add docs

Rdmp.Core/Curation/Data/Datasets/DatasetProviderConfiguration.cs

@@ -10,6 +10,7 @@
 
 namespace Rdmp.Core.Curation.Data.Datasets;
 
+/// <inheritdoc/>
 public class DatasetProviderConfiguration : DatabaseEntity, IDatasetProviderConfiguration
 {
 

Rdmp.Core/Curation/Data/Datasets/IDatasetProviderConfiguration.cs

@@ -1,20 +1,36 @@
-using Org.BouncyCastle.Bcpg.OpenPgp;
-using System;
-using System.Collections.Generic;
-using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
+using Rdmp.Core.MapsDirectlyToDatabaseTable;
 
 namespace Rdmp.Core.Curation.Data.Datasets;
 
-public interface IDatasetProviderConfiguration
+
+/// <summary>
+/// Remords configuration for accessing external dataset providers, such as PURE
+/// </summary>
+public interface IDatasetProviderConfiguration: IMapsDirectlyToDatabaseTable
 {
+    /// <summary>
+    /// The assembly name of the provider this configuration is used for
+    /// </summary>
     public string Type { get; }
+
+    /// <summary>
+    /// A friendly name for the configuration
+    /// </summary>
     public string Name { get; }
+
+    /// <summary>
+    /// The API url
+    /// </summary>
     public string Url { get; }
 
+    /// <summary>
+    /// Reference to which credentials should be used to access the API
+    /// </summary>
     public int DataAccessCredentials_ID { get; }
 
+    /// <summary>
+    /// The organisation ID to use with the remote provider
+    /// </summary>
     public string Organisation_ID { get; }
 
 

Rdmp.Core/DataLoad/Modules/Mutilators/PostLoad/PureDatasetPostLoadUpdater.cs

@@ -10,6 +10,7 @@
 using Rdmp.Core.DataLoad.Engine.Mutilators;
 using Rdmp.Core.DataLoad.Triggers;
 using Rdmp.Core.Datasets;
+using Rdmp.Core.Datasets.PureItems;
 using Rdmp.Core.MapsDirectlyToDatabaseTable;
 using Rdmp.Core.QueryBuilding;
 using Rdmp.Core.ReusableLibraryCode.Checks;
@@ -25,6 +26,10 @@
 
 namespace Rdmp.Core.DataLoad.Modules.Mutilators.PostLoad
 {
+    /// <summary>
+    /// Used to update a Pure dataset with updated temporal data to include the new records
+    /// and update the description of the dataset
+    /// </summary>
     public class PureDatasetPostLoadUpdater : IMutilateDataTables
     {
         private readonly string _type = typeof(PureDatasetProvider).ToString();
@@ -97,7 +102,7 @@ public ExitCodeType Mutilate(IDataLoadJob job)
 
             var dt = new DataTable();
             dt.BeginLoadData();
-            var server = catalogue.GetDistinctLiveDatabaseServer(ReusableLibraryCode.DataAccess.DataAccessContext.DataLoad,false);
+            var server = catalogue.GetDistinctLiveDatabaseServer(ReusableLibraryCode.DataAccess.DataAccessContext.DataLoad, false);
             var con = server.GetConnection();
             con.Open();
             using (var cmd = server.GetCommand(sql, con))
@@ -106,7 +111,7 @@ public ExitCodeType Mutilate(IDataLoadJob job)
                 da.Fill(dt);
             }
             dt.EndLoadData();
-            if (dt.Rows.Count ==0) return ExitCodeType.OperationNotRequired;
+            if (dt.Rows.Count == 0) return ExitCodeType.OperationNotRequired;
             _newRecordsCount = dt.Rows.Count;
             _earliestDate = new PureDate(dt.AsEnumerable().Min(row => DateTime.Parse(row[0].ToString())));
             _latestDate = new PureDate(dt.AsEnumerable().Max(row => DateTime.Parse(row[0].ToString())));
@@ -130,10 +135,10 @@ public ExitCodeType Mutilate(IDataLoadJob job)
         private TemporalCoveragePeriod GetTemporalCoveragePeriod()
         {
             var coverage = _pureDataset.TemporalCoveragePeriod ?? new TemporalCoveragePeriod();
-            if(_pureDataset.TemporalCoveragePeriod is null || _pureDataset.TemporalCoveragePeriod.StartDate is null || _earliestDate.IsBefore(_pureDataset.TemporalCoveragePeriod.StartDate))
+            if (_pureDataset.TemporalCoveragePeriod is null || _pureDataset.TemporalCoveragePeriod.StartDate is null || _earliestDate.IsBefore(_pureDataset.TemporalCoveragePeriod.StartDate))
                 coverage.StartDate = _earliestDate;
 
-            if(_pureDataset.TemporalCoveragePeriod is null ||  _pureDataset.TemporalCoveragePeriod.EndDate is null || _pureDataset.TemporalCoveragePeriod.EndDate.IsBefore(_latestDate))
+            if (_pureDataset.TemporalCoveragePeriod is null || _pureDataset.TemporalCoveragePeriod.EndDate is null || _pureDataset.TemporalCoveragePeriod.EndDate.IsBefore(_latestDate))
                 coverage.EndDate = _latestDate;
             return coverage;
         }
@@ -150,7 +155,7 @@ private List<PureDescription> GetDescriptions()
             var datasetDescriptionTerm = "/dk/atira/pure/dataset/descriptions/datasetdescription";
             foreach (var description in _pureDataset.Descriptions.Where(d => d.Term.URI == datasetDescriptionTerm))
             {
-                description.Value.en_GB += @$"
+                description.Value.En_GB += @$"
 {GetUpdateText()}";
                 descriptions.Add(description);
             }

Rdmp.Core/Datasets/DatasetConfigurationUICommon.cs

@@ -6,7 +6,7 @@
 
 using Rdmp.Core.CommandExecution;
 
-namespace Rdmp.Core.Dataset;
+namespace Rdmp.Core.Datasets;
 
 /// <summary>
 /// Common methods used by Cohort Builder UI implementations.  Eliminates

Rdmp.Core/Datasets/IDatasetProvider.cs

@@ -1,17 +1,25 @@
 using Rdmp.Core.Curation.Data.Datasets;
-using System;
 using System.Collections.Generic;
-using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
 
 namespace Rdmp.Core.Datasets;
-
+/// <summary>
+/// Base interface for dataset providers to impliment
+/// </summary>
 public interface IDatasetProvider
 {
 
-    List<Curation.Data.Datasets.Dataset> FetchDatasets();
+    /// <summary>
+    /// Fetch known datasets
+    /// </summary>
+    /// <returns></returns>
+    List<Dataset> FetchDatasets();
+
 
-    Curation.Data.Datasets.Dataset FetchDatasetByID(int id);
+    /// <summary>
+    /// Fetch a specific dataset by its ID
+    /// </summary>
+    /// <param name="id"></param>
+    /// <returns></returns>
+    Dataset FetchDatasetByID(int id);
 
 }

Rdmp.Core/Datasets/InternalDatasetProvider.cs

@@ -1,12 +1,12 @@
 using Rdmp.Core.CommandExecution;
-using System;
 using System.Collections.Generic;
 using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
 
 namespace Rdmp.Core.Datasets;
 
+/// <summary>
+/// Provider for internal datasets
+/// </summary>
 public class InternalDatasetProvider : IDatasetProvider
 {
     private readonly IBasicActivateItems _activator;
@@ -15,11 +15,13 @@ public InternalDatasetProvider(IBasicActivateItems activator)
         _activator = activator;
     }
 
+    /// <inheritdoc/>
     public Curation.Data.Datasets.Dataset FetchDatasetByID(int id)
     {
         return _activator.RepositoryLocator.CatalogueRepository.GetAllObjectsWhere<Curation.Data.Datasets.Dataset>("ID", id).FirstOrDefault();
     }
 
+    /// <inheritdoc/>
     public List<Curation.Data.Datasets.Dataset> FetchDatasets()
     {
         return _activator.RepositoryLocator.CatalogueRepository.GetAllObjects<Curation.Data.Datasets.Dataset>().ToList();

Rdmp.Core/Datasets/PluginDataset.cs

@@ -1,12 +1,12 @@
-using System;
-using System.Collections.Generic;
-using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
+using Rdmp.Core.Curation.Data.Datasets;
+
 
 namespace Rdmp.Core.Datasets
 {
-    public class PluginDataset: Curation.Data.Datasets.Dataset
+    /// <summary>
+    /// Base class to allow all plugin dataset types to be based off
+    /// </summary>
+    public class PluginDataset: Dataset
     {
 
         public PluginDataset() { }

Rdmp.Core/Datasets/PureDataset.cs

@@ -1,140 +1,21 @@
-using Amazon.Auth.AccessControlPolicy.ActionIdentifiers;
-using NPOI.SS.Formula.Atp;
-using NPOI.SS.Formula.Functions;
-using SynthEHR;
+// Copyright (c) The University of Dundee 2024-2024
+// This file is part of the Research Data Management Platform (RDMP).
+// RDMP is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+// RDMP is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+// You should have received a copy of the GNU General Public License along with RDMP. If not, see <https://www.gnu.org/licenses/>.
+
+
+using Rdmp.Core.Datasets.PureItems;
 using System;
 using System.Collections.Generic;
 using System.Text.Json.Serialization;
 
 namespace Rdmp.Core.Datasets;
 #nullable enable
 
-public class ENGBWrapper
-{
-    public ENGBWrapper(string? text) { en_GB = text; }
-    public string? en_GB { get; set; }
-}
-
-public class URITerm
-{
-    public URITerm(string? uri, ENGBWrapper enGBWrapper)
-    {
-        URI = uri;
-        term = enGBWrapper;
-    }
-    public string? URI { get; set; }
-    public ENGBWrapper term { get; set; }
-}
-public class PureDescription
-{
-    public int? PureId { get; set; }
-    public ENGBWrapper? Value { get; set; }
-
-    public URITerm Term { get => new URITerm("/dk/atira/pure/dataset/descriptions/datasetdescription", new ENGBWrapper("Description")); }
-}
-
-public class Name()
-{
-    public string? FirstName { get; set; }
-    public string? LastName { get; set; }
-}
-
-public class PurePerson
-{
-    public string? TypeDiscriminator { get; set; }
-    public int? PureId { get; set; }
-
-    public Name? Name { get; set; }
-    public URITerm? Role { get; set; }
-
-    public List<PureSystem>? Organizations { get; set; }
-}
-
-public class PureDate
-{
-    public PureDate(DateTime dateTime)
-    {
-        Year = dateTime.Year;
-        Month = dateTime.Month;
-        Day = dateTime.Day;
-    }
-
-    public PureDate() { }
-
-
-    public DateTime ToDateTime()
-    {
-        return new DateTime(Year, Month??1, Day??1, 0, 0, 0);
-    }
-
-    public bool IsBefore(PureDate date)
-    {
-        if (Year < date.Year) return true;
-        if (Year == date.Year)
-        {
-            if (Month < date.Month) return true;
-            if (Month == date.Month)
-            {
-                return Day < date.Day;
-            }
-        }
-
-        return false;
-    }
-
-    public PureDate(int year, int? month = null, int? day = null)
-    {
-        Year = year;
-        if (month != null) Month = month;
-        if (day != null) Day = day;
-    }
-    public int Year { get; set; }
-    public int? Month { get; set; }
-    public int? Day { get; set; }
-}
-
-public class Visibility
-{
-    public Visibility(string? key, ENGBWrapper description)
-    {
-        Key = key;
-        Description = description;
-    }
-    public string? Key { get; set; }
-    public ENGBWrapper Description { get; set; }
-}
-
-public class Workflow
-{
-    public string? Step { get; set; }
-    public ENGBWrapper? Description { get; set; }
-}
-
-public class Geolocation
-{
-    public ENGBWrapper? GeographicalCoverage { get; set; }
-    public string? Point { get; set; }
-
-    public string? Polygon { get; set; }
-}
-
-public class TemporalCoveragePeriod
-{
-    public PureDate? StartDate { get; set; }
-    public PureDate? EndDate { get; set; }
-}
-
-public class PureSystem
-{
-    public PureSystem(string? uuid, string? systemName)
-    {
-        UUID = uuid;
-        SystemName = systemName;
-    }
-    public string? SystemName { get; set; }
-    public string? UUID { get; set; }
-}
-
+/// <summary>
+/// Used for mapping Pure datasets from the API into a C# object.
+/// </summary>
 public class PureDataset : PluginDataset
 {
     [JsonIgnore(Condition = JsonIgnoreCondition.WhenWritingNull)]