Merge branch 'master' into fix-sync-state-excepiton

benchmark/build.gradle.kts

@@ -1,3 +1,6 @@
+import Dependencies.forceHapiVersion
+import Dependencies.removeIncompatibleDependencies
+
 plugins {
   id(Plugins.BuildPlugins.androidLib)
   id(Plugins.BuildPlugins.kotlinAndroid)
@@ -67,15 +70,8 @@ android {
 
 configurations {
   all {
-    exclude(module = "xpp3")
-    exclude(module = "xpp3_min")
-    exclude(module = "xmlpull")
-    exclude(module = "javax.json")
-    exclude(module = "jcl-over-slf4j")
-    exclude(group = "org.apache.httpcomponents")
-    // Remove this after this issue has been fixed:
-    // https://github.com/cqframework/clinical_quality_language/issues/799
-    exclude(module = "antlr4")
+    removeIncompatibleDependencies()
+    forceHapiVersion()
   }
 }
 

buildSrc/build.gradle.kts

@@ -20,5 +20,4 @@ dependencies {
   implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:6.0.1")
   implementation("com.squareup:kotlinpoet:1.9.0")
   implementation("org.jetbrains.kotlin:kotlin-stdlib-jdk7:1.6.21")
-  implementation("org.jetbrains.dokka:dokka-gradle-plugin:1.6.10")
 }

buildSrc/src/main/kotlin/Dependencies.kt

@@ -1,3 +1,22 @@
+/*
+ * 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.
+ */
+
+import org.gradle.api.artifacts.Configuration
+import org.gradle.kotlin.dsl.exclude
+
 /*
  * Copyright 2022 Google LLC
  *
@@ -34,10 +53,6 @@ object Dependencies {
     const val openCdsGroup = "org.opencds.cqf.cql"
     const val translatorGroup = "info.cqframework"
 
-    // Remove this after this issue has been fixed:
-    // https://github.com/cqframework/clinical_quality_language/issues/799
-    const val antlr4Runtime = "org.antlr:antlr4-runtime:${Versions.Cql.antlr}"
-
     const val engine = "$openCdsGroup:engine:${Versions.Cql.engine}"
     const val engineJackson = "$openCdsGroup:engine.jackson:${Versions.Cql.engine}"
 
@@ -53,9 +68,37 @@ object Dependencies {
     const val translatorModelJackson = "$translatorGroup:model-jackson:${Versions.Cql.translator}"
   }
 
+  object Glide {
+    const val glide = "com.github.bumptech.glide:glide:${Versions.Glide.glide}"
+  }
+
   object HapiFhir {
+    const val fhirBase = "ca.uhn.hapi.fhir:hapi-fhir-base:${Versions.hapiFhir}"
+    const val fhirClient = "ca.uhn.hapi.fhir:hapi-fhir-client:${Versions.hapiFhir}"
+    const val structuresDstu2 = "ca.uhn.hapi.fhir:hapi-fhir-structures-dstu2:${Versions.hapiFhir}"
+    const val structuresDstu3 = "ca.uhn.hapi.fhir:hapi-fhir-structures-dstu3:${Versions.hapiFhir}"
     const val structuresR4 = "ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${Versions.hapiFhir}"
+    const val structuresR4b = "ca.uhn.hapi.fhir:hapi-fhir-structures-r4b:${Versions.hapiFhir}"
+    const val structuresR5 = "ca.uhn.hapi.fhir:hapi-fhir-structures-r5:${Versions.hapiFhir}"
+
     const val validation = "ca.uhn.hapi.fhir:hapi-fhir-validation:${Versions.hapiFhir}"
+    const val validationDstu3 =
+      "ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu3:${Versions.hapiFhir}"
+    const val validationR4 =
+      "ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r4:${Versions.hapiFhir}"
+    const val validationR5 =
+      "ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r5:${Versions.hapiFhir}"
+
+    const val fhirCoreDstu2 = "ca.uhn.hapi.fhir:org.hl7.fhir.dstu2:${Versions.hapiFhirCore}"
+    const val fhirCoreDstu2016 =
+      "ca.uhn.hapi.fhir:org.hl7.fhir.dstu2016may:${Versions.hapiFhirCore}"
+    const val fhirCoreDstu3 = "ca.uhn.hapi.fhir:org.hl7.fhir.dstu3:${Versions.hapiFhirCore}"
+    const val fhirCoreR4 = "ca.uhn.hapi.fhir:org.hl7.fhir.r4:${Versions.hapiFhirCore}"
+    const val fhirCoreR4b = "ca.uhn.hapi.fhir:org.hl7.fhir.r4b:${Versions.hapiFhirCore}"
+    const val fhirCoreR5 = "ca.uhn.hapi.fhir:org.hl7.fhir.r5:${Versions.hapiFhirCore}"
+    const val fhirCoreUtils = "ca.uhn.hapi.fhir:org.hl7.fhir.utilities:${Versions.hapiFhirCore}"
+    const val fhirCoreConvertors =
+      "ca.uhn.hapi.fhir:org.hl7.fhir.convertors:${Versions.hapiFhirCore}"
 
     // Runtime dependency that is required to run FhirPath (also requires minSDK of 26).
     // Version 3.0 uses java.lang.System.Logger, which is not available on Android
@@ -64,9 +107,19 @@ object Dependencies {
   }
 
   object Jackson {
-    const val annotations = "com.fasterxml.jackson.core:jackson-annotations:${Versions.jackson}"
-    const val core = "com.fasterxml.jackson.core:jackson-core:${Versions.jackson}"
-    const val databind = "com.fasterxml.jackson.core:jackson-databind:${Versions.jackson}"
+    const val mainGroup = "com.fasterxml.jackson"
+    const val coreGroup = "$mainGroup.core"
+    const val dataformatGroup = "$mainGroup.dataformat"
+    const val datatypeGroup = "$mainGroup.datatype"
+    const val moduleGroup = "$mainGroup.module"
+
+    const val annotations = "$coreGroup:jackson-annotations:${Versions.jackson}"
+    const val bom = "$mainGroup:jackson-bom:${Versions.jackson}"
+    const val core = "$coreGroup:jackson-core:${Versions.jackson}"
+    const val databind = "$coreGroup:jackson-databind:${Versions.jackson}"
+    const val dataformatXml = "$dataformatGroup:jackson-dataformat-xml:${Versions.jackson}"
+    const val jaxbAnnotations = "$moduleGroup:jackson-module-jaxb-annotations:${Versions.jackson}"
+    const val jsr310 = "$datatypeGroup:jackson-datatype-jsr310:${Versions.jackson}"
   }
 
   object Kotlin {
@@ -188,9 +241,13 @@ object Dependencies {
 
     object Cql {
       const val antlr = "4.10.1"
-      const val engine = "2.1.0"
-      const val evaluator = "2.1.0"
-      const val translator = "2.2.0"
+      const val engine = "2.4.0"
+      const val evaluator = "2.4.0"
+      const val translator = "2.4.0"
+    }
+
+    object Glide {
+      const val glide = "4.14.2"
     }
 
     object Kotlin {
@@ -204,9 +261,17 @@ object Dependencies {
     const val caffeine = "2.9.1"
     const val fhirUcum = "1.0.3"
     const val guava = "28.2-android"
+
+    // Hapi FHIR and HL7 Core Components are interlinked.
+    // Newer versions of HapiFhir don't work on Android due to the use of Caffeine 3+
+    // Wait for this to release (6.3): https://github.com/hapifhir/hapi-fhir/pull/4196
     const val hapiFhir = "6.0.1"
+    // Newer versions don't work on Android due to Apache Commons Codec:
+    // Wait for this fix: https://github.com/hapifhir/org.hl7.fhir.core/issues/1046
+    const val hapiFhirCore = "5.6.36"
+
     const val http = "4.9.1"
-    const val jackson = "2.12.2"
+    const val jackson = "2.14.1"
     const val jsonToolsPatch = "1.13"
     const val jsonAssert = "1.5.1"
     const val kotlinPoet = "1.9.0"
@@ -245,4 +310,45 @@ object Dependencies {
       const val objectDetectionCustom = "16.3.1"
     }
   }
+
+  fun Configuration.removeIncompatibleDependencies() {
+    exclude(module = "xpp3")
+    exclude(module = "xpp3_min")
+    exclude(module = "xmlpull")
+    exclude(module = "javax.json")
+    exclude(module = "jcl-over-slf4j")
+    exclude(group = "org.apache.httpcomponents")
+  }
+
+  fun Configuration.forceHapiVersion() {
+    // Removes newer versions of caffeine and manually imports 2.9
+    // Removes newer versions of hapi and keeps on 6.0.1
+    // Removes newer versions of HL7 core and keeps it on 5.6.36
+    // (newer versions don't work on Android)
+    resolutionStrategy {
+      force(HapiFhir.caffeine)
+
+      force(HapiFhir.fhirBase)
+      force(HapiFhir.fhirClient)
+      force(HapiFhir.fhirCoreConvertors)
+
+      force(HapiFhir.fhirCoreDstu2)
+      force(HapiFhir.fhirCoreDstu2016)
+      force(HapiFhir.fhirCoreDstu3)
+      force(HapiFhir.fhirCoreR4)
+      force(HapiFhir.fhirCoreR4b)
+      force(HapiFhir.fhirCoreR5)
+      force(HapiFhir.fhirCoreUtils)
+
+      force(HapiFhir.structuresDstu2)
+      force(HapiFhir.structuresDstu3)
+      force(HapiFhir.structuresR4)
+      force(HapiFhir.structuresR5)
+
+      force(HapiFhir.validation)
+      force(HapiFhir.validationDstu3)
+      force(HapiFhir.validationR4)
+      force(HapiFhir.validationR5)
+    }
+  }
 }

buildSrc/src/main/kotlin/LicenseeConfig.kt

@@ -100,10 +100,6 @@ fun Project.configureLicensee() {
     allowDependency("org.antlr", "antlr4-runtime", "4.10.1") {
       because("BSD 3-clause. http://www.antlr.org/license.html")
     }
-    // ANTLR 4
-    allowDependency("org.antlr", "antlr4", "4.10.1") {
-      because("BSD 3-clause. http://www.antlr.org/license.html")
-    }
 
     // Utilities
     // https://developers.google.com/android/reference/com/google/android/gms/common/package-summary
@@ -149,6 +145,26 @@ fun Project.configureLicensee() {
     // Vision Common
     // https://developers.google.com/android/reference/com/google/mlkit/vision/common/package-summary
     allowDependency("com.google.mlkit", "vision-internal-vkp", "18.0.0") { because("") }
+
+    // Glide
+    allowDependency("com.github.bumptech.glide", "glide", "4.14.2") {
+      because("BSD, part MIT and Apache 2.0. https://github.com/bumptech/glide#license")
+    }
+
+    // Glide Annotations
+    allowDependency("com.github.bumptech.glide", "annotations", "4.14.2") {
+      because("BSD, part MIT and Apache 2.0. https://github.com/bumptech/glide#license")
+    }
+
+    // Glide Disk LRU Cache
+    allowDependency("com.github.bumptech.glide", "disklrucache", "4.14.2") {
+      because("BSD, part MIT and Apache 2.0. https://github.com/bumptech/glide#license")
+    }
+
+    // Glide GIF Decoder
+    allowDependency("com.github.bumptech.glide", "gifdecoder", "4.14.2") {
+      because("BSD, part MIT and Apache 2.0. https://github.com/bumptech/glide#license")
+    }
   }
 }
 

buildSrc/src/main/kotlin/Plugins.kt

@@ -21,7 +21,6 @@ object Plugins {
     const val application = "com.android.application"
     const val benchmark = "androidx.benchmark"
     const val jetbrainsKotlinAndroid = "org.jetbrains.kotlin.android"
-    // Use Dokka 1.6.10 until https://github.com/Kotlin/dokka/issues/2452 is resolved.
     const val dokka = "org.jetbrains.dokka"
     const val kotlin = "kotlin"
     const val kotlinAndroid = "kotlin-android"
@@ -45,7 +44,7 @@ object Plugins {
   object Versions {
     const val androidGradlePlugin = "7.2.1"
     const val benchmarkPlugin = "1.1.0"
-    // Use Dokka 1.6.10 until https://github.com/Kotlin/dokka/issues/2472 is resolved.
+    // Change dokka to 1.7.20 once androidGradlePlugin upgrades to 7.3+
     const val dokka = "1.6.10"
   }
 }

catalog/src/main/AndroidManifest.xml

@@ -16,12 +16,16 @@
 -->
 <manifest
     xmlns:android="http://schemas.android.com/apk/res/android"
+    xmlns:tools="http://schemas.android.com/tools"
     package="com.google.android.fhir.catalog"
 >
 
     <uses-feature android:name="android.hardware.camera" />
 
-    <uses-permission android:name="android.permission.CAMERA" />
+    <uses-permission
+        android:name="android.permission.CAMERA"
+        android:required="false"
+    />
 
     <application
         android:allowBackup="true"
@@ -40,6 +44,19 @@
                 <category android:name="android.intent.category.LAUNCHER" />
             </intent-filter>
         </activity>
+
+        <provider
+            android:name="androidx.core.content.FileProvider"
+            android:authorities="com.google.android.fhir.catalog.fileprovider"
+            android:exported="false"
+            android:grantUriPermissions="true"
+        >
+            <meta-data
+                android:name="android.support.FILE_PROVIDER_PATHS"
+                android:resource="@xml/file_paths"
+            >
+            </meta-data>
+        </provider>
     </application>
 
 </manifest>

catalog/src/main/assets/component_attachment.json

@@ -0,0 +1,52 @@
+{
+  "resourceType": "Questionnaire",
+  "item": [
+    {
+      "extension": [
+        {
+          "url": "http://hl7.org/fhir/StructureDefinition/mimeType",
+          "valueCode": "image/*"
+        },
+        {
+          "url": "http://hl7.org/fhir/StructureDefinition/mimeType",
+          "valueCode": "audio/*"
+        },
+        {
+          "url": "http://hl7.org/fhir/StructureDefinition/mimeType",
+          "valueCode": "video/*"
+        },
+        {
+          "url": "http://hl7.org/fhir/StructureDefinition/mimeType",
+          "valueCode": "application/pdf"
+        },
+        {
+          "url": "http://hl7.org/fhir/StructureDefinition/maxSize",
+          "valueDecimal": 5242880
+        }
+      ],
+      "linkId": "1",
+      "text": "Select an image or file to upload",
+      "type": "attachment",
+      "item": [
+        {
+          "extension": [
+            {
+              "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-displayCategory",
+              "valueCodeableConcept": {
+                "coding": [
+                  {
+                    "system": "http://hl7.org/fhir/questionnaire-display-category",
+                    "code": "instructions"
+                  }
+                ]
+              }
+            }
+          ],
+          "linkId": "1-media-types-supported",
+          "text": "Media types supported: .jpg, .png, .mp3, .mp4, .pdf",
+          "type": "display"
+        }
+      ]
+    }
+  ]
+}