9758065908

Committed 02 Jul 2024 09:03AM UTC coverage: 56.679% (-0.2%) from 56.914%

Build # 9758065908

Build Type

push

github

Committed by

web-flow

Commit Message

Release/8.2.0 (#1867)

* add extraction additions

* interim

* add test

* interim

* working dedupe

* improved checking

* add timestamp option

* fix extra looping

* add check

* start on tests

* tidy up code

* update link

* tidy up

* Rename executeFullExtractionToDatabaseMSSql.md to ExecuteFullExtractionToDatabaseMSSql.md

* fix typo

* add docs

* update

* update documentation

* attempt fix docs

* update docs

* tidy up code

* better tests

* add real test

* tidy up

* interim

* grab existiing entity

* no new data

* add basic tests

* attempt to fix test

* interim

* interim commit

* working clash

* add test

* fix test

* improved clash checker

* tidy up

* update test

* fix up test

* update from codeql

* tidy up code

* fix bad merge

* fix typo

* skip over for now

* revert change

* Task/RDMP-180 Add instance settings table (#1820)

* working settings interface

* add documentation

* add missing files

* update namespace

* add icon

* update from run

* make key unique

* add tests

* update tests

* update for tests

* fix unique name issue

* tidy up

* tidy up from review

* works

* nested deprications

* recursive deprication

* tidy up

* add newline

* Task/rdmp 174 dqe improvements (#1849)

* working scallable graph

* add changelog

* add axis override

* interim

* working increments

* working ui refresh

* update changelog

* tidy up code

* add missing file

* tidy up

* Task/rdmp 155 migrate catalogue tables (#1805)

* start of UI

* interim

* working switch

* improved ui

* fix build

* rename duped file

* imterim

* add checks

* start of tests

* local tests  working

* add tests

* improved ui

* tidy up

* add single item use

* broken test

* updated tests

* tidy up imports

* add some documentation

* fix docume... (continued)

Run Details

10912 of 20750 branches covered (52.59%)

Branch coverage included in aggregate %.

369 of 831 new or added lines in 38 files covered. (44.4%)

375 existing lines in 25 files now uncovered.

30965 of 53135 relevant lines covered (58.28%)

7845.71 hits per line

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

8.21

/Rdmp.Core/Curation/Data/LoadModuleAssembly.cs

// Copyright (c) The University of Dundee 2018-2024
// 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.IO;
using System.Linq;
using System.Xml;
using ICSharpCode.SharpZipLib.Zip;
using Rdmp.Core.ReusableLibraryCode.Checks;

namespace Rdmp.Core.Curation.Data;

/// <summary>
/// This entity wraps references to plugin .nupkg files on disk.
/// </summary>
public sealed class LoadModuleAssembly
{
    private static readonly bool IsWin = AppDomain.CurrentDomain.GetAssemblies()
        .Any(static a => a.FullName?.StartsWith("Rdmp.UI", StringComparison.Ordinal) == true);

    private static readonly string PluginsList = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, "rdmpplugins.txt");

    internal static readonly List<LoadModuleAssembly> Assemblies = [];
    private readonly FileInfo _file;

    private LoadModuleAssembly(FileInfo file)
    {
        _file = file;
    }


    private static bool IsReleaseCandidcate(string filename)
    {
        return filename.Split('.')[^2].Contains("-rc");
    }

    private static int GetReleaseCandidateId(string filename)
    {
        //expects the rc to be something like My.Plugin.3.0.0-rc2
        int.TryParse(filename.Split("-rc")[1].Split('.')[0], out var result);
        return result;
    }

    private static Dictionary<string, string> HandlePluginVersioning()
    {
        var PluginVersionLookup = new Dictionary<string, string>();
        var PluginPathLookup = new Dictionary<string, string>();
        var pluginFiles = Directory.EnumerateFiles(AppDomain.CurrentDomain.BaseDirectory, "*.rdmp");
        foreach (var pluginFile in pluginFiles)
        {
            using FileStream fs = new(pluginFile, FileMode.Open);
            using ZipFile zip = new(fs);
            foreach (ZipEntry ze in zip)
            {
                if (ze.Name.Contains(".nuspec"))
                {
                    using StreamReader sr = new StreamReader(zip.GetInputStream(ze.ZipFileIndex));
                    var content = sr.ReadToEnd();
                    var xmlDoc = new XmlDocument();
                    xmlDoc.LoadXml(content);

                    var name = xmlDoc.GetElementsByTagName("id").Item(0).InnerText;
                    var version = xmlDoc.GetElementsByTagName("version").Item(0).InnerText;
                    if (PluginVersionLookup.TryGetValue(name, out var currentVersion))
                    {
                        //already found a version
                        var result = new Version(currentVersion).CompareTo(new Version(version));
                        if (result < 0)
                        {
                            //this version is the latest version
                            PluginVersionLookup[name] = version;
                            PluginPathLookup[name] = pluginFile;
                        }
                        if(result == 0)
                        {
                            //check for RC in the name
                            var currentIsReleaseCandidate = IsReleaseCandidcate(PluginPathLookup[name]);
                            var newIsReleaseCandidate = IsReleaseCandidcate(pluginFile);
                            if(newIsReleaseCandidate && currentIsReleaseCandidate)
                            {
                                var newIsLatest = GetReleaseCandidateId(pluginFile) > GetReleaseCandidateId(PluginPathLookup[name]);
                                if (newIsLatest)
                                {
                                    PluginVersionLookup[name] = version;
                                    PluginPathLookup[name] = pluginFile;
                                }
                            } else if (newIsReleaseCandidate)
                            {
                                //new version is the latest
                                PluginVersionLookup[name] = version;
                                PluginPathLookup[name] = pluginFile;
                            }
                        }
                    }
                    else
                    {
                        PluginVersionLookup[name] = version;
                        PluginPathLookup[name] = pluginFile;
                    }
                    break;
                }

            }

        }

        return PluginPathLookup;
    }

    /// <summary>
    /// List the plugin files to load
    /// </summary>
    /// <returns></returns>
    internal static IEnumerable<string> PluginFiles()
    {
        if (Directory.EnumerateFiles(AppDomain.CurrentDomain.BaseDirectory, "*.rdmp").Count() > 0)
        {
            //use the modern .RDMP plugins
            var plugins = HandlePluginVersioning();
            return plugins.Values.ToArray();

        }
        return File.Exists(PluginsList)
            ? File.ReadAllLines(PluginsList)
                .Select(static name => Path.Combine(AppDomain.CurrentDomain.BaseDirectory, name))
            : Directory.EnumerateFiles(AppDomain.CurrentDomain.BaseDirectory, "*.nupkg");
    }

    /// <summary>
    /// Unpack the plugin DLL files, excluding any Windows UI specific dlls when not running a Windows GUI
    /// </summary>
    internal static IEnumerable<(string, MemoryStream)> GetContents(string path)
    {
        var info = new FileInfo(path);
        if (!info.Exists || info.Length < 100) yield break; // Ignore missing or empty files

        var pluginStream = info.OpenRead();
        if (!pluginStream.CanSeek)
            throw new ArgumentException("Seek needed", nameof(path));

        Assemblies.Add(new LoadModuleAssembly(info));

        using var zip = new ZipFile(pluginStream);
        foreach (var e in zip.Cast<ZipEntry>()
                     .Where(static e => e.IsFile && e.Name.EndsWith(".dll", StringComparison.OrdinalIgnoreCase) &&
                                        (IsWin || !e.Name.Contains("/windows/"))))
        {
            using var s = zip.GetInputStream(e);
            using var ms2 = new MemoryStream();
            s.CopyTo(ms2);
            ms2.Position = 0;
            yield return (e.Name, ms2);
        }
    }

    /// <summary>
    /// Copy the plugin nupkg to the given directory
    /// </summary>
    /// <param name="downloadDirectory"></param>
    public void DownloadAssembly(DirectoryInfo downloadDirectory)
    {
        if (!downloadDirectory.Exists)
            downloadDirectory.Create();
        var targetFile = Path.Combine(downloadDirectory.FullName, _file.Name);
        _file.CopyTo(targetFile, true);
    }

    /// <summary>
    /// Delete the plugin file from disk, and remove it from rdmpplugins.txt if in use
    /// </summary>
    public void Delete()
    {
        _file.Delete();
        if (!File.Exists(PluginsList)) return;

        var tmp = $"{PluginsList}.tmp";
        File.WriteAllLines(tmp, File.ReadAllLines(PluginsList).Where(l => !l.Contains(_file.Name)));
        File.Move(tmp, PluginsList, true);
    }

    public override string ToString() => _file.Name;

    public static void UploadFile(ICheckNotifier checkNotifier, FileInfo toCommit)
    {
        try
        {
            toCommit.CopyTo(Path.Combine(AppDomain.CurrentDomain.BaseDirectory, toCommit.Name), true);
            if (!File.Exists(PluginsList)) return;

            // Now the tricky bit: add this new file, and remove any other versions of the same
            // e.g. adding DummyPlugin-1.2.3 should delete DummyPlugin-2.0 and DummyPlugin-1.0 if present
            var list = File.ReadAllLines(PluginsList);
            var tmp = $"{PluginsList}.tmp";

            var versionPos = toCommit.Name.IndexOf('-');
            if (versionPos != -1)
            {
                var stub = toCommit.Name[..(versionPos + 1)];
                list = list.Where(l => !l.StartsWith(stub, StringComparison.OrdinalIgnoreCase)).ToArray();
            }

            File.WriteAllLines(tmp, list.Union([toCommit.Name]));
            File.Move(tmp, PluginsList, true);
        }
        catch (Exception e)
        {
            checkNotifier.OnCheckPerformed(new CheckEventArgs($"Failed copying plugin {toCommit.Name}",
                CheckResult.Fail, e));
            throw;
        }
    }
}

1	// Copyright (c) The University of Dundee 2018-2024
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.IO;
10	using System.Linq;
11	using System.Xml;
12	using ICSharpCode.SharpZipLib.Zip;
13	using Rdmp.Core.ReusableLibraryCode.Checks;
14
15	namespace Rdmp.Core.Curation.Data;
16
17	/// <summary>
18	/// This entity wraps references to plugin .nupkg files on disk.
19	/// </summary>
20	public sealed class LoadModuleAssembly
21	{
22	private static readonly bool IsWin = AppDomain.CurrentDomain.GetAssemblies()	4✔
23	.Any(static a => a.FullName?.StartsWith("Rdmp.UI", StringComparison.Ordinal) == true);	354!
24
25	private static readonly string PluginsList = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, "rdmpplugins.txt");	4✔
26
27	internal static readonly List<LoadModuleAssembly> Assemblies = [];	4✔
28	private readonly FileInfo _file;
29
30	private LoadModuleAssembly(FileInfo file)	×
31	{
32	_file = file;	×
33	}	×
34
35
36	private static bool IsReleaseCandidcate(string filename)
37	{
NEW 38	return filename.Split('.')[^2].Contains("-rc");	×
39	}
40
41	private static int GetReleaseCandidateId(string filename)
42	{
43	//expects the rc to be something like My.Plugin.3.0.0-rc2
NEW 44	int.TryParse(filename.Split("-rc")[1].Split('.')[0], out var result);	×
NEW 45	return result;	×
46	}
47
48	private static Dictionary<string, string> HandlePluginVersioning()
49	{
NEW 50	var PluginVersionLookup = new Dictionary<string, string>();	×
NEW 51	var PluginPathLookup = new Dictionary<string, string>();	×
NEW 52	var pluginFiles = Directory.EnumerateFiles(AppDomain.CurrentDomain.BaseDirectory, "*.rdmp");	×
NEW 53	foreach (var pluginFile in pluginFiles)	×
54	{
NEW 55	using FileStream fs = new(pluginFile, FileMode.Open);	×
NEW 56	using ZipFile zip = new(fs);	×
NEW 57	foreach (ZipEntry ze in zip)	×
58	{
NEW 59	if (ze.Name.Contains(".nuspec"))	×
60	{
NEW 61	using StreamReader sr = new StreamReader(zip.GetInputStream(ze.ZipFileIndex));	×
NEW 62	var content = sr.ReadToEnd();	×
NEW 63	var xmlDoc = new XmlDocument();	×
NEW 64	xmlDoc.LoadXml(content);	×
65
NEW 66	var name = xmlDoc.GetElementsByTagName("id").Item(0).InnerText;	×
NEW 67	var version = xmlDoc.GetElementsByTagName("version").Item(0).InnerText;	×
NEW 68	if (PluginVersionLookup.TryGetValue(name, out var currentVersion))	×
69	{
70	//already found a version
NEW 71	var result = new Version(currentVersion).CompareTo(new Version(version));	×
NEW 72	if (result < 0)	×
73	{
74	//this version is the latest version
NEW 75	PluginVersionLookup[name] = version;	×
NEW 76	PluginPathLookup[name] = pluginFile;	×
77	}
NEW 78	if(result == 0)	×
79	{
80	//check for RC in the name
NEW 81	var currentIsReleaseCandidate = IsReleaseCandidcate(PluginPathLookup[name]);	×
NEW 82	var newIsReleaseCandidate = IsReleaseCandidcate(pluginFile);	×
NEW 83	if(newIsReleaseCandidate && currentIsReleaseCandidate)	×
84	{
NEW 85	var newIsLatest = GetReleaseCandidateId(pluginFile) > GetReleaseCandidateId(PluginPathLookup[name]);	×
NEW 86	if (newIsLatest)	×
87	{
NEW 88	PluginVersionLookup[name] = version;	×
NEW 89	PluginPathLookup[name] = pluginFile;	×
90	}
NEW 91	} else if (newIsReleaseCandidate)	×
92	{
93	//new version is the latest
NEW 94	PluginVersionLookup[name] = version;	×
NEW 95	PluginPathLookup[name] = pluginFile;	×
96	}
97	}
98	}
99	else
100	{
NEW 101	PluginVersionLookup[name] = version;	×
NEW 102	PluginPathLookup[name] = pluginFile;	×
103	}
NEW 104	break;	×
105	}
106
107	}
108
109	}
110
NEW 111	return PluginPathLookup;	×
112	}
113
114	/// <summary>
115	/// List the plugin files to load
116	/// </summary>
117	/// <returns></returns>
118	internal static IEnumerable<string> PluginFiles()
119	{
120	if (Directory.EnumerateFiles(AppDomain.CurrentDomain.BaseDirectory, "*.rdmp").Count() > 0)	16!
121	{
122	//use the modern .RDMP plugins
NEW 123	var plugins = HandlePluginVersioning();	×
NEW 124	return plugins.Values.ToArray();	×
125
126	}
127	return File.Exists(PluginsList)	16!
128	? File.ReadAllLines(PluginsList)	16✔
129	.Select(static name => Path.Combine(AppDomain.CurrentDomain.BaseDirectory, name))	×
130	: Directory.EnumerateFiles(AppDomain.CurrentDomain.BaseDirectory, "*.nupkg");	16✔
131	}
132
133	/// <summary>
134	/// Unpack the plugin DLL files, excluding any Windows UI specific dlls when not running a Windows GUI
135	/// </summary>
136	internal static IEnumerable<(string, MemoryStream)> GetContents(string path)
137	{
138	var info = new FileInfo(path);	×
139	if (!info.Exists \|\| info.Length < 100) yield break; // Ignore missing or empty files	×
140
141	var pluginStream = info.OpenRead();	×
142	if (!pluginStream.CanSeek)	×
143	throw new ArgumentException("Seek needed", nameof(path));	×
144
145	Assemblies.Add(new LoadModuleAssembly(info));	×
146
147	using var zip = new ZipFile(pluginStream);	×
148	foreach (var e in zip.Cast<ZipEntry>()	×
149	.Where(static e => e.IsFile && e.Name.EndsWith(".dll", StringComparison.OrdinalIgnoreCase) &&
150	(IsWin \|\| !e.Name.Contains("/windows/"))))
151	{
152	using var s = zip.GetInputStream(e);	×
153	using var ms2 = new MemoryStream();	×
154	s.CopyTo(ms2);	×
155	ms2.Position = 0;	×
156	yield return (e.Name, ms2);	×
157	}	×
158	}	×
159
160	/// <summary>
161	/// Copy the plugin nupkg to the given directory
162	/// </summary>
163	/// <param name="downloadDirectory"></param>
164	public void DownloadAssembly(DirectoryInfo downloadDirectory)
165	{
166	if (!downloadDirectory.Exists)	×
167	downloadDirectory.Create();	×
168	var targetFile = Path.Combine(downloadDirectory.FullName, _file.Name);	×
169	_file.CopyTo(targetFile, true);	×
170	}	×
171
172	/// <summary>
173	/// Delete the plugin file from disk, and remove it from rdmpplugins.txt if in use
174	/// </summary>
175	public void Delete()
176	{
177	_file.Delete();	×
178	if (!File.Exists(PluginsList)) return;	×
179
180	var tmp = $"{PluginsList}.tmp";	×
181	File.WriteAllLines(tmp, File.ReadAllLines(PluginsList).Where(l => !l.Contains(_file.Name)));	×
182	File.Move(tmp, PluginsList, true);	×
183	}	×
184
185	public override string ToString() => _file.Name;	×
186
187	public static void UploadFile(ICheckNotifier checkNotifier, FileInfo toCommit)
188	{
189	try
190	{
191	toCommit.CopyTo(Path.Combine(AppDomain.CurrentDomain.BaseDirectory, toCommit.Name), true);	×
192	if (!File.Exists(PluginsList)) return;	×
193
194	// Now the tricky bit: add this new file, and remove any other versions of the same
195	// e.g. adding DummyPlugin-1.2.3 should delete DummyPlugin-2.0 and DummyPlugin-1.0 if present
196	var list = File.ReadAllLines(PluginsList);	×
197	var tmp = $"{PluginsList}.tmp";	×
198
199	var versionPos = toCommit.Name.IndexOf('-');	×
200	if (versionPos != -1)	×
201	{
202	var stub = toCommit.Name[..(versionPos + 1)];	×
203	list = list.Where(l => !l.StartsWith(stub, StringComparison.OrdinalIgnoreCase)).ToArray();	×
204	}
205
206	File.WriteAllLines(tmp, list.Union([toCommit.Name]));	×
207	File.Move(tmp, PluginsList, true);	×
208	}	×
209	catch (Exception e)	×
210	{
211	checkNotifier.OnCheckPerformed(new CheckEventArgs($"Failed copying plugin {toCommit.Name}",	×
212	CheckResult.Fail, e));	×
213	throw;	×
214	}
215	}	×
216	}

HicServices / RDMP / 9758065908

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