@Test
public void test_write_interaction_registered()
throws XMLStreamException, IOException, IllegalRangeException {
BinaryInteractionEvidence interaction = new DefaultNamedBinaryInteractionEvidence();
ParticipantEvidence participant =
new DefaultNamedParticipantEvidence(InteractorUtils.createUnknownBasicInteractor());
interaction.addParticipant(participant);
elementCache.clear();
elementCache.extractIdForInteraction(new DefaultInteraction());
elementCache.extractIdForInteraction(interaction);
XmlNamedBinaryInteractionEvidenceWriter writer =
new XmlNamedBinaryInteractionEvidenceWriter(createStreamWriter(), this.elementCache);
writer.write(interaction);
streamWriter.flush();
Assert.assertEquals(this.interaction_registered, output.toString());
}
@Test
public void test_write_participant_complex_no_participants()
throws XMLStreamException, IOException, IllegalRangeException {
BinaryInteractionEvidence interaction = new DefaultNamedBinaryInteractionEvidence();
Complex complex = new DefaultComplex("test complex");
ParticipantEvidence participant = new DefaultNamedParticipantEvidence(complex);
interaction.addParticipant(participant);
elementCache.clear();
XmlNamedBinaryInteractionEvidenceWriter writer =
new XmlNamedBinaryInteractionEvidenceWriter(createStreamWriter(), this.elementCache);
writer.write(interaction);
streamWriter.flush();
Assert.assertEquals(this.interaction, output.toString());
}
@Test
public void test_write_interaction_type()
throws XMLStreamException, IOException, IllegalRangeException {
BinaryInteractionEvidence interaction = new DefaultNamedBinaryInteractionEvidence();
ParticipantEvidence participant =
new DefaultNamedParticipantEvidence(InteractorUtils.createUnknownBasicInteractor());
interaction.addParticipant(participant);
interaction.setInteractionType(CvTermUtils.createMICvTerm("association", "MI:0914"));
elementCache.clear();
XmlNamedInteractionEvidenceWriter writer =
new XmlNamedInteractionEvidenceWriter(createStreamWriter(), this.elementCache);
writer.write(interaction);
streamWriter.flush();
Assert.assertEquals(this.interaction_type, output.toString());
}
@Test
public void test_write_interaction_fullName()
throws XMLStreamException, IOException, IllegalRangeException {
NamedInteraction interaction = new DefaultNamedBinaryInteractionEvidence();
interaction.setFullName("interaction test");
ParticipantEvidence participant =
new DefaultNamedParticipantEvidence(InteractorUtils.createUnknownBasicInteractor());
interaction.addParticipant(participant);
elementCache.clear();
XmlNamedBinaryInteractionEvidenceWriter writer =
new XmlNamedBinaryInteractionEvidenceWriter(createStreamWriter(), this.elementCache);
writer.write((BinaryInteractionEvidence) interaction);
streamWriter.flush();
Assert.assertEquals(this.interaction_fullName, output.toString());
}
@Test
public void test_write_interaction_xref()
throws XMLStreamException, IOException, IllegalRangeException {
BinaryInteractionEvidence interaction = new DefaultNamedBinaryInteractionEvidence();
ParticipantEvidence participant =
new DefaultNamedParticipantEvidence(InteractorUtils.createUnknownBasicInteractor());
interaction.addParticipant(participant);
interaction.getXrefs().add(new DefaultXref(new DefaultCvTerm("test2"), "xxxx2"));
interaction.getXrefs().add(new DefaultXref(new DefaultCvTerm("test"), "xxxx1"));
elementCache.clear();
XmlNamedBinaryInteractionEvidenceWriter writer =
new XmlNamedBinaryInteractionEvidenceWriter(createStreamWriter(), this.elementCache);
writer.write(interaction);
streamWriter.flush();
Assert.assertEquals(this.interaction_xref, output.toString());
}
@Test
public void test_write_interaction_attributes()
throws XMLStreamException, IOException, IllegalRangeException {
BinaryInteractionEvidence interaction = new DefaultNamedBinaryInteractionEvidence();
ParticipantEvidence participant =
new DefaultNamedParticipantEvidence(InteractorUtils.createUnknownBasicInteractor());
interaction.addParticipant(participant);
interaction.getAnnotations().add(new DefaultAnnotation(new DefaultCvTerm("test2")));
interaction.getAnnotations().add(new DefaultAnnotation(new DefaultCvTerm("test3")));
interaction.setComplexExpansion(CvTermUtils.createMICvTerm("spoke expansion", "MI:1060"));
elementCache.clear();
XmlNamedBinaryInteractionEvidenceWriter writer =
new XmlNamedBinaryInteractionEvidenceWriter(createStreamWriter(), this.elementCache);
writer.write(interaction);
streamWriter.flush();
Assert.assertEquals(this.interaction_attributes, output.toString());
}
@Test
@Ignore
public void test_write_interaction_inferred()
throws XMLStreamException, IOException, IllegalRangeException {
BinaryInteractionEvidence interaction = new DefaultNamedBinaryInteractionEvidence();
ParticipantEvidence participant =
new DefaultNamedParticipantEvidence(InteractorUtils.createUnknownBasicInteractor());
ParticipantEvidence participant2 =
new DefaultNamedParticipantEvidence(InteractorUtils.createUnknownBasicInteractor());
ParticipantEvidence participant3 =
new DefaultNamedParticipantEvidence(InteractorUtils.createUnknownBasicInteractor());
ParticipantEvidence participant4 =
new DefaultNamedParticipantEvidence(InteractorUtils.createUnknownBasicInteractor());
// two inferred interactiosn f1, f2, f3 and f3,f4
FeatureEvidence f1 = new DefaultFeatureEvidence();
f1.getRanges().add(RangeUtils.createRangeFromString("1-4"));
FeatureEvidence f2 = new DefaultFeatureEvidence();
f2.getRanges().add(RangeUtils.createRangeFromString("1-4"));
FeatureEvidence f3 = new DefaultFeatureEvidence();
f1.getLinkedFeatures().add(f2);
f1.getLinkedFeatures().add(f3);
f2.getLinkedFeatures().add(f1);
f2.getLinkedFeatures().add(f3);
f3.getLinkedFeatures().add(f1);
f3.getLinkedFeatures().add(f2);
participant.addFeature(f1);
participant2.addFeature(f2);
participant3.addFeature(f3);
interaction.addParticipant(participant);
interaction.addParticipant(participant2);
elementCache.clear();
XmlNamedBinaryInteractionEvidenceWriter writer =
new XmlNamedBinaryInteractionEvidenceWriter(createStreamWriter(), this.elementCache);
writer.write(interaction);
streamWriter.flush();
Assert.assertEquals(this.interaction_inferred, output.toString());
}