gov.nih.nci.common.persistence.enhanced.Experiment
Class ExperimentByTissueTypeQuery

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

public final class ExperimentByTissueTypeQuery
extends BaseQueryImpl
implements ESCriterionQuery

Used to find all Experiment(s) with BioMaterial(s) with characteristics, OntologyEntry(s) with a category of value 'OrganismPart'

Author:
smatyas
     1.1 Find all BioSources with characteristics.category = 'OrganismPart'
     1.2. Find all BioSamples with characteristics.category = 'OrganismPart', recurse through BioSamples 
     1.3. Find all LabeledExtracts with characteristics.category = 'OrganismPart'
     2  Find all LabeledExtracts from the resultset from step 1.1, 1.2, 1.3
     3. 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.) 
        Do so using the found PhysicalBioAssay(s) = PhysicalBioAssay.bioAssayTreatments.target 
     4. Find all Experiments for the given the PhysicalBioAssays found
 

Field Summary
 
Fields inherited from class gov.nih.nci.common.persistence.enhanced.BaseQueryImpl
EMPTY_LONG_COLLECTION
 
Constructor Summary
ExperimentByTissueTypeQuery()
           
 
Method Summary
protected  java.util.Collection<java.lang.Long> findAllBioSamplesFromBioSourcesWithCharacteristicsCategoryMatchingOrganismPart()
           
protected  java.util.Collection<java.lang.Long> findAllBioSamplesWithCharacteristicsCategoryMatchingOrganismPart()
           
protected  java.util.Collection findAllBioSourcesWithCharacteristicsCategoryMatchingOrganismPart()
           
protected  java.util.Collection findAllExperiments()
           
protected  java.util.Collection<java.lang.Long> findAllLabeledExtractsFromBioMaterialsFound()
           
protected  java.util.Collection<java.lang.Long> findAllLabeledExtractsFromBioSamples(java.util.Collection<java.lang.Long> bioSampleIds)
           
protected  java.util.Collection<java.lang.Long> findAllLabeledExtractsWithCharacteristicsCategoryMatchingOrganismPart()
           
protected  java.util.Collection<java.lang.Long> findAllPhysicalBioAssays()
           
 java.lang.Long[] getIdsForQuery()
           
protected  org.apache.ojb.broker.query.ReportQueryByCriteria query_findAllBioSourcesWithCharacteristicsCategoryMatchingOrganismPart()
           
protected  org.apache.ojb.broker.query.ReportQueryByCriteria query_findAllExperiments(java.util.Collection<java.lang.Long> physicalBioAssayIds)
           
protected  org.apache.ojb.broker.query.ReportQueryByCriteria query_findAllLabeledExtractsFromBioSamples(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
 

Constructor Detail

ExperimentByTissueTypeQuery

public ExperimentByTissueTypeQuery()
Method Detail

getIdsForQuery

public java.lang.Long[] getIdsForQuery()
Specified by:
getIdsForQuery in interface ESCriterionQuery

setCriterion

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

findAllBioSourcesWithCharacteristicsCategoryMatchingOrganismPart

protected java.util.Collection findAllBioSourcesWithCharacteristicsCategoryMatchingOrganismPart()

query_findAllBioSourcesWithCharacteristicsCategoryMatchingOrganismPart

protected org.apache.ojb.broker.query.ReportQueryByCriteria query_findAllBioSourcesWithCharacteristicsCategoryMatchingOrganismPart()

findAllBioSamplesWithCharacteristicsCategoryMatchingOrganismPart

protected java.util.Collection<java.lang.Long> findAllBioSamplesWithCharacteristicsCategoryMatchingOrganismPart()

findAllLabeledExtractsWithCharacteristicsCategoryMatchingOrganismPart

protected java.util.Collection<java.lang.Long> findAllLabeledExtractsWithCharacteristicsCategoryMatchingOrganismPart()

findAllLabeledExtractsFromBioSamples

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

query_findAllLabeledExtractsFromBioSamples

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

findAllLabeledExtractsFromBioMaterialsFound

protected java.util.Collection<java.lang.Long> findAllLabeledExtractsFromBioMaterialsFound()

findAllBioSamplesFromBioSourcesWithCharacteristicsCategoryMatchingOrganismPart

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

findAllPhysicalBioAssays

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

findAllExperiments

protected java.util.Collection findAllExperiments()

query_findAllExperiments

protected org.apache.ojb.broker.query.ReportQueryByCriteria query_findAllExperiments(java.util.Collection<java.lang.Long> physicalBioAssayIds)