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)

Run Details

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30685 of 52388 relevant lines covered (58.57%)

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57.75

/Rdmp.Core/QueryBuilding/ReleaseIdentifierSubstitution.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.Text.RegularExpressions;
using FAnsi.Discovery.QuerySyntax;
using Rdmp.Core.Curation.Data;
using Rdmp.Core.Curation.Data.Spontaneous;
using Rdmp.Core.DataExport.Data;
using Rdmp.Core.MapsDirectlyToDatabaseTable;
using Rdmp.Core.MapsDirectlyToDatabaseTable.Attributes;
using Rdmp.Core.QueryBuilding.SyntaxChecking;
using Rdmp.Core.ReusableLibraryCode.Checks;

namespace Rdmp.Core.QueryBuilding;

/// <summary>
/// Records how (via SQL) replace the private patient identifier column (e.g. CHI) with the release identifier (e.g. swap [biochemistry]..[chi] for
/// [cohort]..[ReleaseId]).  Also includes the Join SQL string for linking the cohort table (which contains the ReleaseId e.g. [cohort]) with the dataset
/// table (e.g. [biochemistry]).
/// 
/// <para>This class is an IColumn and is designed to be added as a new Column to a QueryBuilder as normal (See ExtractionQueryBuilder)</para>
/// </summary>
public class ReleaseIdentifierSubstitution : SpontaneousObject, IColumn
{
    public string JoinSQL { get; private set; }

    /// <summary>
    /// The identifiable column which is being substituted on
    /// </summary>
    public IColumn OriginalDatasetColumn;

    private readonly IQuerySyntaxHelper _querySyntaxHelper;

    [Sql] public string SelectSQL { get; set; }

    public string Alias { get; private set; }

    //all these are hard coded to null or false really
    public ColumnInfo ColumnInfo => OriginalDatasetColumn.ColumnInfo;

    public int Order
    {
        get => OriginalDatasetColumn.Order;
        set { }
    }

    public bool HashOnDataRelease => false;
    public bool IsExtractionIdentifier => OriginalDatasetColumn.IsExtractionIdentifier;
    public bool IsPrimaryKey => OriginalDatasetColumn.IsPrimaryKey;

    public ReleaseIdentifierSubstitution(MemoryRepository repo, IColumn extractionIdentifierToSubFor,
        IExtractableCohort extractableCohort, bool isPartOfMultiCHISubstitution,
        IQuerySyntaxHelper querySyntaxHelper) : base(repo)
    {
        if (!extractionIdentifierToSubFor.IsExtractionIdentifier)
            throw new Exception(
                $"Column {extractionIdentifierToSubFor} is not marked IsExtractionIdentifier so cannot be substituted for a ReleaseIdentifier");

        OriginalDatasetColumn = extractionIdentifierToSubFor;
        _querySyntaxHelper = querySyntaxHelper;
        if (OriginalDatasetColumn.ColumnInfo == null)
            throw new Exception(
                $"The column {OriginalDatasetColumn.GetRuntimeName()} references a ColumnInfo that has been deleted");

        var syntaxHelper = extractableCohort.GetQuerySyntaxHelper();

        //the externally referenced Cohort table
        var privateCol = extractableCohort.ExternalCohortTable.DiscoverPrivateIdentifier();

        var collateStatement = "";

        //the release identifier join might require collation

        //if the private has a collation
        if (!string.IsNullOrWhiteSpace(privateCol.Collation))
        {
            var cohortCollation = privateCol.Collation;
            var otherTableCollation = OriginalDatasetColumn.ColumnInfo.Collation;


            //only collate if the server types match and if the collations differ
            if (privateCol.Table.Database.Server.DatabaseType ==
                OriginalDatasetColumn.ColumnInfo.TableInfo.DatabaseType)
                if (!string.IsNullOrWhiteSpace(otherTableCollation) &&
                    !string.Equals(cohortCollation, otherTableCollation))
                    collateStatement = $" collate {cohortCollation}";
        }


        if (!isPartOfMultiCHISubstitution)
        {
            SelectSQL = extractableCohort.GetReleaseIdentifier();
            Alias = syntaxHelper.GetRuntimeName(SelectSQL);
        }
        else
        {
            SelectSQL =
                $"(SELECT DISTINCT {extractableCohort.GetReleaseIdentifier()} FROM {privateCol.Table.GetFullyQualifiedName()} WHERE {extractableCohort.WhereSQL()} AND {privateCol.GetFullyQualifiedName()}={OriginalDatasetColumn.SelectSQL}{collateStatement})";

            if (!string.IsNullOrWhiteSpace(OriginalDatasetColumn.Alias))
            {
                var toReplace = extractableCohort.GetPrivateIdentifier(true);
                var toReplaceWith = extractableCohort.GetReleaseIdentifier(true);

                //take the same name as the underlying column
                Alias = OriginalDatasetColumn.Alias;

                //but replace all instances of CHI with PROCHI (or Barcode, or whatever)
                if (!Alias.Contains(toReplace) || Regex.Matches(Alias, Regex.Escape(toReplace)).Count > 1)
                    throw new Exception(
                        $"Failed to resolve multiple extraction identifiers in dataset.  Either mark a single column as the IsExtractionIdentifier for this extraction or ensure all columns are of compatible type and have the text \"{toReplace}\" appearing once (and only once in its name)");

                Alias = Alias.Replace(toReplace, toReplaceWith);
            }
            else
            {
                throw new Exception(
                    $"In cases where you have multiple columns marked IsExtractionIdentifier, they must all have Aliases, the column {OriginalDatasetColumn.SelectSQL} does not have one");
            }
        }

        JoinSQL = $"{OriginalDatasetColumn.SelectSQL}={privateCol.GetFullyQualifiedName()}{collateStatement}";
    }

    public string GetRuntimeName() =>
        string.IsNullOrWhiteSpace(Alias) ? _querySyntaxHelper.GetRuntimeName(SelectSQL) : Alias;

    public void Check(ICheckNotifier notifier)
    {
        new ColumnSyntaxChecker(this).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;
8	using System.Text.RegularExpressions;
9	using FAnsi.Discovery.QuerySyntax;
10	using Rdmp.Core.Curation.Data;
11	using Rdmp.Core.Curation.Data.Spontaneous;
12	using Rdmp.Core.DataExport.Data;
13	using Rdmp.Core.MapsDirectlyToDatabaseTable;
14	using Rdmp.Core.MapsDirectlyToDatabaseTable.Attributes;
15	using Rdmp.Core.QueryBuilding.SyntaxChecking;
16	using Rdmp.Core.ReusableLibraryCode.Checks;
17
18	namespace Rdmp.Core.QueryBuilding;
19
20	/// <summary>
21	/// Records how (via SQL) replace the private patient identifier column (e.g. CHI) with the release identifier (e.g. swap [biochemistry]..[chi] for
22	/// [cohort]..[ReleaseId]). Also includes the Join SQL string for linking the cohort table (which contains the ReleaseId e.g. [cohort]) with the dataset
23	/// table (e.g. [biochemistry]).
24	///
25	/// <para>This class is an IColumn and is designed to be added as a new Column to a QueryBuilder as normal (See ExtractionQueryBuilder)</para>
26	/// </summary>
27	public class ReleaseIdentifierSubstitution : SpontaneousObject, IColumn
28	{
29	public string JoinSQL { get; private set; }	224✔
30
31	/// <summary>
32	/// The identifiable column which is being substituted on
33	/// </summary>
34	public IColumn OriginalDatasetColumn;
35
36	private readonly IQuerySyntaxHelper _querySyntaxHelper;
37
38	[Sql] public string SelectSQL { get; set; }	476✔
39
40	public string Alias { get; private set; }	1,352✔
41
42	//all these are hard coded to null or false really
43	public ColumnInfo ColumnInfo => OriginalDatasetColumn.ColumnInfo;	112✔
44
45	public int Order
46	{
47	get => OriginalDatasetColumn.Order;	208✔
48	set { }	×
49	}
50
51	public bool HashOnDataRelease => false;	126✔
52	public bool IsExtractionIdentifier => OriginalDatasetColumn.IsExtractionIdentifier;	×
53	public bool IsPrimaryKey => OriginalDatasetColumn.IsPrimaryKey;	16✔
54
55	public ReleaseIdentifierSubstitution(MemoryRepository repo, IColumn extractionIdentifierToSubFor,
56	IExtractableCohort extractableCohort, bool isPartOfMultiCHISubstitution,
57	IQuerySyntaxHelper querySyntaxHelper) : base(repo)	112✔
58	{
59	if (!extractionIdentifierToSubFor.IsExtractionIdentifier)	112!
60	throw new Exception(	×
61	$"Column {extractionIdentifierToSubFor} is not marked IsExtractionIdentifier so cannot be substituted for a ReleaseIdentifier");	×
62
63	OriginalDatasetColumn = extractionIdentifierToSubFor;	112✔
64	_querySyntaxHelper = querySyntaxHelper;	112✔
65	if (OriginalDatasetColumn.ColumnInfo == null)	112!
66	throw new Exception(	×
67	$"The column {OriginalDatasetColumn.GetRuntimeName()} references a ColumnInfo that has been deleted");	×
68
69	var syntaxHelper = extractableCohort.GetQuerySyntaxHelper();	112✔
70
71	//the externally referenced Cohort table
72	var privateCol = extractableCohort.ExternalCohortTable.DiscoverPrivateIdentifier();	112✔
73
74	var collateStatement = "";	112✔
75
76	//the release identifier join might require collation
77
78	//if the private has a collation
79	if (!string.IsNullOrWhiteSpace(privateCol.Collation))	112✔
80	{
81	var cohortCollation = privateCol.Collation;	112✔
82	var otherTableCollation = OriginalDatasetColumn.ColumnInfo.Collation;	112✔
83
84
85	//only collate if the server types match and if the collations differ
86	if (privateCol.Table.Database.Server.DatabaseType ==	112✔
87	OriginalDatasetColumn.ColumnInfo.TableInfo.DatabaseType)	112✔
88	if (!string.IsNullOrWhiteSpace(otherTableCollation) &&	112!
89	!string.Equals(cohortCollation, otherTableCollation))	112✔
90	collateStatement = $" collate {cohortCollation}";	×
91	}
92
93
94	if (!isPartOfMultiCHISubstitution)	112!
95	{
96	SelectSQL = extractableCohort.GetReleaseIdentifier();	112✔
97	Alias = syntaxHelper.GetRuntimeName(SelectSQL);	112✔
98	}
99	else
100	{
101	SelectSQL =	×
102	$"(SELECT DISTINCT {extractableCohort.GetReleaseIdentifier()} FROM {privateCol.Table.GetFullyQualifiedName()} WHERE {extractableCohort.WhereSQL()} AND {privateCol.GetFullyQualifiedName()}={OriginalDatasetColumn.SelectSQL}{collateStatement})";	×
103
104	if (!string.IsNullOrWhiteSpace(OriginalDatasetColumn.Alias))	×
105	{
106	var toReplace = extractableCohort.GetPrivateIdentifier(true);	×
107	var toReplaceWith = extractableCohort.GetReleaseIdentifier(true);	×
108
109	//take the same name as the underlying column
110	Alias = OriginalDatasetColumn.Alias;	×
111
112	//but replace all instances of CHI with PROCHI (or Barcode, or whatever)
113	if (!Alias.Contains(toReplace) \|\| Regex.Matches(Alias, Regex.Escape(toReplace)).Count > 1)	×
114	throw new Exception(	×
115	$"Failed to resolve multiple extraction identifiers in dataset. Either mark a single column as the IsExtractionIdentifier for this extraction or ensure all columns are of compatible type and have the text \"{toReplace}\" appearing once (and only once in its name)");	×
116
117	Alias = Alias.Replace(toReplace, toReplaceWith);	×
118	}
119	else
120	{
121	throw new Exception(	×
122	$"In cases where you have multiple columns marked IsExtractionIdentifier, they must all have Aliases, the column {OriginalDatasetColumn.SelectSQL} does not have one");	×
123	}
124	}
125
126	JoinSQL = $"{OriginalDatasetColumn.SelectSQL}={privateCol.GetFullyQualifiedName()}{collateStatement}";	112✔
127	}	112✔
128
129	public string GetRuntimeName() =>
130	string.IsNullOrWhiteSpace(Alias) ? _querySyntaxHelper.GetRuntimeName(SelectSQL) : Alias;	242!
131
132	public void Check(ICheckNotifier notifier)
133	{
134	new ColumnSyntaxChecker(this).Check(notifier);	126✔
135	}	126✔
136	}

HicServices / RDMP / 6245535001

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