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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48141 of 48141 new or added lines in 1086 files covered. (100.0%)

30685 of 52388 relevant lines covered (58.57%)

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0.0

/Rdmp.Core/DataLoad/Modules/DataFlowOperations/ExtractCatalogueMetadata.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.Data;
using System.IO;
using Rdmp.Core.CommandExecution;
using Rdmp.Core.CommandExecution.AtomicCommands;
using Rdmp.Core.Curation.Data;
using Rdmp.Core.DataExport.DataExtraction;
using Rdmp.Core.DataExport.DataExtraction.Commands;
using Rdmp.Core.DataFlowPipeline;
using Rdmp.Core.DataFlowPipeline.Requirements;
using Rdmp.Core.ReusableLibraryCode.Checks;
using Rdmp.Core.ReusableLibraryCode.Progress;

namespace Rdmp.Core.DataLoad.Modules.DataFlowOperations;

/// <summary>
/// Extraction component that will generate share definition files for the catalogues involved in the extraction.
/// 
/// <para>The Metadata Naming Pattern will also override the table name in the DataTable flow object.</para>
/// </summary>
public class ExtractCatalogueMetadata : IPluginDataFlowComponent<DataTable>, IPipelineRequirement<IExtractCommand>,
    IPipelineRequirement<IBasicActivateItems>
{
    private IExtractCommand _request;
    private IBasicActivateItems _activator;

    [DemandsInitialization(@"How do you want to name datasets, use the following tokens if you need them:   
         $p - Project Name ('e.g. My Project')
         $n - Project Number (e.g. 234)
         $c - Configuration Name (e.g. 'Cases')
         $d - Dataset name (e.g. 'Prescribing')
         $a - Dataset acronym (e.g. 'Presc') 

         You must have either $a or $d
         THIS WILL OVERRIDE THE TableNamingPattern at the destination!
         ", Mandatory = true, DefaultValue = "$d")]
    public string MetadataNamingPattern { get; set; }

    public DataTable ProcessPipelineData(DataTable toProcess, IDataLoadEventListener listener,
        GracefulCancellationToken cancellationToken)
    {
        toProcess.TableName = GetTableName();
        toProcess.ExtendedProperties.Add("ProperlyNamed", true);

        if (_request is ExtractDatasetCommand extractDatasetCommand)
        {
            var catalogue = extractDatasetCommand.Catalogue;

            var sourceFolder = _request.GetExtractionDirectory() ??
                               throw new Exception(
                                   "Could not find Source Folder. Does the project have an Extraction Directory defined?");
            var outputFolder = sourceFolder.Parent.CreateSubdirectory(ExtractionDirectory.METADATA_FOLDER_NAME);
            var outputFile = new FileInfo(Path.Combine(outputFolder.FullName, $"{toProcess.TableName}.sd"));

            catalogue.Name = toProcess.TableName;
            var cmd = new ExecuteCommandExportObjectsToFile(_activator, catalogue, outputFile);
            cmd.Execute();
            catalogue.RevertToDatabaseState();
        }

        return toProcess;
    }

    public string GetTableName()
    {
        var tblName = MetadataNamingPattern;
        var project = _request.Configuration.Project;

        tblName = tblName.Replace("$p", project.Name);
        tblName = tblName.Replace("$n", project.ProjectNumber.ToString());
        tblName = tblName.Replace("$c", _request.Configuration.Name);

        switch (_request)
        {
            case ExtractDatasetCommand extractDatasetCommand:
                tblName = tblName.Replace("$d", extractDatasetCommand.DatasetBundle.DataSet.Catalogue.Name);
                tblName = tblName.Replace("$a", extractDatasetCommand.DatasetBundle.DataSet.Catalogue.Acronym);
                break;
            case ExtractGlobalsCommand:
                tblName = tblName.Replace("$d", ExtractionDirectory.GLOBALS_DATA_NAME);
                tblName = tblName.Replace("$a", "G");
                break;
        }

        return tblName;
    }

    public void Dispose(IDataLoadEventListener listener, Exception pipelineFailureExceptionIfAny)
    {
    }

    public void Abort(IDataLoadEventListener listener)
    {
    }

    public void Check(ICheckNotifier notifier)
    {
        if (MetadataNamingPattern != null && MetadataNamingPattern.Contains("$a"))
            if (_request is ExtractDatasetCommand dsRequest && string.IsNullOrWhiteSpace(dsRequest.Catalogue.Acronym))
                notifier.OnCheckPerformed(new CheckEventArgs(
                    $"Catalogue '{dsRequest.Catalogue}' does not have an Acronym but MetadataNamingPattern contains $a",
                    CheckResult.Fail));
    }

    public void PreInitialize(IExtractCommand value, IDataLoadEventListener listener)
    {
        _request = value;
    }

    public void PreInitialize(IBasicActivateItems value, IDataLoadEventListener listener)
    {
        _activator = value;
    }
}

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.Data;
9	using System.IO;
10	using Rdmp.Core.CommandExecution;
11	using Rdmp.Core.CommandExecution.AtomicCommands;
12	using Rdmp.Core.Curation.Data;
13	using Rdmp.Core.DataExport.DataExtraction;
14	using Rdmp.Core.DataExport.DataExtraction.Commands;
15	using Rdmp.Core.DataFlowPipeline;
16	using Rdmp.Core.DataFlowPipeline.Requirements;
17	using Rdmp.Core.ReusableLibraryCode.Checks;
18	using Rdmp.Core.ReusableLibraryCode.Progress;
19
20	namespace Rdmp.Core.DataLoad.Modules.DataFlowOperations;
21
22	/// <summary>
23	/// Extraction component that will generate share definition files for the catalogues involved in the extraction.
24	///
25	/// <para>The Metadata Naming Pattern will also override the table name in the DataTable flow object.</para>
26	/// </summary>
27	public class ExtractCatalogueMetadata : IPluginDataFlowComponent<DataTable>, IPipelineRequirement<IExtractCommand>,
28	IPipelineRequirement<IBasicActivateItems>
29	{
30	private IExtractCommand _request;
31	private IBasicActivateItems _activator;
32
33	[DemandsInitialization(@"How do you want to name datasets, use the following tokens if you need them:
34	$p - Project Name ('e.g. My Project')
35	$n - Project Number (e.g. 234)
36	$c - Configuration Name (e.g. 'Cases')
37	$d - Dataset name (e.g. 'Prescribing')
38	$a - Dataset acronym (e.g. 'Presc')
39
40	You must have either $a or $d
41	THIS WILL OVERRIDE THE TableNamingPattern at the destination!
42	", Mandatory = true, DefaultValue = "$d")]
43	public string MetadataNamingPattern { get; set; }	×
44
45	public DataTable ProcessPipelineData(DataTable toProcess, IDataLoadEventListener listener,
46	GracefulCancellationToken cancellationToken)
47	{
48	toProcess.TableName = GetTableName();	×
49	toProcess.ExtendedProperties.Add("ProperlyNamed", true);	×
50
51	if (_request is ExtractDatasetCommand extractDatasetCommand)	×
52	{
53	var catalogue = extractDatasetCommand.Catalogue;	×
54
55	var sourceFolder = _request.GetExtractionDirectory() ??	×
56	throw new Exception(	×
57	"Could not find Source Folder. Does the project have an Extraction Directory defined?");	×
58	var outputFolder = sourceFolder.Parent.CreateSubdirectory(ExtractionDirectory.METADATA_FOLDER_NAME);	×
59	var outputFile = new FileInfo(Path.Combine(outputFolder.FullName, $"{toProcess.TableName}.sd"));	×
60
61	catalogue.Name = toProcess.TableName;	×
62	var cmd = new ExecuteCommandExportObjectsToFile(_activator, catalogue, outputFile);	×
63	cmd.Execute();	×
64	catalogue.RevertToDatabaseState();	×
65	}
66
67	return toProcess;	×
68	}
69
70	public string GetTableName()
71	{
72	var tblName = MetadataNamingPattern;	×
73	var project = _request.Configuration.Project;	×
74
75	tblName = tblName.Replace("$p", project.Name);	×
76	tblName = tblName.Replace("$n", project.ProjectNumber.ToString());	×
77	tblName = tblName.Replace("$c", _request.Configuration.Name);	×
78
79	switch (_request)	×
80	{
81	case ExtractDatasetCommand extractDatasetCommand:
82	tblName = tblName.Replace("$d", extractDatasetCommand.DatasetBundle.DataSet.Catalogue.Name);	×
83	tblName = tblName.Replace("$a", extractDatasetCommand.DatasetBundle.DataSet.Catalogue.Acronym);	×
84	break;	×
85	case ExtractGlobalsCommand:
86	tblName = tblName.Replace("$d", ExtractionDirectory.GLOBALS_DATA_NAME);	×
87	tblName = tblName.Replace("$a", "G");	×
88	break;
89	}
90
91	return tblName;	×
92	}
93
94	public void Dispose(IDataLoadEventListener listener, Exception pipelineFailureExceptionIfAny)
95	{
96	}	×
97
98	public void Abort(IDataLoadEventListener listener)
99	{
100	}	×
101
102	public void Check(ICheckNotifier notifier)
103	{
104	if (MetadataNamingPattern != null && MetadataNamingPattern.Contains("$a"))	×
105	if (_request is ExtractDatasetCommand dsRequest && string.IsNullOrWhiteSpace(dsRequest.Catalogue.Acronym))	×
106	notifier.OnCheckPerformed(new CheckEventArgs(	×
107	$"Catalogue '{dsRequest.Catalogue}' does not have an Acronym but MetadataNamingPattern contains $a",	×
108	CheckResult.Fail));	×
109	}	×
110
111	public void PreInitialize(IExtractCommand value, IDataLoadEventListener listener)
112	{
113	_request = value;	×
114	}	×
115
116	public void PreInitialize(IBasicActivateItems value, IDataLoadEventListener listener)
117	{
118	_activator = value;	×
119	}	×
120	}

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