Validation Package invenio
v2.1.0 released on 08/08/2024
by Oliver Maus; Christopher Lux; Lukas Weil
88 Downloads
Validates if the ARC contains the necessary metadata to be publishable via Invenio.
Install with arc-validate
arc-validate package install invenio --version 2.1.0
Include in a PLANTDataHUB CQC pipeline
validation_packages:
- name: invenio
version: 2.1.0
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
Release notes
- Fix package passing validation against Investigation file containing only section keys
Browse code (v2.1.0)
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: 1
PatchVersion: 0
Publish: true
Authors:
- FullName: Oliver Maus
Affiliation: DataPLANT
- FullName: Christopher Lux
Email: lux@csbiology.de
Affiliation: RPTU Kaiserslautern
AffiliationLink: http://rptu.de/startseite
- FullName: Lukas Weil
Email: weil@rptu.de
Affiliation: DataPLANT
Tags:
- Name: ARC
- Name: data publication
ReleaseNotes: |
- Fix package passing validation against Investigation file containing only section keys
---
*)"""
#r "nuget: ARCExpect, 4.0.1"
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.ContainsNonKeyParamWithTerm
INVMSO.``Investigation Metadata``.INVESTIGATION.``Investigation Title``
}
// Investigation has description
ARCExpect.validationCase (TestID.Name INVMSO.``Investigation Metadata``.INVESTIGATION.``Investigation Description``.Name) {
investigationMetadata
|> Validate.ParamCollection.ContainsNonKeyParamWithTerm
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.ContainsNonKeyParamWithTerm 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.ContainsNonKeyParamWithTerm 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.ContainsNonKeyParamWithTerm 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.filter (Param.getValueAsString >> (<>) "Metadata Section Key")
|> 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.ContainsNonKeyParamWithTerm 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.filter (Param.getValueAsString >> (<>) "Metadata Section Key")
|> Seq.iter (Validate.Param.ValueMatchesRegex StringValidationPattern.email)
}
]
// Execution:
Setup.ValidationPackage(
metadata = Setup.Metadata(PACKAGE_METADATA),
CriticalValidationCases = [cases]
)
|> Execute.ValidationPipeline(
basePath = arcDir
)