/**
* 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;
}
@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);
}
}