@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);
}
/**
* @param pt paged table
* @param request request
* @return all results of pathquery corresponding specified paged table.
*/
public ExportResultsIterator getResultRows(PagedTable pt, HttpServletRequest request) {
PathQuery pathQuery = pt.getWebTable().getPathQuery();
HttpSession session = request.getSession();
final InterMineAPI im = SessionMethods.getInterMineAPI(session);
Profile profile = SessionMethods.getProfile(session);
executor = im.getPathQueryExecutor(profile);
executor.setBatchSize(BATCH_SIZE);
return executor.execute(pathQuery);
}
@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;
}
}
}
}