Add global settings to JSON dokka cli input

integration-tests/cli/build.gradle.kts

@@ -12,6 +12,8 @@ evaluationDependsOn(":plugins:base")
 dependencies {
     implementation(kotlin("stdlib"))
     implementation(kotlin("test-junit"))
+    val jackson_version: String by project
+    implementation("com.fasterxml.jackson.module:jackson-module-kotlin:$jackson_version")
 }
 
 /* Create a fat base plugin jar for cli tests */
@@ -23,6 +25,7 @@ val basePluginShadow: Configuration by configurations.creating {
 
 dependencies {
     basePluginShadow(project(":plugins:base"))
+
 }
 val basePluginShadowJar by tasks.register("basePluginShadowJar", ShadowJar::class) {
     configurations = listOf(basePluginShadow)

integration-tests/cli/src/integrationTest/kotlin/org/jetbrains/dokka/it/cli/CliIntegrationTest.kt

@@ -2,6 +2,8 @@ package org.jetbrains.dokka.it.cli
 
 import org.jetbrains.dokka.it.awaitProcessResult
 import java.io.File
+import java.io.PrintWriter
+import java.lang.IllegalStateException
 import kotlin.test.*
 
 class CliIntegrationTest : AbstractCliIntegrationTest() {
@@ -193,7 +195,7 @@ class CliIntegrationTest : AbstractCliIntegrationTest() {
     }
 
     @Test
-    fun `logging level should be respected`(){
+    fun `logging level should be respected`() {
         val dokkaOutputDir = File(projectDir, "output")
         assertTrue(dokkaOutputDir.mkdirs())
         val process = ProcessBuilder(
@@ -259,4 +261,111 @@ class CliIntegrationTest : AbstractCliIntegrationTest() {
             )
         )
     }
+
+
+    @Test
+    fun json() {
+        val dokkaOutputDir = File(projectDir, "output")
+        assertTrue(dokkaOutputDir.mkdirs())
+        val jsonPath = javaClass.getResource("/my-file.json")?.path ?: throw IllegalStateException("No JSON found!")
+        PrintWriter(jsonPath).run {
+            write(jsonBuilder(dokkaOutputDir.path, basePluginJarFile.path, File(projectDir, "src").path, reportUndocumented = true))
+            close()
+        }
+
+        val process = ProcessBuilder(
+            "java", "-jar", cliJarFile.path, jsonPath
+        ).redirectErrorStream(true).start()
+
+        val result = process.awaitProcessResult()
+        assertEquals(0, result.exitCode, "Expected exitCode 0 (Success)")
+
+        val extensionLoadedRegex = Regex("""Extension: org\.jetbrains\.dokka\.base\.DokkaBase""")
+        val amountOfExtensionsLoaded = extensionLoadedRegex.findAll(result.output).count()
+
+        assertTrue(
+            amountOfExtensionsLoaded > 10,
+            "Expected more than 10 extensions being present (found $amountOfExtensionsLoaded)"
+        )
+
+        val undocumentedReportRegex = Regex("""Undocumented:""")
+        val amountOfUndocumentedReports = undocumentedReportRegex.findAll(result.output).count()
+        assertTrue(
+            amountOfUndocumentedReports > 0,
+            "Expected at least one report of undocumented code (found $amountOfUndocumentedReports)"
+        )
+
+        assertTrue(dokkaOutputDir.isDirectory, "Missing dokka output directory")
+    }
+
+    /**
+     * This test disables global `reportUndocumneted` property and set `reportUndocumented` via perPackageOptions to
+     * make sure that global settings apply to dokka context.
+     */
+    @Test
+    fun jsonWithGlobals() {
+        val dokkaOutputDir = File(projectDir, "output")
+        assertTrue(dokkaOutputDir.mkdirs())
+        val jsonPath = javaClass.getResource("/my-file.json")?.path ?: throw IllegalStateException("No JSON found!")
+        PrintWriter(jsonPath).run {
+            write(
+                jsonBuilder(
+                    outputPath = dokkaOutputDir.path,
+                    pluginsClasspath = basePluginJarFile.path,
+                    projectPath = File(projectDir, "src").path,
+                    globalSourceLinks = """
+                        {
+                          "localDirectory": "/home/Vadim.Mishenev/dokka/examples/cli/src/main/kotlin",
+                          "remoteUrl": "https://github.com/Kotlin/dokka/tree/master/examples/gradle/dokka-gradle-example/src/main/kotlin",
+                          "remoteLineSuffix": "#L"
+                        }
+                    """.trimIndent(),
+                    globalExternalDocumentationLinks = """
+                        {
+                          "url": "https://docs.oracle.com/javase/8/docs/api/",
+                          "packageListUrl": "https://docs.oracle.com/javase/8/docs/api/package-list"
+                        },
+                        {
+                          "url": "https://kotlinlang.org/api/latest/jvm/stdlib/",
+                          "packageListUrl": "https://kotlinlang.org/api/latest/jvm/stdlib/package-list"
+                        }
+                        """.trimIndent(),
+                    globalPerPackageOptions = """
+                        {
+                          "matchingRegex": ".*",
+                          "skipDeprecated": "true",
+                          "reportUndocumented": "true", 
+                          "includeNonPublic": "true"
+                        }
+                    """.trimIndent(),
+                    reportUndocumented = false
+                ),
+            )
+            close()
+        }
+
+        val process = ProcessBuilder(
+            "java", "-jar", cliJarFile.path, jsonPath
+        ).redirectErrorStream(true).start()
+
+        val result = process.awaitProcessResult()
+        assertEquals(0, result.exitCode, "Expected exitCode 0 (Success)")
+
+        val extensionLoadedRegex = Regex("""Extension: org\.jetbrains\.dokka\.base\.DokkaBase""")
+        val amountOfExtensionsLoaded = extensionLoadedRegex.findAll(result.output).count()
+
+        assertTrue(
+            amountOfExtensionsLoaded > 10,
+            "Expected more than 10 extensions being present (found $amountOfExtensionsLoaded)"
+        )
+
+        val undocumentedReportRegex = Regex("""Undocumented:""")
+        val amountOfUndocumentedReports = undocumentedReportRegex.findAll(result.output).count()
+        assertTrue(
+            amountOfUndocumentedReports > 0,
+            "Expected at least one report of undocumented code (found $amountOfUndocumentedReports)"
+        )
+
+        assertTrue(dokkaOutputDir.isDirectory, "Missing dokka output directory")
+    }
 }

integration-tests/cli/src/integrationTest/kotlin/org/jetbrains/dokka/it/cli/jsonBuilder.kt

@@ -0,0 +1,52 @@
+package org.jetbrains.dokka.it.cli
+
+fun jsonBuilder(
+    outputPath: String,
+    pluginsClasspath: String,
+    projectPath: String,
+    globalSourceLinks: String = "",
+    globalExternalDocumentationLinks: String = "",
+    globalPerPackageOptions: String = "",
+    reportUndocumented: Boolean = false
+
+): String {
+   return """{
+  "moduleName": "Dokka Example",
+  "moduleVersion": null,
+  "outputDir": "$outputPath",
+  "pluginsClasspath": ["$pluginsClasspath"],
+  "cacheRoot": null,
+  "offlineMode": false,
+  "sourceLinks": [$globalSourceLinks],
+  "externalDocumentationLinks": [$globalExternalDocumentationLinks],
+  "perPackageOptions": [$globalPerPackageOptions],
+  "sourceSets": [
+    {
+      "displayName": "jvm",
+      "sourceSetID": {
+        "scopeId": ":dokkaHtml",
+        "sourceSetName": "main"
+      },
+      "sourceRoots": [
+        "$projectPath"
+      ],
+      "dependentSourceSets": [],
+      "samples": [],
+      "includes": [],
+      "includeNonPublic": false,
+      "reportUndocumented": $reportUndocumented,
+      "skipEmptyPackages": true,
+      "skipDeprecated": false,
+      "jdkVersion": 8,
+      "sourceLinks": [],
+      "perPackageOptions": [],
+      "externalDocumentationLinks": [],
+      "noStdlibLink": false,
+      "noJdkLink": false,
+      "suppressedFiles": [],
+      "analysisPlatform": "jvm"
+    }
+  ]
+}
+"""
+}

plugins/all-modules-page/out/index.md

@@ -0,0 +1,10 @@
+/
+
+# Sample project
+
+Sample documentation with [external link](https://www.google.pl)
+
+## All modules:
+
+| Name |
+|---|

runners/cli/build.gradle.kts

@@ -10,6 +10,10 @@ dependencies {
     implementation("org.jetbrains.kotlinx:kotlinx-cli-jvm:0.3.3")
     implementation(project(":core"))
     implementation(kotlin("stdlib"))
+    val jackson_version: String by project
+    implementation("com.fasterxml.jackson.module:jackson-module-kotlin:$jackson_version")
+
+    testImplementation(kotlin("test-junit"))
 }
 
 tasks {

runners/cli/src/main/kotlin/cli/JsonMapperForCLI.kt

@@ -0,0 +1,48 @@
+package org.jetbrains.dokka
+
+import com.fasterxml.jackson.core.JsonGenerator
+import com.fasterxml.jackson.databind.DeserializationFeature
+import com.fasterxml.jackson.databind.SerializerProvider
+import com.fasterxml.jackson.databind.module.SimpleModule
+import com.fasterxml.jackson.databind.ser.std.StdScalarSerializer
+import com.fasterxml.jackson.module.kotlin.jacksonObjectMapper
+import com.fasterxml.jackson.module.kotlin.jacksonTypeRef
+import java.io.File
+
+// THIS IS COPIED FROM BASE SINCE IT NEEDS TO BE INSTANTIATED ON THE SAME CLASS LOADER AS PLUGINS
+
+private val objectMapper = run {
+    val module = SimpleModule().apply {
+        addSerializer(FileSerializer)
+    }
+    jacksonObjectMapper()
+        .registerModule(module)
+        .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false)
+}
+
+@PublishedApi
+internal class TypeReference<T> private constructor(
+    internal val jackson: com.fasterxml.jackson.core.type.TypeReference<T>
+) {
+    companion object {
+        internal inline operator fun <reified T> invoke(): TypeReference<T> = TypeReference(jacksonTypeRef())
+    }
+}
+
+inline fun <reified T : Any> parseJson(json: String): T = parseJson(json, TypeReference())
+
+@PublishedApi
+internal fun <T : Any> parseJson(json: String, typeReference: TypeReference<T>): T =
+    objectMapper.readValue(json, typeReference.jackson)
+
+private object FileSerializer : StdScalarSerializer<File>(File::class.java) {
+    override fun serialize(value: File, g: JsonGenerator, provider: SerializerProvider) {
+        g.writeString(value.path)
+    }
+}
+
+data class GlobalDokkaConfiguration(
+    val perPackageOptions: List<PackageOptionsImpl>?,
+    val externalDocumentationLinks: List<ExternalDocumentationLinkImpl>?,
+    val sourceLinks: List<SourceLinkDefinitionImpl>?
+)

runners/cli/src/main/kotlin/cli/main.kt

@@ -2,10 +2,7 @@ package org.jetbrains.dokka
 
 import kotlinx.cli.*
 import org.jetbrains.dokka.DokkaConfiguration.ExternalDocumentationLink
-import org.jetbrains.dokka.utilities.DokkaConsoleLogger
-import org.jetbrains.dokka.utilities.DokkaLogger
-import org.jetbrains.dokka.utilities.LoggingLevel
-import org.jetbrains.dokka.utilities.cast
+import org.jetbrains.dokka.utilities.*
 import java.io.*
 import java.net.MalformedURLException
 import java.net.URL
@@ -80,6 +77,7 @@ class GlobalArguments(args: Array<String>) : DokkaConfiguration {
 
     private val _includes by parser.option(
         ArgTypeFile,
+        fullName = "includes",
         description = "Markdown files that would be displayed in multi-module page separated by the semicolon `;`)"
     ).delimiter(";")
 
@@ -406,14 +404,35 @@ fun parseLinks(links: List<String>): List<ExternalDocumentationLink> {
             }
 }
 
+fun initializeConfiguration(globalArguments: GlobalArguments): DokkaConfiguration = if (globalArguments.json != null) {
+        val jsonContent = Paths.get(checkNotNull(globalArguments.json)).toFile().readText()
+        val globals: GlobalDokkaConfiguration = parseJson(jsonContent)
+        val dokkaConfigurationImpl = DokkaConfigurationImpl(jsonContent)
+        dokkaConfigurationImpl.run {
+            sourceSets.forEach {
+                it.perPackageOptions.cast<MutableList<DokkaConfiguration.PackageOptions>>().addAll(globals.perPackageOptions ?: emptyList())
+            }
+
+            sourceSets.forEach {
+                it.externalDocumentationLinks.cast<MutableSet<ExternalDocumentationLink>>().addAll(globals.externalDocumentationLinks ?: emptyList())
+            }
+
+            sourceSets.forEach {
+                it.sourceLinks.cast<MutableSet<SourceLinkDefinitionImpl>>().addAll(globals.sourceLinks ?: emptyList())
+            }
+
+            sourceSets.forEach {
+                it.externalDocumentationLinks.cast<MutableSet<ExternalDocumentationLink>>().addAll(defaultLinks(it))
+            }
+        }
+        dokkaConfigurationImpl
+    } else {
+        globalArguments
+    }
+
 fun main(args: Array<String>) {
     val globalArguments = GlobalArguments(args)
-    val configuration = if (globalArguments.json != null)
-        DokkaConfigurationImpl(
-            Paths.get(checkNotNull(globalArguments.json)).toFile().readText()
-        )
-    else
-        globalArguments
+    val configuration = initializeConfiguration(globalArguments)
     DokkaGenerator(configuration, globalArguments.logger).generate()
 }
 

runners/cli/src/test/kotlin/cli/CliTest.kt

@@ -0,0 +1,29 @@
+package org.jetbrains.dokka
+
+import junit.framework.Assert.assertTrue
+import org.junit.Test
+import java.lang.IllegalStateException
+import kotlin.test.assertEquals
+
+class CliIntegrationTest {
+
+    @Test
+    fun testGlobalArgs() {
+        val jsonPath = javaClass.getResource("/my-file.json")?.path ?: throw IllegalStateException("No JSON found!")
+        val globalArguments = GlobalArguments(arrayOf(jsonPath))
+
+        val configuration = initializeConfiguration(globalArguments)
+
+        configuration.sourceSets.forEach {
+            assertTrue(it.perPackageOptions.isNotEmpty())
+            assertTrue(it.sourceLinks.isNotEmpty())
+            assertTrue(it.externalDocumentationLinks.isNotEmpty())
+
+            assertTrue(it.externalDocumentationLinks.any { it.url.toString() == "https://docs.oracle.com/javase/8/docs/api/" })
+            assertEquals(it.sourceLinks.single().localDirectory, "/home/Vadim.Mishenev/dokka/examples/cli/src/main/kotlin")
+            assertEquals(it.perPackageOptions.single().matchingRegex, "my-custom-regex")
+        }
+
+    }
+
+}