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

91.89

/Rdmp.Core/CohortCreation/Execution/ExamplePluginCohortCompiler.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.Collections.Generic;
using System.Data;
using System.Linq;
using System.Threading;
using BadMedicine;
using Rdmp.Core.Curation.Data;
using Rdmp.Core.Curation.Data.Aggregation;
using Rdmp.Core.QueryCaching.Aggregation;

namespace Rdmp.Core.CohortCreation.Execution;

/// <summary>
/// Demonstration class for how to implement a plugin cohort e.g. to a REST API.
/// This class generates a number of random chis when prompted to query the 'api'.
/// 
/// <para>If deployed as a patient index table, also returns random dates of birth and death</para>
/// </summary>
public class ExamplePluginCohortCompiler : PluginCohortCompiler
{
    public const string ExampleAPIName = $"{ApiPrefix}GenerateRandomChisExample";

    public override void Run(AggregateConfiguration ac, CachedAggregateConfigurationResultsManager cache,
        CancellationToken token)
    {
        token.ThrowIfCancellationRequested();

        // The user of RDMP will have configured ac as either patient index table or normal cohort aggregate
        if (ac.IsJoinablePatientIndexTable())
            // user expects multiple columns from the API
            RunAsPatientIndexTable(ac, cache, token);
        else
            // user expects only a single linkage identifier to be returned by the API
            RunAsIdentifierList(ac, cache, token);
    }

    private void RunAsPatientIndexTable(AggregateConfiguration ac, CachedAggregateConfigurationResultsManager cache,
        CancellationToken token)
    {
        using var dt = new DataTable();
        dt.Columns.Add("chi", typeof(string));
        dt.Columns.Add("dateOfBirth", typeof(DateTime));
        dt.Columns.Add("dateOfDeath", typeof(DateTime));

        // generate a list of random chis + date of birth/death
        var pc = new PersonCollection();
        pc.GeneratePeople(GetNumberToGenerate(ac), new Random());

        foreach (var p in pc.People) dt.Rows.Add(p.CHI, p.DateOfBirth, p.DateOfDeath ?? (object)DBNull.Value);

        SubmitPatientIndexTable(dt, ac, cache, true);
    }

    private void RunAsIdentifierList(AggregateConfiguration ac, CachedAggregateConfigurationResultsManager cache,
        CancellationToken token)
    {
        var pc = new PersonCollection();
        var requiredNumber = GetNumberToGenerate(ac);
        var rand = new Random();
        pc.GeneratePeople(requiredNumber, rand);

        var set = new HashSet<string>(pc.People.Select(p => p.CHI));

        // there may be duplicates, if so we need to bump up the number to match the required count
        while (set.Count < requiredNumber)
        {
            pc.GeneratePeople(1, rand);
            set.Add(pc.People[0].CHI);
        }

        // generate a list of random chis
        SubmitIdentifierList("chi", set, ac, cache);
    }

    private static int GetNumberToGenerate(AggregateConfiguration ac) =>
        // You can persist configuration info about how to query the API any way
        // you want.  Here we just use the Description field
        int.TryParse(ac.Description, out var result) ? result : 5;

    public override bool ShouldRun(ICatalogue cata) =>
        // we will handle any dataset where the associated Catalogue has this name
        // you can customise how to spot your API calls however you want
        cata.Name.Equals(ExampleAPIName);

    protected override string GetJoinColumnNameFor(AggregateConfiguration joinedTo) =>
        // when RunAsPatientIndexTable is being used the column that can be linked
        // to other datasets is called "chi"
        "chi";
}

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.Collections.Generic;
9	using System.Data;
10	using System.Linq;
11	using System.Threading;
12	using BadMedicine;
13	using Rdmp.Core.Curation.Data;
14	using Rdmp.Core.Curation.Data.Aggregation;
15	using Rdmp.Core.QueryCaching.Aggregation;
16
17	namespace Rdmp.Core.CohortCreation.Execution;
18
19	/// <summary>
20	/// Demonstration class for how to implement a plugin cohort e.g. to a REST API.
21	/// This class generates a number of random chis when prompted to query the 'api'.
22	///
23	/// <para>If deployed as a patient index table, also returns random dates of birth and death</para>
24	/// </summary>
25	public class ExamplePluginCohortCompiler : PluginCohortCompiler
26	{
27	public const string ExampleAPIName = $"{ApiPrefix}GenerateRandomChisExample";
28
29	public override void Run(AggregateConfiguration ac, CachedAggregateConfigurationResultsManager cache,
30	CancellationToken token)
31	{
32	token.ThrowIfCancellationRequested();	6✔
33
34	// The user of RDMP will have configured ac as either patient index table or normal cohort aggregate
35	if (ac.IsJoinablePatientIndexTable())	6✔
36	// user expects multiple columns from the API
37	RunAsPatientIndexTable(ac, cache, token);	2✔
38	else
39	// user expects only a single linkage identifier to be returned by the API
40	RunAsIdentifierList(ac, cache, token);	4✔
41	}	4✔
42
43	private void RunAsPatientIndexTable(AggregateConfiguration ac, CachedAggregateConfigurationResultsManager cache,
44	CancellationToken token)
45	{
46	using var dt = new DataTable();	2✔
47	dt.Columns.Add("chi", typeof(string));	2✔
48	dt.Columns.Add("dateOfBirth", typeof(DateTime));	2✔
49	dt.Columns.Add("dateOfDeath", typeof(DateTime));	2✔
50
51	// generate a list of random chis + date of birth/death
52	var pc = new PersonCollection();	2✔
53	pc.GeneratePeople(GetNumberToGenerate(ac), new Random());	2✔
54
55	foreach (var p in pc.People) dt.Rows.Add(p.CHI, p.DateOfBirth, p.DateOfDeath ?? (object)DBNull.Value);	34✔
56
57	SubmitPatientIndexTable(dt, ac, cache, true);	2✔
58	}	4✔
59
60	private void RunAsIdentifierList(AggregateConfiguration ac, CachedAggregateConfigurationResultsManager cache,
61	CancellationToken token)
62	{
63	var pc = new PersonCollection();	4✔
64	var requiredNumber = GetNumberToGenerate(ac);	4✔
65	var rand = new Random();	4✔
66	pc.GeneratePeople(requiredNumber, rand);	4✔
67
68	var set = new HashSet<string>(pc.People.Select(p => p.CHI));	18✔
69
70	// there may be duplicates, if so we need to bump up the number to match the required count
71	while (set.Count < requiredNumber)	4!
72	{
73	pc.GeneratePeople(1, rand);	×
74	set.Add(pc.People[0].CHI);	×
75	}
76
77	// generate a list of random chis
78	SubmitIdentifierList("chi", set, ac, cache);	4✔
79	}	4✔
80
81	private static int GetNumberToGenerate(AggregateConfiguration ac) =>
82	// You can persist configuration info about how to query the API any way
83	// you want. Here we just use the Description field
84	int.TryParse(ac.Description, out var result) ? result : 5;	6✔
85
86	public override bool ShouldRun(ICatalogue cata) =>
87	// we will handle any dataset where the associated Catalogue has this name
88	// you can customise how to spot your API calls however you want
89	cata.Name.Equals(ExampleAPIName);	358✔
90
91	protected override string GetJoinColumnNameFor(AggregateConfiguration joinedTo) =>
92	// when RunAsPatientIndexTable is being used the column that can be linked
93	// to other datasets is called "chi"
94	"chi";	8✔
95	}

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