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 (see Performing an RF2 Release) and the following tools are used to enact those stages. 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
  • test.mode.flag - a flag indicating whether to run in test mode, which avoids making database changes, defaults to false
  • NOTE:  this mojo will avoid making database changes if any of the validation steps fail.
     

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.
  • test.mode.flag - a flag indicating whether to run in test mode, which avoids making database changes, defaults to false


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
  • input.file - the final RF2 snapshot file from the release process to reload
  • test.mode.flag - a flag indicating whether to run in test mode, which avoids making database changes, defaults to false

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

 

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/data/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 -Dinput.file=/home/ihtsdo/data/doc/release/der2_iisssccRefset_ExtendedMapSnapshot_INT_20150131.txt

 

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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