Serialized Form (molgenis-omx-core 0.0.4 API)

Package org.molgenis.omx.auth
- Class org.molgenis.omx.auth.GroupAuthority extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - role
```
String role
```
    - id
```
Integer id
```
    - molgenisGroup
```
MolgenisGroup molgenisGroup
```
    - molgenisGroup_id
```
Integer molgenisGroup_id
```
- Class org.molgenis.omx.auth.Institute extends Characteristic implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - address
```
String address
```
    - phone
```
String phone
```
    - email
```
String email
```
    - fax
```
String fax
```
    - tollFreePhone
```
String tollFreePhone
```
    - city
```
String city
```
    - country
```
String country
```
    - name
```
String name
```
- Class org.molgenis.omx.auth.MolgenisGroup extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
Integer id
```
    - name
```
String name
```
- Class org.molgenis.omx.auth.MolgenisGroupMember extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
Integer id
```
    - molgenisUser
```
MolgenisUser molgenisUser
```
    - molgenisUser_id
```
Integer molgenisUser_id
```
    - molgenisUser_Email
```
String molgenisUser_Email
```
    - molgenisGroup
```
MolgenisGroup molgenisGroup
```
    - molgenisGroup_id
```
Integer molgenisGroup_id
```
- Class org.molgenis.omx.auth.MolgenisUser extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
Integer id
```
    - username
```
String username
```
    - password_
```
String password_
```
    - activationCode
```
String activationCode
```
    - active
```
Boolean active
```
    - superuser
```
Boolean superuser
```
    - firstName
```
String firstName
```
    - midInitials
```
String midInitials
```
    - lastName
```
String lastName
```
    - title
```
String title
```
    - affiliation
```
String affiliation
```
    - department
```
String department
```
    - role
```
String role
```
    - address
```
String address
```
    - phone
```
String phone
```
    - email
```
String email
```
    - fax
```
String fax
```
    - tollFreePhone
```
String tollFreePhone
```
    - city
```
String city
```
    - country
```
String country
```
- Class org.molgenis.omx.auth.Person extends Characteristic implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - address
```
String address
```
    - phone
```
String phone
```
    - email
```
String email
```
    - fax
```
String fax
```
    - tollFreePhone
```
String tollFreePhone
```
    - city
```
String city
```
    - country
```
String country
```
    - firstName
```
String firstName
```
    - midInitials
```
String midInitials
```
    - lastName
```
String lastName
```
    - title
```
String title
```
    - affiliation
```
Institute affiliation
```
    - affiliation_id
```
Integer affiliation_id
```
    - affiliation_Name
```
String affiliation_Name
```
    - department
```
String department
```
    - roles
```
PersonRole roles
```
    - roles_id
```
Integer roles_id
```
    - roles_Identifier
```
String roles_Identifier
```
- Class org.molgenis.omx.auth.PersonRole extends OntologyTerm implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.molgenis.omx.auth.UserAuthority extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - role
```
String role
```
    - id
```
Integer id
```
    - molgenisUser
```
MolgenisUser molgenisUser
```
    - molgenisUser_id
```
Integer molgenisUser_id
```
    - molgenisUser_Email
```
String molgenisUser_Email
```
Package org.molgenis.omx.converters
- Class org.molgenis.omx.converters.ValueConverterException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
Package org.molgenis.omx.core
- Class org.molgenis.omx.core.MolgenisEntity extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
Integer id
```
    - name
```
String name
```
    - type_
```
String type_
```
    - className
```
String className
```
- Class org.molgenis.omx.core.MolgenisFile extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
Integer id
```
    - identifier
```
String identifier
```
    - name
```
String name
```
    - extension
```
String extension
```
- Class org.molgenis.omx.core.RuntimeProperty extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
Integer id
```
    - identifier
```
String identifier
```
    - name
```
String name
```
    - value
```
String value
```
Package org.molgenis.omx.decorators
- Class org.molgenis.omx.decorators.MolgenisFileHandler.TypeUnknownException extends Exception implements Serializable
  
  serialVersionUID:
  
  7026641720938935426L
Package org.molgenis.omx.observ
- Class org.molgenis.omx.observ.Category extends Characteristic implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - observableFeature
```
ObservableFeature observableFeature
```
    - observableFeature_id
```
Integer observableFeature_id
```
    - observableFeature_Identifier
```
String observableFeature_Identifier
```
    - valueCode
```
String valueCode
```
    - definition
```
OntologyTerm definition
```
    - definition_id
```
Integer definition_id
```
    - definition_Identifier
```
String definition_Identifier
```
    - isMissing
```
Boolean isMissing
```
- Class org.molgenis.omx.observ.Characteristic extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
Integer id
```
    - identifier
```
String identifier
```
    - name
```
String name
```
    - __Type
```
String __Type
```
    - __Type_label
```
String __Type_label
```
    - description
```
String description
```
    - valueMrefValueCollection
```
Collection<E> valueMrefValueCollection
```
- Class org.molgenis.omx.observ.DataSet extends Characteristic implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - protocolUsed
```
Protocol protocolUsed
```
    - protocolUsed_id
```
Integer protocolUsed_id
```
    - protocolUsed_Identifier
```
String protocolUsed_Identifier
```
    - startTime
```
Date startTime
```
    - endTime
```
Date endTime
```
    - active
```
Boolean active
```
- Class org.molgenis.omx.observ.ObservableFeature extends Characteristic implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - unit
```
OntologyTerm unit
```
    - unit_id
```
Integer unit_id
```
    - unit_Identifier
```
String unit_Identifier
```
    - definitions
```
List<E> definitions
```
    - definitions_id
```
List<E> definitions_id
```
    - definitions_Identifier
```
List<E> definitions_Identifier
```
    - dataType
```
String dataType
```
    - dataType_label
```
String dataType_label
```
    - temporal
```
Boolean temporal
```
    - featuresProtocolCollection
```
Collection<E> featuresProtocolCollection
```
    - requiredFeaturesProtocolCollection
```
Collection<E> requiredFeaturesProtocolCollection
```
- Class org.molgenis.omx.observ.ObservableFeature_Definitions extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - autoid
```
Integer autoid
```
    - definitions
```
OntologyTerm definitions
```
    - definitions_id
```
Integer definitions_id
```
    - definitions_Identifier
```
String definitions_Identifier
```
    - observableFeature
```
ObservableFeature observableFeature
```
    - observableFeature_id
```
Integer observableFeature_id
```
    - observableFeature_Identifier
```
String observableFeature_Identifier
```
- Class org.molgenis.omx.observ.ObservationSet extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
Integer id
```
    - identifier
```
String identifier
```
    - partOfDataSet
```
DataSet partOfDataSet
```
    - partOfDataSet_id
```
Integer partOfDataSet_id
```
    - partOfDataSet_Identifier
```
String partOfDataSet_Identifier
```
    - time
```
Date time
```
- Class org.molgenis.omx.observ.ObservationTarget extends Characteristic implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.molgenis.omx.observ.ObservedValue extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
Integer id
```
    - observationSet
```
ObservationSet observationSet
```
    - observationSet_id
```
Integer observationSet_id
```
    - observationSet_Identifier
```
String observationSet_Identifier
```
    - feature
```
ObservableFeature feature
```
    - feature_id
```
Integer feature_id
```
    - feature_Identifier
```
String feature_Identifier
```
    - value
```
Value value
```
    - value_id
```
Integer value_id
```
- Class org.molgenis.omx.observ.Protocol extends Characteristic implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - protocolType
```
OntologyTerm protocolType
```
    - protocolType_id
```
Integer protocolType_id
```
    - protocolType_Identifier
```
String protocolType_Identifier
```
    - subprotocols
```
List<E> subprotocols
```
    - subprotocols_id
```
List<E> subprotocols_id
```
    - subprotocols_Identifier
```
List<E> subprotocols_Identifier
```
    - features
```
List<E> features
```
    - features_id
```
List<E> features_id
```
    - features_Identifier
```
List<E> features_Identifier
```
    - requiredFeatures
```
List<E> requiredFeatures
```
    - requiredFeatures_id
```
List<E> requiredFeatures_id
```
    - requiredFeatures_Identifier
```
List<E> requiredFeatures_Identifier
```
    - root
```
Boolean root
```
    - subprotocolsProtocolCollection
```
Collection<E> subprotocolsProtocolCollection
```
- Class org.molgenis.omx.observ.Protocol_Features extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - autoid
```
Integer autoid
```
    - features
```
ObservableFeature features
```
    - features_id
```
Integer features_id
```
    - features_Identifier
```
String features_Identifier
```
    - protocol
```
Protocol protocol
```
    - protocol_id
```
Integer protocol_id
```
    - protocol_Identifier
```
String protocol_Identifier
```
- Class org.molgenis.omx.observ.Protocol_RequiredFeatures extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - autoid
```
Integer autoid
```
    - requiredFeatures
```
ObservableFeature requiredFeatures
```
    - requiredFeatures_id
```
Integer requiredFeatures_id
```
    - requiredFeatures_Identifier
```
String requiredFeatures_Identifier
```
    - protocol
```
Protocol protocol
```
    - protocol_id
```
Integer protocol_id
```
    - protocol_Identifier
```
String protocol_Identifier
```
- Class org.molgenis.omx.observ.Protocol_Subprotocols extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - autoid
```
Integer autoid
```
    - subprotocols
```
Protocol subprotocols
```
    - subprotocols_id
```
Integer subprotocols_id
```
    - subprotocols_Identifier
```
String subprotocols_Identifier
```
    - protocol
```
Protocol protocol
```
    - protocol_id
```
Integer protocol_id
```
    - protocol_Identifier
```
String protocol_Identifier
```
Package org.molgenis.omx.observ.target
- Class org.molgenis.omx.observ.target.Accession extends OntologyTerm implements Serializable
  
  serialVersionUID:
  
  1L
- Class org.molgenis.omx.observ.target.Individual extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mother
```
Individual mother
```
    - mother_id
```
Integer mother_id
```
    - mother_Identifier
```
String mother_Identifier
```
    - father
```
Individual father
```
    - father_id
```
Integer father_id
```
    - father_Identifier
```
String father_Identifier
```
    - individualsPanelCollection
```
Collection<E> individualsPanelCollection
```
- Class org.molgenis.omx.observ.target.Ontology extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
Integer id
```
    - identifier
```
String identifier
```
    - name
```
String name
```
    - ontologyAccession
```
String ontologyAccession
```
    - ontologyURI
```
String ontologyURI
```
- Class org.molgenis.omx.observ.target.OntologyTerm extends Characteristic implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - ontology
```
Ontology ontology
```
    - ontology_id
```
Integer ontology_id
```
    - ontology_Identifier
```
String ontology_Identifier
```
    - termAccession
```
String termAccession
```
    - definition
```
String definition
```
    - definitionsObservableFeatureCollection
```
Collection<E> definitionsObservableFeatureCollection
```
- Class org.molgenis.omx.observ.target.Panel extends ObservationTarget implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - panelType
```
OntologyTerm panelType
```
    - panelType_id
```
Integer panelType_id
```
    - panelType_Identifier
```
String panelType_Identifier
```
    - numberOfIndividuals
```
Integer numberOfIndividuals
```
    - species
```
Species species
```
    - species_id
```
Integer species_id
```
    - species_Identifier
```
String species_Identifier
```
    - individuals
```
List<E> individuals
```
    - individuals_id
```
List<E> individuals_id
```
    - individuals_Identifier
```
List<E> individuals_Identifier
```
- Class org.molgenis.omx.observ.target.Panel_Individuals extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - autoid
```
Integer autoid
```
    - individuals
```
Individual individuals
```
    - individuals_id
```
Integer individuals_id
```
    - individuals_Identifier
```
String individuals_Identifier
```
    - panel
```
Panel panel
```
    - panel_id
```
Integer panel_id
```
    - panel_Identifier
```
String panel_Identifier
```
- Class org.molgenis.omx.observ.target.PanelSource extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
Integer id
```
    - currentPanel
```
Panel currentPanel
```
    - currentPanel_id
```
Integer currentPanel_id
```
    - currentPanel_Identifier
```
String currentPanel_Identifier
```
    - sourcePanel
```
Panel sourcePanel
```
    - sourcePanel_id
```
Integer sourcePanel_id
```
    - sourcePanel_Identifier
```
String sourcePanel_Identifier
```
    - numberOfIndividuals
```
Integer numberOfIndividuals
```
    - selectionCriteria
```
String selectionCriteria
```
- Class org.molgenis.omx.observ.target.Species extends OntologyTerm implements Serializable
  
  serialVersionUID:
  
  1L
Package org.molgenis.omx.observ.value
- Class org.molgenis.omx.observ.value.BoolValue extends Value implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
Boolean value
```
- Class org.molgenis.omx.observ.value.CategoricalValue extends Value implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
Category value
```
    - value_id
```
Integer value_id
```
    - value_Identifier
```
String value_Identifier
```
- Class org.molgenis.omx.observ.value.DateTimeValue extends Value implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
Date value
```
- Class org.molgenis.omx.observ.value.DateValue extends Value implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
Date value
```
- Class org.molgenis.omx.observ.value.DecimalValue extends Value implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
Double value
```
- Class org.molgenis.omx.observ.value.EmailValue extends Value implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
String value
```
- Class org.molgenis.omx.observ.value.HtmlValue extends Value implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
String value
```
- Class org.molgenis.omx.observ.value.HyperlinkValue extends Value implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
String value
```
- Class org.molgenis.omx.observ.value.IntValue extends Value implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
Integer value
```
- Class org.molgenis.omx.observ.value.LongValue extends Value implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
Long value
```
- Class org.molgenis.omx.observ.value.MrefValue extends Value implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
List<E> value
```
    - value_id
```
List<E> value_id
```
    - value_Identifier
```
List<E> value_Identifier
```
- Class org.molgenis.omx.observ.value.MrefValue_Value extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - autoid
```
Integer autoid
```
    - value
```
Characteristic value
```
    - value_id
```
Integer value_id
```
    - value_Identifier
```
String value_Identifier
```
    - mrefValue
```
MrefValue mrefValue
```
    - mrefValue_id
```
Integer mrefValue_id
```
- Class org.molgenis.omx.observ.value.StringValue extends Value implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
String value
```
- Class org.molgenis.omx.observ.value.TextValue extends Value implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
String value
```
- Class org.molgenis.omx.observ.value.Value extends AbstractEntity implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - id
```
Integer id
```
    - __Type
```
String __Type
```
    - __Type_label
```
String __Type_label
```
- Class org.molgenis.omx.observ.value.XrefValue extends Value implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
Characteristic value
```
    - value_id
```
Integer value_id
```
    - value_Identifier
```
String value_Identifier
```

Serialized Form

Package org.molgenis.omx.auth

Class org.molgenis.omx.auth.GroupAuthority extends AbstractEntity implements Serializable

Serialized Fields

role

id

molgenisGroup

molgenisGroup_id

Class org.molgenis.omx.auth.Institute extends Characteristic implements Serializable

Serialized Fields

address

phone

email

fax

tollFreePhone

city

country

name

Class org.molgenis.omx.auth.MolgenisGroup extends AbstractEntity implements Serializable

Serialized Fields

id

name

Class org.molgenis.omx.auth.MolgenisGroupMember extends AbstractEntity implements Serializable

Serialized Fields

id

molgenisUser

molgenisUser_id

molgenisUser_Email

molgenisGroup

molgenisGroup_id

Class org.molgenis.omx.auth.MolgenisUser extends AbstractEntity implements Serializable

Serialized Fields

id

username

password_

activationCode

active

superuser

firstName

midInitials

lastName

title

affiliation

department

role

address

phone

email

fax

tollFreePhone

city

country

Class org.molgenis.omx.auth.Person extends Characteristic implements Serializable

Serialized Fields

address

phone

email

fax

tollFreePhone

city

country

firstName

midInitials

lastName

title

affiliation

affiliation_id

affiliation_Name

department

roles

roles_id

roles_Identifier

Class org.molgenis.omx.auth.PersonRole extends OntologyTerm implements Serializable

Class org.molgenis.omx.auth.UserAuthority extends AbstractEntity implements Serializable

Serialized Fields

role

id

molgenisUser

molgenisUser_id

molgenisUser_Email