update arctrl.net dependency

nfdi4plants · Oct 7, 2023 · dee2ba1 · dee2ba1
1 parent a3e4994
commit dee2ba1
Show file tree

Hide file tree

Showing 4 changed files with 26 additions and 17 deletions.
diff --git a/src/ArcCommander/APIs/ArcAPI.fs b/src/ArcCommander/APIs/ArcAPI.fs
@@ -132,10 +132,10 @@ module ArcAPI =
         let output =
             if arcArgs.ContainsFlag ProcessSequence then
                 API.ARC.getProcesses arc
-                |> ARCtrl.ISA.Json.ProcessSequence.toString
+                |> ARCtrl.ISA.Json.ProcessSequence.toJsonString
             else 
                 arc.ISA.Value
-                |> ARCtrl.ISA.Json.ArcInvestigation.toString
+                |> ARCtrl.ISA.Json.ArcInvestigation.toJsonString
 
         match arcArgs.TryGetFieldValue Output with
         | Some p -> System.IO.File.WriteAllText(p, output)

diff --git a/src/ArcCommander/APIs/AssayAPI.fs b/src/ArcCommander/APIs/AssayAPI.fs
@@ -49,17 +49,26 @@ module AssayAPI =
 
         let assayFileName = Identifier.Assay.fileNameFromIdentifier assayIdentifier
 
+        let mt = 
+            OntologyAnnotation.fromString(
+                ?termName = (assayArgs.TryGetFieldValue AssayInitArgs.MeasurementType),
+                ?tan = (assayArgs.TryGetFieldValue AssayInitArgs.MeasurementTypeTermAccessionNumber),
+                ?tsr = (assayArgs.TryGetFieldValue AssayInitArgs.MeasurementTypeTermSourceREF)
+                    )
+            |> Aux.Option.fromValueWithDefault OntologyAnnotation.empty
+        let tt = 
+            OntologyAnnotation.fromString(
+                ?termName = (assayArgs.TryGetFieldValue AssayInitArgs.TechnologyType),
+                ?tan = (assayArgs.TryGetFieldValue AssayInitArgs.TechnologyTypeTermAccessionNumber),
+                ?tsr = (assayArgs.TryGetFieldValue AssayInitArgs.TechnologyTypeTermSourceREF)
+                    )
+            |> Aux.Option.fromValueWithDefault OntologyAnnotation.empty
+        let tp = 
+            assayArgs.TryGetFieldValue AssayInitArgs.TechnologyPlatform
+            |> Option.map ArcAssay.decomposeTechnologyPlatform
+
         let assay = 
-            Assays.fromString
-                (assayArgs.TryGetFieldValue  AssayInitArgs.MeasurementType)
-                (assayArgs.TryGetFieldValue  AssayInitArgs.MeasurementTypeTermAccessionNumber)
-                (assayArgs.TryGetFieldValue  AssayInitArgs.MeasurementTypeTermSourceREF)
-                (assayArgs.TryGetFieldValue  AssayInitArgs.TechnologyType)
-                (assayArgs.TryGetFieldValue  AssayInitArgs.TechnologyTypeTermAccessionNumber)
-                (assayArgs.TryGetFieldValue  AssayInitArgs.TechnologyTypeTermSourceREF)
-                (assayArgs.TryGetFieldValue  AssayInitArgs.TechnologyPlatform)
-                assayFileName
-                [||]
+            ArcAssay.create(assayIdentifier, ?measurementType = mt,?technologyType = tt, ?technologyPlatform = tp)
 
         let arc = ARC.load(arcConfiguration)
         let isa = arc.ISA |> Option.defaultValue (ArcInvestigation(Identifier.createMissingIdentifier()))
@@ -371,10 +380,10 @@ module AssayAPI =
                 if assayArgs.ContainsFlag AssayExportArgs.ProcessSequence then               
                     a.Tables |> Seq.collect (fun t -> t.GetProcesses())
                     |> Seq.toList
-                    |> ARCtrl.ISA.Json.ProcessSequence.toString
+                    |> ARCtrl.ISA.Json.ProcessSequence.toJsonString
                 else 
                     Study.create(Contacts = (a.Performers |> Array.toList),Assays = [a.ToAssay()])
-                    |> ARCtrl.ISA.Json.Study.toString
+                    |> ARCtrl.ISA.Json.Study.toJsonString
 
             match assayArgs.TryGetFieldValue AssayExportArgs.Output with
             | Some p -> System.IO.File.WriteAllText(p, output)
@@ -405,7 +414,7 @@ module AssayAPI =
                     ass
                     |> Seq.collect (fun a -> a.Tables |> Seq.collect (fun t -> t.GetProcesses()))
                     |> Seq.toList
-                    |> ARCtrl.ISA.Json.ProcessSequence.toString
+                    |> ARCtrl.ISA.Json.ProcessSequence.toJsonString
                 else 
                     ass
                     |> Seq.map (fun a -> 

diff --git a/src/ArcCommander/ArcCommander.fsproj b/src/ArcCommander/ArcCommander.fsproj
@@ -71,7 +71,7 @@
   <!--References-->
   <ItemGroup>
     <PackageReference Update="FSharp.Core" Version="7.0.400" />
-    <PackageReference Include="ARCtrl.NET" Version="1.0.0-alpha2" />
+    <PackageReference Include="ARCtrl.NET" Version="1.0.0-alpha3" />
     <PackageReference Include="Argu" Version="6.1.1" />
     <PackageReference Include="Fake.IO.FileSystem" Version="6.0.0" />
     <PackageReference Include="Fake.Tools.Git" Version="6.0.0" />

diff --git a/src/ArcCommander/Server/ArcAPIHandler.fs b/src/ArcCommander/Server/ArcAPIHandler.fs
@@ -63,7 +63,7 @@ let arcImportHandler : HttpHandler =
             let tmpDir = Path.Combine(Path.GetTempPath(), "tmpArc")
             let tmpZip = Path.Combine(Path.GetTempPath(), "tmpArc.zip")
 
-            ArcInvestigation.fromString isaJsonString
+            ArcInvestigation.fromJsonString isaJsonString
             //|> fun i -> {i with Remarks = []}
             |> fun i -> ARC(i).Write(tmpDir)