Package ome.model.core

Class OriginalFile

  • 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 OriginalFile
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_PIXELSFILEMAPS

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

      • GROUP_FILTER_PIXELSFILEMAPS

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

      • EVENT_FILTER_PIXELSFILEMAPS

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

      • PERMS_FILTER_PIXELSFILEMAPS

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

      • path

        protected java.lang.String path

      • repo

        protected java.lang.String repo

      • size

        protected java.lang.Long size

      • atime

        protected java.sql.Timestamp atime

      • mtime

        protected java.sql.Timestamp mtime

      • ctime

        protected java.sql.Timestamp ctime

      • hash

        protected java.lang.String hash

      • mimetype

        protected java.lang.String mimetype

      • filesetEntries

        protected java.util.Set<FilesetEntry> filesetEntries

      • OWNER_FILTER_FILESETENTRIES

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

      • GROUP_FILTER_FILESETENTRIES

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

      • EVENT_FILTER_FILESETENTRIES

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

      • PERMS_FILTER_FILESETENTRIES

        public static final java.lang.String PERMS_FILTER_FILESETENTRIES
        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

      • details

        protected Details details

      • PIXELSFILEMAPSCOUNTPEROWNER

        public static final java.lang.String PIXELSFILEMAPSCOUNTPEROWNER
        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

      • OriginalFile

        public OriginalFile()

      • OriginalFile

        protected OriginalFile​(java.lang.Long id)

      • OriginalFile

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

      • OriginalFile

        public OriginalFile​(java.lang.String _path,
                    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.

      • getPixelsFileMaps

        protected java.util.Set<PixelsOriginalFileMap> getPixelsFileMaps()
        returns pixelsFileMaps . You should not modify this collection unless you know what you are doing. Use the iterate method instead. one-to-many Set ome.model.core.OriginalFile.pixelsFileMaps (ome.model.core.PixelsOriginalFileMap)

      • setPixelsFileMaps

        protected void setPixelsFileMaps​(java.util.Set<PixelsOriginalFileMap> pixelsFileMaps)
        setter for pixelsFileMaps should be avoided. Does not fulfill normal semantics.

      • sizeOfPixelsFileMaps

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

      • iteratePixelsFileMaps

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

      • unmodifiablePixelsFileMaps

        public java.util.Collection<PixelsOriginalFileMap> unmodifiablePixelsFileMaps()
        Returns an unmodifiable collection-view

      • collectPixelsFileMaps

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

      • addPixelsOriginalFileMap

        public void addPixelsOriginalFileMap​(PixelsOriginalFileMap target)
        use instead of setPixelsFileMaps . Makes the necessary call on ome.model.core.PixelsOriginalFileMap as well.

      • addPixelsOriginalFileMapSet

        public void addPixelsOriginalFileMapSet​(java.util.Collection<PixelsOriginalFileMap> targets)
        use like addPixelsOriginalFileMap.

      • removePixelsOriginalFileMap

        public void removePixelsOriginalFileMap​(PixelsOriginalFileMap target)
        removes a single element from this set and makes the inverse call on ome.model.core.PixelsOriginalFileMap

      • removePixelsOriginalFileMapSet

        public void removePixelsOriginalFileMapSet​(java.util.Collection<PixelsOriginalFileMap> targets)
        use like removePixelsOriginalFileMap

      • linkPixels

        public PixelsOriginalFileMap linkPixels​(Pixels addition)
        Adds a ome.model.core.PixelsOriginalFileMap to pixelsFileMaps . This entails changing our pixelsFileMaps Set, creating a new ome.model.core.PixelsOriginalFileMap and calling linkPixels on the ome.model.core.Pixels.

      • addPixelsOriginalFileMap

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

      • linkedPixelsIterator

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

      • findPixelsOriginalFileMap

        public java.util.Set<PixelsOriginalFileMap> findPixelsOriginalFileMap​(Pixels target)
        find all ome.model.core.PixelsOriginalFileMap which have the argument as their child.

      • linkedPixelsList

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

      • eachLinkedPixels

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

      • unlinkPixels

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

      • removePixelsOriginalFileMap

        public void removePixelsOriginalFileMap​(PixelsOriginalFileMap link,
                                        boolean bothSides)
        removes the given PixelsOriginalFileMap from pixelsFileMaps, allowing for recursion -- whether or not the removal will call unlinkOriginalFile again if loaded.

      • clearPixelsLinks

        public void clearPixelsLinks()
        clears the set.

      • setPixelsFileMapsCountPerOwner

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

      • getPixelsFileMapsCountPerOwner

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

      • getPath

        @Field(index=TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields")
public java.lang.String getPath()
        Simple field ome.model.core.OriginalFile.path (java.lang.String)

      • setPath

        public void setPath​(java.lang.String path)

      • getRepo

        @Field(index=TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields")
public java.lang.String getRepo()
        Simple field ome.model.core.OriginalFile.repo (java.lang.String)

      • setRepo

        public void setRepo​(java.lang.String repo)

      • getSize

        @Field(index=UN_TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields")
public java.lang.Long getSize()
        Simple field ome.model.core.OriginalFile.size (java.lang.Long)

      • setSize

        public void setSize​(java.lang.Long size)

      • getAtime

        @DateBridge(resolution=MINUTE)
@Fields(@Field(index=UN_TOKENIZED))
public java.sql.Timestamp getAtime()
        Simple field ome.model.core.OriginalFile.atime (java.sql.Timestamp)

      • setAtime

        public void setAtime​(java.sql.Timestamp atime)

      • getMtime

        @DateBridge(resolution=MINUTE)
@Fields(@Field(index=UN_TOKENIZED))
public java.sql.Timestamp getMtime()
        Simple field ome.model.core.OriginalFile.mtime (java.sql.Timestamp)

      • setMtime

        public void setMtime​(java.sql.Timestamp mtime)

      • getCtime

        @DateBridge(resolution=MINUTE)
@Fields(@Field(index=UN_TOKENIZED))
public java.sql.Timestamp getCtime()
        Simple field ome.model.core.OriginalFile.ctime (java.sql.Timestamp)

      • setCtime

        public void setCtime​(java.sql.Timestamp ctime)

      • getHasher

        public ChecksumAlgorithm getHasher()
        Many-to-one field ome.model.core.OriginalFile.hasher (ome.model.enums.ChecksumAlgorithm)

      • getHash

        @Field(index=TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields")
public java.lang.String getHash()
        Simple field ome.model.core.OriginalFile.hash (java.lang.String)

      • setHash

        public void setHash​(java.lang.String hash)

      • getMimetype

        @Field(index=TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields")
public java.lang.String getMimetype()
        Simple field ome.model.core.OriginalFile.mimetype (java.lang.String)

      • setMimetype

        public void setMimetype​(java.lang.String mimetype)

      • getFilesetEntries

        protected java.util.Set<FilesetEntry> getFilesetEntries()
        returns filesetEntries . You should not modify this collection unless you know what you are doing. Use the iterate method instead. one-to-many Set ome.model.core.OriginalFile.filesetEntries (ome.model.fs.FilesetEntry)

      • setFilesetEntries

        protected void setFilesetEntries​(java.util.Set<FilesetEntry> filesetEntries)
        setter for filesetEntries should be avoided. Does not fulfill normal semantics.

      • sizeOfFilesetEntries

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

      • iterateFilesetEntries

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

      • unmodifiableFilesetEntries

        public java.util.Collection<FilesetEntry> unmodifiableFilesetEntries()
        Returns an unmodifiable collection-view

      • collectFilesetEntries

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

      • addFilesetEntry

        public void addFilesetEntry​(FilesetEntry target)
        use instead of setFilesetEntries . Makes the necessary call on ome.model.fs.FilesetEntry as well.

      • addFilesetEntrySet

        public void addFilesetEntrySet​(java.util.Collection<FilesetEntry> targets)
        use like addFilesetEntry.

      • removeFilesetEntry

        public void removeFilesetEntry​(FilesetEntry target)
        removes a single element from this set and makes the inverse call on ome.model.fs.FilesetEntry

      • removeFilesetEntrySet

        public void removeFilesetEntrySet​(java.util.Collection<FilesetEntry> targets)
        use like removeFilesetEntry

      • clearFilesetEntries

        public void clearFilesetEntries()
        clears the set.

      • getAnnotationLinks

        protected java.util.Set<OriginalFileAnnotationLink> 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.core.OriginalFile.annotationLinks (ome.model.annotations.OriginalFileAnnotationLink)

      • setAnnotationLinks

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

      • addOriginalFileAnnotationLink

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

      • addOriginalFileAnnotationLinkSet

        public void addOriginalFileAnnotationLinkSet​(java.util.Collection<OriginalFileAnnotationLink> targets)
        use like addOriginalFileAnnotationLink.

      • removeOriginalFileAnnotationLink

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

      • removeOriginalFileAnnotationLinkSet

        public void removeOriginalFileAnnotationLinkSet​(java.util.Collection<OriginalFileAnnotationLink> targets)
        use like removeOriginalFileAnnotationLink

      • linkAnnotation

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

      • addOriginalFileAnnotationLink

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

      • findOriginalFileAnnotationLink

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

      • removeOriginalFileAnnotationLink

        public void removeOriginalFileAnnotationLink​(OriginalFileAnnotationLink link,
                                             boolean bothSides)
        removes the given OriginalFileAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkOriginalFile 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.OriginalFileAnnotationLink 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.core.OriginalFile.name (java.lang.String)

      • setName

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

      • 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.

      • 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)