fix querymodel node updating

nfdi4plants · Jun 15, 2022 · af3dc20 · af3dc20
1 parent 36831dc
commit af3dc20
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Showing 3 changed files with 52 additions and 44 deletions.
diff --git a/src/ISADotnet/QueryModel/Assay.fs b/src/ISADotnet/QueryModel/Assay.fs
@@ -18,21 +18,22 @@ type QAssay(FileName : string option,MeasurementType : OntologyAnnotation option
     member this.TechnologyType = TechnologyType
     member this.TechnologyPlatform = TechnologyPlatform
 
-    static member fromAssay (assay : Assay) =
+    static member fromAssay (assay : Assay, ?ReferenceSheets : QSheet list) =
         let sheets = 
-            assay.ProcessSequence |> Option.defaultValue []
-            |> List.groupBy (fun x -> 
-                if x.ExecutesProtocol.IsSome && x.ExecutesProtocol.Value.Name.IsSome then
-                    x.ExecutesProtocol.Value.Name.Value 
-                else
-                    // Data Stewards use '_' as seperator to distinguish between protocol template types.
-                    // Exmp. 1SPL01_plants, in these cases we need to find the last '_' char and remove from that index.
-                    let lastUnderScoreIndex = x.Name.Value.LastIndexOf '_'
-                    x.Name.Value.Remove lastUnderScoreIndex
-            )
-            |> List.map (fun (name,processes) -> QSheet.fromProcesses name processes)
+            match ReferenceSheets with
+            | Some ref -> 
+                assay.ProcessSequence 
+                |> Option.defaultValue []
+                |> fun sheets -> QProcessSequence(sheets,ref)
+            | None ->
+                assay.ProcessSequence 
+                |> Option.defaultValue []
+                |> QProcessSequence
+            |> Seq.toList
+
         QAssay(assay.FileName,assay.MeasurementType,assay.TechnologyType,assay.TechnologyPlatform,sheets)
 
+
     member this.Protocol (sheetName : string) =
         base.Protocol(sheetName, $"Assay \"{this.FileName}\"")
 

diff --git a/src/ISADotnet/QueryModel/ProcessSequence.fs b/src/ISADotnet/QueryModel/ProcessSequence.fs
@@ -13,26 +13,33 @@ type QProcessSequence (sheets : QSheet list) =
 
     member this.Sheets = sheets
 
-    new (processSequence : Process list) =
-        let updateNodes (sheets : QSheet list) =
-            let mapping = 
-                sheets
-                |> List.collect (fun s -> 
-                    s.Rows
-                    |> List.collect (fun r -> [r.Input, r.InputType.Value; r.Output, r.OutputType.Value])
-                )
-                |> List.groupBy fst
-                |> List.map (fun (name,vs) -> name, vs |> List.map snd |> IOType.reduce)
-                |> Map.ofList
-            let updateRow row = 
-                {row with 
-                    InputType = Some mapping.[row.Input]
-                    OutputType = Some mapping.[row.Output]
-                }
-            sheets
-            |> List.map (fun sheet ->
-                {sheet with Rows = sheet.Rows |> List.map updateRow}
+    static member internal updateNodesAgainst (reference : QSheet list) (sheets : QSheet list) =
+        let mapping = 
+            reference
+            |> List.collect (fun s -> 
+                s.Rows
+                |> List.collect (fun r -> [r.Input, r.InputType.Value; r.Output, r.OutputType.Value])
             )
+            |> List.groupBy fst
+            |> List.map (fun (name,vs) -> name, vs |> List.map snd |> IOType.reduce)
+            |> Map.ofList
+        let updateRow row = 
+            {row with 
+                InputType = Some mapping.[row.Input]
+                OutputType = Some mapping.[row.Output]
+            }
+        sheets
+        |> List.map (fun sheet ->
+            {sheet with Rows = sheet.Rows |> List.map updateRow}
+        )
+
+    new (processSequence : Process list, ?ReferenceSheets : QSheet list) =
+        let updateNodes (sheets : QSheet list) =
+            match ReferenceSheets with
+            | Some ref ->
+                QProcessSequence.updateNodesAgainst (ref @ sheets) sheets
+            | None ->
+                QProcessSequence.updateNodesAgainst sheets sheets
         let sheets = 
             processSequence
             |> List.groupBy (fun x -> 

diff --git a/src/ISADotnet/QueryModel/Study.fs b/src/ISADotnet/QueryModel/Study.fs
@@ -25,20 +25,20 @@ type QStudy(FileName : string option,Identifier : string option,Title : string o
     member this.Assays = Assays
 
     static member fromStudy (study : Study) =
-        let assays = study.Assays |> Option.map (List.map QAssay.fromAssay) |> Option.defaultValue []
+               
         let sheets = 
-            study.ProcessSequence |> Option.defaultValue []
-            |> List.groupBy (fun x -> 
-                if x.ExecutesProtocol.IsSome && x.ExecutesProtocol.Value.Name.IsSome then
-                    x.ExecutesProtocol.Value.Name.Value 
-                else
-                    // Data Stewards use '_' as seperator to distinguish between protocol template types.
-                    // Exmp. 1SPL01_plants, in these cases we need to find the last '_' char and remove from that index.
-                    let lastUnderScoreIndex = x.Name.Value.LastIndexOf '_'
-                    x.Name.Value.Remove lastUnderScoreIndex
-            )
-            |> List.map (fun (name,processes) -> QSheet.fromProcesses name processes)
-            |> List.append (assays |> List.collect (fun a -> a.Protocols))
+            study.Assays 
+            |> Option.map (List.collect (fun a -> a.ProcessSequence |> Option.defaultValue []) )
+            |> Option.defaultValue []
+            |> List.append (study.ProcessSequence |> Option.defaultValue [])
+            |> QProcessSequence
+            |> Seq.toList
+
+        let assays = 
+            study.Assays 
+            |> Option.map (List.map (fun a -> QAssay.fromAssay(a,sheets)))
+            |> Option.defaultValue []
+
         QStudy(study.FileName,study.Identifier,study.Title,study.Description,study.SubmissionDate,study.PublicReleaseDate,study.Publications,study.Contacts,study.StudyDesignDescriptors,assays,sheets)
 
     member this.Protocol (sheetName : string) =