From f7c9d33ad4c0be416e21eab59343a08010bc0a0e Mon Sep 17 00:00:00 2001
From: omaus <omaus@bio.uni-kl.de>
Date: Tue, 19 Nov 2024 15:26:33 +0100
Subject: [PATCH 1/9] Make validation check for non-emptiness

Addresses #5.
PRIDE package bumped to v1.0.4.
---
 validation_packages/pride/pride@1.0.4.fsx | 384 ++++++++++++++++++++++
 1 file changed, 384 insertions(+)
 create mode 100644 validation_packages/pride/pride@1.0.4.fsx

diff --git a/validation_packages/pride/pride@1.0.4.fsx b/validation_packages/pride/pride@1.0.4.fsx
new file mode 100644
index 0000000..7e44127
--- /dev/null
+++ b/validation_packages/pride/pride@1.0.4.fsx
@@ -0,0 +1,384 @@
+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, tissue & species in correct format
+        - Assay has protocol, technology type, instrument model, and fixed and/or variable modification in correct format
+MajorVersion: 1
+MinorVersion: 0
+PatchVersion: 4
+Publish: true
+Authors:
+  - FullName: Oliver Maus
+    Affiliation: DataPLANT
+  - FullName: Christopher Lux
+    Email: lux@csbiology.de
+    Affiliation: RPTU Kaiserslautern
+    AffiliationLink: http://rptu.de/startseite
+Tags:
+  - Name: validation
+  - Name: pride
+  - Name: proteomics
+ReleaseNotes: |
+  - Bug fix: Fixed/variable modification values must not be empty
+---
+*)"""
+
+
+#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()
+let arcDir = @"C:\Repos\nfdi4plants\arc-validation-packages\tests\fixtures\testARC_proteomicsCorrect"
+
+
+// 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 modification","MS")) ||
+            cvpList.Head |> Param.getValueAsTerm = (CvTerm.create("MS:1003022","Variable modification","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 -> RegularExpressions.Regex(@"^.{0,}$")
+    | Some ll, None -> RegularExpressions.Regex($"^.{{{ll},}}$")
+    | None, Some ul -> RegularExpressions.Regex($"^.{{0,{ul}}}$")
+    | Some ll, Some ul -> RegularExpressions.Regex($"^.{{{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 investigationCases = 
+    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)
+        }
+
+        // Investigation hast Keywords comment
+        //ARCExpect.validationCase (TestID.Name $"{INVMSO.``Investigation Metadata``.INVESTIGATION.key}.Keywords exists") {
+        //    investigationMetadata
+        //    //|> Validate.ParamCollection.ContainsNonKeyParamWithTerm INVMSO.``Investigation Metadata``.``INVESTIGATION CONTACTS``.``Investigation Person Last Name``
+        //    |> Validate.ParamCollection.ContainsParamWithTerm (CvTerm.create "Keywords")
+        //}
+    ]
+
+let studyCases =
+    testList STDMSO.``Study Metadata``.STUDY.key.Name [
+        // 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") {
+            organismTokens
+            |> 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)
+        }
+    ]
+
+let assayCases =
+    testList ASSMSO.``Assay Metadata``.ASSAY.key.Name [
+        // Assay has protocol
+        //ARCExpect.validationCase (TestID.Name techTypeTAN.Name) {
+        //    assayMetadata
+        //    |> Validate.ParamCollection.ContainsParamWithTerm techTypeTAN
+        //}
+
+        // Assay has protocol in correct format
+        //ARCExpect.validationCase (TestID.Name "ASSAY PROTOCOLS description") {
+        //    assayMetadata
+        //    |> Seq.filter (fun iparam -> Param.getTerm iparam = techTypeTAN)
+        //    |> Seq.filter (Param.getValueAsString >> (<>) "Metadata Section Key")
+        //    |> Seq.iter (Validate.Param.ValueMatchesRegex (characterLimit (Some 50) (Some 500)))
+        //}
+
+        // 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
+        ARCExpect.validationCase (TestID.Name "modification") {
+            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"))
+                    )
+            )
+        }
+
+        // Assay has fixed or variable modification and values are not empty
+        ARCExpect.validationCase (TestID.Name "modification values") {
+            modTokens
+            |> Validate.ParamCollection.SatisfiesPredicate (
+                fun iparams ->
+                    iparams
+                    |> List.forall (
+                        fun iparam -> 
+                            iparam.Value 
+                            |> ParamValue.getValueAsString
+                            <> System.String.Empty
+                    )
+            )
+        }
+    ]
+
+
+// Execution:
+
+Setup.ValidationPackage(
+    metadata = Setup.Metadata(PACKAGE_METADATA),
+    CriticalValidationCases = [investigationCases; studyCases; assayCases]
+)
+|> Execute.ValidationPipeline(
+    basePath = arcDir
+)
\ No newline at end of file

From c569de280259eaeeeb307c8f69aedf51deca197b Mon Sep 17 00:00:00 2001
From: omaus <omaus@bio.uni-kl.de>
Date: Wed, 20 Nov 2024 12:20:10 +0100
Subject: [PATCH 2/9] Add test ARC with modifications missing

---
 .../assays/.gitkeep                             |   0
 .../assays/testAssayOther/README.md             |   0
 .../assays/testAssayOther/dataset/.gitkeep      |   0
 .../assays/testAssayOther/isa.assay.xlsx        | Bin 0 -> 6894 bytes
 .../assays/testAssayOther/protocols/.gitkeep    |   0
 .../assays/testAssayPRIDE/README.md             |   0
 .../assays/testAssayPRIDE/dataset/.gitkeep      |   0
 .../assays/testAssayPRIDE/isa.assay.xlsx        | Bin 0 -> 11419 bytes
 .../assays/testAssayPRIDE/protocols/.gitkeep    |   0
 .../isa.investigation.xlsx                      | Bin 0 -> 7169 bytes
 .../runs/.gitkeep                               |   0
 .../studies/.gitkeep                            |   0
 .../studies/testStudyOther/README.md            |   0
 .../studies/testStudyOther/isa.study.xlsx       | Bin 0 -> 7516 bytes
 .../studies/testStudyOther/protocols/.gitkeep   |   0
 .../studies/testStudyOther/resources/.gitkeep   |   0
 .../studies/testStudyPRIDE/README.md            |   0
 .../studies/testStudyPRIDE/isa.study.xlsx       | Bin 0 -> 9702 bytes
 .../studies/testStudyPRIDE/protocols/.gitkeep   |   0
 .../studies/testStudyPRIDE/resources/.gitkeep   |   0
 .../workflows/.gitkeep                          |   0
 21 files changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/assays/.gitkeep
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayOther/README.md
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayOther/dataset/.gitkeep
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayOther/isa.assay.xlsx
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayOther/protocols/.gitkeep
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayPRIDE/README.md
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayPRIDE/dataset/.gitkeep
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayPRIDE/isa.assay.xlsx
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayPRIDE/protocols/.gitkeep
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/isa.investigation.xlsx
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/runs/.gitkeep
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/studies/.gitkeep
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyOther/README.md
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyOther/isa.study.xlsx
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyOther/protocols/.gitkeep
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyOther/resources/.gitkeep
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyPRIDE/README.md
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyPRIDE/isa.study.xlsx
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyPRIDE/protocols/.gitkeep
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyPRIDE/resources/.gitkeep
 create mode 100644 tests/fixtures/testARC_proteomicsModifValueMissing/workflows/.gitkeep

diff --git a/tests/fixtures/testARC_proteomicsModifValueMissing/assays/.gitkeep b/tests/fixtures/testARC_proteomicsModifValueMissing/assays/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayOther/README.md b/tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayOther/README.md
new file mode 100644
index 0000000..e69de29
diff --git a/tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayOther/dataset/.gitkeep b/tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayOther/dataset/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayOther/isa.assay.xlsx b/tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayOther/isa.assay.xlsx
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new file mode 100644
index 0000000..e69de29
diff --git a/tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayPRIDE/README.md b/tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayPRIDE/README.md
new file mode 100644
index 0000000..e69de29
diff --git a/tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayPRIDE/dataset/.gitkeep b/tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayPRIDE/dataset/.gitkeep
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diff --git a/tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayPRIDE/protocols/.gitkeep b/tests/fixtures/testARC_proteomicsModifValueMissing/assays/testAssayPRIDE/protocols/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/tests/fixtures/testARC_proteomicsModifValueMissing/isa.investigation.xlsx b/tests/fixtures/testARC_proteomicsModifValueMissing/isa.investigation.xlsx
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diff --git a/tests/fixtures/testARC_proteomicsModifValueMissing/studies/.gitkeep b/tests/fixtures/testARC_proteomicsModifValueMissing/studies/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyOther/README.md b/tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyOther/README.md
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diff --git a/tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyOther/isa.study.xlsx b/tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyOther/isa.study.xlsx
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index 0000000..e69de29
diff --git a/tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyOther/resources/.gitkeep b/tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyOther/resources/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyPRIDE/README.md b/tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyPRIDE/README.md
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index 0000000..e69de29
diff --git a/tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyPRIDE/isa.study.xlsx b/tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyPRIDE/isa.study.xlsx
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diff --git a/tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyPRIDE/protocols/.gitkeep b/tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyPRIDE/protocols/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyPRIDE/resources/.gitkeep b/tests/fixtures/testARC_proteomicsModifValueMissing/studies/testStudyPRIDE/resources/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/tests/fixtures/testARC_proteomicsModifValueMissing/workflows/.gitkeep b/tests/fixtures/testARC_proteomicsModifValueMissing/workflows/.gitkeep
new file mode 100644
index 0000000..e69de29

From af37cbbafcbfdee47fae1997d8ab51ab966ec981 Mon Sep 17 00:00:00 2001
From: omaus <omaus@bio.uni-kl.de>
Date: Wed, 20 Nov 2024 12:20:52 +0100
Subject: [PATCH 3/9] Update old packages' tests structure

---
 tests/invenio@3.0.0.fs | 26 +++++++++++++-------------
 tests/pride@1.0.3.fs   |  6 +++---
 2 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/tests/invenio@3.0.0.fs b/tests/invenio@3.0.0.fs
index a01d8da..d0c17e6 100644
--- a/tests/invenio@3.0.0.fs
+++ b/tests/invenio@3.0.0.fs
@@ -1,4 +1,4 @@
-module invenio
+module invenio_3_0_0
 
 
 open ValidationPackages.Tests
@@ -75,8 +75,8 @@ type ArcPrototype() =
 
     [<Fact>]
     member this.``validation_summary JSON is equal`` () =
-        Assert.Equal(ReferenceObjects.invenio.ArcPrototype.validationResultCritical, this.Fixture.ArcExpectValidationResult.Critical)
-        Assert.Equal(ReferenceObjects.invenio.ArcPrototype.validationResultNonCritical, this.Fixture.ArcExpectValidationResult.NonCritical)
+        Assert.Equal(ReferenceObjects.invenio.``3_0_0``.ArcPrototype.validationResultCritical, this.Fixture.ArcExpectValidationResult.Critical)
+        Assert.Equal(ReferenceObjects.invenio.``3_0_0``.ArcPrototype.validationResultNonCritical, this.Fixture.ArcExpectValidationResult.NonCritical)
 
     [<Fact>]
     member this.``validation_report XML is equal`` () =
@@ -102,8 +102,8 @@ type testARC_empty() =
 
     [<Fact>]
     member this.``validation_summary JSON is equal`` () =
-        Assert.Equal(ReferenceObjects.invenio.testARC_empty.validationResultCritical, this.Fixture.ArcExpectValidationResult.Critical)
-        Assert.Equal(ReferenceObjects.invenio.testARC_empty.validationResultNonCritical, this.Fixture.ArcExpectValidationResult.NonCritical)
+        Assert.Equal(ReferenceObjects.invenio.``3_0_0``.testARC_empty.validationResultCritical, this.Fixture.ArcExpectValidationResult.Critical)
+        Assert.Equal(ReferenceObjects.invenio.``3_0_0``.testARC_empty.validationResultNonCritical, this.Fixture.ArcExpectValidationResult.NonCritical)
 
     [<Fact>]
     member this.``validation_report XML is equal`` () =
@@ -129,8 +129,8 @@ type testARC_emptyContactsColumn() =
 
     [<Fact>]
     member this.``validation_summary JSON is equal`` () =
-        Assert.Equal(ReferenceObjects.invenio.testARC_emptyContactsColumn.validationResultCritical, this.Fixture.ArcExpectValidationResult.Critical)
-        Assert.Equal(ReferenceObjects.invenio.testARC_emptyContactsColumn.validationResultNonCritical, this.Fixture.ArcExpectValidationResult.NonCritical)
+        Assert.Equal(ReferenceObjects.invenio.``3_0_0``.testARC_emptyContactsColumn.validationResultCritical, this.Fixture.ArcExpectValidationResult.Critical)
+        Assert.Equal(ReferenceObjects.invenio.``3_0_0``.testARC_emptyContactsColumn.validationResultNonCritical, this.Fixture.ArcExpectValidationResult.NonCritical)
 
     [<Fact>]
     member this.``validation_report XML is equal`` () =
@@ -156,8 +156,8 @@ type testARC_shiftedContactsCells() =
 
     [<Fact>]
     member this.``validation_summary JSON is equal`` () =
-        Assert.Equal(ReferenceObjects.invenio.testARC_shiftedContactsCells.validationResultCritical, this.Fixture.ArcExpectValidationResult.Critical)
-        Assert.Equal(ReferenceObjects.invenio.testARC_shiftedContactsCells.validationResultNonCritical, this.Fixture.ArcExpectValidationResult.NonCritical)
+        Assert.Equal(ReferenceObjects.invenio.``3_0_0``.testARC_shiftedContactsCells.validationResultCritical, this.Fixture.ArcExpectValidationResult.Critical)
+        Assert.Equal(ReferenceObjects.invenio.``3_0_0``.testARC_shiftedContactsCells.validationResultNonCritical, this.Fixture.ArcExpectValidationResult.NonCritical)
 
     [<Fact>]
     member this.``validation_report XML is equal`` () =
@@ -183,8 +183,8 @@ type testARC_shiftedTitleCell() =
 
     [<Fact>]
     member this.``validation_summary JSON is equal`` () =
-        Assert.Equal(ReferenceObjects.invenio.testARC_shiftedTitleCell.validationResultCritical, this.Fixture.ArcExpectValidationResult.Critical)
-        Assert.Equal(ReferenceObjects.invenio.testARC_shiftedTitleCell.validationResultNonCritical, this.Fixture.ArcExpectValidationResult.NonCritical)
+        Assert.Equal(ReferenceObjects.invenio.``3_0_0``.testARC_shiftedTitleCell.validationResultCritical, this.Fixture.ArcExpectValidationResult.Critical)
+        Assert.Equal(ReferenceObjects.invenio.``3_0_0``.testARC_shiftedTitleCell.validationResultNonCritical, this.Fixture.ArcExpectValidationResult.NonCritical)
 
     [<Fact>]
     member this.``validation_report XML is equal`` () =
@@ -210,8 +210,8 @@ type testARC_wrongEmail() =
 
     [<Fact>]
     member this.``validation_summary JSON is equal`` () =
-        Assert.Equal(ReferenceObjects.invenio.testARC_wrongEmail.validationResultCritical, this.Fixture.ArcExpectValidationResult.Critical)
-        Assert.Equal(ReferenceObjects.invenio.testARC_wrongEmail.validationResultNonCritical, this.Fixture.ArcExpectValidationResult.NonCritical)
+        Assert.Equal(ReferenceObjects.invenio.``3_0_0``.testARC_wrongEmail.validationResultCritical, this.Fixture.ArcExpectValidationResult.Critical)
+        Assert.Equal(ReferenceObjects.invenio.``3_0_0``.testARC_wrongEmail.validationResultNonCritical, this.Fixture.ArcExpectValidationResult.NonCritical)
 
     [<Fact>]
     member this.``validation_report XML is equal`` () =
diff --git a/tests/pride@1.0.3.fs b/tests/pride@1.0.3.fs
index 70f8148..f104120 100644
--- a/tests/pride@1.0.3.fs
+++ b/tests/pride@1.0.3.fs
@@ -1,4 +1,4 @@
-module pride
+module pride_1_0_3
 
 
 open ValidationPackages.Tests
@@ -53,8 +53,8 @@ type testARC_proteomicsCorrect() =
 
     [<Fact>]
     member this.``validation_summary JSON is equal`` () =
-        Assert.Equal(ReferenceObjects.pride.testARC_proteomicsCorrect.validationResultCritical, this.Fixture.ArcExpectValidationResult.Critical)
-        Assert.Equal(ReferenceObjects.pride.testARC_proteomicsCorrect.validationResultNonCritical, this.Fixture.ArcExpectValidationResult.NonCritical)
+        Assert.Equal(ReferenceObjects.pride.``1_0_3``.testARC_proteomicsCorrect.validationResultCritical, this.Fixture.ArcExpectValidationResult.Critical)
+        Assert.Equal(ReferenceObjects.pride.``1_0_3``.testARC_proteomicsCorrect.validationResultNonCritical, this.Fixture.ArcExpectValidationResult.NonCritical)
 
     [<Fact>]
     member this.``validation_report XML is equal`` () =

From 3b9f2ecccbbcc26c34b41ee2e1525979aca6422c Mon Sep 17 00:00:00 2001
From: omaus <omaus@bio.uni-kl.de>
Date: Wed, 20 Nov 2024 12:21:15 +0100
Subject: [PATCH 4/9] Add validation report for correct proteomics ARC

---
 .../validation_report.xml                     | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 tests/fixtures/validationReport/pride/1.0.4/testARC_proteomicsCorrect/validation_report.xml

diff --git a/tests/fixtures/validationReport/pride/1.0.4/testARC_proteomicsCorrect/validation_report.xml b/tests/fixtures/validationReport/pride/1.0.4/testARC_proteomicsCorrect/validation_report.xml
new file mode 100644
index 0000000..bbe287f
--- /dev/null
+++ b/tests/fixtures/validationReport/pride/1.0.4/testARC_proteomicsCorrect/validation_report.xml
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="utf-8"?>
+<testsuites>
+    <testsuite name="fsi">
+        <testcase name="[ Critical; INVESTIGATION; Investigation Title ]" time="0.003" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Description ]" time="0.003" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Person First Name exists ]" time="0.003" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Person First Name is not empty ]" time="0.003" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Person Last Name exists ]" time="0.003" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Person Last Name is not empty ]" time="0.003" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Person Affiliation exists ]" time="0.003" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Person Affiliation is not empty ]" time="0.003" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Person Email ]" time="0.001" />
+        <testcase name="[ Critical; STUDY; STUDY PROTOCOLS ]" time="0.001" />
+        <testcase name="[ Critical; STUDY; STUDY PROTOCOLS description ]" time="0.001" />
+        <testcase name="[ Critical; STUDY; Tissue ]" time="0.001" />
+        <testcase name="[ Critical; STUDY; Organism ]" time="0.001" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Person Email exists ]" time="0.000" />
+        <testcase name="[ Critical; STUDY; Tissue terms ]" time="0.000" />
+        <testcase name="[ Critical; STUDY; Organism terms ]" time="0.000" />
+        <testcase name="[ Critical; ASSAY; Assay Technology Type Term Accession Number ]" time="0.000" />
+        <testcase name="[ Critical; ASSAY; Assay Technology Type ]" time="0.000" />
+        <testcase name="[ Critical; ASSAY; Assay Technology Type Term Source REF ]" time="0.000" />
+        <testcase name="[ Critical; ASSAY; instrument model ]" time="0.000" />
+        <testcase name="[ Critical; ASSAY; instrument model terms ]" time="0.000" />
+        <testcase name="[ Critical; ASSAY; modification ]" time="0.000" />
+    </testsuite>
+</testsuites>
\ No newline at end of file

From decd846f89739423f66db682689a3c6a3a659b2c Mon Sep 17 00:00:00 2001
From: omaus <omaus@bio.uni-kl.de>
Date: Wed, 20 Nov 2024 12:21:36 +0100
Subject: [PATCH 5/9] Add unit tests for PRIDE 1.0.4 (WIP)

---
 tests/ValidationPackages.Tests.fsproj |  1 +
 tests/pride@1.0.4.fs                  | 88 +++++++++++++++++++++++++++
 2 files changed, 89 insertions(+)
 create mode 100644 tests/pride@1.0.4.fs

diff --git a/tests/ValidationPackages.Tests.fsproj b/tests/ValidationPackages.Tests.fsproj
index 783fa50..a7b13b0 100644
--- a/tests/ValidationPackages.Tests.fsproj
+++ b/tests/ValidationPackages.Tests.fsproj
@@ -17,6 +17,7 @@
     <Compile Include="GitSubmodulesTests.fs" />
     <Compile Include="invenio%403.0.0.fs" />
     <Compile Include="pride%401.0.3.fs" />
+    <Compile Include="pride%401.0.4.fs" />
     <Compile Include="Program.fs" />
   </ItemGroup>
 
diff --git a/tests/pride@1.0.4.fs b/tests/pride@1.0.4.fs
new file mode 100644
index 0000000..0a75b4f
--- /dev/null
+++ b/tests/pride@1.0.4.fs
@@ -0,0 +1,88 @@
+module pride_1_0_4
+
+
+open ValidationPackages.Tests
+open TestUtils
+
+open Xunit
+open ARCExpect
+
+open System.IO
+open System
+
+
+type BaseTool_Fixture(scriptName : string, version : string, arcfolder : string) =
+
+    let result = runTool "dotnet" [|"fsi"; $"../../validation_packages/{scriptName}/{scriptName}@{version}.fsx"|] $"fixtures/{arcfolder}"
+
+    let arcExpectValidationResult = ARCExpect.ValidationSummary.fromJson (File.ReadAllText $"fixtures/{arcfolder}/.arc-validate-results/{scriptName}@{version}/validation_summary.json")
+
+    let jUnitResult = JUnitResults.fromJUnitFile $"fixtures/{arcfolder}/.arc-validate-results/{scriptName}@{version}/validation_report.xml"
+
+    let jUnitExpected = JUnitResults.fromJUnitFile $"fixtures/validationReport/{scriptName}/{version}/{arcfolder}/validation_report.xml"
+
+    interface IDisposable with
+        override this.Dispose() =
+            Directory.Delete($"fixtures/{arcfolder}/.arc-validate-results/{scriptName}@{version}/", true)
+
+    member this.Result = result
+
+    member this.ArcExpectValidationResult = arcExpectValidationResult
+
+    member this.JUnitResult = jUnitResult
+
+    member this.JUnitExpected = jUnitExpected
+
+
+type testARC_proteomicsCorrect_Fixture() =
+
+    inherit BaseTool_Fixture("pride", "1.0.4", "testARC_proteomicsCorrect")
+
+
+type testARC_proteomicsCorrect() =
+
+    let tool_fixture = new testARC_proteomicsCorrect_Fixture()
+
+    interface IClassFixture<testARC_proteomicsCorrect_Fixture>
+
+    member this.Fixture with get() = tool_fixture
+
+    [<Fact>]
+    member this.``result Exitcode is 0`` () =
+        Assert.Equal(0, this.Fixture.Result.ExitCode)
+
+    [<Fact>]
+    member this.``validation_summary JSON is equal`` () =
+        Assert.Equal(ReferenceObjects.pride.``1_0_4``.testARC_proteomicsCorrect.validationResultCritical, this.Fixture.ArcExpectValidationResult.Critical)
+        Assert.Equal(ReferenceObjects.pride.``1_0_4``.testARC_proteomicsCorrect.validationResultNonCritical, this.Fixture.ArcExpectValidationResult.NonCritical)
+
+    [<Fact>]
+    member this.``validation_report XML is equal`` () =
+        Assert.Equal(this.Fixture.JUnitExpected, this.Fixture.JUnitResult)
+
+
+type testARC_proteomicsModifValueMissing_Fixture() =
+
+    inherit BaseTool_Fixture("pride", "1.0.4", "testARC_proteomicsCorrect")
+
+
+type testARC_proteomicsModifValueMissing() =
+
+    let tool_fixture = new testARC_proteomicsModifValueMissing_Fixture()
+
+    interface IClassFixture<testARC_proteomicsModifValueMissing_Fixture>
+
+    member this.Fixture with get() = tool_fixture
+
+    [<Fact>]
+    member this.``result Exitcode is 0`` () =
+        Assert.Equal(0, this.Fixture.Result.ExitCode)
+
+    [<Fact>]
+    member this.``validation_summary JSON is equal`` () =
+        Assert.Equal(ReferenceObjects.pride.``1_0_4``.testARC_proteomicsCorrect.validationResultCritical, this.Fixture.ArcExpectValidationResult.Critical)
+        Assert.Equal(ReferenceObjects.pride.``1_0_4``.testARC_proteomicsCorrect.validationResultNonCritical, this.Fixture.ArcExpectValidationResult.NonCritical)
+
+    [<Fact>]
+    member this.``validation_report XML is equal`` () =
+        Assert.Equal(this.Fixture.JUnitExpected, this.Fixture.JUnitResult)
\ No newline at end of file

From 5ab2f26efc77a4db7cd5e5744e4758bd35317a6b Mon Sep 17 00:00:00 2001
From: omaus <omaus@bio.uni-kl.de>
Date: Wed, 20 Nov 2024 12:21:44 +0100
Subject: [PATCH 6/9] Update ref objects accordingly

---
 tests/ReferenceObjects.fs | 94 ++++++++++++++++++++++++---------------
 1 file changed, 59 insertions(+), 35 deletions(-)

diff --git a/tests/ReferenceObjects.fs b/tests/ReferenceObjects.fs
index aa09eda..4a08b21 100644
--- a/tests/ReferenceObjects.fs
+++ b/tests/ReferenceObjects.fs
@@ -12,66 +12,90 @@ module General =
 
 module invenio =
 
-    module ArcPrototype =
+    module ``3_0_0`` =
 
-        let validationResultCritical =
-            ValidationResult.create(10,10,0,0)
+        module ArcPrototype =
 
-        let validationResultNonCritical =
-            ValidationResult.create(0,0,0,0)
+            let validationResultCritical =
+                ValidationResult.create(10,10,0,0)
 
+            let validationResultNonCritical =
+                ValidationResult.create(0,0,0,0)
 
-    module testARC_empty =
 
-        let validationResultCritical =
-            ValidationResult.create(10,4,6,0)
+        module testARC_empty =
 
-        let validationResultNonCritical =
-            ValidationResult.create(0,0,0,0)
+            let validationResultCritical =
+                ValidationResult.create(10,4,6,0)
 
+            let validationResultNonCritical =
+                ValidationResult.create(0,0,0,0)
 
-    module testARC_emptyContactsColumn =
 
-        let validationResultCritical =
-            ValidationResult.create(10,6,4,0)
+        module testARC_emptyContactsColumn =
 
-        let validationResultNonCritical =
-            ValidationResult.create(0,0,0,0)
+            let validationResultCritical =
+                ValidationResult.create(10,6,4,0)
 
+            let validationResultNonCritical =
+                ValidationResult.create(0,0,0,0)
 
-    module testARC_shiftedContactsCells =
 
-        let validationResultCritical =
-            ValidationResult.create(10,9,1,0)
+        module testARC_shiftedContactsCells =
 
-        let validationResultNonCritical =
-            ValidationResult.create(0,0,0,0)
+            let validationResultCritical =
+                ValidationResult.create(10,9,1,0)
 
+            let validationResultNonCritical =
+                ValidationResult.create(0,0,0,0)
 
-    module testARC_shiftedTitleCell =
 
-        let validationResultCritical =
-            ValidationResult.create(10,10,0,0)
+        module testARC_shiftedTitleCell =
 
-        let validationResultNonCritical =
-            ValidationResult.create(0,0,0,0)
+            let validationResultCritical =
+                ValidationResult.create(10,10,0,0)
 
+            let validationResultNonCritical =
+                ValidationResult.create(0,0,0,0)
 
-    module testARC_wrongEmail =
 
-        let validationResultCritical =
-            ValidationResult.create(10,9,1,0)
+        module testARC_wrongEmail =
 
-        let validationResultNonCritical =
-            ValidationResult.create(0,0,0,0)
+            let validationResultCritical =
+                ValidationResult.create(10,9,1,0)
+
+            let validationResultNonCritical =
+                ValidationResult.create(0,0,0,0)
 
 
 module pride =
 
-    module testARC_proteomicsCorrect =
+    module ``1_0_3`` =
+
+        module testARC_proteomicsCorrect =
+
+            let validationResultCritical =
+                ValidationResult.create(22,22,0,0)
+
+            let validationResultNonCritical =
+                ValidationResult.create(0,0,0,0)
+
+
+    module ``1_0_4`` =
+
+        module testARC_proteomicsCorrect =
+
+            let validationResultCritical =
+                ValidationResult.create(22,22,0,0)
+
+            let validationResultNonCritical =
+                ValidationResult.create(0,0,0,0)
+
+
+        module testARC_proteomicsModifValueMissing =
 
-        let validationResultCritical =
-            ValidationResult.create(22,22,0,0)
+            let validationResultCritical =
+                ValidationResult.create(22,21,1,0)
 
-        let validationResultNonCritical =
-            ValidationResult.create(0,0,0,0)
\ No newline at end of file
+            let validationResultNonCritical =
+                ValidationResult.create(0,0,0,0)
\ No newline at end of file

From 0ead0660a9bbadb9510d2ccfd1d9ecc627e420bf Mon Sep 17 00:00:00 2001
From: Oliver Maus <oliver.maus@eclipso.de>
Date: Tue, 26 Nov 2024 20:19:30 +0100
Subject: [PATCH 7/9] Modify validation report for correct proteomics test ARC

---
 .../pride/1.0.4/testARC_proteomicsCorrect/validation_report.xml  | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/fixtures/validationReport/pride/1.0.4/testARC_proteomicsCorrect/validation_report.xml b/tests/fixtures/validationReport/pride/1.0.4/testARC_proteomicsCorrect/validation_report.xml
index bbe287f..999e619 100644
--- a/tests/fixtures/validationReport/pride/1.0.4/testARC_proteomicsCorrect/validation_report.xml
+++ b/tests/fixtures/validationReport/pride/1.0.4/testARC_proteomicsCorrect/validation_report.xml
@@ -23,5 +23,6 @@
         <testcase name="[ Critical; ASSAY; instrument model ]" time="0.000" />
         <testcase name="[ Critical; ASSAY; instrument model terms ]" time="0.000" />
         <testcase name="[ Critical; ASSAY; modification ]" time="0.000" />
+        <testcase name="[ Critical; ASSAY; modification values ]" time="0.000" />
     </testsuite>
 </testsuites>
\ No newline at end of file

From 09b01b75e52568ebc3dd741b841d7ba7df2daac1 Mon Sep 17 00:00:00 2001
From: Oliver Maus <oliver.maus@eclipso.de>
Date: Tue, 26 Nov 2024 20:19:50 +0100
Subject: [PATCH 8/9] Add validation report for ARC with modification missing

---
 .../validation_report.xml                     | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 tests/fixtures/validationReport/pride/1.0.4/testARC_proteomicsModifValueMissing/validation_report.xml

diff --git a/tests/fixtures/validationReport/pride/1.0.4/testARC_proteomicsModifValueMissing/validation_report.xml b/tests/fixtures/validationReport/pride/1.0.4/testARC_proteomicsModifValueMissing/validation_report.xml
new file mode 100644
index 0000000..999e619
--- /dev/null
+++ b/tests/fixtures/validationReport/pride/1.0.4/testARC_proteomicsModifValueMissing/validation_report.xml
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="utf-8"?>
+<testsuites>
+    <testsuite name="fsi">
+        <testcase name="[ Critical; INVESTIGATION; Investigation Title ]" time="0.003" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Description ]" time="0.003" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Person First Name exists ]" time="0.003" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Person First Name is not empty ]" time="0.003" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Person Last Name exists ]" time="0.003" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Person Last Name is not empty ]" time="0.003" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Person Affiliation exists ]" time="0.003" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Person Affiliation is not empty ]" time="0.003" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Person Email ]" time="0.001" />
+        <testcase name="[ Critical; STUDY; STUDY PROTOCOLS ]" time="0.001" />
+        <testcase name="[ Critical; STUDY; STUDY PROTOCOLS description ]" time="0.001" />
+        <testcase name="[ Critical; STUDY; Tissue ]" time="0.001" />
+        <testcase name="[ Critical; STUDY; Organism ]" time="0.001" />
+        <testcase name="[ Critical; INVESTIGATION; Investigation Person Email exists ]" time="0.000" />
+        <testcase name="[ Critical; STUDY; Tissue terms ]" time="0.000" />
+        <testcase name="[ Critical; STUDY; Organism terms ]" time="0.000" />
+        <testcase name="[ Critical; ASSAY; Assay Technology Type Term Accession Number ]" time="0.000" />
+        <testcase name="[ Critical; ASSAY; Assay Technology Type ]" time="0.000" />
+        <testcase name="[ Critical; ASSAY; Assay Technology Type Term Source REF ]" time="0.000" />
+        <testcase name="[ Critical; ASSAY; instrument model ]" time="0.000" />
+        <testcase name="[ Critical; ASSAY; instrument model terms ]" time="0.000" />
+        <testcase name="[ Critical; ASSAY; modification ]" time="0.000" />
+        <testcase name="[ Critical; ASSAY; modification values ]" time="0.000" />
+    </testsuite>
+</testsuites>
\ No newline at end of file

From 3249ca6723d99dddc52ea75220882a9a042a722a Mon Sep 17 00:00:00 2001
From: Oliver Maus <oliver.maus@eclipso.de>
Date: Tue, 26 Nov 2024 20:20:12 +0100
Subject: [PATCH 9/9] Update reference objects according to new tests

---
 tests/ReferenceObjects.fs | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/ReferenceObjects.fs b/tests/ReferenceObjects.fs
index 4a08b21..2b77fbd 100644
--- a/tests/ReferenceObjects.fs
+++ b/tests/ReferenceObjects.fs
@@ -86,7 +86,7 @@ module pride =
         module testARC_proteomicsCorrect =
 
             let validationResultCritical =
-                ValidationResult.create(22,22,0,0)
+                ValidationResult.create(23,23,0,0)
 
             let validationResultNonCritical =
                 ValidationResult.create(0,0,0,0)
@@ -95,7 +95,7 @@ module pride =
         module testARC_proteomicsModifValueMissing =
 
             let validationResultCritical =
-                ValidationResult.create(22,21,1,0)
+                ValidationResult.create(23,22,1,0)
 
             let validationResultNonCritical =
                 ValidationResult.create(0,0,0,0)
\ No newline at end of file