first commit

.circleci/config.yml

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+# Scala CircleCI 2.0 configuration file
+# See: https://circleci.com/docs/sample-config/
+version: 2.1
+orbs:
+  node: circleci/[email protected]
+workflows:
+  compile-workflow:
+    jobs:
+      - build:
+          context:
+            - DOCKER_CONTEXT
+# Define a job to be invoked later in a workflow.
+# See: https://circleci.com/docs/configuration-reference/#jobs
+jobs:
+  build:
+    # Specify the execution environment. You can specify an image from Dockerhub or use one of our Convenience Images from CircleCI's Developer Hub.
+    # See: https://circleci.com/docs/configuration-reference/#docker-machine-macos-windows-executor
+    docker:
+      # specify the version you desire here
+      - image: cimg/openjdk:19.0.2
+        auth:
+          username: ${DOCKER_USER}
+          password: ${DOCKER_PASS}
+
+      # Specify service dependencies here if necessary
+      # CircleCI maintains a library of pre-built images
+      # documented at https://circleci.com/docs/circleci-images/
+      # - image: circleci/postgres:9.4
+
+    working_directory: ~/repo
+
+    environment:
+      # Customize the JVM maximum heap limit
+      JVM_OPTS: -Xmx3200m
+      TERM: dumb
+
+    # Add steps to the job
+    # See: https://circleci.com/docs/configuration-reference/#steps
+    steps:
+      - checkout
+      - node/install:
+          node-version: '19.6'
+      # Download and cache dependencies
+      - restore_cache:
+          keys:
+            - v1-dependencies-{{ checksum "build.sbt" }}
+            # fallback to using the latest cache if no exact match is found
+            - v1-dependencies-
+
+      - run: cat /dev/null | sbt test:compile
+
+      - save_cache:
+          paths:
+            - ~/.m2
+          key: v1-dependencies--{{ checksum "build.sbt" }}
+
+      # run tests!
+      - run:
+          name: Compile/Tests
+          command: |
+            export NODE_OPTIONS=--openssl-legacy-provider
+            cat /dev/null | sbt test:test

.gitignore

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+*.class
+*.log
+target/
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*

LICENSE

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+MIT License
+
+Copyright (c) 2023 The Metabolic Profiling and Metabolomic Platform
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# xcms-p2m2-tools
+[![CircleCI](https://circleci.com/gh/p2m2/experiment-ions-p2m2-tools.svg?style=shield)](https://circleci.com/gh/p2m2/experiment-ions-p2m2-tools)
+[![Codacy Badge](https://app.codacy.com/project/badge/Grade/516456a87a7447ce9c02290c4fe13bea)](https://app.codacy.com/gh/p2m2/experiment-ions-p2m2-tools/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
+
+https://p2m2.github.io/xcms-p2m2-tools/
+
+### Html
+
+#### Development version
+
+npm should be installed.
+
+```shell 
+export NODE_OPTIONS=--openssl-legacy-provider
+# fastOptJS or fullOptJS check html/index.html
+sbt fastOptJS 
+sbt fullOptJS 
+# open html/index.html
+```
+
+#### Release
+
+```shell 
+sbt fullOptJS::webpack
+cp target/scala-2.13/scalajs-bundler/main/xcms-p2m2-tools-opt-bundle.js docs/
+# open docs/index.html
+```

build.sbt

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+
+scalaVersion := "2.13.12"
+name := "xcms-p2m2-tools"
+organization := "com.github.p2m2"
+version := "1.0"
+organizationName := "p2m2"
+organizationHomepage := Some(url("https://www6.inrae.fr/p2m2"))
+licenses := Seq("MIT License" -> url("http://www.opensource.org/licenses/mit-license.php"))
+
+scmInfo := Some(
+  ScmInfo(
+    url("https://github.com/p2m2/xcms-p2m2-tools"),
+    "scm:[email protected]:p2m2/xcms-p2m2-tools.git"
+  )
+)
+
+developers := List(
+  Developer("ofilangi", "Olivier Filangi", "[email protected]",url("https://github.com/ofilangi"))
+)
+
+lazy val root = (project in file(".")).
+  enablePlugins(ScalaJSPlugin).
+  enablePlugins(ScalaJSBundlerPlugin).
+  settings(
+    name := "xcms-p2m2-tools",
+    version := "1.0",
+    credentials += {
+      val realm = scala.util.Properties.envOrElse("REALM_CREDENTIAL", "")
+      val host = scala.util.Properties.envOrElse("HOST_CREDENTIAL", "")
+      val login = scala.util.Properties.envOrElse("LOGIN_CREDENTIAL", "")
+      val pass = scala.util.Properties.envOrElse("PASSWORD_CREDENTIAL", "")
+
+      val file_credential = Path.userHome / ".sbt" / ".credentials"
+
+      if (reflect.io.File(file_credential).exists) {
+        Credentials(file_credential)
+      } else {
+        Credentials(realm, host, login, pass)
+      }
+    },
+    publishTo := {
+      if (isSnapshot.value)
+        Some("Sonatype Snapshots Nexus" at "https://oss.sonatype.org/content/repositories/snapshots")
+      else
+        Some("Sonatype Snapshots Nexus" at "https://oss.sonatype.org/service/local/staging/deploy/maven2")
+    },
+    publishConfiguration := publishConfiguration.value.withOverwrite(true),
+    publishLocalConfiguration := publishLocalConfiguration.value.withOverwrite(true),
+    pomIncludeRepository := { _ => false },
+    publishMavenStyle := true,
+    coverageMinimumStmtTotal := 20,
+    coverageFailOnMinimum := false,
+    coverageHighlighting := true,
+    libraryDependencies ++= Seq(
+      "com.lihaoyi" %%% "utest" % "0.8.2" % Test,
+      "com.lihaoyi" %%% "scalatags" % "0.12.0",
+      "org.scala-js" %%% "scala-js-macrotask-executor" % "1.1.1"
+    ),
+    testFrameworks += new TestFramework("utest.runner.Framework"),
+    Compile / fastOptJS / scalaJSLinkerConfig ~= {
+      _.withOptimizer(false)
+        .withPrettyPrint(true)
+        .withSourceMap(true)
+    },
+    Compile / fullOptJS / scalaJSLinkerConfig ~= {
+      _.withSourceMap(false)
+        .withModuleKind(ModuleKind.CommonJSModule)
+    },
+    Compile / scalaJSUseMainModuleInitializer := true,
+    Compile / mainClass := Some("fr.inrae.p2m2.webapp.WebApp"),
+    webpackBundlingMode := BundlingMode.LibraryAndApplication(),
+    assembly / assemblyMergeStrategy := {
+      case PathList("META-INF", _*) => MergeStrategy.discard
+      case _ => MergeStrategy.first
+    }
+  )
+
+Global / onChangedBuildSource := ReloadOnSourceChanges
+

docs/index.html

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+<!DOCTYPE html>
+<html>
+  <head>
+    <meta charset="UTF-8">
+    <title>Identifying Common Ions of Interest Across XCMS Files</title>
+    <link rel="stylesheet" href="p2m2.css">
+    <script src="https://grist-static.com/csv-viewer.js"></script>
+  </head>
+  <header>
+    <a href="https://github.com/p2m2/" target="_blank"><img src="https://img.shields.io/badge/github-p2m2-blue.svg"/></a>
+  </header>
+  <body>
+
+  <h1><a href="javascript:window.location.reload(true)">Identifying Common Ions of Interest Across XCMS Files</a></h1>
+
+  <div id="boardTools" class="centered-element" >
+<!--
+  // PANE 1 - Reader
+-->
+
+    <h2>Input file (CSV, TSV)</h2>
+    <table>
+      <tbody>
+      <tr>
+        <td>
+        <div id="inputFilesDiv" ></div>
+      </td>
+      </tr>
+        <tr>
+          <td>
+            <button onclick="document.getElementById('exportCsvTable').innerHTML = '';">Clean</button>
+          </td>
+        </tr>
+      <tr>
+          <td>
+            <label for="ppm">ppm:</label>
+            <input type="text" id="ppm" name="ppm" required maxlength="8" size="10" value="5.0" />
+          </td>
+      </tr>
+      <tr>
+          <td>
+            <label for="rt">rt delta:</label>
+            <input type="text" id="rt" name="rt" required maxlength="8" size="10" value="0.1" />
+          </td>
+      </tr>
+      </tbody>
+    </table>
+
+    <div id="exportCsvTable"></div>
+  </div>
+
+
+  <!-- Include Scala.js compiled code -->
+  <script type="text/javascript" src="../target/scala-2.13/experiment-ions-p2m2-tools-fastopt/main.js"></script>
+
+  </body>
+    <footer>
+      <a href="https://www6.inrae.fr/p2m2" target="_blank"><img src="p2m2.png" width="120"></a>
+      <a href="https://www.metabohub.fr/" target="_blank"><img src="metabohub.png" width="120"></a>
+    </footer>
+
+</html>
+

docs/p2m2.css

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+body {
+    background: #F5F5F5;
+}
+
+.centered-element{
+     margin-left: auto;
+     margin-right: auto;
+     padding: 35px;
+     width: 520px;
+}
+
+h1,h2 {
+     text-align: center;
+}
+
+footer {
+  text-align: center;
+  padding: 3px;
+  //background-color: Grey;
+  color: grey;
+}
+textarea {
+  white-space: pre;
+}
+
+.results table, .results th, .results td {
+  border: 1px solid white;
+  border-collapse: collapse;
+}
+.results th, .results td {
+  background-color: #96D4D4;
+}