Merge branch 'google:master' into master

buildSrc/src/main/kotlin/Dependencies.kt

@@ -19,14 +19,6 @@ import org.gradle.api.artifacts.DependencyConstraint
 import org.gradle.kotlin.dsl.exclude
 
 object Dependencies {
-  object Cql {
-    const val evaluator = "org.opencds.cqf.fhir:cqf-fhir-cr:${Versions.Cql.clinicalReasoning}"
-    const val evaluatorFhirJackson =
-      "org.opencds.cqf.fhir:cqf-fhir-jackson:${Versions.Cql.clinicalReasoning}"
-    const val evaluatorFhirUtilities =
-      "org.opencds.cqf.fhir:cqf-fhir-utility:${Versions.Cql.clinicalReasoning}"
-  }
-
   object HapiFhir {
     const val fhirBaseModule = "ca.uhn.hapi.fhir:hapi-fhir-base"
     const val fhirClientModule = "ca.uhn.hapi.fhir:hapi-fhir-client"
@@ -139,11 +131,6 @@ object Dependencies {
   const val xmlUnit = "org.xmlunit:xmlunit-core:${Versions.xmlUnit}"
 
   object Versions {
-
-    object Cql {
-      const val clinicalReasoning = "3.0.0-PRE9-SNAPSHOT"
-    }
-
     const val androidFhirCommon = "0.1.0-alpha05"
     const val androidFhirEngine = "0.1.0-beta05"
     const val androidFhirKnowledge = "0.1.0-alpha03"
@@ -195,16 +182,17 @@ object Dependencies {
   }
 
   fun Configuration.removeIncompatibleDependencies() {
-    exclude(module = "xpp3")
-    exclude(module = "xpp3_min")
-    exclude(module = "xmlpull")
+    exclude(module = "hapi-fhir-caching-caffeine")
     exclude(module = "javax.json")
     exclude(module = "jcl-over-slf4j")
-    exclude(group = "org.apache.httpcomponents")
-    exclude(group = "org.antlr", module = "antlr4")
-    exclude(group = "org.eclipse.persistence", module = "org.eclipse.persistence.moxy")
-    exclude(module = "hapi-fhir-caching-caffeine")
+    exclude(module = "xmlpull")
+    exclude(module = "xpp3")
+    exclude(module = "xpp3_min")
+    exclude(group = "ch.qos.logback", module = "logback-classic")
     exclude(group = "com.github.ben-manes.caffeine", module = "caffeine")
+    exclude(group = "org.eclipse.persistence", module = "org.eclipse.persistence.moxy")
+    exclude(group = "org.antlr", module = "antlr4")
+    exclude(group = "org.apache.httpcomponents")
   }
 
   fun hapiFhirConstraints(): Map<String, DependencyConstraint.() -> Unit> {

buildSrc/src/main/kotlin/LicenseeConfig.kt

@@ -72,17 +72,24 @@ fun Project.configureLicensee() {
     }
 
     // Jakarta XML Binding API
-    allowDependency("jakarta.xml.bind", "jakarta.xml.bind-api", "2.3.3") {
+    allowDependency("jakarta.xml.bind", "jakarta.xml.bind-api", "4.0.1") {
       because("BSD 3-clause.")
     }
 
     // Jakarta Activation API 2.1 Specification
-    allowDependency("jakarta.activation", "jakarta.activation-api", "1.2.2") {
+    allowDependency("jakarta.activation", "jakarta.activation-api", "2.1.2") {
       because(
         "Licensed under Eclipse Distribution License 1.0. http://www.eclipse.org/org/documents/edl-v10.php",
       )
     }
 
+    // Jakarta Annotation API 2.1 Specification
+    allowDependency("jakarta.annotation", "jakarta.annotation-api", "2.1.1") {
+      because(
+        "Licensed under EPL 2.0",
+      )
+    }
+
     // Javax Annotation API
     allowDependency("javax.annotation", "javax.annotation-api", "1.3.2") {
       because("Dual-licensed under CDDL 1.1 and GPL v2 with classpath exception.")
@@ -108,7 +115,7 @@ fun Project.configureLicensee() {
       because("BSD 3-clause. http://www.antlr.org/license.html")
     }
     // ANTLR 4
-    allowDependency("org.antlr", "antlr4-runtime", "4.10.1") {
+    allowDependency("org.antlr", "antlr4-runtime", "4.13.1") {
       because("BSD 3-clause. http://www.antlr.org/license.html")
     }
 
@@ -195,6 +202,12 @@ fun Project.configureLicensee() {
     allowDependency("com.ibm.icu", "icu4j", "72.1") {
       because("BSD, part MIT and Apache 2.0. https://github.com/unicode-org/icu/blob/main/LICENSE")
     }
+
+    // Logback
+    allowDependency("ch.qos.logback", "logback-classic", "1.4.14") { because("LGPL") }
+
+    // Logback
+    allowDependency("ch.qos.logback", "logback-core", "1.4.14") { because("LGPL") }
   }
 }
 

catalog/src/main/assets/behavior_calculated_expression.json

@@ -2,48 +2,20 @@
   "resourceType": "Questionnaire",
   "item": [
     {
-      "linkId": "a-birthdate",
-      "text": "Birth Date (select age to auto calculate if not known)",
-      "type": "date",
-      "extension": [
-        {
-          "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-calculatedExpression",
-          "valueExpression": {
-            "language": "text/fhirpath",
-            "expression": "%resource.repeat(item).where(linkId='a-age-years' and answer.empty().not()).select(today() - answer.value)"
-          }
-        }
-      ]
+      "linkId": "birthdate",
+      "text": "Date of birth",
+      "type": "date"
     },
     {
-      "linkId": "a-age-years",
+      "linkId": "age",
       "text": "Age",
-      "type": "quantity",
+      "type": "integer",
       "extension": [
         {
-          "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-unitOption",
-          "valueCoding": {
-            "system": "http://unitsofmeasure.org",
-            "code": "years",
-            "display": "years"
-          }
-        },
-        {
-          "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-unitOption",
-          "valueCoding": {
-            "system": "http://unitsofmeasure.org",
-            "code": "months",
-            "display": "months"
-          }
-        }
-      ],
-      "initial": [
-        {
-          "valueQuantity": {
-            "value": 1,
-            "unit": "months",
-            "system": "http://unitsofmeasure.org",
-            "code": "months"
+          "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-calculatedExpression",
+          "valueExpression": {
+            "language": "text/fhirpath",
+            "expression": "%resource.repeat(item).where(linkId='birthdate' and answer.empty().not()).select(today().toString().substring(0,4).toInteger() - answer.value.toString().substring(0,4).toInteger() + iif(today().toString().substring(5,2) & today().toString().substring(8,2) > answer.value.toString().substring(5,2) & answer.value.toString().substring(8,2), 1, 0) - 1)"
           }
         }
       ]

catalog/src/main/res/values/strings.xml

@@ -58,7 +58,7 @@
     <string name="component_name_initial_value">Initial Value</string>
     <string
         name="behavior_name_calculated_expression_info"
-    >Input age to automatically calculate birthdate until birthdate is updated manually.</string>
+    >Input date of birth to automatically calculate age until age is updated manually.</string>
     <string
         name="behavior_name_calculated_expression"
     >Calculated Expression</string>

docs/contrib/git.md

@@ -4,6 +4,27 @@ This page documents [Git](https://git-scm.com) tips for contributors to this pro
 
 This project generally follows [these guidelines](https://github.com/google/fhir-data-pipes/blob/master/doc/review_process.md) from our `fhir-data-pipes` sister project.
 
+## Overview
+
+We use the following workflow:
+
+1. Contributors can open "draft" PRs for any Work In Progress (WIP) which does not require review yet.
+   It's OK if the checks do not pass yet.
+
+1. When a PR is ready for code review, the contributor marks the PR as "Ready for review". For a smooth review, the PR must pass all the checks.
+   At this point, the PR should only have 1 single commit; please "squash" (or use `--amend`) your "local history",
+   before pushing to a branch to open a PR (or when your WIP Draft PR is ready for review). The commit message
+   of this initial commit should explain what this PR is all about.
+
+1. Maintainers, or other Contributors, will now review the PR. They may add comments requesting changes.
+
+1. When contributors update PRs to make changes requested by reviewers, those should be added as
+   additional new single commits per round of review,
+   typically with a generic message such as _"Incorporated review feedback."_
+   Do NOT squash (or amend) these review updates into the original commit.
+
+1. Maintainers (with write acces) _squash_ all commits of PRs into a single commit when merging.
+
 ## Usage
 
 ### Edit on GitHub Web UI

docs/contrib/index.md

@@ -324,3 +324,18 @@ This section defines the process one goes through when making changes to any of
 * Update your/any dependent PR (PR using the library) with the new _Artifact ID_ and make/trigger the CI
 
 **NB:** For a specific example on working with FHIR SDK's Common Library during development, see [Common Library](#common-library).
+
+# Database migration
+
+If you are making changes to the database schema (in the `engine` or the `knowledge` module), you
+need to consider how applications with Android FHIR SDK dependencies can upgrade to the new schema
+without losing or corrupting existing data already on device. This can be done with [Room database
+migration](https://developer.android.com/training/data-storage/room/migrating-db-versions).
+
+> [!TIP]
+> A new JSON schema file will be generated under the `schemas` folder in the module when you
+update the database version. If you are having trouble with this, make sure you run the gradle
+> command with `--rerun-tasks`: 
+> ```
+> ./gradlew :<module>:build --rerun-tasks
+> ```

engine/build.gradle.kts

@@ -14,6 +14,9 @@ publishArtifact(Releases.Engine)
 
 createJacocoTestReportTask()
 
+// Generate database schema in the schemas folder
+ksp { arg("room.schemaLocation", "$projectDir/schemas") }
+
 val generateSearchParamsTask =
   project.tasks.register("generateSearchParamsTask", GenerateSearchParamsTask::class) {
     srcOutputDir.set(project.layout.buildDirectory.dir("gen/main"))
@@ -39,12 +42,6 @@ android {
     // need to specify this to prevent junit runner from going deep into our dependencies
     testInstrumentationRunnerArguments["package"] = "com.google.android.fhir"
     consumerProguardFile("proguard-rules.pro")
-
-    javaCompileOptions {
-      annotationProcessorOptions {
-        compilerArgumentProviders(RoomSchemaArgProvider(File(projectDir, "schemas")))
-      }
-    }
   }
 
   sourceSets {