Package ome.api

Interface Search

    • Method Summary

      All Methods Instance Methods Abstract Methods Deprecated Methods 
      Modifier and Type Method Description
      int activeQueries()
      Returns the number of active queries.
      void addOrderByAsc​(java.lang.String path)
      A path from the target entity which will be added to the current stack of order statements applied to the query.
      void addOrderByDesc​(java.lang.String path)
      A path from the target entity which will be added to the current stack of order statements applied to the query.
      void allTypes()
      Permits all types to be returned.
      void and()
      Applies the next by* method to the previous by* method, so that a call hasNext(), next(), or results() sees only the intersection of the two calls.
      void byAnnotatedWith​(ome.model.annotations.Annotation... examples)
      Finds entities annotated with an Annotation similar to the example.
      void byFullText​(java.lang.String query)
      Passes the query as is to the Lucene backend.
      void byGroupForTags​(java.lang.String group)
      Returns transient (without ID) TagAnnotation instances which represent all the tags in the given group.
      void byHqlQuery​(java.lang.String query, ome.parameters.Parameters p)
      Delegates to IQuery.findAllByQuery(String, Parameters) method to take advantage of the and(), or(), and not() methods, or queue-semantics.
      void byLuceneQueryBuilder​(java.lang.String fields, java.lang.String from, java.lang.String to, java.lang.String dateType, java.lang.String query)
      Builds a Lucene query and passes it to the Lucene backend.
      void bySimilarTerms​(java.lang.String... terms)
      Returns transient (without ID) TextAnnotation instances which represent terms which are similar to the given terms.
      void bySomeMustNone​(java.lang.String[] some, java.lang.String[] must, java.lang.String[] none)
      Builds a Lucene query and passes it to byFullText(String).
      void byTagForGroups​(java.lang.String tag)
      Creates a query which will return transient (without ID) TagAnnotation instances which represent all the tag groups which the given tag belongs to.
      void clearQueries()
      Removes all active queries (leaving settings alone), such that activeQueries() will return 0.
      java.util.Map<java.lang.String,​ome.model.annotations.Annotation> currentMetadata()
      Provides access to the extra query information (for example Lucene score and boost values) for a single call to next().
      java.util.List<java.util.Map<java.lang.String,​ome.model.annotations.Annotation>> currentMetadataList()
      Provides access to the extra query information (for example Lucene score and boost values) for a single call to results().
      void fetchAlso​(java.lang.String... fetches)
      Adds a fetch clause for loading non-annotation fields of returned entities.
      void fetchAnnotations​(java.lang.Class... classes)
      Queries the database for all annotations of the given types for all returned instances.
      int getBatchSize()
      Returns the current batch size.
      boolean hasNext()
      Returns true if another call to next() is valid.
      boolean isAllowLeadingWildcard()
      Returns the current leading-wildcard setting.
      boolean isCaseSensitive()
      Returns the current case sensitivity setting.
      boolean isMergedBatches()
      Returns the current merged-batches setting.
      boolean isReturnUnloaded()
      Returns the current return-unloaded setting.
      boolean isUseProjections()
      Returns the current use-projection setting.
      ome.model.IObject next()
      Returns the next entity from the current query.
      void not()
      Applies the next by* method to the previous by* method, so that a call hasNext(), next(), or results() sees only the intersection of the two calls.
      void notAnnotatedBy​(ome.model.internal.Details d)
      Restricts entities by who has not annotated them with an Annotation matching the other filters.
      void notOwnedBy​(ome.model.internal.Details d)
      Uses the Details.getOwner() and Details.getGroup() information to restrict the entities which will be returned.
      void onlyAnnotatedBetween​(java.sql.Timestamp start, java.sql.Timestamp stop)
      Restricts entities by the time in which any annotation (which matches the other filters) was added them.
      void onlyAnnotatedBy​(ome.model.internal.Details d)
      Restricts entities by who has annotated them with an Annotation matching the other filters.
      void onlyAnnotatedWith​(java.lang.Class... classes)
      Restricts entities to having an Annotation of all the given types.
      void onlyCreatedBetween​(java.sql.Timestamp start, java.sql.Timestamp stop)
      Restricts the time between which an entity may have been created.
      void onlyIds​(java.lang.Long... ids)
      Restricts the set of ids which will be checked.
      void onlyModifiedBetween​(java.sql.Timestamp start, java.sql.Timestamp stop)
      Restricts the time between which an entity may have last been modified.
      void onlyOwnedBy​(ome.model.internal.Details d)
      Uses the Details.getOwner() and Details.getGroup() information to restrict the entities which will be returned.
      <T extends ome.model.IObject>
      void      		 onlyType​(java.lang.Class<T> klass)
      Restricts the search to a single type.
      <T extends ome.model.IObject>
      void      		 onlyTypes​(java.lang.Class<T>... classes)
      Restricts searches to a set of types.
      void or()
      Applies the next by* method to the previous by* method, so that a call hasNext(), next(), or results() sees only the union of the two calls.
      void remove()
      Unsupported operation.
      void resetDefaults()
      Resets all settings (non-query state) to the original default values, as if the instance had just be created.
      <T extends ome.model.IObject>
      java.util.List<T>      		 results()
      Returns up to batch size number of results along with the related query metadata.
      void setAllowLeadingWildcard​(boolean allowLeadingWildcard)
      Permits full-text queries with a leading query if true.
      void setBatchSize​(int size)
      Sets the maximum number of results that will be returned by one call to results().
      void setCaseSensitive​(boolean caseSensitive)
      Sets the case sensitivity on all queries where case-sensitivity is supported.
      void setCaseSentivice​(boolean caseSensitive)
      Deprecated.
      use setCaseSensitive(boolean)
      void setMergedBatches​(boolean merge)
      Set whether or not results from two separate queries can be returned in the same call to results().
      void setReturnUnloaded​(boolean returnUnloaded)
      Determines if all results should be returned as unloaded objects.
      void setUseProjections​(boolean useProjections)
      Determines if Lucene queries should not hit the database.
      void unordered()
      Removes the current stack of order statements.

      • Methods inherited from interface java.util.Iterator

        forEachRemaining

    • Method Detail

      • activeQueries

        int activeQueries()
        Returns the number of active queries. This means that activeQueries gives the minimum number of remaining calls to results() when batches are not merged.
        Returns:
        number of active queries

      • setBatchSize

        void setBatchSize​(int size)
        Sets the maximum number of results that will be returned by one call to results(). If batches are not merged, then results may often be less than the batch size. If batches are merged, then only the last call to results() can be less than batch size. Note: some query types may not support batching at the query level, and all instances must then be loaded into memory simultaneously.
        Parameters:
        size - maximum number of results per call to results()

      • setMergedBatches

        void setMergedBatches​(boolean merge)
        Set whether or not results from two separate queries can be returned in the same call to results().

      • setCaseSentivice

        @Deprecated
void setCaseSentivice​(boolean caseSensitive)
        Deprecated.
        use setCaseSensitive(boolean)
        Sets the case sensitivity on all queries where case-sensitivity is supported.

      • setCaseSensitive

        void setCaseSensitive​(boolean caseSensitive)
        Sets the case sensitivity on all queries where case-sensitivity is supported.

      • setUseProjections

        void setUseProjections​(boolean useProjections)
        Determines if Lucene queries should not hit the database. Instead all values which are stored in the index will be loaded into the object, which includes the id. However, the entity will not be marked unloaded and therefore it is especially important to not allow a projection-instance to be saved back to the server. This can result in DATA LOSS.

      • setReturnUnloaded

        void setReturnUnloaded​(boolean returnUnloaded)
        Determines if all results should be returned as unloaded objects. This is particularly useful for creating lists for further querying via IQuery. This value overrides the setUseProjections(boolean) setting.

      • isReturnUnloaded

        boolean isReturnUnloaded()
        Returns the current return-unloaded setting. If true, all returned entities will be unloaded. If setReturnUnloaded(boolean) has not been called, the default value will be in effect.

      • onlyType

        <T extends ome.model.IObject> void onlyType​(java.lang.Class<T> klass)
        Restricts the search to a single type. All return values will match this type.

      • onlyTypes

        <T extends ome.model.IObject> void onlyTypes​(java.lang.Class<T>... classes)
        Restricts searches to a set of types. The entities returned are guaranteed to be one of these types.

      • allTypes

        void allTypes()
        Permits all types to be returned. For some types of queries, this carries a performance penalty as every database table must be hit.

      • onlyIds

        void onlyIds​(java.lang.Long... ids)
        Restricts the set of ids which will be checked. This is useful for testing one of the given restrictions on a reduced set of objects.
        Parameters:
        ids - Can be null, in which case the previous restriction is removed.

      • onlyOwnedBy

        void onlyOwnedBy​(ome.model.internal.Details d)
        Uses the Details.getOwner() and Details.getGroup() information to restrict the entities which will be returned. If both are non-null, the two restrictions are joined by an AND.
        Parameters:
        d - Can be null, in which case the previous restriction is removed.

      • notOwnedBy

        void notOwnedBy​(ome.model.internal.Details d)
        Uses the Details.getOwner() and Details.getGroup() information to restrict the entities which will be returned. If both are non-null, the two restrictions are joined by an AND.
        Parameters:
        d - Can be null, in which case the previous restriction is removed.

      • onlyCreatedBetween

        void onlyCreatedBetween​(java.sql.Timestamp start,
                        java.sql.Timestamp stop)
        Restricts the time between which an entity may have been created.
        Parameters:
        start - Can be null, i.e. interval open to negative infinity.
        stop - Can be null, i.e. interval opens to positive infinity.

      • onlyModifiedBetween

        void onlyModifiedBetween​(java.sql.Timestamp start,
                         java.sql.Timestamp stop)
        Restricts the time between which an entity may have last been modified.
        Parameters:
        start - Can be null, i.e. interval open to negative infinity.
        stop - Can be null, i.e. interval open to positive infinity.

      • onlyAnnotatedBetween

        void onlyAnnotatedBetween​(java.sql.Timestamp start,
                          java.sql.Timestamp stop)
        Restricts entities by the time in which any annotation (which matches the other filters) was added them. This matches the creation event of the Annotation.
        Parameters:
        start - Can be null, i.e. interval open to negative infinity.
        stop - Can be null, i.e. interval open to positive infinity.

      • onlyAnnotatedBy

        void onlyAnnotatedBy​(ome.model.internal.Details d)
        Restricts entities by who has annotated them with an Annotation matching the other filters. As onlyOwnedBy(Details), the Details.getOwner() and Details.getGroup() information is combined with an AND condition.
        Parameters:
        d - Can be null, in which case any previous restriction is removed.

      • notAnnotatedBy

        void notAnnotatedBy​(ome.model.internal.Details d)
        Restricts entities by who has not annotated them with an Annotation matching the other filters. As notOwnedBy(Details), the Details.getOwner() and Details.getGroup() information is combined with an AND condition.
        Parameters:
        d - Can be null, in which case any previous restriction is removed.

      • onlyAnnotatedWith

        void onlyAnnotatedWith​(java.lang.Class... classes)
        Restricts entities to having an Annotation of all the given types. This is useful in combination with the other onlyAnnotated* methods to say, e.g., only annotated with a file by user X. By default, this value is null and imposes no restriction. Passing an empty array implies an object that is not annotated at all. Note: If the semantics were OR, then a client would have to query each class individually, and compare all the various values, checking which ids are where. However, since this method defaults to AND, multiple calls (optionally with isMergedBatches() and isReturnUnloaded()) and combine the results. Duplicate ids are still possible, so a set of some form should be used to collect the results.
        Parameters:
        classes - Can be empty, in which case restriction is removed.

      • addOrderByAsc

        void addOrderByAsc​(java.lang.String path)
        A path from the target entity which will be added to the current stack of order statements applied to the query.
        Parameters:
        path - Non-null.
        See Also:
        unordered()

      • addOrderByDesc

        void addOrderByDesc​(java.lang.String path)
        A path from the target entity which will be added to the current stack of order statements applied to the query.
        Parameters:
        path - Non-null.
        See Also:
        unordered()

      • fetchAnnotations

        void fetchAnnotations​(java.lang.Class... classes)
        Queries the database for all annotations of the given types for all returned instances.
        Parameters:
        classes - Can be empty, which removes previous fetch setting.

      • fetchAlso

        void fetchAlso​(java.lang.String... fetches)
        Adds a fetch clause for loading non-annotation fields of returned entities. Each fetch is a hibernate clause in dot notation.
        Parameters:
        fetches - Can be empty, which removes previous fetch setting.

      • resetDefaults

        void resetDefaults()
        Resets all settings (non-query state) to the original default values, as if the instance had just be created.

      • bySimilarTerms

        void bySimilarTerms​(java.lang.String... terms)
        Returns transient (without ID) TextAnnotation instances which represent terms which are similar to the given terms. For example, if the argument is "cell", one return value might have as its textValue: "cellular" while another has "cellularize". No filtering or fetching is performed.
        Parameters:
        terms - Cannot be empty.

      • byGroupForTags

        void byGroupForTags​(java.lang.String group)
        Returns transient (without ID) TagAnnotation instances which represent all the tags in the given group. The entities are transient and without ownership since multiple users can own the same tag. This method will override settings for types.
        Parameters:
        group - Can be null or empty to return all tags.

      • byTagForGroups

        void byTagForGroups​(java.lang.String tag)
        Creates a query which will return transient (without ID) TagAnnotation instances which represent all the tag groups which the given tag belongs to. The entities are transient and without ownership since multiple users can own the same tag group. This method will override settings for types.
        Parameters:
        tag - Can be null or empty to return all groups.

      • byFullText

        void byFullText​(java.lang.String query)
        Passes the query as is to the Lucene backend.
        Parameters:
        query - May not be null or of zero length.

      • byLuceneQueryBuilder

        void byLuceneQueryBuilder​(java.lang.String fields,
                          java.lang.String from,
                          java.lang.String to,
                          java.lang.String dateType,
                          java.lang.String query)
        Builds a Lucene query and passes it to the Lucene backend.
        Parameters:
        fields - The fields (comma separated) to search in (name, description, ...)
        from - The date range from, in the form YYYYMMDD (may be null)
        to - The date range to (inclusive), in the form YYYYMMDD (may be null)
        dateType - DATE_TYPE_ACQUISITION or DATE_TYPE_IMPORT
        query - May not be null or of zero length.

      • bySomeMustNone

        void bySomeMustNone​(java.lang.String[] some,
                    java.lang.String[] must,
                    java.lang.String[] none)
        Builds a Lucene query and passes it to byFullText(String).
        Parameters:
        some - Some (at least one) of these terms must be present in the document. May be null.
        must - All of these terms must be present in the document. May be null.
        none - None of these terms may be present in the document. May be null.

      • byAnnotatedWith

        void byAnnotatedWith​(ome.model.annotations.Annotation... examples)
        Finds entities annotated with an Annotation similar to the example. This does not use Hibernate's Query-By-Example mechanism, since that cannot handle joins. The fields which are used are:
        • the main content of the annotation : String, OriginalFile.getId(), etc.

        If the main content is null it is assumed to be a wildcard searched, and only the type of the annotation is searched. Currently, ListAnnotations are not supported.

        Parameters:
        examples - Not empty.

      • or

        void or()
        Applies the next by* method to the previous by* method, so that a call hasNext(), next(), or results() sees only the union of the two calls. For example, 
         service.onlyType(Image.class);
 service.byFullText("foo");
 service.or();
 service.onlyType(Dataset.class);
 service.byFullText("foo");
        will return both Images and Datasets together. Calling this method overrides a previous setting of and() or not(). If there is no active queries (i.e. activeQueries() greater than 0), then an ApiUsageException will be thrown.

      • and

        void and()
        Applies the next by* method to the previous by* method, so that a call hasNext(), next(), or results() sees only the intersection of the two calls. For example, 
         service.onlyType(Image.class);
 service.byFullText("foo");
 service.intersection();
 service.byAnnotatedWith(TagAnnotation.class);
        will return only the Images with TagAnnotations.

        Calling this method overrides a previous setting of or() or not(). If there is no active queries (i.e. activeQueries() greater than 0), then an ApiUsageException will be thrown.

      • not

        void not()
        Applies the next by* method to the previous by* method, so that a call hasNext(), next(), or results() sees only the intersection of the two calls. For example, 
         service.onlyType(Image.class);
 service.byFullText("foo");
 service.complement();
 service.byAnnotatedWith(TagAnnotation.class);
        will return all the Images not annotated with TagAnnotation.

        Calling this method overrides a previous setting of or() or and(). If there is no active queries (i.e. activeQueries() greater than 0), then an ApiUsageException will be thrown.

      • clearQueries

        void clearQueries()
        Removes all active queries (leaving settings alone), such that activeQueries() will return 0.

      • hasNext

        boolean hasNext()
        Returns true if another call to next() is valid. A call to next() may throw an exception for another reason, however.
        Specified by:
        hasNext in interface java.util.Iterator<ome.model.IObject>

      • next

        ome.model.IObject next()
                throws ome.conditions.ApiUsageException
        Returns the next entity from the current query. If the previous call returned the last entity from a given query, the first entity from the next query will be returned and activeQueries() decremented. Since this method only returns the entity itself, a single call to currentMetadata() may follow this call to gather the extra metadata which is returned in the map via results().
        Specified by:
        next in interface java.util.Iterator<ome.model.IObject>
        Throws:
        ome.conditions.ApiUsageException - if hasNext() returns false.

      • currentMetadata

        java.util.Map<java.lang.String,​ome.model.annotations.Annotation> currentMetadata()
        Provides access to the extra query information (for example Lucene score and boost values) for a single call to next(). This method may only be called once for any given call to next().

      • remove

        void remove()
     throws java.lang.UnsupportedOperationException
        Unsupported operation.
        Specified by:
        remove in interface java.util.Iterator<ome.model.IObject>
        Throws:
        java.lang.UnsupportedOperationException

      • results

        <T extends ome.model.IObject> java.util.List<T> results()
                                                 throws ome.conditions.ApiUsageException
        Returns up to batch size number of results along with the related query metadata. If batches are merged then the results from multiple queries may be returned together.
        Throws:
        ome.conditions.ApiUsageException - if hasNext() returns false.

      • currentMetadataList

        java.util.List<java.util.Map<java.lang.String,​ome.model.annotations.Annotation>> currentMetadataList()
        Provides access to the extra query information (for example Lucene score and boost values) for a single call to results(). This method may only be called once for any given call to results().