@SuppressWarnings("unchecked")
@Override
public void display(HttpServletRequest request, ReportObject reportObject) {
// get the gene/protein in question from the request
InterMineObject object = reportObject.getObject();
// wrapper for the result so we can say what type it is
HashMap<String, Object> result = new HashMap();
// API connection
HttpSession session = request.getSession();
final InterMineAPI im = SessionMethods.getInterMineAPI(session);
Model model = im.getModel();
PathQuery query = new PathQuery(model);
// dealing with genes...
if (object instanceof Gene) {
// cast me Gene
Gene gene = (Gene) object;
String geneID = String.valueOf(gene.getId());
query = geneCommentsQuery(geneID, query);
Profile profile = SessionMethods.getProfile(session);
PathQueryExecutor executor = im.getPathQueryExecutor(profile);
ExportResultsIterator values;
try {
values = executor.execute(query);
} catch (ObjectStoreException e) {
throw new RuntimeException(e);
}
result.put("gene", geneComments2(values));
// result.put("gene", geneComments(gene));
} else if (object instanceof Protein) {
// cast me Protein
Protein protein = (Protein) object;
String proteinID = String.valueOf(protein.getId());
query = proteinCommentsQuery(proteinID, query);
Profile profile = SessionMethods.getProfile(session);
PathQueryExecutor executor = im.getPathQueryExecutor(profile);
ExportResultsIterator values;
try {
values = executor.execute(query);
} catch (ObjectStoreException e) {
throw new RuntimeException(e);
}
result.put("protein", proteinComments2(values));
// result.put("protein", proteinComments(protein));
} else {
// big fat fail
}
request.setAttribute("response", result);
}
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());
}
@Override
public void display(HttpServletRequest request, ReportObject reportObject) {
// get the gene/protein in question from the request
InterMineObject object = reportObject.getObject();
// API connection
HttpSession session = request.getSession();
final InterMineAPI im = SessionMethods.getInterMineAPI(session);
Model model = im.getModel();
PathQuery query = new PathQuery(model);
// cast me Gene
Gene gene = (Gene) object;
Object genePrimaryIDObj = gene.getPrimaryIdentifier();
if (genePrimaryIDObj != null) {
// fetch the expression
String genePrimaryID = String.valueOf(genePrimaryIDObj);
query = geneExpressionAtlasQuery(genePrimaryID, query);
// execute the query
Profile profile = SessionMethods.getProfile(session);
PathQueryExecutor executor = im.getPathQueryExecutor(profile);
ExportResultsIterator values = executor.execute(query);
// convert to a map
GeneExpressionAtlasDiseasesExpressions geae =
new GeneExpressionAtlasDiseasesExpressions(values);
// attach to results
request.setAttribute("expressions", geae);
request.setAttribute("url", "http://www.ebi.ac.uk/gxa/experiment/E-MTAB-62/" + genePrimaryID);
request.setAttribute("defaultPValue", "1e-4");
request.setAttribute("defaultTValue", "4");
// get the corresponding collection
for (FieldDescriptor fd : reportObject.getClassDescriptor().getAllFieldDescriptors()) {
if ("atlasExpression".equals(fd.getName()) && fd.isCollection()) {
// fetch the collection
Collection<?> collection = null;
try {
collection = (Collection<?>) reportObject.getObject().getFieldValue("atlasExpression");
} catch (IllegalAccessException e) {
e.printStackTrace();
}
List<Class<?>> lc =
PathQueryResultHelper.queryForTypesInCollection(
reportObject.getObject(), "atlasExpression", im.getObjectStore());
// create an InlineResultsTable
InlineResultsTable t =
new InlineResultsTable(
collection,
fd.getClassDescriptor().getModel(),
SessionMethods.getWebConfig(request),
im.getClassKeys(),
collection.size(),
false,
lc);
request.setAttribute("collection", t);
break;
}
}
}
}