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Alexander Nozik 2022-05-21 13:38:15 +03:00
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11
build.gradle.kts
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@ -3,6 +3,7 @@ import ru.mipt.npm.gradle.KScienceVersions
plugins {
id("ru.mipt.npm.gradle.project")
id("ru.mipt.npm.gradle.jvm")
id("org.hidetake.ssh") version "2.10.1"
application
}
@ -21,7 +22,7 @@ application {
}
val dataforgeVersion by extra("0.6.0-dev-7")
val dataforgeVersion by extra("0.6.0-dev-9")
val ktorVersion = KScienceVersions.ktorVersion
dependencies {
@ -42,11 +43,11 @@ dependencies {
kotlin {
explicitApi = org.jetbrains.kotlin.gradle.dsl.ExplicitApiMode.Disabled
sourceSets.all {
languageSettings {
languageVersion = "1.7"
apiVersion = "1.7"
}
tasks.withType<org.jetbrains.kotlin.gradle.tasks.KotlinCompile>{
kotlinOptions{
freeCompilerArgs = freeCompilerArgs + "-Xcontext-receivers"
}
}

75
data/home/content/people/Nozik.md Normal file
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@ -0,0 +1,75 @@
---
type: team
title: Alexander Nozik
id: nozik
order: 1
image: images/people/nozik_2.png
language: en
---
* PhD in particle physics.
* Director of [Scientific Programming Centre](/).
* Senior researcher at https://npm.mipt.ru.
* (ex) Team lead at [JetBrains Research](https://research.jetbrains.org/groups/npm/).
* Google developer expert in Kotlin.
<blockquote>
<ul>
<li> I am against the war in Ukraine. It must be stopped. </li>
<li> I did not vote for Putin. I do not think that Putin is the legitimate president of Russia. </li>
<li> I hope for the better future. I publicly express my position in <a href="https://twitter.com/noraltavir">my twitter</a>.</li>
<li> I do not speak for the whole laboratory. </li>
</ul>
</blockquote>
## About me
When I finished the school, I had two choices: I liked physics and I liked programming. In the end I decided that physics is more interesting. Now I am doing programming in physics. Currently I am doing software and physical data analysis for a number of experiments in particle physics (Troitsk nu-mass, IAXO and other experiments). I am leading development of scientific libraries and leading the development of new simulation software and models.
The laboratory at MIPT, we created in the last years includes young passionate researchers in different fields connected to particle and nuclear physics methods. The aim of the laboratory is to prepare the new generation of researchers, familiar with modern scientific tools and able to develop new ones.
## Social
* [ResearchGate profile](https://www.researchgate.net/profile/Alexander_Nozik)
* [Twitter](https://twitter.com/noraltavir)
* [Telegram](https://t.me/noraltavir)
## Education
* Lyceum “2nd school” 1997 - 2002
* MIPT (bachelor, problems of physics and energetics) 2002 - 2006. Finished with honors.
* MIPT (master, fundamental particles and cosmology) 2006 - 2008
* [PhD in physics](https://www.researchgate.net/publication/260058278_Rezultaty_obrabotki_dannyh_eksperimenta_Troick_nu-mass_po_pramomu_izmereniu_massy_elektronnogo_nejtrino), INR RAS 2012 .
## Work experience
* INR RAS Laboratory assistant, 2004–2008
* INR RAS Researcher, 2008–2012
* INR RAS Senior researcher, 2012–present
* MIPT Assistant, 2013–2018, The department of general physics laboratory practice and seminars. Special courses on programming and statistics.
* MIPT Associate professor, 2019–present
* MIPT Senior researcher, 2019–present, Deputy head of the nuclear physics methods laboratory.
* JetBrains Research, 2020–present, Head of the research group.
## The code
* Private GitHub account: https://github.com/altavir
* Laboratory / centre GitHub account: https://github.com/mipt-npm
## Achievements
* The best (until 2020) limit on electron neutrino mass: https://arxiv.org/abs/1108.5034
* The best limit on sterile neutrino contribution to the electron neutrino with masses up to 2 keV: https://arxiv.org/abs/1307.5687, https://arxiv.org/abs/1703.10779
* The data acquisition and analysis software in Troitsk nu-mass experiment.
* The Reactor model for TGF generation in thunderclouds.
* KMath library: https://github.com/mipt-npm/kmath.
## Publications
* ORCID: https://orcid.org/0000-0001-9075-0080
* Scopus ID: 24071435300
* Web of Science ID: H-3844-2019
## Keywords
Particle physics, Neutrino, Data analysis, Mathematical statistics, Scientific programming, Java, Kotlin

5
data/home/content/people/Nozik[info].md Normal file
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@ -0,0 +1,5 @@
* PhD in particle physics.
* Director of [Scientific Programming Centre](/).
* Senior researcher at https://npm.mipt.ru.
* (ex) Team lead at [JetBrains Research](https://research.jetbrains.org/groups/npm/).
* Google developer expert in Kotlin.

10
data/home/content/projects/kmath.md Normal file
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@ -0,0 +1,10 @@
---
type: project
title: KMath
order: 2
language: en
---
An experimental Kotlin library for mathematical operations, built on the principle of context-oriented programming using mathematical abstractions.
[Repository and documentation](https://github.com/altavir/kmath)

1
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@ -0,0 +1 @@
An experimental Kotlin library for mathematical operations, built on the principle of context-oriented programming using mathematical abstractions.

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data/magprog/content/team/muhina.md → data/magprog/content/team/Muhina.md
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data/magprog/content/team/nozik.md → data/magprog/content/team/Nozik.md
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data/magprog/content/team/svetlichnii.md → data/magprog/content/team/Svetlichnii.md
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2
gradle.properties
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@ -1,3 +1,3 @@
kotlin.code.style=official
toolsVersion=0.11.4-kotlin-1.6.20
toolsVersion=0.11.5-kotlin-1.6.21

2
src/main/kotlin/ru/mipt/spc/master.kt
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@ -268,7 +268,7 @@ internal fun Application.spcMaster(context: Context, dataPath: Path, prefix: Str
val snark = context.fetch(SnarkPlugin)
val magProgPageContext = snark.parse(prefix, dataPath.resolve("content"))
val magProgPageContext: PageContext = snark.parse(prefix, dataPath.resolve("content"))
routing {
route(prefix) {

194
src/main/kotlin/ru/mipt/spc/home.kt → src/main/kotlin/ru/mipt/spc/spcHome.kt
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@ -11,166 +11,20 @@ import io.ktor.server.routing.*
import kotlinx.html.*
import space.kscience.dataforge.context.Context
import space.kscience.dataforge.context.fetch
import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.meta.get
import space.kscience.dataforge.meta.string
import space.kscience.dataforge.names.Name
import space.kscience.dataforge.names.parseAsName
import space.kscience.snark.*
import java.nio.file.Path
private const val SPC_TITLE = "Scientific Programming Centre"
context(PageContext) private fun HTML.spcHead(title: String = SPC_TITLE) {
head {
title {
+title
}
meta {
charset = "utf-8"
}
meta {
name = "viewport"
content = "width=device-width, initial-scale=1, user-scalable=no"
}
link(rel = "stylesheet", href = resolveRef("assets/css/main.css"))
noScript {
link(rel = "stylesheet", href = resolveRef("assets/css/noscript.css"))
}
}
}
context(PageContext) private fun FlowContent.spcHomeMenu() {
nav {
id = "menu"
ul("links") {
li {
a {
href = homeRef
+"""Home"""
}
}
li {
a {
href = resolveRef("magprog")
+"""Master"""
}
}
li {
a {
href = resolveRef("research")
+"""Research"""
}
}
li {
a {
href = resolveRef("consulting")
+"""Consulting"""
}
}
li {
a {
href = resolveRef("team")
+"""Team"""
}
}
}
// ul("actions stacked") {
// li {
// a(classes = "button primary fit") {
// href = "#"
// +"""Get Started"""
// }
// }
// li {
// a(classes = "button fit") {
// href = "#"
// +"""Log In"""
// }
// }
// }
}
}
context(PageContext) private fun FlowContent.spcFooter() {
footer {
id = "footer"
div("inner") {
ul("icons") {
// li {
// a(classes = "icon brands alt fa-twitter") {
// href = "#"
// span("label") { +"""Twitter""" }
// }
// }
// li {
// a(classes = "icon brands alt fa-facebook-f") {
// href = "#"
// span("label") { +"""Facebook""" }
// }
// }
// li {
// a(classes = "icon brands alt fa-instagram") {
// href = "#"
// span("label") { +"""Instagram""" }
// }
// }
li {
a(classes = "icon brands alt fa-github") {
href = "https://github.com/mipt-npm"
span("label") { +"""GitHub""" }
}
}
// li {
// a(classes = "icon brands alt fa-linkedin-in") {
// href = "#"
// span("label") { +"""LinkedIn""" }
// }
// }
}
ul("copyright") {
li { +"""SPC""" }
li {
+"""Design:"""
a {
href = "https://html5up.net"
+"""HTML5 UP"""
}
}
}
}
}
}
context(PageContext) private fun FlowContent.wrapper(contentBody: FlowContent.() -> Unit) {
div {
id = "wrapper"
// Header
header("alt") {
id = "header"
a(classes = "logo") {
href = homeRef
strong { +"""SPC""" }
span { +"""Scientific Programming Centre""" }
}
nav {
a {
href = "#menu"
+"""Menu"""
}
}
}
// Menu
spcHomeMenu()
//Body
contentBody()
// Footer
spcFooter()
}
}
context(PageContext) private fun HTML.spcPage(data: HtmlData) {
val title = data.meta["title"].string ?: SPC_TITLE
context(PageContext) internal fun HTML.spcPageContent(
meta: Meta,
title: String = meta["title"].string ?: SPC_TITLE,
fragment: FlowContent.() -> Unit,
) {
spcHead(title)
body("is-preload") {
wrapper {
@ -183,7 +37,7 @@ context(PageContext) private fun HTML.spcPage(data: HtmlData) {
header("major") {
h1 { +title }
}
data.meta["image"].string?.let { imagePath ->
meta["image"].string?.let { imagePath ->
span("image main") {
img {
src = resolveRef(imagePath)
@ -191,7 +45,7 @@ context(PageContext) private fun HTML.spcPage(data: HtmlData) {
}
}
}
htmlData(data)
fragment()
}
}
}
@ -201,26 +55,41 @@ context(PageContext) private fun HTML.spcPage(data: HtmlData) {
}
}
context(PageContext) private fun Route.spcPage(subRoute: String, data: HtmlData) {
context(PageContext) internal fun Route.spcPage(subRoute: String, meta: Meta, fragment: FlowContent.() -> Unit) {
get(subRoute) {
withRequest(call.request) {
call.respondHtml {
spcPage(data)
spcPageContent(meta, fragment = fragment)
}
}
}
}
context(PageContext) private fun Route.spcPage(subRoute: String, dataPath: String = subRoute) {
val data = resolveHtml(dataPath.parseAsName())
context(PageContext) internal fun Route.spcPage(
subRoute: String,
dataPath: Name = subRoute.parseAsName(),
more: FlowContent.() -> Unit = {},
) {
val data = resolveHtml(dataPath)
if (data != null) {
spcPage(subRoute, data)
spcPage(subRoute, data.meta) {
htmlData(data)
more()
}
} else {
application.log.error("Content for page with path $dataPath not found")
}
}
context(PageContext) internal fun Route.spcPage(
name: Name,
more: FlowContent.() -> Unit = {},
) {
spcPage(name.tokens.joinToString("/"), name, more)
}
context(PageContext) private fun HTML.spcHome() {
spcHead()
body("is-preload") {
@ -420,8 +289,9 @@ internal fun Application.spcHome(context: Context, rootPath: Path, prefix: Strin
}
spcPage("consulting")
spcPage("research")
spcPage("team")
spcLanding("team") { _, m -> m["type"].string == "team" }
spcLanding("research"){ _, m -> m["type"].string == "project" }
}
}
}

119
src/main/kotlin/ru/mipt/spc/spcLanding.kt Normal file
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@ -0,0 +1,119 @@
package ru.mipt.spc
import html5up.forty.fortyScripts
import io.ktor.server.application.call
import io.ktor.server.html.respondHtml
import io.ktor.server.routing.Route
import io.ktor.server.routing.get
import kotlinx.html.*
import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.meta.get
import space.kscience.dataforge.meta.string
import space.kscience.dataforge.names.Name
import space.kscience.dataforge.names.parseAsName
import space.kscience.dataforge.names.withIndex
import space.kscience.snark.*
context(PageContext) private fun FlowContent.spcTeamContent(
landing: HtmlData,
content: Map<Name, HtmlData>,
) {
// Banner
// Note: The "styleN" class below should match that of the header element.
section("style2") {
id = "banner"
div("inner") {
span("image") {
img {
src = "images/pic07.jpg"
alt = ""
}
}
header("major") {
h1 { +(landing.meta["title"].string ?: "???") }
}
div("content") {
htmlData(landing)
}
}
}
// Main
div {
id = "main"
content.forEach { (name, data) ->
val ref = resolveRef(name)
section("spotlights") {
id = data.meta["id"].string ?: name.toString()
section {
data.meta["image"].string?.let { imagePath ->
a(classes = "image") {
href = ref
img {
src = resolveRef(imagePath)
alt = name.toString()
attributes["data-position"] = "center center"
}
}
}
div("content") {
div("inner") {
header("major") {
h3 { +(data.meta["title"].string ?: "???") }
}
resolveHtml(name.withIndex("info"))?.let {
htmlData(it)
}
ul("actions") {
li {
a(classes = "button") {
href = ref
+"""Learn more"""
}
}
}
}
}
}
}
}
}
}
context(PageContext) internal fun Route.spcLanding(
name: String,
contentFilter: (Name, Meta) -> Boolean,
) {
val body = resolveHtml(name.parseAsName()) ?: error("Could not find body for $name")
val content = resolveAllHtml(contentFilter)
val meta = body.meta
get(name) {
withRequest(call.request) {
call.respondHtml {
val title = meta["title"].string ?: SPC_TITLE
spcHead(title)
body("is-preload") {
wrapper {
spcTeamContent(body, content)
}
fortyScripts()
}
}
}
}
content.forEach { (name, contentBody) ->
get(name.tokens.joinToString("/")) {
withRequest(call.request) {
call.respondHtml {
spcPageContent(contentBody.meta) {
htmlData(contentBody)
}
}
}
}
}
}

157
src/main/kotlin/ru/mipt/spc/spcMisc.kt Normal file
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@ -0,0 +1,157 @@
package ru.mipt.spc
import kotlinx.html.*
import space.kscience.snark.PageContext
import space.kscience.snark.homeRef
import space.kscience.snark.resolveRef
internal const val SPC_TITLE = "Scientific Programming Centre"
context(PageContext) internal fun HTML.spcHead(title: String = SPC_TITLE) {
head {
title {
+title
}
meta {
charset = "utf-8"
}
meta {
name = "viewport"
content = "width=device-width, initial-scale=1, user-scalable=no"
}
link(rel = "stylesheet", href = resolveRef("assets/css/main.css"))
noScript {
link(rel = "stylesheet", href = resolveRef("assets/css/noscript.css"))
}
}
}
context(PageContext) internal fun FlowContent.spcHomeMenu() {
nav {
id = "menu"
ul("links") {
li {
a {
href = homeRef
+"""Home"""
}
}
li {
a {
href = resolveRef("magprog")
+"""Master"""
}
}
li {
a {
href = resolveRef("research")
+"""Research"""
}
}
li {
a {
href = resolveRef("consulting")
+"""Consulting"""
}
}
li {
a {
href = resolveRef("team")
+"""Team"""
}
}
}
// ul("actions stacked") {
// li {
// a(classes = "button primary fit") {
// href = "#"
// +"""Get Started"""
// }
// }
// li {
// a(classes = "button fit") {
// href = "#"
// +"""Log In"""
// }
// }
// }
}
}
context(PageContext) internal fun FlowContent.spcFooter() {
footer {
id = "footer"
div("inner") {
ul("icons") {
// li {
// a(classes = "icon brands alt fa-twitter") {
// href = "#"
// span("label") { +"""Twitter""" }
// }
// }
// li {
// a(classes = "icon brands alt fa-facebook-f") {
// href = "#"
// span("label") { +"""Facebook""" }
// }
// }
// li {
// a(classes = "icon brands alt fa-instagram") {
// href = "#"
// span("label") { +"""Instagram""" }
// }
// }
li {
a(classes = "icon brands alt fa-github") {
href = "https://github.com/mipt-npm"
span("label") { +"""GitHub""" }
}
}
// li {
// a(classes = "icon brands alt fa-linkedin-in") {
// href = "#"
// span("label") { +"""LinkedIn""" }
// }
// }
}
ul("copyright") {
li { +"""SPC""" }
li {
+"""Design:"""
a {
href = "https://html5up.net"
+"""HTML5 UP"""
}
}
}
}
}
}
context(PageContext) internal fun FlowContent.wrapper(contentBody: FlowContent.() -> Unit) {
div {
id = "wrapper"
// Header
header("alt") {
id = "header"
a(classes = "logo") {
href = homeRef
strong { +"""SPC""" }
span { +"""Scientific Programming Centre""" }
}
nav {
a {
href = "#menu"
+"""Menu"""
}
}
}
// Menu
spcHomeMenu()
//Body
contentBody()
// Footer
spcFooter()
}
}

105
src/main/kotlin/space/kscience/snark/DirectoryDataTree.kt
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@ -1,105 +0,0 @@
package space.kscience.snark
import kotlinx.coroutines.flow.SharedFlow
import kotlinx.coroutines.flow.SharingStarted
import kotlinx.coroutines.flow.flow
import kotlinx.coroutines.flow.shareIn
import space.kscience.dataforge.data.Data
import space.kscience.dataforge.data.DataSource
import space.kscience.dataforge.data.DataTree
import space.kscience.dataforge.data.DataTreeItem
import space.kscience.dataforge.io.IOPlugin
import space.kscience.dataforge.io.readEnvelopeFile
import space.kscience.dataforge.io.readMetaFile
import space.kscience.dataforge.io.toByteArray
import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.meta.copy
import space.kscience.dataforge.names.*
import java.nio.file.Path
import java.nio.file.StandardWatchEventKinds
import java.nio.file.attribute.BasicFileAttributes
import kotlin.coroutines.CoroutineContext
import kotlin.io.path.*
import kotlin.reflect.KType
import kotlin.reflect.typeOf
class DirectoryDataTree(val io: IOPlugin, val path: Path) : DataTree<ByteArray>, DataSource<ByteArray> {
override val coroutineContext: CoroutineContext get() = io.context.coroutineContext
override val dataType: KType
get() = typeOf<ByteArray>()
override val meta: Meta get() = try {
//TODO replace by readMetaFileOrNull
io.readMetaFile(path)
} catch (ise: java.lang.IllegalStateException){
Meta.EMPTY
}
private fun readFile(filePath: Path): Data<ByteArray> {
val envelope = io.readEnvelopeFile(filePath, readNonEnvelopes = true)
val meta = envelope.meta.copy {
META_FILE_PATH_KEY put filePath.toString()
META_FILE_EXTENSION_KEY put filePath.extension
val attributes = filePath.readAttributes<BasicFileAttributes>()
META_FILE_UPDATE_TIME_KEY put attributes.lastModifiedTime().toInstant().toString()
META_FILE_CREATE_TIME_KEY put attributes.creationTime().toInstant().toString()
}
return Data(meta) {
envelope.data?.toByteArray() ?: ByteArray(0)
}
}
private fun Path.toName(): Name = Name(flatMap {it.nameWithoutExtension.parseAsName().tokens})
override val items: Map<NameToken, DataTreeItem<ByteArray>>
get() = path.listDirectoryEntries().associate { childPath ->
//val fileName = childPath.fileName.nameWithoutExtension
val item: DataTreeItem<ByteArray> = if (childPath.isDirectory()) {
DataTreeItem.Node(DirectoryDataTree(io, childPath))
} else {
DataTreeItem.Leaf(readFile(childPath))
}
val name = childPath.fileName.toName()//Name.parse(fileName)
if (name.length == 1) {
name.first() to item
} else {
TODO("Segmented names are not supported")
}
}
override val updates: SharedFlow<Name> by lazy {
val watchService = path.fileSystem.newWatchService()
path.register(
watchService,
StandardWatchEventKinds.ENTRY_CREATE,
StandardWatchEventKinds.ENTRY_MODIFY,
StandardWatchEventKinds.ENTRY_DELETE
)
flow {
while (true) {
val key = watchService.take() ?: break
key.pollEvents().map { it.context() }.filterIsInstance<Path>().forEach {
emit(it.toName())
}
key.reset()
}
}.shareIn(this, SharingStarted.Eagerly)
}
companion object {
val META_FILE_KEY = "file".asName()
val META_FILE_PATH_KEY = META_FILE_KEY + "path"
val META_FILE_EXTENSION_KEY = META_FILE_KEY + "extension"
val META_FILE_CREATE_TIME_KEY = META_FILE_KEY + "created"
val META_FILE_UPDATE_TIME_KEY = META_FILE_KEY + "update"
}
}

5
src/main/kotlin/space/kscience/snark/HtmlData.kt
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@ -1,5 +1,6 @@
package space.kscience.snark
import kotlinx.coroutines.Dispatchers
import kotlinx.coroutines.runBlocking
import kotlinx.html.FlowContent
import kotlinx.html.TagConsumer
@ -23,11 +24,11 @@ val HtmlData.language: String? get() = meta["language"].string?.lowercase()
val HtmlData.order: Int? get() = meta["order"]?.int
fun TagConsumer<*>.htmlData(data: HtmlData) = runBlocking {
fun TagConsumer<*>.htmlData(data: HtmlData) = runBlocking(Dispatchers.IO) {
data.await().invoke(this@htmlData)
}
fun FlowContent.htmlData(data: HtmlData) = runBlocking {
fun FlowContent.htmlData(data: HtmlData) = runBlocking(Dispatchers.IO) {
data.await().invoke(consumer)
}

7
src/main/kotlin/space/kscience/snark/PageContext.kt
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@ -6,7 +6,6 @@ import io.ktor.server.plugins.origin
import io.ktor.server.request.ApplicationRequest
import io.ktor.server.request.host
import io.ktor.server.request.port
import space.kscience.dataforge.actions.invoke
import space.kscience.dataforge.data.*
import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.meta.get
@ -24,6 +23,8 @@ data class PageContext(val path: String, val pageMeta: Meta, val data: DataSet<*
*/
fun PageContext.resolveRef(name: String): String = "${path.removeSuffix("/")}/$name"
fun PageContext.resolveRef(name: Name): String = "${path.removeSuffix("/")}/${name.tokens.joinToString ("/")}"
/**
* Resolve a Html builder by its full name
*/
@ -53,9 +54,7 @@ internal val Data<*>.published: Boolean get() = meta["published"].string != "fal
fun PageContext(rootUrl: String, data: DataSet<*>): PageContext = PageContext(rootUrl, data.meta, data)
fun SnarkPlugin.parse(rootUrl: String, path: Path): PageContext {
val directoryDataTree = DirectoryDataTree(io, path)
val parsedData: DataSet<Any> = parseAction(directoryDataTree)
val parsedData: DataSet<Any> = readDirectory(path)
return PageContext(rootUrl, parsedData)
}

8
src/main/kotlin/space/kscience/snark/SnarkHtmlParser.kt
View File

@ -1,20 +1,20 @@
package space.kscience.snark
import io.ktor.http.ContentType
import io.ktor.utils.io.core.Input
import kotlinx.html.div
import kotlinx.html.unsafe
import space.kscience.dataforge.meta.Meta
import kotlin.reflect.KType
import kotlin.reflect.typeOf
object SnarkHtmlParser : SnarkParser<HtmlFragment> {
override val contentType: ContentType = ContentType.Text.Html
override val fileExtensions: Set<String> = setOf("html")
override val resultType: KType = typeOf<HtmlFragment>()
override val type: KType = typeOf<HtmlFragment>()
override suspend fun parse(bytes: ByteArray, meta: Meta): HtmlFragment = {
override fun readObject(input: Input): HtmlFragment = {
div {
unsafe { +bytes.decodeToString() }
unsafe { +input.readText() }
}
}
}

17
src/main/kotlin/space/kscience/snark/SnarkJsonParser.kt
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@ -1,17 +0,0 @@
package space.kscience.snark
import io.ktor.http.ContentType
import kotlinx.serialization.json.Json
import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.meta.toMeta
import kotlin.reflect.KType
import kotlin.reflect.typeOf
object SnarkJsonParser: SnarkParser<Meta> {
override val contentType: ContentType = ContentType.Application.Json
override val fileExtensions: Set<String> = setOf("json")
override val resultType: KType= typeOf<Meta>()
override suspend fun parse(bytes: ByteArray, meta: Meta): Meta =
Json.parseToJsonElement(bytes.decodeToString()).toMeta()
}

8
src/main/kotlin/space/kscience/snark/SnarkMarkdownParser.kt
View File

@ -1,25 +1,25 @@
package space.kscience.snark
import io.ktor.http.ContentType
import io.ktor.utils.io.core.Input
import kotlinx.html.div
import kotlinx.html.unsafe
import org.intellij.markdown.flavours.commonmark.CommonMarkFlavourDescriptor
import org.intellij.markdown.html.HtmlGenerator
import org.intellij.markdown.parser.MarkdownParser
import space.kscience.dataforge.meta.Meta
import kotlin.reflect.KType
import kotlin.reflect.typeOf
object SnarkMarkdownParser:SnarkParser<HtmlFragment> {
override val contentType: ContentType = ContentType.Text.Html
override val fileExtensions: Set<String> = setOf("markdown", "mdown", "mkdn", "mkd", "md")
override val resultType: KType = typeOf<HtmlFragment>()
override val type: KType = typeOf<HtmlFragment>()
private val markdownFlavor = CommonMarkFlavourDescriptor()
private val markdownParser = MarkdownParser(markdownFlavor)
override suspend fun parse(bytes: ByteArray, meta: Meta): HtmlFragment {
val src = bytes.decodeToString()
override fun readObject(input: Input): HtmlFragment {
val src = input.readText()
val parsedTree = markdownParser.buildMarkdownTreeFromString(src)
val htmlString = HtmlGenerator(src, parsedTree, markdownFlavor).generateHtml()

80
src/main/kotlin/space/kscience/snark/SnarkPlugin.kt
View File

@ -1,9 +1,14 @@
package space.kscience.snark
import io.ktor.http.ContentType
import space.kscience.dataforge.actions.Action
import space.kscience.dataforge.actions.map
import io.ktor.util.extension
import io.ktor.utils.io.core.readBytes
import space.kscience.dataforge.context.*
import space.kscience.dataforge.data.DataTree
import space.kscience.dataforge.io.IOReader
import space.kscience.dataforge.io.JsonMetaFormat
import space.kscience.dataforge.io.asBinary
import space.kscience.dataforge.io.yaml.YamlMetaFormat
import space.kscience.dataforge.io.yaml.YamlPlugin
import space.kscience.dataforge.meta.Meta
import space.kscience.dataforge.meta.get
@ -12,20 +17,24 @@ import space.kscience.dataforge.misc.DFExperimental
import space.kscience.dataforge.misc.Type
import space.kscience.dataforge.names.Name
import space.kscience.dataforge.names.asName
import space.kscience.dataforge.workspace.FileData
import space.kscience.dataforge.workspace.readDataDirectory
import java.nio.file.Path
import kotlin.reflect.KClass
import kotlin.reflect.KType
import kotlin.reflect.typeOf
@Type(SnarkParser.TYPE)
interface SnarkParser<R : Any> {
interface SnarkParser<out R : Any> : IOReader<R> {
val contentType: ContentType
val fileExtensions: Set<String>
val priority: Int get() = DEFAULT_PRIORITY
val resultType: KType
suspend fun parse(bytes: ByteArray, meta: Meta): R
suspend fun parse(bytes: ByteArray, meta: Meta): R = bytes.asBinary().read {
readObject(this)
}
companion object {
const val TYPE = "snark.parser"
@ -33,6 +42,20 @@ interface SnarkParser<R : Any> {
}
}
@PublishedApi
internal class SnarkParserWrapper<R : Any>(
val reader: IOReader<R>,
override val type: KType,
override val contentType: ContentType,
override val fileExtensions: Set<String>,
) : SnarkParser<R>, IOReader<R> by reader
inline fun <reified R : Any> SnarkParser(
reader: IOReader<R>,
contentType: ContentType,
vararg fileExtensions: String,
): SnarkParser<R> = SnarkParserWrapper(reader, typeOf<R>(), contentType, fileExtensions.toSet())
@OptIn(DFExperimental::class)
class SnarkPlugin : AbstractPlugin() {
@ -45,31 +68,46 @@ class SnarkPlugin : AbstractPlugin() {
context.gather(SnarkParser.TYPE, true)
}
val parseAction = Action.map {
// val parseAction: Action<ByteArray, Any> = Action.map {
// val parser: SnarkParser<*>? = parsers.values.filter { parser ->
// parser.contentType.toString() == meta["contentType"].string ||
// meta[META_FILE_EXTENSION_KEY].string in parser.fileExtensions
// }.maxByOrNull {
// it.priority
// }
//
// //ensure that final type is correct
// if (parser == null) {
// logger.warn { "The parser is not found for data with meta $meta" }
// result { it }
// } else {
// result(parser.resultType) { bytes ->
// parser.parse(bytes, meta)
// }
// }
// }
fun readDirectory(path: Path): DataTree<Any> = io.readDataDirectory(path) { dataPath, meta ->
val fileExtension = meta[FileData.META_FILE_EXTENSION_KEY].string ?: dataPath.extension
val parser: SnarkParser<*>? = parsers.values.filter { parser ->
parser.contentType.toString() == meta["contentType"].string ||
meta[DirectoryDataTree.META_FILE_EXTENSION_KEY].string in parser.fileExtensions
fileExtension in parser.fileExtensions
}.maxByOrNull {
it.priority
}
//ensure that final type is correct
if (parser == null) {
logger.warn { "The parser is not found for data with meta $meta" }
result { it }
} else {
result(parser.resultType) { bytes ->
parser.parse(bytes, meta)
}
parser ?: run {
logger.warn { "The parser is not found for file $dataPath with meta $meta" }
byteArrayIOReader
}
}
override fun content(target: String): Map<Name, Any> = when (target) {
SnarkParser.TYPE -> mapOf(
"html".asName() to SnarkHtmlParser,
"markdown".asName() to SnarkMarkdownParser,
"json".asName() to SnarkJsonParser,
"yaml".asName() to SnarkYamlParser
"json".asName() to SnarkParser(JsonMetaFormat, ContentType.Application.Json, "json"),
"yaml".asName() to SnarkParser(YamlMetaFormat, ContentType.Application.Json, "yaml", "yml")
)
else -> super.content(target)
}
@ -79,5 +117,9 @@ class SnarkPlugin : AbstractPlugin() {
override val type: KClass<out SnarkPlugin> = SnarkPlugin::class
override fun build(context: Context, meta: Meta): SnarkPlugin = SnarkPlugin()
private val byteArrayIOReader = IOReader {
readBytes()
}
}
}

18
src/main/kotlin/space/kscience/snark/SnarkYamlParser.kt
View File

@ -1,18 +0,0 @@
package space.kscience.snark
import io.ktor.http.ContentType
import space.kscience.dataforge.io.asBinary
import space.kscience.dataforge.io.readObject
import space.kscience.dataforge.io.yaml.YamlMetaFormat
import space.kscience.dataforge.meta.Meta
import kotlin.reflect.KType
import kotlin.reflect.typeOf
object SnarkYamlParser : SnarkParser<Meta> {
override val contentType: ContentType = ContentType.Application.Json
override val fileExtensions: Set<String> = setOf("yaml", "yml")
override val resultType: KType = typeOf<Meta>()
override suspend fun parse(bytes: ByteArray, meta: Meta): Meta =
YamlMetaFormat.readObject(bytes.asBinary())
}