6237307473

Committed 19 Sep 2023 04:02PM UTC coverage: 57.015% (-0.4%) from 57.44%

Build # 6237307473

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push

github

Committed by

web-flow

Commit Message

Feature/rc4 (#1570)

* Syntax tidying
* Dependency updates
* Event handling singletons (ThrowImmediately and co)

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: James A Sutherland <>
Co-authored-by: James Friel <jfriel001@dundee.ac.uk>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

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49.59

/Rdmp.Core/CommandExecution/AtomicCommands/ExecuteCommandImportFilterContainerTree.cs

﻿// Copyright (c) The University of Dundee 2018-2019
// 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;
using Rdmp.Core.Curation.Data;
using Rdmp.Core.Curation.Data.Aggregation;
using Rdmp.Core.Curation.Data.Cohort;
using Rdmp.Core.Curation.FilterImporting;
using Rdmp.Core.Curation.FilterImporting.Construction;
using Rdmp.Core.DataExport.Data;
using Rdmp.Core.Icons.IconProvision;
using Rdmp.Core.Providers;
using Rdmp.Core.Repositories.Construction;
using Rdmp.Core.ReusableLibraryCode.Icons.IconProvision;
using SixLabors.ImageSharp;
using SixLabors.ImageSharp.PixelFormats;

namespace Rdmp.Core.CommandExecution.AtomicCommands;

/// <summary>
/// Imports the entire tree from another <see cref="ISelectedDataSets"/> or <see cref="AggregateConfiguration"/> into a given <see cref="SelectedDataSets"/> (as new copies)
/// </summary>
public class ExecuteCommandImportFilterContainerTree : BasicCommandExecution
{
    /// <summary>
    /// ID of the Catalogue that is being extracted by <see cref="_into"/> to ensure that we only import filters from the same table
    /// </summary>
    private readonly ICatalogue _catalogue;

    private readonly IRootFilterContainerHost _into;
    private const float DEFAULT_WEIGHT = 1.2f;

    /// <summary>
    /// May be null, if populated this is the explicit subcontainer into which the tree should be imported i.e. not <see cref="_into"/>
    /// </summary>
    private IContainer _intoSubContainer;

    /// <summary>
    /// May be null, if populated then this is the explicit one the user wants and we shouldn't ask them again
    /// </summary>
    private IContainer _explicitChoice;

    private ExecuteCommandImportFilterContainerTree(IBasicActivateItems activator) : base(activator)
    {
        Weight = DEFAULT_WEIGHT;

        if (activator.CoreChildProvider is not DataExportChildProvider)
            SetImpossible("Data export functions unavailable");
    }

    public ExecuteCommandImportFilterContainerTree(IBasicActivateItems activator, IRootFilterContainerHost into) :
        this(activator)
    {
        Weight = DEFAULT_WEIGHT;

        _into = into;

        if (into.RootFilterContainer_ID != null)
            SetImpossible("Dataset already has a root container");


        if (into is AggregateConfiguration ac && ac.Catalogue.IsApiCall())
            SetImpossible(ExecuteCommandAddNewFilterContainer.FiltersCannotBeAddedToApiCalls);

        _catalogue = _into.GetCatalogue();

        SetImpossibleIfReadonly(into);
    }

    /// <summary>
    /// constructor for explicit choices, use this aggregates root container
    /// </summary>
    /// <param name="activator"></param>
    /// <param name="into"></param>
    /// <param name="from"></param>
    [UseWithObjectConstructor]
    public ExecuteCommandImportFilterContainerTree(IBasicActivateItems activator, IRootFilterContainerHost into,
        IRootFilterContainerHost from) : this(activator, into)
    {
        Weight = DEFAULT_WEIGHT;

        if (from.RootFilterContainer_ID == null)
            SetImpossible("AggregateConfiguration has no root container");
        else
            _explicitChoice = from.RootFilterContainer;
    }

    /// <summary>
    /// Constructor for explicitly specifying the container to import
    /// </summary>
    /// <param name="activator"></param>
    /// <param name="into"></param>
    /// <param name="explicitChoice"></param>
    public ExecuteCommandImportFilterContainerTree(IBasicActivateItems activator, IRootFilterContainerHost into,
        IContainer explicitChoice) : this(activator, into)
    {
        Weight = DEFAULT_WEIGHT;

        _explicitChoice = explicitChoice;
    }

    /// <summary>
    /// Constructor for importing into a sub container
    /// </summary>
    /// <param name="activator"></param>
    /// <param name="into"></param>
    /// <param name="explicitChoice"></param>
    public ExecuteCommandImportFilterContainerTree(IBasicActivateItems activator, IContainer into,
        IContainer explicitChoice) : this(activator)
    {
        Weight = DEFAULT_WEIGHT;

        _intoSubContainer = into;
        _explicitChoice = explicitChoice;
    }

    public override Image<Rgba32> GetImage(IIconProvider iconProvider) =>
        iconProvider.GetImage(RDMPConcept.FilterContainer, OverlayKind.Import);

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

        if (_explicitChoice != null)
        {
            Import(_explicitChoice);
        }
        else
        {
            if (_into == null)
                throw new NotSupportedException(
                    "Interactive mode is only supported when specifying a root object to import into");

            //prompt user to pick one
            var childProvider = (DataExportChildProvider)BasicActivator.CoreChildProvider;

            var ecById = childProvider.ExtractionConfigurations.ToDictionary(k => k.ID);

            // The root object that makes most sense to the user e.g. they select an extraction
            var fromConfiguration
                =
                childProvider.AllCohortIdentificationConfigurations.Where(IsEligible)
                    .Cast<DatabaseEntity>()
                    .Union(childProvider.SelectedDataSets.Where(IsEligible)
                        .Select(sds => ecById[sds.ExtractionConfiguration_ID])).ToList();

            if (!fromConfiguration.Any())
            {
                Show("There are no extractions or cohort builder configurations of this dataset that use filters");
                return;
            }

            if (SelectOne(fromConfiguration, out var selected))
            {
                if (selected is ExtractionConfiguration ec) Import(GetEligibleChild(ec).RootFilterContainer);
                if (selected is CohortIdentificationConfiguration cic)
                {
                    var chosen = SelectOne(GetEligibleChildren(cic).ToList(), null, true);

                    if (chosen != null)
                        Import(chosen.RootFilterContainer);
                }
            }
        }

        Publish((DatabaseEntity)_into ?? (DatabaseEntity)_intoSubContainer);
    }

    private void Import(IContainer from)
    {
        var factory =
            _into != null ? _into.GetFilterFactory() : _intoSubContainer.GetFilterFactory();

        IContainer intoContainer;

        if (_into != null)
        {
            var newRoot = factory.CreateNewContainer();
            newRoot.Operation = from.Operation;
            newRoot.SaveToDatabase();
            _into.RootFilterContainer_ID = newRoot.ID;
            _into.SaveToDatabase();

            intoContainer = newRoot;
        }
        else
        {
            intoContainer = _intoSubContainer;
        }

        DeepClone(intoContainer, from, factory);
    }

    private void DeepClone(IContainer into, IContainer from, IFilterFactory factory)
    {
        //clone the subcontainers
        foreach (var container in from.GetSubContainers())
        {
            var subContainer = factory.CreateNewContainer();
            subContainer.Operation = container.Operation;
            subContainer.SaveToDatabase();
            into.AddChild(subContainer);

            DeepClone(subContainer, container, factory);
        }

        var wizard = new FilterImportWizard(BasicActivator);

        //clone the filters
        foreach (var filter in from.GetFilters())
            into.AddChild(wizard.Import(into, filter));
    }

    private bool IsEligible(CohortIdentificationConfiguration arg) => GetEligibleChildren(arg).Any();


    /// <summary>
    /// Returns all <see cref="AggregateConfiguration"/> from the <paramref name="arg"/> where the dataset is the same and there are filters defined
    /// </summary>
    /// <param name="arg"></param>
    /// <returns></returns>
    private IEnumerable<AggregateConfiguration> GetEligibleChildren(CohortIdentificationConfiguration arg)
    {
        return arg.RootCohortAggregateContainer_ID == null
            ? Array.Empty<AggregateConfiguration>()
            : arg.RootCohortAggregateContainer.GetAllAggregateConfigurationsRecursively()
                .Where(ac => ac.Catalogue_ID == _catalogue.ID && ac.RootFilterContainer_ID != null);
    }

    /// <summary>
    /// Returns the <see cref="ISelectedDataSets"/> that matches the dataset <see cref="_into"/> if it is one of the datasets in the <see cref="ExtractionConfiguration"/> <paramref name="arg"/> (each dataset can only be extracted once in a given <see cref="ExtractionConfiguration"/>)
    /// </summary>
    /// <param name="arg"></param>
    /// <returns></returns>
    private ISelectedDataSets GetEligibleChild(ExtractionConfiguration arg) =>
        arg.SelectedDataSets.FirstOrDefault(IsEligible);

    private bool IsEligible(ISelectedDataSets arg) => arg.RootFilterContainer_ID != null;
}

1	// Copyright (c) The University of Dundee 2018-2019
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;
11	using Rdmp.Core.Curation.Data;
12	using Rdmp.Core.Curation.Data.Aggregation;
13	using Rdmp.Core.Curation.Data.Cohort;
14	using Rdmp.Core.Curation.FilterImporting;
15	using Rdmp.Core.Curation.FilterImporting.Construction;
16	using Rdmp.Core.DataExport.Data;
17	using Rdmp.Core.Icons.IconProvision;
18	using Rdmp.Core.Providers;
19	using Rdmp.Core.Repositories.Construction;
20	using Rdmp.Core.ReusableLibraryCode.Icons.IconProvision;
21	using SixLabors.ImageSharp;
22	using SixLabors.ImageSharp.PixelFormats;
23
24	namespace Rdmp.Core.CommandExecution.AtomicCommands;
25
26	/// <summary>
27	/// Imports the entire tree from another <see cref="ISelectedDataSets"/> or <see cref="AggregateConfiguration"/> into a given <see cref="SelectedDataSets"/> (as new copies)
28	/// </summary>
29	public class ExecuteCommandImportFilterContainerTree : BasicCommandExecution
30	{
31	/// <summary>
32	/// ID of the Catalogue that is being extracted by <see cref="_into"/> to ensure that we only import filters from the same table
33	/// </summary>
34	private readonly ICatalogue _catalogue;
35
36	private readonly IRootFilterContainerHost _into;
37	private const float DEFAULT_WEIGHT = 1.2f;
38
39	/// <summary>
40	/// May be null, if populated this is the explicit subcontainer into which the tree should be imported i.e. not <see cref="_into"/>
41	/// </summary>
42	private IContainer _intoSubContainer;
43
44	/// <summary>
45	/// May be null, if populated then this is the explicit one the user wants and we shouldn't ask them again
46	/// </summary>
47	private IContainer _explicitChoice;
48
49	private ExecuteCommandImportFilterContainerTree(IBasicActivateItems activator) : base(activator)	6✔
50	{
51	Weight = DEFAULT_WEIGHT;	6✔
52
53	if (activator.CoreChildProvider is not DataExportChildProvider)	6!
54	SetImpossible("Data export functions unavailable");	×
55	}	6✔
56
57	public ExecuteCommandImportFilterContainerTree(IBasicActivateItems activator, IRootFilterContainerHost into) :
58	this(activator)	6✔
59	{
60	Weight = DEFAULT_WEIGHT;	6✔
61
62	_into = into;	6✔
63
64	if (into.RootFilterContainer_ID != null)	6!
65	SetImpossible("Dataset already has a root container");	×
66
67
68	if (into is AggregateConfiguration ac && ac.Catalogue.IsApiCall())	6!
69	SetImpossible(ExecuteCommandAddNewFilterContainer.FiltersCannotBeAddedToApiCalls);	×
70
71	_catalogue = _into.GetCatalogue();	6✔
72
73	SetImpossibleIfReadonly(into);	6✔
74	}	6✔
75
76	/// <summary>
77	/// constructor for explicit choices, use this aggregates root container
78	/// </summary>
79	/// <param name="activator"></param>
80	/// <param name="into"></param>
81	/// <param name="from"></param>
82	[UseWithObjectConstructor]
83	public ExecuteCommandImportFilterContainerTree(IBasicActivateItems activator, IRootFilterContainerHost into,
84	IRootFilterContainerHost from) : this(activator, into)	6✔
85	{
86	Weight = DEFAULT_WEIGHT;	6✔
87
88	if (from.RootFilterContainer_ID == null)	6!
89	SetImpossible("AggregateConfiguration has no root container");	×
90	else
91	_explicitChoice = from.RootFilterContainer;	6✔
92	}	6✔
93
94	/// <summary>
95	/// Constructor for explicitly specifying the container to import
96	/// </summary>
97	/// <param name="activator"></param>
98	/// <param name="into"></param>
99	/// <param name="explicitChoice"></param>
100	public ExecuteCommandImportFilterContainerTree(IBasicActivateItems activator, IRootFilterContainerHost into,
101	IContainer explicitChoice) : this(activator, into)	×
102	{
103	Weight = DEFAULT_WEIGHT;	×
104
105	_explicitChoice = explicitChoice;	×
106	}	×
107
108	/// <summary>
109	/// Constructor for importing into a sub container
110	/// </summary>
111	/// <param name="activator"></param>
112	/// <param name="into"></param>
113	/// <param name="explicitChoice"></param>
114	public ExecuteCommandImportFilterContainerTree(IBasicActivateItems activator, IContainer into,
115	IContainer explicitChoice) : this(activator)	×
116	{
117	Weight = DEFAULT_WEIGHT;	×
118
119	_intoSubContainer = into;	×
120	_explicitChoice = explicitChoice;	×
121	}	×
122
123	public override Image<Rgba32> GetImage(IIconProvider iconProvider) =>
124	iconProvider.GetImage(RDMPConcept.FilterContainer, OverlayKind.Import);	×
125
126	public override void Execute()
127	{
128	base.Execute();	6✔
129
130	if (_explicitChoice != null)	6!
131	{
132	Import(_explicitChoice);	6✔
133	}
134	else
135	{
136	if (_into == null)	×
137	throw new NotSupportedException(	×
138	"Interactive mode is only supported when specifying a root object to import into");	×
139
140	//prompt user to pick one
141	var childProvider = (DataExportChildProvider)BasicActivator.CoreChildProvider;	×
142
143	var ecById = childProvider.ExtractionConfigurations.ToDictionary(k => k.ID);	×
144
145	// The root object that makes most sense to the user e.g. they select an extraction
146	var fromConfiguration	×
147	=	×
148	childProvider.AllCohortIdentificationConfigurations.Where(IsEligible)	×
149	.Cast<DatabaseEntity>()	×
150	.Union(childProvider.SelectedDataSets.Where(IsEligible)	×
151	.Select(sds => ecById[sds.ExtractionConfiguration_ID])).ToList();	×
152
153	if (!fromConfiguration.Any())	×
154	{
155	Show("There are no extractions or cohort builder configurations of this dataset that use filters");	×
156	return;	×
157	}
158
159	if (SelectOne(fromConfiguration, out var selected))	×
160	{
161	if (selected is ExtractionConfiguration ec) Import(GetEligibleChild(ec).RootFilterContainer);	×
162	if (selected is CohortIdentificationConfiguration cic)	×
163	{
164	var chosen = SelectOne(GetEligibleChildren(cic).ToList(), null, true);	×
165
166	if (chosen != null)	×
167	Import(chosen.RootFilterContainer);	×
168	}
169	}
170	}
171
172	Publish((DatabaseEntity)_into ?? (DatabaseEntity)_intoSubContainer);	6!
173	}	6✔
174
175	private void Import(IContainer from)
176	{
177	var factory =	6!
178	_into != null ? _into.GetFilterFactory() : _intoSubContainer.GetFilterFactory();	6✔
179
180	IContainer intoContainer;
181
182	if (_into != null)	6!
183	{
184	var newRoot = factory.CreateNewContainer();	6✔
185	newRoot.Operation = from.Operation;	6✔
186	newRoot.SaveToDatabase();	6✔
187	_into.RootFilterContainer_ID = newRoot.ID;	6✔
188	_into.SaveToDatabase();	6✔
189
190	intoContainer = newRoot;	6✔
191	}
192	else
193	{
194	intoContainer = _intoSubContainer;	×
195	}
196
197	DeepClone(intoContainer, from, factory);	6✔
198	}	6✔
199
200	private void DeepClone(IContainer into, IContainer from, IFilterFactory factory)
201	{
202	//clone the subcontainers
203	foreach (var container in from.GetSubContainers())	28✔
204	{
205	var subContainer = factory.CreateNewContainer();	4✔
206	subContainer.Operation = container.Operation;	4✔
207	subContainer.SaveToDatabase();	4✔
208	into.AddChild(subContainer);	4✔
209
210	DeepClone(subContainer, container, factory);	4✔
211	}
212
213	var wizard = new FilterImportWizard(BasicActivator);	10✔
214
215	//clone the filters
216	foreach (var filter in from.GetFilters())	32✔
217	into.AddChild(wizard.Import(into, filter));	6✔
218	}	10✔
219
220	private bool IsEligible(CohortIdentificationConfiguration arg) => GetEligibleChildren(arg).Any();	×
221
222
223	/// <summary>
224	/// Returns all <see cref="AggregateConfiguration"/> from the <paramref name="arg"/> where the dataset is the same and there are filters defined
225	/// </summary>
226	/// <param name="arg"></param>
227	/// <returns></returns>
228	private IEnumerable<AggregateConfiguration> GetEligibleChildren(CohortIdentificationConfiguration arg)
229	{
230	return arg.RootCohortAggregateContainer_ID == null	×
231	? Array.Empty<AggregateConfiguration>()	×
232	: arg.RootCohortAggregateContainer.GetAllAggregateConfigurationsRecursively()	×
233	.Where(ac => ac.Catalogue_ID == _catalogue.ID && ac.RootFilterContainer_ID != null);	×
234	}
235
236	/// <summary>
237	/// Returns the <see cref="ISelectedDataSets"/> that matches the dataset <see cref="_into"/> if it is one of the datasets in the <see cref="ExtractionConfiguration"/> <paramref name="arg"/> (each dataset can only be extracted once in a given <see cref="ExtractionConfiguration"/>)
238	/// </summary>
239	/// <param name="arg"></param>
240	/// <returns></returns>
241	private ISelectedDataSets GetEligibleChild(ExtractionConfiguration arg) =>
242	arg.SelectedDataSets.FirstOrDefault(IsEligible);	×
243
244	private bool IsEligible(ISelectedDataSets arg) => arg.RootFilterContainer_ID != null;	×
245	}

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