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

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83.02

/Rdmp.Core/DataExport/Checks/ExtractionConfigurationChecker.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.IO;
using System.Linq;
using Rdmp.Core.CommandExecution;
using Rdmp.Core.Curation.Data;
using Rdmp.Core.DataExport.Data;
using Rdmp.Core.DataExport.DataExtraction;
using Rdmp.Core.Repositories;
using Rdmp.Core.ReusableLibraryCode.Checks;

namespace Rdmp.Core.DataExport.Checks;

/// <summary>
/// Checks <see cref="ExtractionConfiguration"/> to ensure they are in a valid state for execution (have a cohort, linkable patient columns etc).  Optionally also checks
/// each dataset in the configuration with a <see cref="SelectedDataSetsChecker"/>
/// </summary>
public class ExtractionConfigurationChecker : ICheckable
{
    private IExtractionConfiguration _config;
    private IBasicActivateItems _activator;

    /// <summary>
    /// True to fetch all <see cref="ISelectedDataSets"/> and check with <see cref="SelectedDataSetsChecker"/>
    /// </summary>
    public bool CheckDatasets { get; set; }

    /// <summary>
    /// True to also check all globals with a <see cref="GlobalExtractionChecker"/>
    /// </summary>
    public bool CheckGlobals { get; set; }

    /// <summary>
    /// Prepares checking of the given <paramref name="config"/>
    /// </summary>
    /// <param name="activator"></param>
    /// <param name="config"></param>
    public ExtractionConfigurationChecker(IBasicActivateItems activator, IExtractionConfiguration config)
    {
        _config = config;
        _activator = activator;
    }

    /// <summary>
    /// Checks that the configuration is in a valid state.  Supports both released (frozen) <see cref="ExtractionConfiguration"/> and unreleased ones.
    /// </summary>
    /// <param name="notifier"></param>
    public void Check(ICheckNotifier notifier)
    {
        if (_config.IsReleased)
            CheckReleaseConfiguration(notifier);
        else
            CheckInProgressConfiguration(notifier);
    }

    private void CheckReleaseConfiguration(ICheckNotifier notifier)
    {
        var projectDirectory = new DirectoryInfo(_config.Project.ExtractionDirectory);

        notifier.OnCheckPerformed(new CheckEventArgs($"Found Frozen/Released configuration '{_config}'",
            CheckResult.Success));

        foreach (var directoryInfo in projectDirectory.GetDirectories(
                     $"{ExtractionDirectory.GetExtractionDirectoryPrefix(_config)}*").ToArray())
            if (DirectoryIsEmpty(directoryInfo, out var firstFileFound))
            {
                var deleteIt =
                    notifier.OnCheckPerformed(
                        new CheckEventArgs(
                            $"Found empty folder {directoryInfo.Name} which is left over extracted folder after data release",
                            CheckResult.Warning, null,
                            "Delete empty folder"));

                if (deleteIt)
                    directoryInfo.Delete(true);
            }
            else
            {
                notifier.OnCheckPerformed(
                    new CheckEventArgs(
                        $"Found non-empty folder {directoryInfo.Name} which is left over extracted folder after data release (First file found was '{firstFileFound}' but there may be others)",
                        CheckResult.Fail));
            }
    }

    private bool DirectoryIsEmpty(DirectoryInfo d, out string firstFileFound)
    {
        var found = d.GetFiles().FirstOrDefault();
        if (found != null)
        {
            firstFileFound = found.FullName;
            return false;
        }

        foreach (var directory in d.GetDirectories())
            if (!DirectoryIsEmpty(directory, out firstFileFound))
                return false;

        firstFileFound = null;
        return true;
    }

    private void CheckInProgressConfiguration(ICheckNotifier notifier)
    {
        var repo = (IDataExportRepository)_config.Repository;
        notifier.OnCheckPerformed(new CheckEventArgs($"Found configuration '{_config}'", CheckResult.Success));

        var datasets = _config.GetAllExtractableDataSets().ToArray();

        foreach (ExtractableDataSet dataSet in datasets)
            if (dataSet.DisableExtraction)
                notifier.OnCheckPerformed(
                    new CheckEventArgs(
                        $"Dataset {dataSet} is set to DisableExtraction=true, probably someone doesn't want you extracting this dataset at the moment",
                        CheckResult.Fail));

        if (!datasets.Any())
            notifier.OnCheckPerformed(
                new CheckEventArgs(
                    $"There are no datasets selected for open configuration '{_config}'",
                    CheckResult.Fail));

        if (_config.Cohort_ID == null)
        {
            notifier.OnCheckPerformed(
                new CheckEventArgs(
                    $"Open configuration '{_config}' does not have a cohort yet",
                    CheckResult.Fail));
            return;
        }

        //make sure that its cohort is retrievable
        var cohort = repo.GetObjectByID<ExtractableCohort>((int)_config.Cohort_ID);
        if (cohort.IsDeprecated)
            notifier.OnCheckPerformed(
                new CheckEventArgs(
                    $"Cohort '{cohort}' is marked IsDeprecated",
                    CheckResult.Fail));

        if (CheckDatasets)
            foreach (var s in _config.SelectedDataSets)
                new SelectedDataSetsChecker(_activator, s).Check(notifier);

        //globals
        if (CheckGlobals)
            if (datasets.Any())
                foreach (var table in _config.GetGlobals().OfType<SupportingSQLTable>())
                    new SupportingSQLTableChecker(table).Check(notifier);
    }
}

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.IO;
8	using System.Linq;
9	using Rdmp.Core.CommandExecution;
10	using Rdmp.Core.Curation.Data;
11	using Rdmp.Core.DataExport.Data;
12	using Rdmp.Core.DataExport.DataExtraction;
13	using Rdmp.Core.Repositories;
14	using Rdmp.Core.ReusableLibraryCode.Checks;
15
16	namespace Rdmp.Core.DataExport.Checks;
17
18	/// <summary>
19	/// Checks <see cref="ExtractionConfiguration"/> to ensure they are in a valid state for execution (have a cohort, linkable patient columns etc). Optionally also checks
20	/// each dataset in the configuration with a <see cref="SelectedDataSetsChecker"/>
21	/// </summary>
22	public class ExtractionConfigurationChecker : ICheckable
23	{
24	private IExtractionConfiguration _config;
25	private IBasicActivateItems _activator;
26
27	/// <summary>
28	/// True to fetch all <see cref="ISelectedDataSets"/> and check with <see cref="SelectedDataSetsChecker"/>
29	/// </summary>
30	public bool CheckDatasets { get; set; }	12✔
31
32	/// <summary>
33	/// True to also check all globals with a <see cref="GlobalExtractionChecker"/>
34	/// </summary>
35	public bool CheckGlobals { get; set; }	2✔
36
37	/// <summary>
38	/// Prepares checking of the given <paramref name="config"/>
39	/// </summary>
40	/// <param name="activator"></param>
41	/// <param name="config"></param>
42	public ExtractionConfigurationChecker(IBasicActivateItems activator, IExtractionConfiguration config)	10✔
43	{
44	_config = config;	10✔
45	_activator = activator;	10✔
46	}	10✔
47
48	/// <summary>
49	/// Checks that the configuration is in a valid state. Supports both released (frozen) <see cref="ExtractionConfiguration"/> and unreleased ones.
50	/// </summary>
51	/// <param name="notifier"></param>
52	public void Check(ICheckNotifier notifier)
53	{
54	if (_config.IsReleased)	10✔
55	CheckReleaseConfiguration(notifier);	4✔
56	else
57	CheckInProgressConfiguration(notifier);	6✔
58	}	2✔
59
60	private void CheckReleaseConfiguration(ICheckNotifier notifier)
61	{
62	var projectDirectory = new DirectoryInfo(_config.Project.ExtractionDirectory);	4✔
63
64	notifier.OnCheckPerformed(new CheckEventArgs($"Found Frozen/Released configuration '{_config}'",	4✔
65	CheckResult.Success));	4✔
66
67	foreach (var directoryInfo in projectDirectory.GetDirectories(	16✔
68	$"{ExtractionDirectory.GetExtractionDirectoryPrefix(_config)}*").ToArray())	4✔
69	if (DirectoryIsEmpty(directoryInfo, out var firstFileFound))	4✔
70	{
71	var deleteIt =	2✔
72	notifier.OnCheckPerformed(	2✔
73	new CheckEventArgs(	2✔
74	$"Found empty folder {directoryInfo.Name} which is left over extracted folder after data release",	2✔
75	CheckResult.Warning, null,	2✔
76	"Delete empty folder"));	2✔
77
78	if (deleteIt)	2✔
79	directoryInfo.Delete(true);	2✔
80	}
81	else
82	{
83	notifier.OnCheckPerformed(	2✔
84	new CheckEventArgs(	2✔
85	$"Found non-empty folder {directoryInfo.Name} which is left over extracted folder after data release (First file found was '{firstFileFound}' but there may be others)",	2✔
86	CheckResult.Fail));	2✔
87	}
88	}	4✔
89
90	private bool DirectoryIsEmpty(DirectoryInfo d, out string firstFileFound)
91	{
92	var found = d.GetFiles().FirstOrDefault();	12✔
93	if (found != null)	12✔
94	{
95	firstFileFound = found.FullName;	2✔
96	return false;	2✔
97	}
98
99	foreach (var directory in d.GetDirectories())	32✔
100	if (!DirectoryIsEmpty(directory, out firstFileFound))	8✔
101	return false;	4✔
102
103	firstFileFound = null;	6✔
104	return true;	6✔
105	}
106
107	private void CheckInProgressConfiguration(ICheckNotifier notifier)
108	{
109	var repo = (IDataExportRepository)_config.Repository;	6✔
110	notifier.OnCheckPerformed(new CheckEventArgs($"Found configuration '{_config}'", CheckResult.Success));	6✔
111
112	var datasets = _config.GetAllExtractableDataSets().ToArray();	6✔
113
114	foreach (ExtractableDataSet dataSet in datasets)	18✔
115	if (dataSet.DisableExtraction)	4✔
116	notifier.OnCheckPerformed(	2✔
117	new CheckEventArgs(	2✔
118	$"Dataset {dataSet} is set to DisableExtraction=true, probably someone doesn't want you extracting this dataset at the moment",	2✔
119	CheckResult.Fail));	2✔
120
121	if (!datasets.Any())	4✔
122	notifier.OnCheckPerformed(	2✔
123	new CheckEventArgs(	2✔
124	$"There are no datasets selected for open configuration '{_config}'",	2✔
125	CheckResult.Fail));	2✔
126
127	if (_config.Cohort_ID == null)	2!
128	{
129	notifier.OnCheckPerformed(	×
130	new CheckEventArgs(	×
131	$"Open configuration '{_config}' does not have a cohort yet",	×
132	CheckResult.Fail));	×
133	return;	×
134	}
135
136	//make sure that its cohort is retrievable
137	var cohort = repo.GetObjectByID<ExtractableCohort>((int)_config.Cohort_ID);	2✔
138	if (cohort.IsDeprecated)	2!
139	notifier.OnCheckPerformed(	×
140	new CheckEventArgs(	×
141	$"Cohort '{cohort}' is marked IsDeprecated",	×
142	CheckResult.Fail));	×
143
144	if (CheckDatasets)	2✔
145	foreach (var s in _config.SelectedDataSets)	8✔
146	new SelectedDataSetsChecker(_activator, s).Check(notifier);	2✔
147
148	//globals
149	if (CheckGlobals)	2!
150	if (datasets.Any())	×
151	foreach (var table in _config.GetGlobals().OfType<SupportingSQLTable>())	×
152	new SupportingSQLTableChecker(table).Check(notifier);	×
153	}	2✔
154	}

HicServices / RDMP / 6245535001

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