Merge pull request #488 from nfdi4plants/rocrate-fixes

RO-Crate Fixes
nfdi4plants · Jan 23, 2025 · 6f8dac4 · 6f8dac4
2 parents 5af193c + 134caf8
commit 6f8dac4
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Showing 8 changed files with 27 additions and 9 deletions.
diff --git a/src/Json/Assay.fs b/src/Json/Assay.fs
@@ -76,7 +76,7 @@ module Assay =
             | "" -> "#EmptyAssay"
             | i -> 
                 let identifier = i.Replace(" ","_")
-                $"#assay/{identifier}"
+                $"assays/{identifier}/"
 
         let encoder (studyName:string Option) (a : ArcAssay) = 
             let fileName = Identifier.Assay.fileNameFromIdentifier a.Identifier

diff --git a/src/Json/Investigation.fs b/src/Json/Investigation.fs
@@ -108,7 +108,7 @@ module Investigation =
                 Encode.tryInclude "title" Encode.string oa.Title
                 Encode.tryInclude "description" Encode.string oa.Description
                 Encode.tryInclude "submissionDate" Encode.string oa.SubmissionDate
-                Encode.tryInclude "publicReleaseDate" Encode.string oa.PublicReleaseDate
+                "publicReleaseDate", Encode.string (oa.PublicReleaseDate |> (Option.defaultValue (System.DateTime.Today.ToString "yyyy-MM-dd"))) |> Some
                 Encode.tryIncludeSeq "ontologySourceReferences" OntologySourceReference.ROCrate.encoder oa.OntologySourceReferences
                 Encode.tryIncludeSeq "publications" Publication.ROCrate.encoder oa.Publications
                 Encode.tryIncludeSeq "people" Person.ROCrate.encoder oa.Contacts

diff --git a/src/Json/Study.fs b/src/Json/Study.fs
@@ -109,7 +109,7 @@ module Study =
             | "" -> "#EmptyStudy"
             | i -> 
                 let identifier = i.Replace(" ","_")
-                $"#study/{identifier}"
+                $"studies/{identifier}/"
 
         let encoder (assays: ArcAssay list option) (s : ArcStudy) = 
             let fileName = Identifier.Study.tryFileNameFromIdentifier s.Identifier
@@ -129,7 +129,8 @@ module Study =
                 Encode.tryIncludeSeq "publications" Publication.ROCrate.encoder s.Publications
                 Encode.tryIncludeSeq "people" Person.ROCrate.encoder s.Contacts
                 Encode.tryIncludeList "processSequence" (Process.ROCrate.encoder (Some s.Identifier) None) processes
-                Encode.tryIncludeSeq "assays" (Assay.ROCrate.encoder (Some s.Identifier)) assays           
+                Encode.tryIncludeSeq "assays" (Assay.ROCrate.encoder (Some s.Identifier)) assays 
+                Encode.tryIncludeList "dataFiles" Data.ROCrate.encoder (ARCtrl.Process.ProcessSequence.getData processes)        
                 Encode.tryIncludeSeq "comments" Comment.ROCrate.encoder s.Comments
                 "@context", ROCrateContext.Study.context_jsonvalue |> Some
             ]

diff --git a/src/Json/context/rocrate/isa_investigation_context.fs b/src/Json/context/rocrate/isa_investigation_context.fs
@@ -32,7 +32,7 @@ module Investigation =
       "Investigation", Encode.string "sdo:Dataset"
 
       "identifier", Encode.string "sdo:identifier"
-      "title", Encode.string "sdo:headline"
+      "title", Encode.string "sdo:name"
       "additionalType", Encode.string "sdo:additionalType"
       "description", Encode.string "sdo:description"
       "submissionDate", Encode.string "sdo:dateCreated"
@@ -55,7 +55,7 @@ module Investigation =
     "Investigation": "sdo:Dataset",
 
     "identifier" : "sdo:identifier",
-    "title": "sdo:headline",
+    "title": "sdo:name",
     "description": "sdo:description",
     "submissionDate": "sdo:dateCreated",
     "publicReleaseDate": "sdo:datePublished",

diff --git a/src/Json/context/rocrate/isa_study_context.fs b/src/Json/context/rocrate/isa_study_context.fs
@@ -49,6 +49,7 @@ module Study =
       "publications", Encode.string "sdo:citation"
       "people", Encode.string "sdo:creator"
       "assays", Encode.string "sdo:hasPart"
+      "dataFiles",Encode.string "sdo:hasPart"
       "filename", Encode.string "sdo:alternateName"
       "comments", Encode.string "sdo:comment"
       "processSequence", Encode.string "sdo:about"

diff --git a/src/Json/context/rocrate/rocrate_context.fs b/src/Json/context/rocrate/rocrate_context.fs
@@ -27,5 +27,5 @@ module ROCrate =
       "CreativeWork", Encode.string "sdo:CreativeWork"
 
       "about", Encode.string "sdo:about"
-      "conformsTo", Encode.string "sdo:conformsTo"
+      "conformsTo", Encode.string "http://purl.org/dc/terms/conformsTo"
     ]
diff --git a/tests/Json/Investigation.Tests.fs b/tests/Json/Investigation.Tests.fs
@@ -88,14 +88,29 @@ let private test_isaEmpty =
         compareFields
 
 let private test_roCrateEmpty =
+    let removePublicationDate (inv : ArcInvestigation) =
+        inv.PublicReleaseDate <- None
+        inv
     createBaseJsonTests
         "ROCrate-empty"
         create_empty
         ArcInvestigation.toROCrateJsonString
-        ArcInvestigation.fromROCrateJsonString
+        (ArcInvestigation.fromROCrateJsonString >> removePublicationDate)
         None
         compareFields
 
+let test_defaultDate = testList "ROCrate-defaultDate" [
+    testCase "roundabout" <| fun _ ->
+        let addPublicationDate (inv : ArcInvestigation) =
+            inv.PublicReleaseDate <- Some (System.DateTime.Today.ToString "yyyy-MM-dd")
+            inv
+        let obj = create_empty()
+        let json = ArcInvestigation.toROCrateJsonString () obj
+        let res = ArcInvestigation.fromROCrateJsonString json
+        let inv = obj |> addPublicationDate
+        Expect.equal inv res ""
+]
+
 let private test_core =
     createBaseJsonTests
         "core"
@@ -147,4 +162,5 @@ let main = testList "Investigation" [
     test_isa
     test_roCrateEmpty
     test_roCrate
+    test_defaultDate
 ]
diff --git a/tests/TestingUtils/TestObjects.Json/Study.fs b/tests/TestingUtils/TestObjects.Json/Study.fs
@@ -3,7 +3,7 @@
 let studyWithIDTable =
     """
     {
-        "@id": "#study/Study1",
+        "@id": "studies/Study1/",
         "filename" : "studies/Study1/isa.study.xlsx",
         "identifier" : "Study1",
         "protocols" : [