kscience/dataforge-core
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Merge remote-tracking branch 'remotes/origin/dev' into dev-zelenyy-2

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This commit is contained in:
Mikhail Zelenyy 2019-11-19 18:05:34 +03:00
commit 0cf060e93d
31 changed files with 483 additions and 157 deletions
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17
.github/workflows/gradle.yml vendored Normal file
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@ -0,0 +1,17 @@
name: Gradle build
on: [push]
jobs:
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v1
- name: Set up JDK 11
uses: actions/setup-java@v1
with:
java-version: 11
- name: Build with Gradle
run: ./gradlew build

2
README.md
View File

@ -1,5 +1,5 @@
[![DOI](https://zenodo.org/badge/148831678.svg)](https://zenodo.org/badge/latestdoi/148831678)
# Questions and Answers #

8
build.gradle.kts
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@ -1,12 +1,12 @@
import scientifik.ScientifikExtension
plugins {
id("scientifik.mpp") version "0.2.2" apply false
id("scientifik.jvm") version "0.2.2" apply false
id("scientifik.publish") version "0.2.2" apply false
id("scientifik.mpp") version "0.2.4" apply false
id("scientifik.jvm") version "0.2.4" apply false
id("scientifik.publish") version "0.2.4" apply false
}
val dataforgeVersion by extra("0.1.5-dev-2")
val dataforgeVersion by extra("0.1.5-dev-3")
val bintrayRepo by extra("dataforge")
val githubProject by extra("dataforge-core")

38
dataforge-data/src/commonMain/kotlin/hep/dataforge/data/DataNode.kt
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@ -15,20 +15,20 @@ sealed class DataItem<out T : Any> : MetaRepr {
abstract val meta: Meta
class Node<out T : Any>(val value: DataNode<T>) : DataItem<T>() {
override val type: KClass<out T> get() = value.type
class Node<out T : Any>(val node: DataNode<T>) : DataItem<T>() {
override val type: KClass<out T> get() = node.type
override fun toMeta(): Meta = value.toMeta()
override fun toMeta(): Meta = node.toMeta()
override val meta: Meta get() = value.meta
override val meta: Meta get() = node.meta
}
class Leaf<out T : Any>(val value: Data<T>) : DataItem<T>() {
override val type: KClass<out T> get() = value.type
class Leaf<out T : Any>(val data: Data<T>) : DataItem<T>() {
override val type: KClass<out T> get() = data.type
override fun toMeta(): Meta = value.toMeta()
override fun toMeta(): Meta = data.toMeta()
override val meta: Meta get() = value.meta
override val meta: Meta get() = data.meta
}
}
@ -68,8 +68,8 @@ interface DataNode<out T : Any> : MetaRepr {
}
}
val <T : Any> DataItem<T>?.node: DataNode<T>? get() = (this as? DataItem.Node<T>)?.value
val <T : Any> DataItem<T>?.data: Data<T>? get() = (this as? DataItem.Leaf<T>)?.value
val <T : Any> DataItem<T>?.node: DataNode<T>? get() = (this as? DataItem.Node<T>)?.node
val <T : Any> DataItem<T>?.data: Data<T>? get() = (this as? DataItem.Leaf<T>)?.data
/**
* Start computation for all goals in data node and return a job for the whole node
@ -77,8 +77,8 @@ val <T : Any> DataItem<T>?.data: Data<T>? get() = (this as? DataItem.Leaf<T>)?.v
fun DataNode<*>.launchAll(scope: CoroutineScope): Job = scope.launch {
items.values.forEach {
when (it) {
is DataItem.Node<*> -> it.value.launchAll(scope)
is DataItem.Leaf<*> -> it.value.start(scope)
is DataItem.Node<*> -> it.node.launchAll(scope)
is DataItem.Leaf<*> -> it.data.start(scope)
}
}
}
@ -98,7 +98,7 @@ fun <T : Any> DataNode<T>.asSequence(): Sequence<Pair<Name, DataItem<T>>> = sequ
items.forEach { (head, item) ->
yield(head.asName() to item)
if (item is DataItem.Node) {
val subSequence = item.value.asSequence()
val subSequence = item.node.asSequence()
.map { (name, data) -> (head.asName() + name) to data }
yieldAll(subSequence)
}
@ -111,9 +111,9 @@ fun <T : Any> DataNode<T>.asSequence(): Sequence<Pair<Name, DataItem<T>>> = sequ
fun <T : Any> DataNode<T>.dataSequence(): Sequence<Pair<Name, Data<T>>> = sequence {
items.forEach { (head, item) ->
when (item) {
is DataItem.Leaf -> yield(head.asName() to item.value)
is DataItem.Leaf -> yield(head.asName() to item.data)
is DataItem.Node -> {
val subSequence = item.value.dataSequence()
val subSequence = item.node.dataSequence()
.map { (name, data) -> (head.asName() + name) to data }
yieldAll(subSequence)
}
@ -188,8 +188,8 @@ class DataTreeBuilder<T : Any>(val type: KClass<out T>) {
operator fun set(name: Name, node: DataNode<T>) = set(name, node.builder())
operator fun set(name: Name, item: DataItem<T>) = when (item) {
is DataItem.Node<T> -> set(name, item.value.builder())
is DataItem.Leaf<T> -> set(name, item.value)
is DataItem.Node<T> -> set(name, item.node.builder())
is DataItem.Leaf<T> -> set(name, item.data)
}
/**
@ -223,6 +223,10 @@ class DataTreeBuilder<T : Any>(val type: KClass<out T>) {
fun meta(block: MetaBuilder.() -> Unit) = meta.apply(block)
fun meta(meta: Meta) {
this.meta = meta.builder()
}
fun build(): DataTree<T> {
val resMap = map.mapValues { (_, value) ->
when (value) {

4
dataforge-data/src/commonMain/kotlin/hep/dataforge/data/dataCast.kt
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@ -28,8 +28,8 @@ expect fun <R : Any> DataNode<*>.canCast(type: KClass<out R>): Boolean
expect fun <R : Any> Data<*>.canCast(type: KClass<out R>): Boolean
fun <R : Any> DataItem<*>.canCast(type: KClass<out R>): Boolean = when (this) {
is DataItem.Node -> value.canCast(type)
is DataItem.Leaf -> value.canCast(type)
is DataItem.Node -> node.canCast(type)
is DataItem.Leaf -> data.canCast(type)
}
/**

4
dataforge-data/src/jvmMain/kotlin/hep/dataforge/data/TypeFilteredDataNode.kt
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@ -14,12 +14,12 @@ class TypeFilteredDataNode<out T : Any>(val origin: DataNode<*>, override val ty
origin.items.mapNotNull { (key, item) ->
when (item) {
is DataItem.Leaf -> {
(item.value.filterIsInstance(type))?.let {
(item.data.filterIsInstance(type))?.let {
key to DataItem.Leaf(it)
}
}
is DataItem.Node -> {
key to DataItem.Node(item.value.filterIsInstance(type))
key to DataItem.Node(item.node.filterIsInstance(type))
}
}
}.associate { it }

4
dataforge-data/src/jvmMain/kotlin/hep/dataforge/data/dataJVM.kt
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@ -42,8 +42,8 @@ fun <R : Any> DataNode<*>.filterIsInstance(type: KClass<out R>): DataNode<R> {
*/
fun <R : Any> DataItem<*>?.filterIsInstance(type: KClass<out R>): DataItem<R>? = when (this) {
null -> null
is DataItem.Node -> DataItem.Node(this.value.filterIsInstance(type))
is DataItem.Leaf -> this.value.filterIsInstance(type)?.let { DataItem.Leaf(it) }
is DataItem.Node -> DataItem.Node(this.node.filterIsInstance(type))
is DataItem.Leaf -> this.data.filterIsInstance(type)?.let { DataItem.Leaf(it) }
}
inline fun <reified R : Any> DataItem<*>?.filterIsInstance(): DataItem<R>? = this@filterIsInstance.filterIsInstance(R::class)

2
dataforge-io/dataforge-io-yaml/build.gradle.kts
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@ -7,6 +7,4 @@ description = "YAML meta IO"
dependencies {
api(project(":dataforge-io"))
api("org.yaml:snakeyaml:1.25")
testImplementation(kotlin("test"))
testImplementation(kotlin("test-junit"))
}

2
dataforge-io/dataforge-io-yaml/src/test/kotlin/hep/dataforge/io/yaml/YamlMetaFormatTest.kt
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@ -6,7 +6,7 @@ import hep.dataforge.meta.Meta
import hep.dataforge.meta.buildMeta
import hep.dataforge.meta.get
import hep.dataforge.meta.seal
import org.junit.Test
import org.junit.jupiter.api.Test
import kotlin.test.assertEquals

8
dataforge-io/src/commonMain/kotlin/hep/dataforge/io/Binary.kt
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@ -10,7 +10,7 @@ interface Binary {
/**
* The size of binary in bytes. [ULong.MAX_VALUE] if size is not defined and input should be read until its end is reached
*/
val size: ULong
val size: ULong get() = ULong.MAX_VALUE
/**
* Read continuous [Input] from this binary stating from the beginning.
@ -41,7 +41,11 @@ interface RandomAccessBinary : Binary {
}
fun Binary.toBytes(): ByteArray = read {
this.readBytes()
readBytes()
}
fun Binary.contentToString(): String = read {
readText()
}
@ExperimentalUnsignedTypes

1
dataforge-io/src/commonMain/kotlin/hep/dataforge/io/Envelope.kt
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@ -83,4 +83,3 @@ fun Envelope.withMetaLayers(vararg layers: Meta): Envelope {
else -> ProxyEnvelope(this, *layers)
}
}

8
dataforge-io/src/commonMain/kotlin/hep/dataforge/io/EnvelopeFormat.kt
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@ -23,11 +23,15 @@ interface EnvelopeFormat : IOFormat<Envelope> {
fun Input.readPartial(): PartialEnvelope
fun Output.writeEnvelope(envelope: Envelope, metaFormatFactory: MetaFormatFactory, formatMeta: Meta = EmptyMeta)
fun Output.writeEnvelope(
envelope: Envelope,
metaFormatFactory: MetaFormatFactory = defaultMetaFormat,
formatMeta: Meta = EmptyMeta
)
override fun Input.readObject(): Envelope
override fun Output.writeObject(obj: Envelope): Unit = writeEnvelope(obj, defaultMetaFormat)
override fun Output.writeObject(obj: Envelope): Unit = writeEnvelope(obj)
}
@Type(ENVELOPE_FORMAT_TYPE)

35
dataforge-io/src/commonMain/kotlin/hep/dataforge/io/EnvelopeParts.kt
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@ -3,6 +3,7 @@ package hep.dataforge.io
import hep.dataforge.context.Global
import hep.dataforge.io.EnvelopeParts.FORMAT_META_KEY
import hep.dataforge.io.EnvelopeParts.FORMAT_NAME_KEY
import hep.dataforge.io.EnvelopeParts.INDEX_KEY
import hep.dataforge.io.EnvelopeParts.MULTIPART_DATA_TYPE
import hep.dataforge.io.EnvelopeParts.SIZE_KEY
import hep.dataforge.meta.*
@ -13,6 +14,7 @@ import hep.dataforge.names.toName
object EnvelopeParts {
val MULTIPART_KEY = "multipart".asName()
val SIZE_KEY = Envelope.ENVELOPE_NODE_KEY + MULTIPART_KEY + "size"
val INDEX_KEY = Envelope.ENVELOPE_NODE_KEY + MULTIPART_KEY + "index"
val FORMAT_NAME_KEY = Envelope.ENVELOPE_NODE_KEY + MULTIPART_KEY + "format"
val FORMAT_META_KEY = Envelope.ENVELOPE_NODE_KEY + MULTIPART_KEY + "meta"
@ -37,8 +39,37 @@ fun EnvelopeBuilder.multipart(format: EnvelopeFormatFactory, envelopes: Collecti
}
}
fun EnvelopeBuilder.multipart(formatFactory: EnvelopeFormatFactory, builder: suspend SequenceScope<Envelope>.() -> Unit) =
multipart(formatFactory, sequence(builder).toList())
/**
* Create a multipart partition in the envelope adding additional name-index mapping in meta
*/
@DFExperimental
fun EnvelopeBuilder.multipart(format: EnvelopeFormatFactory, envelopes: Map<String, Envelope>) {
dataType = MULTIPART_DATA_TYPE
meta {
SIZE_KEY put envelopes.size
FORMAT_NAME_KEY put format.name.toString()
}
data {
format.run {
var counter = 0
envelopes.forEach {(key, envelope)->
writeObject(envelope)
meta{
append(INDEX_KEY, buildMeta {
"key" put key
"index" put counter
})
}
counter++
}
}
}
}
fun EnvelopeBuilder.multipart(
formatFactory: EnvelopeFormatFactory,
builder: suspend SequenceScope<Envelope>.() -> Unit
) = multipart(formatFactory, sequence(builder).toList())
/**
* If given envelope supports multipart data, return a sequence of those parts (could be empty). Otherwise return null.

4
dataforge-io/src/commonMain/kotlin/hep/dataforge/io/IOFormat.kt
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@ -79,8 +79,10 @@ inline fun buildPacketWithoutPool(headerSizeHint: Int = 0, block: BytePacketBuil
}
fun <T : Any> IOFormat<T>.writePacket(obj: T): ByteReadPacket = buildPacket { writeObject(obj) }
//TODO Double buffer copy. fix all that with IO-2
@Deprecated("Not to be used outside tests due to double buffer write")
fun <T : Any> IOFormat<T>.writeBytes(obj: T): ByteArray = buildPacket { writeObject(obj) }.readBytes()
@Deprecated("Not to be used outside tests due to double buffer write")
fun <T : Any> IOFormat<T>.readBytes(array: ByteArray): T = buildPacket { writeFully(array) }.readObject()
object DoubleIOFormat : IOFormat<Double>, IOFormatFactory<Double> {

4
dataforge-io/src/commonMain/kotlin/hep/dataforge/io/IOPlugin.kt
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@ -20,7 +20,7 @@ class IOPlugin(meta: Meta) : AbstractPlugin(meta) {
metaFormatFactories.find { it.key == key }?.invoke(meta)
fun metaFormat(name: String, meta: Meta = EmptyMeta): MetaFormat? =
metaFormatFactories.find { it.name.toString() == name }?.invoke(meta)
metaFormatFactories.find { it.name.last().toString() == name }?.invoke(meta)
val envelopeFormatFactories by lazy {
context.content<EnvelopeFormatFactory>(ENVELOPE_FORMAT_TYPE).values
@ -52,7 +52,7 @@ class IOPlugin(meta: Meta) : AbstractPlugin(meta) {
companion object : PluginFactory<IOPlugin> {
val defaultMetaFormats: List<MetaFormatFactory> = listOf(JsonMetaFormat, BinaryMetaFormat)
val defaultEnvelopeFormats = listOf(TaggedEnvelopeFormat)
val defaultEnvelopeFormats = listOf(TaggedEnvelopeFormat, TaglessEnvelopeFormat)
override val tag: PluginTag = PluginTag("io", group = PluginTag.DATAFORGE_GROUP)

6
dataforge-io/src/commonMain/kotlin/hep/dataforge/io/TaggedEnvelopeFormat.kt
View File

@ -38,15 +38,15 @@ class TaggedEnvelopeFormat(
override fun Output.writeEnvelope(envelope: Envelope, metaFormatFactory: MetaFormatFactory, formatMeta: Meta) {
val metaFormat = metaFormatFactory.invoke(formatMeta, io.context)
val metaBytes = metaFormat.writeBytes(envelope.meta)
val metaBytes = metaFormat.writePacket(envelope.meta)
val actualSize: ULong = if (envelope.data == null) {
0u
} else {
envelope.data?.size ?: ULong.MAX_VALUE
}
val tag = Tag(metaFormatFactory.key, metaBytes.size.toUInt() + 2u, actualSize)
val tag = Tag(metaFormatFactory.key, metaBytes.remaining.toUInt() + 2u, actualSize)
writePacket(tag.toBytes())
writeFully(metaBytes)
writePacket(metaBytes)
writeText("\r\n")
envelope.data?.read { copyTo(this@writeEnvelope) }
flush()

8
dataforge-io/src/commonMain/kotlin/hep/dataforge/io/TaglessEnvelopeFormat.kt
View File

@ -37,10 +37,10 @@ class TaglessEnvelopeFormat(
//Printing meta
if (!envelope.meta.isEmpty()) {
val metaBytes = metaFormat.writeBytes(envelope.meta)
writeProperty(META_LENGTH_PROPERTY, metaBytes.size)
val metaBytes = metaFormat.writePacket(envelope.meta)
writeProperty(META_LENGTH_PROPERTY, metaBytes.remaining)
writeText(metaStart + "\r\n")
writeFully(metaBytes)
writePacket(metaBytes)
writeText("\r\n")
}
@ -192,7 +192,7 @@ class TaglessEnvelopeFormat(
return try {
val buffer = ByteArray(TAGLESS_ENVELOPE_HEADER.length)
input.readFully(buffer)
return if (buffer.toString() == TAGLESS_ENVELOPE_HEADER) {
return if (String(buffer) == TAGLESS_ENVELOPE_HEADER) {
TaglessEnvelopeFormat(io)
} else {
null

132
dataforge-io/src/jvmMain/kotlin/hep/dataforge/io/fileIO.kt
View File

@ -4,6 +4,9 @@ import hep.dataforge.descriptors.NodeDescriptor
import hep.dataforge.meta.DFExperimental
import hep.dataforge.meta.EmptyMeta
import hep.dataforge.meta.Meta
import hep.dataforge.meta.isEmpty
import kotlinx.io.core.Output
import kotlinx.io.core.copyTo
import kotlinx.io.nio.asInput
import kotlinx.io.nio.asOutput
import java.nio.file.Files
@ -12,10 +15,15 @@ import java.nio.file.StandardOpenOption
import kotlin.reflect.full.isSuperclassOf
import kotlin.streams.asSequence
/**
* Resolve IOFormat based on type
*/
@DFExperimental
inline fun <reified T : Any> IOPlugin.resolveIOFormat(): IOFormat<T>? {
return ioFormats.values.find { it.type.isSuperclassOf(T::class) } as IOFormat<T>?
}
/**
* Read file containing meta using given [formatOverride] or file extension to infer meta type.
* If [path] is a directory search for file starting with `meta` in it
@ -43,11 +51,12 @@ fun IOPlugin.readMetaFile(path: Path, formatOverride: MetaFormat? = null, descri
*/
fun IOPlugin.writeMetaFile(
path: Path,
meta: Meta,
metaFormat: MetaFormatFactory = JsonMetaFormat,
descriptor: NodeDescriptor? = null
) {
val actualPath = if (Files.isDirectory(path)) {
path.resolve(metaFormat.name.toString())
path.resolve("@" + metaFormat.name.toString())
} else {
path
}
@ -58,6 +67,28 @@ fun IOPlugin.writeMetaFile(
}
}
/**
* Return inferred [EnvelopeFormat] if only one format could read given file. If no format accepts file, return null. If
* multiple formats accepts file, throw an error.
*/
fun IOPlugin.peekBinaryFormat(path: Path): EnvelopeFormat? {
val binary = path.asBinary()
val formats = envelopeFormatFactories.mapNotNull { factory ->
binary.read {
factory.peekFormat(this@peekBinaryFormat, this@read)
}
}
return when (formats.size) {
0 -> null
1 -> formats.first()
else -> error("Envelope format binary recognition clash")
}
}
val IOPlugin.Companion.META_FILE_NAME: String get() = "@meta"
val IOPlugin.Companion.DATA_FILE_NAME: String get() = "@data"
/**
* Read and envelope from file if the file exists, return null if file does not exist.
*
@ -72,13 +103,17 @@ fun IOPlugin.writeMetaFile(
* Return null otherwise.
*/
@DFExperimental
fun IOPlugin.readEnvelopeFile(path: Path, readNonEnvelopes: Boolean = false): Envelope? {
fun IOPlugin.readEnvelopeFile(
path: Path,
readNonEnvelopes: Boolean = false,
formatPeeker: IOPlugin.(Path) -> EnvelopeFormat? = IOPlugin::peekBinaryFormat
): Envelope? {
if (!Files.exists(path)) return null
//read two-files directory
if (Files.isDirectory(path)) {
val metaFile = Files.list(path).asSequence()
.singleOrNull { it.fileName.toString().startsWith("meta") }
.singleOrNull { it.fileName.toString().startsWith(IOPlugin.META_FILE_NAME) }
val meta = if (metaFile == null) {
EmptyMeta
@ -86,7 +121,7 @@ fun IOPlugin.readEnvelopeFile(path: Path, readNonEnvelopes: Boolean = false): En
readMetaFile(metaFile)
}
val dataFile = path.resolve("data")
val dataFile = path.resolve(IOPlugin.DATA_FILE_NAME)
val data: Binary? = if (Files.exists(dataFile)) {
dataFile.asBinary()
@ -97,41 +132,76 @@ fun IOPlugin.readEnvelopeFile(path: Path, readNonEnvelopes: Boolean = false): En
return SimpleEnvelope(meta, data)
}
val binary = path.asBinary()
return formatPeeker(path)?.let { format ->
FileEnvelope(path, format)
} ?: if (readNonEnvelopes) { // if no format accepts file, read it as binary
SimpleEnvelope(Meta.empty, path.asBinary())
} else null
}
val formats = envelopeFormatFactories.mapNotNull { factory ->
binary.read {
factory.peekFormat(this@readEnvelopeFile, this@read)
}
}
return when (formats.size) {
0 -> if (readNonEnvelopes) {
SimpleEnvelope(Meta.empty, binary)
} else {
null
}
1 -> formats.first().run {
binary.read {
readObject()
}
}
else -> error("Envelope format file recognition clash")
private fun Path.useOutput(consumer: Output.() -> Unit) {
//TODO forbid rewrite?
Files.newByteChannel(
this,
StandardOpenOption.CREATE, StandardOpenOption.WRITE, StandardOpenOption.TRUNCATE_EXISTING
).asOutput().use {
it.consumer()
it.flush()
}
}
/**
* Write a binary into file. Throws an error if file already exists
*/
fun <T : Any> IOFormat<T>.writeToFile(path: Path, obj: T) {
path.useOutput {
writeObject(obj)
flush()
}
}
/**
* Write envelope file to given [path] using [envelopeFormat] and optional [metaFormat]
*/
@DFExperimental
fun IOPlugin.writeEnvelopeFile(
path: Path,
envelope: Envelope,
format: EnvelopeFormat = TaggedEnvelopeFormat
envelopeFormat: EnvelopeFormat = TaggedEnvelopeFormat,
metaFormat: MetaFormatFactory? = null
) {
val output = Files.newByteChannel(
path,
StandardOpenOption.WRITE,
StandardOpenOption.CREATE,
StandardOpenOption.TRUNCATE_EXISTING
).asOutput()
path.useOutput {
with(envelopeFormat) {
writeEnvelope(envelope, metaFormat ?: envelopeFormat.defaultMetaFormat)
}
}
}
with(format) {
output.writeObject(envelope)
/**
* Write separate meta and data files to given directory [path]
*/
@DFExperimental
fun IOPlugin.writeEnvelopeDirectory(
path: Path,
envelope: Envelope,
metaFormat: MetaFormatFactory = JsonMetaFormat
) {
if (!Files.exists(path)) {
Files.createDirectories(path)
}
if (!Files.isDirectory(path)) {
error("Can't write envelope directory to file")
}
if (!envelope.meta.isEmpty()) {
writeMetaFile(path, envelope.meta, metaFormat)
}
val dataFile = path.resolve(IOPlugin.DATA_FILE_NAME)
dataFile.useOutput {
envelope.data?.read {
val copied = copyTo(this@useOutput)
if (envelope.data?.size != ULong.MAX_VALUE && copied != envelope.data?.size?.toLong()) {
error("The number of copied bytes does not equal data size")
}
}
}
}

23
dataforge-io/src/jvmTest/kotlin/hep/dataforge/io/FileEnvelopeTest.kt
View File

@ -26,11 +26,24 @@ class FileEnvelopeTest {
@Test
fun testFileWriteRead() {
val tmpPath = Files.createTempFile("dataforge_test", ".df")
Global.io.writeEnvelopeFile(tmpPath,envelope)
println(tmpPath.toUri())
val restored: Envelope = Global.io.readEnvelopeFile(tmpPath)!!
assertTrue { envelope.contentEquals(restored) }
Global.io.run {
val tmpPath = Files.createTempFile("dataforge_test", ".df")
writeEnvelopeFile(tmpPath, envelope)
println(tmpPath.toUri())
val restored: Envelope = readEnvelopeFile(tmpPath)!!
assertTrue { envelope.contentEquals(restored) }
}
}
@Test
fun testFileWriteReadTagless() {
Global.io.run {
val tmpPath = Files.createTempFile("dataforge_test_tagless", ".df")
writeEnvelopeFile(tmpPath, envelope, envelopeFormat = TaglessEnvelopeFormat)
println(tmpPath.toUri())
val restored: Envelope = readEnvelopeFile(tmpPath)!!
assertTrue { envelope.contentEquals(restored) }
}
}
@Test

10
dataforge-io/src/jvmTest/kotlin/hep/dataforge/io/tcp/EnvelopeServerTest.kt
View File

@ -7,9 +7,9 @@ import hep.dataforge.io.TaggedEnvelopeFormat
import hep.dataforge.io.writeBytes
import kotlinx.coroutines.GlobalScope
import kotlinx.coroutines.runBlocking
import org.junit.AfterClass
import org.junit.BeforeClass
import org.junit.Test
import org.junit.jupiter.api.AfterAll
import org.junit.jupiter.api.BeforeAll
import kotlin.test.Test
import kotlin.test.assertEquals
import kotlin.time.ExperimentalTime
@ -30,13 +30,13 @@ class EnvelopeServerTest {
@JvmStatic
val echoEnvelopeServer = EnvelopeServer(Global, 7778, EchoResponder, GlobalScope)
@BeforeClass
@BeforeAll
@JvmStatic
fun start() {
echoEnvelopeServer.start()
}
@AfterClass
@AfterAll
@JvmStatic
fun close() {
echoEnvelopeServer.stop()

2
dataforge-scripting/build.gradle.kts
View File

@ -19,8 +19,6 @@ kotlin {
}
val jvmTest by getting {
dependencies {
implementation(kotlin("test"))
implementation(kotlin("test-junit"))
implementation("ch.qos.logback:logback-classic:1.2.3")
}
}

2
dataforge-scripting/src/jvmTest/kotlin/hep/dataforge/scripting/BuildersKtTest.kt
View File

@ -6,7 +6,7 @@ import hep.dataforge.meta.int
import hep.dataforge.workspace.SimpleWorkspaceBuilder
import hep.dataforge.workspace.context
import hep.dataforge.workspace.target
import org.junit.Test
import kotlin.test.Test
import kotlin.test.assertEquals

14
dataforge-workspace/src/commonMain/kotlin/hep/dataforge/workspace/dataUtils.kt
View File

@ -1,14 +0,0 @@
package hep.dataforge.workspace
import hep.dataforge.data.Data
import hep.dataforge.io.Envelope
import hep.dataforge.io.IOFormat
import hep.dataforge.io.readWith
import kotlin.reflect.KClass
/**
* Convert an [Envelope] to a data via given format. The actual parsing is done lazily.
*/
fun <T : Any> Envelope.toData(type: KClass<out T>, format: IOFormat<T>): Data<T> = Data(type, meta) {
data?.readWith(format) ?: error("Can't convert envelope without data to Data")
}

33
dataforge-workspace/src/commonMain/kotlin/hep/dataforge/workspace/envelopeData.kt Normal file
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@ -0,0 +1,33 @@
package hep.dataforge.workspace
import hep.dataforge.data.Data
import hep.dataforge.data.await
import hep.dataforge.io.*
import kotlinx.coroutines.coroutineScope
import kotlinx.io.core.Input
import kotlinx.io.core.buildPacket
import kotlin.reflect.KClass
/**
* Convert an [Envelope] to a data via given format. The actual parsing is done lazily.
*/
fun <T : Any> Envelope.toData(type: KClass<out T>, format: IOFormat<T>): Data<T> = Data(type, meta) {
data?.readWith(format) ?: error("Can't convert envelope without data to Data")
}
suspend fun <T : Any> Data<T>.toEnvelope(format: IOFormat<T>): Envelope {
val obj = coroutineScope {
await(this)
}
val binary = object : Binary {
override fun <R> read(block: Input.() -> R): R {
//TODO optimize away additional copy by creating inputs that reads directly from output
val packet = buildPacket {
format.run { writeObject(obj) }
}
return packet.block()
}
}
return SimpleEnvelope(meta, binary)
}

162
dataforge-workspace/src/jvmMain/kotlin/hep/dataforge/workspace/fileData.kt
View File

@ -1,17 +1,27 @@
package hep.dataforge.workspace
//import jdk.nio.zipfs.ZipFileSystemProvider
import hep.dataforge.data.*
import hep.dataforge.io.Envelope
import hep.dataforge.io.IOFormat
import hep.dataforge.io.IOPlugin
import hep.dataforge.io.readEnvelopeFile
import hep.dataforge.meta.Meta
import hep.dataforge.meta.get
import hep.dataforge.meta.string
import hep.dataforge.io.*
import hep.dataforge.meta.*
import kotlinx.coroutines.Dispatchers
import kotlinx.coroutines.withContext
import java.nio.file.FileSystem
import java.nio.file.Files
import java.nio.file.Path
import java.nio.file.StandardCopyOption
import java.nio.file.spi.FileSystemProvider
import kotlin.reflect.KClass
typealias FileFormatResolver<T> = (Path, Meta) -> IOFormat<T>
//private val zipFSProvider = ZipFileSystemProvider()
private fun newZFS(path: Path): FileSystem {
val fsProvider = FileSystemProvider.installedProviders().find { it.scheme == "jar" }
?: error("Zip file system provider not found")
return fsProvider.newFileSystem(path, mapOf("create" to "true"))
}
/**
* Read data with supported envelope format and binary format. If envelope format is null, then read binary directly from file.
@ -22,62 +32,152 @@ import kotlin.reflect.KClass
* @param metaFile the relative file for optional meta override
* @param metaFileFormat the meta format for override
*/
@DFExperimental
fun <T : Any> IOPlugin.readDataFile(
path: Path,
type: KClass<out T>,
formatResolver: (Meta) -> IOFormat<T>
formatResolver: FileFormatResolver<T>
): Data<T> {
val envelope = readEnvelopeFile(path, true) ?: error("Can't read data from $path")
val format = formatResolver(envelope.meta)
val format = formatResolver(path, envelope.meta)
return envelope.toData(type, format)
}
//TODO wants multi-receiver
@DFExperimental
inline fun <reified T : Any> IOPlugin.readDataFile(path: Path): Data<T> =
readDataFile(path, T::class) { _, _ ->
resolveIOFormat<T>() ?: error("Can't resolve IO format for ${T::class}")
}
/**
* Add file/directory-based data tree item
*/
@DFExperimental
fun <T : Any> DataTreeBuilder<T>.file(
plugin: IOPlugin,
path: Path,
formatResolver: (Meta) -> IOFormat<T>
formatResolver: FileFormatResolver<T>
) {
plugin.run {
val data = readDataFile(path, type, formatResolver)
val name = data.meta[Envelope.ENVELOPE_NAME_KEY].string
?: path.fileName.toString().replace(".df", "")
datum(name, data)
//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("@") }) {
plugin.run {
val data = readDataFile(path, type, formatResolver)
val name = data.meta[Envelope.ENVELOPE_NAME_KEY].string
?: path.fileName.toString().replace(".df", "")
datum(name, data)
}
} else {
//otherwise, read as directory
plugin.run {
val data = readDataDirectory(path, type, formatResolver)
val name = data.meta[Envelope.ENVELOPE_NAME_KEY].string
?: path.fileName.toString().replace(".df", "")
node(name, data)
}
}
}
/**
* Read the directory as a data node
* Read the directory as a data node. If [path] is a zip archive, read it as directory
*/
@DFExperimental
fun <T : Any> IOPlugin.readDataDirectory(
path: Path,
type: KClass<out T>,
formatResolver: (Meta) -> IOFormat<T>
formatResolver: FileFormatResolver<T>
): DataNode<T> {
if (!Files.isDirectory(path)) error("Provided path $this is not a directory")
//read zipped data node
if (path.fileName != null && path.fileName.toString().endsWith(".zip")) {
//Using explicit Zip file system to avoid bizarre compatibility bugs
val fs = newZFS(path)
return readDataDirectory(fs.rootDirectories.first(), type, formatResolver)
}
if (!Files.isDirectory(path)) error("Provided path $path is not a directory")
return DataNode(type) {
Files.list(path).forEach { path ->
if (!path.fileName.toString().endsWith(".meta")) {
val fileName = path.fileName.toString()
if (fileName.startsWith(IOPlugin.META_FILE_NAME)) {
meta(readMetaFile(path))
} else if (!fileName.startsWith("@")) {
file(this@readDataDirectory, path, formatResolver)
}
}
}
}
fun <T : Any> DataTreeBuilder<T>.directory(
plugin: IOPlugin,
@DFExperimental
inline fun <reified T : Any> IOPlugin.readDataDirectory(path: Path): DataNode<T> =
readDataDirectory(path, T::class) { _, _ ->
resolveIOFormat<T>() ?: error("Can't resolve IO format for ${T::class}")
}
/**
* Write data tree to existing directory or create a new one using default [java.nio.file.FileSystem] provider
*/
@DFExperimental
suspend fun <T : Any> IOPlugin.writeDataDirectory(
path: Path,
formatResolver: (Meta) -> IOFormat<T>
node: DataNode<T>,
format: IOFormat<T>,
envelopeFormat: EnvelopeFormat? = null,
metaFormat: MetaFormatFactory? = null
) {
plugin.run {
val data = readDataDirectory(path, type, formatResolver)
val name = data.meta[Envelope.ENVELOPE_NAME_KEY].string
?: path.fileName.toString().replace(".df", "")
node(name, data)
withContext(Dispatchers.IO) {
if (!Files.exists(path)) {
Files.createDirectories(path)
} else if (!Files.isDirectory(path)) {
error("Can't write a node into file")
}
node.items.forEach { (token, item) ->
val childPath = path.resolve(token.toString())
when (item) {
is DataItem.Node -> {
writeDataDirectory(childPath, item.node, format, envelopeFormat)
}
is DataItem.Leaf -> {
val envelope = item.data.toEnvelope(format)
if (envelopeFormat != null) {
writeEnvelopeFile(childPath, envelope, envelopeFormat, metaFormat)
} else {
writeEnvelopeDirectory(childPath, envelope, metaFormat ?: JsonMetaFormat)
}
}
}
}
if (!node.meta.isEmpty()) {
writeMetaFile(path, node.meta, metaFormat ?: JsonMetaFormat)
}
}
}
suspend fun <T : Any> IOPlugin.writeZip(
path: Path,
node: DataNode<T>,
format: IOFormat<T>,
envelopeFormat: EnvelopeFormat? = null,
metaFormat: MetaFormatFactory? = null
) {
withContext(Dispatchers.IO) {
val actualFile = if (path.toString().endsWith(".zip")) {
path
} else {
path.resolveSibling(path.fileName.toString() + ".zip")
}
if (Files.exists(actualFile) && Files.size(path) == 0.toLong()) {
Files.delete(path)
}
//Files.createFile(actualFile)
newZFS(actualFile).use { zipfs ->
val internalTargetPath = zipfs.getPath("/")
Files.createDirectories(internalTargetPath)
val tmp = Files.createTempDirectory("df_zip")
writeDataDirectory(tmp, node, format, envelopeFormat, metaFormat)
Files.list(tmp).forEach { sourcePath ->
val targetPath = sourcePath.fileName.toString()
val internalTargetPath = internalTargetPath.resolve(targetPath)
Files.copy(sourcePath, internalTargetPath, StandardCopyOption.REPLACE_EXISTING)
}
}
}
}

2
dataforge-workspace/src/jvmTest/kotlin/hep/dataforge/workspace/DataPropagationTest.kt
View File

@ -6,8 +6,8 @@ import hep.dataforge.context.PluginTag
import hep.dataforge.data.*
import hep.dataforge.meta.Meta
import hep.dataforge.names.asName
import org.junit.Test
import kotlin.reflect.KClass
import kotlin.test.Test
import kotlin.test.assertEquals

72
dataforge-workspace/src/jvmTest/kotlin/hep/dataforge/workspace/FileDataTest.kt Normal file
View File

@ -0,0 +1,72 @@
package hep.dataforge.workspace
import hep.dataforge.context.Global
import hep.dataforge.data.*
import hep.dataforge.io.IOFormat
import hep.dataforge.io.io
import hep.dataforge.meta.DFExperimental
import kotlinx.coroutines.runBlocking
import kotlinx.io.core.Input
import kotlinx.io.core.Output
import kotlinx.io.core.readText
import kotlinx.io.core.writeText
import java.nio.file.Files
import kotlin.test.Ignore
import kotlin.test.Test
import kotlin.test.assertEquals
class FileDataTest {
val dataNode = DataNode<String> {
node("dir") {
static("a", "Some string") {
"content" put "Some string"
}
}
static("b", "root data")
meta {
"content" put "This is root meta node"
}
}
object StringIOFormat : IOFormat<String> {
override fun Output.writeObject(obj: String) {
writeText(obj)
}
override fun Input.readObject(): String {
return readText()
}
}
@Test
@DFExperimental
fun testDataWriteRead() {
Global.io.run {
val dir = Files.createTempDirectory("df_data_node")
runBlocking {
writeDataDirectory(dir, dataNode, StringIOFormat)
}
println(dir.toUri().toString())
val reconstructed = readDataDirectory(dir, String::class) { _, _ -> StringIOFormat }
assertEquals(dataNode["dir.a"]?.meta, reconstructed["dir.a"]?.meta)
assertEquals(dataNode["b"]?.data?.get(), reconstructed["b"]?.data?.get())
}
}
@Test
@Ignore
fun testZipWriteRead() {
Global.io.run {
val zip = Files.createTempFile("df_data_node", ".zip")
runBlocking {
writeZip(zip, dataNode, StringIOFormat)
}
println(zip.toUri().toString())
val reconstructed = readDataDirectory(zip, String::class) { _, _ -> StringIOFormat }
assertEquals(dataNode["dir.a"]?.meta, reconstructed["dir.a"]?.meta)
assertEquals(dataNode["b"]?.data?.get(), reconstructed["b"]?.data?.get())
}
}
}

2
dataforge-workspace/src/jvmTest/kotlin/hep/dataforge/workspace/SimpleWorkspaceTest.kt
View File

@ -7,7 +7,7 @@ import hep.dataforge.meta.builder
import hep.dataforge.meta.get
import hep.dataforge.meta.int
import hep.dataforge.names.plus
import org.junit.Test
import kotlin.test.Test
import kotlin.test.assertEquals
import kotlin.test.assertTrue

BIN
gradle/wrapper/gradle-wrapper.jar vendored
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Binary file not shown.

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-5.6.2-bin.zip
distributionUrl=https\://services.gradle.org/distributions/gradle-6.0-bin.zip
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists

29
gradlew vendored Normal file → Executable file
View File

@ -154,19 +154,19 @@ if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
else
eval `echo args$i`="\"$arg\""
fi
i=$((i+1))
i=`expr $i + 1`
done
case $i in
(0) set -- ;;
(1) set -- "$args0" ;;
(2) set -- "$args0" "$args1" ;;
(3) set -- "$args0" "$args1" "$args2" ;;
(4) set -- "$args0" "$args1" "$args2" "$args3" ;;
(5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
(6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
(7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
(8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
(9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
0) set -- ;;
1) set -- "$args0" ;;
2) set -- "$args0" "$args1" ;;
3) set -- "$args0" "$args1" "$args2" ;;
4) set -- "$args0" "$args1" "$args2" "$args3" ;;
5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
esac
fi
@ -175,14 +175,9 @@ save () {
for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
echo " "
}
APP_ARGS=$(save "$@")
APP_ARGS=`save "$@"`
# Collect all arguments for the java command, following the shell quoting and substitution rules
eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
cd "$(dirname "$0")"
fi
exec "$JAVACMD" "$@"