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MatchEngine V2.1

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@ethansiegl ethansiegl released this 10 Aug 15:23
· 665 commits to master since this release
2.1
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Learn about vigilant mode.

Major Updates

  • Extend configuration to allow allow user to set new collections to use in matching and trial curations. Set new defaults in config.json using prior_treatments as an example.

Bug Fixes

  • Check for patients who have aged in/out of trial eligibility since last time patient was run against trial and ensure patients are added to runs
  • Allow user to specify custom trial_status field instead of defaulting to using _summary.status to determine trial open/closed status
  • When using a Mongo _id as a trial identifier, remove _id from trial match pre-processing to avoid _id collisions
  • Use BIRHTDATEINT field instead of BIRTHDATE to calculate age eligibilities (BIRHTDATEINT is the patient's birth date as an integer using the format YYYYMMDD)

Minor Updates

  • Update Jenkinsfile to include graph viz lib
  • Update README
  • Move debug flag higher in init to avoid missing extra logs
  • add bypass_warnings flag to continue runs when run flags have been toggled
  • Add try/catch to asyncio init
  • Add comments and additional logging
  • Chunk all queries to avoid hitting MongoDB query size limits
  • Add tests to verify that patients can age in/out of trial eligibilities
  • Various performance improvements

Co-authored-by: Ethan Siegel esiegel@ds.dfci.harvard.edu
Co-authored-by: Eric Marriott marriott@ds.dfci.harvard.edu
Co-authored-by: Eric Marriott marriott@bcb.dfci.harvard.edu
Co-authored-by: Roshni Biswas rbiswas@ds.dfci.harvard.edu
Co-authored-by: emarriott

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