Merge remote-tracking branch 'spc/dev' into dev

docs/README-TEMPLATE.md

@@ -58,5 +58,14 @@ Postprocessors are functions that transform fragments of HTML wrapped in them ac
 
 Other details on HTML rendering could be found in [snark-html](./snark-html) module
 
+## Examples
+
+### Scientific document builder
+
+The idea of [the project](examples/document) is to produce a tree of scientific documents or papers. It does that in following steps:
+
+1. Read data tree from `data` directory (data path could be overridden by either ktor configuration or manually).
+2. Search all directories for a files called `document.yaml` or any other format that could be treated as value-tree (for example `document.json`). Use that file as a document descriptor that defines linear document structure.
+3. 
 
 ${modules}

examples/README.md

@@ -0,0 +1,4 @@
+# Module examples
+
+
+

examples/document/README.md

@@ -0,0 +1,4 @@
+# Module document
+
+
+

examples/document/data/loremIpsum/document.yaml

@@ -2,7 +2,7 @@ route: lorem.ipsum
 title: Lorem Ipsum
 authors:
   - name: Alexander Nozik
-    affiliation: MIPT
+    affiliation: SPC
 fragments:
   - type: image
     ref: SPC-logo.png

examples/document/data/simple/body.md

@@ -0,0 +1,2 @@
+
+This is a document body for a simple document

examples/document/data/simple/document.json

@@ -0,0 +1,13 @@
+{
+  "title": "A simple document",
+  "fragments": [
+    {
+      "type": "data",
+      "name": "body"
+    },
+    {
+      "type": "data",
+      "name": "footer"
+    }
+  ]
+}

examples/document/data/simple/footer.html

@@ -0,0 +1,4 @@
+
+<p>
+    <strong>This is HTML footer</strong>
+</p>

examples/document/src/jvmMain/kotlin/main.kt

@@ -1,8 +1,12 @@
 package center.sciprog.snark.documents
 
 import io.ktor.server.application.Application
+import io.ktor.server.application.call
 import io.ktor.server.cio.CIO
 import io.ktor.server.engine.embeddedServer
+import io.ktor.server.response.respondRedirect
+import io.ktor.server.routing.get
+import io.ktor.server.routing.routing
 import kotlinx.html.ScriptCrossorigin
 import kotlinx.html.link
 import kotlinx.html.script
@@ -14,6 +18,7 @@ import space.kscience.snark.ktor.snarkApplication
 fun Application.renderAllDocuments() = snarkApplication {
     allDocuments(
         headers = {
+            //add katex headers
             link {
                 rel = "stylesheet"
                 href = "https://cdn.jsdelivr.net/npm/katex@0.16.10/dist/katex.min.css"
@@ -33,6 +38,7 @@ fun Application.renderAllDocuments() = snarkApplication {
                 crossorigin = ScriptCrossorigin.anonymous
                 attributes["onload"] = "renderMathInElement(document.body);"
             }
+            // Auto-render latex expressions with katex
             script {
                 unsafe {
                     +"""
@@ -51,6 +57,12 @@ fun Application.renderAllDocuments() = snarkApplication {
             }
         }
     )
+
+    routing {
+        get("/"){
+            call.respondRedirect("lorem/ipsum")
+        }
+    }
 }
 
 

snark-core/README.md

@@ -0,0 +1,21 @@
+# Module snark-core
+
+
+
+## Usage
+
+## Artifact:
+
+The Maven coordinates of this project are `space.kscience:snark-core:0.2.0-dev-1`.
+
+**Gradle Kotlin DSL:**
+```kotlin
+repositories {
+    maven("https://repo.kotlin.link")
+    mavenCentral()
+}
+
+dependencies {
+    implementation("space.kscience:snark-core:0.2.0-dev-1")
+}
+```

snark-gradle-plugin/README.md

@@ -0,0 +1,21 @@
+# Module snark-gradle-plugin
+
+
+
+## Usage
+
+## Artifact:
+
+The Maven coordinates of this project are `space.kscience:snark-gradle-plugin:0.2.0-dev-1`.
+
+**Gradle Kotlin DSL:**
+```kotlin
+repositories {
+    maven("https://repo.kotlin.link")
+    mavenCentral()
+}
+
+dependencies {
+    implementation("space.kscience:snark-gradle-plugin:0.2.0-dev-1")
+}
+```

snark-html/src/jvmMain/kotlin/space/kscience/snark/html/ParseAction.kt

@@ -1,68 +0,0 @@
-package space.kscience.snark.html
-
-import space.kscience.dataforge.actions.AbstractAction
-import space.kscience.dataforge.data.*
-import space.kscience.dataforge.io.Binary
-import space.kscience.dataforge.io.toByteArray
-import space.kscience.dataforge.meta.Meta
-import space.kscience.dataforge.meta.get
-import space.kscience.dataforge.misc.DFInternal
-import space.kscience.snark.SnarkReader
-import space.kscience.snark.TextProcessor
-import kotlin.coroutines.CoroutineContext
-import kotlin.coroutines.EmptyCoroutineContext
-import kotlin.reflect.KType
-import kotlin.reflect.typeOf
-
-@OptIn(DFInternal::class)
-internal fun <T, R> Data<T>.transform(
-    type: KType,
-    meta: Meta = this.meta,
-    coroutineContext: CoroutineContext = EmptyCoroutineContext,
-    block: suspend (T) -> R,
-): Data<R> {
-    val data = Data(type, meta, coroutineContext, listOf(this)) {
-        block(await())
-    }
-    return data
-}
-
-public class ParseAction(private val snarkHtml: SnarkHtml) :
-    AbstractAction<Binary, Any>(typeOf<PageFragment>()) {
-
-    private fun parseOne(data: NamedData<Binary>): NamedData<Any>? = with(snarkHtml) {
-        val contentType = getContentType(data.name, data.meta)
-
-        val parser: SnarkReader<Any>? = snark.readers.values.filter { parser ->
-            contentType in parser.inputContentTypes
-        }.maxByOrNull {
-            it.priority
-        }
-
-        //ignore data for which parser is not found
-        if (parser != null) {
-            val preprocessor = meta[TextProcessor.TEXT_PREPROCESSOR_KEY]?.let { snark.preprocessor(it) }
-            data.transform(parser.outputType) {
-                if (preprocessor == null) {
-                    parser.readFrom(it)
-                } else {
-                    //TODO provide encoding
-                    val string = it.toByteArray().decodeToString()
-                    parser.readFrom(preprocessor.process(string))
-                }
-            }.named(data.name)
-        } else {
-            null
-        }
-    }
-
-    override fun DataSink<Any>.generate(data: DataTree<Binary>, meta: Meta) {
-        data.forEach {
-            parseOne(it)?.let { put(it) }
-        }
-    }
-
-    override fun DataSink<Any>.update(source: DataTree<Binary>, meta: Meta, namedData: NamedData<Binary>) {
-        parseOne(namedData)?.let { put(it) }
-    }
-}

snark-html/src/jvmMain/kotlin/space/kscience/snark/html/SnarkHtml.kt

@@ -3,7 +3,6 @@
 package space.kscience.snark.html
 
 import io.ktor.http.ContentType
-import kotlinx.coroutines.CoroutineScope
 import kotlinx.io.readByteArray
 import space.kscience.dataforge.actions.Action
 import space.kscience.dataforge.actions.mapping
@@ -11,11 +10,11 @@ import space.kscience.dataforge.actions.transform
 import space.kscience.dataforge.context.Context
 import space.kscience.dataforge.context.PluginFactory
 import space.kscience.dataforge.context.PluginTag
-import space.kscience.dataforge.data.*
-import space.kscience.dataforge.io.Binary
-import space.kscience.dataforge.io.IOPlugin
-import space.kscience.dataforge.io.IOReader
-import space.kscience.dataforge.io.JsonMetaFormat
+import space.kscience.dataforge.data.DataSink
+import space.kscience.dataforge.data.DataTree
+import space.kscience.dataforge.data.filterByType
+import space.kscience.dataforge.data.putAll
+import space.kscience.dataforge.io.*
 import space.kscience.dataforge.io.yaml.YamlMetaFormat
 import space.kscience.dataforge.io.yaml.YamlPlugin
 import space.kscience.dataforge.meta.Meta
@@ -106,7 +105,34 @@ public class SnarkHtml : WorkspacePlugin() {
         }
     }
 
-    public val parseAction: Action<Binary, Any> = ParseAction(this)
+    public val parseAction: Action<Binary, Any> = Action.mapping {
+        val contentType = getContentType(name, meta)
+
+        val parser: SnarkReader<Any>? = snark.readers.values.filter { parser ->
+            contentType in parser.inputContentTypes
+        }.maxByOrNull {
+            it.priority
+        }
+
+        result(parser?.outputType ?: typeOf<Binary>()) { data ->
+
+            //ignore data for which parser is not found
+            if (parser != null) {
+                val preprocessor =
+                    meta[TextProcessor.TEXT_PREPROCESSOR_KEY]?.let { snark.preprocessor(it) }
+                if (preprocessor == null) {
+                    parser.readFrom(data)
+                } else {
+                    //TODO provide encoding
+                    val string = data.toByteArray().decodeToString()
+                    parser.readFrom(preprocessor.process(string))
+                }
+            } else {
+                data
+            }
+        }
+
+    }
 
     public val layoutAction: Action<Any, Any> = Action.mapping {
 
@@ -134,7 +160,7 @@ public class SnarkHtml : WorkspacePlugin() {
 
         override fun build(context: Context, meta: Meta): SnarkHtml = SnarkHtml()
 
-        private val byteArrayIOReader = IOReader { source->
+        private val byteArrayIOReader = IOReader { source ->
             source.readByteArray()
         }
 
@@ -143,21 +169,24 @@ public class SnarkHtml : WorkspacePlugin() {
     }
 }
 
-
-public fun SnarkHtml.readSiteData(
+/**
+ * Parse raw data tree into html primitives
+ */
+public fun SnarkHtml.parseDataTree(
     binaries: DataTree<Binary>,
     meta: Meta = Meta.EMPTY,
-): DataTree<Any> = ObservableDataTree(context) {
+): DataTree<Any> = DataTree {
     //put all binaries
     putAll(binaries)
     //override ones which could be parsed
     putAll(binaries.transform(parseAction, meta))
 }.transform(prepareHeaderAction, meta).transform(removeIndexAction, meta)
 
-
-public fun SnarkHtml.readSiteData(
-    coroutineScope: CoroutineScope,
+/**
+ * Read the parsed data tree by providing [builder] for raw binary data tree
+ */
+public fun SnarkHtml.parseDataTree(
     meta: Meta = Meta.EMPTY,
     //TODO add IO plugin as a context parameter
     builder: DataSink<Binary>.() -> Unit,
-): DataTree<Any> = readSiteData(ObservableDataTree(coroutineScope) { builder() }, meta)
+): DataTree<Any> = parseDataTree(DataTree { builder() }, meta)

snark-html/src/jvmMain/kotlin/space/kscience/snark/html/SnarkHtmlReader.kt

@@ -14,7 +14,7 @@ public interface SnarkHtmlReader : SnarkReader<PageFragment>{
 }
 
 public object RawHtmlReader : SnarkHtmlReader {
-    override val inputContentTypes: Set<String> = setOf("html")
+    override val inputContentTypes: Set<String> = setOf("text/html", "html")
 
     override fun readFrom(source: String): PageFragment = PageFragment {
         div {

snark-html/src/jvmMain/resources/application.conf

@@ -1,12 +0,0 @@
-ktor {
-    application {
-        modules = [ ru.mipt.spc.ApplicationKt.spcModule ]
-    }
-
-    deployment {
-        port = 7080
-        watch = ["classes", "data/"]
-    }
-
-    development = true
-}

snark-html/src/jvmMain/resources/logback.xml

@@ -1,29 +0,0 @@
-<configuration>
-    <timestamp key="bySecond" datePattern="yyyyMMdd'T'HHmmss"/>
-
-    <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
-        <encoder>
-            <pattern>%d{YYYY-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n</pattern>
-        </encoder>
-    </appender>
-
-    <root level="trace">
-        <appender-ref ref="STDOUT"/>
-    </root>
-
-    <appender name="FILE" class="ch.qos.logback.core.FileAppender">
-        <!-- use the previously created timestamp to create a uniquely
-             named log file -->
-        <file>logs/${bySecond}.txt</file>
-        <encoder>
-            <pattern>%d{YYYY-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n</pattern>
-        </encoder>
-    </appender>
-
-    <root level="DEBUG">
-        <appender-ref ref="FILE" />
-    </root>
-
-    <logger name="org.eclipse.jetty" level="INFO"/>
-    <logger name="io.netty" level="INFO"/>
-</configuration>

snark-ktor/README.md

@@ -0,0 +1,21 @@
+# Module snark-ktor
+
+
+
+## Usage
+
+## Artifact:
+
+The Maven coordinates of this project are `space.kscience:snark-ktor:0.2.0-dev-1`.
+
+**Gradle Kotlin DSL:**
+```kotlin
+repositories {
+    maven("https://repo.kotlin.link")
+    mavenCentral()
+}
+
+dependencies {
+    implementation("space.kscience:snark-ktor:0.2.0-dev-1")
+}
+```

snark-ktor/src/jvmMain/kotlin/space/kscience/snark/ktor/extractData.kt

@@ -18,6 +18,7 @@ private const val BUILD_DATE_FILE = "/buildDate"
  *
  * @return true if cache is valid and false if it is reset
  */
+@Deprecated("To be removed")
 fun Application.prepareSnarkDataCacheDirectory(dataPath: Path): Boolean {
 
     // Clear data directory if it is outdated

snark-ktor/src/jvmMain/kotlin/space/kscience/snark/ktor/snarkApplication.kt

@@ -15,7 +15,7 @@ import space.kscience.dataforge.workspace.FileData
 import space.kscience.dataforge.workspace.directory
 import space.kscience.snark.html.HtmlSite
 import space.kscience.snark.html.SnarkHtml
-import space.kscience.snark.html.readSiteData
+import space.kscience.snark.html.parseDataTree
 import kotlin.io.path.Path
 import kotlin.io.path.exists
 
@@ -47,7 +47,7 @@ public fun Route.site(
         error("Data directory at $dataDirectory is not resolved")
     }
 
-    val siteData = snark.readSiteData(context) {
+    val siteData = snark.parseDataTree {
         directory(snark.io, Name.EMPTY, dataDirectory)
     }