kscience/dataforge-core
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Merge branch 'kotlinx-io' into dev

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# Conflicts:
#	dataforge-io/build.gradle.kts
#	dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/JsonMetaFormat.kt
#	gradle.properties
This commit is contained in:
Alexander Nozik 2023-10-08 16:55:47 +03:00
commit dc2bf5da83
29 changed files with 405 additions and 305 deletions
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1
CHANGELOG.md
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@ -5,6 +5,7 @@
### Added
### Changed
- Kotlin 1.9
### Deprecated

14
dataforge-io/build.gradle.kts
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@ -1,11 +1,11 @@
import space.kscience.gradle.KScienceVersions
plugins {
id("space.kscience.gradle.mpp")
}
description = "IO module"
val ioVersion = "0.2.0"
kscience {
jvm()
js()
@ -15,11 +15,13 @@ kscience {
cbor()
}
dependencies {
api(project(":dataforge-context"))
api("io.ktor:ktor-io:${KScienceVersions.ktorVersion}")
api(projects.dataforgeContext)
api("org.jetbrains.kotlinx:kotlinx-io-core:$ioVersion")
api("org.jetbrains.kotlinx:kotlinx-io-bytestring:$ioVersion")
//api("io.ktor:ktor-io:${KScienceVersions.ktorVersion}")
}
}
readme {
maturity = space.kscience.gradle.Maturity.PROTOTYPE
readme{
maturity = space.kscience.gradle.Maturity.EXPERIMENTAL
}

38
dataforge-io/dataforge-io-yaml/src/commonMain/kotlin/space/kscience/dataforge/io/yaml/FrontMatterEnvelopeFormat.kt
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@ -1,7 +1,11 @@
package space.kscience.dataforge.io.yaml
import io.ktor.utils.io.core.Input
import io.ktor.utils.io.core.Output
import kotlinx.io.Sink
import kotlinx.io.Source
import kotlinx.io.bytestring.ByteString
import kotlinx.io.bytestring.encodeToByteString
import kotlinx.io.readByteString
import kotlinx.io.writeString
import space.kscience.dataforge.context.Context
import space.kscience.dataforge.context.Global
import space.kscience.dataforge.io.*
@ -19,18 +23,18 @@ public class FrontMatterEnvelopeFormat(
var offset = 0
offset += discardWithSeparator(
SEPARATOR.encodeToByteArray(),
SEPARATOR,
atMost = 1024,
)
val line = ByteArray {
offset += readWithSeparatorTo(this, "\n".encodeToByteArray())
offset += readWithSeparatorTo(this, "\n".encodeToByteString())
}.decodeToString()
val readMetaFormat = line.trim().takeIf { it.isNotBlank() }?.let { io.resolveMetaFormat(it) } ?: YamlMetaFormat
val packet = ByteArray {
offset += readWithSeparatorTo(this, SEPARATOR.encodeToByteArray())
offset += readWithSeparatorTo(this, SEPARATOR)
}
offset += discardLine()
@ -39,25 +43,25 @@ public class FrontMatterEnvelopeFormat(
Envelope(meta, binary.view(offset))
}
override fun readObject(input: Input): Envelope = readObject(input.readBinary())
override fun readObject(source: Source): Envelope = readObject(source.readBinary())
override fun writeObject(
output: Output,
sink: Sink,
obj: Envelope,
) {
val metaFormat = metaFormatFactory.build(io.context, meta)
val formatSuffix = if (metaFormat is YamlMetaFormat) "" else metaFormatFactory.shortName
output.writeRawString("$SEPARATOR${formatSuffix}\r\n")
metaFormat.run { metaFormat.writeObject(output, obj.meta) }
output.writeRawString("$SEPARATOR\r\n")
sink.writeString("$SEPARATOR${formatSuffix}\r\n")
metaFormat.run { metaFormat.writeObject(sink, obj.meta) }
sink.writeString("$SEPARATOR\r\n")
//Printing data
obj.data?.let { data ->
output.writeBinary(data)
sink.writeBinary(data)
}
}
public companion object : EnvelopeFormatFactory {
public const val SEPARATOR: String = "---"
public val SEPARATOR: ByteString = "---".encodeToByteString()
private val metaTypeRegex = "---(\\w*)\\s*".toRegex()
@ -69,8 +73,8 @@ public class FrontMatterEnvelopeFormat(
override fun peekFormat(io: IOPlugin, binary: Binary): EnvelopeFormat? = binary.read {
//read raw string to avoid UTF issues
val line = readRawString(3)
return@read if (line == "---") {
val line = readByteString(3)
return@read if (line == "---".encodeToByteString()) {
default
} else {
null
@ -82,12 +86,12 @@ public class FrontMatterEnvelopeFormat(
override fun readObject(binary: Binary): Envelope = default.readObject(binary)
override fun writeObject(
output: Output,
sink: Sink,
obj: Envelope,
): Unit = default.writeObject(output, obj)
): Unit = default.writeObject(sink, obj)
override fun readObject(input: Input): Envelope = default.readObject(input)
override fun readObject(source: Source): Envelope = default.readObject(source)
}
}

24
dataforge-io/dataforge-io-yaml/src/commonMain/kotlin/space/kscience/dataforge/io/yaml/YamlMetaFormat.kt
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@ -1,13 +1,13 @@
package space.kscience.dataforge.io.yaml
import io.ktor.utils.io.core.Input
import io.ktor.utils.io.core.Output
import kotlinx.io.Sink
import kotlinx.io.Source
import kotlinx.io.readString
import kotlinx.io.writeString
import net.mamoe.yamlkt.*
import space.kscience.dataforge.context.Context
import space.kscience.dataforge.io.MetaFormat
import space.kscience.dataforge.io.MetaFormatFactory
import space.kscience.dataforge.io.readUtf8String
import space.kscience.dataforge.io.writeUtf8String
import space.kscience.dataforge.meta.*
import space.kscience.dataforge.meta.descriptors.MetaDescriptor
import space.kscience.dataforge.meta.descriptors.get
@ -89,14 +89,14 @@ public fun YamlMap.toMeta(): Meta = YamlMeta(this)
*/
public class YamlMetaFormat(private val meta: Meta) : MetaFormat {
override fun writeMeta(output: Output, meta: Meta, descriptor: MetaDescriptor?) {
override fun writeMeta(sink: Sink, meta: Meta, descriptor: MetaDescriptor?) {
val yaml: YamlMap = meta.toYaml()
val string = Yaml.encodeToString(YamlMap.serializer(), yaml)
output.writeUtf8String(string)
sink.writeString(string)
}
override fun readMeta(input: Input, descriptor: MetaDescriptor?): Meta {
val yaml = Yaml.decodeYamlMapFromString(input.readUtf8String())
override fun readMeta(source: Source, descriptor: MetaDescriptor?): Meta {
val yaml = Yaml.decodeYamlMapFromString(source.readString())
return yaml.toMeta()
}
@ -109,10 +109,10 @@ public class YamlMetaFormat(private val meta: Meta) : MetaFormat {
private val default = YamlMetaFormat(Meta.EMPTY)
override fun writeMeta(output: Output, meta: Meta, descriptor: MetaDescriptor?): Unit =
default.writeMeta(output, meta, descriptor)
override fun writeMeta(sink: Sink, meta: Meta, descriptor: MetaDescriptor?): Unit =
default.writeMeta(sink, meta, descriptor)
override fun readMeta(input: Input, descriptor: MetaDescriptor?): Meta =
default.readMeta(input, descriptor)
override fun readMeta(source: Source, descriptor: MetaDescriptor?): Meta =
default.readMeta(source, descriptor)
}
}

39
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/Binary.kt
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@ -1,6 +1,9 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.*
import kotlinx.io.Sink
import kotlinx.io.Source
import kotlinx.io.buffered
import kotlinx.io.readByteArray
import kotlin.math.min
/**
@ -17,13 +20,13 @@ public interface Binary {
* Read maximum of [atMost] bytes as input from the binary, starting at [offset]. The generated input is always closed
* when leaving scope, so it could not be leaked outside of scope of [block].
*/
public fun <R> read(offset: Int = 0, atMost: Int = size - offset, block: Input.() -> R): R
public fun <R> read(offset: Int = 0, atMost: Int = size - offset, block: Source.() -> R): R
public suspend fun <R> readSuspend(offset: Int = 0, atMost: Int = size - offset, block: suspend Input.() -> R): R
public suspend fun <R> readSuspend(offset: Int = 0, atMost: Int = size - offset, block: suspend Source.() -> R): R
/**
* Read a binary with given [offset] relative to this binary and given [binarySize].
* In general, resulting binary is of the same type as this one, but it is not guaranteed.
* In general, the resulting binary is of the same type as this one, but it is not guaranteed.
*/
public fun view(offset: Int, binarySize: Int = size - offset): Binary
@ -38,25 +41,27 @@ internal class ByteArrayBinary(
override val size: Int = array.size - start,
) : Binary {
override fun <R> read(offset: Int, atMost: Int, block: Input.() -> R): R {
override fun <R> read(offset: Int, atMost: Int, block: Source.() -> R): R {
require(offset >= 0) { "Offset must be positive" }
require(offset < array.size) { "Offset $offset is larger than array size" }
val input = ByteReadPacket(
return ByteArraySource(
array,
offset + start,
min(atMost, size - offset)
)
return input.use(block)
).buffered().use(block)
}
override suspend fun <R> readSuspend(offset: Int, atMost: Int, block: suspend Input.() -> R): R {
override suspend fun <R> readSuspend(offset: Int, atMost: Int, block: suspend Source.() -> R): R {
require(offset >= 0) { "Offset must be positive" }
require(offset < array.size) { "Offset $offset is larger than array size" }
val input = ByteReadPacket(
val input = ByteArraySource(
array,
offset + start,
min(atMost, size - offset)
)
).buffered()
return try {
block(input)
} finally {
@ -77,26 +82,26 @@ public fun Binary.toByteArray(): ByteArray = if (this is ByteArrayBinary) {
array.copyOfRange(start, start + size) // TODO do we need to ensure data safety here?
} else {
read {
readBytes()
readByteArray()
}
}
//TODO optimize for file-based Inputs
public fun Input.readBinary(size: Int? = null): Binary {
val array = if (size == null) readBytes() else readBytes(size)
public fun Source.readBinary(size: Int? = null): Binary {
val array = if (size == null) readByteArray() else readByteArray(size)
return ByteArrayBinary(array)
}
/**
* Direct write of binary to the output. Returns the number of bytes written
*/
public fun Output.writeBinary(binary: Binary): Int {
public fun Sink.writeBinary(binary: Binary): Int {
return if (binary is ByteArrayBinary) {
writeFully(binary.array, binary.start, binary.start + binary.size)
write(binary.array, binary.start, binary.start + binary.size)
binary.size
} else {
binary.read {
copyTo(this@writeBinary).toInt()
transferTo(this@writeBinary).toInt()
}
}
}

4
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/EnvelopeBuilder.kt
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@ -1,6 +1,6 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.Output
import kotlinx.io.Sink
import space.kscience.dataforge.meta.*
public class EnvelopeBuilder : Envelope {
@ -33,7 +33,7 @@ public class EnvelopeBuilder : Envelope {
/**
* Construct a data binary from given builder
*/
public inline fun data(block: Output.() -> Unit) {
public inline fun data(block: Sink.() -> Unit) {
data = ByteArray { block() }.asBinary()
}

4
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/EnvelopeFormat.kt
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@ -1,6 +1,6 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.Input
import kotlinx.io.Source
import space.kscience.dataforge.context.Context
import space.kscience.dataforge.io.EnvelopeFormatFactory.Companion.ENVELOPE_FORMAT_TYPE
import space.kscience.dataforge.meta.Meta
@ -15,7 +15,7 @@ public interface EnvelopeFormat : IOFormat<Envelope> {
override val type: KType get() = typeOf<Envelope>()
}
public fun EnvelopeFormat.read(input: Input): Envelope = readObject(input)
public fun EnvelopeFormat.read(input: Source): Envelope = readObject(input)
@Type(ENVELOPE_FORMAT_TYPE)
public interface EnvelopeFormatFactory : IOFormatFactory<Envelope>, EnvelopeFormat {

15
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/EnvelopeParts.kt
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@ -1,5 +1,8 @@
package space.kscience.dataforge.io
import kotlinx.io.bytestring.ByteString
import kotlinx.io.bytestring.decodeToString
import kotlinx.io.write
import space.kscience.dataforge.io.Envelope.Companion.ENVELOPE_NODE_KEY
import space.kscience.dataforge.io.PartDescriptor.Companion.DEFAULT_MULTIPART_DATA_SEPARATOR
import space.kscience.dataforge.io.PartDescriptor.Companion.MULTIPART_DATA_TYPE
@ -20,7 +23,7 @@ private class PartDescriptor : Scheme() {
val PARTS_KEY = MULTIPART_KEY + "parts"
val SEPARATOR_KEY = MULTIPART_KEY + "separator"
const val DEFAULT_MULTIPART_DATA_SEPARATOR = "\r\n#~PART~#\r\n"
val DEFAULT_MULTIPART_DATA_SEPARATOR = "\r\n#~PART~#\r\n".toAsciiByteString()
const val MULTIPART_DATA_TYPE = "envelope.multipart"
}
@ -32,12 +35,12 @@ public typealias EnvelopeParts = List<EnvelopePart>
public fun EnvelopeBuilder.multipart(
parts: EnvelopeParts,
separator: String = DEFAULT_MULTIPART_DATA_SEPARATOR,
separator: ByteString = DEFAULT_MULTIPART_DATA_SEPARATOR,
) {
dataType = MULTIPART_DATA_TYPE
var offsetCounter = 0
val separatorSize = separator.length
val separatorSize = separator.size
val partDescriptors = parts.map { (binary, description) ->
offsetCounter += separatorSize
PartDescriptor {
@ -51,14 +54,14 @@ public fun EnvelopeBuilder.multipart(
meta {
if (separator != DEFAULT_MULTIPART_DATA_SEPARATOR) {
SEPARATOR_KEY put separator
SEPARATOR_KEY put separator.decodeToString()
}
setIndexed(PARTS_KEY, partDescriptors.map { it.toMeta() })
}
data {
parts.forEach {
writeRawString(separator)
write(separator)
writeBinary(it.binary)
}
}
@ -69,7 +72,7 @@ public fun EnvelopeBuilder.multipart(
*/
public fun EnvelopeBuilder.envelopes(
envelopes: List<Envelope>,
separator: String = DEFAULT_MULTIPART_DATA_SEPARATOR,
separator: ByteString = DEFAULT_MULTIPART_DATA_SEPARATOR,
) {
val parts = envelopes.map {
val binary = Binary(it, TaggedEnvelopeFormat)

26
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/IOFormat.kt
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@ -1,6 +1,8 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.*
import kotlinx.io.Sink
import kotlinx.io.Source
import kotlinx.io.readByteArray
import space.kscience.dataforge.context.Context
import space.kscience.dataforge.context.Factory
import space.kscience.dataforge.io.IOFormatFactory.Companion.IO_FORMAT_TYPE
@ -21,7 +23,7 @@ public interface IOReader<out T> {
*/
public val type: KType
public fun readObject(input: Input): T
public fun readObject(source: Source): T
public fun readObject(binary: Binary): T = binary.read { readObject(this) }
@ -32,21 +34,21 @@ public interface IOReader<out T> {
public val binary: IOReader<Binary> = object : IOReader<Binary> {
override val type: KType = typeOf<Binary>()
override fun readObject(input: Input): Binary = input.readBytes().asBinary()
override fun readObject(source: Source): Binary = source.readByteArray().asBinary()
override fun readObject(binary: Binary): Binary = binary
}
}
}
public inline fun <reified T> IOReader(crossinline read: Input.() -> T): IOReader<T> = object : IOReader<T> {
public inline fun <reified T> IOReader(crossinline read: Source.() -> T): IOReader<T> = object : IOReader<T> {
override val type: KType = typeOf<T>()
override fun readObject(input: Input): T = input.read()
override fun readObject(source: Source): T = source.read()
}
public fun interface IOWriter<in T> {
public fun writeObject(output: Output, obj: T)
public fun writeObject(sink: Sink, obj: T)
}
/**
@ -54,20 +56,20 @@ public fun interface IOWriter<in T> {
*/
public interface IOFormat<T> : IOReader<T>, IOWriter<T>
public fun <T : Any> Input.readObject(format: IOReader<T>): T = format.readObject(this@readObject)
public fun <T : Any> Source.readObject(format: IOReader<T>): T = format.readObject(this@readObject)
public fun <T : Any> IOFormat<T>.readObjectFrom(binary: Binary): T = binary.read {
readObject(this)
}
/**
* Read given binary as object using given format
* Read given binary as an object using given format
*/
public fun <T : Any> Binary.readWith(format: IOReader<T>): T = read {
readObject(format)
}
public fun <T : Any> Output.writeObject(format: IOWriter<T>, obj: T): Unit =
public fun <T : Any> Sink.writeObject(format: IOWriter<T>, obj: T): Unit =
format.writeObject(this@writeObject, obj)
@ -94,9 +96,9 @@ public object DoubleIOFormat : IOFormat<Double>, IOFormatFactory<Double> {
override val type: KType get() = typeOf<Double>()
override fun writeObject(output: Output, obj: Double) {
output.writeDouble(obj)
override fun writeObject(sink: Sink, obj: Double) {
sink.writeLong(obj.toBits())
}
override fun readObject(input: Input): Double = input.readDouble()
override fun readObject(source: Source): Double = Double.fromBits(source.readLong())
}

24
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/JsonMetaFormat.kt
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@ -1,10 +1,10 @@
@file:Suppress("UNUSED_PARAMETER")
package space.kscience.dataforge.io
import io.ktor.utils.io.core.Input
import io.ktor.utils.io.core.Output
import kotlinx.io.Sink
import kotlinx.io.Source
import kotlinx.io.readString
import kotlinx.io.writeString
import kotlinx.serialization.json.Json
import kotlinx.serialization.json.JsonElement
import space.kscience.dataforge.context.Context
@ -18,13 +18,13 @@ import space.kscience.dataforge.meta.toMeta
*/
public class JsonMetaFormat(private val json: Json = DEFAULT_JSON) : MetaFormat {
override fun writeMeta(output: Output, meta: Meta, descriptor: MetaDescriptor?) {
override fun writeMeta(sink: Sink, meta: Meta, descriptor: MetaDescriptor?) {
val jsonElement = meta.toJson(descriptor)
output.writeUtf8String(json.encodeToString(JsonElement.serializer(), jsonElement))
sink.writeString(json.encodeToString(JsonElement.serializer(), jsonElement))
}
override fun readMeta(input: Input, descriptor: MetaDescriptor?): Meta {
val str = input.readUtf8String()//readByteArray().decodeToString()
override fun readMeta(source: Source, descriptor: MetaDescriptor?): Meta {
val str = source.readString()
val jsonElement = json.parseToJsonElement(str)
return jsonElement.toMeta(descriptor)
}
@ -39,10 +39,10 @@ public class JsonMetaFormat(private val json: Json = DEFAULT_JSON) : MetaFormat
private val default = JsonMetaFormat()
override fun writeMeta(output: Output, meta: Meta, descriptor: MetaDescriptor?): Unit =
default.run { writeMeta(output, meta, descriptor) }
override fun writeMeta(sink: Sink, meta: Meta, descriptor: MetaDescriptor?): Unit =
default.run { writeMeta(sink, meta, descriptor) }
override fun readMeta(input: Input, descriptor: MetaDescriptor?): Meta =
default.run { readMeta(input, descriptor) }
override fun readMeta(source: Source, descriptor: MetaDescriptor?): Meta =
default.run { readMeta(source, descriptor) }
}
}

22
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/MetaFormat.kt
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@ -1,9 +1,9 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.ByteReadPacket
import io.ktor.utils.io.core.Input
import io.ktor.utils.io.core.Output
import io.ktor.utils.io.core.use
import kotlinx.io.Sink
import kotlinx.io.Source
import kotlinx.io.buffered
import space.kscience.dataforge.context.Context
import space.kscience.dataforge.context.Global
import space.kscience.dataforge.io.MetaFormatFactory.Companion.META_FORMAT_TYPE
@ -23,19 +23,19 @@ public interface MetaFormat : IOFormat<Meta> {
override val type: KType get() = typeOf<Meta>()
override fun writeObject(output: Output, obj: Meta) {
writeMeta(output, obj, null)
override fun writeObject(sink: Sink, obj: Meta) {
writeMeta(sink, obj, null)
}
override fun readObject(input: Input): Meta = readMeta(input)
override fun readObject(source: Source): Meta = readMeta(source)
public fun writeMeta(
output: Output,
sink: Sink,
meta: Meta,
descriptor: MetaDescriptor? = null,
)
public fun readMeta(input: Input, descriptor: MetaDescriptor? = null): Meta
public fun readMeta(source: Source, descriptor: MetaDescriptor? = null): Meta
}
@Type(META_FORMAT_TYPE)
@ -63,9 +63,7 @@ public fun Meta.toString(format: MetaFormat): String = ByteArray {
public fun Meta.toString(formatFactory: MetaFormatFactory): String = toString(formatFactory.build(Global, Meta.EMPTY))
public fun MetaFormat.parse(str: String): Meta {
return ByteReadPacket(str.encodeToByteArray()).use { readObject(it) }
}
public fun MetaFormat.parse(str: String): Meta = readObject(StringSource(str).buffered())
public fun MetaFormatFactory.parse(str: String, formatMeta: Meta): Meta = build(Global, formatMeta).parse(str)

67
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/TaggedEnvelopeFormat.kt
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@ -1,6 +1,7 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.*
import kotlinx.io.*
import kotlinx.io.bytestring.decodeToString
import space.kscience.dataforge.context.Context
import space.kscience.dataforge.context.Global
import space.kscience.dataforge.meta.Meta
@ -18,7 +19,7 @@ import space.kscience.dataforge.names.plus
public class TaggedEnvelopeFormat(
public val io: IOPlugin,
public val version: VERSION = VERSION.DF02,
public val metaFormatFactory: MetaFormatFactory = JsonMetaFormat
public val metaFormatFactory: MetaFormatFactory = JsonMetaFormat,
) : EnvelopeFormat {
// private val metaFormat = io.metaFormat(metaFormatKey)
@ -26,59 +27,60 @@ public class TaggedEnvelopeFormat(
private fun Tag.toBinary() = Binary {
writeRawString(START_SEQUENCE)
writeRawString(version.name)
write(START_SEQUENCE)
writeString(version.name)
writeShort(metaFormatKey)
writeUInt(metaSize)
when (version) {
VERSION.DF02 -> {
writeUInt(dataSize.toUInt())
}
VERSION.DF03 -> {
writeULong(dataSize)
}
}
writeRawString(END_SEQUENCE)
write(END_SEQUENCE)
}
override fun writeObject(
output: Output,
sink: Sink,
obj: Envelope,
) {
val metaFormat = metaFormatFactory.build(io.context, Meta.EMPTY)
val metaBytes = Binary(obj.meta,metaFormat)
val metaBytes = Binary(obj.meta, metaFormat)
val actualSize: ULong = (obj.data?.size ?: 0).toULong()
val tag = Tag(metaFormatFactory.key, metaBytes.size.toUInt() + 2u, actualSize)
output.writeBinary(tag.toBinary())
output.writeBinary(metaBytes)
output.writeRawString("\r\n")
sink.writeBinary(tag.toBinary())
sink.writeBinary(metaBytes)
sink.writeString("\r\n")
obj.data?.let {
output.writeBinary(it)
sink.writeBinary(it)
}
}
/**
* Read an envelope from input into memory
*
* @param input an input to read from
* @param source an input to read from
* @param formats a collection of meta formats to resolve
*/
override fun readObject(input: Input): Envelope {
val tag = input.readTag(this.version)
override fun readObject(source: Source): Envelope {
val tag = source.readTag(this.version)
val metaFormat = io.resolveMetaFormat(tag.metaFormatKey)
?: error("Meta format with key ${tag.metaFormatKey} not found")
val metaBinary = input.readBinary(tag.metaSize.toInt())
val metaBinary = source.readBinary(tag.metaSize.toInt())
val meta: Meta = metaFormat.readObjectFrom(metaBinary)
val data = input.readBinary(tag.dataSize.toInt())
val data = source.readBinary(tag.dataSize.toInt())
return SimpleEnvelope(meta, data)
}
override fun readObject(binary: Binary): Envelope = binary.read{
override fun readObject(binary: Binary): Envelope = binary.read {
val tag = readTag(version)
val metaFormat = io.resolveMetaFormat(tag.metaFormatKey)
@ -104,8 +106,8 @@ public class TaggedEnvelopeFormat(
}
public companion object : EnvelopeFormatFactory {
private const val START_SEQUENCE = "#~"
private const val END_SEQUENCE = "~#\r\n"
private val START_SEQUENCE = "#~".toAsciiByteString()
private val END_SEQUENCE = "~#\r\n".toAsciiByteString()
override val name: Name = EnvelopeFormatFactory.ENVELOPE_FACTORY_NAME + "tagged"
@ -121,27 +123,26 @@ public class TaggedEnvelopeFormat(
return TaggedEnvelopeFormat(io, version)
}
private fun Input.readTag(version: VERSION): Tag {
val start = readRawString(2)
private fun Source.readTag(version: VERSION): Tag {
val start = readByteString(2)
if (start != START_SEQUENCE) error("The input is not an envelope")
val versionString = readRawString(4)
if (version.name != versionString) error("Wrong version of DataForge: expected $version but found $versionString")
val versionString = readByteString(4)
if (version.name.toAsciiByteString() != versionString) error("Wrong version of DataForge: expected $version but found $versionString")
val metaFormatKey = readShort()
val metaLength = readUInt()
val dataLength: ULong = when (version) {
VERSION.DF02 -> readUInt().toULong()
VERSION.DF03 -> readULong()
}
val end = readRawString(4)
val end = readByteString(4)
if (end != END_SEQUENCE) error("The input is not an envelope")
return Tag(metaFormatKey, metaLength, dataLength)
}
override fun peekFormat(io: IOPlugin, binary: Binary): EnvelopeFormat? {
return try {
override fun peekFormat(io: IOPlugin, binary: Binary): EnvelopeFormat? = try {
binary.read {
val header = readRawString(6)
return@read when (header.substring(2..5)) {
val header = readByteString(6)
when (header.substring(2, 6).decodeToString()) {
VERSION.DF02.name -> TaggedEnvelopeFormat(io, VERSION.DF02)
VERSION.DF03.name -> TaggedEnvelopeFormat(io, VERSION.DF03)
else -> null
@ -150,7 +151,6 @@ public class TaggedEnvelopeFormat(
} catch (ex: Exception) {
null
}
}
private val default by lazy { build(Global, Meta.EMPTY) }
@ -158,16 +158,13 @@ public class TaggedEnvelopeFormat(
default.run { readObject(binary) }
override fun writeObject(
output: Output,
sink: Sink,
obj: Envelope,
): Unit = default.run {
writeObject(
output,
obj,
)
writeObject(sink, obj)
}
override fun readObject(input: Input): Envelope = default.readObject(input)
override fun readObject(source: Source): Envelope = default.readObject(source)
}
}

56
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/TaglessEnvelopeFormat.kt
View File

@ -1,9 +1,9 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.ByteReadPacket
import io.ktor.utils.io.core.Input
import io.ktor.utils.io.core.Output
import io.ktor.utils.io.core.readUTF8UntilDelimiterTo
import kotlinx.io.*
import kotlinx.io.bytestring.ByteString
import kotlinx.io.bytestring.encodeToByteString
import space.kscience.dataforge.context.Context
import space.kscience.dataforge.context.Global
import space.kscience.dataforge.meta.Meta
@ -29,34 +29,35 @@ public class TaglessEnvelopeFormat(
// }
override fun writeObject(
output: Output,
sink: Sink,
obj: Envelope,
) {
val metaFormat = metaFormatFactory.build(this.io.context, meta)
//printing header
output.writeRawString(TAGLESS_ENVELOPE_HEADER + "\r\n")
sink.write(TAGLESS_ENVELOPE_HEADER)
sink.writeString("\r\n")
//Printing meta
if (!obj.meta.isEmpty()) {
val metaBinary = Binary(obj.meta, metaFormat)
output.writeUtf8String(META_START + "-${metaFormatFactory.shortName}\r\n")
output.writeBinary(metaBinary)
output.writeRawString("\r\n")
sink.writeString(META_START + "-${metaFormatFactory.shortName}\r\n")
sink.writeBinary(metaBinary)
sink.writeString("\r\n")
}
//Printing data
obj.data?.let { data ->
//val actualSize: Int = envelope.data?.size ?: 0
output.writeUtf8String(DATA_START + "\r\n")
output.writeBinary(data)
sink.writeString(DATA_START + "\r\n")
sink.writeBinary(data)
}
}
override fun readObject(input: Input): Envelope {
override fun readObject(source: Source): Envelope {
//read preamble
input.discardWithSeparator(
TAGLESS_ENVELOPE_HEADER.encodeToByteArray(),
source.discardWithSeparator(
TAGLESS_ENVELOPE_HEADER,
atMost = 1024,
)
@ -64,22 +65,22 @@ public class TaglessEnvelopeFormat(
var data: Binary? = null
input.discardWithSeparator(
source.discardWithSeparator(
SEPARATOR_PREFIX,
atMost = 1024,
)
var header: String = ByteArray {
input.readUTF8UntilDelimiterTo(this, "\n")
source.readWithSeparatorTo(this, "\n".encodeToByteString())
}.decodeToString()
while (!input.endOfInput) {
while (!source.exhausted()) {
val block = ByteArray {
input.readWithSeparatorTo(this, SEPARATOR_PREFIX)
source.readWithSeparatorTo(this, SEPARATOR_PREFIX)
}
val nextHeader = ByteArray {
input.readWithSeparatorTo(this, "\n".encodeToByteArray())
source.readWithSeparatorTo(this, "\n".encodeToByteString())
}.decodeToString()
//terminate on end
@ -89,7 +90,7 @@ public class TaglessEnvelopeFormat(
if (header.startsWith("META")) {
//TODO check format
val metaFormat: MetaFormatFactory = JsonMetaFormat
meta = metaFormat.readMeta(ByteReadPacket(block))
meta = metaFormat.readMeta(ByteArraySource(block).buffered())
}
if (header.startsWith("DATA")) {
@ -111,9 +112,9 @@ public class TaglessEnvelopeFormat(
public const val TAGLESS_ENVELOPE_TYPE: String = "tagless"
public val SEPARATOR_PREFIX: ByteArray = "\n#~".encodeToByteArray()
public val SEPARATOR_PREFIX: ByteString = "\n#~".encodeToByteString()
public const val TAGLESS_ENVELOPE_HEADER: String = "#~DFTL"
public val TAGLESS_ENVELOPE_HEADER: ByteString = "#~DFTL".encodeToByteString()
// public const val META_START_PROPERTY: String = "metaSeparator"
public const val META_START: String = "#~META"
@ -134,21 +135,18 @@ public class TaglessEnvelopeFormat(
override fun readObject(binary: Binary): Envelope = default.run { readObject(binary) }
override fun writeObject(
output: Output,
sink: Sink,
obj: Envelope,
): Unit = default.run {
writeObject(
output,
obj,
)
writeObject(sink, obj)
}
override fun readObject(input: Input): Envelope = default.readObject(input)
override fun readObject(source: Source): Envelope = default.readObject(source)
override fun peekFormat(io: IOPlugin, binary: Binary): EnvelopeFormat? {
return try {
binary.read {
val string = readRawString(TAGLESS_ENVELOPE_HEADER.length)
val string = readByteString(TAGLESS_ENVELOPE_HEADER.size)
return@read if (string == TAGLESS_ENVELOPE_HEADER) {
TaglessEnvelopeFormat(io)
} else {

166
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/ioMisc.kt
View File

@ -1,40 +1,41 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.bits.Memory
import io.ktor.utils.io.charsets.Charsets
import io.ktor.utils.io.charsets.decodeExactBytes
import io.ktor.utils.io.core.*
import io.ktor.utils.io.core.internal.ChunkBuffer
import kotlinx.io.*
import kotlinx.io.bytestring.ByteString
import kotlinx.io.bytestring.decodeToString
import kotlinx.io.bytestring.encodeToByteString
import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.misc.DFExperimental
import kotlin.math.min
public fun Output.writeRawString(str: String) {
writeFully(str.toByteArray(Charsets.ISO_8859_1))
/**
* Convert a string literal, containing only ASCII characters to a [ByteString].
* Throws an error if there are non-ASCII characters.
*/
public fun String.toAsciiByteString(): ByteString {
val bytes = ByteArray(length) {
val char = get(it)
val code = char.code
if (code > Byte.MAX_VALUE) error("Symbol $char is not ASCII symbol") else code.toByte()
}
return ByteString(bytes)
}
public fun Output.writeUtf8String(str: String) {
writeFully(str.encodeToByteArray())
}
public inline fun Buffer(block: Sink.() -> Unit): Buffer = Buffer().apply(block)
public fun Input.readRawString(size: Int): String {
return Charsets.ISO_8859_1.newDecoder().decodeExactBytes(this, size)
}
//public fun Source.readSafeUtf8Line(): String = readUTF8Line() ?: error("Line not found")
public fun Input.readUtf8String(): String = readBytes().decodeToString()
public inline fun ByteArray(block: Sink.() -> Unit): ByteArray =
Buffer(block).readByteArray()
public fun Input.readSafeUtf8Line(): String = readUTF8Line() ?: error("Line not found")
public inline fun ByteArray(block: Output.() -> Unit): ByteArray =
buildPacket(block).readBytes()
public inline fun Binary(block: Output.() -> Unit): Binary =
public inline fun Binary(block: Sink.() -> Unit): Binary =
ByteArray(block).asBinary()
public operator fun Binary.get(range: IntRange): Binary = view(range.first, range.last - range.first)
/**
* Return inferred [EnvelopeFormat] if only one format could read given file. If no format accepts the binary, return null. If
* multiple formats accepts binary, throw an error.
* multiple formats accept binary, throw an error.
*/
public fun IOPlugin.peekBinaryEnvelopeFormat(binary: Binary): EnvelopeFormat? {
val formats = envelopeFormatFactories.mapNotNull { factory ->
@ -96,74 +97,139 @@ private class RingByteArray(
else -> inputArray.indices.all { inputArray[it] == get(it) }
}
fun contentEquals(byteString: ByteString): Boolean = when {
byteString.size != buffer.size -> false
size < buffer.size -> false
else -> (0 until byteString.size).all { byteString[it] == get(it) }
}
}
private fun RingByteArray.toArray(): ByteArray = ByteArray(size) { get(it) }
/**
* Read [Input] into [output] until designated multibyte [separator] and optionally continues until
* Read [Source] into [output] until designated multibyte [separator] and optionally continues until
* the end of the line after it. Throw error if [separator] not found and [atMost] bytes are read.
* Also fails if [separator] not found until the end of input.
*
* Separator itself is not read into Output.
* The Separator itself is not read into [Sink].
*
* @param errorOnEof if true error is thrown if separator is never encountered
*
* @return bytes actually being read, including separator
*/
public fun Input.readWithSeparatorTo(
output: Output,
separator: ByteArray,
public fun Source.readWithSeparatorTo(
output: Sink?,
separator: ByteString,
atMost: Int = Int.MAX_VALUE,
errorOnEof: Boolean = false,
): Int {
var counter = 0
val rb = RingByteArray(ByteArray(separator.size))
takeWhile { buffer ->
while (buffer.canRead()) {
val byte = buffer.readByte()
while (!exhausted()) {
val byte = readByte()
counter++
if (counter >= atMost) error("Maximum number of bytes to be read $atMost reached.")
rb.push(byte)
if (rb.contentEquals(separator)) {
return counter
} else if (rb.isFull()) {
output.writeByte(rb[0])
output?.writeByte(rb[0])
}
}
!endOfInput
}
if (errorOnEof) {
error("Read to the end of input without encountering ${separator.decodeToString()}")
} else {
for(i in 1 until rb.size){
output.writeByte(rb[i])
for (i in 1 until rb.size) {
output?.writeByte(rb[i])
}
counter += (rb.size - 1)
return counter
}
}
public fun Input.discardLine(): Int {
return discardUntilDelimiter('\n'.code.toByte()).also {
discard(1)
}.toInt() + 1
}
public fun Input.discardWithSeparator(
separator: ByteArray,
/**
* Discard all bytes until [separator] is encountered. Separator is discarded sa well.
* Return the total number of bytes read.
*/
public fun Source.discardWithSeparator(
separator: ByteString,
atMost: Int = Int.MAX_VALUE,
errorOnEof: Boolean = false,
): Int {
val dummy: Output = object : Output(ChunkBuffer.Pool) {
override fun closeDestination() {
): Int = readWithSeparatorTo(null, separator, atMost, errorOnEof)
/**
* Discard all symbol until newline is discovered. Carriage return is not discarded.
*/
public fun Source.discardLine(
atMost: Int = Int.MAX_VALUE,
errorOnEof: Boolean = false,
): Int = discardWithSeparator("\n".encodeToByteString(), atMost, errorOnEof)
/**
* A [Source] based on [ByteArray]
*/
public class ByteArraySource(
private val byteArray: ByteArray,
private val offset: Int = 0,
private val size: Int = byteArray.size - offset,
) : RawSource {
init {
require(offset >= 0) { "Offset must be positive" }
require(offset + size <= byteArray.size) { "End index is ${offset + size}, but the array size is ${byteArray.size}" }
}
private var pointer = offset
override fun close() {
// Do nothing
}
override fun flush(source: Memory, offset: Int, length: Int) {
// Do nothing
override fun readAtMostTo(sink: Buffer, byteCount: Long): Long {
if (pointer == offset + size) return -1
val byteRead = min(byteCount.toInt(), (size + offset - pointer))
sink.write(byteArray, pointer, pointer + byteRead)
pointer += byteRead
return byteRead.toLong()
}
}
return readWithSeparatorTo(dummy, separator, atMost, errorOnEof)
}
/**
* A [Source] based on [String]
*/
public class StringSource(
public val string: String,
public val offset: Int = 0,
public val size: Int = string.length - offset,
) : RawSource {
private var pointer = offset
override fun close() {
// Do nothing
}
override fun readAtMostTo(sink: Buffer, byteCount: Long): Long {
if (pointer == offset + size) return -1
val byteRead = min(byteCount.toInt(), (size + offset - pointer))
sink.writeString(string, pointer, pointer + byteRead)
pointer += byteRead
return byteRead.toLong()
}
}
public fun Sink.writeDouble(value: Double) {
writeLong(value.toBits())
}
public fun Source.readDouble(): Double = Double.fromBits(readLong())
public fun Sink.writeFloat(value: Float) {
writeInt(value.toBits())
}
public fun Source.readFloat(): Float = Float.fromBits(readInt())

1
dataforge-io/src/commonTest/kotlin/space/kscience/dataforge/io/BinaryTest.kt
View File

@ -1,6 +1,5 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.readInt
import kotlin.test.Test
import kotlin.test.assertEquals

13
dataforge-io/src/commonTest/kotlin/space/kscience/dataforge/io/EnvelopeFormatTest.kt
View File

@ -1,6 +1,7 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.readBytes
import kotlinx.io.readByteArray
import kotlinx.io.writeString
import kotlin.test.Test
import kotlin.test.assertEquals
@ -12,7 +13,7 @@ class EnvelopeFormatTest {
"d" put 22.2
}
data {
writeUtf8String("12345678")
writeString("12345678")
}
}
@ -22,7 +23,7 @@ class EnvelopeFormatTest {
val res = readFromByteArray(byteArray)
assertEquals(envelope.meta, res.meta)
val bytes = res.data?.read {
readBytes()
readByteArray()
}
assertEquals("12345678", bytes?.decodeToString())
}
@ -34,13 +35,13 @@ class EnvelopeFormatTest {
val res = readFromByteArray(byteArray)
assertEquals(envelope.meta, res.meta)
val bytes = res.data?.read {
readBytes()
readByteArray()
}
assertEquals("12345678", bytes?.decodeToString())
}
@Test
fun testManualDftl(){
fun testManualDftl() {
val envelopeString = """
#~DFTL
#~META
@ -56,7 +57,7 @@ class EnvelopeFormatTest {
val res = TaglessEnvelopeFormat.readFromByteArray(envelopeString.encodeToByteArray())
assertEquals(envelope.meta, res.meta)
val bytes = res.data?.read {
readBytes()
readByteArray()
}
assertEquals("12345678", bytes?.decodeToString())
}

21
dataforge-io/src/commonTest/kotlin/space/kscience/dataforge/io/IOTest.kt
View File

@ -1,8 +1,9 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.ByteReadPacket
import io.ktor.utils.io.core.readBytes
import io.ktor.utils.io.core.readUTF8Line
import kotlinx.io.buffered
import kotlinx.io.bytestring.encodeToByteString
import kotlinx.io.readByteArray
import kotlinx.io.readLine
import kotlin.test.Test
import kotlin.test.assertEquals
import kotlin.test.assertFails
@ -11,9 +12,9 @@ class IOTest {
@Test
fun readBytes() {
val bytes = ByteArray(8) { it.toByte() }
val input = ByteReadPacket(bytes)
@Suppress("UNUSED_VARIABLE") val first = input.readBytes(4)
val second = input.readBytes(4)
val input = ByteArraySource(bytes).buffered()
@Suppress("UNUSED_VARIABLE") val first = input.readByteArray(4)
val second = input.readByteArray(4)
assertEquals(4.toByte(), second[0])
}
@ -31,25 +32,25 @@ class IOTest {
binary.read {
val array = ByteArray {
val read = readWithSeparatorTo(this, "---".encodeToByteArray()) + discardLine()
val read = readWithSeparatorTo(this, "---".encodeToByteString()) + discardLine()
assertEquals(12, read)
}
assertEquals("""
aaa
bbb
""".trimIndent(),array.decodeToString().trim())
assertEquals("ccc", readUTF8Line()?.trim())
assertEquals("ccc", readLine()?.trim())
}
assertFails {
binary.read {
discardWithSeparator("---".encodeToByteArray(), atMost = 3 )
discardWithSeparator("---".encodeToByteString(), atMost = 3 )
}
}
assertFails {
binary.read{
discardWithSeparator("-+-".encodeToByteArray(), errorOnEof = true)
discardWithSeparator("-+-".encodeToByteString(), errorOnEof = true)
}
}

5
dataforge-io/src/commonTest/kotlin/space/kscience/dataforge/io/MultipartTest.kt
View File

@ -1,5 +1,6 @@
package space.kscience.dataforge.io
import kotlinx.io.writeString
import space.kscience.dataforge.context.Global
import space.kscience.dataforge.meta.get
import space.kscience.dataforge.meta.int
@ -18,9 +19,9 @@ class MultipartTest {
"value" put it
}
data {
writeUtf8String("Hello World $it")
writeString("Hello World $it")
repeat(300) {
writeRawString("$it ")
writeString("$it ")
}
}
}

5
dataforge-io/src/commonTest/kotlin/space/kscience/dataforge/io/ioTestUtils.kt
View File

@ -1,12 +1,11 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.ByteReadPacket
import io.ktor.utils.io.core.use
import kotlinx.io.buffered
fun <T : Any> IOFormat<T>.writeToByteArray(obj: T): ByteArray = ByteArray {
writeObject(this, obj)
}
fun <T : Any> IOFormat<T>.readFromByteArray(array: ByteArray): T = ByteReadPacket(array).use {
fun <T : Any> IOFormat<T>.readFromByteArray(array: ByteArray): T = ByteArraySource(array).buffered().use {
readObject(it)
}

29
dataforge-io/src/jvmMain/kotlin/space/kscience/dataforge/io/fileIO.kt
View File

@ -1,8 +1,11 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.*
import io.ktor.utils.io.streams.asOutput
import kotlinx.coroutines.runBlocking
import kotlinx.io.Sink
import kotlinx.io.Source
import kotlinx.io.asSink
import kotlinx.io.buffered
import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.meta.descriptors.MetaDescriptor
import space.kscience.dataforge.meta.isEmpty
@ -23,18 +26,18 @@ internal class PathBinary(
override val size: Int = Files.size(path).toInt() - fileOffset,
) : Binary {
override fun <R> read(offset: Int, atMost: Int, block: Input.() -> R): R = runBlocking {
override fun <R> read(offset: Int, atMost: Int, block: Source.() -> R): R = runBlocking {
readSuspend(offset, atMost, block)
}
override suspend fun <R> readSuspend(offset: Int, atMost: Int, block: suspend Input.() -> R): R {
override suspend fun <R> readSuspend(offset: Int, atMost: Int, block: suspend Source.() -> R): R {
val actualOffset = offset + fileOffset
val actualSize = min(atMost, size - offset)
val array = path.inputStream().use {
it.skip(actualOffset.toLong())
it.readNBytes(actualSize)
}
return ByteReadPacket(array).block()
return ByteArraySource(array).buffered().use { it.block() }
}
override fun view(offset: Int, binarySize: Int) = PathBinary(path, fileOffset + offset, binarySize)
@ -42,36 +45,36 @@ internal class PathBinary(
public fun Path.asBinary(): Binary = PathBinary(this)
public fun <R> Path.read(block: Input.() -> R): R = asBinary().read(block = block)
public fun <R> Path.read(block: Source.() -> R): R = asBinary().read(block = block)
/**
* Write a live output to a newly created file. If file does not exist, throws error
*/
public fun Path.write(block: Output.() -> Unit): Unit {
public fun Path.write(block: Sink.() -> Unit): Unit {
val stream = Files.newOutputStream(this, StandardOpenOption.WRITE, StandardOpenOption.CREATE_NEW)
stream.asOutput().use(block)
stream.asSink().buffered().use(block)
}
/**
* Create a new file or append to exiting one with given output [block]
*/
public fun Path.append(block: Output.() -> Unit): Unit {
public fun Path.append(block: Sink.() -> Unit): Unit {
val stream = Files.newOutputStream(
this,
StandardOpenOption.WRITE, StandardOpenOption.APPEND, StandardOpenOption.CREATE
)
stream.asOutput().use(block)
stream.asSink().buffered().use(block)
}
/**
* Create a new file or replace existing one using given output [block]
*/
public fun Path.rewrite(block: Output.() -> Unit): Unit {
public fun Path.rewrite(block: Sink.() -> Unit): Unit {
val stream = Files.newOutputStream(
this,
StandardOpenOption.WRITE, StandardOpenOption.TRUNCATE_EXISTING, StandardOpenOption.CREATE
)
stream.asOutput().use(block)
stream.asSink().buffered().use(block)
}
@DFExperimental
@ -260,7 +263,7 @@ public fun IOPlugin.writeEnvelopeDirectory(
val dataFile = path.resolve(IOPlugin.DATA_FILE_NAME)
dataFile.write {
envelope.data?.read {
val copied = copyTo(this@write)
val copied = transferTo(this@write)
if (copied != envelope.data?.size?.toLong()) {
error("The number of copied bytes does not equal data size")
}

12
dataforge-io/src/jvmMain/kotlin/space/kscience/dataforge/io/resourceIO.kt
View File

@ -1,9 +1,11 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.Input
import io.ktor.utils.io.streams.asInput
import kotlinx.io.Source
import kotlinx.io.asSource
import kotlinx.io.buffered
public fun IOPlugin.resource(name: String): Binary? = context.javaClass.getResource(name)?.readBytes()?.asBinary()
public inline fun <R> IOPlugin.readResource(name: String, block: Input.() -> R): R =
context.javaClass.getResource(name)?.openStream()?.asInput()?.block() ?: error("Can't read resource $name")
public fun IOPlugin.resource(name: String): Binary? = { }.javaClass.getResource(name)?.readBytes()?.asBinary()
public inline fun <R> IOPlugin.readResource(name: String, block: Source.() -> R): R =
{ }.javaClass.getResource(name)?.openStream()?.asSource()?.buffered()?.block() ?: error("Can't read resource $name")

1
dataforge-io/src/jvmTest/kotlin/space/kscience/dataforge/io/FileBinaryTest.kt
View File

@ -1,6 +1,5 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.writeDouble
import space.kscience.dataforge.context.Global
import space.kscience.dataforge.misc.DFExperimental
import java.nio.file.Files

1
dataforge-io/src/jvmTest/kotlin/space/kscience/dataforge/io/FileEnvelopeTest.kt
View File

@ -1,6 +1,5 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.writeDouble
import space.kscience.dataforge.context.Global
import space.kscience.dataforge.misc.DFExperimental
import java.nio.file.Files

36
dataforge-workspace/build.gradle.kts
View File

@ -10,17 +10,35 @@ kscience{
useSerialization{
protobuf()
}
dependencies {
api(projects.dataforgeContext)
api(projects.dataforgeData)
api(projects.dataforgeIo)
}
dependencies(jvmTest){
implementation(spclibs.logback.classic)
implementation(projects.dataforgeIo.dataforgeIoYaml)
}
// dependencies {
// api(projects.dataforgeContext)
// api(projects.dataforgeData)
// api(projects.dataforgeIo)
// }
// dependencies(jvmTest){
// implementation(spclibs.logback.classic)
// implementation(projects.dataforgeIo.dataforgeIoYaml)
// }
}
readme{
maturity = space.kscience.gradle.Maturity.EXPERIMENTAL
}
kotlin{
sourceSets{
commonMain{
dependencies {
api(projects.dataforgeContext)
api(projects.dataforgeData)
api(projects.dataforgeIo)
}
}
getByName("jvmTest"){
dependencies {
implementation(spclibs.logback.classic)
implementation(projects.dataforgeIo.dataforgeIoYaml)
}
}
}
}

17
dataforge-workspace/src/jvmMain/kotlin/space/kscience/dataforge/workspace/FileWorkspaceCache.kt
View File

@ -1,9 +1,6 @@
package space.kscience.dataforge.workspace
import io.ktor.utils.io.core.Input
import io.ktor.utils.io.core.Output
import io.ktor.utils.io.core.readBytes
import io.ktor.utils.io.core.writeFully
import kotlinx.io.*
import kotlinx.serialization.ExperimentalSerializationApi
import kotlinx.serialization.KSerializer
import kotlinx.serialization.json.Json
@ -30,10 +27,10 @@ public class JsonIOFormat<T : Any>(override val type: KType) : IOFormat<T> {
@Suppress("UNCHECKED_CAST")
private val serializer: KSerializer<T> = serializer(type) as KSerializer<T>
override fun readObject(input: Input): T = Json.decodeFromString(serializer, input.readUtf8String())
override fun readObject(input: Source): T = Json.decodeFromString(serializer, input.readString())
override fun writeObject(output: Output, obj: T) {
output.writeUtf8String(Json.encodeToString(serializer, obj))
override fun writeObject(output: Sink, obj: T) {
output.writeString(Json.encodeToString(serializer, obj))
}
}
@ -43,10 +40,10 @@ public class ProtobufIOFormat<T : Any>(override val type: KType) : IOFormat<T> {
@Suppress("UNCHECKED_CAST")
private val serializer: KSerializer<T> = serializer(type) as KSerializer<T>
override fun readObject(input: Input): T = ProtoBuf.decodeFromByteArray(serializer, input.readBytes())
override fun readObject(input: Source): T = ProtoBuf.decodeFromByteArray(serializer, input.readByteArray())
override fun writeObject(output: Output, obj: T) {
output.writeFully(ProtoBuf.encodeToByteArray(serializer, obj))
override fun writeObject(output: Sink, obj: T) {
output.write(ProtoBuf.encodeToByteArray(serializer, obj))
}
}

15
dataforge-workspace/src/jvmMain/kotlin/space/kscience/dataforge/workspace/zipData.kt
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@ -1,13 +1,10 @@
package space.kscience.dataforge.workspace
import io.ktor.utils.io.streams.asOutput
import kotlinx.coroutines.Dispatchers
import kotlinx.coroutines.withContext
import space.kscience.dataforge.data.DataTree
import space.kscience.dataforge.data.DataTreeItem
import space.kscience.dataforge.io.EnvelopeFormat
import space.kscience.dataforge.io.IOFormat
import space.kscience.dataforge.io.TaggedEnvelopeFormat
import space.kscience.dataforge.io.*
import space.kscience.dataforge.misc.DFExperimental
import java.nio.file.Files
import java.nio.file.Path
@ -28,11 +25,15 @@ private suspend fun <T : Any> ZipOutputStream.writeNode(
val envelope = treeItem.data.toEnvelope(dataFormat)
val entry = ZipEntry(name)
putNextEntry(entry)
asOutput().run {
envelopeFormat.writeObject(this, envelope)
flush()
//TODO remove additional copy
val bytes = ByteArray {
writeObject(envelopeFormat, envelope)
}
write(bytes)
}
is DataTreeItem.Node -> {
val entry = ZipEntry("$name/")
putNextEntry(entry)

17
dataforge-workspace/src/jvmTest/kotlin/space/kscience/dataforge/workspace/FileDataTest.kt
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@ -1,8 +1,11 @@
package space.kscience.dataforge.workspace
import io.ktor.utils.io.core.Input
import io.ktor.utils.io.core.Output
import kotlinx.coroutines.runBlocking
import kotlinx.coroutines.test.runTest
import kotlinx.io.Sink
import kotlinx.io.Source
import kotlinx.io.readString
import kotlinx.io.writeString
import space.kscience.dataforge.context.Context
import space.kscience.dataforge.context.Global
import space.kscience.dataforge.data.*
@ -36,11 +39,11 @@ class FileDataTest {
object StringIOFormat : IOFormat<String> {
override val type: KType get() = typeOf<String>()
override fun writeObject(output: Output, obj: String) {
output.writeUtf8String(obj)
override fun writeObject(output: Sink, obj: String) {
output.writeString(obj)
}
override fun readObject(input: Input): String = input.readUtf8String()
override fun readObject(input: Source): String = input.readString()
}
@Test
@ -59,9 +62,9 @@ class FileDataTest {
@Test
@DFExperimental
fun testZipWriteRead() = with(Global.io) {
fun testZipWriteRead() = runTest {
with(Global.io) {
val zip = Files.createTempFile("df_data_node", ".zip")
runBlocking {
dataNode.writeZip(zip, StringIOFormat)
println(zip.toUri().toString())
val reconstructed = readDataDirectory(zip) { _, _ -> StringIOFormat }

3
gradle.properties
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@ -6,4 +6,5 @@ kotlin.mpp.stability.nowarn=true
kotlin.incremental.js.ir=true
kotlin.native.ignoreDisabledTargets=true
toolsVersion=0.14.9-kotlin-1.8.20
toolsVersion=0.14.9-kotlin-1.9.0
kotlin.experimental.tryK2=true

2
gradle/wrapper/gradle-wrapper.properties vendored
View File

@ -1,5 +1,5 @@
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
distributionUrl=https\://services.gradle.org/distributions/gradle-8.2-bin.zip
distributionUrl=https\://services.gradle.org/distributions/gradle-8.2.1-bin.zip
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists