Merge branch 'develop'

.circleci/config.yml

@@ -12,6 +12,9 @@
 #  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
 workflows:
   compile-workflow:
@@ -56,6 +59,17 @@ workflows:
             branches:
               ignore: /.*/
 
+#      - publish_npm:
+#          requires:
+#            - lib_js
+#          context:
+#            - NPM_CONTEXT
+#          filters:
+#            tags:
+#              only: /.*/
+#            branches:
+#              only: strategySourceRequest
+
       - check_discovery_valid_fullopjs_cdn_jsdelivr:
           filters:
             tags:
@@ -64,6 +78,7 @@ workflows:
 executors:
 
   openjdk:
+      working_directory: ~/repo
       docker:
         - image: circleci/openjdk:8-jdk
           auth:
@@ -76,6 +91,7 @@ executors:
           auth:
             username: ${DOCKER_USER}
             password: ${DOCKER_PASS}
+
         - image: tenforce/virtuoso:virtuoso7.2.5
           auth:
             username: ${DOCKER_USER}
@@ -93,6 +109,9 @@ executors:
             SPARQL_UPDATE: true
             DEFAULT_GRAPH: "graph:test:discovery:default:"
 
+orbs:
+  node: circleci/[email protected]
+
 jobs:
   compile:
     executor: openjdk
@@ -117,9 +136,7 @@ jobs:
 
   lib_js:
     executor: openjdk
-    environment:
-      JVM_OPTS: -Xmx3200m
-      TERM: dumb
+    working_directory: ~/repo
     steps:
       - checkout
       - setup_remote_docker
@@ -135,6 +152,10 @@ jobs:
           name: fullOptJS
           command: cat /dev/null | sbt discoveryJS/fullOptJS
 
+      - persist_to_workspace:
+          root: ./js/target/scala-2.13/scalajs-bundler/main/
+          paths: discovery-opt.js
+
   test_and_coverage_jvm:
     executor: virtuoso_environment_executor
     environment:
@@ -149,7 +170,7 @@ jobs:
             # fallback to using the latest cache if no exact match is found
             - v1-dependencies-
       - run:
-          name: Test and Coverage
+          name: Test JVM env and Coverage
           command: |
             cat /dev/null | sbt clean coverage discoveryJVM/test:test
             sbt discoveryJVM/coverageReport
@@ -206,8 +227,37 @@ jobs:
             F2=./dist/checksum
 
             if [ "$(diff -q $F1 $F2)" != ""  ]; then
-               echo "discovery and discovery-web have to be updated with update_cdn_libjs.sh !" ;
                echo "current checksum : "$(cat checksum)
                echo "repo checksum    : "$(cat dist/checksum)
                exit 1;
             fi ;
+
+  publish_npm:
+    docker:
+      - image: circleci/node:12.20
+        auth:
+          username: ${DOCKER_USER}
+          password: ${DOCKER_PASS}
+    working_directory: ~/repo
+    steps:
+        - checkout
+        - setup_remote_docker
+        - restore_cache:
+            keys:
+              - v1-dependencies-{{ checksum "build.sbt" }}
+              # fallback to using the latest cache if no exact match is found
+              - v1-dependencies-
+
+        - attach_workspace:
+            at: ~/repo/js/target/scala-2.13/scalajs-bundler/main/
+
+        - run:
+            name: Authenticate with registry
+            command: echo "//registry.npmjs.org/:_authToken=${NPM_TOKEN}" > ~/.npmrc
+
+        - run:
+            name: Js Opt Lib generation
+            command: |
+              npm config set registry http://registry.npmjs.org
+              npm version 0.0.4
+              npm publish --access public

README.md

@@ -5,93 +5,91 @@
 [![CodeFactor](https://www.codefactor.io/repository/github/p2m2/discovery/badge)](https://www.codefactor.io/repository/github/p2m2/discovery)
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/8d8ecb66f9ff4963a22efab3c693b629)](https://www.codacy.com/gh/p2m2/Discovery/dashboard?utm_source=github.com&utm_medium=referral&utm_content=p2m2/Discovery&utm_campaign=Badge_Grade)
 
-## Installation
 
-```sbt
-resolvers += Resolver.bintrayRepo("hmil", "maven")
-libraryDependencies += "com.github.p2m2" %%% "discovery" % "0.0.2-SNAPSHOT"
-```
+- easy sparql query construct using a simple editor and a web browser
+- display rich information on the web page or console 
+- offers building blocks to facilitate queries
 
-## Library generation 
-
-```
-sbt discoveryJS/fullOptJS
-sbt discoveryJVM/package
-sbt publishLocal 
-```
-
-### Library generation html/nodejs  
-
-```bash
-./update_cdn_libjs.sh
-```
-
-## test
-```
-sbt discoveryJVM/test  
-```
-
-## coverage
-```
-sbt discoveryJVM/coverageReport 
-```
 
 ### Html/Js example
 
 #### Html import 
 
 ```html 
-<script type="text/javascript" src="https://cdn.jsdelivr.net/gh/p2m2/Discovery@master/dist/discovery-web.js"></script> 
+<script type="text/javascript" src="https://cdn.jsdelivr.net/gh/p2m2/discovery@develop/dist/discovery-web.min.js"> </script> 
 <script>
-
-var SWDiscovery = discovery.SWDiscovery ;
-var SWDiscoveryConfiguration = discovery.SWDiscoveryConfiguration ;
-var URI = discovery.URI ;
-
-</script>
-```
-
-[js fiddle example](https://jsfiddle.net/ofilangi/3xkay1f6/10/)
+      let config = SWDiscoveryConfiguration.setConfigString(`
+          {
+          "sources" : [{
+          "id"  : "peakforest",
+          "url" : "https://peakforest.semantic-metabolomics.fr/sparql"
+           }]}
+          `)
+        let r = SWDiscovery(config)
+                     .prefix("peak_class","https://metabohub.peakforest.org/ontology/class#")
+                     .prefix("peak_prop","https://metabohub.peakforest.org/ontology/property#")
+                     .root()
+                      .something("i")
+                        .setList(18,19,20)
+                     .root()
+                       .something("m1")
+                         .isA("peak_class:Compound")
+                         .datatype("rdfs:label","label1")
+                         .isSubjectOf("peak_prop:InChIKey","inchikey1")
+                           .bind("block1").subStr(0,"?i")
+                     .root()
+                       .something("m2")
+                         .filter.notEqual("?m1")
+                         .isA("peak_class:Compound")
+                         .datatype("rdfs:label","label2")
+                         .isSubjectOf("peak_prop:InChIKey","inchikey2")
+                           .bind("block2").subStr(0,"?i")
+                           .filter.equal("?block1")
+                      .focus("m1")
+                        .console() // display information on the console
+                        .helper("metabo") // display information on the web page and propose new building block.
+                     .select("m1","m2","label1","label2","block1","block2")
+                     .limit(10);
+      
+       
+        r.commit().raw().then((response) => {
+          
+          for (let i=0;i<response.results.bindings.length;i++) {
+            let m1 =response.results.bindings[i]["m1"].value;
+            let m2 =response.results.bindings[i]["m2"].value;
+            /* decorations/datatype properties management */ 
+            let label1=response.results.datatypes["label1"][m1][0].value; // all studies with all languages, here we take the first one arbitrarily.
+            let label2=response.results.datatypes["label2"][m2][0].value;
+            
+            let b1 =response.results.bindings[i]["block1"].value;
+            let b2 =response.results.bindings[i]["block2"].value;
+
+            console.log(label1 + "-" + label2 + " block1:"+b1 + " block2:"+b2 );
+          }
+
+        }).catch( (error) => {
+          console.error(" -- catch exception --")
+          console.error(error)
+        } );
+
+    </script>
+ ```
+
+
+[js fiddle example](https://jsfiddle.net/ofilangi/h6fbg845/)
 
 #### Node import 
 
 ##### dependencies 
 
-```bash
-npm install require-from-url
-```
-
-```node
-var requireFromUrl = require('require-from-url/sync');
-var discoveryjs = requireFromUrl("https://cdn.jsdelivr.net/gh/p2m2/Discovery@master/dist/discovery.js")
-
-var SWDiscoveryConfiguration = discoveryjs.SWDiscoveryConfiguration ;
-var SWDiscovery = discoveryjs.SWDiscovery ;
-var URI = discoveryjs.URI ;
-```
+### html examples
 
 [discovery-tutorial-html-js](https://github.com/p2m2/discovery-tutorial-html-js)
 
-### NodeJs example
+### NodeJs examples
 
 [discovery-tutorial-nodejs](https://github.com/p2m2/discovery-tutorial-nodejs)
 
-### Scala Exemple 
+### Scala examples 
 
 full example with [table view implementation](https://github.com/p2m2/discovery-table-view) using [scalatags](https://github.com/lihaoyi/scalatags)
-
-
-## note dev
-
-```
-sbt compile
-sbt run   # run web app http://localhost:9000
-sbt package
-sbt test
-sbt fastOptJS => generer le JS
-sbt discoveryJVM/testOnly inrae.semantic_web.QueryPlannerTest
-## local publication -> .ivy2
-sbt publishLocal
-## osssonatype maven centra repository publication
-sbt publish
-```

build.sbt

@@ -1,18 +1,20 @@
 import sbt.Keys.scalacOptions
 import sbtcrossproject.CrossPlugin.autoImport.crossProject
 
-lazy val utestVersion = "0.7.5"
+lazy val utestVersion = "0.7.7"
 lazy val upickleVersion  = "1.2.2"
 lazy val airframeLogVersion = "20.11.0"
 lazy val scalaParserCombinatorVersion = "1.1.2"
-lazy val scalaReflectVersion = "1.0.0"
 lazy val RosHttpVersion = "3.0.0"
 lazy val scalaJsDOMVersion = "1.1.0"
 lazy val scalaStubVersion = "1.0.0"
 lazy val scalatagVersion = "0.9.2"
-lazy val jenaVersion = "3.16.0"
+lazy val rdf4jVersion = "3.6.0-M2"
+
+//https://jitpack.io/
 
 releaseIgnoreUntrackedFiles := true
+
 val version_build = scala.util.Properties.envOrElse("DISCOVERY_VERSION", "local-SNAPSHOT" )
 val SWDiscoveryVersionAtBuildTimeFile = "./shared/src/main/scala/inrae/semantic_web/SWDiscoveryVersionAtBuildTime.scala"
 
@@ -25,7 +27,7 @@ val buildSWDiscoveryVersionAtBuildTimeFile =
       |package inrae.semantic_web
       |
       |object SWDiscoveryVersionAtBuildTime {
-      |   val version : String = "${version_build}"
+      |   val version : String = " build ${java.time.LocalDate.now.toString}"
       |}""").stripMargin)
 
 
@@ -45,6 +47,9 @@ def getPackageSetting() = Seq(
       "scm:[email protected]:p2m2/Discovery.git"
     )
   ),
+  developers := List(
+    Developer("ofilangi", "Olivier Filangi", "[email protected]",url("https://github.com/ofilangi"))
+  ),
   credentials += {
 
     val realm = scala.util.Properties.envOrElse("REALM_CREDENTIAL", "" )
@@ -85,35 +90,49 @@ lazy val discovery=crossProject(JSPlatform, JVMPlatform).in(file("."))
   .settings(
     resolvers += Resolver.bintrayRepo("hmil", "maven"),
     libraryDependencies ++= Seq(
-      "com.lihaoyi" %%% "utest" % utestVersion % "test",
+      "com.lihaoyi" %%% "utest" % utestVersion % Test,
+      "fr.hmil" %%% "roshttp" % RosHttpVersion % Test ,
       "com.lihaoyi" %%% "upickle" % upickleVersion,
       "org.wvlet.airframe" %%% "airframe-log" % airframeLogVersion,
-      "org.scala-lang.modules" %%% "scala-parser-combinators" % scalaParserCombinatorVersion,
-      "org.portable-scala" %%% "portable-scala-reflect" % scalaReflectVersion,
-      "fr.hmil" %%% "roshttp" % RosHttpVersion,
-      "com.softwaremill.sttp.client3" %%% "core" % "3.0.0"
+      "org.scala-lang.modules" %%% "scala-parser-combinators" % scalaParserCombinatorVersion
     ),
     testFrameworks += new TestFramework("utest.runner.Framework"),
     scalacOptions ++= Seq("-deprecation", "-feature"),
     classLoaderLayeringStrategy := ClassLoaderLayeringStrategy.AllLibraryJars,
     coverageMinimum := 70,
     coverageFailOnMinimum := false,
-    coverageHighlighting := true
+    coverageHighlighting := true,
+    parallelExecution in Test := false
   )
+  .jsConfigure(_.enablePlugins(ScalaJSBundlerPlugin))
   .jsSettings(
-    scalaJSLinkerConfig ~= { _.withModuleKind(ModuleKind.CommonJSModule) } ,
-    scalaJSLinkerConfig in (Compile, fullOptJS) ~= { _.withSourceMap(false) },
-    libraryDependencies ++= Seq(
-      "org.scala-js" %%% "scalajs-dom" % scalaJsDOMVersion
+    webpackBundlingMode := BundlingMode.LibraryAndApplication(),
+    npmDependencies in Compile ++= Seq(
+      "axios" -> "0.21.1",
+      "qs" -> "6.9.6",
+      "showdown" -> "1.9.1"
     ),
-    jsEnv := new org.scalajs.jsenv.jsdomnodejs.JSDOMNodeJSEnv()
+    scalaJSLinkerConfig in (Compile, fastOptJS ) ~= {
+      _.withOptimizer(false)
+        .withPrettyPrint(true)
+        .withSourceMap(true)
+    },
+    scalaJSLinkerConfig in (Compile, fullOptJS) ~= {
+      _.withSourceMap(false)
+        .withModuleKind(ModuleKind.CommonJSModule)
+    },
+    libraryDependencies ++= Seq(
+      "org.scala-js" %%% "scalajs-dom" % "1.1.0"
+    )
   )
   .jvmSettings(
     libraryDependencies ++= Seq(
       "org.scala-js" %% "scalajs-stubs" % scalaStubVersion % "provided",
-      "org.apache.jena" % "apache-jena" % jenaVersion pomOnly()
+      "org.slf4j" % "slf4j-api" % "1.7.9",
+      "org.slf4j" % "slf4j-simple" % "1.7.9",
+      "org.eclipse.rdf4j" % "rdf4j-storage" % rdf4jVersion,
+      "org.eclipse.rdf4j" % "rdf4j-tools-federation" % rdf4jVersion
     ))
-  //.enablePlugins(ScalaJSBundlerPlugin)
 
 Global / onChangedBuildSource := ReloadOnSourceChanges
 //publishTo in ThisBuild :=