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Merge thehyve/cross_trial into thehyve/master
Conflicts: TransmartCoreGrailsPlugin.groovy grails-app/conf/BuildConfig.groovy transmart-core-db-tests/TransmartCoreDbTestsGrailsPlugin.groovy
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47 changes: 47 additions & 0 deletions
47
grails-app/domain/org/transmartproject/db/ontology/ModifierDimensionCoreDb.groovy
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,47 @@ | ||
| package org.transmartproject.db.ontology | ||
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| class ModifierDimensionCoreDb { | ||
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| String path | ||
| String code | ||
| String name | ||
| Long level | ||
| String studyId | ||
| String nodeType | ||
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| // unused | ||
| // String modifierBlob | ||
| // Date updateDate | ||
| // Date downloadDate | ||
| // Date importDate | ||
| // Long uploadId | ||
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| static mapping = { | ||
| table schema: 'i2b2demodata', name: 'modifier_dimension' | ||
| id name: 'path', generator: 'assigned' | ||
| version false | ||
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| path column: 'modifier_path' | ||
| code column: 'modifier_cd' | ||
| name column: 'name_char' | ||
| level column: 'modifier_level' | ||
| studyId column: 'sourcesystem_cd' | ||
| nodeType column: 'modifier_node_type' // known values: {L, F} | ||
| } | ||
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| static constraints = { | ||
| path maxSize: 700 | ||
| code nullable: true, maxSize: 50 | ||
| name nullable: true, maxSize: 2000 | ||
| level nullable: true | ||
| studyId nullable: true, maxSize: 50 | ||
| nodeType nullable: true, maxSize: 10 | ||
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| // unused: | ||
| // modifierBlob nullable: true | ||
| // updateDate nullable: true | ||
| // downloadDate nullable: true | ||
| // importDate nullable: true | ||
| // uploadId nullable: true | ||
| } | ||
| } |
69 changes: 69 additions & 0 deletions
69
grails-app/domain/org/transmartproject/db/ontology/ModifierDimensionView.groovy
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| /* | ||
| * Copyright © 2013-2014 The Hyve B.V. | ||
| * | ||
| * This file is part of transmart-core-db. | ||
| * | ||
| * Transmart-core-db is free software: you can redistribute it and/or modify it | ||
| * under the terms of the GNU General Public License as published by the Free | ||
| * Software Foundation, either version 3 of the License, or (at your option) any | ||
| * later version. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, but WITHOUT | ||
| * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS | ||
| * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more | ||
| * details. | ||
| * | ||
| * You should have received a copy of the GNU General Public License along with | ||
| * transmart-core-db. If not, see <http://www.gnu.org/licenses/>. | ||
| */ | ||
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| package org.transmartproject.db.ontology | ||
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| /** | ||
| * View that joins {@link ModifierDimensionView} and | ||
| * {@link ModifierMetadataCoreDb}. It has to be done on a view because | ||
| * modifier_metadata inexplicably doesn't use modifier_dimension's primary key, | ||
| * though modifier_cd functions as a de facto second primary key. | ||
| */ | ||
| class ModifierDimensionView { | ||
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| // it's a view! | ||
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| String path | ||
| String code | ||
| String name | ||
| Long level | ||
| String studyId | ||
| String nodeType | ||
| String valueType | ||
| String unit | ||
| String visitInd = 'N' | ||
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| static transients = ['visit'] | ||
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| Boolean visit | ||
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| Boolean isVisit() { | ||
| visitInd == 'Y' | ||
| } | ||
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| void setVisit(Boolean visit) { | ||
| visitInd == visit == null ? null : | ||
| visit ? 'Y' : 'N' | ||
| } | ||
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| static mapping = { | ||
| table schema: 'i2b2demodata', name: 'modifier_dimension_view' | ||
| id name: 'path', generator: 'assigned' | ||
| version false | ||
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| path column: 'modifier_path' | ||
| code column: 'modifier_cd' | ||
| name column: 'name_char' | ||
| level column: 'modifier_level' | ||
| studyId column: 'sourcesystem_cd' | ||
| nodeType column: 'modifier_node_type' // known values: {L, F} | ||
| valueType column: 'valtype_cd' | ||
| unit column: 'std_units' | ||
| } | ||
| } |
46 changes: 46 additions & 0 deletions
46
grails-app/domain/org/transmartproject/db/ontology/ModifierMetadataCoreDb.groovy
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| package org.transmartproject.db.ontology | ||
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| class ModifierMetadataCoreDb implements Serializable { | ||
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| /* why the tables were designed in a way that this one has no reference | ||
| * modifier_dimension's primary key is beyond me. | ||
| * Add to that oddity that this table that it stores a boolean as a string | ||
| * and doesn't even have a primary key (though in this mapping I chose | ||
| * modifierCode as the primary key (the queries make it clear modifierCode | ||
| * must be unique) */ | ||
| String code //id | ||
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| String valueType | ||
| String unit | ||
| Character visitInd = 'N' as Character | ||
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| static transients = ['visit'] | ||
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| Boolean visit | ||
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| Boolean isVisit() { | ||
| visitInd == 'Y' | ||
| } | ||
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| void setVisit(Boolean visit) { | ||
| visitInd == visit == null ? null : | ||
| visit ? 'Y' : 'N' | ||
| } | ||
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| static mapping = { | ||
| table schema: 'i2b2demodata', name: 'modifier_metadata' | ||
| id generator: 'assigned', name: 'code' | ||
| version false | ||
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| code column: 'modifier_cd' | ||
| valueType column: 'valtype_cd' | ||
| unit column: 'std_units' | ||
| } | ||
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| static constraints = { | ||
| code maxSize: 50 | ||
| valueType nullable: true, maxSize: 10 | ||
| unit nullable: true, maxSize: 50 | ||
| visitInd nullable: false | ||
| } | ||
| } |
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