Refactor namespaces, add Globals namespace with default strings

nfdi4plants · Jan 10, 2024 · 4d84f7f · 4d84f7f
1 parent ce71ac4
commit 4d84f7f
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Showing 8 changed files with 261 additions and 119 deletions.
diff --git a/src/ARCTokenization/ARCTokenization.fsproj b/src/ARCTokenization/ARCTokenization.fsproj
@@ -33,6 +33,7 @@
     <None Include="structural_ontologies/investigation_metadata_structural_ontology.yml" />
     <None Include="structural_ontologies/study_metadata_structural_ontology.yml" />
     <None Include="structural_ontologies/assay_metadata_structural_ontology.yml" />
+    <Compile Include="Globals.fs" />
     <Compile Include="Address.fs" />
     <Compile Include="Terms.fs" />
     <Compile Include="Regex.fs" />
@@ -43,7 +44,6 @@
     <Compile Include="Worksheet.fs" />
     <Compile Include="FileSystem.fs" />
     <Compile Include="TopLevelParsers.fs" />
-    <Compile Include="ParamBasedParsers.fs" />
     <Compile Include="ARCMock.fs" />
   </ItemGroup>
 

diff --git a/src/ARCTokenization/Globals.fs b/src/ARCTokenization/Globals.fs
@@ -0,0 +1,15 @@
+module Globals
+
+open ARCtrl
+open ARCtrl.ISA
+
+let [<Literal>] INVESTIGATION_FILE_NAME = Path.InvestigationFileName
+let [<Literal>] INVESTIGATION_METADATA_SHEET_NAME = ARCtrl.ISA.Spreadsheet.ArcInvestigation.metaDataSheetName
+
+let [<Literal>] STUDY_FILE_NAME = Path.StudyFileName
+let [<Literal>] STUDY_METADATA_SHEET_NAME = ARCtrl.ISA.Spreadsheet.ArcStudy.metaDataSheetName
+let [<Literal>] STUDY_OBSOLETE_METADATA_SHEET_NAME= ARCtrl.ISA.Spreadsheet.ArcStudy.obsoleteMetaDataSheetName
+
+let [<Literal>] ASSAY_FILE_NAME = Path.AssayFileName
+let [<Literal>] ASSAY_METADATA_SHEET_NAME = ARCtrl.ISA.Spreadsheet.ArcAssay.metaDataSheetName
+let [<Literal>] ASSAY_OBSOLETE_METADATA_SHEET_NAME = ARCtrl.ISA.Spreadsheet.ArcAssay.obsoleteMetaDataSheetName
diff --git a/src/ARCTokenization/ParamBasedParsers.fs b/src/ARCTokenization/ParamBasedParsers.fs
diff --git a/src/ARCTokenization/TopLevelParsers.fs b/src/ARCTokenization/TopLevelParsers.fs
diff --git a/src/ARCTokenization/Workbook.fs b/src/ARCTokenization/Workbook.fs
@@ -9,7 +9,7 @@ module Workbook =
 
     let getInvestigationMetadataSheet (useLastSheetOnIncorrectName: bool) investigation =
         try
-            FsWorkbook.getWorksheetByName "isa_investigation" investigation
+            FsWorkbook.getWorksheetByName Globals.INVESTIGATION_METADATA_SHEET_NAME investigation
         with _ ->
             if useLastSheetOnIncorrectName then
                 FsWorkbook.getWorksheets investigation
@@ -19,22 +19,22 @@ module Workbook =
 
     let getStudyMetadataSheet (useLastSheetOnIncorrectName: bool) study =
         try
-            FsWorkbook.tryGetWorksheetByName "Study" study
-            |> Option.defaultValue (FsWorkbook.getWorksheetByName "isa_study" study)
+            FsWorkbook.tryGetWorksheetByName Globals.STUDY_OBSOLETE_METADATA_SHEET_NAME study
+            |> Option.defaultValue (FsWorkbook.getWorksheetByName Globals.STUDY_METADATA_SHEET_NAME study)
         with _ ->
             if useLastSheetOnIncorrectName then
                 FsWorkbook.getWorksheets study
                 |> Seq.last
             else
-                failwith "No worksheet named 'Study' or 'isa_study' found in the workbook"
+                failwith $"No worksheet named {Globals.STUDY_OBSOLETE_METADATA_SHEET_NAME} or {Globals.STUDY_METADATA_SHEET_NAME} found in the workbook"
 
     let getAssayMetadataSheet (useLastSheetOnIncorrectName: bool) assay =
         try
-            FsWorkbook.tryGetWorksheetByName "Assay" assay
-            |> Option.defaultValue (FsWorkbook.getWorksheetByName "isa_assay" assay)
+            FsWorkbook.tryGetWorksheetByName Globals.ASSAY_OBSOLETE_METADATA_SHEET_NAME assay
+            |> Option.defaultValue (FsWorkbook.getWorksheetByName Globals.ASSAY_METADATA_SHEET_NAME assay)
         with _ ->
             if useLastSheetOnIncorrectName then
                 FsWorkbook.getWorksheets assay
                 |> Seq.last
             else
-                failwith "No worksheet named 'Assay' or 'isa_assay' found in the workbook"
+                failwith $"No worksheet named {Globals.ASSAY_OBSOLETE_METADATA_SHEET_NAME} or {Globals.ASSAY_METADATA_SHEET_NAME} found in the workbook"
diff --git a/tests/ARCTokenization.Tests/IntegrationTests/AssayMetadata.fs b/tests/ARCTokenization.Tests/IntegrationTests/AssayMetadata.fs
@@ -33,7 +33,12 @@ module AssayMetadata =
     [<Fact>]
     let ``Simple study is parsed from filepath CvParam with all structural ontology terms in order`` () =
         let fakePath = CvParam(cvTerm = AFSO.``File Path``, v = "Fixtures/correct/assay_simple.xlsx")
-        let actual = ParamBasedParsers.parseIsaMetadataSheetFromCvp "assay_simple.xlsx" Assay.parseMetadataSheetFromFile [fakePath] |> Seq.head
+        let actual = 
+            [fakePath]
+            |> Assay.parseMetadataSheetsFromTokens(
+                FileName = "assay_simple.xlsx"
+            ) 
+            |> Seq.head
         Assert.All((List.zip allExpectedMetadataTermsFull actual), (fun (expected,actual) ->
             CvParam.structuralEquality (expected) (actual :?> CvParam)
         ))
diff --git a/tests/ARCTokenization.Tests/IntegrationTests/InvestigationMetadata.fs b/tests/ARCTokenization.Tests/IntegrationTests/InvestigationMetadata.fs
@@ -10,8 +10,8 @@ module InvestigationMetadata =
 
     open TestUtils
 
-    let parsedInvestigationMetadataEmpty = Investigation.parseMetadataSheetFromFile "Fixtures/incorrect/investigation_empty.xlsx"
-    let parsedInvestigationMetadataSimple = Investigation.parseMetadataSheetFromFile "Fixtures/correct/investigation_simple.xlsx"
+    let parsedInvestigationMetadataEmpty = Investigation.parseMetadataSheetFromFile() "Fixtures/incorrect/investigation_empty.xlsx"
+    let parsedInvestigationMetadataSimple = Investigation.parseMetadataSheetFromFile() "Fixtures/correct/investigation_simple.xlsx"
 
     let allExpectedMetadataTermsEmpty = 
         Terms.InvestigationMetadata.nonObsoleteNonRootCvTerms
@@ -62,7 +62,13 @@ module InvestigationMetadata =
     [<Fact>]
     let ``Simple investigation is parsed from filepath CvParam with all structural ontology terms in order`` () =
         let fakePath = CvParam(cvTerm = AFSO.``File Path``, v = "Fixtures/correct/investigation_simple.xlsx")
-        let actual = ParamBasedParsers.parseIsaMetadataSheetFromCvp "investigation_simple.xlsx" Investigation.parseMetadataSheetFromFile [fakePath] |> Seq.head
+        let actual = 
+            [fakePath]
+            |> Investigation.parseMetadataSheetsFromTokens(
+                FileName = "investigation_simple.xlsx"
+            ) 
+            |> Seq.head
+
         Assert.All((List.zip allExpectedMetadataTermsFull actual), (fun (expected,actual) ->
             CvParam.structuralEquality (expected) (actual :?> CvParam)
         ))
diff --git a/tests/ARCTokenization.Tests/IntegrationTests/StudyMetadata.fs b/tests/ARCTokenization.Tests/IntegrationTests/StudyMetadata.fs
@@ -28,7 +28,12 @@ module StudyMetadata =
     [<Fact>]
     let ``Simple study is parsed from filepath CvParam with all structural ontology terms in order`` () =
         let fakePath = CvParam(cvTerm = AFSO.``File Path``, v = "Fixtures/correct/study_simple.xlsx")
-        let actual = ParamBasedParsers.parseIsaMetadataSheetFromCvp "study_simple.xlsx" Study.parseMetadataSheetfromFile [fakePath] |> Seq.head
+        let actual = 
+            [fakePath]
+            |> Study.parseMetadataSheetsFromTokens(
+                FileName = "study_simple.xlsx"
+            ) 
+            |> Seq.head
         Assert.All((List.zip allExpectedMetadataTermsFull actual), (fun (expected,actual) ->
             CvParam.structuralEquality (expected) (actual :?> CvParam)
         ))