Use sane fallbacks when reading empty files

advisor/src/main/kotlin/Advisor.kt

@@ -66,6 +66,10 @@ class Advisor(
             "Read ORT result from '${ortFile.name}' (${ortFile.formatSizeInMib}) in ${duration.inMilliseconds}ms."
         }
 
+        requireNotNull(ortResult) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
         if (ortResult.analyzer == null) {
             log.warn {
                 "Cannot run the advisor as the provided ORT result file '${ortFile.canonicalPath}' does not contain " +

advisor/src/test/kotlin/advisors/VulnerableCodeTest.kt

@@ -268,7 +268,7 @@ private fun resultFile(): File = File(TEST_FILES_ROOT).resolve(TEST_RESULT_NAME)
  * Return a list with [Package]s from the analyzer result file that serve as input for the [VulnerableCode] advisor.
  */
 private fun inputPackages(): List<Package> =
-    resultFile().readValue<OrtResult>().getPackages(false).map { it.pkg }
+    resultFile().readValue<OrtResult>()?.getPackages(false)?.map { it.pkg }.orEmpty()
 
 /**
  * Generate the JSON body of the request to query information about packages. It mainly consists of an array with the

analyzer/src/main/kotlin/Analyzer.kt

@@ -60,7 +60,7 @@ class Analyzer(private val config: AnalyzerConfiguration) {
         val repositoryConfiguration = if (actualRepositoryConfigurationFile.isFile) {
             log.info { "Using configuration file '${actualRepositoryConfigurationFile.absolutePath}'." }
 
-            actualRepositoryConfigurationFile.readValue()
+            actualRepositoryConfigurationFile.readValue() ?: RepositoryConfiguration()
         } else {
             RepositoryConfiguration()
         }

analyzer/src/main/kotlin/curation/FilePackageCurationProvider.kt

@@ -33,7 +33,7 @@ import org.ossreviewtoolkit.model.readValue
  */
 class FilePackageCurationProvider(curationFile: File) : PackageCurationProvider {
     internal val packageCurations: List<PackageCuration> by lazy {
-        curationFile.readValue<List<PackageCuration>>()
+        curationFile.readValue<List<PackageCuration>>().orEmpty()
     }
 
     override fun getCurationsFor(pkgId: Identifier) = packageCurations.filter { it.isApplicable(pkgId) }

analyzer/src/main/kotlin/managers/Npm.kt

@@ -223,7 +223,7 @@ open class Npm(
 
             log.debug { "Found a 'package.json' file in '$packageDir'." }
 
-            val json = file.readValue<ObjectNode>()
+            val json = file.readValue<ObjectNode>() ?: return@forEach
             val rawName = json["name"].textValue()
             val (namespace, name) = splitNamespaceAndName(rawName)
             val version = json["version"].textValue()

analyzer/src/main/kotlin/managers/utils/NodeSupport.kt

@@ -23,13 +23,12 @@ package org.ossreviewtoolkit.analyzer.managers.utils
 
 import com.fasterxml.jackson.core.JsonProcessingException
 import com.fasterxml.jackson.databind.node.ArrayNode
-import com.fasterxml.jackson.databind.node.ObjectNode
 
 import java.io.File
 import java.nio.file.FileSystems
 import java.nio.file.PathMatcher
 
-import org.ossreviewtoolkit.model.readValue
+import org.ossreviewtoolkit.model.readJsonFile
 import org.ossreviewtoolkit.utils.AuthenticatedProxy
 import org.ossreviewtoolkit.utils.ProtocolProxyMap
 import org.ossreviewtoolkit.utils.collectMessagesAsString
@@ -176,7 +175,7 @@ private fun getPackageJsonInfo(definitionFiles: Set<File>): Collection<PackageJs
 
 private fun isYarnWorkspaceRoot(definitionFile: File) =
     try {
-        definitionFile.readValue<ObjectNode>()["workspaces"] != null
+        readJsonFile(definitionFile).has("workspaces")
     } catch (e: JsonProcessingException) {
         e.showStackTrace()
 
@@ -211,7 +210,7 @@ private fun getYarnWorkspaceSubmodules(definitionFiles: Set<File>): Set<File> {
 
 private fun getWorkspaceMatchers(definitionFile: File): List<PathMatcher> {
     var workspaces = try {
-        definitionFile.readValue<ObjectNode>()["workspaces"]
+        readJsonFile(definitionFile).get("workspaces")
     } catch (e: JsonProcessingException) {
         e.showStackTrace()
 

cli/src/funTest/kotlin/ExamplesFunTest.kt

@@ -93,8 +93,8 @@ class ExamplesFunTest : StringSpec() {
 
         "license-classifications.yml can be deserialized" {
             shouldNotThrow<IOException> {
-                val classifications =
-                    takeExampleFile("license-classifications.yml").readValue<LicenseClassifications>()
+                val classifications = takeExampleFile("license-classifications.yml").readValue()
+                    ?: LicenseClassifications()
 
                 classifications.categories.filter { it.description.isNotEmpty() } shouldNot beEmpty()
                 classifications.categoryNames shouldContain "public-domain"
@@ -130,19 +130,21 @@ class ExamplesFunTest : StringSpec() {
             val resultFile = File("src/funTest/assets/semver4j-analyzer-result.yml")
             val licenseFile = File("../examples/license-classifications.yml")
             val ortResult = resultFile.readValue<OrtResult>()
-            val evaluator = Evaluator(
-                ortResult = ortResult,
-                licenseInfoResolver = ortResult.createLicenseInfoResolver(),
-                licenseClassifications = licenseFile.readValue()
-            )
 
-            val script = takeExampleFile("rules.kts").readText()
+            ortResult shouldNotBeNull {
+                val evaluator = Evaluator(
+                    ortResult = this,
+                    licenseInfoResolver = createLicenseInfoResolver(),
+                    licenseClassifications = licenseFile.readValue() ?: LicenseClassifications()
+                )
 
-            val result = evaluator.run(script)
+                val script = takeExampleFile("rules.kts").readText()
+                val result = evaluator.run(script)
 
-            result.violations shouldHaveSize 2
-            val failedRules = result.violations.map { it.rule }
-            failedRules shouldContainExactlyInAnyOrder listOf("UNHANDLED_LICENSE", "COPYLEFT_LIMITED_IN_SOURCE")
+                result.violations shouldHaveSize 2
+                val failedRules = result.violations.map { it.rule }
+                failedRules shouldContainExactlyInAnyOrder listOf("UNHANDLED_LICENSE", "COPYLEFT_LIMITED_IN_SOURCE")
+            }
         }
 
         "asciidoctor-pdf-theme.yml is a valid asciidoctor-pdf theme" {

cli/src/main/kotlin/commands/DownloaderCommand.kt

@@ -187,6 +187,10 @@ class DownloaderCommand : CliktCommand(name = "download", help = "Fetch source c
                             "${duration.inMilliseconds}ms."
                 }
 
+                requireNotNull(ortResult) {
+                    "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+                }
+
                 val analyzerResult = ortResult.analyzer?.result
 
                 if (analyzerResult == null) {

cli/src/main/kotlin/commands/EvaluatorCommand.kt

@@ -45,9 +45,11 @@ import org.ossreviewtoolkit.GroupTypes.StringType
 import org.ossreviewtoolkit.evaluator.Evaluator
 import org.ossreviewtoolkit.model.FileFormat
 import org.ossreviewtoolkit.model.OrtResult
+import org.ossreviewtoolkit.model.PackageCuration
 import org.ossreviewtoolkit.model.Severity
 import org.ossreviewtoolkit.model.config.CopyrightGarbage
 import org.ossreviewtoolkit.model.config.LicenseFilenamePatterns
+import org.ossreviewtoolkit.model.config.RepositoryConfiguration
 import org.ossreviewtoolkit.model.config.createFileArchiver
 import org.ossreviewtoolkit.model.config.orEmpty
 import org.ossreviewtoolkit.model.licenses.DefaultLicenseInfoProvider
@@ -239,12 +241,12 @@ class EvaluatorCommand : CliktCommand(name = "evaluate", help = "Evaluate ORT re
             }
         }
 
-        repositoryConfigurationFile?.let {
-            ortResultInput = ortResultInput?.replaceConfig(it.readValue())
+        repositoryConfigurationFile?.readValue<RepositoryConfiguration>()?.let {
+            ortResultInput = ortResultInput?.replaceConfig(it)
         }
 
-        packageCurationsFile?.let {
-            ortResultInput = ortResultInput?.replacePackageCurations(it.readValue())
+        packageCurationsFile?.readValue<List<PackageCuration>>()?.let {
+            ortResultInput = ortResultInput?.replacePackageCurations(it)
         }
 
         val finalOrtResult = requireNotNull(ortResultInput) {

cli/src/main/kotlin/commands/ReporterCommand.kt

@@ -45,6 +45,7 @@ import org.ossreviewtoolkit.GlobalOptions
 import org.ossreviewtoolkit.model.OrtResult
 import org.ossreviewtoolkit.model.config.CopyrightGarbage
 import org.ossreviewtoolkit.model.config.LicenseFilenamePatterns
+import org.ossreviewtoolkit.model.config.RepositoryConfiguration
 import org.ossreviewtoolkit.model.config.Resolutions
 import org.ossreviewtoolkit.model.config.createFileArchiver
 import org.ossreviewtoolkit.model.config.orEmpty
@@ -200,14 +201,18 @@ class ReporterCommand : CliktCommand(
     private val globalOptionsForSubcommands by requireObject<GlobalOptions>()
 
     override fun run() {
-        var (ortResult, duration) = measureTimedValue { ortFile.readValue<OrtResult>() }
+        var (originalOrtResult, duration) = measureTimedValue { ortFile.readValue<OrtResult>() }
 
         log.perf {
             "Read ORT result from '${ortFile.name}' (${ortFile.formatSizeInMib}) in ${duration.inMilliseconds}ms."
         }
 
-        repositoryConfigurationFile?.let {
-            ortResult = ortResult.replaceConfig(it.readValue())
+        repositoryConfigurationFile?.readValue<RepositoryConfiguration>()?.let {
+            originalOrtResult = originalOrtResult?.replaceConfig(it)
+        }
+
+        val ortResult = requireNotNull(originalOrtResult) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
         }
 
         val resolutionProvider = DefaultResolutionProvider()

cli/src/main/kotlin/commands/UploadCurationsCommand.kt

@@ -95,7 +95,7 @@ class UploadCurationsCommand : CliktCommand(
         }
 
     override fun run() {
-        val curations = inputFile.readValue<List<PackageCuration>>()
+        val curations = inputFile.readValue<List<PackageCuration>>().orEmpty()
         val curationsToCoordinates = curations.mapNotNull { curation ->
             curation.id.toClearlyDefinedCoordinates()?.let { coordinates ->
                 curation to coordinates

cli/src/main/kotlin/commands/UploadResultToPostgresCommand.kt

@@ -93,6 +93,10 @@ class UploadResultToPostgresCommand : CliktCommand(
             "Read ORT result from '${ortFile.name}' (${ortFile.formatSizeInMib}) in ${duration.inMilliseconds}ms."
         }
 
+        requireNotNull(ortResult) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
         val postgresConfig = globalOptionsForSubcommands.config.scanner.storages?.values
             ?.filterIsInstance<PostgresStorageConfiguration>()?.singleOrNull()
 

cli/src/main/kotlin/commands/UploadResultToSw360Command.kt

@@ -82,6 +82,10 @@ class UploadResultToSw360Command : CliktCommand(
             "Read ORT result from '${ortFile.name}' (${ortFile.formatSizeInMib}) in ${duration.inMilliseconds}ms."
         }
 
+        requireNotNull(ortResult) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
         val sw360Config = globalOptionsForSubcommands.config.scanner.storages?.values
             ?.filterIsInstance<Sw360StorageConfiguration>()?.singleOrNull()
 

helper-cli/src/main/kotlin/commands/ExportLicenseFindingCurationsCommand.kt

@@ -68,18 +68,17 @@ internal class ExportLicenseFindingCurationsCommand : CliktCommand(
     ).flag()
 
     override fun run() {
-        val ortResult = ortFile.readValue<OrtResult>().replaceConfig(repositoryConfigurationFile)
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }.replaceConfig(repositoryConfigurationFile)
 
         val localLicenseFindingCurations = getLicenseFindingCurationsByRepository(
             curations = ortResult.repository.config.curations.licenseFindings,
             nestedRepositories = ortResult.repository.nestedRepositories
         )
 
-        val globalLicenseFindingCurations = if (licenseFindingCurationsFile.isFile) {
-            licenseFindingCurationsFile.readValue<RepositoryLicenseFindingCurations>()
-        } else {
-            mapOf()
-        }
+        val globalLicenseFindingCurations = licenseFindingCurationsFile.takeIf { it.isFile }
+            ?.readValue<RepositoryLicenseFindingCurations>().orEmpty()
 
         globalLicenseFindingCurations
             .mergeLicenseFindingCurations(localLicenseFindingCurations, updateOnlyExisting = updateOnlyExisting)

helper-cli/src/main/kotlin/commands/ExportPathExcludesCommand.kt

@@ -68,16 +68,15 @@ internal class ExportPathExcludesCommand : CliktCommand(
     ).flag()
 
     override fun run() {
-        val localPathExcludes = ortFile
-            .readValue<OrtResult>()
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
+        val localPathExcludes = ortResult
             .replaceConfig(repositoryConfigurationFile)
             .getRepositoryPathExcludes()
 
-        val globalPathExcludes = if (pathExcludesFile.isFile) {
-            pathExcludesFile.readValue<RepositoryPathExcludes>()
-        } else {
-            mapOf()
-        }
+        val globalPathExcludes = pathExcludesFile.takeIf { it.isFile }?.readValue<RepositoryPathExcludes>().orEmpty()
 
         globalPathExcludes
             .mergePathExcludes(localPathExcludes, updateOnlyExisting = updateOnlyExisting)

helper-cli/src/main/kotlin/commands/ExtractRepositoryConfigurationCommand.kt

@@ -50,9 +50,10 @@ class ExtractRepositoryConfigurationCommand : CliktCommand(
         .required()
 
     override fun run() {
-        ortFile
-            .readValue<OrtResult>()
-            .repository
-            .config.write(repositoryConfigurationFile)
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
+        ortResult.repository.config.write(repositoryConfigurationFile)
     }
 }

helper-cli/src/main/kotlin/commands/FormatRepositoryConfigurationCommand.kt

@@ -41,8 +41,10 @@ internal class FormatRepositoryConfigurationCommand : CliktCommand(
         .convert { it.absoluteFile.normalize() }
 
     override fun run() {
-        repositoryConfigurationFile
-            .readValue<RepositoryConfiguration>()
-            .write(repositoryConfigurationFile)
+        val repoConfig = requireNotNull(repositoryConfigurationFile.readValue<RepositoryConfiguration>()) {
+            "The provided ORT result file '${repositoryConfigurationFile.canonicalPath}' has no content."
+        }
+
+        repoConfig.write(repositoryConfigurationFile)
     }
 }

helper-cli/src/main/kotlin/commands/GenerateProjectExcludesCommand.kt

@@ -57,14 +57,12 @@ internal class GenerateProjectExcludesCommand : CliktCommand(
         .required()
 
     override fun run() {
-        val repositoryConfiguration = if (repositoryConfigurationFile.isFile) {
-            repositoryConfigurationFile.readValue()
-        } else {
-            RepositoryConfiguration()
-        }
+        val repositoryConfiguration = repositoryConfigurationFile.takeIf { it.isFile }?.readValue()
+            ?: RepositoryConfiguration()
 
-        val ortResult = ortFile.readValue<OrtResult>()
-            .replaceConfig(repositoryConfiguration)
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }.replaceConfig(repositoryConfiguration)
 
         val generatedPathExcludes = ortResult
             .getProjects()

helper-cli/src/main/kotlin/commands/GenerateRuleViolationResolutionsCommand.kt

@@ -66,8 +66,11 @@ internal class GenerateRuleViolationResolutionsCommand : CliktCommand(
     ).enum<Severity>().split(",").default(enumValues<Severity>().asList())
 
     override fun run() {
-        val repositoryConfiguration = repositoryConfigurationFile.readValue<RepositoryConfiguration>()
-        val ortResult = ortFile.readValue<OrtResult>().replaceConfig(repositoryConfiguration)
+        val repositoryConfiguration = repositoryConfigurationFile.readValue() ?: RepositoryConfiguration()
+
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }.replaceConfig(repositoryConfiguration)
 
         val generatedResolutions = ortResult
             .getUnresolvedRuleViolations()

helper-cli/src/main/kotlin/commands/GenerateScopeExcludesCommand.kt

@@ -57,14 +57,17 @@ internal class GenerateScopeExcludesCommand : CliktCommand(
         .required()
 
     override fun run() {
-        val ortResult = ortFile.readValue<OrtResult>()
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }
+
         val scopeExcludes = ortResult.generateScopeExcludes()
 
-        repositoryConfigurationFile
-            .readValue<RepositoryConfiguration>()
-            .replaceScopeExcludes(scopeExcludes)
-            .sortScopeExcludes()
-            .write(repositoryConfigurationFile)
+        val repoConfig = requireNotNull(repositoryConfigurationFile.readValue<RepositoryConfiguration>()) {
+            "The provided ORT result file '${repositoryConfigurationFile.canonicalPath}' has no content."
+        }
+
+        repoConfig.replaceScopeExcludes(scopeExcludes).sortScopeExcludes().write(repositoryConfigurationFile)
     }
 }
 

helper-cli/src/main/kotlin/commands/GenerateTimeoutErrorResolutionsCommand.kt

@@ -68,13 +68,15 @@ internal class GenerateTimeoutErrorResolutionsCommand : CliktCommand(
     ).flag()
 
     override fun run() {
-        val ortResult = ortFile.readValue<OrtResult>().replaceConfig(repositoryConfigurationFile)
+        val ortResult = requireNotNull(ortFile.readValue<OrtResult>()) {
+            "The provided ORT result file '${ortFile.canonicalPath}' has no content."
+        }.replaceConfig(repositoryConfigurationFile)
 
         val resolutionProvider = DefaultResolutionProvider().apply {
             var resolutions = Resolutions()
 
-            resolutionsFile?.let {
-                resolutions = resolutions.merge(it.readValue())
+            resolutionsFile?.readValue<Resolutions>()?.let {
+                resolutions = resolutions.merge(it)
             }
 
             resolutions = resolutions.merge(ortResult.getResolutions())

helper-cli/src/main/kotlin/commands/ImportCopyrightGarbageCommand.kt

@@ -59,11 +59,8 @@ internal class ImportCopyrightGarbageCommand : CliktCommand(
     override fun run() {
         val entriesToImport = inputCopyrightGarbageFile.readLines().filterNot { it.isBlank() }
 
-        val existingCopyrightGarbage = if (outputCopyrightGarbageFile.isFile) {
-            outputCopyrightGarbageFile.readValue<CopyrightGarbage>().items
-        } else {
-            emptySet<String>()
-        }
+        val existingCopyrightGarbage = outputCopyrightGarbageFile.takeIf { it.isFile }
+                ?.readValue<CopyrightGarbage>()?.items.orEmpty()
 
         val collator = Collator.getInstance(Locale("en", "US.utf-8", "POSIX"))
         CopyrightGarbage((entriesToImport + existingCopyrightGarbage).toSortedSet(collator)).let {