Changeset 1604
- Timestamp:
- Mar 8, 2011, 6:01:16 PM (13 years ago)
- File:
-
- 1 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/grails-app/conf/dbnp/configuration/ExampleTemplates.groovy
r1588 r1604 66 66 ncboId: '1007', 67 67 ncboVersionedId: '44746' 68 ).save(failOnError:true )68 ).save(failOnError:true, flush:true) 69 69 70 70 } … … 666 666 new TemplateFieldListItem(name: 'HPLC') 667 667 ]) 668 ).save(failOnError:true )668 ).save(failOnError:true, flush:true) 669 669 } 670 670 671 671 } 672 673 ///**674 // * @Author kees675 // * @Since Jun 25, 2010676 // *677 // * Revision information:678 // * $Rev$679 // * $Author$680 // * $Date$681 // */682 //package dbnp.configuration683 //684 //685 //import dbnp.studycapturing.*686 //import org.dbnp.gdt.*687 //import org.codehaus.groovy.grails.commons.GrailsApplication688 //689 //class ExampleTemplates {690 //691 // /**692 // * Add the ontologies that are necessary for the templates below manually693 // * This function can be called to avoid the HTTP requests to BioPortal each time694 // * (e.g. in development or automated test environments)695 // */696 // public static void initTemplateOntologies() {697 // "inserting initial ontologies".grom()698 //699 // // If running in development or test mode, add ontologies manually to speed up development and allow running offline700 // if (grails.util.GrailsUtil.environment == GrailsApplication.ENV_DEVELOPMENT || grails.util.GrailsUtil.environment == GrailsApplication.ENV_TEST) {701 //702 // // add Species ontology which is used for a.o. the Subject domain field 'species'703 // def speciesOntology = new Ontology(704 // name: 'NCBI organismal classification',705 // description: 'A taxonomic classification of living organisms and associated artifacts for their controlled description within the context of databases.',706 // url: 'http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/',707 // versionNumber: '1.2',708 // ncboId: '1132',709 // ncboVersionedId: '38802'710 // ).with { if (!validate()) { errors.each { println it} } else save()}711 //712 // // add Sample>material ontology713 // def brendaOntology = new Ontology(714 // name: 'BRENDA tissue / enzyme source',715 // 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.',716 // url: 'http://www.brenda-enzymes.info',717 // versionNumber: '1.3',718 // ncboId: '1005',719 // ncboVersionedId: '40643'720 // ).with { if (!validate()) { errors.each { println it} } else save()}721 //722 // // add NCI ontology which is used in Mouse genotype template field723 // def nciOntology = new Ontology(724 // name: 'NCI Thesaurus',725 // description: 'A vocabulary for clinical care, translational and basic research, and public information and administrative activities.',726 // url: 'http://ncicb.nci.nih.gov/core/EVS',727 // versionNumber: '10.03',728 // ncboId: '1032',729 // ncboVersionedId: '42838'730 // ).with { if (!validate()) { errors.each { println it} } else save()}731 //732 // // add CHEBI ontology which is used for describing chemicals in e.g. events733 // def chebiOntology = new Ontology(734 // name: 'Chemical entities of biological interest',735 // description: 'A structured classification of chemical compounds of biological relevance.',736 // url: 'http://www.ebi.ac.uk/chebi',737 // versionNumber: '1.73',738 // ncboId: '1007',739 // ncboVersionedId: '44746'740 // ).with { if (!validate()) { errors.each { println it} } else save()}741 //742 // }743 // // otherwise, this may be a production demo instance, so initialize the ontologies dynamically from BioPortal744 // else {745 //746 // def speciesOntology = Ontology.getOrCreateOntologyByNcboId(1132)747 // def brendaOntology = Ontology.getOrCreateOntologyByNcboId(1005)748 // def nciOntology = Ontology.getOrCreateOntologyByNcboId(1032)749 // def chebiOntology = Ontology.getOrCreateOntologyByNcboId(1007)750 // }751 // }752 //753 //754 // /**755 // * Add example templates, this function would normally be called on an empty database756 // */757 // public static void initTemplates() {758 // "inserting initial templates".grom()759 //760 // def genderField = new TemplateField(761 // name: 'Gender',type: TemplateFieldType.STRINGLIST, entity: Subject,762 // listEntries: [new TemplateFieldListItem(name:'Male'),new TemplateFieldListItem(name: 'Female'),new TemplateFieldListItem(name: 'Unknown')])763 // .with { if (!validate()) { errors.each { println it} } else save()}764 //765 // def ageField = new TemplateField(766 // name: 'Age',type: TemplateFieldType.LONG,entity: Subject,unit: 'years',comment: 'Either include age at the start of the study or date of birth (if known)')767 // .with { if (!validate()) { errors.each { println it} } else save()}768 //769 // def genotypeField = new TemplateField(770 // name: 'Genotype', type: TemplateFieldType.ONTOLOGYTERM,entity: Subject,771 // comment: 'If present, indicate the genetic variance of the subject (e.g., mutagenized populations,knock-out/in,transgene etc)')772 // .with { if (!validate()) { errors.each { println it} } else save()}773 //774 // def genotypeTypeField = new TemplateField(775 // name: 'Genotype type',type: TemplateFieldType.STRINGLIST,entity: Subject,776 // listEntries: [new TemplateFieldListItem(name:'wildtype'),777 // new TemplateFieldListItem(name:'transgenic'),778 // new TemplateFieldListItem(name:'knock-out'),779 // new TemplateFieldListItem(name:'knock-in')],780 // comment: 'If a genotype was specified, please indicate here the type of the genotype')781 // .with { if (!validate()) { errors.each { println it} } else save()}782 //783 // def varietyField = new TemplateField(784 // name: 'Variety', type: TemplateFieldType.STRING,entity: Subject,785 // comment: 'taxonomic category consisting of members of a species that differ from others of the same species in minor but heritable characteristics')786 // .with { if (!validate()) { errors.each { println it} } else save()}787 //788 // def ecotypeField = new TemplateField(789 // name: 'Ecotype', type: TemplateFieldType.STRING,entity: Subject,790 // comment: 'a type or subspecies of life that is especially well adapted to a certain environment'791 // )792 // .with { if (!validate()) { errors.each { println it} } else save()}793 //794 // // Nutritional study template795 // def studyTemplate = new Template(796 // name: 'Academic study',797 // entity: dbnp.studycapturing.Study798 // )799 // .addToFields(new TemplateField(name: 'Objectives',type: TemplateFieldType.TEXT,entity: Study,comment:'Fill out the aim or questions of the study'))800 // .addToFields(new TemplateField(name: 'Consortium',type: TemplateFieldType.STRING,entity: Study,comment:'If the study was performed within a consortium (e.g. NMC, NuGO), you can indicate this here'))801 // .addToFields(new TemplateField(name: 'Cohort name',type: TemplateFieldType.STRING,entity: Study,comment:'If a cohort was used the name or code of the cohort can be define here (define a cohort template)'))802 // .addToFields(new TemplateField(name: 'Lab id',type: TemplateFieldType.STRING,entity: Study,comment:'In which lab was the study performed; indicate the roomnumber.'))803 // .addToFields(new TemplateField(name: 'Institute',type: TemplateFieldType.STRING,entity: Study,comment:'In which institute was the study performed; indicate the full address information (to be replaced by persons-affiliations?)'))804 // .addToFields(new TemplateField(name: 'Study protocol',type: TemplateFieldType.FILE,entity: Study,comment:'Optionally attach a file in which the protocol in the study is described'))805 // .with { if (!validate()) { errors.each { println it} } else save()}806 //807 // // Mouse template808 // def mouseTemplate = new Template(809 // name: 'Mouse', entity: dbnp.studycapturing.Subject)810 // .addToFields(new TemplateField(811 // name: 'Strain', type: TemplateFieldType.ONTOLOGYTERM, ontologies: [Ontology.getOrCreateOntologyByNcboId(1032)], entity: Subject, comment: "This is an ontology term, if the right strain is not in the list please add it with 'add more'"))812 // .addToFields(genotypeField)813 // .addToFields(genotypeTypeField)814 // .addToFields(genderField)815 // .addToFields(new TemplateField(816 // name: 'Age', type: TemplateFieldType.LONG, entity: Subject, unit: 'weeks', comment: 'Age at start of study'))817 // .addToFields(new TemplateField(818 // name: 'Age type',type: TemplateFieldType.STRINGLIST,entity: Subject,819 // listEntries: [new TemplateFieldListItem(name:'postnatal'),new TemplateFieldListItem(name:'embryonal')]))820 // .addToFields(new TemplateField(821 // name: 'Cage',type: TemplateFieldType.STRING,entity: Subject,comment:'Indicate the cage used for housing (type and/or size)'))822 // .addToFields(new TemplateField(823 // name: '#Mice in cage',type: TemplateFieldType.LONG,entity: Subject,comment:'If known, indicate the number of mice per cage'))824 // .addToFields(new TemplateField(825 // name: 'Litter size',type: TemplateFieldType.LONG,entity: Subject,comment:'If known, indicate the litter size of the litter from which the subject originates'))826 // .addToFields(new TemplateField(827 // name: 'Weight', type: TemplateFieldType.DOUBLE, unit: 'gram',entity: Subject,comment:'If known indicate the weight of the subject in grams at the start of the study'))828 // .with { if (!validate()) { errors.each { println it} } else save()}829 //830 // // Human template831 // def humanTemplate = new Template(832 // name: 'Human', entity: dbnp.studycapturing.Subject)833 // .addToFields(genderField)834 // .addToFields(ageField)835 // .addToFields(new TemplateField(836 // name: 'DOB',type: TemplateFieldType.DATE,entity: Subject,comment:'Date of birth'))837 // .addToFields(new TemplateField(838 // name: 'Height',type: TemplateFieldType.DOUBLE, entity: Subject, unit: 'm'))839 // .addToFields(new TemplateField(840 // name: 'Weight',type: TemplateFieldType.DOUBLE, entity: Subject, unit: 'kg'))841 // .addToFields(new TemplateField(842 // name: 'BMI',type: TemplateFieldType.DOUBLE, entity: Subject, unit: 'kg/m2',comment:'Body-mass-index'))843 // .addToFields(new TemplateField(844 // name: 'Race',type: TemplateFieldType.STRING,entity: Subject, comment:'If known and of interest the ethnic group can be indicated'))845 // .addToFields(new TemplateField(846 // name: 'Waist circumference',type: TemplateFieldType.DOUBLE, unit: 'cm',entity: Subject, comment:'The waist circumference is measured just above the hip bone. Indicate the measure at the start of the study.'))847 // .addToFields(new TemplateField(848 // name: 'Hip circumference',type: TemplateFieldType.DOUBLE, unit: 'cm',entity: Subject, 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.'))849 // .addToFields(new TemplateField(850 // name: 'Systolic blood pressure',type: TemplateFieldType.DOUBLE, unit: 'mmHg',entity: Subject, comment:'Indicate the levels at the start of the study in mmHG'))851 // .addToFields(new TemplateField(852 // name: 'Diastolic blood pressure',type: TemplateFieldType.DOUBLE, unit: 'mmHg',entity: Subject, comment:'Indicate the levels at the start of the study in mmHG'))853 // .addToFields(new TemplateField(854 // name: 'Heart rate',type: TemplateFieldType.DOUBLE, unit: 'beats/min',entity: Subject, comment:'Indicate the heart rate at the start of in study in beats per minute'))855 // .addToFields(new TemplateField(856 // name: 'Run-in-food',type: TemplateFieldType.TEXT,entity: Subject, comment:'If defined, give a short description of the food used before the measurements'))857 // .with { if (!validate()) { errors.each { println it} } else save()}858 //859 // def sampleRemarksField = new TemplateField(860 // name: 'Remarks',861 // type: TemplateFieldType.TEXT,862 // entity: Sample863 // )864 // .with { if (!validate()) { errors.each { println it} } else save()}865 //866 // def sampleVialTextField = new TemplateField(867 // name: 'Text on vial',868 // type: TemplateFieldType.STRING,869 // entity: Sample870 // )871 // .with { if (!validate()) { errors.each { println it} } else save()}872 //873 // // Human tissue sample template874 // def humanSampleTemplate = new Template(875 // name: 'Human tissue sample',876 // entity: dbnp.studycapturing.Sample877 // )878 // .addToFields(sampleRemarksField)879 // .addToFields(sampleVialTextField)880 // .addToFields(881 // new TemplateField(882 // name: 'Sample measured weight',883 // unit: 'mg',884 // type: TemplateFieldType.DOUBLE,885 // entity: Sample886 // )887 // )888 // .with { if (!validate()) { errors.each { println it} } else save()}889 //890 // // Human blood sample template891 // def humanBloodSampleTemplate = new Template(892 // name: 'Human blood sample',893 // entity: dbnp.studycapturing.Sample894 // )895 // .addToFields(sampleRemarksField)896 // .addToFields(sampleVialTextField)897 // .addToFields(898 // new TemplateField(899 // name: 'Sample measured volume',900 // unit: 'ml',901 // type: TemplateFieldType.DOUBLE,902 // entity: Sample903 // )904 // )905 // .with { if (!validate()) { errors.each { println it} } else save()}906 //907 //908 // /*909 // * Add NMC - DCL Sample Mapping Template910 // * by Michael van Vliet911 // *912 // * For the Pilot running in Leiden (NOV2010)913 // */914 // def sampleDCLTextField = new TemplateField(915 // name: 'DCL Sample Reference',916 // type: TemplateFieldType.STRING,917 // entity: Sample918 // )919 // .with { if (!validate()) { errors.each { println it} } else save()}920 //921 // // Human tissue sample template922 // def dclSampleTemplate = new Template(923 // name: 'DCL Sample information',924 // entity: dbnp.studycapturing.Sample925 // )926 // .addToFields(sampleDCLTextField)927 // .with { if (!validate()) { errors.each { println it} } else save()}928 // // EO DCL Sample Mapping Template**********************************929 //930 //931 // /*932 // def GrowthTreatmentTemplate = new Template(933 // name: 'Growth treatment',934 // entity: dbnp.studycapturing.Event935 // )936 // .addToFields(sampleDescriptionField)937 // .addToFields(new TemplateField(name: 'position X',type: TemplateFieldType.STRING))938 // .addToFields(new TemplateField(name: 'position Y',type: TemplateFieldType.STRING))939 // .addToFields(new TemplateField(name: 'Block',type: TemplateFieldType.STRING))940 // .addToFields(new TemplateField(name: 'Temparature Day',type: TemplateFieldType.STRING))941 // .addToFields(new TemplateField(name: 'Temparature Night',type: TemplateFieldType.STRING))942 // .addToFields(new TemplateField(name: 'Light Intensity',type: TemplateFieldType.STRING))943 // .addToFields(new TemplateField(name: 'Harvest Delay',type: TemplateFieldType.STRING))944 // .with { if (!validate()) { errors.each { println it} } else save()}945 // */946 //947 // //Plant template948 // def greenHouseTemplate = new Template(949 // name: 'Plant-green house ',950 // entity: dbnp.studycapturing.Subject951 // )952 // .addToFields(varietyField)953 // .addToFields(ecotypeField)954 // .addToFields(genotypeField)955 // /*956 // .addToFields(genotypeTypeField)957 // .addToFields(958 // new TemplateField(959 // name: 'Growth location', type: TemplateFieldType.STRINGLIST,960 // listEntries: [961 // new TemplateFieldListItem(name:'Greenhouse'),962 // new TemplateFieldListItem(name: 'Field')963 // ]964 // )965 // )966 // .addToFields(967 // new TemplateField(968 // name: 'Room', type: TemplateFieldType.STRING,969 // comment: 'Chamber number in case of Greenhouse'970 // )971 // )972 // */973 // .addToFields(974 // new TemplateField(975 // name: 'Chamber no.',976 // type: TemplateFieldType.STRING,977 // entity: Subject,978 // comment: 'Chamber number in the Greenhouse'979 // )980 // )981 // .addToFields(982 // new TemplateField(983 // name: 'Growth type',984 // entity: Subject,985 // type: TemplateFieldType.STRINGLIST,986 // listEntries: [987 // new TemplateFieldListItem(name:'Standard'),988 // new TemplateFieldListItem(name: 'Experimental'),989 // new TemplateFieldListItem(name: 'Unknown')990 // ]991 // )992 // )993 // .addToFields(new TemplateField(994 // name: 'Growth protocol', entity: Subject, type: TemplateFieldType.TEXT))995 // .addToFields(new TemplateField(996 // name: 'Position X', entity: Subject, type: TemplateFieldType.DOUBLE))997 // .addToFields(new TemplateField(998 // name: 'Position Y', entity: Subject, type: TemplateFieldType.DOUBLE))999 // .addToFields(new TemplateField(1000 // name: 'Block', entity: Subject, type: TemplateFieldType.STRING))1001 // .addToFields(new TemplateField(1002 // name: 'Temperature at day', entity: Subject, type: TemplateFieldType.DOUBLE))1003 // .addToFields(new TemplateField(1004 // name: 'Temperature at night', entity: Subject, type: TemplateFieldType.DOUBLE))1005 // .addToFields(new TemplateField(1006 // name: 'Photo period', entity: Subject, type: TemplateFieldType.STRING))1007 // .addToFields(new TemplateField(1008 // name: 'Light intensity', entity: Subject, type: TemplateFieldType.STRING))1009 // .addToFields(new TemplateField(1010 // name: 'Start date', entity: Subject, type: TemplateFieldType.DATE))1011 // .addToFields(new TemplateField(1012 // name: 'Harvest date', entity: Subject, type: TemplateFieldType.DATE))1013 // .addToFields(new TemplateField(1014 // name: 'Harvest delay', entity: Subject, type: TemplateFieldType.TEXT))1015 // .addToFields(new TemplateField(1016 // name: 'Additional info', entity: Subject, type: TemplateFieldType.TEXT))1017 // .with { if (!validate()) { errors.each { println it} } else save()}1018 //1019 // def FieldTemplate = new Template(1020 // name: 'Plant-open field',1021 // entity: dbnp.studycapturing.Subject1022 // )1023 // .addToFields(varietyField)1024 // .addToFields(ecotypeField)1025 // .addToFields(genotypeField)1026 // .addToFields(new TemplateField(1027 // name: 'Start date', entity: Subject, type: TemplateFieldType.DATE))1028 // .addToFields(new TemplateField(1029 // name: 'Harvest date', entity: Subject, type: TemplateFieldType.DATE))1030 // .addToFields(new TemplateField(1031 // name: 'Growth type', entity: Subject, type: TemplateFieldType.STRINGLIST,1032 // listEntries: [new TemplateFieldListItem(name:'Standard'),new TemplateFieldListItem(name: 'Experimental')]))1033 // .addToFields(new TemplateField(1034 // name: 'Growth protocol', entity: Subject, type: TemplateFieldType.TEXT))1035 // .addToFields(new TemplateField(1036 // name: 'Harvest delay', entity: Subject, type: TemplateFieldType.TEXT))1037 // .with { if (!validate()) { errors.each { println it} } else save()}1038 //1039 // //Plant template1040 // def chamberTemplate = new Template(1041 // name: 'Plant-chamber',1042 // entity: dbnp.studycapturing.Subject1043 // )1044 // .addToFields(varietyField)1045 // .addToFields(ecotypeField)1046 // .addToFields(genotypeField)1047 // /*1048 // .addToFields(genotypeTypeField)1049 // .addToFields(1050 // new TemplateField(1051 // name: 'Growth location',1052 // type: TemplateFieldType.STRINGLIST,1053 // listEntries: [1054 // new TemplateFieldListItem(name:'Greenhouse'),1055 // new TemplateFieldListItem(name: 'Field')1056 // ]1057 // )1058 // )1059 // */1060 // .addToFields(new TemplateField(1061 // name: 'Room', type: TemplateFieldType.STRING, entity: Subject,1062 // comment: 'room number'))1063 // .addToFields(new TemplateField(1064 // name: 'Chamber no.', type: TemplateFieldType.STRING, entity: Subject,1065 // comment: 'Chamber number'))1066 // .addToFields(new TemplateField(1067 // name: 'Block', type: TemplateFieldType.STRING, entity: Subject))1068 // .addToFields(new TemplateField(1069 // name: 'Position X', type: TemplateFieldType.DOUBLE, entity: Subject))1070 // .addToFields(new TemplateField(1071 // name: 'Position Y', type: TemplateFieldType.DOUBLE, entity: Subject))1072 // .addToFields(new TemplateField(1073 // name: 'Temperature at day', type: TemplateFieldType.DOUBLE, entity: Subject))1074 // .addToFields(new TemplateField(1075 // name: 'Temperature at night', type: TemplateFieldType.DOUBLE, entity: Subject))1076 // .addToFields(new TemplateField(1077 // name: 'Photo period', type: TemplateFieldType.STRING, entity: Subject))1078 // .addToFields(new TemplateField(1079 // name: 'Light intensity', type: TemplateFieldType.STRING, entity: Subject))1080 // .addToFields(new TemplateField(1081 // name: 'Start date', type: TemplateFieldType.DATE, entity: Subject))1082 // .addToFields(new TemplateField(1083 // name: 'Harvest date', type: TemplateFieldType.DATE, entity: Subject))1084 // .addToFields(new TemplateField(1085 // name: 'Growth type', type: TemplateFieldType.STRINGLIST, entity: Subject,1086 // listEntries: [new TemplateFieldListItem(name:'Standard'),new TemplateFieldListItem(name: 'Experimental')]))1087 // .addToFields(new TemplateField(1088 // name: 'Growth protocol', type: TemplateFieldType.TEXT, entity: Subject))1089 // .addToFields(new TemplateField(1090 // name: 'Harvest delay', type: TemplateFieldType.TEXT, entity: Subject))1091 // .with { if (!validate()) { errors.each { println it} } else save()}1092 //1093 // def plantSampleTemplate = new Template(1094 // name: 'Plant sample',1095 // entity: dbnp.studycapturing.Sample1096 // )1097 // .addToFields(sampleRemarksField)1098 // .addToFields(sampleVialTextField)1099 // .with { if (!validate()) { errors.each { println it} } else save()}1100 //1101 // def materialPrepTemplate = new Template(1102 // name: 'Plant-material preparation',1103 // description: 'material preparation',1104 // entity: dbnp.studycapturing.Event1105 // )1106 // .addToFields(new TemplateField(1107 // name: 'Tissue',1108 // type: TemplateFieldType.STRING,1109 // entity: Event,1110 // comment: 'organ/ fraction of culture/ plant part')1111 // )1112 // .addToFields(1113 // new TemplateField(1114 // name: 'Grinding',1115 // type: TemplateFieldType.STRINGLIST,1116 // entity: Event,1117 // listEntries: [1118 // new TemplateFieldListItem(name:'yes'),1119 // new TemplateFieldListItem(name: 'no'),1120 // new TemplateFieldListItem(name: 'unknown')1121 // ]1122 // )1123 // )1124 // .addToFields(1125 // new TemplateField(1126 // name: 'Storage location',1127 // type: TemplateFieldType.STRING,1128 // entity: Event1129 // )1130 // )1131 // .addToFields(1132 // new TemplateField(1133 // name: 'protocol reference',1134 // type: TemplateFieldType.STRING,1135 // entity: Event1136 // )1137 // )1138 // .with { if (!validate()) { errors.each { println it} } else save()}1139 //1140 // def protocolField = new TemplateField(1141 // name: 'Protocol',1142 // type: TemplateFieldType.FILE,1143 // entity: Event,1144 // comment: 'You can upload a protocol here which describes the procedure which was used when carrying out the event'1145 // )1146 // .with { if (!validate()) { errors.each { println it} } else save()}1147 //1148 // // diet treatment template1149 // def dietTreatmentTemplate = new Template(1150 // name: 'Diet treatment',1151 // entity: dbnp.studycapturing.Event1152 // )1153 // .addToFields(1154 // new TemplateField(1155 // name: 'Diet',1156 // type: TemplateFieldType.STRINGLIST,1157 // entity: Event,1158 // listEntries: [1159 // new TemplateFieldListItem(name:'low fat'),1160 // new TemplateFieldListItem(name: 'high fat')1161 // ]1162 // )1163 // )1164 // .addToFields(protocolField)1165 // .with { if (!validate()) { errors.each { println it} } else save(flush:true)}1166 // dietTreatmentTemplate.refresh()1167 //1168 // // boost treatment template1169 // def boostTreatmentTemplate = new Template(1170 // name: 'Compound challenge',1171 // entity: dbnp.studycapturing.Event1172 // )1173 // .addToFields(1174 // new TemplateField(1175 // name: 'Compound',1176 // type: TemplateFieldType.ONTOLOGYTERM,1177 // entity: Event,1178 // ontologies: [Ontology.getOrCreateOntologyByNcboId(1007)]1179 // )1180 // )1181 // .addToFields(1182 // new TemplateField(1183 // name: 'Control',1184 // type: TemplateFieldType.BOOLEAN,1185 // entity: Event1186 // )1187 // )1188 // .addToFields(protocolField)1189 // .with { if (!validate()) { errors.each { println it} } else save(flush:true)}1190 // boostTreatmentTemplate.refresh()1191 //1192 // // fasting treatment template1193 // def fastingTreatment = new Template(1194 // name: 'Fasting treatment',1195 // description: 'Fasting for a specific amount of time',1196 // entity: dbnp.studycapturing.Event1197 // )1198 // .addToFields(1199 // new TemplateField(1200 // name: 'Fasting period',1201 // type: TemplateFieldType.RELTIME,1202 // entity: Event1203 // )1204 // )1205 // .with { if (!validate()) { errors.each { println it} } else save()}1206 //1207 // // SamplingEvent templates1208 // def samplingProtocolField = new TemplateField(1209 // name: 'Sample Protocol',1210 // entity: SamplingEvent,1211 // type: TemplateFieldType.FILE,1212 // comment: 'You can upload a protocol here which describes the procedure which was used when carrying out the sampling event'1213 // )1214 // .with { if (!validate()) { errors.each { println it} } else save()}1215 //1216 // // liver sampling event template1217 // def liverSamplingEventTemplate = new Template(1218 // name: 'Liver extraction',1219 // description: 'Liver sampling for transcriptomics arrays',1220 // entity: dbnp.studycapturing.SamplingEvent1221 // )1222 // .addToFields(samplingProtocolField)1223 // .addToFields(1224 // new TemplateField(1225 // name: 'Sample weight',1226 // unit: 'mg',1227 // entity: SamplingEvent,1228 // type: TemplateFieldType.DOUBLE1229 // )1230 // )1231 // .with { if (!validate()) { errors.each { println it} } else save(flush:true)}1232 // liverSamplingEventTemplate.refresh()1233 //1234 // // blood sampling1235 // def bloodSamplingEventTemplate = new Template(1236 // name: 'Blood extraction',1237 // description: 'Blood extraction targeted at lipid assays',1238 // entity: dbnp.studycapturing.SamplingEvent1239 // )1240 // .addToFields(samplingProtocolField)1241 // .addToFields(1242 // new TemplateField(1243 // name: 'Sample volume',1244 // entity: SamplingEvent,1245 // unit: 'ml',1246 // type: TemplateFieldType.DOUBLE1247 // )1248 // )1249 // .with { if (!validate()) { errors.each { println it} } else save(flush:true)}1250 // bloodSamplingEventTemplate.refresh()1251 //1252 // // plant sample extraction event template1253 // def plantSamplingExtractEventTemplate = new Template(1254 // name: 'Plant sample extraction',1255 // description: 'sample extraction',1256 // entity: dbnp.studycapturing.SamplingEvent,1257 // sampleTemplates: [plantSampleTemplate]1258 // )1259 // .addToFields(samplingProtocolField)1260 // .addToFields(1261 // new TemplateField(1262 // name: 'Sample weight',1263 // unit: 'ul',1264 // entity: SamplingEvent,1265 // type: TemplateFieldType.DOUBLE1266 // )1267 // )1268 // .addToFields(1269 // new TemplateField(1270 // name: 'Sample when measured',1271 // type: TemplateFieldType.STRINGLIST,1272 // entity: SamplingEvent,1273 // listEntries: [1274 // new TemplateFieldListItem(name:'Dried'),1275 // new TemplateFieldListItem(name: 'Fresh'),1276 // new TemplateFieldListItem(name: 'Unknown')1277 // ]1278 // )1279 // )1280 // .with { if (!validate()) { errors.each { println it} } else save()}1281 //1282 // // plant sampling event template1283 // def plantSamplingEventTemplate = new Template(1284 // name: 'Plant-sample',1285 // description: 'plant sample ',1286 // entity: dbnp.studycapturing.SamplingEvent,1287 // sampleTemplates: [plantSampleTemplate]1288 // )1289 // //.addToFields(samplingProtocolField)1290 // .addToFields(1291 // new TemplateField(1292 // name: 'material',1293 // comment: 'physical charecteristic. e.g, grounded powder of tomato seed or liquid',1294 // entity: SamplingEvent,1295 // type: TemplateFieldType.STRING1296 // )1297 // )1298 // .addToFields(1299 // new TemplateField(1300 // name: 'Description',1301 // type: TemplateFieldType.STRING,1302 // entity: SamplingEvent1303 // )1304 // )1305 // .addToFields(1306 // new TemplateField(1307 // name: 'extracted material',1308 // comment: 'substance to be extracted. e.g., lipids, volatiles, primary metabolites etc',1309 // type: TemplateFieldType.STRING,1310 // entity: SamplingEvent1311 // )1312 // )1313 // .addToFields(1314 // new TemplateField(1315 // name: 'Text on vial',1316 // entity: SamplingEvent,1317 // type: TemplateFieldType.STRING1318 // )1319 // )1320 // .with { if (!validate()) { errors.each { println it} } else save()}1321 //1322 //1323 // // assay templates1324 // def assayDescriptionField = new TemplateField(1325 // name: 'Description',1326 // comment: 'add general assay information here',1327 // entity: Assay,1328 // type: TemplateFieldType.STRING1329 // );1330 // assayDescriptionField.with { if (!validate()) { errors.each { println it} } else save()}1331 //1332 // def ccAssayTemplate = new Template(1333 // name: 'Clinical chemistry assay',1334 // description: 'Clinical chemistry assay stored in a SAM module',1335 // entity: dbnp.studycapturing.Assay1336 // )1337 // .addToFields(assayDescriptionField)1338 // .with { if (!validate()) { errors.each { println it} } else save()}1339 //1340 // def metAssayTemplate = new Template(1341 // name: 'Metabolomics assay',1342 // description: 'Metabolomics assay stored in a metabolomics module',1343 // entity: dbnp.studycapturing.Assay1344 // )1345 // .addToFields(assayDescriptionField)1346 // .addToFields(1347 // new TemplateField(1348 // name: 'Spectrometry technique',1349 // comment: 'Select the used metabolomics technique',1350 // entity: Assay,1351 // type: TemplateFieldType.STRINGLIST,1352 // listEntries: [1353 // new TemplateFieldListItem(name: 'GC/MS'),1354 // new TemplateFieldListItem(name: 'LC/MS'),1355 // new TemplateFieldListItem(name: 'NMR'),1356 // new TemplateFieldListItem(name: 'HPLC')1357 // ])1358 // )1359 // .with { if (!validate()) { errors.each { println it} } else save(flush:true)}1360 // metAssayTemplate.refresh()1361 // }1362 //1363 //}
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