| 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 | |
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| 6 | /** |
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| 7 | * Application Bootstrapper |
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| 8 | * @Author Jeroen Wesbeek |
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| 9 | * @Since 20091021 |
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| 10 | * |
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| 11 | * Revision information: |
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| 12 | * $Rev: 370 $ |
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| 13 | * $Author: roberth $ |
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| 14 | * $Date: 2010-04-22 07:31:50 +0000 (do, 22 apr 2010) $ |
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| 15 | */ |
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| 16 | class BootStrap { |
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| 17 | def init = {servletContext -> |
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| 18 | // define timezone |
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| 19 | System.setProperty('user.timezone', 'CET') |
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| 20 | |
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| 21 | // we could also check if we are in development by GrailsUtil.environment == GrailsApplication.ENV_DEVELOPMENT |
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| 22 | if (Study.count() == 0) { |
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| 23 | println ".development bootstrapping..."; |
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| 24 | |
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| 25 | // add NCBI species ontology |
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| 26 | println ".adding NCBI species ontology" |
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| 27 | def speciesOntology = new Ontology( |
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| 28 | name: 'NCBI organismal classification', |
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| 29 | description: 'A taxonomic classification of living organisms and associated artifacts for their controlled description within the context of databases.', |
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| 30 | url: 'http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/', |
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| 31 | versionNumber: '1.2', |
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| 32 | ncboId: '1132', |
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| 33 | ncboVersionedId: '38802' |
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| 34 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 35 | |
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| 36 | // add TERMS |
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| 37 | println ".adding mouse term" |
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| 38 | def mouseTerm = new Term( |
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| 39 | name: 'Mus musculus', |
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| 40 | ontology: speciesOntology, |
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| 41 | accession: '10090' |
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| 42 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 43 | println ".adding human term" |
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| 44 | def humanTerm = new Term( |
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| 45 | name: 'Homo sapiens', |
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| 46 | ontology: speciesOntology, |
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| 47 | accession: '9606' |
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| 48 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 49 | |
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| 50 | // Create a few persons, roles and Affiliations |
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| 51 | println ".adding persons, roles and affiliations" |
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| 52 | def affiliation1 = new PersonAffiliation( |
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| 53 | name: "Science Institute NYC" |
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| 54 | ).save(); |
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| 55 | def affiliation2 = new PersonAffiliation( |
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| 56 | name: "InfoStats GmbH, Hamburg" |
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| 57 | ).save(); |
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| 58 | def role1 = new PersonRole( |
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| 59 | name: "Principal Investigator" |
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| 60 | ).save(); |
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| 61 | def role2 = new PersonRole( |
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| 62 | name: "Statician" |
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| 63 | ).save(); |
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| 64 | def person1 = new Person( |
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| 65 | lastName: "Scientist", |
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| 66 | firstName: "John", |
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| 67 | midInitials: "R", |
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| 68 | email: "john@scienceinstitute.com", |
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| 69 | phone: "1-555-3049", |
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| 70 | address: "First street 2,NYC" |
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| 71 | ) |
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| 72 | .addToAffiliations( affiliation1 ) |
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| 73 | .addToAffiliations( affiliation2 ) |
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| 74 | .save(); |
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| 75 | |
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| 76 | def person2 = new Person( |
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| 77 | lastName: "Statician", |
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| 78 | firstName: "Jane", |
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| 79 | midInitials: "W", |
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| 80 | email: "jane@statisticalcompany.de", |
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| 81 | phone: "49-555-8291", |
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| 82 | address: "Dritten strasse 38, Hamburg, Germany" |
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| 83 | ) |
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| 84 | .addToAffiliations( affiliation2 ) |
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| 85 | .save(); |
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| 86 | |
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| 87 | /* COMMENTED OUT BECAUSE IT BREAKS EVERYTHING AFTER REFACTORING THE DATAMODEL |
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| 88 | |
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| 89 | // ontologies |
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| 90 | def speciesOntology = new Ontology( |
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| 91 | name: 'NCBI Taxonomy', |
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| 92 | shortName: 'Taxon', |
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| 93 | url: 'http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncbi_taxonomy' |
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| 94 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 95 | |
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| 96 | def humanBodyOntology = new Ontology( |
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| 97 | name: 'Foundational Model of Anatomy', |
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| 98 | shortName: 'HumanBody', |
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| 99 | url: 'http://bioportal.bioontology.org/ontologies/39966' |
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| 100 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 101 | |
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| 102 | def nciOntology = new Ontology( |
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| 103 | name: 'NCI Thesaurus', |
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| 104 | shortName: 'NCI', |
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| 105 | url: 'http://bioportal.bioontology.org/ontologies/42331' |
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| 106 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 107 | |
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| 108 | // terms |
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| 109 | def mouseTerm = new Term( |
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| 110 | name: 'Mus musculus', |
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| 111 | ontology: speciesOntology, |
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| 112 | accession: '10090' |
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| 113 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 114 | def humanTerm = new Term( |
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| 115 | name: 'Homo sapiens', |
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| 116 | ontology: speciesOntology, |
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| 117 | accession: '9606' |
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| 118 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 119 | def arabTerm = new Term( |
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| 120 | name: 'Arabidopsis thaliana', |
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| 121 | ontology: speciesOntology, |
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| 122 | accession: '3702' |
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| 123 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 124 | |
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| 125 | def bloodTerm = new Term( |
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| 126 | name: 'Portion of blood', |
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| 127 | ontology: humanBodyOntology, |
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| 128 | accession: '9670' |
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| 129 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 130 | |
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| 131 | def c57bl6Term = new Term( |
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| 132 | name: 'C57BL/6 Mouse', |
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| 133 | ontology: nciOntology, |
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| 134 | accession: 'C14424' |
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| 135 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 136 | |
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| 137 | def madmaxOntology = new Ontology( |
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| 138 | name: 'Madmax ontology', |
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| 139 | shortName: 'MDMX', |
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| 140 | url: 'madmax.bioinformatics.nl' |
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| 141 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 142 | |
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| 143 | def treatmentTerm = new Term( |
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| 144 | name: 'ExperimentalProtocol', |
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| 145 | ontology: madmaxOntology, |
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| 146 | accession: 'P-MDMXGE-264' |
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| 147 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 148 | |
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| 149 | def dietProtocol = new Protocol( |
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| 150 | name: 'Diet treatment Protocol NuGO PPS3 leptin module', |
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| 151 | reference: treatmentTerm |
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| 152 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 153 | |
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| 154 | def boostProtocol = new Protocol( |
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| 155 | name: 'Boost treatment Protocol NuGO PPS3 leptin module', |
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| 156 | reference: treatmentTerm |
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| 157 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 158 | |
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| 159 | def fastingProtocol = new Protocol( |
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| 160 | name: 'Fasting', |
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| 161 | reference: treatmentTerm |
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| 162 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 163 | |
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| 164 | |
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| 165 | // ParameterStringListItems |
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| 166 | def oil10= new ParameterStringListItem( |
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| 167 | name: '10% fat (palm oil)' |
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| 168 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 169 | def oil45= new ParameterStringListItem( |
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| 170 | name: '45% fat (palm oil)' |
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| 171 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 172 | def vehicle= new ParameterStringListItem( |
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| 173 | name: 'Vehicle' |
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| 174 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 175 | def leptin= new ParameterStringListItem( |
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| 176 | name: 'Leptin' |
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| 177 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 178 | |
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| 179 | |
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| 180 | dietProtocol |
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| 181 | .addToParameters(new ProtocolParameter( |
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| 182 | name: 'Diet', |
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| 183 | type: ProtocolParameterType.STRINGLIST, |
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| 184 | listEntries: [oil10,oil45])) |
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| 185 | .save() |
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| 186 | |
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| 187 | boostProtocol |
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| 188 | .addToParameters(new ProtocolParameter( |
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| 189 | name: 'Compound', |
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| 190 | type: ProtocolParameterType.STRINGLIST, |
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| 191 | listEntries: [vehicle,leptin])) |
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| 192 | .save() |
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| 193 | |
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| 194 | fastingProtocol |
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| 195 | .addToParameters(new ProtocolParameter( |
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| 196 | name: 'Fasting period', |
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| 197 | type: ProtocolParameterType.STRING)) |
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| 198 | .save() |
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| 199 | |
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| 200 | |
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| 201 | // sampling event protocols |
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| 202 | |
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| 203 | def liverSamplingProtocol = new Protocol( |
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| 204 | name: 'Liver sampling' |
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| 205 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 206 | |
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| 207 | liverSamplingProtocol |
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| 208 | .addToParameters(new ProtocolParameter( |
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| 209 | name: 'Sample weight', |
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| 210 | unit: 'mg', |
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| 211 | type: ProtocolParameterType.FLOAT)) |
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| 212 | .save() |
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| 213 | |
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| 214 | def bloodSamplingProtocol = new Protocol( |
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| 215 | name: 'Blood sampling' |
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| 216 | ).with { if (!validate()) { errors.each { println it} } else save()} |
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| 217 | |
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| 218 | bloodSamplingProtocol |
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| 219 | .addToParameters(new ProtocolParameter( |
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| 220 | name: 'Sample volume', |
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| 221 | unit: 'ml', |
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| 222 | type: ProtocolParameterType.FLOAT)) |
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| 223 | .save() |
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| 224 | */ |
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| 225 | // create system user |
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| 226 | |
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| 227 | /*def systemUser = userService.createUser(InstanceGenerator.user( |
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| 228 | username: 'system', |
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| 229 | pass: 'system', |
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| 230 | passConfirm: 'system', |
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| 231 | enabled: true |
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| 232 | ))*/ |
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| 233 | |
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| 234 | |
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| 235 | def genderField = new TemplateField( |
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| 236 | name: 'Gender',type: TemplateFieldType.STRINGLIST, |
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| 237 | listEntries: [new TemplateFieldListItem(name:'Male'),new TemplateFieldListItem(name: 'Female')]) |
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| 238 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 239 | |
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| 240 | def ageField = new TemplateField( |
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| 241 | name: 'Age (years)',type: TemplateFieldType.INTEGER,unit: 'years') |
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| 242 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 243 | |
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| 244 | def genotypeField = new TemplateField( |
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| 245 | name: 'Genotype', type: TemplateFieldType.ONTOLOGYTERM) |
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| 246 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 247 | |
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| 248 | def genotypeTypeField = new TemplateField( |
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| 249 | name: 'Genotype type',type: TemplateFieldType.STRINGLIST, |
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| 250 | listEntries: [new TemplateFieldListItem(name:'transgenic'), |
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| 251 | new TemplateFieldListItem(name:'knock-out'), |
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| 252 | new TemplateFieldListItem(name:'knock-in')]) |
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| 253 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 254 | |
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| 255 | |
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| 256 | // Nutritional study template |
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| 257 | |
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| 258 | println ".adding academic study template..." |
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| 259 | def studyTemplate = new Template( |
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| 260 | name: 'Academic study', entity: dbnp.studycapturing.Study) |
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| 261 | //.addToFields(new TemplateField(name: 'Description',type: TemplateFieldType.TEXT)) |
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| 262 | .addToFields(new TemplateField(name: 'Study code',type: TemplateFieldType.STRING)) |
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| 263 | .addToFields(new TemplateField(name: 'Objectives',type: TemplateFieldType.TEXT)) |
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| 264 | .addToFields(new TemplateField(name: 'Consortium',type: TemplateFieldType.STRING)) |
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| 265 | .addToFields(new TemplateField(name: 'Cohort name',type: TemplateFieldType.STRING)) |
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| 266 | .addToFields(new TemplateField(name: 'Time zone',type: TemplateFieldType.STRING)) |
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| 267 | .addToFields(new TemplateField(name: 'Responsible scientist',type: TemplateFieldType.STRING)) |
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| 268 | .addToFields(new TemplateField(name: 'Lab id',type: TemplateFieldType.STRING)) |
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| 269 | .addToFields(new TemplateField(name: 'Institute',type: TemplateFieldType.STRING)) |
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| 270 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 271 | |
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| 272 | // Mouse template |
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| 273 | println ".adding mouse subject template..." |
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| 274 | def mouseTemplate = new Template( |
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| 275 | name: 'Mouse', entity: dbnp.studycapturing.Subject) |
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| 276 | .addToFields(new TemplateField( |
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| 277 | name: 'Strain', type: TemplateFieldType.ONTOLOGYTERM)) |
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| 278 | .addToFields(genotypeField) |
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| 279 | .addToFields(genotypeTypeField) |
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| 280 | .addToFields(genderField) |
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| 281 | .addToFields(new TemplateField( |
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| 282 | name: 'Age (weeks)', type: TemplateFieldType.INTEGER, unit: 'weeks')) |
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| 283 | .addToFields(new TemplateField( |
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| 284 | name: 'Age type',type: TemplateFieldType.STRINGLIST, |
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| 285 | listEntries: [new TemplateFieldListItem(name:'postnatal'),new TemplateFieldListItem(name:'embryonal')])) |
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| 286 | .addToFields(new TemplateField( |
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| 287 | name: 'Cage',type: TemplateFieldType.STRING)) |
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| 288 | .addToFields(new TemplateField( |
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| 289 | name: '#Mice in cage',type: TemplateFieldType.INTEGER)) |
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| 290 | .addToFields(new TemplateField( |
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| 291 | name: 'Litter size',type: TemplateFieldType.INTEGER)) |
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| 292 | .addToFields(new TemplateField( |
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| 293 | name: 'Weight (g)', type: TemplateFieldType.DOUBLE, unit: 'gram')) |
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| 294 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 295 | |
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| 296 | // Human template |
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| 297 | println ".adding human subject template..." |
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| 298 | def humanTemplate = new Template( |
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| 299 | name: 'Human', entity: dbnp.studycapturing.Subject) |
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| 300 | .addToFields(genderField) |
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| 301 | .addToFields(ageField) |
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| 302 | .addToFields(new TemplateField( |
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| 303 | name: 'DOB',type: TemplateFieldType.DATE)) |
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| 304 | .addToFields(new TemplateField( |
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| 305 | name: 'Height',type: TemplateFieldType.DOUBLE, unit: 'm')) |
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| 306 | .addToFields(new TemplateField( |
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| 307 | name: 'Weight (kg)',type: TemplateFieldType.DOUBLE, unit: 'kg')) |
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| 308 | .addToFields(new TemplateField( |
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| 309 | name: 'BMI',type: TemplateFieldType.DOUBLE, unit: 'kg/m2')) |
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| 310 | .addToFields(new TemplateField( |
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| 311 | name: 'Race',type: TemplateFieldType.STRING)) |
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| 312 | .addToFields(new TemplateField( |
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| 313 | name: 'Waist circumference',type: TemplateFieldType.FLOAT, unit: 'cm')) |
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| 314 | .addToFields(new TemplateField( |
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| 315 | name: 'Hip circumference',type: TemplateFieldType.FLOAT, unit: 'cm')) |
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| 316 | .addToFields(new TemplateField( |
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| 317 | name: 'Systolic blood pressure',type: TemplateFieldType.FLOAT, unit: 'mmHg')) |
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| 318 | .addToFields(new TemplateField( |
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| 319 | name: 'Diastolic blood pressure',type: TemplateFieldType.FLOAT, unit: 'mmHg')) |
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| 320 | .addToFields(new TemplateField( |
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| 321 | name: 'Heart rate',type: TemplateFieldType.FLOAT, unit: 'beats/min')) |
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| 322 | .addToFields(new TemplateField( |
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| 323 | name: 'Run-in-food',type: TemplateFieldType.TEXT)) |
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| 324 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 325 | |
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| 326 | |
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| 327 | def sampleDescriptionField = new TemplateField( |
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| 328 | name: 'Description',type: TemplateFieldType.TEXT) |
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| 329 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 330 | def sampleTypeField = new TemplateField( |
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| 331 | name: 'SampleType',type: TemplateFieldType.STRING) |
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| 332 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 333 | def sampleProtocolField = new TemplateField( |
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| 334 | name: 'SampleProtocol',type: TemplateFieldType.STRING) |
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| 335 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 336 | def sampleVialTextField = new TemplateField( |
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| 337 | name: 'Text on vial',type: TemplateFieldType.STRING) |
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| 338 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 339 | |
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| 340 | // Human sample template |
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| 341 | def humanSampleTemplate = new Template( |
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| 342 | name: 'Human tissue sample', entity: dbnp.studycapturing.Sample) |
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| 343 | .addToFields(sampleDescriptionField) |
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| 344 | .addToFields(sampleTypeField) |
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| 345 | .addToFields(sampleProtocolField) |
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| 346 | .addToFields(sampleVialTextField) |
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| 347 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 348 | |
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| 349 | //Plant template |
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| 350 | def plantTemplate = new Template( |
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| 351 | name: 'Plant template', entity: dbnp.studycapturing.Subject) |
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| 352 | .addToFields(new TemplateField( |
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| 353 | name: 'Variety', type: TemplateFieldType.STRING)) |
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| 354 | .addToFields(new TemplateField( |
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| 355 | name: 'Ecotype', type: TemplateFieldType.STRING)) |
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| 356 | .addToFields(genotypeField) |
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| 357 | .addToFields(genotypeTypeField) |
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| 358 | .addToFields(new TemplateField( |
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| 359 | name: 'Growth location', type: TemplateFieldType.STRINGLIST, |
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| 360 | listEntries: [new TemplateFieldListItem(name:'Greenhouse'),new TemplateFieldListItem(name: 'Field')])) |
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| 361 | .addToFields(new TemplateField( |
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| 362 | name: 'Room', type: TemplateFieldType.STRING, |
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| 363 | comment: 'Chamber number in case of Greenhouse')) |
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| 364 | .addToFields(new TemplateField( |
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| 365 | name: 'Position X', type: TemplateFieldType.FLOAT)) |
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| 366 | .addToFields(new TemplateField( |
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| 367 | name: 'Position Y', type: TemplateFieldType.FLOAT)) |
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| 368 | .addToFields(new TemplateField( |
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| 369 | name: 'Block', type: TemplateFieldType.STRING)) |
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| 370 | .addToFields(new TemplateField( |
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| 371 | name: 'Temperature at day', type: TemplateFieldType.FLOAT)) |
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| 372 | .addToFields(new TemplateField( |
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| 373 | name: 'Temperature at night', type: TemplateFieldType.FLOAT)) |
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| 374 | .addToFields(new TemplateField( |
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| 375 | name: 'Photo period', type: TemplateFieldType.STRING)) |
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| 376 | .addToFields(new TemplateField( |
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| 377 | name: 'Light intensity', type: TemplateFieldType.STRING)) |
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| 378 | .addToFields(new TemplateField( |
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| 379 | name: 'Start date', type: TemplateFieldType.DATE)) |
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| 380 | .addToFields(new TemplateField( |
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| 381 | name: 'Harvest date', type: TemplateFieldType.DATE)) |
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| 382 | .addToFields(new TemplateField( |
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| 383 | name: 'Growth type', type: TemplateFieldType.STRINGLIST, |
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| 384 | listEntries: [new TemplateFieldListItem(name:'Standard'),new TemplateFieldListItem(name: 'Experimental')])) |
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| 385 | .addToFields(new TemplateField( |
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| 386 | name: 'Growth protocol', type: TemplateFieldType.TEXT)) |
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| 387 | .addToFields(new TemplateField( |
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| 388 | name: 'Harvest delay', type: TemplateFieldType.TEXT)) |
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| 389 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 390 | |
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| 391 | def plantSampleTemplate = new Template( |
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| 392 | name: 'Plant sample', entity: dbnp.studycapturing.Sample) |
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| 393 | .addToFields(sampleDescriptionField) |
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| 394 | .addToFields(sampleTypeField) |
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| 395 | .addToFields(sampleProtocolField) |
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| 396 | .addToFields(sampleVialTextField) |
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| 397 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 398 | |
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| 399 | |
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| 400 | // Event template |
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| 401 | def dietTreatmentTemplate = new Template( |
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| 402 | name: 'Diet treatment ', entity: dbnp.studycapturing.Event) |
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| 403 | .addToFields(sampleDescriptionField) |
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| 404 | .addToFields(new TemplateField( |
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| 405 | name: 'Diet', type: TemplateFieldType.STRING)) |
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| 406 | .with { if (!validate()) { errors.each { println it} } else save()} |
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| 407 | |
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| 408 | def boostTreatmentTemplate = new Template( |
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| 409 | name: 'Boost treatment ', entity: dbnp.studycapturing.Event) |
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| 410 | .addToFields(sampleDescriptionField) |
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| 411 | .addToFields(new TemplateField( |
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| 412 | name: 'Compound', type: TemplateFieldType.STRING)) |
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| 413 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 414 | |
|---|
| 415 | /* |
|---|
| 416 | //events |
|---|
| 417 | def eventDiet = new EventDescription( |
|---|
| 418 | name: 'Diet treatment', |
|---|
| 419 | description: 'Diet treatment (fat percentage)', |
|---|
| 420 | classification: treatmentTerm, |
|---|
| 421 | protocol: dietProtocol, |
|---|
| 422 | isSamplingEvent: false |
|---|
| 423 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 424 | |
|---|
| 425 | def eventBoost = new EventDescription( |
|---|
| 426 | name: 'Boost treatment', |
|---|
| 427 | description: 'Boost treatment (leptin or vehicle)', |
|---|
| 428 | classification: treatmentTerm, |
|---|
| 429 | protocol: boostProtocol, |
|---|
| 430 | isSamplingEvent: false |
|---|
| 431 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 432 | |
|---|
| 433 | def samplingEvent = new EventDescription( |
|---|
| 434 | name: 'Liver extraction', |
|---|
| 435 | description: 'Liver sampling for transcriptomics arrays', |
|---|
| 436 | protocol: liverSamplingProtocol, |
|---|
| 437 | isSamplingEvent: true |
|---|
| 438 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 439 | |
|---|
| 440 | def bloodSamplingEventDescription = new EventDescription( |
|---|
| 441 | name: 'Blood extraction', |
|---|
| 442 | description: 'Blood extraction targeted at lipid assays', |
|---|
| 443 | protocol: bloodSamplingProtocol, |
|---|
| 444 | isSamplingEvent: true |
|---|
| 445 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 446 | |
|---|
| 447 | |
|---|
| 448 | def fastingTreatment = new EventDescription( |
|---|
| 449 | name: 'Fasting treatment', |
|---|
| 450 | description: 'Fasting Protocol NuGO PPSH', |
|---|
| 451 | protocol: fastingProtocol, |
|---|
| 452 | isSamplingEvent: false |
|---|
| 453 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 454 | |
|---|
| 455 | println('Adding PPS3 study...') |
|---|
| 456 | */ |
|---|
| 457 | // studies |
|---|
| 458 | def exampleStudy = new Study( |
|---|
| 459 | template: studyTemplate, |
|---|
| 460 | title:"NuGO PPS3 mouse study leptin module", |
|---|
| 461 | code:"PPS3_leptin_module", |
|---|
| 462 | researchQuestion:"Leptin etc.", |
|---|
| 463 | ecCode:"2007117.c", |
|---|
| 464 | startDate: Date.parse('yyyy-MM-dd','2007-12-11') |
|---|
| 465 | ) |
|---|
| 466 | //.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." ) |
|---|
| 467 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 468 | |
|---|
| 469 | def exampleHumanStudy = new Study( |
|---|
| 470 | template: humanTemplate, |
|---|
| 471 | title:"Human example template", |
|---|
| 472 | code:"Human example code", |
|---|
| 473 | researchQuestion:"Leptin etc.", |
|---|
| 474 | ecCode:"2007117.c", |
|---|
| 475 | startDate: Date.parse('yyyy-MM-dd','2007-12-11') |
|---|
| 476 | ) |
|---|
| 477 | //.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." ) |
|---|
| 478 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 479 | |
|---|
| 480 | def evLF = new Event( |
|---|
| 481 | startTime: Date.parse('yyyy-MM-dd','2008-01-07'), |
|---|
| 482 | endTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
|---|
| 483 | template: dietTreatmentTemplate |
|---|
| 484 | ) |
|---|
| 485 | .setFieldValue( 'Diet','10% fat (palm oil)' ) |
|---|
| 486 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 487 | |
|---|
| 488 | def evHF = new Event( |
|---|
| 489 | startTime: Date.parse('yyyy-MM-dd','2008-01-07'), |
|---|
| 490 | endTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
|---|
| 491 | template: dietTreatmentTemplate |
|---|
| 492 | ) |
|---|
| 493 | .setFieldValue( 'Diet','45% fat (palm oil)' ) |
|---|
| 494 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 495 | |
|---|
| 496 | def evBV = new Event( |
|---|
| 497 | startTime: Date.parse('yyyy-MM-dd','2008-01-07'), |
|---|
| 498 | endTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
|---|
| 499 | template: boostTreatmentTemplate |
|---|
| 500 | ) |
|---|
| 501 | .setFieldValue( 'Compound','Vehicle' ) |
|---|
| 502 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 503 | |
|---|
| 504 | def evBL = new Event( |
|---|
| 505 | startTime: Date.parse('yyyy-MM-dd','2008-01-07'), |
|---|
| 506 | endTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
|---|
| 507 | template: boostTreatmentTemplate |
|---|
| 508 | ) |
|---|
| 509 | .setFieldValue( 'Compound','Leptin' ) |
|---|
| 510 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 511 | |
|---|
| 512 | /* |
|---|
| 513 | def evLF4 = new Event( |
|---|
| 514 | startTime: Date.parse('yyyy-MM-dd','2008-01-07'), |
|---|
| 515 | endTime: Date.parse('yyyy-MM-dd','2008-02-04'), |
|---|
| 516 | eventDescription: eventDiet, |
|---|
| 517 | parameterStringValues: ['Diet':'10% fat (palm oil)'] |
|---|
| 518 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 519 | |
|---|
| 520 | def evHF4 = new Event( |
|---|
| 521 | startTime: Date.parse('yyyy-MM-dd','2008-01-07'), |
|---|
| 522 | endTime: Date.parse('yyyy-MM-dd','2008-02-04'), |
|---|
| 523 | eventDescription: eventDiet, |
|---|
| 524 | parameterStringValues: ['Diet':'45% fat (palm oil)'] |
|---|
| 525 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 526 | |
|---|
| 527 | def evBV4 = new Event( |
|---|
| 528 | startTime: Date.parse('yyyy-MM-dd','2008-01-07'), |
|---|
| 529 | endTime: Date.parse('yyyy-MM-dd','2008-02-04'), |
|---|
| 530 | eventDescription: eventBoost, |
|---|
| 531 | parameterStringValues: ['Compound':'Vehicle'] |
|---|
| 532 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 533 | |
|---|
| 534 | def evBL4 = new Event( |
|---|
| 535 | startTime: Date.parse('yyyy-MM-dd','2008-01-07'), |
|---|
| 536 | endTime: Date.parse('yyyy-MM-dd','2008-02-04'), |
|---|
| 537 | eventDescription: eventBoost, |
|---|
| 538 | parameterStringValues: ['Compound':'Leptin'] |
|---|
| 539 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 540 | |
|---|
| 541 | def evS = new SamplingEvent( |
|---|
| 542 | startTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
|---|
| 543 | endTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
|---|
| 544 | eventDescription: samplingEvent, |
|---|
| 545 | parameterFloatValues: ['Sample weight':5F] |
|---|
| 546 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 547 | |
|---|
| 548 | def evS4 = new SamplingEvent( |
|---|
| 549 | startTime: Date.parse('yyyy-MM-dd','2008-02-04'), |
|---|
| 550 | endTime: Date.parse('yyyy-MM-dd','2008-02-04'), |
|---|
| 551 | eventDescription: samplingEvent, |
|---|
| 552 | parameterFloatValues: ['Sample weight':5F] |
|---|
| 553 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 554 | */ |
|---|
| 555 | |
|---|
| 556 | // Add events to study |
|---|
| 557 | exampleStudy |
|---|
| 558 | .addToEvents(evLF) |
|---|
| 559 | .addToEvents(evHF) |
|---|
| 560 | .addToEvents(evBV) |
|---|
| 561 | .addToEvents(evBL) |
|---|
| 562 | /* |
|---|
| 563 | .addToEvents(evLF4) |
|---|
| 564 | .addToEvents(evHF4) |
|---|
| 565 | .addToEvents(evBV4) |
|---|
| 566 | .addToEvents(evBL4) |
|---|
| 567 | .addToSamplingEvents(evS) |
|---|
| 568 | .addToSamplingEvents(evS4) |
|---|
| 569 | */ |
|---|
| 570 | .save() |
|---|
| 571 | |
|---|
| 572 | def LFBV1 = new EventGroup(name:"10% fat + vehicle for 1 week") |
|---|
| 573 | .addToEvents(evLF) |
|---|
| 574 | .addToEvents(evBV) |
|---|
| 575 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 576 | |
|---|
| 577 | def LFBL1 = new EventGroup(name:"10% fat + leptin for 1 week") |
|---|
| 578 | .addToEvents(evLF) |
|---|
| 579 | .addToEvents(evBL) |
|---|
| 580 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 581 | |
|---|
| 582 | def HFBV1 = new EventGroup(name:"45% fat + vehicle for 1 week") |
|---|
| 583 | .addToEvents(evHF) |
|---|
| 584 | .addToEvents(evBV) |
|---|
| 585 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 586 | |
|---|
| 587 | def HFBL1 = new EventGroup(name:"45% fat + leptin for 1 week") |
|---|
| 588 | .addToEvents(evHF) |
|---|
| 589 | .addToEvents(evBL) |
|---|
| 590 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 591 | |
|---|
| 592 | /* |
|---|
| 593 | def LFBV4 = new EventGroup(name:"10% fat + vehicle for 4 weeks") |
|---|
| 594 | .addToEvents(evLF4) |
|---|
| 595 | .addToEvents(evBV4) |
|---|
| 596 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 597 | |
|---|
| 598 | def LFBL4 = new EventGroup(name:"10% fat + leptin for 4 weeks") |
|---|
| 599 | .addToEvents(evLF4) |
|---|
| 600 | .addToEvents(evBL4) |
|---|
| 601 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 602 | |
|---|
| 603 | def HFBV4 = new EventGroup(name:"45% fat + vehicle for 4 weeks") |
|---|
| 604 | .addToEvents(evHF4) |
|---|
| 605 | .addToEvents(evBV4) |
|---|
| 606 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 607 | |
|---|
| 608 | def HFBL4 = new EventGroup(name:"45% fat + leptin for 4 weeks") |
|---|
| 609 | .addToEvents(evHF4) |
|---|
| 610 | .addToEvents(evBL4) |
|---|
| 611 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 612 | */ |
|---|
| 613 | |
|---|
| 614 | // Add subjects and samples and compose EventGroups |
|---|
| 615 | |
|---|
| 616 | def x=1 |
|---|
| 617 | 40.times { |
|---|
| 618 | def currentSubject = new Subject( |
|---|
| 619 | name: "A" + x++, |
|---|
| 620 | species: mouseTerm, |
|---|
| 621 | template: mouseTemplate, |
|---|
| 622 | ) |
|---|
| 623 | .setFieldValue("Gender", "Male") |
|---|
| 624 | //.setFieldValue("Genotype", c57bl6Term) |
|---|
| 625 | .setFieldValue("Age (weeks)", 17) |
|---|
| 626 | .setFieldValue("Cage", "" + (int)(x/2)) |
|---|
| 627 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 628 | |
|---|
| 629 | exampleStudy.addToSubjects(currentSubject) |
|---|
| 630 | .with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 631 | |
|---|
| 632 | // Add subject to appropriate EventGroup |
|---|
| 633 | /* |
|---|
| 634 | if (x > 70) { HFBL4.addToSubjects(currentSubject).save() } |
|---|
| 635 | else if (x > 60) { HFBV4.addToSubjects(currentSubject).save() } |
|---|
| 636 | else if (x > 50) { LFBL4.addToSubjects(currentSubject).save() } |
|---|
| 637 | else if (x > 40) { LFBV4.addToSubjects(currentSubject).save() } |
|---|
| 638 | else if (x > 30) { HFBL1.addToSubjects(currentSubject).save() } |
|---|
| 639 | else if (x > 20) { HFBV1.addToSubjects(currentSubject).save() } |
|---|
| 640 | else if (x > 10) { LFBL1.addToSubjects(currentSubject).save() } |
|---|
| 641 | else { LFBV1.addToSubjects(currentSubject).save() } |
|---|
| 642 | */ |
|---|
| 643 | |
|---|
| 644 | if (x > 30) { HFBL1.addToSubjects(currentSubject).save() } |
|---|
| 645 | else if (x > 20) { HFBV1.addToSubjects(currentSubject).save() } |
|---|
| 646 | else if (x > 10) { LFBL1.addToSubjects(currentSubject).save() } |
|---|
| 647 | else { LFBV1.addToSubjects(currentSubject).save() } |
|---|
| 648 | |
|---|
| 649 | } |
|---|
| 650 | |
|---|
| 651 | // Add EventGroups to study |
|---|
| 652 | exampleStudy |
|---|
| 653 | .addToEventGroups(LFBV1) |
|---|
| 654 | .addToEventGroups(LFBL1) |
|---|
| 655 | .addToEventGroups(HFBV1) |
|---|
| 656 | .addToEventGroups(HFBL1) |
|---|
| 657 | //.addToEventGroups(LFBV4) |
|---|
| 658 | //.addToEventGroups(LFBL4) |
|---|
| 659 | //.addToEventGroups(HFBV4) |
|---|
| 660 | //.addToEventGroups(HFBL4) |
|---|
| 661 | |
|---|
| 662 | // Add persons to study |
|---|
| 663 | def studyperson1 = new StudyPerson( person: person1, role: role1 ).save(); |
|---|
| 664 | def studyperson2 = new StudyPerson( person: person2, role: role2 ).save(); |
|---|
| 665 | |
|---|
| 666 | exampleStudy |
|---|
| 667 | .addToPersons( studyperson1 ) |
|---|
| 668 | .addToPersons( studyperson2 ) |
|---|
| 669 | .save() |
|---|
| 670 | |
|---|
| 671 | /* |
|---|
| 672 | println 'Adding PPSH study' |
|---|
| 673 | |
|---|
| 674 | def humanStudy = new Study( |
|---|
| 675 | template: studyTemplate, |
|---|
| 676 | title:"NuGO PPS human study", |
|---|
| 677 | code:"PPSH", |
|---|
| 678 | researchQuestion:"How much are fasting plasma and urine metabolite levels affected by prolonged fasting ?", |
|---|
| 679 | description:"Human study", |
|---|
| 680 | ecCode:"unknown", |
|---|
| 681 | startDate: Date.parse('yyyy-MM-dd','2009-01-01') |
|---|
| 682 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 683 | |
|---|
| 684 | def fastingEvent = new Event( |
|---|
| 685 | startTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
|---|
| 686 | endTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
|---|
| 687 | eventDescription: fastingTreatment, |
|---|
| 688 | parameterStringValues: ['Fasting period':'8h']); |
|---|
| 689 | |
|---|
| 690 | def bloodSamplingEvent = new SamplingEvent( |
|---|
| 691 | startTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
|---|
| 692 | endTime: Date.parse('yyyy-MM-dd','2008-01-14'), |
|---|
| 693 | eventDescription: bloodSamplingEventDescription, |
|---|
| 694 | parameterFloatValues: ['Sample volume':4.5F]); |
|---|
| 695 | |
|---|
| 696 | def rootGroup = new EventGroup(name: 'Root group'); |
|---|
| 697 | rootGroup.addToEvents fastingEvent |
|---|
| 698 | rootGroup.addToEvents bloodSamplingEvent |
|---|
| 699 | rootGroup.save() |
|---|
| 700 | |
|---|
| 701 | def y = 1 |
|---|
| 702 | 11.times { |
|---|
| 703 | def currentSubject = new Subject( |
|---|
| 704 | name: "" + y++, |
|---|
| 705 | species: humanTerm, |
|---|
| 706 | template: humanTemplate).setFieldValue("Gender", (boolean) (x / 2) ? "Male" : "Female").setFieldValue("DOB", new java.text.SimpleDateFormat("dd-mm-yy").parse("01-02-19" + (10 + (int) (Math.random() * 80)))).setFieldValue("Age (years)", 30).setFieldValue("Height", Math.random() * 2F).setFieldValue("Weight (kg)", Math.random() * 150F).setFieldValue("BMI", 20 + Math.random() * 10F).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 707 | |
|---|
| 708 | rootGroup.addToSubjects currentSubject |
|---|
| 709 | rootGroup.save() |
|---|
| 710 | |
|---|
| 711 | def currentSample = new Sample( |
|---|
| 712 | name: currentSubject.name + '_B', |
|---|
| 713 | material: bloodTerm, |
|---|
| 714 | parentSubject: currentSubject, |
|---|
| 715 | parentEvent: bloodSamplingEvent); |
|---|
| 716 | |
|---|
| 717 | |
|---|
| 718 | humanStudy.addToSubjects(currentSubject).addToSamples(currentSample).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 719 | } |
|---|
| 720 | |
|---|
| 721 | humanStudy.addToEvents(fastingEvent) |
|---|
| 722 | humanStudy.addToSamplingEvents(bloodSamplingEvent) |
|---|
| 723 | humanStudy.addToEventGroups rootGroup |
|---|
| 724 | humanStudy.save() |
|---|
| 725 | |
|---|
| 726 | // Add clinical data |
|---|
| 727 | |
|---|
| 728 | def lipidAssay = new dbnp.clinicaldata.ClinicalAssay( |
|---|
| 729 | name: 'Lipid profile', |
|---|
| 730 | approved: true |
|---|
| 731 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 732 | |
|---|
| 733 | def ldlMeasurement = new dbnp.clinicaldata.ClinicalMeasurement( |
|---|
| 734 | name: 'LDL', |
|---|
| 735 | unit: 'mg/dL', |
|---|
| 736 | type: dbnp.data.FeatureType.QUANTITATIVE, |
|---|
| 737 | referenceValues: '100 mg/dL', |
|---|
| 738 | detectableLimit: 250, |
|---|
| 739 | isDrug: false, isIntake: true, inSerum: true |
|---|
| 740 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 741 | |
|---|
| 742 | def hdlMeasurement = new dbnp.clinicaldata.ClinicalMeasurement( |
|---|
| 743 | name: 'HDL', |
|---|
| 744 | unit: 'mg/dL', |
|---|
| 745 | type: dbnp.data.FeatureType.QUANTITATIVE, |
|---|
| 746 | referenceValues: '50 mg/dL', |
|---|
| 747 | detectableLimit: 100, |
|---|
| 748 | isDrug: false, isIntake: true, inSerum: true |
|---|
| 749 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 750 | |
|---|
| 751 | lipidAssay.addToMeasurements ldlMeasurement |
|---|
| 752 | lipidAssay.addToMeasurements hdlMeasurement |
|---|
| 753 | |
|---|
| 754 | def lipidAssayInstance = new dbnp.clinicaldata.ClinicalAssayInstance( |
|---|
| 755 | assay: lipidAssay |
|---|
| 756 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 757 | |
|---|
| 758 | humanStudy.samples*.each { |
|---|
| 759 | new dbnp.clinicaldata.ClinicalFloatData( |
|---|
| 760 | assay: lipidAssayInstance, |
|---|
| 761 | measurement: ldlMeasurement, |
|---|
| 762 | sample: it.name, |
|---|
| 763 | value: Math.round(Math.random()*ldlMeasurement.detectableLimit) |
|---|
| 764 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 765 | |
|---|
| 766 | new dbnp.clinicaldata.ClinicalFloatData( |
|---|
| 767 | assay: lipidAssayInstance, |
|---|
| 768 | measurement: hdlMeasurement, |
|---|
| 769 | sample: it.name, |
|---|
| 770 | value: Math.round(Math.random()*hdlMeasurement.detectableLimit) |
|---|
| 771 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 772 | } |
|---|
| 773 | |
|---|
| 774 | // Add assay to study capture module |
|---|
| 775 | |
|---|
| 776 | def clinicalModule = new AssayModule( |
|---|
| 777 | name: 'Clinical data', |
|---|
| 778 | type: AssayType.CLINICAL_DATA, |
|---|
| 779 | platform: 'clinical measurements', |
|---|
| 780 | url: 'http://localhost:8080/gscf' |
|---|
| 781 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 782 | |
|---|
| 783 | def lipidAssayRef = new Assay( |
|---|
| 784 | name: 'Lipid profiling', |
|---|
| 785 | module: clinicalModule, |
|---|
| 786 | externalAssayId: lipidAssayInstance.id |
|---|
| 787 | ).with { if (!validate()) { errors.each { println it} } else save()} |
|---|
| 788 | |
|---|
| 789 | humanStudy.samples*.each { |
|---|
| 790 | lipidAssayRef.addToSamples(it) |
|---|
| 791 | } |
|---|
| 792 | lipidAssayRef.save() |
|---|
| 793 | |
|---|
| 794 | humanStudy.addToAssays(lipidAssayRef); |
|---|
| 795 | humanStudy.save() |
|---|
| 796 | */ |
|---|
| 797 | } |
|---|
| 798 | } |
|---|
| 799 | |
|---|
| 800 | def destroy = { |
|---|
| 801 | } |
|---|
| 802 | } |
|---|
