Package ome.model.containers

Class Dataset

  • All Implemented Interfaces:
    java.io.Serializable, IAnnotated, IMutable, IObject, Filterable
    @Entity
@Indexed(index="FullText")
@ClassBridge(name="details",
             impl=DetailsFieldBridge.class,
             index=UN_TOKENIZED,
             store=NO)
public class Dataset
extends java.lang.Object
implements java.io.Serializable, IObject, IMutable, IAnnotated
    These filter definitions are used by the security system to eliminate non-readable objects from queries. The regular user does not need to worry about them, as they will be injected directly into the SQL (not HQL)
    See Also:
    Serialized Form

    • Field Detail

      • id

        protected java.lang.Long id

      • version

        protected java.lang.Integer version

      • OWNER_FILTER_PROJECTLINKS

        public static final java.lang.String OWNER_FILTER_PROJECTLINKS
        See Also:
        Constant Field Values

      • GROUP_FILTER_PROJECTLINKS

        public static final java.lang.String GROUP_FILTER_PROJECTLINKS
        See Also:
        Constant Field Values

      • EVENT_FILTER_PROJECTLINKS

        public static final java.lang.String EVENT_FILTER_PROJECTLINKS
        See Also:
        Constant Field Values

      • PERMS_FILTER_PROJECTLINKS

        public static final java.lang.String PERMS_FILTER_PROJECTLINKS
        See Also:
        Constant Field Values

      • OWNER_FILTER_IMAGELINKS

        public static final java.lang.String OWNER_FILTER_IMAGELINKS
        See Also:
        Constant Field Values

      • GROUP_FILTER_IMAGELINKS

        public static final java.lang.String GROUP_FILTER_IMAGELINKS
        See Also:
        Constant Field Values

      • EVENT_FILTER_IMAGELINKS

        public static final java.lang.String EVENT_FILTER_IMAGELINKS
        See Also:
        Constant Field Values

      • PERMS_FILTER_IMAGELINKS

        public static final java.lang.String PERMS_FILTER_IMAGELINKS
        See Also:
        Constant Field Values

      • OWNER_FILTER_ANNOTATIONLINKS

        public static final java.lang.String OWNER_FILTER_ANNOTATIONLINKS
        See Also:
        Constant Field Values

      • GROUP_FILTER_ANNOTATIONLINKS

        public static final java.lang.String GROUP_FILTER_ANNOTATIONLINKS
        See Also:
        Constant Field Values

      • EVENT_FILTER_ANNOTATIONLINKS

        public static final java.lang.String EVENT_FILTER_ANNOTATIONLINKS
        See Also:
        Constant Field Values

      • PERMS_FILTER_ANNOTATIONLINKS

        public static final java.lang.String PERMS_FILTER_ANNOTATIONLINKS
        See Also:
        Constant Field Values

      • name

        protected java.lang.String name

      • description

        protected java.lang.String description

      • details

        protected Details details

      • PROJECTLINKSCOUNTPEROWNER

        public static final java.lang.String PROJECTLINKSCOUNTPEROWNER
        See Also:
        Constant Field Values

      • IMAGELINKSCOUNTPEROWNER

        public static final java.lang.String IMAGELINKSCOUNTPEROWNER
        See Also:
        Constant Field Values

      • ANNOTATIONLINKSCOUNTPEROWNER

        public static final java.lang.String ANNOTATIONLINKSCOUNTPEROWNER
        See Also:
        Constant Field Values

      • FIELDS

        public static final java.util.Set<java.lang.String> FIELDS

      • _dynamicFields

        protected java.util.Map<java.lang.String,​java.lang.Object> _dynamicFields

      • _loaded

        protected boolean _loaded

    • Constructor Detail

      • Dataset

        public Dataset()

      • Dataset

        protected Dataset​(java.lang.Long id)

      • Dataset

        public Dataset​(java.lang.Long id,
               boolean loaded)
        Main constructor.

      • Dataset

        public Dataset​(java.lang.String _name)

    • Method Detail

      • getId

        @DocumentId
public java.lang.Long getId()
        The DB unique identifier for this object. You are not responsible for setting the id; however, it can be useful for creating "unloaded" versions of your objects. Each top-level entity contains an id field of type long. For all objects returned from the server, this value will be non-null, which doesn't necessarily hold for the other fields.
        Specified by:
        getId in interface IObject
        Returns:
        Long primary key. May be null.

      • setId

        public void setId​(java.lang.Long id)
        Description copied from interface: IObject
        usually unneeded. Ids are managed by the backend.
        Specified by:
        setId in interface IObject
        Parameters:
        id - Long value for this id.

      • getVersion

        public java.lang.Integer getVersion()
        This version number is controlled by the database for optimisitic locking.
        Specified by:
        getVersion in interface IMutable

      • setVersion

        public void setVersion​(java.lang.Integer version)
        Description copied from interface: IMutable
        use with caution. In general, the version should only be altered by the backend. In the best case, an exception will be thrown for a version not equal to the current DB value. In the worst (though rare) case, the new version could match the database, and override optimistic lock checks that are supposed to prevent data loss.
        Specified by:
        setVersion in interface IMutable
        Parameters:
        version - Value for this objects version.

      • getProjectLinks

        protected java.util.Set<ProjectDatasetLink> getProjectLinks()
        returns projectLinks . You should not modify this collection unless you know what you are doing. Use the iterate method instead. one-to-many Set ome.model.containers.Dataset.projectLinks (ome.model.containers.ProjectDatasetLink)

      • setProjectLinks

        protected void setProjectLinks​(java.util.Set<ProjectDatasetLink> projectLinks)
        setter for projectLinks should be avoided. Does not fulfill normal semantics.

      • sizeOfProjectLinks

        public int sizeOfProjectLinks()
        returns the size of projectLinks. If less than zero, the Set was null.

      • iterateProjectLinks

        public java.util.Iterator<ProjectDatasetLink> iterateProjectLinks()
        should be used rather than accessing the projectLinks set directly. This method will never return null, but rather will return an instance of EmptyIterator. To test for a null collection, see of sizeOfProjectLinks() is less than zero.

      • unmodifiableProjectLinks

        public java.util.Collection<ProjectDatasetLink> unmodifiableProjectLinks()
        Returns an unmodifiable collection-view

      • collectProjectLinks

        public <E> java.util.List<E> collectProjectLinks​(CBlock<E> block)
        takes a CBlock and calls the block once for each ome.model.containers.ProjectDatasetLink while collecting the results. If block == null, then the iterator values themselves are collected. This method uses iterateProjectLinks() internally and so will return a value even if the underlying collection is null.

      • addProjectDatasetLink

        public void addProjectDatasetLink​(ProjectDatasetLink target)
        use instead of setProjectLinks . Makes the necessary call on ome.model.containers.ProjectDatasetLink as well.

      • addProjectDatasetLinkSet

        public void addProjectDatasetLinkSet​(java.util.Collection<ProjectDatasetLink> targets)
        use like addProjectDatasetLink.

      • removeProjectDatasetLink

        public void removeProjectDatasetLink​(ProjectDatasetLink target)
        removes a single element from this set and makes the inverse call on ome.model.containers.ProjectDatasetLink

      • removeProjectDatasetLinkSet

        public void removeProjectDatasetLinkSet​(java.util.Collection<ProjectDatasetLink> targets)
        use like removeProjectDatasetLink

      • linkProject

        public ProjectDatasetLink linkProject​(Project addition)
        Adds a ome.model.containers.ProjectDatasetLink to projectLinks . This entails changing our projectLinks Set, creating a new ome.model.containers.ProjectDatasetLink and calling linkProject on the ome.model.containers.Project.

      • addProjectDatasetLink

        public void addProjectDatasetLink​(ProjectDatasetLink link,
                                  boolean bothSides)
        Adds a ome.model.containers.ProjectDatasetLink to projectLinks, allowing for recursion -- whether or not addProjectDatasetLink will be called on the addition if it is loaded

      • linkedProjectIterator

        public java.util.Iterator<Project> linkedProjectIterator()
        provides an iterator over the child values of the projectLinks. Like with most Collection iterators, modifications to the underlying collection while iterating will result in an ConcurrentModificationException. Use linkedProjectList() instead.

      • findProjectDatasetLink

        public java.util.Set<ProjectDatasetLink> findProjectDatasetLink​(Project target)
        find all ome.model.containers.ProjectDatasetLink which have the argument as their parent.

      • linkedProjectList

        public java.util.List<Project> linkedProjectList()
        produces a List-copy of the underlying collection. Unlike, linkedProjectIterator(), while using the returned List, modifications can be made to the underlying collection without throwing ConcurrentModificationException.

      • eachLinkedProject

        public <E> java.util.List<E> eachLinkedProject​(CBlock<E> block)
        takes a CBlock and calls the block once for each ome.model.containers.Project while collecting the results. If block == null, then the iterator values themselves are collected.

      • unlinkProject

        public void unlinkProject​(Project removal)
        unlinks all ome.model.containers.Project instances from this instance.

      • removeProjectDatasetLink

        public void removeProjectDatasetLink​(ProjectDatasetLink link,
                                     boolean bothSides)
        removes the given ProjectDatasetLink from projectLinks, allowing for recursion -- whether or not the removal will call unlinkDataset again if loaded.

      • clearProjectLinks

        public void clearProjectLinks()
        clears the set.

      • setProjectLinksCountPerOwner

        protected void setProjectLinksCountPerOwner​(java.util.Map<java.lang.Long,​java.lang.Long> map)

      • getProjectLinksCountPerOwner

        public java.util.Map<java.lang.Long,​java.lang.Long> getProjectLinksCountPerOwner()
        If fetched, returns the count(*) of ome.model.containers.ProjectDatasetLink that a user has. If unfetched, returns null. No entries in the collection should be null.

      • getImageLinks

        protected java.util.Set<DatasetImageLink> getImageLinks()
        returns imageLinks . You should not modify this collection unless you know what you are doing. Use the iterate method instead. one-to-many Set ome.model.containers.Dataset.imageLinks (ome.model.containers.DatasetImageLink)

      • setImageLinks

        protected void setImageLinks​(java.util.Set<DatasetImageLink> imageLinks)
        setter for imageLinks should be avoided. Does not fulfill normal semantics.

      • sizeOfImageLinks

        public int sizeOfImageLinks()
        returns the size of imageLinks. If less than zero, the Set was null.

      • iterateImageLinks

        public java.util.Iterator<DatasetImageLink> iterateImageLinks()
        should be used rather than accessing the imageLinks set directly. This method will never return null, but rather will return an instance of EmptyIterator. To test for a null collection, see of sizeOfImageLinks() is less than zero.

      • unmodifiableImageLinks

        public java.util.Collection<DatasetImageLink> unmodifiableImageLinks()
        Returns an unmodifiable collection-view

      • collectImageLinks

        public <E> java.util.List<E> collectImageLinks​(CBlock<E> block)
        takes a CBlock and calls the block once for each ome.model.containers.DatasetImageLink while collecting the results. If block == null, then the iterator values themselves are collected. This method uses iterateImageLinks() internally and so will return a value even if the underlying collection is null.

      • addDatasetImageLink

        public void addDatasetImageLink​(DatasetImageLink target)
        use instead of setImageLinks . Makes the necessary call on ome.model.containers.DatasetImageLink as well.

      • addDatasetImageLinkSet

        public void addDatasetImageLinkSet​(java.util.Collection<DatasetImageLink> targets)
        use like addDatasetImageLink.

      • removeDatasetImageLink

        public void removeDatasetImageLink​(DatasetImageLink target)
        removes a single element from this set and makes the inverse call on ome.model.containers.DatasetImageLink

      • removeDatasetImageLinkSet

        public void removeDatasetImageLinkSet​(java.util.Collection<DatasetImageLink> targets)
        use like removeDatasetImageLink

      • linkImage

        public DatasetImageLink linkImage​(Image addition)
        Adds a ome.model.containers.DatasetImageLink to imageLinks . This entails changing our imageLinks Set, creating a new ome.model.containers.DatasetImageLink and calling linkImage on the ome.model.core.Image.

      • addDatasetImageLink

        public void addDatasetImageLink​(DatasetImageLink link,
                                boolean bothSides)
        Adds a ome.model.containers.DatasetImageLink to imageLinks, allowing for recursion -- whether or not addDatasetImageLink will be called on the addition if it is loaded

      • linkedImageIterator

        public java.util.Iterator<Image> linkedImageIterator()
        provides an iterator over the parent values of the imageLinks. Like with most Collection iterators, modifications to the underlying collection while iterating will result in an ConcurrentModificationException. Use linkedImageList() instead.

      • findDatasetImageLink

        public java.util.Set<DatasetImageLink> findDatasetImageLink​(Image target)
        find all ome.model.containers.DatasetImageLink which have the argument as their child.

      • linkedImageList

        public java.util.List<Image> linkedImageList()
        produces a List-copy of the underlying collection. Unlike, linkedImageIterator(), while using the returned List, modifications can be made to the underlying collection without throwing ConcurrentModificationException.

      • eachLinkedImage

        public <E> java.util.List<E> eachLinkedImage​(CBlock<E> block)
        takes a CBlock and calls the block once for each ome.model.core.Image while collecting the results. If block == null, then the iterator values themselves are collected.

      • unlinkImage

        public void unlinkImage​(Image removal)
        unlinks all ome.model.core.Image instances from this instance.

      • removeDatasetImageLink

        public void removeDatasetImageLink​(DatasetImageLink link,
                                   boolean bothSides)
        removes the given DatasetImageLink from imageLinks, allowing for recursion -- whether or not the removal will call unlinkDataset again if loaded.

      • clearImageLinks

        public void clearImageLinks()
        clears the set.

      • setImageLinksCountPerOwner

        protected void setImageLinksCountPerOwner​(java.util.Map<java.lang.Long,​java.lang.Long> map)

      • getImageLinksCountPerOwner

        public java.util.Map<java.lang.Long,​java.lang.Long> getImageLinksCountPerOwner()
        If fetched, returns the count(*) of ome.model.containers.DatasetImageLink that a user has. If unfetched, returns null. No entries in the collection should be null.

      • getAnnotationLinks

        protected java.util.Set<DatasetAnnotationLink> getAnnotationLinks()
        returns annotationLinks . You should not modify this collection unless you know what you are doing. Use the iterate method instead. one-to-many Set ome.model.containers.Dataset.annotationLinks (ome.model.annotations.DatasetAnnotationLink)

      • setAnnotationLinks

        protected void setAnnotationLinks​(java.util.Set<DatasetAnnotationLink> annotationLinks)
        setter for annotationLinks should be avoided. Does not fulfill normal semantics.

      • sizeOfAnnotationLinks

        public int sizeOfAnnotationLinks()
        returns the size of annotationLinks. If less than zero, the Set was null.
        Specified by:
        sizeOfAnnotationLinks in interface IAnnotated

      • collectAnnotationLinks

        public <E> java.util.List<E> collectAnnotationLinks​(CBlock<E> block)
        takes a CBlock and calls the block once for each ome.model.annotations.DatasetAnnotationLink while collecting the results. If block == null, then the iterator values themselves are collected. This method uses iterateAnnotationLinks() internally and so will return a value even if the underlying collection is null.
        Specified by:
        collectAnnotationLinks in interface IAnnotated

      • addDatasetAnnotationLink

        public void addDatasetAnnotationLink​(DatasetAnnotationLink target)
        use instead of setAnnotationLinks . Makes the necessary call on ome.model.annotations.DatasetAnnotationLink as well.

      • addDatasetAnnotationLinkSet

        public void addDatasetAnnotationLinkSet​(java.util.Collection<DatasetAnnotationLink> targets)
        use like addDatasetAnnotationLink.

      • removeDatasetAnnotationLink

        public void removeDatasetAnnotationLink​(DatasetAnnotationLink target)
        removes a single element from this set and makes the inverse call on ome.model.annotations.DatasetAnnotationLink

      • removeDatasetAnnotationLinkSet

        public void removeDatasetAnnotationLinkSet​(java.util.Collection<DatasetAnnotationLink> targets)
        use like removeDatasetAnnotationLink

      • linkAnnotation

        public DatasetAnnotationLink linkAnnotation​(Annotation addition)
        Adds a ome.model.annotations.DatasetAnnotationLink to annotationLinks . This entails changing our annotationLinks Set, creating a new ome.model.annotations.DatasetAnnotationLink and calling linkAnnotation on the ome.model.annotations.Annotation.
        Specified by:
        linkAnnotation in interface IAnnotated

      • addDatasetAnnotationLink

        public void addDatasetAnnotationLink​(DatasetAnnotationLink link,
                                     boolean bothSides)
        Adds a ome.model.annotations.DatasetAnnotationLink to annotationLinks, allowing for recursion -- whether or not addDatasetAnnotationLink will be called on the addition if it is loaded

      • linkedAnnotationIterator

        public java.util.Iterator<Annotation> linkedAnnotationIterator()
        provides an iterator over the parent values of the annotationLinks. Like with most Collection iterators, modifications to the underlying collection while iterating will result in an ConcurrentModificationException. Use linkedAnnotationList() instead.
        Specified by:
        linkedAnnotationIterator in interface IAnnotated

      • findDatasetAnnotationLink

        public java.util.Set<DatasetAnnotationLink> findDatasetAnnotationLink​(Annotation target)
        find all ome.model.annotations.DatasetAnnotationLink which have the argument as their child.

      • linkedAnnotationList

        public java.util.List<Annotation> linkedAnnotationList()
        produces a List-copy of the underlying collection. Unlike, linkedAnnotationIterator(), while using the returned List, modifications can be made to the underlying collection without throwing ConcurrentModificationException.
        Specified by:
        linkedAnnotationList in interface IAnnotated

      • eachLinkedAnnotation

        public <E> java.util.List<E> eachLinkedAnnotation​(CBlock<E> block)
        takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results. If block == null, then the iterator values themselves are collected.
        Specified by:
        eachLinkedAnnotation in interface IAnnotated

      • unlinkAnnotation

        public void unlinkAnnotation​(Annotation removal)
        unlinks all ome.model.annotations.Annotation instances from this instance.
        Specified by:
        unlinkAnnotation in interface IAnnotated

      • removeDatasetAnnotationLink

        public void removeDatasetAnnotationLink​(DatasetAnnotationLink link,
                                        boolean bothSides)
        removes the given DatasetAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkDataset again if loaded.

      • setAnnotationLinksCountPerOwner

        protected void setAnnotationLinksCountPerOwner​(java.util.Map<java.lang.Long,​java.lang.Long> map)

      • getAnnotationLinksCountPerOwner

        public java.util.Map<java.lang.Long,​java.lang.Long> getAnnotationLinksCountPerOwner()
        If fetched, returns the count(*) of ome.model.annotations.DatasetAnnotationLink that a user has. If unfetched, returns null. No entries in the collection should be null.

      • getName

        @Field(index=TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields")
public java.lang.String getName()
        Simple field ome.model.containers.Dataset.name (java.lang.String)

      • setName

        public void setName​(java.lang.String name)

      • getDescription

        @Field(index=TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields")
public java.lang.String getDescription()
        Simple field ome.model.containers.Dataset.description (java.lang.String)

      • setDescription

        public void setDescription​(java.lang.String description)

      • getDetails

        public Details getDetails()
        The details of this object correspond to low-level system information. Owner, permissions, Details is always guaranteed to be non-null, unless the user actively nulls it. Every entity also contains a Detail reference, which doesn't refer to a separate table but rather to a collection of fields collected into a Hibernate "component" which is embedded in the object. HQL queries which refer to the Details component cannot directly fetch the entity like this: select o from Object join fetch o.details but rather each field of the Details instance must be explicitly joined: select o from Object join fetch o.details.owner It should also be noted that not all types have all the fields which are present on Details. For example, select e from Experimenter e join fetch e.details.owner will fail. Experimenter has no owner, for obvious reasons. Note: subclasses of this class will return a subclass of the Details type.
        Specified by:
        getDetails in interface IObject

      • setDetails

        protected void setDetails​(Details details)

      • isValid

        public boolean isValid()
        Description copied from interface: IObject
        calls the class-specific validator for this instance and returns the value from Validation.isValid()
        Specified by:
        isValid in interface IObject

      • validate

        public Validation validate()
        Description copied from interface: IObject
        calls the class-specific validator for this instance and returns the Validation object.
        Specified by:
        validate in interface IObject
        Returns:
        Validation collecting parameter.

      • newInstance

        public Dataset newInstance()

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • fields

        public java.util.Set<java.lang.String> fields()
        Description copied from interface: IObject
        returns a Set of field names that belong to this class
        Specified by:
        fields in interface IObject

      • retrieve

        public java.lang.Object retrieve​(java.lang.String field)
        Description copied from interface: IObject
        retrieves a value from this instance. Values for field which match a field of this instance will be delegated to the accessors. Otherwise, values will be retrieved from a lazy-loaded map filled by calls to IObject.putAt(String, Object)
        Specified by:
        retrieve in interface IObject

      • putAt

        public void putAt​(java.lang.String field,
                  java.lang.Object value)
        Description copied from interface: IObject
        stores a value in this instance. Values for field which match a field of this instance will be delegated to the accessors. Otherwise, values will be stored in a lazy-loaded map.
        Specified by:
        putAt in interface IObject
        Parameters:
        field - Field name
        value - Any object to be stored.

      • isLoaded

        public boolean isLoaded()
        Description copied from interface: IObject
        transient field (not stored in the DB) which specifies whether this object has been loaded from the DB or is only a wrapper around the ID.
        Specified by:
        isLoaded in interface IObject

      • errorIfUnloaded

        protected void errorIfUnloaded()

      • unload

        public void unload()
        Description copied from interface: IObject
        set the loaded field to false, and set all non-ID fields to null. Subsequent calls to all accessors other than getId/setId will throw an ApiUsageException
        Specified by:
        unload in interface IObject

      • getGraphHolder

        public final GraphHolder getGraphHolder()
        Description copied from interface: IObject
        retrieves the GraphHolder for this entity. If the GraphHolder has not been actively set, a new one will be instatiated.
        Specified by:
        getGraphHolder in interface IObject
        Returns:
        Non-null GraphHolder

      • throwNullCollectionException

        protected void throwNullCollectionException​(java.lang.String propertyName)