Changeset 84 for trunk/grails-app
- Timestamp:
- Jan 13, 2010, 1:55:45 PM (11 years ago)
- Location:
- trunk/grails-app/domain/dbnp/studycapturing
- Files:
-
- 3 added
- 16 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/grails-app/domain/dbnp/studycapturing/Assay.groovy
r81 r84 1 1 package dbnp.studycapturing 2 2 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 */ 3 8 class Assay { 4 9 -
trunk/grails-app/domain/dbnp/studycapturing/AssayType.groovy
r81 r84 1 1 package dbnp.studycapturing 2 2 3 /** 4 * Enum describing the different assay types (aka omics submodules). 5 */ 3 6 public enum AssayType { 4 7 TRANSCRIPTOMICS('Transcriptomics'), -
trunk/grails-app/domain/dbnp/studycapturing/Event.groovy
r81 r84 1 1 package dbnp.studycapturing 2 2 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 */ 3 8 class Event { 4 9 -
trunk/grails-app/domain/dbnp/studycapturing/EventDescription.groovy
r81 r84 1 1 package dbnp.studycapturing 2 2 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 */ 3 8 class EventDescription { 4 9 -
trunk/grails-app/domain/dbnp/studycapturing/Ontology.groovy
r80 r84 1 1 package dbnp.studycapturing 2 2 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 */ 3 7 class Ontology { 4 8 -
trunk/grails-app/domain/dbnp/studycapturing/Protocol.groovy
r80 r84 4 4 * Class describing the available protocols in the database, and their respective protocol parameters 5 5 * 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. 6 8 */ 7 9 class Protocol { -
trunk/grails-app/domain/dbnp/studycapturing/ProtocolInstance.groovy
r81 r84 1 1 package dbnp.studycapturing 2 2 3 /** 4 * Class describing a concrete application of a protocol (which goes with numbers/values for the protocol parameters). 5 */ 3 6 class ProtocolInstance { 4 7 -
trunk/grails-app/domain/dbnp/studycapturing/ProtocolParameter.groovy
r80 r84 1 1 package dbnp.studycapturing 2 2 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 */ 3 7 class ProtocolParameter { 4 8 … … 9 13 Term reference 10 14 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' 12 16 13 17 static constraints = { -
trunk/grails-app/domain/dbnp/studycapturing/ProtocolParameterType.groovy
r80 r84 1 1 package dbnp.studycapturing 2 2 3 /** 4 * Enum describing the type of a protocol parameter. 5 */ 3 6 public enum ProtocolParameterType { 4 7 STRING('String'), … … 16 19 } 17 20 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 18 25 /*def String toString() { 19 26 return this.name -
trunk/grails-app/domain/dbnp/studycapturing/Sample.groovy
r81 r84 1 1 package dbnp.studycapturing 2 2 3 /** 4 * The Sample class describes an actual sample which results from a SamplingEvent. 5 */ 3 6 class Sample { 4 7 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 6 15 Term material 7 16 -
trunk/grails-app/domain/dbnp/studycapturing/SamplingEvent.groovy
r81 r84 1 1 package dbnp.studycapturing 2 2 3 /** 4 * The SamplingEvent class describes a sampling event, an event that also results in one or more samples. 5 */ 3 6 class SamplingEvent extends Event { 4 7 -
trunk/grails-app/domain/dbnp/studycapturing/Study.groovy
r77 r84 17 17 Template template 18 18 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] 20 22 21 23 static constraints = { -
trunk/grails-app/domain/dbnp/studycapturing/Subject.groovy
r77 r84 1 1 package dbnp.studycapturing 2 2 3 /** 4 * This domain class describes the subjects in a study. 5 */ 3 6 class Subject { 4 7 5 Study study6 8 String name 7 9 Term species -
trunk/grails-app/domain/dbnp/studycapturing/SubjectGroup.groovy
r77 r84 1 1 package dbnp.studycapturing 2 2 3 /** 4 * This class describes groupings in the subjects of a study. 5 */ 3 6 class SubjectGroup { 4 5 Study study6 7 7 8 static hasMany = [ subjects : Subject] -
trunk/grails-app/domain/dbnp/studycapturing/Template.groovy
r80 r84 1 1 package dbnp.studycapturing 2 2 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 */ 3 8 class Template { 4 9 5 10 String name 6 11 nimble.User owner 12 13 static hasMany = [subjectFields : TemplateSubjectField] 7 14 8 15 static constraints = { -
trunk/grails-app/domain/dbnp/studycapturing/Term.groovy
r80 r84 1 1 package dbnp.studycapturing 2 2 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 */ 3 8 class Term { 4 9
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