gov.nih.nci.common.persistence.enhanced.Experiment
Class ExperimentByOrganismNameQuery
java.lang.Object
gov.nih.nci.common.persistence.enhanced.BaseQueryImpl
gov.nih.nci.common.persistence.enhanced.Experiment.ExperimentByOrganismNameQuery
- All Implemented Interfaces:
- ESCriterionQuery, ESQuery
public class ExperimentByOrganismNameQuery
- extends BaseQueryImpl
- implements ESCriterionQuery
Used to find all Experiment(s) with BioMaterial(s) with characteristics,
OntologyEntry(s) with a category of value 'Organism' OR BioMaterial(s) with
descriptions.annotations with a category of value 'species'
- Author:
- smatyas
1.1a Find all BioSource(s).descriptions.annotations.category='species' AND descriptions.annotations.value is LIKE "%?%"
1.2a Find all BioSample(s).descriptions.annotations.category='species' AND descriptions.annotations.value is LIKE "%?%"
1.3a Find all LabeledExtract(s).descriptions.annotations.category='species' AND descriptions.annotations.value is LIKE "%?%"
1.1. Find all BioSources with characteristics.category = 'Organism'
1.2. Find all BioSamples with characteristics.category = 'Organism', recurse through BioSamples
1.3. Find all LabeledExtracts with characteristics.category = 'Organism'
2. Find all LabeledExtracts from the resultset from step 1.1, 1.1a, 1.2, 1.2a, 1.3, 1.3a
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 founds PhysicalBioAssay(s) = PhysicalBioAssay.bioAssayTreatments.target
4. Find all Experiments for the given the PhysicalBioAssays founds
| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
ExperimentByOrganismNameQuery
public ExperimentByOrganismNameQuery()
setCriterion
public void setCriterion(EnhancedSearchCriterion criterion)
- Specified by:
setCriterion in interface ESCriterionQuery
getIdsForQuery
public java.lang.Long[] getIdsForQuery()
- Specified by:
getIdsForQuery in interface ESCriterionQuery
findAllBioSourcesWithOntologyEntryOfCategorySpecies
protected java.util.Collection<java.lang.Long> findAllBioSourcesWithOntologyEntryOfCategorySpecies()
findAllBioSamplesWithOntologyEntryOfCategorySpecies
protected java.util.Collection<java.lang.Long> findAllBioSamplesWithOntologyEntryOfCategorySpecies()
findAllLabeledExtractsWithOntologyEntryOfCategorySpecies
protected java.util.Collection<java.lang.Long> findAllLabeledExtractsWithOntologyEntryOfCategorySpecies()
findAllBioSourcesWithCharacteristicsCategoryMatchingOrganism
protected java.util.Collection<java.lang.Long> findAllBioSourcesWithCharacteristicsCategoryMatchingOrganism()
query_findAllBioSourcesWithCharacteristicsCategoryMatchingOrganism
protected org.apache.ojb.broker.query.ReportQueryByCriteria query_findAllBioSourcesWithCharacteristicsCategoryMatchingOrganism(java.lang.String[] values)
findAllBioSamplesWithCharacteristicsCategoryMatchingOrganism
protected java.util.Collection<java.lang.Long> findAllBioSamplesWithCharacteristicsCategoryMatchingOrganism()
query_findAllBioSamplesWithCharacteristicsCategoryMatchingOrganism
protected org.apache.ojb.broker.query.ReportQueryByCriteria query_findAllBioSamplesWithCharacteristicsCategoryMatchingOrganism(java.lang.String[] values)
findAllLabeledExtractsWithCharacteristicsCategoryMatchingOrganism
protected java.util.Collection<java.lang.Long> findAllLabeledExtractsWithCharacteristicsCategoryMatchingOrganism()
findAllLabeledExtractsFromBioMaterialsFound
protected java.util.Collection<java.lang.Long> findAllLabeledExtractsFromBioMaterialsFound()
findAllBioSamplesFromBioSourcesWithCharacteristicsCategoryMatchingOrganismOrWithOntologyEntryOfCategorySpecies
protected java.util.Collection<java.lang.Long> findAllBioSamplesFromBioSourcesWithCharacteristicsCategoryMatchingOrganismOrWithOntologyEntryOfCategorySpecies()
- Returns:
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:
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)