Changeset 339

Timestamp:

Apr 12, 2010, 4:19:28 PM (13 years ago)

Author:

keesvb

Message:

added plant template to BootStrap?

Location:

trunk/grails-app

Files:

• conf/BootStrap.groovy (modified) (9 diffs)
• domain/dbnp/studycapturing/TemplateField.groovy (modified) (1 diff)

trunk/grails-app/conf/BootStrap.groovy

@@ -39 +39 @@
                         ).with { if (!validate()) { errors.each { println it} } else save()}
 
+                        def nciOntology = new Ontology(
+                                name: 'NCI Thesaurus',
+                                shortName: 'NCI',
+                                url: 'http://bioportal.bioontology.org/ontologies/42331'
+                        ).with { if (!validate()) { errors.each { println it} } else save()}
+
                         // terms
                         def mouseTerm = new Term(
@@ -50 +56 @@
                                 accession: '9606'
                         ).with { if (!validate()) { errors.each { println it} } else save()}
-
+                        def arabTerm = new Term(
+                                name: 'Arabidopsis thaliana',
+                                ontology: speciesOntology,
+                                accession: '3702'
+                        ).with { if (!validate()) { errors.each { println it} } else save()}
+                        
                         def bloodTerm = new Term(
                                 name: 'Portion of blood',
                                 ontology: humanBodyOntology,
                                 accession: '9670'
+                        ).with { if (!validate()) { errors.each { println it} } else save()}
+
+                        def c57bl6Term = new Term(
+                                name: 'C57BL/6 Mouse',
+                                ontology: nciOntology,
+                                accession: 'C14424'
                         ).with { if (!validate()) { errors.each { println it} } else save()}
 
@@ -163 +180 @@
                                 name: 'Age (years)',type: TemplateFieldType.INTEGER,unit: 'years')
                         .with { if (!validate()) { errors.each { println it} } else save()}
+
+                        def genotypeField = new TemplateField(
+                                name: 'Genotype', type: TemplateFieldType.ONTOLOGYTERM)
+                        .with { if (!validate()) { errors.each { println it} } else save()}
+
+                        def genotypeTypeField = new TemplateField(
+                                name: 'Genotype type',type: TemplateFieldType.STRINGLIST,
+                                listEntries: [new TemplateFieldListItem(name:'transgenic'),
+                                        new TemplateFieldListItem(name:'knock-out'),
+                                        new TemplateFieldListItem(name:'knock-in')])
+                        .with { if (!validate()) { errors.each { println it} } else save()}
+
 
                         // Nutritional study template
@@ -175 +204 @@
                                 .addToFields(new TemplateField(name: 'Lab code',type: TemplateFieldType.STRING))
                                 .addToFields(new TemplateField(name: 'Institute',type: TemplateFieldType.STRING))
-                                .addToFields(new TemplateField(name: 'Some Integer',type: TemplateFieldType.INTEGER))
                         .with { if (!validate()) { errors.each { println it} } else save()}
 
@@ -183 +211 @@
                         .addToFields(new TemplateField(
                                 name: 'Strain', type: TemplateFieldType.ONTOLOGYTERM))
-                        .addToFields(new TemplateField(
-                                name: 'Genotype', type: TemplateFieldType.STRING))
-                        .addToFields(new TemplateField(
-                                name: 'Genotype type',type: TemplateFieldType.STRINGLIST,
-                                listEntries: [new TemplateFieldListItem(name:'transgenic'),new TemplateFieldListItem(name:'knock-out'),new TemplateFieldListItem(name:'knock-in')]))
+                        .addToFields(genotypeField)
+                        .addToFields(genotypeTypeField)
                         .addToFields(genderField)
                         .addToFields(new TemplateField(
@@ -202 +227 @@
                         .addToFields(new TemplateField(
                                 name: 'Weight (g)', type: TemplateFieldType.DOUBLE, unit: 'gram'))
-                        .addToFields(new TemplateField(
-                                name: 'SomeOntology', type: TemplateFieldType.ONTOLOGYTERM))
                         .with { if (!validate()) { errors.each { println it} } else save()}
 
@@ -222 +245 @@
                                 name: 'Race',type: TemplateFieldType.STRING))
                         .addToFields(new TemplateField(
-                                name: 'Waist circumvence',type: TemplateFieldType.FLOAT, unit: 'cm'))
-                        .addToFields(new TemplateField(
-                                name: 'Hip circumvence',type: TemplateFieldType.FLOAT, unit: 'cm'))
+                                name: 'Waist circumference',type: TemplateFieldType.FLOAT, unit: 'cm'))
+                        .addToFields(new TemplateField(
+                                name: 'Hip circumference',type: TemplateFieldType.FLOAT, unit: 'cm'))
                         .addToFields(new TemplateField(
                                 name: 'Systolic blood pressure',type: TemplateFieldType.FLOAT, unit: 'mmHg'))
@@ -235 +258 @@
                         .with { if (!validate()) { errors.each { println it} } else save()}
 
+
+                        def sampleDescriptionField = new TemplateField(
+                                name: 'Description',type: TemplateFieldType.TEXT)
+                        .with { if (!validate()) { errors.each { println it} } else save()}
+                        def sampleTypeField = new TemplateField(
+                                name: 'SampleType',type: TemplateFieldType.STRING)
+                        .with { if (!validate()) { errors.each { println it} } else save()}
+                        def sampleProtocolField = new TemplateField(
+                                name: 'SampleProtocol',type: TemplateFieldType.STRING)
+                        .with { if (!validate()) { errors.each { println it} } else save()}
+                        def sampleVialTextField = new TemplateField(
+                                name: 'Text on vial',type: TemplateFieldType.STRING)
+                        .with { if (!validate()) { errors.each { println it} } else save()}
 
                         // Human sample template
                         def humanSampleTemplate = new Template(
                                 name: 'Human tissue sample', entity: dbnp.studycapturing.Sample)
-                        .addToFields(new TemplateField(
-                                name: 'Description',type: TemplateFieldType.TEXT))
-                        .addToFields(new TemplateField(
-                                name: 'SampleType',type: TemplateFieldType.STRING))
-                        .addToFields(new TemplateField(
-                                name: 'SampleProtocol',type: TemplateFieldType.STRING))
-                        .addToFields(new TemplateField(
-                                name: 'Text on vial',type: TemplateFieldType.STRING))
-                        .with { if (!validate()) { errors.each { println it} } else save()}
+                        .addToFields(sampleDescriptionField)
+                        .addToFields(sampleTypeField)
+                        .addToFields(sampleProtocolField)
+                        .addToFields(sampleVialTextField)
+                        .with { if (!validate()) { errors.each { println it} } else save()}
+
+                        //Plant template
+                        def plantTemplate = new Template(
+                                name: 'Plant template', entity: dbnp.studycapturing.Subject)
+                        .addToFields(new TemplateField(
+                                name: 'Variety', type: TemplateFieldType.STRING))
+                        .addToFields(new TemplateField(
+                                name: 'Ecotype', type: TemplateFieldType.STRING))
+                        .addToFields(genotypeField)
+                        .addToFields(genotypeTypeField)
+                        .addToFields(new TemplateField(
+                                name: 'Growth location', type: TemplateFieldType.STRINGLIST,
+                                listEntries: [new TemplateFieldListItem(name:'Greenhouse'),new TemplateFieldListItem(name: 'Field')]))
+                        .addToFields(new TemplateField(
+                                name: 'Room', type: TemplateFieldType.STRING,
+                                comment: 'Chamber number in case of Greenhouse'))
+                        .addToFields(new TemplateField(
+                                name: 'Position X', type: TemplateFieldType.FLOAT))
+                        .addToFields(new TemplateField(
+                                name: 'Position Y', type: TemplateFieldType.FLOAT))
+                        .addToFields(new TemplateField(
+                                name: 'Block', type: TemplateFieldType.STRING))
+                        .addToFields(new TemplateField(
+                                name: 'Temperature at day', type: TemplateFieldType.FLOAT))
+                        .addToFields(new TemplateField(
+                                name: 'Temperature at night', type: TemplateFieldType.FLOAT))
+                        .addToFields(new TemplateField(
+                                name: 'Photo period', type: TemplateFieldType.STRING))
+                        .addToFields(new TemplateField(
+                                name: 'Light intensity', type: TemplateFieldType.STRING))
+                        .addToFields(new TemplateField(
+                                name: 'Start date', type: TemplateFieldType.DATE))
+                        .addToFields(new TemplateField(
+                                name: 'Harvest date', type: TemplateFieldType.DATE))
+                        .addToFields(new TemplateField(
+                                name: 'Growth type', type: TemplateFieldType.STRINGLIST,
+                                listEntries: [new TemplateFieldListItem(name:'Standard'),new TemplateFieldListItem(name: 'Experimental')]))
+                        .addToFields(new TemplateField(
+                                name: 'Growth protocol', type: TemplateFieldType.TEXT))
+                        .addToFields(new TemplateField(
+                                name: 'Harvest delay', type: TemplateFieldType.TEXT))
+                        .with { if (!validate()) { errors.each { println it} } else save()}
+
+                        def plantSampleTemplate = new Template(
+                                name: 'Plant sample', entity: dbnp.studycapturing.Sample)
+                        .addToFields(sampleDescriptionField)
+                        .addToFields(sampleTypeField)
+                        .addToFields(sampleProtocolField)
+                        .addToFields(sampleVialTextField)
+                        .with { if (!validate()) { errors.each { println it} } else save()}
+
 
                         //events
@@ -445 +528 @@
                                 )
                                 .setFieldValue("Gender", "Male")
-                                .setFieldValue("Genotype", "C57/Bl6j")
+                                .setFieldValue("Genotype", c57bl6Term)
                                 .setFieldValue("Age (weeks)", 17)
                                 .setFieldValue("Cage", "" + (int)(x/2))

trunk/grails-app/domain/dbnp/studycapturing/TemplateField.groovy

@@ -2 +2 @@
 
 /**
- * This is the superclass for template fields. Normally, this class will not be instantiated.
+ * This is the class for template fields. These should be part of one or more templates via Template.fields
  *
  * Revision information: