/**
* Return the query specified in the request, shorn of all duplicate classes in the view. Note, it
* is the users responsibility to ensure that there are only SequenceFeatures in the view.
*
* @return A query.
*/
protected PathQuery getQuery() {
String xml = getRequiredParameter(XML_PARAM);
PathQueryBuilder builder = getQueryBuilder(xml);
PathQuery pq = builder.getQuery();
List<String> newView = new ArrayList<String>();
Set<ClassDescriptor> seenTypes = new HashSet<ClassDescriptor>();
for (String viewPath : pq.getView()) {
Path p;
try {
p = new Path(pq.getModel(), viewPath);
} catch (PathException e) {
throw new BadRequestException("Query is invalid", e);
}
ClassDescriptor cd = p.getLastClassDescriptor();
if (!seenTypes.contains(cd)) {
newView.add(viewPath);
}
seenTypes.add(cd);
}
if (!newView.equals(pq.getView())) {
pq.clearView();
pq.addViews(newView);
}
return pq;
}
@Override
protected void execute() throws Exception {
Profile profile = getPermission().getProfile();
PathQueryExecutor executor = this.im.getPathQueryExecutor(profile);
// For FASTA/BED/GFF only set Gene.id in the view in im-tables system
PathQuery pathQuery = getQuery();
checkPathQuery(pathQuery);
// Bring back original views for extra fields to be included in data export
// NB: Functional but bad practice?
// view in http request will look like: view=Gene.name&view=Gene.length...
// Support the standard mechanism for accepting multiple parameter values
List<String> views = getPathQueryViews(request.getParameterValues(VIEW_PARAM));
if (views != null) {
try {
pathQuery.addViews(views);
} catch (IllegalArgumentException e) {
throw new BadRequestException("Bad value for view parameter", e);
}
// Remove duplicates in views
ArrayList<String> al = new ArrayList<String>();
al.clear();
al.addAll(new LinkedHashSet<String>(pathQuery.getView()));
pathQuery.clearView();
pathQuery.addViews(al);
}
Exporter exporter = getExporter(pathQuery);
ExportResultsIterator iter = null;
try {
iter = executor.execute(pathQuery, 0, WebServiceRequestParser.DEFAULT_LIMIT);
iter.goFaster();
exporter.export(iter);
} finally {
if (iter != null) {
iter.releaseGoFaster();
}
}
}
