Merge pull request #141 from nfdi4plants/kevinf-patch-0.4.5

Kevinf patch 0.4.5

.assets/assets/manifest.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
 <OfficeApp xmlns="http://schemas.microsoft.com/office/appforoffice/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.microsoft.com/office/officeappbasictypes/1.0" xmlns:ov="http://schemas.microsoft.com/office/taskpaneappversionoverrides" xsi:type="TaskPaneApp">
   <Id>5d6f5462-3401-48ec-9406-d12882e9ad83</Id>
-  <Version>0.4.4</Version>
+  <Version>0.4.5</Version>
   <ProviderName>Computational Systems Biology</ProviderName>
   <DefaultLocale>en-US</DefaultLocale>
   <DisplayName DefaultValue="Swate"/>

RELEASE_NOTES.md

@@ -1,3 +1,11 @@
+### 0.4.5+b360273 (Released 2021-3-12)
+* Additions:
+    * latest commit #b360273
+    * [[#d630a76](https://github.com/nfdi4plants/Swate/commit/d630a76445f1845bb93de9ae89bf1e983f81c51f)] Save darkmode as cookie and improve darkmode (Issue #134).
+* Bugfixes:
+    * [[#b360273](https://github.com/nfdi4plants/Swate/commit/b36027369f60a612e2660ec3b8bfefb09cbe5664)] Fix bug, removing protocol groups if one column is not an ontology.
+    * [[#402a220](https://github.com/nfdi4plants/Swate/commit/402a220824ee69ebd1cb5e6f4ecd2ba4cf1627f7)] Fix pointer .json generator (Issue #139).
+
 ### 0.4.4+4ae3198 (Released 2021-3-11)
 * Additions:
     * latest commit #4ae3198

manifest.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
 <OfficeApp xmlns="http://schemas.microsoft.com/office/appforoffice/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.microsoft.com/office/officeappbasictypes/1.0" xmlns:ov="http://schemas.microsoft.com/office/taskpaneappversionoverrides" xsi:type="TaskPaneApp">
   <Id>5d6f5462-3401-48ec-9406-d12882e9ad83</Id>
-  <Version>0.4.4</Version>
+  <Version>0.4.5</Version>
   <ProviderName>Computational Systems Biology</ProviderName>
   <DefaultLocale>en-US</DefaultLocale>
   <DisplayName DefaultValue="Swate"/>

src/Client/CustomComponents/AnnotationTableMissingWarning.fs

@@ -13,6 +13,11 @@ let annotationTableMissingWarningComponent (model:Model) (dispatch: Msg-> unit)
     Notification.notification [
         Notification.Color IsWarning
         Notification.Props [
+            Style [
+                BackgroundColor (if model.SiteStyleState.IsDarkMode = false then NFDIColors.Yellow.Base else model.SiteStyleState.ColorMode.ControlBackground)
+                Color model.SiteStyleState.ColorMode.Text
+                //yield! colorControlInArray model.SiteStyleState.ColorMode
+            ]
         ]
     ] [
         Notification.delete [ Props [
@@ -21,12 +26,14 @@ let annotationTableMissingWarningComponent (model:Model) (dispatch: Msg-> unit)
             )
         ]] [ ]
         Heading.h5 [] [str "Warning: No Annotation table found in worksheet"]
-        Text.p [] [
+        Field.div [] [
             str "Your worksheet seems to contain no annotation table. You can create one by pressing the button below"
         ]
-        Button.buttonComponent
-            model.SiteStyleState.ColorMode
-            true
-            "create annotation table"
-            (fun _ -> CreateAnnotationTable (model.SiteStyleState.IsDarkMode) |> ExcelInterop |> dispatch )
+        Field.div [][
+            Button.buttonComponent
+                model.SiteStyleState.ColorMode
+                model.SiteStyleState.IsDarkMode
+                "create annotation table"
+                (fun _ -> CreateAnnotationTable model.SiteStyleState.IsDarkMode |> ExcelInterop |> dispatch )
+        ]
     ]

src/Client/CustomComponents/Button.fs

@@ -4,11 +4,15 @@ open Fulma
 open Fable.React
 open Fable.React.Props
 
-let buttonComponent (colorMode: ExcelColors.ColorMode) (isActive:bool) txt onClick =
+let buttonComponent (colorMode: ExcelColors.ColorMode) (isDarkMode:bool) txt onClick =
 
     Button.button [
+        if isDarkMode then
+            Button.Color IsWarning
+            Button.IsOutlined
+        else
+            Button.Props [Style [BackgroundColor colorMode.BodyForeground; Color colorMode.Text]]
         Button.IsFullWidth
-        Button.Props [Style [BackgroundColor colorMode.BodyForeground; Color colorMode.Text]]
         Button.OnClick onClick
         ][
         str txt

src/Client/CustomComponents/Navbar.fs

@@ -89,7 +89,7 @@ let navbarShortCutIconList model dispatch =
 
 let dropdownShortCutIconList model dispatch =
     Table.table [
-        Table.Props [Style [ BackgroundColor model.SiteStyleState.ColorMode.ElementBackground; Color "white"; Cursor "default" ]]
+        Table.Props [Style [BackgroundColor model.SiteStyleState.ColorMode.ElementBackground; Color "white"; Cursor "default" ]]
     ][
         tbody [][
             for icon in shortCutIconList model do
@@ -99,7 +99,11 @@ let dropdownShortCutIconList model dispatch =
                         td [][
                             let padding = "0.5rem"
                             Button.a [
-                                Button.Props [ Style [BackgroundColor model.SiteStyleState.ColorMode.ElementBackground; PaddingLeft padding; PaddingRight padding]]
+                                Button.Props [ Style [
+                                    if model.SiteStyleState.IsDarkMode |> not then
+                                        BackgroundColor model.SiteStyleState.ColorMode.ElementBackground
+                                    PaddingLeft padding; PaddingRight padding
+                                ]]
                                 Button.OnClick (fun _ ->
                                     icon.Msg |> dispatch
                                 )
@@ -121,9 +125,18 @@ let quickAccessDropdownElement model dispatch =
     ] [
         div [Style [
             Position PositionOptions.Relative
+            BackgroundColor model.SiteStyleState.ColorMode.ElementBackground
+            if model.SiteStyleState.IsDarkMode then
+                BorderColor model.SiteStyleState.ColorMode.ControlForeground
+            else
+                BorderColor model.SiteStyleState.ColorMode.Fade
         ]] [
             Button.a [
-                Button.Props [Style [BackgroundColor model.SiteStyleState.ColorMode.ElementBackground; PaddingLeft "0"; PaddingRight "0"]]
+                Button.Props [Style [
+                    if model.SiteStyleState.IsDarkMode |> not then
+                        BackgroundColor model.SiteStyleState.ColorMode.ElementBackground
+                    PaddingLeft "0"; PaddingRight "0"]
+                ]
                 Button.Color Color.IsWhite
                 Button.IsInverted
             ][

src/Client/CustomComponents/WarningModal.fs

@@ -15,12 +15,12 @@ let warningModal (model:Model) dispatch =
     let msg = fun e -> model.WarningModal.Value.NextMsg |> dispatch
     let closeMsg = fun e -> UpdateWarningModal None |> dispatch
     let message = model.WarningModal.Value.ModalMessage
-    Modal.modal [ Modal.IsActive true ] [
+    Modal.modal [ Modal.IsActive true] [
         Modal.background [
             Props [ OnClick closeMsg ]
         ] [ ]
         Notification.notification [
-            Notification.Props [Style [MaxWidth "80%"; MaxHeight "80%"; OverflowX OverflowOptions.Auto ]]
+            Notification.Props [Style [MaxWidth "80%"; MaxHeight "80%"; OverflowX OverflowOptions.Auto; yield! colorControlInArray model.SiteStyleState.ColorMode ]]
         ] [
             Notification.delete [
                 Props [OnClick closeMsg]

src/Client/Messages.fs

@@ -303,23 +303,39 @@ and Msg =
 
 open Routing
 
-let initializeModel (pageOpt: Route option) = {
-    DebouncerState              = Debouncer                 .create ()
-    PageState                   = PageState                 .init pageOpt
-    PersistentStorageState      = PersistentStorageState    .init ()
-    DevState                    = DevState                  .init ()
-    SiteStyleState              = SiteStyleState            .init ()
-    TermSearchState             = TermSearchState           .init ()
-    AdvancedSearchState         = AdvancedSearchState       .init ()
-    ExcelState                  = ExcelState                .init ()
-    ApiState                    = ApiState                  .init ()
-    FilePickerState             = FilePickerState           .init ()
-    AddBuildingBlockState       = AddBuildingBlockState     .init ()
-    ValidationState             = ValidationState           .init ()
-    ProtocolInsertState         = ProtocolInsertState       .init ()
-    BuildingBlockDetailsState   = BuildingBlockDetailsState .init ()
-    SettingsXmlState            = SettingsXmlState          .init ()
-    SettingsDataStewardState    = SettingsDataStewardState  .init ()
-    SettingsProtocolState       = SettingsProtocolState     .init ()
-    WarningModal                = None
-}
+let initializeModel (pageOpt: Route option) =
+    let isDarkMode =
+        let cookies = Browser.Dom.document.cookie
+        let cookiesSplit = cookies.Split([|";"|], System.StringSplitOptions.RemoveEmptyEntries)
+        cookiesSplit
+        |> Array.tryFind (fun x -> x.StartsWith (Cookies.IsDarkMode.toCookieString + "="))
+        |> fun cookieOpt ->
+            if cookieOpt.IsSome then
+                cookieOpt.Value.Replace(Cookies.IsDarkMode.toCookieString + "=","")
+                |> fun cookie ->
+                    match cookie with
+                    | "false"| "False"  -> false
+                    | "true" | "True"   -> true
+                    | anyElse -> false
+            else
+                false
+    {
+        DebouncerState              = Debouncer                 .create ()
+        PageState                   = PageState                 .init pageOpt
+        PersistentStorageState      = PersistentStorageState    .init ()
+        DevState                    = DevState                  .init ()
+        SiteStyleState              = SiteStyleState            .init (darkMode=isDarkMode)
+        TermSearchState             = TermSearchState           .init ()
+        AdvancedSearchState         = AdvancedSearchState       .init ()
+        ExcelState                  = ExcelState                .init ()
+        ApiState                    = ApiState                  .init ()
+        FilePickerState             = FilePickerState           .init ()
+        AddBuildingBlockState       = AddBuildingBlockState     .init ()
+        ValidationState             = ValidationState           .init ()
+        ProtocolInsertState         = ProtocolInsertState       .init ()
+        BuildingBlockDetailsState   = BuildingBlockDetailsState .init ()
+        SettingsXmlState            = SettingsXmlState          .init ()
+        SettingsDataStewardState    = SettingsDataStewardState  .init ()
+        SettingsProtocolState       = SettingsProtocolState     .init ()
+        WarningModal                = None
+    }

src/Client/Model.fs

@@ -7,6 +7,18 @@ open Shared
 open Thoth.Elmish
 open Routing
 
+type Cookies =
+| IsDarkMode
+
+    member this.toCookieString =
+        match this with
+        | IsDarkMode    -> "isDarkmode"
+
+    static member ofString str =
+        match str with
+        | "isDarkmode"  -> IsDarkMode
+        | anyElse       -> failwith (sprintf "Cookie-Parser encountered unknown cookie name: %s" anyElse)
+
 type LogItem =
     | Debug of (System.DateTime*string)
     | Info  of (System.DateTime*string)
@@ -115,11 +127,11 @@ type SiteStyleState = {
     IsDarkMode      : bool
     ColorMode       : ExcelColors.ColorMode
 } with
-    static member init () = {
+    static member init (?darkMode) = {
         QuickAcessIconsShown    = false
         BurgerVisible           = false
-        IsDarkMode              = false
-        ColorMode               = ExcelColors.colorfullMode
+        IsDarkMode              = if darkMode.IsSome then darkMode.Value else false
+        ColorMode               = if darkMode.IsSome && darkMode.Value = true then ExcelColors.darkMode else ExcelColors.colorfullMode
     }
 
 type DevState = {

src/Client/OfficeInterop/HelperFunctions.fs

@@ -86,10 +86,12 @@ let tryFindSpannedBuildingBlocks (currentProtocolGroup:Xml.GroupTypes.Protocol)
             buildingBlocks
             |> Array.tryFind (fun foundBuildingBlock ->
                 let isSameAccession =
-                    if spannedBlock.TermAccession <> "" && foundBuildingBlock.MainColumn.Header.Value.Ontology.IsSome then
-                        foundBuildingBlock.MainColumn.Header.Value.Ontology.Value.TermAccession = spannedBlock.TermAccession
+                    if spannedBlock.TermAccession <> "" || foundBuildingBlock.MainColumn.Header.Value.Ontology.IsSome then
+                        // As in the above only one option is that ontology is some we need a default in the next step.
+                        // We default to an empty termaccession, as 'spannedBlock' MUST be <> "" to trigger the default
+                        (Option.defaultValue (OntologyInfo.create "" "") foundBuildingBlock.MainColumn.Header.Value.Ontology).TermAccession = spannedBlock.TermAccession
                     else
-                        false
+                        true
                 foundBuildingBlock.MainColumn.Header.Value.Header = spannedBlock.ColumnName
                 && isSameAccession
             )
@@ -791,7 +793,7 @@ let updateRemoveSwateProtocolGroup (protocolGroup:Xml.GroupTypes.ProtocolGroup)
                     if remove then
                         filteredChildren
                     else
-                        newProtocolGroupXml::filteredChildren
+                        if filteredChildren.IsEmpty then [newProtocolGroupXml] else newProtocolGroupXml::filteredChildren
             }
         else
             let initNewSwateTableXml =
@@ -815,15 +817,15 @@ let updateRemoveSwateProtocolGroup (protocolGroup:Xml.GroupTypes.ProtocolGroup)
         Children = nextTableXml::filterPrevTableFromRootChildren
     }
 
-let removeSwateProtocolGroup (protocolGroup:Xml.GroupTypes.ProtocolGroup) (previousCompleteCustomXml:XmlElement) =
-    updateRemoveSwateProtocolGroup protocolGroup previousCompleteCustomXml true
+//let removeSwateProtocolGroup (protocolGroup:Xml.GroupTypes.ProtocolGroup) (previousCompleteCustomXml:XmlElement) =
+//    updateRemoveSwateProtocolGroup protocolGroup previousCompleteCustomXml true
 
-let updateSwateProtocolGroup (protocolGroup:Xml.GroupTypes.ProtocolGroup) (previousCompleteCustomXml:XmlElement) =
-    updateRemoveSwateProtocolGroup protocolGroup previousCompleteCustomXml false
+//let updateSwateProtocolGroup (protocolGroup:Xml.GroupTypes.ProtocolGroup) (previousCompleteCustomXml:XmlElement) =
+//    updateRemoveSwateProtocolGroup protocolGroup previousCompleteCustomXml false
 
 let replaceProtGroupByProtGroup protGroup1 protGroup2 (previousCompleteCustomXml:XmlElement) =
-    let removeProtGroup1 = removeSwateProtocolGroup protGroup1 previousCompleteCustomXml
-    let addProtGroup2 = updateSwateProtocolGroup protGroup2 removeProtGroup1
+    let removeProtGroup1 = updateRemoveSwateProtocolGroup protGroup1 previousCompleteCustomXml true
+    let addProtGroup2 = updateRemoveSwateProtocolGroup protGroup2 removeProtGroup1 false
     addProtGroup2
 
 /// Use the 'remove' parameter to remove any Swate protocol xml for the worksheet annotation table name combination in 'protocolGroup'
@@ -846,16 +848,16 @@ let updateRemoveSwateProtocol (protocol:Xml.GroupTypes.Protocol) (previousComple
                 if remove then
                     filteredProtocolChildren
                 else
-                    protocol::filteredProtocolChildren
+                    if filteredProtocolChildren.IsEmpty then [protocol] else protocol::filteredProtocolChildren
         }
 
-    updateSwateProtocolGroup nextProtocolGroup previousCompleteCustomXml
+    updateRemoveSwateProtocolGroup nextProtocolGroup previousCompleteCustomXml false
 
-let removeSwateProtocol (protocol:Xml.GroupTypes.Protocol) (previousCompleteCustomXml:XmlElement) =
-    updateRemoveSwateProtocol protocol previousCompleteCustomXml true
+//let removeSwateProtocol (protocol:Xml.GroupTypes.Protocol) (previousCompleteCustomXml:XmlElement) =
+//    updateRemoveSwateProtocol protocol previousCompleteCustomXml true
 
-let updateSwateProtocol (protocol:Xml.GroupTypes.Protocol) (previousCompleteCustomXml:XmlElement) =
-    updateRemoveSwateProtocol protocol previousCompleteCustomXml false
+//let updateSwateProtocol (protocol:Xml.GroupTypes.Protocol) (previousCompleteCustomXml:XmlElement) =
+//    updateRemoveSwateProtocol protocol previousCompleteCustomXml false
 
 let updateProtocolFromXml (protocol:Xml.GroupTypes.Protocol) (remove:bool) =
     Excel.run(fun context ->
@@ -876,10 +878,7 @@ let updateProtocolFromXml (protocol:Xml.GroupTypes.Protocol) (remove:bool) =
             let securityUpdateForProtocol = {protocol with AnnotationTable = AnnotationTable.create annotationTable activeSheet.name}
 
             let nextCustomXml =
-                if remove then
-                    removeSwateProtocol securityUpdateForProtocol xmlParsed
-                else
-                    updateSwateProtocol securityUpdateForProtocol xmlParsed
+                updateRemoveSwateProtocol securityUpdateForProtocol xmlParsed remove
 
             let nextCustomXmlString = nextCustomXml |> xmlElementToXmlString
 

src/Client/OfficeInterop/OfficeInterop.fs

@@ -1317,7 +1317,7 @@ let updateProtocolGroupHeader () =
 
                 let getGroupHeaderIndicesForProtocol (buildingBlocks:BuildingBlock []) (protocol:Xml.GroupTypes.Protocol) =
                     let buildingBlockOpts = tryFindSpannedBuildingBlocks protocol buildingBlocks
-                    // caluclate list of indices fro group blocks
+                    // caluclate list of indices for group blocks
                     if buildingBlockOpts.IsSome then
                         let getStartAndEnd (mainColIndices:int list) =
                             let startInd = List.min mainColIndices
@@ -1855,9 +1855,9 @@ let removeXmlType(xmlType:XmlTypes) =
                 | ValidationType tableValidation ->
                     removeSwateValidation tableValidation xmlParsed
                 | GroupType protGroup ->
-                    removeSwateProtocolGroup protGroup xmlParsed
+                    updateRemoveSwateProtocolGroup protGroup xmlParsed true
                 | ProtocolType protocol ->
-                    removeSwateProtocol protocol xmlParsed
+                    updateRemoveSwateProtocol protocol xmlParsed true
 
             let nextCustomXmlString = nextCustomXml |> OfficeInterop.HelperFunctions.xmlElementToXmlString
 
@@ -1941,7 +1941,7 @@ let createPointerJson() =
             [
                 "name"          , Fable.SimpleJson.JString  ""
                 "version"       , Fable.SimpleJson.JString  ""     
-                "author"        , Fable.SimpleJson.JString  ""
+                "author"        , Fable.SimpleJson.JArray   []
                 "description"   , Fable.SimpleJson.JString  ""
                 "docslink"      , Fable.SimpleJson.JString  ""
                 "tags"          , Fable.SimpleJson.JArray   []