diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index e2640f0b3ecfafcf9d143f661a8d4dd6807b37c1..12f391a07b0474df7bfcbeda5e93ab8ccbc328e1 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -114,6 +114,8 @@ public class ComplexZipConverter {
ZipEntry entry = entries.nextElement();
if (!entry.isDirectory()) {
ZipEntryFile zef = params.getEntry(entry.getName());
+ logger.debug(entry.getName());
+ logger.debug(zef);
if (zef instanceof ModelZipEntryFile) {
ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
InputStream is = zipFile.getInputStream(entry);
@@ -133,7 +135,7 @@ public class ComplexZipConverter {
// imageEntries.add((ImageZipEntryFile) zef);
} else if (zef instanceof DataMiningZipEntryFile) {
dataMiningSets.add(dataMiningZipEntryToDataMiningSet(zipFile, entry, (DataMiningZipEntryFile) zef));
- } else {
+ } else if (!isIgnoredFile(entry.getName())) {
throw new NotImplementedException("Unknwon entry type: " + zef.getClass());
}
}
@@ -181,6 +183,19 @@ public class ComplexZipConverter {
}
}
+ protected boolean isIgnoredFile(String name) {
+ if (name == null) {
+ return true;
+ } else if (name.isEmpty()) {
+ return true;
+ } else if (name.startsWith(".DS_Store")) {
+ return true;
+ } else if (name.startsWith("__MACOSX")) {
+ return true;
+ }
+ return false;
+ }
+
/**
* Process a single reaction in mapping file (transfomring reaction into
* connection between submodels).
@@ -278,13 +293,12 @@ public class ComplexZipConverter {
String root = null;
String mapping = null;
- logger.debug(params.getFilenames());
while (entries.hasMoreElements()) {
ZipEntry entry = entries.nextElement();
if (!entry.isDirectory()) {
String name = entry.getName();
ZipEntryFile zef = params.getEntry(name);
- if (zef == null) {
+ if (zef == null && !isIgnoredFile(name)) {
throw new InvalidArgumentException("No information found in params about file: " + name);
}
if (zef instanceof ModelZipEntryFile) {
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
index 6d8f7acb690f1c8cda2b868de108b1c462ae506a..4d768d5aa99d4578a1ffe8b58f9b0efd74d7c9e1 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
@@ -1,8 +1,10 @@
package lcsb.mapviewer.converter;
import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
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 java.io.File;
@@ -35,461 +37,494 @@ import lcsb.mapviewer.model.map.species.Species;
public class ComplexZipConverterTest {
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ComplexZipConverterTest.class);
-
- private abstract class AbstractConverter implements IConverter {
-
- }
-
- private interface InterfaceConverter extends IConverter {
-
- }
-
- public static class MockConverter implements IConverter {
-
- @Override
- public Model createModel(ConverterParams params) {
- Model result = new ModelFullIndexed(null);
-
- Species sa1 = new GenericProtein("sa1");
- result.addElement(sa1);
-
- Species sa2 = new GenericProtein("sa2");
- result.addElement(sa2);
-
- Species sa3 = new GenericProtein("sa3");
- result.addElement(sa3);
-
- Species sa4 = new Phenotype("sa4");
- result.addElement(sa4);
-
- Complex ca1 = new Complex("ca1");
- ca1.setName("main");
- result.addElement(ca1);
- Species sa5 = new GenericProtein("sa5");
- sa5.setName("sa1");
- result.addElement(sa5);
- ca1.addSpecies(sa5);
- Species sa6 = new Phenotype("sa6");
- sa6.setName("sa4");
- result.addElement(sa6);
- ca1.addSpecies(sa6);
-
- Complex ca2 = new Complex("ca2");
- ca2.setName("s1");
- result.addElement(ca2);
- Species sa7 = new GenericProtein("sa7");
- sa7.setName("sa1");
- result.addElement(sa7);
- ca2.addSpecies(sa7);
-
- Complex ca3 = new Complex("cs3");
- ca3.setName("s2");
- result.addElement(ca3);
-
- Complex ca4 = new Complex("cs4");
- ca4.setName("s3");
- result.addElement(ca4);
-
- Reaction r1 = new TransportReaction("re1");
- r1.addReactant(new Reactant(sa5));
- r1.addProduct(new Product(sa7));
- result.addReaction(r1);
-
- Reaction r2 = new TransportReaction("re2");
- r2.addReactant(new Reactant(sa6));
- r2.addProduct(new Product(ca3));
- result.addReaction(r2);
-
- Reaction r3 = new TransportReaction("re3");
- r3.addReactant(new Reactant(sa7));
- r3.addProduct(new Product(ca4));
- result.addReaction(r3);
- return result;
- }
-
- @Override
- public InputStream exportModelToInputStream(Model model) throws InconsistentModelException {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public File exportModelToFile(Model model, String filePath) throws InconsistentModelException {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public String getCommonName() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public MimeType getMimeType() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public String getFileExtension() {
- // TODO Auto-generated method stub
- return null;
- }
-
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() throws Exception {
- try {
- new ComplexZipConverter(AbstractConverter.class);
- fail("Exception expected");
-
- } catch (InvalidClassException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testConstructor2() throws Exception {
- try {
- new ComplexZipConverter(InterfaceConverter.class);
- fail("Exception expected");
-
- } catch (InvalidClassException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testConstructor3() throws Exception {
- try {
- new ComplexZipConverter(MockConverter.class);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testParamsOk() throws Exception {
- try {
- ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/complex_model.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
- params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
- params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
- params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
- params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- Model model = converter.createModel(params);
- assertNotNull(model);
- assertEquals("main", model.getName());
- assertEquals(3, model.getSubmodelConnections().size());
-
- Model s1Model = null;
- Model s2Model = null;
- Model s3Model = null;
-
- for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
- if (submodel.getName().equals("s1")) {
- s1Model = submodel.getSubmodel().getModel();
- }
- if (submodel.getName().equals("s2")) {
- s2Model = submodel.getSubmodel().getModel();
- }
- if (submodel.getName().equals("s3")) {
- s3Model = submodel.getSubmodel().getModel();
- }
- }
- assertNotNull(s1Model);
- assertNotNull(s2Model);
- assertNotNull(s3Model);
-
- Element al1 = model.getElementByElementId("sa1");
- assertNotNull(al1.getSubmodel());
- assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
- assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
-
- Element al2 = model.getElementByElementId("sa2");
- assertNull(al2.getSubmodel());
-
- Element al4 = model.getElementByElementId("sa4");
- assertNotNull(al4.getSubmodel());
- assertEquals(SubmodelType.PATHWAY, al4.getSubmodel().getType());
- assertEquals(s2Model, al4.getSubmodel().getSubmodel().getModel());
-
- Element s1_al1 = s1Model.getElementByElementId("sa1");
- assertNotNull(s1_al1.getSubmodel());
- assertEquals(SubmodelType.DOWNSTREAM_TARGETS, s1_al1.getSubmodel().getType());
- assertEquals(s3Model, s1_al1.getSubmodel().getSubmodel().getModel());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testChangeModelZipEntry() throws Exception {
- try {
- ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/complex_model.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
- params.entry(new ModelZipEntryFile("s1.xml", "s12", false, false, SubmodelType.DOWNSTREAM_TARGETS));
- params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
- params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
- params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- Model model = converter.createModel(params);
- assertNotNull(model);
- assertEquals("main", model.getName());
- assertEquals(3, model.getSubmodelConnections().size());
-
- Model s1Model = null;
- Model s2Model = null;
- Model s3Model = null;
-
- for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
- if (submodel.getName().equals("s12")) {
- s1Model = submodel.getSubmodel().getModel();
- }
- if (submodel.getName().equals("s2")) {
- s2Model = submodel.getSubmodel().getModel();
- }
- if (submodel.getName().equals("s3")) {
- s3Model = submodel.getSubmodel().getModel();
- }
- }
- assertNotNull(s1Model);
- assertNotNull(s2Model);
- assertNotNull(s3Model);
-
- Element al1 = model.getElementByElementId("sa1");
- assertNotNull(al1.getSubmodel());
- assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
- assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
-
- Element al2 = model.getElementByElementId("sa2");
- assertNull(al2.getSubmodel());
-
- Element al4 = model.getElementByElementId("sa4");
- assertNotNull(al4.getSubmodel());
- assertEquals(SubmodelType.PATHWAY, al4.getSubmodel().getType());
- assertEquals(s2Model, al4.getSubmodel().getSubmodel().getModel());
-
- Element s1_al1 = s1Model.getElementByElementId("sa1");
- assertNotNull(s1_al1.getSubmodel());
- assertEquals(SubmodelType.DOWNSTREAM_TARGETS, s1_al1.getSubmodel().getType());
- assertEquals(s3Model, s1_al1.getSubmodel().getSubmodel().getModel());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testParamsMissing() throws Exception {
- try {
- ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/complex_model.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
- params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
- params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
- params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- try {
- converter.createModel(params);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testParamsInvalid1() throws Exception {
- try {
- // two mains
- ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/complex_model.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
- params.entry(new ModelZipEntryFile("s1.xml", "s1", true, false, SubmodelType.DOWNSTREAM_TARGETS));
- params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
- params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
- params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- try {
- converter.createModel(params);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testParamsInvalid2() throws Exception {
- try {
- // zero mains
- ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/complex_model.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", false, false, null));
- params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
- params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
- params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
- params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- try {
- converter.createModel(params);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testParamsInvalid3() throws Exception {
- try {
- // two mappings
- ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/complex_model.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
- params.entry(new ModelZipEntryFile("s1.xml", "s1", false, true, SubmodelType.DOWNSTREAM_TARGETS));
- params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
- params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
- params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- try {
- converter.createModel(params);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testParamsMissingMapping() throws Exception {
- try {
- // zero mappings (should be ok)
- ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/complex_model.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
- params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
- params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
- params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
- params.entry(new ModelZipEntryFile("mapping.xml", "", false, false, null));
- Model model = converter.createModel(params);
-
- assertNotNull(model);
-
- assertEquals(4, model.getSubmodelConnections().size());
-
- for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
- if (submodel.getName().equals("s1")) {
- assertEquals(SubmodelType.DOWNSTREAM_TARGETS, submodel.getType());
- } else if (submodel.getName().equals("s2")) {
- assertEquals(SubmodelType.PATHWAY, submodel.getType());
- } else if (submodel.getName().equals("s3")) {
- assertEquals(SubmodelType.UNKNOWN, submodel.getType());
- } else if (submodel.getName().equals("mapping")) {
- assertEquals(SubmodelType.UNKNOWN, submodel.getType());
- }
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testTooManyParams() throws Exception {
- try {
- // zero mappings (should be ok)
- ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/complex_model.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
- params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
- params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
- params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
- params.entry(new ModelZipEntryFile("mapping.xml", "", false, false, null));
- params.entry(new ModelZipEntryFile("blabla.xml", "s3", false, false, SubmodelType.UNKNOWN));
- try {
- converter.createModel(params);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidMappingFile() throws Exception {
- try {
- // zero mappings (should be ok)
- ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(new ZipFile("testFiles/invalid_mapping.zip"));
- params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
- params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- try {
- converter.createModel(params);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ComplexZipConverterTest.class);
+
+ private abstract class AbstractConverter implements IConverter {
+
+ }
+
+ private interface InterfaceConverter extends IConverter {
+
+ }
+
+ public static class MockConverter implements IConverter {
+
+ @Override
+ public Model createModel(ConverterParams params) {
+ Model result = new ModelFullIndexed(null);
+
+ Species sa1 = new GenericProtein("sa1");
+ result.addElement(sa1);
+
+ Species sa2 = new GenericProtein("sa2");
+ result.addElement(sa2);
+
+ Species sa3 = new GenericProtein("sa3");
+ result.addElement(sa3);
+
+ Species sa4 = new Phenotype("sa4");
+ result.addElement(sa4);
+
+ Complex ca1 = new Complex("ca1");
+ ca1.setName("main");
+ result.addElement(ca1);
+ Species sa5 = new GenericProtein("sa5");
+ sa5.setName("sa1");
+ result.addElement(sa5);
+ ca1.addSpecies(sa5);
+ Species sa6 = new Phenotype("sa6");
+ sa6.setName("sa4");
+ result.addElement(sa6);
+ ca1.addSpecies(sa6);
+
+ Complex ca2 = new Complex("ca2");
+ ca2.setName("s1");
+ result.addElement(ca2);
+ Species sa7 = new GenericProtein("sa7");
+ sa7.setName("sa1");
+ result.addElement(sa7);
+ ca2.addSpecies(sa7);
+
+ Complex ca3 = new Complex("cs3");
+ ca3.setName("s2");
+ result.addElement(ca3);
+
+ Complex ca4 = new Complex("cs4");
+ ca4.setName("s3");
+ result.addElement(ca4);
+
+ Reaction r1 = new TransportReaction("re1");
+ r1.addReactant(new Reactant(sa5));
+ r1.addProduct(new Product(sa7));
+ result.addReaction(r1);
+
+ Reaction r2 = new TransportReaction("re2");
+ r2.addReactant(new Reactant(sa6));
+ r2.addProduct(new Product(ca3));
+ result.addReaction(r2);
+
+ Reaction r3 = new TransportReaction("re3");
+ r3.addReactant(new Reactant(sa7));
+ r3.addProduct(new Product(ca4));
+ result.addReaction(r3);
+ return result;
+ }
+
+ @Override
+ public InputStream exportModelToInputStream(Model model) throws InconsistentModelException {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public File exportModelToFile(Model model, String filePath) throws InconsistentModelException {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getCommonName() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public MimeType getMimeType() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getFileExtension() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor() throws Exception {
+ try {
+ new ComplexZipConverter(AbstractConverter.class);
+ fail("Exception expected");
+
+ } catch (InvalidClassException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testConstructor2() throws Exception {
+ try {
+ new ComplexZipConverter(InterfaceConverter.class);
+ fail("Exception expected");
+
+ } catch (InvalidClassException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testConstructor3() throws Exception {
+ try {
+ new ComplexZipConverter(MockConverter.class);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testParamsOk() throws Exception {
+ try {
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+ params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+ params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+ params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+ Model model = converter.createModel(params);
+ assertNotNull(model);
+ assertEquals("main", model.getName());
+ assertEquals(3, model.getSubmodelConnections().size());
+
+ Model s1Model = null;
+ Model s2Model = null;
+ Model s3Model = null;
+
+ for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
+ if (submodel.getName().equals("s1")) {
+ s1Model = submodel.getSubmodel().getModel();
+ }
+ if (submodel.getName().equals("s2")) {
+ s2Model = submodel.getSubmodel().getModel();
+ }
+ if (submodel.getName().equals("s3")) {
+ s3Model = submodel.getSubmodel().getModel();
+ }
+ }
+ assertNotNull(s1Model);
+ assertNotNull(s2Model);
+ assertNotNull(s3Model);
+
+ Element al1 = model.getElementByElementId("sa1");
+ assertNotNull(al1.getSubmodel());
+ assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
+ assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
+
+ Element al2 = model.getElementByElementId("sa2");
+ assertNull(al2.getSubmodel());
+
+ Element al4 = model.getElementByElementId("sa4");
+ assertNotNull(al4.getSubmodel());
+ assertEquals(SubmodelType.PATHWAY, al4.getSubmodel().getType());
+ assertEquals(s2Model, al4.getSubmodel().getSubmodel().getModel());
+
+ Element s1_al1 = s1Model.getElementByElementId("sa1");
+ assertNotNull(s1_al1.getSubmodel());
+ assertEquals(SubmodelType.DOWNSTREAM_TARGETS, s1_al1.getSubmodel().getType());
+ assertEquals(s3Model, s1_al1.getSubmodel().getSubmodel().getModel());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testChangeModelZipEntry() throws Exception {
+ try {
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+ params.entry(new ModelZipEntryFile("s1.xml", "s12", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+ params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+ params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+ Model model = converter.createModel(params);
+ assertNotNull(model);
+ assertEquals("main", model.getName());
+ assertEquals(3, model.getSubmodelConnections().size());
+
+ Model s1Model = null;
+ Model s2Model = null;
+ Model s3Model = null;
+
+ for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
+ if (submodel.getName().equals("s12")) {
+ s1Model = submodel.getSubmodel().getModel();
+ }
+ if (submodel.getName().equals("s2")) {
+ s2Model = submodel.getSubmodel().getModel();
+ }
+ if (submodel.getName().equals("s3")) {
+ s3Model = submodel.getSubmodel().getModel();
+ }
+ }
+ assertNotNull(s1Model);
+ assertNotNull(s2Model);
+ assertNotNull(s3Model);
+
+ Element al1 = model.getElementByElementId("sa1");
+ assertNotNull(al1.getSubmodel());
+ assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
+ assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
+
+ Element al2 = model.getElementByElementId("sa2");
+ assertNull(al2.getSubmodel());
+
+ Element al4 = model.getElementByElementId("sa4");
+ assertNotNull(al4.getSubmodel());
+ assertEquals(SubmodelType.PATHWAY, al4.getSubmodel().getType());
+ assertEquals(s2Model, al4.getSubmodel().getSubmodel().getModel());
+
+ Element s1_al1 = s1Model.getElementByElementId("sa1");
+ assertNotNull(s1_al1.getSubmodel());
+ assertEquals(SubmodelType.DOWNSTREAM_TARGETS, s1_al1.getSubmodel().getType());
+ assertEquals(s3Model, s1_al1.getSubmodel().getSubmodel().getModel());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testParamsMissing() throws Exception {
+ try {
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+ params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+ params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+ try {
+ converter.createModel(params);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testParamsInvalid1() throws Exception {
+ try {
+ // two mains
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+ params.entry(new ModelZipEntryFile("s1.xml", "s1", true, false, SubmodelType.DOWNSTREAM_TARGETS));
+ params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+ params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+ try {
+ converter.createModel(params);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testParamsInvalid2() throws Exception {
+ try {
+ // zero mains
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", false, false, null));
+ params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+ params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+ params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+ try {
+ converter.createModel(params);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testParamsInvalid3() throws Exception {
+ try {
+ // two mappings
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+ params.entry(new ModelZipEntryFile("s1.xml", "s1", false, true, SubmodelType.DOWNSTREAM_TARGETS));
+ params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+ params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+ try {
+ converter.createModel(params);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testParamsMissingMapping() throws Exception {
+ try {
+ // zero mappings (should be ok)
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+ params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+ params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+ params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ params.entry(new ModelZipEntryFile("mapping.xml", "", false, false, null));
+ Model model = converter.createModel(params);
+
+ assertNotNull(model);
+
+ assertEquals(4, model.getSubmodelConnections().size());
+
+ for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
+ if (submodel.getName().equals("s1")) {
+ assertEquals(SubmodelType.DOWNSTREAM_TARGETS, submodel.getType());
+ } else if (submodel.getName().equals("s2")) {
+ assertEquals(SubmodelType.PATHWAY, submodel.getType());
+ } else if (submodel.getName().equals("s3")) {
+ assertEquals(SubmodelType.UNKNOWN, submodel.getType());
+ } else if (submodel.getName().equals("mapping")) {
+ assertEquals(SubmodelType.UNKNOWN, submodel.getType());
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testTooManyParams() throws Exception {
+ try {
+ // zero mappings (should be ok)
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+ params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+ params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+ params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ params.entry(new ModelZipEntryFile("mapping.xml", "", false, false, null));
+ params.entry(new ModelZipEntryFile("blabla.xml", "s3", false, false, SubmodelType.UNKNOWN));
+ try {
+ converter.createModel(params);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidMappingFile() throws Exception {
+ try {
+ // zero mappings (should be ok)
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(new ZipFile("testFiles/invalid_mapping.zip"));
+ params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+ params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+ try {
+ converter.createModel(params);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIsIgnoredFileForMac() throws Exception {
+ try {
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
+ assertTrue(converter.isIgnoredFile("__MACOSX/.desc"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIsIgnoredFileForOldMacEntries() throws Exception {
+ try {
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
+ assertTrue(converter.isIgnoredFile(".DS_Store/.desc"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIsIgnoredFileForValidFiles() throws Exception {
+ try {
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
+ assertFalse(converter.isIgnoredFile("mapping.xml"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
index 64679faba0f0d005725549c27637b2b8674edd21..d9eb87fa1d9a5df2e2082ba39e432538396b986d 100644
--- a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
@@ -159,7 +159,7 @@ AddProjectDialog.prototype.createGeneralTabContent = function () {
name: "project-file"
});
fileInput.addEventListener("change", function () {
- return self.callListeners("onFileUpload", fileInput.files[0]);
+ return self.callListeners("onFileUpload", fileInput.files[0]).then(null, GuiConnector.alert);
}, false);
self.addListener("onFileUpload", function (e) {
var file = e.arg;
@@ -936,6 +936,8 @@ AddProjectDialog.prototype.createZipEntry = function (jsZipEntry, zipObject) {
data.description = "";
}
});
+ } else if (this.isIgnoredZipEntry(filename)) {
+ type = undefined;
} else if (filename.indexOf("\\") === -1 && filename.indexOf("/") === -1) {
type = "MAP";
data.root = true;
@@ -972,7 +974,11 @@ AddProjectDialog.prototype.createZipEntry = function (jsZipEntry, zipObject) {
}
return processingPromise.then(function () {
- return new ZipEntry({filename: filename, type: type, data: data});
+ if (type !== undefined) {
+ return new ZipEntry({filename: filename, type: type, data: data});
+ } else {
+ return null;
+ }
});
};
@@ -986,6 +992,15 @@ AddProjectDialog.prototype.setZipEntries = function (entries) {
};
+AddProjectDialog.prototype.isIgnoredZipEntry = function (filename) {
+ var lowercaseString = filename.toLowerCase();
+ if (lowercaseString.startsWith("__macosx") || lowercaseString.startsWith(".ds_store")) {
+ return true;
+ } else {
+ return false;
+ }
+};
+
AddProjectDialog.prototype.getEntryByFilename = function (filename) {
var self = this;
var entries = self.getZipEntries();
diff --git a/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js b/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js
index 97133089ed9a036b5aff78fde3454033eca57107..f76d54a2d73f8d2c9ffd53312fc935a7d159137d 100644
--- a/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js
+++ b/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js
@@ -172,7 +172,7 @@ describe('AddProjectDialog', function () {
dialog.setProjectId("(invalid id)");
return dialog.checkValidity().then(function () {
assert.notOk("Expected validity to reject");
- }).catch(function(error){
+ }).catch(function (error) {
assert.ok(error instanceof ValidationError);
});
}).then().finally(function () {
@@ -198,4 +198,38 @@ describe('AddProjectDialog', function () {
});
});
+ describe('isIgnoredZipEntry', function () {
+ it('valid entry', function () {
+ var dialog = new AddProjectDialog({
+ element: testDiv,
+ customMap: null
+ });
+
+ assert.notOk(dialog.isIgnoredZipEntry("images/a.png"));
+ assert.notOk(dialog.isIgnoredZipEntry("main.xml"));
+ return dialog.destroy();
+ });
+ it('invalid MAC OS entry', function () {
+ var dialog = new AddProjectDialog({
+ element: testDiv,
+ customMap: null
+ });
+
+ // noinspection SpellCheckingInspection
+ assert.ok(dialog.isIgnoredZipEntry("__MACOSX/.desc"));
+ assert.ok(dialog.isIgnoredZipEntry("__macosx/.desc"));
+ return dialog.destroy();
+ });
+ it('invalid old MAC OS entry', function () {
+ var dialog = new AddProjectDialog({
+ element: testDiv,
+ customMap: null
+ });
+
+ assert.ok(dialog.isIgnoredZipEntry(".DS_Store/.desc"));
+ assert.ok(dialog.isIgnoredZipEntry(".ds_store/.desc"));
+ return dialog.destroy();
+ });
+ });
+
});
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 8a2bb71c2e8b3afdb4e8146548fa511a5fe72864..1fd990051d085ab60b4805162da30871cabcecac 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
@@ -616,4 +616,6 @@ public interface Model {
void addFunction(SbmlFunction sbmlFunction);
SbmlArgument getFunctionById(String id);
+
+ void removeReactions(Collection<Reaction> reactions);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index 4d2d833420676c82b172552749a3ab298e50c014..893134e99c718bcccc81398d58152bf607d86a64 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
@@ -734,4 +734,13 @@ public class ModelFullIndexed implements Model {
}
return null;
}
+
+ @Override
+ public void removeReactions(Collection<Reaction> reactions) {
+ Set<Reaction> reactionsToRemove = new HashSet<>();
+ reactionsToRemove.addAll(reactions);
+ for (Reaction reaction : reactionsToRemove) {
+ removeReaction(reaction);
+ }
+ }
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java
index ad2bd21b548a27e2cf1ea9f15fa5b55b87ac04b4..e65556f1044b7cf57849214923809461a2670647 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java
@@ -35,495 +35,506 @@ import lcsb.mapviewer.services.utils.data.ExportFileType;
import lcsb.mapviewer.services.view.PubmedAnnotatedElementsView;
public class ExporterServiceTest extends ServiceTestFunctions {
- Logger logger = Logger.getLogger(ExporterServiceTest.class);
- @Autowired
- IExporterService exporter2;
-
- ExporterService exporter;
-
- @Before
- public void setUp() throws Exception {
- exporter = (ExporterService) exporter2;
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetExportSpeciesStringForTabSeparatedFile() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
- ExportColumn columns[] = { ExportColumn.NAME, ExportColumn.ID, ExportColumn.COMPONENT_NAME, ExportColumn.COMPARTMENT_NAME, ExportColumn.TYPE };
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED);
-
- // full export (all elements)
- String string = exporter.getExportSpeciesString(params);
- String lines[] = string.split("\n");
- assertTrue("Not enough elements in the result file", lines.length > 1);
-
- String response = lines[0];
- String textColumns[] = response.split("\t");
- assertEquals(5, textColumns.length);
-
- // only proteins for self-made modules
- new CreateHierarchyCommand(model, 8, 80).execute();
- string = exporter.getExportSpeciesString(params.type(GenericProtein.class));
- lines = string.split("\n");
- assertTrue(lines.length > 1);
-
- boolean differenceBetweenComponentCompartmnet = false;
- int lineCount = 0;
- for (String string2 : lines) {
- if (lineCount == 0) {
- textColumns = string2.split("\t");
- assertEquals(ExportColumn.TYPE.getTitle(), textColumns[4]);
- } else {
- textColumns = string2.split("\t");
- assertEquals(GenericProtein.class.getSimpleName(), textColumns[4]);
- if (!textColumns[2].equalsIgnoreCase(textColumns[3])) {
- differenceBetweenComponentCompartmnet = true;
- }
- }
- lineCount++;
- }
- assertTrue(differenceBetweenComponentCompartmnet);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDuplicatesInGetExportSpeciesString() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export_duplicate_elements.xml", false);
- ExportColumn columns[] = { ExportColumn.NAME, ExportColumn.COMPONENT_NAME, ExportColumn.TYPE };
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED);
-
- // full export (all elements)
- String string = exporter.getExportSpeciesString(params);
-
- String lines[] = string.split("\n");
- Set<String> uniqueNames = new HashSet<String>();
- for (String string2 : lines) {
- uniqueNames.add(string2);
- }
- assertEquals(uniqueNames.size(), lines.length);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetExportStringForOneSpecies_Complex() {
- try {
- Model model = getModelForFile("testFiles/export/hsp70.xml", true);
-
- Species alias = (Species) model.getElementByElementId("csa1");
- ExportColumn columns[] = { ExportColumn.NAME };
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
- column(columns).//
- complexElementsName(false).//
- fileType(ExportFileType.TAB_SEPARATED);
-
- List<String> elements = exporter.getExportStringForOneSpecies(alias, params);
- assertTrue(elements.contains("HSP70:chaperon"));
-
- // now the results are concatenated children
- params.complexElementsName(true);
-
- elements = exporter.getExportStringForOneSpecies(alias, params);
- assertTrue(elements.size() > 0);
- String string = elements.get(0);
- assertFalse(string.equals("HSP70:chaperon"));
- assertTrue(string.contains("HSP70"));
- assertTrue(string.contains("STUB1"));
- assertTrue(string.contains("DNAJB2"));
- assertTrue(string.contains("BAG1"));
-
- // and now check complexes with mix of proteins and molecules
- alias = (Species) model.getElementByElementId("csa3");
-
- elements = exporter.getExportStringForOneSpecies(alias, params);
- assertTrue(elements.size() > 0);
- string = elements.get(0);
- assertTrue(string.contains("UBA1"));
- assertTrue(string.contains("UBA6"));
- assertTrue(string.contains("AMP"));
-
- elements = exporter.getExportStringForOneSpecies(alias, params.type(Protein.class));
- assertTrue(elements.size() > 0);
- string = elements.get(0);
- assertTrue(string.contains("UBA1"));
- assertTrue(string.contains("UBA6"));
- assertFalse(string.contains("AMP"));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occured");
- }
- }
-
- @Test
- public void testGetExportStringForOneReaction() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/reaction.xml", false);
- Set<Compartment> aliases = new HashSet<>();
- for (Compartment alias : model.getCompartments()) {
- if (alias.getName().equalsIgnoreCase("Dopamine loaded synaptic vesicle"))
- aliases.add(alias);
- }
-
- Reaction reaction = model.getReactionByReactionId("re2");
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
- fileType(ExportFileType.SIF).//
- type(Protein.class).//
- type(Complex.class).//
- fileType(ExportFileType.SIF).//
- complexElementsName(false).//
- excluded(aliases);
-
- String string = exporter.getExportSingleInteractionString(reaction, params).get(0);
- assertNotNull(string);
- assertTrue(string.contains("Calcium channel:RIMBP:RIM:MUNC13:RAB"));
- assertTrue(string.contains("CSP:Hsc70:SGT"));
- assertTrue(string.contains("SNCA"));
- assertTrue(string.contains("trans-SNARE complex"));
- assertFalse(string.contains("VAMP2"));
-
- params = new IExporterService.ExporterParameters().model(model).fileType(ExportFileType.SIF).type(Complex.class).type(Protein.class);
- string = exporter.getExportSingleInteractionString(reaction, params).get(0);
- assertTrue(string.contains("VAMP2"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetExportStringForOneReactionInGeneral() {
- try {
- Model model = getModelForFile("testFiles/export/reaction.xml", true);
- Reaction reaction = model.getReactionByReactionId("re2");
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
- fileType(ExportFileType.SIF).//
- complexElementsName(false).//
- type(Complex.class).type(Protein.class);
- String string = exporter.getExportSingleInteractionString(reaction, params).get(0);
- assertNotNull(string);
- assertTrue(string.contains("Calcium channel:RIMBP:RIM:MUNC13:RAB"));
- assertTrue(string.contains("CSP:Hsc70:SGT"));
- assertTrue(string.contains("SNCA"));
- assertTrue(string.contains("trans-SNARE complex"));
- assertTrue(string.contains("SNAP25"));
- assertFalse(string.contains("RAB3A"));
-
- params.complexElementsName(true);
- string = exporter.getExportSingleInteractionString(reaction, params).get(0);
- assertFalse(string.contains("trans-SNARE complex"));
- assertTrue(string.contains("RAB3A"));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occured");
- }
-
- }
-
- @Test
- public void testGetExportStringForOneReactionInGeneralWithOnlyOneElement() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/reaction.xml", false);
- Reaction reaction = model.getReactionByReactionId("re11");
- model.getReactions().clear();
- model.addReaction(reaction);
- Set<Compartment> aliases = new HashSet<Compartment>();
- aliases.add((Compartment) model.getElementByElementId("ca1"));
- ExporterParameters params = new IExporterService.ExporterParameters()
- .model(model).fileType(ExportFileType.SIF).included("dopamine loaded synaptic vesicle");
- assertEquals(0, exporter.getExportSingleInteractionString(reaction, params).size());
-
- params = new IExporterService.ExporterParameters().model(model).fileType(ExportFileType.SIF);
- assertEquals(1, exporter.getExportSingleInteractionString(reaction, params).size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetExportSingleInteractionString_text() {
- try {
- Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
- for (Reaction reaction : model.getReactions()) {
- String str = exporter
- .getExportSingleInteractionString(
- reaction, new IExporterService.ExporterParameters().fileType(ExportFileType.TAB_SEPARATED).type(Species.class))
- .get(0);
-
- List<String> strings = new ArrayList<String>();
- strings.add(ReactionLineData.getByReactionType(reaction.getClass()).getCellDesignerString());
- strings.add(reaction.getIdReaction());
- for (ReactionNode node : reaction.getReactionNodes()) {
- strings.add(node.getElement().getName());
-
- }
- for (String string : strings) {
- assertTrue("Description \"" + str + "\" doesn't contain " + string + ". reactionId=" + reaction.getIdReaction(), str.contains(string));
- }
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occured");
- }
- }
-
- @Test
- public void testGetExportComponentAndCompartments() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/export_model.xml", false);
- new CreateHierarchyCommand(model, 7, 80).execute();
- ExporterParameters params = new IExporterService.ExporterParameters()
- .model(model).fileType(ExportFileType.TAB_SEPARATED).column(ExportColumn.NAME).column(ExportColumn.COMPONENT_NAME)
- .column(ExportColumn.COMPARTMENT_NAME);
-
- List<String> list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa1"), params);
- String desc = list.get(0);
- String compartment = desc.split("\t")[2];
- assertEquals("c1", compartment);
- String component = desc.split("\t")[1];
- assertEquals("Test3", component);
-
- list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa2"), params);
- desc = null;
- for (String string : list) {
- if (string.contains("Test 1")) {
- desc = string;
- }
- }
- compartment = desc.split("\t")[2];
- assertEquals("c2", compartment);
- component = desc.split("\t")[1];
- assertEquals("Test 1", component);
-
- for (String string : list) {
- if (string.contains("Test2")) {
- desc = string;
- }
- }
- compartment = desc.split("\t")[2];
- assertEquals("c2", compartment);
- component = desc.split("\t")[1];
- assertEquals("Test2", component);
-
- for (String string : list) {
- if (string.contains("Test3")) {
- desc = string;
- }
- }
- compartment = desc.split("\t")[2];
- assertEquals("c2", compartment);
- component = desc.split("\t")[1];
- assertEquals("Test3", component);
-
- list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa3"), params);
- boolean ok = false;
- for (String string : list) {
- if (string.split("\t")[2].equals("null") && string.split("\t")[1].equals("Test2")) {
- ok = true;
- }
- }
- assertTrue(ok);
-
- list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa4"), params);
- desc = list.get(0);
- compartment = desc.split("\t")[2];
- assertEquals("null", compartment);
- component = desc.split("\t")[1];
- assertEquals("Test3", component);
-
- list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa5"), params);
- desc = list.get(0);
- compartment = desc.split("\t")[2];
- assertEquals("c3", compartment);
- component = desc.split("\t")[1];
- assertEquals("null", component);
-
- list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa6"), params);
- desc = list.get(0);
- compartment = desc.split("\t")[2];
- assertEquals("null", compartment);
- component = desc.split("\t")[1];
- assertEquals("null", component);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetExportSpeciesStringForTabSeparatedFile2() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
- ExportColumn columns[] = { ExportColumn.NAME, ExportColumn.ID, ExportColumn.COMPONENT_NAME, ExportColumn.COMPARTMENT_NAME, ExportColumn.TYPE };
-
- ExporterParameters params = new IExporterService.ExporterParameters()
- .model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED).type(Object.class);
-
- // full export (all elements)
- String string = exporter.getExportSpeciesString(params);
- String lines[] = string.split("\n");
- assertTrue("Not enough elements in the result file", lines.length > 1);
-
- String response = lines[0];
- String textColumns[] = response.split("\t");
- assertEquals(columns.length, textColumns.length);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetExportCompartmentsString() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/export_compartments.xml", false);
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).fileType(ExportFileType.TAB_SEPARATED).type(Object.class);
-
- // full export (all compartments)
- String string = exporter.getExportCompartmentsString(params);
- String lines[] = string.split("\n");
- assertTrue("Not enough elements in the result file", lines.length >= 2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAllExportColumnsSpecies() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
- List<ExportColumn> columns = new ArrayList<ExportColumn>();
- for (ExportColumn column : ExportColumn.values()) {
- if (column.getClazz().isAssignableFrom(Species.class)) {
- columns.add(column);
- }
- }
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED);
-
- // full export (all elements)
- String string = exporter.getExportSpeciesString(params);
- assertNotNull(string);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAllExportColumnsReaction() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
- List<ExportColumn> columns = new ArrayList<ExportColumn>();
- for (ExportColumn column : ExportColumn.values()) {
- if (column.getClazz().isAssignableFrom(Reaction.class)) {
- columns.add(column);
- }
- }
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED);
-
- // full export (all elements)
- String string = exporter.getExportInteractionString(params);
- assertNotNull(string);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetTabSeparatedReaction() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/reaction.xml", false);
- Set<Compartment> aliases = new HashSet<>();
- for (Compartment alias : model.getCompartments()) {
- if (alias.getName().equalsIgnoreCase("Dopamine loaded synaptic vesicle"))
- aliases.add(alias);
- }
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
- fileType(ExportFileType.TAB_SEPARATED).//
- column(ExportColumn.REACTION_ID).//
- column(ExportColumn.REACTION_TYPE).//
- type(Species.class);
-
- String string = exporter.getExportInteractionString(params);
- assertTrue(string.indexOf("STATE_TRANSITION REACTANT") >= 0);
- assertTrue(string.indexOf("sa7") >= 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void test() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/new_line_file.xml", false);
- List<ExportColumn> columns = new ArrayList<ExportColumn>();
- for (ExportColumn column : ExportColumn.values()) {
- if (column.getClazz().isAssignableFrom(Species.class)) {
- columns.add(column);
- }
- }
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED);
-
- // full export (all elements)
- String string = exporter.getExportSpeciesString(params);
- String tmp[] = string.split("\n");
- for (String string2 : tmp) {
- assertTrue(string2, columns.size() <= string2.split("\t", -1).length);
- }
- assertNotNull(string);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPubmedSummary() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/reaction.xml", false);
- List<PubmedAnnotatedElementsView> result = exporter.getPublicationModelSummary(model);
- assertNotNull(result);
- for (PubmedAnnotatedElementsView pubmedAnnotatedElementsView : result) {
- assertNotNull(pubmedAnnotatedElementsView.getArticle());
- assertNotNull(pubmedAnnotatedElementsView.getArticle().getTitle());
- assertTrue(pubmedAnnotatedElementsView.getElements().size() > 0);
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Logger logger = Logger.getLogger(ExporterServiceTest.class);
+ @Autowired
+ IExporterService exporter2;
+
+ ExporterService exporter;
+
+ @Before
+ public void setUp() throws Exception {
+ exporter = (ExporterService) exporter2;
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetExportSpeciesStringForTabSeparatedFile() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
+ ExportColumn columns[] = { ExportColumn.NAME, ExportColumn.ID, ExportColumn.COMPONENT_NAME,
+ ExportColumn.COMPARTMENT_NAME, ExportColumn.TYPE };
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns)
+ .fileType(ExportFileType.TAB_SEPARATED);
+
+ // full export (all elements)
+ String string = exporter.getExportSpeciesString(params);
+ String lines[] = string.split("\n");
+ assertTrue("Not enough elements in the result file", lines.length > 1);
+
+ String response = lines[0];
+ String textColumns[] = response.split("\t");
+ assertEquals(5, textColumns.length);
+
+ // only proteins for self-made modules
+ new CreateHierarchyCommand(model, 8, 80).execute();
+ string = exporter.getExportSpeciesString(params.type(GenericProtein.class));
+ lines = string.split("\n");
+ assertTrue(lines.length > 1);
+
+ boolean differenceBetweenComponentCompartmnet = false;
+ int lineCount = 0;
+ for (String string2 : lines) {
+ if (lineCount == 0) {
+ textColumns = string2.split("\t");
+ assertEquals(ExportColumn.TYPE.getTitle(), textColumns[4]);
+ } else {
+ textColumns = string2.split("\t");
+ assertEquals(GenericProtein.class.getSimpleName(), textColumns[4]);
+ if (!textColumns[2].equalsIgnoreCase(textColumns[3])) {
+ differenceBetweenComponentCompartmnet = true;
+ }
+ }
+ lineCount++;
+ }
+ assertTrue(differenceBetweenComponentCompartmnet);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDuplicatesInGetExportSpeciesString() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export_duplicate_elements.xml", false);
+ ExportColumn columns[] = { ExportColumn.NAME, ExportColumn.COMPONENT_NAME, ExportColumn.TYPE };
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns)
+ .fileType(ExportFileType.TAB_SEPARATED);
+
+ // full export (all elements)
+ String string = exporter.getExportSpeciesString(params);
+
+ String lines[] = string.split("\n");
+ Set<String> uniqueNames = new HashSet<String>();
+ for (String string2 : lines) {
+ uniqueNames.add(string2);
+ }
+ assertEquals(uniqueNames.size(), lines.length);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetExportStringForOneSpecies_Complex() {
+ try {
+ Model model = getModelForFile("testFiles/export/hsp70.xml", true);
+
+ Species alias = (Species) model.getElementByElementId("csa1");
+ ExportColumn columns[] = { ExportColumn.NAME };
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
+ column(columns).//
+ complexElementsName(false).//
+ fileType(ExportFileType.TAB_SEPARATED);
+
+ List<String> elements = exporter.getExportStringForOneSpecies(alias, params);
+ assertTrue(elements.contains("HSP70:chaperon"));
+
+ // now the results are concatenated children
+ params.complexElementsName(true);
+
+ elements = exporter.getExportStringForOneSpecies(alias, params);
+ assertTrue(elements.size() > 0);
+ String string = elements.get(0);
+ assertFalse(string.equals("HSP70:chaperon"));
+ assertTrue(string.contains("HSP70"));
+ assertTrue(string.contains("STUB1"));
+ assertTrue(string.contains("DNAJB2"));
+ assertTrue(string.contains("BAG1"));
+
+ // and now check complexes with mix of proteins and molecules
+ alias = (Species) model.getElementByElementId("csa3");
+
+ elements = exporter.getExportStringForOneSpecies(alias, params);
+ assertTrue(elements.size() > 0);
+ string = elements.get(0);
+ assertTrue(string.contains("UBA1"));
+ assertTrue(string.contains("UBA6"));
+ assertTrue(string.contains("AMP"));
+
+ elements = exporter.getExportStringForOneSpecies(alias, params.type(Protein.class));
+ assertTrue(elements.size() > 0);
+ string = elements.get(0);
+ assertTrue(string.contains("UBA1"));
+ assertTrue(string.contains("UBA6"));
+ assertFalse(string.contains("AMP"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Exception occured");
+ }
+ }
+
+ @Test
+ public void testGetExportStringForOneReaction() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export/reaction.xml", false);
+ Set<Compartment> aliases = new HashSet<>();
+ for (Compartment alias : model.getCompartments()) {
+ if (alias.getName().equalsIgnoreCase("Dopamine loaded synaptic vesicle"))
+ aliases.add(alias);
+ }
+
+ Reaction reaction = model.getReactionByReactionId("re2");
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
+ fileType(ExportFileType.SIF).//
+ type(Protein.class).//
+ type(Complex.class).//
+ fileType(ExportFileType.SIF).//
+ complexElementsName(false).//
+ excluded(aliases);
+
+ String string = exporter.getExportSingleInteractionString(reaction, params).get(0);
+ assertNotNull(string);
+ assertTrue(string.contains("Calcium channel:RIMBP:RIM:MUNC13:RAB"));
+ assertTrue(string.contains("CSP:Hsc70:SGT"));
+ assertTrue(string.contains("SNCA"));
+ assertTrue(string.contains("trans-SNARE complex"));
+ assertFalse(string.contains("VAMP2"));
+
+ params = new IExporterService.ExporterParameters().model(model).fileType(ExportFileType.SIF).type(Complex.class)
+ .type(Protein.class);
+ string = exporter.getExportSingleInteractionString(reaction, params).get(0);
+ assertTrue(string.contains("VAMP2"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetExportStringForOneReactionInGeneral() {
+ try {
+ Model model = getModelForFile("testFiles/export/reaction.xml", true);
+ Reaction reaction = model.getReactionByReactionId("re2");
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
+ fileType(ExportFileType.SIF).//
+ complexElementsName(false).//
+ type(Complex.class).type(Protein.class);
+ String string = exporter.getExportSingleInteractionString(reaction, params).get(0);
+ assertNotNull(string);
+ assertTrue(string.contains("Calcium channel:RIMBP:RIM:MUNC13:RAB"));
+ assertTrue(string.contains("CSP:Hsc70:SGT"));
+ assertTrue(string.contains("SNCA"));
+ assertTrue(string.contains("trans-SNARE complex"));
+ assertTrue(string.contains("SNAP25"));
+ assertFalse(string.contains("RAB3A"));
+
+ params.complexElementsName(true);
+ string = exporter.getExportSingleInteractionString(reaction, params).get(0);
+ assertFalse(string.contains("trans-SNARE complex"));
+ assertTrue(string.contains("RAB3A"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Exception occured");
+ }
+
+ }
+
+ @Test
+ public void testGetExportStringForOneReactionInGeneralWithOnlyOneElement() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export/reaction.xml", false);
+ Reaction reaction = model.getReactionByReactionId("re11");
+ model.removeReactions(model.getReactions());
+ model.addReaction(reaction);
+ Set<Compartment> aliases = new HashSet<>();
+ aliases.add((Compartment) model.getElementByElementId("ca1"));
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).fileType(ExportFileType.SIF)
+ .included("dopamine loaded synaptic vesicle");
+ assertEquals(0, exporter.getExportSingleInteractionString(reaction, params).size());
+
+ params = new IExporterService.ExporterParameters().model(model).fileType(ExportFileType.SIF);
+ assertEquals(1, exporter.getExportSingleInteractionString(reaction, params).size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetExportSingleInteractionString_text() {
+ try {
+ Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
+ for (Reaction reaction : model.getReactions()) {
+ String str = exporter
+ .getExportSingleInteractionString(reaction,
+ new IExporterService.ExporterParameters().fileType(ExportFileType.TAB_SEPARATED).type(Species.class))
+ .get(0);
+
+ List<String> strings = new ArrayList<String>();
+ strings.add(ReactionLineData.getByReactionType(reaction.getClass()).getCellDesignerString());
+ strings.add(reaction.getIdReaction());
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ strings.add(node.getElement().getName());
+
+ }
+ for (String string : strings) {
+ assertTrue(
+ "Description \"" + str + "\" doesn't contain " + string + ". reactionId=" + reaction.getIdReaction(),
+ str.contains(string));
+ }
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Exception occured");
+ }
+ }
+
+ @Test
+ public void testGetExportComponentAndCompartments() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export/export_model.xml", false);
+ new CreateHierarchyCommand(model, 7, 80).execute();
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model)
+ .fileType(ExportFileType.TAB_SEPARATED).column(ExportColumn.NAME).column(ExportColumn.COMPONENT_NAME)
+ .column(ExportColumn.COMPARTMENT_NAME);
+
+ List<String> list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa1"), params);
+ String desc = list.get(0);
+ String compartment = desc.split("\t")[2];
+ assertEquals("c1", compartment);
+ String component = desc.split("\t")[1];
+ assertEquals("Test3", component);
+
+ list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa2"), params);
+ desc = null;
+ for (String string : list) {
+ if (string.contains("Test 1")) {
+ desc = string;
+ }
+ }
+ compartment = desc.split("\t")[2];
+ assertEquals("c2", compartment);
+ component = desc.split("\t")[1];
+ assertEquals("Test 1", component);
+
+ for (String string : list) {
+ if (string.contains("Test2")) {
+ desc = string;
+ }
+ }
+ compartment = desc.split("\t")[2];
+ assertEquals("c2", compartment);
+ component = desc.split("\t")[1];
+ assertEquals("Test2", component);
+
+ for (String string : list) {
+ if (string.contains("Test3")) {
+ desc = string;
+ }
+ }
+ compartment = desc.split("\t")[2];
+ assertEquals("c2", compartment);
+ component = desc.split("\t")[1];
+ assertEquals("Test3", component);
+
+ list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa3"), params);
+ boolean ok = false;
+ for (String string : list) {
+ if (string.split("\t")[2].equals("null") && string.split("\t")[1].equals("Test2")) {
+ ok = true;
+ }
+ }
+ assertTrue(ok);
+
+ list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa4"), params);
+ desc = list.get(0);
+ compartment = desc.split("\t")[2];
+ assertEquals("null", compartment);
+ component = desc.split("\t")[1];
+ assertEquals("Test3", component);
+
+ list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa5"), params);
+ desc = list.get(0);
+ compartment = desc.split("\t")[2];
+ assertEquals("c3", compartment);
+ component = desc.split("\t")[1];
+ assertEquals("null", component);
+
+ list = exporter.getExportStringForOneSpecies((Species) model.getElementByElementId("sa6"), params);
+ desc = list.get(0);
+ compartment = desc.split("\t")[2];
+ assertEquals("null", compartment);
+ component = desc.split("\t")[1];
+ assertEquals("null", component);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetExportSpeciesStringForTabSeparatedFile2() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
+ ExportColumn columns[] = { ExportColumn.NAME, ExportColumn.ID, ExportColumn.COMPONENT_NAME,
+ ExportColumn.COMPARTMENT_NAME, ExportColumn.TYPE };
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns)
+ .fileType(ExportFileType.TAB_SEPARATED).type(Object.class);
+
+ // full export (all elements)
+ String string = exporter.getExportSpeciesString(params);
+ String lines[] = string.split("\n");
+ assertTrue("Not enough elements in the result file", lines.length > 1);
+
+ String response = lines[0];
+ String textColumns[] = response.split("\t");
+ assertEquals(columns.length, textColumns.length);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetExportCompartmentsString() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export/export_compartments.xml", false);
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model)
+ .fileType(ExportFileType.TAB_SEPARATED).type(Object.class);
+
+ // full export (all compartments)
+ String string = exporter.getExportCompartmentsString(params);
+ String lines[] = string.split("\n");
+ assertTrue("Not enough elements in the result file", lines.length >= 2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAllExportColumnsSpecies() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
+ List<ExportColumn> columns = new ArrayList<ExportColumn>();
+ for (ExportColumn column : ExportColumn.values()) {
+ if (column.getClazz().isAssignableFrom(Species.class)) {
+ columns.add(column);
+ }
+ }
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns)
+ .fileType(ExportFileType.TAB_SEPARATED);
+
+ // full export (all elements)
+ String string = exporter.getExportSpeciesString(params);
+ assertNotNull(string);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAllExportColumnsReaction() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
+ List<ExportColumn> columns = new ArrayList<ExportColumn>();
+ for (ExportColumn column : ExportColumn.values()) {
+ if (column.getClazz().isAssignableFrom(Reaction.class)) {
+ columns.add(column);
+ }
+ }
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns)
+ .fileType(ExportFileType.TAB_SEPARATED);
+
+ // full export (all elements)
+ String string = exporter.getExportInteractionString(params);
+ assertNotNull(string);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetTabSeparatedReaction() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export/reaction.xml", false);
+ Set<Compartment> aliases = new HashSet<>();
+ for (Compartment alias : model.getCompartments()) {
+ if (alias.getName().equalsIgnoreCase("Dopamine loaded synaptic vesicle"))
+ aliases.add(alias);
+ }
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
+ fileType(ExportFileType.TAB_SEPARATED).//
+ column(ExportColumn.REACTION_ID).//
+ column(ExportColumn.REACTION_TYPE).//
+ type(Species.class);
+
+ String string = exporter.getExportInteractionString(params);
+ assertTrue(string.indexOf("STATE_TRANSITION REACTANT") >= 0);
+ assertTrue(string.indexOf("sa7") >= 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void test() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export/new_line_file.xml", false);
+ List<ExportColumn> columns = new ArrayList<ExportColumn>();
+ for (ExportColumn column : ExportColumn.values()) {
+ if (column.getClazz().isAssignableFrom(Species.class)) {
+ columns.add(column);
+ }
+ }
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns)
+ .fileType(ExportFileType.TAB_SEPARATED);
+
+ // full export (all elements)
+ String string = exporter.getExportSpeciesString(params);
+ String tmp[] = string.split("\n");
+ for (String string2 : tmp) {
+ assertTrue(string2, columns.size() <= string2.split("\t", -1).length);
+ }
+ assertNotNull(string);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPubmedSummary() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export/reaction.xml", false);
+ List<PubmedAnnotatedElementsView> result = exporter.getPublicationModelSummary(model);
+ assertNotNull(result);
+ for (PubmedAnnotatedElementsView pubmedAnnotatedElementsView : result) {
+ assertNotNull(pubmedAnnotatedElementsView.getArticle());
+ assertNotNull(pubmedAnnotatedElementsView.getArticle().getTitle());
+ assertTrue(pubmedAnnotatedElementsView.getElements().size() > 0);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/data/FullAliasViewFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/search/data/FullAliasViewFactoryTest.java
index 538ec5894c2b3dc05c62f2d74065b3aa4b6dd833..0e1577f840cb18a675253a920e1db457d0662a8c 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/data/FullAliasViewFactoryTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/data/FullAliasViewFactoryTest.java
@@ -40,195 +40,197 @@ import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.overlay.ChebiTreeRow;
public class FullAliasViewFactoryTest extends ServiceTestFunctions {
- Logger logger = Logger.getLogger(FullAliasViewFactoryTest.class);
-
- @Autowired
- FullAliasViewFactory fullAliasViewFactory;
-
- @Autowired
- private ChebiAnnotator backend;
- private Species alias;
- private Species alias2;
- private Point2D midPoint;
- private Reaction reaction;
- private Species alias3;
-
- private Model model;
-
- private Compartment compartmentAlias;
-
- @Before
- public void setUp() throws Exception {
-
- model = new ModelFullIndexed(null);
- model.setWidth(20010);
- model.setHeight(20010);
- model.setTileSize(256);
- model.setZoomLevels(7);
- model.addLayout(new Layout());
- model.getModelData().setId(-12);
-
- alias = new GenericProtein("AL1");
- alias.setName("blablabla");
- alias.setNotes("nottttttes");
- alias.setX(10.0);
- alias.setY(12.0);
- alias.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.WIKIPEDIA, "144352"));
- alias.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "43345"));
-
- model.addElement(alias);
-
- alias2 = new GenericProtein("AL2");
- alias2.setName("blablabla2");
- alias2.setX(100.0);
- alias2.setY(120.0);
-
- model.addElement(alias2);
-
- midPoint = new Point2D.Double(30, 100);
-
- reaction = new Reaction();
-
- Reactant reactant = new Reactant(alias);
- reactant.setLine(new PolylineData(alias.getCenter(), midPoint));
- reaction.addReactant(reactant);
-
- Product product = new Product(alias2);
- product.setLine(new PolylineData(alias2.getCenter(), midPoint));
- reaction.addProduct(product);
-
- model.addReaction(reaction);
-
- alias3 = new GenericProtein("AL3");
- alias3.setName("blablabla3");
- alias3.setX(200.0);
- alias3.setY(120.0);
-
- model.addElement(alias3);
-
- reaction = new NegativeInfluenceReaction(reaction);
- reaction.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CAS, "cc"));
-
- model.addReaction(reaction);
-
- compartmentAlias = new Compartment("AL4");
- compartmentAlias.setX(10);
- compartmentAlias.setY(10);
- compartmentAlias.setWidth(10);
- compartmentAlias.setHeight(10);
- model.addElement(compartmentAlias);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCreateGson() {
- try {
- Element alias = new GenericProtein("id");
- alias.setName("12");
- alias.setModel(new ModelFullIndexed(null));
- FullAliasView object = fullAliasViewFactory.create(alias);
- String gson = fullAliasViewFactory.createGson(object);
- assertNotNull(gson);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAliasOverlay() throws Exception {
- try {
- FullAliasView result = fullAliasViewFactory.create(alias);
- assertNotNull(result);
- assertEquals(model.getId(), result.getModelId());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAliasOverlay2() throws Exception {
- try {
- FullAliasView result = fullAliasViewFactory.create(alias2);
- assertNotNull(result);
- assertEquals(model.getId(), result.getModelId());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetNotes() throws Exception {
- try {
- Model model = getModelForFile("testFiles/protein_with_modification.xml", true);
- model.setTileSize(256);
- Species alias = (Species) model.getElementByElementId("sa1");
- FullAliasView marker = fullAliasViewFactory.create(alias);
- List<?> list = (List<?>) marker.getOther("posttranslationalModifications");
- assertNotNull(list);
- assertEquals(2, list.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateChebiTree() throws Exception {
- try {
- Chebi chebi = backend.getChebiElementForChebiId(new MiriamData(MiriamType.CHEBI, "CHEBI:15377"));
-
- TreeNode root = fullAliasViewFactory.createTreeForChebi(chebi);
-
- Set<String> el = new HashSet<String>();
- assertNotNull(root);
-
- Queue<TreeNode> elements = new LinkedList<TreeNode>();
-
- elements.add(root);
-
- while (!elements.isEmpty()) {
- TreeNode node = elements.peek();
- elements.remove();
- el.add(((ChebiTreeRow) node.getData()).getName());
- for (TreeNode child : node.getChildren()) {
- elements.add(child);
- }
- }
-
- assertTrue(el.size() > 3);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotationsInConversionForChebiTree() throws Exception {
- try {
- Model model = getModelForFile("testFiles/graph_path_example3.xml", false);
- model.setTileSize(256);
- Species alias = (Species) model.getElementByElementId("sa4");
- assertNotNull(alias);
- FullAliasView result = fullAliasViewFactory.create(alias);
- assertNotNull(result.getOther("chebiTree"));
-
- alias = (Species) model.getElementByElementId("sa3");
- result = fullAliasViewFactory.create(alias);
- assertNull(result.getOther("chebiTree"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Logger logger = Logger.getLogger(FullAliasViewFactoryTest.class);
+
+ @Autowired
+ FullAliasViewFactory fullAliasViewFactory;
+
+ @Autowired
+ private ChebiAnnotator backend;
+ private Species alias;
+ private Species alias2;
+ private Point2D midPoint;
+ private Reaction reaction;
+ private Species alias3;
+
+ private Model model;
+
+ private Compartment compartmentAlias;
+
+ @Before
+ public void setUp() throws Exception {
+
+ model = new ModelFullIndexed(null);
+ model.setWidth(20010);
+ model.setHeight(20010);
+ model.setTileSize(256);
+ model.setZoomLevels(7);
+ model.addLayout(new Layout());
+ model.getModelData().setId(-12);
+
+ alias = new GenericProtein("AL1");
+ alias.setName("blablabla");
+ alias.setNotes("nottttttes");
+ alias.setX(10.0);
+ alias.setY(12.0);
+ alias.getMiriamData()
+ .add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.WIKIPEDIA, "144352"));
+ alias.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "43345"));
+
+ model.addElement(alias);
+
+ alias2 = new GenericProtein("AL2");
+ alias2.setName("blablabla2");
+ alias2.setX(100.0);
+ alias2.setY(120.0);
+
+ model.addElement(alias2);
+
+ midPoint = new Point2D.Double(30, 100);
+
+ reaction = new Reaction("re1");
+
+ Reactant reactant = new Reactant(alias);
+ reactant.setLine(new PolylineData(alias.getCenter(), midPoint));
+ reaction.addReactant(reactant);
+
+ Product product = new Product(alias2);
+ product.setLine(new PolylineData(alias2.getCenter(), midPoint));
+ reaction.addProduct(product);
+
+ model.addReaction(reaction);
+
+ alias3 = new GenericProtein("AL3");
+ alias3.setName("blablabla3");
+ alias3.setX(200.0);
+ alias3.setY(120.0);
+
+ model.addElement(alias3);
+
+ reaction = new NegativeInfluenceReaction(reaction);
+ reaction.setIdReaction("re2");
+ reaction.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CAS, "cc"));
+
+ model.addReaction(reaction);
+
+ compartmentAlias = new Compartment("AL4");
+ compartmentAlias.setX(10);
+ compartmentAlias.setY(10);
+ compartmentAlias.setWidth(10);
+ compartmentAlias.setHeight(10);
+ model.addElement(compartmentAlias);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCreateGson() {
+ try {
+ Element alias = new GenericProtein("id");
+ alias.setName("12");
+ alias.setModel(new ModelFullIndexed(null));
+ FullAliasView object = fullAliasViewFactory.create(alias);
+ String gson = fullAliasViewFactory.createGson(object);
+ assertNotNull(gson);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAliasOverlay() throws Exception {
+ try {
+ FullAliasView result = fullAliasViewFactory.create(alias);
+ assertNotNull(result);
+ assertEquals(model.getId(), result.getModelId());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAliasOverlay2() throws Exception {
+ try {
+ FullAliasView result = fullAliasViewFactory.create(alias2);
+ assertNotNull(result);
+ assertEquals(model.getId(), result.getModelId());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetNotes() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/protein_with_modification.xml", true);
+ model.setTileSize(256);
+ Species alias = (Species) model.getElementByElementId("sa1");
+ FullAliasView marker = fullAliasViewFactory.create(alias);
+ List<?> list = (List<?>) marker.getOther("posttranslationalModifications");
+ assertNotNull(list);
+ assertEquals(2, list.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateChebiTree() throws Exception {
+ try {
+ Chebi chebi = backend.getChebiElementForChebiId(new MiriamData(MiriamType.CHEBI, "CHEBI:15377"));
+
+ TreeNode root = fullAliasViewFactory.createTreeForChebi(chebi);
+
+ Set<String> el = new HashSet<String>();
+ assertNotNull(root);
+
+ Queue<TreeNode> elements = new LinkedList<TreeNode>();
+
+ elements.add(root);
+
+ while (!elements.isEmpty()) {
+ TreeNode node = elements.peek();
+ elements.remove();
+ el.add(((ChebiTreeRow) node.getData()).getName());
+ for (TreeNode child : node.getChildren()) {
+ elements.add(child);
+ }
+ }
+
+ assertTrue(el.size() > 3);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotationsInConversionForChebiTree() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/graph_path_example3.xml", false);
+ model.setTileSize(256);
+ Species alias = (Species) model.getElementByElementId("sa4");
+ assertNotNull(alias);
+ FullAliasView result = fullAliasViewFactory.create(alias);
+ assertNotNull(result.getOther("chebiTree"));
+
+ alias = (Species) model.getElementByElementId("sa3");
+ result = fullAliasViewFactory.create(alias);
+ assertNull(result.getOther("chebiTree"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}