diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
index 15bacd4c643e0d7321abcf12b01f2d0013097498..32a11b6dfda8deff66377492939c558927d2219d 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
@@ -23,7 +23,6 @@ import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.cache.XmlSerializer;
import lcsb.mapviewer.annotation.data.Article;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
@@ -100,8 +99,8 @@ public class PubmedParser extends CachableInterface implements IExternalService
}
/**
- * Constructor. Initializes structures used for transforming
- * {@link Article} from/to xml.
+ * Constructor. Initializes structures used for transforming {@link Article}
+ * from/to xml.
*/
@Autowired
public PubmedParser(MiriamConnector miriamConnector) {
@@ -209,7 +208,7 @@ public class PubmedParser extends CachableInterface implements IExternalService
}
public Article getPubmedArticleById(String id) throws PubmedSearchException {
- if (id==null) {
+ if (id == null) {
return null;
}
return getPubmedArticleById(Integer.valueOf(id.trim()));
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 c4c0151c50e86e47c3ad378437224eb04c4d0c0a..0b4f0d4dd5f38e0d2dae09e2d16cd72dcf0f2e24 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
@@ -24,7 +24,6 @@ import org.w3c.dom.Node;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache;
import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
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 0ef26253308c893606da6664106e753b9931e215..c718c9afebb7f805e564027ba56044e20b3d284c 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
@@ -5,9 +5,9 @@ import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.when;
import java.io.IOException;
@@ -23,8 +23,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
-import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache;
import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
@@ -82,7 +80,8 @@ 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(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
chemicalParser.setWebPageDownloader(mockDownloader);
// Parkinson disease
chemicalParser.getChemicalsForDisease(parkinsonDiseaseId);
@@ -447,7 +446,8 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
WebPageDownloader downloader = chemicalParser.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
chemicalParser.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, chemicalParser.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -544,7 +544,8 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
chemicalParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
chemicalParser.setWebPageDownloader(mockDownloader);
try {
chemicalParser.getChemicals(parkinsonDiseaseId, 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 b230cba338260aaa0e2cc7466825e0da2230640c..a9b5ee9131e7d30c79218b57138e2336aadf7a89 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
@@ -6,8 +6,8 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.when;
import java.io.IOException;
@@ -21,7 +21,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache;
import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
@@ -549,7 +548,8 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
WebPageDownloader downloader = drugBankHTMLParser.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
drugBankHTMLParser.setWebPageDownloader(mockDownloader);
drugBankHTMLParser.refreshCacheQuery("http://google.pl/");
fail("Exception expected");
@@ -568,7 +568,8 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
GeneralCacheInterface cache = drugBankHTMLParser.getCache();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
drugBankHTMLParser.setWebPageDownloader(mockDownloader);
drugBankHTMLParser.setCache(null);
@@ -661,7 +662,8 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
WebPageDownloader downloader = drugBankHTMLParser.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
drugBankHTMLParser.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, drugBankHTMLParser.getServiceStatus().getStatus());
} catch (Exception e) {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNAParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNAParserTest.java
index ac1e12c007a1b3cdcc779573c752409b8ce0e228..8132a0fd81c9c0322921e36f3b82e1cf4f84950e 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNAParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNAParserTest.java
@@ -23,7 +23,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache;
import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.data.MiRNA;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
index fe7b5e52e484c45266a6bd501b1dc6e1b383c705..7918cb4ca6c1316afebd99f7f1369b4154cc21d1 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
@@ -6,7 +6,7 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
-import static org.mockito.Matchers.any;
+import static org.mockito.ArgumentMatchers.any;
import java.util.ArrayList;
import java.util.Collection;
@@ -25,7 +25,6 @@ import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.services.annotators.AnnotationParameters;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
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 b8c100cc028f3af61bb4600a1f7fde2307200827..5d2f97a890d5fae1973e481717c6c1f0bc1a2946 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java
@@ -6,8 +6,8 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.when;
import java.io.IOException;
@@ -18,7 +18,6 @@ import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import org.mockito.Mock;
import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
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 ef6138383b8ff2e866f5e8cdfe6551343a8f3574..3566680735812abfa8b0198678ab69dedba47d4f 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
@@ -5,10 +5,10 @@ import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyBoolean;
+import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyBoolean;
-import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.when;
import java.io.IOException;
@@ -26,7 +26,6 @@ import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import org.mockito.Mock;
import org.mockito.Mockito;
import org.mockito.invocation.InvocationOnMock;
import org.mockito.stubbing.Answer;
diff --git a/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java b/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java
index a796375a3ca3fd7a4e5b880dcf9e1da55f74def2..99070dc3729a839ec2afa04f9542545afca6d15f 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java
@@ -11,14 +11,9 @@ import java.awt.Color;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
-import java.lang.reflect.Field;
import java.nio.charset.StandardCharsets;
import java.util.List;
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-
import org.apache.log4j.Logger;
import org.apache.xerces.dom.DocumentImpl;
import org.apache.xerces.dom.ElementImpl;
@@ -32,391 +27,395 @@ import org.w3c.dom.Node;
import org.xml.sax.InputSource;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
public class XmlParserTest {
- Logger logger = Logger.getLogger(XmlParserTest.class);
-
- XmlParser parser = new XmlParser();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testColorParsing() {
- try {
- String strColor = "ffcbcd09";
-
- Color c = parser.stringToColor(strColor);
- String resultString = parser.colorToString(c);
- assertTrue("Different string representation: " + strColor + " - " + resultString, strColor.equalsIgnoreCase(resultString));
-
- Color c2 = parser.stringToColor(resultString);
-
- assertEquals(c.getRed(), c2.getRed());
- assertEquals(c.getGreen(), c2.getGreen());
- assertEquals(c.getBlue(), c2.getBlue());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidColorParsing() {
- try {
- String strColor = "hello world";
-
- parser.stringToColor(strColor);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testColorParsingWithAlpha() {
- try {
- String strColor = "fecbcd09";
-
- Color c = parser.stringToColor(strColor);
- String resultString = parser.colorToString(c);
- assertTrue("Different string representation: " + strColor + " - " + resultString, strColor.equalsIgnoreCase(resultString));
-
- Color c2 = parser.stringToColor(resultString);
-
- assertEquals(c.getRed(), c2.getRed());
- assertEquals(c.getGreen(), c2.getGreen());
- assertEquals(c.getBlue(), c2.getBlue());
- assertEquals(c.getAlpha(), c2.getAlpha());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetXmlDocumentFromString() throws Exception {
- try {
- Document validDoc = parser.getXmlDocumentFromString("<node>test</node>");
- assertNotNull(validDoc);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testNodeToString() throws Exception {
- try {
- String xml = "<test_node>test_x</test_node>";
- Document validDoc = parser.getXmlDocumentFromString(xml);
- String str = parser.nodeToString(validDoc);
- assertEquals(xml.trim(), str.trim());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testEmptyNodeToString() throws Exception {
- try {
- String str = parser.nodeToString(null);
- assertNull(str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testNodeToStringWithHeader() throws Exception {
- try {
- String xml = "<test_node>test_x</test_node>";
- Document validDoc = parser.getXmlDocumentFromString(xml);
- String str = parser.nodeToString(validDoc, true);
- assertTrue(str.contains(xml));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidNodeToString() throws Exception {
- try {
- final DocumentImpl xmlDoc = new DocumentImpl();
-
- Element root = xmlDoc.createElement("booking");
-
- class Tmp extends ElementImpl {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public Tmp() {
- this.ownerDocument = xmlDoc;
- }
-
- @Override
- public NamedNodeMap getAttributes() {
- return null;
- }
-
- }
- ;
- Element el = new Tmp();
- root.appendChild(el);
- assertNotNull(parser.nodeToString(root, true));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetXmlDocumentFromInvalidString() throws Exception {
- try {
- parser.getXmlDocumentFromString("<node>test<node>");
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetXmlDocumentFromInvalidInputStream() throws Exception {
- try {
- parser.getXmlDocumentFromInputSource(new InputSource(), true);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testEscapeXml() throws Exception {
- try {
- String str = parser.escapeXml("<xml>node</xml>");
- assertFalse(str.contains("<"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testEscapeNullXml() throws Exception {
- try {
- String str = parser.escapeXml(null);
- assertNull(str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFileToString() throws Exception {
- try {
- String str = parser.fileToString("testFiles/test.txt");
- assertTrue(str.contains("test"));
- assertTrue(str.contains("file"));
- assertTrue(str.contains("with some content"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testInputStreamToString() throws Exception {
- try {
- InputStream stream = new ByteArrayInputStream("stream string".getBytes(StandardCharsets.UTF_8));
- String str = parser.inputStreamToString(stream);
- assertEquals("stream string", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodeValue() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node>content</node>");
- Node node = parser.getNode("node", document);
- String str = parser.getNodeValue(node);
- assertEquals("content", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodeValue2() throws Exception {
- try {
- String str = parser.getNodeValue(null);
- assertEquals("", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodeValue3() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node></node>");
- Node node = parser.getNode("node", document);
- String str = parser.getNodeValue(node);
- assertEquals("", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodeValue4() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node><subnode/></node>");
- Node node = parser.getNode("node", document);
- String str = parser.getNodeValue(node);
- assertEquals("", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testInputStreamToStringThrowsException() throws Exception {
- try {
- parser.inputStreamToString(new InputStream() {
- @Override
- public int read() throws IOException {
- throw new IOException();
- }
- });
- fail("Exception expected");
- } catch (IOException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFileToStringThrowsException() throws Exception {
- try {
- parser.fileToString("testFiles/unknown file.txt");
- fail("Exception expected");
- } catch (IOException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodeAttr() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node attr=\"val\">content</node>");
- Node node = parser.getNode("node", document);
- String str = parser.getNodeAttr("attr", node);
- assertEquals("val", str);
- str = parser.getNodeAttr("attr2", node);
- assertEquals("", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodes() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
- Node node = parser.getNode("node", document);
- List<Node> nodes = parser.getNodes("subnode", node.getChildNodes());
- assertEquals(2, nodes.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNode() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
- Node node = parser.getNode("node", document);
- Node child = parser.getNode("other", node.getChildNodes());
- assertNotNull(child);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNode2() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node attr=\"x\"><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
- Node node = parser.getNode("node", document);
- Node child = parser.getNode("other2", node.getChildNodes());
- assertNull(child);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNode3() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node attr=\"x\">xxx</node>");
- Node node = parser.getNode("node", document);
- Node child = parser.getNode("other2", node.getChildNodes());
- assertNull(child);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Logger logger = Logger.getLogger(XmlParserTest.class);
+
+ XmlParser parser = new XmlParser();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testColorParsing() {
+ try {
+ String strColor = "ffcbcd09";
+
+ Color c = parser.stringToColor(strColor);
+ String resultString = parser.colorToString(c);
+ assertTrue("Different string representation: " + strColor + " - " + resultString,
+ strColor.equalsIgnoreCase(resultString));
+
+ Color c2 = parser.stringToColor(resultString);
+
+ assertEquals(c.getRed(), c2.getRed());
+ assertEquals(c.getGreen(), c2.getGreen());
+ assertEquals(c.getBlue(), c2.getBlue());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidColorParsing() {
+ try {
+ String strColor = "hello world";
+
+ parser.stringToColor(strColor);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testColorParsingWithAlpha() {
+ try {
+ String strColor = "fecbcd09";
+
+ Color c = parser.stringToColor(strColor);
+ String resultString = parser.colorToString(c);
+ assertTrue("Different string representation: " + strColor + " - " + resultString,
+ strColor.equalsIgnoreCase(resultString));
+
+ Color c2 = parser.stringToColor(resultString);
+
+ assertEquals(c.getRed(), c2.getRed());
+ assertEquals(c.getGreen(), c2.getGreen());
+ assertEquals(c.getBlue(), c2.getBlue());
+ assertEquals(c.getAlpha(), c2.getAlpha());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetXmlDocumentFromString() throws Exception {
+ try {
+ Document validDoc = parser.getXmlDocumentFromString("<node>test</node>");
+ assertNotNull(validDoc);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testNodeToString() throws Exception {
+ try {
+ String xml = "<test_node>test_x</test_node>";
+ Document validDoc = parser.getXmlDocumentFromString(xml);
+ String str = parser.nodeToString(validDoc);
+ assertEquals(xml.trim(), str.trim());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testEmptyNodeToString() throws Exception {
+ try {
+ String str = parser.nodeToString(null);
+ assertNull(str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testNodeToStringWithHeader() throws Exception {
+ try {
+ String xml = "<test_node>test_x</test_node>";
+ Document validDoc = parser.getXmlDocumentFromString(xml);
+ String str = parser.nodeToString(validDoc, true);
+ assertTrue(str.contains(xml));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidNodeToString() throws Exception {
+ try {
+ final DocumentImpl xmlDoc = new DocumentImpl();
+
+ Element root = xmlDoc.createElement("booking");
+
+ class Tmp extends ElementImpl {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public Tmp() {
+ this.ownerDocument = xmlDoc;
+ }
+
+ @Override
+ public NamedNodeMap getAttributes() {
+ return null;
+ }
+
+ }
+ ;
+ Element el = new Tmp();
+ root.appendChild(el);
+ assertNotNull(parser.nodeToString(root, true));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetXmlDocumentFromInvalidString() throws Exception {
+ try {
+ parser.getXmlDocumentFromString("<node>test<node>");
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetXmlDocumentFromInvalidInputStream() throws Exception {
+ try {
+ parser.getXmlDocumentFromInputSource(new InputSource(), true);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testEscapeXml() throws Exception {
+ try {
+ String str = parser.escapeXml("<xml>node</xml>");
+ assertFalse(str.contains("<"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testEscapeNullXml() throws Exception {
+ try {
+ String str = parser.escapeXml(null);
+ assertNull(str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFileToString() throws Exception {
+ try {
+ String str = parser.fileToString("testFiles/test.txt");
+ assertTrue(str.contains("test"));
+ assertTrue(str.contains("file"));
+ assertTrue(str.contains("with some content"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testInputStreamToString() throws Exception {
+ try {
+ InputStream stream = new ByteArrayInputStream("stream string".getBytes(StandardCharsets.UTF_8));
+ String str = parser.inputStreamToString(stream);
+ assertEquals("stream string", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodeValue() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node>content</node>");
+ Node node = parser.getNode("node", document);
+ String str = parser.getNodeValue(node);
+ assertEquals("content", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodeValue2() throws Exception {
+ try {
+ String str = parser.getNodeValue(null);
+ assertEquals("", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodeValue3() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node></node>");
+ Node node = parser.getNode("node", document);
+ String str = parser.getNodeValue(node);
+ assertEquals("", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodeValue4() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node><subnode/></node>");
+ Node node = parser.getNode("node", document);
+ String str = parser.getNodeValue(node);
+ assertEquals("", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testInputStreamToStringThrowsException() throws Exception {
+ try {
+ parser.inputStreamToString(new InputStream() {
+ @Override
+ public int read() throws IOException {
+ throw new IOException();
+ }
+ });
+ fail("Exception expected");
+ } catch (IOException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFileToStringThrowsException() throws Exception {
+ try {
+ parser.fileToString("testFiles/unknown file.txt");
+ fail("Exception expected");
+ } catch (IOException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodeAttr() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node attr=\"val\">content</node>");
+ Node node = parser.getNode("node", document);
+ String str = parser.getNodeAttr("attr", node);
+ assertEquals("val", str);
+ str = parser.getNodeAttr("attr2", node);
+ assertEquals("", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodes() throws Exception {
+ try {
+ Document document = parser
+ .getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
+ Node node = parser.getNode("node", document);
+ List<Node> nodes = parser.getNodes("subnode", node.getChildNodes());
+ assertEquals(2, nodes.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNode() throws Exception {
+ try {
+ Document document = parser
+ .getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
+ Node node = parser.getNode("node", document);
+ Node child = parser.getNode("other", node.getChildNodes());
+ assertNotNull(child);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNode2() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString(
+ "<node attr=\"x\"><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
+ Node node = parser.getNode("node", document);
+ Node child = parser.getNode("other2", node.getChildNodes());
+ assertNull(child);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNode3() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node attr=\"x\">xxx</node>");
+ Node node = parser.getNode("node", document);
+ Node child = parser.getNode("other2", node.getChildNodes());
+ assertNull(child);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
index 0928447874812b444a8054ae552c8d62b8435fcd..d529314f4a9be7f6e57c4f776532784c294cea3b 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
@@ -1,10 +1,10 @@
package lcsb.mapviewer.converter.graphics.bioEntity.reaction;
import static org.junit.Assert.assertTrue;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyDouble;
+import static org.mockito.ArgumentMatchers.anyInt;
import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyDouble;
-import static org.mockito.Matchers.anyInt;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
@@ -41,7 +41,6 @@ import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.SplitOperator;
-import lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
import lcsb.mapviewer.model.map.species.GenericProtein;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index f0fddefe0a1bb12c06b36b5e3bb7d289fdec430f..b6d037fd550412790b999f9687c61c054610723e 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -19,7 +19,6 @@ import org.sbml.jsbml.ext.SBasePlugin;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
import org.sbml.jsbml.ext.multi.MultiModelPlugin;
-import org.sbml.jsbml.ext.render.LocalStyle;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.commands.layout.ApplySimpleLayoutModelCommand;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
index 327a0049438001361e51d172762d9351aa0a0084..e2ddd817d450483be08464bca6f5bc854ffe71b6 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
@@ -19,7 +19,6 @@ import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
index eec9afd5e7ce0630275fc1a9f336767476dca191..1e2ecd69f2fe52546509453e9edc7ed2e6dbebf2 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
@@ -5,7 +5,6 @@ import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
-import java.awt.Color;
import java.io.FileNotFoundException;
import java.util.List;
@@ -15,7 +14,6 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
@@ -199,7 +197,8 @@ public class SbmlParserTest {
@Test
public void testParseConflictingTypesFromMulti() throws Exception {
- Model model = parser.createModel(new ConverterParams().filename("testFiles/multi_features/conflicting_species_type.xml"));
+ Model model = parser
+ .createModel(new ConverterParams().filename("testFiles/multi_features/conflicting_species_type.xml"));
assertTrue(model.getElementByElementId("species_0") instanceof GenericProtein);
assertEquals(1, getWarnings().size());
}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index 175bbfd01674a95e95ee820f88dd980a1164fbce..639b864a4eaf6304406eb413437f44f96a29a595 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -5,11 +5,9 @@ import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.lang.reflect.Modifier;
-import java.util.ArrayList;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.HashSet;
-import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
index c310515b20c0c9f5f29dd0fc36910d701a452a8a..6afd588a365b16021b2805ecd88fbac0a7399dfe 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
@@ -17,7 +17,6 @@ import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
-import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
index 6cc46e9d4266aaf4d7bf6ac25a376e4a7453f003..c19980657d23d3a5ff5ef3e85565a3dce6812190 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
@@ -10,7 +10,6 @@ import java.awt.geom.Point2D;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
-import java.util.ArrayList;
import org.junit.After;
import org.junit.Before;
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
index d4e7f30e6ed84db9ffad7a6caa4a5ebdacddf562..9056b2a2698be8f48ac5df373e5754e92ffb4299 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
@@ -2,7 +2,6 @@ package lcsb.mapviewer.commands;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
import java.awt.geom.Path2D;
import java.io.ByteArrayInputStream;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
index bcabc050f42a742757c05d55251d5b93a4a4ea52..737126987a4de8c0800caac394d8e5919c188deb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
@@ -36,7 +36,6 @@ import org.apache.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.model.map.BioEntity;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
index 801b026b7021fb5cbb736ffade5f55aa537d6feb..088eac1a1378914c5708dbfd61b19d00d299a6f5 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
@@ -1,7 +1,6 @@
package lcsb.mapviewer.model.map.species;
import java.util.ArrayList;
-import java.util.Collection;
import java.util.List;
import javax.persistence.DiscriminatorValue;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java
index 5d41bcd193058162e9d164dfb992fd9c2ca443e3..d34d431b1cf6cf94b4833b6289d8966a7b4949b2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java
@@ -1,7 +1,6 @@
package lcsb.mapviewer.model.map.species;
import java.util.ArrayList;
-import java.util.Collection;
import java.util.List;
import javax.persistence.DiscriminatorValue;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/SpeciesWithModificationResidue.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/SpeciesWithModificationResidue.java
index da6163349278b52a898872ac0677692b6b694ef3..e9ad4b731bf03871e05af06c49ca68059b478c2e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/SpeciesWithModificationResidue.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/SpeciesWithModificationResidue.java
@@ -1,6 +1,5 @@
package lcsb.mapviewer.model.map.species.field;
-import java.util.Collection;
import java.util.List;
/**
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java
index f931b099c9a2e62ca1f9e2ed31866d518cba324a..c2baa22270230d405a116b002cf837cab7840cfb 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java
@@ -17,7 +17,6 @@ import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
index 9881b49693d977ff83c3ffad9988e3ae1e2f79bb..54a8d516ab1b8fbe0f7433a72354f47339248d11 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
@@ -20,7 +20,6 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.layout.BlockDiagram;
-import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java
index 7b7d6d48694044e69cb299bedf6dd0663e3be914..4af40967c90ac8c0764e2c41f5fb376eb2c3724d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java
@@ -12,7 +12,6 @@ import org.junit.Test;
import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
import lcsb.mapviewer.model.map.species.field.ModificationSite;
import lcsb.mapviewer.model.map.species.field.ModificationState;
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java b/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java
index 0cef750d7c6f32a15f312a2c731e0cdab6b0d169..6ac53ee658630da86304d224f86dbf92fe1c13f0 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java
@@ -5,8 +5,6 @@ import java.util.Map;
import java.util.Map.Entry;
import java.util.Observable;
-import javax.transaction.TransactionManager;
-
import org.apache.log4j.Logger;
import org.hibernate.SQLQuery;
import org.hibernate.Session;
@@ -14,9 +12,9 @@ import org.hibernate.SessionFactory;
import org.hibernate.dialect.Dialect;
import org.hibernate.internal.SessionFactoryImpl;
import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
import lcsb.mapviewer.common.exception.InvalidStateException;
-import org.springframework.stereotype.Service;
/**
* This class contains a set of methods that allow to manage hibernate sessions
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/LayoutDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/LayoutDao.java
index 64b93782826a93ef92076a719e964b20ae9a76d9..c754aef096bc03df8511ed6ca5d0ff789d5810c5 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/LayoutDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/LayoutDao.java
@@ -7,14 +7,13 @@ import org.apache.log4j.Logger;
import org.hibernate.Criteria;
import org.hibernate.criterion.Projections;
import org.hibernate.criterion.Restrictions;
+import org.springframework.stereotype.Repository;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.BaseDao;
-import org.springframework.stereotype.Repository;
/**
* Data access object for {@link Layout} class.
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
index f44acde754fb9d737dfe59928134ee319654545c..4bd24a91427422c4ba0fb91be3fbd1b97b52415e 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
@@ -25,7 +25,6 @@ import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.Residue;
import lcsb.mapviewer.persist.PersistTestFunctions;
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomePhysicalEntity.java b/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomePhysicalEntity.java
index 9638284291fd0ea37797e48c9d3fa96cf715f4ba..ef8691b527ed7900dbff0b7a130b020c2cffd1ca 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomePhysicalEntity.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/model/ReactomePhysicalEntity.java
@@ -3,8 +3,6 @@ package lcsb.mapviewer.reactome.model;
import java.util.ArrayList;
import java.util.List;
-import org.apache.log4j.Logger;
-
/**
* Object representing Reactome <a href=
* "http://www.reactome.org/cgi-bin/classbrowser?DB=gk_current&CLASS=PhysicalEntity"
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndSimpleEntityComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndSimpleEntityComparator.java
index 6c93422860e89a4988d3332aa8f2681fcf3e987b..099b291b908317e5324b54a50a0e5a41706095a4 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndSimpleEntityComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndSimpleEntityComparator.java
@@ -3,15 +3,15 @@ package lcsb.mapviewer.reactome.utils.comparators;
import java.util.HashSet;
import java.util.Set;
+import org.springframework.stereotype.Service;
+
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.reactome.model.ReactomeReferenceEntity;
import lcsb.mapviewer.reactome.model.ReactomeReferenceMolecule;
import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
import lcsb.mapviewer.reactome.utils.ComparatorException;
-import org.springframework.stereotype.Service;
/**
* This class allows to compare {@link Complex} element (internal
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndCatalystComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndCatalystComparator.java
index 83e7bedd0ae39799fe1813b0e1a920be2c940639..e562eb8c69191b957f7d5340cec3f69f9d2027e5 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndCatalystComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndCatalystComparator.java
@@ -1,5 +1,7 @@
package lcsb.mapviewer.reactome.utils.comparators;
+import org.springframework.stereotype.Service;
+
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
@@ -9,8 +11,6 @@ import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
import lcsb.mapviewer.reactome.model.ReactomePhysicalEntity;
import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
import lcsb.mapviewer.reactome.utils.ComparatorException;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Service;
/**
* This class allows to compare {@link SimpleMolecule} element (internal
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
index e7b443111d26d84cfb33fb20e40d476970389258..57916b9d19923dfdb612b95a445d9e2f4ac2014f 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -31,14 +31,11 @@ import lcsb.mapviewer.annotation.services.MiriamConnector;
import lcsb.mapviewer.annotation.services.PubmedParser;
import lcsb.mapviewer.annotation.services.PubmedSearchException;
import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
-import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
-import lcsb.mapviewer.converter.graphics.ImageGenerators;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
import lcsb.mapviewer.converter.model.sbml.SbmlParser;
@@ -320,8 +317,8 @@ public abstract class BaseRestImpl {
*/
public void setProjectService(IProjectService projectService) {
this.projectService = projectService;
- }
-
+ }
+
protected IConverter getModelParser(String handlerClass) throws QueryException {
for (IConverter converter : getModelConverters()) {
if (converter.getClass().getCanonicalName().equals(handlerClass)) {
@@ -338,7 +335,6 @@ public abstract class BaseRestImpl {
result.add(new SbmlParser());
return result;
}
-
protected String getFirstValue(List<Object> list) {
if (list == null) {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/files/FileRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/files/FileRestImpl.java
index 0100b22104c53cc825ec7b473d04735cd6b3df9b..937aa13f666c2d931abebf2ce288be3fddc7fead 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/files/FileRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/files/FileRestImpl.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.api.files;
-import java.util.TreeMap;
import java.util.Map;
+import java.util.TreeMap;
import org.apache.commons.lang3.ArrayUtils;
import org.hibernate.QueryException;
@@ -13,7 +13,6 @@ import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.ObjectNotFoundException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
import lcsb.mapviewer.services.SecurityException;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index 1da0a9b5261fd32b6957c8992c5fcf932362311b..a0177609c3388be8c71187d62e72959b1d3e8edc 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
@@ -1,7 +1,6 @@
package lcsb.mapviewer.api.projects;
import java.awt.geom.Point2D;
-import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.Serializable;
import java.security.MessageDigest;
@@ -16,7 +15,6 @@ import java.util.Set;
import java.util.TreeMap;
import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.util.MultiValueMap;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
index b735ce360ec9e480c7254edf78006c017e99a8e7..549213de52c85a626fb6d97c7c056678324f063d 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
@@ -23,7 +23,6 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.search.DbSearchCriteria;
import lcsb.mapviewer.services.search.drug.IDrugService;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
index 3b1cf58d62fc68b7d0ecc0b41e7ecbf73441a2ee..256a9996a1a6729d15d41cf1bae8076514978ed1 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
@@ -17,9 +17,7 @@ import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.UserAccessException;
-import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.ISearchService;
-import lcsb.mapviewer.services.interfaces.IUserService;
@Transactional
@Service
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java
index 2b29e95d8e015f4411f93dea2bdf25390f37b6a5..2e59795a7844cf6e5aa7ac136f4ec5d0f8e64f68 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java
@@ -4,13 +4,10 @@ import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
-import java.io.BufferedWriter;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileOutputStream;
-import java.io.FileWriter;
import java.io.IOException;
-import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
@@ -28,7 +25,6 @@ import org.junit.Test;
import org.sbml.jsbml.SBMLException;
import org.springframework.beans.factory.annotation.Autowired;
-
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.api.RestTestFunctions;
import lcsb.mapviewer.converter.ConverterException;
@@ -56,314 +52,307 @@ public class ConvertRestImplTest extends RestTestFunctions {
@After
public void tearDown() throws Exception {
}
-
- @SuppressWarnings("unchecked")
+
+ @SuppressWarnings("unchecked")
@Test
public void testGetInformation() throws Exception {
try {
- Map<String, Object> result = convertRestImpl.getInformationImage(token);
- assertTrue(result.keySet().size() == 2);
- assertNotNull(result.get("inputs"));
- assertNotNull(result.get("outputs"));
-
- List<Object> inputs = (List<Object>) result.get("inputs");
- List<Object> outputs = (List<Object>) result.get("outputs");
-
- assertTrue(inputs.size() > 0);
- assertTrue(outputs.size() > 0);
-
+ Map<String, Object> result = convertRestImpl.getInformationImage(token);
+ assertTrue(result.keySet().size() == 2);
+ assertNotNull(result.get("inputs"));
+ assertNotNull(result.get("outputs"));
+
+ List<Object> inputs = (List<Object>) result.get("inputs");
+ List<Object> outputs = (List<Object>) result.get("outputs");
+
+ assertTrue(inputs.size() > 0);
+ assertTrue(outputs.size() > 0);
+
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
-
+
@SuppressWarnings("unchecked")
@Test
public void testGetInformationImage() throws Exception {
try {
- Map<String, Object> result = convertRestImpl.getInformationImage(token);
- assertTrue(result.keySet().size() == 2);
- assertNotNull(result.get("inputs"));
- assertNotNull(result.get("outputs"));
-
- List<Object> inputs = (List<Object>) result.get("inputs");
- List<Object> outputs = (List<Object>) result.get("outputs");
-
- assertTrue(inputs.size() > 0);
- assertTrue(outputs.size() > 0);
-
+ Map<String, Object> result = convertRestImpl.getInformationImage(token);
+ assertTrue(result.keySet().size() == 2);
+ assertNotNull(result.get("inputs"));
+ assertNotNull(result.get("outputs"));
+
+ List<Object> inputs = (List<Object>) result.get("inputs");
+ List<Object> outputs = (List<Object>) result.get("outputs");
+
+ assertTrue(inputs.size() > 0);
+ assertTrue(outputs.size() > 0);
+
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
-
@Test
public void testCelDesigner2Sbml1() throws Exception {
try {
- File file = new File("testFiles/convert/sample-cd.xml");
- String content = FileUtils.readFileToString(file);
- String result = convertRestImpl.convert(token, "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser",
- "lcsb.mapviewer.converter.model.sbml.SbmlParser", content);
- assertTrue(result.length() > 0);
- assertTrue(result.contains("</layout:speciesReferenceGlyph>"));
+ File file = new File("testFiles/convert/sample-cd.xml");
+ String content = FileUtils.readFileToString(file);
+ String result = convertRestImpl.convert(token,
+ "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser",
+ "lcsb.mapviewer.converter.model.sbml.SbmlParser", content);
+ assertTrue(result.length() > 0);
+ assertTrue(result.contains("</layout:speciesReferenceGlyph>"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
-
+
/*
* this test does not work because the generator is not deterministic
- @Test
- public void testCelDesigner2Sbml2() throws Exception {
- try {
- File file = new File("testFiles/convert/sample-cd.xml");
- String content = FileUtils.readFileToString(file);
- String result = convertRestImpl.convert(token, "CellDesigner_SBML", "SBML", content);
- //String result2 = convertRestImpl.convert(token, "CellDesigner_SBML", "SBML", content);
- String result2 = convertRestImpl.convert(token, "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser",
- "lcsb.mapviewer.converter.model.sbml.SbmlParser", content);
-
- assertTrue(result.equals(result2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- */
-
+ *
+ * @Test public void testCelDesigner2Sbml2() throws Exception { try { File file
+ * = new File("testFiles/convert/sample-cd.xml"); String content =
+ * FileUtils.readFileToString(file); String result =
+ * convertRestImpl.convert(token, "CellDesigner_SBML", "SBML", content);
+ * //String result2 = convertRestImpl.convert(token, "CellDesigner_SBML",
+ * "SBML", content); String result2 = convertRestImpl.convert(token,
+ * "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser",
+ * "lcsb.mapviewer.converter.model.sbml.SbmlParser", content);
+ *
+ * assertTrue(result.equals(result2));
+ *
+ * } catch (Exception e) { e.printStackTrace(); throw e; } }
+ */
+
@Test
public void testCelDesigner2Svg() throws Exception {
try {
- File file = new File("testFiles/convert/sample-cd.xml");
- String content = FileUtils.readFileToString(file);
- String result = convertRestImpl.converToImage(token, "CellDesigner_SBML", "svg", content).toString();
-
- // FileOutputStream outputStream = new FileOutputStream("sample-cd.png");
- // outputStream.write(convertRestImpl.converToImage(token, "CellDesigner_SBML", "png", content).toByteArray());
- // outputStream.close();
-
- assertTrue(result.contains("<rect"));
+ File file = new File("testFiles/convert/sample-cd.xml");
+ String content = FileUtils.readFileToString(file);
+ String result = convertRestImpl.converToImage(token, "CellDesigner_SBML", "svg", content).toString();
+
+ // FileOutputStream outputStream = new FileOutputStream("sample-cd.png");
+ // outputStream.write(convertRestImpl.converToImage(token, "CellDesigner_SBML",
+ // "png", content).toByteArray());
+ // outputStream.close();
+
+ assertTrue(result.contains("<rect"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
-
+
@Test
public void testCellDesigner2Sbml2Svg() throws Exception {
try {
- File file = new File("testFiles/convert/neuron_cd.xml");
- String content = FileUtils.readFileToString(file);
- String resultSbml = convertRestImpl.convert(token, "CellDesigner_SBML", "SBML", content).toString();
- String resultSvg = convertRestImpl.converToImage(token, "SBML", "svg", resultSbml).toString();
-
- // FileOutputStream outputStream = new FileOutputStream("sample-cd.png");
- // outputStream.write(convertRestImpl.converToImage(token, "CellDesigner_SBML", "png", content).toByteArray());
- // outputStream.close();
-
- assertTrue(resultSvg.contains("<rect"));
+ File file = new File("testFiles/convert/neuron_cd.xml");
+ String content = FileUtils.readFileToString(file);
+ String resultSbml = convertRestImpl.convert(token, "CellDesigner_SBML", "SBML", content).toString();
+ String resultSvg = convertRestImpl.converToImage(token, "SBML", "svg", resultSbml).toString();
+
+ // FileOutputStream outputStream = new FileOutputStream("sample-cd.png");
+ // outputStream.write(convertRestImpl.converToImage(token, "CellDesigner_SBML",
+ // "png", content).toByteArray());
+ // outputStream.close();
+
+ assertTrue(resultSvg.contains("<rect"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
-
+
@Test
public void testCellDesigner2Sbml2CellDesignerSvg() throws Exception {
try {
- File file = new File("testFiles/convert/neuron_cd.xml");
- String content = FileUtils.readFileToString(file);
- String resultSbml = convertRestImpl.convert(token, "CellDesigner_SBML", "SBML", content).toString();
- String resultCellDesignerSbml = convertRestImpl.convert(token, "SBML", "CellDesigner_SBML", resultSbml).toString();
- String resultSvg = convertRestImpl.converToImage(token, "CellDesigner_SBML", "svg", resultCellDesignerSbml).toString();
-
- // FileOutputStream outputStream = new FileOutputStream("sample-cd.png");
- // outputStream.write(convertRestImpl.converToImage(token, "CellDesigner_SBML", "png", content).toByteArray());
- // outputStream.close();
-
- assertTrue(resultSvg.contains("<rect"));
+ File file = new File("testFiles/convert/neuron_cd.xml");
+ String content = FileUtils.readFileToString(file);
+ String resultSbml = convertRestImpl.convert(token, "CellDesigner_SBML", "SBML", content).toString();
+ String resultCellDesignerSbml = convertRestImpl.convert(token, "SBML", "CellDesigner_SBML", resultSbml)
+ .toString();
+ String resultSvg = convertRestImpl.converToImage(token, "CellDesigner_SBML", "svg", resultCellDesignerSbml)
+ .toString();
+
+ // FileOutputStream outputStream = new FileOutputStream("sample-cd.png");
+ // outputStream.write(convertRestImpl.converToImage(token, "CellDesigner_SBML",
+ // "png", content).toByteArray());
+ // outputStream.close();
+
+ assertTrue(resultSvg.contains("<rect"));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
-
+
@Test
public void testScaling() throws Exception {
try {
- File file = new File("testFiles/convert/sample-cd.xml");
- String content = FileUtils.readFileToString(file);
- String result1 = convertRestImpl.converToImage(token, "CellDesigner_SBML", "svg", content, 50.0, 50.0).toString();
- String result2 = convertRestImpl.converToImage(token, "CellDesigner_SBML", "svg", content, 100.0, 100.0).toString();
-
-
- Pattern pattern = Pattern.compile(".*scale\\(([0-9]+\\.[0-9]+),([0-9]+\\.[0-9]+)\\).*");
- Matcher matcher1 = pattern.matcher(result1);
- Matcher matcher2 = pattern.matcher(result2);
-
- assertTrue(matcher1.find());
- assertTrue(matcher2.find());
-
- assertFalse(matcher1.group(1).toString().equals(matcher2.group(1).toString()));
-
+ File file = new File("testFiles/convert/sample-cd.xml");
+ String content = FileUtils.readFileToString(file);
+ String result1 = convertRestImpl.converToImage(token, "CellDesigner_SBML", "svg", content, 50.0, 50.0).toString();
+ String result2 = convertRestImpl.converToImage(token, "CellDesigner_SBML", "svg", content, 100.0, 100.0)
+ .toString();
+
+ Pattern pattern = Pattern.compile(".*scale\\(([0-9]+\\.[0-9]+),([0-9]+\\.[0-9]+)\\).*");
+ Matcher matcher1 = pattern.matcher(result1);
+ Matcher matcher2 = pattern.matcher(result2);
+
+ assertTrue(matcher1.find());
+ assertTrue(matcher2.find());
+
+ assertFalse(matcher1.group(1).toString().equals(matcher2.group(1).toString()));
+
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
-
+
@Test
public void test1() throws Exception {
try {
- File file = new File("testFiles/convert/glycolysis2.xml");
- String content = FileUtils.readFileToString(file);
-
- String result = convertRestImpl.convert(token, "CellDesigner_SBML", "SBML", content);
- ByteArrayOutputStream result1 = convertRestImpl.converToImage(token, "SBML", "svg", result);
-
- File output = new File("testFiles/convert/glycolysis2.svg");
-
- FileOutputStream outputStream = new FileOutputStream(output);
- outputStream.write(result1.toByteArray());
- outputStream.close();
- assertTrue(output.exists());
- output.delete();
-
-
+ File file = new File("testFiles/convert/glycolysis2.xml");
+ String content = FileUtils.readFileToString(file);
+
+ String result = convertRestImpl.convert(token, "CellDesigner_SBML", "SBML", content);
+ ByteArrayOutputStream result1 = convertRestImpl.converToImage(token, "SBML", "svg", result);
+
+ File output = new File("testFiles/convert/glycolysis2.svg");
+
+ FileOutputStream outputStream = new FileOutputStream(output);
+ outputStream.write(result1.toByteArray());
+ outputStream.close();
+ assertTrue(output.exists());
+ output.delete();
+
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
-
+
@Test
public void test2() throws Exception {
try {
- File file = new File("testFiles/convert/glycolysis2.xml");
- String content = FileUtils.readFileToString(file);
-
- String result = convertRestImpl.convert(token, "CellDesigner_SBML", "SBML", content);
- String result1 = convertRestImpl.convert(token, "SBML", "CellDesigner_SBML", result);
-
-
+ File file = new File("testFiles/convert/glycolysis2.xml");
+ String content = FileUtils.readFileToString(file);
+
+ String result = convertRestImpl.convert(token, "CellDesigner_SBML", "SBML", content);
+ String result1 = convertRestImpl.convert(token, "SBML", "CellDesigner_SBML", result);
+
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
-
-
+
@Test
public void testCelDesigner2Sbgn() throws Exception {
try {
- File file = new File("testFiles/convert/sample-cd.xml");
- String content = FileUtils.readFileToString(file);
- String result = convertRestImpl.convert(token, "CellDesigner_SBML", "SBGN-ML", content).toString();
- assertTrue(result.contains("glyph class=\"complex\""));
+ File file = new File("testFiles/convert/sample-cd.xml");
+ String content = FileUtils.readFileToString(file);
+ String result = convertRestImpl.convert(token, "CellDesigner_SBML", "SBGN-ML", content).toString();
+ assertTrue(result.contains("glyph class=\"complex\""));
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
-
+
/*
* this test does not work because the generator is not deterministic
- @Test
- public void testCelDesigner2Svg2() throws Exception {
- try {
- File file = new File("testFiles/convert/sample-cd.xml");
- String content = FileUtils.readFileToString(file);
- String result = convertRestImpl.converToImage(token, "CellDesigner_SBML", "svg", content).toString();
- String result2 = convertRestImpl.converToImage(token, "CellDesigner_SBML",
- "lcsb.mapviewer.converter.graphics.SvgImageGenerator", content).toString();
-
- assertTrue(result.equals(result2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- */
-
+ *
+ * @Test public void testCelDesigner2Svg2() throws Exception { try { File file =
+ * new File("testFiles/convert/sample-cd.xml"); String content =
+ * FileUtils.readFileToString(file); String result =
+ * convertRestImpl.converToImage(token, "CellDesigner_SBML", "svg",
+ * content).toString(); String result2 = convertRestImpl.converToImage(token,
+ * "CellDesigner_SBML", "lcsb.mapviewer.converter.graphics.SvgImageGenerator",
+ * content).toString();
+ *
+ * assertTrue(result.equals(result2));
+ *
+ * } catch (Exception e) { e.printStackTrace(); throw e; } }
+ */
+
@SuppressWarnings("unchecked")
private List<String> extractIdsFromOutputs(Map<String, Object> infoObject) {
- List<String> ids = new ArrayList<>();
- for (Map<String, List<String>> o : (List<Map<String, List<String>>>) infoObject.get("outputs")) {
- ids.add(o.get("available_names").get(0));
- }
- return ids;
+ List<String> ids = new ArrayList<>();
+ for (Map<String, List<String>> o : (List<Map<String, List<String>>>) infoObject.get("outputs")) {
+ ids.add(o.get("available_names").get(0));
+ }
+ return ids;
}
-
- private void test2All(String content, String converter)
- throws SBMLException, SecurityException, InvalidInputDataExecption, InconsistentModelException,
- IOException, ConverterException, XMLStreamException, DrawingException, QueryException
- {
-
- Map<String, Object> info = convertRestImpl.getInformation(token);
- Map<String, Object> infoImage = convertRestImpl.getInformationImage(token);
-
- List<String> targets = new ArrayList<>();
-
- targets.addAll(extractIdsFromOutputs(info));
- for (String target: targets) {
- String result = convertRestImpl.convert(token, converter, target, content).toString();
- assertTrue(result.length() > 0);
- }
-
- targets.clear();
- targets.addAll(extractIdsFromOutputs(infoImage));
- for (String target: targets) {
- String result = convertRestImpl.converToImage(token, converter, target, content).toString();
- assertTrue(result.length() > 0);
- }
+
+ private void test2All(String content, String converter)
+ throws SBMLException, SecurityException, InvalidInputDataExecption, InconsistentModelException,
+ IOException, ConverterException, XMLStreamException, DrawingException, QueryException {
+
+ Map<String, Object> info = convertRestImpl.getInformation(token);
+ Map<String, Object> infoImage = convertRestImpl.getInformationImage(token);
+
+ List<String> targets = new ArrayList<>();
+
+ targets.addAll(extractIdsFromOutputs(info));
+ for (String target : targets) {
+ String result = convertRestImpl.convert(token, converter, target, content).toString();
+ assertTrue(result.length() > 0);
+ }
+
+ targets.clear();
+ targets.addAll(extractIdsFromOutputs(infoImage));
+ for (String target : targets) {
+ String result = convertRestImpl.converToImage(token, converter, target, content).toString();
+ assertTrue(result.length() > 0);
+ }
}
-
+
@Test
public void testCelDesigner2All() throws Exception {
-
- try {
- File file = new File("testFiles/convert/sample-cd.xml");
- String content = FileUtils.readFileToString(file);
- test2All(content, "CellDesigner_SBML");
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+
+ try {
+ File file = new File("testFiles/convert/sample-cd.xml");
+ String content = FileUtils.readFileToString(file);
+ test2All(content, "CellDesigner_SBML");
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
}
-
+
@Test
public void testSbml2All() throws Exception {
-
- try {
- File file = new File("testFiles/convert/sample-sbml.xml");
- String content = FileUtils.readFileToString(file);
- test2All(content, "SBML");
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+
+ try {
+ File file = new File("testFiles/convert/sample-sbml.xml");
+ String content = FileUtils.readFileToString(file);
+ test2All(content, "SBML");
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
}
-
+
@Test
public void testSbgn2All() throws Exception {
-
- try {
- File file = new File("testFiles/convert/sample.sbgn");
- String content = FileUtils.readFileToString(file);
- test2All(content, "SBGN-ML");
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+
+ try {
+ File file = new File("testFiles/convert/sample.sbgn");
+ String content = FileUtils.readFileToString(file);
+ test2All(content, "SBGN-ML");
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
}
-
+
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesControllerTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesControllerTest.java
index 5b1aa78aef09f05c7a9230090d1049f0a9fe0a36..29e64d174a28381a8941ccd31f599bd8156db7b9 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesControllerTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesControllerTest.java
@@ -2,11 +2,10 @@ package lcsb.mapviewer.api.projects.models.bioEntities;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyString;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyString;
import java.awt.geom.Point2D;
-import java.util.ArrayList;
import java.util.List;
import java.util.Map;
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
index dcc5bfd727af2ba1b4e2c24f8f2ec9967d441932..a536521da9ea4706d6b94948d982d0286b74e17f 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
@@ -12,7 +12,6 @@ import java.util.Map;
import java.util.Set;
import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
@@ -25,7 +24,6 @@ import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.SearchIndex;
-import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.reaction.Reaction;
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/mirna/MiRNAService.java b/service/src/main/java/lcsb/mapviewer/services/search/mirna/MiRNAService.java
index d63e6838cc989d2c20cc499476f37bde37a931fa..67b670d25c880a6bb854078242ca273087642cab 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/mirna/MiRNAService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/mirna/MiRNAService.java
@@ -7,10 +7,7 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
-import javax.annotation.PostConstruct;
-
import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
index 4a95ab7f9b6ec398b7e2265f8a82287ed0cb765f..3fd35f90e71b6aff2bbd283a057c2f90e41121c6 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
@@ -23,8 +23,6 @@ import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
@@ -153,19 +151,19 @@ public class SearchServiceTest extends ServiceTestFunctions {
}
}
- @Test
- public void testSearchByUnknwonElementId() throws Exception {
- try {
- Model model = createFullModel();
- Element element =model.getElements().iterator().next();
- element.setId(907);
- List<BioEntity> global = searchService.searchByQuery(model, "species:90111117", 50, null, "127.0.0.1");
- assertEquals(0, global.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
+ @Test
+ public void testSearchByUnknwonElementId() throws Exception {
+ try {
+ Model model = createFullModel();
+ Element element = model.getElements().iterator().next();
+ element.setId(907);
+ List<BioEntity> global = searchService.searchByQuery(model, "species:90111117", 50, null, "127.0.0.1");
+ assertEquals(0, global.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
}
+ }
@Test
public void testSearchByName4() throws Exception {