Package ome.model.screen

Class Reagent

  • 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 Reagent
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

      • name

        protected java.lang.String name

      • reagentIdentifier

        protected java.lang.String reagentIdentifier

      • screen

        protected Screen screen

      • OWNER_FILTER_WELLLINKS

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

      • GROUP_FILTER_WELLLINKS

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

      • EVENT_FILTER_WELLLINKS

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

      • PERMS_FILTER_WELLLINKS

        public static final java.lang.String PERMS_FILTER_WELLLINKS
        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

      • description

        protected java.lang.String description

      • details

        protected Details details

      • REAGENTIDENTIFIER

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

      • WELLLINKSCOUNTPEROWNER

        public static final java.lang.String WELLLINKSCOUNTPEROWNER
        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

      • Reagent

        public Reagent()

      • Reagent

        protected Reagent​(java.lang.Long id)

      • Reagent

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

      • Reagent

        public Reagent​(Screen _screen)

    • 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.

      • getName

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

      • setName

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

      • getReagentIdentifier

        @Field(index=TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields")
public java.lang.String getReagentIdentifier()
        Simple field ome.model.screen.Reagent.reagentIdentifier (java.lang.String)

      • setReagentIdentifier

        public void setReagentIdentifier​(java.lang.String reagentIdentifier)

      • getScreen

        public Screen getScreen()
        Many-to-one field ome.model.screen.Reagent.screen (ome.model.screen.Screen)

      • setScreen

        public void setScreen​(Screen screen)

      • getWellLinks

        protected java.util.Set<WellReagentLink> getWellLinks()
        returns wellLinks . You should not modify this collection unless you know what you are doing. Use the iterate method instead. one-to-many Set ome.model.screen.Reagent.wellLinks (ome.model.screen.WellReagentLink)

      • setWellLinks

        protected void setWellLinks​(java.util.Set<WellReagentLink> wellLinks)
        setter for wellLinks should be avoided. Does not fulfill normal semantics.

      • sizeOfWellLinks

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

      • iterateWellLinks

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

      • unmodifiableWellLinks

        public java.util.Collection<WellReagentLink> unmodifiableWellLinks()
        Returns an unmodifiable collection-view

      • collectWellLinks

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

      • addWellReagentLink

        public void addWellReagentLink​(WellReagentLink target)
        use instead of setWellLinks . Makes the necessary call on ome.model.screen.WellReagentLink as well.

      • addWellReagentLinkSet

        public void addWellReagentLinkSet​(java.util.Collection<WellReagentLink> targets)
        use like addWellReagentLink.

      • removeWellReagentLink

        public void removeWellReagentLink​(WellReagentLink target)
        removes a single element from this set and makes the inverse call on ome.model.screen.WellReagentLink

      • removeWellReagentLinkSet

        public void removeWellReagentLinkSet​(java.util.Collection<WellReagentLink> targets)
        use like removeWellReagentLink

      • linkWell

        public WellReagentLink linkWell​(Well addition)
        Adds a ome.model.screen.WellReagentLink to wellLinks . This entails changing our wellLinks Set, creating a new ome.model.screen.WellReagentLink and calling linkWell on the ome.model.screen.Well.

      • addWellReagentLink

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

      • linkedWellIterator

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

      • findWellReagentLink

        public java.util.Set<WellReagentLink> findWellReagentLink​(Well target)
        find all ome.model.screen.WellReagentLink which have the argument as their parent.

      • linkedWellList

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

      • eachLinkedWell

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

      • unlinkWell

        public void unlinkWell​(Well removal)
        unlinks all ome.model.screen.Well instances from this instance.

      • removeWellReagentLink

        public void removeWellReagentLink​(WellReagentLink link,
                                  boolean bothSides)
        removes the given WellReagentLink from wellLinks, allowing for recursion -- whether or not the removal will call unlinkReagent again if loaded.

      • clearWellLinks

        public void clearWellLinks()
        clears the set.

      • setWellLinksCountPerOwner

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

      • getWellLinksCountPerOwner

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

      • getAnnotationLinks

        protected java.util.Set<ReagentAnnotationLink> 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.screen.Reagent.annotationLinks (ome.model.annotations.ReagentAnnotationLink)

      • setAnnotationLinks

        protected void setAnnotationLinks​(java.util.Set<ReagentAnnotationLink> 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.ReagentAnnotationLink 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

      • addReagentAnnotationLink

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

      • addReagentAnnotationLinkSet

        public void addReagentAnnotationLinkSet​(java.util.Collection<ReagentAnnotationLink> targets)
        use like addReagentAnnotationLink.

      • removeReagentAnnotationLink

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

      • removeReagentAnnotationLinkSet

        public void removeReagentAnnotationLinkSet​(java.util.Collection<ReagentAnnotationLink> targets)
        use like removeReagentAnnotationLink

      • linkAnnotation

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

      • addReagentAnnotationLink

        public void addReagentAnnotationLink​(ReagentAnnotationLink link,
                                     boolean bothSides)
        Adds a ome.model.annotations.ReagentAnnotationLink to annotationLinks, allowing for recursion -- whether or not addReagentAnnotationLink 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

      • findReagentAnnotationLink

        public java.util.Set<ReagentAnnotationLink> findReagentAnnotationLink​(Annotation target)
        find all ome.model.annotations.ReagentAnnotationLink 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

      • removeReagentAnnotationLink

        public void removeReagentAnnotationLink​(ReagentAnnotationLink link,
                                        boolean bothSides)
        removes the given ReagentAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkReagent 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.ReagentAnnotationLink that a user has. If unfetched, returns null. No entries in the collection should be null.

      • getDescription

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