Migrate API to use AVPRIndex lib, add custom migration

nfdi4plants · Feb 29, 2024 · ee0ee58 · ee0ee58
1 parent 592dd65
commit ee0ee58
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Showing 14 changed files with 381 additions and 18 deletions.
diff --git a/src/AVPRIndex/AVPRIndex.fsproj b/src/AVPRIndex/AVPRIndex.fsproj
@@ -5,7 +5,23 @@
     <GenerateDocumentationFile>true</GenerateDocumentationFile>
   </PropertyGroup>
 
+  <PropertyGroup>
+    <Authors>Kevin Schneider</Authors>
+    <Description>Type system for the indexing backend of avpr.nfdi4plants.org</Description>
+    <Summary>Type system for the indexing backend of avpr.nfdi4plants.org</Summary>
+    <PackageLicenseExpression>MIT</PackageLicenseExpression>
+    <PackageTags>C# F# ARC annotated-research-context rdm research-data-management validation</PackageTags>
+    <PackageProjectUrl>https://github.com/nfdi4plants/arc-validate-package-registry</PackageProjectUrl>
+    <RepositoryUrl>https://github.com/nfdi4plants/arc-validate-package-registry</RepositoryUrl>
+    <RepositoryType>git</RepositoryType>
+    <PackageReleaseNotes>$([System.IO.File]::ReadAllText("$(MSBuildProjectDirectory)/RELEASE_NOTES.md"))</PackageReleaseNotes>
+    <PackageReadmeFile>README.md</PackageReadmeFile>
+    <PackageVersion>0.0.1</PackageVersion>
+  </PropertyGroup>
+
   <ItemGroup>
+    <None Include="README.md" Pack="true" PackagePath="\"/>
+    <None Include="RELEASE_NOTES.md" />
     <Compile Include="Globals.fs" />
     <Compile Include="Domain.fs" />
     <Compile Include="Utils.fs" />

diff --git a/src/AVPRIndex/Domain.fs b/src/AVPRIndex/Domain.fs
@@ -39,22 +39,51 @@ 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, 
@@ -70,6 +99,7 @@ module Domain =
             | :? ValidationPackageMetadata as vpm -> 
                 (
                     this.Name, 
+                    this.Summary, 
                     this.Description, 
                     this.MajorVersion, 
                     this.MinorVersion, 
@@ -80,6 +110,7 @@ module Domain =
                     this.ReleaseNotes
                 ) = (
                     vpm.Name, 
+                    vpm.Summary, 
                     vpm.Description, 
                     vpm.MajorVersion, 
                     vpm.MinorVersion, 

diff --git a/src/AVPRIndex/README.md b/src/AVPRIndex/README.md
@@ -0,0 +1,5 @@
+# AVPR Index
+
+Type system for the indexing backend of https://avpr.nfdi4plants.org.
+
+This lib exposes the type system and utilities needed to parse and index arc validation packages with yaml frontmatter.
diff --git a/src/AVPRIndex/RELEASE_NOTES.md b/src/AVPRIndex/RELEASE_NOTES.md
@@ -0,0 +1,3 @@
+## v0.0.1
+
+- Initial release for AVPR API v1
diff --git a/src/PackageRegistryService/Data/DataInitializer.cs b/src/PackageRegistryService/Data/DataInitializer.cs
@@ -10,15 +10,15 @@
 using static AVPRIndex.Frontmatter;
 
 namespace PackageRegistryService.Data
-
+    
 {
     public class DataInitializer
     {
         public static List<ValidationPackageIndex> ReadIndex()
         {
             var json = File.ReadAllText(@"Data/arc-validate-package-index.json");
             var index = JsonSerializer.Deserialize<List<ValidationPackageIndex>>(json);
-            return index;
+            return index ?? [];
         }
         public static void SeedData(ValidationPackageDb context)
         {
@@ -39,6 +39,7 @@ public static void SeedData(ValidationPackageDb context)
                             return new ValidationPackage
                             {
                                 Name = i.Metadata.Name,
+                                Summary = i.Metadata.Summary,
                                 Description = i.Metadata.Description,
                                 MajorVersion = i.Metadata.MajorVersion,
                                 MinorVersion = i.Metadata.MinorVersion,

diff --git a/src/PackageRegistryService/Data/arc-validate-package-index.json b/src/PackageRegistryService/Data/arc-validate-package-index.json
@@ -2,7 +2,7 @@
   {
     "RepoPath": "src/PackageRegistryService/StagingArea/invenio/invenio@1.0.0.fsx",
     "FileName": "invenio@1.0.0.fsx",
-    "LastUpdated": "2024-02-29T14:45:26+01:00",
+    "LastUpdated": "2024-02-29T14:45:24+01:00",
     "ContentHash": "864458DA6C7B0F08A546210CFD3CCA4A",
     "Metadata": {
       "Name": "invenio",
@@ -74,7 +74,7 @@
   {
     "RepoPath": "src/PackageRegistryService/StagingArea/test/test@2.0.0.fsx",
     "FileName": "test@2.0.0.fsx",
-    "LastUpdated": "2024-02-29T14:45:26+01:00",
+    "LastUpdated": "2024-02-29T14:45:24+01:00",
     "ContentHash": "40729E451689807AEFF17F5932843A4C",
     "Metadata": {
       "Name": "test",
@@ -121,7 +121,7 @@
   {
     "RepoPath": "src/PackageRegistryService/StagingArea/test/test@3.0.0.fsx",
     "FileName": "test@3.0.0.fsx",
-    "LastUpdated": "2024-02-29T14:45:26+01:00",
+    "LastUpdated": "2024-02-29T14:45:24+01:00",
     "ContentHash": "0537642158095CE84F4FA8363225831E",
     "Metadata": {
       "Name": "test",

diff --git a/src/PackageRegistryService/Migrations/20240229124121_AddSummaryAndOntologyTags.Designer.cs b/src/PackageRegistryService/Migrations/20240229124121_AddSummaryAndOntologyTags.Designer.cs