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)

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92.0

/Rdmp.Core/Curation/Data/ExtractionFilterParameterSet.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.Data.Common;
using System.Linq;
using Rdmp.Core.MapsDirectlyToDatabaseTable;
using Rdmp.Core.Repositories;
using Rdmp.Core.ReusableLibraryCode.Annotations;

namespace Rdmp.Core.Curation.Data;

/// <summary>
/// Often an ExtractionFilter will have a parameter associated with it (or more than one).  In this case it can be that you want to curate various values and give them
/// meaningful titles.  For exmaple if you have a filter 'Hospitalised with condition X' which has parameter @ConditionList.  Then you decide that you want to curate
/// a list 'A101.23,B21.1' as 'People hospitalised with drug dependency'.  This 'known meaningful parameter values set' is called a ExtractionFilterParameterSet.  You
/// can provide a name and a description for the concept.  Then you create a value for each parameter in the associated filter.  See ExtractionFilterParameterSetValue for
/// the value recordings.
/// </summary>
public class ExtractionFilterParameterSet : DatabaseEntity, ICollectSqlParameters, INamed
{
    #region Database Properties

    private string _name;
    private string _description;
    private int _extractionFilterID;

    /// <inheritdoc/>
    [NotNull]
    public string Name
    {
        get => _name;
        set => SetField(ref _name, value);
    }

    /// <summary>
    /// Human readable description of what the parameter set identifies e.g. 'Diabetes Drugs' and any supporting information about how it works, quirks etc
    /// </summary>
    public string Description
    {
        get => _description;
        set => SetField(ref _description, value);
    }

    /// <summary>
    /// The filter which the parameter values are designed to work with
    /// </summary>
    public int ExtractionFilter_ID
    {
        get => _extractionFilterID;
        set => SetField(ref _extractionFilterID, value);
    }

    #endregion

    #region Relationships

    /// <inheritdoc cref ="ExtractionFilter_ID"/>
    [NoMappingToDatabase]
    public ExtractionFilter ExtractionFilter => Repository.GetObjectByID<ExtractionFilter>(ExtractionFilter_ID);

    /// <summary>
    /// Gets all the individual parameter values required for populating the filter to achieve this concept (e.g. 'Diabetes Drugs' might have 2 parameter values @DrugList='123.122.1,1.2... etc' and @DrugCodeFormat='bnf')
    /// </summary>
    [NoMappingToDatabase]
    public IEnumerable<ExtractionFilterParameterSetValue> Values =>
        Repository.GetAllObjectsWithParent<ExtractionFilterParameterSetValue>(this);

    #endregion

    public ExtractionFilterParameterSet()
    {
    }

    internal ExtractionFilterParameterSet(ICatalogueRepository repository, DbDataReader r)
        : base(repository, r)
    {
        Name = r["Name"].ToString();
        Description = r["Description"] as string;
        ExtractionFilter_ID = Convert.ToInt32(r["ExtractionFilter_ID"]);
    }

    /// <summary>
    /// Defines a new set of known parameter values to achieve a given goal (e.g. identify 'diabetic drugs' in dataset prescriptions) in combination with a parent <see cref="IFilter"/>.
    /// <para>A single <see cref="ExtractionFilter"/> (e.g. 'Drug Prescriptions of X' with parameter @DrugList) could have many <see cref="ExtractionFilterParameterSet"/></para>
    /// </summary>
    /// <param name="repository"></param>
    /// <param name="filter"></param>
    /// <param name="name"></param>
    public ExtractionFilterParameterSet(ICatalogueRepository repository, ExtractionFilter filter, string name = null)
    {
        name ??= $"New ExtractionFilterParameterSet {Guid.NewGuid()}";

        repository.InsertAndHydrate(this, new Dictionary<string, object>
        {
            { "Name", name },
            { "ExtractionFilter_ID", filter.ID }
        });
    }


    /// <inheritdoc/>
    public override string ToString() => Name;

    /// <inheritdoc cref="Values"/>
    public ISqlParameter[] GetAllParameters() => Values.ToArray();

    /// <summary>
    /// Identifies all parameters which do not exist yet as declared values
    /// </summary>
    /// <returns></returns>
    public IEnumerable<ExtractionFilterParameter> GetMissingEntries()
    {
        var existingCatalogueParameters =
            ExtractionFilter.GetAllParameters().Cast<ExtractionFilterParameter>().ToArray();

        var personalChildren = Values.ToArray();

        foreach (var catalogueParameter in existingCatalogueParameters)
            if (personalChildren.All(c => c.ExtractionFilterParameter_ID != catalogueParameter.ID))
                yield return catalogueParameter;
    }

    /// <summary>
    /// Creates new value entries for each parameter in the filter that does not yet have a value in this value set
    /// </summary>
    /// <returns></returns>
    public ExtractionFilterParameterSetValue[] CreateNewValueEntries()
    {
        var toReturn = new List<ExtractionFilterParameterSetValue>();

        foreach (var catalogueParameter in GetMissingEntries())
            //we have a master that does not have any child values yet
            toReturn.Add(new ExtractionFilterParameterSetValue((ICatalogueRepository)Repository, this,
                catalogueParameter));

        return toReturn.ToArray();
    }

    public override void DeleteInDatabase()
    {
        foreach (var v in Values) v.DeleteInDatabase();

        base.DeleteInDatabase();
    }
}

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.Data.Common;
10	using System.Linq;
11	using Rdmp.Core.MapsDirectlyToDatabaseTable;
12	using Rdmp.Core.Repositories;
13	using Rdmp.Core.ReusableLibraryCode.Annotations;
14
15	namespace Rdmp.Core.Curation.Data;
16
17	/// <summary>
18	/// Often an ExtractionFilter will have a parameter associated with it (or more than one). In this case it can be that you want to curate various values and give them
19	/// meaningful titles. For exmaple if you have a filter 'Hospitalised with condition X' which has parameter @ConditionList. Then you decide that you want to curate
20	/// a list 'A101.23,B21.1' as 'People hospitalised with drug dependency'. This 'known meaningful parameter values set' is called a ExtractionFilterParameterSet. You
21	/// can provide a name and a description for the concept. Then you create a value for each parameter in the associated filter. See ExtractionFilterParameterSetValue for
22	/// the value recordings.
23	/// </summary>
24	public class ExtractionFilterParameterSet : DatabaseEntity, ICollectSqlParameters, INamed
25	{
26	#region Database Properties
27
28	private string _name;
29	private string _description;
30	private int _extractionFilterID;
31
32	/// <inheritdoc/>
33	[NotNull]
34	public string Name
35	{
36	get => _name;	24✔
37	set => SetField(ref _name, value);	34✔
38	}
39
40	/// <summary>
41	/// Human readable description of what the parameter set identifies e.g. 'Diabetes Drugs' and any supporting information about how it works, quirks etc
42	/// </summary>
43	public string Description
44	{
45	get => _description;	10✔
46	set => SetField(ref _description, value);	14✔
47	}
48
49	/// <summary>
50	/// The filter which the parameter values are designed to work with
51	/// </summary>
52	public int ExtractionFilter_ID
53	{
54	get => _extractionFilterID;	30✔
55	set => SetField(ref _extractionFilterID, value);	32✔
56	}
57
58	#endregion
59
60	#region Relationships
61
62	/// <inheritdoc cref ="ExtractionFilter_ID"/>
63	[NoMappingToDatabase]
64	public ExtractionFilter ExtractionFilter => Repository.GetObjectByID<ExtractionFilter>(ExtractionFilter_ID);	6✔
65
66	/// <summary>
67	/// Gets all the individual parameter values required for populating the filter to achieve this concept (e.g. 'Diabetes Drugs' might have 2 parameter values @DrugList='123.122.1,1.2... etc' and @DrugCodeFormat='bnf')
68	/// </summary>
69	[NoMappingToDatabase]
70	public IEnumerable<ExtractionFilterParameterSetValue> Values =>
71	Repository.GetAllObjectsWithParent<ExtractionFilterParameterSetValue>(this);	14✔
72
73	#endregion
74
75	public ExtractionFilterParameterSet()	×
76	{
77	}	×
78
79	internal ExtractionFilterParameterSet(ICatalogueRepository repository, DbDataReader r)
80	: base(repository, r)	8✔
81	{
82	Name = r["Name"].ToString();	8✔
83	Description = r["Description"] as string;	8✔
84	ExtractionFilter_ID = Convert.ToInt32(r["ExtractionFilter_ID"]);	8✔
85	}	8✔
86
87	/// <summary>
88	/// Defines a new set of known parameter values to achieve a given goal (e.g. identify 'diabetic drugs' in dataset prescriptions) in combination with a parent <see cref="IFilter"/>.
89	/// <para>A single <see cref="ExtractionFilter"/> (e.g. 'Drug Prescriptions of X' with parameter @DrugList) could have many <see cref="ExtractionFilterParameterSet"/></para>
90	/// </summary>
91	/// <param name="repository"></param>
92	/// <param name="filter"></param>
93	/// <param name="name"></param>
94	public ExtractionFilterParameterSet(ICatalogueRepository repository, ExtractionFilter filter, string name = null)	24✔
95	{
96	name ??= $"New ExtractionFilterParameterSet {Guid.NewGuid()}";	24!
97
98	repository.InsertAndHydrate(this, new Dictionary<string, object>	24✔
99	{	24✔
100	{ "Name", name },	24✔
101	{ "ExtractionFilter_ID", filter.ID }	24✔
102	});	24✔
103	}	24✔
104
105
106	/// <inheritdoc/>
107	public override string ToString() => Name;	12✔
108
109	/// <inheritdoc cref="Values"/>
110	public ISqlParameter[] GetAllParameters() => Values.ToArray();	×
111
112	/// <summary>
113	/// Identifies all parameters which do not exist yet as declared values
114	/// </summary>
115	/// <returns></returns>
116	public IEnumerable<ExtractionFilterParameter> GetMissingEntries()
117	{
118	var existingCatalogueParameters =	4✔
119	ExtractionFilter.GetAllParameters().Cast<ExtractionFilterParameter>().ToArray();	4✔
120
121	var personalChildren = Values.ToArray();	4✔
122
123	foreach (var catalogueParameter in existingCatalogueParameters)	16✔
124	if (personalChildren.All(c => c.ExtractionFilterParameter_ID != catalogueParameter.ID))	4✔
125	yield return catalogueParameter;	4✔
126	}	4✔
127
128	/// <summary>
129	/// Creates new value entries for each parameter in the filter that does not yet have a value in this value set
130	/// </summary>
131	/// <returns></returns>
132	public ExtractionFilterParameterSetValue[] CreateNewValueEntries()
133	{
134	var toReturn = new List<ExtractionFilterParameterSetValue>();	4✔
135
136	foreach (var catalogueParameter in GetMissingEntries())	16✔
137	//we have a master that does not have any child values yet
138	toReturn.Add(new ExtractionFilterParameterSetValue((ICatalogueRepository)Repository, this,	4✔
139	catalogueParameter));	4✔
140
141	return toReturn.ToArray();	4✔
142	}
143
144	public override void DeleteInDatabase()
145	{
146	foreach (var v in Values) v.DeleteInDatabase();	18✔
147
148	base.DeleteInDatabase();	6✔
149	}	6✔
150	}

HicServices / RDMP / 6245535001

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