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Commit 1331ea0a authored by Piotr Gawron's avatar Piotr Gawron
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unit tests fixed (model cannot contain reactions with the same id)

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model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+ 2
− 0
View file @ 1331ea0a
......@@ -616,4 +616,6 @@ public interface Model {
void addFunction(SbmlFunction sbmlFunction);
SbmlArgument getFunctionById(String id);
void removeReactions(Collection<Reaction> reactions);
}
model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+ 9
− 0
View file @ 1331ea0a
......@@ -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);
}
}
}
service/src/test/java/lcsb/mapviewer/services/search/data/FullAliasViewFactoryTest.java
+ 192
− 190
View file @ 1331ea0a
......@@ -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;
}
}
}
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