Package org.incenp.obofoundry.sssom.transform

Class MappingEditor

  • All Implemented Interfaces:
    ISimpleSlotVisitor<Mapping,​Void>, IMappingTransformer<Mapping>
    public class MappingEditor
extends Object
implements IMappingTransformer<Mapping>, ISimpleSlotVisitor<Mapping,​Void>
    A mapping transformer that applies arbitrary changes to a mapping.

    There are three ways to specify a change to apply. The simplest one is to use addSimpleAssign(String, String), when the value to assign is static and therefore fully known at the time the function is called: 

     // Set a mapping justification
 editor.addSimpleAssign("mapping_justification", "semapv:ManualMappingCuration");

    If the value to assign is to be generated from the mapping the change must be applied to, then use addDelayedAssign(String, IMappingTransformer). For example, to set the object label to a value derived from the subject label: 

     editor.addDelayedAssign("object_label", (mapping) -> String.format("same as %s", mapping -> getSubjectLabel()));

    Lastly, use addReplacement(String, String, String) to change the value of a slot by searching and replacing a pattern within the original value: 

     editor.addReplacement("subject_id", "https://meshb.nlm.nih.gov/record/ui[?]ui=", "http://id.nlm.nih.gov/mesh/");

    • Constructor Detail

      • MappingEditor

        public MappingEditor()
        Creates a new instance with the default SSSOM prefix manager.

      • MappingEditor

        public MappingEditor​(PrefixManager prefixManager)
        Creates a new instance with the specified prefix manager. The prefix manager is used to expand short identifiers in arguments to addSimpleAssign(String, String).
        Parameters:
        prefixManager - The prefix manager to use.

    • Method Detail

      • visit

        public Void visit​(Slot<Mapping> slot,
                  Mapping object,
                  Object value)
        Description copied from interface: ISimpleSlotVisitor
        Visits a SSSOM slot.
        Specified by:
        visit in interface ISimpleSlotVisitor<Mapping,​Void>
        Parameters:
        slot - The slot that is being visited.
        object - The object to which the slot is attached.
        value - The value of the slot.
        Returns:
        Whatever value the visitor wishes to return once the slot has been visited.

      • addSimpleAssign

        public void addSimpleAssign​(String slotName,
                            String value)
        Adds a change to be applied by this transformer. This is a simple change where the value to assign is already fully known when the method is called: the value does not depend on the mapping the change is applied to.
        Parameters:
        slotName - The name of the mapping slot to change.
        value - The new value of the slot. May be null or an empty string to remove an existing value. For multi-value slots, the values must be separated by a | character.
        Throws:
        IllegalArgumentException - If slotName is not a valid slot name, or if the value is invalid.

      • addDelayedAssign

        public void addDelayedAssign​(String slotName,
                             IMappingTransformer<String> value)
        Adds a change to be applied by transformer, when the new value to assign will only be known at the time the change is applied because it may depend on the mapping the change is applied to.

        Of note, because the new value is not known at the time the change is registered, we cannot perform any check on the value. We only check whether the given slot name is a valid one.

        Parameters:
        slotName - The name of the mapping slot to change.
        value - The transformer that will derive the new value to assign from a mapping.
        Throws:
        IllegalArgumentException - If slotName is not a valid slot name.

      • addReplacement

        public void addReplacement​(String slotName,
                           String pattern,
                           String replacement)
        Adds a replacement operation to be applied by this transformer. The new value of the edited slot is computed by finding all occurrences of the specified pattern in the original slot value, and replacing them with the specified replacement value.
        Parameters:
        slotName - The name of the mapping slot to change.
        pattern - The pattern to replace in the slot's original value.
        replacement - The value the pattern should be replaced by.
        Throws:
        IllegalArgumentException - If slotName is not a valid slot name, if the pattern is not a valid regular expression, or if the slot type is unsupported (only string and list-of-strings slots are supported for now).