Add PRIDE package v1.0.2 (#61)

nfdi4plants · Nov 15, 2024 · ade17a4 · ade17a4
1 parent 4cb728e
commit ade17a4
Showing 1 changed file with 342 additions and 0 deletions.
diff --git a/StagingArea/pride/[email protected] b/StagingArea/pride/[email protected]
@@ -0,0 +1,342 @@
+let [<Literal>]PACKAGE_METADATA = """(*
+---
+Name: pride
+Summary: Validates if the ARC contains the necessary metadata to be publishable via PRIDE.
+Description: |
+    Validates if the ARC contains the necessary metadata to be publishable via PRIDE.
+    The following metadata is required:
+        - Investigation has title and description
+        - Investigation has Keywords comment in correct format
+        - All persons in Investigation Contacts must have a first name, last name, affiliation and valid email
+        - Study has protocol in correct format
+        - Assay has protocol, technology type in correct format
+MajorVersion: 1
+MinorVersion: 0
+PatchVersion: 2
+Publish: true
+Authors:
+  - FullName: Oliver Maus
+    Affiliation: DataPLANT
+  - FullName: Christopher Lux
+    Email: [email protected]
+    Affiliation: RPTU Kaiserslautern
+    AffiliationLink: http://rptu.de/startseite
+Tags:
+  - Name: validation
+  - Name: pride
+  - Name: proteomics
+ReleaseNotes: |
+  - First release
+---
+*)"""
+
+
+#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 
+
+let studyMetadata =
+    absoluteDirectoryPaths
+    |> Study.parseMetadataSheetsFromTokens() arcDir
+    |> List.concat
+
+let assayMetadata =
+    absoluteDirectoryPaths
+    |> Assay.parseMetadataSheetsFromTokens() arcDir
+    |> List.concat
+
+let studyProcessGraphTokens = 
+    try 
+        absoluteDirectoryPaths
+        |> Study.parseProcessGraphColumnsFromTokens arcDir
+        |> Seq.collect Map.values
+        |> List.concat
+    with
+        | _ -> List.empty
+
+let assayProcessGraphTokens =
+    try 
+        absoluteDirectoryPaths
+        |> Assay.parseProcessGraphColumnsFromTokens arcDir
+        |> Seq.collect Map.values
+        |> List.concat
+    with
+        | _ -> List.empty
+
+let organismTokens =
+    studyProcessGraphTokens
+    |> List.tryFind (fun cvpList -> cvpList.Head |> Param.getValueAsTerm = (CvTerm.create("OBI:0100026","organism","OBI")))
+    |> Option.defaultValue []
+
+let tissueTokens =
+    studyProcessGraphTokens
+    |> List.tryFind (fun cvpList -> cvpList.Head |> Param.getValueAsTerm = (CvTerm.create("NCIT:C12801","Tissue","NCIT")))
+    |> Option.defaultValue []
+
+let instrumentTokens =
+    assayProcessGraphTokens
+    |> List.tryFind (fun cvpList -> cvpList.Head |> Param.getValueAsTerm = (CvTerm.create("MS:1000031","instrument model","MS")))
+    |> Option.defaultValue []
+
+let modTokens =
+    assayProcessGraphTokens
+    |> List.filter (
+        fun cvpList -> 
+            cvpList.Head |> Param.getValueAsTerm = (CvTerm.create("MS:1003021","Fixed model","MS")) ||
+            cvpList.Head |> Param.getValueAsTerm = (CvTerm.create("MS:1003022","Variable model","MS"))
+    )
+    |> List.concat
+
+let techTypeName = CvTerm.create("ASSMSO:00000011", "Assay Technology Type", "ASSMSO")
+let techTypeTAN = CvTerm.create("ASSMSO:00000013", "Assay Technology Type Term Accession Number", "ASSMSO")
+let techTypeTSR = CvTerm.create("ASSMSO:00000015", "Assay Technology Type Term Source REF", "ASSMSO")
+
+
+// Helper functions (to deposit in ARCExpect later):
+
+open System.Text
+
+
+let characterLimit (lowerLimit : int option) (upperLimit : int option) =
+    match lowerLimit, upperLimit with
+    | None, None -> System.Text.RegularExpressions.Regex(@"^.{0,}$")
+    | Some ll, None -> System.Text.RegularExpressions.Regex($"^.{{{ll},}}$")
+    | None, Some ul -> System.Text.RegularExpressions.Regex($"^.{{0,{ul}}}$")
+    | Some ll, Some ul -> System.Text.RegularExpressions.Regex($"^.{{{ll},{ul}}}$")
+
+
+type ErrorMessage with
+
+    static member ofIParamCollection error iParamCollection =
+
+        let iParam = Seq.head iParamCollection
+
+        let str = new StringBuilder()    
+        str.AppendFormat("['{0}', ..] {1}\n",  Param.getCvName iParam, error) |> ignore 
+
+        match Param.tryGetValueOfCvParamAttr "FilePath" iParam with
+        | Some path ->
+            str.AppendFormat(" > filePath '{0}'\n", path) |> ignore         
+        | None -> ()
+
+        match Param.tryGetValueOfCvParamAttr "Worksheet" iParam with
+        | Some sheet ->
+            str.AppendFormat(" > sheet '{0}'", sheet) |> ignore         
+        | None -> ()
+
+        match Param.tryGetValueOfCvParamAttr "Row" iParam with
+        | Some row -> 
+            str.AppendFormat(" > row '{0}'", row) |> ignore
+        | None -> ()
+
+        match Param.tryGetValueOfCvParamAttr "Column" iParam with
+        | Some column -> 
+            str.AppendFormat(" > column '{0}'", column) |> ignore
+        | None -> ()        
+
+        match Param.tryGetValueOfCvParamAttr "Line" iParam with
+        | Some line ->
+            str.AppendFormat(" > line '{0}'", line) |> ignore
+        | None -> ()
+
+        match Param.tryGetValueOfCvParamAttr "Position" iParam with
+        | Some position -> 
+            str.AppendFormat(" > position '{0}'", position) |> ignore
+        | None -> ()
+        str.ToString()
+
+
+type Validate.ParamCollection with
+
+    static member AllTermsSatisfyPredicate (projection : #IParam -> bool) (paramCollection : #seq<#IParam>) =
+        match Seq.forall projection paramCollection with
+        | true  -> ()
+        | false ->
+            ErrorMessage.ofIParamCollection $"does not satisfy the requirements" paramCollection
+            |> Expecto.Tests.failtestNoStackf "%s"
+
+
+// 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)
+        }
+
+        // Study has protocol in correct format
+        ARCExpect.validationCase (TestID.Name STDMSO.``Study Metadata``.``STUDY PROTOCOLS``.key.Name) {
+            studyMetadata
+            |> Validate.ParamCollection.ContainsParamWithTerm STDMSO.``Study Metadata``.``STUDY PROTOCOLS``.key
+        }
+
+        // Study protocol is in correct format
+        ARCExpect.validationCase (TestID.Name "STUDY PROTOCOLS description") {
+            studyMetadata|> Seq.filter (fun iparam -> Param.getTerm iparam = STDMSO.``Study Metadata``.``STUDY PROTOCOLS``.``Study Protocol Description``)
+            |> Seq.filter (Param.getValueAsString >> (<>) "Metadata Section Key")
+            |> Seq.iter (Validate.Param.ValueMatchesRegex (characterLimit (Some 50) (Some 500)))
+        }
+
+        // Study has tissue header in process graph
+        ARCExpect.validationCase (TestID.Name "Tissue") {
+            tissueTokens
+            |> Validate.ParamCollection.SatisfiesPredicate (
+                fun iparams ->
+                    iparams
+                    |> List.exists (fun iparam -> iparam.Value = ParamValue.CvValue (CvTerm.create("NCIT:C12801","Tissue","NCIT")))
+            )
+        }
+
+        // Study has tissue values as terms (CvValues)
+        ARCExpect.validationCase (TestID.Name "Tissue terms") {
+            tissueTokens
+            |> Validate.ParamCollection.AllTermsSatisfyPredicate (fun ip -> match ip.Value with CvValue _ -> true | _ -> false)
+        }
+
+        // Study has species in correct format
+        ARCExpect.validationCase (TestID.Name "Organism") {
+            tissueTokens
+            |> Validate.ParamCollection.SatisfiesPredicate (
+                fun iparams ->
+                    iparams
+                    |> List.exists (fun iparam -> iparam.Value = ParamValue.CvValue (CvTerm.create("OBI:0100026","organism","OBI")))
+            )
+        }
+
+        // Study has species values as terms (CvValues)
+        ARCExpect.validationCase (TestID.Name "Organism terms") {
+            tissueTokens
+            |> Validate.ParamCollection.AllTermsSatisfyPredicate (fun ip -> match ip.Value with CvValue _ -> true | _ -> false)
+        }
+
+        // Assay has technology type in correct format
+        ARCExpect.validationCase (TestID.Name techTypeTAN.Name) {
+            assayMetadata
+            |> Validate.ParamCollection.ContainsParamWithTerm techTypeTAN
+        }
+        ARCExpect.validationCase (TestID.Name techTypeName.Name) {
+            assayMetadata
+            |> Validate.ParamCollection.ContainsParamWithTerm techTypeName
+        }
+        ARCExpect.validationCase (TestID.Name techTypeTSR.Name) {
+            assayMetadata
+            |> Validate.ParamCollection.ContainsParamWithTerm techTypeTSR
+        }
+
+        // Assay has instrument model
+        ARCExpect.validationCase (TestID.Name "instrument model") {
+            instrumentTokens
+            |> Validate.ParamCollection.SatisfiesPredicate (
+                fun iparams ->
+                    iparams
+                    |> List.exists (fun iparam -> iparam.Value = ParamValue.CvValue (CvTerm.create("MS:1000031","instrument model","MS")))
+            )
+        }
+
+        // Assay has instrument model in correct format
+        ARCExpect.validationCase (TestID.Name "instrument model terms") {
+            instrumentTokens
+            |> Validate.ParamCollection.AllTermsSatisfyPredicate (fun ip -> match ip.Value with CvValue _ -> true | _ -> false)
+        }
+
+        // Assay has fixed or variable modification in correct format
+        ARCExpect.validationCase (TestID.Name "instrument model") {
+            modTokens
+            |> Validate.ParamCollection.SatisfiesPredicate (
+                fun iparams ->
+                    iparams
+                    |> List.exists (
+                        fun iparam -> 
+                            iparam.Value = ParamValue.CvValue (CvTerm.create("MS:1003021","Fixed modification","MS")) ||
+                            iparam.Value = ParamValue.CvValue (CvTerm.create("MS:1003022","Variable modification","MS"))
+                    )
+            )
+        }
+
+    ]
+
+
+// Execution:
+
+Setup.ValidationPackage(
+    metadata = Setup.Metadata(PACKAGE_METADATA),
+    CriticalValidationCases = [cases]
+)
+|> Execute.ValidationPipeline(
+    basePath = arcDir
+)