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Implement StructureMap-based extraction (#566)
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datacapture/src/main/assets/packages.fhir.org-hl7.fhir.r4.core-4.0.1.tgz
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datacapture/src/main/java/com/google/android/fhir/datacapture/MoreQuestionnaires.kt
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| /* | ||
| * Copyright 2020 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. | ||
| */ | ||
|
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| package com.google.android.fhir.datacapture | ||
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| import org.hl7.fhir.r4.model.CanonicalType | ||
| import org.hl7.fhir.r4.model.Questionnaire | ||
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| /** | ||
| * The StructureMap url in the | ||
| * [target structure-map extension](http://build.fhir.org/ig/HL7/sdc/StructureDefinition-sdc-questionnaire-targetStructureMap.html) | ||
| * s. | ||
| */ | ||
| val Questionnaire.targetStructureMap: String? | ||
| get() { | ||
| val extensionValue = | ||
| this.extension.singleOrNull { it.url == TARGET_STRUCTURE_MAP }?.value ?: return null | ||
| return if (extensionValue is CanonicalType) extensionValue.valueAsString else null | ||
| } | ||
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| /** | ||
| * See | ||
| * [Extension: target structure map](http://build.fhir.org/ig/HL7/sdc/StructureDefinition-sdc-questionnaire-targetStructureMap.html) | ||
| * . | ||
| */ | ||
| private const val TARGET_STRUCTURE_MAP: String = | ||
| "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-targetStructureMap" |
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...rc/main/java/com/google/android/fhir/datacapture/mapping/NpmPackageInitializationError.kt
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| /* | ||
| * Copyright 2020 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. | ||
| */ | ||
|
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| package com.google.android.fhir.datacapture.mapping | ||
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| /** Thrown to indicate that the FHIR core package could not be initialized successfully */ | ||
| class NpmPackageInitializationError : Exception { | ||
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| constructor(cause: Throwable?) : super(cause) | ||
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| constructor(message: String, cause: Throwable?) : super(message, cause) | ||
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| constructor(message: String) : super(message) | ||
| } |
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...capture/src/main/java/com/google/android/fhir/datacapture/utilities/NpmPackageProvider.kt
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| /* | ||
| * Copyright 2020 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. | ||
| */ | ||
|
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| package com.google.android.fhir.datacapture.utilities | ||
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| import android.content.Context | ||
| import android.os.Environment | ||
| import android.util.Log | ||
| import com.google.android.fhir.datacapture.mapping.NpmPackageInitializationError | ||
| import java.io.File | ||
| import java.io.FileOutputStream | ||
| import java.io.IOException | ||
| import java.io.InputStream | ||
| import org.apache.commons.compress.utils.IOUtils | ||
| import org.hl7.fhir.utilities.npm.NpmPackage | ||
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| /** | ||
| * Manages extracting the fhir core package into app storage and loading it into memory. Extracting | ||
| * the fhir core package should preferably be done after installation since it is a long running | ||
| * operation that takes 1-2 minutes. Loading the package into memory also takes considerable time | ||
| * (20 seconds to 1 minute) and should be preferably done at application start. | ||
| * | ||
| * However, both operations will be done automatically where required during StructureMap-based | ||
| * extraction. | ||
| */ | ||
| object NpmPackageProvider { | ||
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| private const val FHIR_R4_CORE_PACKAGE_FILENAME = "packages.fhir.org-hl7.fhir.r4.core-4.0.1.tgz" | ||
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| /** | ||
| * | ||
| * NpmPackage containing all the [org.hl7.fhir.r4.model.StructureDefinition]s takes around 20 | ||
| * seconds to load. Therefore, reloading for each extraction is not desirable. This should happen | ||
| * once and cache the variable throughout the app's lifecycle. | ||
| * | ||
| * Call [loadNpmPackage] to load it. The method handles skips the operation if it's already | ||
| * loaded. | ||
| */ | ||
| private lateinit var npmPackage: NpmPackage | ||
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| /** | ||
| * Decompresses the hl7.fhir.r4.core archived package into app storage and loads it into memory. | ||
| * It loads the package into [npmPackage]. The method skips any unnecessary operations. This | ||
| * method can be called during initial app installation and run in the background so as to reduce | ||
| * the time it takes for the whole process. | ||
| * | ||
| * The whole process can take 1-2 minutes on a clean installation. | ||
| */ | ||
| fun loadNpmPackage(context: Context): NpmPackage { | ||
| setupNpmPackage(context) | ||
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| if (!this::npmPackage.isInitialized) { | ||
| npmPackage = NpmPackage.fromFolder(getLocalFhirCorePackageDirectory(context)) | ||
| } | ||
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| return npmPackage | ||
| } | ||
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| /** | ||
| * Decompresses the hl7.fhir.r4.core archived package into app storage. | ||
| * | ||
| * The whole process can take 1-2 minutes. | ||
| * | ||
| * @Throws NpmPackageInitializationError | ||
| */ | ||
| private fun setupNpmPackage(context: Context) { | ||
| val outDir = getLocalFhirCorePackageDirectory(context) | ||
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| if (File(outDir + "/package/package.json").exists()) { | ||
| return | ||
| } | ||
| // Create any missing folders | ||
| File(outDir).mkdirs() | ||
|
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| // Copy the tgz package to private app storage | ||
| var inputStream: InputStream? = null | ||
| var outputStream: FileOutputStream? = null | ||
| try { | ||
| inputStream = context.assets.open(FHIR_R4_CORE_PACKAGE_FILENAME) | ||
| outputStream = | ||
| FileOutputStream( | ||
| File(getLocalNpmPackagesDirectory(context) + FHIR_R4_CORE_PACKAGE_FILENAME) | ||
| ) | ||
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| IOUtils.copy(inputStream, outputStream) | ||
| } catch (e: IOException) { | ||
| // Delete the folders | ||
| try { | ||
| val packageDirectory = File(outDir) | ||
| if (packageDirectory.exists()) { | ||
| packageDirectory.delete() | ||
| } | ||
| } catch (securityException: SecurityException) { | ||
| Log.e(NpmPackageProvider.javaClass.name, securityException.stackTraceToString()) | ||
| } | ||
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| throw NpmPackageInitializationError( | ||
| "Could not copy archived package [$FHIR_R4_CORE_PACKAGE_FILENAME] to app private storage", | ||
| e | ||
| ) | ||
| } finally { | ||
| IOUtils.closeQuietly(inputStream) | ||
| IOUtils.closeQuietly(outputStream) | ||
| } | ||
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| // decompress the .tgz package | ||
| TarGzipUtility.decompress( | ||
| getLocalNpmPackagesDirectory(context) + FHIR_R4_CORE_PACKAGE_FILENAME, | ||
| File(outDir) | ||
| ) | ||
| } | ||
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| /** Generates the path to the local npm packages directory. */ | ||
| private fun getLocalNpmPackagesDirectory(context: Context): String = | ||
| Environment.getDataDirectory().getAbsolutePath() + | ||
| "/data/${context.applicationContext.packageName}/npm_packages/" | ||
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| /** Generates the path to the local hl7.fhir.r4.core package. */ | ||
| private fun getLocalFhirCorePackageDirectory(context: Context): String { | ||
| return getLocalNpmPackagesDirectory(context) + "hl7.fhir.r4.core#4.0.1" | ||
| } | ||
| } |
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