public void setUp() throws Exception {
super.setUp();
userprofileOS.setModel(Model.getInstanceByName("userprofile"));
Model testmodel = Model.getInstanceByName("testmodel");
query = new PathQuery(testmodel);
query.addView("Employee");
query.addView("Employee.name");
queryBag = new PathQuery(testmodel);
queryBag.addView("Employee");
queryBag.addView("Employee.name");
queryBag.addConstraint(Constraints.in("Employee", "bag2"));
sq = new SavedQuery("query1", date, query);
sqBag = new SavedQuery("query3", date, queryBag);
hist = new SavedQuery("query2", date, (PathQuery) query.clone());
hist2 = new SavedQuery("query1", date, query.clone());
template = new TemplateQuery("template", "ttitle", "tdesc", new PathQuery(testmodel));
SessionMethods.initSession(this.getSession());
Profile profile = (Profile) getSession().getAttribute(Constants.PROFILE);
profile.saveQuery(sq.getName(), sq);
profile.saveQuery(sqBag.getName(), sqBag);
profile.saveHistory(hist);
profile.saveHistory(hist2);
}
@AfterClass
public static void shutdown() {
int deleted = 0;
if (osw != null) {
try {
osw.beginTransaction();
PathQuery pq = new PathQuery(osw.getModel());
pq.addView("Types.id");
pq.addConstraint(Constraints.eq("Types.name", "histo*"));
Query q = MainHelper.makeQuery(pq, new HashMap(), new HashMap(), null, new HashMap());
Results res = osw.execute(q, 50000, true, false, true);
for (Object row : res) {
Types thing = (Types) ((List) row).get(0);
osw.delete(thing);
deleted++;
}
osw.commitTransaction();
} catch (ObjectStoreException e) {
LOG.warn(e);
}
try {
osw.close();
} catch (ObjectStoreException e) {
LOG.warn(e);
}
}
System.out.printf("\n[CLEAN UP] Deleted %d things\n", deleted);
}
@SuppressWarnings("unchecked")
@Override
public boolean removeAll(@SuppressWarnings("rawtypes") Collection c) {
int priorSize = getSize();
if (c instanceof ItemList) {
ItemList res = subtract(((ItemList) c));
update(res);
delete();
res.rename(getName());
} else if (!c.isEmpty()) {
try {
Item[] is = (Item[]) c.toArray(new Item[0]);
String path = is[0].getType() + ".id";
PathQuery pq = new PathQuery(services.getModel());
pq.addView(path);
pq.addConstraint(
Constraints.oneOfValues(
path,
collect(
collect(Arrays.asList(is), invokerTransformer("getId")),
stringValueTransformer())));
createListAndSubtract(pq);
} catch (ArrayStoreException e) {
// Do nothing - we didn't get a collection of items.
}
}
return priorSize != getSize();
}
/**
* Used for making a query for a reference or collection. Only used when a user clicks on [show
* all] under an inline table on an Object's report page. The type of that object is
* "startingPath", eg. Department. This path will be prepended to every path in the query. The
* "type" is the type of the reference/collection, eg. Employee.
*
* <p>TODO use getDefaultViewForClass() instead
*
* @param objType class of object we are querying for eg. Manager
* @param model the model
* @param webConfig the webconfig
* @param fieldType the type of the field this object is in, eg Employee
* @return query, eg. Department.employees.name
*/
protected static PathQuery getQueryWithDefaultView(
String objType, Model model, WebConfig webConfig, String fieldType) {
String prefix = fieldType;
PathQuery query = new PathQuery(model);
ClassDescriptor cld = model.getClassDescriptorByName(objType);
List<FieldConfig> fieldConfigs = getClassFieldConfigs(webConfig, cld);
if (!StringUtils.isBlank(prefix)) {
try {
// if the type is different to the end of the prefix path, add a subclass constraint
Path fieldPath = new Path(model, fieldType);
String fieldEndType = TypeUtil.unqualifiedName(fieldPath.getEndType().getName());
if (!fieldEndType.equals(objType)) {
query.addConstraint(Constraints.type(fieldType, objType));
}
} catch (PathException e) {
LOG.error("Invalid path configured in webconfig for class: " + objType);
}
}
for (FieldConfig fieldConfig : fieldConfigs) {
if (fieldConfig.getShowInResults()) {
String path = prefix + "." + fieldConfig.getFieldExpr();
int from = prefix.length() + 1;
while (path.indexOf('.', from) != -1) {
int dotPos = path.indexOf('.', from);
int nextDot = path.indexOf('.', dotPos + 1);
String outerJoin = nextDot == -1 ? path.substring(0, dotPos) : path.substring(0, nextDot);
query.setOuterJoinStatus(outerJoin, OuterJoinStatus.OUTER);
from = dotPos + 1;
}
query.addView(path);
}
}
if (query.getView().size() == 0) {
for (AttributeDescriptor att : cld.getAllAttributeDescriptors()) {
if (!"id".equals(att.getName())) {
query.addView(prefix + "." + att.getName());
}
}
}
return query;
}
@Override
public boolean remove(Object i) {
int priorSize = getSize();
if (i instanceof Item) {
Item item = (Item) i;
String path = item.getType() + ".id";
PathQuery pq = new PathQuery(services.getModel());
pq.addView(path);
pq.addConstraint(Constraints.eq(path, Integer.toString(item.getId())));
createListAndSubtract(pq);
}
return priorSize != getSize();
}
/**
* Tell the requester about all the reference sequences that have data (are of non-zero length)
* and are in the correct domain.
*/
private void serveRefSeqs() {
Model m = im.getModel();
ClassDescriptor ref = m.getClassDescriptorByName(refType);
if (ref == null) {
throw new ResourceNotFoundException("No class called " + ref);
}
PathQuery pq = new PathQuery(m);
pq.addView(refType + ".id");
pq.addConstraint(Constraints.greaterThan(refType + "." + lengthPath, "0"));
pq.addConstraint(Constraints.eq(refType + "." + domainPath, domain));
Query q = pathQueryToOSQ(pq);
SingletonResults res = im.getObjectStore().executeSingleton(q);
if (res.size() == 0) {
throw new ResourceNotFoundException("No " + refType + "s on " + domain);
}
Iterator<Object> it = res.iterator();
while (it.hasNext()) {
FastPathObject o = (FastPathObject) it.next();
Map<String, Object> refseq = makeRefSeq(o);
addResultItem(refseq, it.hasNext());
}
}
/** {@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;
}
