/**
* Generates the getElementType method.
*
* @param cld the ClassDescriptor
* @return a String with the method
*/
public String generateGetElementType(ClassDescriptor cld) {
StringBuffer sb = new StringBuffer();
sb.append(INDENT).append("public Class<?> getElementType(final String fieldName) {\n");
for (FieldDescriptor field : cld.getAllFieldDescriptors()) {
if (field.isCollection()) {
sb.append(INDENT + INDENT)
.append("if (\"" + field.getName() + "\".equals(fieldName)) {\n")
.append(INDENT + INDENT + INDENT)
.append(
"return " + ((CollectionDescriptor) field).getReferencedClassName() + ".class;\n")
.append(INDENT + INDENT)
.append("}\n");
}
}
sb.append(INDENT + INDENT)
.append("if (!" + cld.getName() + ".class.equals(getClass())) {\n")
.append(INDENT + INDENT + INDENT)
.append("return TypeUtil.getElementType(" + cld.getName() + ".class, fieldName);\n")
.append(INDENT + INDENT)
.append("}\n")
.append(INDENT + INDENT)
.append("throw new IllegalArgumentException(\"Unknown field \" + fieldName);\n")
.append(INDENT)
.append("}\n");
return sb.toString();
}
private String getTaggedType(FieldDescriptor fd) {
if (fd.isCollection()) {
return "collection";
} else if (fd.isReference()) {
return "reference";
}
return "attribute";
}
/**
* Generates the addCollectionElement method.
*
* @param cld the ClassDescriptor
* @return a String with the method
*/
public String generateAddCollectionElement(ClassDescriptor cld) {
StringBuffer sb = new StringBuffer();
sb.append(INDENT)
.append("public void addCollectionElement(final String fieldName,")
.append(" final org.intermine.model.InterMineObject element) {\n")
.append(INDENT + INDENT);
for (FieldDescriptor field : cld.getAllFieldDescriptors()) {
if (field.isCollection()) {
String fieldName = field.getName();
if ("fieldName".equals(fieldName)) {
fieldName = "this.fieldName";
} else if ("element".equals(fieldName)) {
fieldName = "this.element";
}
sb.append("if (\"" + field.getName() + "\".equals(fieldName)) {\n")
.append(INDENT + INDENT + INDENT)
.append(
fieldName
+ ".add(("
+ ((CollectionDescriptor) field).getReferencedClassName()
+ ") element);\n")
.append(INDENT + INDENT)
.append("} else ");
}
}
sb.append("{\n")
.append(INDENT + INDENT + INDENT)
.append("if (!" + cld.getName() + ".class.equals(getClass())) {\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append("TypeUtil.addCollectionElement(this, fieldName, element);\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append("return;\n")
.append(INDENT + INDENT + INDENT)
.append("}\n")
.append(INDENT + INDENT + INDENT)
.append("throw new IllegalArgumentException(\"Unknown collection \" + fieldName);\n")
.append(INDENT + INDENT)
.append("}\n")
.append(INDENT)
.append("}\n");
return sb.toString();
}
@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;
}
}
}
}
