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++;
}
}
private static Map<String, List<FieldDescriptor>> getClassKeys(ObjectStore os) {
Properties classKeyProps = new Properties();
try {
InputStream inputStream =
ProfileManagerBinding.class.getClassLoader().getResourceAsStream("class_keys.properties");
classKeyProps.load(inputStream);
} catch (IOException ioe) {
throw new BuildException("class_keys.properties not found", ioe);
}
return ClassKeyHelper.readKeys(os.getModel(), classKeyProps);
}
@Override
public void execute() {
System.out.println("Creating lucene index for keyword search...");
ObjectStore os;
try {
os = getObjectStore();
} catch (Exception e) {
throw new BuildException(e);
}
if (!(os instanceof ObjectStoreInterMineImpl)) {
// Yes, yes, this is horrific...
throw new RuntimeException(
"Got invalid ObjectStore - must be an " + "instance of ObjectStoreInterMineImpl!");
}
/*
String configFileName = "objectstoresummary.config.properties";
InputStream configStream = classLoader.getResourceAsStream(configFileName);
if (configStream == null) {
throw new RuntimeException("can't find resource: " + configFileName);
}
Properties properties = new Properties();
properties.load(configStream);*/
// read class keys to figure out what are keyFields during indexing
InputStream is = this.getClass().getClassLoader().getResourceAsStream("class_keys.properties");
Properties classKeyProperties = new Properties();
try {
classKeyProperties.load(is);
} catch (NullPointerException e) {
throw new BuildException("Could not find the class keys");
} catch (IOException e) {
throw new BuildException("Could not read the class keys", e);
}
Map<String, List<FieldDescriptor>> classKeys =
ClassKeyHelper.readKeys(os.getModel(), classKeyProperties);
// index and save
KeywordSearch.saveIndexToDatabase(os, classKeys);
KeywordSearch.deleteIndexDirectory();
}
// 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);
}
}