SNOMED International Mapping Tool

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Overview

This page documents the use of admin tools to perform an RF2 release of mapping project data.

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 and data is loaded.
  • A map project must exist for the specified refset id and have publication ready records.
  • IMPORTANT: The Tomcat server must not be running while this is run, otherwise indexes can get corrupted.

Details

There are three stages to the process:

  • Begin a release
    • Generate a "release QA report"
    • Verify all records are through the workflow
    • Run validation
    • Remove map records for retired/out of scope concepts
  • Process a release - iterate over this until perfect
    • Create RF2 delta files
    • Create "active snapshot" human readable files
    • Create a statistics report
  • Finish a release
    • Mark READY_FOR_PUBLICATION records as PUBLISHED
    • Update the "complex map refset members" table to reflect the published/snapshot state (for future comparisons).

  

Following are some details about the release tooling implementations:

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

Project: admin/release

Configuration Parameters

  • A profile of "BeginRelease" must be specified
  • run.config - the standard configuration file specified as a -D parameter
  • refset.id - the refset id of the mapping project to release specified as a -D parameter
    • A map project with this refset id must exist
  • remove.records - a flag indicating whether to remove out of scope map records
     

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

Project: admin/release

Configuration Parameters

  • A profile of "Release" must be specified
  • run.config - the standard configuration file specified as a -D parameter
  • refset.id - the refset id of the mapping project to release specified as a -D parameter
    • A map project with this refset id must exist
  • output.dir - the output directory specified as a -D parameter
  • time - the date to use for the effectiveTime of the RF2 files created
  • module.id - the moduleId to use for the RF2 files - this is specific to the individual map project. 

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

Project: admin/release

Configuration Parameters

  • A profile of "FinishRelease" must be specified
  • run.config - the standard configuration file specified as a -D parameter
  • refset.id - the refset id of the mapping project to release specified as a -D parameter
    • A map project with this refset id must exist

Samples

Sample command line call of the RF2 release tooling to begin a release for refset 447563008:

% cd ~/code/admin/release
% mvn install -Drun.config=/home/ihtsdo/config/config.properties -PBeginRelease -Drefset.id=447563008 -Dremove.records=true

 

Sample command line call of the RF2 release tooling to process a release for refset 447563008:

% cd ~/code/admin/release
% mvn install -Drun.config=/home/ihtsdo/config/config.properties -PRelease -Drefset.id=447563008 -Doutput.dir=/home/ihtsdo/doc/release -Dmodule.id=900000000000207008 -Dtime=20150131

 

Sample command line call of the RF2 release tooling to finish a release for refset 447563008:

% cd ~/code/admin/release
% mvn install -Drun.config=/home/ihtsdo/config/config.properties -PFinishRelease -Drefset.id=447563008

 

Sample Eclipse run configuration to begin a release for refset 447563008:

Sample Eclipse run configuration to process a release for refset 447563008:

Sample Eclipse run configuration to finish a release for refset 447563008:

Troubleshooting

The most likely issue is that QA errors are discovered in the generated files. This step can be repeatedly re-run until the results look right, including edits along the way to the underlying data (as long as mid-stream workflow states are not created).

Another way to avoid problems is to run the process in a cloned environment (e.g. UAT) which supports the ability to revert to the initial state at any time without interfering with production activities.

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