/** {@inheritDoc} */
@Override
public ActionForward execute(
@SuppressWarnings("unused") ActionMapping mapping,
@SuppressWarnings("unused") ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
HttpSession session = request.getSession();
final InterMineAPI im = SessionMethods.getInterMineAPI(session);
ObjectStore os = im.getObjectStore();
WebConfig webConfig = SessionMethods.getWebConfig(request);
Integer objectId = new Integer(request.getParameter("object"));
String fieldName = request.getParameter("field");
String fileType = request.getParameter("type");
InterMineObject object = os.getObjectById(objectId);
FieldExporter fieldExporter = null;
Set classes = DynamicUtil.decomposeClass(object.getClass());
Iterator classIter = classes.iterator();
while (classIter.hasNext()) {
Class c = (Class) classIter.next();
Type thisTypeConfig = webConfig.getTypes().get(c.getName());
FieldConfig fc = thisTypeConfig.getFieldConfigMap().get(fieldName);
if (fc != null) {
String fieldExporterClassName = fc.getFieldExporter();
if (fieldExporterClassName != null) {
fieldExporter = (FieldExporter) Class.forName(fieldExporterClassName).newInstance();
break;
}
}
}
if (fieldExporter == null) {
Object fieldValue = object.getFieldValue(fieldName);
if (fileType == null || fileType.length() == 0) {
response.setContentType("text/plain; charset=UTF-8");
response.setHeader("Content-Disposition ", "inline; filename=" + fieldName + ".txt");
} else {
response.setContentType("text/" + fileType);
response.setHeader(
"Content-Disposition ", "inline; filename=" + fieldName + "." + fileType);
}
PrintStream out = new PrintStream(response.getOutputStream());
if (fieldValue instanceof ClobAccess) {
((ClobAccess) fieldValue).drainToPrintStream(out);
} else {
out.print(fieldValue);
}
out.flush();
} else {
fieldExporter.exportField(object, fieldName, os, response);
}
return null;
}
private InterMineObject getRequestedObject(InterMineAPI im, HttpServletRequest request) {
String idString = request.getParameter("id");
Integer id = new Integer(Integer.parseInt(idString));
ObjectStore os = im.getObjectStore();
InterMineObject requestedObject = null;
try {
requestedObject = os.getObjectById(id);
} catch (ObjectStoreException e) {
Log.warn("Accessed report page with id: " + id + " but failed to find object.", e);
}
return requestedObject;
}
/** {@inheritDoc} */
@Override
public ActionForward execute(
ComponentContext context,
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
boolean canExportAsBED = false;
HttpSession session = request.getSession();
final InterMineAPI im = SessionMethods.getInterMineAPI(session);
Model model = im.getModel();
PathQuery query = new PathQuery(model);
// org and dbkey for galaxy use
Set<String> orgSet = new HashSet<String>();
Set<String> genomeBuildSet = new HashSet<String>();
// Build GenomicRegion pathquery, the request is from GenomicRegionSearch "export to Galaxy"
if (request.getParameter("featureIds") != null) {
String featureIds = request.getParameter("featureIds").trim();
String orgName = request.getParameter("orgName");
if (orgName != null && !"".equals(orgName)) {
orgSet.add(orgName);
}
// Refer to GenomicRegionSearchService.getExportFeaturesQuery method
String path = "SequenceFeature";
query.addView(path + ".primaryIdentifier");
query.addView(path + ".chromosomeLocation.locatedOn.primaryIdentifier");
query.addView(path + ".chromosomeLocation.start");
query.addView(path + ".chromosomeLocation.end");
query.addView(path + ".organism.name");
// use ids or pids
String[] idsInStr = featureIds.split(",");
Set<Integer> ids = new HashSet<Integer>();
boolean isIds = true;
for (String id : idsInStr) {
id = id.trim();
if (!Pattern.matches("^\\d+$", id)) {
isIds = false;
break;
}
ids.add(Integer.valueOf(id));
}
if (isIds) {
query.addConstraint(Constraints.inIds(path, ids));
} else {
if (featureIds.contains("'")) {
featureIds = featureIds.replaceAll("'", "\\\\'");
}
query.addConstraint(Constraints.lookup(path, featureIds, null));
}
canExportAsBED = true;
} else { // request from normal result table
String tableName = request.getParameter("table");
request.setAttribute("table", tableName);
PagedTable pt = SessionMethods.getResultsTable(session, tableName);
// Null check to page table, maybe session timeout?
if (pt == null) {
LOG.error("Page table is NULL...");
return null;
}
// Check if can export as BED
TableHttpExporter tableExporter = new BEDHttpExporter();
try {
canExportAsBED = tableExporter.canExport(pt);
} catch (Exception e) {
canExportAsBED = false;
LOG.error("Caught an error running canExport() for: BEDHttpExporter. " + e);
e.printStackTrace();
}
LinkedHashMap<Path, Integer> exportClassPathsMap = getExportClassPaths(pt);
List<Path> exportClassPaths = new ArrayList<Path>(exportClassPathsMap.keySet());
Map<String, String> pathMap = new LinkedHashMap<String, String>();
for (Path path : exportClassPaths) {
String pathString = path.toStringNoConstraints();
String displayPath = pathString.replace(".", " > ");
pathMap.put(pathString, displayPath);
}
Map<String, Integer> pathIndexMap = new LinkedHashMap<String, Integer>();
for (int index = 0; index < exportClassPaths.size(); index++) {
String pathString = exportClassPaths.get(index).toStringNoConstraints();
Integer idx = exportClassPathsMap.get(exportClassPaths.get(index));
pathIndexMap.put(pathString, idx);
}
request.setAttribute("exportClassPaths", pathMap);
request.setAttribute("pathIndexMap", pathIndexMap);
// Support export public and private lists to Galaxy
query = pt.getWebTable().getPathQuery();
ObjectStore os = im.getObjectStore();
Map<PathConstraint, String> constrains = query.getConstraints();
for (PathConstraint constraint : constrains.keySet()) {
if (constraint instanceof PathConstraintBag) {
String bagName = ((PathConstraintBag) constraint).getBag();
InterMineBag imBag =
im.getBagManager().getBag(SessionMethods.getProfile(session), bagName);
// find the classKeys
Set<String> classKeySet = new LinkedHashSet<String>();
for (Integer id : imBag.getContentsAsIds()) {
String classKey = pt.findClassKeyValue(im.getClassKeys(), os.getObjectById(id));
classKeySet.add(classKey);
}
String path = ((PathConstraintBag) constraint).getPath();
// replace constraint in the pathquery
PathConstraintLookup newConstraint =
new PathConstraintLookup(
path,
classKeySet.toString().substring(1, classKeySet.toString().length() - 1),
null);
query.replaceConstraint(constraint, newConstraint);
}
}
orgSet = SequenceFeatureExportUtil.getOrganisms(query, session);
}
if (query instanceof TemplateQuery) {
TemplateQuery templateQuery = (TemplateQuery) query;
Map<PathConstraint, SwitchOffAbility> constraintSwitchOffAbilityMap =
templateQuery.getConstraintSwitchOffAbility();
for (Map.Entry<PathConstraint, SwitchOffAbility> entry :
constraintSwitchOffAbilityMap.entrySet()) {
if (entry.getValue().compareTo(SwitchOffAbility.OFF) == 0) {
templateQuery.removeConstraint(entry.getKey());
}
}
}
String queryXML =
PathQueryBinding.marshal(query, "", model.getName(), PathQuery.USERPROFILE_VERSION);
// String encodedQueryXML = URLEncoder.encode(queryXML, "UTF-8");
String tableViewURL =
new URLGenerator(request).getPermanentBaseURL() + "/service/query/results";
request.setAttribute("tableURL", tableViewURL);
request.setAttribute("queryXML", queryXML);
request.setAttribute("size", 1000000);
// If can export as BED
request.setAttribute("canExportAsBED", canExportAsBED);
if (canExportAsBED) {
String bedURL =
new URLGenerator(request).getPermanentBaseURL() + "/service/query/results/bed";
request.setAttribute("bedURL", bedURL);
genomeBuildSet =
(Set<String>) OrganismGenomeBuildLookup.getGenomeBuildByOrgansimCollection(orgSet);
String org =
(orgSet.size() < 1) ? "Organism information not available" : StringUtil.join(orgSet, ",");
// possible scenario: [null, ce3, null], should remove all null element and then join
genomeBuildSet.removeAll(Collections.singleton(null));
String dbkey =
(genomeBuildSet.size() < 1)
? "Genome Build information not available"
: StringUtil.join(genomeBuildSet, ",");
request.setAttribute("org", org);
request.setAttribute("dbkey", dbkey);
}
// PathMap
Map<String, String> pathsMap = new LinkedHashMap<String, String>();
List<String> views = query.getView();
for (String view : views) {
String title = query.getGeneratedPathDescription(view);
title = WebUtil.formatColumnName(title);
pathsMap.put(view, title);
}
request.setAttribute("pathsMap", pathsMap);
return null;
}
public void testSetChromosomeLocationsAndLengths() throws Exception {
Chromosome chr1 =
(Chromosome) DynamicUtil.createObject(Collections.singleton(Chromosome.class));
chr1.setPrimaryIdentifier("1");
chr1.setId(new Integer(101));
Chromosome chr2 =
(Chromosome) DynamicUtil.createObject(Collections.singleton(Chromosome.class));
chr1.setPrimaryIdentifier("2");
chr1.setId(new Integer(102));
Exon exon1 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
exon1.setId(new Integer(107));
exon1.setLength(new Integer(1000));
Exon exon2 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
exon2.setId(new Integer(108));
Exon exon3 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
exon3.setId(new Integer(109));
// exon 2 has two chromosome locations, shouldn't get chromosome[Location] references
Location exon1OnChr = createLocation(chr1, exon1, "1", 51, 100, Location.class);
exon1OnChr.setId(new Integer(1010));
Location exon2OnChr = createLocation(chr2, exon2, "1", 201, 250, Location.class);
exon2OnChr.setId(new Integer(1011));
Location exon2OnChrDup = createLocation(chr1, exon2, "1", 501, 550, Location.class);
exon2OnChrDup.setId(new Integer(1012));
Location exon3OnChr = createLocation(chr2, exon3, "1", 601, 650, Location.class);
exon3OnChr.setId(new Integer(1013));
Set<InterMineObject> toStore =
new HashSet<InterMineObject>(
Arrays.asList(
new InterMineObject[] {
chr1, chr2, exon1, exon2, exon3, exon1OnChr, exon2OnChr, exon2OnChrDup, exon3OnChr
}));
for (InterMineObject imo : toStore) {
osw.store(imo);
}
CalculateLocations cl = new CalculateLocations(osw);
cl.setChromosomeLocationsAndLengths();
ObjectStore os = osw.getObjectStore();
Exon resExon1 = (Exon) os.getObjectById(new Integer(107));
Exon resExon2 = (Exon) os.getObjectById(new Integer(108));
Exon resExon3 = (Exon) os.getObjectById(new Integer(109));
assertEquals(chr1.getId(), resExon1.getChromosome().getId());
assertEquals(exon1OnChr.getId(), resExon1.getChromosomeLocation().getId());
assertNull(resExon2.getChromosome());
assertNull(resExon2.getChromosomeLocation());
assertEquals(chr2.getId(), resExon3.getChromosome().getId());
assertEquals(exon3OnChr.getId(), resExon3.getChromosomeLocation().getId());
// exon1 has length set so should stay as 1000, exon3 should get length 50 set from location
assertEquals(new Integer(1000), resExon1.getLength());
assertEquals(new Integer(50), resExon3.getLength());
// nothing done to exon2
assertNull(resExon2.getLength());
}
public void testCreateSpanningLocations() throws Exception {
Exon exon1 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
exon1.setId(new Integer(107));
Exon exon2 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
exon2.setId(new Integer(108));
Exon exon3 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
exon3.setId(new Integer(109));
Location exon1OnChr = createLocation(getChromosome(), exon1, "1", 51, 100, Location.class);
exon1OnChr.setId(new Integer(1010));
Location exon2OnChr = createLocation(getChromosome(), exon2, "1", 201, 250, Location.class);
exon2OnChr.setId(new Integer(1011));
Location exon3OnChr = createLocation(getChromosome(), exon3, "1", 201, 400, Location.class);
exon3OnChr.setId(new Integer(1012));
Transcript trans1 =
(Transcript) DynamicUtil.createObject(Collections.singleton(Transcript.class));
trans1.setId(new Integer(201));
Transcript trans2 =
(Transcript) DynamicUtil.createObject(Collections.singleton(Transcript.class));
trans2.setId(new Integer(202));
Location trans2OnChr = createLocation(getChromosome(), trans2, "1", 61, 300, Location.class);
Gene gene = (Gene) DynamicUtil.createObject(Collections.singleton(Gene.class));
gene.setId(new Integer(301));
exon1.setTranscripts(new HashSet<Transcript>(Arrays.asList(new Transcript[] {trans1})));
exon2.setTranscripts(new HashSet<Transcript>(Arrays.asList(new Transcript[] {trans1})));
// the location of exon3 should be ignored by createSpanningLocations() because trans2
// already has a location
exon3.setTranscripts(new HashSet<Transcript>(Arrays.asList(new Transcript[] {trans2})));
trans1.setGene(gene);
trans2.setGene(gene);
Set<InterMineObject> toStore =
new HashSet<InterMineObject>(
Arrays.asList(
new InterMineObject[] {
getChromosome(),
gene,
trans1,
trans2,
exon1,
exon2,
exon3,
exon1OnChr,
exon2OnChr,
trans2OnChr
}));
for (InterMineObject imo : toStore) {
osw.store(imo);
}
CalculateLocations cl = new CalculateLocations(osw);
cl.createSpanningLocations("Transcript", "Exon", "exons");
cl.createSpanningLocations("Gene", "Transcript", "transcripts");
ObjectStore os = osw.getObjectStore();
Transcript resTrans1 = (Transcript) os.getObjectById(new Integer(201));
Assert.assertEquals(1, resTrans1.getLocations().size());
Location resTrans1Location = (Location) resTrans1.getLocations().iterator().next();
Assert.assertEquals(51, resTrans1Location.getStart().intValue());
Assert.assertEquals(250, resTrans1Location.getEnd().intValue());
Transcript resTrans2 = (Transcript) os.getObjectById(new Integer(202));
Assert.assertEquals(1, resTrans2.getLocations().size());
Location resTrans2Location = (Location) resTrans2.getLocations().iterator().next();
Assert.assertEquals(61, resTrans2Location.getStart().intValue());
Assert.assertEquals(300, resTrans2Location.getEnd().intValue());
Gene resGene = (Gene) os.getObjectById(new Integer(301));
Assert.assertEquals(1, resGene.getLocations().size());
Location resGeneLocation = (Location) resGene.getLocations().iterator().next();
Assert.assertEquals(51, resGeneLocation.getStart().intValue());
Assert.assertEquals(300, resGeneLocation.getEnd().intValue());
}