Add location attributes to all metadata section cv params, annotate k…

…eys with special term
nfdi4plants · Aug 4, 2023 · ae6c20a · ae6c20a
1 parent cd4f08b
commit ae6c20a
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Showing 3 changed files with 39 additions and 66 deletions.
diff --git a/src/ArcGraphModel/Terms.fs b/src/ArcGraphModel/Terms.fs
@@ -46,58 +46,6 @@ module AssayMetadata =
         ontology.Terms
         |> List.map (fun t -> CvTerm(t.Id,t.Name,"ASSMSO"))
 
-module Terms = 
-
-    let filepath = "http://purl.obolibrary.org/obo/NCIT_C47922","Pathname","NCIT"
-
-    let person = "http://purl.obolibrary.org/obo/NCIT_C25190","Person","NCIT"
-
-    let name = "http://semanticscience.org/resource/SIO_000116","name","SIO"
-
-    let identifier = "http://semanticscience.org/resource/SIO_000115","identifier","SIO"
-
-    let title = "http://semanticscience.org/resource/SIO_000185","title","SIO"
-
-    let descriptor = "http://semanticscience.org/resource/SIO_000133","descriptor","SIO"
-
-    let familyName = "http://purl.obolibrary.org/obo/IAO_0020017","family name","IAO"
-
-    let givenName = "http://purl.obolibrary.org/obo/IAO_0020016","given name","IAO"
-
-    let midInitials = "http://purl.obolibrary.org/obo/NCIT_C25536","Initials","NCIT"
-
-    let email = "http://purl.obolibrary.org/obo/NCIT_C42775","E-mail Address","NCIT"
-
-    let phone = "http://purl.obolibrary.org/obo/NCIT_C40978","Telephone Number","NCIT"
+module StructuralTerms =
 
-    let design = "http://semanticscience.org/resource/SIO_000705","Design","SIO"
-
-    let investigation = "ARCO:1234","Investigation","ARCO"
-
-    let study = "ARCO:1234","Study","ARCO"
-
-    let assay = "ARCO:1234","Assay","ARCO"
-
-    let publication = "ARCO:1234","Publication","ARCO"
-
-    let status = "ARCO:1234","Status","ARCO"
-
-    let factor = "ARCO:12345","Factor","ARCO"
-
-    let parameter = "ARCO:12346","Parameter","ARCO"
-
-    let characteristic = "ARCO:12347","Characteristic","ARCO"
-
-    let rawData = "http://purl.obolibrary.org/obo/NCIT_C142663","Raw Data","NCIT"
-
-    let processedData = "http://purl.obolibrary.org/obo/NCIT_C84340","Processed Data","NCIT"
-
-    let data = "http://purl.obolibrary.org/obo/NCIT_C25474","Data","NCIT"
-
-    let source = "ARCO:12349","Source Material","ARCO"
-
-    let sample = "ARCO:12350","Sample","ARCO"
-
-    let annotationID = "ARCO:1","AnnotationID","ARCO"
-
-    let termSourceRef = "ARCO:2","termSourceRef","ARCO"
+    let metadataSectionKey = CvTerm("AGMO:00000001","Metadata Section Key","AGMO")
diff --git a/src/ArcGraphModel/Tokenization.fs b/src/ArcGraphModel/Tokenization.fs
@@ -12,13 +12,31 @@ module Tokenization =
         | [] -> failwith "Cannot convert nothin"
         | key :: [] -> 
             let f = keyParser [] key.Value
-            [f (ParamValue.CvValue ("","MetadataSectionKey",""))]
+
+            let keyTerm = 
+                let tmp = f (ParamValue.CvValue Terms.StructuralTerms.metadataSectionKey)
+                CvAttributeCollection.tryAddAttribute (Address.createRowParam(key.RowNumber)) tmp       |> ignore
+                CvAttributeCollection.tryAddAttribute (Address.createColumnParam(key.ColumnNumber)) tmp |> ignore
+                tmp
+
+            [keyTerm]
+
         | key :: cells ->
             let f = keyParser [] key.Value
-            cells
-            |> List.map (fun c -> 
-                let param = f (ParamValue.Value c.Value)
-                CvAttributeCollection.tryAddAttribute (Address.createRowParam(c.RowNumber)) param       |> ignore
-                CvAttributeCollection.tryAddAttribute (Address.createColumnParam(c.ColumnNumber)) param |> ignore
-                param
-            )
+
+            let keyTerm = 
+                let tmp = f (ParamValue.CvValue Terms.StructuralTerms.metadataSectionKey)
+                CvAttributeCollection.tryAddAttribute (Address.createRowParam(key.RowNumber)) tmp       |> ignore
+                CvAttributeCollection.tryAddAttribute (Address.createColumnParam(key.ColumnNumber)) tmp |> ignore
+                tmp
+
+            let cellTerms =
+                cells
+                |> List.map (fun c -> 
+                    let param = f (ParamValue.Value c.Value)
+                    CvAttributeCollection.tryAddAttribute (Address.createRowParam(c.RowNumber)) param       |> ignore
+                    CvAttributeCollection.tryAddAttribute (Address.createColumnParam(c.ColumnNumber)) param |> ignore
+                    param
+
+                )
+            keyTerm :: cellTerms
diff --git a/src/ArcGraphModel/TopLevelParsers.fs b/src/ArcGraphModel/TopLevelParsers.fs
@@ -5,7 +5,7 @@ open FSharpAux
 open FsSpreadsheet
 open FsSpreadsheet.ExcelIO
 
-type Investigation() =
+type Investigation =
 
     /// <summary>
     /// Parses the metadata sheet from an ISA Investigation  XLSX file as a row-based 2D list of `IParam`s.
@@ -38,7 +38,7 @@ type Investigation() =
         )
         |> List.concat
 
-type Study() =
+type Study =
 
     /// <summary>
     /// Parses the metadata sheet from an ISA Study XLSX file as a row-based 2D list of `IParam`s.
@@ -71,7 +71,15 @@ type Study() =
         )
         |> List.concat
 
-type Assay() =
+    /// <summary>
+    /// Parses all annotation tables from an ISA Study XLSX file as a list of `TokenizedAnnotationTable`s, a type that contains IO columns separated from the other columns.
+    /// </summary>
+    /// <param name="path">he path to the study xlsx file</param>
+    static member parseAnnotationTablesFromFile (path: string) =
+        FsWorkbook.fromXlsxFile path
+        |> AnnotationTable.parseWorkbook
+
+type Assay =
 
     /// <summary>
     /// Parses the metadata sheet from an ISA Assay XLSX file as a row-based 2D list of `IParam`s.
@@ -104,7 +112,6 @@ type Assay() =
         )
         |> List.concat
 
-
     /// <summary>
     /// Parses all annotation tables from an ISA Assay XLSX file as a list of `TokenizedAnnotationTable`s, a type that contains IO columns separated from the other columns.
     /// </summary>