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Releases: dfci/matchengine-V2

MatchEngine V2.1

10 Aug 15:23
@ethansiegl ethansiegl
2.1
ad5ddc6
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MatchEngine V2.1 Latest
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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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MatchEngine V2

16 Sep 16:01
@marriott-er marriott-er
2.0.0
90c44de
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MatchEngine V2

The MatchEngine is designed to match cancer patients to genomically driven, precision medicine clinical trials. While this version is a complete re-write from the ground up, it maintains feature parity and most default behaviors from the V1 MatchEngine, as well as integration with the MatchminerAPI (>=V1.0), and MatchminerUI (>=V1.0).

For documentation please see https://matchminer.gitbook.io/matchminer/

CHANGELOG:

  • Add command line flag for matching to individual, or batches of trials
  • Add command line flag for matching based on single sample IDs, or multiple IDs
  • Add command line flag to output digraph visualizations of matching algorithm
  • Adds support by default for new patient genomic criteria including tumor mutational burden, structural variations, and POLE, tobacco, temozolomide, and APOBEC signature statuses
  • Allow for single or batch importing of JSON documents for all data types
  • Introduce asynchronous query behavior
  • Introduce plugin architecture for easy trial configuration/extensibility
  • Trial matching criteria moved to extensible configuration files
  • Fix bug related to reporting trial match reasons
  • Fix sorting bug related to variant level match exclusions
  • Fix bug related to matching on protein wildcard curations
  • Add run_log to track additions, updates, and deletions to individual trials
  • Expand documentation to include tutorials on getting started, trial curation, and engine configuration
  • Add clinical reason(s) to trial match output documents
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