SNOMED International Mapping Tool

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  • Map Note Loader and Remover

Overview

This page documents the use of admin tools to load or remove map notes.  This is used to take mapping notes from a legacy system and install them into the new environment.  It can also be used as a generic means to attach arbitrary note information to mapped concepts for a map project.  For example, this mechanism was used to load "legacy" information about specialists/leads and when concepts were mapped from the old Cartographer system.

Prerequisites

  • MySQL database must already exist (e.g. "mappingservicedb").
  • MySQL database connection parameters must be defined in the properties file specified by "run.config".
  • Create/Update DB mojo must also have already run so that the database schema exists.
  • A map project must exist with a refset id matching the data intended to be loaded
    • Either create a map project and configure it properly
    • Or import a map project
  • Map records must exist already to which the notes will be attached.
  • IMPORTANT: The Tomcat server must not be running while this is run, otherwise indexes can get corrupted.

Details

This tool is used to load or remove map notes from a pseudo RF2 file.  This is a mechanism to migrate notes information from a legacy environment into the new environment.  The expected format is in the style of an RF2 file with these fields (including a header line):

  • id - a UUID based on refSetId, referencedComponentId, and annotation
  • effectiveTime - publication date
  • active - should always be 1, inactive notes not supported
  • moduleId - ignored
  • refSetId - must match the refset id of one of the configured and installed map projects.
  • referencedComponentId - the note will be attached to the map record whose "conceptId" field matches this within the project specified by the refset id.
  • fullySpecifiedName - ignored
  • annotation - the note, and it may contain HTML.

  

Following are some details about the loader implementation:

Mojo: MapNoteRf2LoaderMojo.java (in admin/mojo/src/main/resources/java/org/ihtsdo/otf/mapping/mojo)

Project: admin/loader

Configuration Parameters

  • A profile of "MapNotes" must be specified
  • run.config - the standard configuration file specified as a -D parameter
  • input.file - the input file specified as a -D parameter
    • Map records with matching concept ids should exist within map projects that also share the refset id.
    • If not, the notes are skipped.

 

Following are some details about the remover implementation:

Mojo: MapNoteRemoverMojo.java (in admin/mojo/src/main/resources/java/org/ihtsdo/otf/mapping/mojo)

Project: admin/remover

Configuration Parameters

  • A profile of "MapNotes" must be specified
  • run.config - the standard configuration file specified as a -D parameter
  • refset.id - a comma-separated list of refset ids to remove map notes for specified as a -D parameter
    • Map projects with these refset ids must exist.

Samples

Sample command line call of the admin tool to load map notes from an RF2 file:

% cd ~/code/admin/loader
% mvn install -Drun.config=/home/ihtsdo/config/config.properties -PMapNotes -Dinput.file=/home/ihtsdo/data/der2_sRefset_MapNotesSnapshot_INT_20140131.txt


Sample command line call of the admin tool to remove map notes for refsets 447563008 and 447562003:

% cd ~/code/admin/remover
% mvn install -Drun.config=/home/ihtsdo/config/config.properties -PMapNotes -Drefset.id=447563008,447562003

 

Sample Eclipse run configuration to load map notes from an RF2 file:

Sample Eclipse run configuration to remove map notes for refsets 447563008 and 447562003:

Troubleshooting

If anything goes wrong loading map notes, they can be removed with the remover and simply reloaded.

  • n/a

 

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