Uses of Class
org.molgenis.model.MolgenisModelException

Packages that use MolgenisModelException

Package	Description
org.molgenis	MOLGENIS generative platform for life sciences having framework, generators, models and util.
org.molgenis.fieldtypes	Helper functions for each field type.
org.molgenis.generators	MOLGENIS generators.
org.molgenis.model	MOLGENIS meta model parser.
org.molgenis.model.elements	Currently known model elements like 'entity' and 'field'.

Uses of MolgenisModelException in org.molgenis

Methods in org.molgenis that throw MolgenisModelException

Modifier and Type	Method and Description
static FieldType	MolgenisFieldTypes.get(Field f)

Uses of MolgenisModelException in org.molgenis.fieldtypes

Methods in org.molgenis.fieldtypes that throw MolgenisModelException

Modifier and Type	Method and Description
String	MrefField.getCppJavaPropertyType()
String	CompoundField.getCppJavaPropertyType()
String	XrefField.getCppJavaPropertyType()
abstract String	FieldType.getCppJavaPropertyType()
String	HyperlinkField.getCppPropertyType()
String	DateField.getCppPropertyType()
String	LongField.getCppPropertyType()
String	MrefField.getCppPropertyType()
String	TextField.getCppPropertyType()
String	CompoundField.getCppPropertyType()
String	DecimalField.getCppPropertyType()
String	DatetimeField.getCppPropertyType()
String	XrefField.getCppPropertyType()
String	StringField.getCppPropertyType()
String	BoolField.getCppPropertyType()
String	EmailField.getCppPropertyType()
String	IntField.getCppPropertyType()
String	FileField.getCppPropertyType() Deprecated.
String	EnumField.getCppPropertyType()
abstract String	FieldType.getCppPropertyType() Product the Java type of this field type.
FieldType	FieldType.getFieldType(Field f) Get the field type from a field.
String	MrefField.getHsqlType()
String	TextField.getHsqlType()
String	CompoundField.getHsqlType()
String	XrefField.getHsqlType()
String	StringField.getHsqlType()
String	EmailField.getHsqlType()
abstract String	FieldType.getHsqlType() Produce a valid hsql snippet indicating the mysql type.
String	StringField.getJavaAssignment(String value)
String	EmailField.getJavaAssignment(String value)
abstract String	FieldType.getJavaAssignment(String value) Produce a valid Java snippet to set a value for field.
String	MrefField.getJavaPropertyDefault()
String	StringField.getJavaPropertyDefault()
String	EmailField.getJavaPropertyDefault()
abstract String	FieldType.getJavaPropertyDefault() Produce a valid Java snippet to set the default of a field, using the 'getDefault' function of that field.
String	DateField.getJavaPropertyType()
String	MrefField.getJavaPropertyType()
String	TextField.getJavaPropertyType()
String	CompoundField.getJavaPropertyType()
String	DatetimeField.getJavaPropertyType()
String	XrefField.getJavaPropertyType()
String	StringField.getJavaPropertyType()
String	EmailField.getJavaPropertyType()
String	IntField.getJavaPropertyType()
abstract String	FieldType.getJavaPropertyType() Product the Java type of this field type.
String	DateField.getJavaSetterType()
String	MrefField.getJavaSetterType()
String	CompoundField.getJavaSetterType()
String	DatetimeField.getJavaSetterType()
String	XrefField.getJavaSetterType()
String	IntField.getJavaSetterType()
String	FieldType.getJavaSetterType()
Class<?>	XrefField.getJavaType()
abstract Class<?>	FieldType.getJavaType() Produce the Java class corresponding to the value
String	HyperlinkField.getMysqlType()
String	DateField.getMysqlType()
String	LongField.getMysqlType()
String	MrefField.getMysqlType()
String	TextField.getMysqlType()
String	CompoundField.getMysqlType()
String	DecimalField.getMysqlType()
String	DatetimeField.getMysqlType()
String	XrefField.getMysqlType()
String	StringField.getMysqlType()
String	BoolField.getMysqlType()
String	EmailField.getMysqlType()
String	IntField.getMysqlType()
String	FileField.getMysqlType() Deprecated.
String	EnumField.getMysqlType()
abstract String	FieldType.getMysqlType() Produce a valid mysql snippet indicating the mysql type.
String	HyperlinkField.getOracleType()
String	DateField.getOracleType()
String	LongField.getOracleType()
String	MrefField.getOracleType()
String	CompoundField.getOracleType()
String	DecimalField.getOracleType()
String	DatetimeField.getOracleType()
String	XrefField.getOracleType()
String	StringField.getOracleType()
String	BoolField.getOracleType()
String	EmailField.getOracleType()
String	IntField.getOracleType()
String	FileField.getOracleType() Deprecated.
String	EnumField.getOracleType()
abstract String	FieldType.getOracleType()
String	MrefField.getXsdType()
String	TextField.getXsdType()
String	CompoundField.getXsdType()
String	XrefField.getXsdType()
String	StringField.getXsdType()
String	EmailField.getXsdType()
abstract String	FieldType.getXsdType() Produce valid XSD type

Uses of MolgenisModelException in org.molgenis.generators

Methods in org.molgenis.generators that throw MolgenisModelException

Modifier and Type	Method and Description
Vector<Unique>	GeneratorHelper.getAllKeys(Entity e)
String	GeneratorHelper.getImports(Model m, Entity e, String subpackage, String suffix)
String	GeneratorHelper.getJavaAssignment(Field field, String value)
Vector<Field>	GeneratorHelper.getKeyFields(Entity e)
Vector<Field>	GeneratorHelper.getKeyFields(List<Unique> keys) Return all secondary key fields.
Vector<Field>	GeneratorHelper.getKeyFields(Unique u)
Vector<Field>	GeneratorHelper.getSecondaryKeyFields(Entity e)
Vector<Unique>	GeneratorHelper.getSecondaryKeys(Entity e) Return all secondary keys for an entity
Vector<Unique>	GeneratorHelper.getTableKeys(Entity e) A table can only contain the keys for columns that are actually in the table.
boolean	GeneratorHelper.isPrimaryKey(Field f, Entity e)

Uses of MolgenisModelException in org.molgenis.model

Methods in org.molgenis.model that throw MolgenisModelException

Modifier and Type	Method and Description
static void	MolgenisModelValidator.addInterfaces(Model model) Add interfaces as artificial entities to the model
static void	MolgenisModelValidator.addTypeFieldInSubclasses(Model model) In each entity of an entity subclass hierarchy a 'type' field is added to enable filtering.
static void	MolgenisModelValidator.addXrefLabelsToEntities(Model model)
static void	MolgenisModelValidator.copyDecoratorsToSubclass(Model model)
static void	MolgenisModelValidator.copyDefaultXrefLabels(Model model) Default xref labels can come from: - the xref_entity (or one of its superclasses)
static void	MolgenisModelValidator.copyFieldsToSubclassToEnforceConstraints(Model model) Copy fields to subclasses (redundantly) so this field can be part of an extra constraint.
static void	MolgenisModelValidator.correctXrefCaseSensitivity(Model model) test for case sensitivity
static void	MolgenisModelValidator.createLinkTablesForMrefs(Model model, MolgenisOptions options) Add link tables for many to many relationships A link table entity will have the name of [from_entity]_[to_entity] A link table has two xrefs to the from/to entity respectively The column names are those of the respective fields In case of a self reference, the second column name is '_self'
static void	MolgenisModelValidator.moveMrefsFromInterfaceAndCopyToSubclass(Model model) As mrefs are a linking table between to other tables, interfaces cannot be part of mrefs (as they don't have a linking table).
static Model	MolgenisModelParser.parseDbSchema(ArrayList<String> filenames)
static Model	MolgenisModelParser.parseDbSchema(ArrayList<String> filenames, String modelName)
static Model	MolgenisModelParser.parseDbSchema(String xml) Simple parse an xml string
static Entity	MolgenisModelParser.parseEntity(Model model, Element element)
static void	MolgenisModelParser.parseField(Entity entity, Element element)
static void	MolgenisModelParser.parseMatrix(Model model, Element element)
static void	MolgenisModelParser.parseMethod(Model model, Element element)
static void	MolgenisModelParser.parseModule(Model model, Element element)
static void	MolgenisModelParser.parseParameter(Method method, Element element)
static void	MolgenisModelParser.parseQuery(Model model, Method method, Element element)
static void	MolgenisModelParser.parseQueryRule(Model model, MethodQuery query, Element element)
static void	MolgenisModelParser.parseReturnType(Model model, Method method, Element element)
static void	MolgenisModelParser.parseView(Model model, Element element)
static List<Entity>	MolgenisModel.sortEntitiesByDependency(List<Entity> entityList, Model model)
static void	MolgenisModelValidator.validate(Model model, MolgenisOptions options)
static void	MolgenisModelValidator.validateExtendsAndImplements(Model model) Validate extends and implements relationships: Do superclasses actually exist Do 'implements' refer to abstract superclasses (interfaces) Do 'extends' refer to non-abstract superclasses Copy primary key to subclass to form parent/child relationships
static void	MolgenisModelValidator.validateForeignKeys(Model model) Validate foreign key relationships: Do the xref_field and xref_label refer to fields actually exist Is the entity refered to non-abstract Does the xref_field refer to a unique field (i.e.
static void	MolgenisModelValidator.validateHideFields(Model model)
static void	MolgenisModelValidator.validateKeys(Model model) Validate the unique constraints Do unique field names refer to existing fields? Is there a unique column id + unique label?
static void	MolgenisModelValidator.validateNamesAndReservedWords(Model model, MolgenisOptions options)
static void	MolgenisModelValidator.validateNameSize(Model model, MolgenisOptions options)
static void	MolgenisModelValidator.validatePrimaryKeys(Model model)
static void	MolgenisModelValidator.validateViews(Model model) Check if the view objects are an aggregate of known entities.

Uses of MolgenisModelException in org.molgenis.model.elements

Methods in org.molgenis.model.elements that throw MolgenisModelException

Modifier and Type	Method and Description
void	Processor.addDataset(Dataset dataset) Deprecated.
void	Entity.addField(Field field) Adds the given field to the list of fields associated with this entity.
void	Entity.addField(Integer pos, Field field) Adds the given field to the list of fields associated with this entity.
void	Index.addField(String field) Adds the field-name to the list of fields.
void	Entity.addKey(List<String> keys, boolean subclass, String description) Adds the given list of fields to the key-list.
void	Method.addParameter(Parameter parameter)
Map<String,List<Field>>	Field.allPossibleXrefLabels()
Field	Model.findField(String f)
Vector<Field>	Entity.getAddFields()
Vector<Field>	Entity.getAllAddFields()
Field	Entity.getAllField(String name) Returns the field with the given name from entity or any of its parents.
List<Field>	View.getAllFields()
Vector<Field>	Entity.getAllFields()
Vector<Field>	Entity.getAllFieldsOf(FieldType type)
Vector<Field>	Entity.getAllFieldsOf(String typeName)
Vector<Entity>	Entity.getAllImplements()
Vector<Index>	Entity.getAllIndices()
Vector<Unique>	Entity.getAllKeys()
Vector<Field>	Entity.getAllLocalFields() Returns a vector with all the fields that are actualy located in this entity.
Vector<Field>	Entity.getAllUpdateFields()
Entity	Matrix.getColEntity() Return the Entity that contains the labels for the columns.
Entity	Matrix.getContainerEntity() Return the Entity that contains the container
List<Entity>	Entity.getDependencies()
List<String>	Parameter.getEnumOptions()
Vector<String>	Field.getEnumOptions()
Field	Entity.getField(String name)
Field	Entity.getField(String name, boolean required, boolean recursive, boolean systemFields) Returns the field with the given name.
Field	Entity.getFieldRecusive(String name)
List<Field>	Record.getFields()
List<Field>	View.getFields()
List<Field>	Entity.getFields() Returns a vector with all the fields associated with this entity.
Vector<Field>	Unique.getFields() Returns a list of all the fields that make up this unique.
List<Field>	Entity.getFields(boolean required, boolean recursive, boolean systemField)
List<Field>	Entity.getFields(boolean required, boolean recursive, boolean systemField, boolean implementing) Returns a vector with all the fields associated with this entity.
Vector<Field>	Entity.getFieldsOf(FieldType type) Returns a vector with all the fields associated with this entity and are of the given type.
Vector<Field>	Entity.getImplementedFields() Get fields for this entity as well as from the interfaces it implements.
Vector<Field>	Entity.getImplementedFieldsOf(FieldType type)
Vector<Field>	Entity.getImplementedFieldsOf(String typeName)
Vector<Entity>	Entity.getImplements()
Index	Entity.getIndex(String name) Returns the index with the given name.
Vector<Index>	Entity.getIndices() Returns a vector with all the indices associated with this entity.
Vector<Field>	Entity.getInheritedFields()
Unique	Entity.getKey(int index) Returns the key at the given index.
Vector<Field>	Entity.getKeyFields(int index) Returns a list of the fields that make up the key at the given index.
Vector<Unique>	Entity.getKeys() Returns a list with all the keys.
Integer	Field.getLength()
Vector<Field>	Entity.getLocalFields() Returns a vector with all the fields that are actualy located in this entity.
List<Field>	Entity.getNonSystemFields(boolean all) Returns all the fields belonging to this entity, which have not set the system-property.
int	Entity.getNumberOfMrefTo(Entity e)
int	Entity.getNumberOfMrefTo(Entity e, Field f)
int	Entity.getNumberOfReferencesTo(Entity e)
int	Model.getNumberOfReferencesTo(Entity e)
int	Entity.getNumberOfReferencesTo(Entity e, Field f)
static Plugin.Flavor	Plugin.Flavor.getPluginMethod(String method)
static Menu.Position	Menu.Position.getPosition(String position)
Field	Entity.getPrimaryKey()
Vector<Field>	Entity.getRemoteFields() Returns a vector with all the fields that are located in other tables, but belong to this entity (xref_multiple).
Entity	Matrix.getRowEntity() Return the Entity that contains the labels for the rows.
List<Field>	Entity.getSystemFields(boolean all)
List<Unique>	Entity.getUniqueKeysWithoutPk()
List<Field>	Entity.getUserFields()
int	Field.getVarCharLength() When this field is of type Type.VARCHAR, this method returns the maximum length the varchar can be.
Entity	Field.getXrefEntity() Returns the name of the entity this field is referencing to.
String	Field.getXrefEntityName()
Field	Field.getXrefField() Returns the name of the field of the entity this field is referencing to.
List<Field>	Entity.getXRefFields()
List<String>	Field.getXrefLabelNames() Returns the label of this reference.
List<Field>	Field.getXrefLabelPath(String label)
List<String>	Entity.getXrefLabels()
List<Field>	Field.getXrefLabels()
List<String>	Field.getXrefLabelsTemp()
SimpleTree<SimpleTree<?>>	Field.getXrefLabelTree() Return a tree wich describes the path to xref labels.
SimpleTree<SimpleTree<?>>	Field.getXrefLabelTree(boolean useJavaNames)
protected void	Field.getXrefLabelTree(List<String> labels, SimpleTree<?> parent) Creates a tree with leafs that match labels and nodes that match entities.
protected void	Field.getXrefLabelTree(List<String> labels, SimpleTree<?> parent, boolean useJavaNames) Creates a tree with leafs that match labels and nodes that match entities.
List<String>	Entity.getXrefLookupFields()
List<Field>	View.getXRefsFor(Entity e, List<Entity> entities)
boolean	Entity.hasSuperclassField(String fieldname)
boolean	Field.isCyclic()
boolean	Field.isUnique() If this a unique field? If this field is part of a compound key it will return false
static Form.SortOrder	Form.SortOrder.parse(String str)
static Form.ViewType	Form.ViewType.parseViewType(String str)
static Tree.ViewType	Tree.ViewType.parseViewType(String str)
void	Parameter.setEnumOptions(List<String> options)