Update the invenio and pride packages (#36)

* Update [email protected] - Rework the tokenisation and acess to the metadata in Accordance to ARKTokenization 5.0.0 - Add checks for token existence to the checks for token value * Create [email protected] - Rework the tokenisation and acess to the metadata in Accordance to ARKTokenization 5.0.0 - Add checks for token existence to the checks for token value * use in-package frontmatter metadata extraction for [email protected] and [email protected] * simplify sanity checks: instead of compiling via fsc, check wether the package can be run via fsi. Revisit compilation in the future, since this is not ideal. * only publish preview index on push --------- Co-authored-by: Kevin Schneider <[email protected]>
nfdi4plants · Jun 6, 2024 · 25904a4 · 25904a4
1 parent 50a81ce
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diff --git a/.github/workflows/pipeline.yml b/.github/workflows/pipeline.yml
@@ -245,7 +245,7 @@ jobs:
   update-preview-index:
     needs: staging-area-pre-publish-checks
     runs-on: ubuntu-latest
-    if: needs.staging-area-pre-publish-checks.outputs.trigger-update-preview-index == 'true'
+    if: needs.staging-area-pre-publish-checks.outputs.trigger-update-preview-index == 'true' && github.event_name == 'push'
     steps:
       - uses: actions/checkout@v4
       - name: Set up .NET

diff --git a/StagingArea/invenio/[email protected] b/StagingArea/invenio/[email protected]
@@ -0,0 +1,116 @@
+let [<Literal>]PACKAGE_METADATA = """(*
+---
+Name: invenio
+Summary: Validates if the ARC contains the necessary metadata to be publishable via Invenio.
+Description: |
+  Validates if the ARC contains the necessary metadata to be publishable via Invenio.
+  The following metadata is required:
+  - Investigation has title and description
+  - All persons in Investigation Contacts must have a name, last name, affiliation and valid email
+MajorVersion: 2
+MinorVersion: 0
+PatchVersion: 0
+Publish: true
+Authors:
+  - FullName: Oliver Maus
+    Affiliation: DataPLANT
+  - FullName: Christopher Lux
+    Email: [email protected]
+    Affiliation: RPTU Kaiserslautern
+    AffiliationLink: http://rptu.de/startseite
+Tags:
+  - Name: ARC
+  - Name: data publication
+ReleaseNotes: |
+  - Rework the tokenisation and acess to the metadata in Accordance to ARKTokenization 6.0.0/ARCExpect 2.0.0
+---
+*)"""
+
+#r "nuget: ARCExpect, 2.0.0"
+
+open ControlledVocabulary
+open Expecto
+open ARCExpect
+open ARCTokenization
+open ARCTokenization.StructuralOntology
+open System.IO
+
+// Input:
+let arcDir = Directory.GetCurrentDirectory()
+
+// Values:
+let absoluteDirectoryPaths = FileSystem.parseARCFileSystem arcDir
+
+let investigationMetadata = 
+    absoluteDirectoryPaths
+    |> Investigation.parseMetadataSheetsFromTokens() arcDir 
+    |> List.concat 
+
+
+// Validation Cases:
+let cases = 
+    testList INVMSO.``Investigation Metadata``.INVESTIGATION.key.Name [
+        // Investigation has title
+        ARCExpect.validationCase (TestID.Name INVMSO.``Investigation Metadata``.INVESTIGATION.``Investigation Title``.Name) {
+            investigationMetadata
+            |> Validate.ParamCollection.ContainsParamWithTerm
+                INVMSO.``Investigation Metadata``.INVESTIGATION.``Investigation Title``
+        }
+        // Investigation has description
+        ARCExpect.validationCase (TestID.Name INVMSO.``Investigation Metadata``.INVESTIGATION.``Investigation Description``.Name) {
+            investigationMetadata
+            |> Validate.ParamCollection.ContainsParamWithTerm
+                INVMSO.``Investigation Metadata``.INVESTIGATION.``Investigation Description``
+        }
+        // Investigation has contacts with name, last name, affiliation and email
+        // Investigation Person First Name
+        ARCExpect.validationCase (TestID.Name $"{INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person First Name``.Name} exists") {
+            investigationMetadata
+            |> Validate.ParamCollection.ContainsParamWithTerm INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person First Name``
+        }
+        ARCExpect.validationCase (TestID.Name $"{INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person First Name``.Name} is not empty") {
+            investigationMetadata
+            |> Seq.filter (Param.getTerm >> (=) INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person First Name``)
+            |> Seq.iter Validate.Param.ValueIsNotEmpty
+        }
+        // Investigation Person Last Name
+        ARCExpect.validationCase (TestID.Name $"{INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Last Name``.Name} exists") {
+            investigationMetadata
+            |> Validate.ParamCollection.ContainsParamWithTerm INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Last Name``
+        }
+        ARCExpect.validationCase (TestID.Name $"{INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Last Name``.Name} is not empty") {
+            investigationMetadata
+            |> Seq.filter (Param.getTerm >> (=) INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Last Name``)
+            |> Seq.iter Validate.Param.ValueIsNotEmpty
+        }
+        // Investigation Person Affiliation
+        ARCExpect.validationCase (TestID.Name $"{INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Affiliation``.Name} exists") {
+            investigationMetadata
+            |> Validate.ParamCollection.ContainsParamWithTerm INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Affiliation``
+        }
+        ARCExpect.validationCase (TestID.Name $"{INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Affiliation``.Name} is not empty") {
+            investigationMetadata
+            |> Seq.filter (Param.getTerm >> (=) INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Affiliation``)
+            |> Seq.iter Validate.Param.ValueIsNotEmpty
+        }
+        // Investigation Person Email
+        ARCExpect.validationCase (TestID.Name $"{INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Email``.Name} exists") {
+        investigationMetadata
+        |> Validate.ParamCollection.ContainsParamWithTerm INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Email``
+        }
+        ARCExpect.validationCase (TestID.Name INVMSO.``Investigation Metadata``. ``INVESTIGATION CONTACTS``.``Investigation Person Email``.Name) {
+            investigationMetadata
+            |> Seq.filter (Param.getTerm >> (=) INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Email``)
+            |> Seq.iter (Validate.Param.ValueMatchesRegex StringValidationPattern.email)
+        }
+    ]
+
+// Execution:
+
+Setup.ValidationPackage(
+    metadata = Setup.Metadata(PACKAGE_METADATA),
+    CriticalValidationCases = [cases]
+)
+|> Execute.ValidationPipeline(
+    basePath = arcDir
+)