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[WIP] change data structure

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This commit is contained in:
Alexander Nozik 2024-01-29 22:10:06 +03:00
parent 5fec0518d4
commit 90999f424f
30 changed files with 316 additions and 398 deletions
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8
dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/actions/Action.kt
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@ -10,7 +10,7 @@ import space.kscience.dataforge.misc.DFExperimental
/**
* A simple data transformation on a data node. Actions should avoid doing actual dependency evaluation in [execute].
*/
public fun interface Action<T : Any, R : Any> {
public fun interface Action<T, R> {
/**
* Transform the data in the node, producing a new node. By default, it is assumed that all calculations are lazy
@ -24,7 +24,7 @@ public fun interface Action<T : Any, R : Any> {
/**
* A convenience method to transform data using given [action]
*/
public fun <T : Any, R : Any> DataTree<T>.transform(
public fun <T, R> DataTree<T>.transform(
action: Action<T, R>,
scope: CoroutineScope,
meta: Meta = Meta.EMPTY,
@ -33,11 +33,11 @@ public fun <T : Any, R : Any> DataTree<T>.transform(
/**
* Action composition. The result is terminal if one of its parts is terminal
*/
public infix fun <T : Any, I : Any, R : Any> Action<T, I>.then(action: Action<I, R>): Action<T, R> =
public infix fun <T , I, R> Action<T, I>.then(action: Action<I, R>): Action<T, R> =
Action { scope, dataSet, meta -> action.execute(scope, this@then.execute(scope, dataSet, meta), meta) }
@DFExperimental
public suspend operator fun <T : Any, R : Any> Action<T, R>.invoke(
public suspend operator fun <T, R> Action<T, R>.invoke(
dataSet: DataTree<T>,
meta: Meta = Meta.EMPTY,
): DataTree<R> = coroutineScope { execute(this, dataSet, meta) }

2
dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/actions/MapAction.kt
View File

@ -79,7 +79,7 @@ internal class MapAction<T : Any, R : Any>(
builder.result(env, data.await())
}
//setting the data node
emit(newName, newData)
data(newName, newData)
}
override fun DataSink<R>.generate(data: DataTree<T>, meta: Meta) {

2
dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/actions/ReduceAction.kt
View File

@ -103,7 +103,7 @@ internal class ReduceAction<T : Any, R : Any>(
meta = groupMeta
) { group.result.invoke(env, it) }
emit(env.name, res)
data(env.name, res)
}
}
}

2
dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/actions/SplitAction.kt
View File

@ -64,7 +64,7 @@ internal class SplitAction<T : Any, R : Any>(
).apply(rule)
//data.map<R>(outputType, meta = env.meta) { env.result(it) }.named(fragmentName)
emit(
data(
fragmentName,
@Suppress("OPT_IN_USAGE") Data(outputType, meta = env.meta, dependencies = listOf(data)) {
env.result(data.await())

2
dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/data/Data.kt
View File

@ -15,7 +15,7 @@ import kotlin.reflect.typeOf
* A data element characterized by its meta
*/
@DfType(Data.TYPE)
public interface Data<T> : Goal<T>, MetaRepr {
public interface Data<out T> : Goal<T>, MetaRepr {
/**
* Type marker for the data. The type is known before the calculation takes place so it could be checked.
*/

36
dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/data/DataSource.kt
View File

@ -12,7 +12,7 @@ import kotlin.reflect.typeOf
/**
* A generic data provider
*/
public interface DataSource<T> {
public interface DataSource<out T> {
/**
* The minimal common ancestor to all data in the node
@ -28,7 +28,7 @@ public interface DataSource<T> {
/**
* A data provider with possible dynamic updates
*/
public interface ObservableDataSource<T> : DataSource<T> {
public interface ObservableDataSource<out T> : DataSource<T> {
/**
* Flow updates made to the data
@ -39,7 +39,7 @@ public interface ObservableDataSource<T> : DataSource<T> {
/**
* A tree like structure for data holding
*/
public interface GenericDataTree<T, out TR : GenericDataTree<T, TR>> : DataSource<T> {
public interface GenericDataTree<out T, out TR : GenericDataTree<T, TR>> : DataSource<T> {
public val self: TR
public val data: Data<T>?
@ -66,7 +66,12 @@ public interface GenericDataTree<T, out TR : GenericDataTree<T, TR>> : DataSourc
}
}
public typealias DataTree<T> = GenericDataTree<T, *>
public typealias DataTree<T> = GenericDataTree<T, GenericDataTree<T,*>>
/**
* Return a single data in this tree. Throw error if it is not single.
*/
public fun <T> DataTree<T>.single(): NamedData<T> = asSequence().single()
/**
* An alias for easier access to tree values
@ -79,7 +84,7 @@ public operator fun <T> DataTree<T>.get(name: String): Data<T>? = read(name.pars
* Return a sequence of all data items in this tree.
* This method does not take updates into account.
*/
public fun <T> GenericDataTree<T, DataTree<T>>.asSequence(
public fun <T> DataTree<T>.asSequence(
namePrefix: Name = Name.EMPTY,
): Sequence<NamedData<T>> = sequence {
data?.let { yield(it.named(Name.EMPTY)) }
@ -100,6 +105,9 @@ public tailrec fun <T, TR : GenericDataTree<T, TR>> GenericDataTree<T, TR>.branc
else -> items[name.first()]?.branch(name.cutFirst())
}
public fun <T, TR : GenericDataTree<T, TR>> GenericDataTree<T, TR>.branch(name: String): TR? =
branch(name.parseAsName())
public fun GenericDataTree<*, *>.isEmpty(): Boolean = data == null && items.isEmpty()
@PublishedApi
@ -113,7 +121,7 @@ internal class FlatDataTree<T>(
override val items: Map<NameToken, FlatDataTree<T>>
get() = dataSet.keys
.filter { it.startsWith(prefix) && it.length > prefix.length }
.map { it.tokens[prefix.length + 1] }
.map { it.tokens[prefix.length] }
.associateWith { FlatDataTree(dataType, dataSet, prefix + it) }
override fun read(name: Name): Data<T>? = dataSet[prefix + name]
@ -133,20 +141,20 @@ internal fun <T> Sequence<NamedData<T>>.toTree(type: KType): DataTree<T> =
public inline fun <reified T> Sequence<NamedData<T>>.toTree(): DataTree<T> =
FlatDataTree(typeOf<T>(), associate { it.name to it.data }, Name.EMPTY)
public interface GenericObservableDataTree<T, TR : GenericObservableDataTree<T, TR>> : GenericDataTree<T, TR>,
public interface GenericObservableDataTree<out T, out TR : GenericObservableDataTree<T, TR>> : GenericDataTree<T, TR>,
ObservableDataSource<T>
public typealias ObservableDataTree<T> = GenericObservableDataTree<T, *>
public typealias ObservableDataTree<T> = GenericObservableDataTree<T, GenericObservableDataTree<T, *>>
public fun <T> DataTree<T>.updates(): Flow<NamedData<T>> = if (this is ObservableDataTree<T>) updates() else emptyFlow()
public fun <T> DataTree<T>.updates(): Flow<NamedData<T>> = if (this is GenericObservableDataTree<T,*>) updates() else emptyFlow()
public fun interface DataSink<T> {
public fun emit(name: Name, data: Data<T>?)
public fun interface DataSink<in T> {
public fun data(name: Name, data: Data<T>?)
}
public class DataTreeBuilder<T>(private val type: KType) : DataSink<T> {
private val map = HashMap<Name, Data<T>>()
override fun emit(name: Name, data: Data<T>?) {
override fun data(name: Name, data: Data<T>?) {
if (data == null) {
map.remove(name)
} else {
@ -182,7 +190,7 @@ public interface MutableDataTree<T> : GenericObservableDataTree<T, MutableDataTr
public operator fun set(token: NameToken, data: Data<T>?)
override fun emit(name: Name, data: Data<T>?): Unit = set(name, data)
override fun data(name: Name, data: Data<T>?): Unit = set(name, data)
}
public tailrec operator fun <T> MutableDataTree<T>.set(name: Name, data: Data<T>?): Unit {
@ -266,6 +274,6 @@ public fun <T> Sequence<NamedData<T>>.toObservableTree(dataType: KType, scope: C
MutableDataTree<T>(dataType, scope).apply {
emitAll(this@toObservableTree)
updates.onEach {
emit(it.name, it.data)
data(it.name, it.data)
}.launchIn(scope)
}

2
dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/data/GroupRule.kt
View File

@ -42,7 +42,7 @@ public interface GroupRule {
set.forEach { data ->
val tagValue: String = data.meta[key]?.string ?: defaultTagValue
map.getOrPut(tagValue) { DataTreeBuilder(set.dataType) }.emit(data.name,data.data)
map.getOrPut(tagValue) { DataTreeBuilder(set.dataType) }.data(data.name,data.data)
}

2
dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/data/NamedData.kt
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@ -4,7 +4,7 @@ import space.kscience.dataforge.meta.isEmpty
import space.kscience.dataforge.misc.Named
import space.kscience.dataforge.names.Name
public interface NamedData<T> : Named, Data<T> {
public interface NamedData<out T> : Named, Data<T> {
override val name: Name
public val data: Data<T>
}

48
dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/data/dataBuilders.kt
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@ -7,23 +7,24 @@ import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.meta.MutableMeta
import space.kscience.dataforge.misc.DFExperimental
import space.kscience.dataforge.names.Name
import space.kscience.dataforge.names.asName
import space.kscience.dataforge.names.isEmpty
import space.kscience.dataforge.names.plus
public fun <T> DataSink<T>.emit(value: NamedData<T>) {
emit(value.name, value.data)
public fun <T> DataSink<T>.data(value: NamedData<T>) {
data(value.name, value.data)
}
public fun <T> DataSink<T>.emitAll(sequence: Sequence<NamedData<T>>) {
sequence.forEach { emit(it) }
sequence.forEach { data(it) }
}
public fun <T> DataSink<T>.emitAll(dataTree: DataTree<T>) {
public fun <T> DataSink<T>.branch(dataTree: DataTree<T>) {
emitAll(dataTree.asSequence())
}
public inline fun <T> DataSink<T>.emitAll(
public inline fun <T> DataSink<T>.branch(
prefix: Name,
block: DataSink<T>.() -> Unit,
) {
@ -31,45 +32,50 @@ public inline fun <T> DataSink<T>.emitAll(
apply(block)
} else {
val proxyDataSink = DataSink { nameWithoutPrefix, data ->
this.emit(prefix + nameWithoutPrefix, data)
this.data(prefix + nameWithoutPrefix, data)
}
proxyDataSink.apply(block)
}
}
public inline fun <T> DataSink<T>.branch(
prefix: String,
block: DataSink<T>.() -> Unit,
): Unit = branch(prefix.asName(), block)
public fun <T> DataSink<T>.emit(name: String, value: Data<T>) {
emit(Name.parse(name), value)
public fun <T> DataSink<T>.data(name: String, value: Data<T>) {
data(Name.parse(name), value)
}
public fun <T> DataSink<T>.emitAll(name: Name, set: DataTree<T>) {
emitAll(name) { emitAll(set.asSequence()) }
public fun <T> DataSink<T>.branch(name: Name, set: DataTree<T>) {
branch(name) { emitAll(set.asSequence()) }
}
public fun <T> DataSink<T>.emitAll(name: String, set: DataTree<T>) {
emitAll(Name.parse(name)) { emitAll(set.asSequence()) }
public fun <T> DataSink<T>.branch(name: String, set: DataTree<T>) {
branch(Name.parse(name)) { emitAll(set.asSequence()) }
}
/**
* Produce lazy [Data] and emit it into the [MutableDataTree]
*/
public inline fun <reified T> DataSink<T>.produce(
public inline fun <reified T> DataSink<T>.data(
name: String,
meta: Meta = Meta.EMPTY,
noinline producer: suspend () -> T,
) {
val data = Data(meta, block = producer)
emit(name, data)
data(name, data)
}
public inline fun <reified T> DataSink<T>.produce(
public inline fun <reified T> DataSink<T>.data(
name: Name,
meta: Meta = Meta.EMPTY,
noinline producer: suspend () -> T,
) {
val data = Data(meta, block = producer)
emit(name, data)
data(name, data)
}
/**
@ -79,24 +85,24 @@ public inline fun <reified T> DataSink<T>.static(
name: String,
data: T,
meta: Meta = Meta.EMPTY,
): Unit = emit(name, Data.static(data, meta))
): Unit = data(name, Data.static(data, meta))
public inline fun <reified T> DataSink<T>.static(
name: Name,
data: T,
meta: Meta = Meta.EMPTY,
): Unit = emit(name, Data.static(data, meta))
): Unit = data(name, Data.static(data, meta))
public inline fun <reified T> DataSink<T>.static(
name: String,
data: T,
mutableMeta: MutableMeta.() -> Unit,
): Unit = emit(Name.parse(name), Data.static(data, Meta(mutableMeta)))
): Unit = data(Name.parse(name), Data.static(data, Meta(mutableMeta)))
public fun <T> DataSink<T>.populateFrom(sequence: Sequence<NamedData<T>>) {
sequence.forEach {
emit(it.name, it.data)
data(it.name, it.data)
}
}
@ -111,7 +117,7 @@ public fun <T> DataSink<T>.populateFrom(tree: DataTree<T>) {
@DFExperimental
public fun <T> MutableDataTree<T>.populateFrom(flow: ObservableDataSource<T>): Job = flow.updates().onEach {
//TODO check if the place is occupied
emit(it.name, it.data)
data(it.name, it.data)
}.launchIn(scope)
//public fun <T > DataSetBuilder<T>.populateFrom(flow: Flow<NamedData<T>>) {

38
dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/data/dataTransform.kt
View File

@ -9,14 +9,14 @@ import kotlin.coroutines.EmptyCoroutineContext
import kotlin.reflect.KType
import kotlin.reflect.typeOf
public data class ValueWithMeta<T>(val meta: Meta, val value: T)
public data class ValueWithMeta<T>(val value: T, val meta: Meta)
public suspend fun <T> Data<T>.awaitWithMeta(): ValueWithMeta<T> = ValueWithMeta(meta, await())
public suspend fun <T> Data<T>.awaitWithMeta(): ValueWithMeta<T> = ValueWithMeta(await(), meta)
public data class NamedValueWithMeta<T>(val name: Name, val meta: Meta, val value: T)
public data class NamedValueWithMeta<T>(val name: Name, val value: T, val meta: Meta)
public suspend fun <T> NamedData<T>.awaitWithMeta(): NamedValueWithMeta<T> =
NamedValueWithMeta(name, meta, await())
NamedValueWithMeta(name, await(), meta)
/**
@ -25,7 +25,7 @@ public suspend fun <T> NamedData<T>.awaitWithMeta(): NamedValueWithMeta<T> =
* @param meta for the resulting data. By default equals input data.
* @param block the transformation itself
*/
public inline fun <T : Any, reified R : Any> Data<T>.transform(
public inline fun <T, reified R> Data<T>.transform(
meta: Meta = this.meta,
coroutineContext: CoroutineContext = EmptyCoroutineContext,
crossinline block: suspend (T) -> R,
@ -36,7 +36,7 @@ public inline fun <T : Any, reified R : Any> Data<T>.transform(
/**
* Combine this data with the other data using [block]. See [Data::map] for other details
*/
public inline fun <T1 : Any, T2 : Any, reified R : Any> Data<T1>.combine(
public inline fun <T1, T2, reified R> Data<T1>.combine(
other: Data<T2>,
meta: Meta = this.meta,
coroutineContext: CoroutineContext = EmptyCoroutineContext,
@ -69,7 +69,7 @@ internal fun Map<*, Data<*>>.joinMeta(): Meta = Meta {
}
@DFInternal
public fun <K, T : Any, R : Any> Map<K, Data<T>>.reduceToData(
public fun <K, T, R> Map<K, Data<T>>.reduceToData(
outputType: KType,
meta: Meta = joinMeta(),
coroutineContext: CoroutineContext = EmptyCoroutineContext,
@ -89,7 +89,7 @@ public fun <K, T : Any, R : Any> Map<K, Data<T>>.reduceToData(
* @param T type of the input goal
* @param R type of the result goal
*/
public inline fun <K, T : Any, reified R : Any> Map<K, Data<T>>.reduceToData(
public inline fun <K, T, reified R> Map<K, Data<T>>.reduceToData(
meta: Meta = joinMeta(),
coroutineContext: CoroutineContext = EmptyCoroutineContext,
crossinline block: suspend (Map<K, ValueWithMeta<T>>) -> R,
@ -104,7 +104,7 @@ public inline fun <K, T : Any, reified R : Any> Map<K, Data<T>>.reduceToData(
//Iterable operations
@DFInternal
public inline fun <T : Any, R : Any> Iterable<Data<T>>.reduceToData(
public inline fun <T, R> Iterable<Data<T>>.reduceToData(
outputType: KType,
meta: Meta = joinMeta(),
coroutineContext: CoroutineContext = EmptyCoroutineContext,
@ -119,7 +119,7 @@ public inline fun <T : Any, R : Any> Iterable<Data<T>>.reduceToData(
}
@OptIn(DFInternal::class)
public inline fun <T : Any, reified R : Any> Iterable<Data<T>>.reduceToData(
public inline fun <T, reified R> Iterable<Data<T>>.reduceToData(
meta: Meta = joinMeta(),
coroutineContext: CoroutineContext = EmptyCoroutineContext,
crossinline transformation: suspend (Collection<ValueWithMeta<T>>) -> R,
@ -127,7 +127,7 @@ public inline fun <T : Any, reified R : Any> Iterable<Data<T>>.reduceToData(
transformation(it)
}
public inline fun <T : Any, reified R : Any> Iterable<Data<T>>.foldToData(
public inline fun <T, reified R> Iterable<Data<T>>.foldToData(
initial: R,
meta: Meta = joinMeta(),
coroutineContext: CoroutineContext = EmptyCoroutineContext,
@ -142,7 +142,7 @@ public inline fun <T : Any, reified R : Any> Iterable<Data<T>>.foldToData(
* Transform an [Iterable] of [NamedData] to a single [Data].
*/
@DFInternal
public inline fun <T : Any, R : Any> Iterable<NamedData<T>>.reduceNamedToData(
public inline fun <T, R> Iterable<NamedData<T>>.reduceNamedToData(
outputType: KType,
meta: Meta = joinMeta(),
coroutineContext: CoroutineContext = EmptyCoroutineContext,
@ -157,7 +157,7 @@ public inline fun <T : Any, R : Any> Iterable<NamedData<T>>.reduceNamedToData(
}
@OptIn(DFInternal::class)
public inline fun <T : Any, reified R : Any> Iterable<NamedData<T>>.reduceNamedToData(
public inline fun <T, reified R> Iterable<NamedData<T>>.reduceNamedToData(
meta: Meta = joinMeta(),
coroutineContext: CoroutineContext = EmptyCoroutineContext,
crossinline transformation: suspend (Collection<NamedValueWithMeta<T>>) -> R,
@ -168,7 +168,7 @@ public inline fun <T : Any, reified R : Any> Iterable<NamedData<T>>.reduceNamedT
/**
* Fold a [Iterable] of named data into a single [Data]
*/
public inline fun <T : Any, reified R : Any> Iterable<NamedData<T>>.foldNamedToData(
public inline fun <T, reified R> Iterable<NamedData<T>>.foldNamedToData(
initial: R,
meta: Meta = joinMeta(),
coroutineContext: CoroutineContext = EmptyCoroutineContext,
@ -194,18 +194,18 @@ public suspend fun <T, R> DataTree<T>.transform(
val d = Data(outputType, newMeta, coroutineContext, listOf(namedData)) {
block(namedData.awaitWithMeta())
}
emit(namedData.name, d)
data(namedData.name, d)
}
}
@OptIn(DFInternal::class)
public suspend inline fun <T : Any, reified R : Any> DataTree<T>.transform(
public suspend inline fun <T, reified R> DataTree<T>.transform(
noinline metaTransform: MutableMeta.() -> Unit = {},
coroutineContext: CoroutineContext = EmptyCoroutineContext,
noinline block: suspend (NamedValueWithMeta<T>) -> R,
): DataTree<R> = this@transform.transform(typeOf<R>(), metaTransform, coroutineContext, block)
public inline fun <T : Any> DataTree<T>.forEach(block: (NamedData<T>) -> Unit) {
public inline fun <T> DataTree<T>.forEach(block: (NamedData<T>) -> Unit) {
asSequence().forEach(block)
}
@ -219,13 +219,13 @@ internal fun DataTree<*>.joinMeta(): Meta = Meta {
}
}
public inline fun <T : Any, reified R : Any> DataTree<T>.reduceToData(
public inline fun <T, reified R> DataTree<T>.reduceToData(
meta: Meta = joinMeta(),
coroutineContext: CoroutineContext = EmptyCoroutineContext,
crossinline transformation: suspend (Iterable<NamedValueWithMeta<T>>) -> R,
): Data<R> = asSequence().asIterable().reduceNamedToData(meta, coroutineContext, transformation)
public inline fun <T : Any, reified R : Any> DataTree<T>.foldToData(
public inline fun <T, reified R> DataTree<T>.foldToData(
initial: R,
meta: Meta = joinMeta(),
coroutineContext: CoroutineContext = EmptyCoroutineContext,

4
dataforge-data/src/jvmMain/kotlin/space/kscience/dataforge/data/dataFilterJvm.kt
View File

@ -14,7 +14,7 @@ import kotlin.reflect.typeOf
* Cast the node to given type if the cast is possible or return null
*/
@Suppress("UNCHECKED_CAST")
private fun <R : Any> Data<*>.castOrNull(type: KType): Data<R>? =
private fun <R> Data<*>.castOrNull(type: KType): Data<R>? =
if (!this.type.isSubtypeOf(type)) {
null
} else {
@ -55,7 +55,7 @@ public inline fun <reified R : Any> DataTree<*>.filterByType(
/**
* Select a single datum if it is present and of given [type]
*/
public fun <R : Any> DataTree<*>.getByType(type: KType, name: Name): NamedData<R>? =
public fun <R> DataTree<*>.getByType(type: KType, name: Name): NamedData<R>? =
get(name)?.castOrNull<R>(type)?.named(name)
public inline fun <reified R : Any> DataTree<*>.getByType(name: Name): NamedData<R>? =

10
dataforge-data/src/jvmMain/kotlin/space/kscience/dataforge/data/dataSetBuilderInContext.kt
View File

@ -12,14 +12,14 @@ import space.kscience.dataforge.names.plus
*/
context(DataSink<T>)
public infix fun <T : Any> String.put(data: Data<T>): Unit =
emit(Name.parse(this), data)
data(Name.parse(this), data)
/**
* Append node
*/
context(DataSink<T>)
public infix fun <T : Any> String.put(dataSet: DataTree<T>): Unit =
emitAll(this, dataSet)
branch(this, dataSet)
/**
* Build and append node
@ -27,7 +27,7 @@ public infix fun <T : Any> String.put(dataSet: DataTree<T>): Unit =
context(DataSink<T>)
public infix fun <T : Any> String.put(
block: DataSink<T>.() -> Unit,
): Unit = emitAll(Name.parse(this), block)
): Unit = branch(Name.parse(this), block)
/**
* Copy given data set and mirror its changes to this [LegacyDataTreeBuilder] in [this@setAndObserve]. Returns an update [Job]
@ -37,8 +37,8 @@ public fun <T : Any> CoroutineScope.setAndWatch(
name: Name,
dataSet: DataTree<T>,
): Job = launch {
emitAll(name, dataSet)
branch(name, dataSet)
dataSet.updates().collect {
emit(name + it.name, it.data)
data(name + it.name, it.data)
}
}

2
dataforge-data/src/jvmTest/kotlin/space/kscience/dataforge/data/LegacyGenericDataTreeBuilderTest.kt → dataforge-data/src/jvmTest/kotlin/space/kscience/dataforge/data/DataTreeBuilderTest.kt
View File

@ -7,7 +7,7 @@ import kotlin.test.Test
import kotlin.test.assertEquals
internal class LegacyGenericDataTreeBuilderTest {
internal class DataTreeBuilderTest {
@Test
fun testTreeBuild() = runBlocking {
val node = DataTree<Any> {

5
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/EnvelopeFormat.kt
View File

@ -10,10 +10,7 @@ import space.kscience.dataforge.names.asName
import kotlin.reflect.KType
import kotlin.reflect.typeOf
public interface EnvelopeFormat : IOFormat<Envelope> {
override val type: KType get() = typeOf<Envelope>()
}
public interface EnvelopeFormat : IOFormat<Envelope>
public fun EnvelopeFormat.read(input: Source): Envelope = readFrom(input)

4
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/IOFormat.kt
View File

@ -49,13 +49,13 @@ public fun interface IOWriter<in T> {
*/
public interface IOFormat<T> : IOReader<T>, IOWriter<T>
public fun <T : Any> Source.readWith(format: IOReader<T>): T = format.readFrom(this)
public fun <T> Source.readWith(format: IOReader<T>): T = format.readFrom(this)
/**
* Read given binary as an object using given format
*/
public fun <T> Binary.readWith(format: IOReader<T>): T = read {
readWith(format)
this.readWith(format)
}
/**

2
dataforge-io/src/commonMain/kotlin/space/kscience/dataforge/io/MetaFormat.kt
View File

@ -21,8 +21,6 @@ import kotlin.reflect.typeOf
*/
public interface MetaFormat : IOFormat<Meta> {
override val type: KType get() = typeOf<Meta>()
override fun writeTo(sink: Sink, obj: Meta) {
writeMeta(sink, obj, null)
}

22
dataforge-workspace/src/commonMain/kotlin/space/kscience/dataforge/workspace/TaskResult.kt
View File

@ -1,9 +1,13 @@
package space.kscience.dataforge.workspace
import kotlinx.coroutines.CoroutineScope
import kotlinx.coroutines.Job
import kotlinx.coroutines.launch
import space.kscience.dataforge.data.ObservableDataTree
import space.kscience.dataforge.data.asSequence
import space.kscience.dataforge.data.launch
import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.names.Name
import kotlin.reflect.KType
/**
* A result of a [Task]
@ -12,16 +16,24 @@ import kotlin.reflect.KType
* @param taskMeta The configuration of the task that produced the result
*/
public data class TaskResult<T>(
public val data: ObservableDataTree<T>,
public val content: ObservableDataTree<T>,
public val workspace: Workspace,
public val taskName: Name,
public val taskMeta: Meta,
) {
val dataType: KType get() = data.dataType
}
): ObservableDataTree<T> by content
/**
* Wrap data into [TaskResult]
*/
public fun <T> Workspace.wrapResult(data: ObservableDataTree<T>, taskName: Name, taskMeta: Meta): TaskResult<T> =
TaskResult(data, this, taskName, taskMeta)
/**
* Start computation for all data elements of this node.
* The resulting [Job] is completed only when all of them are completed.
*/
public fun TaskResult<*>.compute(scope: CoroutineScope): Job = scope.launch {
asSequence().forEach {
it.data.launch(scope)
}
}

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

@ -53,7 +53,7 @@ public interface Workspace : ContextAware, Provider, CoroutineScope {
}
public suspend fun produceData(taskName: Name, taskMeta: Meta, name: Name): Data<*>? =
produce(taskName, taskMeta).data[name]
produce(taskName, taskMeta)[name]
public companion object {
public const val TYPE: String = "workspace"

6
dataforge-workspace/src/commonMain/kotlin/space/kscience/dataforge/workspace/WorkspaceBuilder.kt
View File

@ -19,12 +19,12 @@ import kotlin.properties.PropertyDelegateProvider
import kotlin.properties.ReadOnlyProperty
import kotlin.reflect.typeOf
public data class TaskReference<T : Any>(public val taskName: Name, public val task: Task<T>) : DataSelector<T> {
public data class TaskReference<T>(public val taskName: Name, public val task: Task<T>) : DataSelector<T> {
@Suppress("UNCHECKED_CAST")
override suspend fun select(workspace: Workspace, meta: Meta): DataTree<T> {
if (workspace.tasks[taskName] == task) {
return workspace.produce(taskName, meta).data as DataTree<T>
return workspace.produce(taskName, meta) as DataTree<T>
} else {
error("Task $taskName does not belong to the workspace")
}
@ -125,7 +125,7 @@ public class WorkspaceBuilder(
/**
* Define intrinsic data for the workspace
*/
public fun data(builder: DataSink<*>.() -> Unit) {
public fun data(builder: DataSink<Any?>.() -> Unit) {
data.apply(builder)
}

20
dataforge-workspace/src/commonMain/kotlin/space/kscience/dataforge/workspace/taskBuilders.kt
View File

@ -3,7 +3,7 @@ package space.kscience.dataforge.workspace
import space.kscience.dataforge.actions.Action
import space.kscience.dataforge.context.PluginFactory
import space.kscience.dataforge.data.DataTree
import space.kscience.dataforge.data.emitAll
import space.kscience.dataforge.data.branch
import space.kscience.dataforge.data.forEach
import space.kscience.dataforge.data.transform
import space.kscience.dataforge.meta.*
@ -25,12 +25,12 @@ public val TaskResultBuilder<*>.defaultDependencyMeta: Meta
* @param selector a workspace data selector. Could be either task selector or initial data selector.
* @param dependencyMeta meta used for selector. The same meta is used for caching. By default, uses [defaultDependencyMeta].
*/
public suspend fun <T : Any> TaskResultBuilder<*>.from(
public suspend fun <T> TaskResultBuilder<*>.from(
selector: DataSelector<T>,
dependencyMeta: Meta = defaultDependencyMeta,
): DataTree<T> = selector.select(workspace, dependencyMeta)
public suspend inline fun <T : Any, reified P : WorkspacePlugin> TaskResultBuilder<*>.from(
public suspend inline fun <T, reified P : WorkspacePlugin> TaskResultBuilder<*>.from(
plugin: P,
dependencyMeta: Meta = defaultDependencyMeta,
selectorBuilder: P.() -> TaskReference<T>,
@ -50,7 +50,7 @@ public suspend inline fun <T : Any, reified P : WorkspacePlugin> TaskResultBuild
* @param dependencyMeta meta used for selector. The same meta is used for caching. By default, uses [defaultDependencyMeta].
* @param selectorBuilder a builder of task from the plugin.
*/
public suspend inline fun <reified T : Any, reified P : WorkspacePlugin> TaskResultBuilder<*>.from(
public suspend inline fun <reified T, reified P : WorkspacePlugin> TaskResultBuilder<*>.from(
pluginFactory: PluginFactory<P>,
dependencyMeta: Meta = defaultDependencyMeta,
selectorBuilder: P.() -> TaskReference<T>,
@ -77,7 +77,7 @@ public val TaskResultBuilder<*>.allData: DataSelector<*>
* @param action process individual data asynchronously.
*/
@DFExperimental
public suspend inline fun <T : Any, reified R : Any> TaskResultBuilder<R>.transformEach(
public suspend inline fun <T, reified R> TaskResultBuilder<R>.transformEach(
selector: DataSelector<T>,
dependencyMeta: Meta = defaultDependencyMeta,
dataMetaTransform: MutableMeta.(name: Name) -> Unit = {},
@ -93,27 +93,27 @@ public suspend inline fun <T : Any, reified R : Any> TaskResultBuilder<R>.transf
action(it, data.name, meta)
}
emit(data.name, res)
data(data.name, res)
}
}
/**
* Set given [dataSet] as a task result.
*/
public fun <T : Any> TaskResultBuilder<T>.result(dataSet: DataTree<T>) {
emitAll(dataSet)
public fun <T> TaskResultBuilder<T>.result(dataSet: DataTree<T>) {
branch(dataSet)
}
/**
* Use provided [action] to fill the result
*/
@DFExperimental
public suspend inline fun <T : Any, reified R : Any> TaskResultBuilder<R>.actionFrom(
public suspend inline fun <T, reified R> TaskResultBuilder<R>.actionFrom(
selector: DataSelector<T>,
action: Action<T, R>,
dependencyMeta: Meta = defaultDependencyMeta,
) {
emitAll(action.execute(workspace.context, from(selector, dependencyMeta), dependencyMeta))
branch(action.execute(workspace.context, from(selector, dependencyMeta), dependencyMeta))
}

4
dataforge-workspace/src/jvmMain/kotlin/space/kscience/dataforge/workspace/FileWorkspaceCache.kt
View File

@ -95,8 +95,8 @@ public class FileWorkspaceCache(public val cacheDirectory: Path) : WorkspaceCach
}
val cachedTree = result.data.asSequence().map { cacheOne(it) }
.toObservableTree(result.dataType, result.workspace, result.data.updates().map { cacheOne(it) })
val cachedTree = result.asSequence().map { cacheOne(it) }
.toObservableTree(result.dataType, result.workspace, result.updates().map { cacheOne(it) })
return result.workspace.wrapResult(cachedTree, result.taskName, result.taskMeta)
}

38
dataforge-workspace/src/jvmMain/kotlin/space/kscience/dataforge/workspace/InMemoryWorkspaceCache.kt
View File

@ -1,39 +1,39 @@
package space.kscience.dataforge.workspace
import kotlinx.coroutines.flow.map
import space.kscience.dataforge.data.*
import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.names.Name
import kotlin.reflect.KType
import kotlin.reflect.full.isSubtypeOf
private typealias TaskResultId = Pair<Name, Meta>
private data class TaskResultId(val name: Name, val meta: Meta)
public class InMemoryWorkspaceCache : WorkspaceCache {
// never do that at home!
private val cache = HashMap<TaskResultId, HashMap<Name, TaskData<*>>>()
private val cache = HashMap<TaskResultId, HashMap<Name, Data<*>>>()
@Suppress("UNCHECKED_CAST")
private fun <T : Any> TaskData<*>.checkType(taskType: KType): TaskData<T> =
if (type.isSubtypeOf(taskType)) this as TaskData<T>
private fun <T> Data<*>.checkType(taskType: KType): Data<T> =
if (type.isSubtypeOf(taskType)) this as Data<T>
else error("Cached data type mismatch: expected $taskType but got $type")
override suspend fun <T : Any> cache(result: TaskResult<T>): TaskResult<T> {
for (d: TaskData<T> in result) {
cache.getOrPut(result.taskName to result.taskMeta) { HashMap() }.getOrPut(d.name) { d }
}
return object : TaskResult<T> by result {
override fun iterator(): Iterator<TaskData<T>> = (cache[result.taskName to result.taskMeta]
?.values?.map { it.checkType<T>(result.dataType) }
?: emptyList()).iterator()
override fun get(name: Name): TaskData<T>? {
val cached: TaskData<*> = cache[result.taskName to result.taskMeta]?.get(name) ?: return null
//TODO check types
return cached.checkType(result.dataType)
override suspend fun <T> cache(result: TaskResult<T>): TaskResult<T> {
fun cacheOne(data: NamedData<T>): NamedData<T> {
val cachedData = cache.getOrPut(TaskResultId(result.taskName, result.taskMeta)){
HashMap()
}.getOrPut(data.name){
data.data
}
return cachedData.checkType<T>(result.dataType).named(data.name)
}
val cachedTree = result.asSequence().map { cacheOne(it) }
.toObservableTree(result.dataType, result.workspace, result.updates().map { cacheOne(it) })
return result.workspace.wrapResult(cachedTree, result.taskName, result.taskMeta)
}
}

293
dataforge-workspace/src/jvmMain/kotlin/space/kscience/dataforge/workspace/fileData.kt
View File

@ -1,30 +1,24 @@
package space.kscience.dataforge.workspace
import kotlinx.coroutines.Dispatchers
import kotlinx.coroutines.isActive
import kotlinx.coroutines.launch
import kotlinx.coroutines.withContext
import space.kscience.dataforge.context.error
import space.kscience.dataforge.context.logger
import space.kscience.dataforge.context.warn
import kotlinx.coroutines.*
import space.kscience.dataforge.data.*
import space.kscience.dataforge.io.*
import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.meta.copy
import space.kscience.dataforge.meta.string
import space.kscience.dataforge.misc.DFExperimental
import space.kscience.dataforge.misc.DFInternal
import space.kscience.dataforge.names.*
import space.kscience.dataforge.workspace.FileData.Companion.defaultPathToName
import space.kscience.dataforge.names.Name
import space.kscience.dataforge.names.NameToken
import space.kscience.dataforge.names.asName
import space.kscience.dataforge.names.plus
import space.kscience.dataforge.workspace.FileData.defaultPathToName
import java.nio.file.Files
import java.nio.file.Path
import java.nio.file.StandardWatchEventKinds
import java.nio.file.WatchEvent
import java.nio.file.attribute.BasicFileAttributes
import java.nio.file.spi.FileSystemProvider
import java.time.Instant
import kotlin.io.path.*
import kotlin.reflect.KType
import kotlin.reflect.typeOf
@ -33,40 +27,28 @@ import kotlin.reflect.typeOf
public typealias FileFormatResolver<T> = (path: Path, meta: Meta) -> IOReader<T>?
/**
* A data based on a filesystem [Path]
*/
public class FileData<T> internal constructor(private val data: Data<T>, public val path: Path) : Data<T> by data {
public object FileData {
public val FILE_KEY: Name = "file".asName()
public val FILE_PATH_KEY: Name = FILE_KEY + "path"
public val FILE_EXTENSION_KEY: Name = FILE_KEY + "extension"
public val FILE_CREATE_TIME_KEY: Name = FILE_KEY + "created"
public val FILE_UPDATE_TIME_KEY: Name = FILE_KEY + "updated"
public const val DF_FILE_EXTENSION: String = "df"
public val DEFAULT_IGNORE_EXTENSIONS: Set<String> = setOf(DF_FILE_EXTENSION)
// public val path: String? get() = meta[META_FILE_PATH_KEY].string
// public val extension: String? get() = meta[META_FILE_EXTENSION_KEY].string
//
public val createdTime: Instant? get() = meta[FILE_CREATE_TIME_KEY].string?.let { Instant.parse(it) }
public val updatedTime: Instant? get() = meta[FILE_UPDATE_TIME_KEY].string?.let { Instant.parse(it) }
public companion object {
public val FILE_KEY: Name = "file".asName()
public val FILE_PATH_KEY: Name = FILE_KEY + "path"
public val FILE_EXTENSION_KEY: Name = FILE_KEY + "extension"
public val FILE_CREATE_TIME_KEY: Name = FILE_KEY + "created"
public val FILE_UPDATE_TIME_KEY: Name = FILE_KEY + "updated"
public const val DF_FILE_EXTENSION: String = "df"
public val DEFAULT_IGNORE_EXTENSIONS: Set<String> = setOf(DF_FILE_EXTENSION)
/**
* Transform file name into DataForg name. Ignores DataForge file extensions.
*/
public val defaultPathToName: (Path) -> Name = { path ->
Name(
path.map { segment ->
if (segment.isRegularFile() && segment.extension in DEFAULT_IGNORE_EXTENSIONS) {
NameToken(path.nameWithoutExtension)
} else {
NameToken(path.name)
}
/**
* Transform file name into DataForg name. Ignores DataForge file extensions.
*/
public val defaultPathToName: (Path) -> Name = { path ->
Name(
path.map { segment ->
if (segment.isRegularFile() && segment.extension in DEFAULT_IGNORE_EXTENSIONS) {
NameToken(path.nameWithoutExtension)
} else {
NameToken(path.name)
}
)
}
}
)
}
}
@ -75,14 +57,11 @@ public class FileData<T> internal constructor(private val data: Data<T>, public
* Read data with supported envelope format and binary format. If the envelope format is null, then read binary directly from file.
* The operation is blocking since it must read the meta header. The reading of envelope body is lazy
*/
@OptIn(DFInternal::class)
@DFExperimental
public fun <T : Any> IOPlugin.readDataFile(
@OptIn(DFExperimental::class)
public fun IOPlugin.readFileData(
path: Path,
formatResolver: FileFormatResolver<T>,
): FileData<T>? {
): Data<Binary> {
val envelope = readEnvelopeFile(path, true)
val format = formatResolver(path, envelope.meta) ?: return null
val updatedMeta = envelope.meta.copy {
FileData.FILE_PATH_KEY put path.toString()
FileData.FILE_EXTENSION_KEY put path.extension
@ -91,146 +70,104 @@ public fun <T : Any> IOPlugin.readDataFile(
FileData.FILE_UPDATE_TIME_KEY put attributes.lastModifiedTime().toInstant().toString()
FileData.FILE_CREATE_TIME_KEY put attributes.creationTime().toInstant().toString()
}
return FileData(
Data(format.type, updatedMeta) {
(envelope.data ?: Binary.EMPTY).readWith(format)
},
path
return StaticData(
typeOf<Binary>(),
envelope.data ?: Binary.EMPTY,
updatedMeta
)
}
public fun DataSink<Binary>.file(io: IOPlugin, path: Path, name: Name) {
if (!path.isRegularFile()) error("Only regular files could be handled by this function")
data(name, io.readFileData(path))
}
context(IOPlugin) @DFExperimental
public fun <T : Any> DataSetBuilder<T>.directory(
public fun DataSink<Binary>.directory(
io: IOPlugin,
path: Path,
pathToName: (Path) -> Name = defaultPathToName,
formatResolver: FileFormatResolver<T>,
) {
if (!path.isDirectory()) error("Only directories could be handled by this function")
val metaFile = path.resolve(IOPlugin.META_FILE_NAME)
val dataFile = path.resolve(IOPlugin.DATA_FILE_NAME)
//process root data
if (metaFile.exists() || dataFile.exists()) {
data(
Name.EMPTY,
StaticData(
typeOf<Binary>(),
dataFile.takeIf { it.exists() }?.asBinary() ?: Binary.EMPTY,
io.readMetaFileOrNull(metaFile) ?: Meta.EMPTY
)
)
}
Files.list(path).forEach { childPath ->
val fileName = childPath.fileName.toString()
if (fileName.startsWith(IOPlugin.META_FILE_NAME)) {
meta(readMetaFile(childPath))
} else if (!fileName.startsWith("@")) {
file(childPath, pathToName, formatResolver)
if (!fileName.startsWith("@")) {
files(io, childPath, pathToName)
}
}
}
/**
* Read the directory as a data node. If [path] is a zip archive, read it as directory
*/
@DFExperimental
@DFInternal
public fun <T : Any> IOPlugin.readDataDirectory(
type: KType,
path: Path,
pathToName: (Path) -> Name = defaultPathToName,
formatResolver: FileFormatResolver<T>,
): LegacyDataTree<T> {
//read zipped data node
if (path.fileName != null && path.fileName.toString().endsWith(".zip")) {
public fun DataSink<Binary>.files(io: IOPlugin, path: Path, pathToName: (Path) -> Name = defaultPathToName) {
if (path.isRegularFile() && path.extension == "zip") {
//Using explicit Zip file system to avoid bizarre compatibility bugs
val fsProvider = FileSystemProvider.installedProviders().find { it.scheme == "jar" }
?: error("Zip file system provider not found")
val fs = fsProvider.newFileSystem(path, mapOf("create" to "true"))
return readDataDirectory(type, fs.rootDirectories.first(), pathToName, formatResolver)
return files(io, fs.rootDirectories.first(), pathToName)
}
if (!Files.isDirectory(path)) error("Provided path $path is not a directory")
return DataTree(type) {
meta {
FileData.FILE_PATH_KEY put path.toString()
}
directory(path, pathToName, formatResolver)
if (path.isRegularFile()) {
file(io, path, pathToName(path))
} else {
directory(io, path, pathToName)
}
}
@OptIn(DFInternal::class)
@DFExperimental
public inline fun <reified T : Any> IOPlugin.readDataDirectory(
path: Path,
noinline pathToName: (Path) -> Name = defaultPathToName,
noinline formatResolver: FileFormatResolver<T>,
): LegacyDataTree<T> = readDataDirectory(typeOf<T>(), path, pathToName, formatResolver)
/**
* Read a raw binary data tree from the directory. All files are read as-is (save for meta files).
*/
@DFExperimental
public fun IOPlugin.readRawDirectory(
path: Path,
pathToName: (Path) -> Name = defaultPathToName,
): LegacyDataTree<Binary> = readDataDirectory(path, pathToName) { _, _ -> IOReader.binary }
private fun Path.toName() = Name(map { NameToken.parse(it.nameWithoutExtension) })
@DFInternal
@DFExperimental
public fun <T : Any> IOPlugin.monitorDataDirectory(
type: KType,
public fun DataSink<Binary>.monitorFiles(
io: IOPlugin,
path: Path,
pathToName: (Path) -> Name = defaultPathToName,
formatResolver: FileFormatResolver<T>,
): DataSource<T> {
if (path.fileName.toString().endsWith(".zip")) error("Monitoring not supported for ZipFS")
if (!Files.isDirectory(path)) error("Provided path $path is not a directory")
return DataSource(type, context) {
directory(path, pathToName, formatResolver)
launch(Dispatchers.IO) {
val watchService = path.fileSystem.newWatchService()
scope: CoroutineScope = io.context,
): Job {
files(io, path, pathToName)
return scope.launch(Dispatchers.IO) {
val watchService = path.fileSystem.newWatchService()
path.register(
watchService,
StandardWatchEventKinds.ENTRY_DELETE,
StandardWatchEventKinds.ENTRY_MODIFY,
StandardWatchEventKinds.ENTRY_CREATE
)
path.register(
watchService,
StandardWatchEventKinds.ENTRY_DELETE,
StandardWatchEventKinds.ENTRY_MODIFY,
StandardWatchEventKinds.ENTRY_CREATE
)
do {
val key = watchService.take()
if (key != null) {
for (event: WatchEvent<*> in key.pollEvents()) {
val eventPath = event.context() as Path
if (event.kind() == StandardWatchEventKinds.ENTRY_DELETE) {
remove(eventPath.toName())
} else {
val fileName = eventPath.fileName.toString()
if (fileName.startsWith(IOPlugin.META_FILE_NAME)) {
meta(readMetaFile(eventPath))
} else if (!fileName.startsWith("@")) {
file(eventPath, pathToName, formatResolver)
}
do {
val key = watchService.take()
if (key != null) {
for (event: WatchEvent<*> in key.pollEvents()) {
val eventPath = event.context() as Path
if (event.kind() == StandardWatchEventKinds.ENTRY_DELETE) {
data(eventPath.toName(), null)
} else {
val fileName = eventPath.fileName.toString()
if (!fileName.startsWith("@")) {
files(io, eventPath, pathToName)
}
}
key.reset()
}
} while (isActive && key != null)
}
key.reset()
}
} while (isActive && key != null)
}
}
/**
* Start monitoring given directory ([path]) as a [DataSource].
*/
@OptIn(DFInternal::class)
@DFExperimental
public inline fun <reified T : Any> IOPlugin.monitorDataDirectory(
path: Path,
noinline pathToName: (Path) -> Name = defaultPathToName,
noinline formatResolver: FileFormatResolver<T>,
): DataSource<T> = monitorDataDirectory(typeOf<T>(), path, pathToName, formatResolver)
/**
* Read and monitor raw binary data tree from the directory. All files are read as-is (save for meta files).
*/
@DFExperimental
public fun IOPlugin.monitorRawDirectory(
path: Path,
pathToName: (Path) -> Name = defaultPathToName,
): DataSource<Binary> = monitorDataDirectory(path, pathToName) { _, _ -> IOReader.binary }
/**
* Write the data tree to existing directory or create a new one using default [java.nio.file.FileSystem] provider
*
@ -239,7 +176,7 @@ public fun IOPlugin.monitorRawDirectory(
@DFExperimental
public suspend fun <T : Any> IOPlugin.writeDataDirectory(
path: Path,
dataSet: DataSet<T>,
dataSet: DataTree<T>,
format: IOWriter<T>,
envelopeFormat: EnvelopeFormat? = null,
nameToPath: (name: Name, data: Data<T>) -> Path = { name, _ ->
@ -262,62 +199,28 @@ public suspend fun <T : Any> IOPlugin.writeDataDirectory(
writeEnvelopeDirectory(childPath, envelope)
}
}
val directoryMeta = dataSet.meta
writeMetaFile(path, directoryMeta)
dataSet.meta?.let { writeMetaFile(path, it) }
}
}
/**
* Reads the specified resources and returns a [LegacyDataTree] containing the data.
*
* @param resources The names of the resources to read.
* @param classLoader The class loader to use for loading the resources. By default, it uses the current thread's context class loader.
* @return A DataTree containing the data read from the resources.
*/
@DFExperimental
public fun IOPlugin.readResources(
public fun DataSink<Binary>.resources(
io: IOPlugin,
vararg resources: String,
pathToName: (Path) -> Name = defaultPathToName,
classLoader: ClassLoader = Thread.currentThread().contextClassLoader,
): LegacyDataTree<Binary> = GenericDataTree {
) {
resources.forEach { resource ->
val path = classLoader.getResource(resource)?.toURI()?.toPath() ?: error(
"Resource with name $resource is not resolved"
)
node(resource, readRawDirectory(path, pathToName))
}
}
/**
* Add file/directory-based data tree item
*/
context(IOPlugin)
@OptIn(DFInternal::class)
@DFExperimental
public fun <T : Any> DataSetBuilder<T>.file(
path: Path,
pathToName: (Path) -> Name = defaultPathToName,
formatResolver: FileFormatResolver<out T>,
) {
try {
//If path is a single file or a special directory, read it as single datum
if (!Files.isDirectory(path) || Files.list(path).allMatch { it.fileName.toString().startsWith("@") }) {
val data = readDataFile(path, formatResolver)
if (data == null) {
logger.warn { "File format is not resolved for $path. Skipping." }
return
}
val name: Name = data.meta[Envelope.ENVELOPE_NAME_KEY].string?.parseAsName() ?: pathToName(path.last())
data(name, data)
} else {
//otherwise, read as directory
val data: LegacyDataTree<T> = readDataDirectory(dataType, path, pathToName, formatResolver)
val name = data.meta[Envelope.ENVELOPE_NAME_KEY].string?.parseAsName() ?: pathToName(path.last())
node(name, data)
branch(resource.asName()) {
files(io, path, pathToName)
}
} catch (ex: Exception) {
logger.error(ex) { "Failed to read file or directory at $path: ${ex.message}" }
}
}

6
dataforge-workspace/src/jvmMain/kotlin/space/kscience/dataforge/workspace/workspaceJvm.kt
View File

@ -16,8 +16,8 @@ import space.kscience.dataforge.names.matches
*/
@OptIn(DFExperimental::class)
public inline fun <reified T : Any> TaskResultBuilder<*>.dataByType(namePattern: Name? = null): DataSelector<T> =
DataSelector<T> { workspace, meta ->
workspace.data.filterByType { name, _ ->
DataSelector<T> { workspace, _ ->
workspace.data.filterByType { name, _, _ ->
namePattern == null || name.matches(namePattern)
}
}
@ -25,4 +25,4 @@ public inline fun <reified T : Any> TaskResultBuilder<*>.dataByType(namePattern:
public suspend inline fun <reified T : Any> TaskResultBuilder<*>.fromTask(
task: Name,
taskMeta: Meta = Meta.EMPTY,
): DataTree<T> = workspace.produce(task, taskMeta).data.filterByType()
): DataTree<T> = workspace.produce(task, taskMeta).filterByType()

52
dataforge-workspace/src/jvmMain/kotlin/space/kscience/dataforge/workspace/zipData.kt
View File

@ -2,8 +2,7 @@ package space.kscience.dataforge.workspace
import kotlinx.coroutines.Dispatchers
import kotlinx.coroutines.withContext
import space.kscience.dataforge.data.DataTreeItem
import space.kscience.dataforge.data.LegacyDataTree
import space.kscience.dataforge.data.DataTree
import space.kscience.dataforge.io.*
import space.kscience.dataforge.misc.DFExperimental
import java.nio.file.Files
@ -15,42 +14,39 @@ import java.util.zip.ZipOutputStream
private suspend fun <T : Any> ZipOutputStream.writeNode(
name: String,
treeItem: DataTreeItem<T>,
tree: DataTree<T>,
dataFormat: IOFormat<T>,
envelopeFormat: EnvelopeFormat = TaggedEnvelopeFormat,
): Unit = withContext(Dispatchers.IO) {
when (treeItem) {
is DataTreeItem.Leaf -> {
//TODO add directory-based envelope writer
val envelope = treeItem.data.toEnvelope(dataFormat)
val entry = ZipEntry(name)
putNextEntry(entry)
//TODO remove additional copy
val bytes = ByteArray {
writeWith(envelopeFormat, envelope)
}
write(bytes)
//TODO add directory-based envelope writer
tree.data?.let {
val envelope = it.toEnvelope(dataFormat)
val entry = ZipEntry(name)
putNextEntry(entry)
//TODO remove additional copy
val bytes = ByteArray {
writeWith(envelopeFormat, envelope)
}
is DataTreeItem.Node -> {
val entry = ZipEntry("$name/")
putNextEntry(entry)
closeEntry()
treeItem.tree.items.forEach { (token, item) ->
val childName = "$name/$token"
writeNode(childName, item, dataFormat, envelopeFormat)
}
}
write(bytes)
}
val entry = ZipEntry("$name/")
putNextEntry(entry)
closeEntry()
tree.items.forEach { (token, item) ->
val childName = "$name/$token"
writeNode(childName, item, dataFormat, envelopeFormat)
}
}
/**
* Write this [LegacyDataTree] as a zip archive
* Write this [DataTree] as a zip archive
*/
@DFExperimental
public suspend fun <T : Any> LegacyDataTree<T>.writeZip(
public suspend fun <T : Any> DataTree<T>.writeZip(
path: Path,
format: IOFormat<T>,
envelopeFormat: EnvelopeFormat = TaggedEnvelopeFormat,
@ -68,6 +64,6 @@ public suspend fun <T : Any> LegacyDataTree<T>.writeZip(
)
val zos = ZipOutputStream(fos)
zos.use {
it.writeNode("", DataTreeItem.Node(this@writeZip), format, envelopeFormat)
it.writeNode("", this@writeZip, format, envelopeFormat)
}
}

10
dataforge-workspace/src/jvmTest/kotlin/space/kscience/dataforge/workspace/CachingWorkspaceTest.kt
View File

@ -4,7 +4,6 @@ import kotlinx.coroutines.ExperimentalCoroutinesApi
import kotlinx.coroutines.coroutineScope
import kotlinx.coroutines.test.runTest
import org.junit.jupiter.api.Test
import space.kscience.dataforge.data.startAll
import space.kscience.dataforge.data.static
import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.meta.boolean
@ -37,7 +36,6 @@ internal class CachingWorkspaceTest {
}
}
@Suppress("UNUSED_VARIABLE")
val doSecond by task<Any> {
transformEach(
doFirst,
@ -54,11 +52,11 @@ internal class CachingWorkspaceTest {
val secondB = workspace.produce("doSecond", Meta { "flag" put true })
val secondC = workspace.produce("doSecond")
coroutineScope {
first.startAll(this)
secondA.startAll(this)
secondB.startAll(this)
first.compute(this)
secondA.compute(this)
secondB.compute(this)
//repeat to check caching
secondC.startAll(this)
secondC.compute(this)
}
assertEquals(10, firstCounter)
assertEquals(10, secondCounter)

8
dataforge-workspace/src/jvmTest/kotlin/space/kscience/dataforge/workspace/DataPropagationTest.kt
View File

@ -20,13 +20,13 @@ class DataPropagationTestPlugin : WorkspacePlugin() {
val result: Data<Int> = selectedData.foldToData(0) { result, data ->
result + data.value
}
emit("result", result)
data("result", result)
}
val singleData by task<Int> {
workspace.data.filterByType<Int>()["myData[12]"]?.let {
emit("result", it)
data("result", it)
}
}
@ -55,12 +55,12 @@ class DataPropagationTest {
@Test
fun testAllData() = runTest {
val node = testWorkspace.produce("Test.allData")
assertEquals(4950, node.asSequence().single().await())
assertEquals(4950, node.content.asSequence().single().await())
}
@Test
fun testSingleData() = runTest {
val node = testWorkspace.produce("Test.singleData")
assertEquals(12, node.asSequence().single().await())
assertEquals(12, node.content.asSequence().single().await())
}
}

39
dataforge-workspace/src/jvmTest/kotlin/space/kscience/dataforge/workspace/FileDataTest.kt
View File

@ -9,38 +9,32 @@ import kotlinx.io.writeString
import space.kscience.dataforge.context.Context
import space.kscience.dataforge.context.Global
import space.kscience.dataforge.data.*
import space.kscience.dataforge.io.Envelope
import space.kscience.dataforge.io.IOFormat
import space.kscience.dataforge.io.io
import space.kscience.dataforge.io.readEnvelopeFile
import space.kscience.dataforge.io.*
import space.kscience.dataforge.io.yaml.YamlPlugin
import space.kscience.dataforge.meta.get
import space.kscience.dataforge.misc.DFExperimental
import java.nio.file.Files
import kotlin.io.path.fileSize
import kotlin.io.path.toPath
import kotlin.reflect.KType
import kotlin.reflect.typeOf
import kotlin.test.Test
import kotlin.test.assertEquals
class FileDataTest {
val dataNode = GenericDataTree<String> {
node("dir") {
val dataNode = DataTree<String> {
branch("dir") {
static("a", "Some string") {
"content" put "Some string"
}
}
static("b", "root data")
meta {
"content" put "This is root meta node"
}
// meta {
// "content" put "This is root meta node"
// }
}
object StringIOFormat : IOFormat<String> {
override val type: KType get() = typeOf<String>()
override fun writeTo(sink: Sink, obj: String) {
sink.writeString(obj)
@ -52,11 +46,13 @@ class FileDataTest {
@Test
@DFExperimental
fun testDataWriteRead() = with(Global.io) {
val io = Global.io
val dir = Files.createTempDirectory("df_data_node")
runBlocking {
writeDataDirectory(dir, dataNode, StringIOFormat)
println(dir.toUri().toString())
val reconstructed = readDataDirectory(dir) { _, _ -> StringIOFormat }
val reconstructed = DataTree { files(io, dir) }
.transform { (_, value) -> value.toByteArray().decodeToString() }
assertEquals(dataNode["dir.a"]?.meta?.get("content"), reconstructed["dir.a"]?.meta?.get("content"))
assertEquals(dataNode["b"]?.await(), reconstructed["b"]?.await())
}
@ -66,14 +62,15 @@ class FileDataTest {
@Test
@DFExperimental
fun testZipWriteRead() = runTest {
with(Global.io) {
val zip = Files.createTempFile("df_data_node", ".zip")
dataNode.writeZip(zip, StringIOFormat)
println(zip.toUri().toString())
val reconstructed = readDataDirectory(zip) { _, _ -> StringIOFormat }
assertEquals(dataNode["dir.a"]?.meta?.get("content"), reconstructed["dir.a"]?.meta?.get("content"))
assertEquals(dataNode["b"]?.await(), reconstructed["b"]?.await())
}
val io = Global.io
val zip = Files.createTempFile("df_data_node", ".zip")
dataNode.writeZip(zip, StringIOFormat)
println(zip.toUri().toString())
val reconstructed = DataTree { files(io, zip) }
.transform { (_, value) -> value.toByteArray().decodeToString() }
assertEquals(dataNode["dir.a"]?.meta?.get("content"), reconstructed["dir.a"]?.meta?.get("content"))
assertEquals(dataNode["b"]?.await(), reconstructed["b"]?.await())
}
@OptIn(DFExperimental::class)

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

@ -3,7 +3,6 @@ package space.kscience.dataforge.workspace
import kotlinx.coroutines.ExperimentalCoroutinesApi
import kotlinx.coroutines.test.runTest
import org.junit.jupiter.api.Test
import space.kscience.dataforge.data.startAll
import space.kscience.dataforge.data.static
import space.kscience.dataforge.misc.DFExperimental
import java.nio.file.Files
@ -22,13 +21,12 @@ class FileWorkspaceCacheTest {
}
fileCache(Files.createTempDirectory("dataforge-temporary-cache"))
@Suppress("UNUSED_VARIABLE")
val echo by task<String> {
transformEach(dataByType<String>()) { arg, _, _ -> arg }
}
}
workspace.produce("echo").startAll(this)
workspace.produce("echo").compute(this)
}
}

39
dataforge-workspace/src/jvmTest/kotlin/space/kscience/dataforge/workspace/SimpleWorkspaceTest.kt
View File

@ -27,8 +27,8 @@ public fun <P : Plugin> P.toFactory(): PluginFactory<P> = object : PluginFactory
override val tag: PluginTag = this@toFactory.tag
}
public fun Workspace.produceBlocking(task: String, block: MutableMeta.() -> Unit = {}): DataSet<Any> = runBlocking {
produce(task, block)
public fun Workspace.produceBlocking(task: String, block: MutableMeta.() -> Unit = {}): DataTree<*> = runBlocking {
produce(task, block).content
}
@OptIn(DFExperimental::class)
@ -68,8 +68,8 @@ internal class SimpleWorkspaceTest {
val filterOne by task<Int> {
val name by taskMeta.string { error("Name field not defined") }
from(testPluginFactory) { test }.getByType<Int>(name)?.let { source ->
data(source.name, source.map { it })
from(testPluginFactory) { test }[name]?.let { source: Data<Int> ->
data(name, source)
}
}
@ -110,14 +110,14 @@ internal class SimpleWorkspaceTest {
}
val averageByGroup by task<Int> {
val evenSum = workspace.data.filterByType<Int> { name, _ ->
val evenSum = workspace.data.filterByType<Int> { name, _, _ ->
name.toString().toInt() % 2 == 0
}.foldToData(0) { l, r ->
l + r.value
}
data("even", evenSum)
val oddSum = workspace.data.filterByType<Int> { name, _ ->
val oddSum = workspace.data.filterByType<Int> { name, _, _ ->
name.toString().toInt() % 2 == 1
}.foldToData(0) { l, r ->
l + r.value
@ -159,7 +159,7 @@ internal class SimpleWorkspaceTest {
@Timeout(1)
fun testMetaPropagation() = runTest {
val node = workspace.produce("sum") { "testFlag" put true }
val res = node.asSequence().single().await()
val res = node.single().await()
}
@Test
@ -170,20 +170,25 @@ internal class SimpleWorkspaceTest {
}
@Test
fun testFullSquare() {
runBlocking {
val node = workspace.produce("fullSquare")
println(node.toMeta())
fun testFullSquare() = runTest {
val result = workspace.produce("fullSquare")
result.forEach {
println(
"""
Name: ${it.name}
Meta: ${it.meta}
Data: ${it.data.await()}
""".trimIndent()
)
}
}
@Test
fun testFilter() {
runBlocking {
val node = workspace.produce("filterOne") {
"name" put "myData[12]"
}
assertEquals(12, node.single().await())
fun testFilter() = runTest {
val node = workspace.produce("filterOne") {
"name" put "myData[12]"
}
assertEquals(12, node.single().await())
}
}