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public interface SearchService
Remote service for search and data enumeration. Used by the grid service, and can also be used directly by EJB clients. Several methods in this service accept a LimitOffset parameter to allow the client to request a subset of the results that would otherwise be matched by the provided criteria. For these methods, there may also be a maximum number of results that the system is willing to return for that query, regardless of the limit requested by the client. This maximum is not specified in the method definition (and varies between the methods), but will be be indicated in the return value. The actual number of results returned for these methods will then be the smaller of { maximum system threshold, limit requested by client in the LimitOffset parameter, actual number of results available (taking into account the offset specified)
Field Summary | |
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static java.lang.String |
JNDI_NAME
The JNDI name to look up this Remote EJB under. |
Method Summary | ||
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java.util.List<Category> |
getAllCharacteristicCategories(CaArrayEntityReference experimentRef)
Retrieve the list of all categories of characteristics, either in the entire system, or for given experiment. |
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java.util.List<Person> |
getAllPrincipalInvestigators()
Retrieve list of Person entities that are Principal Investigators on at least one experiment in the system. |
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AnnotationSet |
getAnnotationSet(AnnotationSetRequest request)
Returns an annotation set matching the given request. |
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java.util.List<Term> |
getTermsForCategory(CaArrayEntityReference categoryRef,
java.lang.String valuePrefix)
Retrieve the list of all terms belonging to given category in the system. |
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searchByExample(ExampleSearchCriteria<T> criteria,
LimitOffset limitOffset)
Search for entities based on a specified example. |
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SearchResult<Biomaterial> |
searchForBiomaterials(BiomaterialSearchCriteria criteria,
LimitOffset limitOffset)
Search for biomaterials satisfying the given search criteria. |
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SearchResult<Biomaterial> |
searchForBiomaterialsByKeyword(BiomaterialKeywordSearchCriteria criteria,
LimitOffset limitOffset)
Search for biomaterials matching the given keyword criteria. |
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SearchResult<Experiment> |
searchForExperiments(ExperimentSearchCriteria criteria,
LimitOffset limitOffset)
Search for experiments satisfying the given search criteria. |
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SearchResult<Experiment> |
searchForExperimentsByKeyword(KeywordSearchCriteria criteria,
LimitOffset limitOffset)
Search for experiments matching the given keyword keyword criteria. |
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SearchResult<File> |
searchForFiles(FileSearchCriteria criteria,
LimitOffset limitOffset)
Search for files satisfying the given search criteria. |
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SearchResult<Hybridization> |
searchForHybridizations(HybridizationSearchCriteria criteria,
LimitOffset limitOffset)
Search for hybridizations satisfying the given search criteria. |
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java.util.List<QuantitationType> |
searchForQuantitationTypes(QuantitationTypeSearchCriteria criteria)
Returns a list of quantitation types satisfying the given search criteria. |
Field Detail |
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static final java.lang.String JNDI_NAME
Method Detail |
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java.util.List<Person> getAllPrincipalInvestigators()
java.util.List<Category> getAllCharacteristicCategories(CaArrayEntityReference experimentRef) throws InvalidReferenceException
experimentRef
- if not null, then only categories of characteristics of biomaterials in the given experiment
are returned, otherwise categories of all characteristics in the system are returned.
InvalidReferenceException
- if the given reference does not identify an existing experiment in the system.java.util.List<Term> getTermsForCategory(CaArrayEntityReference categoryRef, java.lang.String valuePrefix) throws InvalidReferenceException
categoryRef
- reference identifying the categoryvaluePrefix
- if not null, only include terms whose value starts with given prefix, using case insensitive
matching
InvalidReferenceException
- if the given reference does not identify an existing category in the system.SearchResult<Experiment> searchForExperiments(ExperimentSearchCriteria criteria, LimitOffset limitOffset) throws InvalidReferenceException, UnsupportedCategoryException
criteria
- the search criteria.limitOffset
- an optional parameter specifying the number of results to return, and the offset of the first
result to return within the overall result set. May be left null to indicate the entire result set is
requested.
InvalidReferenceException
- if any references within the given criteria are not valid, e.g. refer to
entities that do not exist or are not of the correct types
UnsupportedCategoryException
- if the search criteria includes an annotation criterion with a category
other that disease state, cell type, material type, tissue site.SearchResult<Experiment> searchForExperimentsByKeyword(KeywordSearchCriteria criteria, LimitOffset limitOffset)
criteria
- the keyword criteria to search for.limitOffset
- an optional parameter specifying the number of results to return, and the offset of the first
result to return within the overall result set. May be left null to indicate the entire result set is
requested.
SearchResult<Biomaterial> searchForBiomaterials(BiomaterialSearchCriteria criteria, LimitOffset limitOffset) throws InvalidReferenceException, UnsupportedCategoryException
criteria
- the search criterialimitOffset
- an optional parameter specifying the number of results to return, and the offset of the first
result to return within the overall result set. May be left null to indicate the entire result set is
requested.
InvalidReferenceException
- if any references within the given criteria are not valid, e.g. refer to
entities that do not exist or are not of the correct types
UnsupportedCategoryException
- if the search criteria includes an annotation criterion with a category
other that disease state, cell type, material type, tissue site.SearchResult<Biomaterial> searchForBiomaterialsByKeyword(BiomaterialKeywordSearchCriteria criteria, LimitOffset limitOffset)
criteria
- the keyword criteria to search for; this identifies the string to look for, and the types of
biomaterials to include in the results.limitOffset
- an optional parameter specifying the number of results to return, and the offset of the first
result to return within the overall result set. May be left null to indicate the entire result set is
requested.
SearchResult<Hybridization> searchForHybridizations(HybridizationSearchCriteria criteria, LimitOffset limitOffset) throws InvalidReferenceException
criteria
- the search criterialimitOffset
- an optional parameter specifying the number of results to return, and the offset of the first
result to return within the overall result set. May be left null to indicate the entire result set is
requested.
InvalidReferenceException
- if any references within the given criteria are not valid, e.g. refer to
entities that do not exist or are not of the correct typesSearchResult<File> searchForFiles(FileSearchCriteria criteria, LimitOffset limitOffset) throws InvalidReferenceException
criteria
- the search criteria.limitOffset
- an optional parameter specifying the number of results to return, and the offset of the first
result to return within the overall result set. May be left null to indicate the entire result set is
requested.
InvalidReferenceException
- if any references within the given criteria are not valid, e.g. refer to
entities that do not exist or are not of the correct typesDataService
java.util.List<QuantitationType> searchForQuantitationTypes(QuantitationTypeSearchCriteria criteria) throws InvalidReferenceException, InvalidInputException
criteria
- the search criteria. The criteria must, at a minimum, include a reference to a Hybridization.
InvalidReferenceException
- if any references within the given criteria are not valid, e.g. refer to
entities that do not exist or are not of the correct types
InvalidInputException
- if the search criteria does not have a non-null Hybridization reference<T extends AbstractCaArrayEntity> SearchResult<T> searchByExample(ExampleSearchCriteria<T> criteria, LimitOffset limitOffset) throws InvalidInputException
T
- type of the example entitycriteria
- the criteria specifying the example entity, as well as rules defining how candidate entities are
matched against the examplelimitOffset
- an optional parameter specifying the number of results to return, and the offset of the first
result to return within the overall result set. May be left null to indicate the entire result set is
requested.
InvalidInputException
- if a null example is givenAnnotationSet getAnnotationSet(AnnotationSetRequest request) throws InvalidReferenceException
The annotation set will include an AnnotationColumn for each ExperimentGraphNode included in the request; each AnnotationColumn will include an AnnotationValueSet for each Category included in the request. The AnnotationValueSet for a given experiment node and characteristic category is calculated as follows:
request
- the annotation set request
InvalidReferenceException
- if any references within the given criteria are not valid, e.g. refer to
entities that do not exist or are not of the correct types
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