gov.nih.nci.common.persistence.enhanced.Experiment
Class ExperimentByTissueTypeQuery
java.lang.Object
gov.nih.nci.common.persistence.enhanced.BaseQueryImpl
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
| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
ExperimentByTissueTypeQuery
public ExperimentByTissueTypeQuery()
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)