Merge branch 'master' into master-release

.github/workflows/build.yml

@@ -34,6 +34,13 @@ env:
   GRADLE_BUILD_ACTION_CACHE_DEBUG_ENABLED: true
   GRADLE_BUILD_ACTION_CACHE_KEY_PREFIX: "fhir" # change this to invalidate cache
 
+concurrency:
+  # github.head_ref uniquely identifies Pull Requests (but is not available when building branches like main or master)
+  # github.ref is the fallback used when building for workflows triggered by push
+  # Note that || are fallback values (not "concatenations")
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
+  cancel-in-progress: true # Use e.g. ${{ github.ref != 'refs/heads/main' }} (or master, until #2180) to only cancel for PRs not on branch
+
   # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   # Build will compile APK, test APK and run tests, lint, etc.
@@ -49,10 +56,6 @@ jobs:
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-      - name: Cancel previous
-        uses: styfle/cancel-workflow-action@0.12.0
-        with:
-          access_token: ${{ github.token }}
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Checkout Repo

.github/workflows/codeql.yaml

@@ -28,6 +28,10 @@ on:
   schedule:
     - cron: '32 13 * * 2'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref || || github.run_id }}
+  cancel-in-progress: true
+
 jobs:
   analyze:
     name: Analyze

.github/workflows/runFlank.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+#
+# Copyright 2022 Google LLC
+#
+# 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
+#
+#       http://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.
+#
+
+# Fail on any error.
+set -e
+
+lib_names=("workflow:benchmark" "engine:benchmark" "datacapture" "engine" "knowledge" "workflow")
+firebase_pids=()
+
+for lib_name in "${lib_names[@]}"; do
+  ./gradlew :$lib_name:runFlank --scan --stacktrace &
+  firebase_pids+=("$!")
+done
+
+for firebase_pid in ${firebase_pids[*]}; do
+    wait $firebase_pid
+done

buildSrc/build.gradle.kts

@@ -11,7 +11,7 @@ repositories {
 dependencies {
   implementation("com.diffplug.spotless:spotless-plugin-gradle:6.22.0")
 
-  implementation("com.android.tools.build:gradle:8.1.2")
+  implementation("com.android.tools.build:gradle:8.1.4")
 
   implementation("app.cash.licensee:licensee-gradle-plugin:1.8.0")
   implementation("com.osacky.flank.gradle:fladle:0.17.4")

engine/src/main/java/com/google/android/fhir/search/MoreSearch.kt

@@ -293,6 +293,7 @@ internal fun Search.getQuery(
     filterArgs.addAll(it.args)
   }
   val whereArgs = mutableListOf<Any>()
+  val nestedArgs = mutableListOf<Any>()
   val query =
     when {
         isCount -> {
@@ -311,11 +312,12 @@ internal fun Search.getQuery(
         nestedContext != null -> {
           whereArgs.add(nestedContext.param.paramName)
           val start = "${nestedContext.parentType.name}/".length + 1
+          nestedArgs.add(nestedContext.parentType.name)
           //  spotless:off
         """
         SELECT resourceUuid
         FROM ResourceEntity a
-        WHERE a.resourceId IN (
+        WHERE a.resourceType = ? AND a.resourceId IN (
         SELECT substr(a.index_value, $start)
         FROM ReferenceIndexEntity a
         $sortJoinStatement
@@ -342,7 +344,7 @@ internal fun Search.getQuery(
       .split("\n")
       .filter { it.isNotBlank() }
       .joinToString("\n") { it.trim() }
-  return SearchQuery(query, sortArgs + type.name + whereArgs + filterArgs + limitArgs)
+  return SearchQuery(query, nestedArgs + sortArgs + type.name + whereArgs + filterArgs + limitArgs)
 }
 
 private val Order?.sqlString: String

engine/src/test/java/com/google/android/fhir/search/SearchTest.kt

@@ -1827,7 +1827,7 @@ class SearchTest {
         AND a.resourceUuid IN (
         SELECT resourceUuid
         FROM ResourceEntity a
-        WHERE a.resourceId IN (
+        WHERE a.resourceType = ? AND a.resourceId IN (
         SELECT substr(a.index_value, 9)
         FROM ReferenceIndexEntity a
         WHERE a.resourceType = ? AND a.index_name = ?
@@ -1844,6 +1844,7 @@ class SearchTest {
     assertThat(query.args)
       .isEqualTo(
         listOf(
+          ResourceType.Patient.name,
           ResourceType.Patient.name,
           ResourceType.Condition.name,
           Condition.SUBJECT.paramName,
@@ -1906,7 +1907,7 @@ class SearchTest {
         AND a.resourceUuid IN (
         SELECT resourceUuid
         FROM ResourceEntity a
-        WHERE a.resourceId IN (
+        WHERE a.resourceType = ? AND a.resourceId IN (
         SELECT substr(a.index_value, 9)
         FROM ReferenceIndexEntity a
         WHERE a.resourceType = ? AND a.index_name = ?
@@ -1931,6 +1932,7 @@ class SearchTest {
           ResourceType.Patient.name,
           Patient.ADDRESS_COUNTRY.paramName,
           "IN",
+          ResourceType.Patient.name,
           ResourceType.Immunization.name,
           Immunization.PATIENT.paramName,
           ResourceType.Immunization.name,
@@ -1974,7 +1976,7 @@ class SearchTest {
         AND a.resourceUuid IN (
         SELECT resourceUuid
         FROM ResourceEntity a
-        WHERE a.resourceId IN (
+        WHERE a.resourceType = ? AND a.resourceId IN (
         SELECT substr(a.index_value, 9)
         FROM ReferenceIndexEntity a
         WHERE a.resourceType = ? AND a.index_name = ?
@@ -1986,7 +1988,7 @@ class SearchTest {
         )  AND a.resourceUuid IN(
         SELECT resourceUuid
         FROM ResourceEntity a
-        WHERE a.resourceId IN (
+        WHERE a.resourceType = ? AND a.resourceId IN (
         SELECT substr(a.index_value, 9)
         FROM ReferenceIndexEntity a
         WHERE a.resourceType = ? AND a.index_name = ?
@@ -2003,13 +2005,15 @@ class SearchTest {
     assertThat(query.args)
       .isEqualTo(
         listOf(
+          ResourceType.Patient.name,
           ResourceType.Patient.name,
           ResourceType.Condition.name,
           Condition.SUBJECT.paramName,
           ResourceType.Condition.name,
           Condition.CODE.paramName,
           "44054006",
           "http://snomed.info/sct",
+          ResourceType.Patient.name,
           ResourceType.Condition.name,
           Condition.SUBJECT.paramName,
           ResourceType.Condition.name,

gradle/libs.versions.toml

@@ -1,7 +1,7 @@
 # see https://docs.gradle.org/current/userguide/platforms.html
 
 [versions]
-glide = "4.14.2"
+glide = "4.16.0"
 
 [libraries]
 glide = { module = "com.github.bumptech.glide:glide", version.ref = "glide" }

kokoro/gcp_ubuntu/kokoro_build.sh

@@ -92,16 +92,7 @@ function build_only() {
 function device_tests() {
   ./gradlew packageDebugAndroidTest --scan --stacktrace
   ./gradlew packageReleaseAndroidTest --scan --stacktrace
-    local lib_names=("workflow:benchmark" "engine:benchmark" "datacapture" "engine" "knowledge" "workflow")
-    firebase_pids=()
-    for lib_name in "${lib_names[@]}"; do
-      ./gradlew :$lib_name:runFlank  --scan --stacktrace &
-      firebase_pids+=("$!")
-    done
-
-    for firebase_pid in ${firebase_pids[*]}; do
-        wait $firebase_pid
-    done
+  .github/workflows/runFlank.sh
 }
 
 # Generates JaCoCo reports and uploads to Codecov: https://about.codecov.io/

settings.gradle.kts

@@ -35,7 +35,7 @@ buildscript {
     classpath("com.fasterxml.jackson.core:jackson-annotations:2.15.3")
     classpath("com.fasterxml.jackson.core:jackson-databind:2.15.3")
     classpath("com.fasterxml.jackson.dataformat:jackson-dataformat-xml:2.15.3")
-    classpath("com.fasterxml.jackson.module:jackson-module-jaxb-annotations:2.15.3")
+    classpath("com.fasterxml.jackson.module:jackson-module-jaxb-annotations:2.16.0")
     classpath("com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.15.3")
     classpath("com.fasterxml.jackson.module:jackson-module-kotlin:2.15.3")
   }