/**
* Unmarshal an XML file to an object.
*
* @param is the InputStream to read from
* @return a collection of business objects
* @throws InterMineException if an error occurs during unmarshalling
*/
public List<FastPathObject> unmarshal(InputStream is) throws InterMineException {
try {
return FullParser.realiseObjects(FullParser.parse(is), model, false);
} catch (Exception e) {
throw new InterMineException("Error during unmarshalling", e);
}
}
public void testEntrezPublicationRetriever() throws Exception {
EntrezPublicationsRetriever eor = new TestEntrezPublicationsRetriever();
// Create temp file.
File temp = File.createTempFile("EntrezPublicationsRetriever", ".tmp");
// Delete temp file when program exits.
temp.deleteOnExit();
eor.setLoadFullRecord(fullRecord); // use eFetch URL instead of summary
eor.setOsAlias("os.bio-test");
eor.setOutputFile(temp.getPath());
// eor.setOutputFile("entrez-pub-tgt-items.xml");
eor.setCacheDirName("build/");
eor.execute();
Collection<Item> actual = FullParser.parse(new FileInputStream(temp));
Set<Item> expected;
if ("true".equals(fullRecord)) {
expected = readItemSet("EntrezPublicationsFullRecord_tgt.xml");
} else {
expected = readItemSet("EntrezPublicationsSummary_tgt.xml");
}
assertEquals(expected, new HashSet<Item>(actual));
}
@SuppressWarnings({"unchecked", "rawtypes"})
protected List getPublications(ObjectStore os) {
try {
List<Item> items =
FullParser.parse(
getClass()
.getClassLoader()
.getResourceAsStream("EntrezPublicationsRetrieverTest_src.xml"));
return FullParser.realiseObjects(items, Model.getInstanceByName("genomic"), false);
} catch (Exception e) {
throw new RuntimeException(e);
}
}
public Set<Item> readItemSet(String fileName) throws Exception {
return new LinkedHashSet<Item>(
FullParser.parse(getClass().getClassLoader().getResourceAsStream(fileName)));
}