Merge thehyve/master into london_hackaton

.gitattributes

@@ -0,0 +1 @@
+* text=auto

TransmartCoreGrailsPlugin.groovy

@@ -1,4 +1,6 @@
 import org.springframework.stereotype.Component
+import org.transmartproject.db.accesscontrol.AccessControlChecks
+import org.transmartproject.db.dataquery.clinical.variables.ClinicalVariableFactory
 import org.transmartproject.db.dataquery.highdim.AbstractHighDimensionDataTypeModule
 import org.transmartproject.db.http.BusinessExceptionResolver
 import org.transmartproject.db.support.DatabasePortabilityService
@@ -49,6 +51,10 @@ A runtime dependency for tranSMART that implements the Core API
 
         businessExceptionResolver(BusinessExceptionResolver)
 
+        accessControlChecks(AccessControlChecks)
+
+        clinicalVariableFactory(ClinicalVariableFactory)
+
         context.'component-scan'('base-package': 'org.transmartproject.db.dataquery.highdim') {
             context.'include-filter'(
                     type:       'assignable',

grails-app/conf/BuildConfig.groovy

@@ -2,6 +2,20 @@ grails.project.class.dir = "target/classes"
 grails.project.test.class.dir = "target/test-classes"
 grails.project.test.reports.dir = "target/test-reports"
 
+def defaultVMSettings = [
+        maxMemory: 768,
+        minMemory: 64,
+        debug:     false,
+        maxPerm:   256
+]
+
+grails.project.fork = [
+        test:    [*: defaultVMSettings, daemon:      true],
+        run:     [*: defaultVMSettings, forkReserve: false],
+        war:     [*: defaultVMSettings, forkReserve: false],
+        console: defaultVMSettings
+]
+
 grails.project.repos.default = 'repo.thehyve.nl-snapshots'
 grails.project.repos."${grails.project.repos.default}".url = 'https://repo.thehyve.nl/content/repositories/snapshots/'
 
@@ -34,7 +48,7 @@ grails.project.dependency.resolution = {
         test 'org.hamcrest:hamcrest-core:1.3',
              'org.hamcrest:hamcrest-library:1.3'
 
-        test 'org.gmock:gmock:0.8.3', {
+        test 'org.gmock:gmock:0.9.0-r435-hyve2', {
             transitive = false /* don't bring groovy-all */
         }
     }

grails-app/domain/org/transmartproject/db/accesscontrol/AccessLevel.groovy

@@ -31,15 +31,22 @@ class AccessLevel implements Permission {
 
     /**
      * This is not in the database for now.
+     *
+     * Note that {@link Permission}s are only used for Studies at this
+     * point. This mapping between permissions and operations are
+     * specific for Studies.
+     *
+     * Access to QueryDefinitions don't need to rely on QueryDefinition
+     * specific permissions because are implemented in function of
+     * Study access and access to QueryResults is implemented in function of
+     * the user that submitted the query. AccessLevels are not involved.
      */
     @Lazy
     static Multimap<String, ProtectedOperation> permissionToOperations = {
         def mapBuilder = ImmutableMultimap.builder()
 
         [API_READ, BUILD_COHORT, SHOW_SUMMARY_STATISTICS, RUN_ANALYSIS, EXPORT,
                 SHOW_IN_TABLE].each {
-            // don't iterate over WellKnownOperations.values() to avoid bugs in
-            // the future
             mapBuilder.put 'OWN', it
             mapBuilder.put 'EXPORT', it
         }

grails-app/domain/org/transmartproject/db/dataquery/highdim/DeGplInfo.groovy

@@ -10,25 +10,25 @@ class DeGplInfo implements Platform {
     String  organism
     Date    annotationDate
     String  markerType
-    Integer releaseNumber
+    String  genomeReleaseId
 
     static mapping = {
         table         schema: 'deapp'
 
-        id            column: 'platform',   generator: 'assigned'
-        releaseNumber column: 'release_nbr'
+        id              column: 'platform',   generator: 'assigned'
+        genomeReleaseId column: 'release_nbr'
 
         version      false
     }
 
     static constraints = {
         id             maxSize:  50
 
-        title          nullable: true, maxSize: 500
-        organism       nullable: true, maxSize: 100
-        annotationDate nullable: true
-        markerType     nullable: true, maxSize: 100
-        releaseNumber  nullable: true
+        title           nullable: true, maxSize: 500
+        organism        nullable: true, maxSize: 100
+        annotationDate  nullable: true
+        markerType      nullable: true, maxSize: 100
+        genomeReleaseId nullable: true
     }
 
     @Override

grails-app/domain/org/transmartproject/db/dataquery/highdim/acgh/DeSubjectAcghData.groovy

@@ -1,10 +1,10 @@
 package org.transmartproject.db.dataquery.highdim.acgh
 
 import groovy.transform.EqualsAndHashCode
-import org.transmartproject.db.dataquery.highdim.chromoregion.DeChromosomalRegion
 import org.transmartproject.core.dataquery.highdim.acgh.AcghValues
 import org.transmartproject.core.dataquery.highdim.acgh.CopyNumberState
 import org.transmartproject.db.dataquery.highdim.DeSubjectSampleMapping
+import org.transmartproject.db.dataquery.highdim.chromoregion.DeChromosomalRegion
 import org.transmartproject.db.i2b2data.PatientDimension
 
 @EqualsAndHashCode(includes = [ 'assay', 'region' ])

grails-app/domain/org/transmartproject/db/dataquery/highdim/chromoregion/DeChromosomalRegion.groovy

@@ -11,10 +11,10 @@ class DeChromosomalRegion implements Region {
     Integer numberOfProbes
     String  name
     String  cytoband
-
-    /* unused */
     String  geneSymbol
     Long    geneId
+
+    /* unused */
     String  organism
 
     static belongsTo = [platform: DeGplInfo]

grails-app/domain/org/transmartproject/db/dataquery/highdim/rbm/DeSubjectRbmData.groovy

@@ -18,7 +18,7 @@ class DeSubjectRbmData {
 
     static mapping = {
         table schema: 'deapp', name: 'de_subject_rbm_data'
-        id generator: 'sequence', params: [sequence: 'de_subject_rbm_data_seq']
+        id generator: 'sequence', params: [sequence: 'de_subject_rbm_data_seq', schema: 'deapp']
         assay column: 'assay_id'
         annotations joinTable: [
                 name: 'de_rbm_data_annotation_join',

grails-app/domain/org/transmartproject/db/dataquery/highdim/rnaseq/DeSubjectRnaseqData.groovy

@@ -1,9 +1,9 @@
 package org.transmartproject.db.dataquery.highdim.rnaseq
 
 import groovy.transform.EqualsAndHashCode
-import org.transmartproject.db.dataquery.highdim.chromoregion.DeChromosomalRegion
 import org.transmartproject.core.dataquery.highdim.rnaseq.RnaSeqValues
 import org.transmartproject.db.dataquery.highdim.DeSubjectSampleMapping
+import org.transmartproject.db.dataquery.highdim.chromoregion.DeChromosomalRegion
 import org.transmartproject.db.i2b2data.PatientDimension
 
 @EqualsAndHashCode(includes = [ 'assay', 'region' ])

grails-app/domain/org/transmartproject/db/dataquery/highdim/vcf/DeVariantDatasetCoreDb.groovy

@@ -21,8 +21,7 @@ class DeVariantDatasetCoreDb {
     }
 
     static mapping = {
-        table schema: 'deapp'
-        table   name:  'de_variant_dataset'
+        table schema: 'deapp', name:  'de_variant_dataset'
         version false
         id column:'dataset_id', generator: 'assigned'
     }

grails-app/domain/org/transmartproject/db/dataquery/highdim/vcf/DeVariantSubjectDetailCoreDb.groovy

@@ -1,17 +1,12 @@
 package org.transmartproject.db.dataquery.highdim.vcf
 
 import groovy.transform.EqualsAndHashCode
-import org.transmartproject.core.dataquery.highdim.vcf.GenomicVariantType
-import org.transmartproject.db.dataquery.highdim.DeSubjectSampleMapping
-
-import static org.transmartproject.core.dataquery.highdim.vcf.GenomicVariantType.*
-import org.transmartproject.core.dataquery.highdim.vcf.VcfValues
 
 @EqualsAndHashCode()
 class DeVariantSubjectDetailCoreDb implements Serializable {
 
     String chr
-    Long pos
+    Long   pos
     String rsId
     String ref
     String alt
@@ -21,34 +16,32 @@ class DeVariantSubjectDetailCoreDb implements Serializable {
     String format
     String variant
 
-    static belongsTo = [dataset: DeVariantDatasetCoreDb]          //TODO: implement constraint on dataset
+    static belongsTo = [dataset: DeVariantDatasetCoreDb] //TODO: implement constraint on dataset
 
     static constraints = {
-        alt(nullable: true)
-        quality(nullable: true)
-        filter(nullable: true)
-        info(nullable: true)
-        format(nullable: true)
-        variant(nullable: true)
+        alt     nullable: true
+        quality nullable: true
+        filter  nullable: true
+        info    nullable: true
+        format  nullable: true
+        variant nullable: true
     }
 
     static mapping = {
-        table schema: 'deapp'
-        table   name:  'de_variant_subject_detail'
-        version false
+        table     schema:  'deapp', name: 'de_variant_subject_detail'
+        version   false
+
         id composite: ['chr', 'pos']
+
         dataset column: 'dataset_id'
-        rsId column: 'rs_id'
-        ref column: 'ref'
-        alt column: 'alt'
+        rsId    column: 'rs_id'
+        ref     column: 'ref'
+        alt     column: 'alt'
         quality column: 'qual'
-        filter column: 'filter'
-        info column: 'info'
-        format column: 'format'
+        filter  column: 'filter'
+        info    column: 'info'
+        format  column: 'format'
         variant column: 'variant_value', sqlType: 'clob'
     }
 
-
-
-
 }

grails-app/domain/org/transmartproject/db/dataquery/highdim/vcf/DeVariantSubjectIdxCoreDb.groovy

@@ -0,0 +1,18 @@
+package org.transmartproject.db.dataquery.highdim.vcf
+
+class DeVariantSubjectIdxCoreDb implements Serializable {
+    DeVariantDatasetCoreDb dataset
+    String subjectId
+    Long position
+
+    static mapping = {
+        table schema: 'deapp', name: 'de_variant_subject_idx'
+        version false
+        id composite: ['dataset', 'subjectId']
+
+        dataset   column: 'dataset_id'
+        subjectId column: 'subject_id'
+        position  column: 'position'
+    }
+
+}

grails-app/domain/org/transmartproject/db/dataquery/highdim/vcf/DeVariantSubjectSummaryCoreDb.groovy

@@ -15,31 +15,39 @@ class DeVariantSubjectSummaryCoreDb {
     Integer allele2
 
     DeVariantSubjectDetailCoreDb jDetail
+    DeVariantSubjectIdxCoreDb subjectIndex
 
     static belongsTo = [dataset: DeVariantDatasetCoreDb, assay: DeSubjectSampleMapping]   //TODO: implement constraint on dataset
 
-
-
     static constraints = {
         variant(nullable: true)
         variantFormat(nullable: true)
         variantType(nullable: true)
+        subjectIndex(nullable: true)
     }
 
     static mapping = {
-        table schema: 'deapp'
-        table   name:  'de_variant_subject_summary'
+        table schema: 'deapp', name: 'de_variant_subject_summary'
         version false
-        id column:'variant_subject_summary_id', generator: 'sequence', params: [sequence: 'de_variant_subject_summary_seq']
-        dataset column: 'dataset_id'
+        id  column:'variant_subject_summary_id',
+            generator: 'sequence',
+            params: [sequence: 'de_variant_subject_summary_seq', schema: 'deapp']
+
+        dataset column: 'dataset_id', insertable: false, updateable: false
         assay   column: 'assay_id'
+        subjectId column: 'subject_id', insertable: false, updateable: false
+
         // this is needed due to a Criteria bug.
         // see https://forum.hibernate.org/viewtopic.php?f=1&t=1012372
         columns {
             jDetail {
                 column name: 'chr'
                 column name: 'pos'
             }
+            subjectIndex {
+                column name: 'dataset_id'
+                column name: 'subject_id'
+            }
         }
     }
 }

grails-app/domain/org/transmartproject/db/ontology/I2b2.groovy

@@ -1,5 +1,8 @@
 package org.transmartproject.db.ontology
 
+import org.transmartproject.core.exceptions.UnexpectedResultException
+import org.transmartproject.core.ontology.Study
+
 class I2b2 extends AbstractI2b2Metadata implements Serializable {
 
     BigDecimal   cTotalnum
@@ -27,9 +30,9 @@ class I2b2 extends AbstractI2b2Metadata implements Serializable {
 
         AbstractI2b2Metadata.mapping.delegate = delegate
         AbstractI2b2Metadata.mapping()
-	}
+    }
 
-	static constraints = {
+    static constraints = {
         cTotalnum           nullable:   true
         cComment            nullable:   true
         mAppliedPath        nullable:   false,   maxSize:   700
@@ -44,6 +47,37 @@ class I2b2 extends AbstractI2b2Metadata implements Serializable {
 
         AbstractI2b2Metadata.constraints.delegate = delegate
         AbstractI2b2Metadata.constraints()
-	}
+    }
+
+    @Override
+    Study getStudy() {
+        def trial
+
+        def matcher = cComment =~ /(?<=^trial:).+/
+        if (matcher.find()) {
+            trial = matcher.group 0
+        }
+
+        if (!trial) {
+            return null
+        }
+
+        def query = sessionFactory.currentSession.createQuery '''
+                SELECT I
+                FROM I2b2 I, I2b2TrialNodes TN
+                WHERE (I.fullName = TN.fullName) AND
+                TN.trial = :trial'''
+
+        query.setParameter 'trial', trial
+
+        def res = query.list()
+        if (res.size() > 1) {
+            throw new UnexpectedResultException("More than one study with name $trial")
+        } else if (res.size() == 1) {
+            new StudyImpl(ontologyTerm: res[0])
+        } else {
+            null
+        }
+    }
 
 }

grails-app/domain/org/transmartproject/db/ontology/I2b2Secure.groovy

@@ -12,7 +12,7 @@ class I2b2Secure extends AbstractI2b2Metadata implements Serializable {
 
         id composite: ['fullName', 'name']
 
-        secureObjectToken name: 'secure_obj_token'
+        secureObjectToken column: 'secure_obj_token'
 
         AbstractI2b2Metadata.mapping.delegate = delegate
         AbstractI2b2Metadata.mapping()