Changeset 84


Ignore:
Timestamp:
Jan 13, 2010, 1:55:45 PM (7 years ago)
Author:
keesvb
Message:

updated domain classes: added comments, carried out some normalization

Location:
trunk
Files:
5 added
16 edited

Legend:

Unmodified
Added
Removed
  • trunk/grails-app/domain/dbnp/studycapturing/Assay.groovy

    r81 r84  
    11package dbnp.studycapturing
    22
     3/**
     4 * This class describes an Assay, which describes the application of a certain (omics) measurement to multiple samples.
     5 * The actual data of these measurements are described in submodules of dbNP. The type property describes in which module
     6 * this data can be found.
     7 */
    38class Assay {
    49
  • trunk/grails-app/domain/dbnp/studycapturing/AssayType.groovy

    r81 r84  
    11package dbnp.studycapturing
    22
     3/**
     4 * Enum describing the different assay types (aka omics submodules).
     5 */
    36public enum AssayType {
    47    TRANSCRIPTOMICS('Transcriptomics'),
  • trunk/grails-app/domain/dbnp/studycapturing/Event.groovy

    r81 r84  
    11package dbnp.studycapturing
    22
     3/**
     4 * The Event class describes an actual event, as it has happened to a certain subject. Often, the same event occurs
     5 * to multiple subjects at the same time. That is why the actual description of the event is factored out into a more
     6 * general EventDescription class. Events that also lead to sample(s) should be instantiated as SamplingEvents.
     7 */
    38class Event {
    49
  • trunk/grails-app/domain/dbnp/studycapturing/EventDescription.groovy

    r81 r84  
    11package dbnp.studycapturing
    22
     3/**
     4 * Description of an event. Actual events are described by instances of the Event class.
     5 * For the moment, EventDescription is not linked to a specific study or user.
     6 * This means that the user can add events of all possible event types as defined by the (global) EventDescription collection.
     7 */
    38class EventDescription {
    49
  • trunk/grails-app/domain/dbnp/studycapturing/Ontology.groovy

    r80 r84  
    11package dbnp.studycapturing
    22
     3/**
     4 * This class describes an existing ontology, of which terms can be stored (actually 'cached' would be a better description)
     5 * in the (global) Term store.
     6 */
    37class Ontology {
    48
  • trunk/grails-app/domain/dbnp/studycapturing/Protocol.groovy

    r80 r84  
    44 * Class describing the available protocols in the database, and their respective protocol parameters
    55 * Concrete instances of protocol application (and parameter values) should be stored as ProtocolInstance
     6 * For the moment, there is one global Protocol store. From user experience, it should become clear if this store
     7 * has to remain global or should be bound to specific templates, users, user groups or even studies.
    68 */
    79class Protocol {
  • trunk/grails-app/domain/dbnp/studycapturing/ProtocolInstance.groovy

    r81 r84  
    11package dbnp.studycapturing
    22
     3/**
     4 * Class describing a concrete application of a protocol (which goes with numbers/values for the protocol parameters).
     5 */
    36class ProtocolInstance {
    47
  • trunk/grails-app/domain/dbnp/studycapturing/ProtocolParameter.groovy

    r80 r84  
    11package dbnp.studycapturing
    22
     3/**
     4 * The ProtocolParameter class describes a protocol parameter, and belongs to the Protocol class.
     5 * Actual values of this parameter are stored in the corresponding field of the ProtocolInstance class.
     6 */
    37class ProtocolParameter {
    48
     
    913    Term reference
    1014
    11     static hasMany = [listEntries : String]
     15    static hasMany = [listEntries : String] // to store the entries to choose from when the type is 'item from predefined list'
    1216
    1317    static constraints = {
  • trunk/grails-app/domain/dbnp/studycapturing/ProtocolParameterType.groovy

    r80 r84  
    11package dbnp.studycapturing
    22
     3/**
     4 * Enum describing the type of a protocol parameter.
     5 */
    36public enum ProtocolParameterType {
    47    STRING('String'),
     
    1619    }
    1720
     21
     22    // It would be nice to see the description string in the scaffolding,
     23    // and the following works, but then the item cannot be saved properly.
     24    // TODO: find a way to display the enum description but save the enum value in the scaffolding
    1825    /*def String toString() {
    1926        return this.name
  • trunk/grails-app/domain/dbnp/studycapturing/Sample.groovy

    r81 r84  
    11package dbnp.studycapturing
    22
     3/**
     4 * The Sample class describes an actual sample which results from a SamplingEvent.
     5 */
    36class Sample {
    47
    5     String name
     8    // TODO: should Sample also carry a reference to its parent study,
     9    // or should this be inferred via the parent SamplingEvent?
     10
     11    // TODO: should Sample also carry a reference to its parent subject,
     12    // or should this be inferred via the parent SamplingEvent?
     13
     14    String name // should be unique with respect to the parent study (which can be inferred
    615    Term material
    716
  • trunk/grails-app/domain/dbnp/studycapturing/SamplingEvent.groovy

    r81 r84  
    11package dbnp.studycapturing
    22
     3/**
     4 * The SamplingEvent class describes a sampling event, an event that also results in one or more samples.
     5 */
    36class SamplingEvent extends Event {
    47
  • trunk/grails-app/domain/dbnp/studycapturing/Study.groovy

    r77 r84  
    1717    Template template
    1818
    19     static hasMany = [ editors : nimble.User, subjects: Subject, protocols: Protocol ]
     19    static hasMany = [ editors : nimble.User, readers : nimble.User,
     20            subjects: Subject, groups : SubjectGroup,
     21            events: Event, samplingEvents : SamplingEvent]
    2022
    2123    static constraints = {
  • trunk/grails-app/domain/dbnp/studycapturing/Subject.groovy

    r77 r84  
    11package dbnp.studycapturing
    22
     3/**
     4 * This domain class describes the subjects in a study.
     5 */
    36class Subject {
    47
    5     Study study
    68    String name
    79    Term species
  • trunk/grails-app/domain/dbnp/studycapturing/SubjectGroup.groovy

    r77 r84  
    11package dbnp.studycapturing
    22
     3/**
     4 * This class describes groupings in the subjects of a study.
     5 */
    36class SubjectGroup {
    4 
    5     Study study
    67
    78    static hasMany = [ subjects : Subject]
  • trunk/grails-app/domain/dbnp/studycapturing/Template.groovy

    r80 r84  
    11package dbnp.studycapturing
    22
     3/**
     4 * The Template class describes a study template, which is basically an extension of the study capture entities
     5 * in terms of extra fields (described by classes that extend the TemplateField class).
     6 * At this moment, only extension of the subject entity is implemented.
     7 */
    38class Template {
    49
    510    String name
    611    nimble.User owner
     12
     13    static hasMany = [subjectFields : TemplateSubjectField]
    714 
    815    static constraints = {
  • trunk/grails-app/domain/dbnp/studycapturing/Term.groovy

    r80 r84  
    11package dbnp.studycapturing
    22
     3/**
     4 * The Term object describes a term in the ontology that is referred to in other entities such as events.
     5 * The Term object should point to an existing term in an online ontology, therefore instances of this class can also
     6 * be seen as a cache of elements of the external ontology.
     7 */
    38class Term {
    49
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