Fixes in Envelope format and data tre

CHANGELOG.md

@@ -11,6 +11,7 @@
 - More fine-grained types in Action builders.
 
 ### Changed
+- `Name::replaceLast` API
 - `PluginFactory` no longer requires plugin class
 - Collection<Named> toMap -> associateByName
 - Simplified `DFTL` envelope format. Closing symbols are unnecessary. Properties are discontinued.
@@ -36,6 +37,8 @@
 ### Removed
 
 ### Fixed
+- `readDataDirectory` does not split names with dots
+- Front matter reader does not crash on non-UTF files
 - Meta file name in readMeta from directory
 - Tagless and FrontMatter envelope partial readers fix.
 

build.gradle.kts

@@ -9,7 +9,7 @@ plugins {
 
 allprojects {
     group = "space.kscience"
-    version = "0.6.1-dev-5"
+    version = "0.6.1-dev-6"
 }
 
 subprojects {

dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/data/DataSet.kt

@@ -107,7 +107,7 @@ public fun <T : Any> DataSet<T>.startAll(coroutineScope: CoroutineScope): Job =
     }.joinAll()
 }
 
-public suspend fun <T : Any> DataSet<T>.join(): Unit = coroutineScope { startAll(this).join() }
+public suspend fun <T : Any> DataSet<T>.computeAndJoinAll(): Unit = coroutineScope { startAll(this).join() }
 
 public fun DataSet<*>.toMeta(): Meta = Meta {
     forEach {

dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/data/DataTree.kt

@@ -1,6 +1,7 @@
 package space.kscience.dataforge.data
 
 import space.kscience.dataforge.meta.Meta
+import space.kscience.dataforge.misc.DFInternal
 import space.kscience.dataforge.misc.Type
 import space.kscience.dataforge.names.*
 import kotlin.collections.component1
@@ -65,11 +66,16 @@ public interface DataTree<out T : Any> : DataSet<T> {
          */
         public val META_ITEM_NAME_TOKEN: NameToken = NameToken("@meta")
 
-        public inline fun <reified T : Any> empty(meta: Meta = Meta.EMPTY): DataTree<T> = object : DataTree<T> {
+        @DFInternal
+        public fun <T : Any> emptyWithType(type: KType, meta: Meta = Meta.EMPTY): DataTree<T> = object : DataTree<T> {
             override val items: Map<NameToken, DataTreeItem<T>> get() = emptyMap()
-            override val dataType: KType get() = typeOf<T>()
+            override val dataType: KType get() = type
             override val meta: Meta get() = meta
         }
+
+        @OptIn(DFInternal::class)
+        public inline fun <reified T : Any> empty(meta: Meta = Meta.EMPTY): DataTree<T> =
+            emptyWithType<T>(typeOf<T>(), meta)
     }
 }
 
@@ -106,12 +112,8 @@ public fun <T : Any> DataTree<T>.traverseItems(): Sequence<Pair<Name, DataTreeIt
  * Get a branch of this [DataTree] with a given [branchName].
  * The difference from similar method for [DataSet] is that internal logic is more simple and the return value is a [DataTree]
  */
-public fun <T : Any> DataTree<T>.branch(branchName: Name): DataTree<T> = object : DataTree<T> {
+@OptIn(DFInternal::class)
-    override val dataType: KType get() = this@branch.dataType
+public fun <T : Any> DataTree<T>.branch(branchName: Name): DataTree<T> =
+    getItem(branchName)?.tree ?: DataTree.emptyWithType(dataType)
 
-    override val meta: Meta
+public fun <T : Any> DataTree<T>.branch(branchName: String): DataTree<T> = branch(branchName.parseAsName())
-        get() = getItem(branchName)?.meta ?: Meta.EMPTY
-
-    override val items: Map<NameToken, DataTreeItem<T>>
-        get() = getItem(branchName).tree?.items ?: emptyMap()
-}

dataforge-io/dataforge-io-yaml/src/commonMain/kotlin/space/kscience/dataforge/io/yaml/FrontMatterEnvelopeFormat.kt

@@ -68,8 +68,9 @@ public class FrontMatterEnvelopeFormat(
         }
 
         override fun peekFormat(io: IOPlugin, binary: Binary): EnvelopeFormat? = binary.read {
-            val line = readSafeUtf8Line()
+            //read raw string to avoid UTF issues
-            return@read if (line.startsWith("---")) {
+            val line = readRawString(3)
+            return@read if (line == "---") {
                 default
             } else {
                 null

dataforge-meta/src/commonMain/kotlin/space/kscience/dataforge/names/Name.kt

@@ -144,6 +144,15 @@ public fun Name.firstOrNull(): NameToken? = tokens.firstOrNull()
  */
 public fun Name.first(): NameToken = tokens.first()
 
+/**
+ * Return a [Name] with its last token replaced via [replacement] rule.
+ * If initial [Name] is empty, return empty name.
+ */
+public fun Name.replaceLast(replacement: (NameToken) -> NameToken): Name {
+    if (isEmpty()) return Name.EMPTY
+    return cutLast() + replacement(lastOrNull()!!)
+}
+
 
 /**
  * Convert the [String] to a [Name] by simply wrapping it in a single name token without parsing.
@@ -227,7 +236,6 @@ public fun Name.removeFirstOrNull(first: Name): Name? = if (startsWith(first)) {
     null
 }
 
-
 @ThreadLocal
 private val nameCache = HashMap<String, Name>()
 

dataforge-workspace/build.gradle.kts

@@ -17,6 +17,7 @@ kscience{
     }
     dependencies(jvmTest){
         implementation(spclibs.logback.classic)
+        implementation(projects.dataforgeIo.dataforgeIoYaml)
     }
 }
 

dataforge-workspace/src/jvmMain/kotlin/space/kscience/dataforge/workspace/fileData.kt

@@ -19,6 +19,7 @@ import space.kscience.dataforge.names.Name
 import space.kscience.dataforge.names.NameToken
 import space.kscience.dataforge.names.asName
 import space.kscience.dataforge.names.plus
+import space.kscience.dataforge.workspace.FileData.Companion.DEFAULT_IGNORE_EXTENSIONS
 import java.nio.file.Files
 import java.nio.file.Path
 import java.nio.file.StandardWatchEventKinds
@@ -27,6 +28,7 @@ import java.nio.file.attribute.BasicFileAttributes
 import java.nio.file.spi.FileSystemProvider
 import java.time.Instant
 import kotlin.io.path.extension
+import kotlin.io.path.name
 import kotlin.io.path.nameWithoutExtension
 import kotlin.io.path.readAttributes
 import kotlin.reflect.KType
@@ -54,6 +56,8 @@ public class FileData<T> internal constructor(private val data: Data<T>, public
         public val FILE_EXTENSION_KEY: Name = FILE_KEY + "extension"
         public val FILE_CREATE_TIME_KEY: Name = FILE_KEY + "created"
         public val FILE_UPDATE_TIME_KEY: Name = FILE_KEY + "updated"
+        public const val DF_FILE_EXTENSION: String = "df"
+        public val DEFAULT_IGNORE_EXTENSIONS: Set<String> = setOf(DF_FILE_EXTENSION)
     }
 }
 
@@ -88,13 +92,17 @@ public fun <T : Any> IOPlugin.readDataFile(
 
 
 context(IOPlugin) @DFExperimental
-private fun <T : Any> DataSetBuilder<T>.directory(path: Path, formatResolver: FileFormatResolver<T>) {
+private fun <T : Any> DataSetBuilder<T>.directory(
+    path: Path,
+    ignoreExtensions: Set<String>,
+    formatResolver: FileFormatResolver<T>,
+) {
     Files.list(path).forEach { childPath ->
         val fileName = childPath.fileName.toString()
         if (fileName.startsWith(IOPlugin.META_FILE_NAME)) {
             meta(readMetaFile(childPath))
         } else if (!fileName.startsWith("@")) {
-            file(childPath, formatResolver)
+            file(childPath, ignoreExtensions, formatResolver)
         }
     }
 }
@@ -107,6 +115,7 @@ private fun <T : Any> DataSetBuilder<T>.directory(path: Path, formatResolver: Fi
 public fun <T : Any> IOPlugin.readDataDirectory(
     type: KType,
     path: Path,
+    ignoreExtensions: Set<String> = DEFAULT_IGNORE_EXTENSIONS,
     formatResolver: FileFormatResolver<T>,
 ): DataTree<T> {
     //read zipped data node
@@ -116,14 +125,14 @@ public fun <T : Any> IOPlugin.readDataDirectory(
             ?: error("Zip file system provider not found")
         val fs = fsProvider.newFileSystem(path, mapOf("create" to "true"))
 
-        return readDataDirectory(type, fs.rootDirectories.first(), formatResolver)
+        return readDataDirectory(type, fs.rootDirectories.first(), ignoreExtensions, formatResolver)
     }
     if (!Files.isDirectory(path)) error("Provided path $path is not a directory")
     return DataTree(type) {
         meta {
-          FileData.FILE_PATH_KEY put path.toString()
+            FileData.FILE_PATH_KEY put path.toString()
         }
-        directory(path, formatResolver)
+        directory(path, ignoreExtensions, formatResolver)
     }
 }
 
@@ -131,8 +140,9 @@ public fun <T : Any> IOPlugin.readDataDirectory(
 @DFExperimental
 public inline fun <reified T : Any> IOPlugin.readDataDirectory(
     path: Path,
+    ignoreExtensions: Set<String> = DEFAULT_IGNORE_EXTENSIONS,
     noinline formatResolver: FileFormatResolver<T>,
-): DataTree<T> = readDataDirectory(typeOf<T>(), path, formatResolver)
+): DataTree<T> = readDataDirectory(typeOf<T>(), path, ignoreExtensions, formatResolver)
 
 /**
  * Read raw binary data tree from the directory. All files are read as-is (save for meta files).
@@ -140,7 +150,8 @@ public inline fun <reified T : Any> IOPlugin.readDataDirectory(
 @DFExperimental
 public fun IOPlugin.readRawDirectory(
     path: Path,
-): DataTree<Binary> = readDataDirectory(path) { _, _ -> IOReader.binary }
+    ignoreExtensions: Set<String> = emptySet(),
+): DataTree<Binary> = readDataDirectory(path, ignoreExtensions) { _, _ -> IOReader.binary }
 
 
 private fun Path.toName() = Name(map { NameToken.parse(it.nameWithoutExtension) })
@@ -150,12 +161,13 @@ private fun Path.toName() = Name(map { NameToken.parse(it.nameWithoutExtension)
 public fun <T : Any> IOPlugin.monitorDataDirectory(
     type: KType,
     path: Path,
+    ignoreExtensions: Set<String> = DEFAULT_IGNORE_EXTENSIONS,
     formatResolver: FileFormatResolver<T>,
 ): DataSource<T> {
     if (path.fileName.toString().endsWith(".zip")) error("Monitoring not supported for ZipFS")
     if (!Files.isDirectory(path)) error("Provided path $path is not a directory")
     return DataSource(type, context) {
-        directory(path, formatResolver)
+        directory(path, ignoreExtensions, formatResolver)
         launch(Dispatchers.IO) {
             val watchService = path.fileSystem.newWatchService()
 
@@ -178,7 +190,7 @@ public fun <T : Any> IOPlugin.monitorDataDirectory(
                             if (fileName.startsWith(IOPlugin.META_FILE_NAME)) {
                                 meta(readMetaFile(eventPath))
                             } else if (!fileName.startsWith("@")) {
-                                file(eventPath, formatResolver)
+                                file(eventPath, ignoreExtensions, formatResolver)
                             }
                         }
                     }
@@ -197,8 +209,9 @@ public fun <T : Any> IOPlugin.monitorDataDirectory(
 @DFExperimental
 public inline fun <reified T : Any> IOPlugin.monitorDataDirectory(
     path: Path,
+    ignoreExtensions: Set<String> = DEFAULT_IGNORE_EXTENSIONS,
     noinline formatResolver: FileFormatResolver<T>,
-): DataSource<T> = monitorDataDirectory(typeOf<T>(), path, formatResolver)
+): DataSource<T> = monitorDataDirectory(typeOf<T>(), path, ignoreExtensions, formatResolver)
 
 /**
  * Read and monitor raw binary data tree from the directory. All files are read as-is (save for meta files).
@@ -206,7 +219,8 @@ public inline fun <reified T : Any> IOPlugin.monitorDataDirectory(
 @DFExperimental
 public fun IOPlugin.monitorRawDirectory(
     path: Path,
-): DataSource<Binary> = monitorDataDirectory(path) { _, _ -> IOReader.binary }
+    ignoreExtensions: Set<String> = DEFAULT_IGNORE_EXTENSIONS,
+): DataSource<Binary> = monitorDataDirectory(path, ignoreExtensions) { _, _ -> IOReader.binary }
 
 /**
  * Write data tree to existing directory or create a new one using default [java.nio.file.FileSystem] provider
@@ -248,14 +262,20 @@ public suspend fun <T : Any> IOPlugin.writeDataDirectory(
 
 /**
  * Add file/directory-based data tree item
+ *
+ * @param ignoreExtensions a list of file extensions for which extension should be cut from the resulting item name
  */
 context(IOPlugin)
 @OptIn(DFInternal::class)
 @DFExperimental
 public fun <T : Any> DataSetBuilder<T>.file(
     path: Path,
+    ignoreExtensions: Set<String> = DEFAULT_IGNORE_EXTENSIONS,
     formatResolver: FileFormatResolver<out T>,
 ) {
+
+    fun defaultPath() = if (path.extension in ignoreExtensions) path.nameWithoutExtension else path.name
+
     try {
         //If path is a single file or a special directory, read it as single datum
         if (!Files.isDirectory(path) || Files.list(path).allMatch { it.fileName.toString().startsWith("@") }) {
@@ -264,13 +284,13 @@ public fun <T : Any> DataSetBuilder<T>.file(
                 logger.warn { "File format is not resolved for $path. Skipping." }
                 return
             }
-            val name = data.meta[Envelope.ENVELOPE_NAME_KEY].string ?: path.nameWithoutExtension
+            val name: String = data.meta[Envelope.ENVELOPE_NAME_KEY].string ?: defaultPath()
-            data(name, data)
+            data(name.asName(), data)
         } else {
             //otherwise, read as directory
-            val data: DataTree<T> = readDataDirectory(dataType, path, formatResolver)
+            val data: DataTree<T> = readDataDirectory(dataType, path, ignoreExtensions, formatResolver)
-            val name = data.meta[Envelope.ENVELOPE_NAME_KEY].string ?: path.nameWithoutExtension
+            val name = data.meta[Envelope.ENVELOPE_NAME_KEY].string ?: defaultPath()
-            node(name, data)
+            node(name.asName(), data)
         }
     } catch (ex: Exception) {
         logger.error { "Failed to read file or directory at $path: ${ex.message}" }

dataforge-workspace/src/jvmTest/kotlin/space/kscience/dataforge/workspace/FileDataTest.kt

@@ -3,15 +3,16 @@ package space.kscience.dataforge.workspace
 import io.ktor.utils.io.core.Input
 import io.ktor.utils.io.core.Output
 import kotlinx.coroutines.runBlocking
+import space.kscience.dataforge.context.Context
 import space.kscience.dataforge.context.Global
 import space.kscience.dataforge.data.*
-import space.kscience.dataforge.io.IOFormat
+import space.kscience.dataforge.io.*
-import space.kscience.dataforge.io.io
+import space.kscience.dataforge.io.yaml.YamlPlugin
-import space.kscience.dataforge.io.readUtf8String
-import space.kscience.dataforge.io.writeUtf8String
 import space.kscience.dataforge.meta.get
 import space.kscience.dataforge.misc.DFExperimental
 import java.nio.file.Files
+import kotlin.io.path.fileSize
+import kotlin.io.path.toPath
 import kotlin.reflect.KType
 import kotlin.reflect.typeOf
 import kotlin.test.Test
@@ -44,32 +45,38 @@ class FileDataTest {
 
     @Test
     @DFExperimental
-    fun testDataWriteRead() {
+    fun testDataWriteRead() = with(Global.io) {
-        Global.io.run {
+        val dir = Files.createTempDirectory("df_data_node")
-            val dir = Files.createTempDirectory("df_data_node")
+        runBlocking {
-            runBlocking {
+            writeDataDirectory(dir, dataNode, StringIOFormat)
-                writeDataDirectory(dir, dataNode, StringIOFormat)
+            println(dir.toUri().toString())
-                println(dir.toUri().toString())
+            val reconstructed = readDataDirectory(dir) { _, _ -> StringIOFormat }
-                val reconstructed = readDataDirectory(dir) { _, _ -> StringIOFormat }
+            assertEquals(dataNode["dir.a"]?.meta?.get("content"), reconstructed["dir.a"]?.meta?.get("content"))
-                assertEquals(dataNode["dir.a"]?.meta?.get("content"), reconstructed["dir.a"]?.meta?.get("content"))
+            assertEquals(dataNode["b"]?.await(), reconstructed["b"]?.await())
-                assertEquals(dataNode["b"]?.await(), reconstructed["b"]?.await())
-            }
         }
     }
 
 
     @Test
     @DFExperimental
-    fun testZipWriteRead() {
+    fun testZipWriteRead() = with(Global.io) {
-        Global.io.run {
+        val zip = Files.createTempFile("df_data_node", ".zip")
-            val zip = Files.createTempFile("df_data_node", ".zip")
+        runBlocking {
-            runBlocking {
+            dataNode.writeZip(zip, StringIOFormat)
-                dataNode.writeZip(zip, StringIOFormat)
+            println(zip.toUri().toString())
-                println(zip.toUri().toString())
+            val reconstructed = readDataDirectory(zip) { _, _ -> StringIOFormat }
-                val reconstructed = readDataDirectory(zip) { _, _ -> StringIOFormat }
+            assertEquals(dataNode["dir.a"]?.meta?.get("content"), reconstructed["dir.a"]?.meta?.get("content"))
-                assertEquals(dataNode["dir.a"]?.meta?.get("content"), reconstructed["dir.a"]?.meta?.get("content"))
+            assertEquals(dataNode["b"]?.await(), reconstructed["b"]?.await())
-                assertEquals(dataNode["b"]?.await(), reconstructed["b"]?.await())
-            }
         }
     }
+
+    @Test
+    fun testNonEnvelope() {
+        val context = Context {
+            plugin(YamlPlugin)
+        }
+        val resource = javaClass.classLoader.getResource("SPC.png")!!
+        val data: Envelope = context.io.readEnvelopeFile(resource.toURI().toPath(), true)
+        assertEquals(resource.toURI().toPath().fileSize(), data.data?.size?.toLong())
+    }
 }