Changeset 662

Timestamp:

Jul 19, 2010, 4:28:10 PM (13 years ago)

Author:

keesvb

Message:

restructured BootStrap?, it should now run faster because there are no BioPortal? connections, and it adds sample studies in development mode (outcomment the addExampleStudies call in the BootStrap? if you don't want that). Renamed TemplateEntity?.getFieldType to giveFieldType and added tests to SampleTests? for the method.

Location:

trunk

Files:

• grails-app/conf/BootStrap.groovy (modified) (2 diffs)
• grails-app/conf/BootStrapStudies.groovy (modified) (4 diffs)
• grails-app/conf/BootStrapTemplates.groovy (modified) (1 diff)
• grails-app/domain/dbnp/studycapturing/TemplateEntity.groovy (modified) (2 diffs)
• test/integration/gscf/SampleTests.groovy (modified) (2 diffs)

trunk/grails-app/conf/BootStrap.groovy

@@ -22 +22 @@
                 System.setProperty('user.timezone', 'CET')
 
+                // If there are no templates yet in the database
                 if (Template.count() == 0) {
                         println "No templates in the current database.";
+
+                        // If in development or test mode, add the ontologies manually to the database
+                        // without contacting the BioPortal website, to avoid annoying hiccups when the server is busy
+                        if (grails.util.GrailsUtil.environment != GrailsApplication.ENV_PRODUCTION) {
+                                println "Adding ontology descriptors"
+                                BootStrapTemplates.initTemplateOntologies()
+                        }
+
                         // Add example study, subject, event etc. templates
                         BootStrapTemplates.initTemplates()
 
-                        // Add example studies
+                        // If in development mode and no studies are present, add example studies
                         if (Study.count() == 0 && grails.util.GrailsUtil.environment == GrailsApplication.ENV_DEVELOPMENT) {
-
-                                // When the code is properly refactored, BootStrapStudies.addExampleStudies() may be called here
+                                BootStrapStudies.addExampleStudies()
                         }
                 }
@@ -45 +53 @@
                 // register methods for accessing SAM's Rest services 
                 CommunicationManager.SAMServerURL = 'nbx5.nugo.org/sam'
-        CommunicationManager.registerRestWrapperMethodsSAMtoGSCF()
+                CommunicationManager.registerRestWrapperMethodsSAMtoGSCF()
         }
 

trunk/grails-app/conf/BootStrapStudies.groovy

@@ -10 +10 @@
 
 import dbnp.studycapturing.*
+import dbnp.data.Term
+import dbnp.data.Ontology
 
 class BootStrapStudies {
 
+        /**
+         * Add example studies. This function is meant to be called only in development mode
+         */
+
         public static void addExampleStudies() {
 
-                // TODO: Strip this code from all references to template and term objects
-                // which now are not there anymore because this code was separated from the template bootstrapping
-                // and because terms should be dynamically added
-
-                /*
+                // Look up the used ontologies which should be in the database by now
+                def speciesOntology = Ontology.getOrCreateOntologyByNcboId(1132)
+                def brendaOntology = Ontology.getOrCreateOntologyByNcboId(1005)
+                def nciOntology = Ontology.getOrCreateOntologyByNcboId(1032)
+                def chebiOntology = Ontology.getOrCreateOntologyByNcboId(1007)
+
+                // Look up the used templates which should also be in the database by now
+                def studyTemplate = Template.findByName("Academic study")
+                def mouseTemplate = Template.findByName("Mouse")
+                def humanTemplate = Template.findByName("Human")
+                def dietTreatmentTemplate = Template.findByName("Diet treatment")
+                def boostTreatmentTemplate = Template.findByName("Compound challenge")
+                def liverSamplingEventTemplate = Template.findByName("Liver extraction")
+                def fastingTreatmentTemplate = Template.findByName("Fasting treatment")
+                def bloodSamplingEventTemplate = Template.findByName("Blood extraction")
+                def humanBloodSampleTemplate = Template.findByName("Human blood sample")
+                
+
+                // Add terms manually, to avoid having to do many HTTP requests to the BioPortal website
+                println ".adding terms"
+
+
+                def mouseTerm = new Term(
+                        name: 'Mus musculus',
+                        ontology: speciesOntology,
+                        accession: '10090'
+                ).with { if (!validate()) { errors.each { println it} } else save()}
+
+                def humanTerm = new Term(
+                        name: 'Homo sapiens',
+                        ontology: speciesOntology,
+                        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 tomatoTerm = new Term(
+                        name: 'Solanum lycopersicum',
+                        ontology: speciesOntology,
+                        accession: '4081'
+                ).with { if (!validate()) { errors.each { println it} } else save()}
+
+                def potatoTerm = new Term(
+                        name: 'Solanum tuberosum',
+                        ontology: speciesOntology,
+                        accession: '0000'
+                ).with { if (!validate()) { errors.each { println it} } else save()}
+
+                def bloodTerm = new Term(
+                        name: 'blood plasma',
+                        ontology: brendaOntology,
+                        accession: 'BTO:0000131'
+                ).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()}
+
+                def glucoseTerm = new Term(
+                        name: 'Glucose',
+                        ontology: chebiOntology,
+                        accession: 'CHEBI:17234'
+                ).with { if (!validate()) { errors.each { println it} } else save()}
+
                 // Create a few persons, roles and Affiliations
                 println ".adding persons, roles and affiliations"
@@ -313 +384 @@
                         startTime: 3 * 24 * 3600 + 22 * 3600,
                         endTime: 3 * 24 * 3600 + 30 * 3600,
-                        template: fastingTreatment)
+                        template: fastingTreatmentTemplate)
                 .setFieldValue('Fasting period','8h');
 
@@ -421 +492 @@
 
                 def clinicalModule = new AssayModule(
-                        name: 'Clinical data',
-                        type: AssayType.CLINICAL_DATA,
+                        name: 'SAM module for clinical data',
+                        type: AssayType.SIMPLE_ASSAY,
                         platform: 'clinical measurements',
-                        url: 'http://localhost:8080/gscf'
+                        url: 'http://sam.dbnp.org'
                 ).with { if (!validate()) { errors.each { println it} } else save()}
 
@@ -441 +512 @@
                 humanStudy.save()
 
-               mouseStudy.addToAssays(lipidAssayRef);
+                mouseStudy.addToAssays(lipidAssayRef);
                 mouseStudy.save()
-                */
         }
 

trunk/grails-app/conf/BootStrapTemplates.groovy

@@ -14 +14 @@
 class BootStrapTemplates {
 
+        /**
+         * Add the ontologies that are necessary for the templates below manually
+         * This function can be called to avoid the HTTP requests to BioPortal each time
+         * (e.g. in development or automated test environments)
+         */
+        public static void initTemplateOntologies() {
+
+                // add Subject>species ontology
+                println ".adding NCBI species ontology"
+                def speciesOntology = new Ontology(
+                        name: 'NCBI organismal classification',
+                        description: 'A taxonomic classification of living organisms and associated artifacts for their controlled description within the context of databases.',
+                        url: 'http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/',
+                        versionNumber: '1.2',
+                        ncboId: '1132',
+                        ncboVersionedId: '38802'
+                ).with { if (!validate()) { errors.each { println it} } else save()}
+
+                // add Sample>material ontology
+                println ".adding BRENDA source material ontology"
+                def brendaOntology = new Ontology(
+                        name: 'BRENDA tissue / enzyme source',
+                        description: 'A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.',
+                        url: 'http://www.brenda-enzymes.info',
+                        versionNumber: '1.3',
+                        ncboId: '1005',
+                        ncboVersionedId: '40643'
+                ).with { if (!validate()) { errors.each { println it} } else save()}
+
+                // add NCI ontology which is used in Mouse genotype template field
+                def nciOntology = new Ontology(
+                        name: 'NCI Thesaurus',
+                        description: 'A vocabulary for clinical care, translational and basic research, and public information and administrative activities.',
+                        url: 'http://ncicb.nci.nih.gov/core/EVS',
+                        versionNumber: '10.01',
+                        ncboId: '1032',
+                        ncboVersionedId: '42693'
+                ).with { if (!validate()) { errors.each { println it} } else save()}
+
+                // add CHEBI ontology which is used in Mouse genotype template field
+                def chebiOntology = new Ontology(
+                        name: 'Chemical entities of biological interest',
+                        description: 'A structured classification of chemical compounds of biological relevance.',
+                        url: 'http://www.ebi.ac.uk/chebi',
+                        versionNumber: '1.68',
+                        ncboId: '1007',
+                        ncboVersionedId: '42878'
+                ).with { if (!validate()) { errors.each { println it} } else save()}
+                
+        }
+
+        /**
+         * Add example templates, this function would normally be called on an empty database
+         */
         public static void initTemplates() {
 

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

@@ -623 +623 @@
 
         /**
+         * Look up the type of a certain template field
+         * @param String fieldName The name of the template field
+         * @return String The type (static member of TemplateFieldType) of the field, or null of the field does not exist
+         */
+        TemplateFieldType giveFieldType(String fieldName) {
+                def field = giveFields().find {
+                        it.name == fieldName
+                }
+                field?.type
+        }
+
+        /**
          * Return all relevant 'built-in' domain fields of the super class. Should be implemented by a static method
          * @return List with DomainTemplateFields
@@ -659 +671 @@
         }
 
-                    /**
-         * Look up the type of a certain template subject field
-         * @param String fieldName The name of the template field
-         * @return String       The type (static member of TemplateFieldType) of the field, or null of the field does not exist
-         */
-        def TemplateFieldType getFieldType(String fieldName) {
-                def field = this.giveFields().find {
-                        it.name == fieldName
-                }
-                field?.type
-        }
 }

trunk/test/integration/gscf/SampleTests.groovy

@@ -6 +6 @@
 import dbnp.studycapturing.SamplingEvent
 import dbnp.studycapturing.Sample
+import dbnp.studycapturing.TemplateFieldType
 
 /**
@@ -177 +178 @@
                 assert sample.isDomainField('material')
 
+                // Make sure that they have the right type
+                assert sample.giveFieldType('name') == TemplateFieldType.STRING
+                assert sample.giveFieldType('material') == TemplateFieldType.ONTOLOGYTERM
+
         }