/** Test loading a FASTA data source. */
@Test
public void testLoadFastaSource() {
SourceInfoLoader loader = SourceInfoLoader.getInstance();
SourceInfo fastaInfo = loader.getSourceInfo("fasta");
assertNotNull("No source info for 'fasta'", fastaInfo);
assertEquals("Type wrong", "fasta", fastaInfo.getType());
SourceDescriptor source = fastaInfo.getSource();
assertEquals("SourceDescriptor type wrong", "fasta", source.getType());
assertEquals("Incorrect number of properties in source", 9, source.getProperty().size());
Map<String, PropertyDescriptor> propMap = new HashMap<String, PropertyDescriptor>();
for (PropertyDescriptor p : source.getProperty()) {
propMap.put(p.getName(), p);
}
PropertyDescriptor srcDataDir = propMap.get("src.data.dir");
assertNotNull("No property 'src.data.dir'", srcDataDir);
assertEquals(
"'src.data.dir' not required when it should be", Boolean.TRUE, srcDataDir.isRequired());
assertEquals("'src.data.dir' type wrong", PropertyType.DIRECTORY, srcDataDir.getType());
assertNull("'src.data.dir' has validation", srcDataDir.getValidation());
PropertyDescriptor taxonId = propMap.get("fasta.taxonId");
assertNotNull("No property 'fasta.taxonId'", taxonId);
assertEquals(
"'fasta.taxonId' required when it should not be", Boolean.TRUE, taxonId.isRequired());
assertEquals("'fasta.taxonId' type wrong", PropertyType.STRING, taxonId.getType());
assertEquals("'fasta.taxonId' validation wrong", "^\\d+(\\s\\d+)*$", taxonId.getValidation());
}
/**
* Test loading a named derived source. Searches under the project directory <code>
* src/test/sourcetest/project</code>, which in this distribution has a dummy Intermine directory
* structure.
*
* @throws IOException if there is an I/O problem during the test.
* @see SourceInfoLoader#findDerivedSourceInfo(String, Project, File)
*/
@Test
public void testDerivedTypeLoad() throws IOException {
File projectHome = new File("src/test/sourcetest/project");
org.intermine.modelviewer.project.ObjectFactory factory =
new org.intermine.modelviewer.project.ObjectFactory();
Project project = factory.createProject();
project.setSources(factory.createProjectSources());
Property p = factory.createProperty();
p.setName(SourceInfoLoader.SOURCE_PATH_PROPERTY);
p.setLocation("../bio/sources");
project.getProperty().add(p);
p = factory.createProperty();
p.setName(SourceInfoLoader.SOURCE_PATH_PROPERTY);
p.setLocation("../bio/sources/example-sources");
project.getProperty().add(p);
// Source s = factory.createSource();
// s.setName("malaria");
// s.setType("malaria-gff");
// project.getSources().getSource().add(s);
SourceInfo info =
SourceInfoLoader.getInstance().findDerivedSourceInfo("malaria-gff", project, projectHome);
assertNotNull("Could not find derived source type for malaria-gff", info);
assertEquals("Derived type is not gff", "malaria-gff", info.getType());
}
/**
* Set up by initialising the SourceInfoLoader instance.
*
* @throws IOException thrown from {@link SourceInfoLoader#initialise()}
* @throws JAXBException thrown from {@link SourceInfoLoader#initialise()}
*/
@Before
public void setup() throws IOException, JAXBException {
try {
SourceInfoLoader.getInstance().initialise();
} catch (IllegalStateException e) {
// Already loaded.
}
}
