CA observation transforms from local code to LOINC or PLT #1306
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Copied from the previous set of HL7 test data, with added OBX examples of the new mapping
Fixed typo on some local codes
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.../cdc/trustedintermediary/etor/ruleengine/transformation/custom/MapLocalObservationCodes.java
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Add the mapped coding at the beginning of the coding list
…/github.com/CDCgov/trusted-intermediary into story/1277-observation-local-codes-to-loinc
…/github.com/CDCgov/trusted-intermediary into story/1277-observation-local-codes-to-loinc
…e edge case unnacounted for
…/github.com/CDCgov/trusted-intermediary into story/1277-observation-local-codes-to-loinc
jbiskie
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Sep 17, 2024
.../cdc/trustedintermediary/etor/ruleengine/transformation/custom/MapLocalObservationCodes.java
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Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Replace unused assignment with inline return
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
* Updating hurl scripts * Fixed typo in readme, create temp folder, write scrambled file into temp folder * Fixed directory creation, resolved issue with sed command not copying rest of file * updated readme to include toggle in options, add comments to scramble doing, alerted user to scrambling, removed folder creation for individual file * replaced msh header for oru and orm message types * added msh header replacement for oml message type * switched to msh-9.2 as subfield in conditional * remove temp directory after hurl script runs --------- Co-authored-by: jcrichlake <jeff.crichlake@agile6.com> Co-authored-by: Sylvie <sschuresko@flexion.us> Co-authored-by: jcrichlake <145698165+jcrichlake@users.noreply.github.com> Co-authored-by: saquino0827 <saquino@flexion.us>
Co-Authored-By: halprin <halprin@users.noreply.github.com>
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
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* Create 020_CA_ORU_R01_CDPH_OBX_to_LOINC_0_initial_message.hl7 Copied from the previous set of HL7 test data, with added OBX examples of the new mapping * Update 020_CA_ORU_R01_CDPH_OBX_to_LOINC_0_initial_message.hl7 Fixed typo on some local codes * Adding translated example file #20 * Addin skeleton for transformation * WIP - add initial implementation of MapLocalObservationCode transform * Adding unit test for a single observation * Adding test for local code mappable to a PLT * Update MapLocalObservationCodes.java Add the mapped coding at the beginning of the coding list * Small code cleanup * Add tests for when the initial code is a LOINC code * Refactor tests to remove duplicated code * Add assertion to evaluateCoding * Adding test for when primary code is also populated * Add tests for an unmapped local code and empty observation identifer * Updates to transformation to pass first 2 test cases * WIP - multiple observation test * All curent tests pass, but the code is not pretty and has at least one edge case unnacounted for * Complete the multiple observations test, add the remaining mappings to the lookup * Minor cleanup and refactoring * Replace for() loop with if check for a single coding on the observation * Add MapLocalObservationCodes to transformation_definitions.json * refactor: logging for when local codes not found added method to extract MSH10 to HapiHelper class * Update sender in log warning, restore mock logger in unit tests * Commenting out the PLT codes that haven't been mapped yet so they will cause warnings for now * refactor helper method for msh10 * Minor naming tweaks and comment updates * add null check for cwe extension * Address null check for getSystem method * Missing paren * refactor: added hascodingExtensionWithUrl helper method to HapiHelper added getCodingExtensionByUrl helper method to HapiHelper * refactor: added hasCodingSytem helper method to HapiHelper added getCodingSystem helper method to HapiHelper * Removed comments and empty lines * spotlessApply * WIP: transform refactoring - flatten conditional blocks * Refactor transform into simpler methods * Update minor dependencies to v5.4 (#1339) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update HapiHelper.java Replace unused assignment with inline return * Update dependency com.azure:azure-storage-blob to v12.28.0 (#1344) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update Terraform azurerm to v4.3.0 (#1345) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Move urlForCodeType to HapiHelper for future reusability * Adding tests for code coverage and addressing Sonar findings * Adding tests for code coverage and addressing Sonar findings * Adding tests for null and empty bundle for resourcesInBundle * Adding tests for urlForCodeType * HapiHelper: unit test for when bundle is null * Updated RS Hurl Script to Replace MSH Header When Not Toggled (#1342) * Updating hurl scripts * Fixed typo in readme, create temp folder, write scrambled file into temp folder * Fixed directory creation, resolved issue with sed command not copying rest of file * updated readme to include toggle in options, add comments to scramble doing, alerted user to scrambling, removed folder creation for individual file * replaced msh header for oru and orm message types * added msh header replacement for oml message type * switched to msh-9.2 as subfield in conditional * remove temp directory after hurl script runs --------- Co-authored-by: jcrichlake <jeff.crichlake@agile6.com> Co-authored-by: Sylvie <sschuresko@flexion.us> Co-authored-by: jcrichlake <145698165+jcrichlake@users.noreply.github.com> Co-authored-by: saquino0827 <saquino@flexion.us> * Add control id test, update test name * Fix order of mockLogger registration and injection * Fixed prod prefix mapping Co-Authored-By: halprin <halprin@users.noreply.github.com> * Add post-TI and post-RS example files * Update dependency gradle to v8.10.2 (#1347) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Add final 5 PLT mappings; update mapping for 99717-50 * Add comment to clarify behavior of adding the mapped code --------- Co-authored-by: Joel Biskie <jbiskie@flexion.us> Co-authored-by: jorge Lopez <jlopez@flexion.us> Co-authored-by: Tiffini Johnson <tjohnson@flexion.us> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Bella L. Quintero <96704946+pluckyswan@users.noreply.github.com> Co-authored-by: jcrichlake <jeff.crichlake@agile6.com> Co-authored-by: Sylvie <sschuresko@flexion.us> Co-authored-by: jcrichlake <145698165+jcrichlake@users.noreply.github.com> Co-authored-by: saquino0827 <saquino@flexion.us> Co-authored-by: James Herr <jherr@flexion.us> Co-authored-by: halprin <halprin@users.noreply.github.com> Co-authored-by: Jorge Lopez <49923512+jorg3lopez@users.noreply.github.com>
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CA observation transforms from local code to LOINC or PLT
This PR adds a new transform that converts local observation codes in the CA result messages to LOINC or PLT codes. The tranform checks each observation in the message, and the mapped LOINC/PLT codes are added to the observation's coding resource as an additional code. Following the ReportStream conversion from fhir back to HL7, the mapped codes are placed in OBX-3.1/2/3, and the local code remains in OBX-3.4/5/6.
Issue
#1277
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