/**
* 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);
}
/**
* Generates the getElementType method.
*
* @param cld the ClassDescriptor
* @return a String with the method
*/
public String generateGetElementType(ClassDescriptor cld) {
StringBuffer sb = new StringBuffer();
sb.append(INDENT).append("public Class<?> getElementType(final String fieldName) {\n");
for (FieldDescriptor field : cld.getAllFieldDescriptors()) {
if (field.isCollection()) {
sb.append(INDENT + INDENT)
.append("if (\"" + field.getName() + "\".equals(fieldName)) {\n")
.append(INDENT + INDENT + INDENT)
.append(
"return " + ((CollectionDescriptor) field).getReferencedClassName() + ".class;\n")
.append(INDENT + INDENT)
.append("}\n");
}
}
sb.append(INDENT + INDENT)
.append("if (!" + cld.getName() + ".class.equals(getClass())) {\n")
.append(INDENT + INDENT + INDENT)
.append("return TypeUtil.getElementType(" + cld.getName() + ".class, fieldName);\n")
.append(INDENT + INDENT)
.append("}\n")
.append(INDENT + INDENT)
.append("throw new IllegalArgumentException(\"Unknown field \" + fieldName);\n")
.append(INDENT)
.append("}\n");
return sb.toString();
}
/**
* Generates code for a single collection.
*
* @param col the CollectionDescriptor
* @param field true if the class should have the associated field, or false if the field is in
* the superclass
* @return java code
*/
protected String generate(CollectionDescriptor col, boolean field) {
String type = "java.util.Set<" + col.getReferencedClassName() + ">";
String impl = "java.util.HashSet<" + col.getReferencedClassName() + ">";
StringBuffer sb = new StringBuffer();
if (field) {
sb.append(
INDENT + "// Col: " + col.getClassDescriptor().getName() + "." + col.getName() + ENDL)
.append(INDENT)
.append("protected ")
.append(type)
.append(" ")
.append(col.getName())
.append(" = new ")
.append(impl)
.append("();" + ENDL);
}
sb.append(generateGetSet(col, field)).append(ENDL);
return sb.toString();
}
/**
* Search for the classes in a collection for a given InterMineObject, for example find all of the
* sub-classes of Employee in the Department.employees collection of a given Department. If there
* are no subclasses or the collection is empty a list with the type of the collection is
* returned.
*
* @param object an InterMineObject to inspect
* @param field the name if the collection to check
* @param os the ObjectStore in which to execute the query
* @return a list of classes in the collection
*/
public static List<Class<?>> queryForTypesInCollection(
InterMineObject object, String field, ObjectStore os) {
List<Class<?>> typesInCollection = new ArrayList<Class<?>>();
// if there are no subclasses there can only be one type in the collection
Model model = os.getModel();
ClassDescriptor startCld =
model.getClassDescriptorByName(DynamicUtil.getSimpleClassName(object));
CollectionDescriptor col = startCld.getCollectionDescriptorByName(field, true);
ClassDescriptor colCld = col.getReferencedClassDescriptor();
if (model.getAllSubs(colCld).isEmpty()) {
// there aren't any subclasses, so no need to do a query
typesInCollection.add(colCld.getType());
} else {
// there may be multiple subclasses in the collection, need to run a query
Query query = new Query();
QueryClass qc = new QueryClass(colCld.getType());
query.addFrom(qc);
query.addToSelect(new QueryField(qc, "class"));
query.setDistinct(true);
query.setConstraint(
new ContainsConstraint(
new QueryCollectionReference(object, field), ConstraintOp.CONTAINS, qc));
for (Object o : os.executeSingleton(query)) {
typesInCollection.add((Class<?>) o);
}
// Collection was empty but add collection type to be consistent with collection types
// without subclasses.
if (typesInCollection.isEmpty()) {
typesInCollection.add(colCld.getType());
}
}
return typesInCollection;
}
/**
* Generates the addCollectionElement method.
*
* @param cld the ClassDescriptor
* @return a String with the method
*/
public String generateAddCollectionElement(ClassDescriptor cld) {
StringBuffer sb = new StringBuffer();
sb.append(INDENT)
.append("public void addCollectionElement(final String fieldName,")
.append(" final org.intermine.model.InterMineObject element) {\n")
.append(INDENT + INDENT);
for (FieldDescriptor field : cld.getAllFieldDescriptors()) {
if (field.isCollection()) {
String fieldName = field.getName();
if ("fieldName".equals(fieldName)) {
fieldName = "this.fieldName";
} else if ("element".equals(fieldName)) {
fieldName = "this.element";
}
sb.append("if (\"" + field.getName() + "\".equals(fieldName)) {\n")
.append(INDENT + INDENT + INDENT)
.append(
fieldName
+ ".add(("
+ ((CollectionDescriptor) field).getReferencedClassName()
+ ") element);\n")
.append(INDENT + INDENT)
.append("} else ");
}
}
sb.append("{\n")
.append(INDENT + INDENT + INDENT)
.append("if (!" + cld.getName() + ".class.equals(getClass())) {\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append("TypeUtil.addCollectionElement(this, fieldName, element);\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append("return;\n")
.append(INDENT + INDENT + INDENT)
.append("}\n")
.append(INDENT + INDENT + INDENT)
.append("throw new IllegalArgumentException(\"Unknown collection \" + fieldName);\n")
.append(INDENT + INDENT)
.append("}\n")
.append(INDENT)
.append("}\n");
return sb.toString();
}
/**
* Generates the setoBJECT method for deserialising objects.
*
* @param cld a ClassDescriptor
* @return a String containing the method
*/
public String generateSetObject(ClassDescriptor cld) {
StringBuffer sb = new StringBuffer();
sb.append(INDENT)
.append("public void setoBJECT(String notXml, ObjectStore os) {\n")
.append(INDENT + INDENT)
.append("setoBJECT(NotXmlParser.SPLITTER.split(notXml), os);\n")
.append(INDENT)
.append("}\n")
.append(INDENT)
.append("public void setoBJECT(final String[] notXml, final ObjectStore os) {\n")
.append(INDENT + INDENT)
.append(
"if (!"
+ cld.getName()
+ (cld.isInterface() ? "Shadow" : "")
+ ".class.equals(getClass())) {\n")
.append(INDENT + INDENT + INDENT)
.append(
"throw new IllegalStateException(\"Class \" + getClass().getName() + \""
+ " does not match code ("
+ cld.getName()
+ ")\");\n")
.append(INDENT + INDENT)
.append("}\n")
.append(INDENT + INDENT)
.append("for (int i = 2; i < notXml.length;) {\n")
.append(INDENT + INDENT + INDENT)
.append("int startI = i;\n");
for (FieldDescriptor field : cld.getAllFieldDescriptors()) {
String fieldName = field.getName();
if ("notXml".equals(fieldName)) {
fieldName = "this.notXml";
} else if ("os".equals(fieldName)) {
fieldName = "this.os";
}
if (field instanceof AttributeDescriptor) {
AttributeDescriptor attribute = (AttributeDescriptor) field;
sb.append(INDENT + INDENT + INDENT)
.append("if ((i < notXml.length) && \"a" + fieldName + "\".equals(notXml[i])) {\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append("i++;\n")
.append(INDENT + INDENT + INDENT + INDENT);
if ("boolean".equals(attribute.getType())) {
sb.append(fieldName + " = Boolean.parseBoolean(notXml[i]);\n");
} else if ("short".equals(attribute.getType())) {
sb.append(fieldName + " = Short.parseShort(notXml[i]);\n");
} else if ("int".equals(attribute.getType())) {
sb.append(fieldName + " = Integer.parseInt(notXml[i]);\n");
} else if ("long".equals(attribute.getType())) {
sb.append(fieldName + " = Long.parseLong(notXml[i]);\n");
} else if ("float".equals(attribute.getType())) {
sb.append(fieldName + " = Float.parseFloat(notXml[i]);\n");
} else if ("double".equals(attribute.getType())) {
sb.append(fieldName + " = Double.parseDouble(notXml[i]);\n");
} else if ("java.lang.Boolean".equals(attribute.getType())) {
sb.append(fieldName + " = Boolean.valueOf(notXml[i]);\n");
} else if ("java.lang.Short".equals(attribute.getType())) {
sb.append(fieldName + " = Short.valueOf(notXml[i]);\n");
} else if ("java.lang.Integer".equals(attribute.getType())) {
sb.append(fieldName + " = Integer.valueOf(notXml[i]);\n");
} else if ("java.lang.Long".equals(attribute.getType())) {
sb.append(fieldName + " = Long.valueOf(notXml[i]);\n");
} else if ("java.lang.Float".equals(attribute.getType())) {
sb.append(fieldName + " = Float.valueOf(notXml[i]);\n");
} else if ("java.lang.Double".equals(attribute.getType())) {
sb.append(fieldName + " = Double.valueOf(notXml[i]);\n");
} else if ("java.util.Date".equals(attribute.getType())) {
sb.append(fieldName + " = new java.util.Date(Long.parseLong(notXml[i]));\n");
} else if ("java.math.BigDecimal".equals(attribute.getType())) {
sb.append(fieldName + " = new java.math.BigDecimal(notXml[i]);\n");
} else if ("org.intermine.objectstore.query.ClobAccess".equals(attribute.getType())) {
sb.append(
fieldName
+ " = org.intermine.objectstore.query.ClobAccess"
+ ".decodeDbDescription(os, notXml[i]);\n");
} else if ("java.lang.String".equals(attribute.getType())) {
sb.append("StringBuilder string = null;\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append(
"while ((i + 1 < notXml.length) && (notXml[i + 1].charAt(0) == '"
+ ENCODED_DELIM
+ "')) {\n")
.append(INDENT + INDENT + INDENT + INDENT + INDENT)
.append("if (string == null) string = new StringBuilder(notXml[i]);\n")
.append(INDENT + INDENT + INDENT + INDENT + INDENT)
.append("i++;\n")
.append(INDENT + INDENT + INDENT + INDENT + INDENT)
.append("string.append(\"" + DELIM + "\").append(notXml[i].substring(1));\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append("}\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append(fieldName + " = string == null ? notXml[i] : string.toString();\n");
} else {
throw new IllegalArgumentException("Unknown type " + attribute.getType());
}
sb.append(INDENT + INDENT + INDENT + INDENT)
.append("i++;\n")
.append(INDENT + INDENT + INDENT)
.append("}\n");
} else if (field.isReference()) {
ReferenceDescriptor reference = (ReferenceDescriptor) field;
sb.append(INDENT + INDENT + INDENT)
.append("if ((i < notXml.length) &&\"r" + fieldName + "\".equals(notXml[i])) {\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append("i++;\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append(
fieldName
+ " = new ProxyReference(os, Integer.valueOf(notXml[i])"
+ ", "
+ reference.getReferencedClassName()
+ ".class);\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append("i++;\n")
.append(INDENT + INDENT + INDENT)
.append("};\n");
}
}
sb.append(INDENT + INDENT + INDENT)
.append("if (startI == i) {\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append("throw new IllegalArgumentException(\"Unknown field \" + notXml[i]);\n")
.append(INDENT + INDENT + INDENT)
.append("}\n")
.append(INDENT + INDENT)
.append("}\n");
for (FieldDescriptor field : cld.getAllFieldDescriptors()) {
String fieldName = field.getName();
if ("notXml".equals(fieldName)) {
fieldName = "this.notXml";
} else if ("os".equals(fieldName)) {
fieldName = "this.os";
}
if (field instanceof CollectionDescriptor) {
CollectionDescriptor coll = (CollectionDescriptor) field;
sb.append(INDENT + INDENT)
.append(
fieldName
+ " = new ProxyCollection<"
+ coll.getReferencedClassName()
+ ">(os, this, \""
+ fieldName
+ "\", "
+ coll.getReferencedClassName()
+ ".class);\n");
}
}
sb.append(INDENT).append("}\n");
return sb.toString();
}
/**
* Write code for getters and setters for given field.
*
* @param field descriptor for field
* @param fieldPresent true if this class has the associated field
* @return string with generated java code
*/
protected String generateGetSet(FieldDescriptor field, boolean fieldPresent) {
String name = field.getName();
String type = getType(field);
StringBuffer sb = new StringBuffer();
// Get method
sb.append(INDENT)
.append("public ")
.append(type)
.append(" get")
.append(StringUtil.reverseCapitalisation(name))
.append("()");
if (!fieldPresent) {
sb.append(";" + ENDL);
} else {
sb.append(" { ");
if ((field instanceof ReferenceDescriptor) && (!(field instanceof CollectionDescriptor))) {
// This is an object reference.
sb.append("if (")
.append(name)
.append(" instanceof org.intermine.objectstore.proxy.ProxyReference) { return ")
.append("((")
.append(type)
.append(") ((org.intermine.objectstore.proxy.ProxyReference) ")
.append(name)
.append(").getObject()); }; return (")
.append(type)
.append(") ")
.append(name)
.append("; }" + ENDL);
} else {
sb.append("return ").append(name).append("; }" + ENDL);
}
}
// Set method
sb.append(INDENT)
.append("public void ")
.append("set")
.append(StringUtil.reverseCapitalisation(name))
.append("(final ")
.append(type)
.append(" ")
.append(name)
.append(")");
if (!fieldPresent) {
sb.append(";" + ENDL);
} else {
sb.append(" { ").append("this.").append(name).append(" = ").append(name).append("; }" + ENDL);
}
if (field instanceof ReferenceDescriptor) {
if (field instanceof CollectionDescriptor) {
sb.append(INDENT)
.append("public void add")
.append(StringUtil.reverseCapitalisation(name))
.append("(final ")
.append(((CollectionDescriptor) field).getReferencedClassDescriptor().getName())
.append(" arg)");
if (fieldPresent) {
sb.append(" { ").append(name).append(".add(arg); }" + ENDL);
} else {
sb.append(";" + ENDL);
}
} else {
// This is an object reference.
sb.append(INDENT)
.append("public void proxy")
.append(StringUtil.reverseCapitalisation(name))
.append("(final org.intermine.objectstore.proxy.ProxyReference ")
.append(name)
.append(")");
if (fieldPresent) {
sb.append(" { this.").append(name).append(" = ").append(name).append("; }" + ENDL);
} else {
sb.append(";" + ENDL);
}
sb.append(INDENT)
.append("public org.intermine.model.InterMineObject proxGet")
.append(StringUtil.reverseCapitalisation(name))
.append("()");
if (fieldPresent) {
sb.append(" { return ").append(name).append("; }" + ENDL);
} else {
sb.append(";" + ENDL);
}
}
}
return sb.toString();
}
/**
* Add a collection of objects of type X to objects of type Y by using a connecting class. Eg. Add
* a collection of Protein objects to Gene by examining the Transcript objects in the transcripts
* collection of the Gene, which would use a query like: SELECT DISTINCT gene FROM Gene AS gene,
* Transcript AS transcript, Protein AS protein WHERE (gene.transcripts CONTAINS transcript AND
* transcript.protein CONTAINS protein) ORDER BY gene and then set protected gene.protein (if
* created BioEntity1 -> BioEntity2 -> BioEntity3 ==> BioEntity1 -> BioEntity3
*
* @param firstClsName the first class in the query
* @param firstClassFieldName the field in the firstClass which should contain the connectingClass
* @param connectingClsName the class referred to by firstClass.sourceFieldName
* @param connectingClassFieldName the field in connectingClass which should contain secondClass
* @param secondClsName the class referred to by connectingClass.connectingClassFieldName
* @param createFieldName the collection field in the secondClass - the collection to create/set
* @param createInFirstClass if true create the new collection field in firstClass, otherwise
* create in secondClass
* @throws Exception if anything goes wrong
*/
protected void insertCollectionField(
String firstClsName,
String firstClassFieldName,
String connectingClsName,
String connectingClassFieldName,
String secondClsName,
String createFieldName,
boolean createInFirstClass)
throws Exception {
InterMineObject lastDestObject = null;
Set<InterMineObject> newCollection = new HashSet<InterMineObject>();
String insertMessage =
"insertCollectionField("
+ firstClsName
+ ", "
+ firstClassFieldName
+ ", "
+ connectingClsName
+ ", "
+ connectingClassFieldName
+ ","
+ secondClsName
+ ", "
+ createFieldName
+ ", "
+ createInFirstClass
+ ")";
// Check that classes and fields specified exist in model
try {
String errorMessage = "Not performing " + insertMessage;
PostProcessUtil.checkFieldExists(model, firstClsName, firstClassFieldName, errorMessage);
PostProcessUtil.checkFieldExists(
model, connectingClsName, connectingClassFieldName, errorMessage);
PostProcessUtil.checkFieldExists(model, secondClsName, createFieldName, errorMessage);
} catch (MetaDataException e) {
return;
}
LOG.info("Beginning " + insertMessage);
long startTime = System.currentTimeMillis();
// if this is a many to many collection we can use ObjectStore.addToCollection which will
// write directly to the database.
boolean manyToMany = false;
ClassDescriptor destCld;
if (createInFirstClass) {
destCld = model.getClassDescriptorByName(firstClsName);
} else {
destCld = model.getClassDescriptorByName(secondClsName);
}
CollectionDescriptor col = destCld.getCollectionDescriptorByName(createFieldName);
if (col == null) {
String msg =
"Error running post-process `create-references` for `"
+ createFieldName
+ "` since this collection doesn't exist in the model.";
LOG.error(msg);
return;
}
if (col.relationType() == CollectionDescriptor.M_N_RELATION) {
manyToMany = true;
}
Iterator<ResultsRow<InterMineObject>> resIter =
PostProcessUtil.findConnectingClasses(
osw.getObjectStore(),
model.getClassDescriptorByName(firstClsName).getType(),
firstClassFieldName,
model.getClassDescriptorByName(connectingClsName).getType(),
connectingClassFieldName,
model.getClassDescriptorByName(secondClsName).getType(),
createInFirstClass);
// results will be firstClass ; destClass (ordered by firstClass)
osw.beginTransaction();
int count = 0;
while (resIter.hasNext()) {
ResultsRow<InterMineObject> rr = resIter.next();
InterMineObject thisSourceObject;
InterMineObject thisDestObject;
if (createInFirstClass) {
thisDestObject = rr.get(0);
thisSourceObject = rr.get(1);
} else {
thisDestObject = rr.get(1);
thisSourceObject = rr.get(0);
}
if (!manyToMany
&& (lastDestObject == null || !thisDestObject.getId().equals(lastDestObject.getId()))) {
if (lastDestObject != null) {
try {
InterMineObject tempObject = PostProcessUtil.cloneInterMineObject(lastDestObject);
Set<InterMineObject> oldCollection =
(Set<InterMineObject>) tempObject.getFieldValue(createFieldName);
newCollection.addAll(oldCollection);
tempObject.setFieldValue(createFieldName, newCollection);
count += newCollection.size();
osw.store(tempObject);
} catch (IllegalAccessException e) {
LOG.error(
"Object with ID "
+ thisDestObject.getId()
+ " has no "
+ createFieldName
+ " field",
e);
}
}
newCollection = new HashSet<InterMineObject>();
}
if (manyToMany) {
osw.addToCollection(
thisDestObject.getId(), destCld.getType(), createFieldName, thisSourceObject.getId());
} else {
newCollection.add(thisSourceObject);
}
lastDestObject = thisDestObject;
}
if (!manyToMany && lastDestObject != null) {
// clone so we don't change the ObjectStore cache
InterMineObject tempObject = PostProcessUtil.cloneInterMineObject(lastDestObject);
tempObject.setFieldValue(createFieldName, newCollection);
count += newCollection.size();
osw.store(tempObject);
}
LOG.info(
"Finished: created "
+ count
+ " references in "
+ secondClsName
+ " to "
+ firstClsName
+ " via "
+ connectingClsName
+ " - took "
+ (System.currentTimeMillis() - startTime)
+ " ms.");
osw.commitTransaction();
// now ANALYSE tables relation to class that has been altered - may be rows added
// to indirection tables
if (osw instanceof ObjectStoreWriterInterMineImpl) {
ClassDescriptor cld = model.getClassDescriptorByName(secondClsName);
DatabaseUtil.analyse(((ObjectStoreWriterInterMineImpl) osw).getDatabase(), cld, false);
}
}