CA Transform: Remove Accession Number

[JohnNKing]

Story

As UCSD, so that I can ingest an NBS result message, I need the accession number OBX removed (as this uses a local code that can't be supported).

Pre-conditions

• Work for story #1277 is complete. These stories have similar requirements, so this will build on the work we've done for the previous story.

Acceptance Criteria

• [x] For ORUs sent by ReportStream to UCSD, the accession number OBX (as identified by OBX-3.4 as '99717-5' AND OBX-3.6 as 'L') is removed.
• [x] The Observation set ID (OBX-1) values for all OBX segments are renumbered to be sequential (Note: This happens automatically as part of the RS FHIR => HL7 conversion; if not, we should discuss this as a team to see how essential this scope is)

Tasks

Research

• [x] Determine if the transformation should be configurable for "coding" and "alt-coding" matches (OBX-3.1/2/3 vs 4/5/6). [Yes]
• [x] Based on the above, should it still be considered a match if the other triplet has other data? [Yes, as long as we get a match in the fields we're looking for, anything else can be in the other triplet]

Engineering

Phase 1: Working code for testing session with CA and UCSD

• [x] Implement the transform class. See notes below.
• [x] Tests
  • [x] Happy path - remove observation when code, coding system, and cwe-coding match the arguments (e.g. 99717-5/L/alt-coding) @jbiskie
  • [x] Similar to above, but use coding instead of alt-coding. Might also use different code and coding system. @jbiskie
  • [x] Similar to above, but has data in both coding and alt-coding. Should still remove the observation. @jbiskie
  • [x] No removal when there is only a partial match of the code, coding system, and/or cwe-coding @jbiskie
  • [x] No removal when there is no observation identifier (OBX-3 is completely empty)
  • [x] Ensure all matching observations are removed if there's >1 matching observation (corner case to ensure correctness, but not an expected scenario for CA)
  • [x] Ensure matching observation is removed with an example message (can use 002 or other examples)
• [x] Configure the transformation in transformation_definitions.json

Phase 2: Refactor

• [x] Refactor similar code to the mapping transform #1277

Definition of Done

• [x] Documentation tasks completed
  • [x] Documentation and diagrams created or updated
  • [x] ADRs (/adr folder)
  • [x] Main README.md
  • [x] Other READMEs in the repo
  • [x] If applicable, update the ReportStream Setup section in README.md
  • [x] Threat model updated
  • [x] API documentation updated
• [x] Code quality tasks completed
  • [x] Code refactored for clarity and no design/technical debt
  • [x] Adhere to separation of concerns; code is not tightly coupled, especially to 3rd party dependencies
  • [x] Code is reviewed or developed by pair; 1 approval is needed but consider requiring an outside-the-pair reviewer
  • [x] Code quality checks passed
• [x] Security & Privacy tasks completed
  • [x] Security & privacy gates passed
• [x] Testing tasks completed
  • [x] Load tests passed
  • [x] Unit test coverage of our code >= 90%
• [x] Build & Deploy tasks completed
  • [x] Build process updated
  • [x] API(s) are versioned
  • [x] Feature toggles created and/or deleted. Document the feature toggle
  • [x] Source code is merged to the main branch

Research Questions

• Optional: Any initial questions for research

Decisions

• Optional: Any decisions we've made while working on this story

Notes

• Accession Number OBX example: https://github.com/CDCgov/trusted-intermediary/blob/be06050119e62de42ada797a79ee4ab35857bd45/examples/CA/002_CA_ORU_R01.hl7#L65

Implementation

After discussing with @dbgolson, we've decided to generalize the transformation function to accept three parameters. For the accession number in OBX-3.4/5/6, the implementation will resemble:

arguments
---------
code                         99717-5
extension-coding system      L
extension-coding             alt-coding

By examining the coding extension (which can be either "coding" or "alt-coding"), the transform will be more flexible. This allows us to retrieve codes from either OBX-3.1/2/3 or OBX-3.4/5/6, depending on partner-specific requirements.

[jbiskie]

Story tasks and notes updated after discussion with @dbgolson. Tentatively, @luis-pabon-tf is going to start on the implementation and @jbiskie will start on tests.