first commit

Author: ofilangi

Readme.md

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+
+

build.sbt

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+
+// The simplest possible sbt build file is just one line:
+
+scalaVersion := "2.13.8"
+// That is, to create a valid sbt build, all you've got to do is define the
+// version of Scala you'd like your project to use.
+
+// ============================================================================
+
+// Lines like the above defining `scalaVersion` are called "settings". Settings
+// are key/value pairs. In the case of `scalaVersion`, the key is "scalaVersion"
+// and the value is "2.13.8"
+
+// It's possible to define many kinds of settings, such as:
+
+name := "mzXML-stream"
+organization := "com.github.p2m2"
+version := "1.0"
+
+
+libraryDependencies ++= Seq(
+  "org.scalaxb" %% "scalaxb" % "1.11.1",
+  "org.scala-lang.modules" %% "scala-xml" % "2.1.0",
+  "javax.xml.bind" % "jaxb-api" % "2.3.1",
+  "co.fs2" %% "fs2-core" % "3.9.2",
+  "co.fs2" %% "fs2-io" % "3.9.2",
+  "co.fs2" %%"fs2-core"%"3.9.2",
+  "org.gnieh" %%"fs2-data-xml"%"1.8.0"
+)
+
+Global / onChangedBuildSource := ReloadOnSourceChanges

dev.md

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+## scalaxb
+
+- install scalaxb = https://github.com/eed3si9n/scalaxb/
+- generate class from XSD
+  wget https://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_3.2.xsd
+  mkdir separations
+  pushd separations
+  wget http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/separations/separation_technique_1.0.xsd
+  popd
+  wget http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/general_types_1.0.xsd
+
+scalaxb mzXML_3.2.xsd separations/separation_technique_1.0.xsd general_types_1.0.xsd -p mzxml

project/build.properties

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+sbt.version=1.9.6

project/plugins.sbt

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+addSbtPlugin("com.eed3si9n"       % "sbt-assembly"                  % "1.2.0")
+addSbtPlugin("org.scoverage"      % "sbt-scoverage"                 % "2.0.0")
+addSbtPlugin("io.crashbox"        % "sbt-gpg"                       % "0.2.1")
+addSbtPlugin("com.github.sbt"     % "sbt-release"                   % "1.1.0")
+

src/main/scala/Main.scala

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+import cats.Show
+import fs2.Stream
+import cats.effect.{IO, IOApp}
+import cats.effect.unsafe.implicits.global
+import fs2._
+import fs2.data.xml
+import fs2.io.file.{Files, Flags, Path}
+import fs2.data.xml._
+import fs2.data.xml.xpath.{XPath, XPathParser}
+import fs2.data.xml.xpath.literals._
+import mzxml.ScanOrigin
+
+import scala.xml.{NodeSeq, XML}
+
+object Main extends IOApp.Simple {
+  println("Hello, World!")
+  val base= "/media/ofilangi/hdd-local/workspace/INRAE"
+  val data1 = s"$base/P2M2/mzxml-glucosinolate-analyser/src/test/resources/test.mzXML"
+  val data2 = s"$base/P2M2/mzxml-glucosinolate-analyser/src/test/resources/20181018-037.mzXML"
+  val data3 = s"$base/P2M2/brachemdb-workflow/fragmentation/MetFrag/matchms_processing/Brassinet F 20 A 1500 uL 0.14 ug Api Neg_01_7768.mzXML"
+
+  def converter (path: XPath): Stream[IO, String] = {
+    val stream: Stream[IO, Byte] = Files[IO].readAll(fs2.io.file.Path("test.mzXML"))
+    //.through(text.utf8.decode)
+    //.through(text.lines)
+    // .through(events[IO, String]())
+    IO{ println("Hello World !!!2") }
+
+    val streamTxt: Stream[IO, XmlEvent] = stream.through(text.utf8.decode).through(events[IO, String]())
+    //val nsResolved = streamTxt.through(namespaceResolver[IO])
+    //val entityResolved = nsResolved.through(referenceResolver[IO]())
+
+
+
+    streamTxt
+      .through(xml.xpath.filter.raw(path))
+      .parEvalMapUnbounded(_.map(Show[XmlEvent].show(_)).compile.foldMonoid)
+      //.through(xml.xpath.filter.collect(path, scalaxb.fromXML[mzxml.Scan]))
+     // .through(normalize)
+    //  .map( eventXml => scalaxb.fromXML[mzxml.Scan](XML.loadString(eventXml)) )
+
+ //   eventXmlsIo.map( eventXmls => eventXmls.map( e => scalaxb.fromXML[mzxml.Scan](XML.loadString(e))) )
+  }
+
+  val msRun: Stream[IO, mzxml.MsRun] =
+    converter(xpath"//msRun")
+      .map(eventXml => scalaxb.fromXML[mzxml.MsRun](XML.loadString(eventXml)))
+
+  val msInstrument: Stream[IO, mzxml.MsInstrument] =
+    converter(xpath"//msInstrument")
+      .map(eventXml => { println(eventXml);scalaxb.fromXML[mzxml.MsInstrument](XML.loadString(eventXml)) })
+
+  val dataProcessing: Stream[IO, mzxml.DataProcessing] =
+    converter(xpath"/mzXML/msRun/dataProcessing")
+      .map(eventXml => scalaxb.fromXML[mzxml.DataProcessing](XML.loadString(eventXml)))
+
+  val scans : Stream[IO, mzxml.ScanOrigin] =
+    converter(xpath"//scan")
+      .map( eventXml => scalaxb.fromXML[mzxml.ScanOrigin](XML.loadString(eventXml)) )
+
+
+
+  def run: IO[Unit] =
+    {
+      IO {
+        println(
+          scans
+            .filter(x => x.num == 10)
+            .compile
+            .toList
+            .unsafeRunSync())
+      }
+      //scans.compile.drain
+    }
+
+}

src/main/scala/mzxml/general_types_1.01.scala

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+// Generated by <a href="http://scalaxb.org/">scalaxb</a>.
+package mzxml
+
+
+case class NamevalueType(value: scalaxb.DataRecord[Any],
+  attributes: Map[String, scalaxb.DataRecord[Any]] = Map.empty) {
+  lazy val name = attributes.get("@name") map { _.as[String]}
+  lazy val valueAttribute = attributes.get("@value") map { _.as[scalaxb.DataRecord[Any]]}
+  lazy val typeValue = attributes.get("@type") map { _.as[scalaxb.DataRecord[Any]]}
+}
+
+      
+      
+
+
+trait OntologyEntryTypable {
+  def category: String
+  def valueAttribute: String
+}
+
+
+case class OntologyEntryType(attributes: Map[String, scalaxb.DataRecord[Any]] = Map.empty) extends OntologyEntryTypable {
+  lazy val category = attributes("@category").as[String]
+  lazy val valueAttribute = attributes("@value").as[String]
+}
+
+      
+      
+