Merge remote-tracking branch 'origin/developer' into ISADotnetViz

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,32 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: "[BUG]"
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**OS and framework information (please complete the following information):**
+ - OS: [e.g. Windows 10]
+ - OS Version [e.g. 1809] 
+ - .Net core SDK version [e.g. 2.2.101 ]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/documentation.md

@@ -0,0 +1,16 @@
+---
+name: Documentation
+about: Found missing documentation or Errors in the docs? this is the place to go.
+title: "[Docs]"
+labels: documentation
+assignees: ''
+
+---
+
+**Found undocumented code? Please link it here**
+A link to the code in the repository.
+
+**Found a problem with existing documentation?**
+Describe the issue you have with existing documentation e.g. "The example code is rather complex, it can be simplified by ..."
+
+**

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: "[Feature Request]"
+labels: FeatureRequest
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/build-test.yml

@@ -0,0 +1,38 @@
+name: Build and test
+
+on:
+  push:
+    branches: [ developer ]
+  pull_request:
+    branches: [ developer ]
+
+jobs:
+  build-and-test-linux:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup .NET
+      uses: actions/setup-dotnet@v1
+      with:
+        dotnet-version: 5.x.x
+    - name: Restore local tools
+      run: dotnet tool restore
+    - name: Build and test
+      run: dotnet fake build -t runTests
+
+  build-and-test-windows:
+
+    runs-on: windows-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup .NET
+      uses: actions/setup-dotnet@v1
+      with:
+        dotnet-version: 5.x.x
+    - name: Restore local tools
+      run: dotnet tool restore
+    - name: Build and test
+      run: dotnet fake build -t runTests

RELEASE_NOTES.md

@@ -1,4 +1,24 @@
-### 0.3.0-preview.1+993781f (Released 2021-9-6)
+### 0.3.3+2da8c3a (Released 2021-9-10)
+* Additions:
+    * latest commit #2da8c3a
+* Bugfixes:
+    * [[#2da8c3a](https://github.com/nfdi4plants/ISADotNet/commit/2da8c3a2e73aa110b1696d41932c32dc80c91967)] fix prerelease targets
+
+### 0.3.2+4233b78 (Released 2021-9-9)
+* Additions:
+    * latest commit #4233b78
+    * [[#4233b78](https://github.com/nfdi4plants/ISADotNet/commit/4233b780896380764cb10a90af4b1902c8006ac9)] move SwateCustomXml datamodel to ISADotNet
+    * [[#f7511ad](https://github.com/nfdi4plants/ISADotNet/commit/f7511ad7855ba10b652c38feb2c09b993d6df779)] increase function parameter consistency
+    * [[#249f1af](https://github.com/nfdi4plants/ISADotNet/commit/249f1af066d0dfd9682016f6c207cf5c159bc1da)] add ISA Assay Common API parser
+    * [[#9890b6a](https://github.com/nfdi4plants/ISADotNet/commit/9890b6a7932813281546d3eb2621a5ace62265ab)] Unify naming as requested (PR #31).
+    * [[#a48d571](https://github.com/nfdi4plants/ISADotNet/commit/a48d5712a742631d0205dfdc35665acb7592e2df)] Add FromStringWithNumber for ProtocolParameter (Issue #24).
+    * [[#b511949](https://github.com/nfdi4plants/ISADotNet/commit/b511949f3463bb1c3f6053a836c83ddd686103f7)] add isa xlsx stream reader/writer functions
+    * [[#91e9ea5](https://github.com/nfdi4plants/ISADotNet/commit/91e9ea5bbfaa74e5ac5db1152be54a4b149e1f69)] Add GetName, GetNameWithNumber for xxValue DataModel (Issue #24).
+    * [[#035ed55](https://github.com/nfdi4plants/ISADotNet/commit/035ed55b0fa3a417aa32627f20ca037bac129b3c)] Add FromString, FromStringWithNumber for OntologyAnnotation, Factor, MaterialAttribute (Issue #24)
+    * [[#6f883e6](https://github.com/nfdi4plants/ISADotNet/commit/6f883e614e456817fcf6af8e15ce241b7d8c01b1)] Add GetValue logic for FactorValue, MaterialAttributeValue, ProcessParameterValue (Issue #24)
+    * [[#01db12b](https://github.com/nfdi4plants/ISADotNet/commit/01db12ba03014ef062d6f81b662be2042ee8ebbf)] add json readers/writers
+
+### 0.3.0+993781f (Released 2021-9-6)
 * Additions:
     * latest commit #993781f
     * [[#993781f](https://github.com/nfdi4plants/ISADotNet/commit/993781fe3b9ea7d2516ee1a823894b0705db87f9)] small adjustment to assay.xlsx reader

build.fsx

@@ -1,3 +1,5 @@
+#if FAKE
+
 #r "paket:
 nuget BlackFox.Fake.BuildTask
 nuget Fake.Extensions.Release
@@ -16,7 +18,26 @@ nuget Fake.Api.Github
 nuget Fake.DotNet.Testing.Expecto 
 nuget Fake.Tools.Git //"
 
+#endif
+
 #if !FAKE
+
+#r "nuget: BlackFox.Fake.BuildTask"
+#r "nuget: Fake.Extensions.Release"
+#r "nuget: Fake.Core.Target"
+#r "nuget: Fake.Core.Process"
+#r "nuget: Fake.Core.ReleaseNotes"
+#r "nuget: Fake.IO.FileSystem"
+#r "nuget: Fake.DotNet.Cli"
+#r "nuget: Fake.DotNet.MSBuild"
+#r "nuget: Fake.DotNet.AssemblyInfoFile"
+#r "nuget: Fake.DotNet.Paket"
+#r "nuget: Fake.DotNet.FSFormatting"
+#r "nuget: Fake.DotNet.Fsi"
+#r "nuget: Fake.DotNet.NuGet"
+#r "nuget: Fake.Api.Github"
+#r "nuget: Fake.DotNet.Testing.Expecto"
+#r "nuget: Fake.Tools.Git"
 #load "./.fake/build.fsx/intellisense.fsx"
 #r "netstandard" // Temp fix for https://github.com/dotnet/fsharp/issues/5216
 #endif
@@ -102,7 +123,7 @@ module BasicTasks =
         printfn "Please enter pre-release package suffix"
         let suffix = System.Console.ReadLine()
         prereleaseSuffix <- suffix
-        prereleaseTag <- (sprintf "%s-%s" release.NugetVersion suffix)
+        prereleaseTag <- (sprintf "%i.%i.%i-%s" release.SemVer.Major release.SemVer.Minor release.SemVer.Patch suffix)
         isPrerelease <- true
     }
 
@@ -119,6 +140,14 @@ module BasicTasks =
         |> Seq.iter (DotNet.build id)
     }
 
+    //let buildFable = BuildTask.create "BuildFable" [clean] {
+    //    !! "src/**/*.*proj"
+    //    |> Seq.iter (DotNet.build (fun p -> 
+    //        let properties = (("DefineConstants","FABLE") :: p.MSBuildParams.Properties)
+    //        {p with MSBuildParams = {p.MSBuildParams with Properties = properties}
+    //        }))
+    //}
+
     let copyBinaries = BuildTask.create "CopyBinaries" [clean; build] {
         let targets = 
             !! "src/**/*.??proj"
@@ -231,6 +260,26 @@ module PackageTasks =
                                     MSBuildParams = msBuildParams
                             }
                 ))
+                "src/ISADotNet/ISADotNet.fsproj"
+                |> Fake.DotNet.DotNet.pack (fun p ->
+                    let msBuildParams =
+                        {p.MSBuildParams with 
+                            Properties = ([
+                                "PackageId", "ISADotNet.Fable"
+                                "Version",prereleaseTag
+                                "Description","Fable compliant release for the ISA compliant experimental metadata toolkit in F#. Additionally to the compiled library, it is shipped with the uncompiled code."
+                                "PackageTags","F# FSharp dotnet .Net bioinformatics biology datascience metadata investigation study assay ISA Json Fable"
+                                "PackageReleaseNotes",  (release.Notes |> List.map replaceCommitLink |> String.concat "\r\n")
+                            ] @ p.MSBuildParams.Properties)
+                        }
+                    let test = p
+                    {
+                        p with 
+                            VersionSuffix = Some prereleaseSuffix
+                            MSBuildParams = msBuildParams
+                            OutputPath = Some pkgDir
+                    }
+                )
         else
             failwith "aborted"
     }

build.fsx.lock

@@ -214,7 +214,7 @@ NUGET
     Microsoft.NET.StringTools (1.0)
       System.Memory (>= 4.5.4)
       System.Runtime.CompilerServices.Unsafe (>= 5.0)
-    Microsoft.NETCore.Platforms (5.0.2)
+    Microsoft.NETCore.Platforms (5.0.3)
     Microsoft.NETCore.Targets (5.0)
     Microsoft.Win32.Primitives (4.3)
       Microsoft.NETCore.Platforms (>= 1.1)

src/ISADotNet.XLSX/AssayFile/AnnotationColumn.fs

@@ -1,13 +1,15 @@
 namespace ISADotNet.XLSX.AssayFile
 
-open FSharpSpreadsheetML
 open ISADotNet
 open ISADotNet.XLSX
 open System.Text.RegularExpressions
 
 /// Functions for parsing single column headers of an annotation table
 module AnnotationColumn =
 
+    [<Literal>]
+    let OboPurlURL = @"http://purl.obolibrary.org/obo/"
+
     /// Typed depiction of a Swate Header: Kind [TermName] (#Number, #tOntology)
     type ColumnHeader =
         {
@@ -56,7 +58,11 @@ module AnnotationColumn =
                 let ontology = 
                     if ontologySourceRegex.Success then 
                         ontologySourceRegex.Value.Split ':'
-                        |> fun o -> OntologyAnnotation.fromString ""  o.[0] o.[1] 
+                        |> fun o -> 
+                            let tsr = o.[0]
+                            let tanNumberOnly = o.[1] 
+                            let tan = sprintf "%s%s_%s" OboPurlURL tsr tanNumberOnly//$"{OboPurlURL}{tsr}_{tanNumberOnly}"
+                            OntologyAnnotation.fromString "" tsr tan
                         |> fun ontology -> {ontology with Comments = numberComment}
                         |> Some
                     else None