12427673626

Committed 20 Dec 2024 07:55AM UTC coverage: 57.448%. Remained the same

Build # 12427673626

Build Type

push

github

Committed by

web-flow

Commit Message

Fix up some codeql/inspection code issues (#2087)

* Update OverviewModel.cs

Fix up some .Dispose/using issues, make finding most recent load ID more efficient

* LINQ tidying

* CodeQL fixups

* Update Catalogue.cs

Add Hashcode, Equals methods.

* Update Catalogue.cs

Tweak equality semantics for RDMP DB oddities

Run Details

11301 of 21223 branches covered (53.25%)

Branch coverage included in aggregate %.

35 of 95 new or added lines in 13 files covered. (36.84%)

5 existing lines in 2 files now uncovered.

32153 of 54417 relevant lines covered (59.09%)

8580.89 hits per line

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0.0

/Rdmp.Core/CommandExecution/AtomicCommands/ExecuteCommandCloneExtractionConfiguration.cs

// Copyright (c) The University of Dundee 2018-2024
// 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 System.Collections.Generic;
using System.Linq;
using Rdmp.Core.Curation.Data;
using Rdmp.Core.DataExport.Data;
using Rdmp.Core.Icons.IconProvision;
using Rdmp.Core.ReusableLibraryCode.Icons.IconProvision;
using SixLabors.ImageSharp;
using SixLabors.ImageSharp.PixelFormats;

namespace Rdmp.Core.CommandExecution.AtomicCommands;

public class ExecuteCommandCloneExtractionConfiguration : BasicCommandExecution
{
    private readonly ExtractionConfiguration _extractionConfiguration;
    private readonly IBasicActivateItems _activeItems;
    private readonly List<IExtractableDataSet> _toRemove = [];
    private readonly List<Catalogue> _toAdd = [];

    private void CheckForDeprecatedCatalogues()
    {
        if (!_extractionConfiguration.SelectedDataSets.Any(static sd => sd.GetCatalogue().IsDeprecated) ||
            !_activeItems.IsInteractive) return;
        if (!YesNo(
                "There are Deprecated catalogues in this Extraction Configuration. Would you like to replace them with their replacement (where available)?",
                "Replace Deprecated Catalogues")) return;

        var repo = _activeItems.RepositoryLocator.CatalogueRepository;
        var deprecatedDatasets = _extractionConfiguration.SelectedDataSets.Where(static sd => sd.GetCatalogue().IsDeprecated).ToList();
        var replacedBy = repo.GetExtendedProperties(ExtendedProperty.ReplacedBy).ToArray();
        foreach (var ds in deprecatedDatasets)
        {
            var replacement = replacedBy.FirstOrDefault(rb => rb.ReferencedObjectID == ds.GetCatalogue().ID);
            if (replacement is null) continue;

            var replacementCatalogue = repo.GetObjectByID<Catalogue>(int.Parse(replacement.Value));
            while (replacementCatalogue.IsDeprecated)
            {
                var replacementCatalogueIsReplacedBy = replacedBy.FirstOrDefault(rb => rb.ReferencedObjectID == replacementCatalogue.ID);
                if (replacementCatalogueIsReplacedBy is not null)
                {
                    //have found further down the tree
                    replacementCatalogue = repo.GetObjectByID<Catalogue>(int.Parse(replacementCatalogueIsReplacedBy.Value));
                }
                else
                {
                    //there is no replacement
                    break;
                }
            }

            _toRemove.Add(ds.ExtractableDataSet);
            _toAdd.Add(replacementCatalogue);
        }
    }

    public ExecuteCommandCloneExtractionConfiguration(IBasicActivateItems activator,
        ExtractionConfiguration extractionConfiguration) : base(activator)
    {
        _extractionConfiguration = extractionConfiguration;
        _activeItems = activator;
        if (!_extractionConfiguration.SelectedDataSets.Any())
            SetImpossible("ExtractionConfiguration does not have any selected datasets");
    }

    public override string GetCommandHelp() =>
        "Creates an exact copy of the Extraction Configuration including the cohort selection, all selected datasets, parameters, filter containers, filters etc";

    public override Image<Rgba32> GetImage(IIconProvider iconProvider) =>
        Image.Load<Rgba32>(CatalogueIcons.CloneExtractionConfiguration);

    public override void Execute()
    {
        base.Execute();
        CheckForDeprecatedCatalogues();

        var clone = _extractionConfiguration.DeepCloneWithNewIDs();
        foreach (var ds in _toRemove.Cast<ExtractableDataSet>())
        {
            clone.RemoveDatasetFromConfiguration(ds);
        }

        foreach (var c in _toAdd)
        {
            //check if the eds already exis
            var eds = _activeItems.RepositoryLocator.DataExportRepository.GetAllObjectsWhere<ExtractableDataSet>("Catalogue_ID", c.ID).FirstOrDefault();
            if (eds is null)
            {
                eds = new ExtractableDataSet(_activeItems.RepositoryLocator.DataExportRepository, c);
                eds.SaveToDatabase();
            }

            clone.AddDatasetToConfiguration(eds);
        }

        Publish((DatabaseEntity)clone.Project);
        Emphasise(clone);
    }
}

1	// Copyright (c) The University of Dundee 2018-2024
2	// This file is part of the Research Data Management Platform (RDMP).
3	// 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.
4	// 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.
5	// You should have received a copy of the GNU General Public License along with RDMP. If not, see <https://www.gnu.org/licenses/>.
6
7	using System.Collections.Generic;
8	using System.Linq;
9	using Rdmp.Core.Curation.Data;
10	using Rdmp.Core.DataExport.Data;
11	using Rdmp.Core.Icons.IconProvision;
12	using Rdmp.Core.ReusableLibraryCode.Icons.IconProvision;
13	using SixLabors.ImageSharp;
14	using SixLabors.ImageSharp.PixelFormats;
15
16	namespace Rdmp.Core.CommandExecution.AtomicCommands;
17
18	public class ExecuteCommandCloneExtractionConfiguration : BasicCommandExecution
19	{
20	private readonly ExtractionConfiguration _extractionConfiguration;
21	private readonly IBasicActivateItems _activeItems;
NEW 22	private readonly List<IExtractableDataSet> _toRemove = [];	×
NEW 23	private readonly List<Catalogue> _toAdd = [];	×
24
25	private void CheckForDeprecatedCatalogues()
26	{
NEW 27	if (!_extractionConfiguration.SelectedDataSets.Any(static sd => sd.GetCatalogue().IsDeprecated) \|\|	×
NEW 28	!_activeItems.IsInteractive) return;	×
NEW 29	if (!YesNo(	×
NEW 30	"There are Deprecated catalogues in this Extraction Configuration. Would you like to replace them with their replacement (where available)?",	×
NEW 31	"Replace Deprecated Catalogues")) return;	×
32
NEW 33	var repo = _activeItems.RepositoryLocator.CatalogueRepository;	×
NEW 34	var deprecatedDatasets = _extractionConfiguration.SelectedDataSets.Where(static sd => sd.GetCatalogue().IsDeprecated).ToList();	×
NEW 35	var replacedBy = repo.GetExtendedProperties(ExtendedProperty.ReplacedBy).ToArray();	×
NEW 36	foreach (var ds in deprecatedDatasets)	×
37	{
NEW 38	var replacement = replacedBy.FirstOrDefault(rb => rb.ReferencedObjectID == ds.GetCatalogue().ID);	×
NEW 39	if (replacement is null) continue;	×
40
NEW 41	var replacementCatalogue = repo.GetObjectByID<Catalogue>(int.Parse(replacement.Value));	×
NEW 42	while (replacementCatalogue.IsDeprecated)	×
43	{
NEW 44	var replacementCatalogueIsReplacedBy = replacedBy.FirstOrDefault(rb => rb.ReferencedObjectID == replacementCatalogue.ID);	×
NEW 45	if (replacementCatalogueIsReplacedBy is not null)	×
46	{
47	//have found further down the tree
NEW 48	replacementCatalogue = repo.GetObjectByID<Catalogue>(int.Parse(replacementCatalogueIsReplacedBy.Value));	×
49	}
50	else
51	{
52	//there is no replacement
53	break;
54	}
55	}
56
NEW 57	_toRemove.Add(ds.ExtractableDataSet);	×
NEW 58	_toAdd.Add(replacementCatalogue);	×
59	}
60	}	×
61
62	public ExecuteCommandCloneExtractionConfiguration(IBasicActivateItems activator,
63	ExtractionConfiguration extractionConfiguration) : base(activator)	×
64	{
65	_extractionConfiguration = extractionConfiguration;	×
66	_activeItems = activator;	×
67	if (!_extractionConfiguration.SelectedDataSets.Any())	×
68	SetImpossible("ExtractionConfiguration does not have any selected datasets");	×
69	}	×
70
71	public override string GetCommandHelp() =>
72	"Creates an exact copy of the Extraction Configuration including the cohort selection, all selected datasets, parameters, filter containers, filters etc";	×
73
74	public override Image<Rgba32> GetImage(IIconProvider iconProvider) =>
75	Image.Load<Rgba32>(CatalogueIcons.CloneExtractionConfiguration);	×
76
77	public override void Execute()
78	{
79	base.Execute();	×
80	CheckForDeprecatedCatalogues();	×
81
82	var clone = _extractionConfiguration.DeepCloneWithNewIDs();	×
NEW 83	foreach (var ds in _toRemove.Cast<ExtractableDataSet>())	×
84	{
85	clone.RemoveDatasetFromConfiguration(ds);	×
86	}
87
NEW 88	foreach (var c in _toAdd)	×
89	{
90	//check if the eds already exis
91	var eds = _activeItems.RepositoryLocator.DataExportRepository.GetAllObjectsWhere<ExtractableDataSet>("Catalogue_ID", c.ID).FirstOrDefault();	×
92	if (eds is null)	×
93	{
94	eds = new ExtractableDataSet(_activeItems.RepositoryLocator.DataExportRepository, c);	×
95	eds.SaveToDatabase();	×
96	}
97
UNCOV 98	clone.AddDatasetToConfiguration(eds);	×
99	}
100
101	Publish((DatabaseEntity)clone.Project);	×
102	Emphasise(clone);	×
103	}	×
104	}

HicServices / RDMP / 12427673626

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