Merge pull request #2 from p2m2/develop

v1
p2m2 · Sep 23, 2022 · 9c0fceb · 9c0fceb
2 parents 06a0b15 + 913ed2e
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -0,0 +1,142 @@
+#
+#  - Compile JVM/Js
+#  - Tests JVM
+#  - publish JVM Sonatype Snapshot for branches : main/master/develop
+#  - publish JVM Sonatype Stagge/Release (wait approval) for tags release
+#
+#  DOCKER_CONTEXT is a context global env variable for all application github p2m2 organization
+#   - DOCKER_USER          -> login
+#   - DOCKER_PASS          -> password
+#   - ORGANIZATION_NAME    -> organization register on dockerhub
+#
+#  CREDENTIAL_CONTEXT used by build.sbt
+#   - REALM_CREDENTIAL,HOST_CREDENTIAL,LOGIN_CREDENTIAL,PASSWORD_CREDENTIAL
+#
+#  NPM_CONTEXT
+#   - NPM_TOKEN : token (from ~/.npmrc) to publish nodejs lib
+#
+version: 2.1
+orbs:
+  node: circleci/[email protected]
+workflows:
+  compile-workflow:
+    jobs:
+      - compile:
+          context:
+            - DOCKER_CONTEXT
+      - test_and_coverage_jvm:
+          requires:
+            - compile
+          context:
+            - DOCKER_CONTEXT
+      - publish_snapshot:
+          requires:
+            - test_and_coverage_jvm
+          context:
+            - DOCKER_CONTEXT
+            - CREDENTIAL_CONTEXT
+            - GPG_CONTEXT
+          filters:
+            tags:
+              ignore: /.*/
+            branches:
+              only:
+                - develop
+                - main
+                - master
+
+      - publish_tag_to_sonatype_stagge_for_release:
+          context:
+            - DOCKER_CONTEXT
+            - CREDENTIAL_CONTEXT
+            - GPG_CONTEXT
+          filters:
+            tags:
+              only: /.*/
+            branches:
+              ignore: /.*/
+executors:
+
+  openjdk:
+    working_directory: ~/repo
+    docker:
+      - image: circleci/openjdk:8-jdk
+        auth:
+          username: ${DOCKER_USER}
+          password: ${DOCKER_PASS}
+
+jobs:
+  compile:
+    executor: openjdk
+    environment:
+      JVM_OPTS: -Xmx3200m
+      TERM: dumb
+    steps:
+      - checkout
+      - setup_remote_docker
+      - restore_cache:
+          keys:
+            - v1-dependencies-{{ checksum "build.sbt" }}
+            # fallback to using the latest cache if no exact match is found
+            - v1-dependencies-
+      - run:
+          name: Compile - JVM
+          command: cat /dev/null | sbt test:compile
+
+  test_and_coverage_jvm:
+    executor: openjdk
+    environment:
+      JVM_OPTS: -Xmx3200m
+      TERM: dumb
+    steps:
+      - checkout
+      - setup_remote_docker
+      - restore_cache:
+          keys:
+            - v1-dependencies-{{ checksum "build.sbt" }}
+            # fallback to using the latest cache if no exact match is found
+            - v1-dependencies-
+      - run:
+          name: Test JVM env and Coverage
+          command: |
+            cat /dev/null | sbt clean coverage Test/test coverageReport
+            bash <(curl -s https://codecov.io/bash)
+
+      - store_artifacts:
+          path: target/test-reports
+
+  publish_snapshot:
+    executor: openjdk
+    steps:
+      - checkout
+      - setup_remote_docker
+      - restore_cache:
+          keys:
+            - v1-dependencies-{{ checksum "build.sbt" }}
+            # fallback to using the latest cache if no exact match is found
+            - v1-dependencies-
+      - run:
+          name: Snapshot publication
+          command: |
+            export PROG_VERSION="${CIRCLE_BRANCH}-SNAPSHOT"
+            echo "Importing key"
+            echo -e "$GPG_KEY" | gpg --import
+            sbt publish
+
+  publish_tag_to_sonatype_stagge_for_release:
+    executor: openjdk
+    steps:
+      - checkout
+      - setup_remote_docker
+      - restore_cache:
+          keys:
+            - v1-dependencies-{{ checksum "build.sbt" }}
+            # fallback to using the latest cache if no exact match is found
+            - v1-dependencies-
+      - run:
+          name: Snapshot publication
+          command: |
+            export PROG_VERSION="${CIRCLE_TAG}"
+            echo "Importing key"
+            echo -e "$GPG_KEY" | gpg --import
+            sbt publish
diff --git a/README.md b/README.md
@@ -1,5 +1,8 @@
 # Glucosinolates and Phenolics Brassica napus
 
+[![p2m2](https://circleci.com/gh/p2m2/mzxml-glucosinolate-analyser.svg?style=shield)](https://app.circleci.com/pipelines/github/p2m2)
+[![codecov](https://codecov.io/gh/p2m2/mzxml-glucosinolate-analyser/branch/develop/graph/badge.svg)](https://codecov.io/gh/p2m2/mzxml-glucosinolate-analyser)
+
 ## assembly
 
 ```bash
@@ -12,4 +15,18 @@ sbt assembly
 java -jar ./assembly/pack.jar ./src/test/resources/test.mzXML
 ```
 
+ - https://www.ebi.ac.uk/chebi/advancedSearchFT.do
+
 [Identification and Quantification of Glucosinolates and Phenolics in a Large Panel of Brassica napus Highlight Valuable Genetic Resources for Chemical Ecology and Breeding](https://pubs.acs.org/doi/10.1021/acs.jafc.1c08118)
+
+
+``` 
+java -jar ./assembly/pack.jar -i 10000  ./src/test/resources/20181018-038.mzXML
+java -jar ./assembly/pack.jar -i 10000 -s 3.0 -e 3.5 ./src/test/resources/20181018-038.mzXML
+```
+
+## Chebi Glucosinolate
+
+1) https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=glucosinolate
+2) "Download your results"
+=>ChEBI_Results.tsv
diff --git a/build.sbt b/build.sbt
@@ -1,13 +1,68 @@
 scalaVersion := "2.13.8"
-name := "mzxml-analyser-test"
+name := "mzxml-glucosinolates-phenolics-analyser"
 organization := "com.github.p2m2"
+organizationName := "p2m2"
+organizationHomepage := Some(url("https://www6.inrae.fr/p2m2"))
+licenses := Seq("MIT License" -> url("http://www.opensource.org/licenses/mit-license.php"))
 version := "1.0"
+
+scmInfo := Some(
+  ScmInfo(
+    url("https://github.com/p2m2/mzxml-glucosinolate-analyser"),
+    "scm:[email protected]:p2m2/mzxml-glucosinolate-analyser.git"
+  )
+)
+
+developers := List(
+  Developer("ofilangi", "Olivier Filangi", "[email protected]",url("https://github.com/ofilangi"))
+)
+
 libraryDependencies ++= Seq(
   "com.github.scopt" %% "scopt" % "4.1.0",
   "com.github.chhh" % "msftbx" % "1.8.8",
+  "com.lihaoyi" %% "ujson" % "2.0.0",
   "org.scala-lang.modules" %% "scala-parser-combinators" % "2.1.1",
   "com.lihaoyi" %% "utest" % "0.8.1" % Test,
 )
+
+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
+
+// Coverage
+
+coverageMinimumStmtTotal := 0
+coverageMinimumBranchTotal := 0
+coverageMinimumStmtPerPackage := 0
+coverageMinimumBranchPerPackage := 0
+coverageMinimumStmtPerFile := 0
+coverageMinimumBranchPerFile := 0
+coverageFailOnMinimum := true
+coverageHighlighting := true
+
+
 testFrameworks += new TestFramework("utest.runner.Framework")
 assembly / target := file("assembly")
 assembly / assemblyJarName := "pack.jar"
@@ -18,4 +73,5 @@ assembly / assemblyMergeStrategy := {
     val oldStrategy = (ThisBuild / assemblyMergeStrategy).value
     oldStrategy(x)
 }
+
 Global / onChangedBuildSource := ReloadOnSourceChanges
diff --git a/project/plugins.sbt b/project/plugins.sbt
@@ -1 +1,4 @@
-addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.2.0")
+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")  
diff --git a/src/main/resources/default.json b/src/main/resources/default.json
@@ -0,0 +1,60 @@
+{
+  "Glucosinolate" : {
+    "deltaMp0Mp2" : 1.996,
+    "numberSulfurMin" : 2,
+    "neutralLoss" :
+      {
+        "gluconolactone" : 178.0,
+        "sulfureTrioxide" : 80.0,
+        "anhydroglucose" : 162.0,
+        "thioglucose_s03" : 242.0,
+        "thioglucose" : 196.0,
+        "glucosinolate_223" : 223.0
+      },
+    "daughterIons" : {
+      "C6H11O9S_259" : 259.0,
+      "C6H11O8S2_275" : 275.0,
+      "C6H9NO8S_241" : 241.0,
+      "C6H11O7S_227" : 227.0
+    },
+    "databaseReference" : {
+      "G01" : 406.029,
+      "G02" : 422.025,
+      "G03" : 358.027,
+      "G04" : 420.043,
+      "G05" : 436.039,
+      "G06" : 372.041,
+      "G07" : 388.035,
+      "G08" : 388.036,
+      "G09" : 434.06,
+      "G10" : 450.054,
+      "G11" : 386.056,
+      "G12" : 402.051,
+      "G13" : 448.077,
+      "G14" : 422.056,
+      "G15" : 438.052,
+      "G16" : 438.052,
+      "G17" : 438.052,
+      "G18" : 438.051,
+      "G19" : 447.051,
+      "G20" : 477.062,
+      "G21" : 477.061,
+      "G22" : 463.047,
+      "G23" : 463.046,
+      "G24" : 360.042,
+      "G25" : 360.042,
+      "G26" : 374.057,
+      "G27" : 374.057,
+      "G28" : 390.052,
+      "G29" : 390.052,
+      "G30" : 388.073,
+      "G31" : 402.088,
+      "G32" : 402.088,
+      "G33" : 402.088,
+      "G34" : 416.104,
+      "G35" : 416.104,
+      "G36" : 416.104
+    }
+  }
+}
+