1 | package dbnp.studycapturing |
---|
2 | |
---|
3 | import dbnp.data.Term |
---|
4 | import dbnp.data.Ontology |
---|
5 | |
---|
6 | /** |
---|
7 | * The Sample class describes an actual sample which results from a SamplingEvent. |
---|
8 | */ |
---|
9 | class Sample extends TemplateEntity { |
---|
10 | static searchable = { [only: ['name']] } |
---|
11 | |
---|
12 | static belongsTo = [ parent : Study] |
---|
13 | |
---|
14 | Subject parentSubject |
---|
15 | SamplingEvent parentEvent |
---|
16 | |
---|
17 | String name // should be unique with respect to the parent study (which can be inferred) |
---|
18 | Term material // material of the sample (should normally be bound to the BRENDA ontology) |
---|
19 | |
---|
20 | def getExternalSampleId() { name } |
---|
21 | |
---|
22 | /** |
---|
23 | * return the domain fields for this domain class |
---|
24 | * @return List |
---|
25 | */ |
---|
26 | static List<TemplateField> giveDomainFields() { return Sample.domainFields } |
---|
27 | static List<TemplateField> domainFields = [ |
---|
28 | new TemplateField( |
---|
29 | name: 'name', |
---|
30 | type: TemplateFieldType.STRING, |
---|
31 | preferredIdentifier: true, |
---|
32 | required: true |
---|
33 | ), |
---|
34 | new TemplateField( |
---|
35 | name: 'material', |
---|
36 | type: TemplateFieldType.ONTOLOGYTERM |
---|
37 | ) |
---|
38 | ] |
---|
39 | |
---|
40 | static constraints = { |
---|
41 | parentSubject(nullable:true) |
---|
42 | material(nullable: true) |
---|
43 | |
---|
44 | // TODO: Write a validation method that checks if the externalSampleId (currently defined as name) |
---|
45 | // is really unique within each parent study of this sample. |
---|
46 | // Maybe this could also be a constraint, but we might run into trouble creating new Sample objects in e.g. the create wizard. |
---|
47 | // To be checked. |
---|
48 | // This feature is tested by integration test SampleTests.testSampleUniqueNameConstraint |
---|
49 | |
---|
50 | /*name(validator: { fields, obj, errors -> |
---|
51 | def error = false |
---|
52 | |
---|
53 | if (fields) { |
---|
54 | // Search through all study |
---|
55 | if (obj.parent.samples.findAll({ it.name == fields}).size() != 1) { |
---|
56 | errors.rejectValue( |
---|
57 | 'name', |
---|
58 | 'sample.name.NotUnique', |
---|
59 | ['name',fields] as Object[], |
---|
60 | 'The sample name is not unique within the study' |
---|
61 | ) |
---|
62 | } |
---|
63 | } |
---|
64 | else { |
---|
65 | // If no value for name is specified, the sample should not validate |
---|
66 | error = true |
---|
67 | } |
---|
68 | |
---|
69 | return (!error) |
---|
70 | })*/ |
---|
71 | } |
---|
72 | |
---|
73 | /*static def getParentStudies() { |
---|
74 | Study.findAll { |
---|
75 | it.samples.findAll { |
---|
76 | it.name == this.name |
---|
77 | } |
---|
78 | } |
---|
79 | }*/ |
---|
80 | |
---|
81 | static getSamplesFor( event ) { |
---|
82 | return Sample.findAll( 'from Sample s where s.parentEvent =:event', [event:event] ) |
---|
83 | } |
---|
84 | |
---|
85 | } |
---|