Merge pull request #549 from nfdi4plants/issues_521_539_544

Fixes to multiple smaller issues

Swate.sln

@@ -14,8 +14,6 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution
 		.assets\assets\install.cmd = .assets\assets\install.cmd
 		build\manifest.xml = build\manifest.xml
 		package.json = package.json
-		paket.dependencies = paket.dependencies
-		paket.lock = paket.lock
 		README.md = README.md
 		RELEASE_NOTES.md = RELEASE_NOTES.md
 	EndProjectSection
@@ -24,8 +22,8 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "src", "src", "{E0FF3176-0B7
 EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "ISSUE_TEMPLATE", "ISSUE_TEMPLATE", "{54B2B950-6393-4086-8AF4-3D211495433C}"
 	ProjectSection(SolutionItems) = preProject
-		.github\ISSUE_TEMPLATE\config.yml = .github\ISSUE_TEMPLATE\config.yml
 		.github\ISSUE_TEMPLATE\bug_report.yml = .github\ISSUE_TEMPLATE\bug_report.yml
+		.github\ISSUE_TEMPLATE\config.yml = .github\ISSUE_TEMPLATE\config.yml
 		.github\ISSUE_TEMPLATE\feature_request.yml = .github\ISSUE_TEMPLATE\feature_request.yml
 	EndProjectSection
 EndProject

package.json

@@ -6,6 +6,7 @@
   },
   "scripts": {},
   "devDependencies": {
+    "@tailwindcss/typography": "^0.5.15",
     "@types/node": "^20.10.3",
     "@vitejs/plugin-basic-ssl": "^1.0.2",
     "@vitejs/plugin-react": "^4.2.1",

src/Client/MainComponents/FooterTabs.fs

@@ -318,7 +318,7 @@ let MainMetadata(model: Model, dispatch: Messages.Msg -> unit) =
         prop.children [
             Html.a  [
                 Bulma.icon [Html.i [prop.className "fa-solid fa-circle-info"]]
-                Html.text "Metadata"
+                Html.text model.SpreadsheetModel.FileType
             ]
         ]
     ]

src/Client/MainComponents/Navbar.fs

@@ -9,14 +9,29 @@ open Messages
 open Components.QuickAccessButton
 open MainComponents
 open Model
+open Shared
 
-let private quickAccessButtonListStart (state: LocalHistory.Model) dispatch =
+let private FileName (model: Model) =
+    let txt =
+        match model.SpreadsheetModel.ArcFile with
+        | Some (ArcFiles.Assay a) -> a.Identifier
+        | Some (ArcFiles.Study (s,_)) -> s.Identifier
+        | Some (ArcFiles.Investigation i) -> i.Identifier
+        | Some (ArcFiles.Template t) -> t.FileName
+        | _ -> ""
+    Html.div [
+        prop.className "text-white text-lg font-bold flex items-center max-w-[125px] p-2 truncate inline-block"
+        prop.text txt
+        prop.title txt
+    ]
+
+let private quickAccessButtonListStart (model: Model) (state: LocalHistory.Model) dispatch =
     Html.div [
         prop.style [
             style.display.flex; style.flexDirection.row
         ]
         prop.children [
-
+            FileName model
             QuickAccessButton.create(
                 "Back",
                 [
@@ -167,7 +182,7 @@ let Main(model: Model, dispatch, widgets, setWidgets) =
                     Bulma.navbarStart.div [
                         prop.style [style.display.flex; style.alignItems.stretch; style.justifyContent.flexStart; style.custom("marginRight", "auto")]
                         prop.children [
-                            quickAccessButtonListStart model.History dispatch
+                            quickAccessButtonListStart model model.History dispatch
                             WidgetNavbarList(model, dispatch, addWidget)
                         ]
                     ]

src/Client/Messages.fs

@@ -71,10 +71,10 @@ module BuildingBlock =
     open TermSearch
 
     type Msg =
-    | UpdateHeaderWithIO of BuildingBlock.HeaderCellType * IOType
-    | UpdateHeaderCellType of BuildingBlock.HeaderCellType
+    | UpdateHeaderWithIO of CompositeHeaderDiscriminate * IOType
+    | UpdateHeaderCellType of CompositeHeaderDiscriminate
     | UpdateHeaderArg of U2<OntologyAnnotation,IOType> option
-    | UpdateBodyCellType of BuildingBlock.BodyCellType
+    | UpdateBodyCellType of CompositeCellDiscriminate
     | UpdateBodyArg of U2<string, OntologyAnnotation> option
 
 module Protocol =

src/Client/Modals/EditColumn.fs

@@ -13,7 +13,7 @@ open ARCtrl
 
 type private State =
     {
-        NextHeaderType: BuildingBlock.HeaderCellType option
+        NextHeaderType: CompositeHeaderDiscriminate option
         NextIOType: IOType option
     } with
         static member init() = {
@@ -37,33 +37,34 @@ module private EditColumnComponents =
             prop.onClick submit
         ]
 
-    let SelectHeaderTypeOption(headerType: BuildingBlock.HeaderCellType) =
+    let SelectHeaderTypeOption(headerType: CompositeHeaderDiscriminate) =
         let txt = headerType.ToString()
         Html.option [
             prop.value txt
             prop.text txt
         ]
 
-    let SelectHeaderType(state, setState) =
+    let SelectHeaderType(header, state, setState) =
         Bulma.select [
-            prop.onChange (fun (e: string) -> {state with NextHeaderType = Some (BuildingBlock.HeaderCellType.fromString e)} |> setState )
+            prop.value (header.ToString())
+            prop.onChange (fun (e: string) -> {state with NextHeaderType = Some (CompositeHeaderDiscriminate.fromString e)} |> setState )
             prop.children [
                 // -- term columns --
-                SelectHeaderTypeOption BuildingBlock.HeaderCellType.Characteristic
-                SelectHeaderTypeOption BuildingBlock.HeaderCellType.Component
-                SelectHeaderTypeOption BuildingBlock.HeaderCellType.Factor
-                SelectHeaderTypeOption BuildingBlock.HeaderCellType.Parameter
+                SelectHeaderTypeOption CompositeHeaderDiscriminate.Characteristic
+                SelectHeaderTypeOption CompositeHeaderDiscriminate.Component
+                SelectHeaderTypeOption CompositeHeaderDiscriminate.Factor
+                SelectHeaderTypeOption CompositeHeaderDiscriminate.Parameter
                 // -- io columns --
-                SelectHeaderTypeOption BuildingBlock.HeaderCellType.Input
-                SelectHeaderTypeOption BuildingBlock.HeaderCellType.Output
+                SelectHeaderTypeOption CompositeHeaderDiscriminate.Input
+                SelectHeaderTypeOption CompositeHeaderDiscriminate.Output
                 // -- single columns --
-                SelectHeaderTypeOption BuildingBlock.HeaderCellType.Date
-                SelectHeaderTypeOption BuildingBlock.HeaderCellType.Performer
-                SelectHeaderTypeOption BuildingBlock.HeaderCellType.ProtocolDescription
-                SelectHeaderTypeOption BuildingBlock.HeaderCellType.ProtocolREF
-                SelectHeaderTypeOption BuildingBlock.HeaderCellType.ProtocolType
-                SelectHeaderTypeOption BuildingBlock.HeaderCellType.ProtocolUri
-                SelectHeaderTypeOption BuildingBlock.HeaderCellType.ProtocolVersion
+                SelectHeaderTypeOption CompositeHeaderDiscriminate.Date
+                SelectHeaderTypeOption CompositeHeaderDiscriminate.Performer
+                SelectHeaderTypeOption CompositeHeaderDiscriminate.ProtocolDescription
+                SelectHeaderTypeOption CompositeHeaderDiscriminate.ProtocolREF
+                SelectHeaderTypeOption CompositeHeaderDiscriminate.ProtocolType
+                SelectHeaderTypeOption CompositeHeaderDiscriminate.ProtocolUri
+                SelectHeaderTypeOption CompositeHeaderDiscriminate.ProtocolVersion
             ]
         ]
 
@@ -136,43 +137,44 @@ let Main (columnIndex: int) (model: Model) (dispatch) (rmv: _ -> unit) =
         match state.NextHeaderType, state.NextIOType with
         | None, _ -> column
         // -- term columns --
-        | Some BuildingBlock.HeaderCellType.Characteristic, _  ->
+        | Some CompositeHeaderDiscriminate.Characteristic, _  ->
             CompositeColumn.create(CompositeHeader.Characteristic (header.ToTerm()), cellsToTermCells(column))
-        | Some BuildingBlock.HeaderCellType.Parameter, _ ->
+        | Some CompositeHeaderDiscriminate.Parameter, _ ->
             CompositeColumn.create(CompositeHeader.Parameter (header.ToTerm()), cellsToTermCells(column))
-        | Some BuildingBlock.HeaderCellType.Component, _ ->
+        | Some CompositeHeaderDiscriminate.Component, _ ->
             CompositeColumn.create(CompositeHeader.Component (header.ToTerm()), cellsToTermCells(column))
-        | Some BuildingBlock.HeaderCellType.Factor, _ ->
+        | Some CompositeHeaderDiscriminate.Factor, _ ->
             CompositeColumn.create(CompositeHeader.Factor (header.ToTerm()), cellsToTermCells(column))
         // -- input columns --
-        | Some BuildingBlock.HeaderCellType.Input, Some IOType.Data ->
+        | Some CompositeHeaderDiscriminate.Input, Some IOType.Data ->
             CompositeColumn.create(CompositeHeader.Input IOType.Data, cellsToDataOrFreeText(column))
-        | Some BuildingBlock.HeaderCellType.Input, Some io ->
+        | Some CompositeHeaderDiscriminate.Input, Some io ->
             CompositeColumn.create(CompositeHeader.Input io, cellsToFreeText(column))
-        | Some BuildingBlock.HeaderCellType.Input, None ->
+        | Some CompositeHeaderDiscriminate.Input, None ->
             CompositeColumn.create(CompositeHeader.Input IOType.Sample, cellsToFreeText(column))
         // -- output columns --
-        | Some BuildingBlock.HeaderCellType.Output, Some IOType.Data ->
+        | Some CompositeHeaderDiscriminate.Output, Some IOType.Data ->
             CompositeColumn.create(CompositeHeader.Output IOType.Data, cellsToDataOrFreeText(column))
-        | Some BuildingBlock.HeaderCellType.Output, Some io ->
+        | Some CompositeHeaderDiscriminate.Output, Some io ->
             CompositeColumn.create(CompositeHeader.Output io, cellsToFreeText(column))
-        | Some BuildingBlock.HeaderCellType.Output, None ->
+        | Some CompositeHeaderDiscriminate.Output, None ->
             CompositeColumn.create(CompositeHeader.Output IOType.Sample, cellsToFreeText(column))
         // -- single columns --
-        | Some BuildingBlock.HeaderCellType.ProtocolREF, _ ->
+        | Some CompositeHeaderDiscriminate.ProtocolREF, _ ->
             CompositeColumn.create(CompositeHeader.ProtocolREF, cellsToFreeText(column))
-        | Some BuildingBlock.HeaderCellType.Date, _ ->
+        | Some CompositeHeaderDiscriminate.Date, _ ->
             CompositeColumn.create(CompositeHeader.Date, cellsToFreeText(column))
-        | Some BuildingBlock.HeaderCellType.Performer, _ ->
+        | Some CompositeHeaderDiscriminate.Performer, _ ->
             CompositeColumn.create(CompositeHeader.Performer, cellsToFreeText(column))
-        | Some BuildingBlock.HeaderCellType.ProtocolDescription, _ ->
+        | Some CompositeHeaderDiscriminate.ProtocolDescription, _ ->
             CompositeColumn.create(CompositeHeader.ProtocolDescription, cellsToFreeText(column))
-        | Some BuildingBlock.HeaderCellType.ProtocolType, _ ->
+        | Some CompositeHeaderDiscriminate.ProtocolType, _ ->
             CompositeColumn.create(CompositeHeader.ProtocolType, cellsToTermCells(column))
-        | Some BuildingBlock.HeaderCellType.ProtocolUri, _ ->
+        | Some CompositeHeaderDiscriminate.ProtocolUri, _ ->
             CompositeColumn.create(CompositeHeader.ProtocolUri, cellsToFreeText(column))
-        | Some BuildingBlock.HeaderCellType.ProtocolVersion, _ ->
+        | Some CompositeHeaderDiscriminate.ProtocolVersion, _ ->
             CompositeColumn.create(CompositeHeader.ProtocolVersion, cellsToFreeText(column))
+        | Some CompositeHeaderDiscriminate.Comment, _ -> failwith "Comment header type is not yet implemented"
     let submit (e) =
         let nxtCol = updateColumn column0
         Spreadsheet.SetColumn (columnIndex, nxtCol) |> SpreadsheetMsg |> dispatch
@@ -196,9 +198,9 @@ let Main (columnIndex: int) (model: Model) (dispatch) (rmv: _ -> unit) =
                         Bulma.field.div [
                             Bulma.buttons [
                                 prop.children [
-                                    SelectHeaderType(state, setState)
+                                    SelectHeaderType(column0.Header.AsDiscriminate, state, setState)
                                     match state.NextHeaderType with
-                                    | Some BuildingBlock.HeaderCellType.Output | Some BuildingBlock.HeaderCellType.Input ->
+                                    | Some CompositeHeaderDiscriminate.Output | Some CompositeHeaderDiscriminate.Input ->
                                         SelectIOType(state, setState)
                                     | _ -> Html.none
                                 ]

src/Client/Modals/TermModal.fs

@@ -4,6 +4,7 @@ open Shared.TermTypes
 open Feliz
 open Feliz.Bulma
 open ARCtrl
+open Shared
 
 type private State =
     | Loading
@@ -46,25 +47,36 @@ let Main (oa: OntologyAnnotation, dispatch) (rmv: _ -> unit) =
                         ]
                     ]
                     Bulma.modalCardBody [
-                        prop.className "has-text-justified"
+                        prop.className "content"
                         prop.children [
-                            Bulma.content [
+                            Html.div [
                                 match state with
                                 | Loading -> Html.p "loading .."
                                 | NotFound ->
                                     Html.p [
                                         prop.dangerouslySetInnerHTML $"Unable to find term with id <b>{oa.TermAccessionShort}</b> in database."
                                     ]
                                 | Found term ->
-                                    Html.h6 "Description"
+                                    Html.h5 "Description"
                                     Html.p term.Description
-                                    Html.h6 "Source Ontology"
+                                    Html.h5 "Source Ontology"
                                     Html.p term.FK_Ontology
                                     if term.IsObsolete then
                                         Html.p [
                                             color.hasTextDanger
                                             prop.text "Obsolete"
-                                        ] 
+                                        ]
+                                    Html.a [
+                                        prop.className "space-x-2 float-right"
+                                        prop.href (OntologyAnnotation.fromTerm term |> _.TermAccessionOntobeeUrl)
+                                        prop.target.blank
+                                        prop.children [
+                                            Html.span "Ref"
+                                            Html.i [
+                                                prop.className "fas fa-external-link-alt"
+                                            ]
+                                        ]
+                                    ]
                             ]
                         ]
                     ]