9758065908

Committed 02 Jul 2024 09:03AM UTC coverage: 56.679% (-0.2%) from 56.914%

Build # 9758065908

Build Type

push

github

Committed by

web-flow

Commit Message

Release/8.2.0 (#1867)

* add extraction additions

* interim

* add test

* interim

* working dedupe

* improved checking

* add timestamp option

* fix extra looping

* add check

* start on tests

* tidy up code

* update link

* tidy up

* Rename executeFullExtractionToDatabaseMSSql.md to ExecuteFullExtractionToDatabaseMSSql.md

* fix typo

* add docs

* update

* update documentation

* attempt fix docs

* update docs

* tidy up code

* better tests

* add real test

* tidy up

* interim

* grab existiing entity

* no new data

* add basic tests

* attempt to fix test

* interim

* interim commit

* working clash

* add test

* fix test

* improved clash checker

* tidy up

* update test

* fix up test

* update from codeql

* tidy up code

* fix bad merge

* fix typo

* skip over for now

* revert change

* Task/RDMP-180 Add instance settings table (#1820)

* working settings interface

* add documentation

* add missing files

* update namespace

* add icon

* update from run

* make key unique

* add tests

* update tests

* update for tests

* fix unique name issue

* tidy up

* tidy up from review

* works

* nested deprications

* recursive deprication

* tidy up

* add newline

* Task/rdmp 174 dqe improvements (#1849)

* working scallable graph

* add changelog

* add axis override

* interim

* working increments

* working ui refresh

* update changelog

* tidy up code

* add missing file

* tidy up

* Task/rdmp 155 migrate catalogue tables (#1805)

* start of UI

* interim

* working switch

* improved ui

* fix build

* rename duped file

* imterim

* add checks

* start of tests

* local tests  working

* add tests

* improved ui

* tidy up

* add single item use

* broken test

* updated tests

* tidy up imports

* add some documentation

* fix docume... (continued)

Run Details

10912 of 20750 branches covered (52.59%)

Branch coverage included in aggregate %.

369 of 831 new or added lines in 38 files covered. (44.4%)

375 existing lines in 25 files now uncovered.

30965 of 53135 relevant lines covered (58.28%)

7845.71 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

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;
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, IAtomicCommand
{
    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(sd => sd.GetCatalogue().IsDeprecated) && _activeItems.IsInteractive)
        {
            if (YesNo("There are Deprecated catalogues in this Extraction Configuration. Would you like to replace them with their replacement (where available)?", "Replace Deprecated Catalogues"))
            {
                var repo = _activeItems.RepositoryLocator.CatalogueRepository;
                var DeprecatedDatasets = _extractionConfiguration.SelectedDataSets.Where(sd => sd.GetCatalogue().IsDeprecated).ToList();
                var replacedBy = repo.GetExtendedProperties(ExtendedProperty.ReplacedBy);
                foreach (ISelectedDataSets ds in DeprecatedDatasets)
                {
                    var replacement = replacedBy.Where(rb => rb.ReferencedObjectID == ds.GetCatalogue().ID).FirstOrDefault();
                    if (replacement is not null)
                    {
                        var replacementCatalogue = repo.GetObjectByID<Catalogue>(Int32.Parse(replacement.Value));
                        while (replacementCatalogue.IsDeprecated)
                        {
                            var replacementCatalogueIsReplacedBy = replacedBy.Where(rb => rb.ReferencedObjectID == replacementCatalogue.ID).FirstOrDefault();
                            if(replacementCatalogueIsReplacedBy is not null)
                            {
                                //have found further down the tree
                                replacementCatalogue = repo.GetObjectByID<Catalogue>(Int32.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 (ExtractableDataSet ds in toRemove)
        {
            clone.RemoveDatasetFromConfiguration(ds);
        }
        foreach (Catalogue 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;
8	using System.Collections.Generic;
9	using System.Linq;
10	using Rdmp.Core.Curation.Data;
11	using Rdmp.Core.DataExport.Data;
12	using Rdmp.Core.Icons.IconProvision;
13	using Rdmp.Core.ReusableLibraryCode.Icons.IconProvision;
14	using SixLabors.ImageSharp;
15	using SixLabors.ImageSharp.PixelFormats;
16
17	namespace Rdmp.Core.CommandExecution.AtomicCommands;
18
19	public class ExecuteCommandCloneExtractionConfiguration : BasicCommandExecution, IAtomicCommand
20	{
21	private readonly ExtractionConfiguration _extractionConfiguration;
22	private readonly IBasicActivateItems _activeItems;
NEW 23	private readonly List<IExtractableDataSet> toRemove = [];	×
NEW 24	private readonly List<Catalogue> toAdd = [];	×
25	private void CheckForDeprecatedCatalogues()
26	{
NEW 27	if (_extractionConfiguration.SelectedDataSets.Any(sd => sd.GetCatalogue().IsDeprecated) && _activeItems.IsInteractive)	×
28	{
NEW 29	if (YesNo("There are Deprecated catalogues in this Extraction Configuration. Would you like to replace them with their replacement (where available)?", "Replace Deprecated Catalogues"))	×
30	{
NEW 31	var repo = _activeItems.RepositoryLocator.CatalogueRepository;	×
NEW 32	var DeprecatedDatasets = _extractionConfiguration.SelectedDataSets.Where(sd => sd.GetCatalogue().IsDeprecated).ToList();	×
NEW 33	var replacedBy = repo.GetExtendedProperties(ExtendedProperty.ReplacedBy);	×
NEW 34	foreach (ISelectedDataSets ds in DeprecatedDatasets)	×
35	{
NEW 36	var replacement = replacedBy.Where(rb => rb.ReferencedObjectID == ds.GetCatalogue().ID).FirstOrDefault();	×
NEW 37	if (replacement is not null)	×
38	{
NEW 39	var replacementCatalogue = repo.GetObjectByID<Catalogue>(Int32.Parse(replacement.Value));	×
NEW 40	while (replacementCatalogue.IsDeprecated)	×
41	{
NEW 42	var replacementCatalogueIsReplacedBy = replacedBy.Where(rb => rb.ReferencedObjectID == replacementCatalogue.ID).FirstOrDefault();	×
NEW 43	if(replacementCatalogueIsReplacedBy is not null)	×
44	{
45	//have found further down the tree
NEW 46	replacementCatalogue = repo.GetObjectByID<Catalogue>(Int32.Parse(replacementCatalogueIsReplacedBy.Value));	×
47	}
48	else
49	{
50	//there is no replacement
51	break;
52	}
53	}
NEW 54	toRemove.Add(ds.ExtractableDataSet);	×
NEW 55	toAdd.Add(replacementCatalogue);	×
56	}
57	}
58
59
60	}
61	}
NEW 62	}	×
63
64	public ExecuteCommandCloneExtractionConfiguration(IBasicActivateItems activator,
65	ExtractionConfiguration extractionConfiguration) : base(activator)	×
66	{
67	_extractionConfiguration = extractionConfiguration;	×
NEW 68	_activeItems = activator;	×
69	if (!_extractionConfiguration.SelectedDataSets.Any())	×
70	SetImpossible("ExtractionConfiguration does not have any selected datasets");	×
71	}	×
72
73	public override string GetCommandHelp() =>
74	"Creates an exact copy of the Extraction Configuration including the cohort selection, all selected datasets, parameters, filter containers, filters etc";	×
75
76	public override Image<Rgba32> GetImage(IIconProvider iconProvider) =>
77	Image.Load<Rgba32>(CatalogueIcons.CloneExtractionConfiguration);	×
78
79	public override void Execute()
80	{
81	base.Execute();	×
NEW 82	CheckForDeprecatedCatalogues();	×
83
84	var clone = _extractionConfiguration.DeepCloneWithNewIDs();	×
NEW 85	foreach (ExtractableDataSet ds in toRemove)	×
86	{
NEW 87	clone.RemoveDatasetFromConfiguration(ds);	×
88	}
NEW 89	foreach (Catalogue c in toAdd)	×
90	{
91	//check if the eds already exis
NEW 92	var eds = _activeItems.RepositoryLocator.DataExportRepository.GetAllObjectsWhere<ExtractableDataSet>("Catalogue_ID", c.ID).FirstOrDefault();	×
NEW 93	if (eds is null)	×
94	{
NEW 95	eds = new ExtractableDataSet(_activeItems.RepositoryLocator.DataExportRepository, c);	×
NEW 96	eds.SaveToDatabase();	×
97	}
NEW 98	clone.AddDatasetToConfiguration(eds);	×
99	}
100	Publish((DatabaseEntity)clone.Project);	×
101	Emphasise(clone);	×
102	}	×
103	}

HicServices / RDMP / 9758065908

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous