/** 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());
}
/**
* Prints all results stored in this object to the given writer
*
* @param wr The writer to which to print the results
* @throws IOException Thrown when data writing fails
*/
public void printResults(Writer wr) throws IOException {
for (SinkInfo sink : this.results.keySet()) {
wr.write("Found a flow to sink " + sink + ", from the following sources:\n");
for (SourceInfo source : this.results.get(sink)) {
wr.write("\t- " + source.getSource() + "\n");
if (source.getPath() != null && !source.getPath().isEmpty())
wr.write("\t\ton Path " + source.getPath() + "\n");
}
}
}
/** Prints all results stored in this object to the standard output */
public void printResults() {
for (SinkInfo sink : this.results.keySet()) {
logger.info("Found a flow to sink {}, from the following sources:", sink);
for (SourceInfo source : this.results.get(sink)) {
logger.info("\t- {}", source.getSource());
if (source.getPath() != null && !source.getPath().isEmpty())
logger.info("\t\ton Path {}", source.getPath());
}
}
}
