Merge pull request #178 from nfdi4plants/Kevinf-patch-0.5.1

Kevinf patch 0.5.1

.assets/assets/manifest.xml

@@ -1,14 +1,14 @@
-<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<?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>0.5.0</Version>
+  <Version>0.5.1</Version>
   <ProviderName>Computational Systems Biology</ProviderName>
   <DefaultLocale>en-US</DefaultLocale>
   <DisplayName DefaultValue="Swate"/>
   <Description DefaultValue="Utility functions to annotate data in a fast and safe way."/>
   <IconUrl DefaultValue="https://swate.nfdi4plants.de/assets/swate_32x32.png"/>
   <HighResolutionIconUrl DefaultValue="https://swate.nfdi4plants.de/assets/swate_80x80.png"/>
-  <SupportUrl DefaultValue="https://csb.bio.uni-kl.de/"/>
+  <SupportUrl DefaultValue="https://github.com/nfdi4plants/Swate/issues"/>
   <AppDomains>
     <AppDomain>bio.uni-kl.de</AppDomain>
   </AppDomains>

.config/dotnet-tools.json

@@ -1,36 +1,30 @@
 {
-  "version": 1,
-  "isRoot": true,
-  "tools": {
-    "paket": {
-      "version": "6.0.0-rc002",
-      "commands": [
-        "paket"
-      ]
-    },
-    "fake-cli": {
-      "version": "5.20.3",
-      "commands": [
-        "fake"
-      ]
-    },
-    "fable": {
-      "version": "3.2.1",
-      "commands": [
-        "fable"
-      ]
-    },
-    "fantomas-tool": {
-      "version": "4.4.0",
-      "commands": [
-        "fantomas"
-      ]
-    },
-    "femto": {
-      "version": "0.8.6",
-      "commands": [
-        "femto"
-      ]
+    "version": 1,
+    "isRoot": true,
+    "tools": {
+        "paket": {
+            "version": "6.0.7",
+            "commands": [
+                "paket"
+            ]
+        },
+        "fable": {
+            "version": "3.2.11",
+            "commands": [
+                "fable"
+            ]
+        },
+        "fantomas-tool": {
+            "version": "4.5.2",
+            "commands": [
+                "fantomas"
+            ]
+        },
+        "femto": {
+            "version": "0.9.0",
+            "commands": [
+                "femto"
+            ]
+        }
     }
-  }
 }

.db/docker-compose.yml

@@ -7,16 +7,14 @@ services:
     # newer version fail with .net
     image: mariadb:10.4
     # command: --default-authentication-plugin=mysql_native_password
-    restart: always
     volumes:
       - ./mysql-dump:/docker-entrypoint-initdb.d
     environment:
-      MYSQL_ROOT_PASSWORD: {PASSWORD}
+      MYSQL_ROOT_PASSWORD: example
     ports:
         - 42333:3306
 
   adminer:
     image: adminer
-    restart: always
     ports:
         - 8085:8080

.dockerignore

@@ -0,0 +1,19 @@
+.fable/
+*.fs.js
+.fake/
+.farmer/
+.idea/
+.ionide/
+.vs/
+deploy/
+obj/
+bin/
+packages/
+paket-files/
+node_modules/
+release.cmd
+release.sh
+*.orig
+*.DotSettings.user
+.assets/swate.zip
+.git

.gitignore

@@ -1,5 +1,6 @@
 .fable/
 *.fs.js
+*.fs.js.map
 .fake/
 .farmer/
 .idea/

.paket/Paket.Restore.targets

@@ -159,7 +159,7 @@
 		This value should match the version in the props generated by paket
 		If they differ, this means we need to do a restore in order to ensure correct dependencies
 	-->
-    <PropertyGroup Condition="'$(PaketPropsVersion)' != '5.185.3' ">
+    <PropertyGroup Condition="'$(PaketPropsVersion)' != '6.0.0' ">
       <PaketRestoreRequired>true</PaketRestoreRequired>
     </PropertyGroup>
 
@@ -236,13 +236,16 @@
         <PackageName>$([System.String]::Copy('%(PaketReferencesFileLines.Identity)').Split(',')[0])</PackageName>
         <PackageVersion>$([System.String]::Copy('%(PaketReferencesFileLines.Identity)').Split(',')[1])</PackageVersion>
         <AllPrivateAssets>$([System.String]::Copy('%(PaketReferencesFileLines.Identity)').Split(',')[4])</AllPrivateAssets>
-        <CopyLocal Condition="'%(PaketReferencesFileLinesInfo.Splits)' == '6'">$([System.String]::Copy('%(PaketReferencesFileLines.Identity)').Split(',')[5])</CopyLocal>
+        <CopyLocal Condition="%(PaketReferencesFileLinesInfo.Splits) &gt;= 6">$([System.String]::Copy('%(PaketReferencesFileLines.Identity)').Split(',')[5])</CopyLocal>
+        <OmitContent Condition="%(PaketReferencesFileLinesInfo.Splits) &gt;= 7">$([System.String]::Copy('%(PaketReferencesFileLines.Identity)').Split(',')[6])</OmitContent>
+        <ImportTargets Condition="%(PaketReferencesFileLinesInfo.Splits) &gt;= 8">$([System.String]::Copy('%(PaketReferencesFileLines.Identity)').Split(',')[7])</ImportTargets>
       </PaketReferencesFileLinesInfo>
       <PackageReference Include="%(PaketReferencesFileLinesInfo.PackageName)">
         <Version>%(PaketReferencesFileLinesInfo.PackageVersion)</Version>
         <PrivateAssets Condition=" ('%(PaketReferencesFileLinesInfo.AllPrivateAssets)' == 'true') Or ('$(PackAsTool)' == 'true') ">All</PrivateAssets>
-        <ExcludeAssets Condition=" '%(PaketReferencesFileLinesInfo.Splits)' == '6' And %(PaketReferencesFileLinesInfo.CopyLocal) == 'false'">runtime</ExcludeAssets>
-        <ExcludeAssets Condition=" '%(PaketReferencesFileLinesInfo.Splits)' != '6' And %(PaketReferencesFileLinesInfo.AllPrivateAssets) == 'exclude'">runtime</ExcludeAssets>
+        <ExcludeAssets Condition=" %(PaketReferencesFileLinesInfo.CopyLocal) == 'false' or %(PaketReferencesFileLinesInfo.AllPrivateAssets) == 'exclude'">runtime</ExcludeAssets>
+        <ExcludeAssets Condition=" %(PaketReferencesFileLinesInfo.OmitContent) == 'true'">$(ExcludeAssets);contentFiles</ExcludeAssets>
+        <ExcludeAssets Condition=" %(PaketReferencesFileLinesInfo.ImportTargets) == 'false'">$(ExcludeAssets);build;buildMultitargeting;buildTransitive</ExcludeAssets>
         <Publish Condition=" '$(PackAsTool)' == 'true' ">true</Publish>
         <AllowExplicitVersion>true</AllowExplicitVersion>
       </PackageReference>
@@ -362,7 +365,9 @@
               PackageLicenseFile="$(PackageLicenseFile)"
               PackageLicenseExpression="$(PackageLicenseExpression)"
               PackageLicenseExpressionVersion="$(PackageLicenseExpressionVersion)"
-              PackageReadmeFile="$(PackageReadmeFile)" />
+              Readme="$(PackageReadmeFile)"
+              NoDefaultExcludes="$(NoDefaultExcludes)"/>
+
     <PackTask Condition="$(UseMSBuild16_0_Pack)"
               PackItem="$(PackProjectInputFile)"
               PackageFiles="@(_PackageFiles)"
@@ -410,7 +415,8 @@
               NuspecProperties="$(NuspecProperties)"
               PackageLicenseFile="$(PackageLicenseFile)"
               PackageLicenseExpression="$(PackageLicenseExpression)"
-              PackageLicenseExpressionVersion="$(PackageLicenseExpressionVersion)" />
+              PackageLicenseExpressionVersion="$(PackageLicenseExpressionVersion)"
+              NoDefaultExcludes="$(NoDefaultExcludes)" />
 
     <PackTask Condition="$(UseMSBuild15_9_Pack)"
               PackItem="$(PackProjectInputFile)"

AssemblyVersion.fs

@@ -3,11 +3,11 @@ namespace System
 open System.Reflection
 
 [<assembly: AssemblyTitleAttribute("Swate")>]
-[<assembly: AssemblyVersionAttribute("0.5.0")>]
-[<assembly: AssemblyMetadataAttribute("ReleaseDate","22-Oct-21")>]
+[<assembly: AssemblyVersionAttribute("0.5.1")>]
+[<assembly: AssemblyMetadataAttribute("ReleaseDate","02-Nov-21")>]
 do ()
 
 module internal AssemblyVersionInformation =
     let [<Literal>] AssemblyTitle = "Swate"
-    let [<Literal>] AssemblyVersion = "0.5.0"
-    let [<Literal>] AssemblyMetadata_ReleaseDate = "22-Oct-21"
+    let [<Literal>] AssemblyVersion = "0.5.1"
+    let [<Literal>] AssemblyMetadata_ReleaseDate = "02-Nov-21"

Build.fs

@@ -16,6 +16,8 @@ let clientTestsPath = Path.getFullName "tests/Client"
 
 let dockerComposePath = Path.getFullName ".db\docker-compose.yml"
 
+let developmentUrl = "https://localhost:3000"
+
 module ProjectInfo =
 
     let gitOwner = "nfdi4plants"
@@ -191,29 +193,30 @@ Target.create "InstallClient" (fun _ ->
     run npm "install" "."
 )
 
-Target.create "Bundle" (fun _ ->
+Target.create "bundle" (fun _ ->
     [ "server", dotnet $"publish -c Release -o \"{deployPath}\"" serverPath
-      "client", dotnet "fable --run webpack -p" clientPath ]
+      "client", dotnet "fable src/Client -s --run webpack --config webpack.config.js" "" ]
     |> runParallel
 )
 
-Target.create "Bundle-Linux" (fun _ ->
+Target.create "bundle-linux" (fun _ ->
     [ "server", dotnet $"publish -c Release -r linux-x64 -o \"{deployPath}\"" serverPath
-      "client", dotnet "fable --run webpack -p" clientPath ]
+      "client", dotnet "fable src/Client -s --run webpack --config webpack.config.js" "" ]
     |> runParallel
 )
 
 Target.create "Run" (fun _ ->
     run dotnet "build" sharedPath
     [ "server", dotnet "watch run" serverPath
-      "client", dotnet "fable watch --run webpack-dev-server" clientPath ]
+      "client", dotnet "fable watch src/Client -s --run webpack-dev-server" "" ]
     |> runParallel
 )
 
 Target.create "officedebug" (fun _ ->
     run dotnet "build" sharedPath
+    openBrowser developmentUrl
     [ "server", dotnet "watch run" serverPath
-      "client", dotnet "fable watch --run webpack-dev-server" clientPath
+      "client", dotnet "fable watch src/Client -s --run webpack-dev-server" ""
       /// start up mysql db from docker-compose
       "database", dockerCompose $"-f {dockerComposePath} up" __SOURCE_DIRECTORY__
       /// sideload webapp in excel

Dockerfile

@@ -0,0 +1,18 @@
+FROM mcr.microsoft.com/dotnet/sdk:5.0 as build
+
+# Install node
+RUN curl -sL https://deb.nodesource.com/setup_14.x | bash
+RUN apt-get update && apt-get install -y nodejs
+
+WORKDIR /workspace
+COPY . .
+RUN dotnet tool restore
+
+RUN dotnet run Bundle
+
+
+FROM mcr.microsoft.com/dotnet/aspnet:5.0-alpine
+COPY --from=build /workspace/deploy /app
+WORKDIR /app
+EXPOSE 5000
+ENTRYPOINT [ "dotnet", "Server.dll" ]

Helpers.fs

@@ -1,6 +1,7 @@
 module Helpers
 
 open Fake.Core
+open System.Runtime.InteropServices
 
 let initializeContext () =
     let execContext = Context.FakeExecutionContext.Create false "build.fsx" [ ]
@@ -102,6 +103,17 @@ let node =
 
 let dockerCompose = createProcess "docker-compose"
 
+///Choose process to open plots with depending on OS. Thanks to @zyzhu for hinting at a solution (https://github.com/plotly/Plotly.NET/issues/31)
+let openBrowser url =
+    if RuntimeInformation.IsOSPlatform(OSPlatform.Windows) then
+        CreateProcess.fromRawCommand "cmd.exe" [ "/C"; $"start {url}" ] |> Proc.run |> ignore
+    elif RuntimeInformation.IsOSPlatform(OSPlatform.Linux) then
+        CreateProcess.fromRawCommand "xdg-open" [ url ] |> Proc.run |> ignore
+    elif RuntimeInformation.IsOSPlatform(OSPlatform.OSX) then
+        CreateProcess.fromRawCommand "open" [ url ] |> Proc.run |> ignore
+    else
+        failwith "Cannot open Browser. OS not supported."
+
 let run proc arg dir =
     proc arg dir
     |> Proc.run

README.md

@@ -13,14 +13,14 @@ Swate aims to provide a low-friction workflow annotation experience that makes t
 
 - [Swate](#swate)
   - [Features](#features)
+    - [Swate Features sorted by Excel Versions](#swate-features-sorted-by-excel-versions)
   - [Install/Use](#installuse)
     - [Excel desktop](#excel-desktop)
-      - [Using the Swate Installer](#using-the-swate-installer)
+      - [Using the Swate installer](#using-the-swate-installer)
       - [Using a shared folder](#using-a-shared-folder)
     - [Excel online](#excel-online)
   - [Discuss/Get help](#discussget-help)
     - [Documentation](#documentation)
-      - [API docs](#api-docs)
       - [Feature documentation](#feature-documentation)
       - [Guides](#guides)
     - [Report problems and request features](#report-problems-and-request-features)
@@ -47,13 +47,28 @@ The base features of Swate are:
 There are many more small and incremental features. Check the [latest release notes](https://github.com/nfdi4plants/Swate/releases) for the newest additions.
 
 
+### Swate Features sorted by Excel Versions
+
+Feature | Excel 365/ Office online  	| Excel 2019  	|
+|---            |:---:	        |:---:	        |
+|  **Core**     |  	            |
+| Adding and managing <br> building blocks|<span style="color:#1FC2A7">✓</span>|<span style="color:#1FC2A7">✓</span>|
+| Ontology Term search <br> and insert|<span style="color:#1FC2A7">✓</span>| <span style="color:#1FC2A7">✓</span>
+| Ontology Term update | <span style="color:#1FC2A7">✓</span> |<span style="color:#1FC2A7">✓</span>|
+| Add Templates|<span style="color:#1FC2A7">✓</span>|<span style="color:#1FC2A7">✓</span>
+| Copy filenames into table| <span style="color:#1FC2A7">✓</span>| <span style="color:#1FC2A7">✓</span>
+| Display DAG| <span style="color:#1FC2A7">✓</span>| <span style="color:#c21f3a">x</span>
+|  **Experts**     |  	            |
+| Export Swate information | <span style="color:#1FC2A7">✓</span>| <span style="color:#c21f3a">x</span>
+| Create Template Metadata | <span style="color:#1FC2A7">✓</span>| <span style="color:#c21f3a">x</span>
+| Write Checklist Custom Xml | <span style="color:#1FC2A7">✓</span>| <span style="color:#1FC2A7">✓</span>
+| Edit Custom Xml | <span style="color:#1FC2A7">✓</span>| <span style="color:#1FC2A7">✓</span>
+
 ## Install/Use
 
 You can test swate by following the steps below. If you decide to do so, please take the time to set up a Github account to report your issues and suggestions [here](https://github.com/nfdi4plants/Swate/issues).
 You can also search existing issues for solutions for your questions and/or discussions about your suggestions.
 
-___N O T E___ : Swate runs **only** on MS Excel 365, and MS Excel Online. We test on and develop for explicitly these versions. (It is possible though that some older versions like MS Excel 2019 work.)
-
 ### Excel desktop
 
 
@@ -88,10 +103,6 @@ If you have administrative access in your organization, you can create a network
 
 ### Documentation
 
-#### API docs 
-
-The RPC API docs of Swate are available [here](https://swate.denbi.uni-tuebingen.de/api/IAnnotatorAPIv1/docs)
-
 #### Feature documentation
 
 Documentation of the features is now a top priority as we completed the POC stage :rocket:. You can discuss needed docs and the available ones [here](https://github.com/nfdi4plants/Swate/issues/47)
@@ -170,31 +181,23 @@ By installing this repo via the install.cmd file the MySql password will default
 
 ### Set up Sql Dump
 
-The database became too large for GitHub to upload the dump directly. Therefore we now provide the basic Database structure as .sql dump file in this repo, including the data for ontologiesand all template related tables. Only Terms and TermRelationships are missing. These tables can be populated via the private repository SwateDB (v2 branch). If you can't access this repository, please post an issue and you will get a complete dump.
-
-The following instructions can help to import that dump into the database:
-
-After following the instructions above:
-1. Open powershell in the folder with the sql dump. 
-2. Use `cmd /c "docker exec -i db_db_1 mysql -uroot -pexample SwateDB<SwateDB.sql"`
-3. Observe in Adminer how the tables are created and slowly filled.
+The database became too large for GitHub to upload the dump directly. Therefore we now provide the basic Database structure as .sql dump file in this repo, including the data for ontologies and all template related tables. If you wish to participate in development open an issue and we can figure out how to share a ready-to-use database dump.
 
 ### Project Decription
 
 This project uses the [SAFE Stack](https://github.com/SAFE-Stack) to create a website that uses [office.js](https://github.com/OfficeDev/office-js) to interop with Excel.
 
-The file [OfficeJS.fs](src/Client/OfficeJS.fs) contains Fable bindings autogenerated from the office.js typescript definitions.
+The utilized Fable bindings for office-js can be found in [office-fable](https://github.com/Freymaurer/office-fable).
 
-to debug the AddIn locally, use the build target `OfficeDebug`:
+To debug the AddIn locally, use the build target `officedebug`:
 
-`fake build -t OfficeDebug`
+`dotnet run officedebug`
 
 this will launch an Excel instance with the AddIn sideloaded, while also running docker with a MySql- and a Adminer instance.
 The MySql user/password will be root/example and can be set in .db/docker-compose.yml.
 Adminer can be accessed at localhost:8085, MySql at localhost:42333, and the app runs at localhost:3000 for client and localhost:8080 for the server.
 
-However it is currently pretty hard to attach a debugger to the instance of edge that runs in
-the Excel window (update: you can now use [EdgeDevToolsPreview](https://www.microsoft.com/en-us/p/microsoft-edge-devtools-preview/9mzbfrmz0mnj?activetab=pivot:overviewtab) for that aswell). You can circumvent this issue by additionally testing in Excel online:
+To debug add-in instances you can now easily open debug console/inspect for newer Excel versions. For Excel 2019 and earlier you can use the create a `.cmd` file with `C:\Windows\SysWOW64\F12\IEChooser.exe` to easily open the f12 tools (on windows). Alternatively use office online:
 
  - open Excel online in your favorite browser
  - create a blank new workbook (or use any workbook, but be warned that you can't undo stuff done via Office.js) 

RELEASE_NOTES.md

@@ -1,3 +1,14 @@
+### 0.5.1+0c90a83 (Released 2021-12-8)
+* Additions:
+    * latest commit #0c90a83
+    * Add support for Excel 2019 :tada:
+    * [[#48d8d61](https://github.com/nfdi4plants/Swate/commit/48d8d61409d1404b9bd254241e54742ced36b357)] Replace drag and drop for filepicker with simplified table sorting element
+    * [[#e16c861](https://github.com/nfdi4plants/Swate/commit/e16c8613acde31738ecf0af09bee503feea7246a)] Add whitespace between authors.
+    * [[#7b0884f](https://github.com/nfdi4plants/Swate/commit/7b0884f9d2c76bae5d59148acecd7b4165739587)] add pure json return for common api
+* Bugfixes:
+    * [[#2a09a55](https://github.com/nfdi4plants/Swate/commit/2a09a55120261db8527b1c80e63a50cb0ecfe4e3)] Split template tags by "," instead of ";"
+    * [[#c82dd4f](https://github.com/nfdi4plants/Swate/commit/c82dd4f3ef72a21af8f0896ea0cb103811f2c198)] Fix server port error for production.
+
 ### 0.5.0+70632951 (Released 2021-10-22)
 * Additions:
     * latest commit #70632951