6245535001

Committed 20 Sep 2023 07:44AM UTC coverage: 57.013%. First build

Build # 6245535001

Build Type

push

github

Committed by

web-flow

Commit Message

8.1.0 Release (#1628)

* Bump Newtonsoft.Json from 13.0.1 to 13.0.2

Bumps [Newtonsoft.Json](https://github.com/JamesNK/Newtonsoft.Json) from 13.0.1 to 13.0.2.
- [Release notes](https://github.com/JamesNK/Newtonsoft.Json/releases)
- [Commits](https://github.com/JamesNK/Newtonsoft.Json/compare/13.0.1...13.0.2)

---
updated-dependencies:
- dependency-name: Newtonsoft.Json
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump NLog from 5.0.5 to 5.1.0

Bumps [NLog](https://github.com/NLog/NLog) from 5.0.5 to 5.1.0.
- [Release notes](https://github.com/NLog/NLog/releases)
- [Changelog](https://github.com/NLog/NLog/blob/dev/CHANGELOG.md)
- [Commits](https://github.com/NLog/NLog/compare/v5.0.5...v5.1.0)

---
updated-dependencies:
- dependency-name: NLog
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump NLog from 5.0.5 to 5.1.0

* Fix -r flag - should have been --results-directory all along

* Bump Newtonsoft.Json from 13.0.1 to 13.0.2

* Bump YamlDotNet from 12.0.2 to 12.1.0

Bumps [YamlDotNet](https://github.com/aaubry/YamlDotNet) from 12.0.2 to 12.1.0.
- [Release notes](https://github.com/aaubry/YamlDotNet/releases)
- [Commits](https://github.com/aaubry/YamlDotNet/compare/v12.0.2...v12.1.0)

---
updated-dependencies:
- dependency-name: YamlDotNet
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump Moq from 4.18.2 to 4.18.3

Bumps [Moq](https://github.com/moq/moq4) from 4.18.2 to 4.18.3.
- [Release notes](https://github.com/moq/moq4/releases)
- [Changelog](https://github.com/moq/moq4/blob/main/CHANGELOG.md)
- [Commits](https://github.com/moq/moq4/compare/v4.18.2...v4.18.3)

---
updated-dependencies:
- dependency-name: Moq
... (continued)

Run Details

10732 of 20257 branches covered (0.0%)

Branch coverage included in aggregate %.

48141 of 48141 new or added lines in 1086 files covered. (100.0%)

30685 of 52388 relevant lines covered (58.57%)

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Source File
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38.89

/Rdmp.Core/CommandExecution/AtomicCommands/ExecuteCommandSetExtractionIdentifier.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 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;

/// <summary>
/// Change which column is used to perform linkage against a cohort.  This command supports both changing the global setting on a <see cref="Catalogue"/>
/// or changing it only for a specific <see cref="ExtractionConfiguration"/>
/// </summary>
public sealed class ExecuteCommandSetExtractionIdentifier : ExecuteCommandSetColumnSettingBase, IAtomicCommand
{
    /// <summary>
    /// Change which column is the linkage identifier in a <see cref="Catalogue"/> either at a global level or for a specific <paramref name="inConfiguration"/>
    /// </summary>
    /// <param name="activator"></param>
    /// <param name="catalogue"></param>
    /// <param name="inConfiguration"></param>
    /// <param name="column"></param>
    public ExecuteCommandSetExtractionIdentifier(IBasicActivateItems activator,
            [DemandsInitialization("The dataset you want to change the extraction identifier for")]
            ICatalogue catalogue,
            [DemandsInitialization(
                "Optional - The specific extraction you want the change made in or Null for the Catalogue itself (will affect all future extractions)")]
            IExtractionConfiguration inConfiguration,
            [DemandsInitialization(
                "Optional - The Column name(s) you want to select as the new linkage identifier(s).  Comma separate multiple entries if needed")]
            string column)
        // base class args
        : base(activator, catalogue, inConfiguration, column,
            "Set Extraction Identifier",
            "Extraction Identifier")
    {
    }

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

    public override string GetCommandHelp() =>
        "Change which column(s) contain the patient id / linkage column e.g. CHI";

    protected override bool IsValidSelection(ConcreteColumn[] selected) =>
        selected is not { Length: > 1 } // if multiple selected warn user
        ||
        YesNo(
            "Are you sure you want multiple linkable extraction identifier columns (most datasets only have 1 person ID column in them)?",
            "Multiple IsExtractionIdentifier columns?");

    protected override bool Getter(ConcreteColumn c) => c.IsExtractionIdentifier;

    protected override void Setter(ConcreteColumn c, bool newValue)
    {
        c.IsExtractionIdentifier = newValue;
    }
}

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 Rdmp.Core.Curation.Data;
8	using Rdmp.Core.DataExport.Data;
9	using Rdmp.Core.Icons.IconProvision;
10	using Rdmp.Core.ReusableLibraryCode.Icons.IconProvision;
11	using SixLabors.ImageSharp;
12	using SixLabors.ImageSharp.PixelFormats;
13
14	namespace Rdmp.Core.CommandExecution.AtomicCommands;
15
16	/// <summary>
17	/// Change which column is used to perform linkage against a cohort. This command supports both changing the global setting on a <see cref="Catalogue"/>
18	/// or changing it only for a specific <see cref="ExtractionConfiguration"/>
19	/// </summary>
20	public sealed class ExecuteCommandSetExtractionIdentifier : ExecuteCommandSetColumnSettingBase, IAtomicCommand
21	{
22	/// <summary>
23	/// Change which column is the linkage identifier in a <see cref="Catalogue"/> either at a global level or for a specific <paramref name="inConfiguration"/>
24	/// </summary>
25	/// <param name="activator"></param>
26	/// <param name="catalogue"></param>
27	/// <param name="inConfiguration"></param>
28	/// <param name="column"></param>
29	public ExecuteCommandSetExtractionIdentifier(IBasicActivateItems activator,
30	[DemandsInitialization("The dataset you want to change the extraction identifier for")]
31	ICatalogue catalogue,
32	[DemandsInitialization(
33	"Optional - The specific extraction you want the change made in or Null for the Catalogue itself (will affect all future extractions)")]
34	IExtractionConfiguration inConfiguration,
35	[DemandsInitialization(
36	"Optional - The Column name(s) you want to select as the new linkage identifier(s). Comma separate multiple entries if needed")]
37	string column)
38	// base class args
39	: base(activator, catalogue, inConfiguration, column,	8✔
40	"Set Extraction Identifier",	8✔
41	"Extraction Identifier")	8✔
42	{
43	}	8✔
44
45	public override Image<Rgba32> GetImage(IIconProvider iconProvider) =>
46	iconProvider.GetImage(RDMPConcept.ExtractableCohort, OverlayKind.Key);	×
47
48	public override string GetCommandHelp() =>
49	"Change which column(s) contain the patient id / linkage column e.g. CHI";	×
50
51	protected override bool IsValidSelection(ConcreteColumn[] selected) =>
52	selected is not { Length: > 1 } // if multiple selected warn user	×
53	\|\|	×
54	YesNo(	×
55	"Are you sure you want multiple linkable extraction identifier columns (most datasets only have 1 person ID column in them)?",	×
56	"Multiple IsExtractionIdentifier columns?");	×
57
58	protected override bool Getter(ConcreteColumn c) => c.IsExtractionIdentifier;	18✔
59
60	protected override void Setter(ConcreteColumn c, bool newValue)
61	{
62	c.IsExtractionIdentifier = newValue;	8✔
63	}	8✔
64	}

HicServices / RDMP / 6245535001

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