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Simplify DFTL. fix io bugs

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This commit is contained in:
Alexander Nozik 2023-01-25 18:56:19 +03:00
parent 82838b6a92
commit 5d7ddb4e00
21 changed files with 216 additions and 372 deletions
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1
CHANGELOG.md
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@ -9,6 +9,7 @@
- More fine-grained types in Action builders.
### Changed
- Simplified `DFTL` envelope format. Closing symbols are unnecessary. Properties are discontinued.
- Meta `get` method allows nullable receiver
- `withDefault` functions do not add new keys to meta children and are consistent.
- `dataforge.meta.values` package is merged into `dataforge.meta` for better star imports

2
build.gradle.kts
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@ -9,7 +9,7 @@ plugins {
allprojects {
group = "space.kscience"
version = "0.6.0-dev-15"
version = "0.6.1-dev-1"
}
subprojects {

4
dataforge-io/dataforge-io-yaml/build.gradle.kts
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@ -1,13 +1,13 @@
plugins {
id("space.kscience.gradle.mpp")
// id("space.kscience.gradle.native")
}
description = "YAML meta IO"
kscience {
native()
useSerialization{
yamlKt("0.9.0-dev-1")
yamlKt()
}
}

61
dataforge-io/dataforge-io-yaml/src/commonMain/kotlin/space/kscience/dataforge/io/yaml/FrontMatterEnvelopeFormat.kt
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@ -2,8 +2,6 @@ package space.kscience.dataforge.io.yaml
import io.ktor.utils.io.core.Input
import io.ktor.utils.io.core.Output
import io.ktor.utils.io.core.buildPacket
import io.ktor.utils.io.core.readBytes
import space.kscience.dataforge.context.Context
import space.kscience.dataforge.context.Global
import space.kscience.dataforge.io.*
@ -14,50 +12,46 @@ import space.kscience.dataforge.names.plus
public class FrontMatterEnvelopeFormat(
private val io: IOPlugin,
private val meta: Meta = Meta.EMPTY,
private val metaFormatFactory: MetaFormatFactory = YamlMetaFormat,
) : EnvelopeFormat {
override fun readPartial(input: Input): PartialEnvelope {
override fun readObject(binary: Binary): Envelope = binary.read {
var offset = 0
offset += input.discardWithSeparator(
offset += discardWithSeparator(
SEPARATOR.encodeToByteArray(),
atMost = 1024,
skipUntilEndOfLine = false
)
val line = input.readSafeUtf8Line()
val line = ByteArray {
offset += readWithSeparatorTo(this, "\n".encodeToByteArray())
}.decodeToString()
val readMetaFormat = line.trim().takeIf { it.isNotBlank() }?.let { io.resolveMetaFormat(it) } ?: YamlMetaFormat
//TODO replace by preview
val packet = buildPacket {
offset += input.readBytesWithSeparatorTo(
this,
SEPARATOR.encodeToByteArray(),
skipUntilEndOfLine = true
)
}
val meta = readMetaFormat.readMeta(packet)
return PartialEnvelope(meta, offset, null)
val packet = ByteArray {
offset += readWithSeparatorTo(this, SEPARATOR.encodeToByteArray())
}
override fun readObject(input: Input): Envelope {
val partial = readPartial(input)
val data = input.readBytes().asBinary()
return SimpleEnvelope(partial.meta, data)
offset += discardLine()
val meta = readMetaFormat.readObject(packet.asBinary())
Envelope(meta, binary.view(offset))
}
override fun writeEnvelope(
override fun readObject(input: Input): Envelope = readObject(input.readBinary())
override fun writeObject(
output: Output,
envelope: Envelope,
metaFormatFactory: MetaFormatFactory,
formatMeta: Meta,
obj: Envelope,
) {
val metaFormat = metaFormatFactory.build(this@FrontMatterEnvelopeFormat.io.context, formatMeta)
output.writeRawString("$SEPARATOR\r\n")
metaFormat.run { this.writeObject(output, envelope.meta) }
val metaFormat = metaFormatFactory.build(io.context, meta)
val formatSuffix = if (metaFormat is YamlMetaFormat) "" else metaFormatFactory.shortName
output.writeRawString("$SEPARATOR${formatSuffix}\r\n")
metaFormat.run { metaFormat.writeObject(output, obj.meta) }
output.writeRawString("$SEPARATOR\r\n")
//Printing data
envelope.data?.let { data ->
obj.data?.let { data ->
output.writeBinary(data)
}
}
@ -84,15 +78,12 @@ public class FrontMatterEnvelopeFormat(
private val default by lazy { build(Global, Meta.EMPTY) }
override fun readPartial(input: Input): PartialEnvelope =
default.readPartial(input)
override fun readObject(binary: Binary): Envelope = default.readObject(binary)
override fun writeEnvelope(
override fun writeObject(
output: Output,
envelope: Envelope,
metaFormatFactory: MetaFormatFactory,
formatMeta: Meta,
): Unit = default.writeEnvelope(output, envelope, metaFormatFactory, formatMeta)
obj: Envelope,
): Unit = default.writeObject(output, obj)
override fun readObject(input: Input): Envelope = default.readObject(input)

15
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/Binary.kt
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@ -21,6 +21,12 @@ public interface Binary {
public suspend fun <R> readSuspend(offset: Int = 0, atMost: Int = size - offset, block: suspend Input.() -> 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.
*/
public fun view(offset: Int, binarySize: Int = size - offset): Binary
public companion object {
public val EMPTY: Binary = ByteArrayBinary(ByteArray(0))
}
@ -57,6 +63,9 @@ internal class ByteArrayBinary(
input.close()
}
}
override fun view(offset: Int, binarySize: Int): ByteArrayBinary =
ByteArrayBinary(array, start + offset, binarySize)
}
public fun ByteArray.asBinary(): Binary = ByteArrayBinary(this)
@ -65,7 +74,7 @@ public fun ByteArray.asBinary(): Binary = ByteArrayBinary(this)
* Produce a [ByteArray] representing an exact copy of this [Binary]
*/
public fun Binary.toByteArray(): ByteArray = if (this is ByteArrayBinary) {
array.copyOf() // TODO do we need to ensure data safety here?
array.copyOfRange(start, start + size) // TODO do we need to ensure data safety here?
} else {
read {
readBytes()
@ -73,8 +82,8 @@ public fun Binary.toByteArray(): ByteArray = if (this is ByteArrayBinary) {
}
//TODO optimize for file-based Inputs
public fun Input.readBinary(size: Int): Binary {
val array = readBytes(size)
public fun Input.readBinary(size: Int? = null): Binary {
val array = if (size == null) readBytes() else readBytes(size)
return ByteArrayBinary(array)
}

2
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/Envelope.kt
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@ -34,7 +34,7 @@ public interface Envelope {
}
}
public class SimpleEnvelope(override val meta: Meta, override val data: Binary?) : Envelope
internal class SimpleEnvelope(override val meta: Meta, override val data: Binary?) : Envelope
public fun Envelope(meta: Meta, data: Binary?): Envelope = SimpleEnvelope(meta, data)

21
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/EnvelopeFormat.kt
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@ -1,7 +1,6 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.Input
import io.ktor.utils.io.core.Output
import space.kscience.dataforge.context.Context
import space.kscience.dataforge.io.EnvelopeFormatFactory.Companion.ENVELOPE_FORMAT_TYPE
import space.kscience.dataforge.meta.Meta
@ -11,29 +10,9 @@ import space.kscience.dataforge.names.asName
import kotlin.reflect.KType
import kotlin.reflect.typeOf
/**
* A partially read envelope with meta, but without data
*/
public data class PartialEnvelope(val meta: Meta, val dataOffset: Int, val dataSize: ULong?)
public interface EnvelopeFormat : IOFormat<Envelope> {
override val type: KType get() = typeOf<Envelope>()
public val defaultMetaFormat: MetaFormatFactory get() = JsonMetaFormat
public fun readPartial(input: Input): PartialEnvelope
public fun writeEnvelope(
output: Output,
envelope: Envelope,
metaFormatFactory: MetaFormatFactory = defaultMetaFormat,
formatMeta: Meta = Meta.EMPTY,
)
override fun readObject(input: Input): Envelope
override fun writeObject(output: Output, obj: Envelope): Unit = writeEnvelope(output, obj)
}
public fun EnvelopeFormat.read(input: Input): Envelope = readObject(input)

27
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/EnvelopeParts.kt
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@ -1,12 +1,10 @@
package space.kscience.dataforge.io
import space.kscience.dataforge.context.invoke
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
import space.kscience.dataforge.io.PartDescriptor.Companion.MULTIPART_KEY
import space.kscience.dataforge.io.PartDescriptor.Companion.PARTS_KEY
import space.kscience.dataforge.io.PartDescriptor.Companion.PART_FORMAT_KEY
import space.kscience.dataforge.io.PartDescriptor.Companion.SEPARATOR_KEY
import space.kscience.dataforge.meta.*
import space.kscience.dataforge.names.asName
@ -24,8 +22,6 @@ private class PartDescriptor : Scheme() {
const val DEFAULT_MULTIPART_DATA_SEPARATOR = "\r\n#~PART~#\r\n"
val PART_FORMAT_KEY = "format".asName()
const val MULTIPART_DATA_TYPE = "envelope.multipart"
}
}
@ -73,21 +69,12 @@ public fun EnvelopeBuilder.multipart(
*/
public fun EnvelopeBuilder.envelopes(
envelopes: List<Envelope>,
formatFactory: EnvelopeFormatFactory = TaggedEnvelopeFormat,
formatMeta: Meta? = null,
separator: String = DEFAULT_MULTIPART_DATA_SEPARATOR,
) {
val parts = envelopes.map {
val format = formatMeta?.let { formatFactory(formatMeta) } ?: formatFactory
val binary = Binary(it, format)
val binary = Binary(it, TaggedEnvelopeFormat)
EnvelopePart(binary, null)
}
meta {
(MULTIPART_KEY + PART_FORMAT_KEY) put {
IOFormatFactory.NAME_KEY put formatFactory.name.toString()
formatMeta?.let { IOFormatFactory.META_KEY put formatMeta }
}
}
multipart(parts, separator)
}
@ -115,14 +102,4 @@ public val EnvelopePart.name: String? get() = description?.get("name").string
/**
* Represent envelope part by an envelope
*/
public fun EnvelopePart.envelope(plugin: IOPlugin): Envelope {
val formatItem = description?.get(PART_FORMAT_KEY)
return if (formatItem != null) {
val format: EnvelopeFormat = plugin.resolveEnvelopeFormat(formatItem)
?: error("Envelope format for $formatItem is not resolved")
binary.readWith(format)
} else {
error("Envelope description not found")
//SimpleEnvelope(description ?: Meta.EMPTY, binary)
}
}
public fun EnvelopePart.envelope(): Envelope = binary.readWith(TaggedEnvelopeFormat)

2
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/IOFormat.kt
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@ -25,6 +25,8 @@ public interface IOReader<out T> {
public val type: KType
public fun readObject(input: Input): T
public fun readObject(binary: Binary): T = binary.read { readObject(this) }
}
public inline fun <reified T> IOReader(crossinline read: Input.() -> T): IOReader<T> = object : IOReader<T> {

39
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/TaggedEnvelopeFormat.kt
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@ -18,6 +18,7 @@ import space.kscience.dataforge.names.plus
public class TaggedEnvelopeFormat(
public val io: IOPlugin,
public val version: VERSION = VERSION.DF02,
public val metaFormatFactory: MetaFormatFactory = JsonMetaFormat
) : EnvelopeFormat {
// private val metaFormat = io.metaFormat(metaFormatKey)
@ -40,20 +41,18 @@ public class TaggedEnvelopeFormat(
writeRawString(END_SEQUENCE)
}
override fun writeEnvelope(
override fun writeObject(
output: Output,
envelope: Envelope,
metaFormatFactory: MetaFormatFactory,
formatMeta: Meta,
obj: Envelope,
) {
val metaFormat = metaFormatFactory.build(this@TaggedEnvelopeFormat.io.context, formatMeta)
val metaBytes = Binary(envelope.meta,metaFormat)
val actualSize: ULong = (envelope.data?.size ?: 0).toULong()
val metaFormat = metaFormatFactory.build(io.context, Meta.EMPTY)
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")
envelope.data?.let {
obj.data?.let {
output.writeBinary(it)
}
}
@ -79,18 +78,18 @@ public class TaggedEnvelopeFormat(
return SimpleEnvelope(meta, data)
}
override fun readPartial(input: Input): PartialEnvelope {
val tag = input.readTag(this.version)
override fun readObject(binary: Binary): Envelope = binary.read{
val tag = readTag(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 = readBinary(tag.metaSize.toInt())
val meta: Meta = metaFormat.readObjectFrom(metaBinary)
return PartialEnvelope(meta, (version.tagSize + tag.metaSize).toInt(), tag.dataSize)
SimpleEnvelope(meta, binary.view((version.tagSize + tag.metaSize).toInt(), tag.dataSize.toInt()))
}
private data class Tag(
@ -155,20 +154,16 @@ public class TaggedEnvelopeFormat(
private val default by lazy { build(Global, Meta.EMPTY) }
override fun readPartial(input: Input): PartialEnvelope =
default.run { readPartial(input) }
override fun readObject(binary: Binary): Envelope =
default.run { readObject(binary) }
override fun writeEnvelope(
override fun writeObject(
output: Output,
envelope: Envelope,
metaFormatFactory: MetaFormatFactory,
formatMeta: Meta,
obj: Envelope,
): Unit = default.run {
writeEnvelope(
writeObject(
output,
envelope,
metaFormatFactory,
formatMeta
obj,
)
}

206
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/TaglessEnvelopeFormat.kt
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@ -1,64 +1,54 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.*
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 space.kscience.dataforge.context.Context
import space.kscience.dataforge.context.Global
import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.meta.get
import space.kscience.dataforge.meta.isEmpty
import space.kscience.dataforge.meta.string
import space.kscience.dataforge.names.Name
import space.kscience.dataforge.names.plus
import kotlin.collections.set
/**
* A text envelope format with human-readable tag.
* A text envelope format based on block separators.
* TODO add description
*/
public class TaglessEnvelopeFormat(
public val io: IOPlugin,
public val meta: Meta = Meta.EMPTY,
public val metaFormatFactory: MetaFormatFactory = JsonMetaFormat,
) : EnvelopeFormat {
private val metaStart = meta[META_START_PROPERTY].string ?: DEFAULT_META_START
private val dataStart = meta[DATA_START_PROPERTY].string ?: DEFAULT_DATA_START
// private val metaStart = meta[META_START_PROPERTY].string ?: DEFAULT_META_START
// private val dataStart = meta[DATA_START_PROPERTY].string ?: DEFAULT_DATA_START
private fun Output.writeProperty(key: String, value: Any) {
writeFully("#? $key: $value;\r\n".encodeToByteArray())
}
// private fun Output.writeProperty(key: String, value: Any) {
// writeFully("#? $key: $value;\r\n".encodeToByteArray())
// }
override fun writeEnvelope(
override fun writeObject(
output: Output,
envelope: Envelope,
metaFormatFactory: MetaFormatFactory,
formatMeta: Meta,
obj: Envelope,
) {
val metaFormat = metaFormatFactory.build(this.io.context, formatMeta)
val metaFormat = metaFormatFactory.build(this.io.context, meta)
//printing header
output.writeRawString(TAGLESS_ENVELOPE_HEADER + "\r\n")
//printing all properties
output.writeProperty(META_TYPE_PROPERTY,
metaFormatFactory.shortName)
//TODO add optional metaFormat properties
val actualSize: Int = envelope.data?.size ?: 0
output.writeProperty(DATA_LENGTH_PROPERTY, actualSize)
//Printing meta
if (!envelope.meta.isEmpty()) {
val metaBinary = Binary(envelope.meta, metaFormat)
output.writeProperty(META_LENGTH_PROPERTY,
metaBinary.size + 2)
output.writeUtf8String(this.metaStart + "\r\n")
if (!obj.meta.isEmpty()) {
val metaBinary = Binary(obj.meta, metaFormat)
output.writeUtf8String(META_START + "-${metaFormatFactory.shortName}\r\n")
output.writeBinary(metaBinary)
output.writeRawString("\r\n")
}
//Printing data
envelope.data?.let { data ->
output.writeUtf8String(this.dataStart + "\r\n")
obj.data?.let { data ->
//val actualSize: Int = envelope.data?.size ?: 0
output.writeUtf8String(DATA_START + "\r\n")
output.writeBinary(data)
}
}
@ -68,121 +58,46 @@ public class TaglessEnvelopeFormat(
input.discardWithSeparator(
TAGLESS_ENVELOPE_HEADER.encodeToByteArray(),
atMost = 1024,
skipUntilEndOfLine = true
)
val properties = HashMap<String, String>()
var line = ""
while (line.isBlank() || line.startsWith("#?")) {
if (line.startsWith("#?")) {
val match = propertyPattern.find(line)
?: error("Line $line does not match property declaration pattern")
val (key, value) = match.destructured
properties[key] = value
}
try {
line = ByteArray {
try {
input.readBytesWithSeparatorTo(this, byteArrayOf('\n'.code.toByte()), 1024)
} catch (ex: BufferLimitExceededException) {
throw IllegalStateException("Property line exceeds maximum line length (1024)", ex)
}
}.decodeToString().trim()
} catch (ex: EOFException) {
return SimpleEnvelope(Meta.EMPTY, Binary.EMPTY)
}
}
var meta: Meta = Meta.EMPTY
if (line.startsWith(metaStart)) {
val metaFormat = properties[META_TYPE_PROPERTY]?.let { io.resolveMetaFormat(it) } ?: JsonMetaFormat
val metaSize = properties[META_LENGTH_PROPERTY]?.toInt()
meta = if (metaSize != null) {
metaFormat.readObjectFrom(input.readBinary(metaSize))
} else {
error("Can't partially read an envelope with undefined meta size")
}
}
var data: Binary? = null
//skip until data start
input.discardWithSeparator(
dataStart.encodeToByteArray(),
SEPARATOR_PREFIX,
atMost = 1024,
skipUntilEndOfLine = true
)
val data: Binary = if (properties.containsKey(DATA_LENGTH_PROPERTY)) {
input.readBinary(properties[DATA_LENGTH_PROPERTY]!!.toInt())
// val bytes = ByteArray(properties[DATA_LENGTH_PROPERTY]!!.toInt())
// readByteArray(bytes)
// bytes.asBinary()
} else {
input.readBytes().asBinary()
var header: String = ByteArray {
input.readUTF8UntilDelimiterTo(this, "\n")
}.decodeToString()
while (!input.endOfInput) {
val block = ByteArray {
input.readWithSeparatorTo(this, SEPARATOR_PREFIX)
}
return SimpleEnvelope(meta, data)
val nextHeader = ByteArray {
input.readWithSeparatorTo(this, "\n".encodeToByteArray())
}.decodeToString()
//terminate on end
if (header.startsWith("END")) break
if (header.startsWith("META")) {
//TODO check format
val metaFormat: MetaFormatFactory = JsonMetaFormat
meta = metaFormat.readMeta(ByteReadPacket(block))
}
override fun readPartial(input: Input): PartialEnvelope {
var offset = 0
//read preamble
offset += input.discardWithSeparator(
TAGLESS_ENVELOPE_HEADER.encodeToByteArray(),
atMost = 1024,
skipUntilEndOfLine = true
)
val properties = HashMap<String, String>()
var line = ""
while (line.isBlank() || line.startsWith("#?")) {
if (line.startsWith("#?")) {
val match = propertyPattern.find(line)
?: error("Line $line does not match property declaration pattern")
val (key, value) = match.destructured
properties[key] = value
if (header.startsWith("DATA")) {
data = block.asBinary()
}
try {
line = ByteArray {
val read = try {
input.readBytesWithSeparatorTo(this, byteArrayOf('\n'.code.toByte()), 1024)
} catch (ex: BufferLimitExceededException) {
throw IllegalStateException("Property line exceeds maximum line length (1024)", ex)
header = nextHeader
}
offset += read
}.decodeToString().trim()
} catch (ex: EOFException) {
return PartialEnvelope(Meta.EMPTY, offset, 0.toULong())
}
}
var meta: Meta = Meta.EMPTY
if (line.startsWith(metaStart)) {
val metaFormat = properties[META_TYPE_PROPERTY]?.let { io.resolveMetaFormat(it) } ?: JsonMetaFormat
val metaSize = properties[META_LENGTH_PROPERTY]?.toInt()
meta = if (metaSize != null) {
offset += metaSize
metaFormat.readObjectFrom(input.readBinary(metaSize))
} else {
error("Can't partially read an envelope with undefined meta size")
}
}
//skip until data start
offset += input.discardWithSeparator(
dataStart.encodeToByteArray(),
atMost = 1024,
skipUntilEndOfLine = true
)
val dataSize = properties[DATA_LENGTH_PROPERTY]?.toULong()
return PartialEnvelope(meta, offset, dataSize)
return Envelope(meta, data)
}
public companion object : EnvelopeFormatFactory {
@ -196,11 +111,17 @@ public class TaglessEnvelopeFormat(
public const val TAGLESS_ENVELOPE_TYPE: String = "tagless"
public const val TAGLESS_ENVELOPE_HEADER: String = "#~DFTL~#"
public const val META_START_PROPERTY: String = "metaSeparator"
public const val DEFAULT_META_START: String = "#~META~#"
public const val DATA_START_PROPERTY: String = "dataSeparator"
public const val DEFAULT_DATA_START: String = "#~DATA~#"
public val SEPARATOR_PREFIX: ByteArray = "\n#~".encodeToByteArray()
public const val TAGLESS_ENVELOPE_HEADER: String = "#~DFTL"
// public const val META_START_PROPERTY: String = "metaSeparator"
public const val META_START: String = "#~META"
// public const val DATA_START_PROPERTY: String = "dataSeparator"
public const val DATA_START: String = "#~DATA"
public const val END: String = "#~END"
public const val code: Int = 0x4446544c //DFTL
@ -210,20 +131,15 @@ public class TaglessEnvelopeFormat(
private val default by lazy { build(Global, Meta.EMPTY) }
override fun readPartial(input: Input): PartialEnvelope =
default.run { readPartial(input) }
override fun readObject(binary: Binary): Envelope = default.run { readObject(binary) }
override fun writeEnvelope(
override fun writeObject(
output: Output,
envelope: Envelope,
metaFormatFactory: MetaFormatFactory,
formatMeta: Meta,
obj: Envelope,
): Unit = default.run {
writeEnvelope(
writeObject(
output,
envelope,
metaFormatFactory,
formatMeta
obj,
)
}

86
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/ioMisc.kt
View File

@ -7,7 +7,6 @@ import io.ktor.utils.io.core.*
import io.ktor.utils.io.core.internal.ChunkBuffer
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))
@ -31,26 +30,7 @@ public inline fun ByteArray(block: Output.() -> Unit): ByteArray =
public inline fun Binary(block: Output.() -> Unit): Binary =
ByteArray(block).asBinary()
/**
* View section of a [Binary] as an independent binary
*/
public class BinaryView(private val source: Binary, private val start: Int, override val size: Int) : Binary {
init {
require(start > 0)
require(start + size <= source.size) { "View boundary is outside source binary size" }
}
override fun <R> read(offset: Int, atMost: Int, block: Input.() -> R): R =
source.read(start + offset, min(size, atMost), block)
override suspend fun <R> readSuspend(offset: Int, atMost: Int, block: suspend Input.() -> R): R =
source.readSuspend(start + offset, min(size, atMost), block)
}
public fun Binary.view(start: Int, size: Int): BinaryView = BinaryView(this, start, size)
public operator fun Binary.get(range: IntRange): BinaryView = view(range.first, range.last - range.first)
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
@ -68,22 +48,6 @@ public fun IOPlugin.peekBinaryEnvelopeFormat(binary: Binary): EnvelopeFormat? {
}
}
/**
* Zero-copy read this binary as an envelope using given [this@toEnvelope]
*/
@DFExperimental
public fun EnvelopeFormat.readBinary(binary: Binary): Envelope {
val partialEnvelope: PartialEnvelope = binary.read {
run {
readPartial(this@read)
}
}
val offset: Int = partialEnvelope.dataOffset.toInt()
val size: Int = partialEnvelope.dataSize?.toInt() ?: (binary.size - offset)
val envelopeBinary = BinaryView(binary, offset, size)
return SimpleEnvelope(partialEnvelope.meta, envelopeBinary)
}
/**
* A zero-copy read from
*/
@ -92,9 +56,9 @@ public fun IOPlugin.readEnvelope(
binary: Binary,
readNonEnvelopes: Boolean = false,
formatPicker: IOPlugin.(Binary) -> EnvelopeFormat? = IOPlugin::peekBinaryEnvelopeFormat,
): Envelope = formatPicker(binary)?.readBinary(binary) ?: if (readNonEnvelopes) {
): Envelope = formatPicker(binary)?.readObject(binary) ?: if (readNonEnvelopes) {
// if no format accepts file, read it as binary
SimpleEnvelope(Meta.EMPTY, binary)
Envelope(Meta.EMPTY, binary)
} else error("Can't infer format for $binary")
@DFExperimental
@ -126,62 +90,70 @@ private class RingByteArray(
private fun Int.forward(n: Int): Int = (this + n) % (buffer.size)
fun compare(inputArray: ByteArray): Boolean = when {
fun contentEquals(inputArray: ByteArray): Boolean = when {
inputArray.size != buffer.size -> false
size < buffer.size -> false
else -> inputArray.indices.all { inputArray[it] == get(it) }
}
}
private fun RingByteArray.toArray(): ByteArray = ByteArray(size) { get(it) }
/**
* Read [Input] into [output] until designated multy-byte [separator] and optionally continues until
* Read [Input] 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.
*
* @param errorOnEof if true error is thrown if separator is never encountered
*
* @return bytes actually being read, including separator
*/
public fun Input.readBytesWithSeparatorTo(
public fun Input.readWithSeparatorTo(
output: Output,
separator: ByteArray,
atMost: Int = Int.MAX_VALUE,
skipUntilEndOfLine: Boolean = false,
errorOnEof: Boolean = false,
): Int {
var counter = 0
val rb = RingByteArray(ByteArray(separator.size))
var separatorFound = false
takeWhile { buffer ->
while (buffer.canRead()) {
val byte = buffer.readByte()
counter++
if (counter >= atMost) error("Maximum number of bytes to be read $atMost reached.")
//If end-of-line-search is on, terminate
if (separatorFound) {
if (endOfInput || byte == '\n'.code.toByte()) {
return counter
}
} else {
rb.push(byte)
if (rb.compare(separator)) {
separatorFound = true
if (!skipUntilEndOfLine) {
if (rb.contentEquals(separator)) {
return counter
}
} else if (rb.isFull()) {
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])
}
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,
atMost: Int = Int.MAX_VALUE,
skipUntilEndOfLine: Boolean = false,
errorOnEof: Boolean = false,
): Int {
val dummy: Output = object : Output(ChunkBuffer.Pool) {
override fun closeDestination() {
@ -193,5 +165,5 @@ public fun Input.discardWithSeparator(
}
}
return readBytesWithSeparatorTo(dummy, separator, atMost, skipUntilEndOfLine)
return readWithSeparatorTo(dummy, separator, atMost, errorOnEof)
}

56
dataforge-io/src/commonTest/kotlin/space/kscience/dataforge/io/EnvelopeFormatTest.kt
View File

@ -1,8 +1,6 @@
package space.kscience.dataforge.io
import io.ktor.utils.io.core.ByteReadPacket
import io.ktor.utils.io.core.readDouble
import io.ktor.utils.io.core.writeDouble
import io.ktor.utils.io.core.readBytes
import kotlin.test.Test
import kotlin.test.assertEquals
@ -14,40 +12,52 @@ class EnvelopeFormatTest {
"d" put 22.2
}
data {
writeDouble(22.2)
// repeat(2000){
// writeInt(it)
// }
writeUtf8String("12345678")
}
}
@Test
fun testTaggedFormat() {
TaggedEnvelopeFormat.run {
fun testTaggedFormat() = with(TaggedEnvelopeFormat) {
val byteArray = writeToByteArray(envelope)
//println(byteArray.decodeToString())
val res = readFromByteArray(byteArray)
assertEquals(envelope.meta, res.meta)
val double = res.data?.read {
readDouble()
}
assertEquals(22.2, double)
val bytes = res.data?.read {
readBytes()
}
assertEquals("12345678", bytes?.decodeToString())
}
@Test
fun testTaglessFormat() {
TaglessEnvelopeFormat.run {
fun testTaglessFormat() = with(TaglessEnvelopeFormat) {
val byteArray = writeToByteArray(envelope)
//println(byteArray.decodeToString())
val partial = readPartial(ByteReadPacket(byteArray))
assertEquals(8, partial.dataSize?.toInt())
println(byteArray.decodeToString())
val res = readFromByteArray(byteArray)
assertEquals(envelope.meta, res.meta)
val double = res.data?.read {
readDouble()
}
assertEquals(22.2, double)
val bytes = res.data?.read {
readBytes()
}
assertEquals("12345678", bytes?.decodeToString())
}
@Test
fun testManualDftl(){
val envelopeString = """
#~DFTL
#~META
{
"@envelope": {
"type": "test.format"
},
"d": 22.2
}
#~DATA
12345678
""".trimIndent()
val res = TaglessEnvelopeFormat.readFromByteArray(envelopeString.encodeToByteArray())
assertEquals(envelope.meta, res.meta)
val bytes = res.data?.read {
readBytes()
}
assertEquals("12345678", bytes?.decodeToString())
}
}

4
dataforge-io/src/commonTest/kotlin/space/kscience/dataforge/io/IOTest.kt
View File

@ -31,7 +31,7 @@ class IOTest {
binary.read {
val array = ByteArray {
val read = readBytesWithSeparatorTo(this, "---".encodeToByteArray(), skipUntilEndOfLine = true)
val read = readWithSeparatorTo(this, "---".encodeToByteArray()) + discardLine()
assertEquals(12, read)
}
assertEquals("""
@ -49,7 +49,7 @@ class IOTest {
assertFails {
binary.read{
discardWithSeparator("-+-".encodeToByteArray())
discardWithSeparator("-+-".encodeToByteArray(), errorOnEof = true)
}
}

6
dataforge-io/src/commonTest/kotlin/space/kscience/dataforge/io/MultipartTest.kt
View File

@ -27,12 +27,12 @@ class MultipartTest {
}
val partsEnvelope = Envelope {
envelopes(envelopes, TaglessEnvelopeFormat)
envelopes(envelopes)
}
@Test
fun testParts() {
val format = TaglessEnvelopeFormat
val format = TaggedEnvelopeFormat
val singleEnvelopeData = Binary(envelopes[0], format)
val singleEnvelopeSize = singleEnvelopeData.size
val bytes = Binary(partsEnvelope, format)
@ -40,7 +40,7 @@ class MultipartTest {
val reconstructed = bytes.readWith(format)
println(reconstructed.meta)
val parts = reconstructed.parts()
val envelope = parts[2].envelope(io)
val envelope = parts[2].envelope()
assertEquals(2, envelope.meta["value"].int)
println(reconstructed.data!!.size)
}

15
dataforge-io/src/jvmMain/kotlin/space/kscience/dataforge/io/fileIO.kt
View File

@ -36,6 +36,8 @@ internal class PathBinary(
}
return ByteReadPacket(array).block()
}
override fun view(offset: Int, binarySize: Int) = PathBinary(path, fileOffset + offset, binarySize)
}
public fun Path.asBinary(): Binary = PathBinary(this)
@ -73,15 +75,7 @@ public fun Path.rewrite(block: Output.() -> Unit): Unit {
}
@DFExperimental
public fun EnvelopeFormat.readFile(path: Path): Envelope {
val partialEnvelope: PartialEnvelope = path.asBinary().read {
readPartial(this@read)
}
val offset: Int = partialEnvelope.dataOffset.toInt()
val size: Int = partialEnvelope.dataSize?.toInt() ?: (Files.size(path).toInt() - offset)
val binary = PathBinary(path, offset, size)
return SimpleEnvelope(partialEnvelope.meta, binary)
}
public fun EnvelopeFormat.readFile(path: Path): Envelope = readObject(path.asBinary())
/**
* Resolve IOFormat based on type
@ -239,10 +233,9 @@ public fun IOPlugin.writeEnvelopeFile(
path: Path,
envelope: Envelope,
envelopeFormat: EnvelopeFormat = TaggedEnvelopeFormat,
metaFormat: MetaFormatFactory? = null,
) {
path.rewrite {
envelopeFormat.writeEnvelope(this, envelope, metaFormat ?: envelopeFormat.defaultMetaFormat)
envelopeFormat.writeObject(this, envelope)
}
}

2
dataforge-workspace/src/commonMain/kotlin/space/kscience/dataforge/workspace/envelopeData.kt
View File

@ -17,5 +17,5 @@ public fun <T : Any> Envelope.toData(format: IOReader<T>): Data<T> = Data(format
public suspend fun <T : Any> Data<T>.toEnvelope(format: IOWriter<T>): Envelope {
val obj = await()
val binary = Binary(obj, format)
return SimpleEnvelope(meta, binary)
return Envelope(meta, binary)
}

8
dataforge-workspace/src/jvmMain/kotlin/space/kscience/dataforge/workspace/fileData.kt
View File

@ -30,7 +30,6 @@ import kotlin.io.path.nameWithoutExtension
import kotlin.io.path.readAttributes
import kotlin.reflect.KType
import kotlin.reflect.typeOf
import kotlin.streams.toList
//public typealias FileFormatResolver<T> = (Path, Meta) -> IOFormat<T>
@ -193,7 +192,6 @@ public suspend fun <T : Any> IOPlugin.writeDataDirectory(
tree: DataTree<T>,
format: IOWriter<T>,
envelopeFormat: EnvelopeFormat? = null,
metaFormat: MetaFormatFactory? = null,
) {
withContext(Dispatchers.IO) {
if (!Files.exists(path)) {
@ -210,15 +208,15 @@ public suspend fun <T : Any> IOPlugin.writeDataDirectory(
is DataTreeItem.Leaf -> {
val envelope = item.data.toEnvelope(format)
if (envelopeFormat != null) {
writeEnvelopeFile(childPath, envelope, envelopeFormat, metaFormat)
writeEnvelopeFile(childPath, envelope, envelopeFormat)
} else {
writeEnvelopeDirectory(childPath, envelope, metaFormat ?: JsonMetaFormat)
writeEnvelopeDirectory(childPath, envelope)
}
}
}
}
val treeMeta = tree.meta
writeMetaFile(path, treeMeta, metaFormat ?: JsonMetaFormat)
writeMetaFile(path, treeMeta)
}
}

2
dataforge-workspace/src/jvmMain/kotlin/space/kscience/dataforge/workspace/zipData.kt
View File

@ -29,7 +29,7 @@ private suspend fun <T : Any> ZipOutputStream.writeNode(
val entry = ZipEntry(name)
putNextEntry(entry)
asOutput().run {
envelopeFormat.writeEnvelope(this, envelope)
envelopeFormat.writeObject(this, envelope)
flush()
}
}

4
dataforge-workspace/src/jvmTest/kotlin/space/kscience/dataforge/workspace/CachingWorkspaceTest.kt
View File

@ -23,13 +23,13 @@ internal class CachingWorkspaceTest {
useCache()
val doFirst by task<Any> {
pipeFrom(data()) { _, name, meta ->
pipeFrom(data()) { _, name, _ ->
println("Done first on $name with flag=${taskMeta["flag"].boolean ?: false}")
}
}
val doSecond by task<Any>{
pipeFrom(doFirst) { _, name, meta ->
pipeFrom(doFirst) { _, name, _ ->
println("Done second on $name with flag=${taskMeta["flag"].boolean ?: false}")
}
}

1
gradle.properties
View File

@ -4,5 +4,6 @@ org.gradle.jvmargs=-Xmx4096m
kotlin.code.style=official
kotlin.mpp.stability.nowarn=true
kotlin.incremental.js.ir=true
kotlin.native.ignoreDisabledTargets=true
toolsVersion=0.13.3-kotlin-1.7.20