/**
* 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();
}
private String getTaggedType(FieldDescriptor fd) {
if (fd.isCollection()) {
return "collection";
} else if (fd.isReference()) {
return "reference";
}
return "attribute";
}
/**
* Generates the getFieldType method.
*
* @param cld the ClassDescriptor
* @return a String with the method
*/
public String generateGetFieldType(ClassDescriptor cld) {
StringBuffer sb = new StringBuffer();
sb.append(INDENT).append("public Class<?> getFieldType(final String fieldName) {\n");
for (FieldDescriptor field : cld.getAllFieldDescriptors()) {
sb.append(INDENT + INDENT)
.append("if (\"" + field.getName() + "\".equals(fieldName)) {\n")
.append(INDENT + INDENT + INDENT);
if (field instanceof AttributeDescriptor) {
AttributeDescriptor attribute = (AttributeDescriptor) field;
if ("boolean".equals(attribute.getType())) {
sb.append("return Boolean.TYPE;\n");
} else if ("short".equals(attribute.getType())) {
sb.append("return Short.TYPE;\n");
} else if ("int".equals(attribute.getType())) {
sb.append("return Integer.TYPE;\n");
} else if ("long".equals(attribute.getType())) {
sb.append("return Long.TYPE;\n");
} else if ("float".equals(attribute.getType())) {
sb.append("return Float.TYPE;\n");
} else if ("double".equals(attribute.getType())) {
sb.append("return Double.TYPE;\n");
} else {
sb.append("return " + attribute.getType() + ".class;\n");
}
} else if (field.isReference()) {
sb.append("return " + ((ReferenceDescriptor) field).getReferencedClassName() + ".class;\n");
} else {
sb.append("return java.util.Set.class;\n");
}
sb.append(INDENT + INDENT).append("}\n");
}
sb.append(INDENT + INDENT)
.append("if (!" + cld.getName() + ".class.equals(getClass())) {\n")
.append(INDENT + INDENT + INDENT)
.append("return TypeUtil.getFieldType(" + 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 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();
}
/**
* Returns whether this primary key can be fetched now.
*
* @param pk the PrimaryKey
* @param cld the ClassDescriptor that the PrimaryKey is in
* @param pksNotDone a Map of pks not yet fetched
* @return a boolean
*/
protected boolean canDoPkNow(
PrimaryKey pk, ClassDescriptor cld, Map<PrimaryKey, ClassDescriptor> pksNotDone) {
boolean canDoPkNow = true;
Iterator<String> fieldNameIter = pk.getFieldNames().iterator();
while (fieldNameIter.hasNext() && canDoPkNow) {
String fieldName = fieldNameIter.next();
FieldDescriptor fd = cld.getFieldDescriptorByName(fieldName);
if (fd.isReference()) {
Iterator<ClassDescriptor> otherCldIter = pksNotDone.values().iterator();
while (otherCldIter.hasNext() && canDoPkNow) {
ClassDescriptor otherCld = otherCldIter.next();
Class<? extends FastPathObject> fieldClass =
((ReferenceDescriptor) fd).getReferencedClassDescriptor().getType();
if (otherCld.getType().isAssignableFrom(fieldClass)
|| fieldClass.isAssignableFrom(otherCld.getType())) {
canDoPkNow = false;
}
}
}
}
return canDoPkNow;
}
/**
* Generate a .toString() method for the given class .
*
* @param cld descriptor for the class in question
* @return generated java code as a string
*/
protected String generateToString(ClassDescriptor cld) {
String unqualifiedName = TypeUtil.unqualifiedName(cld.getName());
StringBuilder sb = new StringBuilder();
Set<FieldDescriptor> keyFields = cld.getAllFieldDescriptors();
if (keyFields.size() > 0) {
sb.append(INDENT)
.append("@Override public String toString() { ")
.append("return \"")
.append(unqualifiedName)
.append(" [");
TreeMap<String, FieldDescriptor> sortedMap = new TreeMap<String, FieldDescriptor>();
for (FieldDescriptor field : keyFields) {
sortedMap.put(field.getName(), field);
}
boolean needComma = false;
for (Map.Entry<String, FieldDescriptor> entry : sortedMap.entrySet()) {
FieldDescriptor field = entry.getValue();
if (!(field instanceof CollectionDescriptor)) {
if (needComma) {
sb.append(", ");
}
needComma = true;
sb.append(field.getName());
if (field instanceof AttributeDescriptor) {
sb.append("=\\\"\" + " + field.getName() + " + \"\\\"");
} else {
sb.append(
"=\" + ("
+ field.getName()
+ " == null ? \"null\" : ("
+ field.getName()
+ ".getId() == null ? \"no id\" : "
+ field.getName()
+ ".getId().toString())) + \"");
}
}
}
sb.append("]\"; }" + ENDL);
}
return sb.toString();
}
/**
* For a given FieldDescriptor, look up its 'aspect:' tags and place it in the correct map within
* placementRefsAndCollections. If categorised, remove it from the supplied miscRefs map.
*
* @param fd the FieldDecriptor (a references or collection)
* @param taggedType 'reference' or 'collection'
* @param dispRef the corresponding DisplayReference or DisplayCollection
* @param miscRefs map that contains dispRef (may be removed by this method)
* @param tagManager the tag manager
* @param sup the superuser account name
* @param placementRefsAndCollections take from the ReportObject
* @param isSuperUser if current user is superuser
*/
public static void categoriseBasedOnTags(
FieldDescriptor fd,
String taggedType,
DisplayField dispRef,
Map<String, DisplayField> miscRefs,
TagManager tagManager,
String sup,
Map<String, Map<String, DisplayField>> placementRefsAndCollections,
boolean isSuperUser) {
List<Tag> tags =
tagManager.getTags(
null,
fd.getClassDescriptor().getUnqualifiedName() + "." + fd.getName(),
taggedType,
sup);
for (Tag tag : tags) {
String tagName = tag.getTagName();
if (!isSuperUser && tagName.equals(TagNames.IM_HIDDEN)) {
// miscRefs.remove(fd.getName());
// Maybe it was added already to some placement and
// that's why it must be removed
removeField(fd.getName(), placementRefsAndCollections);
return;
}
if (AspectTagUtil.isAspectTag(tagName)) {
Map<String, DisplayField> refs = placementRefsAndCollections.get(tagName);
if (refs != null) {
refs.put(fd.getName(), dispRef);
miscRefs.remove(fd.getName());
}
} else if (tagName.equals(TagNames.IM_SUMMARY)) {
Map<String, DisplayField> summary = placementRefsAndCollections.get(TagNames.IM_SUMMARY);
if (summary != null) {
summary.put(fd.getName(), dispRef);
miscRefs.remove(fd.getName());
}
miscRefs.remove(fd.getName());
}
}
}
/**
* Generates the setFieldValue method.
*
* @param cld the ClassDescriptor
* @return a String with the method
*/
public String generateSetFieldValue(ClassDescriptor cld) {
StringBuffer sb = new StringBuffer();
sb.append(INDENT)
.append("public void setFieldValue(final String fieldName, final Object value) {\n")
.append(INDENT + INDENT);
for (FieldDescriptor field : cld.getAllFieldDescriptors()) {
sb.append("if (\"" + field.getName() + "\".equals(fieldName)) {\n");
String fieldName = field.getName();
if ("value".equals(fieldName)) {
fieldName = "this.value";
} else if ("fieldName".equals(fieldName)) {
fieldName = "this.fieldName";
}
if (field instanceof AttributeDescriptor) {
AttributeDescriptor attribute = (AttributeDescriptor) field;
if ("boolean".equals(attribute.getType())) {
sb.append(INDENT + INDENT + INDENT)
.append(fieldName + " = ((Boolean) value).booleanValue();\n");
} else if ("short".equals(attribute.getType())) {
sb.append(INDENT + INDENT + INDENT)
.append(fieldName + " = ((Short) value).shortValue();\n");
} else if ("int".equals(attribute.getType())) {
sb.append(INDENT + INDENT + INDENT)
.append(fieldName + " = ((Integer) value).intValue();\n");
} else if ("long".equals(attribute.getType())) {
sb.append(INDENT + INDENT + INDENT)
.append(fieldName + " = ((Long) value).longValue();\n");
} else if ("float".equals(attribute.getType())) {
sb.append(INDENT + INDENT + INDENT)
.append(fieldName + " = ((Float) value).floatValue();\n");
} else if ("double".equals(attribute.getType())) {
sb.append(INDENT + INDENT + INDENT)
.append(fieldName + " = ((Double) value).doubleValue();\n");
} else {
sb.append(INDENT + INDENT + INDENT)
.append(fieldName + " = (" + attribute.getType() + ") value;\n");
}
} else if (field.isReference()) {
sb.append(INDENT + INDENT + INDENT)
.append(fieldName + " = (org.intermine.model.InterMineObject) value;\n");
} else {
sb.append(INDENT + INDENT + INDENT).append(fieldName + " = (java.util.Set) value;\n");
}
sb.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.setFieldValue(this, fieldName, value);\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append("return;\n")
.append(INDENT + INDENT + INDENT)
.append("}\n")
.append(INDENT + INDENT + INDENT)
.append("throw new IllegalArgumentException(\"Unknown field \" + fieldName);\n")
.append(INDENT + INDENT)
.append("}\n")
.append(INDENT)
.append("}\n");
return sb.toString();
}
/**
* Generates the getFieldValue method.
*
* @param cld the ClassDescriptor
* @param proxy false to make the getFieldValue method, true to make the getFieldProxy method
* @return a String with the method
*/
public String generateGetFieldValue(ClassDescriptor cld, boolean proxy) {
StringBuffer sb = new StringBuffer();
sb.append(INDENT)
.append(
"public Object getField"
+ (proxy ? "Proxy" : "Value")
+ "(final String fieldName) throws IllegalAccessException {\n");
for (FieldDescriptor field : cld.getAllFieldDescriptors()) {
sb.append(INDENT + INDENT).append("if (\"" + field.getName() + "\".equals(fieldName)) {\n");
String fieldName = field.getName();
if ("fieldName".equals(fieldName)) {
fieldName = "this.fieldName";
}
if (field instanceof AttributeDescriptor) {
AttributeDescriptor attribute = (AttributeDescriptor) field;
if ("boolean".equals(attribute.getType())) {
sb.append(INDENT + INDENT + INDENT)
.append("return Boolean.valueOf(" + fieldName + ");\n");
} else if ("short".equals(attribute.getType())) {
sb.append(INDENT + INDENT + INDENT).append("return Short.valueOf(" + fieldName + ");\n");
} else if ("int".equals(attribute.getType())) {
sb.append(INDENT + INDENT + INDENT)
.append("return Integer.valueOf(" + fieldName + ");\n");
} else if ("long".equals(attribute.getType())) {
sb.append(INDENT + INDENT + INDENT).append("return Long.valueOf(" + fieldName + ");\n");
} else if ("float".equals(attribute.getType())) {
sb.append(INDENT + INDENT + INDENT).append("return Float.valueOf(" + fieldName + ");\n");
} else if ("double".equals(attribute.getType())) {
sb.append(INDENT + INDENT + INDENT).append("return Double.valueOf(" + fieldName + ");\n");
} else {
sb.append(INDENT + INDENT + INDENT).append("return " + fieldName + ";\n");
}
} else if (field.isReference()) {
sb.append(INDENT + INDENT + INDENT);
if (proxy) {
sb.append("return " + fieldName + ";\n");
} else {
sb.append("if (" + fieldName + " instanceof ProxyReference) {\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append("return ((ProxyReference) " + fieldName + ").getObject();\n")
.append(INDENT + INDENT + INDENT)
.append("} else {\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append("return " + fieldName + ";\n")
.append(INDENT + INDENT + INDENT)
.append("}\n");
}
} else {
sb.append(INDENT + INDENT + INDENT).append("return " + fieldName + ";\n");
}
sb.append(INDENT + INDENT).append("}\n");
}
sb.append(INDENT + INDENT)
.append("if (!" + cld.getName() + ".class.equals(getClass())) {\n")
.append(INDENT + INDENT + INDENT)
.append("return TypeUtil.getField" + (proxy ? "Proxy" : "Value") + "(this, 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 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();
}
/**
* Generates the getoBJECT method for producing NotXml.
*
* @param cld the ClassDescriptor
* @return generated java code as a String
*/
protected String generateGetObject(ClassDescriptor cld) {
StringBuffer sb = new StringBuffer();
sb.append(INDENT)
.append("public StringConstructor getoBJECT() {\n")
.append(INDENT + INDENT)
.append(
"if (!"
+ cld.getName()
+ (cld.isInterface() ? "Shadow" : "")
+ ".class.equals(getClass())) {\n")
.append(INDENT + INDENT + INDENT)
.append("return NotXmlRenderer.render(this);\n")
.append(INDENT + INDENT)
.append("}\n")
.append(INDENT + INDENT)
.append("StringConstructor sb = new StringConstructor();\n")
.append(INDENT + INDENT)
.append("sb.append(\"" + DELIM + cld.getName() + "\");\n");
for (FieldDescriptor field : cld.getAllFieldDescriptors()) {
if (field instanceof AttributeDescriptor) {
AttributeDescriptor attribute = (AttributeDescriptor) field;
if (attribute.getType().startsWith("java.")) {
sb.append(INDENT + INDENT)
.append("if (" + attribute.getName() + " != null) {\n")
.append(INDENT + INDENT + INDENT)
.append("sb.append(\"" + DELIM + "a" + field.getName() + DELIM + "\")");
if ("java.util.Date".equals(attribute.getType())) {
sb.append(".append(" + attribute.getName() + ".getTime());\n");
} else if ("java.lang.String".equals(attribute.getType())) {
sb.append(";\n")
.append(INDENT + INDENT + INDENT)
.append("String string = " + attribute.getName() + ";\n")
.append(INDENT + INDENT + INDENT)
.append("while (string != null) {\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append("int delimPosition = string.indexOf(\"" + DELIM + "\");\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append("if (delimPosition == -1) {\n")
.append(INDENT + INDENT + INDENT + INDENT + INDENT)
.append("sb.append(string);\n")
.append(INDENT + INDENT + INDENT + INDENT + INDENT)
.append("string = null;\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append("} else {\n")
.append(INDENT + INDENT + INDENT + INDENT + INDENT)
.append("sb.append(string.substring(0, delimPosition + 3));\n")
.append(INDENT + INDENT + INDENT + INDENT + INDENT)
.append("sb.append(\"" + ENCODED_DELIM + "\");\n")
.append(INDENT + INDENT + INDENT + INDENT + INDENT)
.append("string = string.substring(delimPosition + 3);\n")
.append(INDENT + INDENT + INDENT + INDENT)
.append("}\n")
.append(INDENT + INDENT + INDENT)
.append("}\n");
} else {
sb.append(".append(" + attribute.getName() + ");\n");
}
sb.append(INDENT + INDENT).append("}\n");
} else if ("org.intermine.objectstore.query.ClobAccess".equals(attribute.getType())) {
sb.append(INDENT + INDENT)
.append("if (" + attribute.getName() + " != null) {\n")
.append(INDENT + INDENT + INDENT)
.append("sb.append(\"" + DELIM + "a" + field.getName() + DELIM + "\" + ")
.append(attribute.getName() + ".getDbDescription());\n")
.append(INDENT + INDENT)
.append("}\n");
} else {
sb.append(INDENT)
.append(INDENT)
.append("sb.append(\"" + DELIM + "a" + field.getName() + DELIM + "\")")
.append(".append(" + field.getName() + ");\n");
}
} else if (field.isReference()) {
sb.append(INDENT + INDENT)
.append("if (" + field.getName() + " != null) {\n")
.append(INDENT + INDENT + INDENT)
.append("sb.append(\"" + DELIM + "r" + field.getName() + DELIM + "\")")
.append(".append(" + field.getName() + ".getId());\n")
.append(INDENT + INDENT)
.append("}\n");
}
}
sb.append(INDENT + INDENT).append("return sb;\n").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();
}
@Override
public void display(HttpServletRequest request, ReportObject reportObject) {
// get the gene/protein in question from the request
InterMineObject object = reportObject.getObject();
// API connection
HttpSession session = request.getSession();
final InterMineAPI im = SessionMethods.getInterMineAPI(session);
Model model = im.getModel();
PathQuery query = new PathQuery(model);
// cast me Gene
Gene gene = (Gene) object;
Object genePrimaryIDObj = gene.getPrimaryIdentifier();
if (genePrimaryIDObj != null) {
// fetch the expression
String genePrimaryID = String.valueOf(genePrimaryIDObj);
query = geneExpressionAtlasQuery(genePrimaryID, query);
// execute the query
Profile profile = SessionMethods.getProfile(session);
PathQueryExecutor executor = im.getPathQueryExecutor(profile);
ExportResultsIterator values = executor.execute(query);
// convert to a map
GeneExpressionAtlasDiseasesExpressions geae =
new GeneExpressionAtlasDiseasesExpressions(values);
// attach to results
request.setAttribute("expressions", geae);
request.setAttribute("url", "http://www.ebi.ac.uk/gxa/experiment/E-MTAB-62/" + genePrimaryID);
request.setAttribute("defaultPValue", "1e-4");
request.setAttribute("defaultTValue", "4");
// get the corresponding collection
for (FieldDescriptor fd : reportObject.getClassDescriptor().getAllFieldDescriptors()) {
if ("atlasExpression".equals(fd.getName()) && fd.isCollection()) {
// fetch the collection
Collection<?> collection = null;
try {
collection = (Collection<?>) reportObject.getObject().getFieldValue("atlasExpression");
} catch (IllegalAccessException e) {
e.printStackTrace();
}
List<Class<?>> lc =
PathQueryResultHelper.queryForTypesInCollection(
reportObject.getObject(), "atlasExpression", im.getObjectStore());
// create an InlineResultsTable
InlineResultsTable t =
new InlineResultsTable(
collection,
fd.getClassDescriptor().getModel(),
SessionMethods.getWebConfig(request),
im.getClassKeys(),
collection.size(),
false,
lc);
request.setAttribute("collection", t);
break;
}
}
}
}
/**
* Create a new DelimitedFileConfiguration from an InputStream.
*
* @param model The model to use when looking for ClassDescriptors and FieldDescriptors
* @param inputStream The InputStream to read the configuration from
* @throws IOException throws if the read fails
*/
public DelimitedFileConfiguration(Model model, InputStream inputStream) throws IOException {
Properties properties = new Properties();
properties.load(inputStream);
String className = properties.getProperty("className");
if (className == null) {
throw new IllegalArgumentException(
"className not set in property file for " + "DelimitedFileConfiguration");
}
configClassDescriptor = model.getClassDescriptorByName(className);
if (configClassDescriptor == null) {
throw new IllegalArgumentException("cannot find ClassDescriptor for: " + className);
}
Map columnFieldDescriptorMap = new TreeMap();
Enumeration enumeration = properties.propertyNames();
while (enumeration.hasMoreElements()) {
String key = (String) enumeration.nextElement();
if (key.startsWith("column.")) {
String columnNumberString = key.substring(7);
try {
int keyColumnNumber = Integer.valueOf(columnNumberString).intValue();
String fieldName = properties.getProperty(key);
FieldDescriptor columnFD = configClassDescriptor.getFieldDescriptorByName(fieldName);
if (columnFD == null) {
throw new IllegalArgumentException(
"cannot find FieldDescriptor for " + fieldName + " in " + className);
}
if (!columnFD.isAttribute()) {
String message =
"field: "
+ fieldName
+ " in "
+ className
+ " is not an attribute field so cannot be used as a "
+ "className in DelimitedFileConfiguration";
throw new IllegalArgumentException(message);
}
columnFieldDescriptorMap.put(new Integer(keyColumnNumber), columnFD);
} catch (NumberFormatException e) {
throw new IllegalArgumentException(
"column number ("
+ key
+ ") not parsable "
+ "in property file for "
+ "DelimitedFileConfiguration");
}
}
}
int mapMax = findMapMaxKey(columnFieldDescriptorMap);
columnFieldDescriptors = new ArrayList(mapMax + 1);
for (int columnNumber = 0; columnNumber < mapMax + 1; columnNumber++) {
FieldDescriptor columnFD =
(FieldDescriptor) columnFieldDescriptorMap.get(new Integer(columnNumber));
columnFieldDescriptors.add(columnFD);
}
}
/** {@inheritDoc} */
@SuppressWarnings("unused")
@Override
public ActionForward execute(
@SuppressWarnings("unused") ActionMapping mapping,
@SuppressWarnings("unused") ActionForm form,
HttpServletRequest request,
@SuppressWarnings("unused") HttpServletResponse response)
throws Exception {
long startTime = System.currentTimeMillis();
HttpSession session = request.getSession();
InterMineAPI im = SessionMethods.getInterMineAPI(session);
if (im.getBagManager().isAnyBagToUpgrade(SessionMethods.getProfile(session))) {
recordError(new ActionMessage("login.upgradeListManually"), request);
}
// fetch & set requested object
InterMineObject requestedObject = getRequestedObject(im, request);
if (requestedObject != null) {
ReportObjectFactory reportObjectFactory = SessionMethods.getReportObjects(session);
ReportObject reportObject = reportObjectFactory.get(requestedObject);
request.setAttribute("object", reportObject);
request.setAttribute("reportObject", reportObject);
request.setAttribute("requestedObject", requestedObject);
// hell starts here
TagManager tagManager = im.getTagManager();
ServletContext servletContext = session.getServletContext();
ObjectStore os = im.getObjectStore();
String superuser = im.getProfileManager().getSuperuser();
if (superuser.equals(SessionMethods.getProfile(session).getUsername())) {
request.setAttribute("SHOW_TAGS", true);
}
// place InlineLists based on TagManager, reportObject is cached while Controller is not
Map<String, List<InlineList>> placedInlineLists = new TreeMap<String, List<InlineList>>();
// traverse all unplaced (non-header) InlineLists
for (InlineList list : reportObject.getNormalInlineLists()) {
FieldDescriptor fd = list.getDescriptor();
String taggedType = getTaggedType(fd);
// assign lists to any aspects they are tagged to or put in unplaced lists
String fieldPath = fd.getClassDescriptor().getUnqualifiedName() + "." + fd.getName();
List<Tag> tags = tagManager.getTags(null, fieldPath, taggedType, superuser);
for (Tag tag : tags) {
String tagName = tag.getTagName();
if (AspectTagUtil.isAspectTag(tagName)) {
List<InlineList> listsForAspect = placedInlineLists.get(tagName);
if (listsForAspect == null) {
listsForAspect = new ArrayList<InlineList>();
placedInlineLists.put(tagName, listsForAspect);
}
listsForAspect.add(list);
} else if (tagName.equals(TagNames.IM_SUMMARY)) {
List<InlineList> summaryLists = placedInlineLists.get(tagName);
if (summaryLists == null) {
summaryLists = new ArrayList<InlineList>();
placedInlineLists.put(tagName, summaryLists);
}
summaryLists.add(list);
}
}
}
// any lists that aren't tagged will be 'unplaced'
List<InlineList> unplacedInlineLists =
new ArrayList<InlineList>(reportObject.getNormalInlineLists());
unplacedInlineLists.removeAll(placedInlineLists.values());
long now = System.currentTimeMillis();
LOG.info("TIME placed inline lists: " + (now - startTime) + "ms");
long stepTime = now;
request.setAttribute("mapOfInlineLists", placedInlineLists);
request.setAttribute("listOfUnplacedInlineLists", unplacedInlineLists);
Map<String, Map<String, DisplayField>> placementRefsAndCollections =
new TreeMap<String, Map<String, DisplayField>>();
Set<String> aspects = new LinkedHashSet<String>(SessionMethods.getCategories(servletContext));
Set<ClassDescriptor> cds =
os.getModel().getClassDescriptorsForClass(requestedObject.getClass());
for (String aspect : aspects) {
placementRefsAndCollections.put(
TagNames.IM_ASPECT_PREFIX + aspect,
new TreeMap<String, DisplayField>(String.CASE_INSENSITIVE_ORDER));
}
Map<String, DisplayField> miscRefs =
new TreeMap<String, DisplayField>(reportObject.getRefsAndCollections());
placementRefsAndCollections.put(TagNames.IM_ASPECT_MISC, miscRefs);
// summary refs and colls
Map<String, DisplayField> summaryRefsCols = new TreeMap<String, DisplayField>();
placementRefsAndCollections.put(TagNames.IM_SUMMARY, summaryRefsCols);
for (Iterator<Entry<String, DisplayField>> iter =
reportObject.getRefsAndCollections().entrySet().iterator();
iter.hasNext(); ) {
Map.Entry<String, DisplayField> entry = iter.next();
DisplayField df = entry.getValue();
if (df instanceof DisplayReference) {
categoriseBasedOnTags(
((DisplayReference) df).getDescriptor(),
"reference",
df,
miscRefs,
tagManager,
superuser,
placementRefsAndCollections,
SessionMethods.isSuperUser(session));
} else if (df instanceof DisplayCollection) {
categoriseBasedOnTags(
((DisplayCollection) df).getDescriptor(),
"collection",
df,
miscRefs,
tagManager,
superuser,
placementRefsAndCollections,
SessionMethods.isSuperUser(session));
}
}
// remove any fields overridden by displayers
removeFieldsReplacedByReportDisplayers(reportObject, placementRefsAndCollections);
request.setAttribute("placementRefsAndCollections", placementRefsAndCollections);
String type = reportObject.getType();
request.setAttribute("objectType", type);
String stableLink = PortalHelper.generatePortalLink(reportObject.getObject(), im, request);
if (stableLink != null) {
request.setAttribute("stableLink", stableLink);
}
stepTime = System.currentTimeMillis();
startTime = stepTime;
// attach only non empty categories
Set<String> allClasses = new HashSet<String>();
for (ClassDescriptor cld : cds) {
allClasses.add(cld.getUnqualifiedName());
}
TemplateManager templateManager = im.getTemplateManager();
Map<String, List<ReportDisplayer>> displayerMap = reportObject.getReportDisplayers();
stepTime = System.currentTimeMillis();
startTime = stepTime;
List<String> categories = new LinkedList<String>();
for (String aspect : aspects) {
// 1) Displayers
// 2) Inline Lists
if ((displayerMap != null && displayerMap.containsKey(aspect))
|| placedInlineLists.containsKey(aspect)) {
categories.add(aspect);
} else {
// 3) Templates
if (!templateManager.getReportPageTemplatesForAspect(aspect, allClasses).isEmpty()) {
categories.add(aspect);
} else {
// 4) References & Collections
if (placementRefsAndCollections.containsKey("im:aspect:" + aspect)
&& placementRefsAndCollections.get("im:aspect:" + aspect) != null) {
for (DisplayField df :
placementRefsAndCollections.get("im:aspect:" + aspect).values()) {
categories.add(aspect);
break;
}
}
}
}
}
if (!categories.isEmpty()) {
request.setAttribute("categories", categories);
}
now = System.currentTimeMillis();
LOG.info("TIME made list of categories: " + (now - stepTime) + "ms");
}
return null;
}
/**
* Look a the values of the given primary key in the object and return true if and only if some
* part of the primary key is null. If the primary key contains a reference it is sufficient for
* any of the primary keys of the referenced object to be non-null (ie objectPrimaryKeyIsNull()
* returning true).
*
* @param model the Model in which to find ClassDescriptors
* @param obj the Object to check
* @param cld one of the classes that obj is. Only primary keys for this classes will be checked
* @param pk the primary key to check
* @param source the Source database
* @param idMap an IntToIntMap from source IDs to destination IDs
* @return true if the the given primary key is non-null for the given object
* @throws MetaDataException if anything goes wrong
*/
public static boolean objectPrimaryKeyNotNull(
Model model,
InterMineObject obj,
ClassDescriptor cld,
PrimaryKey pk,
Source source,
IntToIntMap idMap)
throws MetaDataException {
for (String fieldName : pk.getFieldNames()) {
FieldDescriptor fd = cld.getFieldDescriptorByName(fieldName);
if (fd instanceof AttributeDescriptor) {
Object value;
try {
value = obj.getFieldValue(fieldName);
} catch (IllegalAccessException e) {
throw new MetaDataException(
"Failed to get field " + fieldName + " for key " + pk + " from " + obj, e);
}
if (value == null) {
return false;
}
} else if (fd instanceof CollectionDescriptor) {
throw new MetaDataException(
"Primary key "
+ pk.getName()
+ " for class "
+ cld.getName()
+ " cannot contain collection "
+ fd.getName()
+ ": collections cannot be part of a primary key. Please edit"
+ model.getName()
+ "_keyDefs.properties");
} else if (fd instanceof ReferenceDescriptor) {
InterMineObject refObj;
try {
refObj = (InterMineObject) obj.getFieldProxy(fieldName);
} catch (IllegalAccessException e) {
throw new MetaDataException(
"Failed to get field " + fieldName + " for key " + pk + " from " + obj, e);
}
if (refObj == null) {
return false;
}
if ((refObj.getId() != null) && (idMap.get(refObj.getId()) != null)) {
// We have previously loaded the object in this reference.
continue;
}
if (refObj instanceof ProxyReference) {
refObj = ((ProxyReference) refObj).getObject();
}
boolean foundNonNullKey = false;
boolean foundKey = false;
Set<ClassDescriptor> classDescriptors =
model.getClassDescriptorsForClass(refObj.getClass());
CLDS:
for (ClassDescriptor refCld : classDescriptors) {
Set<PrimaryKey> primaryKeys;
if (source == null) {
primaryKeys =
new LinkedHashSet<PrimaryKey>(PrimaryKeyUtil.getPrimaryKeys(refCld).values());
} else {
primaryKeys = DataLoaderHelper.getPrimaryKeys(refCld, source, null);
}
for (PrimaryKey refPK : primaryKeys) {
foundKey = true;
if (objectPrimaryKeyNotNull(model, refObj, refCld, refPK, source, idMap)) {
foundNonNullKey = true;
break CLDS;
}
}
}
if (foundKey && (!foundNonNullKey)) {
return false;
}
}
}
return true;
}
