6245535001

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

Build # 6245535001

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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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87.1

/Rdmp.Core/DataExport/Data/DeployedExtractionFilter.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.Curation.Checks;
using Rdmp.Core.Curation.Data;
using Rdmp.Core.Curation.FilterImporting.Construction;
using Rdmp.Core.MapsDirectlyToDatabaseTable;
using Rdmp.Core.MapsDirectlyToDatabaseTable.Attributes;
using Rdmp.Core.Repositories;
using Rdmp.Core.ReusableLibraryCode.Checks;

namespace Rdmp.Core.DataExport.Data;

/// <summary>
/// Sometimes it is necessary to restrict which records are extracted for a given ExtractionConfiguration beyond the linkage against a cohort.  For example you might want to extract
/// 'only paracetamol prescriptions' for your cohort rather than the entire Prescribing dataset.  This is achieved by using a DeployedExtractionFilter.  DeployedExtractionFilters are
/// curated pieces of WHERE SQL with a name and description.  These can either be written bespoke for your extract or copied from a master ExtractionFilter in the Catalogue database.
/// In general if a filter concept is reusable and useful across multiple projects / over time then you should create it in the Catalogue database as an ExtractionFilter and then
/// import a copy into your ExtractionConfiguration each time you need it (or mark it as IsMandatory if it should always be used in data extraction of that Catalogue).
/// 
/// <para>When you import a master filter into your ExtractionConfiguration a copy of the WHERE SQL, any
/// parameters and the name and description will be made as a DeployedExtractionFilter which will also contain a reference back to the original (ClonedFromExtractionFilter_ID).  This
/// allows you to ensure consistency over time and gives you a central location (the ExtractionFilter) to fix errors in the Filter implementation etc.  </para>
/// 
/// </summary>
public class DeployedExtractionFilter : ConcreteFilter
{
    #region Database Properties

    private int? _clonedFromExtractionFilterID;
    private int? _filterContainerID;

    /// <inheritdoc/>
    public override int? ClonedFromExtractionFilter_ID
    {
        get => _clonedFromExtractionFilterID;
        set => SetField(ref _clonedFromExtractionFilterID, value);
    }

    /// <inheritdoc/>
    [Relationship(typeof(FilterContainer), RelationshipType.SharedObject)]
    public override int? FilterContainer_ID
    {
        get => _filterContainerID;
        set => SetField(ref _filterContainerID, value);
    }

    #endregion

    #region Relationships

    /// <summary>
    /// Returns all parameters declared against this filter (does not include other parameters in scope e.g. globals)
    /// </summary>
    [NoMappingToDatabase]
    public DeployedExtractionFilterParameter[] ExtractionFilterParameters => Repository
        .GetAllObjectsWhere<DeployedExtractionFilterParameter>("ExtractionFilter_ID", ID).ToArray();

    /// <inheritdoc/>
    [NoMappingToDatabase]
    public override IContainer FilterContainer => FilterContainer_ID.HasValue
        ? Repository.GetObjectByID<FilterContainer>(FilterContainer_ID.Value)
        : null;

    #endregion

    /// <inheritdoc/>
    public override ColumnInfo GetColumnInfoIfExists() => null;

    /// <inheritdoc/>
    public override IFilterFactory GetFilterFactory() =>
        new DeployedExtractionFilterFactory((IDataExportRepository)Repository);

    /// <inheritdoc/>
    public override Catalogue GetCatalogue()
    {
        var ds = GetDataset().ExtractableDataSet;
        try
        {
            return (Catalogue)ds.Catalogue;
        }
        catch (Exception)
        {
            //could be that the catalogue has been deleted
            return null;
        }
    }

    /// <inheritdoc/>
    public override ISqlParameter[] GetAllParameters() => ExtractionFilterParameters.Cast<ISqlParameter>().ToArray();

    public DeployedExtractionFilter()
    {
    }

    /// <summary>
    /// Creates a new empty WHERE filter in the given <paramref name="container"/> that will be used when
    /// extracting the dataset.
    /// 
    /// <para>This object is created into the data export metadata database</para>
    /// </summary>
    /// <param name="repository"></param>
    /// <param name="name"></param>
    /// <param name="container"></param>
    public DeployedExtractionFilter(IDataExportRepository repository, string name, FilterContainer container)
    {
        Repository = repository;
        Repository.InsertAndHydrate(this, new Dictionary<string, object>
        {
            { "Name", name != null ? (object)name : DBNull.Value },
            { "FilterContainer_ID", container != null ? (object)container.ID : DBNull.Value }
        });
    }

    /// <summary>
    /// Read an existing WHERE filter out of the database
    /// </summary>
    /// <param name="repository"></param>
    /// <param name="r"></param>
    internal DeployedExtractionFilter(IDataExportRepository repository, DbDataReader r)
        : base(repository, r)
    {
        WhereSQL = r["WhereSQL"] as string;
        Description = r["Description"] as string;
        Name = r["Name"] as string;
        IsMandatory = (bool)r["IsMandatory"];

        if (r["FilterContainer_ID"] != null && !string.IsNullOrWhiteSpace(r["FilterContainer_ID"].ToString()))
            FilterContainer_ID = int.Parse(r["FilterContainer_ID"].ToString());
        else
            FilterContainer_ID = null;

        ClonedFromExtractionFilter_ID = ObjectToNullableInt(r["ClonedFromExtractionFilter_ID"]);
    }

    /// <summary>
    /// Returns Name of filters
    /// </summary>
    /// <returns></returns>
    public override string ToString() => Name;


    /// <summary>
    /// Checks the filter is properly defined (e.g. not blank).
    /// </summary>
    /// <param name="notifier"></param>
    public override void Check(ICheckNotifier notifier)
    {
        base.Check(notifier);

        var checker = new ClonedFilterChecker(this, ClonedFromExtractionFilter_ID,
            ((IDataExportRepository)Repository).CatalogueRepository);
        checker.Check(notifier);
    }

    /// <summary>
    /// Returns the configuration and dataset (<see cref="ISelectedDataSets"/>) in which the filter is declared.  This involves traversing
    /// up any nested <see cref="FilterContainer"/>s to the root.
    /// 
    /// <para>Returns null if the filter is an orphan (not in a container or part of an orphan container tree)</para>
    /// </summary>
    /// <returns></returns>
    public SelectedDataSets GetDataset()
    {
        if (FilterContainer_ID == null)
            return null;

        var container = Repository.GetObjectByID<FilterContainer>(FilterContainer_ID.Value);
        return container.GetSelectedDataSetsRecursively();
    }

    public DeployedExtractionFilter ShallowClone(FilterContainer into)
    {
        var clone = new DeployedExtractionFilter(DataExportRepository, Name, into);
        CopyShallowValuesTo(clone);
        return clone;
    }
}

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.Curation.Checks;
12	using Rdmp.Core.Curation.Data;
13	using Rdmp.Core.Curation.FilterImporting.Construction;
14	using Rdmp.Core.MapsDirectlyToDatabaseTable;
15	using Rdmp.Core.MapsDirectlyToDatabaseTable.Attributes;
16	using Rdmp.Core.Repositories;
17	using Rdmp.Core.ReusableLibraryCode.Checks;
18
19	namespace Rdmp.Core.DataExport.Data;
20
21	/// <summary>
22	/// Sometimes it is necessary to restrict which records are extracted for a given ExtractionConfiguration beyond the linkage against a cohort. For example you might want to extract
23	/// 'only paracetamol prescriptions' for your cohort rather than the entire Prescribing dataset. This is achieved by using a DeployedExtractionFilter. DeployedExtractionFilters are
24	/// curated pieces of WHERE SQL with a name and description. These can either be written bespoke for your extract or copied from a master ExtractionFilter in the Catalogue database.
25	/// In general if a filter concept is reusable and useful across multiple projects / over time then you should create it in the Catalogue database as an ExtractionFilter and then
26	/// import a copy into your ExtractionConfiguration each time you need it (or mark it as IsMandatory if it should always be used in data extraction of that Catalogue).
27	///
28	/// <para>When you import a master filter into your ExtractionConfiguration a copy of the WHERE SQL, any
29	/// parameters and the name and description will be made as a DeployedExtractionFilter which will also contain a reference back to the original (ClonedFromExtractionFilter_ID). This
30	/// allows you to ensure consistency over time and gives you a central location (the ExtractionFilter) to fix errors in the Filter implementation etc. </para>
31	///
32	/// </summary>
33	public class DeployedExtractionFilter : ConcreteFilter
34	{
35	#region Database Properties
36
37	private int? _clonedFromExtractionFilterID;
38	private int? _filterContainerID;
39
40	/// <inheritdoc/>
41	public override int? ClonedFromExtractionFilter_ID
42	{
43	get => _clonedFromExtractionFilterID;	74✔
44	set => SetField(ref _clonedFromExtractionFilterID, value);	104✔
45	}
46
47	/// <inheritdoc/>
48	[Relationship(typeof(FilterContainer), RelationshipType.SharedObject)]
49	public override int? FilterContainer_ID
50	{
51	get => _filterContainerID;	386✔
52	set => SetField(ref _filterContainerID, value);	140✔
53	}
54
55	#endregion
56
57	#region Relationships
58
59	/// <summary>
60	/// Returns all parameters declared against this filter (does not include other parameters in scope e.g. globals)
61	/// </summary>
62	[NoMappingToDatabase]
63	public DeployedExtractionFilterParameter[] ExtractionFilterParameters => Repository	48✔
64	.GetAllObjectsWhere<DeployedExtractionFilterParameter>("ExtractionFilter_ID", ID).ToArray();	48✔
65
66	/// <inheritdoc/>
67	[NoMappingToDatabase]
68	public override IContainer FilterContainer => FilterContainer_ID.HasValue	8!
69	? Repository.GetObjectByID<FilterContainer>(FilterContainer_ID.Value)	8✔
70	: null;	8✔
71
72	#endregion
73
74	/// <inheritdoc/>
75	public override ColumnInfo GetColumnInfoIfExists() => null;	26✔
76
77	/// <inheritdoc/>
78	public override IFilterFactory GetFilterFactory() =>
79	new DeployedExtractionFilterFactory((IDataExportRepository)Repository);	8✔
80
81	/// <inheritdoc/>
82	public override Catalogue GetCatalogue()
83	{
84	var ds = GetDataset().ExtractableDataSet;	16✔
85	try
86	{
87	return (Catalogue)ds.Catalogue;	16✔
88	}
89	catch (Exception)	×
90	{
91	//could be that the catalogue has been deleted
92	return null;	×
93	}
94	}	16✔
95
96	/// <inheritdoc/>
97	public override ISqlParameter[] GetAllParameters() => ExtractionFilterParameters.Cast<ISqlParameter>().ToArray();	42✔
98
99	public DeployedExtractionFilter()	×
100	{
101	}	×
102
103	/// <summary>
104	/// Creates a new empty WHERE filter in the given <paramref name="container"/> that will be used when
105	/// extracting the dataset.
106	///
107	/// <para>This object is created into the data export metadata database</para>
108	/// </summary>
109	/// <param name="repository"></param>
110	/// <param name="name"></param>
111	/// <param name="container"></param>
112	public DeployedExtractionFilter(IDataExportRepository repository, string name, FilterContainer container)	36✔
113	{
114	Repository = repository;	36✔
115	Repository.InsertAndHydrate(this, new Dictionary<string, object>	36!
116	{	36✔
117	{ "Name", name != null ? (object)name : DBNull.Value },	36✔
118	{ "FilterContainer_ID", container != null ? (object)container.ID : DBNull.Value }	36✔
119	});	36✔
120	}	36✔
121
122	/// <summary>
123	/// Read an existing WHERE filter out of the database
124	/// </summary>
125	/// <param name="repository"></param>
126	/// <param name="r"></param>
127	internal DeployedExtractionFilter(IDataExportRepository repository, DbDataReader r)
128	: base(repository, r)	86✔
129	{
130	WhereSQL = r["WhereSQL"] as string;	86✔
131	Description = r["Description"] as string;	86✔
132	Name = r["Name"] as string;	86✔
133	IsMandatory = (bool)r["IsMandatory"];	86✔
134
135	if (r["FilterContainer_ID"] != null && !string.IsNullOrWhiteSpace(r["FilterContainer_ID"].ToString()))	86✔
136	FilterContainer_ID = int.Parse(r["FilterContainer_ID"].ToString());	78✔
137	else
138	FilterContainer_ID = null;	8✔
139
140	ClonedFromExtractionFilter_ID = ObjectToNullableInt(r["ClonedFromExtractionFilter_ID"]);	86✔
141	}	86✔
142
143	/// <summary>
144	/// Returns Name of filters
145	/// </summary>
146	/// <returns></returns>
147	public override string ToString() => Name;	10✔
148
149
150	/// <summary>
151	/// Checks the filter is properly defined (e.g. not blank).
152	/// </summary>
153	/// <param name="notifier"></param>
154	public override void Check(ICheckNotifier notifier)
155	{
156	base.Check(notifier);	10✔
157
158	var checker = new ClonedFilterChecker(this, ClonedFromExtractionFilter_ID,	10✔
159	((IDataExportRepository)Repository).CatalogueRepository);	10✔
160	checker.Check(notifier);	10✔
161	}	10✔
162
163	/// <summary>
164	/// Returns the configuration and dataset (<see cref="ISelectedDataSets"/>) in which the filter is declared. This involves traversing
165	/// up any nested <see cref="FilterContainer"/>s to the root.
166	///
167	/// <para>Returns null if the filter is an orphan (not in a container or part of an orphan container tree)</para>
168	/// </summary>
169	/// <returns></returns>
170	public SelectedDataSets GetDataset()
171	{
172	if (FilterContainer_ID == null)	16!
173	return null;	×
174
175	var container = Repository.GetObjectByID<FilterContainer>(FilterContainer_ID.Value);	16✔
176	return container.GetSelectedDataSetsRecursively();	16✔
177	}
178
179	public DeployedExtractionFilter ShallowClone(FilterContainer into)
180	{
181	var clone = new DeployedExtractionFilter(DataExportRepository, Name, into);	4✔
182	CopyShallowValuesTo(clone);	4✔
183	return clone;	4✔
184	}
185	}

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