/** {@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;
}
/**
* Populate the SequenceFeature.locatedFeatures() collection for: Gene, Transcript, Exon and CDS
*
* @throws Exception if anything goes wrong
*/
public void populateCollection() throws Exception {
Map<String, SOTerm> soTerms = populateSOTermMap(osw);
Query q = getAllParents();
Results res = osw.getObjectStore().execute(q);
Iterator<Object> resIter = res.iterator();
osw.beginTransaction();
int parentCount = 0;
int childCount = 0;
while (resIter.hasNext()) {
ResultsRow<InterMineObject> rr = (ResultsRow<InterMineObject>) resIter.next();
InterMineObject parent = rr.get(0);
SOTerm soTerm = (SOTerm) rr.get(1);
InterMineObject o = PostProcessUtil.cloneInterMineObject(parent);
Set<InterMineObject> newCollection = getChildFeatures(soTerms, soTerm, o);
if (newCollection != null && !newCollection.isEmpty()) {
o.setFieldValue(TARGET_COLLECTION, newCollection);
osw.store(o);
parentCount++;
childCount += newCollection.size();
}
}
osw.commitTransaction();
LOG.info("Stored " + childCount + " child features for " + parentCount + " parent features");
}
/**
* Calls ObjectStore.releaseGoFaster() if this object wraps a Results object from an
* ObjectStoreInterMineImpl.
*
* @throws ObjectStoreException if ObjectStoreInterMineImpl.releaseGoFaster() throws the exception
*/
public synchronized void releaseGoFaster() throws ObjectStoreException {
goingFaster--;
if (goingFaster == 0) {
ObjectStore os = osResults.getObjectStore();
if (os instanceof ObjectStoreInterMineImpl) {
((ObjectStoreInterMineImpl) os).releaseGoFaster(osResults.getQuery());
}
}
}
/**
* Calls ObjectStore.goFaster() if this object wraps a Results object from an
* ObjectStoreInterMineImpl.
*
* @throws ObjectStoreException if ObjectStoreInterMineImpl.goFaster() throws the exception
*/
public synchronized void goFaster() throws ObjectStoreException {
goingFaster++;
if (goingFaster == 1) {
osResults = changeResultBatchSize(osResults, BIG_BATCH_SIZE);
ObjectStore os = osResults.getObjectStore();
if (os instanceof ObjectStoreInterMineImpl) {
((ObjectStoreInterMineImpl) os).goFaster(osResults.getQuery());
}
}
}
@Test
public void test() throws Exception {
Model m = osw.getModel();
Long start = System.currentTimeMillis();
PathQuery pq = new PathQuery(m);
pq.addViews("Types.name", "Types.intType", "Types.doubleType");
pq.addConstraint(Constraints.eq("Types.name", "histo*"));
Query q = MainHelper.makeSummaryQuery(pq, "Types.intType", new HashMap(), new HashMap(), null);
Results res = osw.execute(q, 100000, true, false, false);
Long sum = 0L;
Map<Integer, Long> actual = new TreeMap<Integer, Long>();
for (Object o : res) {
// System.out.println("ROW:" + o);
List row = (List) o;
Integer bucket = (Integer) row.get(5);
Integer min = (Integer) row.get(0);
Integer max = (Integer) row.get(1);
Integer buckets = (Integer) row.get(4);
Integer width = (max - min) / (buckets - 1);
Integer group = min + ((bucket - 1) * width);
Long count = ((BigDecimal) row.get(6)).longValue();
actual.put(group, count);
sum += count;
}
Long postExecution = System.currentTimeMillis();
showHistogram("Actual", actual);
System.out.printf(
"MIN: %d\nMAX: %d\nAVG: %.03f\nSTD-DEV: %.03f\n",
((List) res.get(0)).subList(0, 4).toArray());
System.out.println("TOTAL THINGS: " + sum);
System.out.printf(
"Query composition and execution took %.4f seconds",
Double.valueOf(postExecution - start) / 1000);
res = osw.execute(getCheckQuery());
Long countFromOSQ = null;
for (Object o : res) {
List row = (List) o;
countFromOSQ = (Long) row.get(0);
}
// int scale = generator.nextInt(MAX_SCALE - MIN_SCALE) + MIN_SCALE;
assertEquals("Sum of buckets and total count agrees", sum, countFromOSQ);
assertEquals("Sum of buckets agrees with what we inserted", made, sum.intValue());
}
public void testFailFast() throws Exception {
Query q1 = new Query();
QueryClass qc1 = new QueryClass(Employee.class);
q1.addFrom(qc1);
q1.addToSelect(qc1);
Results r1 = writer.execute(q1);
writer.store(data.get("EmployeeA1"));
try {
r1.iterator().hasNext();
fail("Expected: ConcurrentModificationException");
} catch (ConcurrentModificationException e) {
}
}
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());
}
/**
* Create a new WebResults object.
*
* @param pathQuery used to get the paths of the columns
* @param results the underlying Results object
* @param im intermine API
* @param pathToQueryNode the mapping between Paths (in the columnPaths argument) and the
* QueryNodes in the results object
* @param pathToBagQueryResult a Map containing results from LOOKUP operations
*/
public WebResults(
InterMineAPI im,
PathQuery pathQuery,
Results results,
Map<String, QuerySelectable> pathToQueryNode,
Map<String, BagQueryResult> pathToBagQueryResult) {
this.im = im;
this.osResults = results;
this.flatResults = new ResultsFlatOuterJoinsImpl(((List) osResults), osResults.getQuery());
model = im.getModel();
this.columnPaths = new ArrayList<Path>();
try {
for (String pathString : pathQuery.getView()) {
this.columnPaths.add(pathQuery.makePath(pathString));
}
} catch (PathException e) {
throw new RuntimeException("Error creating WebResults because PathQuery is invalid", e);
}
classKeys = im.getClassKeys();
this.pathToQueryNode = new HashMap<String, QuerySelectable>();
if (pathToQueryNode != null) {
this.pathToQueryNode.putAll(pathToQueryNode);
}
this.pathToBagQueryResult = new HashMap<String, BagQueryResult>();
if (pathToBagQueryResult != null) {
this.pathToBagQueryResult.putAll(pathToBagQueryResult);
}
this.pathQuery = pathQuery;
pathToIndex = getPathToIndex();
redirector = im.getLinkRedirector();
addColumnsInternal(columnPaths);
}
/** Test that transactions do actually commit and that isInTransaction() works. */
public void testCommitTransactions() throws Exception {
Address address1 = new Address();
address1.setAddress("Address 1");
Address address2 = new Address();
address2.setAddress("Address 2");
Query q = new Query();
QueryClass qcAddress = new QueryClass(Address.class);
QueryField qf = new QueryField(qcAddress, "address");
ConstraintSet cs1 = new ConstraintSet(ConstraintOp.OR);
cs1.addConstraint(new SimpleConstraint(qf, ConstraintOp.MATCHES, new QueryValue("Address%")));
q.addToSelect(qcAddress);
q.addFrom(qcAddress);
q.addToOrderBy(qf);
q.setConstraint(cs1);
try {
writer.beginTransaction();
assertTrue(writer.isInTransaction());
writer.store(address1);
writer.store(address2);
// Should be nothing in OS until we commit
Results res = realOs.execute(q);
assertEquals(0, res.size());
// However, they should be in the WRITER.
// TODO: These lines now fail, because we do not allow querying on writers with uncommitted
// data. The writer should relax this restriction.
res = writer.execute(q);
assertEquals(2, res.size());
writer.commitTransaction();
assertFalse(writer.isInTransaction());
res = realOs.execute(q);
assertEquals(2, res.size());
assertEquals(address1, (Address) ((ResultsRow) res.get(0)).get(0));
assertEquals(address2, (Address) ((ResultsRow) res.get(1)).get(0));
} finally {
writer.delete(address1);
writer.delete(address2);
}
}
/**
* Create and ObjectStore query from a PathQuery and execute it, returning results in a format
* appropriate for displaying a web table.
*
* @param pathQuery the query to execute
* @param pathToBagQueryResult will be populated with results from bag queries used in any LOOKUP
* constraints
* @return results in a format appropriate for display in a web page table
* @throws ObjectStoreException if problem running query
*/
public WebResults execute(PathQuery pathQuery, Map<String, BagQueryResult> pathToBagQueryResult)
throws ObjectStoreException {
Map<String, QuerySelectable> pathToQueryNode = new HashMap<String, QuerySelectable>();
Query q = makeQuery(pathQuery, pathToBagQueryResult, pathToQueryNode);
Results results = os.execute(q, Constants.BATCH_SIZE, true, true, false);
Query realQ = results.getQuery();
if (realQ == q) {
queryToPathToQueryNode.put(q, pathToQueryNode);
} else {
pathToQueryNode = queryToPathToQueryNode.get(realQ);
}
WebResults webResults =
new WebResults(im, pathQuery, results, pathToQueryNode, pathToBagQueryResult);
return webResults;
}
/**
* @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;
}
/** {@inheritDoc} */
@Override
public Results execute(
Query q, int batchSize, boolean optimise, boolean explain, boolean prefetch) {
Results retval = new Results(q, this, getSequence(getComponentsForQuery(q)));
if (batchSize != 0) {
retval.setBatchSize(batchSize);
}
if (!optimise) {
retval.setNoOptimise();
}
if (!explain) {
retval.setNoExplain();
}
if (!prefetch) {
retval.setNoPrefetch();
}
retval.setImmutable();
return retval;
}
private static void runSpanValidationQuery(InterMineAPI im) {
// a Map contains orgName and its chrInfo accordingly
// e.g. <D.Melanogaster, (D.Melanogaster, X, 5000)...>
chrInfoMap = new HashMap<String, List<ChromosomeInfo>>();
try {
Query q = new Query();
QueryClass qcOrg = new QueryClass(Organism.class);
QueryClass qcChr = new QueryClass(Chromosome.class);
// Result columns
QueryField qfOrgName = new QueryField(qcOrg, "shortName");
QueryField qfChrPID = new QueryField(qcChr, "primaryIdentifier");
QueryField qfChrLength = new QueryField(qcChr, "length");
// As in SQL SELECT ?,?,?
q.addToSelect(qfOrgName);
q.addToSelect(qfChrPID);
q.addToSelect(qfChrLength);
// As in SQL FROM ?,?
q.addFrom(qcChr);
q.addFrom(qcOrg);
// As in SQL WHERE ?
QueryObjectReference organism = new QueryObjectReference(qcChr, "organism");
ContainsConstraint ccOrg = new ContainsConstraint(organism, ConstraintOp.CONTAINS, qcOrg);
q.setConstraint(ccOrg);
Results results = im.getObjectStore().execute(q);
// a List contains all the chrInfo (organism, chrPID, length)
List<ChromosomeInfo> chrInfoList = new ArrayList<ChromosomeInfo>();
// a Set contains all the orgName
Set<String> orgSet = new HashSet<String>();
// Handle results
for (Iterator<?> iter = results.iterator(); iter.hasNext(); ) {
ResultsRow<?> row = (ResultsRow<?>) iter.next();
String org = (String) row.get(0);
String chrPID = (String) row.get(1);
Integer chrLength = (Integer) row.get(2);
// Add orgName to HashSet to filter out duplication
orgSet.add(org);
if (chrLength != null) {
ChromosomeInfo chrInfo = new ChromosomeInfo();
chrInfo.setOrgName(org);
chrInfo.setChrPID(chrPID);
chrInfo.setChrLength(chrLength);
// Add ChromosomeInfo to Arraylist
chrInfoList.add(chrInfo);
}
}
// Iterate orgSet and chrInfoList to put data in chrInfoMap which has the key as the
// orgName and value as a ArrayList containing a list of chrInfo which has the same
// orgName
for (String o : orgSet) {
// a List to store chrInfo for the same organism
List<ChromosomeInfo> chrInfoSubList = new ArrayList<ChromosomeInfo>();
for (ChromosomeInfo chrInfo : chrInfoList) {
if (o.equals(chrInfo.getOrgName())) {
chrInfoSubList.add(chrInfo);
chrInfoMap.put(o, chrInfoSubList);
}
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
/** The method to run all the queries. */
@SuppressWarnings("rawtypes")
private void queryExecutor() {
// Use spanOverlapFullResultMap to store the data in the session
@SuppressWarnings("unchecked")
Map<String, Map<GenomicRegion, List<SpanQueryResultRow>>> spanOverlapFullResultMap =
(Map<String, Map<GenomicRegion, List<SpanQueryResultRow>>>)
request.getSession().getAttribute("spanOverlapFullResultMap");
if (spanOverlapFullResultMap == null) {
spanOverlapFullResultMap =
new HashMap<String, Map<GenomicRegion, List<SpanQueryResultRow>>>();
}
Map<GenomicRegion, List<SpanQueryResultRow>> spanOverlapResultDisplayMap =
Collections.synchronizedMap(new LinkedHashMap<GenomicRegion, List<SpanQueryResultRow>>());
// GBrowse track
@SuppressWarnings("unchecked")
Map<String, Map<GenomicRegion, LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>>>>
gbrowseFullTrackMap =
(HashMap<
String,
Map<GenomicRegion, LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>>>>)
request.getSession().getAttribute("gbrowseFullTrackMap");
if (gbrowseFullTrackMap == null) {
gbrowseFullTrackMap =
new HashMap<
String, Map<GenomicRegion, LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>>>>();
}
Map<GenomicRegion, LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>>> gbrowseTrackMap =
Collections.synchronizedMap(
new LinkedHashMap<
GenomicRegion, LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>>>());
if (!spanOverlapFullResultMap.containsKey(spanUUIDString)) {
spanOverlapFullResultMap.put(spanUUIDString, spanOverlapResultDisplayMap);
request.getSession().setAttribute("spanOverlapFullResultMap", spanOverlapFullResultMap);
gbrowseFullTrackMap.put(spanUUIDString, gbrowseTrackMap);
request.getSession().setAttribute("gbrowseFullTrackMap", gbrowseFullTrackMap);
try {
Query q;
for (GenomicRegion aSpan : spanList) {
q = new Query();
q.setDistinct(true);
String chrPID = aSpan.getChr();
Integer start = aSpan.getStart();
Integer end = aSpan.getEnd();
/*
>>>>> TEST CODE <<<<<
LOG.info("OrgName: " + orgName);
LOG.info("chrPID: " + chrPID);
LOG.info("start: " + start);
LOG.info("end: " + end);
LOG.info("FeatureTypes: " + ftKeys);
LOG.info("Submissions: " + subKeys);
>>>>> TEST CODE <<<<<
*/
// DB tables
QueryClass qcOrg = new QueryClass(Organism.class);
QueryClass qcChr = new QueryClass(Chromosome.class);
QueryClass qcFeature = new QueryClass(SequenceFeature.class);
QueryClass qcLoc = new QueryClass(Location.class);
QueryClass qcSubmission = new QueryClass(Submission.class);
QueryField qfOrgName = new QueryField(qcOrg, "shortName");
QueryField qfChrPID = new QueryField(qcChr, "primaryIdentifier");
QueryField qfFeaturePID = new QueryField(qcFeature, "primaryIdentifier");
QueryField qfFeatureId = new QueryField(qcFeature, "id");
QueryField qfFeatureClass = new QueryField(qcFeature, "class");
QueryField qfSubmissionTitle = new QueryField(qcSubmission, "title");
QueryField qfSubmissionDCCid = new QueryField(qcSubmission, "DCCid");
QueryField qfChr = new QueryField(qcChr, "primaryIdentifier");
QueryField qfLocStart = new QueryField(qcLoc, "start");
QueryField qfLocEnd = new QueryField(qcLoc, "end");
q.addToSelect(qfFeatureId);
q.addToSelect(qfFeaturePID);
q.addToSelect(qfFeatureClass);
q.addToSelect(qfChr);
q.addToSelect(qfLocStart);
q.addToSelect(qfLocEnd);
q.addToSelect(qfSubmissionDCCid);
q.addToSelect(qfSubmissionTitle);
q.addFrom(qcChr);
q.addFrom(qcOrg);
q.addFrom(qcFeature);
q.addFrom(qcLoc);
q.addFrom(qcSubmission);
q.addToOrderBy(qfLocStart, "ascending");
ConstraintSet constraints = new ConstraintSet(ConstraintOp.AND);
q.setConstraint(constraints);
// SequenceFeature.organism = Organism
QueryObjectReference organism = new QueryObjectReference(qcFeature, "organism");
ContainsConstraint ccOrg = new ContainsConstraint(organism, ConstraintOp.CONTAINS, qcOrg);
constraints.addConstraint(ccOrg);
// Organism.name = orgName
SimpleConstraint scOrg =
new SimpleConstraint(qfOrgName, ConstraintOp.EQUALS, new QueryValue(orgName));
constraints.addConstraint(scOrg);
// Location.feature = SequenceFeature
QueryObjectReference locSubject = new QueryObjectReference(qcLoc, "feature");
ContainsConstraint ccLocSubject =
new ContainsConstraint(locSubject, ConstraintOp.CONTAINS, qcFeature);
constraints.addConstraint(ccLocSubject);
// Location.locatedOn = Chromosome
QueryObjectReference locObject = new QueryObjectReference(qcLoc, "locatedOn");
ContainsConstraint ccLocObject =
new ContainsConstraint(locObject, ConstraintOp.CONTAINS, qcChr);
constraints.addConstraint(ccLocObject);
// Chromosome.primaryIdentifier = chrPID
SimpleConstraint scChr =
new SimpleConstraint(qfChrPID, ConstraintOp.EQUALS, new QueryValue(chrPID));
constraints.addConstraint(scChr);
// SequenceFeature.submissions = Submission
QueryCollectionReference submission =
new QueryCollectionReference(qcFeature, "submissions");
ContainsConstraint ccSubmission =
new ContainsConstraint(submission, ConstraintOp.CONTAINS, qcSubmission);
constraints.addConstraint(ccSubmission);
// SequenceFeature.class in a list
constraints.addConstraint(new BagConstraint(qfFeatureClass, ConstraintOp.IN, ftKeys));
// Submission.CCDid in a list
constraints.addConstraint(new BagConstraint(qfSubmissionDCCid, ConstraintOp.IN, subKeys));
OverlapRange overlapInput =
new OverlapRange(new QueryValue(start), new QueryValue(end), locObject);
OverlapRange overlapFeature =
new OverlapRange(
new QueryField(qcLoc, "start"), new QueryField(qcLoc, "end"), locObject);
OverlapConstraint oc =
new OverlapConstraint(overlapInput, ConstraintOp.OVERLAPS, overlapFeature);
constraints.addConstraint(oc);
Results results = im.getObjectStore().execute(q);
/*
>>>>> TEST CODE <<<<<
LOG.info("Query: " + q.toString());
LOG.info("Result Size: " + results.size());
LOG.info("Result >>>>> " + results);
>>>>> TEST CODE <<<<<
*/
List<SpanQueryResultRow> spanResults = new ArrayList<SpanQueryResultRow>();
if (results == null || results.isEmpty()) {
spanOverlapResultDisplayMap.put(aSpan, null);
gbrowseTrackMap.put(aSpan, null);
} else {
for (Iterator<?> iter = results.iterator(); iter.hasNext(); ) {
ResultsRow<?> row = (ResultsRow<?>) iter.next();
SpanQueryResultRow aRow = new SpanQueryResultRow();
aRow.setFeatureId((Integer) row.get(0));
aRow.setFeaturePID((String) row.get(1));
aRow.setFeatureClass(((Class) row.get(2)).getSimpleName());
aRow.setChr((String) row.get(3));
aRow.setStart((Integer) row.get(4));
aRow.setEnd((Integer) row.get(5));
aRow.setSubDCCid((String) row.get(6));
aRow.setSubTitle((String) row.get(7));
spanResults.add(aRow);
}
spanOverlapResultDisplayMap.put(aSpan, spanResults);
gbrowseTrackMap.put(aSpan, getSubGbrowseTrack(spanResults)); // Gbrowse
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
}
@Override
protected void execute() throws Exception {
String pathString = request.getParameter("path");
Map<String, Object> attributes = getHeaderAttributes();
output.setHeaderAttributes(attributes);
if (isEmpty(pathString)) {
throw new BadRequestException("No path provided");
}
attributes.put("path", pathString);
kvPairs.put("path", pathString);
String typeConstraintStr = request.getParameter("typeConstraints");
Map<String, String> typeMap = new HashMap<String, String>();
if (!isEmpty(typeConstraintStr)) {
logger.debug(typeConstraintStr);
JSONObject typeJO = new JSONObject(typeConstraintStr);
Iterator<String> it = (Iterator<String>) typeJO.keys();
while (it.hasNext()) {
String name = it.next();
String subType = typeJO.getString(name);
typeMap.put(name, subType);
}
}
Model model = im.getModel();
Path path;
try {
if (typeMap.isEmpty()) {
path = new Path(model, pathString);
} else {
path = new Path(model, pathString, typeMap);
}
} catch (PathException e) {
throw new BadRequestException("Bad path given: " + pathString, e);
}
Query q = new Query();
attributes.put("class", path.getLastClassDescriptor().getUnqualifiedName());
attributes.put("field", path.getLastElement());
String type = ((AttributeDescriptor) path.getEndFieldDescriptor()).getType();
String[] parts = split(type, '.');
reverse(parts);
attributes.put("type", parts[0]);
QueryClass qc = new QueryClass(path.getPrefix().getEndType());
q.addFrom(qc);
QueryField qf1 = new QueryField(qc, path.getLastElement());
q.addToSelect(qf1);
QueryFunction qf = new QueryFunction();
q.addToSelect(qf);
q.addToGroupBy(qf1);
int count = im.getObjectStore().count(q, ObjectStore.SEQUENCE_IGNORE);
if (formatIsCount()) {
output.addResultItem(Arrays.asList(String.valueOf(count)));
} else {
attributes.put("count", count);
Results results = im.getObjectStore().execute(q, DEFAULT_BATCH_SIZE, true, true, false);
Iterator<Object> iter = results.iterator();
while (iter.hasNext()) {
@SuppressWarnings("rawtypes")
List row = (List) iter.next();
Map<String, Object> jsonMap = new HashMap<String, Object>();
jsonMap.put("value", row.get(0));
jsonMap.put("count", row.get(1));
JSONObject jo = new JSONObject(jsonMap);
List<String> forOutput = new ArrayList<String>();
forOutput.add(jo.toString());
if (iter.hasNext()) {
// Standard hack to ensure commas
forOutput.add("");
}
output.addResultItem(forOutput);
}
}
}
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));
}
/** {@inheritDoc} */
public boolean isSingleBatch() {
return osResults.isSingleBatch();
}
/**
* Return the ResultsInfo object from the underlying Results object.
*
* @return the ResultsInfo object
* @throws ObjectStoreException if there is an exception while getting the info
*/
public ResultsInfo getInfo() throws ObjectStoreException {
return osResults.getInfo();
}
/**
* 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);
}
}
/**
* Make a copy of a Results object, but with a different batch size.
*
* @param oldResults the original Results objects
* @param newBatchSize the new batch size
* @return a new Results object with a new batch size
*/
private Results changeResultBatchSize(Results oldResults, int newBatchSize) {
Results newResults =
oldResults.getObjectStore().execute(oldResults.getQuery(), newBatchSize, true, true, true);
return newResults;
}
/** Test that transactions can be aborted */
public void testAbortTransactions() throws Exception {
Address address1 = new Address();
address1.setAddress("Address 3");
Address address2 = new Address();
address2.setAddress("Address 4");
Query q = new Query();
QueryClass qcAddress = new QueryClass(Address.class);
QueryField qf = new QueryField(qcAddress, "address");
ConstraintSet cs1 = new ConstraintSet(ConstraintOp.OR);
cs1.addConstraint(new SimpleConstraint(qf, ConstraintOp.MATCHES, new QueryValue("Address%")));
q.addToSelect(qcAddress);
q.addFrom(qcAddress);
q.addToOrderBy(qf);
q.setConstraint(cs1);
Results res = writer.execute(q);
assertEquals(res.toString(), 0, res.size());
res = realOs.execute(q);
assertEquals(res.toString(), 0, res.size());
writer.beginTransaction();
assertTrue(writer.isInTransaction());
writer.store(address1);
writer.store(address2);
// TODO: These lines now fail, because we do not allow querying on writers with uncommitted
// data. The writer should relax this restriction.
res = writer.execute(q);
assertEquals(2, res.size());
res = realOs.execute(q);
assertEquals(res.toString(), 0, res.size());
writer.abortTransaction();
assertFalse(writer.isInTransaction());
// Should be nothing there unless we commit
res = writer.execute(q);
assertEquals(res.toString(), 0, res.size());
res = realOs.execute(q);
assertEquals(res.toString(), 0, res.size());
}
/**
* Returns the ObjectStore's maximum allowable offset.
*
* @return an int
*/
public int getMaxRetrievableIndex() {
return osResults.getObjectStore().getMaxOffset();
}