| 1 | import dbnp.studycapturing.* |
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| 2 | |
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| 3 | import dbnp.data.Ontology |
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| 4 | import dbnp.data.Term |
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| 5 | import org.codehaus.groovy.grails.commons.GrailsApplication |
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| 6 | |
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| 7 | /** |
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| 8 | * Application Bootstrapper |
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| 9 | * @Author Jeroen Wesbeek |
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| 10 | * @Since 20091021 |
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| 11 | * |
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| 12 | * Revision information: |
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| 13 | * $Rev: 458 $ |
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| 14 | * $Author: roberth $ |
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| 15 | * $Date: 2010-05-25 09:18:21 +0000 (di, 25 mei 2010) $ |
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| 16 | */ |
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| 17 | class BootStrap { |
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| 18 | def init = {servletContext -> |
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| 19 | // define timezone |
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| 20 | System.setProperty('user.timezone', 'CET') |
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| 21 | |
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| 22 | // we could also check if we are in development by GrailsUtil.environment == GrailsApplication.ENV_DEVELOPMENT |
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| 23 | if (Study.count() == 0) { |
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| 24 | println ".development bootstrapping..."; |
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| 25 | |
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| 26 | // add Subject>species ontology |
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| 27 | println ".adding NCBI species ontology" |
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| 28 | def speciesOntology = new Ontology( |
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| 29 | name: 'NCBI organismal classification', |
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| 30 | description: 'A taxonomic classification of living organisms and associated artifacts for their controlled description within the context of databases.', |
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| 31 | url: 'http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/', |
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| 32 | versionNumber: '1.2', |
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| 33 | ncboId: '1132', |
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| 34 | ncboVersionedId: '38802' |
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| 35 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 36 | |
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| 37 | // add Sample>material ontology |
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| 38 | println ".adding BRENDA source material ontology" |
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| 39 | def brendaOntology = new Ontology( |
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| 40 | name: 'BRENDA tissue / enzyme source', |
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| 41 | 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.', |
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| 42 | url: 'http://www.brenda-enzymes.info', |
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| 43 | versionNumber: '1.3', |
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| 44 | ncboId: '1005', |
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| 45 | ncboVersionedId: '40643' |
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| 46 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 47 | |
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| 48 | // add NCI ontology which is used in Mouse genotype template field |
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| 49 | def nciOntology = new Ontology( |
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| 50 | name: 'NCI Thesaurus', |
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| 51 | description: 'A vocabulary for clinical care, translational and basic research, and public information and administrative activities.', |
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| 52 | url: 'http://ncicb.nci.nih.gov/core/EVS', |
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| 53 | versionNumber: '10.01', |
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| 54 | ncboId: '1032', |
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| 55 | ncboVersionedId: '42693' |
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| 56 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 57 | |
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| 58 | // add Terms |
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| 59 | println ".adding mouse term" |
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| 60 | def mouseTerm = new Term( |
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| 61 | name: 'Mus musculus', |
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| 62 | ontology: speciesOntology, |
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| 63 | accession: '10090' |
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| 64 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 65 | println ".adding human term" |
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| 66 | def humanTerm = new Term( |
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| 67 | name: 'Homo sapiens', |
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| 68 | ontology: speciesOntology, |
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| 69 | accession: '9606' |
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| 70 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 71 | def arabTerm = new Term( |
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| 72 | name: 'Arabidopsis thaliana', |
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| 73 | ontology: speciesOntology, |
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| 74 | accession: '3702' |
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| 75 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 76 | |
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| 77 | def bloodTerm = new Term( |
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| 78 | name: 'blood plasma', |
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| 79 | ontology: brendaOntology, |
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| 80 | accession: 'BTO:0000131' |
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| 81 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 82 | |
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| 83 | def c57bl6Term = new Term( |
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| 84 | name: 'C57BL/6 Mouse', |
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| 85 | ontology: nciOntology, |
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| 86 | accession: 'C14424' |
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| 87 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 88 | |
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| 89 | // Create a few persons, roles and Affiliations |
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| 90 | println ".adding persons, roles and affiliations" |
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| 91 | def affiliation1 = new PersonAffiliation( |
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| 92 | institute: "Science Institute NYC", |
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| 93 | department: "Department of Mathematics" |
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| 94 | ).save(); |
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| 95 | def affiliation2 = new PersonAffiliation( |
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| 96 | institute: "InfoStats GmbH, Hamburg", |
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| 97 | department: "Life Sciences" |
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| 98 | ).save(); |
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| 99 | def role1 = new PersonRole( |
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| 100 | name: "Principal Investigator" |
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| 101 | ).save(); |
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| 102 | def role2 = new PersonRole( |
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| 103 | name: "Statician" |
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| 104 | ).save(); |
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| 105 | |
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| 106 | // Create persons |
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| 107 | def person1 = new Person( |
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| 108 | lastName: "Scientist", |
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| 109 | firstName: "John", |
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| 110 | gender: "Male", |
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| 111 | initials: "J.R.", |
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| 112 | email: "john@scienceinstitute.com", |
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| 113 | phone: "1-555-3049", |
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| 114 | address: "First street 2,NYC" |
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| 115 | ) |
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| 116 | .addToAffiliations( affiliation1 ) |
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| 117 | .addToAffiliations( affiliation2 ) |
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| 118 | .save(); |
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| 119 | |
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| 120 | def person2 = new Person( |
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| 121 | lastName: "Statician", |
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| 122 | firstName: "Jane", |
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| 123 | gender: "Female", |
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| 124 | initials: "W.J.", |
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| 125 | email: "jane@statisticalcompany.de", |
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| 126 | phone: "49-555-8291", |
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| 127 | address: "Dritten strasse 38, Hamburg, Germany" |
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| 128 | ) |
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| 129 | .addToAffiliations( affiliation2 ) |
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| 130 | .save(); |
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| 131 | |
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| 132 | // Create 30 persons to test pagination |
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| 133 | def personCounter = 1; |
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| 134 | 30.times { new Person( firstName: "Person #${personCounter}", lastName: "Testperson", email: "email${personCounter++}@testdomain.com" ).save() } |
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| 135 | |
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| 136 | // Create a few publications |
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| 137 | println ".adding publications" |
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| 138 | def publication1 = new Publication( |
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| 139 | title: "Postnatal development of hypothalamic leptin receptors", |
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| 140 | authorsList: "Cottrell EC, Mercer JG, Ozanne SE.", |
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| 141 | pubMedID: "20472140", |
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| 142 | comments: "Not published yet", |
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| 143 | DOI: "unknown" |
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| 144 | ) |
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| 145 | .save(); |
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| 146 | |
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| 147 | def publication2 = new Publication( |
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| 148 | title: "Induction of regulatory T cells decreases adipose inflammation and alleviates insulin resistance in ob/ob mice", |
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| 149 | authorsList: "Ilan Y, Maron R, Tukpah AM, Maioli TU, Murugaiyan G, Yang K, Wu HY, Weiner HL.", |
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| 150 | pubMedID: "20445103", |
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| 151 | comments: "", |
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| 152 | DOI: "" |
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| 153 | ) |
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| 154 | .save(); |
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| 155 | |
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| 156 | // Create templates |
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| 157 | |
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| 158 | def genderField = new TemplateField( |
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| 159 | name: 'Gender',type: TemplateFieldType.STRINGLIST, |
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| 160 | listEntries: [new TemplateFieldListItem(name:'Male'),new TemplateFieldListItem(name: 'Female'),new TemplateFieldListItem(name: 'Unknown')]) |
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| 161 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 162 | |
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| 163 | def ageField = new TemplateField( |
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| 164 | name: 'Age',type: TemplateFieldType.INTEGER,unit: 'years',comment: 'Either include age at the start of the study or date of birth (if known)') |
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| 165 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 166 | |
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| 167 | def genotypeField = new TemplateField( |
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| 168 | name: 'Genotype', type: TemplateFieldType.ONTOLOGYTERM, |
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| 169 | comment: 'If present, indicate the genetic variance of the subject (the gene knock-out/in or transgene)') |
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| 170 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 171 | |
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| 172 | def genotypeTypeField = new TemplateField( |
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| 173 | name: 'Genotype type',type: TemplateFieldType.STRINGLIST, |
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| 174 | listEntries: [new TemplateFieldListItem(name:'wildtype'), |
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| 175 | new TemplateFieldListItem(name:'transgenic'), |
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| 176 | new TemplateFieldListItem(name:'knock-out'), |
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| 177 | new TemplateFieldListItem(name:'knock-in')], |
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| 178 | comment: 'If a genotype was specified, please indicate here the type of the genotype') |
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| 179 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 180 | |
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| 181 | |
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| 182 | // Nutritional study template |
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| 183 | |
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| 184 | println ".adding academic study template..." |
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| 185 | def studyTemplate = new Template( |
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| 186 | name: 'Academic study', entity: dbnp.studycapturing.Study) |
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| 187 | .addToFields(new TemplateField(name: 'Description',type: TemplateFieldType.TEXT,comment:'Describe here the type of subjects and the treatment, challenges and sampling.')) |
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| 188 | .addToFields(new TemplateField( |
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| 189 | name: 'Study code', |
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| 190 | type: TemplateFieldType.STRING, |
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| 191 | preferredIdentifier:true, |
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| 192 | comment: 'Fill out the code by which many people will recognize your study')) |
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| 193 | .addToFields(new TemplateField(name: 'Objectives',type: TemplateFieldType.TEXT,comment:'Fill out the aim or questions of the study')) |
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| 194 | .addToFields(new TemplateField(name: 'Consortium',type: TemplateFieldType.STRING,comment:'If the study was performed within a consortium (e.g. NMC, NuGO), you can indicate this here')) |
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| 195 | .addToFields(new TemplateField(name: 'Cohort name',type: TemplateFieldType.STRING,comment:'If a cohort was used the name or code of the cohort can be define here (define a cohort template)')) |
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| 196 | //.addToFields(new TemplateField(name: 'Time zone',type: TemplateFieldType.STRING,comment:'In the database the local time will be stored. This field is essential to be able to generalize time.')) |
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| 197 | .addToFields(new TemplateField(name: 'Responsible scientist',type: TemplateFieldType.STRING,comment:'Fill out the project leader of principle investigator of the study. (soon to be replaced with persons input)')) |
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| 198 | .addToFields(new TemplateField(name: 'Lab id',type: TemplateFieldType.STRING,comment:'In which lab was the study performed; indicate the roomnumber.')) |
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| 199 | .addToFields(new TemplateField(name: 'Institute',type: TemplateFieldType.STRING,comment:'In which institute was the study performed; indicate the full address information (to be replaced by persons-affiliations?)')) |
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| 200 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 201 | |
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| 202 | // Mouse template |
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| 203 | println ".adding mouse subject template..." |
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| 204 | def mouseTemplate = new Template( |
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| 205 | name: 'Mouse', entity: dbnp.studycapturing.Subject) |
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| 206 | .addToFields(new TemplateField( |
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| 207 | name: 'Strain', type: TemplateFieldType.ONTOLOGYTERM, ontologies: [nciOntology], comment: "This is an ontology term, if the right strain is not in the list please add it with 'add more'")) |
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| 208 | .addToFields(genotypeField) |
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| 209 | .addToFields(genotypeTypeField) |
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| 210 | .addToFields(genderField) |
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| 211 | .addToFields(new TemplateField( |
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| 212 | name: 'Age', type: TemplateFieldType.INTEGER, unit: 'weeks', comment: 'Age at start of study')) |
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| 213 | .addToFields(new TemplateField( |
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| 214 | name: 'Age type',type: TemplateFieldType.STRINGLIST, |
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| 215 | listEntries: [new TemplateFieldListItem(name:'postnatal'),new TemplateFieldListItem(name:'embryonal')])) |
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| 216 | .addToFields(new TemplateField( |
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| 217 | name: 'Cage',type: TemplateFieldType.STRING,comment:'Indicate the cage used for housing (type and/or size)')) |
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| 218 | .addToFields(new TemplateField( |
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| 219 | name: '#Mice in cage',type: TemplateFieldType.INTEGER,comment:'If known, indicate the number of mice per cage')) |
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| 220 | .addToFields(new TemplateField( |
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| 221 | name: 'Litter size',type: TemplateFieldType.INTEGER,comment:'If known, indicate the litter size of the litter from which the subject originates')) |
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| 222 | .addToFields(new TemplateField( |
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| 223 | name: 'Weight', type: TemplateFieldType.DOUBLE, unit: 'gram',comment:'If known indicate the weight of the subject in grams at the start of the study')) |
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| 224 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 225 | |
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| 226 | // Human template |
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| 227 | println ".adding human subject template..." |
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| 228 | def humanTemplate = new Template( |
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| 229 | name: 'Human', entity: dbnp.studycapturing.Subject) |
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| 230 | .addToFields(genderField) |
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| 231 | .addToFields(ageField) |
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| 232 | .addToFields(new TemplateField( |
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| 233 | name: 'DOB',type: TemplateFieldType.DATE,comment:'Date of birth')) |
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| 234 | .addToFields(new TemplateField( |
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| 235 | name: 'Height',type: TemplateFieldType.DOUBLE, unit: 'm')) |
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| 236 | .addToFields(new TemplateField( |
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| 237 | name: 'Weight',type: TemplateFieldType.DOUBLE, unit: 'kg')) |
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| 238 | .addToFields(new TemplateField( |
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| 239 | name: 'BMI',type: TemplateFieldType.DOUBLE, unit: 'kg/m2',comment:'Body-mass-index')) |
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| 240 | .addToFields(new TemplateField( |
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| 241 | name: 'Race',type: TemplateFieldType.STRING,comment:'If known and of interest the ethnic group can be indicated')) |
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| 242 | .addToFields(new TemplateField( |
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| 243 | name: 'Waist circumference',type: TemplateFieldType.FLOAT, unit: 'cm',comment:'The waist circumference is measured just above the hip bone. Indicate the measure at the start of the study.')) |
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| 244 | .addToFields(new TemplateField( |
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| 245 | name: 'Hip circumference',type: TemplateFieldType.FLOAT, unit: 'cm',comment:'The hip circumference is measured at the level of the two bony prominences front of the hips. Indicate the measure at the start of the study.')) |
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| 246 | .addToFields(new TemplateField( |
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| 247 | name: 'Systolic blood pressure',type: TemplateFieldType.FLOAT, unit: 'mmHg',comment:'Indicate the levels at the start of the study in mmHG')) |
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| 248 | .addToFields(new TemplateField( |
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| 249 | name: 'Diastolic blood pressure',type: TemplateFieldType.FLOAT, unit: 'mmHg',comment:'Indicate the levels at the start of the study in mmHG')) |
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| 250 | .addToFields(new TemplateField( |
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| 251 | name: 'Heart rate',type: TemplateFieldType.FLOAT, unit: 'beats/min',comment:'Indicate the heart rate at the start of in study in beats per minute')) |
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| 252 | .addToFields(new TemplateField( |
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| 253 | name: 'Run-in-food',type: TemplateFieldType.TEXT,comment:'If defined, give a short description of the food used before the measurements')) |
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| 254 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 255 | |
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| 256 | |
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| 257 | def sampleDescriptionField = new TemplateField( |
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| 258 | name: 'Description',type: TemplateFieldType.TEXT) |
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| 259 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 260 | def sampleTypeField = new TemplateField( |
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| 261 | name: 'SampleType',type: TemplateFieldType.STRING) |
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| 262 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 263 | def sampleProtocolField = new TemplateField( |
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| 264 | name: 'SampleProtocol',type: TemplateFieldType.STRING) |
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| 265 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 266 | def sampleVialTextField = new TemplateField( |
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| 267 | name: 'Text on vial',type: TemplateFieldType.STRING) |
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| 268 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 269 | |
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| 270 | // Human sample template |
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| 271 | println ".adding human sample template..." |
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| 272 | def humanSampleTemplate = new Template( |
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| 273 | name: 'Human tissue sample', entity: dbnp.studycapturing.Sample) |
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| 274 | .addToFields(sampleDescriptionField) |
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| 275 | .addToFields(sampleTypeField) |
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| 276 | .addToFields(sampleProtocolField) |
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| 277 | .addToFields(sampleVialTextField) |
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| 278 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 279 | |
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| 280 | //Plant template |
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| 281 | println ".adding plant template..." |
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| 282 | def plantTemplate = new Template( |
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| 283 | name: 'Plant template', entity: dbnp.studycapturing.Subject) |
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| 284 | .addToFields(new TemplateField( |
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| 285 | name: 'Variety', type: TemplateFieldType.STRING)) |
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| 286 | .addToFields(new TemplateField( |
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| 287 | name: 'Ecotype', type: TemplateFieldType.STRING)) |
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| 288 | .addToFields(genotypeField) |
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| 289 | .addToFields(genotypeTypeField) |
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| 290 | .addToFields(new TemplateField( |
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| 291 | name: 'Growth location', type: TemplateFieldType.STRINGLIST, |
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| 292 | listEntries: [new TemplateFieldListItem(name:'Greenhouse'),new TemplateFieldListItem(name: 'Field')])) |
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| 293 | .addToFields(new TemplateField( |
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| 294 | name: 'Room', type: TemplateFieldType.STRING, |
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| 295 | comment: 'Chamber number in case of Greenhouse')) |
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| 296 | .addToFields(new TemplateField( |
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| 297 | name: 'Position X', type: TemplateFieldType.FLOAT)) |
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| 298 | .addToFields(new TemplateField( |
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| 299 | name: 'Position Y', type: TemplateFieldType.FLOAT)) |
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| 300 | .addToFields(new TemplateField( |
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| 301 | name: 'Block', type: TemplateFieldType.STRING)) |
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| 302 | .addToFields(new TemplateField( |
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| 303 | name: 'Temperature at day', type: TemplateFieldType.FLOAT)) |
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| 304 | .addToFields(new TemplateField( |
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| 305 | name: 'Temperature at night', type: TemplateFieldType.FLOAT)) |
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| 306 | .addToFields(new TemplateField( |
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| 307 | name: 'Photo period', type: TemplateFieldType.STRING)) |
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| 308 | .addToFields(new TemplateField( |
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| 309 | name: 'Light intensity', type: TemplateFieldType.STRING)) |
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| 310 | .addToFields(new TemplateField( |
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| 311 | name: 'Start date', type: TemplateFieldType.DATE)) |
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| 312 | .addToFields(new TemplateField( |
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| 313 | name: 'Harvest date', type: TemplateFieldType.DATE)) |
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| 314 | .addToFields(new TemplateField( |
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| 315 | name: 'Growth type', type: TemplateFieldType.STRINGLIST, |
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| 316 | listEntries: [new TemplateFieldListItem(name:'Standard'),new TemplateFieldListItem(name: 'Experimental')])) |
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| 317 | .addToFields(new TemplateField( |
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| 318 | name: 'Growth protocol', type: TemplateFieldType.TEXT)) |
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| 319 | .addToFields(new TemplateField( |
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| 320 | name: 'Harvest delay', type: TemplateFieldType.TEXT)) |
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| 321 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 322 | |
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| 323 | println ".adding plant sample template..." |
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| 324 | def plantSampleTemplate = new Template( |
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| 325 | name: 'Plant sample', entity: dbnp.studycapturing.Sample) |
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| 326 | .addToFields(sampleDescriptionField) |
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| 327 | .addToFields(sampleTypeField) |
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| 328 | .addToFields(sampleProtocolField) |
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| 329 | .addToFields(sampleVialTextField) |
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| 330 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 331 | |
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| 332 | |
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| 333 | // Event templates |
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| 334 | def dietTreatmentTemplate = new Template( |
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| 335 | name: 'Diet treatment', entity: dbnp.studycapturing.Event) |
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| 336 | .addToFields(sampleDescriptionField) |
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| 337 | .addToFields(new TemplateField( |
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| 338 | name: 'Diet', type: TemplateFieldType.STRINGLIST, |
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| 339 | listEntries: [new TemplateFieldListItem(name:'10% fat (palm oil)'),new TemplateFieldListItem(name: '45% fat (palm oil)')])) |
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| 340 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 341 | |
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| 342 | def boostTreatmentTemplate = new Template( |
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| 343 | name: 'Boost treatment', entity: dbnp.studycapturing.Event) |
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| 344 | .addToFields(sampleDescriptionField) |
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| 345 | .addToFields(new TemplateField( |
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| 346 | name: 'Compound', type: TemplateFieldType.STRING, |
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| 347 | listEntries: [new TemplateFieldListItem(name:'Vehicle'),new TemplateFieldListItem(name: 'Leptin')])) |
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| 348 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 349 | |
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| 350 | def fastingTreatment = new Template( |
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| 351 | name: 'Fasting treatment', |
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| 352 | description: 'Fasting Protocol NuGO PPSH', |
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| 353 | entity: dbnp.studycapturing.Event) |
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| 354 | .addToFields(new TemplateField( |
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| 355 | name: 'Fasting period', |
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| 356 | type: TemplateFieldType.STRING)) |
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| 357 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 358 | |
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| 359 | // SamplingEvent templates |
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| 360 | |
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| 361 | def liverSamplingEventTemplate = new Template( |
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| 362 | name: 'Liver extraction', |
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| 363 | description: 'Liver sampling for transcriptomics arrays', |
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| 364 | entity: dbnp.studycapturing.SamplingEvent) |
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| 365 | .addToFields(new TemplateField( |
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| 366 | name: 'Sample weight', |
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| 367 | unit: 'mg', |
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| 368 | type: TemplateFieldType.FLOAT)) |
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| 369 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 370 | |
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| 371 | def bloodSamplingEventTemplate = new Template( |
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| 372 | name: 'Blood extraction', |
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| 373 | description: 'Blood extraction targeted at lipid assays', |
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| 374 | entity: dbnp.studycapturing.SamplingEvent) |
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| 375 | .addToFields(new TemplateField( |
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| 376 | name: 'Sample volume', |
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| 377 | unit: 'ml', |
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| 378 | type: TemplateFieldType.FLOAT)) |
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| 379 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 380 | |
|---|
| 381 | |
|---|
| 382 | // Add example studies |
|---|
| 383 | if (!(grails.util.GrailsUtil.environment == GrailsApplication.ENV_TEST)) { |
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| 384 | println ".adding NuGO PPS3 leptin example study..." |
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| 385 | def mouseStudy = new Study( |
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| 386 | template: studyTemplate, |
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| 387 | title:"NuGO PPS3 mouse study leptin module", |
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| 388 | code:"PPS3_leptin_module", |
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| 389 | researchQuestion:"Leptin etc.", |
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| 390 | ecCode:"2007117.c", |
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| 391 | startDate: Date.parse('yyyy-MM-dd','2007-12-11') |
|---|
| 392 | ) |
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| 393 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 394 | |
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| 395 | mouseStudy.setFieldValue('Description', "C57Bl/6 mice were fed a high fat (45 en%) or low fat (10 en%) diet after a four week run-in on low fat diet. After 1 week 10 mice that received a low fat diet were given an IP leptin challenge and 10 mice of the low-fat group received placebo injections. The same procedure was performed with mice that were fed the high-fat diet. After 4 weeks the procedure was repeated. In total 80 mice were culled." ) |
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| 396 | mouseStudy.save() |
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| 397 | |
|---|
| 398 | def evLF = new Event( |
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| 399 | startTime: Date.parse('yyyy-MM-dd','2008-01-07'), |
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| 400 | endTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
|---|
| 401 | template: dietTreatmentTemplate |
|---|
| 402 | ) |
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| 403 | .setFieldValue( 'Diet','10% fat (palm oil)') |
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| 404 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 405 | |
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| 406 | def evHF = new Event( |
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| 407 | startTime: Date.parse('yyyy-MM-dd','2008-01-07'), |
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| 408 | endTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
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| 409 | template: dietTreatmentTemplate |
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| 410 | ) |
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| 411 | .setFieldValue( 'Diet','45% fat (palm oil)' ) |
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| 412 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 413 | |
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| 414 | def evBV = new Event( |
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| 415 | startTime: Date.parse('yyyy-MM-dd','2008-01-07'), |
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| 416 | endTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
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| 417 | template: boostTreatmentTemplate |
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| 418 | ) |
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| 419 | .setFieldValue( 'Compound','Vehicle' ) |
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| 420 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 421 | |
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| 422 | def evBL = new Event( |
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| 423 | startTime: Date.parse('yyyy-MM-dd','2008-01-07'), |
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| 424 | endTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
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| 425 | template: boostTreatmentTemplate |
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| 426 | ) |
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| 427 | .setFieldValue( 'Compound','Leptin' ) |
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| 428 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 429 | |
|---|
| 430 | def evLF4 = new Event( |
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| 431 | startTime: Date.parse('yyyy-MM-dd','2008-01-07'), |
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| 432 | endTime: Date.parse('yyyy-MM-dd','2008-02-04'), |
|---|
| 433 | template: dietTreatmentTemplate |
|---|
| 434 | ) |
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| 435 | .setFieldValue( 'Diet','10% fat (palm oil)') |
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| 436 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 437 | |
|---|
| 438 | def evHF4 = new Event( |
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| 439 | startTime: Date.parse('yyyy-MM-dd','2008-01-07'), |
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| 440 | endTime: Date.parse('yyyy-MM-dd','2008-02-04'), |
|---|
| 441 | template: dietTreatmentTemplate |
|---|
| 442 | ) |
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| 443 | .setFieldValue( 'Diet','45% fat (palm oil)' ) |
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| 444 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 445 | |
|---|
| 446 | def evBV4 = new Event( |
|---|
| 447 | startTime: Date.parse('yyyy-MM-dd','2008-01-07'), |
|---|
| 448 | endTime: Date.parse('yyyy-MM-dd','2008-02-04'), |
|---|
| 449 | template: boostTreatmentTemplate |
|---|
| 450 | ) |
|---|
| 451 | .setFieldValue( 'Compound','Vehicle' ) |
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| 452 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 453 | |
|---|
| 454 | def evBL4 = new Event( |
|---|
| 455 | startTime: Date.parse('yyyy-MM-dd','2008-01-07'), |
|---|
| 456 | endTime: Date.parse('yyyy-MM-dd','2008-02-04'), |
|---|
| 457 | template: boostTreatmentTemplate |
|---|
| 458 | ) |
|---|
| 459 | .setFieldValue( 'Compound','Leptin' ) |
|---|
| 460 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 461 | |
|---|
| 462 | def evS = new SamplingEvent( |
|---|
| 463 | startTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
|---|
| 464 | endTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
|---|
| 465 | template: liverSamplingEventTemplate) |
|---|
| 466 | .setFieldValue('Sample weight',5F) |
|---|
| 467 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 468 | |
|---|
| 469 | def evS4 = new SamplingEvent( |
|---|
| 470 | startTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
|---|
| 471 | endTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
|---|
| 472 | template: liverSamplingEventTemplate) |
|---|
| 473 | .setFieldValue('Sample weight',5F) |
|---|
| 474 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 475 | |
|---|
| 476 | // Add events to study |
|---|
| 477 | mouseStudy |
|---|
| 478 | .addToEvents(evLF) |
|---|
| 479 | .addToEvents(evHF) |
|---|
| 480 | .addToEvents(evBV) |
|---|
| 481 | .addToEvents(evBL) |
|---|
| 482 | .addToEvents(evLF4) |
|---|
| 483 | .addToEvents(evHF4) |
|---|
| 484 | .addToEvents(evBV4) |
|---|
| 485 | .addToEvents(evBL4) |
|---|
| 486 | .addToSamplingEvents(evS) |
|---|
| 487 | .addToSamplingEvents(evS4) |
|---|
| 488 | .save() |
|---|
| 489 | |
|---|
| 490 | def LFBV1 = new EventGroup(name:"10% fat + vehicle for 1 week") |
|---|
| 491 | .addToEvents(evLF) |
|---|
| 492 | .addToEvents(evBV) |
|---|
| 493 | .addToEvents(evS) |
|---|
| 494 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 495 | |
|---|
| 496 | def LFBL1 = new EventGroup(name:"10% fat + leptin for 1 week") |
|---|
| 497 | .addToEvents(evLF) |
|---|
| 498 | .addToEvents(evBL) |
|---|
| 499 | .addToEvents(evS) |
|---|
| 500 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 501 | |
|---|
| 502 | def HFBV1 = new EventGroup(name:"45% fat + vehicle for 1 week") |
|---|
| 503 | .addToEvents(evHF) |
|---|
| 504 | .addToEvents(evBV) |
|---|
| 505 | .addToEvents(evS) |
|---|
| 506 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 507 | |
|---|
| 508 | def HFBL1 = new EventGroup(name:"45% fat + leptin for 1 week") |
|---|
| 509 | .addToEvents(evHF) |
|---|
| 510 | .addToEvents(evBL) |
|---|
| 511 | .addToEvents(evS) |
|---|
| 512 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 513 | |
|---|
| 514 | def LFBV4 = new EventGroup(name:"10% fat + vehicle for 4 weeks") |
|---|
| 515 | .addToEvents(evLF4) |
|---|
| 516 | .addToEvents(evBV4) |
|---|
| 517 | .addToEvents(evS4) |
|---|
| 518 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 519 | |
|---|
| 520 | def LFBL4 = new EventGroup(name:"10% fat + leptin for 4 weeks") |
|---|
| 521 | .addToEvents(evLF4) |
|---|
| 522 | .addToEvents(evBL4) |
|---|
| 523 | .addToEvents(evS4) |
|---|
| 524 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 525 | |
|---|
| 526 | def HFBV4 = new EventGroup(name:"45% fat + vehicle for 4 weeks") |
|---|
| 527 | .addToEvents(evHF4) |
|---|
| 528 | .addToEvents(evBV4) |
|---|
| 529 | .addToEvents(evS4) |
|---|
| 530 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 531 | |
|---|
| 532 | def HFBL4 = new EventGroup(name:"45% fat + leptin for 4 weeks") |
|---|
| 533 | .addToEvents(evHF4) |
|---|
| 534 | .addToEvents(evBL4) |
|---|
| 535 | .addToEvents(evS4) |
|---|
| 536 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 537 | |
|---|
| 538 | // Add subjects and samples and compose EventGroups |
|---|
| 539 | def x=1 |
|---|
| 540 | 20.times { |
|---|
| 541 | def currentSubject = new Subject( |
|---|
| 542 | name: "A" + x++, |
|---|
| 543 | species: mouseTerm, |
|---|
| 544 | template: mouseTemplate, |
|---|
| 545 | ) |
|---|
| 546 | .setFieldValue("Gender", "Male") |
|---|
| 547 | .setFieldValue("Genotype", c57bl6Term) |
|---|
| 548 | .setFieldValue("Age", 17) |
|---|
| 549 | .setFieldValue("Cage", "" + (int)(x/2)) |
|---|
| 550 | .with { if (!validate()) { errors.each { println it} } else save(flush:true)} |
|---|
| 551 | |
|---|
| 552 | mouseStudy.addToSubjects(currentSubject) |
|---|
| 553 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 554 | |
|---|
| 555 | // Add subject to appropriate EventGroup |
|---|
| 556 | if (x > 70) { HFBL4.addToSubjects(currentSubject).save() } |
|---|
| 557 | else if (x > 60) { HFBV4.addToSubjects(currentSubject).save() } |
|---|
| 558 | else if (x > 50) { LFBL4.addToSubjects(currentSubject).save() } |
|---|
| 559 | else if (x > 40) { LFBV4.addToSubjects(currentSubject).save() } |
|---|
| 560 | else if (x > 30) { HFBL1.addToSubjects(currentSubject).save() } |
|---|
| 561 | else if (x > 20) { HFBV1.addToSubjects(currentSubject).save() } |
|---|
| 562 | else if (x > 10) { LFBL1.addToSubjects(currentSubject).save() } |
|---|
| 563 | else { LFBV1.addToSubjects(currentSubject).save() } |
|---|
| 564 | |
|---|
| 565 | } |
|---|
| 566 | |
|---|
| 567 | // Add EventGroups to study |
|---|
| 568 | mouseStudy |
|---|
| 569 | .addToEventGroups(LFBV1) |
|---|
| 570 | .addToEventGroups(LFBL1) |
|---|
| 571 | .addToEventGroups(HFBV1) |
|---|
| 572 | .addToEventGroups(HFBL1) |
|---|
| 573 | .addToEventGroups(LFBV4) |
|---|
| 574 | .addToEventGroups(LFBL4) |
|---|
| 575 | .addToEventGroups(HFBV4) |
|---|
| 576 | .addToEventGroups(HFBL4) |
|---|
| 577 | |
|---|
| 578 | // Add persons and publications to study |
|---|
| 579 | def studyperson1 = new StudyPerson( person: person1, role: role1 ).save(); |
|---|
| 580 | def studyperson2 = new StudyPerson( person: person2, role: role2 ).save(); |
|---|
| 581 | |
|---|
| 582 | mouseStudy |
|---|
| 583 | .addToPersons( studyperson1 ) |
|---|
| 584 | .addToPersons( studyperson2 ) |
|---|
| 585 | .addToPublications( publication1 ) |
|---|
| 586 | .addToPublications( publication2 ) |
|---|
| 587 | .save() |
|---|
| 588 | |
|---|
| 589 | println ".adding NuGO PPSH example study..." |
|---|
| 590 | |
|---|
| 591 | def humanStudy = new Study( |
|---|
| 592 | template: studyTemplate, |
|---|
| 593 | title:"NuGO PPS human study", |
|---|
| 594 | code:"PPSH", |
|---|
| 595 | researchQuestion:"How much are fasting plasma and urine metabolite levels affected by prolonged fasting ?", |
|---|
| 596 | description:"Human study", |
|---|
| 597 | ecCode:"unknown", |
|---|
| 598 | startDate: Date.parse('yyyy-MM-dd','2008-01-14')) |
|---|
| 599 | .setFieldValue( 'Description', "Human study performed at RRI; centres involved: RRI, IFR, TUM, Maastricht U." ) |
|---|
| 600 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 601 | |
|---|
| 602 | def rootGroup = new EventGroup(name: 'Root group'); |
|---|
| 603 | |
|---|
| 604 | def fastingEvent = new Event( |
|---|
| 605 | startTime: Date.parse('yyyy-MM-dd HH:mm','2008-01-14 22:00'), |
|---|
| 606 | endTime: Date.parse('yyyy-MM-dd HH:mm','2008-01-15 08:00'), |
|---|
| 607 | template: fastingTreatment) |
|---|
| 608 | .setFieldValue('Fasting period','8h'); |
|---|
| 609 | |
|---|
| 610 | |
|---|
| 611 | def bloodSamplingEvent = new SamplingEvent( |
|---|
| 612 | startTime: Date.parse('yyyy-MM-dd HH:mm','2008-01-15 08:00'), |
|---|
| 613 | endTime: Date.parse('yyyy-MM-dd HH:mm','2008-01-15 08:00'), |
|---|
| 614 | template: bloodSamplingEventTemplate) |
|---|
| 615 | .setFieldValue('Sample volume',4.5F); |
|---|
| 616 | |
|---|
| 617 | rootGroup.addToEvents fastingEvent |
|---|
| 618 | rootGroup.addToEvents bloodSamplingEvent |
|---|
| 619 | rootGroup.save() |
|---|
| 620 | |
|---|
| 621 | def y = 1 |
|---|
| 622 | 11.times { |
|---|
| 623 | def currentSubject = new Subject( |
|---|
| 624 | name: "" + y++, |
|---|
| 625 | species: humanTerm, |
|---|
| 626 | template: humanTemplate) |
|---|
| 627 | .setFieldValue("Gender", (Math.random() > 0.5) ? "Male" : "Female") |
|---|
| 628 | .setFieldValue("DOB", new java.text.SimpleDateFormat("dd-mm-yy").parse("01-02-19" + (10 + (int) (Math.random() * 80)))) |
|---|
| 629 | .setFieldValue("Age", 30) |
|---|
| 630 | .setFieldValue("Height", Math.random() * 2F) |
|---|
| 631 | .setFieldValue("Weight", Math.random() * 150F) |
|---|
| 632 | .setFieldValue("BMI", 20 + Math.random() * 10F) |
|---|
| 633 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 634 | |
|---|
| 635 | rootGroup.addToSubjects currentSubject |
|---|
| 636 | rootGroup.save() |
|---|
| 637 | |
|---|
| 638 | def currentSample = new Sample( |
|---|
| 639 | name: currentSubject.name + '_B', |
|---|
| 640 | material: bloodTerm, |
|---|
| 641 | parentSubject: currentSubject, |
|---|
| 642 | parentEvent: bloodSamplingEvent); |
|---|
| 643 | |
|---|
| 644 | humanStudy.addToSubjects(currentSubject).addToSamples(currentSample).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 645 | } |
|---|
| 646 | |
|---|
| 647 | humanStudy.addToEvents(fastingEvent) |
|---|
| 648 | humanStudy.addToSamplingEvents(bloodSamplingEvent) |
|---|
| 649 | humanStudy.addToEventGroups rootGroup |
|---|
| 650 | |
|---|
| 651 | |
|---|
| 652 | // Add persons to study |
|---|
| 653 | def studyperson3 = new StudyPerson( person: person1, role: role2 ).save(); |
|---|
| 654 | |
|---|
| 655 | humanStudy |
|---|
| 656 | .addToPersons( studyperson3 ) |
|---|
| 657 | .addToPublications( publication2 ) |
|---|
| 658 | .save() |
|---|
| 659 | |
|---|
| 660 | /* |
|---|
| 661 | // Add clinical data |
|---|
| 662 | |
|---|
| 663 | def lipidAssay = new dbnp.clinicaldata.ClinicalAssay( |
|---|
| 664 | name: 'Lipid profile', |
|---|
| 665 | approved: true |
|---|
| 666 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 667 | |
|---|
| 668 | def ldlMeasurement = new dbnp.clinicaldata.ClinicalMeasurement( |
|---|
| 669 | name: 'LDL', |
|---|
| 670 | unit: 'mg/dL', |
|---|
| 671 | type: dbnp.data.FeatureType.QUANTITATIVE, |
|---|
| 672 | referenceValues: '100 mg/dL', |
|---|
| 673 | detectableLimit: 250, |
|---|
| 674 | isDrug: false, isIntake: true, inSerum: true |
|---|
| 675 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 676 | |
|---|
| 677 | def hdlMeasurement = new dbnp.clinicaldata.ClinicalMeasurement( |
|---|
| 678 | name: 'HDL', |
|---|
| 679 | unit: 'mg/dL', |
|---|
| 680 | type: dbnp.data.FeatureType.QUANTITATIVE, |
|---|
| 681 | referenceValues: '50 mg/dL', |
|---|
| 682 | detectableLimit: 100, |
|---|
| 683 | isDrug: false, isIntake: true, inSerum: true |
|---|
| 684 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 685 | |
|---|
| 686 | lipidAssay.addToMeasurements ldlMeasurement |
|---|
| 687 | lipidAssay.addToMeasurements hdlMeasurement |
|---|
| 688 | |
|---|
| 689 | def lipidAssayInstance = new dbnp.clinicaldata.ClinicalAssayInstance( |
|---|
| 690 | assay: lipidAssay |
|---|
| 691 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 692 | |
|---|
| 693 | humanStudy.samples*.each { |
|---|
| 694 | new dbnp.clinicaldata.ClinicalFloatData( |
|---|
| 695 | assay: lipidAssayInstance, |
|---|
| 696 | measurement: ldlMeasurement, |
|---|
| 697 | sample: it.name, |
|---|
| 698 | value: Math.round(Math.random()*ldlMeasurement.detectableLimit) |
|---|
| 699 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 700 | |
|---|
| 701 | new dbnp.clinicaldata.ClinicalFloatData( |
|---|
| 702 | assay: lipidAssayInstance, |
|---|
| 703 | measurement: hdlMeasurement, |
|---|
| 704 | sample: it.name, |
|---|
| 705 | value: Math.round(Math.random()*hdlMeasurement.detectableLimit) |
|---|
| 706 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 707 | } |
|---|
| 708 | */ |
|---|
| 709 | // Add assay to study capture module |
|---|
| 710 | |
|---|
| 711 | def clinicalModule = new AssayModule( |
|---|
| 712 | name: 'Clinical data', |
|---|
| 713 | type: AssayType.CLINICAL_DATA, |
|---|
| 714 | platform: 'clinical measurements', |
|---|
| 715 | url: 'http://localhost:8080/gscf' |
|---|
| 716 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 717 | |
|---|
| 718 | def lipidAssayRef = new Assay( |
|---|
| 719 | name: 'Lipid profiling', |
|---|
| 720 | module: clinicalModule, |
|---|
| 721 | externalAssayId: 0 |
|---|
| 722 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 723 | |
|---|
| 724 | humanStudy.samples*.each { |
|---|
| 725 | lipidAssayRef.addToSamples(it) |
|---|
| 726 | } |
|---|
| 727 | lipidAssayRef.save() |
|---|
| 728 | |
|---|
| 729 | humanStudy.addToAssays(lipidAssayRef); |
|---|
| 730 | humanStudy.save() |
|---|
| 731 | |
|---|
| 732 | mouseStudy.addToAssays(lipidAssayRef); |
|---|
| 733 | mouseStudy.save() |
|---|
| 734 | |
|---|
| 735 | } |
|---|
| 736 | } |
|---|
| 737 | |
|---|
| 738 | // Ontologies must be connected to the templatefields in runtime |
|---|
| 739 | // because the Ontology.findByNcboId is not available otherwise |
|---|
| 740 | TemplateEntity.getField( Subject.domainFields, 'species' ).ontologies = [Ontology.findByNcboId(1132)] |
|---|
| 741 | TemplateEntity.getField( Sample.domainFields, 'material' ).ontologies = [Ontology.findByNcboId(1005)] |
|---|
| 742 | |
|---|
| 743 | } |
|---|
| 744 | |
|---|
| 745 | def destroy = { |
|---|
| 746 | } |
|---|
| 747 | } |
|---|
