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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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1 merge request!190Resolve "uploading zip file from MAC"
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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/impl/ExporterServiceTest.java
+ 502
− 491
View file @ 1331ea0a
......@@ -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;
}
}
}
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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