@Override
protected void initialiseDefaultFetcher() throws BridgeFailedException {
String urlString = getEnricherContext().getConfig().getOboUrl();
InputStream stream = null;
File tempFile = null;
try {
URL url = new URL(urlString);
stream = url.openStream();
tempFile =
MIFileUtils.storeAsTemporaryFile(
stream, "cvFetcher_" + System.currentTimeMillis(), ".obo");
super.setOboFetcher(
new OboSourceFetcher(CvTermUtils.createPsiMiDatabase(), tempFile.getAbsolutePath()));
} catch (MalformedURLException e) {
throw new BridgeFailedException("Cannot open URL " + urlString, e);
} catch (IOException e) {
throw new BridgeFailedException("Cannot read URL " + urlString, e);
} finally {
if (stream != null) {
try {
stream.close();
} catch (IOException e) {
e.printStackTrace();
}
}
if (tempFile != null) {
tempFile.delete();
}
}
}
@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_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());
}