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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,5 @@ | ||
| #Grails Metadata file | ||
| #Thu Feb 28 15:57:41 CET 2013 | ||
| app.grails.version=2.2.1 | ||
| #Wed May 15 15:47:34 CEST 2013 | ||
| app.grails.version=2.2.2 | ||
| app.name=transmart-core | ||
| plugins.hibernate=2.2.1 | ||
| plugins.hibernate=2.2.2 |
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137 changes: 137 additions & 0 deletions
137
grails-app/services/org/transmartproject/db/dataquery/DataQueryResourceNoGormService.groovy
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,137 @@ | ||
| package org.transmartproject.db.dataquery | ||
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| import groovy.transform.CompileStatic | ||
| import org.hibernate.Query | ||
| import org.hibernate.ScrollableResults | ||
| import org.hibernate.Session | ||
| import org.hibernate.StatelessSession | ||
| import org.hibernate.impl.AbstractSessionImpl | ||
| import org.transmartproject.core.dataquery.DataQueryResource | ||
| import org.transmartproject.core.dataquery.acgh.RegionResult | ||
| import org.transmartproject.core.dataquery.assay.Assay | ||
| import org.transmartproject.core.dataquery.constraints.ACGHRegionQuery | ||
| import org.transmartproject.core.dataquery.acgh.Region | ||
| import org.transmartproject.core.dataquery.acgh.ACGHValues | ||
| import org.transmartproject.core.dataquery.acgh.CopyNumberState | ||
| import org.transmartproject.core.dataquery.Platform | ||
| import org.transmartproject.core.dataquery.acgh.RegionRow | ||
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| import static org.hibernate.ScrollMode.FORWARD_ONLY | ||
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| class DataQueryResourceNoGormService extends DataQueryResourceService { | ||
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| @Override | ||
| protected RegionResult getRegionResultForAssays(final List<Assay> assays, AbstractSessionImpl session) { | ||
| def mainHQL = ''' | ||
| select | ||
| acgh.assay.id, | ||
| acgh.chipCopyNumberValue, | ||
| acgh.segmentCopyNumberValue, | ||
| acgh.flag, | ||
| acgh.probabilityOfLoss, | ||
| acgh.probabilityOfNormal, | ||
| acgh.probabilityOfGain, | ||
| acgh.probabilityOfAmplification, | ||
| region.id, | ||
| region.cytoband, | ||
| region.chromosome, | ||
| region.start, | ||
| region.end, | ||
| region.numberOfProbes | ||
| from DeSubjectAcghData as acgh | ||
| inner join acgh.region region | ||
| where acgh.assay.id in (:assayIds) | ||
| order by region.id, acgh.assay.id'''.stripIndent() | ||
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| def mainQuery = createQuery(session, mainHQL, ['assayIds': assays.collect {Assay assay -> assay.id}]).scroll(FORWARD_ONLY) | ||
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| new RegionResultListImpl(assays, mainQuery) | ||
| } | ||
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| @CompileStatic | ||
| class ACGHValuesImpl implements ACGHValues { | ||
| final List rowList | ||
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| ACGHValuesImpl(final List rowList) { | ||
| this.rowList = rowList | ||
| } | ||
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| Long getAssayId() { rowList[0] as Long } | ||
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| Double getChipCopyNumberValue() { rowList[1] as Double } | ||
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| Double getSegmentCopyNumberValue() { rowList[2] as Double } | ||
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| CopyNumberState getCopyNumberState() { CopyNumberState.forInteger((rowList[3] as Short).intValue()) } | ||
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| Double getProbabilityOfLoss() { rowList[4] as Double } | ||
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| Double getProbabilityOfNormal() { rowList[5] as Double } | ||
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| Double getProbabilityOfGain() { rowList[6] as Double } | ||
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| Double getProbabilityOfAmplification() { rowList[7] as Double } | ||
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| } | ||
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| @CompileStatic | ||
| class RegionImpl implements Region { | ||
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| final List rowList | ||
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| RegionImpl(final List rowList) { | ||
| this.rowList = rowList | ||
| } | ||
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| Long getId() { rowList[8] as Long } | ||
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| String getCytoband() { rowList[9] as String } | ||
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| Platform getPlatform() { | ||
| throw new UnsupportedOperationException('Getter for get platform is not implemented') | ||
| } | ||
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| String getChromosome() { rowList[10] as String } | ||
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| Long getStart() { rowList[11] as Long } | ||
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| Long getEnd() { rowList[12] as Long } | ||
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| Integer getNumberOfProbes() { rowList[13] as Integer } | ||
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| } | ||
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| @CompileStatic | ||
| class RegionResultListImpl extends org.transmartproject.db.dataquery.RegionResultImpl { | ||
| RegionResultListImpl(List<Assay> indicesList, ScrollableResults results) { | ||
| super(indicesList, results) | ||
| } | ||
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| @Override | ||
| protected RegionRow getNextRegionRow() { | ||
| List rowList = results.get() as List | ||
| if (rowList == null) { | ||
| return null | ||
| } | ||
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| RegionImpl region = new RegionImpl(rowList) | ||
| ACGHValuesImpl acghValue = new ACGHValuesImpl(rowList) | ||
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| Map values = new HashMap(indicesList.size(), 1) | ||
| while (new RegionImpl(rowList).id == region.id) { | ||
| values[acghValue.assayId] = acghValue | ||
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| if (!results.next()) { | ||
| break | ||
| } | ||
| rowList = results.get() as List | ||
| acghValue = new ACGHValuesImpl(rowList) | ||
| } | ||
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| new RegionRowImpl(region, indicesList, values) | ||
| } | ||
| } | ||
| } | ||
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