Merge pull request #105 from nfdi4plants/kevinf-patch-0.2.1

Up developer version to 0.3.0

tests/manifest.xml → .assets/assets/manifest.xml

@@ -1,13 +1,13 @@
-<?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>1.0.0.0</Version>
+  <Version>0.3.0</Version>
   <ProviderName>Computational Systems Biology</ProviderName>
   <DefaultLocale>en-US</DefaultLocale>
-  <DisplayName DefaultValue="CSBAnnotator"/>
-  <Description DefaultValue="Utility functions to annotate data in a fast and safe way"/>
-  <IconUrl DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/icon-32.png"/>
-  <HighResolutionIconUrl DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/icon-80.png"/>
+  <DisplayName DefaultValue="Swate"/>
+  <Description DefaultValue="Utility functions to annotate data in a fast and safe way."/>
+  <IconUrl DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/swate_32x32.png"/>
+  <HighResolutionIconUrl DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/swate_80x80.png"/>
   <SupportUrl DefaultValue="https://csb.bio.uni-kl.de/"/>
   <AppDomains>
     <AppDomain>bio.uni-kl.de</AppDomain>
@@ -30,8 +30,8 @@
           </GetStarted>
           <ExtensionPoint xsi:type="PrimaryCommandSurface">
             <OfficeTab id="TabData">
-              <Group id="CSBAnnotatorCommands">
-                <Label resid="CSBAnnotatorCommands.Label"/>
+              <Group id="SwateCommands">
+                <Label resid="SwateCommands.Label"/>
                 <Icon>
                   <bt:Image size="16" resid="Icon.16x16"/>
                   <bt:Image size="20" resid="Icon.20x20"/>
@@ -43,7 +43,7 @@
                   <bt:Image size="80" resid="Icon.80x80"/>
                   <bt:Image size="96" resid="Icon.96x96"/>
                 </Icon>
-                <Control xsi:type="Button" id="TermSearch">
+                <!--<Control xsi:type="Button" id="TermSearch">
                   <Label resid="TermSearch.Label"/>
                   <Supertip>
                     <Title resid="TermSearch.Label"/>
@@ -64,7 +64,7 @@
                     <TaskpaneId>ButtonId1</TaskpaneId>
                     <SourceLocation resid="TermSearch.Url"/>
                   </Action>
-                </Control>
+                </Control>-->
                 <Control xsi:type="Button" id="AddBuildingBlock">
                     <Label resid="AddBuildingBlock.Label"/>
                     <Supertip>
@@ -95,32 +95,32 @@
     </Hosts>
     <Resources>
       <bt:Images>
-        <bt:Image id="Icon.16x16" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/icon-16.png"/>
-        <bt:Image id="Icon.20x20" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/icon-20.png"/>
-        <bt:Image id="Icon.24x24" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/icon-24.png"/>
-        <bt:Image id="Icon.32x32" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/icon-32.png"/>
-        <bt:Image id="Icon.40x40" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/icon-40.png"/>
-        <bt:Image id="Icon.48x48" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/icon-48.png"/>
-        <bt:Image id="Icon.64x64" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/icon-64.png"/>
-        <bt:Image id="Icon.80x80" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/icon-80.png"/>
-        <bt:Image id="Icon.96x96" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/icon-96.png"/>
+        <bt:Image id="Icon.16x16" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/swate_16x16.png"/>
+        <bt:Image id="Icon.20x20" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/swate_20x20.png"/>
+        <bt:Image id="Icon.24x24" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/swate_24x24.png"/>
+        <bt:Image id="Icon.32x32" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/swate_32x32.png"/>
+        <bt:Image id="Icon.40x40" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/swate_40x40.png"/>
+        <bt:Image id="Icon.48x48" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/swate_48x48.png"/>
+        <bt:Image id="Icon.64x64" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/swate_64x64.png"/>
+        <bt:Image id="Icon.80x80" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/swate_80x80.png"/>
+        <bt:Image id="Icon.96x96" DefaultValue="https://swate.denbi.uni-tuebingen.de/assets/swate_96x96.png"/>
       </bt:Images>
       <bt:Urls>
         <bt:Url id="GetStarted.LearnMoreUrl" DefaultValue="https://go.microsoft.com/fwlink/?LinkId=276812"/>
-        <bt:Url id="TermSearch.Url" DefaultValue="https://swate.denbi.uni-tuebingen.de/#TermSearch"/>
+        <!--<bt:Url id="TermSearch.Url" DefaultValue="https://swate.denbi.uni-tuebingen.de/#TermSearch"/>-->
         <bt:Url id="AddBuildingBlock.Url" DefaultValue="https://swate.denbi.uni-tuebingen.de/#AddBuildingBlock"/>
       </bt:Urls>
       <bt:ShortStrings>
         <bt:String id="GetStarted.Title" DefaultValue="Get started annotating your data for greater good!"/>
-        <bt:String id="CSBAnnotatorCommands.Label" DefaultValue="CSBAnnotator Commands"/>
-        <bt:String id="TermSearch.Label" DefaultValue="Insert Ontology Term"/>
-        <bt:String id="AddBuildingBlock.Label" DefaultValue="Add Annotation Building Block"/>
+        <bt:String id="SwateCommands.Label" DefaultValue="Swate"/>
+        <!--<bt:String id="TermSearch.Label" DefaultValue="Insert Ontology Term"/>-->
+        <bt:String id="AddBuildingBlock.Label" DefaultValue="Swate"/>
       </bt:ShortStrings>
       <bt:LongStrings>
-        <bt:String id="GetStarted.Description" DefaultValue="CSBAnnotator succesfully. Go to the DATA tab and click the 'Show Annotation Pane' button to get started."/>
-        <bt:String id="TermSearch.Tooltip" DefaultValue="open a taskpane where you can search for ontology terms in multiple ways and fill the results into your sheet."/>
-        <bt:String id="AddBuildingBlock.Tooltip" DefaultValue="open a taskpane where you can select annotation building block and add them to yourt anotation table."/>
+        <bt:String id="GetStarted.Description" DefaultValue="Swate was loaded succesfully. Go to the DATA tab and click the 'Swate' button to get started."/>
+        <!--<bt:String id="TermSearch.Tooltip" DefaultValue="Open a taskpane where you can search for ontology terms in multiple ways and fill the results into your sheet."/>-->
+        <bt:String id="AddBuildingBlock.Tooltip" DefaultValue="Open a task pane to gain full access to the Swate functionality."/>
       </bt:LongStrings>
     </Resources>
   </VersionOverrides>
-</OfficeApp>
+</OfficeApp>

.assets/assets/swate.cmd

@@ -0,0 +1,4 @@
+@ECHO OFF
+echo "Starting Excel instance with the SWATE manifest ..."
+
+npx office-addin-debugging start manifest.xml desktop --debug-method web

.assets/assets/swate.sh

@@ -0,0 +1,3 @@
+echo "Starting Excel instance with the SWATE manifest ..."
+
+npx office-addin-debugging start manifest.xml desktop --debug-method web

RELEASE_NOTES.md

@@ -1,3 +1,26 @@
+### 0.3.0+0d31c43 (Released 2021-2-11)
+* Additions:
+    * latest commit #0d31c43
+    * [[#4bf33cb](https://github.com/nfdi4plants/Swate/commit/4bf33cb478861250a3f1794140821460115e3173)] Add ontology accession number as tag in ref columns (Issue #100).
+    * [[#262dae3](https://github.com/nfdi4plants/Swate/commit/262dae32acef085d3bfff46c1194f80698278387)] Add option to write process.json to Swate annotation table (Issue #84). :sparkles:
+    * [[#09467d9](https://github.com/nfdi4plants/Swate/commit/09467d97813b708ce8bee58935b0b5830aea15f7)] Visually group building blocks to protocols (Issues 101#, #103, #104) :sparkles:
+    * [[#0516353](https://github.com/nfdi4plants/Swate/commit/05163533c6832023301e588ccc59b34af5b18f88)] Add Logos and visually update Swate (Issue #59).
+    * [[#5c2e56a](https://github.com/nfdi4plants/Swate/commit/5c2e56a46b57fa627c5b37b7e8307ab633a4e12b)] Add option to add unit cols to existing building block (Issue #94).
+    * [[#9987184](https://github.com/nfdi4plants/Swate/commit/99871849bc83cfa4bd4fe7760c2f43dae524d76b)] Add sorensen dice sorting to advanced term search (Issue #95).
+    * [[#9158bb7](https://github.com/nfdi4plants/Swate/commit/9158bb75696399492050109ebb0d04be59eeb9b6)] Update unit search to only search UO ontology (Issue #93).
+    * [[#4e0d0c9](https://github.com/nfdi4plants/Swate/commit/4e0d0c9e32c5be606542f9ca0f05b74be6626e1d)] Add easy to access navigation option to advanced search (Issue #91).
+    * [[#374e326](https://github.com/nfdi4plants/Swate/commit/374e326f2123a2f61825f281bc4886b109d5261d)] Add features from #68 to Update Reference Columns (Issue 87#).
+* Deletions:
+    * [[#9da9c55](https://github.com/nfdi4plants/Swate/commit/9da9c55a23d737aa05ff7c12759446ce5387902f)] Remove event handlers (input assist, #87).
+* Bugfixes:
+    * [[#0d31c43](https://github.com/nfdi4plants/Swate/commit/0d31c43ff55961b7eed6d91183c4c91c85356c59)] Fix bug not opening "File Picker" upload window on click.
+    * [[#8606b12](https://github.com/nfdi4plants/Swate/commit/8606b12fe5497c2fbea2659cafd123c9a22dfe34)] Add Protocol Xml logic and fix ISADotNet dependency.
+    * [[#51928c0](https://github.com/nfdi4plants/Swate/commit/51928c0af9b5d5a39dbc54abbadc3aa81e8580f8)] Fix minor routing icon mismatch.
+    * [[#fdcb58c](https://github.com/nfdi4plants/Swate/commit/fdcb58c71ce624879448c4e86e2119b72bc877ae)] Fix minor white/lightgrey mix ups in filepicker view.
+    * [[#cc26e81](https://github.com/nfdi4plants/Swate/commit/cc26e81e895d7ec7fc7abef885e5d7afb4c0a7c2)] Fix bug overloading computers when creating an annotation table for whole rows (Issue #63).
+    * [[#1e5eb3d](https://github.com/nfdi4plants/Swate/commit/1e5eb3d6c2b0f2f0527d4843c8bc0addabdb0b04)] Fix reset of unit search input when unchecking (Issue #92).
+    * [[#474cf73](https://github.com/nfdi4plants/Swate/commit/474cf73cb48227d58e88d239e6e9e50e8676c78a)] Fix bug creating wrong TAN with insertTerm.
+
 ### 0.2.0+899b535 (Released 2021-1-11)
 * Additions:
     * latest commit #899b535

SAFEOfficeAddInn.sln → Swate.sln

@@ -25,10 +25,6 @@ EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "assets", "assets", "{A21844B3-2816-4F6F-B275-308DA4EC2B3E}"
 	ProjectSection(SolutionItems) = preProject
 		src\Client\public\favicon.png = src\Client\public\favicon.png
-		src\Client\public\assets\icon-16.png = src\Client\public\assets\icon-16.png
-		src\Client\public\assets\icon-32.png = src\Client\public\assets\icon-32.png
-		src\Client\public\assets\icon-80.png = src\Client\public\assets\icon-80.png
-		src\Client\public\assets\logo-filled.png = src\Client\public\assets\logo-filled.png
 	EndProjectSection
 EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "docs", "docs", "{DB2C5A73-BF7F-45D5-AEC8-D36539C5C019}"
@@ -63,7 +59,6 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "tools", "tools", "{494903F3
 EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "tests", "tests", "{A7CCC606-3646-4F94-9F59-79C75E413344}"
 	ProjectSection(SolutionItems) = preProject
-		tests\manifest.xml = tests\manifest.xml
 		tests\test.cmd = tests\test.cmd
 		tests\test.sh = tests\test.sh
 	EndProjectSection

build.fsx

@@ -1,17 +1,35 @@
-#r "paket: groupref build //"
+#r "paket:
+nuget BlackFox.Fake.BuildTask
+nuget Fake.Core.Target
+nuget Fake.Core.Process
+nuget Fake.Core.ReleaseNotes
+nuget Fake.IO.FileSystem
+nuget Fake.DotNet.Cli
+nuget Fake.DotNet.MSBuild
+nuget Fake.DotNet.AssemblyInfoFile
+nuget Fake.DotNet.Paket
+nuget Fake.DotNet.FSFormatting
+nuget Fake.DotNet.Fsi
+nuget Fake.DotNet.NuGet
+nuget Fake.Api.Github
+nuget Fake.DotNet.Testing.Expecto 
+nuget Fake.Extensions.Release
+nuget Fake.Tools.Git //
+"
+
+#if !FAKE
 #load "./.fake/build.fsx/intellisense.fsx"
-#r "netstandard"
-
+#r "netstandard" // Temp fix for https://github.com/dotnet/fsharp/issues/5216
+#endif
 
 open System
+open System.Text
 open Fake
 open Fake.Core
 open Fake.DotNet
 open Fake.IO
 open Fake.Api
 open Fake.Tools.Git
-open Farmer
-open Farmer.Builders
 
 Target.initEnvironment ()
 
@@ -354,18 +372,19 @@ Target.create "Release" (fun config ->
     let semVer =
         let opt =
             config.Context.Arguments
+            |> List.map (fun x -> x.ToLower())
             |> List.tryFind (fun x -> x.StartsWith "semver:")
         match opt with
-        | Some "semver:major"| Some "semver:Major" ->
+        | Some "semver:major"->
             Trace.trace "Increase major for next release notes."
             Major
-        | Some "semver:minor"| Some "semver:Minor" ->
+        | Some "semver:minor" ->
             Trace.trace "Increase minor for next release notes."
             Minor
-        | Some "semver:Patch"| Some "semver:patch" ->
+        | Some "semver:patch" ->
             Trace.trace "Increase patch for next release notes."
             Patch
-        | Some "semver:wip"| Some "semver:WIP" ->
+        | Some "semver:wip" ->
             Trace.trace "Add new commits to current release."
             WIP
         | Some x ->
@@ -503,8 +522,6 @@ Target.create "Release" (fun config ->
             "RELEASE_NOTES.md"
             newNotes
 
-    writeNewReleaseNotes
-
     Trace.trace "Update RELEASE_NOTES.md done!"
 
     Trace.trace "Update Version.fs"
@@ -521,6 +538,35 @@ Target.create "Release" (fun config ->
         ]
 
     Trace.trace "Update Version.fs done!"
+
+    /// Update maniefest.xmls
+
+    Trace.trace "Update manifest.xml"
+
+    let _ =
+        let newVer = sprintf "<Version>%i.%i.%i</Version>" newRelease.SemVer.Major newRelease.SemVer.Minor newRelease.SemVer.Patch
+        Shell.regexReplaceInFilesWithEncoding
+            "<Version>[0-9]+.[0-9]+.[0-9]+</Version>"
+            newVer
+            Encoding.UTF8
+            [
+                (Path.combine __SOURCE_DIRECTORY__ @".assets\assets\manifest.xml")
+                (Path.combine __SOURCE_DIRECTORY__ "manifest.xml")
+            ]
+
+    Trace.trace "Update manifest.xml done!"
+)
+
+Target.create "ZipAssets" (fun _ ->
+
+    let assetPath = System.IO.Path.Combine(__SOURCE_DIRECTORY__,@".assets\assets")
+    let assetDir = Fake.IO.DirectoryInfo.ofPath assetPath
+
+    let files =
+        let assetsPaths = Fake.IO.DirectoryInfo.getFiles assetDir
+        assetsPaths |> Array.map (fun x -> x.FullName)
+
+    Zip.zip assetDir.FullName ".assets\swate.zip" files
 )
 
 Target.create "GithubDraft" (fun config ->
@@ -576,7 +622,6 @@ Target.create "GithubDraft" (fun config ->
     let release = ReleaseNotes.load "RELEASE_NOTES.md"
     let semVer = (sprintf "v%i.%i.%i" release.SemVer.Major release.SemVer.Minor release.SemVer.Patch)
 
-
     let token =
         match Environment.environVarOrDefault "github_token" "", tokenOpt with
         | s, None when System.String.IsNullOrWhiteSpace s |> not -> s
@@ -591,6 +636,7 @@ Target.create "GithubDraft" (fun config ->
     let files =
         let assetPath = System.IO.Path.Combine(__SOURCE_DIRECTORY__,@".assets")
         let assetDir = Fake.IO.DirectoryInfo.ofPath assetPath
+        /// This only accesses files and not folders. So in this case it will only access the .zip file created by "ZipAssets"
         let assetsPaths = Fake.IO.DirectoryInfo.getFiles assetDir
         assetsPaths |> Array.map (fun x -> x.FullName)
 
@@ -605,40 +651,9 @@ Target.create "GithubDraft" (fun config ->
         |> Async.RunSynchronously
 
     Trace.trace "Draft successfully created!"
-    //let responseCreate = 
-    //    FSharp.Data.Http.RequestString
-    //        (   "https://api.github.com/repos/nfdi4plants/Swate/releases", 
-    //            headers = [ 
-    //                "accept", "application/vnd.github.v3+json"; 
-    //                "User-Agent", "Swate";
-    //                "Authorization", sprintf "token 5da68a1d1bdd09413f47b4ecdfd6911d641d7a93"
-    //            ],
-    //            body = FSharp.Data.HttpRequestBody.TextRequest textRequestBody
-    //        )
-    //Trace.trace "Draft successfully created!"
-
-    //let upLink = 
-    //    let pattern = "\"upload_url\":\"[a-z]+://[a-zA-Z./0-9]+"
-    //    System.Text.RegularExpressions.Regex.Match(responseCreate,pattern)
-    //    |> fun x -> x.Value.Replace("\"upload_url\":","").Replace("\"","")
-
-    //let uploadResponse =
-    //    let readInZipAsBinary = 
-    //        let path = System.IO.Path.Combine(__SOURCE_DIRECTORY__,@".assets\swate.zip")
-    //        System.IO.File.ReadAllBytes(path)
-    //    FSharp.Data.Http.RequestString
-    //        (   upLink, 
-    //            query = ["name","swate.zip"; "label","Swate"],
-    //            headers = [ 
-    //                "accept", "application/vnd.github.v3+json"; 
-    //                "User-Agent", "Swate";
-    //                "Authorization", sprintf "token 5da68a1d1bdd09413f47b4ecdfd6911d641d7a93"
-    //                "Content-Type", "application\zip"
-    //            ],
-    //            body = FSharp.Data.HttpRequestBody.BinaryUpload readInZipAsBinary
-    //        )
 )
 
+
 Target.create "Bundle" (fun _ ->
     runDotNet (sprintf "publish -c Release -o \"%s\"" deployDir) serverPath
     npm "run build" "."
@@ -691,6 +706,9 @@ open Fake.Core.TargetOperators
 "IsExistingReleaseNotes"
     ==> "Release"
 
+"ZipAssets"
+    ==> "GithubDraft"
+
 "InstallOfficeAddinTooling"
     ==> "WebpackConfigSetup"
     ==> "LocalConnectionStringSetup"