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Data tree refactored to a uniform tree instead of sealed class.

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This commit is contained in:
Alexander Nozik 2024-02-03 17:25:49 +03:00
parent 90999f424f
commit 466e460989
23 changed files with 353 additions and 346 deletions
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28
dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/actions/AbstractAction.kt
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@ -1,9 +1,11 @@
package space.kscience.dataforge.actions
import kotlinx.coroutines.CoroutineScope
import kotlinx.coroutines.flow.launchIn
import kotlinx.coroutines.flow.onEach
import kotlinx.coroutines.launch
import space.kscience.dataforge.data.*
import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.misc.DFInternal
import space.kscience.dataforge.names.Name
import space.kscience.dataforge.names.startsWith
import kotlin.reflect.KType
@ -33,26 +35,38 @@ public abstract class AbstractAction<T : Any, R : Any>(
/**
* Update part of the data set using provided data
*
* @param source the source data tree in case we need several data items to update
*/
protected open fun DataSink<R>.update(
allData: DataTree<T>,
source: DataTree<T>,
meta: Meta,
namedData: NamedData<T>,
){
//by default regenerate the whole data set
generate(allData,meta)
generate(source,meta)
}
@OptIn(DFInternal::class)
override fun execute(
scope: CoroutineScope,
dataSet: DataTree<T>,
meta: Meta,
): ObservableDataTree<R> = MutableDataTree<R>(outputType, scope).apply {
): DataTree<R> = if(dataSet.isObservable()) {
MutableDataTree<R>(outputType, dataSet.updatesScope).apply {
generate(dataSet, meta)
scope.launch {
dataSet.updates().collect {
dataSet.updates().onEach {
update(dataSet, meta, it)
}.launchIn(updatesScope)
//close updates when the source is closed
updatesScope.launch {
dataSet.awaitClose()
close()
}
}
} else{
DataTree(outputType){
generate(dataSet, meta)
}
}
}

18
dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/actions/Action.kt
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@ -1,9 +1,6 @@
package space.kscience.dataforge.actions
import kotlinx.coroutines.CoroutineScope
import kotlinx.coroutines.coroutineScope
import space.kscience.dataforge.data.DataTree
import space.kscience.dataforge.data.ObservableDataTree
import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.misc.DFExperimental
@ -16,7 +13,7 @@ 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
* so not actual computation is started at this moment.
*/
public fun execute(scope: CoroutineScope, dataSet: DataTree<T>, meta: Meta): ObservableDataTree<R>
public fun execute(dataSet: DataTree<T>, meta: Meta): DataTree<R>
public companion object
}
@ -26,20 +23,21 @@ public fun interface Action<T, R> {
*/
public fun <T, R> DataTree<T>.transform(
action: Action<T, R>,
scope: CoroutineScope,
meta: Meta = Meta.EMPTY,
): DataTree<R> = action.execute(scope, this, meta)
): DataTree<R> = action.execute(this, meta)
/**
* Action composition. The result is terminal if one of its parts is terminal
*/
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) }
public infix fun <T, I, R> Action<T, I>.then(action: Action<I, R>): Action<T, R> = Action { dataSet, meta ->
action.execute(this@then.execute(dataSet, meta), meta)
}
@DFExperimental
public suspend operator fun <T, R> Action<T, R>.invoke(
public operator fun <T, R> Action<T, R>.invoke(
dataSet: DataTree<T>,
meta: Meta = Meta.EMPTY,
): DataTree<R> = coroutineScope { execute(this, dataSet, meta) }
): DataTree<R> = execute(dataSet, meta)

4
dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/actions/MapAction.kt
View File

@ -79,14 +79,14 @@ internal class MapAction<T : Any, R : Any>(
builder.result(env, data.await())
}
//setting the data node
data(newName, newData)
put(newName, newData)
}
override fun DataSink<R>.generate(data: DataTree<T>, meta: Meta) {
data.forEach { mapOne(it.name, it.data, meta) }
}
override fun DataSink<R>.update(allData: DataTree<T>, meta: Meta, namedData: NamedData<T>) {
override fun DataSink<R>.update(source: DataTree<T>, meta: Meta, namedData: NamedData<T>) {
mapOne(namedData.name, namedData.data, namedData.meta)
}
}

2
dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/actions/ReduceAction.kt
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@ -103,7 +103,7 @@ internal class ReduceAction<T : Any, R : Any>(
meta = groupMeta
) { group.result.invoke(env, it) }
data(env.name, res)
put(env.name, res)
}
}
}

4
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)
data(
put(
fragmentName,
@Suppress("OPT_IN_USAGE") Data(outputType, meta = env.meta, dependencies = listOf(data)) {
env.result(data.await())
@ -77,7 +77,7 @@ internal class SplitAction<T : Any, R : Any>(
data.forEach { splitOne(it.name, it.data, meta) }
}
override fun DataSink<R>.update(allData: DataTree<T>, meta: Meta, namedData: NamedData<T>) {
override fun DataSink<R>.update(source: DataTree<T>, meta: Meta, namedData: NamedData<T>) {
splitOne(namedData.name, namedData.data, namedData.meta)
}
}

137
dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/data/DataSource.kt
View File

@ -1,11 +1,11 @@
package space.kscience.dataforge.data
import kotlinx.coroutines.CoroutineScope
import kotlinx.coroutines.*
import kotlinx.coroutines.flow.*
import kotlinx.coroutines.launch
import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.misc.DFInternal
import space.kscience.dataforge.names.*
import kotlin.contracts.contract
import kotlin.reflect.KType
import kotlin.reflect.typeOf
@ -66,7 +66,7 @@ public interface GenericDataTree<out T, out TR : GenericDataTree<T, TR>> : DataS
}
}
public typealias DataTree<T> = GenericDataTree<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.
@ -87,7 +87,7 @@ public operator fun <T> DataTree<T>.get(name: String): Data<T>? = read(name.pars
public fun <T> DataTree<T>.asSequence(
namePrefix: Name = Name.EMPTY,
): Sequence<NamedData<T>> = sequence {
data?.let { yield(it.named(Name.EMPTY)) }
data?.let { yield(it.named(namePrefix)) }
items.forEach { (token, tree) ->
yieldAll(tree.asSequence(namePrefix + token))
}
@ -113,8 +113,8 @@ public fun GenericDataTree<*, *>.isEmpty(): Boolean = data == null && items.isEm
@PublishedApi
internal class FlatDataTree<T>(
override val dataType: KType,
val dataSet: Map<Name, Data<T>>,
val prefix: Name,
private val dataSet: Map<Name, Data<T>>,
private val prefix: Name,
) : GenericDataTree<T, FlatDataTree<T>> {
override val self: FlatDataTree<T> get() = this
override val data: Data<T>? get() = dataSet[prefix]
@ -141,20 +141,56 @@ 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<out T, out TR : GenericObservableDataTree<T, TR>> : GenericDataTree<T, TR>,
ObservableDataSource<T>
public interface GenericObservableDataTree<out T, out TR : GenericObservableDataTree<T, TR>> :
GenericDataTree<T, TR>, ObservableDataSource<T>, AutoCloseable {
/**
* A scope that is used to propagate updates. When this scope is closed, no new updates could arrive.
*/
public val updatesScope: CoroutineScope
/**
* Close this data tree updates channel
*/
override fun close() {
updatesScope.cancel()
}
}
public typealias ObservableDataTree<T> = GenericObservableDataTree<T, GenericObservableDataTree<T, *>>
public fun <T> DataTree<T>.updates(): Flow<NamedData<T>> = if (this is GenericObservableDataTree<T,*>) updates() else emptyFlow()
public fun interface DataSink<in T> {
public fun data(name: Name, data: Data<T>?)
/**
* Check if the [DataTree] is observable
*/
public fun <T> DataTree<T>.isObservable(): Boolean {
contract {
returns(true) implies (this@isObservable is GenericObservableDataTree<T, *>)
}
return this is GenericObservableDataTree<T, *>
}
/**
* Wait for this data tree to stop spawning updates (updatesScope is closed).
* If this [DataTree] is not observable, return immediately.
*/
public suspend fun <T> DataTree<T>.awaitClose() {
if (isObservable()) {
updatesScope.coroutineContext[Job]?.join()
}
}
public fun <T> DataTree<T>.updates(): Flow<NamedData<T>> =
if (this is GenericObservableDataTree<T, *>) updates() else emptyFlow()
public fun interface DataSink<in T> {
public fun put(name: Name, data: Data<T>?)
}
@DFInternal
public class DataTreeBuilder<T>(private val type: KType) : DataSink<T> {
private val map = HashMap<Name, Data<T>>()
override fun data(name: Name, data: Data<T>?) {
override fun put(name: Name, data: Data<T>?) {
if (data == null) {
map.remove(name)
} else {
@ -174,6 +210,7 @@ public inline fun <T> DataTree(
/**
* Create and a data tree.
*/
@OptIn(DFInternal::class)
public inline fun <reified T> DataTree(
generator: DataSink<T>.() -> Unit,
): DataTree<T> = DataTreeBuilder<T>(typeOf<T>()).apply(generator).build()
@ -182,77 +219,88 @@ public inline fun <reified T> DataTree(
* A mutable version of [GenericDataTree]
*/
public interface MutableDataTree<T> : GenericObservableDataTree<T, MutableDataTree<T>>, DataSink<T> {
public val scope: CoroutineScope
override var data: Data<T>?
override val items: Map<NameToken, MutableDataTree<T>>
public fun getOrCreateItem(token: NameToken): MutableDataTree<T>
public operator fun set(token: NameToken, data: Data<T>?)
override fun data(name: Name, data: Data<T>?): Unit = set(name, data)
override fun put(name: Name, data: Data<T>?): Unit = set(name, data)
}
public tailrec operator fun <T> MutableDataTree<T>.set(name: Name, data: Data<T>?): Unit {
when (name.length) {
0 -> this.data = data
1 -> set(name.first(), data)
else -> items[name.first()]?.set(name.cutFirst(), data)
else -> getOrCreateItem(name.first())[name.cutFirst()] = data
}
}
private class ObservableMutableDataTreeImpl<T>(
private class MutableDataTreeImpl<T>(
override val dataType: KType,
override val scope: CoroutineScope,
override val updatesScope: CoroutineScope,
) : MutableDataTree<T> {
private val updates = MutableSharedFlow<NamedData<T>>()
private val children = HashMap<NameToken, MutableDataTree<T>>()
override var data: Data<T>? = null
set(value) {
if (!updatesScope.isActive) error("Can't send updates to closed MutableDataTree")
field = value
if (value != null) {
scope.launch {
updatesScope.launch {
updates.emit(value.named(Name.EMPTY))
}
}
}
override val items: Map<NameToken, MutableDataTree<T>> get() = children
override fun getOrCreateItem(token: NameToken): MutableDataTree<T> = children.getOrPut(token){
MutableDataTreeImpl(dataType, updatesScope)
}
override val self: MutableDataTree<T> get() = this
override fun set(token: NameToken, data: Data<T>?) {
children.getOrPut(token) {
ObservableMutableDataTreeImpl<T>(dataType, scope).also { subTree ->
if (!updatesScope.isActive) error("Can't send updates to closed MutableDataTree")
val subTree = getOrCreateItem(token)
subTree.updates().onEach {
updates.emit(it.named(token + it.name))
}.launchIn(scope)
}
}.data = data
}.launchIn(updatesScope)
subTree.data = data
}
override fun updates(): Flow<NamedData<T>> = flow {
//emit this node updates
updates.collect {
emit(it)
}
}
override fun updates(): Flow<NamedData<T>> = updates
}
/**
* Create a new [MutableDataTree]
*
* @param parentScope a [CoroutineScope] to control data propagation. By default uses [GlobalScope]
*/
@OptIn(DelicateCoroutinesApi::class)
public fun <T> MutableDataTree(
type: KType,
scope: CoroutineScope
): MutableDataTree<T> = ObservableMutableDataTreeImpl<T>(type, scope)
parentScope: CoroutineScope = GlobalScope,
): MutableDataTree<T> = MutableDataTreeImpl<T>(
type,
CoroutineScope(parentScope.coroutineContext + Job(parentScope.coroutineContext[Job]))
)
/**
* Create and initialize a observable mutable data tree.
*/
@OptIn(DelicateCoroutinesApi::class)
public inline fun <reified T> MutableDataTree(
scope: CoroutineScope,
parentScope: CoroutineScope = GlobalScope,
generator: MutableDataTree<T>.() -> Unit = {},
): MutableDataTree<T> = MutableDataTree<T>(typeOf<T>(), scope).apply { generator() }
): MutableDataTree<T> = MutableDataTree<T>(typeOf<T>(), parentScope).apply { generator() }
//@DFInternal
//public fun <T> ObservableDataTree(
@ -262,18 +310,21 @@ public inline fun <reified T> MutableDataTree(
//): ObservableDataTree<T> = MutableDataTree<T>(type, scope.coroutineContext).apply(generator)
public inline fun <reified T> ObservableDataTree(
scope: CoroutineScope,
parentScope: CoroutineScope,
generator: MutableDataTree<T>.() -> Unit = {},
): ObservableDataTree<T> = MutableDataTree<T>(typeOf<T>(), scope).apply(generator)
): ObservableDataTree<T> = MutableDataTree<T>(typeOf<T>(), parentScope).apply(generator)
/**
* Collect a [Sequence] into an observable tree with additional [updates]
*/
public fun <T> Sequence<NamedData<T>>.toObservableTree(dataType: KType, scope: CoroutineScope, updates: Flow<NamedData<T>>): ObservableDataTree<T> =
MutableDataTree<T>(dataType, scope).apply {
emitAll(this@toObservableTree)
public fun <T> Sequence<NamedData<T>>.toObservableTree(
dataType: KType,
parentScope: CoroutineScope,
updates: Flow<NamedData<T>>,
): ObservableDataTree<T> = MutableDataTree<T>(dataType, parentScope).apply {
this.putAll(this@toObservableTree)
updates.onEach {
data(it.name, it.data)
}.launchIn(scope)
}
put(it.name, it.data)
}.launchIn(updatesScope)
}

4
dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/data/GroupRule.kt
View File

@ -17,6 +17,7 @@ package space.kscience.dataforge.data
import space.kscience.dataforge.meta.get
import space.kscience.dataforge.meta.string
import space.kscience.dataforge.misc.DFInternal
public interface GroupRule {
public fun <T : Any> gather(set: DataTree<T>): Map<String, DataTree<T>>
@ -30,6 +31,7 @@ public interface GroupRule {
* @param defaultTagValue
* @return
*/
@OptIn(DFInternal::class)
public fun byMetaValue(
key: String,
defaultTagValue: String,
@ -42,7 +44,7 @@ public interface GroupRule {
set.forEach { data ->
val tagValue: String = data.meta[key]?.string ?: defaultTagValue
map.getOrPut(tagValue) { DataTreeBuilder(set.dataType) }.data(data.name,data.data)
map.getOrPut(tagValue) { DataTreeBuilder(set.dataType) }.put(data.name, data.data)
}

75
dataforge-data/src/commonMain/kotlin/space/kscience/dataforge/data/dataBuilders.kt
View File

@ -12,16 +12,12 @@ import space.kscience.dataforge.names.isEmpty
import space.kscience.dataforge.names.plus
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 { data(it) }
public fun <T> DataSink<T>.put(value: NamedData<T>) {
put(value.name, value.data)
}
public fun <T> DataSink<T>.branch(dataTree: DataTree<T>) {
emitAll(dataTree.asSequence())
putAll(dataTree.asSequence())
}
public inline fun <T> DataSink<T>.branch(
@ -32,7 +28,7 @@ public inline fun <T> DataSink<T>.branch(
apply(block)
} else {
val proxyDataSink = DataSink { nameWithoutPrefix, data ->
this.data(prefix + nameWithoutPrefix, data)
this.put(prefix + nameWithoutPrefix, data)
}
proxyDataSink.apply(block)
@ -45,69 +41,69 @@ public inline fun <T> DataSink<T>.branch(
): Unit = branch(prefix.asName(), block)
public fun <T> DataSink<T>.data(name: String, value: Data<T>) {
data(Name.parse(name), value)
public fun <T> DataSink<T>.put(name: String, value: Data<T>) {
put(Name.parse(name), value)
}
public fun <T> DataSink<T>.branch(name: Name, set: DataTree<T>) {
branch(name) { emitAll(set.asSequence()) }
branch(name) { putAll(set.asSequence()) }
}
public fun <T> DataSink<T>.branch(name: String, set: DataTree<T>) {
branch(Name.parse(name)) { emitAll(set.asSequence()) }
branch(Name.parse(name)) { putAll(set.asSequence()) }
}
/**
* Produce lazy [Data] and emit it into the [MutableDataTree]
*/
public inline fun <reified T> DataSink<T>.data(
public inline fun <reified T> DataSink<T>.put(
name: String,
meta: Meta = Meta.EMPTY,
noinline producer: suspend () -> T,
) {
val data = Data(meta, block = producer)
data(name, data)
put(name, data)
}
public inline fun <reified T> DataSink<T>.data(
public inline fun <reified T> DataSink<T>.put(
name: Name,
meta: Meta = Meta.EMPTY,
noinline producer: suspend () -> T,
) {
val data = Data(meta, block = producer)
data(name, data)
put(name, data)
}
/**
* Emit static data with the fixed value
*/
public inline fun <reified T> DataSink<T>.static(
public inline fun <reified T> DataSink<T>.wrap(
name: String,
data: T,
meta: Meta = Meta.EMPTY,
): Unit = data(name, Data.static(data, meta))
): Unit = put(name, Data.static(data, meta))
public inline fun <reified T> DataSink<T>.static(
public inline fun <reified T> DataSink<T>.wrap(
name: Name,
data: T,
meta: Meta = Meta.EMPTY,
): Unit = data(name, Data.static(data, meta))
): Unit = put(name, Data.static(data, meta))
public inline fun <reified T> DataSink<T>.static(
public inline fun <reified T> DataSink<T>.wrap(
name: String,
data: T,
mutableMeta: MutableMeta.() -> Unit,
): Unit = data(Name.parse(name), Data.static(data, Meta(mutableMeta)))
): Unit = put(Name.parse(name), Data.static(data, Meta(mutableMeta)))
public fun <T> DataSink<T>.populateFrom(sequence: Sequence<NamedData<T>>) {
public fun <T> DataSink<T>.putAll(sequence: Sequence<NamedData<T>>) {
sequence.forEach {
data(it.name, it.data)
put(it.name, it.data)
}
}
public fun <T> DataSink<T>.populateFrom(tree: DataTree<T>) {
populateFrom(tree.asSequence())
public fun <T> DataSink<T>.putAll(tree: DataTree<T>) {
this.putAll(tree.asSequence())
}
@ -115,13 +111,22 @@ public fun <T> DataSink<T>.populateFrom(tree: DataTree<T>) {
* Update data with given node data and meta with node meta.
*/
@DFExperimental
public fun <T> MutableDataTree<T>.populateFrom(flow: ObservableDataSource<T>): Job = flow.updates().onEach {
//TODO check if the place is occupied
data(it.name, it.data)
}.launchIn(scope)
public fun <T> MutableDataTree<T>.putAll(source: DataTree<T>) {
source.forEach {
put(it.name, it.data)
}
}
//public fun <T > DataSetBuilder<T>.populateFrom(flow: Flow<NamedData<T>>) {
// flow.collect {
// data(it.name, it.data)
// }
//}
/**
* Copy given data set and mirror its changes to this [DataSink] in [this@setAndObserve]. Returns an update [Job]
*/
public fun <T : Any> DataSink<T>.watchBranch(
name: Name,
dataSet: ObservableDataTree<T>,
): Job {
branch(name, dataSet)
return dataSet.updates().onEach {
put(name + it.name, it.data)
}.launchIn(dataSet.updatesScope)
}

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

@ -194,7 +194,7 @@ public suspend fun <T, R> DataTree<T>.transform(
val d = Data(outputType, newMeta, coroutineContext, listOf(namedData)) {
block(namedData.awaitWithMeta())
}
data(namedData.name, d)
put(namedData.name, d)
}
}

19
dataforge-data/src/jvmMain/kotlin/space/kscience/dataforge/data/dataSetBuilderInContext.kt
View File

@ -1,10 +1,6 @@
package space.kscience.dataforge.data
import kotlinx.coroutines.CoroutineScope
import kotlinx.coroutines.Job
import kotlinx.coroutines.launch
import space.kscience.dataforge.names.Name
import space.kscience.dataforge.names.plus
/**
@ -12,7 +8,7 @@ import space.kscience.dataforge.names.plus
*/
context(DataSink<T>)
public infix fun <T : Any> String.put(data: Data<T>): Unit =
data(Name.parse(this), data)
put(Name.parse(this), data)
/**
* Append node
@ -29,16 +25,3 @@ public infix fun <T : Any> String.put(
block: DataSink<T>.() -> Unit,
): Unit = branch(Name.parse(this), block)
/**
* Copy given data set and mirror its changes to this [LegacyDataTreeBuilder] in [this@setAndObserve]. Returns an update [Job]
*/
context(DataSink<T>)
public fun <T : Any> CoroutineScope.setAndWatch(
name: Name,
dataSet: DataTree<T>,
): Job = launch {
branch(name, dataSet)
dataSet.updates().collect {
data(name + it.name, it.data)
}
}

20
dataforge-data/src/jvmTest/kotlin/space/kscience/dataforge/data/ActionsTest.kt
View File

@ -1,7 +1,7 @@
package space.kscience.dataforge.data
import kotlinx.coroutines.ExperimentalCoroutinesApi
import kotlinx.coroutines.delay
import kotlinx.coroutines.runBlocking
import kotlinx.coroutines.test.runTest
import org.junit.jupiter.api.Test
import space.kscience.dataforge.actions.Action
@ -10,13 +10,13 @@ import space.kscience.dataforge.actions.mapping
import space.kscience.dataforge.misc.DFExperimental
import kotlin.test.assertEquals
@OptIn(DFExperimental::class, ExperimentalCoroutinesApi::class)
@OptIn(DFExperimental::class)
internal class ActionsTest {
@Test
fun testStaticMapAction() = runTest {
val data: DataTree<Int> = DataTree {
repeat(10) {
static(it.toString(), it)
wrap(it.toString(), it)
}
}
@ -28,20 +28,24 @@ internal class ActionsTest {
}
@Test
fun testDynamicMapAction() = runTest {
val data: MutableDataTree<Int> = MutableDataTree(this)
fun testDynamicMapAction() = runBlocking {
val source: MutableDataTree<Int> = MutableDataTree()
val plusOne = Action.mapping<Int, Int> {
result { it + 1 }
}
val result = plusOne(data)
val result = plusOne(source)
repeat(10) {
data.static(it.toString(), it)
source.wrap(it.toString(), it)
}
delay(20)
delay(10)
source.close()
result.awaitClose()
assertEquals(2, result["1"]?.await())
}

69
dataforge-data/src/jvmTest/kotlin/space/kscience/dataforge/data/DataTreeBuilderTest.kt
View File

@ -1,6 +1,8 @@
package space.kscience.dataforge.data
import kotlinx.coroutines.*
import kotlinx.coroutines.delay
import kotlinx.coroutines.runBlocking
import kotlinx.coroutines.test.runTest
import space.kscience.dataforge.misc.DFExperimental
import space.kscience.dataforge.names.asName
import kotlin.test.Test
@ -9,26 +11,25 @@ import kotlin.test.assertEquals
internal class DataTreeBuilderTest {
@Test
fun testTreeBuild() = runBlocking {
fun testTreeBuild() = runTest {
val node = DataTree<Any> {
"primary" put {
static("a", "a")
static("b", "b")
wrap("a", "a")
wrap("b", "b")
}
static("c.d", "c.d")
static("c.f", "c.f")
wrap("c.d", "c.d")
wrap("c.f", "c.f")
}
runBlocking {
assertEquals("a", node["primary.a"]?.await())
assertEquals("b", node["primary.b"]?.await())
assertEquals("c.d", node["c.d"]?.await())
assertEquals("c.f", node["c.f"]?.await())
}
}
@OptIn(DFExperimental::class)
@Test
fun testDataUpdate() = runBlocking {
fun testDataUpdate() = runTest {
val updateData = DataTree<Any> {
"update" put {
"a" put Data.static("a")
@ -38,54 +39,30 @@ internal class DataTreeBuilderTest {
val node = DataTree<Any> {
"primary" put {
static("a", "a")
static("b", "b")
wrap("a", "a")
wrap("b", "b")
}
static("root", "root")
populateFrom(updateData)
wrap("root", "root")
putAll(updateData)
}
runBlocking {
assertEquals("a", node["update.a"]?.await())
assertEquals("a", node["primary.a"]?.await())
}
}
@Test
fun testDynamicUpdates() = runBlocking {
try {
lateinit var updateJob: Job
supervisorScope {
val subNode = ObservableDataTree<Int>(this) {
updateJob = launch {
val subNode = MutableDataTree<Int>()
val rootNode = MutableDataTree<Int> {
watchBranch("sub".asName(), subNode)
}
repeat(10) {
delay(10)
static("value", it)
}
delay(10)
}
}
launch {
subNode.updates().collect {
println(it)
}
}
val rootNode = ObservableDataTree<Int>(this) {
setAndWatch("sub".asName(), subNode)
}
launch {
rootNode.updates().collect {
println(it)
}
}
updateJob.join()
assertEquals(9, rootNode["sub.value"]?.await())
cancel()
}
} catch (t: Throwable) {
if (t !is CancellationException) throw t
subNode.wrap("value[$it]", it)
}
delay(20)
assertEquals(9, rootNode["sub.value[9]"]?.await())
}
}

13
dataforge-workspace/src/commonMain/kotlin/space/kscience/dataforge/workspace/Task.kt
View File

@ -88,12 +88,17 @@ public fun <T : Any> Task(
workspace: Workspace,
taskName: Name,
taskMeta: Meta,
): TaskResult<T> = withContext(GoalExecutionRestriction() + workspace.goalLogger) {
): TaskResult<T> {
//TODO use safe builder and check for external data on add and detects cycles
val dataset = MutableDataTree<T>(resultType, this).apply {
TaskResultBuilder(workspace, taskName, taskMeta, this).apply { builder() }
val dataset = MutableDataTree<T>(resultType, workspace.context).apply {
TaskResultBuilder(workspace, taskName, taskMeta, this).apply {
withContext(GoalExecutionRestriction() + workspace.goalLogger) {
builder()
}
workspace.wrapResult(dataset, taskName, taskMeta)
}
}
return workspace.wrapResult(dataset, taskName, taskMeta)
}
}

10
dataforge-workspace/src/commonMain/kotlin/space/kscience/dataforge/workspace/TaskResult.kt
View File

@ -2,6 +2,7 @@ package space.kscience.dataforge.workspace
import kotlinx.coroutines.CoroutineScope
import kotlinx.coroutines.Job
import kotlinx.coroutines.joinAll
import kotlinx.coroutines.launch
import space.kscience.dataforge.data.ObservableDataTree
import space.kscience.dataforge.data.asSequence
@ -20,7 +21,7 @@ public data class TaskResult<T>(
public val workspace: Workspace,
public val taskName: Name,
public val taskMeta: Meta,
): ObservableDataTree<T> by content
) : ObservableDataTree<T> by content
/**
* Wrap data into [TaskResult]
@ -32,8 +33,9 @@ public fun <T> Workspace.wrapResult(data: ObservableDataTree<T>, taskName: Name,
* 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 {
public fun TaskResult<*>.launch(scope: CoroutineScope): Job {
val jobs = asSequence().map {
it.data.launch(scope)
}
}.toList()
return scope.launch { jobs.joinAll() }
}

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

@ -102,7 +102,7 @@ public inline fun <T : Any, reified R : Any> TaskContainer.action(
noinline descriptorBuilder: MetaDescriptorBuilder.() -> Unit = {},
): PropertyDelegateProvider<Any?, ReadOnlyProperty<Any?, TaskReference<R>>> =
task(MetaDescriptor(descriptorBuilder)) {
result(action.execute(workspace.context, from(selector), taskMeta.copy(metaTransform)))
result(action.execute(from(selector), taskMeta.copy(metaTransform)))
}
public class WorkspaceBuilder(

4
dataforge-workspace/src/commonMain/kotlin/space/kscience/dataforge/workspace/taskBuilders.kt
View File

@ -93,7 +93,7 @@ public suspend inline fun <T, reified R> TaskResultBuilder<R>.transformEach(
action(it, data.name, meta)
}
data(data.name, res)
put(data.name, res)
}
}
@ -113,7 +113,7 @@ public suspend inline fun <T, reified R> TaskResultBuilder<R>.actionFrom(
action: Action<T, R>,
dependencyMeta: Meta = defaultDependencyMeta,
) {
branch(action.execute(workspace.context, from(selector, dependencyMeta), dependencyMeta))
branch(action.execute(from(selector, dependencyMeta), dependencyMeta))
}

96
dataforge-workspace/src/jvmMain/kotlin/space/kscience/dataforge/workspace/fileData.kt
View File

@ -11,7 +11,6 @@ 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
@ -36,20 +35,6 @@ public object FileData {
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)
}
}
)
}
}
@ -77,51 +62,68 @@ public fun IOPlugin.readFileData(
)
}
public fun DataSink<Binary>.file(io: IOPlugin, path: Path, name: Name) {
public fun DataSink<Binary>.file(io: IOPlugin, name: Name, path: Path) {
if (!path.isRegularFile()) error("Only regular files could be handled by this function")
data(name, io.readFileData(path))
put(name, io.readFileData(path))
}
public fun DataSink<Binary>.directory(
io: IOPlugin,
name: Name,
path: Path,
pathToName: (Path) -> Name = defaultPathToName,
) {
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
)
)
}
var dataBinary: Binary? = null
var meta: Meta? = null
Files.list(path).forEach { childPath ->
val fileName = childPath.fileName.toString()
if (!fileName.startsWith("@")) {
files(io, childPath, pathToName)
if (fileName == IOPlugin.DATA_FILE_NAME) {
dataBinary = childPath.asBinary()
} else if (fileName.startsWith(IOPlugin.META_FILE_NAME)) {
meta = io.readMetaFileOrNull(childPath)
} else if (!fileName.startsWith("@")) {
val token = if (childPath.isRegularFile() && childPath.extension in FileData.DEFAULT_IGNORE_EXTENSIONS) {
NameToken(childPath.nameWithoutExtension)
} else {
NameToken(childPath.name)
}
files(io, name + token, childPath)
}
}
//set data if it is relevant
if (dataBinary != null || meta != null) {
put(
name,
StaticData(
typeOf<Binary>(),
dataBinary ?: Binary.EMPTY,
meta ?: Meta.EMPTY
)
)
}
}
public fun DataSink<Binary>.files(io: IOPlugin, path: Path, pathToName: (Path) -> Name = defaultPathToName) {
public fun DataSink<Binary>.files(
io: IOPlugin,
name: Name,
path: Path,
) {
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 files(io, fs.rootDirectories.first(), pathToName)
files(io, name, fs.rootDirectories.first())
}
if (path.isRegularFile()) {
file(io, path, pathToName(path))
file(io, name, path)
} else {
directory(io, path, pathToName)
directory(io, name, path)
}
}
@ -132,11 +134,11 @@ private fun Path.toName() = Name(map { NameToken.parse(it.nameWithoutExtension)
@DFExperimental
public fun DataSink<Binary>.monitorFiles(
io: IOPlugin,
name: Name,
path: Path,
pathToName: (Path) -> Name = defaultPathToName,
scope: CoroutineScope = io.context,
): Job {
files(io, path, pathToName)
files(io, name, path)
return scope.launch(Dispatchers.IO) {
val watchService = path.fileSystem.newWatchService()
@ -153,11 +155,11 @@ public fun DataSink<Binary>.monitorFiles(
for (event: WatchEvent<*> in key.pollEvents()) {
val eventPath = event.context() as Path
if (event.kind() == StandardWatchEventKinds.ENTRY_DELETE) {
data(eventPath.toName(), null)
put(eventPath.toName(), null)
} else {
val fileName = eventPath.fileName.toString()
if (!fileName.startsWith("@")) {
files(io, eventPath, pathToName)
files(io, name, eventPath)
}
}
}
@ -179,18 +181,14 @@ public suspend fun <T : Any> IOPlugin.writeDataDirectory(
dataSet: DataTree<T>,
format: IOWriter<T>,
envelopeFormat: EnvelopeFormat? = null,
nameToPath: (name: Name, data: Data<T>) -> Path = { name, _ ->
Path(name.tokens.joinToString("/") { token -> token.toStringUnescaped() })
},
) {
withContext(Dispatchers.IO) {
): Unit = withContext(Dispatchers.IO) {
if (!Files.exists(path)) {
Files.createDirectories(path)
} else if (!Files.isDirectory(path)) {
error("Can't write a node into file")
}
dataSet.forEach { (name, data) ->
val childPath = path.resolve(nameToPath(name, data))
val childPath = path.resolve(name.tokens.joinToString("/") { token -> token.toStringUnescaped() })
childPath.parent.createDirectories()
val envelope = data.toEnvelope(format)
if (envelopeFormat != null) {
@ -201,7 +199,6 @@ public suspend fun <T : Any> IOPlugin.writeDataDirectory(
}
dataSet.meta?.let { writeMetaFile(path, it) }
}
}
/**
@ -212,15 +209,12 @@ public suspend fun <T : Any> IOPlugin.writeDataDirectory(
public fun DataSink<Binary>.resources(
io: IOPlugin,
vararg resources: String,
pathToName: (Path) -> Name = defaultPathToName,
classLoader: ClassLoader = Thread.currentThread().contextClassLoader,
) {
resources.forEach { resource ->
val path = classLoader.getResource(resource)?.toURI()?.toPath() ?: error(
"Resource with name $resource is not resolved"
)
branch(resource.asName()) {
files(io, path, pathToName)
}
files(io, resource.asName(), path)
}
}

67
dataforge-workspace/src/jvmMain/kotlin/space/kscience/dataforge/workspace/zipData.kt
View File

@ -3,67 +3,36 @@ package space.kscience.dataforge.workspace
import kotlinx.coroutines.Dispatchers
import kotlinx.coroutines.withContext
import space.kscience.dataforge.data.DataTree
import space.kscience.dataforge.io.*
import space.kscience.dataforge.io.EnvelopeFormat
import space.kscience.dataforge.io.IOPlugin
import space.kscience.dataforge.io.IOWriter
import space.kscience.dataforge.misc.DFExperimental
import java.nio.file.Files
import java.nio.file.Path
import java.nio.file.StandardOpenOption
import java.util.zip.ZipEntry
import java.util.zip.ZipOutputStream
private suspend fun <T : Any> ZipOutputStream.writeNode(
name: String,
tree: DataTree<T>,
dataFormat: IOFormat<T>,
envelopeFormat: EnvelopeFormat = TaggedEnvelopeFormat,
): Unit = withContext(Dispatchers.IO) {
//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)
}
write(bytes)
}
val entry = ZipEntry("$name/")
putNextEntry(entry)
closeEntry()
tree.items.forEach { (token, item) ->
val childName = "$name/$token"
writeNode(childName, item, dataFormat, envelopeFormat)
}
}
import java.nio.file.spi.FileSystemProvider
import kotlin.io.path.exists
import kotlin.io.path.extension
/**
* Write this [DataTree] as a zip archive
*/
@DFExperimental
public suspend fun <T : Any> DataTree<T>.writeZip(
public suspend fun <T : Any> IOPlugin.writeZip(
path: Path,
format: IOFormat<T>,
envelopeFormat: EnvelopeFormat = TaggedEnvelopeFormat,
dataSet: DataTree<T>,
format: IOWriter<T>,
envelopeFormat: EnvelopeFormat? = null,
): Unit = withContext(Dispatchers.IO) {
val actualFile = if (path.toString().endsWith(".zip")) {
if (path.exists()) error("Can't override existing zip data file $path")
val actualFile = if (path.extension == "zip") {
path
} else {
path.resolveSibling(path.fileName.toString() + ".zip")
}
val fos = Files.newOutputStream(
actualFile,
StandardOpenOption.WRITE,
StandardOpenOption.CREATE,
StandardOpenOption.TRUNCATE_EXISTING
)
val zos = ZipOutputStream(fos)
zos.use {
it.writeNode("", this@writeZip, format, envelopeFormat)
val fsProvider = FileSystemProvider.installedProviders().find { it.scheme == "jar" }
?: error("Zip file system provider not found")
//val fs = FileSystems.newFileSystem(actualFile, mapOf("create" to true))
val fs = fsProvider.newFileSystem(actualFile, mapOf("create" to true))
fs.use {
writeDataDirectory(fs.rootDirectories.first(), dataSet, format, envelopeFormat)
}
}

19
dataforge-workspace/src/jvmTest/kotlin/space/kscience/dataforge/workspace/CachingWorkspaceTest.kt
View File

@ -1,17 +1,16 @@
package space.kscience.dataforge.workspace
import kotlinx.coroutines.ExperimentalCoroutinesApi
import kotlinx.coroutines.coroutineScope
import kotlinx.coroutines.test.runTest
import org.junit.jupiter.api.Test
import space.kscience.dataforge.data.static
import space.kscience.dataforge.data.wrap
import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.meta.boolean
import space.kscience.dataforge.meta.get
import space.kscience.dataforge.misc.DFExperimental
import kotlin.test.assertEquals
@OptIn(ExperimentalCoroutinesApi::class, DFExperimental::class)
@OptIn(DFExperimental::class)
internal class CachingWorkspaceTest {
@Test
@ -23,7 +22,7 @@ internal class CachingWorkspaceTest {
data {
//statically initialize data
repeat(5) {
static("myData[$it]", it)
wrap("myData[$it]", it)
}
}
@ -39,7 +38,7 @@ internal class CachingWorkspaceTest {
val doSecond by task<Any> {
transformEach(
doFirst,
dependencyMeta = if(taskMeta["flag"].boolean == true) taskMeta else Meta.EMPTY
dependencyMeta = if (taskMeta["flag"].boolean == true) taskMeta else Meta.EMPTY
) { _, name, _ ->
secondCounter++
println("Done second on $name with flag=${taskMeta["flag"].boolean ?: false}")
@ -51,13 +50,15 @@ internal class CachingWorkspaceTest {
val secondA = workspace.produce("doSecond")
val secondB = workspace.produce("doSecond", Meta { "flag" put true })
val secondC = workspace.produce("doSecond")
//use coroutineScope to wait for the result
coroutineScope {
first.compute(this)
secondA.compute(this)
secondB.compute(this)
first.launch(this)
secondA.launch(this)
secondB.launch(this)
//repeat to check caching
secondC.compute(this)
secondC.launch(this)
}
assertEquals(10, firstCounter)
assertEquals(10, secondCounter)
}

6
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
}
data("result", result)
put("result", result)
}
val singleData by task<Int> {
workspace.data.filterByType<Int>()["myData[12]"]?.let {
data("result", it)
put("result", it)
}
}
@ -47,7 +47,7 @@ class DataPropagationTest {
}
data {
repeat(100) {
static("myData[$it]", it)
wrap("myData[$it]", it)
}
}
}

24
dataforge-workspace/src/jvmTest/kotlin/space/kscience/dataforge/workspace/FileDataTest.kt
View File

@ -1,6 +1,5 @@
package space.kscience.dataforge.workspace
import kotlinx.coroutines.runBlocking
import kotlinx.coroutines.test.runTest
import kotlinx.io.Sink
import kotlinx.io.Source
@ -13,7 +12,9 @@ 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 space.kscience.dataforge.names.Name
import java.nio.file.Files
import kotlin.io.path.deleteExisting
import kotlin.io.path.fileSize
import kotlin.io.path.toPath
import kotlin.test.Test
@ -23,11 +24,11 @@ import kotlin.test.assertEquals
class FileDataTest {
val dataNode = DataTree<String> {
branch("dir") {
static("a", "Some string") {
wrap("a", "Some string") {
"content" put "Some string"
}
}
static("b", "root data")
wrap("b", "root data")
// meta {
// "content" put "This is root meta node"
// }
@ -45,18 +46,18 @@ class FileDataTest {
@Test
@DFExperimental
fun testDataWriteRead() = with(Global.io) {
fun testDataWriteRead() = runTest {
val io = Global.io
val dir = Files.createTempDirectory("df_data_node")
runBlocking {
writeDataDirectory(dir, dataNode, StringIOFormat)
io.writeDataDirectory(dir, dataNode, StringIOFormat)
println(dir.toUri().toString())
val reconstructed = DataTree { files(io, dir) }
.transform { (_, value) -> value.toByteArray().decodeToString() }
val data = DataTree {
files(io, Name.EMPTY, dir)
}
val reconstructed = data.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())
}
}
@Test
@ -64,9 +65,10 @@ class FileDataTest {
fun testZipWriteRead() = runTest {
val io = Global.io
val zip = Files.createTempFile("df_data_node", ".zip")
dataNode.writeZip(zip, StringIOFormat)
zip.deleteExisting()
io.writeZip(zip, dataNode, StringIOFormat)
println(zip.toUri().toString())
val reconstructed = DataTree { files(io, zip) }
val reconstructed = DataTree { files(io, Name.EMPTY, 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())

6
dataforge-workspace/src/jvmTest/kotlin/space/kscience/dataforge/workspace/FileWorkspaceCacheTest.kt
View File

@ -3,7 +3,7 @@ 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.static
import space.kscience.dataforge.data.wrap
import space.kscience.dataforge.misc.DFExperimental
import java.nio.file.Files
@ -16,7 +16,7 @@ class FileWorkspaceCacheTest {
data {
//statically initialize data
repeat(5) {
static("myData[$it]", it)
wrap("myData[$it]", it)
}
}
fileCache(Files.createTempDirectory("dataforge-temporary-cache"))
@ -26,7 +26,7 @@ class FileWorkspaceCacheTest {
}
}
workspace.produce("echo").compute(this)
workspace.produce("echo").launch(this)
}
}

16
dataforge-workspace/src/jvmTest/kotlin/space/kscience/dataforge/workspace/SimpleWorkspaceTest.kt
View File

@ -62,14 +62,14 @@ internal class SimpleWorkspaceTest {
data {
//statically initialize data
repeat(100) {
static("myData[$it]", it)
wrap("myData[$it]", it)
}
}
val filterOne by task<Int> {
val name by taskMeta.string { error("Name field not defined") }
from(testPluginFactory) { test }[name]?.let { source: Data<Int> ->
data(name, source)
put(name, source)
}
}
@ -97,7 +97,7 @@ internal class SimpleWorkspaceTest {
val newData: Data<Int> = data.combine(linearData[data.name]!!) { l, r ->
l + r
}
data(data.name, newData)
put(data.name, newData)
}
}
@ -106,7 +106,7 @@ internal class SimpleWorkspaceTest {
val res = from(square).foldToData(0) { l, r ->
l + r.value
}
data("sum", res)
put("sum", res)
}
val averageByGroup by task<Int> {
@ -116,13 +116,13 @@ internal class SimpleWorkspaceTest {
l + r.value
}
data("even", evenSum)
put("even", evenSum)
val oddSum = workspace.data.filterByType<Int> { name, _, _ ->
name.toString().toInt() % 2 == 1
}.foldToData(0) { l, r ->
l + r.value
}
data("odd", oddSum)
put("odd", oddSum)
}
val delta by task<Int> {
@ -132,7 +132,7 @@ internal class SimpleWorkspaceTest {
val res = even.combine(odd) { l, r ->
l - r
}
data("res", res)
put("res", res)
}
val customPipe by task<Int> {
@ -140,7 +140,7 @@ internal class SimpleWorkspaceTest {
val meta = data.meta.toMutableMeta().apply {
"newValue" put 22
}
data(data.name + "new", data.transform { (data.meta["value"].int ?: 0) + it })
put(data.name + "new", data.transform { (data.meta["value"].int ?: 0) + it })
}
}