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working empty investigation metadata test
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@kMutagene
kMutagene committed Aug 1, 2023
1 parent f062e66 commit 59f52e4
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4 changes: 2 additions & 2 deletions src/ArcGraphModel/structural_ontologies/investigation_metadata_structural_ontology.obo
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Expand Up @@ -76,14 +76,14 @@ def: ""
relationship: part_of INVMSO:00000007 ! INVESTIGATION

[Term]
id: INVMSO:0000013
id: INVMSO:00000013
name: INVESTIGATION PUBLICATIONS
def: ""
relationship: part_of INVMSO:00000001 ! Investigation Metadata

[Term]
id: INVMSO:00000014
name: Investigation PubMed ID
name: Investigation Publication PubMed ID
def: ""
relationship: part_of INVMSO:0000014 ! INVESTIGATION PUBLICATIONS

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4 changes: 2 additions & 2 deletions src/ArcGraphModel/structural_ontologies/investigation_metadata_structural_ontology.yml
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Expand Up @@ -76,14 +76,14 @@ def: ""
relationship: part_of INVMSO:00000007 ! INVESTIGATION

[Term]
id: INVMSO:0000013
id: INVMSO:00000013
name: INVESTIGATION PUBLICATIONS
def: ""
relationship: part_of INVMSO:00000001 ! Investigation Metadata

[Term]
id: INVMSO:00000014
name: Investigation PubMed ID
name: Investigation Publication PubMed ID
def: ""
relationship: part_of INVMSO:0000014 ! INVESTIGATION PUBLICATIONS

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7 changes: 5 additions & 2 deletions tests/ArcGraphModel.Tests/ArcGraphModel.Tests.fsproj
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Expand Up @@ -10,8 +10,11 @@
<None Include="Fixtures\**" CopyToOutputDirectory="Always" />
<Compile Include="TestUtils.fs" />
<Compile Include="TestObjects.fs" />
<Compile Include="IntegrationTests\Assay.fs" />
<Compile Include="IntegrationTests\ParseInvestigationTests.fs" />
<Compile Include="IntegrationTests\StudyMetadata.fs" />
<Compile Include="IntegrationTests\StudyAnnotationTable.fs" />
<Compile Include="IntegrationTests\AssayMetadata.fs" />
<Compile Include="IntegrationTests\AssayAnnotationTable.fs" />
<Compile Include="IntegrationTests\InvestigationMetadata.fs" />
<Compile Include="Program.fs" />
</ItemGroup>

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Binary file added tests/ArcGraphModel.Tests/Fixtures/incorrect/investigation_empty.xlsx
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0 ...raphModel.Tests/IntegrationTests/Assay.fs → .../IntegrationTests/AssayAnnotationTable.fs
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17 changes: 17 additions & 0 deletions tests/ArcGraphModel.Tests/IntegrationTests/AssayMetadata.fs
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module IntegrationTests.AssayMetadata

open ControlledVocabulary
open FsSpreadsheet
open FsSpreadsheet.ExcelIO
open ArcGraphModel
open Xunit

open TestUtils



let allExpectedMetadataTerms =

Terms.AssayMetadata.cvTerms
|> List.skip 1 //(ignore root term)
|> List.map (fun p -> CvParam(p, ParamValue.Value "", []))
124 changes: 124 additions & 0 deletions tests/ArcGraphModel.Tests/IntegrationTests/InvestigationMetadata.fs
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module IntegrationTests.InvestigationMetadata

open ControlledVocabulary
open FsSpreadsheet
open FsSpreadsheet.ExcelIO
open ArcGraphModel
open Xunit

open TestUtils

let parsedInvestigationMetadata = Investigation.parseMetadataSheetfromXlsxFile "Fixtures/incorrect/investigation_empty.xlsx"

let allExpectedMetadataTerms =
// maybe we want to not rely on parsed obo? i think we can.
//[
// CvParam(("INVMSO:00000002","ONTOLOGY SOURCE REFERENCE", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000003","Term Source Name", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000004","Term Source File", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000005","Term Source Version", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000006","Term Source Description", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000007","INVESTIGATION", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000008","Investigation Identifier", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000009","Investigation Title", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000010","Investigation Description", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000011","Investigation Submission Date", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000012","Investigation Public Release Date", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000013","INVESTIGATION PUBLICATIONS", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000014","Investigation Publication PubMed ID", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000015","Investigation Publication DOI", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000016","Investigation Publication Author List", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000017","Investigation Publication Title", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000018","Investigation Publication Status", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000019","Investigation Publication Status Term Accession Number", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000020","Investigation Publication Status Term Source REF", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000021","INVESTIGATION CONTACTS", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000022","Investigation Person Last Name", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000023","Investigation Person First Name", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000024","Investigation Person Mid Initials", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000025","Investigation Person Email", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000026","Investigation Person Phone", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000027","Investigation Person Fax", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000028","Investigation Person Address", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000029","Investigation Person Affiliation", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000030","Investigation Person Roles", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000031","Investigation Person Roles Term Accession Number", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000032","Investigation Person Roles Term Source REF", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000033","STUDY", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000034","Study Identifier", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000035","Study Title", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000036","Study Description", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000037","Study Submission Date", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000038","Study Public Release Date", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000039","Study File Name", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000040","STUDY DESIGN DESCRIPTORS", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000041","Study Design Type", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000042","Study Design Type Term Accession Number", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000043","Study Design Type Term Source REF", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000044","STUDY PUBLICATIONS", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000045","Study Publication PubMed ID", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000046","Study Publication DOI", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000047","Study Publication Author List", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000048","Study Publication Title", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000049","Study Publication Status", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000050","Study Publication Status Term Accession Number", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000051","Study Publication Status Term Source REF", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000052","STUDY FACTORS", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000053","Study Factor Name", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000054","Study Factor Type", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000055","Study Factor Type Term Accession Number", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000056","Study Factor Type Term Source REF", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000057","STUDY ASSAYS", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000058","Study Assay Measurement Type", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000059","Study Assay Measurement Type Term Accession Number", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000060","Study Assay Measurement Type Term Source REF", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000061","Study Assay Technology Type", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000062","Study Assay Technology Type Term Accession Number", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000063","Study Assay Technology Type Term Source REF", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000064","Study Assay Technology Platform", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000065","Study Assay File Name", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000066","STUDY PROTOCOLS", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000067","Study Protocol Name", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000068","Study Protocol Type", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000069","Study Protocol Type Term Accession Number", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000070","Study Protocol Type Term Source REF", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000071","Study Protocol Description", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000072","Study Protocol URI", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000073","Study Protocol Version", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000074","Study Protocol Parameters Name", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000075","Study Protocol Parameters Term Accession Number", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000076","Study Protocol Parameters Term Source REF", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000077","Study Protocol Components Name", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000078","Study Protocol Components Type", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000079","Study Protocol Components Type Term Accession Number", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000080","Study Protocol Components Type Term Source REF", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000081","STUDY CONTACTS", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000082","Study Person Last Name", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000083","Study Person First Name", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000084","Study Person Mid Initials", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000085","Study Person Email", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000086","Study Person Phone", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000087","Study Person Fax", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000088","Study Person Address", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000089","Study Person Affiliation", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000090","Study Person Roles", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000091","Study Person Roles Term Accession Number", "INVMSO"), ParamValue.Value "", [])
// CvParam(("INVMSO:00000092","Study Person Roles Term Source REF", "INVMSO"), ParamValue.Value "", [])
//]
Terms.InvestigationMetadata.cvTerms
|> List.skip 1 //(ignore root term)
|> List.map (fun p -> CvParam(p, ParamValue.Value "", []))

[<Fact>]
let ``First Param is CvParam`` () =
Assert.True (parsedInvestigationMetadata.Head |> CvParam.tryCvParam).IsSome

[<Fact>]
let ``First CvParam`` () = CvParam.structuralEquality (parsedInvestigationMetadata.Head :?> CvParam) allExpectedMetadataTerms[0]

[<Fact>]
let ``Empty investigation is parsed with all structural ontology terms in order`` () =
Assert.All((List.zip allExpectedMetadataTerms parsedInvestigationMetadata), (fun (expected,actual) ->
CvParam.structuralEquality (expected) (actual :?> CvParam)
))

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