// 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;
}
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;
}
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;
}
/**
* 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;
}
/**
* 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);
}
// 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);
}
}