Package ome.formats

Class OMEROMetadataStore

  • public class OMEROMetadataStore
extends java.lang.Object
    An OMERO metadata store. This particular metadata store requires the user to be logged into OMERO prior to use with the SecuritySystem.login(ome.system.Principal) method. While attempts have been made to allow the caller to switch back and forth between Images and Pixels during metadata population it is strongly encouraged that at least Images and Pixels are populated in ascending order. For example: Image_1 -> Pixels_1, Pixels_2 followed by Image_2 -> Pixels_1, Pixels2, Pixels_3.

    • Constructor Summary

      Constructors 
      Constructor Description
      OMEROMetadataStore()
      Empty constructor for testing purposes.
      OMEROMetadataStore​(ome.system.ServiceFactory factory, ome.util.SqlAction sql)
      Creates a new instance.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void checkAndCollapseGraph()
      Checks the entire object graph for sections that may be collapsed if the data is derived from a Plate.
      void createRoot()  
      ome.model.IObject getObjectByLSID​(ome.util.LSID lsid)
      Retrieves an object from the internal object graph by LSID.
      void populateMinMax​(double[][][] imageChannelGlobalMinMax)
      Synchronize the minimum and maximum intensity values with those specified by the client and save them in the DB.
      java.util.List<ome.model.core.Pixels> saveToDB​(ome.model.fs.FilesetJobLink link)
      Saves the current object graph to the database.
      void updateObject​(java.lang.String lsid, ome.model.IObject sourceObject, java.util.Map<java.lang.String,​java.lang.Integer> indexes)
      Updates a given model object in our object graph.
      void updateReferences​(java.util.Map<java.lang.String,​java.lang.String[]> referenceCache)
      Updates our object graph references.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • OMEROMetadataStore

        public OMEROMetadataStore()
        Empty constructor for testing purposes.

      • OMEROMetadataStore

        public OMEROMetadataStore​(ome.system.ServiceFactory factory,
                          ome.util.SqlAction sql)
                   throws ome.conditions.ValidationException
        Creates a new instance.
        Parameters:
        factory - a non-null, active ServiceFactory
        sql - the SQL action instance
        Throws:
        ome.conditions.ValidationException - if the factory is null or there is another error instantiating required services.

    • Method Detail

      • updateObject

        public void updateObject​(java.lang.String lsid,
                         ome.model.IObject sourceObject,
                         java.util.Map<java.lang.String,​java.lang.Integer> indexes)
        Updates a given model object in our object graph.
        Parameters:
        lsid - LSID of model object.
        sourceObject - Model object itself.
        indexes - Any indexes that should are used to describe the model object's graph location.

      • updateReferences

        public void updateReferences​(java.util.Map<java.lang.String,​java.lang.String[]> referenceCache)
        Updates our object graph references.
        Parameters:
        referenceCache - Client side LSID reference cache.

      • getObjectByLSID

        public ome.model.IObject getObjectByLSID​(ome.util.LSID lsid)
        Retrieves an object from the internal object graph by LSID.
        Parameters:
        lsid - LSID of the object.
        Returns:
        See above. null if the object is not in the internal LSID map.

      • createRoot

        public void createRoot()

      • checkAndCollapseGraph

        public void checkAndCollapseGraph()
        Checks the entire object graph for sections that may be collapsed if the data is derived from a Plate. Collapsible points:
        • Image -> ObjectiveSettings
        • Image -> Channel -> LogicalChannel -> LightSettings
        • Image -> Channel -> LogicalChannel -> LightPath
        • Image -> Channel -> LogicalChannel -> DetectorSettings

      • saveToDB

        public java.util.List<ome.model.core.Pixels> saveToDB​(ome.model.fs.FilesetJobLink link)
        Saves the current object graph to the database.
        Parameters:
        link - a link from the fileset to be linked from
        Returns:
        List of the Pixels objects with their attached object graphs that have been saved.

      • populateMinMax

        public void populateMinMax​(double[][][] imageChannelGlobalMinMax)
        Synchronize the minimum and maximum intensity values with those specified by the client and save them in the DB.
        Parameters:
        imageChannelGlobalMinMax - Minimums and maximums to update.