/**
* Create summary information of the paths currently in a query and their constraints for display
* in the QueryBuilder summary section. The list of SummaryPath objects collect information for
* simple display in the JSP.
*
* @param query the query to create summary information from
* @return a list if summary information about paths on the query
* @throws PathException if the PathQuery is invalid
*/
public static List<SummaryPath> getDisplaySummary(PathQuery query) throws PathException {
Set<SummaryPath> summaryPaths = new TreeSet<SummaryPath>();
Set<String> constrainedPaths = new HashSet<String>();
for (PathConstraint con : query.getConstraints().keySet()) {
if (con instanceof PathConstraintSubclass) {
// Do nothing
} else if (con instanceof PathConstraintLoop) {
// Put both paths in
constrainedPaths.add(con.getPath());
constrainedPaths.add(((PathConstraintLoop) con).getLoopPath());
} else {
constrainedPaths.add(con.getPath());
}
}
List<String> lockedPaths = findLockedPaths(query);
List<String> forcedInnerJoins = findForcedInnerJoins(query);
Set<String> paths = new HashSet<String>();
paths.addAll(constrainedPaths);
paths.addAll(query.getView());
paths.addAll(query.getOuterJoinGroups().keySet());
for (String stringPath : paths) {
Path path = query.makePath(stringPath);
boolean isLocked = lockedPaths.contains(path.toStringNoConstraints());
boolean isForcedInner = forcedInnerJoins.contains(path.toStringNoConstraints());
SummaryPath summaryPath = new SummaryPath(path, isLocked, isForcedInner);
for (PathConstraint con : query.getConstraintsForPath(path.toStringNoConstraints())) {
boolean editable = false;
String description = null;
String switchable = SwitchOffAbility.LOCKED.toString().toLowerCase();
if (query instanceof TemplateQuery) {
TemplateQuery template = (TemplateQuery) query;
editable = template.getEditableConstraints().contains(con);
description = template.getConstraintDescriptions().get(con);
SwitchOffAbility constraintSwitchOffAbility =
template.getConstraintSwitchOffAbility().get(con);
if (SwitchOffAbility.ON.equals(constraintSwitchOffAbility)) {
switchable = SwitchOffAbility.ON.toString().toLowerCase();
} else if (SwitchOffAbility.OFF.equals(constraintSwitchOffAbility)) {
switchable = SwitchOffAbility.OFF.toString().toLowerCase();
}
}
// subclass constraints aren't display
if (!(con instanceof PathConstraintSubclass)) {
String code = query.getConstraints().get(con);
summaryPath.addSummaryConstraint(
new SummaryConstraint(con, code, editable, description, switchable));
} else {
summaryPath.setSubclass(((PathConstraintSubclass) con).getType());
}
}
summaryPaths.add(summaryPath);
}
return new ArrayList<SummaryPath>(summaryPaths);
}
/**
* 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;
}
/**
* Create a PathQuery to get results for a collection of items from an InterMineObject
*
* @param webConfig the WebConfig
* @param os the production ObjectStore
* @param object the InterMineObject
* @param referencedClassName the collection type
* @param field the name of the field for the collection in the InterMineObject
* @return a PathQuery
*/
public static PathQuery makePathQueryForCollection(
WebConfig webConfig,
ObjectStore os,
InterMineObject object,
String referencedClassName,
String field) {
String className = TypeUtil.unqualifiedName(DynamicUtil.getSimpleClassName(object.getClass()));
Path path;
try {
path = new Path(os.getModel(), className + "." + field);
} catch (PathException e) {
throw new IllegalArgumentException(
"Could not build path for \"" + className + "." + field + "\".");
}
List<Class<?>> types = new ArrayList<Class<?>>();
if (path.endIsCollection()) {
CollectionDescriptor end = (CollectionDescriptor) path.getEndFieldDescriptor();
// Only look for types if the refClass exactly matches the path type.
if (end.getReferencedClassName().equals(referencedClassName)) {
types = queryForTypesInCollection(object, field, os);
}
if (types.isEmpty()) {
// the collection was empty, but still generate a query with the collection type
types.add(os.getModel().getClassDescriptorByName(referencedClassName).getType());
}
} else if (path.endIsReference()) {
types.add(path.getLastClassDescriptor().getType());
}
return makePathQueryForCollectionForClass(webConfig, os.getModel(), object, field, types);
}
// replace final dot in path with '+' if path represents and attribute, used for path ordering
private String replaceAttributeDots(Path p) {
String strPath = p.toStringNoConstraints();
if (p.endIsAttribute()) {
int lastIndex = strPath.lastIndexOf('.');
strPath = strPath.substring(0, lastIndex) + "+" + strPath.substring(lastIndex + 1);
}
return strPath;
}
/**
* Returns a List of paths, being the given path and all its parents.
*
* @param pathString a path String
* @param pathQuery a PathQuery object to use to create a Path object
* @return a List of path Strings
* @throws PathException if something goes wrong
*/
protected static List<String> findParentPaths(String pathString, PathQuery pathQuery)
throws PathException {
Path path = pathQuery.makePath(pathString);
List<String> retval = new ArrayList<String>();
retval.add(path.getNoConstraintsString());
while (!path.isRootPath()) {
path = path.getPrefix();
retval.add(path.getNoConstraintsString());
}
return retval;
}
private static List<String> getSubview(WebConfig webConfig, Model m, Path path)
throws PathException {
List<String> subview = new ArrayList<String>();
String basePath = path.toStringNoConstraints() + ".";
List<FieldConfig> subconfs = getClassFieldConfigs(webConfig, path.getEndClassDescriptor());
for (FieldConfig fc : subconfs) {
String pathString = basePath + fc.getFieldExpr();
Path pathToAdd = new Path(m, pathString);
if (pathToAdd.endIsAttribute() && (fc.getDisplayer() == null && fc.getShowInSummary())) {
subview.add(pathToAdd.getNoConstraintsString());
}
}
return subview;
}
/**
* Return a list of string paths that are defined as WebConfig to be shown in results. This will
* include only attributes of the given class and not follow references. Optionally provide a
* prefix to for creating a view for references/collections.
*
* @param type the class name to create a view for
* @param model the model
* @param webConfig we configuration
* @param startingPath a path to prefix the class, can be null
* @return the configured view paths for the class
*/
public static List<String> getDefaultViewForClass(
String type, Model model, WebConfig webConfig, String startingPath) {
String prefix = startingPath;
List<String> view = new ArrayList<String>();
ClassDescriptor cld = model.getClassDescriptorByName(type);
List<FieldConfig> fieldConfigs = FieldConfigHelper.getClassFieldConfigs(webConfig, cld);
if (!StringUtils.isEmpty(prefix)) {
try {
// we can't add a subclass constraint, type must be same as the end of the prefix
Path prefixPath = new Path(model, prefix);
String prefixEndType = TypeUtil.unqualifiedName(prefixPath.getEndType().getName());
if (!prefixEndType.equals(type)) {
throw new IllegalArgumentException(
"Mismatch between end type of prefix: "
+ prefixEndType
+ " and type parameter: "
+ type);
}
} catch (PathException e) {
LOG.error("Invalid path configured in webconfig for class: " + type);
}
} else {
prefix = type;
}
for (FieldConfig fieldConfig : fieldConfigs) {
String relPath = fieldConfig.getFieldExpr();
// only add attributes, don't follow references, following references can be problematic
// when subclasses get involved.
if (fieldConfig.getShowInResults()) {
try {
Path path = new Path(model, prefix + "." + relPath);
if (path.isOnlyAttribute()) {
view.add(path.getNoConstraintsString());
}
} catch (PathException e) {
LOG.error("Invalid path configured in webconfig for class: " + type);
}
}
}
if (view.size() == 0) {
for (AttributeDescriptor att : cld.getAllAttributeDescriptors()) {
if (!"id".equals(att.getName())) {
view.add(prefix + "." + att.getName());
}
}
}
return view;
}
@Override
protected void checkPathQuery(PathQuery pq) throws Exception {
if (pq.getView().size() > 1) {
throw new BadRequestException("Queries to this service may only have one view.");
}
Path path = pq.makePath(pq.getView().get(0));
ClassDescriptor klazz = path.getLastClassDescriptor();
ClassDescriptor sf = im.getModel().getClassDescriptorByName("SequenceFeature");
ClassDescriptor protein = im.getModel().getClassDescriptorByName("Protein");
if (sf == klazz
|| protein == klazz
|| klazz.getAllSuperDescriptors().contains(sf)
|| klazz.getAllSuperDescriptors().contains(protein)) {
return; // OK
} else {
throw new BadRequestException("Unsuitable type for export: " + klazz);
}
}
private Map<String, Object> getObjectDetails(InterMineObject imo) {
WebConfig webConfig = InterMineContext.getWebConfig();
Model m = im.getModel();
Map<String, Object> objectDetails = new HashMap<String, Object>();
String className = DynamicUtil.getSimpleClassName(imo.getClass());
ClassDescriptor cd = m.getClassDescriptorByName(className);
for (FieldConfig fc : FieldConfigHelper.getClassFieldConfigs(webConfig, cd)) {
try {
Path p = new Path(m, cd.getUnqualifiedName() + "." + fc.getFieldExpr());
if (p.endIsAttribute() && fc.getShowInSummary()) {
objectDetails.put(
p.getNoConstraintsString().replaceAll("^[^.]*\\.", ""), PathUtil.resolvePath(p, imo));
}
} catch (PathException e) {
LOG.error(e);
}
}
return objectDetails;
}
/**
* From the columns of the PagedTable, return a List of the Paths that this exporter will use to
* find sequences to export. The returned Paths are a subset of the prefixes of the column paths.
* eg. if the columns are ("Gene.primaryIdentifier", "Gene.secondaryIdentifier",
* "Gene.proteins.primaryIdentifier") return ("Gene", "Gene.proteins").
*
* @param pt the PagedTable
* @return a list of Paths that have sequence
*/
public static LinkedHashMap<Path, Integer> getExportClassPaths(PagedTable pt) {
LinkedHashMap<Path, Integer> retPaths = new LinkedHashMap<Path, Integer>();
List<Column> columns = pt.getColumns();
for (int index = 0; index < columns.size(); index++) {
Path prefix = columns.get(index).getPath().getPrefix();
ClassDescriptor prefixCD = prefix.getLastClassDescriptor();
Class<? extends FastPathObject> prefixClass = DynamicUtil.getSimpleClass(prefixCD.getType());
// Chromosome is treated as a sequence feature in the model
if (SequenceFeature.class.isAssignableFrom(prefixClass)
&& !Chromosome.class.isAssignableFrom(prefixClass)) {
if (!retPaths.keySet().contains(prefix)) {
retPaths.put(prefix, index);
}
}
}
return retPaths;
}
/**
* 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;
}
/**
* Generate a list from a pathquery.
*
* @param pq The pathquery
* @param name The name of the list
* @param description The description of the list
* @param tags A list of tags to add to the list
* @param profile The profile the list should belong to
* @throws ObjectStoreException If there is an issue running the queries that generate the list.
* @throws PathException If the paths supplied are illegal.
*/
protected void generateListFromQuery(
PathQuery pq, String name, String description, List<String> tags, Profile profile)
throws ObjectStoreException, PathException {
Query q = getQuery(pq, profile);
String tempName = name + TEMP;
String viewPathString = pq.getView().get(0);
Path viewPath = pq.makePath(viewPathString);
String type = viewPath.getLastClassDescriptor().getUnqualifiedName();
try {
InterMineBag newList = profile.createBag(tempName, type, description, im.getClassKeys());
newList.addToBagFromQuery(q);
try {
im.getBagManager().addTagsToBag(tags, newList, profile);
} catch (TagManager.TagNameException e) {
throw new BadRequestException(e.getMessage());
} catch (TagManager.TagNamePermissionException e) {
throw new ServiceForbiddenException(e.getMessage());
}
profile.renameBag(tempName, name);
output.addResultItem(Arrays.asList("" + newList.size()));
} catch (CompletelyFalseException e) {
output.addResultItem(Arrays.asList("0"));
throw new BadRequestException("List not created - it would be of size 0");
} catch (UnknownBagTypeException e) {
output.addResultItem(Arrays.asList("0"));
throw new InternalErrorException(e.getMessage(), e);
} catch (ClassKeysNotFoundException cke) {
throw new BadRequestException("Bag has not class key set", cke);
} finally {
if (profile.getSavedBags().containsKey(tempName)) {
profile.deleteBag(tempName);
}
}
}
private void addColumnsInternal(List<Path> columnPaths) {
List<String> types = new ArrayList<String>();
int i = columns.size();
for (Path columnPath : columnPaths) {
String type = TypeUtil.unqualifiedName(columnPath.getLastClassDescriptor().getName());
Class typeCls = columnPath.getLastClassDescriptor().getType();
String columnDescription =
pathQuery.getGeneratedPathDescription(columnPath.toStringNoConstraints());
Column column;
if (columnDescription.equals(columnPath.toStringNoConstraints())) {
column = new Column(columnPath, i, typeCls);
} else {
column = new Column(columnPath, columnDescription, i, typeCls);
}
if (!types.contains(column.getColumnId())) {
String fieldName = columnPath.getEndFieldDescriptor().getName();
boolean isKeyField = ClassKeyHelper.isKeyField(classKeys, type, fieldName);
if (isKeyField) {
column.setSelectable(true);
types.add(column.getColumnId());
}
}
columns.add(column);
i++;
}
}
/**
* Get the view as configured in the webconfig. Guarantees to return a non-empty non-null list.
*
* @param type The type we are trying to get a view for.
* @param model The data model
* @param webConfig The web-configuration.
* @param fieldConfigs
* @return The list of paths that we can use to construct a query.
* @throws UnconfiguredException if the class has not configured view.
*/
private static List<String> getConfiguredView(ClassDescriptor cld, WebConfig webConfig)
throws UnconfiguredException {
Collection<String> view = new LinkedHashSet<String>(); // Preserve order and uniqueness.
Model m = cld.getModel();
for (FieldConfig fieldConfig : resultConfigs(webConfig, cld)) {
try {
Path p = new Path(m, cld.getUnqualifiedName() + "." + fieldConfig.getFieldExpr());
// add subpaths of references and roots, attrs themselves, ignore collections.
if (p.isRootPath() || p.endIsReference()) {
view.addAll(getSubview(webConfig, m, p));
} else if (p.endIsAttribute()) {
view.add(p.getNoConstraintsString());
}
} catch (PathException e) {
LOG.error("Invalid path configured in webconfig for class: " + cld);
}
}
if (view.isEmpty()) {
throw new UnconfiguredException();
}
return new ArrayList<String>(view);
}
@Override
protected void execute() throws Exception {
String pathString = request.getParameter("path");
Map<String, Object> attributes = getHeaderAttributes();
output.setHeaderAttributes(attributes);
if (isEmpty(pathString)) {
throw new BadRequestException("No path provided");
}
attributes.put("path", pathString);
kvPairs.put("path", pathString);
String typeConstraintStr = request.getParameter("typeConstraints");
Map<String, String> typeMap = new HashMap<String, String>();
if (!isEmpty(typeConstraintStr)) {
logger.debug(typeConstraintStr);
JSONObject typeJO = new JSONObject(typeConstraintStr);
Iterator<String> it = (Iterator<String>) typeJO.keys();
while (it.hasNext()) {
String name = it.next();
String subType = typeJO.getString(name);
typeMap.put(name, subType);
}
}
Model model = im.getModel();
Path path;
try {
if (typeMap.isEmpty()) {
path = new Path(model, pathString);
} else {
path = new Path(model, pathString, typeMap);
}
} catch (PathException e) {
throw new BadRequestException("Bad path given: " + pathString, e);
}
Query q = new Query();
attributes.put("class", path.getLastClassDescriptor().getUnqualifiedName());
attributes.put("field", path.getLastElement());
String type = ((AttributeDescriptor) path.getEndFieldDescriptor()).getType();
String[] parts = split(type, '.');
reverse(parts);
attributes.put("type", parts[0]);
QueryClass qc = new QueryClass(path.getPrefix().getEndType());
q.addFrom(qc);
QueryField qf1 = new QueryField(qc, path.getLastElement());
q.addToSelect(qf1);
QueryFunction qf = new QueryFunction();
q.addToSelect(qf);
q.addToGroupBy(qf1);
int count = im.getObjectStore().count(q, ObjectStore.SEQUENCE_IGNORE);
if (formatIsCount()) {
output.addResultItem(Arrays.asList(String.valueOf(count)));
} else {
attributes.put("count", count);
Results results = im.getObjectStore().execute(q, DEFAULT_BATCH_SIZE, true, true, false);
Iterator<Object> iter = results.iterator();
while (iter.hasNext()) {
@SuppressWarnings("rawtypes")
List row = (List) iter.next();
Map<String, Object> jsonMap = new HashMap<String, Object>();
jsonMap.put("value", row.get(0));
jsonMap.put("count", row.get(1));
JSONObject jo = new JSONObject(jsonMap);
List<String> forOutput = new ArrayList<String>();
forOutput.add(jo.toString());
if (iter.hasNext()) {
// Standard hack to ensure commas
forOutput.add("");
}
output.addResultItem(forOutput);
}
}
}
/** {@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;
}
// TODO javadoc to describe what this does
private MultiRow<ResultsRow<MultiRowValue<ResultElement>>> translateRow(
MultiRow<ResultsRow<MultiRowValue>> multiRow) {
try {
MultiRow<ResultsRow<MultiRowValue<ResultElement>>> retval =
new MultiRow<ResultsRow<MultiRowValue<ResultElement>>>();
for (ResultsRow<MultiRowValue> initialList : multiRow) {
ResultsRow<MultiRowValue<ResultElement>> rowCells =
new ResultsRow<MultiRowValue<ResultElement>>();
for (Path columnPath : columnPaths) {
String columnName = columnPath.toStringNoConstraints();
Integer columnIndexInteger = pathToIndex.get(columnName);
String parentColumnName = columnPath.getPrefix().toStringNoConstraints();
if (columnIndexInteger == null) {
columnIndexInteger = pathToIndex.get(parentColumnName);
}
if (columnIndexInteger == null) {
throw new NullPointerException(
"Path: \""
+ columnName
+ "\", pathToIndex: \""
+ pathToIndex
+ "\", prefix: \""
+ parentColumnName
+ "\", query: \""
+ PathQueryBinding.marshal(
pathQuery,
"",
pathQuery.getModel().getName(),
PathQuery.USERPROFILE_VERSION)
+ "\"");
}
int columnIndex = columnIndexInteger.intValue();
MultiRowValue origO = initialList.get(columnIndex);
FastPathObject o = (FastPathObject) (origO == null ? null : origO.getValue());
int rowspan = -1;
if (origO == null) {
rowspan = 1;
} else if (origO instanceof MultiRowFirstValue) {
rowspan = ((MultiRowFirstValue) origO).getRowspan();
}
String lastCd;
if (columnPath.endIsAttribute()) {
lastCd = columnPath.getLastClassDescriptor().getName();
} else {
// special case for columns that contain objects eg. Gene.chromosomeLocation
lastCd = columnPath.getLastClassDescriptor().getName();
}
String type = TypeUtil.unqualifiedName(lastCd);
Path path;
String fieldName = null;
try {
if (columnPath.endIsAttribute()) {
fieldName = columnName.substring(columnName.lastIndexOf(".") + 1);
path = new Path(model, type + '.' + fieldName);
} else {
// special case for columns that contain objects
path = new Path(model, type);
}
} catch (PathException e) {
// Should never happen if the field name is valid
throw new Error("There must be a bug", e);
}
// Three cases:
// 1) attribute has a value so create a result element
// 2) we have an object but attribute is null -> create a ResultElement with
// value null
// 3) the object is null (outer join) so add null value rowCells
// Object fieldValue;
// try {
// fieldValue = (o == null ? null : PathUtil.resolvePath(path, o));
// } catch (PathException e) {
// throw new IllegalArgumentException("Path: \"" + columnName
// + "\", pathToIndex: \"" + pathToIndex + "\", prefix: \""
// + parentColumnName + "\", query: \""
// + PathQueryBinding.marshal(pathQuery, "",
// pathQuery.getModel()
// .getName(), PathQuery.USERPROFILE_VERSION)
// + "\", columnIndex: \"" + columnIndex + "\",
// initialList: \""
// + initialList + "\"", e);
// }
if (o != null) {
String fieldCDName = path.getLastClassDescriptor().getName();
String unqualifiedFieldCD = TypeUtil.unqualifiedName(fieldCDName);
boolean isKeyField;
if (fieldName == null) {
// special case for columns that contain objects
isKeyField = false;
} else {
isKeyField = ClassKeyHelper.isKeyField(classKeys, unqualifiedFieldCD, fieldName);
}
ResultElement resultElement = new ResultElement(o, path, isKeyField);
// link to report page by default, unless it says otherwise in config
if (redirector != null) {
try {
String linkRedirect = redirector.generateLink(im, (InterMineObject) o);
if (linkRedirect != null) {
resultElement.setLinkRedirect(linkRedirect);
}
} catch (ClassCastException e) {
// Simple objects cannot be consumed by redirectors.
}
}
if (rowspan >= 0) {
rowCells.add(new MultiRowFirstValue(resultElement, rowspan));
} else {
rowCells.add(null);
}
} else {
if (rowspan >= 0) {
rowCells.add(new MultiRowFirstValue(null, rowspan));
} else {
rowCells.add(null);
}
}
}
retval.add(rowCells);
}
return retval;
} catch (IndexOutOfBoundsException e) {
throw new RuntimeException(e);
}
}
/**
* Return a list of string paths that are defined as WebConfig to be shown in results. This will
* include attributes of the given class and follow references.
*
* @param type the class name to create a view for
* @param model the model
* @param webConfig we configuration
* @return the configured view paths for the class
*/
public static List<String> getDefaultViewForClass(String type, Model model, WebConfig webConfig) {
List<String> view = new ArrayList<String>();
ClassDescriptor cld = model.getClassDescriptorByName(type);
List<FieldConfig> fieldConfigs = FieldConfigHelper.getClassFieldConfigs(webConfig, cld);
for (FieldConfig fieldConfig : fieldConfigs) {
String relPath = fieldConfig.getFieldExpr();
// only add attributes, don't follow references, following references can be problematic
// when subclasses get involved.
if (fieldConfig.getShowInResults()) {
try {
Path path = new Path(model, type + "." + relPath);
// add references
if (path.isRootPath() || path.endIsReference()) {
for (FieldConfig fc :
FieldConfigHelper.getClassFieldConfigs(webConfig, path.getEndClassDescriptor())) {
Path pathToAdd =
new Path(model, path.toStringNoConstraints() + "." + fc.getFieldExpr());
if (pathToAdd.endIsAttribute()
&& (!view.contains(pathToAdd.getNoConstraintsString()))
&& (fc.getDisplayer() == null && fc.getShowInSummary())) {
view.add(pathToAdd.getNoConstraintsString());
}
}
// add collections
} else if (!path.endIsCollection()) {
view.add(path.getNoConstraintsString());
}
} catch (PathException e) {
LOG.error("Invalid path configured in webconfig for class: " + type);
}
}
}
if (view.size() == 0) {
for (AttributeDescriptor att : cld.getAllAttributeDescriptors()) {
if (!"id".equals(att.getName())) {
view.add(type + "." + att.getName());
}
}
}
return view;
}