Merge branch 'dev' into 'main'

merge dev into main

See merge request !32

src/SQL2Linked/Implementations/ProjectStructuralData.cs

@@ -28,7 +28,9 @@ public class ProjectStructuralData : StructuralData<ProjectAdminDto>
         AssertToGraphUriNode(coscineGraph, RdfUris.CoscinePrefix, RdfUris.DcatCatalog, RdfUris.CoscineProjects);
         AssertToGraphUriNode(coscineGraph, RdfUris.CoscinePrefix, RdfUris.DcatCatalog, RdfUris.CoscineResources);
 
-        yield return coscineGraph; // yeld coscineGraph first
+        yield return coscineGraph; // yield coscineGraph first
+
+        var trellisGraph = PatchGraph.Empty(RdfUris.TrellisGraph);
 
         await foreach (var entry in entries)
         {
@@ -138,14 +140,42 @@ public class ProjectStructuralData : StructuralData<ProjectAdminDto>
                 Console.WriteLine($"For project '{entry.DisplayName}' will migrate triple '{projectGraphName} {RdfUris.DcTermsCreator} {UriHelper.TryCombineUri(RdfUris.CoscineUsers, entry.Creator.Id)}'. ");
             }
 
-
             if (entry.CreationDate is not null && entry.CreationDate.HasValue)
             {
                 AssertToGraphLiteralNode(graph, projectGraphName, RdfUris.DcTermsCreated, entry.CreationDate.Value.ToString(), RdfUris.XsdDateTime);
                 Console.WriteLine($"For project '{entry.DisplayName}' will migrate triple '{projectGraphName} {RdfUris.DcTermsCreated} {entry.CreationDate}'. ");
             }
 
+            // Add data to the trellis graph
+            AssertToGraphUriNode(trellisGraph,
+                    projectGraphName,
+                    RdfUris.A,
+                    RdfUris.LdpBasicContainerClass);
+            AddModifiedDate(trellisGraph, projectGraphName);
+
+            AssertToGraphUriNode(trellisGraph,
+                    projectGraphName,
+                    RdfUris.DcTermsIsPartOf,
+                    RdfUris.CoscineProjectsEntity);
+            AssertToGraphUriNode(trellisGraph,
+                    RdfUris.CoscineProjectsEntity,
+                    RdfUris.A,
+                    RdfUris.LdpBasicContainerClass);
+            AddModifiedDate(trellisGraph, RdfUris.CoscineProjectsEntity);
+
+            AssertToGraphUriNode(trellisGraph,
+                    RdfUris.CoscineProjectsEntity,
+                    RdfUris.DcTermsIsPartOf,
+                    RdfUris.CoscinePrefix);
+            AssertToGraphUriNode(trellisGraph,
+                    RdfUris.CoscinePrefix,
+                    RdfUris.A,
+                    RdfUris.LdpBasicContainerClass);
+            AddModifiedDate(trellisGraph, RdfUris.CoscinePrefix);
+
             yield return graph;
         }
+
+        yield return trellisGraph;
     }
 }
\ No newline at end of file

src/SQL2Linked/Implementations/ResourceStructuralData.cs

@@ -23,6 +23,8 @@ public class ResourceStructuralData : StructuralData<ResourceAdminDto>
         var coscineHandlePrefix = UriHelper.TryCombinePath(RdfUris.HandlePrefix, _pidConfiguration.Prefix)
             ?? throw new Exception("Could not combine handle prefix with PID prefix");
 
+        var trellisGraph = PatchGraph.Empty(RdfUris.TrellisGraph);
+
         await foreach (var entry in entries)
         {
             var resourceGraphName = UriHelper.TryCombineUri(RdfUris.CoscineResources, entry.Id)
@@ -165,7 +167,57 @@ public class ResourceStructuralData : StructuralData<ResourceAdminDto>
                 Console.WriteLine($"For resource '{entry.DisplayName}' will migrate triple '{resourceGraphName} {RdfUris.DcTermsCreated} {entry.DateCreated}'. ");
             }
 
+            // Add data to the trellis graph
+            AssertToGraphUriNode(trellisGraph,
+                    resourceGraphName,
+                    RdfUris.A,
+                    RdfUris.LdpBasicContainerClass);
+            AddModifiedDate(trellisGraph, resourceGraphName);
+
+            AssertToGraphUriNode(trellisGraph,
+                    resourceGraphName,
+                    RdfUris.DcTermsIsPartOf,
+                    RdfUris.CoscineResourcesEntity);
+            AssertToGraphUriNode(trellisGraph,
+                    RdfUris.CoscineResourcesEntity,
+                    RdfUris.A,
+                    RdfUris.LdpBasicContainerClass);
+            AddModifiedDate(trellisGraph, RdfUris.CoscineResourcesEntity);
+
+            AssertToGraphUriNode(trellisGraph,
+                    RdfUris.CoscineResourcesEntity,
+                    RdfUris.DcTermsIsPartOf,
+                    RdfUris.CoscinePrefix);
+            AssertToGraphUriNode(trellisGraph,
+                    RdfUris.CoscinePrefix,
+                    RdfUris.A,
+                    RdfUris.LdpBasicContainerClass);
+            AddModifiedDate(trellisGraph, RdfUris.CoscinePrefix);
+
+            var resourceACLGraphName = UriHelper.TryCombineUri(resourceGraphName, "?ext=acl");
+            var aclGraph = new Graph()
+            {
+                BaseUri = resourceACLGraphName
+            };
+
+            var aclSubjects = graph.GetTriplesWithObject(RdfUris.AclAuthorizationClass).Select((triple) => triple.Subject);
+            foreach (var subject in aclSubjects)
+            {
+                var subjectNode = aclGraph.CreateBlankNode();
+                foreach (var triple in graph.GetTriplesWithSubject(subject))
+                {
+                    aclGraph.Assert(new Triple(
+                        subjectNode,
+                        triple.Predicate,
+                        triple.Object
+                    ));
+                }
+            }
+
             yield return graph;
+            yield return aclGraph;
         }
+
+        yield return trellisGraph;
     }
 }

src/SQL2Linked/StructuralData.cs

@@ -4,7 +4,10 @@ using Coscine.ApiClient.Core.Client;
 using Coscine.ApiClient.Core.Model;
 using Microsoft.Extensions.Configuration;
 using SQL2Linked.Models.ConfigurationModels;
+using SQL2Linked.Utils;
+using System.Globalization;
 using VDS.RDF;
+using VDS.RDF.Parsing;
 
 namespace SQL2Linked;
 
@@ -97,10 +100,25 @@ public abstract class StructuralData<S>
                 var rdfWriter = MimeTypesHelper.GetWriter(format);
                 var content = VDS.RDF.Writing.StringWriter.Write(graph, rdfWriter);
 
+                if (graph is PatchGraph patchGraph)
+                {
+                    var patchOperations = new List<RdfPatchOperationDto>
+                    {
+                        new(RdfPatchOperationType.A, new RdfDefinitionForManipulationDto(content, formatEnum))
+                    };
+
+                    await _adminApi.PatchMetadataAsync(
+                        graph.BaseUri.AbsoluteUri,
+                        new RdfPatchDocumentDto(patchOperations)
+                    );
+                }
+                else
+                {
                     await _adminApi.UpdateMetadataGraphAsync(
                         graph.BaseUri.AbsoluteUri,
                         new MetadataUpdateAdminParameters(new RdfDefinitionForManipulationDto(content, formatEnum))
                     );
+                }
 
                 Console.WriteLine($" - Graph {graph.BaseUri} added successfully");
                 Console.WriteLine();
@@ -115,6 +133,17 @@ public abstract class StructuralData<S>
         }
     }
 
+    public void AddModifiedDate(IGraph graph, Uri rootUri)
+    {
+        AssertToGraphLiteralNode(
+            graph,
+            rootUri,
+            RdfUris.DcTermsModified,
+            DateTime.UtcNow.ToString("o", CultureInfo.InvariantCulture),
+            new Uri(XmlSpecsHelper.XmlSchemaDataTypeDateTime)
+        );
+    }
+
     /// <summary>
     /// Asserts a triple to the graph with a URI node object.
     /// </summary>

src/SQL2Linked/Utils/PatchGraph.cs

+using VDS.RDF;
+
+namespace SQL2Linked.Utils;
+
+/// <summary>
+/// Represents a specialized RDF graph for small-scale updates.
+/// This class extends the standard Graph class with additional
+/// functionalities for tracking changes (assertions and retractions).
+/// </summary>
+/// <remarks><i>TODO: Consider extending <see cref="ITransactionalGraph"/> to allow for rollback and commit operations.</i></remarks>
+public class PatchGraph : Graph
+{
+    public List<Triple> AssertList { get; set; } = new();
+
+    public List<Triple> RetractList { get; set; } = new();
+
+    /// <summary>
+    /// Initializes a new instance of the <see cref="PatchGraph"/> class.
+    /// </summary>
+    public PatchGraph() : base()
+    {
+    }
+
+    /// <summary>
+    /// Initializes a new instance of the <see cref="PatchGraph"/> class.
+    /// </summary>
+    public PatchGraph(Uri graphUri) : base(graphUri)
+    {
+    }
+
+    /// <summary>
+    /// Initializes a new instance of the <see cref="IPatchGraph"/> class with the specified graph URI.
+    /// </summary>
+    /// <param name="graphUri">The base URI for the graph.</param>
+    /// <returns>A new empty instance of <see cref="IPatchGraph"/> with the provided base URI.</returns>
+    public static PatchGraph Empty(Uri graphUri)
+    {
+        return new PatchGraph(graphUri)
+        {
+            BaseUri = graphUri
+        };
+    }
+
+    /// <summary>
+    /// Initializes a new instance of the <see cref="IPatchGraph"/> class with the specified graph URI.
+    /// </summary>
+    /// <param name="graphUri">The base URI for the graph as a string.</param>
+    /// <returns>A new empty instance of <see cref="IPatchGraph"/> with the provided base URI.</returns>
+    public static PatchGraph Empty(string graphUri)
+    {
+        return Empty(new Uri(graphUri));
+    }
+
+    public override bool Assert(Triple t)
+    {
+        AssertList.Add(t);
+        return base.Assert(t);
+    }
+
+    public override bool Assert(IEnumerable<Triple> triples)
+    {
+        AssertList.AddRange(triples);
+        return base.Assert(triples);
+    }
+
+    public override bool Retract(Triple t)
+    {
+        RetractList.Add(t);
+        return base.Retract(t);
+    }
+
+    public override bool Retract(IEnumerable<Triple> triples)
+    {
+        RetractList.AddRange(triples);
+        return base.Retract(triples);
+    }
+}
\ No newline at end of file

src/SQL2Linked/Utils/RdfUris.cs

@@ -29,8 +29,10 @@ public static class RdfUris
     public static readonly Uri CoscineApplicationProfile = new("https://purl.org/coscine/ap/");
     public static readonly Uri CoscineFixedValue = new("https://purl.org/coscine/fixedValue");
     public static readonly Uri CoscineMetadataExtractionVersion = new("https://purl.org/coscine/terms/metatadataextraction#version");
+    public static readonly Uri CoscineProjectsEntity = new("https://purl.org/coscine/projects");
     public static readonly Uri CoscineProjects = new("https://purl.org/coscine/projects/");
     public static readonly Uri CoscineResourceTypes = new("https://purl.org/coscine/resourcetypes/");
+    public static readonly Uri CoscineResourcesEntity = new("https://purl.org/coscine/resources");
     public static readonly Uri CoscineResources = new("https://purl.org/coscine/resources/");
     public static readonly Uri CoscineRoles = new("https://purl.org/coscine/roles/");
     public static readonly Uri CoscineUsers = new("https://purl.org/coscine/users/");