diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000000000000000000000000000000000000..4c8e77f73dc9ab17d7d6cec19defa40c7f5d9f30
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,12 @@
+image: node
+
+before_script:
+ - cd frontend-js
+ - npm install
+ - cd ..
+
+test_frontend:
+ script:
+ - cd frontend-js
+ - npm test
+
\ No newline at end of file
diff --git a/CHANGELOG b/CHANGELOG
index 5ddd8c6f4e09fcd6ca9040e2e1f8b6b705d83b68..1eb8ddc1b403c90693a938fee296419777858e4b 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,8 @@
+minerva (11.0.1) stable; urgency=medium
+ * Bug fix: logout caused issues with session data
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Fri, 08 Sep 2017 12:00:00 +0200
+
minerva (11.0.0) stable; urgency=medium
* Bug fix: security issue - access to specific map can be restricted
diff --git a/README.md b/README.md
index 861648d99c5e64126470d7438abf13c19892bd67..03e5b1befea38931a7909a47f346b260514e7e99 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,5 @@
+[](https://git-r3lab.uni.lu/piotr.gawron/minerva/commits/207-continous-integration-tests)
+
# Rest API (version 11)
## Introduction
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/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java
index def4fbc887b886ef0abcce359c77e7b2ea308ba3..96bc681dfb4643be61cea44c3d3128d5eff44e00 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java
@@ -54,7 +54,7 @@ public class ImageGenerators {
generatorInstances = new ArrayList<>();
generatorInstances.add(new PngImageGenerator(params));
generatorInstances.add(new PdfImageGenerator(params));
- // generatorInstances.add(new SvgImageGenerator(params));
+ generatorInstances.add(new SvgImageGenerator(params));
// generatorInstances.add(new JpgImageGenerator(params));
for (AbstractImageGenerator abstractImageGenerator : generatorInstances) {
availableGenerators
diff --git a/frontend-js/.idea/codeStyleSettings.xml b/frontend-js/.idea/codeStyleSettings.xml
new file mode 100644
index 0000000000000000000000000000000000000000..5555dd266682059e1b1fed89915c4ef70b2bba45
--- /dev/null
+++ b/frontend-js/.idea/codeStyleSettings.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="ProjectCodeStyleSettingsManager">
+ <option name="PER_PROJECT_SETTINGS">
+ <value />
+ </option>
+ <option name="PREFERRED_PROJECT_CODE_STYLE" value="Default" />
+ </component>
+</project>
\ No newline at end of file
diff --git a/frontend-js/.idea/frontend-js.iml b/frontend-js/.idea/frontend-js.iml
index 24643cc37449b4bde54411a80b8ed61258225e34..b6d6506e8893d7574cd478c3f94f16a0d3a0f679 100644
--- a/frontend-js/.idea/frontend-js.iml
+++ b/frontend-js/.idea/frontend-js.iml
@@ -4,6 +4,7 @@
<content url="file://$MODULE_DIR$">
<excludeFolder url="file://$MODULE_DIR$/.tmp" />
<excludeFolder url="file://$MODULE_DIR$/temp" />
+ <excludeFolder url="file://$MODULE_DIR$/dist" />
<excludeFolder url="file://$MODULE_DIR$/tmp" />
</content>
<orderEntry type="inheritedJdk" />
diff --git a/frontend-js/.idea/preferred-vcs.xml b/frontend-js/.idea/preferred-vcs.xml
new file mode 100644
index 0000000000000000000000000000000000000000..848cfc44550cbfba31b047a54bb77ecd25feb0c7
--- /dev/null
+++ b/frontend-js/.idea/preferred-vcs.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="PreferredVcsStorage">
+ <preferredVcsName>ApexVCS</preferredVcsName>
+ </component>
+</project>
\ No newline at end of file
diff --git a/frontend-js/package.json b/frontend-js/package.json
index 06d8f040f920227de9465f5986979172a0e8d438..f6835c3aa6fbc7e47cdfce0cc8f261720d330d01 100644
--- a/frontend-js/package.json
+++ b/frontend-js/package.json
@@ -26,9 +26,9 @@
"exorcist": "^0.4.0",
"file-url": "^2.0.0",
"istanbul": "0.4.5",
- "jquery": "3.1.1",
- "jquery-ui-dist": "^1.12.1",
- "jsdom": "^11.1.0",
+ "jquery": "1.12.1",
+ "jquery-ui-dist": "1.12.1",
+ "jsdom": "11.1.0",
"jsdom-global": "^2.1.1",
"jshint": "^2.9.4",
"log4js-memory-appender": "1.0.5",
@@ -37,7 +37,8 @@
},
"dependencies": {
"del": "^3.0.0",
- "dual-listbox": "^1.0.3",
+ "dual-listbox": "^1.0.7",
+ "file-saver": "^1.3.3",
"http-status-codes": "^1.1.6",
"js-cookie": "^2.1.3",
"log4js": "0.6.38",
diff --git a/frontend-js/src/main/js/Export.js b/frontend-js/src/main/js/Export.js
index e425dbb06dd9c436840e07ad3b93aa501c9d48d9..d2233fc56f90e66111ccfa589b2337d247e69ff5 100644
--- a/frontend-js/src/main/js/Export.js
+++ b/frontend-js/src/main/js/Export.js
@@ -24,6 +24,7 @@ var Functions = require('./Functions');
function Export(options) {
var self = this;
self._panels = [];
+ self._tabIdCount = 0;
if (!(options instanceof CustomMapOptions)) {
options = new CustomMapOptions(options);
}
@@ -90,7 +91,7 @@ Export.prototype.addTab = function(params, navElement, contentElement) {
var name = params.name;
- var tabId = "left_panel_ab_" + this._tabIdCount;
+ var tabId = "export_panel_tab_" + this._tabIdCount;
self._tabIdCount++;
var navClass = '';
@@ -130,7 +131,7 @@ Export.prototype.addTab = function(params, navElement, contentElement) {
this._panels.push(new params.panelClass({
element : contentDiv,
project : self.getProject(),
- configuration: self.getConfiguration(),
+ configuration : self.getConfiguration(),
}));
};
diff --git a/frontend-js/src/main/js/GuiConnector.js b/frontend-js/src/main/js/GuiConnector.js
index f89dd7c10d0586264413dd6af7eb1b8bb62be362..1e05d57715704904ae833534af9e89bb1f08c29a 100644
--- a/frontend-js/src/main/js/GuiConnector.js
+++ b/frontend-js/src/main/js/GuiConnector.js
@@ -4,6 +4,7 @@ var logger = require('./logger');
var Functions = require('./Functions');
var SecurityError = require('./SecurityError');
+var GuiMessageError = require('./gui/GuiMessageError');
var NetworkError = require('./NetworkError');
/**
@@ -177,6 +178,8 @@ GuiConnector.alert = function (error) {
}
var message = error;
if (message instanceof SecurityError) {
+ message = error.message + "<p>Please <a href=\"login.xhtml\">login</a> to access this resuorce</p>";
+ } else if (message instanceof GuiMessageError) {
message = error.message + "<p>Please <a href=\"login.xhtml\">login</a> to access this resource</p>";
} else if (message instanceof NetworkError && (error.message === "XHR error" || error.message === "Failed to fetch")) {
message = "File to big.<br>Please reduce file size or contact administrators.";
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 8e87692ac119f866cd3cd88cbddd4783c1dfafba..b7454ef5074a92c0c1c33437a43a4ab95854b3e1 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -248,15 +248,14 @@ ServerConnector.getToken = function (token) {
var self = this;
token = self.getSessionData(null).getToken();
- if (token === undefined) {
+ var login = self.getSessionData(null).getLogin()
+ if (token === undefined || login === undefined) {
return self.login();
} else {
// if the project is not initialized then check if we can download data
// using current token
if (self.getSessionData().getProject() === null) {
- return self.getConfiguration({
- token: token
- }).then(function () {
+ return self.getConfiguration().then(function () {
return token;
}, function () {
return self.login();
@@ -376,6 +375,12 @@ ServerConnector.loginUrl = function () {
});
};
+ServerConnector.logoutUrl = function () {
+ return this.getApiUrl({
+ type: "/doLogout",
+ });
+};
+
ServerConnector.getSuggestedQueryListUrl = function (queryParams, filterParams) {
return this.getApiUrl({
url: this.getBioEntitiesUrl(queryParams) + "suggestedQueryList/",
@@ -603,10 +608,7 @@ ServerConnector.getUserUrl = function (queryParams, filterParams) {
});
};
-ServerConnector.getConfiguration = function (params) {
- if (params === undefined) {
- params = {};
- }
+ServerConnector.getConfiguration = function () {
var self = this;
if (this._configuration === undefined) {
return self.readFile(self.getConfigurationUrl()).then(function (content) {
@@ -836,6 +838,12 @@ ServerConnector.getOverlayById = function (overlayId, projectId) {
ServerConnector.getReactions = function (params) {
var self = this;
var queryParams = {};
+ if (params.ids === undefined) {
+ params.ids = [];
+ }
+ if (params.participantId === undefined) {
+ params.participantId = [];
+ }
var filterParams = {
id: params.ids,
columns: params.columns,
@@ -843,7 +851,12 @@ ServerConnector.getReactions = function (params) {
};
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
- return self.readFile(self.getReactionsUrl(queryParams, filterParams));
+ if (filterParams.id.length > 100 || filterParams.participantId.length > 100) {
+ return self.sendPostRequest(self.getReactionsUrl(queryParams), filterParams);
+ } else {
+ return self.readFile(self.getReactionsUrl(queryParams, filterParams));
+ }
+
}).then(function (content) {
var array = JSON.parse(content);
var result = [];
@@ -862,10 +875,19 @@ ServerConnector.getAliases = function (params) {
if (params.ids === undefined) {
params.ids = [];
}
+ if (params.includedCompartmentIds === undefined) {
+ params.includedCompartmentIds = [];
+ }
+ if (params.excludedCompartmentIds === undefined) {
+ params.excludedCompartmentIds = [];
+ }
var filterParams = {
id: params.ids,
columns: params.columns,
type: params.type,
+ excludedCompartmentIds: params.excludedCompartmentIds,
+ includedCompartmentIds: params.includedCompartmentIds,
+
};
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
@@ -947,7 +969,7 @@ ServerConnector.getClosestElementsByCoordinates = function (params) {
ServerConnector.login = function (login, password) {
var self = this;
var params = {};
- if (login !== undefined) {
+ if (login !== undefined && login !== "") {
params.login = login;
params.password = password;
} else {
@@ -970,7 +992,7 @@ ServerConnector.logout = function () {
var self = this;
self.getSessionData().setToken(undefined);
self.getSessionData().setLogin(undefined);
- return Promise.resolve();
+ return self.readFile(self.logoutUrl());
};
ServerConnector.getElementsByQuery = function (params) {
diff --git a/frontend-js/src/main/js/gui/GuiMessageError.js b/frontend-js/src/main/js/gui/GuiMessageError.js
new file mode 100644
index 0000000000000000000000000000000000000000..52ccf03be23abafbcad02be87411e6aeea94734d
--- /dev/null
+++ b/frontend-js/src/main/js/gui/GuiMessageError.js
@@ -0,0 +1,15 @@
+"use strict";
+
+/* exported logger */
+
+var logger = require('../logger');
+
+function GuiMessageError(message) {
+ this.message = message;
+ this.stack = (new Error()).stack;
+}
+
+GuiMessageError.prototype = Object.create(Error.prototype);
+GuiMessageError.prototype.constructor = GuiMessageError;
+
+module.exports = GuiMessageError;
diff --git a/frontend-js/src/main/js/gui/export/AbstractExportPanel.js b/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
new file mode 100644
index 0000000000000000000000000000000000000000..c55f8063bcd6e589b72962ebd8e3cb77c07a7680
--- /dev/null
+++ b/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
@@ -0,0 +1,445 @@
+"use strict";
+
+/* exported logger */
+
+var Panel = require('../Panel');
+
+var GuiConnector = require('../../GuiConnector');
+var logger = require('../../logger');
+var Functions = require('../../Functions');
+var DualListbox = require('dual-listbox').DualListbox;
+var Promise = require("bluebird");
+
+function AbstractExportPanel(params) {
+ params.scrollable = true;
+ Panel.call(this, params);
+
+}
+
+AbstractExportPanel.prototype = Object.create(Panel.prototype);
+AbstractExportPanel.prototype.constructor = AbstractExportPanel;
+
+AbstractExportPanel.prototype.init = function() {
+
+};
+
+function compareSimple(val1, val2) {
+ if (val1 < val2) {
+ return -1;
+ } else if (val1 > val2) {
+ return 1;
+ } else {
+ return 0;
+ }
+}
+
+AbstractExportPanel.prototype._createMiriamTypeDiv = function(annotations) {
+ var self = this;
+ var typeDiv = Functions.createElement({
+ type : "div",
+ name : "miriamSelectDiv",
+ className : "minerva-export-dual-listbox-container",
+ });
+ typeDiv.appendChild(Functions.createElement({
+ type : "h4",
+ content : " Annotations:",
+ }));
+
+ var selectElement = Functions.createElement({
+ type : "select",
+ className : "minerva-multi-select",
+ });
+ typeDiv.appendChild(selectElement);
+
+ function compare(entry1, entry2) {
+ if ((entry1.count === 0 && entry2.count === 0) || (entry1.count !== 0 && entry2.count !== 0)) {
+ return compareSimple(entry1.miriamType.getCommonName(), entry2.miriamType.getCommonName());
+ } else {
+ return compareSimple(-entry1.count, -entry2.count);
+ }
+ }
+ annotations.sort(compare);
+
+ for (var i = 0; i < annotations.length; i++) {
+ var miriamType = annotations[i].miriamType;
+ var count = annotations[i].count;
+
+ var option = new Option();
+ option.value = miriamType.getName();
+ if (count > 0) {
+ option.innerHTML = "<div class='minerva-multi-select-special'>" + miriamType.getCommonName() + " (" + count
+ + ")</div>";
+ } else {
+ option.innerHTML = "<div >" + miriamType.getCommonName() + "</div>";
+ }
+ selectElement.appendChild(option);
+ }
+
+ self.setMiriamTypesDualListbox(self.createDualListbox(selectElement));
+ return typeDiv;
+};
+
+AbstractExportPanel.prototype.createDualListbox = function(selectElement) {
+ return new DualListbox(selectElement, {
+ availableTitle : 'Available',
+ selectedTitle : 'Used',
+ addButtonText : '>',
+ removeButtonText : '<',
+ addAllButtonText : '>>',
+ removeAllButtonText : '<<'
+ });
+};
+
+AbstractExportPanel.prototype._createSelectTypeDiv = function(elementTypes) {
+ var typeDiv = Functions.createElement({
+ type : "div",
+ name : "typeSelectDiv",
+ });
+ typeDiv.appendChild(Functions.createElement({
+ type : "h4",
+ content : " TYPE:",
+ }));
+ var choicesContainer = Functions.createElement({
+ type : "ul",
+ className : "minerva-checkbox-grid"
+ });
+ typeDiv.appendChild(choicesContainer);
+ for (var i = 0; i < elementTypes.length; i++) {
+ var elementType = elementTypes[i];
+ var row = Functions.createElement({
+ type : "li",
+ content : "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"" + elementType + "\" value=\""
+ + elementType + "\" />" + elementType + "</label></div>"
+ });
+ choicesContainer.appendChild(row);
+ }
+ choicesContainer.appendChild(Functions.createElement({
+ type : "li",
+ content : "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"ALL\" value=\"ALL\" />ALL</label></div>"
+ }));
+ return typeDiv;
+};
+
+AbstractExportPanel.prototype.getSelectedTypes = function() {
+ var self = this;
+
+ var div = $("div[name='typeSelectDiv']", $(self.getElement()))[0];
+ var result = [];
+ var selectedAll = false;
+ $(":checked", $(div)).each(function(index, element) {
+ if (element.value === "ALL") {
+ selectedAll = true;
+ }
+ result.push(element.value);
+ });
+ if (selectedAll) {
+ return ServerConnector.getConfiguration().then(function(configuration) {
+ return configuration.getElementTypes();
+ });
+ }
+
+ return Promise.resolve(result);
+};
+
+AbstractExportPanel.prototype.setMiriamTypesDualListbox = function(dualListbox) {
+ this._miriamTypesDualListbox = dualListbox;
+};
+AbstractExportPanel.prototype.getMiriamTypesDualListbox = function() {
+ return this._miriamTypesDualListbox;
+};
+
+AbstractExportPanel.prototype._createSelectColumnDiv = function(columnTypes) {
+ var columnDiv = Functions.createElement({
+ type : "div",
+ name : "columnSelectDiv",
+ });
+ columnDiv.appendChild(Functions.createElement({
+ type : "h4",
+ content : " COLUMN:",
+ }));
+ var choicesContainer = Functions.createElement({
+ type : "ul",
+ className : "minerva-checkbox-grid"
+ });
+
+ columnDiv.appendChild(choicesContainer);
+ for (var i = 0; i < columnTypes.length; i++) {
+ var columnType = columnTypes[i];
+ var row = Functions.createElement({
+ type : "li",
+ content : "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"column_" + columnType.columnName
+ + "\" value=\"" + columnType.columnName + "\" />" + columnType.name + "</label></div>"
+ });
+ choicesContainer.appendChild(row);
+ }
+ choicesContainer.appendChild(Functions.createElement({
+ type : "li",
+ content : "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"ALL\" value=\"ALL\" />ALL</label></div>"
+ }));
+ return columnDiv;
+};
+
+AbstractExportPanel.prototype.getSelectedMiriamTypes = function() {
+ var self = this;
+ return ServerConnector.getConfiguration().then(function(configuration) {
+ var selected = self.getMiriamTypesDualListbox().selected;
+ var result = [];
+ for (var i = 0; i < selected.length; i++) {
+ var miriamType = configuration.getMiriamTypeByName(selected[i].dataset.id);
+ result.push(miriamType);
+ }
+ return result;
+ });
+};
+
+AbstractExportPanel.prototype.getSelectedColumns = function() {
+ var self = this;
+
+ var div = $("div[name='columnSelectDiv']", $(self.getElement()))[0];
+ var selectedColumnMap = [];
+ var selectedAll = false;
+ $(":checked", $(div)).each(function(index, element) {
+ if (element.value === "ALL") {
+ selectedAll = true;
+ }
+ selectedColumnMap[element.value] = true;
+ });
+ var columnTypes = self.getAllColumns();
+
+ if (selectedAll) {
+ return Promise.resolve(columnTypes);
+ }
+
+ var result = [];
+
+ for (var i = 0; i < columnTypes.length; i++) {
+ var columnType = columnTypes[i];
+ if (selectedColumnMap[columnType.columnName] === true) {
+ result.push(columnType);
+ }
+ }
+ return Promise.resolve(result);
+};
+
+AbstractExportPanel.prototype._getCompartmentNames = function() {
+ var self = this;
+ var compartments = [];
+ return self._getAllCompartments().then(function(result) {
+
+ var addedNames = [];
+ for (var i = 0; i < result.length; i++) {
+ if (addedNames[result[i].getName()] === undefined) {
+ compartments.push(result[i].getName());
+ addedNames[result[i].getName()] = true;
+ }
+ }
+ compartments.sort(compareSimple);
+ return compartments;
+ });
+};
+
+AbstractExportPanel.prototype.getModels = function() {
+ var self = this;
+ var models = [ self.getProject().getModel() ];
+ for (var i = 0; i < self.getProject().getModel().getSubmodels().length; i++) {
+ models.push(self.getProject().getModel().getSubmodels()[i]);
+ }
+ return models;
+};
+
+AbstractExportPanel.prototype._getAllCompartments = function() {
+ var self = this;
+ var compartments = [];
+
+ var models = self.getModels();
+
+ var promises = [];
+ for (var i = 0; i < models.length; i++) {
+ promises.push(models[i].getCompartments());
+ }
+
+ return Promise.all(promises).then(function(result) {
+ for (var i = 0; i < result.length; i++) {
+ var modelCompartments = result[i];
+ for (var j = 0; j < modelCompartments.length; j++) {
+ compartments.push(modelCompartments[j]);
+ }
+ }
+ return compartments;
+ });
+};
+
+AbstractExportPanel.prototype._createDownloadButton = function() {
+ var self = this;
+ var downloadDiv = Functions.createElement({
+ type : "div",
+ name : "downloadDiv",
+ style : "clear:both; padding: 10px;",
+ });
+ var button = Functions.createElement({
+ type : "button",
+ name : "downloadButton",
+ content : " Download",
+ onclick : function() {
+ GuiConnector.showProcessing();
+ return self.createResponseString().then(function(result) {
+ var blob = new Blob([ result ], {
+ type : "text/plain;charset=utf-8"
+ });
+ var FileSaver = require("file-saver");
+ return FileSaver.saveAs(blob, self.getSaveFilename());
+ }).then(function() {
+ GuiConnector.hideProcessing();
+ }, function(error) {
+ GuiConnector.hideProcessing();
+ GuiConnector.alert(error);
+ });
+ },
+ });
+ downloadDiv.appendChild(button);
+
+ return downloadDiv;
+};
+
+AbstractExportPanel.prototype.getSaveFilename = function() {
+ var self = this;
+ return self.getProject().getProjectId() + "-" + self.getPanelName() + ".txt";
+};
+
+AbstractExportPanel.prototype._createSelectIncludedCompartmentDiv = function() {
+ var self = this;
+ var typeDiv = Functions.createElement({
+ type : "div",
+ name : "includedCompartmentSelectDiv",
+ className : "minerva-export-dual-listbox-container",
+ });
+ typeDiv.appendChild(Functions.createElement({
+ type : "h4",
+ content : " Included compartment/pathways:",
+ }));
+
+ return self._getCompartmentNames().then(function(compartmentNames) {
+
+ var selectElement = Functions.createElement({
+ type : "select",
+ className : "minerva-multi-select",
+ });
+ typeDiv.appendChild(selectElement);
+
+ for (var i = 0; i < compartmentNames.length; i++) {
+ var name = compartmentNames[i];
+
+ var option = new Option();
+ option.value = name;
+ option.innerHTML = "<div >" + name + "</div>";
+ selectElement.appendChild(option);
+ }
+ self.setIncludedCompartmentsDualListbox(self.createDualListbox(selectElement));
+ return typeDiv;
+ });
+};
+
+AbstractExportPanel.prototype._createSelectExcludedCompartmentDiv = function() {
+ var self = this;
+ var typeDiv = Functions.createElement({
+ type : "div",
+ name : "excludedCompartmentSelectDiv",
+ className : "minerva-export-dual-listbox-container",
+ });
+ typeDiv.appendChild(Functions.createElement({
+ type : "h4",
+ content : " Excluded compartment/pathways:",
+ }));
+
+ return self._getCompartmentNames().then(function(compartmentNames) {
+
+ var selectElement = Functions.createElement({
+ type : "select",
+ className : "minerva-multi-select",
+ });
+ typeDiv.appendChild(selectElement);
+
+ for (var i = 0; i < compartmentNames.length; i++) {
+ var name = compartmentNames[i];
+
+ var option = new Option();
+ option.value = name;
+ option.innerHTML = "<div >" + name + "</div>";
+ selectElement.appendChild(option);
+ }
+ self.setExcludedCompartmentsDualListbox(self.createDualListbox(selectElement));
+ return typeDiv;
+ });
+};
+
+AbstractExportPanel.prototype.setIncludedCompartmentsDualListbox = function(dualListbox) {
+ this._includedCompartmentsDualListbox = dualListbox;
+};
+AbstractExportPanel.prototype.getIncludedCompartmentsDualListbox = function() {
+ return this._includedCompartmentsDualListbox;
+};
+
+AbstractExportPanel.prototype.getSelectedIncludedCompartments = function() {
+ var self = this;
+ var list = self.getIncludedCompartmentsDualListbox().selected;
+ var names = [];
+ var result = [];
+ for (var i = 0; i < list.length; i++) {
+ var element = list[i];
+ names[element.dataset.id] = true;
+ }
+ return self._getAllCompartments().then(function(compartments) {
+ for (var i = 0; i < compartments.length; i++) {
+ var compartment = compartments[i];
+ if (names[compartment.getName()]) {
+ result.push(compartment);
+ }
+ }
+ return result;
+ });
+};
+
+AbstractExportPanel.prototype.setExcludedCompartmentsDualListbox = function(dualListbox) {
+ this._excludedCompartmentsDualListbox = dualListbox;
+};
+AbstractExportPanel.prototype.getExcludedCompartmentsDualListbox = function() {
+ return this._excludedCompartmentsDualListbox;
+};
+
+AbstractExportPanel.prototype.getSelectedExcludedCompartments = function() {
+ var self = this;
+ var list = self.getExcludedCompartmentsDualListbox().selected;
+ var names = [];
+ var result = [];
+ for (var i = 0; i < list.length; i++) {
+ var element = list[i];
+ names[element.dataset.id] = true;
+ }
+ return self._getAllCompartments().then(function(compartments) {
+ for (var i = 0; i < compartments.length; i++) {
+ var compartment = compartments[i];
+ if (names[compartment.getName()]) {
+ result.push(compartment);
+ }
+ }
+ return result;
+ });
+};
+
+AbstractExportPanel.prototype.createResponseHeader = function(columns, miriamTypes) {
+ var stringBuilder = [];
+ var i;
+ for (i = 0; i < columns.length; i++) {
+ var column = columns[i];
+ stringBuilder.push(column.name);
+ }
+ for (i = 0; i < miriamTypes.length; i++) {
+ var miriamType = miriamTypes[i];
+ stringBuilder.push(miriamType.getCommonName());
+ }
+ var result = stringBuilder.join("\t");
+ return result;
+
+};
+
+module.exports = AbstractExportPanel;
diff --git a/frontend-js/src/main/js/gui/export/ElementExportPanel.js b/frontend-js/src/main/js/gui/export/ElementExportPanel.js
index c38301e725da2fb0b0c9198502dcf3afd031cc4f..59868a6b1ba66ad71ef3c8ae2247ff815f027c4b 100644
--- a/frontend-js/src/main/js/gui/export/ElementExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/ElementExportPanel.js
@@ -2,40 +2,21 @@
/* exported logger */
-var Panel = require('../Panel');
+var AbstractExportPanel = require('./AbstractExportPanel');
+var GuiMessageError = require('../GuiMessageError');
-var DualListbox = require('dual-listbox').DualListbox;
var logger = require('../../logger');
-var Functions = require('../../Functions');
var Promise = require("bluebird");
function ElementExportPanel(params) {
params.panelName = "elementExport";
- params.scrollable = true;
- Panel.call(this, params);
-
- var self = this;
- self._createGui();
+ AbstractExportPanel.call(this, params);
}
-ElementExportPanel.prototype = Object.create(Panel.prototype);
+ElementExportPanel.prototype = Object.create(AbstractExportPanel.prototype);
ElementExportPanel.prototype.constructor = ElementExportPanel;
-function compareSimple(val1, val2) {
- if (val1 < val2) {
- return -1;
- } else if (val1 > val2) {
- return 1;
- } else {
- return 0;
- }
-}
-
-ElementExportPanel.prototype._createGui = function() {
-
-};
-
ElementExportPanel.prototype.init = function() {
var self = this;
var element = self.getElement();
@@ -44,148 +25,29 @@ ElementExportPanel.prototype.init = function() {
configuration = result;
var typeDiv = self._createSelectTypeDiv(configuration.getElementTypes());
element.appendChild(typeDiv);
- element.appendChild(self._createSelectColumnDiv());
+ element.appendChild(self._createSelectColumnDiv(self.getAllColumns()));
return ServerConnector.getProjectStatistics(self.getProject().getProjectId());
}).then(function(statistics) {
- var miriamDiv = self._createMiriamTypeDiv(statistics);
- element.appendChild(miriamDiv);
- self.setMiriamTypesDualListbox(new DualListbox("#miriamTypeSelect", {
- availableTitle : 'Available',
- selectedTitle : 'Used',
- addButtonText : '>',
- removeButtonText : '<',
- addAllButtonText : '>>',
- removeAllButtonText : '<<'
- }));
- }).then(function() {
+ return self._createMiriamTypeDiv(statistics.getElementAnnotations());
+ }).then(function(div) {
+ element.appendChild(div);
return self._createSelectIncludedCompartmentDiv();
- }).then(function(selectIncludedCompartmentDiv) {
- element.appendChild(selectIncludedCompartmentDiv);
- self.setIncludedCompartmentsDualListbox(new DualListbox("#includedCompartmentsSelect", {
- availableTitle : 'Available',
- selectedTitle : 'Used',
- addButtonText : '>',
- removeButtonText : '<',
- addAllButtonText : '>>',
- removeAllButtonText : '<<'
- }));
+ }).then(function(div) {
+ element.appendChild(div);
return self._createSelectExcludedCompartmentDiv();
- }).then(function(selectExcludedCompartmentDiv) {
- element.appendChild(selectExcludedCompartmentDiv);
- self.setExcludedCompartmentsDualListbox(new DualListbox("#excludedCompartmentsSelect", {
- availableTitle : 'Available',
- selectedTitle : 'Used',
- addButtonText : '>',
- removeButtonText : '<',
- addAllButtonText : '>>',
- removeAllButtonText : '<<'
- }));
+ }).then(function(div) {
+ element.appendChild(div);
element.appendChild(self._createDownloadButton());
}).then(function() {
$(window).trigger('resize');
});
};
-ElementExportPanel.prototype._createSelectTypeDiv = function(elementTypes) {
- var typeDiv = Functions.createElement({
- type : "div",
- name : "typeSelectDiv",
- });
- typeDiv.appendChild(Functions.createElement({
- type : "h4",
- content : " TYPE:",
- }));
- var choicesContainer = Functions.createElement({
- type : "ul",
- className : "minerva-checkbox-grid"
- });
- typeDiv.appendChild(choicesContainer);
- for (var i = 0; i < elementTypes.length; i++) {
- var elementType = elementTypes[i];
- var row = Functions.createElement({
- type : "li",
- content : "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"" + elementType + "\" value=\""
- + elementType + "\" />" + elementType + "</label></div>"
- });
- choicesContainer.appendChild(row);
- }
- choicesContainer.appendChild(Functions.createElement({
- type : "li",
- content : "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"ALL\" value=\"ALL\" />ALL</label></div>"
- }));
- return typeDiv;
-};
-
-ElementExportPanel.prototype._createMiriamTypeDiv = function(statistics) {
- var typeDiv = Functions.createElement({
- type : "div",
- name : "miriamSelectDiv",
- className : "minerva-export-dual-listbox-container",
- });
- typeDiv.appendChild(Functions.createElement({
- type : "h4",
- content : " Annotations:",
- }));
-
- var annotations = statistics.getElementAnnotations();
-
- var selectElement = Functions.createElement({
- type : "select",
- className : "minerva-multi-select",
- id : "miriamTypeSelect",
- });
- typeDiv.appendChild(selectElement);
-
- function compare(entry1, entry2) {
- if ((entry1.count === 0 && entry2.count === 0) || (entry1.count !== 0 && entry2.count !== 0)) {
- return compareSimple(entry1.miriamType.getCommonName(), entry2.miriamType.getCommonName());
- } else {
- return compareSimple(-entry1.count, -entry2.count);
- }
- }
- annotations.sort(compare);
-
- for (var i = 0; i < annotations.length; i++) {
- var miriamType = annotations[i].miriamType;
- var count = annotations[i].count;
-
- var option = new Option();
- option.value = miriamType.getName();
- if (count > 0) {
- option.innerHTML = "<div class='minerva-multi-select-special'>" + miriamType.getCommonName() + " (" + count
- + ")</div>";
- } else {
- option.innerHTML = "<div >" + miriamType.getCommonName() + "</div>";
- }
- selectElement.appendChild(option);
- }
- return typeDiv;
-};
-
-ElementExportPanel.prototype._createDownloadButton = function() {
- var self = this;
- var downloadDiv = Functions.createElement({
- type : "div",
- name : "downloadDiv",
- style : "clear:both; padding: 10px;",
- });
- var button = Functions.createElement({
- type : "button",
- content : " Download",
- onclick : function() {
- return self.createResponseString().then(function(result) {
- logger.info(result);
- });
- },
- });
- downloadDiv.appendChild(button);
-
- return downloadDiv;
-};
-
ElementExportPanel.prototype.createResponseString = function() {
var self = this;
- var types;
+ var types, miriamTypes;
+ var includedCompartmentIds = [];
+ var excludedCompartmentIds = [];
var models = [ self.getProject().getModel() ];
for (var i = 0; i < self.getProject().getModel().getSubmodels().length; i++) {
models.push(self.getProject().getModel().getSubmodels()[i]);
@@ -193,12 +55,28 @@ ElementExportPanel.prototype.createResponseString = function() {
var elements = [];
return self.getSelectedTypes().then(function(result) {
+ if (result.length === 0) {
+ return Promise.reject(new GuiMessageError("You must select at least one type"));
+ }
types = result;
+ return self.getSelectedIncludedCompartments();
+ }).then(function(result) {
+ result.forEach(function(compartment) {
+ includedCompartmentIds.push(compartment.getId());
+ });
+ return self.getSelectedExcludedCompartments();
+ }).then(function(result) {
+ result.forEach(function(compartment) {
+ excludedCompartmentIds.push(compartment.getId());
+ });
+
var promises = [];
for (var i = 0; i < models.length; i++) {
promises.push(models[i].getAliases({
type : types,
complete : true,
+ includedCompartmentIds : includedCompartmentIds,
+ excludedCompartmentIds : excludedCompartmentIds,
}));
}
return Promise.all(promises);
@@ -208,183 +86,53 @@ ElementExportPanel.prototype.createResponseString = function() {
elements.push(aliasesByModel[i][j]);
}
}
+
+ return self.getSelectedMiriamTypes();
+ }).then(function(result) {
+ miriamTypes = result;
return self.getSelectedColumns();
}).then(function(selectedColumns) {
+ if (selectedColumns.length === 0) {
+ return Promise.reject(new GuiMessageError("You must select at least one column"));
+ }
var rows = [];
- rows.push(self.createResponseHeader(selectedColumns));
+ rows.push(self.createResponseHeader(selectedColumns, miriamTypes));
for (var i = 0; i < elements.length; i++) {
- rows.push(self.createResponseRow(elements[i], selectedColumns));
+ rows.push(self.createResponseRow(elements[i], selectedColumns, miriamTypes));
}
return rows.join("\n");
});
};
-ElementExportPanel.prototype.createResponseHeader = function(columns) {
+ElementExportPanel.prototype.createResponseRow = function(alias, columns, miriamTypes) {
var stringBuilder = [];
- for (var i = 0; i < columns.length; i++) {
+ var i, value;
+ for (i = 0; i < columns.length; i++) {
var column = columns[i];
- stringBuilder.push(column.name);
- }
- var result = stringBuilder.join("\t");
- return result;
-
-};
-
-ElementExportPanel.prototype.createResponseRow = function(alias, columns) {
- var stringBuilder = [];
- for (var i = 0; i < columns.length; i++) {
- var column = columns[i];
- var value = alias[column.method]();
+ value = alias[column.method]();
if (column.formatFunction !== undefined) {
value = column.formatFunction(value);
}
- stringBuilder.push(value);
-
- }
- var result = stringBuilder.join("\t");
- return result;
-};
-
-ElementExportPanel.prototype._createSelectIncludedCompartmentDiv = function() {
- var self = this;
- var typeDiv = Functions.createElement({
- type : "div",
- name : "includedCompartmentSelectDiv",
- className : "minerva-export-dual-listbox-container",
- });
- typeDiv.appendChild(Functions.createElement({
- type : "h4",
- content : " Included compartment/pathways:",
- }));
-
- return self._getCompartmentNames().then(function(compartmentNames) {
-
- var selectElement = Functions.createElement({
- type : "select",
- className : "minerva-multi-select",
- id : "includedCompartmentsSelect",
- });
- typeDiv.appendChild(selectElement);
-
- for (var i = 0; i < compartmentNames.length; i++) {
- var name = compartmentNames[i];
-
- var option = new Option();
- option.value = name;
- option.innerHTML = "<div >" + name + "</div>";
- selectElement.appendChild(option);
- }
- return typeDiv;
- });
-};
-
-ElementExportPanel.prototype._createSelectExcludedCompartmentDiv = function() {
- var self = this;
- var typeDiv = Functions.createElement({
- type : "div",
- name : "excludedCompartmentSelectDiv",
- className : "minerva-export-dual-listbox-container",
- });
- typeDiv.appendChild(Functions.createElement({
- type : "h4",
- content : " Excluded compartment/pathways:",
- }));
-
- return self._getCompartmentNames().then(function(compartmentNames) {
-
- var selectElement = Functions.createElement({
- type : "select",
- className : "minerva-multi-select",
- id : "excludedCompartmentsSelect",
- });
- typeDiv.appendChild(selectElement);
-
- for (var i = 0; i < compartmentNames.length; i++) {
- var name = compartmentNames[i];
-
- var option = new Option();
- option.value = name;
- option.innerHTML = "<div >" + name + "</div>";
- selectElement.appendChild(option);
+ if (value instanceof String || typeof value === "string") {
+ value = value.replace(/[\n\r]/g, ' ');
}
- return typeDiv;
- });
-};
-
-ElementExportPanel.prototype._getAllCompartments = function() {
- var self = this;
- var compartments = [];
- var i;
-
- var models = [ self.getProject().getModel() ];
- for (i = 0; i < self.getProject().getModel().getSubmodels().length; i++) {
- models.push(self.getProject().getModel().getSubmodels()[i]);
- }
-
- var promises = [];
- for (i = 0; i < models.length; i++) {
- promises.push(models[i].getCompartments());
+ stringBuilder.push(value);
}
-
- return Promise.all(promises).then(function(result) {
- for (var i = 0; i < result.length; i++) {
- var modelCompartments = result[i];
- for (var j = 0; j < modelCompartments.length; j++) {
- compartments.push(modelCompartments[j]);
+ for (i = 0; i < miriamTypes.length; i++) {
+ value = "";
+ var miriamType = miriamTypes[i];
+ var references = alias.getReferences();
+ for (var j = 0; j < references.length; j++) {
+ var reference = references[j];
+ if (reference.getType() === miriamType.getName()) {
+ value += reference.getResource() + ",";
}
}
- return compartments;
- });
-};
-ElementExportPanel.prototype._getCompartmentNames = function() {
- var self = this;
- var compartments = [];
- return self._getAllCompartments().then(function(result) {
-
- var addedNames = [];
- for (var i = 0; i < result.length; i++) {
- if (addedNames[result[i].getName()] === undefined) {
- compartments.push(result[i].getName());
- addedNames[result[i].getName()] = true;
- }
- }
- compartments.sort(compareSimple);
- return compartments;
- });
-};
-
-ElementExportPanel.prototype._createSelectColumnDiv = function() {
- var self = this;
- var columnDiv = Functions.createElement({
- type : "div",
- name : "columnSelectDiv",
- });
- columnDiv.appendChild(Functions.createElement({
- type : "h4",
- content : " COLUMN:",
- }));
- var choicesContainer = Functions.createElement({
- type : "ul",
- className : "minerva-checkbox-grid"
- });
- var columnTypes = self.getAllColumns();
-
- columnDiv.appendChild(choicesContainer);
- for (var i = 0; i < columnTypes.length; i++) {
- var columnType = columnTypes[i];
- var row = Functions.createElement({
- type : "li",
- content : "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"column_" + columnType.columnName
- + "\" value=\"" + columnType.columnName + "\" />" + columnType.name + "</label></div>"
- });
- choicesContainer.appendChild(row);
+ stringBuilder.push(value);
}
- choicesContainer.appendChild(Functions.createElement({
- type : "li",
- content : "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"ALL\" value=\"ALL\" />ALL</label></div>"
- }));
- return columnDiv;
+ var result = stringBuilder.join("\t");
+ return result;
};
ElementExportPanel.prototype.getAllColumns = function() {
@@ -467,128 +215,5 @@ ElementExportPanel.prototype.getAllColumns = function() {
}, ];
};
-ElementExportPanel.prototype.getSelectedTypes = function() {
- var self = this;
-
- var div = $("div[name='typeSelectDiv']", $(self.getElement()))[0];
- var result = [];
- var selectedAll = false;
- $(":checked", $(div)).each(function(index, element) {
- if (element.value === "ALL") {
- selectedAll = true;
- }
- result.push(element.value);
- });
- if (selectedAll) {
- return ServerConnector.getConfiguration().then(function(configuration) {
- return configuration.getElementTypes();
- });
- }
-
- return Promise.resolve(result);
-};
-
-ElementExportPanel.prototype.setMiriamTypesDualListbox = function(dualListbox) {
- this._miriamTypesDualListbox = dualListbox;
-};
-ElementExportPanel.prototype.getMiriamTypesDualListbox = function() {
- return this._miriamTypesDualListbox;
-};
-
-ElementExportPanel.prototype.setIncludedCompartmentsDualListbox = function(dualListbox) {
- this._includedCompartmentsDualListbox = dualListbox;
-};
-ElementExportPanel.prototype.getIncludedCompartmentsDualListbox = function() {
- return this._includedCompartmentsDualListbox;
-};
-
-ElementExportPanel.prototype.getSelectedIncludedCompartments = function() {
- var self = this;
- var list = self.getIncludedCompartmentsDualListbox().selected;
- var names = [];
- var result = [];
- for (var i = 0; i < list.length; i++) {
- var element = list[i];
- names[element.dataset.id] = true;
- }
- return self._getAllCompartments().then(function(compartments) {
- for (var i = 0; i < compartments.length; i++) {
- var compartment = compartments[i];
- if (names[compartment.getName()]) {
- result.push(compartment);
- }
- }
- return result;
- });
-};
-
-ElementExportPanel.prototype.setExcludedCompartmentsDualListbox = function(dualListbox) {
- this._excludedCompartmentsDualListbox = dualListbox;
-};
-ElementExportPanel.prototype.getExcludedCompartmentsDualListbox = function() {
- return this._excludedCompartmentsDualListbox;
-};
-
-ElementExportPanel.prototype.getSelectedExcludedCompartments = function() {
- var self = this;
- var list = self.getExcludedCompartmentsDualListbox().selected;
- var names = [];
- var result = [];
- for (var i = 0; i < list.length; i++) {
- var element = list[i];
- names[element.dataset.id] = true;
- }
- return self._getAllCompartments().then(function(compartments) {
- for (var i = 0; i < compartments.length; i++) {
- var compartment = compartments[i];
- if (names[compartment.getName()]) {
- result.push(compartment);
- }
- }
- return result;
- });
-};
-
-ElementExportPanel.prototype.getSelectedMiriamTypes = function() {
- var self = this;
- return ServerConnector.getConfiguration().then(function(configuration) {
- var selected = self.getMiriamTypesDualListbox().selected;
- var result = [];
- for (var i = 0; i < selected.length; i++) {
- var miriamType = configuration.getMiriamTypeByName(selected[i].dataset.id);
- result.push(miriamType);
- }
- return result;
- });
-};
-
-ElementExportPanel.prototype.getSelectedColumns = function() {
- var self = this;
-
- var div = $("div[name='columnSelectDiv']", $(self.getElement()))[0];
- var selectedColumnMap = [];
- var selectedAll = false;
- $(":checked", $(div)).each(function(index, element) {
- if (element.value === "ALL") {
- selectedAll = true;
- }
- selectedColumnMap[element.value] = true;
- });
- var columnTypes = self.getAllColumns();
-
- if (selectedAll) {
- return Promise.resolve(columnTypes);
- }
-
- var result = [];
-
- for (var i = 0; i < columnTypes.length; i++) {
- var columnType = columnTypes[i];
- if (selectedColumnMap[columnType.columnName] === true) {
- result.push(columnType);
- }
- }
- return Promise.resolve(result);
-};
module.exports = ElementExportPanel;
diff --git a/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js b/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js
index 6bf41a4246b1695a8bedde1007e23741acf6ad4c..4e2f7103a850a8a55e62ec42efbb08da47c9ba5c 100644
--- a/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js
@@ -2,21 +2,156 @@
/* exported logger */
-var Panel = require('../Panel');
+var AbstractExportPanel = require('./AbstractExportPanel');
+var Functions = require('../../Functions');
var logger = require('../../logger');
function GraphicsExportPanel(params) {
- params.panelName = "elementExport";
- params.scrollable = true;
- Panel.call(this, params);
+ params.panelName = "graphicsExport";
+ AbstractExportPanel.call(this, params);
}
-GraphicsExportPanel.prototype = Object.create(Panel.prototype);
+GraphicsExportPanel.prototype = Object.create(AbstractExportPanel.prototype);
GraphicsExportPanel.prototype.constructor = GraphicsExportPanel;
GraphicsExportPanel.prototype.init = function() {
+ var self = this;
+ var element = self.getElement();
+ var configuration;
+ element.appendChild(self._createSelectProjectDiv());
+ var configuration;
+ return ServerConnector.getConfiguration().then(function(result) {
+ configuration = result;
+ element.appendChild(self._createSelectGraphicsFormatDiv(configuration.getImageConverters()));
+ element.appendChild(self._createDownloadButton());
+ }).then(function() {
+ $(window).trigger('resize');
+ });
+};
+
+GraphicsExportPanel.prototype._createSelectProjectDiv = function(annotations) {
+ var self = this;
+ var project = self.getProject();
+ var typeDiv = Functions.createElement({
+ type : "div",
+ name : "modelSelectDiv",
+ });
+ typeDiv.appendChild(Functions.createElement({
+ type : "h4",
+ content : "(Sub)map:",
+ }));
+
+ var choicesContainer = Functions.createElement({
+ type : "ul",
+ });
+ typeDiv.appendChild(choicesContainer);
+
+ var models = self.getModels();
+
+ for (var i = 0; i < models.length; i++) {
+ var model = models[i];
+ var checkedString = "";
+ if (i === 0) {
+ checkedString = ' checked="checked" ';
+ }
+ var row = Functions.createElement({
+ type : "li",
+ content : '<div><label> <input type="radio" name="model" value="' + model.getId() + '"' + checkedString + '/>'
+ + model.getName() + '</label></div>',
+ });
+ choicesContainer.appendChild(row);
+ }
+
+ return typeDiv;
+};
+
+GraphicsExportPanel.prototype._createSelectGraphicsFormatDiv = function(formats) {
+ var self = this;
+ var project = self.getProject();
+ var typeDiv = Functions.createElement({
+ type : "div",
+ name : "formatSelectDiv",
+ });
+ typeDiv.appendChild(Functions.createElement({
+ type : "h4",
+ content : "Format:",
+ }));
+
+ var choicesContainer = Functions.createElement({
+ type : "ul",
+ });
+ typeDiv.appendChild(choicesContainer);
+
+ for (var i = 0; i < formats.length; i++) {
+ var format = formats[i];
+ var checkedString = "";
+ if (i === 0) {
+ checkedString = ' checked="checked" ';
+ }
+ var row = Functions.createElement({
+ type : "li",
+ content : '<div><label> <input type="radio" name="format" value="' + format.handler + '"' + checkedString + '/>'
+ + format.name + '</label></div>',
+ });
+ choicesContainer.appendChild(row);
+ }
+
+ return typeDiv;
+};
+
+GraphicsExportPanel.prototype.getSubmapId = function() {
+ var self = this;
+ var div = $("div[name='modelSelectDiv']", $(self.getElement()))[0];
+ var id = null;
+ $(":checked", $(div)).each(function(index, element) {
+ id = element.value;
+ });
+ return id;
+};
+GraphicsExportPanel.prototype.getFormatHandler = function() {
+ var self = this;
+ var div = $("div[name='formatSelectDiv']", $(self.getElement()))[0];
+ var format = null;
+ $(":checked", $(div)).each(function(index, element) {
+ format = element.value;
+ });
+ return format;
+};
+
+GraphicsExportPanel.prototype._createDownloadButton = function() {
+ var self = this;
+ var downloadDiv = Functions.createElement({
+ type : "div",
+ name : "downloadDiv",
+ style : "clear:both; padding: 10px;",
+ });
+ var button = Functions.createElement({
+ type : "button",
+ name : "downloadButton",
+ content : " Download",
+ onclick : function() {
+ var identifier = null;
+ var defaultOverlayName = "Network";
+ for (var i = 0; i < self.getProject().getModel().getLayouts().length; i++) {
+ var layout = self.getProject().getModel().getLayouts()[i];
+ if (identifier === null || layout.getName() === defaultOverlayName) {
+ identifier = layout.getId();
+ }
+ }
+
+ return ServerConnector.getImageDownloadUrl({
+ modelId : self.getSubmapId(),
+ backgroundOverlayId : identifier,
+ handlerClass : self.getFormatHandler(),
+ }).then(function(url) {
+ return self.downloadFile(url);
+ }).then(null, GuiConnector.alert);
+ },
+ });
+ downloadDiv.appendChild(button);
+ return downloadDiv;
};
module.exports = GraphicsExportPanel;
diff --git a/frontend-js/src/main/js/gui/export/NetworkExportPanel.js b/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
index 6f770c99ff870a433843a68a6208d5d8c7031689..d93fdebae2f51ca83c232a5cd181b5d0f5b342ad 100644
--- a/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
@@ -2,22 +2,254 @@
/* exported logger */
-var Panel = require('../Panel');
+var AbstractExportPanel = require('./AbstractExportPanel');
+var Promise = require("bluebird");
var logger = require('../../logger');
+var GuiMessageError = require('../GuiMessageError');
-function NetworkExportPanel(params) {
- params.panelName = "elementExport";
- params.scrollable = true;
- Panel.call(this, params);
+function NetworkExportPanel(params) {
+ params.panelName = "networkExport";
+ AbstractExportPanel.call(this, params);
}
-NetworkExportPanel.prototype = Object.create(Panel.prototype);
+NetworkExportPanel.prototype = Object.create(AbstractExportPanel.prototype);
NetworkExportPanel.prototype.constructor = NetworkExportPanel;
NetworkExportPanel.prototype.init = function() {
+ var self = this;
+ var element = self.getElement();
+ var configuration;
+ return ServerConnector.getConfiguration().then(function(result) {
+ configuration = result;
+ var typeDiv = self._createSelectTypeDiv(configuration.getElementTypes());
+ element.appendChild(typeDiv);
+ element.appendChild(self._createSelectColumnDiv(self.getAllColumns()));
+ return ServerConnector.getProjectStatistics(self.getProject().getProjectId());
+ }).then(function(statistics) {
+ return self._createMiriamTypeDiv(statistics.getReactionAnnotations());
+ }).then(function(div) {
+ element.appendChild(div);
+ return self._createSelectIncludedCompartmentDiv();
+ }).then(function(div) {
+ element.appendChild(div);
+ return self._createSelectExcludedCompartmentDiv();
+ }).then(function(div) {
+ element.appendChild(div);
+ element.appendChild(self._createDownloadButton());
+ }).then(function() {
+ $(window).trigger('resize');
+ });
+
+};
+
+NetworkExportPanel.prototype.getAllColumns = function() {
+ return [ {
+ "columnName" : "elements",
+ "method" : "getElements",
+ "name" : "Elements",
+ "formatFunction" : function(elements, reaction, elementIds) {
+ var stringBuilder = [];
+ var type;
+ var elementFormat = function(element) {
+ if (elementIds[element.getId()]) {
+ stringBuilder.push(type + ":" + element.getId());
+ }
+ };
+ type = "REACTANT";
+ reaction.getReactants().forEach(elementFormat);
+ type = "PRODUCT";
+ reaction.getProducts().forEach(elementFormat);
+ type = "MODIFIER";
+ reaction.getModifiers().forEach(elementFormat);
+
+ return stringBuilder.join(",");
+ },
+ }, {
+ "columnName" : "id",
+ "method" : "getId",
+ "name" : "Id",
+ }, {
+ "columnName" : "description",
+ "method" : "getDescription",
+ "name" : "Description",
+ }, {
+ "columnName" : "modelId",
+ "method" : "getModelId",
+ "name" : "Model",
+ }, {
+ "columnName" : "type",
+ "method" : "getType",
+ "name" : "Type",
+ }, {
+ "columnName" : "symbol",
+ "method" : "getSymbol",
+ "name" : "Symbol",
+ }, {
+ "columnName" : "abbreviation",
+ "method" : "getAbbreviation",
+ "name" : "Abbreviation",
+ }, {
+ "columnName" : "formula",
+ "method" : "getFormula",
+ "name" : "Formula",
+ }, {
+ "columnName" : "synonyms",
+ "method" : "getSynonyms",
+ "name" : "Synonyms",
+ }, {
+ "columnName" : "references",
+ "method" : "getReferences",
+ "name" : "References",
+ "formatFunction" : function(references) {
+ var stringBuilder = [];
+ for (var i = 0; i < references.length; i++) {
+ var reference = references[i];
+ stringBuilder.push(reference.getType() + ":" + reference.getResource());
+ }
+ return stringBuilder.join(",");
+ },
+ }, {
+ "columnName" : "reactionId",
+ "method" : "getReactionId",
+ "name" : "Element external id",
+ }, {
+ "columnName" : "mechanicalConfidenceScore",
+ "method" : "getMechanicalConfidenceScore",
+ "name" : "Mechanical Confidence Score",
+ }, {
+ "columnName" : "lowerBound",
+ "method" : "getLowerBound",
+ "name" : "Lower Bound",
+ }, {
+ "columnName" : "upperBound",
+ "method" : "getUpperBound",
+ "name" : "Upper Bound",
+ }, {
+ "columnName" : "geneProteinReaction",
+ "method" : "getGeneProteinReaction",
+ "name" : "Gene Protein Reaction",
+ }, {
+ "columnName" : "subsystem",
+ "method" : "getSubsystem",
+ "name" : "Subsystem",
+ }, ];
+};
+
+function matchReaction(reaction, elementIds) {
+ var count = 0;
+ reaction.getElements().forEach(function(element) {
+ if (elementIds[element.getId()]) {
+ count++;
+ }
+ });
+ return count > 1;
+}
+
+NetworkExportPanel.prototype.createResponseString = function() {
+ var self = this;
+ var types, miriamTypes;
+ var includedCompartmentIds = [];
+ var excludedCompartmentIds = [];
+ var models = [ self.getProject().getModel() ];
+ for (var i = 0; i < self.getProject().getModel().getSubmodels().length; i++) {
+ models.push(self.getProject().getModel().getSubmodels()[i]);
+ }
+
+ var elementIds = [];
+ var reactions = [];
+ return self.getSelectedTypes().then(function(result) {
+ if (result.length === 0) {
+ return Promise.reject(new GuiMessageError("You must select at least one type"));
+ }
+ types = result;
+ return self.getSelectedIncludedCompartments();
+ }).then(function(result) {
+ result.forEach(function(compartment) {
+ includedCompartmentIds.push(compartment.getId());
+ });
+ return self.getSelectedExcludedCompartments();
+ }).then(function(result) {
+ result.forEach(function(compartment) {
+ excludedCompartmentIds.push(compartment.getId());
+ });
+
+ var promises = [];
+ for (var i = 0; i < models.length; i++) {
+ promises.push(models[i].getAliases({
+ type : types,
+ complete : true,
+ includedCompartmentIds : includedCompartmentIds,
+ excludedCompartmentIds : excludedCompartmentIds,
+ }));
+ }
+ return Promise.all(promises);
+ }).then(function(aliasesByModel) {
+ var promises = [];
+ for (var i = 0; i < models.length; i++) {
+ promises.push(models[i].getReactionsForElements(aliasesByModel[i], true));
+ for (var j = 0; j < aliasesByModel[i].length; j++) {
+ elementIds[aliasesByModel[i][j].getId()] = true;
+ }
+ }
+ return Promise.all(promises);
+ }).then(function(reactionsByModel) {
+ for (var i = 0; i < models.length; i++) {
+ for (var j = 0; j < reactionsByModel[i].length; j++) {
+ var reaction = reactionsByModel[i][j];
+ if (matchReaction(reaction, elementIds)) {
+ reactions.push(reaction);
+ }
+ }
+ }
+ return self.getSelectedMiriamTypes();
+ }).then(function(result) {
+ miriamTypes = result;
+ return self.getSelectedColumns();
+ }).then(function(selectedColumns) {
+ if (selectedColumns.length === 0) {
+ return Promise.reject(new GuiMessageError("You must select at least one column"));
+ }
+
+ var rows = [];
+ rows.push(self.createResponseHeader(selectedColumns, miriamTypes));
+ for (var i = 0; i < reactions.length; i++) {
+ rows.push(self.createResponseRow(reactions[i], selectedColumns, miriamTypes, elementIds));
+ }
+ return rows.join("\n");
+ });
+};
+
+NetworkExportPanel.prototype.createResponseRow = function(reaction, columns, miriamTypes, elementIds) {
+ var stringBuilder = [];
+ var i, value;
+ for (i = 0; i < columns.length; i++) {
+ var column = columns[i];
+ value = reaction[column.method]();
+ if (column.formatFunction !== undefined) {
+ value = column.formatFunction(value, reaction, elementIds);
+ }
+ if (value instanceof String || typeof value === "string") {
+ value = value.replace(/[\n\r]/g, ' ');
+ }
+ stringBuilder.push(value);
+ }
+ for (i = 0; i < miriamTypes.length; i++) {
+ value = "";
+ var miriamType = miriamTypes[i];
+ var references = reaction.getReferences();
+ for (var j = 0; j < references.length; j++) {
+ var reference = references[j];
+ if (reference.getType() === miriamType.getName()) {
+ value += reference.getResource() + ",";
+ }
+ }
+ stringBuilder.push(value);
+ }
+ var result = stringBuilder.join("\t");
+ return result;
};
module.exports = NetworkExportPanel;
diff --git a/frontend-js/src/main/js/map/data/MapModel.js b/frontend-js/src/main/js/map/data/MapModel.js
index fe059bcad1102b1473ec065ed0961fdd9d406226..2d921edb045e3224891e0b539096dec2c8102733 100644
--- a/frontend-js/src/main/js/map/data/MapModel.js
+++ b/frontend-js/src/main/js/map/data/MapModel.js
@@ -103,12 +103,15 @@ MapModel.prototype.getLayouts = function() {
MapModel.prototype.getAliases = function(params) {
var self = this;
return ServerConnector.getAliases({
- columns : "id,bounds,modelId",
+ columns : "id,modelId",
type : params.type,
modelId : self.getId(),
- }).then(function(lightAliases){
+ includedCompartmentIds : params.includedCompartmentIds,
+ excludedCompartmentIds : params.excludedCompartmentIds,
+
+ }).then(function(lightAliases) {
var identifiedElements = [];
- for (var i=0;i<lightAliases.length;i++) {
+ for (var i = 0; i < lightAliases.length; i++) {
self.addAlias(lightAliases[i]);
identifiedElements.push(new IdentifiedElement(lightAliases[i]));
}
@@ -180,45 +183,41 @@ MapModel.prototype.getReactionById = function(id, complete) {
}
};
+MapModel.prototype._getMissingReactionsElementIds = function(reactions) {
+ var self = this;
+ var result = [];
+ var ids = [];
+ for (var i = 0; i < reactions.length; i++) {
+ var reaction = reactions[i];
+ var elements = reaction.getElements();
+ for (var j = 0; j < elements.length; j++) {
+ var element = elements[j];
+ if (!(element instanceof Alias)) {
+ if (self._aliases[element] === undefined || !self._aliases[element].isComplete()) {
+ if (!ids[element]) {
+ ids[element] = true;
+ result.push(element);
+ }
+ }
+ }
+ }
+ }
+ return result;
+};
+
MapModel.prototype.getCompleteReactionById = function(id) {
var self = this;
if (self._reactions[id] instanceof Reaction && self._reactions[id].isComplete()) {
return Promise.resolve(self._reactions[id]);
} else {
var result;
- return self.getReactionById(id).then(
- function(result) {
- var ids = [];
- var i;
- for (i = 0; i < result.getReactants().length; i++) {
- if (!(result.getReactants()[i] instanceof Alias)) {
- if (self._aliases[result.getReactants()[i]] === undefined
- || !self._aliases[result.getReactants()[i]].isComplete()) {
- ids.push(result.getReactants()[i]);
- }
- }
- }
- for (i = 0; i < result.getProducts().length; i++) {
- if (!(result.getProducts()[i] instanceof Alias)) {
- if (self._aliases[result.getProducts()[i]] === undefined
- || !self._aliases[result.getProducts()[i]].isComplete()) {
- ids.push(result.getProducts()[i]);
- }
- }
- }
- for (i = 0; i < result.getModifiers().length; i++) {
- if (!(result.getModifiers()[i] instanceof Alias)) {
- if (self._aliases[result.getModifiers()[i]] === undefined
- || !self._aliases[result.getModifiers()[i]].isComplete()) {
- ids.push(result.getModifiers()[i]);
- }
- }
- }
- return self.getMissingElements({
- aliasIds : ids,
- complete : true
- });
- }).then(function() {
+ return self.getReactionById(id).then(function(result) {
+ var ids = self._getMissingReactionsElementIds([ result ]);
+ return self.getMissingElements({
+ aliasIds : ids,
+ complete : true
+ });
+ }).then(function() {
var i;
result = self._reactions[id];
for (i = 0; i < result.getReactants().length; i++) {
@@ -308,16 +307,20 @@ MapModel.prototype.getMissingElements = function(elements) {
}
}
+ var result = [];
return Promise.all([ reactionPromise, aliasPromise ]).then(function(values) {
- var result = [], i;
+ var i;
var reactions = values[0];
var aliases = values[1];
+ var ids = [];
+
if (reactions !== null) {
for (i = 0; i < reactions.length; i++) {
var reaction = reactions[i];
self.addReaction(reaction);
result.push(reaction);
}
+ ids = self._getMissingReactionsElementIds(reactions);
}
if (aliases !== null) {
for (i = 0; i < aliases.length; i++) {
@@ -326,6 +329,15 @@ MapModel.prototype.getMissingElements = function(elements) {
result.push(alias);
}
}
+ if (ids.length > 0) {
+ return self.getMissingElements({
+ aliasIds : ids,
+ complete : true
+ });
+ } else {
+ return Promise.resolve([]);
+ }
+ }).then(function() {
return result;
});
};
@@ -731,9 +743,13 @@ MapModel.prototype.getReactionsForElements = function(elements, complete) {
return Promise.all(promises);
}
}
+
+ var result = [];
return ServerConnector.getReactions({
participantId : ids,
}).then(function(reactions) {
+ result = reactions;
+
var promises = [];
for (var i = 0; i < reactions.length; i++) {
var reaction = reactions[i];
@@ -743,7 +759,16 @@ MapModel.prototype.getReactionsForElements = function(elements, complete) {
} else {
self._reactions[id].update(reaction);
}
- promises.push(self.getReactionById(id, complete));
+ }
+ var ids = self._getMissingReactionsElementIds(reactions);
+ return self.getMissingElements({
+ aliasIds : ids,
+ complete : true
+ });
+ }).then(function() {
+ var promises = [];
+ for (var i=0;i<result.length;i++) {
+ promises.push(self.getCompleteReactionById(result[i].getId()));
}
return Promise.all(promises);
});
diff --git a/frontend-js/src/main/js/map/data/ProjectStatistics.js b/frontend-js/src/main/js/map/data/ProjectStatistics.js
index e30fe8b0cbb34f7021b6e3fabec5dd60cc5bda45..0e5cd484641a1a04e88b51e38391628854617a04 100644
--- a/frontend-js/src/main/js/map/data/ProjectStatistics.js
+++ b/frontend-js/src/main/js/map/data/ProjectStatistics.js
@@ -49,6 +49,9 @@ ProjectStatistics.prototype.setElementAnnotations = function(elementAnnotations,
ProjectStatistics.prototype.getElementAnnotations = function() {
return this._elementAnnotations;
};
+ProjectStatistics.prototype.getReactionAnnotations = function() {
+ return this._reactionAnnotations;
+};
ProjectStatistics.prototype.setPublicationCount = function(count) {
this._publicationsCount = count;
diff --git a/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js b/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js
index 05146b3859b76a192316df4e0eade26c6c238564..209fd20b97e369a40fdc584c867db855aa3be2b4 100644
--- a/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js
+++ b/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js
@@ -3,6 +3,7 @@
/* exported logger */
var ElementExportPanel = require('../../../../main/js/gui/export/ElementExportPanel');
+var GuiMessageError = require('../../../../main/js/gui/GuiMessageError');
var MiriamType = require('../../../../main/js/map/data/MiriamType');
var logger = require('../../logger');
@@ -217,6 +218,9 @@ describe('ElementExportPanel', function() {
$("input[name='ALL']", $(testDiv)).each(function(index, element) {
element.checked = true;
});
+ var dlb = exportObject.getMiriamTypesDualListbox();
+ var listItem = dlb.available[0];
+ dlb.addSelected(listItem);
return exportObject.createResponseString();
}).then(function(result) {
// protein id
@@ -224,6 +228,62 @@ describe('ElementExportPanel', function() {
assert.ok(result.indexOf("329156") >= 0);
});
});
+ it('get invalid', function() {
+ var exportObject;
+ var project;
+ return ServerConnector.getProject().then(function(result) {
+ project = result;
+ return ServerConnector.getConfiguration();
+ }).then(function(configuration) {
+ exportObject = new ElementExportPanel({
+ element : testDiv,
+ project : project,
+ configuration : configuration,
+ });
+ return exportObject.init();
+ }).then(function() {
+ return exportObject.createResponseString();
+ }).then(null, function(error) {
+ assert.ok(error instanceof GuiMessageError);
+ });
+ });
+ });
+
+ it('download file', function() {
+ var exportObject;
+ var project;
+ return ServerConnector.getProject().then(function(result) {
+ project = result;
+ return ServerConnector.getConfiguration();
+ }).then(function(configuration) {
+ exportObject = new ElementExportPanel({
+ element : testDiv,
+ project : project,
+ configuration : configuration,
+ });
+ return exportObject.init();
+ }).then(function() {
+ $("input[name='ALL']", $(testDiv)).each(function(index, element) {
+ element.checked = true;
+ });
+ var element = $("[name='downloadButton']", $(testDiv))[0];
+ return element.onclick();
+ });
+ });
+
+ describe('createResponseRow', function() {
+ it('description with new line', function() {
+ var exportObject = new ElementExportPanel({
+ element : testDiv,
+ project : helper.createProject(),
+ configuration : helper.getConfiguration(),
+ });
+ var alias = helper.createAlias();
+ var desc = "test\ntest2\n";
+ alias.setDescription(desc);
+ var rowString = exportObject.createResponseRow(alias, exportObject.getAllColumns(), []);
+ assert.ok(rowString.indexOf("test\ntest2\n") === -1);
+ });
});
});
diff --git a/frontend-js/src/test/js/gui/export/GraphicsExportPanel-test.js b/frontend-js/src/test/js/gui/export/GraphicsExportPanel-test.js
new file mode 100644
index 0000000000000000000000000000000000000000..a2b91b43d1f71c2c2ccae68098c6ed749fb6ee06
--- /dev/null
+++ b/frontend-js/src/test/js/gui/export/GraphicsExportPanel-test.js
@@ -0,0 +1,68 @@
+"use strict";
+
+/* exported logger */
+
+var GraphicsExportPanel = require('../../../../main/js/gui/export/GraphicsExportPanel');
+var logger = require('../../logger');
+var assert = require('assert');
+
+describe('GraphicsExportPanel', function() {
+
+ it('getModelId', function() {
+ var exportObject;
+ var project;
+ return ServerConnector.getProject().then(function(result) {
+ project = result;
+ return ServerConnector.getConfiguration();
+ }).then(function(configuration) {
+ exportObject = new GraphicsExportPanel({
+ element : testDiv,
+ project : project,
+ configuration : configuration,
+ });
+ return exportObject.init();
+ }).then(function() {
+ var id = exportObject.getSubmapId();
+ assert.ok(id);
+ });
+ });
+
+ it('getFormatHandler', function() {
+ var exportObject;
+ var project;
+ return ServerConnector.getProject().then(function(result) {
+ project = result;
+ return ServerConnector.getConfiguration();
+ }).then(function(configuration) {
+ exportObject = new GraphicsExportPanel({
+ element : testDiv,
+ project : project,
+ configuration : configuration,
+ });
+ return exportObject.init();
+ }).then(function() {
+ var format = exportObject.getFormatHandler();
+ assert.ok(format);
+ });
+ });
+
+ it('download file', function() {
+ var exportObject;
+ var project;
+ return ServerConnector.getProject().then(function(result) {
+ project = result;
+ return ServerConnector.getConfiguration();
+ }).then(function(configuration) {
+ exportObject = new GraphicsExportPanel({
+ element : testDiv,
+ project : project,
+ configuration : configuration,
+ });
+ return exportObject.init();
+ }).then(function() {
+ var element = $("[name='downloadButton']", $(testDiv))[0];
+ return element.onclick();
+ });
+ });
+
+});
diff --git a/frontend-js/src/test/js/gui/export/NetworkExportPanel-test.js b/frontend-js/src/test/js/gui/export/NetworkExportPanel-test.js
new file mode 100644
index 0000000000000000000000000000000000000000..1badab9af1c93d8f392d50ae969c9e3d34b91b29
--- /dev/null
+++ b/frontend-js/src/test/js/gui/export/NetworkExportPanel-test.js
@@ -0,0 +1,32 @@
+"use strict";
+
+/* exported logger */
+
+var NetworkExportPanel = require('../../../../main/js/gui/export/NetworkExportPanel');
+var logger = require('../../logger');
+
+describe('NetworkExportPanel', function() {
+
+ it('download file', function() {
+ var exportObject;
+ var project;
+ return ServerConnector.getProject().then(function(result) {
+ project = result;
+ return ServerConnector.getConfiguration();
+ }).then(function(configuration) {
+ exportObject = new NetworkExportPanel({
+ element : testDiv,
+ project : project,
+ configuration : configuration,
+ });
+ return exportObject.init();
+ }).then(function() {
+ $("input[name='ALL']", $(testDiv)).each(function(index, element) {
+ element.checked = true;
+ });
+ var element = $("[name='downloadButton']", $(testDiv))[0];
+ return element.onclick();
+ });
+ });
+
+});
diff --git a/frontend-js/src/test/js/mocha-config.js b/frontend-js/src/test/js/mocha-config.js
index 4b4438049ae2ebac08f04cac10d1bc2716cb853a..fa68c112a618f9833c4ab9600a398ff92e48effd 100644
--- a/frontend-js/src/test/js/mocha-config.js
+++ b/frontend-js/src/test/js/mocha-config.js
@@ -24,6 +24,8 @@ global.window.$ = $;
// additions to jsdom implementations:
global.Option = window.Option;
+global.Blob = window.Blob;
+global.MouseEvent = window.MouseEvent;
var originalCreateElement = document.createElement;
document.createElement = function(arg) {
@@ -42,6 +44,9 @@ window.open = function() {
};
return result;
};
+window.URL.createObjectURL = function(){
+
+};
// pileup is using heavily some browser defined javascript
var pileup = require('pileup');
diff --git a/frontend-js/testFiles/apiCalls/doLogout b/frontend-js/testFiles/apiCalls/doLogout
new file mode 100644
index 0000000000000000000000000000000000000000..1a36cf5fc27a0920a9f3668225f9d7aec239566e
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/doLogout
@@ -0,0 +1 @@
+{"status":"ok"}
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/elements/columns=id,modelId&type=Drug,Complex,Phenotype,Gene,RNA,Unknown,Degraded,Antisense RNA,Ion,Simple molecule,Protein,Compartment&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/elements/columns=id,modelId&type=Drug,Complex,Phenotype,Gene,RNA,Unknown,Degraded,Antisense RNA,Ion,Simple molecule,Protein,Compartment&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..b6d21d318c262584cb47a6fa481b462fdfdec7ac
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/elements/columns=id,modelId&type=Drug,Complex,Phenotype,Gene,RNA,Unknown,Degraded,Antisense RNA,Ion,Simple molecule,Protein,Compartment&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"modelId":15781,"id":329180},{"modelId":15781,"id":329166},{"modelId":15781,"id":329183},{"modelId":15781,"id":329158},{"modelId":15781,"id":329175},{"modelId":15781,"id":329160},{"modelId":15781,"id":329176},{"modelId":15781,"id":329161},{"modelId":15781,"id":329164},{"modelId":15781,"id":329171},{"modelId":15781,"id":329157},{"modelId":15781,"id":329181},{"modelId":15781,"id":329165},{"modelId":15781,"id":329184},{"modelId":15781,"id":329156},{"modelId":15781,"id":329185},{"modelId":15781,"id":329169},{"modelId":15781,"id":329162},{"modelId":15781,"id":329167},{"modelId":15781,"id":329178},{"modelId":15781,"id":329170},{"modelId":15781,"id":329163},{"modelId":15781,"id":329173},{"modelId":15781,"id":329168},{"modelId":15781,"id":329174},{"modelId":15781,"id":329182},{"modelId":15781,"id":329159},{"modelId":15781,"id":329172},{"modelId":15781,"id":329177},{"modelId":15781,"id":329179}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/id=329167,329168,329169,329172,329173,329179&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/id=329167,329168,329169,329172,329173,329179&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..ec53d5a3b9547671ae3a2d1bddac3b521d2664db
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/id=329167,329168,329169,329172,329173,329179&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"elementId":"sa5","symbol":null,"formerSymbols":[],"other":{"structuralState":"usual","modifications":[]},"notes":"","references":[],"modelId":15781,"synonyms":[],"fullName":null,"complexId":null,"type":"RNA","abbreviation":null,"compartmentId":null,"name":"s5","bounds":{"x":0.0,"width":90.0,"y":118.5,"height":25.0},"formula":null,"id":329168,"linkedSubmodel":null,"hierarchyVisibilityLevel":"0"},{"elementId":"sa1","symbol":null,"formerSymbols":[],"other":{"structuralState":null,"modifications":[]},"notes":"description of S1\r\nthird line","references":[],"modelId":15781,"synonyms":[],"fullName":null,"complexId":null,"type":"Protein","abbreviation":null,"compartmentId":null,"name":"s1","bounds":{"x":12.0,"width":80.0,"y":6.0,"height":40.0},"formula":null,"id":329173,"linkedSubmodel":null,"hierarchyVisibilityLevel":"0"},{"elementId":"sa6","symbol":null,"formerSymbols":[],"other":{"structuralState":"usual","modifications":[]},"notes":"","references":[],"modelId":15781,"synonyms":[],"fullName":null,"complexId":null,"type":"Antisense RNA","abbreviation":null,"compartmentId":null,"name":"s6","bounds":{"x":101.0,"width":90.0,"y":129.5,"height":25.0},"formula":null,"id":329167,"linkedSubmodel":null,"hierarchyVisibilityLevel":"0"},{"elementId":"sa11","symbol":null,"formerSymbols":[],"other":{"structuralState":null,"modifications":[]},"notes":"","references":[],"modelId":15781,"synonyms":[],"fullName":null,"complexId":null,"type":"Unknown","abbreviation":null,"compartmentId":null,"name":"s11","bounds":{"x":105.0,"width":70.0,"y":203.5,"height":25.0},"formula":null,"id":329169,"linkedSubmodel":null,"hierarchyVisibilityLevel":"0"},{"elementId":"sa7","symbol":null,"formerSymbols":[],"other":{"structuralState":null,"modifications":[]},"notes":"","references":[],"modelId":15781,"synonyms":[],"fullName":null,"complexId":null,"type":"Phenotype","abbreviation":null,"compartmentId":null,"name":"s7","bounds":{"x":213.0,"width":80.0,"y":128.0,"height":30.0},"formula":null,"id":329172,"linkedSubmodel":null,"hierarchyVisibilityLevel":"0"},{"elementId":"sa2","symbol":null,"formerSymbols":[],"other":{"structuralState":null,"modifications":[]},"notes":"","references":[],"modelId":15781,"synonyms":[],"fullName":null,"complexId":null,"type":"Protein","abbreviation":null,"compartmentId":null,"name":"s2","bounds":{"x":165.0,"width":80.0,"y":43.0,"height":50.0},"formula":null,"id":329179,"linkedSubmodel":null,"hierarchyVisibilityLevel":"0"}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/reactions/participantId=329156,329157,329158,329159,329160,329161,329162,329163,329164,329165,329166,329167,329168,329169,329170,329171,329172,329173,329174,329175,329176,329177,329178,329179,329180,329181,329182,329183,329184,329185&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/reactions/participantId=329156,329157,329158,329159,329160,329161,329162,329163,329164,329165,329166,329167,329168,329169,329170,329171,329172,329173,329174,329175,329176,329177,329178,329179,329180,329181,329182,329183,329184,329185&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..90a3c4b7c4fa022979780b493c9d025900e264eb
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/reactions/participantId=329156,329157,329158,329159,329160,329161,329162,329163,329164,329165,329166,329167,329168,329169,329170,329171,329172,329173,329174,329175,329176,329177,329178,329179,329180,329181,329182,329183,329184,329185&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+[{"notes":"","references":[],"modelId":15781,"reactants":"329161","reactionId":"re20","id":153497,"type":"State transition","lines":[{"start":{"x":465.68408727882723,"y":173.00924235519662},"end":{"x":427.95591606364394,"y":159.05933030924652},"type":"START"},{"start":{"x":420.45240587887884,"y":156.28492318210644},"end":{"x":382.72423466369554,"y":142.33501113615634},"type":"END"}],"modifiers":"","centerPoint":{"x":424.2041609712614,"y":157.67212674567648},"products":"329165","hierarchyVisibilityLevel":null},{"notes":"","references":[],"modelId":15781,"reactants":"329172","reactionId":"re12","id":153522,"type":"State transition","lines":[{"start":{"x":282.92735502516456,"y":131.66828304872405},"end":{"x":349.0890546595849,"y":106.61676571141928},"type":"START"},{"start":{"x":356.5706947317768,"y":103.78391170350197},"end":{"x":422.7323943661972,"y":78.73239436619717},"type":"END"}],"modifiers":"","centerPoint":{"x":352.82987469568087,"y":105.20033870746062},"products":"329182","hierarchyVisibilityLevel":null},{"notes":"","references":[],"modelId":15781,"reactants":"329157","reactionId":"re14","id":153502,"type":"State transition","lines":[{"start":{"x":369.0,"y":60.84615384615386},"end":{"x":390.00425356060526,"y":61.8155809335664},"type":"START"},{"start":{"x":397.99574643939474,"y":62.18441906643361},"end":{"x":419.0,"y":63.15384615384615},"type":"END"}],"modifiers":"","centerPoint":{"x":394.0,"y":62.00000000000001},"products":"329182","hierarchyVisibilityLevel":null},{"notes":"","references":[],"modelId":15781,"reactants":"329172","reactionId":"re11","id":153516,"type":"State transition","lines":[{"start":{"x":266.57142857142856,"y":128.0},"end":{"x":286.0544419422188,"y":106.46614311649508},"type":"START"},{"start":{"x":291.4217485339718,"y":100.53385688350491},"end":{"x":310.904761904762,"y":79.0},"type":"END"}],"modifiers":"","centerPoint":{"x":288.7380952380953,"y":103.5},"products":"329157","hierarchyVisibilityLevel":null},{"notes":"","references":[{"resource":"REACT_1493.4","link":null,"id":860354,"type":"REACTOME"}],"modelId":15781,"reactants":"329181","reactionId":"re29","id":153506,"type":"State transition","lines":[{"start":{"x":1065.943922652377,"y":210.4515058436089},"end":{"x":1076.3953582603178,"y":134.9622060910266},"type":"START"},{"start":{"x":1077.4924870444363,"y":127.03779390897431},"end":{"x":1087.943922652377,"y":51.548494156391996},"type":"END"},{"start":{"x":1225.7682370820664,"y":95.9386128624158},"end":{"x":1081.8966802661598,"y":131.68570549007447},"type":"MIDDLE"}],"modifiers":"329170","centerPoint":{"x":1076.943922652377,"y":131.00000000000045},"products":"329164","hierarchyVisibilityLevel":null},{"notes":"","references":[],"modelId":15781,"reactants":"329169","reactionId":"re8","id":153518,"type":"State transition","lines":[{"start":{"x":141.01308884552796,"y":203.5052375718217},"end":{"x":142.676524190943,"y":182.98953497836953},"type":"START"},{"start":{"x":143.32305114107143,"y":175.01570259345215},"end":{"x":144.98648648648648,"y":154.5},"type":"END"}],"modifiers":"","centerPoint":{"x":142.99978766600722,"y":179.00261878591084},"products":"329167","hierarchyVisibilityLevel":null},{"notes":"","references":[],"modelId":15781,"reactants":"329177","reactionId":"re6","id":153507,"type":"State transition","lines":[{"start":{"x":73.33333333333336,"y":205.99999999999997},"end":{"x":86.57623440706466,"y":207.9864351610597},"type":"START"},{"start":{"x":94.48772523001104,"y":209.17315878450162},"end":{"x":107.73062630374235,"y":211.15959394556134},"type":"END"}],"modifiers":"","centerPoint":{"x":90.53197981853785,"y":208.57979697278066},"products":"329169","hierarchyVisibilityLevel":null},{"notes":"","references":[{"resource":"REACT_631.3","link":null,"id":860356,"type":"REACTOME"}],"modelId":15781,"reactants":"329164,329163,329184","reactionId":"re28","id":153517,"type":"State 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\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
index 5df367d06fe0e9da343d11e186252eaea20c8f03..9b09e2708b9244f8798fef693184859756ec2ccc 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
@@ -389,7 +389,7 @@ public interface Model {
* element database identifier ({@link Element#id})
* @return {@link Element} for a given id
*/
- Element getElementByDbId(Integer dbId);
+ <T extends Element> T getElementByDbId(Integer dbId);
/**
* Returns {@link Reaction} for given database identifier.
diff --git a/persist/src/db/11.0.1/fix_db_20170908.sql b/persist/src/db/11.0.1/fix_db_20170908.sql
new file mode 100644
index 0000000000000000000000000000000000000000..a33b6ad89d4881c84fb355b8c56d309760e66b70
--- /dev/null
+++ b/persist/src/db/11.0.1/fix_db_20170908.sql
@@ -0,0 +1 @@
+-- empty file to force directory to be commited to git repo
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
index 668985f097cfc601ef841129dfc8aa372df3eaff..843edf209d9f71f8ea1c36e93041eab82f99ed15 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
@@ -91,12 +91,14 @@ public class ConfigurationRestImpl {
userService.getToken(token);
List<Map<String, Object>> result = new ArrayList<>();
- List<Pair<String, Class<? extends AbstractImageGenerator>>> imageGenerators = new ImageGenerators().getAvailableImageGenerators();
+ ImageGenerators imageGenerators = new ImageGenerators();
+ List<Pair<String, Class<? extends AbstractImageGenerator>>> imageGeneratorList = imageGenerators.getAvailableImageGenerators();
- for (Pair<String, Class<? extends AbstractImageGenerator>> element : imageGenerators) {
+ for (Pair<String, Class<? extends AbstractImageGenerator>> element : imageGeneratorList) {
Map<String, Object> row = new HashMap<>();
row.put("name", element.getLeft());
row.put("handler", element.getRight().getCanonicalName());
+ row.put("extension", imageGenerators.getExtension(element.getRight()));
result.add(row);
}
return result;
@@ -114,6 +116,7 @@ public class ConfigurationRestImpl {
Map<String, Object> row = new HashMap<>();
row.put("name", converter.getCommonName());
row.put("handler", converter.getClass().getCanonicalName());
+ row.put("extension", converter.getFileExtension());
result.add(row);
}
return result;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
index 21b5336199ad0f71bc68dd588c58abfa50d53081..d7bdf466830f02f9d5ee3b8f61d96fe0981415da 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
@@ -29,9 +29,11 @@ public class ElementsController extends BaseController {
@RequestParam(value = "id", defaultValue = "") String id, //
@RequestParam(value = "type", defaultValue = "") String type, //
@RequestParam(value = "columns", defaultValue = "") String columns, //
+ @RequestParam(value = "includedCompartmentIds", defaultValue = "") String includedCompartmentIds, //
+ @RequestParam(value = "excludedCompartmentIds", defaultValue = "") String excludedCompartmentIds, //
@CookieValue(value = Configuration.AUTH_TOKEN) String token//
) throws SecurityException {
- return projectController.getElements(projectId, id, columns, modelId, token, type);
+ return projectController.getElements(projectId, id, columns, modelId, token, type, includedCompartmentIds, excludedCompartmentIds);
}
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
index c30f92abc8903929a1c1ddabb55d9fca647f7acf..9348dc68691f9a30029e51ad2e5a5934b8459939 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
@@ -12,6 +12,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Element;
@@ -35,8 +36,8 @@ public class ElementsRestImpl extends BaseRestImpl {
@Autowired
private OverviewImageViewFactory factory;
- public List<Map<String, Object>> getElements(String projectId, String id, String columns, String modelId, String token, String type)
- throws UserAccessException, SecurityException {
+ public List<Map<String, Object>> getElements(String projectId, String id, String columns, String modelId, String token, String type,
+ String includedCompartmentIds, String excludedCompartmentIds) throws UserAccessException, SecurityException {
Set<Integer> ids = new HashSet<>();
if (!id.equals("")) {
for (String str : id.split(",")) {
@@ -49,18 +50,21 @@ public class ElementsRestImpl extends BaseRestImpl {
types.add(str.toLowerCase());
}
}
+ List<Model> models = getModels(projectId, modelId, token);
+ Set<Compartment> includedCompartments = getCompartments(includedCompartmentIds, models);
+ Set<Compartment> excludedCompartments = getCompartments(excludedCompartmentIds, models);
Set<String> columnsSet = createElementColumnSet(columns);
List<Map<String, Object>> result = new ArrayList<>();
- List<Model> models = getModels(projectId, modelId, token);
-
for (Model model2 : models) {
for (Element element : model2.getElements()) {
if (ids.size() == 0 || ids.contains(element.getId())) {
if (types.size() == 0 || types.contains(element.getStringType().toLowerCase())) {
- result.add(preparedElement(element, columnsSet));
+ if (matchIncludedExcludedCompartments(element, includedCompartments, excludedCompartments)) {
+ result.add(preparedElement(element, columnsSet));
+ }
}
}
}
@@ -69,6 +73,53 @@ public class ElementsRestImpl extends BaseRestImpl {
return result;
}
+ private boolean matchIncludedExcludedCompartments(Element element, Set<Compartment> includedCompartments, Set<Compartment> excludedCompartments) {
+ boolean matchIncluded = true;
+ boolean matchExcluded = false;
+
+ if (includedCompartments.size() > 0) {
+ matchIncluded = matchCompartments(element, includedCompartments);
+ }
+ if (excludedCompartments.size() > 0) {
+ matchExcluded = matchCompartments(element, excludedCompartments);
+ }
+
+ return matchIncluded && !matchExcluded;
+ }
+
+ private boolean matchCompartments(Element element, Set<Compartment> compartmentList) {
+ boolean isInside = false;
+ if (element != null) {
+ for (Compartment compartment : compartmentList) {
+ if (compartment.contains(element) && element.getModel().getId().equals(compartment.getModel().getId())) {
+ isInside = true;
+ }
+ }
+ }
+ return isInside;
+ }
+
+ private Set<Compartment> getCompartments(String includedCompartmentIds, List<Model> models) {
+ Set<Compartment> includedCompartments = new HashSet<>();
+ int count = 0;
+ if (!includedCompartmentIds.isEmpty()) {
+ for (String compartmentId : includedCompartmentIds.split(",")) {
+ Integer integerId = Integer.valueOf(compartmentId);
+ for (Model model : models) {
+ Compartment compartment = model.getElementByDbId(integerId);
+ if (compartment != null) {
+ includedCompartments.add(compartment);
+ }
+ }
+ count++;
+ }
+ if (count > 0 && includedCompartments.size() == 0) {
+ includedCompartments.add(new Compartment("empty_comp_to_reject_all_elements"));
+ }
+ }
+ return includedCompartments;
+ }
+
private Map<String, Object> preparedElement(Element element, Set<String> columnsSet) {
Map<String, Object> result = new HashMap<>();
for (String string : columnsSet) {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
index 0d3e0349126edced91c82d2ad674c564cbd97505..44257fd6b443e375a2b1f6321cb44f8212392170 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
@@ -29,9 +29,7 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.ISearchService;
-import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@Transactional(value = "txManager")
@@ -42,12 +40,6 @@ public class PublicationsRestImpl extends BaseRestImpl {
*/
private Logger logger = Logger.getLogger(PublicationsRestImpl.class);
- @Autowired
- private IUserService userService;
-
- @Autowired
- private IModelService modelService;
-
@Autowired
private ISearchService searchService;
@@ -89,40 +81,6 @@ public class PublicationsRestImpl extends BaseRestImpl {
return publications;
}
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
/**
* @return the searchService
* @see #searchService
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
index a7b6b76983ee2adc818f58b8529eacd1e123fac5..d85484790e2f2380db8344c9dd8418d38ae340f2 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
@@ -78,11 +78,27 @@ public class UserController extends BaseController {
}
@RequestMapping(value = "/doLogout", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, String> logout(@CookieValue(value = Configuration.AUTH_TOKEN) String token) throws SecurityException {
+ public Map<String, String> logout(@CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ HttpServletResponse response //
+ ) throws SecurityException, IOException {
userService.logout(token);
- Map<String, String> response = new HashMap<>();
- response.put("status", "OK");
- return response;
+ Map<String, String> result = new HashMap<>();
+ result.put("status", "OK");
+
+ final Boolean useSecureCookie = false;
+ final String cookiePath = "/";
+
+ Cookie cookie = new Cookie("MINERVA_AUTH_TOKEN", token);
+
+ cookie.setSecure(useSecureCookie);
+ cookie.setMaxAge(0);
+ cookie.setPath(cookiePath);
+
+ response.addCookie(cookie);
+ response.getWriter().write("{\"status\":\"OK\"}");
+ response.getWriter().flush();
+ response.getWriter().close();
+ return result;
}
/**
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java
index 60e3837712d839ffd77e188018a37d6f166f3601..d6b904ceb9dfadc1c4f8b52b554efe6cb6b5d19d 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java
@@ -8,14 +8,12 @@ import lcsb.mapviewer.api.projects.chemicals.AllChemicalTests;
import lcsb.mapviewer.api.projects.drugs.AllDrugTests;
import lcsb.mapviewer.api.projects.mirnas.AllMiRnaTests;
import lcsb.mapviewer.api.projects.models.AllModelsTests;
-import lcsb.mapviewer.api.projects.overlays.AllOverlaysTests;
@RunWith(Suite.class)
@SuiteClasses({ AllChemicalTests.class, //
AllDrugTests.class, //
AllMiRnaTests.class, //
AllModelsTests.class, //
- AllOverlaysTests.class, //
ModelMetaDataTest.class, //
ProjectRestImplTest.class })
public class AllProjectTests {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
index 12a789d393bd4674120a9568735b6ac54bae29e6..0699aadfa0bbbe9acec86e910789e83bb1382c4d 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
@@ -24,6 +24,7 @@ import lcsb.mapviewer.api.RestTestFunctions;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.graphics.PdfImageGenerator;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.cache.FileEntry;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.interfaces.IModelService;
@@ -50,7 +51,7 @@ public class ProjectRestImplTest extends RestTestFunctions {
}
@Test
- public void testGetModelAsImage() throws Exception {
+ public void testGetModelAsImageForInvalidConverter() throws Exception {
try {
ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
projectRest.getModelAsImage(token.getId(), "sample", "0", "", "", "", "", "");
@@ -62,6 +63,18 @@ public class ProjectRestImplTest extends RestTestFunctions {
}
}
+ @Test
+ public void testGetModelAsImage() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ FileEntry result = projectRest.getModelAsImage(token.getId(), "sample", "0", PdfImageGenerator.class.getCanonicalName(), "", "", "", "");
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test(expected = ObjectNotFoundException.class)
public void testGetInvalidMetaData() throws Exception {
_projectRestImpl.getMetaData("unknown_model_id", token.getId());
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
index 7da42635f993dc74e3cbeed463dec330876ce993..19cc3a66c98d2cc2f09e10d94d8709cf6831b841 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
@@ -55,7 +55,7 @@ public class ElementRestImplTest extends RestTestFunctions {
public void testGetElementsProcessAllColumns() throws Exception {
try {
ElementsRestImpl projectRest = createMockElementRest("testFiles/model/sample.xml");
- List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token.getId(), "");
+ List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token.getId(), "", "", "");
for (Map<String, Object> element : result) {
for (String paramName : element.keySet()) {
Object val = element.get(paramName);
@@ -80,7 +80,7 @@ public class ElementRestImplTest extends RestTestFunctions {
try {
String proteinType = new GenericProtein("1").getStringType();
ElementsRestImpl elementRest = createMockElementRest("testFiles/model/sample.xml");
- List<Map<String, Object>> result = elementRest.getElements("sample", "", "", "*", token.getId(), proteinType);
+ List<Map<String, Object>> result = elementRest.getElements("sample", "", "", "*", token.getId(), proteinType, "", "");
assertEquals(12, result.size());
} catch (Exception e) {
@@ -93,7 +93,7 @@ public class ElementRestImplTest extends RestTestFunctions {
public void testGetElementsVisibility() throws Exception {
try {
ElementsRestImpl elementRest = createMockElementRest("testFiles/model/sample.xml");
- List<Map<String, Object>> result = elementRest.getElements("sample", "", "", "*", token.getId(), "");
+ List<Map<String, Object>> result = elementRest.getElements("sample", "", "", "*", token.getId(), "", "", "");
for (Map<String, Object> map : result) {
assertTrue(map.get("hierarchyVisibilityLevel") instanceof String);
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/AllOverlaysTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/AllOverlaysTests.java
deleted file mode 100644
index daf60c8088672175d23a5947536c5a6f62a42f8d..0000000000000000000000000000000000000000
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/AllOverlaysTests.java
+++ /dev/null
@@ -1,11 +0,0 @@
-package lcsb.mapviewer.api.projects.overlays;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ })
-public class AllOverlaysTests {
-
-}