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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25.98

/Rdmp.Core/CommandExecution/AtomicCommands/ExecuteCommandViewData.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.IO;
using System.Linq;
using NLog;
using Rdmp.Core.Curation.Data;
using Rdmp.Core.Curation.Data.Aggregation;
using Rdmp.Core.Curation.Data.Cohort;
using Rdmp.Core.DataExport.Data;
using Rdmp.Core.DataViewing;
using Rdmp.Core.MapsDirectlyToDatabaseTable;
using Rdmp.Core.Repositories.Construction;

namespace Rdmp.Core.CommandExecution.AtomicCommands;

public class ExecuteCommandViewData : ExecuteCommandViewDataBase, IAtomicCommand
{
    private readonly IViewSQLAndResultsCollection _collection;
    private readonly ViewType _viewType;
    private readonly IMapsDirectlyToDatabaseTable _obj;
    private readonly bool _useCache;

    #region Constructors

    /// <summary>
    /// Provides a view of a sample of records in a column/table
    /// </summary>
    /// <param name="activator"></param>
    /// <param name="viewType"></param>
    /// <param name="toFile"></param>
    /// <param name="useCache"></param>
    /// <param name="obj"></param>
    /// <exception cref="ArgumentException"></exception>
    [UseWithObjectConstructor]
    public ExecuteCommandViewData(IBasicActivateItems activator,
        [DemandsInitialization("The object (ColumnInfo, TableInfo etc) you want to view a sample of")]
        IMapsDirectlyToDatabaseTable obj,
        [DemandsInitialization(
            "Optional. The view mode you want to see.  Options include 'TOP_100', 'Aggregate', 'Distribution' or 'All'",
            DefaultValue = ViewType.TOP_100)]
        ViewType viewType = ViewType.TOP_100,
        [DemandsInitialization(ToFileDescription)]
        FileInfo toFile = null,
        [DemandsInitialization(
            "Applies only to CohortIdentificationConfigurations.  Defaults to true.  Set to false to disable query cache use.")]
        bool useCache = true) : base(activator, toFile)
    {
        _viewType = viewType;
        _obj = obj;
        _useCache = useCache;

        switch (obj)
        {
            case TableInfo ti:
                ThrowIfNotSimpleSelectViewType();
                _collection = new ViewTableInfoExtractUICollection(ti, _viewType);
                break;
            case ColumnInfo col:
                _collection = CreateCollection(col);
                break;
            case ExtractionInformation ei:
                _collection = CreateCollection(ei);
                break;
            case Catalogue cata:
                ThrowIfNotSimpleSelectViewType();
                _collection = CreateCollection(cata);
                break;
            case CohortIdentificationConfiguration cic:
                ThrowIfNotSimpleSelectViewType();
                _collection = CreateCollection(cic);
                break;
            case ExtractableCohort ec:
                ThrowIfNotSimpleSelectViewType();
                _collection = CreateCollection(ec);
                break;
            case AggregateConfiguration ac:
                ThrowIfNotSimpleSelectViewType();
                _collection = CreateCollection(ac);
                break;
            default:
                throw new ArgumentException($"Object '{obj}' was not an object type compatible with this command");
        }
    }

    private IViewSQLAndResultsCollection CreateCollection(AggregateConfiguration ac)
    {
        var cic = ac.GetCohortIdentificationConfigurationIfAny();

        var collection = new ViewAggregateExtractUICollection(ac);

        //if it has a cic with a query cache AND it uses joinables.  Since this is a TOP 100 select * from dataset the cache on CHI is useless only patient index tables used by this query are useful if cached
        if (cic is { QueryCachingServer_ID: not null } && ac.PatientIndexJoinablesUsed.Any())
            collection.UseQueryCache = _useCache;

        collection.TopX = _viewType == ViewType.TOP_100 ? 100 : null;

        return collection;
    }

    private IViewSQLAndResultsCollection CreateCollection(ExtractableCohort ec) =>
        new ViewCohortExtractionUICollection(ec)
        {
            Top = _viewType == ViewType.TOP_100 ? 100 : -1,
            IncludeCohortID = false
        };

    private IViewSQLAndResultsCollection CreateCollection(CohortIdentificationConfiguration cic)
    {
        if (_viewType == ViewType.TOP_100)
            LogManager.GetCurrentClassLogger()
                .Warn(
                    $"'{ViewType.TOP_100}' is not supported on '{nameof(CohortIdentificationConfiguration)}', '{ViewType.All}' will be used");

        return new ViewCohortIdentificationConfigurationSqlCollection(cic)
        {
            UseQueryCache = _useCache
        };
    }

    private void ThrowIfNotSimpleSelectViewType()
    {
        if (_viewType != ViewType.TOP_100 && _viewType != ViewType.All)
            throw new ArgumentException(
                $"Only '{nameof(ViewType.TOP_100)}' or '{nameof(ViewType.All)}' can be used for this object Type");
    }

    private IViewSQLAndResultsCollection CreateCollection(Catalogue cata) =>
        new ViewCatalogueDataCollection(cata)
        {
            TopX = _viewType == ViewType.All ? null : 100
        };

    /// <summary>
    /// Fetches the <paramref name="viewType"/> of the data in <see cref="ColumnInfo"/> <paramref name="c"/>
    /// </summary>
    /// <param name="activator"></param>
    /// <param name="viewType"></param>
    /// <param name="c"></param>
    public ExecuteCommandViewData(IBasicActivateItems activator, ViewType viewType, ColumnInfo c) : base(activator,
        null)
    {
        _viewType = viewType;
        _collection = CreateCollection(c);
    }

    public ExecuteCommandViewData(IBasicActivateItems activator, ViewType viewType, ExtractionInformation ei) : base(
        activator, null)
    {
        _viewType = viewType;
        _collection = CreateCollection(ei);
    }

    /// <summary>
    /// Views the top 100 records of the <paramref name="tableInfo"/>
    /// </summary>
    /// <param name="activator"></param>
    /// <param name="tableInfo"></param>
    public ExecuteCommandViewData(IBasicActivateItems activator, TableInfo tableInfo) : base(activator, null)
    {
        _viewType = ViewType.TOP_100;
        _collection = new ViewTableInfoExtractUICollection(tableInfo, _viewType);
    }

    #endregion

    private IViewSQLAndResultsCollection CreateCollection(ColumnInfo c)
    {
        var toReturn = new ViewColumnExtractCollection(c, _viewType);

        if (!c.IsNumerical() && _viewType == ViewType.Distribution)
            SetImpossible("Column is not numerical");

        return toReturn;
    }

    private IViewSQLAndResultsCollection CreateCollection(ExtractionInformation ei)
    {
        var toReturn = new ViewColumnExtractCollection(ei, _viewType);
        if ((!ei.ColumnInfo?.IsNumerical() ?? false) && _viewType == ViewType.Distribution)
            SetImpossible("Column is not numerical");

        return toReturn;
    }

    public override string GetCommandName()
    {
        // if user has set an override, respect it
        if (!string.IsNullOrWhiteSpace(OverrideCommandName))
            return OverrideCommandName;

        return _obj is CohortIdentificationConfiguration
            ? _useCache ? "Query Builder SQL/Results" : "Query Builder SQL/Results (No Cache)"
            : $"View {_viewType.ToString().Replace("_", " ")}";
    }

    protected override IViewSQLAndResultsCollection GetCollection() => _collection;
}

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.IO;
9	using System.Linq;
10	using NLog;
11	using Rdmp.Core.Curation.Data;
12	using Rdmp.Core.Curation.Data.Aggregation;
13	using Rdmp.Core.Curation.Data.Cohort;
14	using Rdmp.Core.DataExport.Data;
15	using Rdmp.Core.DataViewing;
16	using Rdmp.Core.MapsDirectlyToDatabaseTable;
17	using Rdmp.Core.Repositories.Construction;
18
19	namespace Rdmp.Core.CommandExecution.AtomicCommands;
20
21	public class ExecuteCommandViewData : ExecuteCommandViewDataBase, IAtomicCommand
22	{
23	private readonly IViewSQLAndResultsCollection _collection;
24	private readonly ViewType _viewType;
25	private readonly IMapsDirectlyToDatabaseTable _obj;
26	private readonly bool _useCache;
27
28	#region Constructors
29
30	/// <summary>
31	/// Provides a view of a sample of records in a column/table
32	/// </summary>
33	/// <param name="activator"></param>
34	/// <param name="viewType"></param>
35	/// <param name="toFile"></param>
36	/// <param name="useCache"></param>
37	/// <param name="obj"></param>
38	/// <exception cref="ArgumentException"></exception>
39	[UseWithObjectConstructor]
40	public ExecuteCommandViewData(IBasicActivateItems activator,
41	[DemandsInitialization("The object (ColumnInfo, TableInfo etc) you want to view a sample of")]
42	IMapsDirectlyToDatabaseTable obj,
43	[DemandsInitialization(
44	"Optional. The view mode you want to see. Options include 'TOP_100', 'Aggregate', 'Distribution' or 'All'",
45	DefaultValue = ViewType.TOP_100)]
46	ViewType viewType = ViewType.TOP_100,
47	[DemandsInitialization(ToFileDescription)]
48	FileInfo toFile = null,
49	[DemandsInitialization(
50	"Applies only to CohortIdentificationConfigurations. Defaults to true. Set to false to disable query cache use.")]
51	bool useCache = true) : base(activator, toFile)	10✔
52	{
53	_viewType = viewType;	10✔
54	_obj = obj;	10✔
55	_useCache = useCache;	10!
56
57	switch (obj)
58	{
59	case TableInfo ti:
60	ThrowIfNotSimpleSelectViewType();	×
61	_collection = new ViewTableInfoExtractUICollection(ti, _viewType);	×
62	break;	×
63	case ColumnInfo col:
64	_collection = CreateCollection(col);	×
65	break;	×
66	case ExtractionInformation ei:
67	_collection = CreateCollection(ei);	×
68	break;	×
69	case Catalogue cata:
70	ThrowIfNotSimpleSelectViewType();	×
71	_collection = CreateCollection(cata);	×
72	break;	×
73	case CohortIdentificationConfiguration cic:
74	ThrowIfNotSimpleSelectViewType();	×
75	_collection = CreateCollection(cic);	×
76	break;	×
77	case ExtractableCohort ec:
78	ThrowIfNotSimpleSelectViewType();	×
79	_collection = CreateCollection(ec);	×
80	break;	×
81	case AggregateConfiguration ac:
82	ThrowIfNotSimpleSelectViewType();	10✔
83	_collection = CreateCollection(ac);	10✔
84	break;	10✔
85	default:
86	throw new ArgumentException($"Object '{obj}' was not an object type compatible with this command");	×
87	}
88	}
89
90	private IViewSQLAndResultsCollection CreateCollection(AggregateConfiguration ac)
91	{
92	var cic = ac.GetCohortIdentificationConfigurationIfAny();	10✔
93
94	var collection = new ViewAggregateExtractUICollection(ac);	10✔
95
96	//if it has a cic with a query cache AND it uses joinables. Since this is a TOP 100 select * from dataset the cache on CHI is useless only patient index tables used by this query are useful if cached
97	if (cic is { QueryCachingServer_ID: not null } && ac.PatientIndexJoinablesUsed.Any())	10!
98	collection.UseQueryCache = _useCache;	×
99
100	collection.TopX = _viewType == ViewType.TOP_100 ? 100 : null;	10!
101
102	return collection;	10✔
103	}
104
105	private IViewSQLAndResultsCollection CreateCollection(ExtractableCohort ec) =>
106	new ViewCohortExtractionUICollection(ec)	×
107	{	×
108	Top = _viewType == ViewType.TOP_100 ? 100 : -1,	×
109	IncludeCohortID = false	×
110	};	×
111
112	private IViewSQLAndResultsCollection CreateCollection(CohortIdentificationConfiguration cic)
113	{
114	if (_viewType == ViewType.TOP_100)	×
115	LogManager.GetCurrentClassLogger()	×
116	.Warn(	×
117	$"'{ViewType.TOP_100}' is not supported on '{nameof(CohortIdentificationConfiguration)}', '{ViewType.All}' will be used");	×
118
119	return new ViewCohortIdentificationConfigurationSqlCollection(cic)	×
120	{	×
121	UseQueryCache = _useCache	×
122	};	×
123	}
124
125	private void ThrowIfNotSimpleSelectViewType()
126	{
127	if (_viewType != ViewType.TOP_100 && _viewType != ViewType.All)	10!
128	throw new ArgumentException(	×
129	$"Only '{nameof(ViewType.TOP_100)}' or '{nameof(ViewType.All)}' can be used for this object Type");	×
130	}	10✔
131
132	private IViewSQLAndResultsCollection CreateCollection(Catalogue cata) =>
133	new ViewCatalogueDataCollection(cata)	×
134	{	×
135	TopX = _viewType == ViewType.All ? null : 100	×
136	};	×
137
138	/// <summary>
139	/// Fetches the <paramref name="viewType"/> of the data in <see cref="ColumnInfo"/> <paramref name="c"/>
140	/// </summary>
141	/// <param name="activator"></param>
142	/// <param name="viewType"></param>
143	/// <param name="c"></param>
144	public ExecuteCommandViewData(IBasicActivateItems activator, ViewType viewType, ColumnInfo c) : base(activator,	×
145	null)	×
146	{
147	_viewType = viewType;	×
148	_collection = CreateCollection(c);	×
149	}	×
150
151	public ExecuteCommandViewData(IBasicActivateItems activator, ViewType viewType, ExtractionInformation ei) : base(	×
152	activator, null)	×
153	{
154	_viewType = viewType;	×
155	_collection = CreateCollection(ei);	×
156	}	×
157
158	/// <summary>
159	/// Views the top 100 records of the <paramref name="tableInfo"/>
160	/// </summary>
161	/// <param name="activator"></param>
162	/// <param name="tableInfo"></param>
163	public ExecuteCommandViewData(IBasicActivateItems activator, TableInfo tableInfo) : base(activator, null)	×
164	{
165	_viewType = ViewType.TOP_100;	×
166	_collection = new ViewTableInfoExtractUICollection(tableInfo, _viewType);	×
167	}	×
168
169	#endregion
170
171	private IViewSQLAndResultsCollection CreateCollection(ColumnInfo c)
172	{
173	var toReturn = new ViewColumnExtractCollection(c, _viewType);	×
174
175	if (!c.IsNumerical() && _viewType == ViewType.Distribution)	×
176	SetImpossible("Column is not numerical");	×
177
178	return toReturn;	×
179	}
180
181	private IViewSQLAndResultsCollection CreateCollection(ExtractionInformation ei)
182	{
183	var toReturn = new ViewColumnExtractCollection(ei, _viewType);	×
184	if ((!ei.ColumnInfo?.IsNumerical() ?? false) && _viewType == ViewType.Distribution)	×
185	SetImpossible("Column is not numerical");	×
186
187	return toReturn;	×
188	}
189
190	public override string GetCommandName()
191	{
192	// if user has set an override, respect it
193	if (!string.IsNullOrWhiteSpace(OverrideCommandName))	10!
194	return OverrideCommandName;	×
195
196	return _obj is CohortIdentificationConfiguration	10!
197	? _useCache ? "Query Builder SQL/Results" : "Query Builder SQL/Results (No Cache)"	10✔
198	: $"View {_viewType.ToString().Replace("_", " ")}";	10✔
199	}
200
201	protected override IViewSQLAndResultsCollection GetCollection() => _collection;	×
202	}

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