Merge pull request #15 from p2m2/develop

Develop
p2m2 · May 5, 2023 · 2d78af2 · 2d78af2
2 parents 06d9be4 + 67b09d4
commit 2d78af2
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Showing 10 changed files with 198 additions and 13 deletions.
diff --git a/app/controllers/HomeController.scala b/app/controllers/HomeController.scala
@@ -3,8 +3,9 @@ package controllers
 import akka.stream.scaladsl.{Source, StreamConverters}
 import akka.util.ByteString
 import daos.MassSpectrometryFileDAO
-import fr.inrae.metabolomics.p2m2.format.{GenericP2M2, MassSpectrometryResultSet, MassSpectrometryResultSetFactory}
-import fr.inrae.metabolomics.p2m2.parser._
+import fr.inrae.metabolomics.p2m2.format.MassSpectrometryResultSetFactory
+import fr.inrae.metabolomics.p2m2.format.ms.{GCMS, GenericP2M2, MassSpectrometryResultSet, OpenLabCDS, QuantifyCompoundSummaryReportMassLynx, QuantifySampleSummaryReportMassLynx, Xcalibur}
+import fr.inrae.metabolomics.p2m2.parser.{GCMSParser, OpenLabCDSParser, ParserManager, QuantifySummaryReportMassLynxParser, XcaliburXlsParser}
 import fr.inrae.metabolomics.p2m2.stream.ExportData
 import models.MassSpectrometryFile
 import play.api.http.HttpEntity
@@ -62,7 +63,7 @@ class HomeController @Inject()(
           val information = s"($filename,$fileSize,$contentType)" +
           "<br/>\\n \n nGCMSParser:"+GCMSParser.sniffFile(s"/tmp/$filename") +
           "<br/>OpenLabCDSParser:"+OpenLabCDSParser.sniffFile(s"/tmp/$filename") +
-          "<br/>QuantifyCompoundSummaryReportMassLynxParser:"+QuantifyCompoundSummaryReportMassLynxParser.sniffFile(s"/tmp/$filename") +
+          "<br/>QuantifyCompoundSummaryReportMassLynxParser:"+QuantifySummaryReportMassLynxParser.sniffFile(s"/tmp/$filename") +
           "<br/>XcaliburXlsParser:"+XcaliburXlsParser.sniffFile(s"/tmp/$filename")
 
           val ms : Option[MassSpectrometryResultSet] = ParserManager.buildMassSpectrometryObject(s"/tmp/$filename")
@@ -125,4 +126,19 @@ class HomeController @Inject()(
     }
   }
 
+  def preview_file(idMsFile : Long) :  Action[AnyContent] = Action.async {
+    msfiles.findById(idMsFile) map  {
+      case Some(s) => MassSpectrometryResultSetFactory.build(s.fileContent)  match {
+        case Some (obj: GCMS) => Ok (views.html.preview_GCMS (obj) )
+        case Some (obj: OpenLabCDS) => Ok (views.html.preview_OpenLabCDS(obj) )
+        case Some (obj: QuantifyCompoundSummaryReportMassLynx) =>
+          Ok (views.html.preview_QuantifyCompoundSummaryReportMassLynx(obj) )
+        case Some (obj: Xcalibur) => Ok (views.html.preview_Xcalibur(obj) )
+        case None => Ok (s"can not convert string to type [${s.fileContent}]")
+        case _ => Ok (s"can not preview file [id:$idMsFile]")
+        }
+      case None => Ok (s"Can not find Id file  [id:$idMsFile]")
+    }
+  }
+
 }
diff --git a/app/daos/MassSpectrometryFileDAO.scala b/app/daos/MassSpectrometryFileDAO.scala
@@ -1,6 +1,7 @@
 package daos
 
-import fr.inrae.metabolomics.p2m2.format.{GenericP2M2, MassSpectrometryResultSetFactory}
+import fr.inrae.metabolomics.p2m2.format.MassSpectrometryResultSetFactory
+import fr.inrae.metabolomics.p2m2.format.ms.GenericP2M2
 
 import scala.concurrent.{ExecutionContext, Future}
 import javax.inject.Inject
@@ -18,10 +19,14 @@ class MassSpectrometryFileDAO @Inject()
 
   import profile.api._
 
-  def findAll(): Seq[MassSpectrometryFile] = ???
-  def findById(id: String) : MassSpectrometryFile = ???
+  def findById(id: Long) : Future[Option[MassSpectrometryFile]] =
+    db.run(TableQuery[MassSpectrometryFileTable].filter(_.id === id).result).map {
+      case l if l.nonEmpty => Some(l.last)
+      case _ => None
+    }
 
-  def all(): Future[Seq[MassSpectrometryFile]] = db.run(TableQuery[MassSpectrometryFileTable].result)
+  def all(): Future[Seq[MassSpectrometryFile]] =
+    db.run(TableQuery[MassSpectrometryFileTable].result)
 
   def getMergeGenericP2M2() : Future[GenericP2M2] = {
     all().map {

diff --git a/app/views/importMassSpectrometryFile.scala.html b/app/views/importMassSpectrometryFile.scala.html
@@ -17,7 +17,7 @@
     @for(msFile <- listMSFiles ) {
     <tr>
         <td>@msFile.id</td>
-        <td>@msFile.name</td>
+        <td><a href="/preview_file/@msFile.id">@msFile.name</a></td>
         <td>@msFile.className</td>
         <td><a href="/delete/@msFile.id"><span class="material-symbols-outlined">delete</span></a></td>
     </tr>

diff --git a/app/views/preview.scala.html b/app/views/preview.scala.html
@@ -1,4 +1,4 @@
-@import fr.inrae.metabolomics.p2m2.format.GenericP2M2
+@import fr.inrae.metabolomics.p2m2.format.ms.GenericP2M2
 @(obj : GenericP2M2)
 @main("Merge all results file (preview)") {
 <table>
@@ -10,7 +10,7 @@
     </tr>
     </thead>
     <tbody>
-    @for(values <- obj.values) {
+    @for(values <- obj.samples) {
     <tr>
         @for(header <- GenericP2M2.HeaderField.values.toSeq) {
             <td>@values.get(header)</td>

diff --git a/app/views/preview_GCMS.scala.html b/app/views/preview_GCMS.scala.html
@@ -0,0 +1,38 @@
+@**************************************
+* GCMS preview page.                  *
+*                                     *
+* @ob The GCMS information to display *
+**************************************@
+
+@import fr.inrae.metabolomics.p2m2.format.ms._
+@import fr.inrae.metabolomics.p2m2.parser.ParserUtils
+
+@(obj : GCMS)
+@main("GCMS preview") {
+<h2>Header</h2>
+    <table>
+    @for(header <- GCMS.HeaderFileField.values.toSeq) {
+        <tr>
+            <td><b>@ParserUtils.toString(header)</b></td>
+            <td>@obj.header.get(header)</td>
+        </tr>
+    }
+    </table>
+
+<h2>Results</h2>
+
+<table>
+    <tr>
+    @for(header <- GCMS.HeaderField.values.toSeq) {
+        <td><b>@ParserUtils.toString(header)</b></td>
+    }
+    </tr>
+    @for(entry <- obj.msQuantitativeResults) {
+     <tr>
+        @for(header <- GCMS.HeaderField.values.toSeq) {
+            <td>@entry.get(header)</td>
+        }
+     </tr>
+    }
+</table>
+}
diff --git a/app/views/preview_OpenLabCDS.scala.html b/app/views/preview_OpenLabCDS.scala.html
@@ -0,0 +1,38 @@
+@********************************************
+* OpenLabCDS preview page.                  *
+*                                           *
+* @ob The OpenLabCDS information to display *
+*********************************************@
+
+@import fr.inrae.metabolomics.p2m2.format.ms._
+@import fr.inrae.metabolomics.p2m2.parser.ParserUtils
+
+@(obj : OpenLabCDS)
+@main("OpenLabCDS preview") {
+<h2>Header</h2>
+<table>
+    @for(header <- OpenLabCDS.HeaderFileField.values.toSeq) {
+    <tr>
+        <td><b>@ParserUtils.toString(header)</b></td>
+        <td>@obj.header.get(header)</td>
+    </tr>
+    }
+</table>
+
+<h2>Results</h2>
+
+<table>
+    <tr>
+        @for(header <- OpenLabCDS.HeaderField.values.toSeq) {
+        <td><b>@ParserUtils.toString(header)</b></td>
+        }
+    </tr>
+    @for(entry <- obj.results) {
+    <tr>
+        @for(header <- OpenLabCDS.HeaderField.values.toSeq) {
+        <td>@entry.get(header)</td>
+        }
+    </tr>
+    }
+</table>
+}
diff --git a/app/views/preview_QuantifyCompoundSummaryReportMassLynx.scala.html b/app/views/preview_QuantifyCompoundSummaryReportMassLynx.scala.html
@@ -0,0 +1,41 @@
+@***********************************************************************
+* QuantifyCompoundSummaryReportMassLynx preview page.                  *
+*                                                                      *
+* @ob The QuantifyCompoundSummaryReportMassLynx information to display *
+************************************************************************@
+
+@import fr.inrae.metabolomics.p2m2.format.ms._
+@import fr.inrae.metabolomics.p2m2.parser.ParserUtils
+
+@(obj : QuantifyCompoundSummaryReportMassLynx)
+@main("QuantifyCompoundSummaryReportMassLynx preview") {
+<h2>Header</h2>
+<table>
+    <tr>
+        <td><b>Printed Date</b></td>
+        <td>@obj.header.dateStr</td>
+    </tr>
+
+</table>
+
+<h2>Results</h2>
+<table>
+    <tr>
+        <td> - </td>
+        @for(header <- QuantifyCompoundSummaryReportMassLynx.HeaderField.values.toSeq) {
+        <td><b>@ParserUtils.toString(header)</b></td>
+        }
+    </tr>
+    @for(entry <- obj.resultsByCompound) {
+        @for(values <- entry._2) {
+        <tr>
+            <td>@entry._1</td>
+            @for(header <- QuantifyCompoundSummaryReportMassLynx.HeaderField.values.toSeq) {
+                <td>@values.get(header)</td>
+            }
+        </tr>
+        }
+    }
+</table>
+
+}
diff --git a/app/views/preview_Xcalibur.scala.html b/app/views/preview_Xcalibur.scala.html
@@ -0,0 +1,46 @@
+@********************************************
+* Xcalibur preview page.                    *
+*                                           *
+* @ob The Xcalibur information to display   *
+*********************************************@
+
+@import fr.inrae.metabolomics.p2m2.format.ms._
+@import fr.inrae.metabolomics.p2m2.parser.ParserUtils
+
+@(obj : Xcalibur)
+@main("Xcalibur preview") {
+<h2>Sheets</h2>
+
+    @for(sheet <- obj.results) {
+    <h3>Header</h3>
+    <table>
+        @for(header <- Xcalibur.HeaderSheetField.values.toSeq) {
+        <tr>
+            <td><b>@ParserUtils.toString(header)</b></td>
+            <td>@sheet.compoundInformationHeader.get(header)</td>
+        </tr>
+        }
+    </table>
+
+    <h3>Results</h3>
+    <table>
+        <tr>
+        @for(header <- Xcalibur.HeaderField.values.toSeq) {
+            <td><b>@ParserUtils.toString(header)</b></td>
+        }
+        </tr>
+        @for(values <- sheet.compoundByInjection) {
+            <tr>
+                @for(header <- Xcalibur.HeaderField.values.toSeq) {
+                    <td>@values.get(header)</td>
+                }
+            </tr>
+        }
+    </table>
+
+    }
+
+
+
+
+}
diff --git a/build.sbt b/build.sbt
@@ -9,9 +9,9 @@ scalaVersion := "2.13.8"
 
 libraryDependencies ++= Seq(
   guice,
-    "com.github.p2m2" %% "p2m2tools" % "develop-SNAPSHOT" changing(),
-    "com.typesafe.play" %% "play-slick" % "5.0.2",
-    "com.typesafe.play" %% "play-slick-evolutions" % "5.0.2",
+    "com.github.p2m2" %% "p2m2tools" % "0.2.0" changing(),
+    "com.typesafe.play" %% "play-slick" % "5.1.0",
+    "com.typesafe.play" %% "play-slick-evolutions" % "5.1.0",
     "com.h2database" % "h2" % "2.1.214",
     "org.scalatestplus.play" %% "scalatestplus-play" % "5.1.0" % Test
 )

diff --git a/conf/routes b/conf/routes
@@ -11,6 +11,7 @@ GET    /importMSF                  controllers.HomeController.importMassSpectrom
 POST   /upload                     controllers.HomeController.upload()
 GET    /delete/:idMsFileLong       controllers.HomeController.delete(idMsFileLong : Long)
 GET    /preview                    controllers.HomeController.preview()
+GET    /preview_file/:idMsFileLong controllers.HomeController.preview_file(idMsFileLong : Long)
 GET    /clean                      controllers.HomeController.clean()
 GET    /exportXLS                  controllers.HomeController.exportXLS()
 # Map static resources from the /public folder to the /assets URL path