Merge branch 'main' of https://github.com/chronic-care/covid-ed-ig

.github/workflows/build-package.yml

@@ -39,7 +39,7 @@ jobs:
           bundle install
 
       - name: Update Publisher executable
-        run: bash _updatePublisher.sh --force --yes --skip-ping
+        run: bash _updatePublisher.sh --force --yes
 
       - name: Generate Implementation Guide (IG)
         run: bash _genonce.sh

.talismanrc

@@ -1,11 +1,12 @@
 fileignoreconfig:
 - filename: cql-unit-tests/package-lock.json
-  checksum: 1abc3447c829e856923f3031986fadb76ca930f3686d268e1e46cb0b612802e0
-- filename: input/vocabulary/ValueSet/valueset-covid-19-condition-risk-obstructive-sleep-apnea-icd10.json
-  checksum: 2387dad07ac00f6b5ecd0bd346088d5607484205945b2057b07f681692d2a531
+  checksum: 7869cce478539463891fc26b8b1a94b64d02c988c2bbd43e8c80b2b19e596faa
+- filename: input/cql/valueset-db.json
+  checksum: fbba042ed60f0f2c80980e25a4b7ff6b569853431e3cce53686d7bddd20546b7
 - filename: input/vocabulary/ValueSet/valueset-covid-19-condition-risk-downs-syndrome-icd10.json
   checksum: 4cb0e0a2b14d4f37c02f10cf5dd4012f5f61cbb139d0edb5220a5a4f1e782a52
+- filename: input/vocabulary/ValueSet/valueset-covid-19-condition-risk-obstructive-sleep-apnea-icd10.json
+  checksum: 2387dad07ac00f6b5ecd0bd346088d5607484205945b2057b07f681692d2a531
 - filename: input/vocabulary/ValueSet/valueset-vsac-covid19-diabetes-snomed.json
   checksum: 9452adceb8d25afec1621ae487944be99f93c27ad2f1b2a1daa9a68402aa9591
-- filename: input/cql/valueset-db.json
-  checksum: fbba042ed60f0f2c80980e25a4b7ff6b569853431e3cce53686d7bddd20546b7
+version: "1.0"

README.md

@@ -43,11 +43,23 @@ Documentation for the IG-Publisher is available at [https://confluence.hl7.org/d
 
 #### Ruby / Jekyll
 
-Jekyll requires Ruby version 2.1 or greater. Depending on your operating system, you may already have Ruby bundled with it. Otherwise, or if you need a newer version, go to [https://www.ruby-lang.org/en/downloads/](https://www.ruby-lang.org/en/downloads/) for directions.
+FIRST, Install Ruby through a Ruby version manager (rvm/rbenv/chruby) and then install Jekyll.
+`brew install rbenv`
+`rbnev init`
+add `eval "$(rbenv init - zsh)"` to `~/.zshrc` or where your profile settings are.
+`rbenv install 3.1.0`
+`rbenv global 3.1.0`
 
-Jekyll
+Jekyll requires Ruby version 2.1 or greater. 
+`ruby -v`
 
-Go to [https://jekyllrb.com](https://jekyllrb.com) and follow the instructions there, for example gem install jekyll bundler. The end result of this should be that the binary "jekyll" is now in your path.
+Jekyll `gem install --user-install bundler jekyll`
+If `jekyll -v` doesn't work, add `export PATH="/Users/<your-username>/.gem/ruby/3.1.0/bin:$PATH"` to your `~/.zshrc` or where your profile settings are.
+Try `bundle exec jekyll -v` if `jekyll -v` still doesn't work.
+
+If installing on a macOS: [https://jekyllrb.com/docs/installation/macos/](https://jekyllrb.com/docs/installation/macos/)
+
+Go to [https://jekyllrb.com](https://jekyllrb.com) for more information.
 
 ### Build
 
@@ -160,9 +172,7 @@ There are a couple of ways to test the CQL.
 ## Updating Valuesets
 If new codes need to be added to a valueset, follow these steps to manually update the JSON and regenerate the `valueset-db.json` file:
 1. Add new codes to the relevant JSON files in `input/vocabulary/valueset`. For labs, add to both the `compose` and `expansion` objects.
-2. Run `./_updateCQFTooling.sh` script, which updates the [CQF Tooling](https://github.com/cqframework/cqf-tooling) and downloads the `jar` file into `input-cache` directory.
-3. Run `java -jar input-cache/tooling-1.3.1-SNAPSHOT-jar-with-dependencies.jar -ToJsonValueSetDb -path="input/vocabulary/valueset"` (note: this is the path to the entire valueset folder)
-4. The new `valueset-db.json` can be found in `src/main/resources/org/opencds/cqf/tooling/terminology/output`. Copy this over into the `input/cql` directory to replace it.
+2. Run `./_updateValueSet.sh`. This updates the CQF tooling, generates the new valueset, copies it to the `./input/cql` folder and then updates `healthCodes.json` with the new codes as well.
 
 # CQL Development Resources
 

_publishToRepo.sh

@@ -14,6 +14,7 @@ node updatePackage.js --release-tag $releaseTag
 cp ./output/*.cql ./output/package/ # Copy over original CQL
 cp ./output/*-2.json ./output/package/ # Copy over original json+eml
 cp ./input/cql/valueset-db.json ./output/package/
+cp ./input/cql/healthCodes.json ./output/package/
 node localizeLibraryPaths.js ./output/package/*-2.json
 echo "registry=https://npm.pkg.github.com/chronic-care" >> ./output/package/.npmrc
 cd ./output/package

_updatePublisher.bat

@@ -216,4 +216,4 @@ start copy /y "_updatePublisher.new.bat" "_updatePublisher.bat" ^&^& del "_updat
 
 IF "%skipPrompts%"=="true" (
   PAUSE
-}
+)

_updatePublisher.sh

@@ -5,15 +5,14 @@ dlurl=$pubsource$publisher_jar
 
 input_cache_path=$PWD/input-cache/
 
-scriptdlroot=https://raw.githubusercontent.com/FHIR/sample-ig/master
+scriptdlroot=https://raw.githubusercontent.com/HL7/ig-publisher-scripts/main
 update_bat_url=$scriptdlroot/_updatePublisher.bat
 gen_bat_url=$scriptdlroot/_genonce.bat
 gencont_bat_url=$scriptdlroot/_gencontinuous.bat
 gencont_sh_url=$scriptdlroot/_gencontinuous.sh
 gen_sh_url=$scriptdlroot/_genonce.sh
 update_sh_url=$scriptdlroot/_updatePublisher.sh
 
-skipPing=false
 skipPrompts=false
 FORCE=false
 
@@ -24,26 +23,19 @@ fi
 
 while [ "$#" -gt 0 ]; do
     case $1 in
-    --skip-ping)  skipPing=true ;;
     -f|--force)  FORCE=true ;;
     -y|--yes)  skipPrompts=true ; FORCE=true ;;
     *)  echo "Unknown parameter passed: $1.  Exiting"; exit 1 ;;
     esac
     shift
 done
 
-if [[ $skipPing == false ]]; then
-  echo "Checking internet connection"
-  case "$OSTYPE" in
-    linux-gnu* ) ping tx.fhir.org -4 -c 1 -w 30 >/dev/null ;;
-    darwin* )	ping tx.fhir.org -c 1 >/dev/null ;;
-    *) echo "unknown: $OSTYPE"; exit 1 ;;
-  esac
-
-  if [ $? -ne 0 ] ; then
-    echo "Offline (or the terminology server is down), unable to update.  Exiting"
-    exit 1
-  fi
+echo "Checking internet connection"
+curl -sSf tx.fhir.org > /dev/null
+
+if [ $? -ne 0 ] ; then
+  echo "Offline (or the terminology server is down), unable to update.  Exiting"
+  exit 1
 fi
 
 if [ ! -d "$input_cache_path" ] ; then

_updateValueSet.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+
+echo Update CQF Tooling ...
+./_updateCQFTooling.sh
+
+java -jar input-cache/tooling-1.3.1-SNAPSHOT-jar-with-dependencies.jar -ToJsonValueSetDb -path="input/vocabulary/valueset"
+echo Generated valueset at input/vocabulary/valueset
+
+cp src/main/resources/org/opencds/cqf/tooling/terminology/output/valueset-db.json ./input/cql/valueset-db.json
+echo Copied valueset-db.json to ./input/cql folder.
+
+node ./parseHealthCodes.js

cql-unit-tests/bin/run-tests.sh

@@ -2,6 +2,8 @@
 
 echo "Generating compiled CQL..."
 ./_genonce.sh && \
+echo "Updating healthcodes ..." && \
+./_updateValueSet.sh && \
   echo "Localizing library paths..." && \
   node ./localizeLibraryPaths.js ./output/*-2.json && \
   cd cql-unit-tests && \

cql-unit-tests/helpers/builders.ts

@@ -39,40 +39,78 @@ export const buildDefaultPatientDataParameters = (overrides: Partial<PatientData
 
 export const buildDefaultRiskAssessmentScoreParameters = (overrides: Partial<RiskAssessmentScoreParameters> = {}): RiskAssessmentScoreParameters => {
     const riskAssessmentScoreParameters: RiskAssessmentScoreParameters = {
-        Cancer: false,
-        CardiovascularDisease: false,
-        ChronicRespiratoryDisease: false,
-        DiabetesType2: false,
-        DownsSyndrome: false,
-        Hypertension: false,
-        Immunosuppression: false,
-        NeurologicDisease: false,
-        Obesity: false,
-        ObstructiveSleepApnea: false,
-        Pregnancy: false,
-        RenalDisease: false,
-        SteroidUsage: false,
+      Bronchiectasis: false,
+      BronchopulmonaryDysplasia: false,
+      PulmonaryHypertension: false,
+      PulmonaryEmbolism: false,
+      Cancer: false,
+      CerebrovascularDisease: false,
+      ChronicKidneyDisease: false,
+      ChronicLiverDisease: false,
+      COPD: false,
+      DiabetesMellitus: false,
+      HeartConditions: false,
+      InterstitialLungDisease: false,
+      CurrentAndFormerSmoking: false,
+      Tuberculosis: false,
+      Obesity: false,
+      PregnancyAndRecentPregnancy: false,
+      MentalHealthDisorders: false,
+      ChildrenWithCertainUnderlyingConditions: false,
+      DownSyndrome: false,
+      HIV: false,
+      NeurologicConditions: false,
+      Overweight: false,
+      SickleCellDisease: false,
+      SolidOrganOrBloodStemTransplantation: false,
+      SubstanceUseDisorders: false,
+      Corticosteroids: false,
+      ImmunosuppressiveMedications: false,
+      CysticFibrosis: false,
+      Thalassemia: false,
+      Asthma: false,
+      Hypertension: false,
+      ImmuneDeficiencies: false
     };
 
     return buildWithOverrides(riskAssessmentScoreParameters, overrides);
 };
 
 export const buildAllNullRiskAssessmentScoreParameters = (): RiskAssessmentScoreParameters => {
     const riskAssessmentScoreParameters: RiskAssessmentScoreParameters = {
-        Cancer: null,
-        CardiovascularDisease: null,
-        ChronicRespiratoryDisease: null,
-        DiabetesType2: null,
-        DownsSyndrome: null,
-        Hypertension: null,
-        Immunosuppression: null,
-        NeurologicDisease: null,
-        Obesity: null,
-        ObstructiveSleepApnea: null,
-        Pregnancy: null,
-        RenalDisease: null,
-        SteroidUsage: null,
+      Bronchiectasis: null,
+      BronchopulmonaryDysplasia: null,
+      PulmonaryHypertension: null,
+      PulmonaryEmbolism: null,
+      Cancer: null,
+      CerebrovascularDisease: null,
+      ChronicKidneyDisease: null,
+      ChronicLiverDisease: null,
+      COPD: null,
+      DiabetesMellitus: null,
+      HeartConditions: null,
+      InterstitialLungDisease: null,
+      CurrentAndFormerSmoking: null,
+      Tuberculosis: null,
+      Obesity: null,
+      PregnancyAndRecentPregnancy: null,
+      MentalHealthDisorders: null,
+      ChildrenWithCertainUnderlyingConditions: null,
+      DownSyndrome: null,
+      HIV: null,
+      NeurologicConditions: null,
+      Overweight: null,
+      SickleCellDisease: null,
+      SolidOrganOrBloodStemTransplantation: null,
+      SubstanceUseDisorders: null,
+      Corticosteroids: null,
+      ImmunosuppressiveMedications: null,
+      CysticFibrosis: null,
+      Thalassemia: null,
+      Asthma: null,
+      Hypertension: null,
+      ImmuneDeficiencies: null
     };
 
     return buildWithOverrides(riskAssessmentScoreParameters, {});
-};
+};

cql-unit-tests/package.json

@@ -12,7 +12,7 @@
   "dependencies": {
     "@ahryman40k/ts-fhir-types": "^4.0.34",
     "cql-exec-fhir": "^2.0.0",
-    "cql-execution": "^2.3.1"
+    "cql-execution": "^2.3.3"
   },
   "devDependencies": {
     "@babel/plugin-proposal-class-properties": "^7.13.0",