gov.nih.nci.common.persistence.enhanced.BioAssay
Class DerivedBioAssayByBioSourceNameQuery

java.lang.Object
  extended by gov.nih.nci.common.persistence.enhanced.BaseQueryImpl
      extended by gov.nih.nci.common.persistence.enhanced.BioAssay.DerivedBioAssayByBioSourceNameQuery
All Implemented Interfaces:
ESCriterionQuery, ESQuery

public final class DerivedBioAssayByBioSourceNameQuery
extends BaseQueryImpl
implements ESCriterionQuery

Author:
matyass

Field Summary
 
Fields inherited from class gov.nih.nci.common.persistence.enhanced.BaseQueryImpl
EMPTY_LONG_COLLECTION
 
Constructor Summary
DerivedBioAssayByBioSourceNameQuery()
           
 
Method Summary
protected  java.util.Collection<java.lang.Long> findAllBioAssayCreations()
           
protected  java.util.Collection<java.lang.Long> findAllBioSamplesFromBioSources()
           
protected  java.util.Collection findAllBioSourceByName()
           
protected  java.util.Collection<java.lang.Long> findAllLabeledExtracts()
           
protected  java.util.Collection<java.lang.Long> findAllMeasuredBioAssays()
           
protected  java.util.Collection<java.lang.Long> findAllPhysicalBioAssays()
           
protected  java.util.Collection<java.lang.Long> findAllPhysicalBioAssaysAlternate()
           
 java.lang.Long[] getIdsForQuery()
           To find MeasuredBioAssays by BioSource.name or BioSource.identifier =================================================================== 1.
protected  org.apache.ojb.broker.query.ReportQueryByCriteria query_findAllBioSources()
           
protected  org.apache.ojb.broker.query.ReportQueryByCriteria query_findAllLabeledExtracts(java.util.Collection<java.lang.Long> bioSampleIds)
           
 void setCriterion(EnhancedSearchCriterion criterion)
           
 
Methods inherited from class gov.nih.nci.common.persistence.enhanced.BaseQueryImpl
buildLikeCriteria, buildLikeCriteria, getBroker, getCollectionByQuery, getCollectionByQuery, getConnection, getIds, getIdsAsCollection
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface gov.nih.nci.common.persistence.enhanced.ESCriterionQuery
getIdsForQuery
 

Constructor Detail

DerivedBioAssayByBioSourceNameQuery

public DerivedBioAssayByBioSourceNameQuery()
Method Detail

setCriterion

public void setCriterion(EnhancedSearchCriterion criterion)
Specified by:
setCriterion in interface ESCriterionQuery

findAllBioSourceByName

protected java.util.Collection findAllBioSourceByName()
Returns:

query_findAllBioSources

protected org.apache.ojb.broker.query.ReportQueryByCriteria query_findAllBioSources()
Returns:

getIdsForQuery

public java.lang.Long[] getIdsForQuery()
           To find MeasuredBioAssays by BioSource.name or BioSource.identifier
           =================================================================== 
           1. Find all BioSource(s) that match the name/identifier 
           2. Find all BioSample(s) derived from those BioSource(s); BioSample.treatments.sourceBioMaterialMeasurements.bioMaterial = BioSource(s) found 
                this needs to be recursive (might be aBioSource.aBioSample.aBioSample.aBioSample.aLabeledExtract)
           3. Find all LabeledExtract(s) derived from those BioSample(s); LabeledExtract.treatments.sourceBioMaterialMeasurements.bioMaterial = BioSamples(s) found ; 
           4. Find all PhysicalBioAssays that hybridized from LabeledExtracts; PhysicalBioAssay.bioAssayCreation.sourceBioMaterialMeasurement.bioMaterial = LabeledExtract(s) found 
           5. Find all related PhysicalBioAssay(s) recursively (typically there are one or more PhysicalBioAssays per LabeledExtract) (note: caArray doesn't support this however, this is needed to be complete per the MAGE-OM 1.1 Spec.) 
              Using the founds PhysicalBioAssay(s) = PhysicalBioAssay.bioAssayTreatments.target 
           6. Find all MeasuredBioAssays.featureExtraction.physicalBioAssaySource = PhysicalBioAssay(s) found
 


findAllBioSamplesFromBioSources

protected java.util.Collection<java.lang.Long> findAllBioSamplesFromBioSources()
Returns:

findAllLabeledExtracts

protected java.util.Collection<java.lang.Long> findAllLabeledExtracts()
Returns:

query_findAllLabeledExtracts

protected org.apache.ojb.broker.query.ReportQueryByCriteria query_findAllLabeledExtracts(java.util.Collection<java.lang.Long> bioSampleIds)
Parameters:
bioSampleIds -
Returns:

findAllPhysicalBioAssaysAlternate

protected java.util.Collection<java.lang.Long> findAllPhysicalBioAssaysAlternate()
Returns:

findAllBioAssayCreations

protected java.util.Collection<java.lang.Long> findAllBioAssayCreations()
Returns:

findAllPhysicalBioAssays

protected java.util.Collection<java.lang.Long> findAllPhysicalBioAssays()
Returns:

findAllMeasuredBioAssays

protected java.util.Collection<java.lang.Long> findAllMeasuredBioAssays()
Returns: