Modifications to the FuGE-OM for the Hibernate and the EJB3 STK

This document contains the changes to the reference FuGE v1 UML Object model required to properly generate the Hibernate code using the AndroMDA Hibernate+Spring cartridge. It is based extensively on Leandro Hermida's similar document for the FuGE EJB3 STK, so that the two UML documents will be similar. Deviations from his modifications are noted.

  • Rename the copied package to net.sourceforge.fuge
  • Within the net.sourceforge.fuge package change ALL the packages in the entire FuGE hierarchy to lowercase so that it will later produce JavaBeans standard package names (e.g. ConceptualMolecule --> conceptualmolecule)
  • (This step was not needed in the Hibernate STK UML Diagram, as it is already fixed there: Fix typos in UML model, where +referenceAbleCollection between FuGE and ReferenceableCollection should read +referenceableCollection)
  • (This step was also not needed within the Hibernate FuGE-OM) Search and remove all AbstractAssociation stereotyped associations (20 of 26 instances) EXCEPT the following (which don't seem to have a concrete partner - am still checking with developers about this) * +dimensionElements : net.sourceforge.fuge::bio::data::DimensionElement
    • +dimensions : net.sourceforge.fuge::bio::data::Dimension
    • +inputPartitions : net.sourceforge.fuge::bio::data::DataPartition
    • +outputPartitions : net.sourceforge.fuge::bio::data::DataPartition
    • +partitionPairs : net.sourceforge.fuge::bio::data::PartitionPair
    • +supportingData : net.sourceforge.fuge::bio::data::Data
  • Look through all of the associations in the FuGE model and remove any association name numbers that got added during copying (e.g. Provider1 --> Provider)
    • net.sourceforge.fuge.Provider1
    • net.sourceforge.fuge.bio.data.DimensionElementSet1
    • net.sourceforge.fuge.bio.data.PartitionedData1
    • net.sourceforge.fuge.bio.investigation.Conclusion1
    • net.sourceforge.fuge.bio.investigation.Hypothesis1
    • net.sourceforge.fuge.bio.material.Components1
    • net.sourceforge.fuge.bio.material.MeasuredMaterial1
    • net.sourceforge.fuge.common.protocol.Actions1
    • net.sourceforge.fuge.common.protocol.ChildProtocol1
    • net.sourceforge.fuge.common.protocol.Equipment1
    • net.sourceforge.fuge.common.protocol.EquipmentParts1
    • net.sourceforge.fuge.common.protocol.InputCompleteMaterials1
    • net.sourceforge.fuge.common.protocol.ParameterPairs1
    • net.sourceforge.fuge.common.protocol.Parameters1
    • net.sourceforge.fuge.common.protocol.Parameters2
    • net.sourceforge.fuge.common.protocol.Parameters3
    • net.sourceforge.fuge.common.protocol.Parameters4
    • net.sourceforge.fuge.common.protocol.Parameters5
    • net.sourceforge.fuge.common.protocol.Protocol1
    • net.sourceforge.fuge.common.protocol.Software1
    • net.sourceforge.fuge.common.protocol.Software2Equipment1
    • net.sourceforge.fuge.common.protocol.Value1
  • All many-to-many associations with two-way navigability MUST have an aggregation (or composition) end
    • (added to end labelled "equipment", though it then appears on the end labelled "software" in the diagram!) Software2Equipment (between GenericSoftware and GenericEquipment) should be "shared" on +equipment end
  • Fix database table name clashes between certain associations and classes using @andromda.persistence.table tagged value
    Association Tagged Value Location Reason
    Equipment PROTOCOL_EQUIPMENT between GenericEquipment and GenericProtocol clashes with Equipment class
    Software PROTOCOL_SOFTWARE between GenericSoftware and GenericProtocol clashes with Software class
    Provider PARAMETERIZABLE_PROVIDER between Parameterizable and ContactRole clashes with Provider class
  • Create custom table names for classes and associations using @andromda.persistence.table tagged value
    Class Tagged Value Reason
    FuGE F_U_G_E instead of FU_G_E
    Software2Equipment (between GenericSoftware and GenericEquipment) SOFTWARE2EQUIPMENT instead of SOFTWARE2_EQUIPMENT
    Database EXTERNAL_DATABASE DATABASE is SQL reserved word
  • Certain associations need better/corrected table names using @andromda.persistence.table tagged value
    Association Tagged Value Location
    Actions PROTOCOL_ACTION between GenericProtocol and Action
    ActionApplications PROTO_APPL_ACTION_APPL between ProtocolApplication and ActionApplication
    Affiliations AFFILIATION between Person and Organization
    AllBibliographicReferences REF_COLLECT_BIBLIO_REFERENCE ReferenceableCollection and BibliographicReference
    AllContacts AUDIT_COLLECT_CONTACT between AuditCollection and Contact
    AllData DATA_COLLECT_DATA between DataCollection and Data
    AllDatabases REF_COLLECT_EXT_DATABASE between ReferenceableCollection and Database
    AllDataPartitions DATA_COLLECT_DATA_PARTITION between DataCollection and DataPartition
    AllDimensions DATA_COLLECT_DIMENSION between DataCollection and Dimension
    AllEquipment PROTO_COLLECT_EQUIPMENT between ProtocolCollection and Equipment
    AllProtocolApplications INVEST_COMPONENT_PROTO_APPL between InvestigationComponent and ProtocolApplication
    AllSequenceAnnotations CONCEP_MOL_COLLECT_SEQ_ANNOT between ConceptualMoleculeCollection and SequenceAnnotationSet
    AllSoftware PROTO_COLLECT_SOFTWARE between ProtocolCollection and Software
    Annotations DESCRIBABLE_ANNOTATION between Describable and OntologyTerm
    BibliographicReferences IDENT_BIBLIO_REFERENCE Identifiable and BibliographicReference
    Characteristics MATERIAL_CHARACTERISTIC between Material and OntologyTerm
    Components MATERIAL_COMPONENT between GenericMaterial and GenericMaterial
    ComponentDesignTypes COMPONENT_DESIGN_TYPE between InvestigationComponent and OntologyTerm
    ConceptualMolecules CONCEP_MOL_COLLECT_CONCEP_MOL betweeen ConceptualMoleculeCollection and ConceptualMolecule
    Contacts MATERIAL_CONTACT between Material and ContactRole
    DatabaseReferences IDENT_DB_REFERENCE between Identifiable and DatabaseReference
    DataPartitions FACTOR_VALUE_DATA_PARTITION between FactorValue and DataPartition
    Descriptions DESCRIBABLE_DESCRIPTION between Describable and Description
    Dimensions DATA_DIMENSION between Data and Dimension
    DimensionElements DIMENSION_DIMENSION_ELEMENT between Dimension and DimensionElement
    EquipmentApplications PROTO_APPL_EQUIP_APPL between ProtocolApplication and EquipmentApplication
    EquipmentParts EQUIPMENT_PART between GenericEquipment and GenericEquipment
    Factors INVEST_COMPONENT_FACTOR between InvestigationComponent and Factor
    FactorCollection INVEST_COLLECT_FACTOR between InvestigationCollection and Factor
    FactorValues FACTOR_FACTOR_VALUE between Factor and FactorValue
    HigherLevelAnalyses DATA_COLLECT_HIGHER_LEV_ANAL between DataCollection and HigherLevelAnalysis
    InputCompleteMaterials INPUT_COMPLETE_MATERIAL between GenericProtocolApplication and Material
    InputMaterials INPUT_MATERIAL between GenericProtocolApplication and GenericMaterialMeasurement
    InputPartitions INPUT_PARTITION between PartitionPair and DataPartition
    InputTypes INPUT_TYPE between Protocol and OntologyTerm
    Investigations INVEST_COLLECT_INVESTIGATION between InvestigationCollection and Investigation
    InvestigationComponents INVEST_INVEST_COMPONENT between Investigation and InvestigationComponent
    InvestigationTypes INVESTIGATION_TYPE between Investigation and OntologyTerm
    Materials MATERIAL_COLLECT_MATERIAL between MaterialCollection and Material
    Members SECURITY_GROUP_MEMBER between SecurityGroup and Contact
    OntologySources ONTOLOGY_COLLECT_SOURCE between OntologyCollection and OntologySource
    OntologyTerms ONTOLOGY_COLLECT_TERM between OntologyCollection and OntologyTerm
    OutputMaterials OUTPUT_MATERIAL between GenericProtocolApplication and Material
    OutputPartitions OUTPUT_PARTITION between PartitionPair and DataPartition
    OutputTypes OUTPUT_TYPE between Protocol and OntologyTerm
    Owners SECURITY_OWNER between Security and Contact
    Parameters EQUIPMENT_PARAMETER between GenericEquipment and GenericParameter
    Parameters SOFTWARE_PARAMETER between GenericSoftware and GenericParameter
    Parameters PROTOCOL_PARAMETER between GenericProtocol and GenericParameter
    Parameters ACTION_PARAMETER between GenericAction and GenericParameter
    ParameterPairs ACTION_PARAMETER_PAIR between GenericAction and ParameterPair
    ParameterValues PARAM_APPL_PARAM_VALUE between ParameterizableApplication and ParameterValue
    PartitionPairs PROTO_APPL_PARTITION_PAIR between ProtocolApplication and PartitionPair
    Performers PROTO_APPL_PERFORMER between ProtocolApplication and ContactRole
    Properties ONTOLOGY_INDIVIDUAL_PROPERTY between OntologyIndividual and OntologyProperty
    PropertySets DESCRIBABLE_PROPERTY_SET between Describable and NameValueType
    Protocols PROTO_COLLECT_PROTOCOL between ProtocolCollection and Protocol
    ProtocolApplications PROTO_COLLECT_PROTO_APPL between ProtocolCollection and ProtocolApplication
    Providers INVESTIGATION_PROVIDER between Investigation and ContactRole
    QualityControlStatistics QUALITY_CONTROL_STATISTIC between Material and OntologyTerm
    RangeDescriptors RANGE_DESCRIPTOR between Range and OntologyTerm
    SecurityGroups AUDIT_COLLECT_SECURITY_GROUP between AuditCollection and SecurityGroup
    SecurityRights SECURITY_RIGHT between Security and SecurityAccess
    SoftwareApplications PROTO_APPL_SOFTWARE_APPL between ProtocolApplication and SoftwareApplication
    SourceMaterials SOURCE_MATERIAL between Investigation and Material
    SummaryResults SUMMARY_RESULT between Investigation and HigherLevelAnalysis
    Types PARAMETERIZABLE_TYPE between Parameterizable and OntologyTerm
    Types SEQUENCE_ANNOTATION_SET_TYPE between SequenceAnnotationSet and OntologyTerm
  • Certain associations ends need better/corrected column names using @andromda.persistence.column tagged value
    Association End Tagged Value Location Reason
    +parameters PARAMETER_ID Parameters association between GenericAction and GenericParameter override plural association end name
    +parameterPairs PARAMETER_PAIR_ID ParameterPairs association between GenericAction and ParameterPair override plural association end name
    +affiliations AFFILIATION_ID Affliliations association between Person and Organization override plural association end name
    +allContacts CONTACT_ID AllContacts association between AuditCollection and Contact override plural association end name
    +securityGroups SECURITY_GROUP_ID SecurityGroups association between AuditCollection and SecurityGroup override plural association end name
    +componentDesignTypes COMPONENT_DESIGN_TYPE_ID ComponentDesignTypes association between InvestigationComponent and OntologyTerm override plural association end name
    +conceptualMolecules CONCEPTUAL_MOLECULE_ID ConceptualMolecules association between ConceptualMoleculeCollection and ConceptualMolecule override plural association end name
    +allSequenceAnnotations SEQUENCE_ANNOTATION_ID AllSequenceAnnotations association between ConceptualMoleculeCollection and SequenceAnnotationSet override plural association end name
    +allData DATA_ID AllData association between DataCollection and Data override plural association end name
    +allDataPartitions DATA_PARTITION_ID AllDataPartitions association between DataCollection and DataPartition override plural association end name
    +allDimensions DIMENSION_ID AllDimensions association between DataCollection and Dimension override plural association end name
    +higherLevelAnalyses HIGHER_LEVEL_ANALYSIS_ID HigherLevelAnalyses association between DataCollection and HigherLevelAnalysis override plural association end name
    +dimensions DIMENSION_ID Dimensions association between Data and Dimension override plural association end name
    +annotations ANNOTATION_ID Annotations association between Describable and OntologyTerm override plural association end name
    +descriptions DESCRIPTION_ID Descriptions association between Describable and Description override plural association end name
    +propertySets PROPERTY_SET_ID PropertySets assocation between Describable and NameValueType override plural association end name
    +dimensionElements DIMENSION_ELEMENT_ID DimensionElements association between Dimension and DimensionElement override plural association end name
    +parameters PARAMETER_ID Parameters association between GenericEquipment and GenericParameter override plural association end name
    +equipmentParts EQUIPMENT_PART_ID EquipmentParts association between GenericEquipment and GenericEquipment override plural association end name
    +factorCollection FACTOR_ID FactorCollection association between InvestigationCollection and Factor override plural association end name
    +factorValues FACTOR_VALUE_ID FactorValues association between Factor and FactorValue override plural association end name
    +dataPartitions DATA_PARTITION_ID DataPartitions association between FactorValue and DataPartition override plural association end name
    +bibliographicReferences BIBLIOGRAPHIC_REFERENCE_ID BibliographicReferences association between Identifiable and BibliographicReference override plural association end name
    +databaseReferences DATABASE_REFERENCE_ID DatabaseReferences association between Identifiable and DatabaseReference override plural association end name
    +inputCompleteMaterials INPUT_COMPLETE_MATERIAL_ID InputCompleteMaterials association between GenericProtocolApplication and Material override plural association end name
    +inputMaterials INPUT_MATERIAL_ID InputMaterials association between GenericProtocolApplication and GenericMaterialMeasurement override plural association end name
    +inputPartitions INPUT_PARTITION_ID InputPartitions association between ParitionPair and DataPartition override plural association end name
    +inputTypes INPUT_TYPE_ID InputTypes association between Protocol and OntologyTerm override plural association end name
    +providers PROVIDER_ID Providers assoication between Investigation and ContactRole override plural association end name
    +investigationTypes INVESTIGATION_TYPE_ID InvestigationTypes association between Investigation and OntologyTerm override plural association end name
    +investigations INVESTIGATION_ID Investigations association between InvestigationCollection and Investigations override plural association end name
    +factors FACTOR_ID Factors association between InvestigationComponent and Factor override plural association end name
    +allProtocolApplications PROTOCOL_APPLICATION_ID AllProtocolApplications association between InvestigationComponent and ProtocolApplication override plural association end name
    +investigationComponents INVESTIGATION_COMPONENT_ID InvestigationComponents association between Investigation and InvestigationComponent override plural association end name
    +characteristics CHARACTERISTIC_ID Characteristics association between Material and OntologyTerm override plural association end name
    +materials MATERIAL_ID Materials association between MaterialCollection and Material override plural association end name
    +components COMPONENT_ID Components association between GenericMaterial and GenericMaterial override plural association end name
    +contacts CONTACT_ID Contacts association between Material and ContactRole override plural association end name
    +sources SOURCE_ID Sources association between OntologyCollection and OntologySource override plural association end name
    +ontologyTerms ONTOLOGY_TERM_ID OntologyTerms association between OntologyCollection and OntologyTerm override plural association end name
    +properties PROPERTY_ID Properties association between OntologyIndividual and OntologyProperty override plural association end name
    +outputMaterials OUTPUT_MATERIAL_ID OutputMaterials association between GenericProtocolApplication and Material override plural association end name
    +outputPartitions OUTPUT_PARTITION_ID OutputPartitions association between PartitionPair and DataPartition override plural association end name
    +outputTypes OUTPUT_TYPE_ID OutputTypes association between Protocol and OntologyTerm override plural association end name
    +types TYPE_ID Types association between Parameterizable and OntologyTerm override plural association end name
    +parameterValues PARAMETER_VALUE_ID ParameterValues association between ParameterizableApplication and ParameterValue override plural association end name
    +actions ACTION_ID Actions association between GenericProtocol and Action override plural association end name
    +parameters PARAMETER_ID Parameters association between GenericProtocol and GenericParameter override plural association end name
    +actionApplications ACTION_APPLICATION_ID ActionApplications between ProtocolApplication and ActionApplication override plural association end name
    +equipmentApplications EQUIPMENT_APPLICATION_ID EquipmentApplications between ProtocolApplication and EquipmentApplication override plural association end name
    +partitionPairs PARTITION_PAIR_ID PartitionPairs association between ProtocolApplication and PartitionPair override plural association end name
    +performers PERFORMER_ID Performers association between ProtocolApplication and ContactRole override plural association end name
    +softwareApplications SOFTWARE_APPLICATION_ID SoftwareApplications association between ProtocolApplication and SoftwareApplications override plural association end name
    +allEquipment EQUIPMENT_ID AllEquipment association between ProtocolCollection and Equipment override plural association end name
    +protocols PROTOCOL_ID Protocols association between ProtocolCollection and Protocol override plural association end name
    +protocolApplications PROTOCOL_APPLICATION_ID ProtocolApplications association between ProtocolCollection and ProtocolApplications override plural association end name
    +allSoftwares SOFTWARE_ID AllSoftwares association between ProtcolCollection and Software override plural association end name
    +qualityControlStatistics QUALITY_CONTROL_STATISTIC_ID QualityControlStatistics association between Material and OntologyTerm override plural association end name
    +rangeDescriptors RANGE_DESCRIPTOR_ID RangeDescriptor association between Range and OntologyTerm override plural association end name
    +allBibliographicReferences BIBLIOGRAPHIC_REFERENCE_ID AllBibliographicReferences association between ReferenceableCollection and BibliographicReference override plural association end name
    +allDatabases DATABASE_ID AllDatabases association between ReferenceableCollection and Database override plural association end name
    +members MEMBER_ID Members association between SecurityGroup and Contact override plural association end name
    +owners OWNER_ID Owners association between Security and Contact override plural association end name
    +securityRights SECURITY_RIGHT_ID SecurityRights association between Security and SecurityAccess override plural association end name
    +types TYPE_ID Types association between SequenceAnnotationSet and OntologyTerm override plural association end name
    +parameters PARAMETER_ID Parameters association between GenericSoftware and GenericParameter override plural association end name
    +sourceMaterials SOURCE_MATERIAL_ID SourceMaterials association between Investigation and Material override plural association end name
    +summaryResults SUMMARY_RESULT_ID SummaryResults association between Investigation and HigherLevelAnalysis override plural association end name
  • datatype::Object[] within GenericInternalData.storage has been changed to datatype::Blob. Some mapping of this type is required to temporarily fix the inability of PostgreSQL to deal with Object arrays, as there is no default mapping.

Hibernate-only FuGE-OM Modifications

These modifications were only performed on the Hibernate STK's version of the FuGE-OM.

Changes to the standard PostgreSQL Mapping

There is a file, PostgreSQLExtension.xml, within symba-mda/src/main/uml/config/mappings, which specifies any additional mappings between UML data types and Postgres types. Below are a summary of the contents of the file:

  • datatype::Date is mapped to TIMESTAMP WITH TIME ZONE\ I originally tried to map datatype::URI to CHARACTER VARYING(1024) (this datatype::URI mapping has been created to force URIs to be stored as a string, as there is no default mapping). However, this didn't work as it was still being passed as a java.net.URI and ultimately caused exceptions that looked a bit like: "org.springframework.orm.hibernate3.HibernateSystemException: could not deserialize; nested exception is org.hibernate.type.SerializationException: could not deserialize at net.sourceforge.fuge.service.EntityServiceBase.getIdentifiable(EntityServiceBase.java:1113)". Therefore I changed both the PostgreSQL and Java mapping so that both in the database and in Java, the datatype::URI is mapped to CHARACTER VARYING(1024) (for PostgreSQL) and java.lang.String (for Java). This isn't ideal, but until I can figure out a way to have the URI dealt with correctly, at least it doesn't cause problems. This meant that the following URIs are actually strings within the API, though the UML has not changed:
    • net.sourceforge.fuge.common.references.Database.URI
    • net.sourceforge.fuge.common.description.Uri.location
    • net.sourceforge.fuge.bio.data.ExternalData.location
    • net.sourceforge.fuge.common.ontology.OntologySource.ontologyURI

Changes to column attributes

  • Had to set the Unique stereotype for Identifiable.identifier, as this hadn't been done, and without it we cannot retrieve objects based on their identifier.

Changes to entity names

  • The "URI" entity is problematic for Spring, as any class name whose second letter is upper case can cause problems. The best way to solve it is to change the name of this entity to "Uri".

Changes to entity column/property names

  • Certain property names of entities needed to be changed because they were PostgreSQL reserved words. This can be done with the @andromda.persistence.column tagged value.
    Property/Column Name Tagged Value Comments
    +end (hibernate implementation only) END_DATE It is the +end property of the Investigation entity
    +end (hibernate implementation only) END_POSITION It is the +end property of the Sequence entity

Changes from lazy to eager loading

  • The association between AuditCollection and SecurityGroup is composition, but it is still lazily fetched. This is perhaps because it is a 0...* association, and can therefore can have more than one security group? In any case, have set UML to be eager fetched. This means setting @andromda.hibernate.lazy to false within the tag for the association end "securityGroups".
  • In the same way, the following association ends were set to @andromda.hibernate.lazy to false:
    • association end (AE): "securityGroups" (the first instance above)
    • AE: "securityCollection"
    • AE: "securityRights"
    • AE: "annotations" for Describable
    • AE: bibliographicReferences for Identifiable
    • AE: parent for Organization
    • AE: affiliations for Person
    • AE: members for SecurityGroups
    • AE: outputMaterials, inputData, inputCompleteMaterials, outputData for GenericProtocolApplication
    • AE: performer for Audit
    • AE: equipment for GenericSoftware
    • AE: equipment for GenericProtocol
    • AE: software for GenericProtocol
    • AE: inputTypes, outputTypes for Protocol
    • AE: contact for ContactRole
    • AE: ontologySource for OntologyTerm
    • AE: rangeDescriptors for Range
    • AE: measuredMaterial for GenericMaterialMeasurement
    • AE: childProtocolApplication for ActionApplication

Change to Cardinalities

The back cardinality (the side with the diamond in it) of GenericAction to Protocol (named childProtocol) should be 0...* rather than 0...1 . ?It doesn't affect the XSD because these aren't checked but will affect the database. This is something that probably should be fixed in the UML.