/** {@inheritDoc} */
public ActionForward execute(
@SuppressWarnings("unused") ActionMapping mapping,
@SuppressWarnings("unused") ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
String type = request.getParameter("type");
if (type == null) {
type = "webapp";
}
if ("webapp".equals(type)) {
response.getOutputStream().print("OK");
} else if ("query".equals(type)) {
final InterMineAPI im = SessionMethods.getInterMineAPI(request.getSession());
ObjectStore os = im.getObjectStore();
Query q = new Query();
QueryClass c = new QueryClass(InterMineObject.class);
q.addFrom(c);
q.addToSelect(c);
// Add a unique value to the select to avoid caching the query
QueryValue token = new QueryValue(System.currentTimeMillis());
q.addToSelect(token);
Results r = os.execute(q, 1, false, false, false);
if (r.get(0) != null) {
response.getOutputStream().print("OK");
} else {
response.getOutputStream().print("NO RESULTS");
}
}
return null;
}
public void testTranslation() throws Exception {
ObjectStore os2 =
new ObjectStoreTranslatingImpl(
Model.getInstanceByName("testmodel"),
ObjectStoreFactory.getObjectStore("os.unittest"),
new CompanyTranslator());
Query q = new Query();
QueryClass qc = new QueryClass(InterMineObject.class);
q.addToSelect(qc);
q.addFrom(qc);
Results res = os2.execute(q);
assertEquals(2, res.size());
assertEquals("CompanyA", ((Bank) ((ResultsRow) res.get(0)).get(0)).getName());
assertEquals("CompanyB", ((Bank) ((ResultsRow) res.get(1)).get(0)).getName());
}
/**
* @param os object store
* @return map of name to so term
* @throws ObjectStoreException if something goes wrong
*/
protected Map<String, SOTerm> populateSOTermMap(ObjectStore os) throws ObjectStoreException {
Map<String, SOTerm> soTerms = new HashMap<String, SOTerm>();
Query q = new Query();
q.setDistinct(false);
QueryClass qcSOTerm = new QueryClass(SOTerm.class);
q.addToSelect(qcSOTerm);
q.addFrom(qcSOTerm);
q.addToOrderBy(qcSOTerm);
Results res = os.execute(q);
Iterator it = res.iterator();
while (it.hasNext()) {
ResultsRow<InterMineObject> rr = (ResultsRow<InterMineObject>) it.next();
SOTerm soTerm = (SOTerm) rr.get(0);
soTerms.put(soTerm.getName(), soTerm);
}
return soTerms;
}
public void testLoad() throws Exception {
TSVFileReaderTask tsvTask = new TSVFileReaderTask();
tsvTask.setIgnoreDuplicates(true);
tsvTask.setIntegrationWriterAlias("integration.unittestmulti");
tsvTask.setSourceName("testsource");
cleanObjects(tsvTask.getDirectDataLoader().getIntegrationWriter());
File tempFile = File.createTempFile("TSVFileReaderTaskTest", "tmp");
FileWriter fw = new FileWriter(tempFile);
InputStream is = getClass().getClassLoader().getResourceAsStream("TSVFileReaderTaskTest.tsv");
BufferedReader br = new BufferedReader(new InputStreamReader(is));
String line = null;
while ((line = br.readLine()) != null) {
fw.write(line + "\n");
}
fw.close();
FileSet fileSet = new FileSet();
fileSet.setFile(tempFile);
tsvTask.addFileSet(fileSet);
InputStream confInputStream =
getClass().getClassLoader().getResourceAsStream("TSVFileReaderTaskTest.properties");
DelimitedFileConfiguration dfc = new DelimitedFileConfiguration(model, confInputStream);
tsvTask.executeInternal(dfc, tempFile);
// Check the results to see if we have some data...
ObjectStore os = tsvTask.getDirectDataLoader().getIntegrationWriter().getObjectStore();
Query q = new Query();
QueryClass empQueryClass = new QueryClass(Employee.class);
QueryField qf0 = new QueryField(empQueryClass, "age");
QueryField qf1 = new QueryField(empQueryClass, "name");
QueryField qf2 = new QueryField(empQueryClass, "fullTime");
q.addToSelect(qf0);
q.addToSelect(qf1);
q.addToSelect(qf2);
q.addFrom(empQueryClass);
q.addToOrderBy(qf1);
Results r = os.execute(q);
if (r.size() != 3) {
for (List<Object> rr : (List<List<Object>>) ((List) r)) {
System.err.print("row: ");
for (Object obj : rr) {
System.err.print("{" + obj + "} ");
}
System.err.println();
}
}
assertEquals(3, r.size());
List expectedRow0 = Arrays.asList(new Object[] {new Integer(10), "EmployeeA1", Boolean.FALSE});
assertEquals(expectedRow0, r.get(0));
List expectedRow1 = Arrays.asList(new Object[] {new Integer(20), "EmployeeA2", Boolean.TRUE});
assertEquals(expectedRow1, r.get(1));
List expectedRow2 = Arrays.asList(new Object[] {new Integer(0), "EmployeeA3", Boolean.FALSE});
assertEquals(expectedRow2, r.get(2));
}
/**
* Read the UTRs collection of MRNA then set the fivePrimeUTR and threePrimeUTR fields with the
* corresponding UTRs.
*
* @throws Exception if anything goes wrong
*/
public void createUtrRefs() throws Exception {
long startTime = System.currentTimeMillis();
Query q = new Query();
q.setDistinct(false);
QueryClass qcMRNA = new QueryClass(model.getClassDescriptorByName("MRNA").getType());
q.addFrom(qcMRNA);
q.addToSelect(qcMRNA);
q.addToOrderBy(qcMRNA);
QueryClass qcUTR = new QueryClass(model.getClassDescriptorByName("UTR").getType());
q.addFrom(qcUTR);
q.addToSelect(qcUTR);
q.addToOrderBy(qcUTR);
QueryCollectionReference mrnaUtrsRef = new QueryCollectionReference(qcMRNA, "UTRs");
ContainsConstraint mrnaUtrsConstraint =
new ContainsConstraint(mrnaUtrsRef, ConstraintOp.CONTAINS, qcUTR);
QueryObjectReference fivePrimeRef = new QueryObjectReference(qcMRNA, "fivePrimeUTR");
ContainsConstraint fivePrimeNullConstraint =
new ContainsConstraint(fivePrimeRef, ConstraintOp.IS_NULL);
QueryObjectReference threePrimeRef = new QueryObjectReference(qcMRNA, "threePrimeUTR");
ContainsConstraint threePrimeNullConstraint =
new ContainsConstraint(threePrimeRef, ConstraintOp.IS_NULL);
ConstraintSet cs = new ConstraintSet(ConstraintOp.AND);
cs.addConstraint(mrnaUtrsConstraint);
cs.addConstraint(fivePrimeNullConstraint);
cs.addConstraint(threePrimeNullConstraint);
q.setConstraint(cs);
ObjectStore os = osw.getObjectStore();
((ObjectStoreInterMineImpl) os).precompute(q, Constants.PRECOMPUTE_CATEGORY);
Results res = os.execute(q, 500, true, true, true);
int count = 0;
InterMineObject lastMRNA = null;
InterMineObject fivePrimeUTR = null;
InterMineObject threePrimeUTR = null;
osw.beginTransaction();
Class<? extends FastPathObject> fivePrimeUTRCls =
model.getClassDescriptorByName("FivePrimeUTR").getType();
Iterator<?> resIter = res.iterator();
while (resIter.hasNext()) {
ResultsRow<?> rr = (ResultsRow<?>) resIter.next();
InterMineObject mrna = (InterMineObject) rr.get(0);
InterMineObject utr = (InterMineObject) rr.get(1);
if (lastMRNA != null && !mrna.getId().equals(lastMRNA.getId())) {
// clone so we don't change the ObjectStore cache
InterMineObject tempMRNA = PostProcessUtil.cloneInterMineObject(lastMRNA);
if (fivePrimeUTR != null) {
tempMRNA.setFieldValue("fivePrimeUTR", fivePrimeUTR);
fivePrimeUTR = null;
}
if (threePrimeUTR != null) {
tempMRNA.setFieldValue("threePrimeUTR", threePrimeUTR);
threePrimeUTR = null;
}
osw.store(tempMRNA);
count++;
}
if (DynamicUtil.isInstance(utr, fivePrimeUTRCls)) {
fivePrimeUTR = utr;
} else {
threePrimeUTR = utr;
}
lastMRNA = mrna;
}
if (lastMRNA != null) {
// clone so we don't change the ObjectStore cache
InterMineObject tempMRNA = PostProcessUtil.cloneInterMineObject(lastMRNA);
tempMRNA.setFieldValue("fivePrimeUTR", fivePrimeUTR);
tempMRNA.setFieldValue("threePrimeUTR", threePrimeUTR);
osw.store(tempMRNA);
count++;
}
LOG.info(
"Stored MRNA "
+ count
+ " times ("
+ count * 2
+ " fields set)"
+ " - took "
+ (System.currentTimeMillis() - startTime)
+ " ms.");
osw.commitTransaction();
// now ANALYSE tables relating to class that has been altered - may be rows added
// to indirection tables
if (osw instanceof ObjectStoreWriterInterMineImpl) {
ClassDescriptor cld = model.getClassDescriptorByName("MRNA");
DatabaseUtil.analyse(((ObjectStoreWriterInterMineImpl) osw).getDatabase(), cld, false);
}
}