Merged in 2024-artifact-update (pull request #35)

2024 Artifact Update and Integration of CQL-to-ELM Translator task

* Update CQL to version 4.0.0

- Update CQL to version 4.0.0
- Update Naloxone Medication labels/flags to be Naloxone and Nalmefene
- Update Brenda Jackson test patient to have naloxone/nalmefene entries

* Add cql-to-elm translation script

- Add gradle files to invoke CQL-to-ELM translator
- Add npm script for "cql-to-elm"
- Update README to describe how to update CQL and ELM JSON


Approved-by: Julia Afeltra

.gitignore

@@ -6,4 +6,5 @@
 /coverage
 /tx_bundle_dump
 /test_patient_dump
+/.gradle
 *.css

README.md

@@ -45,7 +45,7 @@ Systems integrating the Pain Management Summary will need to expose the correspo
 5. If you'll be launching the app from an Epic EHR, modify `.env` to set `VITE_EPIC_SUPPORTED_QUERIES` to `true`
 6. Serve the code by executing `npm start` (runs on port 8000)
 
-## To build and deploy using a standard web server (static HTML and JS)
+### To build and deploy using a standard web server (static HTML and JS)
 
 The Pain Management Summary can be deployed as static web resources on any HTTP server.  There are several customizations, however, that need to be made based on the site where it is deployed.
 
@@ -65,6 +65,26 @@ The Pain Management Summary can be deployed as static web resources on any HTTP
 
 Optionally to step 9, you can run `npm run serve` to use Vite's built-in server to host the code in `dist`. This approach, however, should not be used in production.
 
+### To update the CQL and/or ELM JSON files
+
+The CQL source and ELM JSON files are kept in the `src/cql/dstu2` and `src/cql/r4` folders. The Pain Management Summary app executes only the ELM JSON files, but it is helpful to keep the CQL source files alongside them.
+
+To update the CQL files:
+
+1. Download the CQL zips from the [CDS Connect artifact](https://cds.ahrq.gov/cdsconnect/artifact/factors-consider-managing-chronic-pain-pain-management-summary) or get them from another source (if applicable).
+2. Unzip the FHIR DSTU2 / 1.0.2 CQL package and copy the CQL and JSON files to `src/cql/dstu2`
+3. Unzip the FHIR R4 / 4.0.1 CQL package and copy the CQL and JSON files to `src/cql/r4`
+
+The ELM JSON files in the distributable zip packages include optional annotations, locators, result types, and signatures. These are not required by this application and significantly increase its file size. The ELM JSON files should be rebuilt without this optional data in order to improve the efficiency of this app.
+
+To rebuild the ELM JSON files without annotations, locators, result types, and unnecessary signatures:
+
+1. Install [JDK 11](https://adoptium.net/temurin/releases/?version=11) or greater (if necessary)
+2. Note the `translatorVersion` in one of the ELM JSON files from the downloaded zip package (e.g., `3.10.0`)
+3. Update the `runtimeOnly` dependency's version in the `build.gradle` file (e.g., `runtimeOnly 'info.cqframework:cql-to-elm-cli:3.10.0'`)
+4. Run `npm run cql-to-elm` to rebuild the ELM JSON files (note: warnings are expected, but there should be no errors)
+5. Review the changes in all ELM JSON files in the `src/cql` folders to ensure they look correct
+
 ### To update the valueset-db.json file
 
 The value set content used by the CQL is cached in a file named `valueset-db.json`.  If the CQL has been modified to add or remove value sets, or if the value sets themselves have been updated, you may wish to update the valueset-db.json with the latest codes.  To do this, you will need a [UMLS Terminology Services account](https://uts.nlm.nih.gov//license.html).

build.gradle

@@ -0,0 +1,19 @@
+plugins {
+  id 'java'
+}
+
+repositories {
+  mavenCentral()
+}
+
+dependencies {
+  runtimeOnly 'info.cqframework:cql-to-elm-cli:3.10.0'
+}
+
+task cql2elm(type: JavaExec) {
+  classpath = sourceSets.main.runtimeClasspath
+  main = 'org.cqframework.cql.cql2elm.cli.Main'
+  // recommended options based on https://build.fhir.org/ig/HL7/cql-ig/using-elm.html#translation-to-elm
+  // but no annotations or locators in order to reduce overall file size
+  args '--input', './src/cql', '--format', 'JSON', '--signatures', 'Overloads', '--disable-list-demotion', '--disable-list-promotion'
+}

gradle/wrapper/gradle-wrapper.properties

@@ -0,0 +1,5 @@
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-bin.zip
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists

gradlew

@@ -0,0 +1,240 @@
+#!/bin/sh
+
+#
+# Copyright © 2015-2021 the original authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+##############################################################################
+#
+#   Gradle start up script for POSIX generated by Gradle.
+#
+#   Important for running:
+#
+#   (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+#       noncompliant, but you have some other compliant shell such as ksh or
+#       bash, then to run this script, type that shell name before the whole
+#       command line, like:
+#
+#           ksh Gradle
+#
+#       Busybox and similar reduced shells will NOT work, because this script
+#       requires all of these POSIX shell features:
+#         * functions;
+#         * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+#           «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+#         * compound commands having a testable exit status, especially «case»;
+#         * various built-in commands including «command», «set», and «ulimit».
+#
+#   Important for patching:
+#
+#   (2) This script targets any POSIX shell, so it avoids extensions provided
+#       by Bash, Ksh, etc; in particular arrays are avoided.
+#
+#       The "traditional" practice of packing multiple parameters into a
+#       space-separated string is a well documented source of bugs and security
+#       problems, so this is (mostly) avoided, by progressively accumulating
+#       options in "$@", and eventually passing that to Java.
+#
+#       Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+#       and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
+#       see the in-line comments for details.
+#
+#       There are tweaks for specific operating systems such as AIX, CygWin,
+#       Darwin, MinGW, and NonStop.
+#
+#   (3) This script is generated from the Groovy template
+#       https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       within the Gradle project.
+#
+#       You can find Gradle at https://github.com/gradle/gradle/.
+#
+##############################################################################
+
+# Attempt to set APP_HOME
+
+# Resolve links: $0 may be a link
+app_path=$0
+
+# Need this for daisy-chained symlinks.
+while
+    APP_HOME=${app_path%"${app_path##*/}"}  # leaves a trailing /; empty if no leading path
+    [ -h "$app_path" ]
+do
+    ls=$( ls -ld "$app_path" )
+    link=${ls#*' -> '}
+    case $link in             #(
+      /*)   app_path=$link ;; #(
+      *)    app_path=$APP_HOME$link ;;
+    esac
+done
+
+APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
+
+APP_NAME="Gradle"
+APP_BASE_NAME=${0##*/}
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD=maximum
+
+warn () {
+    echo "$*"
+} >&2
+
+die () {
+    echo
+    echo "$*"
+    echo
+    exit 1
+} >&2
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "$( uname )" in                #(
+  CYGWIN* )         cygwin=true  ;; #(
+  Darwin* )         darwin=true  ;; #(
+  MSYS* | MINGW* )  msys=true    ;; #(
+  NONSTOP* )        nonstop=true ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD=$JAVA_HOME/jre/sh/java
+    else
+        JAVACMD=$JAVA_HOME/bin/java
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD=java
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+    case $MAX_FD in #(
+      max*)
+        MAX_FD=$( ulimit -H -n ) ||
+            warn "Could not query maximum file descriptor limit"
+    esac
+    case $MAX_FD in  #(
+      '' | soft) :;; #(
+      *)
+        ulimit -n "$MAX_FD" ||
+            warn "Could not set maximum file descriptor limit to $MAX_FD"
+    esac
+fi
+
+# Collect all arguments for the java command, stacking in reverse order:
+#   * args from the command line
+#   * the main class name
+#   * -classpath
+#   * -D...appname settings
+#   * --module-path (only if needed)
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
+
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if "$cygwin" || "$msys" ; then
+    APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+    CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+
+    JAVACMD=$( cygpath --unix "$JAVACMD" )
+
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    for arg do
+        if
+            case $arg in                                #(
+              -*)   false ;;                            # don't mess with options #(
+              /?*)  t=${arg#/} t=/${t%%/*}              # looks like a POSIX filepath
+                    [ -e "$t" ] ;;                      #(
+              *)    false ;;
+            esac
+        then
+            arg=$( cygpath --path --ignore --mixed "$arg" )
+        fi
+        # Roll the args list around exactly as many times as the number of
+        # args, so each arg winds up back in the position where it started, but
+        # possibly modified.
+        #
+        # NB: a `for` loop captures its iteration list before it begins, so
+        # changing the positional parameters here affects neither the number of
+        # iterations, nor the values presented in `arg`.
+        shift                   # remove old arg
+        set -- "$@" "$arg"      # push replacement arg
+    done
+fi
+
+# Collect all arguments for the java command;
+#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
+#     shell script including quotes and variable substitutions, so put them in
+#     double quotes to make sure that they get re-expanded; and
+#   * put everything else in single quotes, so that it's not re-expanded.
+
+set -- \
+        "-Dorg.gradle.appname=$APP_BASE_NAME" \
+        -classpath "$CLASSPATH" \
+        org.gradle.wrapper.GradleWrapperMain \
+        "$@"
+
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+    die "xargs is not available"
+fi
+
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+#   readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+#   set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
+
+eval "set -- $(
+        printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
+        xargs -n1 |
+        sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+        tr '\n' ' '
+    )" '"$@"'
+
+exec "$JAVACMD" "$@"