Code

Merge in cleanup branch#84

Code

Merged

lukeaduncan merged 103 commits intomainWorldHealthOrganization/smart-immunizations:mainfrom cleanupWorldHealthOrganization/smart-immunizations:cleanupCopy head branch name to clipboardFeb 2, 2024

+16,737-61,638

Commits

Commits on Aug 2, 2023

• Initial removal of everything but Measles. Each will be restored as they get updated.

  lukeaduncan

  committed
  40ecebb

• Cleaned up IMMZConcepts.cql to remove currently unsed concepts.

  lukeaduncan

  committed
  0fb6272

Commits on Aug 3, 2023

• Cleaned out indicators and libraries. Added logging to sushi-config.

  lukeaduncan

  committed
  d85ced7

• Added initial logical model for IMMZ.C Register Client.

  lukeaduncan

  committed
  ba9fd76

• Removed so currently not used library files to speed up IG publisher.

  lukeaduncan

  committed
  af136ea

• Updated IMMZ.C logical model to add codes and used HumanName.

  lukeaduncan

  committed
  b7622d0

• Fixed invariant with updated element names.

  lukeaduncan

  committed
  b27edc8

• Replace more complex data types with simple ones in the logical model. Will discuss further to decide on final data types.

  lukeaduncan

  committed
  617568d

• Cleaned up CodeSystem/ValueSet name/ids.

  lukeaduncan

  committed
  43fb2bc

Commits on Aug 4, 2023

• move logical model file

  costateixeira

  committed
  394647a

• add questionnaire

  costateixeira

  committed
  1887d60

• Added in mapping for IMMZ.C logical model.

  lukeaduncan

  committed
  d61bab1

• Removed Identifer type from logical model and some minor fixes to questionnaire.

  lukeaduncan

  committed
  9f551da

• Added in conceptmap for data elements.

  lukeaduncan

  committed
  0f1fd19

• Changed aliases use start with $ to match with recommendations.

  lukeaduncan

  committed
  cf10ea3

• Removed extra logging from sushi config and updated title/desc for IMMZ.C conceptmap.

  lukeaduncan

  committed
  f51fe0f

Commits on Aug 8, 2023

• Fixed issue with questionnaire and added example questionnaire response.

  lukeaduncan

  committed
  3ec6ebc

• Cleaned up example for IMMZ.C questionnaire response.

  lukeaduncan

  committed
  5f8b059

Commits on Aug 9, 2023

• Updated sushi config to include nested directories. Added in StructureMap source and resource for IMMZ.C logical model.

  lukeaduncan

  committed
  68fa492

• Added and corrected maps from QR to LM and Patient, and LM to Patient. Currently unable to test LM to Patient due to issues with the tooling in processing an instance of a LM.

  lukeaduncan

  committed
  0308c86

Commits on Aug 14, 2023

• Updated register client to remove calculated fields and update for changes from DAK.

  lukeaduncan

  committed
  b0f9f18

Commits on Aug 22, 2023

• Updated QR to Patient to pass through the LM instead of duplicating the code.

  lukeaduncan

  committed
  f927d92

Commits on Aug 31, 2023

• Update logical-IMMZ.C.fsh

  costateixeira

  committed
  73f1286

Commits on Sep 18, 2023

• Added logical model and questionnaire for D1 client history.

  lukeaduncan

  committed
  f195ea1

Commits on Sep 20, 2023

• Updated decision logic/scheduling for Measles.

  lukeaduncan

  committed
  d6eaf0b

• Added Library files for updated CQL.

  lukeaduncan

  committed
  1ce96c4

• Fixed measles cql for provisioning the dose to include a max age check and fixed error in plan definition for the expression.

  lukeaduncan

  committed
  2bb67f7

• Created service request activity definition and updated the plan definition to reference that.

  lukeaduncan

  committed
  b14dc4d

Commits on Sep 21, 2023

• Fixed grouping with new activitydefinition for sushi error.

  lukeaduncan

  committed
  d7d5956

• Added status and intent to the servicerequest activitydefinition.

  lukeaduncan

  committed
  d3e2326

• Updated activity definition to remove dyamicvalues which were causing errors.

  lukeaduncan

  committed
  9b411d5

Commits on Sep 25, 2023

• Added in medicationrequest attempt. Still having some issues with dynamicValues and other errors.

  lukeaduncan

  committed
  e6f82dd

Commits on Sep 27, 2023

• Update medicalrequest activitydefinition so it now runs, but the dynamicValues are failing.

  lukeaduncan

  committed
  7239583

• Made changes to work with making structuremaps in IG publisher.

  lukeaduncan

  committed
  8704a02

• Tried to fix publisher issue with LMtoPatient and translate() but it's still occurring.

  lukeaduncan

  committed
  1869c36

Commits on Sep 29, 2023

• Updated activitydefinition that is now working with latest version of cqf-ruler.

  lukeaduncan

  committed
  d4639b7

• Fixed issue with DT08 cql for the scheduled due date and updated maps.http to use the output directory instead of fsh-generated for the questionnaire example.

  lukeaduncan

  committed
  108e10d

• Changed .map to .fml to avoid warnings in IG publisher output.

  lukeaduncan

  committed
  ec0b548

Commits on Oct 2, 2023

• Fixed product dode in medicationrequest activitydefinition.

  lukeaduncan

  committed
  c0584d3

Commits on Oct 3, 2023

• Changed plan and activity definitions to be FSH files. Added in umbrella plan definition.

  lukeaduncan

  committed
  5d29afa

Commits on Oct 4, 2023

• Moved tests for IMMZDT08 under plandefinition directory so bundles are created by the tooling.

  lukeaduncan

  committed
  5cff788

Commits on Oct 5, 2023

• Updated measles activitydefinition to be based off of CPG immunizationactivity.

  lukeaduncan

  committed
  c23c93f

• Renamed Measles based on new id in DAK.

  lukeaduncan

  committed
  e0ff929

• Changed birth dose to zero and updated doses to be based on the primary series. (1 or 2). Updated tests directory to match new CQL file name.

  lukeaduncan

  committed
  c696549

• Fixed compile errors based on file name changes.

  lukeaduncan

  committed
  8755fbd

Commits on Oct 6, 2023

• Updated measures to be continuous variable since the denominator isn't calculable. Only includes clients receiving the dose within the measurement period.

  lukeaduncan

  committed
  3caffc8

Commits on Oct 9, 2023

• Removed pregnant and breastfeeding questions from the client history logical model and questionnaire.

  lukeaduncan

  committed
  a970f2d

• Removed preterm birth from logical model and questionnaire.

  lukeaduncan

  committed
  655a03d

• Added in logical model and questionnaire for contraindications. Removed contraindication check from intial plandefintion. Need to add second plan and activity definitions for contraindications.

  lukeaduncan

  committed
  c98a55c

Commits on Oct 11, 2023

• Removed old activity definition files that are no longer used.

  lukeaduncan

  committed
  c77bad6

Commits on Oct 12, 2023

• Added in logical model/questionnaire for check contraindications. Added template for plan and activity defs for contraindications, but the CQL still needs to be completed.

  lukeaduncan

  committed
  f6fe9a8

• Updated canonical URL.

  lukeaduncan

  committed
  24cd625

Commits on Oct 16, 2023

• Finished plandefinition and activity defintion for contraindications.

  lukeaduncan

  committed
  6f6efcc

• Renamed/organized FSH files to align with the SOP.

  lukeaduncan

  committed
  44f80ed

• Fixed naming errors from previous commit.

  lukeaduncan

  committed
  0b7aba5

• Removed zero and supplementary doses from the measles logic.

  lukeaduncan

  committed
  5d3aa6f

Commits on Oct 18, 2023

• Added in updated questionnaire/logical model/valuesets for client history. Still need to complete the structure map.

  lukeaduncan

  committed
  c95e92b

• Questionnaires - add extraction extension and update reference to contained VS

  costateixeira

  committed
  2cea2b8

• Fixed id in client history questionnaire.

  lukeaduncan

  committed
  984dd65

• Split measures into 2 files for SOP.

  lukeaduncan

  committed
  ce86727

• trim down extensions

  costateixeira

  committed
  5375d86

• Merge branch 'cleanup' of https://github.com/WorldHealthOrganization/smart-immunizations into cleanup

  costateixeira

  committed
  72c0e71

• Added in structuremaps for D1 Client History.

  lukeaduncan

  committed
  e37cd65

Commits on Oct 19, 2023

• rename map files

  costateixeira

  committed
  dacf182

Commits on Oct 20, 2023

• Fixed updated logical model in maps and updated .http file to reference renamed files.

  lukeaduncan

  committed
  fed81ae

Commits on Oct 22, 2023

• align questionnaire names

  costateixeira

  committed
  d9cbabc

• update to canonicals

  costateixeira

  committed
  da317c7

Commits on Nov 6, 2023

• Updated measles quesionnaire/codesystem/structuremaps for new entries in D1. Added rest of D1 codes/valuesets in preparation for next antigens for questionaire/structuremaps.

  lukeaduncan

  committed
  06cd875

Commits on Nov 7, 2023

• Update ghbuild.yaml

  costateixeira

  authored
  e189347

Commits on Nov 29, 2023

• Fixed missing reverse maps for IMMZ.C.

  lukeaduncan

  committed
  82719ec

Commits on Nov 30, 2023

• Added in codesystem for Adminster Vaccine tab because it is needed for contraindications and recommendation status valuesets. Converted from D4 to D5 for contraindication ids because that is what i…

  Show description for 1cd1df7
  lukeaduncan

  committed
  1cd1df7

Commits on Dec 5, 2023

• Updated CQL expressions to match the DAK and updates tests for IMMZD2DTMeasles.

  lukeaduncan

  committed
  d49aaab

Commits on Dec 13, 2023

• Reworked structure of CQL and PlanDefs for measles based on the latest DAK updates. This is split into one input CQL file and output CQL files per decision table (HighTx, LowTx, Dose0, Supplementary).

  lukeaduncan

  committed
  0de2b63

Commits on Dec 15, 2023

• Removed libraries from activitydefinitions and used dynamicValues in the plandefinition so the activitydefinitions can be re-used across the plan definitions to reduce nearly duplicate resources.

  lukeaduncan

  committed
  fdc928f

• Updated template to who.template.root#current in ig.ini.

  lukeaduncan

  committed
  2689e71

Commits on Dec 19, 2023

• Updated contraindications CQL to match the latest table from the DAK and the new format for plandefs.

  lukeaduncan

  committed
  7b37377

Commits on Jan 3, 2024

• Added in CQL/plandefs and tests for measles scheduling logic.

  lukeaduncan

  committed
  c4d3893

• Updated umbrella plandef to include dose0, hightx, and supp measles plandefs.

  lukeaduncan

  committed
  b80c284

Commits on Jan 18, 2024

• Updated indicators for measles and added high/low tx for scheduling dose 0 for the expiration dates.

  lukeaduncan

  committed
  ecb5985

• Added missing Measures and updated Library resources for measles after testing in CQF Ruler.

  lukeaduncan

  committed
  988d473

Commits on Jan 19, 2024

• Replaced contraindication for measles with a generic all antigen questionnaire/model.

  lukeaduncan

  committed
  e813468

• Updated measles LM/questionnaire/structuremaps for updates to the D1 client history data dictionary in the DAK.

  lukeaduncan

  committed
  34c9178

• Added in questionnaire/LM/maps for yellow fever.

  lukeaduncan

  committed
  bada461

Commits on Jan 20, 2024

• Update IMMZD2DTMeaslesHighTx.cql

  Show description for 6c7a892
  jennylthompson

  authored
  6c7a892

• Updated IMMZD2DTMeaslesLowTx.cql guidance to providers per L2 updates

  jennylthompson

  authored
  2dbb8dd

• Update IMMZD2DTMeaslesSupp.cql guidance to providers per L2 updates

  jennylthompson

  authored
  462309b

• Update IMMZD2DTMeaslesDose0.cql guidance to providers per L2 updates

  jennylthompson

  authored
  7d6e5a2

Commits on Jan 22, 2024

• Updated measles CQL/Library files for updated expression names from the L2.

  lukeaduncan

  committed
  20d4904

Commits on Jan 23, 2024

• Added in CQL/plandef for Yellow Fever decision tables and contraindications. Added examples/tests for these. Added MedicationRequest to all Measles contraindication examples.

  lukeaduncan

  committed
  14cf98d

Commits on Jan 24, 2024

• Rolled back change to activitydefs that tried to remove the measles dependency. Each antigen will need its own activitydef. Added in yellow fever CQL/libraries and test examples.

  lukeaduncan

  committed
  0203d94

Commits on Jan 25, 2024

• Updated Measles schedule CQL based on recent updates to the L2.

  lukeaduncan

  committed
  4804ce0

Commits on Jan 26, 2024

• Added in plandef for yellow fever contraindication. Updated plan defs and activity defs to use rulesets to simplify adding new antigens.

  lukeaduncan

  committed
  d70e1e5

• Added in Yellow Fever indicator (26) and measure. Updated measures to use a rulesets.

  lukeaduncan

  committed
  086f220

• Added Polio vaccine valueset.

  lukeaduncan

  committed
  9b47d1e

• Fixed structuremap reference in questionnaires for measles and yellowfever. Added polio LM and questionnaire.

  lukeaduncan

  committed
  ea0c2ed

• Fixed typo and duplicates in polio vaccine valueset.

  lukeaduncan

  committed
  8a020bd

Commits on Jan 29, 2024

• Update decision-logic.md for overview table and measles high tx

  Show description for 0b752ef
  jennylthompson

  authored
  0b752ef

Commits on Jan 30, 2024

• Update decision-logic.md table headers, formatting, and cell merging

  jennylthompson

  authored
  b257611

• Removed extra content from measure 08 with addition of ruleset.

  lukeaduncan

  committed
  e6e67cb

Commits on Jan 31, 2024

• Updated logical models to include an all antigen parent version. Did same for questionnaires. Update structuremaps to have all antigen files for QRtoLM and LMtoResources that are extended by the in…

  Show description for 361f910
  lukeaduncan

  committed
  361f910

• Changed measures to be definitions so they didn't default to be examples for the IG.

  lukeaduncan

  committed
  3c2c0c7

Commits on Feb 1, 2024

• Updated comments to align with updates to latest antigens.

  lukeaduncan

  committed
  9f69dee

Commits on Feb 2, 2024

• Merged in updates from main.

  lukeaduncan

  committed
  36ea67c