1 | package dbnp.studycapturing |
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2 | |
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3 | import dbnp.data.Term |
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4 | import dbnp.data.Ontology |
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5 | |
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6 | /** |
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7 | * The Sample class describes an actual sample which results from a SamplingEvent. |
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8 | */ |
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9 | class Sample extends TemplateEntity { |
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10 | // uncommented due to searchable issue |
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11 | // @see http://jira.codehaus.org/browse/GRAILSPLUGINS-1577 |
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12 | //static searchable = { [only: ['name']] } |
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13 | |
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14 | static belongsTo = [ parent : Study] |
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15 | |
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16 | Subject parentSubject |
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17 | SamplingEvent parentEvent |
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18 | |
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19 | String name // should be unique with respect to the parent study (which can be inferred) |
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20 | Term material // material of the sample (should normally be bound to the BRENDA ontology) |
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21 | |
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22 | def getExternalSampleId() { name } |
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23 | |
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24 | /** |
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25 | * return the domain fields for this domain class |
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26 | * @return List |
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27 | */ |
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28 | static List<TemplateField> giveDomainFields() { return Sample.domainFields } |
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29 | static List<TemplateField> domainFields = [ |
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30 | new TemplateField( |
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31 | name: 'name', |
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32 | type: TemplateFieldType.STRING, |
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33 | preferredIdentifier: true, |
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34 | required: true |
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35 | ), |
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36 | new TemplateField( |
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37 | name: 'material', |
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38 | type: TemplateFieldType.ONTOLOGYTERM |
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39 | ) |
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40 | ] |
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41 | |
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42 | static constraints = { |
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43 | parentSubject(nullable:true) |
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44 | material(nullable: true) |
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45 | |
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46 | // TODO: Write a validation method that checks if the externalSampleId (currently defined as name) |
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47 | // is really unique within each parent study of this sample. |
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48 | // Maybe this could also be a constraint, but we might run into trouble creating new Sample objects in e.g. the create wizard. |
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49 | // To be checked. |
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50 | // This feature is tested by integration test SampleTests.testSampleUniqueNameConstraint |
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51 | |
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52 | /*name(validator: { fields, obj, errors -> |
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53 | def error = false |
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54 | |
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55 | if (fields) { |
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56 | // Search through all study |
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57 | if (obj.parent.samples.findAll({ it.name == fields}).size() != 1) { |
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58 | errors.rejectValue( |
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59 | 'name', |
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60 | 'sample.name.NotUnique', |
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61 | ['name',fields] as Object[], |
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62 | 'The sample name is not unique within the study' |
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63 | ) |
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64 | } |
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65 | } |
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66 | else { |
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67 | // If no value for name is specified, the sample should not validate |
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68 | error = true |
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69 | } |
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70 | |
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71 | return (!error) |
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72 | })*/ |
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73 | } |
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74 | |
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75 | /*static def getParentStudies() { |
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76 | Study.findAll { |
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77 | it.samples.findAll { |
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78 | it.name == this.name |
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79 | } |
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80 | } |
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81 | }*/ |
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82 | |
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83 | static getSamplesFor( event ) { |
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84 | return Sample.findAll( 'from Sample s where s.parentEvent =:event', [event:event] ) |
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85 | } |
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86 | |
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87 | } |
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