SNOMED International Mapping Tool

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Overview

Documents the release process details.  There is an admin page already that indicates how to run the mojo.  See Release Processing Tool for more information.

Assumptions

  • Source terminology is SNOMED CT
  • Release is in RF2 delta format
  • QA of overall release is done by an external system (though project-specific validation rules are processed here)
  • That editing was done in conjunction with a "drip feed" system that brought emerging content into the system as it was being developed, so it could be mapped.
  • That the mapping files are part of the source terminology release

Details

The mapping tool supports a release process that takes into account end-of-editing cycle activities, some quality assurance, production of data files, and upgrading terminology versions when the time comes.  The release processing is specifically tailored to the needs of IHTSDO and maintenance of the RF2 complex and extended map refsets that are part of the SNOMED CT distribution.

 TODO: flowchart

The steps are:

  • Upgrade to latest version - there are two forms of this and it assumes that the version of the map and the "source terminology" are coordinated.  This is to ensure the expected release state of "in scope" concepts is properly represented for workflow and release state computations.  Given processing of "daily build", innaccuracies can build up over an editing cycle.
    • Load a definitive delta release and update the version of all terminology components to latest version.
    • Remove and reload an entire definitive snapshot release. (NOTE: it may be desirable to do this FIRST, before "begin release"). 
  • Finish all editing - assumes drip feed has been processing along the way
  • "Begin" a release
    • Verify all "in scope" concepts are mapped
    • Validate all existing map records against current rules

    • Remove map records for concepts that are retired, deleted, or out of scope. 

      service tomcat7 stop
cd ~/code/admin/release
mvn install -PBeginRelease -Drun.config=/home/ihtsdo/config/config.properties -Drefset.id=447562003 >&! mvn.log
mvn install -PBeginRelease -Drun.config=/home/ihtsdo/config/config.properties -Drefset.id=447563008 >&! mvn2.log
service tomcat7 start
  • Generate release files
    • Create an RF2 delta file
    • Create human readable file

    • Create module dependency file (if needed)

      service tomcat7 stop
cd ~/code/admin/release
mvn install -PRelease -Drun.config=/home/ihtsdo/config/config.properties -Drefset.id=447562003 \
  -Doutput.dir=. -Dtime=20150731 -Dmodule.id=449080006
mvn install -PRelease -Drun.config=/home/ihtsdo/config/config.properties -Drefset.id=447563008 \
  -Doutput.dir=. -Dtime=20150731 -Dmodule.id=900000000000207008
service tomcat7 start
  • "Finish" a release
    • Create complex map refset entries for all delta entries (replacing any there with the same identifiers)

    • Mark all map records for the project that are READY_FOR_PUBLICATION as PUBLISHED.

      service tomcat7 stop
cd ~/code/admin/release
mvn install -PFinishRelease -Drun.config=/home/ihtsdo/config/config.properties -Drefset.id=447562003 >&! mvn.log
mvn install -PFinishRelease -Drun.config=/home/ihtsdo/config/config.properties -Drefset.id=447563008 >&! mvn2.log
service tomcat7 start
  • Begin editing cycle 

    • When ready to start editing for the next cycle, this marks the map project "editing cycle begin date".

      service tomcat7 stop
cd ~/code/admin/loader
mvn install -PBeginEditingCycle -Drun.config=/home/ihtsdo/config/config.properties -Drefset.id=447562003 >&! mvn.log
mvn install -PBeginEditingCycle -Drun.config=/home/ihtsdo/config/config.properties -Drefset.id=447563008 >&! mvn2.log
service tomcat7 start
  • Remove old reports

    • When starting a new editing cycle, it may be useful to remove reports more than a year old to keep the overall size of accumulated reports reasonable.

      service tomcat7 stop
# set date one year ago, e.g. 20140615
set date = 20140615
cd ~/code/parent/admin/remover
mvn install -PReports -Drun.config=/home/ihtsdo/config/config.properties Drefset.id=447562003 -Dend.date=$date >&! mvn.log
mvn install -PReports -Drun.config=/home/ihtsdo/config/config.properties Drefset.id=447563008 -Dend.date=$date >&! mvn.log
service tomcat7 start

Creating Custom Release Processing

If the process above is not needed or desired, alternative release processing can be built as a custom development task.  Things to consider are:

  • The release format
  • Whether the release is part of the source/target terminologies of the map
  • Whether the mapping versioning itself is coordinated with the source/target terminology versioning
  • Whether map records were built completely from scratch or were generated from terminology data
  • Whether a "delta" release is needed - e.g. a release that compares to the previous release and publishes only the changes.

These things are very project specific and are not the same for all projects.

Custom release processing can be implemented via an outside package, or in the mapping-custom project (see Custom Release Process).

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