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++;
}
}
/**
* 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);
}
/**
* 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 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);
}
}
/**
* 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;
}
/**
* 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);
}
}
}
@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);
}
}
}
// 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);
}
}