mockDownloader);
Species protein = new GenericProtein("id");
protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "P01308"));
@@ -279,7 +279,7 @@ public class UniprotAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = uniprotAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
uniprotAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, uniprotAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -295,7 +295,7 @@ public class UniprotAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = uniprotAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("GN Name=ACSS2; Synonyms=ACAS2;");
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("GN Name=ACSS2; Synonyms=ACAS2;");
uniprotAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.CHANGED, uniprotAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnectorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnectorTest.java
index c27bb7764c643c7b9290e1fabd8dc48fea5a387a..5ff31b7460e125167a6e4df0574204fe723c3de1 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnectorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnectorTest.java
@@ -146,7 +146,7 @@ public class UcscReferenceGenomeConnectorTest extends AnnotationTestFunctions {
connector.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
connector.setWebPageDownloader(mockDownloader);
connector.getAvailableOrganisms();
fail("Exception expected");
@@ -760,7 +760,7 @@ public class UcscReferenceGenomeConnectorTest extends AnnotationTestFunctions {
// exclude first cached value
connector.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
connector.setWebPageDownloader(mockDownloader);
connector.refreshCacheQuery("http://google.pl/");
fail("Exception expected");
diff --git a/frontend-js/.idea/frontend-js.iml b/frontend-js/.idea/frontend-js.iml
index fb987bb081cc244b1155f1a001ca98f1ff3c9bd8..4feb4987b6dd589318a78302c0367c39c36535a9 100644
--- a/frontend-js/.idea/frontend-js.iml
+++ b/frontend-js/.idea/frontend-js.iml
@@ -4,8 +4,8 @@
<content url="file://$MODULE_DIR$">
<sourceFolder url="file://$MODULE_DIR$/src/test" isTestSource="true" />
<excludeFolder url="file://$MODULE_DIR$/.tmp" />
- <excludeFolder url="file://$MODULE_DIR$/dist" />
<excludeFolder url="file://$MODULE_DIR$/temp" />
+ <excludeFolder url="file://$MODULE_DIR$/dist" />
<excludeFolder url="file://$MODULE_DIR$/tmp" />
</content>
<orderEntry type="inheritedJdk" />