add datamap contract handling

nfdi4plants · May 14, 2024 · db9fbf8 · db9fbf8
1 parent b54b5a5
commit db9fbf8
Show file tree

Hide file tree

Showing 9 changed files with 43 additions and 11 deletions.
diff --git a/src/ARCtrl/ARC.fs b/src/ARCtrl/ARC.fs
@@ -262,7 +262,7 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
             assay.DataMap <- datamap
             assay.Tables <- updatedTables.Tables
         )
-        investigation.Assays |> Seq.iter (fun a -> a.StaticHash <- a.GetHashCode())
+        investigation.Assays |> Seq.iter (fun a -> a.StaticHash <- a.GetLightHashCode())
         investigation.Studies |> Seq.iter (fun s -> s.StaticHash <- s.GetLightHashCode())
         investigation.StaticHash <- investigation.GetLightHashCode()
         this.ISA <- Some investigation
@@ -303,7 +303,7 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
             )
             inv.Assays
             |> Seq.iter (fun a ->
-                a.StaticHash <- a.GetHashCode()
+                a.StaticHash <- a.GetLightHashCode()
                 workbooks.Add (
                     Identifier.Assay.fileNameFromIdentifier a.Identifier,
                     (DTOType.ISA_Assay, Spreadsheet.ArcAssay.toFsWorkbook a))     
@@ -373,7 +373,7 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
 
                 // Get Assay contracts
                 for a in inv.Assays do
-                    let hash = a.GetHashCode()
+                    let hash = a.GetLightHashCode()
                     if a.StaticHash = 0 then 
                         yield! a.ToCreateContract(WithFolder = true)
                     elif a.StaticHash <> hash then 

diff --git a/src/ARCtrl/ARCtrl.fsproj b/src/ARCtrl/ARCtrl.fsproj
@@ -47,5 +47,7 @@
       <Package Name="requests" Version="&gt;= 2.28.1 &lt; 3.0.0" ResolutionStrategy="Max" />
     </PythonDependencies>
   </PropertyGroup>
-	<ItemGroup />
+	<ItemGroup>
+	  <PackageReference Update="FSharp.Core" Version="7.0.401" />
+	</ItemGroup>
 </Project>
diff --git a/src/Contract/ARCtrl.Contract.fsproj b/src/Contract/ARCtrl.Contract.fsproj
@@ -22,6 +22,9 @@
   <ItemGroup>
     <None Include="../../build/logo.png" Pack="true" PackagePath="\" />
   </ItemGroup>
+  <ItemGroup>
+    <PackageReference Update="FSharp.Core" Version="7.0.401" />
+  </ItemGroup>
   <PropertyGroup>
     <Authors>nfdi4plants, Kevin Frey, Lukas Weil, Kevin Schneider, Oliver Maus</Authors>
     <Description>ARC helper functions for contracts management.</Description>

diff --git a/src/Contract/Datamap.fs b/src/Contract/Datamap.fs
@@ -47,9 +47,12 @@ module DatamapContractExtensions =
         static member tryFromReadContractForAssay (assayIdentifier : string) (c:Contract) =
             let path = Identifier.Assay.datamapFileNameFromIdentifier assayIdentifier
             match c with
-            | {Path = p; Operation = READ; DTOType = Some DTOType.ISA_Datamap; DTO = Some (DTO.Spreadsheet fsworkbook)} when p = path->
-                fsworkbook :?> FsWorkbook
-                |> DataMap.fromFsWorkbook
+            | {Path = p; Operation = READ; DTOType = Some DTOType.ISA_Datamap; DTO = Some (DTO.Spreadsheet fsworkbook)} when p = path ->
+                let dm = 
+                    fsworkbook :?> FsWorkbook
+                    |> DataMap.fromFsWorkbook                
+                dm.StaticHash <- dm.GetHashCode()
+                dm
                 |> Some 
             | _ -> None
 
@@ -81,7 +84,9 @@ module DatamapContractExtensions =
             let path = Identifier.Study.datamapFileNameFromIdentifier studyIdentifier
             match c with
             | {Path = p; Operation = READ; DTOType = Some DTOType.ISA_Datamap; DTO = Some (DTO.Spreadsheet fsworkbook)} when p = path->
-                fsworkbook :?> FsWorkbook
-                |> DataMap.fromFsWorkbook
-                |> Some 
+                let dm = 
+                    fsworkbook :?> FsWorkbook
+                    |> DataMap.fromFsWorkbook                
+                dm.StaticHash <- dm.GetHashCode()
+                Some (dm)
             | _ -> None
diff --git a/src/Core/ArcTypes.fs b/src/Core/ArcTypes.fs
@@ -492,6 +492,20 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno
             this.StructurallyEquals(assay)
         | _ -> false
 
+    // Hashcode without Datamap
+    member this.GetLightHashCode() = 
+        [|
+            box this.Identifier
+            HashCodes.boxHashOption this.MeasurementType
+            HashCodes.boxHashOption this.TechnologyType
+            HashCodes.boxHashOption this.TechnologyPlatform
+            HashCodes.boxHashSeq this.Tables
+            HashCodes.boxHashSeq this.Performers
+            HashCodes.boxHashSeq this.Comments
+        |]
+        |> HashCodes.boxHashArray 
+        |> fun x -> x :?> int
+
     override this.GetHashCode() = 
         [|
             box this.Identifier

diff --git a/src/Json/ARCtrl.Json.fsproj b/src/Json/ARCtrl.Json.fsproj
@@ -87,6 +87,9 @@
     <Content Include="*.fsproj; **\*.fs; **\*.fsi" PackagePath="fable\" />
     <None Include="../../build/logo.png" Pack="true" PackagePath="\" />
   </ItemGroup>
+  <ItemGroup>
+    <PackageReference Update="FSharp.Core" Version="7.0.401" />
+  </ItemGroup>
   <PropertyGroup>
     <Authors>nfdi4plants, Lukas Weil, Florian Wetzels, Kevin Frey</Authors>
     <Description>ARC and ISA json compliant parser for experimental metadata toolkit in F#. This project is meant as an easy means to open, manipulate and save ISA (Investigation,Study,Assay) metadata files in isa-json format.</Description>

diff --git a/src/Spreadsheet/ARCtrl.Spreadsheet.fsproj b/src/Spreadsheet/ARCtrl.Spreadsheet.fsproj
@@ -33,7 +33,7 @@
     <Compile Include="Template.fs" />
   </ItemGroup>
   <ItemGroup>
-    <PackageReference Include="FsSpreadsheet" Version="5.1.3" />
+    <PackageReference Include="FsSpreadsheet" Version="6.1.2" />
   </ItemGroup>
   <ItemGroup>
     <None Include="../../build/logo.png" Pack="true" PackagePath="\" />
@@ -45,6 +45,9 @@
     <ProjectReference Include="..\Core\ARCtrl.Core.fsproj" />
     <ProjectReference Include="..\FileSystem\ARCtrl.FileSystem.fsproj" />
   </ItemGroup>
+  <ItemGroup>
+    <PackageReference Update="FSharp.Core" Version="7.0.401" />
+  </ItemGroup>
   <PropertyGroup>
     <Authors>nfdi4plants, Lukas Weil</Authors>
     <Description>ARC and ISA xlsx compliant parser for experimental metadata toolkit in F#. This project is meant as an easy means to open, manipulate and save ISA (Investigation,Study,Assay) metadata files in isa-xlsx format.</Description>

diff --git a/src/Spreadsheet/Metadata/Assays.fs b/src/Spreadsheet/Metadata/Assays.fs
@@ -35,6 +35,7 @@ module Assays =
             (Option.fromValueWithDefault (OntologyAnnotation()) technologyType) 
             (technologyPlatform |> Option.map JsonTypes.decomposeTechnologyPlatform)
             (ResizeArray())             
+            None
             (ResizeArray())      
             (comments)
 

diff --git a/src/Spreadsheet/Metadata/Study.fs b/src/Spreadsheet/Metadata/Study.fs
@@ -121,6 +121,7 @@ module Studies =
             (ResizeArray contacts)
             (ResizeArray designDescriptors)  
             (ResizeArray())
+            None
             (ResizeArray(assayIdentifiers))
             (ResizeArray studyInfo.Comments)
         |> fun arcstudy ->