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%)

7387.88 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

19.05

/Rdmp.Core/Providers/DataExportProblemProvider.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.Linq;
using Rdmp.Core.DataExport.Data;
using Rdmp.Core.Providers.Nodes;
using Rdmp.Core.Providers.Nodes.ProjectCohortNodes;

namespace Rdmp.Core.Providers;

/// <summary>
/// Identifies all rapidly detectable problems with the configurations of Data Export items
/// </summary>
public class DataExportProblemProvider : ProblemProvider
{
    private DataExportChildProvider _exportChildProvider;

    /// <inheritdoc/>
    public override void RefreshProblems(ICoreChildProvider childProvider)
    {
        _exportChildProvider = childProvider as DataExportChildProvider;
    }


    /// <inheritdoc/>
    protected override string DescribeProblemImpl(object o)
    {
        return o switch
        {
            Project project => DescribeProblem(project),
            ProjectSavedCohortsNode node => DescribeProblem(node),
            ExtractionConfigurationsNode node => DescribeProblem(node),
            SelectedDataSets sets => DescribeProblem(sets),
            ExtractionConfiguration configuration => DescribeProblem(configuration),
            ExternalCohortTable table => DescribeProblem(table),
            ExtractionDirectoryNode node => DescribeProblem(node),
            _ => null
        };
    }

    private string DescribeProblem(ExternalCohortTable externalCohortTable) =>
        _exportChildProvider != null && _exportChildProvider.ForbidListedSources.Contains(externalCohortTable)
            ? "Cohort Source database was unreachable"
            : null;

    private string DescribeProblem(ExtractionConfiguration extractionConfiguration)
    {
        if (extractionConfiguration.Cohort_ID == null)
            return "Configuration has no Cohort configured. You must add a Saved Cohort to enable extraction.";

        if (_exportChildProvider != null)
            if (!_exportChildProvider.GetDatasets(extractionConfiguration).Any()) //there are no selected datasets!
                return
                    "Configuration has no selected datasets. Add existing Datasets or Packages to enable extraction.";

        return null;
    }

    private string DescribeProblem(SelectedDataSets selectedDataSets)
    {
        if (_exportChildProvider.IsMissingExtractionIdentifier(selectedDataSets))
            return "There are no IsExtractionIdentifier columns in dataset";

        return selectedDataSets.GetCatalogue()?.IsDeprecated ?? false ? "Dataset is deprecated" : null;
    }

    private string DescribeProblem(ExtractionConfigurationsNode extractionConfigurationsNode)
    {
        if (_exportChildProvider.Projects.Contains(extractionConfigurationsNode.Project))
            if (!_exportChildProvider.GetConfigurations(extractionConfigurationsNode.Project).Any())
                return
                    "Project has no ExtractionConfigurations. Add a new ExtractionConfiguration to define how data is extracted for this Project.";

        return null;
    }

    private string DescribeProblem(ProjectSavedCohortsNode projectSavedCohortsNode) =>
        _exportChildProvider.ProjectHasNoSavedCohorts(projectSavedCohortsNode.Project)
            ? "Project has no Cohorts. Commit new Cohort(s) from File/Cohort Query Builder to use with this Project's ExtractionConfigurations"
            : null;


    private static string DescribeProblem(ExtractionDirectoryNode edn) => edn.GetDirectoryInfoIfAny() == null
        ? "No Extraction Directory has been specified"
        : null;

    private static string DescribeProblem(Project project)
    {
        if (project.ProjectNumber == null)
            return "Project has no ProjectNumber";

        return string.IsNullOrWhiteSpace(project.ExtractionDirectory)
            ? "Project has no Extraction Directory configured"
            : null;
    }
}

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.Linq;
8	using Rdmp.Core.DataExport.Data;
9	using Rdmp.Core.Providers.Nodes;
10	using Rdmp.Core.Providers.Nodes.ProjectCohortNodes;
11
12	namespace Rdmp.Core.Providers;
13
14	/// <summary>
15	/// Identifies all rapidly detectable problems with the configurations of Data Export items
16	/// </summary>
17	public class DataExportProblemProvider : ProblemProvider
18	{
19	private DataExportChildProvider _exportChildProvider;
20
21	/// <inheritdoc/>
22	public override void RefreshProblems(ICoreChildProvider childProvider)
23	{
24	_exportChildProvider = childProvider as DataExportChildProvider;	×
25	}	×
26
27
28	/// <inheritdoc/>
29	protected override string DescribeProblemImpl(object o)
30	{
31	return o switch	70!
32	{	70✔
33	Project project => DescribeProblem(project),	8✔
34	ProjectSavedCohortsNode node => DescribeProblem(node),	×
35	ExtractionConfigurationsNode node => DescribeProblem(node),	×
36	SelectedDataSets sets => DescribeProblem(sets),	×
37	ExtractionConfiguration configuration => DescribeProblem(configuration),	×
38	ExternalCohortTable table => DescribeProblem(table),	×
39	ExtractionDirectoryNode node => DescribeProblem(node),	×
40	_ => null	62✔
41	};	70✔
42	}
43
44	private string DescribeProblem(ExternalCohortTable externalCohortTable) =>
45	_exportChildProvider != null && _exportChildProvider.ForbidListedSources.Contains(externalCohortTable)	×
46	? "Cohort Source database was unreachable"	×
47	: null;	×
48
49	private string DescribeProblem(ExtractionConfiguration extractionConfiguration)
50	{
51	if (extractionConfiguration.Cohort_ID == null)	×
52	return "Configuration has no Cohort configured. You must add a Saved Cohort to enable extraction.";	×
53
54	if (_exportChildProvider != null)	×
55	if (!_exportChildProvider.GetDatasets(extractionConfiguration).Any()) //there are no selected datasets!	×
56	return	×
57	"Configuration has no selected datasets. Add existing Datasets or Packages to enable extraction.";	×
58
59	return null;	×
60	}
61
62	private string DescribeProblem(SelectedDataSets selectedDataSets)
63	{
64	if (_exportChildProvider.IsMissingExtractionIdentifier(selectedDataSets))	×
65	return "There are no IsExtractionIdentifier columns in dataset";	×
66
67	return selectedDataSets.GetCatalogue()?.IsDeprecated ?? false ? "Dataset is deprecated" : null;	×
68	}
69
70	private string DescribeProblem(ExtractionConfigurationsNode extractionConfigurationsNode)
71	{
72	if (_exportChildProvider.Projects.Contains(extractionConfigurationsNode.Project))	×
73	if (!_exportChildProvider.GetConfigurations(extractionConfigurationsNode.Project).Any())	×
74	return	×
75	"Project has no ExtractionConfigurations. Add a new ExtractionConfiguration to define how data is extracted for this Project.";	×
76
77	return null;	×
78	}
79
80	private string DescribeProblem(ProjectSavedCohortsNode projectSavedCohortsNode) =>
81	_exportChildProvider.ProjectHasNoSavedCohorts(projectSavedCohortsNode.Project)	×
82	? "Project has no Cohorts. Commit new Cohort(s) from File/Cohort Query Builder to use with this Project's ExtractionConfigurations"	×
83	: null;	×
84
85
86	private static string DescribeProblem(ExtractionDirectoryNode edn) => edn.GetDirectoryInfoIfAny() == null	×
87	? "No Extraction Directory has been specified"	×
88	: null;	×
89
90	private static string DescribeProblem(Project project)
91	{
92	if (project.ProjectNumber == null)	8!
93	return "Project has no ProjectNumber";	8✔
94
95	return string.IsNullOrWhiteSpace(project.ExtractionDirectory)	×
96	? "Project has no Extraction Directory configured"	×
97	: null;	×
98	}
99	}

HicServices / RDMP / 6245535001

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous