add new metadata

nfdi4plants · Feb 29, 2024 · 592dd65 · 592dd65
1 parent 62c5fd2
commit 592dd65
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Showing 5 changed files with 118 additions and 29 deletions.
diff --git a/scripts/domain.fsx b/scripts/domain.fsx
@@ -4,10 +4,17 @@
 
 open System
 open System.IO
+open System.Security.Cryptography
 open YamlDotNet.Serialization
 open System.Text.Json
 // open ARCValidationPackages <-- use this (or ARCtrl) once the data model is stable
 
+[<AutoOpen>]
+module Constants =
+
+    let [<Literal>] STAGING_AREA_RELATIVE_PATH = "src/PackageRegistryService/StagingArea"
+    let [<Literal>] PACKAGE_INDEX_RELATIVE_PATH = "src/PackageRegistryService/Data/arc-validate-package-index.json"
+
 // This is the F# version of /src/PackageRegistryService/Models/ValidationPackageIndex.cs
 // and should be equal to the implementation in arc-validate (until there is a common codebase/domain)
 [<AutoOpen>]
@@ -45,22 +52,51 @@ module Domain =
                 )
             | _ -> false
 
+    type OntologyAnnotation() =
+
+        member val Name = "" with get,set
+        member val TermSourceREF = "" with get,set
+        member val TermAccessionNumber = "" with get,set
+
+        override this.GetHashCode() =
+            hash (
+                this.Name, 
+                this.TermSourceREF, 
+                this.TermAccessionNumber
+            )
+
+        override this.Equals(other) =
+            match other with
+            | :? OntologyAnnotation as oa -> 
+                (
+                    this.Name, 
+                    this.TermSourceREF, 
+                    this.TermAccessionNumber
+                ) = (
+                    oa.Name, 
+                    oa.TermSourceREF, 
+                    oa.TermAccessionNumber
+                )
+            | _ -> false
+
     type ValidationPackageMetadata() =
         // mandatory fields
         member val Name = "" with get,set
+        member val Summary = "" with get,set
         member val Description = "" with get,set
         member val MajorVersion = 0 with get,set
         member val MinorVersion = 0 with get,set
         member val PatchVersion = 0 with get,set
         // optional fields
         member val Publish = false with get,set
         member val Authors: Author [] = Array.empty<Author> with get,set
-        member val Tags: string [] = Array.empty<string> with get,set
+        member val Tags: OntologyAnnotation [] = Array.empty<OntologyAnnotation> with get,set
         member val ReleaseNotes = "" with get,set
 
         override this.GetHashCode() =
             hash (
                 this.Name, 
+                this.Summary, 
                 this.Description, 
                 this.MajorVersion, 
                 this.MinorVersion, 
@@ -76,6 +112,7 @@ module Domain =
             | :? ValidationPackageMetadata as vpm -> 
                 (
                     this.Name, 
+                    this.Summary, 
                     this.Description, 
                     this.MajorVersion, 
                     this.MinorVersion, 
@@ -86,6 +123,7 @@ module Domain =
                     this.ReleaseNotes
                 ) = (
                     vpm.Name, 
+                    vpm.Summary, 
                     vpm.Description, 
                     vpm.MajorVersion, 
                     vpm.MinorVersion, 
@@ -125,7 +163,7 @@ module Domain =
                 metadata: ValidationPackageMetadata
             ) = 
 
-                let md5 = System.Security.Cryptography.MD5.Create()
+                let md5 = MD5.Create()
 
                 ValidationPackageIndex.create(
                     repoPath = repoPath,
@@ -212,11 +250,18 @@ module Utils =
             System.Globalization.CultureInfo.InvariantCulture
         )
 
-module AVPRRepo =
+type AVPRRepo =
 
     ///! Paths are relative to the root of the project, since the script is executed from the repo root in CI
-    let getStagedPackages() = 
-        Directory.GetFiles("src/PackageRegistryService/StagingArea", "*.fsx", SearchOption.AllDirectories)
+    /// Path is adjustable by passing `RepoRoot`
+    static member getStagedPackages(?RepoRoot: string) = 
+
+        let path = 
+            defaultArg 
+                (RepoRoot |> Option.map (fun p -> Path.Combine(p, STAGING_AREA_RELATIVE_PATH))) 
+                STAGING_AREA_RELATIVE_PATH
+
+        Directory.GetFiles(path, "*.fsx", SearchOption.AllDirectories)
         |> Array.map (fun x -> x.Replace('\\',Path.DirectorySeparatorChar).Replace('/',Path.DirectorySeparatorChar))
         |> Array.map (fun p -> 
             ValidationPackageIndex.create(
@@ -226,8 +271,15 @@ module AVPRRepo =
         )
 
     ///! Paths are relative to the root of the project, since the script is executed from the repo root in CI
-    let getIndexedPackages() = 
-        "src/PackageRegistryService/Data/arc-validate-package-index.json"
+    /// Path is adjustable by passing `RepoRoot`
+    static member getIndexedPackages(?RepoRoot: string) = 
+
+        let path = 
+            defaultArg 
+                (RepoRoot |> Option.map (fun p -> Path.Combine(p, PACKAGE_INDEX_RELATIVE_PATH))) 
+                PACKAGE_INDEX_RELATIVE_PATH
+
+        path
         |> File.ReadAllText
         |> JsonSerializer.Deserialize<ValidationPackageIndex[]>
 
diff --git a/src/PackageRegistryService/Data/arc-validate-package-index.json b/src/PackageRegistryService/Data/arc-validate-package-index.json
@@ -2,10 +2,11 @@
   {
     "RepoPath": "src/PackageRegistryService/StagingArea/invenio/invenio@1.0.0.fsx",
     "FileName": "invenio@1.0.0.fsx",
-    "LastUpdated": "2024-02-28T15:39:07+01:00",
-    "ContentHash": "1A3CB3CC0538782C864EA37545451FD5",
+    "LastUpdated": "2024-02-29T14:45:26+01:00",
+    "ContentHash": "864458DA6C7B0F08A546210CFD3CCA4A",
     "Metadata": {
       "Name": "invenio",
+      "Summary": "",
       "Description": "Validates if the ARC contains the necessary metadata to be publishable via Invenio.\nThe following metadata is required:\n    - Investigation has title and description\n    - All persons in Investigation Contacts must have a name, last name, affiliation and valid email\n",
       "MajorVersion": 1,
       "MinorVersion": 0,
@@ -20,8 +21,16 @@
         }
       ],
       "Tags": [
-        "ARC",
-        "data publication"
+        {
+          "Name": "ARC",
+          "TermSourceREF": "",
+          "TermAccessionNumber": ""
+        },
+        {
+          "Name": "data publication",
+          "TermSourceREF": "",
+          "TermAccessionNumber": ""
+        }
       ],
       "ReleaseNotes": "Initial release"
     }
@@ -33,6 +42,7 @@
     "ContentHash": "43BFF4CDCC3F3EBB3CA21B6C1F8AC5BA",
     "Metadata": {
       "Name": "test",
+      "Summary": "",
       "Description": "this package is here for testing purposes only.",
       "MajorVersion": 1,
       "MinorVersion": 0,
@@ -50,6 +60,7 @@
     "ContentHash": "0B9CBA89F1CECFAF5EB0BA1CE6A480FA",
     "Metadata": {
       "Name": "test",
+      "Summary": "",
       "Description": "this package is here for testing purposes only.",
       "MajorVersion": 1,
       "MinorVersion": 0,
@@ -63,10 +74,11 @@
   {
     "RepoPath": "src/PackageRegistryService/StagingArea/test/test@2.0.0.fsx",
     "FileName": "test@2.0.0.fsx",
-    "LastUpdated": "2024-02-28T15:39:07+01:00",
-    "ContentHash": "F819359C06456B62F035F2587FBE1EE2",
+    "LastUpdated": "2024-02-29T14:45:26+01:00",
+    "ContentHash": "40729E451689807AEFF17F5932843A4C",
     "Metadata": {
       "Name": "test",
+      "Summary": "",
       "Description": "this package is here for testing purposes only.",
       "MajorVersion": 2,
       "MinorVersion": 0,
@@ -87,20 +99,33 @@
         }
       ],
       "Tags": [
-        "validation",
-        "my-package",
-        "thing"
+        {
+          "Name": "validation",
+          "TermSourceREF": "",
+          "TermAccessionNumber": ""
+        },
+        {
+          "Name": "my-package",
+          "TermSourceREF": "",
+          "TermAccessionNumber": ""
+        },
+        {
+          "Name": "thing",
+          "TermSourceREF": "",
+          "TermAccessionNumber": ""
+        }
       ],
       "ReleaseNotes": "add authors and tags for further testing"
     }
   },
   {
     "RepoPath": "src/PackageRegistryService/StagingArea/test/test@3.0.0.fsx",
     "FileName": "test@3.0.0.fsx",
-    "LastUpdated": "2024-02-28T15:39:07+01:00",
-    "ContentHash": "9E6AB1A9C908DE02F583D9FD0E76D8FA",
+    "LastUpdated": "2024-02-29T14:45:26+01:00",
+    "ContentHash": "0537642158095CE84F4FA8363225831E",
     "Metadata": {
       "Name": "test",
+      "Summary": "",
       "Description": "this package is here for testing purposes only.",
       "MajorVersion": 3,
       "MinorVersion": 0,
@@ -121,9 +146,21 @@
         }
       ],
       "Tags": [
-        "validation",
-        "my-package",
-        "thing"
+        {
+          "Name": "validation",
+          "TermSourceREF": "",
+          "TermAccessionNumber": ""
+        },
+        {
+          "Name": "my-package",
+          "TermSourceREF": "",
+          "TermAccessionNumber": ""
+        },
+        {
+          "Name": "thing",
+          "TermSourceREF": "",
+          "TermAccessionNumber": ""
+        }
       ],
       "ReleaseNotes": "add authors and tags for further testing"
     }

diff --git a/src/PackageRegistryService/StagingArea/invenio/invenio@1.0.0.fsx b/src/PackageRegistryService/StagingArea/invenio/invenio@1.0.0.fsx
@@ -14,8 +14,8 @@ Authors:
     - FullName: Oliver Maus
       Affiliation: DataPLANT
 Tags:
-    - ARC
-    - data publication
+    - Name: ARC
+    - Name: data publication
 ReleaseNotes: "Initial release"
 ---
 *)

diff --git a/src/PackageRegistryService/StagingArea/test/test@2.0.0.fsx b/src/PackageRegistryService/StagingArea/test/test@2.0.0.fsx
@@ -16,9 +16,9 @@ Authors:
     Affiliation: University of Somewhere
     AffiliationLink: https://somewhere.edu
 Tags:
-  - validation
-  - my-package
-  - thing
+  - Name: validation
+  - Name: my-package
+  - Name: thing
 ReleaseNotes: "add authors and tags for further testing"
 ---
 *)

diff --git a/src/PackageRegistryService/StagingArea/test/test@3.0.0.fsx b/src/PackageRegistryService/StagingArea/test/test@3.0.0.fsx
@@ -16,9 +16,9 @@ Authors:
     Affiliation: University of Somewhere
     AffiliationLink: https://somewhere.edu
 Tags:
-  - validation
-  - my-package
-  - thing
+  - Name: validation
+  - Name: my-package
+  - Name: thing
 ReleaseNotes: "add authors and tags for further testing"
 ---
 *)