Finalize the utils module refactoring

.gitattributes

@@ -33,7 +33,7 @@ utils/spdx/src/main/resources/licenserefs/*	linguist-detectable=false
 utils/spdx/src/main/resources/licenses/*	linguist-detectable=false
 
 # Use Unix line endings for the expected control file of a Debian package.
-utils/core/src/test/assets/control-expected.txt  text eol=lf
+utils/common/src/test/assets/control-expected.txt  text eol=lf
 
 # Use Unix line endings for *.graphql files. This is mainly done to prevent that tests need to fiddle with
 # different platform-specific line endings.

analyzer/src/main/kotlin/Analyzer.kt

@@ -35,7 +35,7 @@ import org.ossreviewtoolkit.model.Repository
 import org.ossreviewtoolkit.model.config.AnalyzerConfiguration
 import org.ossreviewtoolkit.model.config.RepositoryConfiguration
 import org.ossreviewtoolkit.model.orEmpty
-import org.ossreviewtoolkit.utils.core.CommandLineTool
+import org.ossreviewtoolkit.utils.common.CommandLineTool
 import org.ossreviewtoolkit.utils.core.Environment
 import org.ossreviewtoolkit.utils.core.log
 

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

@@ -44,12 +44,12 @@ import org.ossreviewtoolkit.model.VcsType
 import org.ossreviewtoolkit.model.config.AnalyzerConfiguration
 import org.ossreviewtoolkit.model.config.RepositoryConfiguration
 import org.ossreviewtoolkit.model.jsonMapper
+import org.ossreviewtoolkit.utils.common.CommandLineTool
 import org.ossreviewtoolkit.utils.common.Os
 import org.ossreviewtoolkit.utils.common.fieldNamesOrEmpty
 import org.ossreviewtoolkit.utils.common.fieldsOrEmpty
+import org.ossreviewtoolkit.utils.common.stashDirectories
 import org.ossreviewtoolkit.utils.common.textValueOrEmpty
-import org.ossreviewtoolkit.utils.core.CommandLineTool
-import org.ossreviewtoolkit.utils.core.stashDirectories
 
 /**
  * The [Bower](https://bower.io/) package manager for JavaScript.

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

@@ -47,8 +47,8 @@ import org.ossreviewtoolkit.model.config.AnalyzerConfiguration
 import org.ossreviewtoolkit.model.config.RepositoryConfiguration
 import org.ossreviewtoolkit.model.jsonMapper
 import org.ossreviewtoolkit.model.orEmpty
+import org.ossreviewtoolkit.utils.common.CommandLineTool
 import org.ossreviewtoolkit.utils.common.textValueOrEmpty
-import org.ossreviewtoolkit.utils.core.CommandLineTool
 import org.ossreviewtoolkit.utils.core.DeclaredLicenseProcessor
 import org.ossreviewtoolkit.utils.core.ProcessedDeclaredLicense
 import org.ossreviewtoolkit.utils.core.log

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

@@ -53,10 +53,10 @@ import org.ossreviewtoolkit.model.createAndLogIssue
 import org.ossreviewtoolkit.model.orEmpty
 import org.ossreviewtoolkit.model.readValue
 import org.ossreviewtoolkit.model.yamlMapper
+import org.ossreviewtoolkit.utils.common.CommandLineTool
+import org.ossreviewtoolkit.utils.common.stashDirectories
 import org.ossreviewtoolkit.utils.common.textValueOrEmpty
-import org.ossreviewtoolkit.utils.core.CommandLineTool
 import org.ossreviewtoolkit.utils.core.log
-import org.ossreviewtoolkit.utils.core.stashDirectories
 
 /**
  * The [CocoaPods](https://cocoapods.org/) package manager for Objective-C.

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

@@ -46,15 +46,15 @@ import org.ossreviewtoolkit.model.config.RepositoryConfiguration
 import org.ossreviewtoolkit.model.createAndLogIssue
 import org.ossreviewtoolkit.model.orEmpty
 import org.ossreviewtoolkit.model.readJsonFile
+import org.ossreviewtoolkit.utils.common.CommandLineTool
 import org.ossreviewtoolkit.utils.common.Os
 import org.ossreviewtoolkit.utils.common.ProcessCapture
 import org.ossreviewtoolkit.utils.common.collectMessagesAsString
 import org.ossreviewtoolkit.utils.common.fieldNamesOrEmpty
+import org.ossreviewtoolkit.utils.common.stashDirectories
 import org.ossreviewtoolkit.utils.common.textValueOrEmpty
-import org.ossreviewtoolkit.utils.core.CommandLineTool
 import org.ossreviewtoolkit.utils.core.log
 import org.ossreviewtoolkit.utils.core.showStackTrace
-import org.ossreviewtoolkit.utils.core.stashDirectories
 
 const val COMPOSER_PHAR_BINARY = "composer.phar"
 const val COMPOSER_LOCK_FILE = "composer.lock"

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

@@ -48,15 +48,15 @@ import org.ossreviewtoolkit.model.config.AnalyzerConfiguration
 import org.ossreviewtoolkit.model.config.RepositoryConfiguration
 import org.ossreviewtoolkit.model.jsonMapper
 import org.ossreviewtoolkit.model.yamlMapper
+import org.ossreviewtoolkit.utils.common.CommandLineTool
 import org.ossreviewtoolkit.utils.common.Os
 import org.ossreviewtoolkit.utils.common.ProcessCapture
 import org.ossreviewtoolkit.utils.common.safeDeleteRecursively
+import org.ossreviewtoolkit.utils.common.stashDirectories
 import org.ossreviewtoolkit.utils.common.textValueOrEmpty
 import org.ossreviewtoolkit.utils.common.toUri
-import org.ossreviewtoolkit.utils.core.CommandLineTool
 import org.ossreviewtoolkit.utils.core.createOrtTempFile
 import org.ossreviewtoolkit.utils.core.log
-import org.ossreviewtoolkit.utils.core.stashDirectories
 
 /**
  * The [Conan](https://conan.io/) package manager for C / C++.

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

@@ -44,13 +44,13 @@ import org.ossreviewtoolkit.model.VcsInfo
 import org.ossreviewtoolkit.model.config.AnalyzerConfiguration
 import org.ossreviewtoolkit.model.config.RepositoryConfiguration
 import org.ossreviewtoolkit.model.createAndLogIssue
+import org.ossreviewtoolkit.utils.common.CommandLineTool
 import org.ossreviewtoolkit.utils.common.ProcessCapture
 import org.ossreviewtoolkit.utils.common.collectMessagesAsString
 import org.ossreviewtoolkit.utils.common.realFile
 import org.ossreviewtoolkit.utils.common.safeCopyRecursively
 import org.ossreviewtoolkit.utils.common.safeDeleteRecursively
 import org.ossreviewtoolkit.utils.common.toUri
-import org.ossreviewtoolkit.utils.core.CommandLineTool
 import org.ossreviewtoolkit.utils.core.ORT_NAME
 import org.ossreviewtoolkit.utils.core.log
 import org.ossreviewtoolkit.utils.core.showStackTrace

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

@@ -40,11 +40,11 @@ import org.ossreviewtoolkit.model.VcsType
 import org.ossreviewtoolkit.model.config.AnalyzerConfiguration
 import org.ossreviewtoolkit.model.config.RepositoryConfiguration
 import org.ossreviewtoolkit.model.orEmpty
+import org.ossreviewtoolkit.utils.common.CommandLineTool
 import org.ossreviewtoolkit.utils.common.Os
+import org.ossreviewtoolkit.utils.common.stashDirectories
 import org.ossreviewtoolkit.utils.common.withoutSuffix
-import org.ossreviewtoolkit.utils.core.CommandLineTool
 import org.ossreviewtoolkit.utils.core.log
-import org.ossreviewtoolkit.utils.core.stashDirectories
 
 /**
  * The [Go Modules](https://github.com/golang/go/wiki/Modules) package manager for Go.

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

@@ -60,16 +60,16 @@ import org.ossreviewtoolkit.model.orEmpty
 import org.ossreviewtoolkit.model.readJsonFile
 import org.ossreviewtoolkit.model.readValue
 import org.ossreviewtoolkit.model.utils.DependencyGraphBuilder
+import org.ossreviewtoolkit.utils.common.CommandLineTool
 import org.ossreviewtoolkit.utils.common.Os
 import org.ossreviewtoolkit.utils.common.fieldNamesOrEmpty
 import org.ossreviewtoolkit.utils.common.isSymbolicLink
 import org.ossreviewtoolkit.utils.common.realFile
+import org.ossreviewtoolkit.utils.common.stashDirectories
 import org.ossreviewtoolkit.utils.common.textValueOrEmpty
-import org.ossreviewtoolkit.utils.core.CommandLineTool
 import org.ossreviewtoolkit.utils.core.OkHttpClientHelper
 import org.ossreviewtoolkit.utils.core.installAuthenticatorAndProxySelector
 import org.ossreviewtoolkit.utils.core.log
-import org.ossreviewtoolkit.utils.core.stashDirectories
 import org.ossreviewtoolkit.utils.spdx.SpdxConstants
 
 const val PUBLIC_NPM_REGISTRY = "https://registry.npmjs.org"

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

@@ -46,14 +46,12 @@ import org.ossreviewtoolkit.model.VcsInfo
 import org.ossreviewtoolkit.model.config.AnalyzerConfiguration
 import org.ossreviewtoolkit.model.config.RepositoryConfiguration
 import org.ossreviewtoolkit.model.jsonMapper
+import org.ossreviewtoolkit.utils.common.CommandLineTool
 import org.ossreviewtoolkit.utils.common.Os
 import org.ossreviewtoolkit.utils.common.ProcessCapture
-import org.ossreviewtoolkit.utils.common.getPathFromEnvironment
 import org.ossreviewtoolkit.utils.common.normalizeLineBreaks
-import org.ossreviewtoolkit.utils.common.resolveWindowsExecutable
 import org.ossreviewtoolkit.utils.common.safeDeleteRecursively
 import org.ossreviewtoolkit.utils.common.textValueOrEmpty
-import org.ossreviewtoolkit.utils.core.CommandLineTool
 import org.ossreviewtoolkit.utils.core.ORT_NAME
 import org.ossreviewtoolkit.utils.core.OkHttpClientHelper
 import org.ossreviewtoolkit.utils.core.log
@@ -141,7 +139,7 @@ object PythonVersion : CommandLineTool {
             // Parse a line like " -2.7-32        C:\Python27\python.exe".
             versionAndPath?.split(' ', limit = 3)?.last()?.trimStart()
         } else {
-            getPathFromEnvironment("python$version")?.path
+            Os.getPathFromEnvironment("python$version")?.path
         }
 }
 
@@ -201,7 +199,7 @@ class Pip(
     ): ProcessCapture {
         val binDir = if (Os.isWindows) "Scripts" else "bin"
         val command = virtualEnvDir.resolve(binDir).resolve(commandName)
-        val resolvedCommand = resolveWindowsExecutable(command)?.takeIf { Os.isWindows } ?: command
+        val resolvedCommand = Os.resolveWindowsExecutable(command)?.takeIf { Os.isWindows } ?: command
 
         // TODO: Maybe work around long shebang paths in generated scripts within a virtualenv by calling the Python
         //       executable in the virtualenv directly, see https://github.com/pypa/virtualenv/issues/997.

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

@@ -28,8 +28,8 @@ import org.ossreviewtoolkit.analyzer.PackageManager
 import org.ossreviewtoolkit.model.ProjectAnalyzerResult
 import org.ossreviewtoolkit.model.config.AnalyzerConfiguration
 import org.ossreviewtoolkit.model.config.RepositoryConfiguration
+import org.ossreviewtoolkit.utils.common.CommandLineTool
 import org.ossreviewtoolkit.utils.common.ProcessCapture
-import org.ossreviewtoolkit.utils.core.CommandLineTool
 import org.ossreviewtoolkit.utils.core.log
 
 class Pipenv(

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

@@ -59,19 +59,18 @@ import org.ossreviewtoolkit.model.config.AnalyzerConfiguration
 import org.ossreviewtoolkit.model.config.RepositoryConfiguration
 import org.ossreviewtoolkit.model.createAndLogIssue
 import org.ossreviewtoolkit.model.yamlMapper
+import org.ossreviewtoolkit.utils.common.CommandLineTool
 import org.ossreviewtoolkit.utils.common.Os
 import org.ossreviewtoolkit.utils.common.ProcessCapture
 import org.ossreviewtoolkit.utils.common.collectMessagesAsString
-import org.ossreviewtoolkit.utils.common.getPathFromEnvironment
 import org.ossreviewtoolkit.utils.common.isSymbolicLink
 import org.ossreviewtoolkit.utils.common.textValueOrEmpty
-import org.ossreviewtoolkit.utils.core.CommandLineTool
+import org.ossreviewtoolkit.utils.common.unpack
 import org.ossreviewtoolkit.utils.core.ORT_NAME
 import org.ossreviewtoolkit.utils.core.OkHttpClientHelper
 import org.ossreviewtoolkit.utils.core.log
 import org.ossreviewtoolkit.utils.core.ortToolsDirectory
 import org.ossreviewtoolkit.utils.core.showStackTrace
-import org.ossreviewtoolkit.utils.core.unpack
 
 private const val GRADLE_VERSION = "5.6.4"
 private const val PUBSPEC_YAML = "pubspec.yaml"
@@ -84,7 +83,7 @@ private val flutterVersion = Os.env["FLUTTER_VERSION"] ?: "2.2.3-stable"
 private val flutterInstallDir = "$ortToolsDirectory/flutter-$flutterVersion"
 
 private val flutterHome by lazy {
-    getPathFromEnvironment(flutterCommand)?.parentFile?.parentFile
+    Os.getPathFromEnvironment(flutterCommand)?.parentFile?.parentFile
         ?: File(Os.env["FLUTTER_HOME"] ?: "$flutterInstallDir/flutter")
 }
 

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

@@ -32,14 +32,14 @@ import org.ossreviewtoolkit.analyzer.AbstractPackageManagerFactory
 import org.ossreviewtoolkit.analyzer.PackageManager
 import org.ossreviewtoolkit.model.config.AnalyzerConfiguration
 import org.ossreviewtoolkit.model.config.RepositoryConfiguration
+import org.ossreviewtoolkit.utils.common.CommandLineTool
 import org.ossreviewtoolkit.utils.common.Os
 import org.ossreviewtoolkit.utils.common.getCommonFileParent
 import org.ossreviewtoolkit.utils.common.safeDeleteRecursively
 import org.ossreviewtoolkit.utils.common.searchUpwardsForSubdirectory
-import org.ossreviewtoolkit.utils.core.CommandLineTool
+import org.ossreviewtoolkit.utils.common.suppressInput
 import org.ossreviewtoolkit.utils.core.createOrtTempDir
 import org.ossreviewtoolkit.utils.core.log
-import org.ossreviewtoolkit.utils.core.suppressInput
 
 /**
  * The [SBT](https://www.scala-sbt.org/) package manager for Scala.

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

@@ -43,9 +43,9 @@ import org.ossreviewtoolkit.model.VcsType
 import org.ossreviewtoolkit.model.config.AnalyzerConfiguration
 import org.ossreviewtoolkit.model.config.RepositoryConfiguration
 import org.ossreviewtoolkit.model.utils.toPurl
+import org.ossreviewtoolkit.utils.common.CommandLineTool
 import org.ossreviewtoolkit.utils.common.ProcessCapture
 import org.ossreviewtoolkit.utils.common.safeDeleteRecursively
-import org.ossreviewtoolkit.utils.core.CommandLineTool
 import org.ossreviewtoolkit.utils.core.OkHttpClientHelper
 import org.ossreviewtoolkit.utils.core.log
 

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

@@ -81,15 +81,15 @@ import org.ossreviewtoolkit.model.RemoteArtifact
 import org.ossreviewtoolkit.model.VcsInfo
 import org.ossreviewtoolkit.model.VcsType
 import org.ossreviewtoolkit.model.yamlMapper
+import org.ossreviewtoolkit.utils.common.DiskCache
 import org.ossreviewtoolkit.utils.common.collectMessagesAsString
+import org.ossreviewtoolkit.utils.common.isMavenCentralUrl
 import org.ossreviewtoolkit.utils.common.searchUpwardsForSubdirectory
 import org.ossreviewtoolkit.utils.common.withoutPrefix
 import org.ossreviewtoolkit.utils.core.DeclaredLicenseProcessor
-import org.ossreviewtoolkit.utils.core.DiskCache
 import org.ossreviewtoolkit.utils.core.OkHttpClientHelper
 import org.ossreviewtoolkit.utils.core.ProcessedDeclaredLicense
 import org.ossreviewtoolkit.utils.core.installAuthenticatorAndProxySelector
-import org.ossreviewtoolkit.utils.core.isMavenCentralUrl
 import org.ossreviewtoolkit.utils.core.log
 import org.ossreviewtoolkit.utils.core.logOnce
 import org.ossreviewtoolkit.utils.core.ortDataDirectory

cli/src/funTest/kotlin/OrtMainFunTest.kt

@@ -32,8 +32,8 @@ import java.io.File
 import org.ossreviewtoolkit.downloader.VersionControlSystem
 import org.ossreviewtoolkit.model.OrtResult
 import org.ossreviewtoolkit.model.readValue
+import org.ossreviewtoolkit.utils.common.redirectStdout
 import org.ossreviewtoolkit.utils.core.normalizeVcsUrl
-import org.ossreviewtoolkit.utils.core.redirectStdout
 import org.ossreviewtoolkit.utils.test.createTestTempDir
 import org.ossreviewtoolkit.utils.test.patchActualResult
 import org.ossreviewtoolkit.utils.test.patchExpectedResult

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

@@ -60,14 +60,14 @@ import org.ossreviewtoolkit.model.licenses.LicenseView
 import org.ossreviewtoolkit.model.licenses.ResolvedLicenseInfo
 import org.ossreviewtoolkit.model.readValue
 import org.ossreviewtoolkit.model.utils.createLicenseInfoResolver
+import org.ossreviewtoolkit.utils.common.ArchiveType
+import org.ossreviewtoolkit.utils.common.archive
 import org.ossreviewtoolkit.utils.common.collectMessagesAsString
 import org.ossreviewtoolkit.utils.common.encodeOrUnknown
 import org.ossreviewtoolkit.utils.common.expandTilde
 import org.ossreviewtoolkit.utils.common.safeDeleteRecursively
-import org.ossreviewtoolkit.utils.core.ArchiveType
 import org.ossreviewtoolkit.utils.core.ORT_CONFIG_FILENAME
 import org.ossreviewtoolkit.utils.core.ORT_LICENSE_CLASSIFICATIONS_FILENAME
-import org.ossreviewtoolkit.utils.core.archive
 import org.ossreviewtoolkit.utils.core.log
 import org.ossreviewtoolkit.utils.core.ortConfigDirectory
 import org.ossreviewtoolkit.utils.core.showStackTrace
@@ -248,11 +248,13 @@ class DownloaderCommand : CliktCommand(name = "download", help = "Fetch source c
                             val zipFile = outputDir.resolve("${pkg.id.toPath("-")}.zip")
 
                             log.info { "Archiving directory '$dir' to '$zipFile'." }
-                            val result = archive(
-                                dir,
-                                zipFile,
-                                "${pkg.id.name.encodeOrUnknown()}/${pkg.id.version.encodeOrUnknown()}/"
-                            )
+                            val result = runCatching {
+                                archive(
+                                    dir,
+                                    zipFile,
+                                    "${pkg.id.name.encodeOrUnknown()}/${pkg.id.version.encodeOrUnknown()}/"
+                                )
+                            }
 
                             result.exceptionOrNull()?.let {
                                 log.error { "Could not archive '$dir': ${it.collectMessagesAsString()}" }
@@ -275,7 +277,7 @@ class DownloaderCommand : CliktCommand(name = "download", help = "Fetch source c
                     val zipFile = outputDir.resolve("archive.zip")
 
                     log.info { "Archiving directory '$outputDir' to '$zipFile'." }
-                    val result = archive(outputDir, zipFile)
+                    val result = runCatching { archive(outputDir, zipFile) }
 
                     result.exceptionOrNull()?.let {
                         log.error { "Could not archive '$outputDir': ${it.collectMessagesAsString()}" }

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

@@ -32,7 +32,7 @@ import org.ossreviewtoolkit.model.config.DownloaderConfiguration
 import org.ossreviewtoolkit.model.config.RepositoryConfiguration
 import org.ossreviewtoolkit.model.config.ScannerConfiguration
 import org.ossreviewtoolkit.scanner.Scanner
-import org.ossreviewtoolkit.utils.core.CommandLineTool
+import org.ossreviewtoolkit.utils.common.CommandLineTool
 import org.ossreviewtoolkit.utils.core.log
 
 import org.reflections.Reflections

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

@@ -50,10 +50,10 @@ import org.ossreviewtoolkit.model.config.Sw360StorageConfiguration
 import org.ossreviewtoolkit.model.jsonMapper
 import org.ossreviewtoolkit.model.utils.toPurl
 import org.ossreviewtoolkit.scanner.storages.Sw360Storage
+import org.ossreviewtoolkit.utils.common.archive
 import org.ossreviewtoolkit.utils.common.collectMessagesAsString
 import org.ossreviewtoolkit.utils.common.expandTilde
 import org.ossreviewtoolkit.utils.common.safeDeleteRecursively
-import org.ossreviewtoolkit.utils.core.archive
 import org.ossreviewtoolkit.utils.core.createOrtTempDir
 import org.ossreviewtoolkit.utils.core.log
 
@@ -119,7 +119,7 @@ class UploadResultToSw360Command : CliktCommand(
 
                         val uploadResult = sw360ReleaseClient.uploadAttachments(
                             AttachmentUploadRequest.builder(release)
-                                .addAttachment(archiveResult.getOrThrow().toPath(), SW360AttachmentType.SOURCE)
+                                .addAttachment(archiveResult.toPath(), SW360AttachmentType.SOURCE)
                                 .build()
                         )
 

clients/github-graphql/src/main/kotlin/GitHubService.kt

@@ -33,7 +33,7 @@ import java.net.URI
 
 import kotlin.time.measureTimedValue
 
-import org.apache.logging.log4j.kotlin.cachedLoggerOf
+import org.apache.logging.log4j.kotlin.Logging
 
 import org.ossreviewtoolkit.clients.github.issuesquery.Issue
 import org.ossreviewtoolkit.clients.github.releasesquery.Release
@@ -62,7 +62,7 @@ class QueryException(
 class GitHubService private constructor(
     val client: GraphQLKtorClient
 ) {
-    companion object {
+    companion object : Logging {
         /**
          * The default endpoint URL for accessing the GitHub GraphQL API.
          */
@@ -132,8 +132,7 @@ private suspend fun <T : Any> GraphQLKtorClient.executeAndCheck(
 ): GraphQLClientResponse<T> {
     val (result, duration) = measureTimedValue { execute(request) }
 
-    cachedLoggerOf(GitHubService::class.java)
-        .debug { "Executed query '${request.operationName}' in $duration." }
+    GitHubService.logger.debug { "Executed query '${request.operationName}' in $duration." }
 
     result.errors?.let { errors ->
         throw QueryException("Result of query '${request.operationName}' contains errors.", errors)

downloader/src/funTest/kotlin/vcs/CvsWorkingTreeFunTest.kt

@@ -29,8 +29,8 @@ import java.io.File
 
 import org.ossreviewtoolkit.model.VcsInfo
 import org.ossreviewtoolkit.model.VcsType
+import org.ossreviewtoolkit.utils.common.unpack
 import org.ossreviewtoolkit.utils.core.ortDataDirectory
-import org.ossreviewtoolkit.utils.core.unpack
 import org.ossreviewtoolkit.utils.test.Ci
 import org.ossreviewtoolkit.utils.test.createSpecTempDir