/** * 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); } }