From 34fbf561731ec6f972f304d9cd03ccacd8e21577 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 12 Feb 2018 17:19:25 +0100
Subject: [PATCH] when importing zip file from max, ignore max specific
"hidden" files
---
.../converter/ComplexZipConverter.java | 20 +-
.../converter/ComplexZipConverterTest.java | 947 +++++++++---------
2 files changed, 508 insertions(+), 459 deletions(-)
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index e2640f0b3e..12f391a07b 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 6d8f7acb69..4d768d5aa9 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;
+ }
+ }
}
--
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