NugetPackageRestorer.cs

using System;
using System.Collections.Concurrent;
using System.Collections.Generic;
using System.IO;
using System.Linq;
using System.Net;
using System.Net.Http;
using System.Security.Cryptography.X509Certificates;
using System.Text;
using System.Text.RegularExpressions;
using System.Threading;
using System.Threading.Tasks;
using NuGet.Versioning;
using Semmle.Util;
using Semmle.Util.Logging;

namespace Semmle.Extraction.CSharp.DependencyFetching
{
    internal sealed partial class NugetPackageRestorer : IDisposable
    {
        internal const string PublicNugetOrgFeed = "https://api.nuget.org/v3/index.json";

        private readonly FileProvider fileProvider;
        private readonly FileContent fileContent;
        private readonly IDotNet dotnet;
        private readonly DependabotProxy? dependabotProxy;
        private readonly IDiagnosticsWriter diagnosticsWriter;
        private readonly DependencyDirectory legacyPackageDirectory;
        private readonly DependencyDirectory missingPackageDirectory;
        private readonly ILogger logger;
        private readonly ICompilationInfoContainer compilationInfoContainer;

        public DependencyDirectory PackageDirectory { get; }

        public NugetPackageRestorer(
            FileProvider fileProvider,
            FileContent fileContent,
            IDotNet dotnet,
            DependabotProxy? dependabotProxy,
            IDiagnosticsWriter diagnosticsWriter,
            ILogger logger,
            ICompilationInfoContainer compilationInfoContainer)
        {
            this.fileProvider = fileProvider;
            this.fileContent = fileContent;
            this.dotnet = dotnet;
            this.dependabotProxy = dependabotProxy;
            this.diagnosticsWriter = diagnosticsWriter;
            this.logger = logger;
            this.compilationInfoContainer = compilationInfoContainer;

            PackageDirectory = new DependencyDirectory("packages", "package", logger);
            legacyPackageDirectory = new DependencyDirectory("legacypackages", "legacy package", logger);
            missingPackageDirectory = new DependencyDirectory("missingpackages", "missing package", logger);
        }

        public string? TryRestore(string package)
        {
            if (TryRestorePackageManually(package))
            {
                var packageDir = DependencyManager.GetPackageDirectory(package, missingPackageDirectory.DirInfo);
                if (packageDir is not null)
                {
                    return GetNewestNugetPackageVersionFolder(packageDir, package);
                }
            }

            return null;
        }

        public string GetNewestNugetPackageVersionFolder(string packagePath, string packageFriendlyName)
        {
            var versionFolders = GetOrderedPackageVersionSubDirectories(packagePath);
            if (versionFolders.Length > 1)
            {
                var versions = string.Join(", ", versionFolders.Select(d => d.Name));
                logger.LogDebug($"Found multiple {packageFriendlyName} DLLs in NuGet packages at {packagePath}. Using the latest version ({versionFolders[0].Name}) from: {versions}.");
            }

            var selectedFrameworkFolder = versionFolders.FirstOrDefault()?.FullName;
            if (selectedFrameworkFolder is null)
            {
                logger.LogDebug($"Found {packageFriendlyName} DLLs in NuGet packages at {packagePath}, but no version folder was found.");
                selectedFrameworkFolder = packagePath;
            }

            logger.LogDebug($"Found {packageFriendlyName} DLLs in NuGet packages at {selectedFrameworkFolder}.");
            return selectedFrameworkFolder;
        }

        public DirectoryInfo[] GetOrderedPackageVersionSubDirectories(string packagePath)
        {
            // Only consider directories with valid NuGet version names.
            return new DirectoryInfo(packagePath)
                .EnumerateDirectories("*", new EnumerationOptions { MatchCasing = MatchCasing.CaseInsensitive, RecurseSubdirectories = false })
                .SelectMany(d =>
                {
                    if (NuGetVersion.TryParse(d.Name, out var version))
                    {
                        return new[] { new { Directory = d, NuGetVersion = version } };
                    }
                    logger.LogInfo($"Ignoring package directory '{d.FullName}' as it does not have a valid NuGet version name.");
                    return [];
                })
                .OrderByDescending(dw => dw.NuGetVersion)
                .Select(dw => dw.Directory)
                .ToArray();
        }

        public HashSet<AssemblyLookupLocation> Restore()
        {
            var assemblyLookupLocations = new HashSet<AssemblyLookupLocation>();
            var checkNugetFeedResponsiveness = EnvironmentVariables.GetBooleanOptOut(EnvironmentVariableNames.CheckNugetFeedResponsiveness);
            logger.LogInfo($"Checking NuGet feed responsiveness: {checkNugetFeedResponsiveness}");
            compilationInfoContainer.CompilationInfos.Add(("NuGet feed responsiveness checked", checkNugetFeedResponsiveness ? "1" : "0"));

            HashSet<string>? explicitFeeds = null;
            HashSet<string>? allFeeds = null;

            try
            {
                if (checkNugetFeedResponsiveness && !CheckFeeds(out explicitFeeds, out allFeeds))
                {
                    // todo: we could also check the reachability of the inherited nuget feeds, but to use those in the fallback we would need to handle authentication too.
                    var unresponsiveMissingPackageLocation = DownloadMissingPackagesFromSpecificFeeds([], explicitFeeds);
                    return unresponsiveMissingPackageLocation is null
                        ? []
                        : [unresponsiveMissingPackageLocation];
                }

                using (var nuget = new NugetExeWrapper(fileProvider, legacyPackageDirectory, logger))
                {
                    var count = nuget.InstallPackages();

                    if (nuget.PackageCount > 0)
                    {
                        compilationInfoContainer.CompilationInfos.Add(("packages.config files", nuget.PackageCount.ToString()));
                        compilationInfoContainer.CompilationInfos.Add(("Successfully restored packages.config files", count.ToString()));
                    }
                }

                var nugetPackageDlls = legacyPackageDirectory.DirInfo.GetFiles("*.dll", new EnumerationOptions { RecurseSubdirectories = true });
                var nugetPackageDllPaths = nugetPackageDlls.Select(f => f.FullName).ToHashSet();
                var excludedPaths = nugetPackageDllPaths
                    .Where(path => IsPathInSubfolder(path, legacyPackageDirectory.DirInfo.FullName, "tools"))
                    .ToList();

                if (nugetPackageDllPaths.Count > 0)
                {
                    logger.LogInfo($"Restored {nugetPackageDllPaths.Count} NuGet DLLs.");
                }
                if (excludedPaths.Count > 0)
                {
                    logger.LogInfo($"Excluding {excludedPaths.Count} NuGet DLLs.");
                }

                foreach (var excludedPath in excludedPaths)
                {
                    logger.LogInfo($"Excluded NuGet DLL: {excludedPath}");
                }

                nugetPackageDllPaths.ExceptWith(excludedPaths);
                assemblyLookupLocations.UnionWith(nugetPackageDllPaths.Select(p => new AssemblyLookupLocation(p)));
            }
            catch (Exception exc)
            {
                logger.LogError($"Failed to restore NuGet packages with nuget.exe: {exc.Message}");
            }

            var restoredProjects = RestoreSolutions(out var container);
            var projects = fileProvider.Projects.Except(restoredProjects);
            RestoreProjects(projects, allFeeds, out var containers);

            var dependencies = containers.Flatten(container);

            var paths = dependencies
                .Paths
                .Select(d => Path.Combine(PackageDirectory.DirInfo.FullName, d))
                .ToList();
            assemblyLookupLocations.UnionWith(paths.Select(p => new AssemblyLookupLocation(p)));

            var usedPackageNames = GetAllUsedPackageDirNames(dependencies);

            var missingPackageLocation = checkNugetFeedResponsiveness
                ? DownloadMissingPackagesFromSpecificFeeds(usedPackageNames, explicitFeeds)
                : DownloadMissingPackages(usedPackageNames);

            if (missingPackageLocation is not null)
            {
                assemblyLookupLocations.Add(missingPackageLocation);
            }
            return assemblyLookupLocations;
        }

        private List<string> GetReachableFallbackNugetFeeds(HashSet<string>? feedsFromNugetConfigs)
        {
            var fallbackFeeds = EnvironmentVariables.GetURLs(EnvironmentVariableNames.FallbackNugetFeeds).ToHashSet();
            if (fallbackFeeds.Count == 0)
            {
                fallbackFeeds.Add(PublicNugetOrgFeed);
                logger.LogInfo($"No fallback NuGet feeds specified. Adding default feed: {PublicNugetOrgFeed}");

                var shouldAddNugetConfigFeeds = EnvironmentVariables.GetBooleanOptOut(EnvironmentVariableNames.AddNugetConfigFeedsToFallback);
                logger.LogInfo($"Adding feeds from nuget.config to fallback restore: {shouldAddNugetConfigFeeds}");

                if (shouldAddNugetConfigFeeds && feedsFromNugetConfigs?.Count > 0)
                {
                    // There are some feeds in `feedsFromNugetConfigs` that have already been checked for reachability, we could skip those.
                    // But we might use different responsiveness testing settings when we try them in the fallback logic, so checking them again is safer.
                    fallbackFeeds.UnionWith(feedsFromNugetConfigs);
                    logger.LogInfo($"Using NuGet feeds from nuget.config files as fallback feeds: {string.Join(", ", feedsFromNugetConfigs.OrderBy(f => f))}");
                }
            }

            logger.LogInfo($"Checking fallback NuGet feed reachability on feeds: {string.Join(", ", fallbackFeeds.OrderBy(f => f))}");
            var (initialTimeout, tryCount) = GetFeedRequestSettings(isFallback: true);
            var reachableFallbackFeeds = fallbackFeeds.Where(feed => IsFeedReachable(feed, initialTimeout, tryCount, allowExceptions: false)).ToList();
            if (reachableFallbackFeeds.Count == 0)
            {
                logger.LogWarning("No fallback NuGet feeds are reachable.");
            }
            else
            {
                logger.LogInfo($"Reachable fallback NuGet feeds: {string.Join(", ", reachableFallbackFeeds.OrderBy(f => f))}");
            }

            compilationInfoContainer.CompilationInfos.Add(("Reachable fallback NuGet feed count", reachableFallbackFeeds.Count.ToString()));

            return reachableFallbackFeeds;
        }

        /// <summary>
        /// Executes `dotnet restore` on all solution files in solutions.
        /// As opposed to RestoreProjects this is not run in parallel using PLINQ
        /// as `dotnet restore` on a solution already uses multiple threads for restoring
        /// the projects (this can be disabled with the `--disable-parallel` flag).
        /// Populates dependencies with the relevant dependencies from the assets files generated by the restore.
        /// Returns a list of projects that are up to date with respect to restore.
        /// </summary>
        private IEnumerable<string> RestoreSolutions(out DependencyContainer dependencies)
        {
            var successCount = 0;
            var nugetSourceFailures = 0;
            var assets = new Assets(logger);

            var isWindows = fileContent.UseWindowsForms || fileContent.UseWpf;

            var projects = fileProvider.Solutions.SelectMany(solution =>
                {
                    logger.LogInfo($"Restoring solution {solution}...");
                    var res = dotnet.Restore(new(solution, PackageDirectory.DirInfo.FullName, ForceDotnetRefAssemblyFetching: true, TargetWindows: isWindows));
                    if (res.Success)
                    {
                        successCount++;
                    }
                    if (res.HasNugetPackageSourceError)
                    {
                        nugetSourceFailures++;
                    }
                    assets.AddDependenciesRange(res.AssetsFilePaths);
                    return res.RestoredProjects;
                }).ToList();
            dependencies = assets.Dependencies;
            compilationInfoContainer.CompilationInfos.Add(("Successfully restored solution files", successCount.ToString()));
            compilationInfoContainer.CompilationInfos.Add(("Failed solution restore with package source error", nugetSourceFailures.ToString()));
            compilationInfoContainer.CompilationInfos.Add(("Restored projects through solution files", projects.Count.ToString()));
            return projects;
        }

        /// <summary>
        /// Executes `dotnet restore` on all projects in projects.
        /// This is done in parallel for performance reasons.
        /// Populates dependencies with the relative paths to the assets files generated by the restore.
        /// </summary>
        /// <param name="projects">A list of paths to project files.</param>
        private void RestoreProjects(IEnumerable<string> projects, HashSet<string>? configuredSources, out ConcurrentBag<DependencyContainer> dependencies)
        {
            // Conservatively, we only set this to a non-null value if a Dependabot proxy is enabled.
            // This ensures that we continue to get the old behaviour where feeds are taken from
            // `nuget.config` files instead of the command-line arguments.
            string? extraArgs = null;

            if (this.dependabotProxy is not null)
            {
                // If the Dependabot proxy is configured, then our main goal is to make `dotnet` aware
                // of the private registry feeds. However, since providing them as command-line arguments
                // to `dotnet` ignores other feeds that may be configured, we also need to add the feeds
                // we have discovered from analysing `nuget.config` files.
                var sources = configuredSources ?? new();
                this.dependabotProxy.RegistryURLs.ForEach(url => sources.Add(url));

                // Add package sources. If any are present, they override all sources specified in
                // the configuration file(s).
                var feedArgs = new StringBuilder();
                foreach (string source in sources)
                {
                    feedArgs.Append($" -s {source}");
                }

                extraArgs = feedArgs.ToString();
            }

            var successCount = 0;
            var nugetSourceFailures = 0;
            ConcurrentBag<DependencyContainer> collectedDependencies = [];

            var isWindows = fileContent.UseWindowsForms || fileContent.UseWpf;

            var sync = new Lock();
            var projectGroups = projects.GroupBy(Path.GetDirectoryName);
            Parallel.ForEach(projectGroups, new ParallelOptions { MaxDegreeOfParallelism = DependencyManager.Threads }, projectGroup =>
            {
                var assets = new Assets(logger);
                foreach (var project in projectGroup)
                {
                    logger.LogInfo($"Restoring project {project}...");
                    var res = dotnet.Restore(new(project, PackageDirectory.DirInfo.FullName, ForceDotnetRefAssemblyFetching: true, extraArgs, TargetWindows: isWindows));
                    assets.AddDependenciesRange(res.AssetsFilePaths);
                    lock (sync)
                    {
                        if (res.Success)
                        {
                            successCount++;
                        }
                        if (res.HasNugetPackageSourceError)
                        {
                            nugetSourceFailures++;
                        }
                    }
                }
                collectedDependencies.Add(assets.Dependencies);
            });
            dependencies = collectedDependencies;
            compilationInfoContainer.CompilationInfos.Add(("Successfully restored project files", successCount.ToString()));
            compilationInfoContainer.CompilationInfos.Add(("Failed project restore with package source error", nugetSourceFailures.ToString()));
        }

        private AssemblyLookupLocation? DownloadMissingPackagesFromSpecificFeeds(IEnumerable<string> usedPackageNames, HashSet<string>? feedsFromNugetConfigs)
        {
            var reachableFallbackFeeds = GetReachableFallbackNugetFeeds(feedsFromNugetConfigs);
            if (reachableFallbackFeeds.Count > 0)
            {
                return DownloadMissingPackages(usedPackageNames, fallbackNugetFeeds: reachableFallbackFeeds);
            }

            logger.LogWarning("Skipping download of missing packages from specific feeds as no fallback NuGet feeds are reachable.");
            return null;
        }

        private AssemblyLookupLocation? DownloadMissingPackages(IEnumerable<string> usedPackageNames, IEnumerable<string>? fallbackNugetFeeds = null)
        {
            var alreadyDownloadedPackages = usedPackageNames.Select(p => p.ToLowerInvariant());
            var alreadyDownloadedLegacyPackages = GetRestoredLegacyPackageNames();

            var notYetDownloadedPackages = new HashSet<PackageReference>(fileContent.AllPackages);
            foreach (var alreadyDownloadedPackage in alreadyDownloadedPackages)
            {
                notYetDownloadedPackages.Remove(new(alreadyDownloadedPackage, PackageReferenceSource.SdkCsProj));
            }
            foreach (var alreadyDownloadedLegacyPackage in alreadyDownloadedLegacyPackages)
            {
                notYetDownloadedPackages.Remove(new(alreadyDownloadedLegacyPackage, PackageReferenceSource.PackagesConfig));
            }

            if (notYetDownloadedPackages.Count == 0)
            {
                return null;
            }

            var multipleVersions = notYetDownloadedPackages
                .GroupBy(p => p.Name)
                .Where(g => g.Count() > 1)
                .Select(g => g.Key)
                .ToList();

            foreach (var package in multipleVersions)
            {
                logger.LogWarning($"Found multiple not yet restored packages with name '{package}'.");
                notYetDownloadedPackages.Remove(new(package, PackageReferenceSource.PackagesConfig));
            }

            logger.LogInfo($"Found {notYetDownloadedPackages.Count} packages that are not yet restored");
            using var tempDir = new TemporaryDirectory(ComputeTempDirectoryPath("nugetconfig"), "generated nuget config", logger);
            var nugetConfig = fallbackNugetFeeds is null
                ? GetNugetConfig()
                : CreateFallbackNugetConfig(fallbackNugetFeeds, tempDir.DirInfo.FullName);

            compilationInfoContainer.CompilationInfos.Add(("Fallback nuget restore", notYetDownloadedPackages.Count.ToString()));

            var successCount = 0;
            var sync = new Lock();

            Parallel.ForEach(notYetDownloadedPackages, new ParallelOptions { MaxDegreeOfParallelism = DependencyManager.Threads }, package =>
            {
                var success = TryRestorePackageManually(package.Name, nugetConfig, package.PackageReferenceSource, tryWithoutNugetConfig: fallbackNugetFeeds is null);
                if (!success)
                {
                    return;
                }

                lock (sync)
                {
                    successCount++;
                }
            });

            compilationInfoContainer.CompilationInfos.Add(("Successfully ran fallback nuget restore", successCount.ToString()));

            return missingPackageDirectory.DirInfo.FullName;
        }

        private string? CreateFallbackNugetConfig(IEnumerable<string> fallbackNugetFeeds, string folderPath)
        {
            var sb = new StringBuilder();
            fallbackNugetFeeds.ForEach((feed, index) => sb.AppendLine($"<add key=\"feed{index}\" value=\"{feed}\" />"));

            var nugetConfigPath = Path.Combine(folderPath, "nuget.config");
            logger.LogInfo($"Creating fallback nuget.config file {nugetConfigPath}.");
            File.WriteAllText(nugetConfigPath,
                $"""
                <?xml version="1.0" encoding="utf-8"?>
                <configuration>
                    <packageSources>
                        <clear />
                {sb}
                    </packageSources>
                </configuration>
                """);

            return nugetConfigPath;
        }

        private string? GetNugetConfig()
        {
            var nugetConfigs = fileProvider.NugetConfigs;
            string? nugetConfig;
            if (nugetConfigs.Count > 1)
            {
                logger.LogInfo($"Found multiple nuget.config files: {string.Join(", ", nugetConfigs)}.");
                nugetConfig = fileProvider.RootNugetConfig;
                if (nugetConfig == null)
                {
                    logger.LogInfo("Could not find a top-level nuget.config file.");
                }
            }
            else
            {
                nugetConfig = nugetConfigs.FirstOrDefault();
            }

            if (nugetConfig != null)
            {
                logger.LogInfo($"Using nuget.config file {nugetConfig}.");
            }

            return nugetConfig;
        }

        private IEnumerable<string> GetAllUsedPackageDirNames(DependencyContainer dependencies)
        {
            var allPackageDirectories = GetAllPackageDirectories();

            logger.LogInfo($"Restored {allPackageDirectories.Count} packages");
            logger.LogInfo($"Found {dependencies.Packages.Count} packages in project.assets.json files");

            var usage = allPackageDirectories.Select(package => (package, isUsed: dependencies.Packages.Contains(package)));

            usage
                .Where(package => !package.isUsed)
                .Order()
                .ForEach(package => logger.LogDebug($"Unused package: {package.package}"));

            return usage
                .Where(package => package.isUsed)
                .Select(package => package.package);
        }

        private ICollection<string> GetAllPackageDirectories()
        {
            return new DirectoryInfo(PackageDirectory.DirInfo.FullName)
                .EnumerateDirectories("*", new EnumerationOptions { MatchCasing = MatchCasing.CaseInsensitive, RecurseSubdirectories = false })
                .Select(d => d.Name)
                .ToList();
        }

        private static bool IsPathInSubfolder(string path, string rootFolder, string subFolder)
        {
            return path.IndexOf(
                $"{Path.DirectorySeparatorChar}{subFolder}{Path.DirectorySeparatorChar}",
                rootFolder.Length,
                StringComparison.InvariantCultureIgnoreCase) >= 0;
        }

        private IEnumerable<string> GetRestoredLegacyPackageNames()
        {
            var oldPackageDirectories = GetRestoredPackageDirectoryNames(legacyPackageDirectory.DirInfo);
            foreach (var oldPackageDirectory in oldPackageDirectories)
            {
                // nuget install restores packages to 'packagename.version' folders (dotnet restore to 'packagename/version' folders)
                // typical folder names look like:
                //   newtonsoft.json.13.0.3
                // there are more complex ones too, such as:
                //   runtime.tizen.4.0.0-armel.Microsoft.NETCore.DotNetHostResolver.2.0.0-preview2-25407-01

                var match = LegacyNugetPackage().Match(oldPackageDirectory);
                if (!match.Success)
                {
                    logger.LogWarning($"Package directory '{oldPackageDirectory}' doesn't match the expected pattern.");
                    continue;
                }

                yield return match.Groups[1].Value.ToLowerInvariant();
            }
        }

        private static IEnumerable<string> GetRestoredPackageDirectoryNames(DirectoryInfo root)
        {
            return Directory.GetDirectories(root.FullName)
                .Select(d => Path.GetFileName(d).ToLowerInvariant());
        }

        private bool TryRestorePackageManually(string package, string? nugetConfig = null, PackageReferenceSource packageReferenceSource = PackageReferenceSource.SdkCsProj,
            bool tryWithoutNugetConfig = true, bool tryPrereleaseVersion = true)
        {
            logger.LogInfo($"Restoring package {package}...");
            using var tempDir = new TemporaryDirectory(
                ComputeTempDirectoryPath(package, "missingpackages_workingdir"), "missing package working", logger);
            var success = dotnet.New(tempDir.DirInfo.FullName);
            if (!success)
            {
                return false;
            }

            if (packageReferenceSource == PackageReferenceSource.PackagesConfig)
            {
                TryChangeTargetFrameworkMoniker(tempDir.DirInfo);
            }

            success = dotnet.AddPackage(tempDir.DirInfo.FullName, package);
            if (!success)
            {
                return false;
            }

            var res = TryRestorePackageManually(package, nugetConfig, tempDir, tryPrereleaseVersion);
            if (res.Success)
            {
                return true;
            }

            if (tryWithoutNugetConfig && res.HasNugetPackageSourceError && nugetConfig is not null)
            {
                logger.LogDebug($"Trying to restore '{package}' without nuget.config.");
                // Restore could not be completed because the listed source is unavailable. Try without the nuget.config:
                res = TryRestorePackageManually(package, nugetConfig: null, tempDir, tryPrereleaseVersion);
                if (res.Success)
                {
                    return true;
                }
            }

            logger.LogInfo($"Failed to restore nuget package {package}");
            return false;
        }

        private RestoreResult TryRestorePackageManually(string package, string? nugetConfig, TemporaryDirectory tempDir, bool tryPrereleaseVersion)
        {
            var res = dotnet.Restore(new(tempDir.DirInfo.FullName, missingPackageDirectory.DirInfo.FullName, ForceDotnetRefAssemblyFetching: false, PathToNugetConfig: nugetConfig, ForceReevaluation: true));

            if (!res.Success && tryPrereleaseVersion && res.HasNugetNoStablePackageVersionError)
            {
                logger.LogDebug($"Failed to restore nuget package {package} because no stable version was found.");
                TryChangePackageVersion(tempDir.DirInfo, "*-*");

                res = dotnet.Restore(new(tempDir.DirInfo.FullName, missingPackageDirectory.DirInfo.FullName, ForceDotnetRefAssemblyFetching: false, PathToNugetConfig: nugetConfig, ForceReevaluation: true));
                if (!res.Success)
                {
                    TryChangePackageVersion(tempDir.DirInfo, "*");
                }
            }

            return res;
        }

        private void TryChangeTargetFrameworkMoniker(DirectoryInfo tempDir)
        {
            TryChangeProjectFile(tempDir, TargetFramework(), $"<TargetFramework>{FrameworkPackageNames.LatestNetFrameworkMoniker}</TargetFramework>", "target framework moniker");
        }

        private void TryChangePackageVersion(DirectoryInfo tempDir, string newVersion)
        {
            TryChangeProjectFile(tempDir, PackageReferenceVersion(), $"Version=\"{newVersion}\"", "package reference version");
        }

        private void TryChangeProjectFile(DirectoryInfo projectDir, Regex pattern, string replacement, string patternName)
        {
            try
            {
                logger.LogDebug($"Changing the {patternName} in {projectDir.FullName}...");

                var csprojs = projectDir.GetFiles("*.csproj", new EnumerationOptions { RecurseSubdirectories = false, MatchCasing = MatchCasing.CaseInsensitive });
                if (csprojs.Length != 1)
                {
                    logger.LogError($"Could not find the .csproj file in {projectDir.FullName}, count = {csprojs.Length}");
                    return;
                }

                var csproj = csprojs[0];
                var content = File.ReadAllText(csproj.FullName);
                var matches = pattern.Matches(content);
                if (matches.Count == 0)
                {
                    logger.LogError($"Could not find the {patternName} in {csproj.FullName}");
                    return;
                }

                content = pattern.Replace(content, replacement, 1);
                File.WriteAllText(csproj.FullName, content);
            }
            catch (Exception exc)
            {
                logger.LogError($"Failed to change the {patternName} in {projectDir.FullName}: {exc}");
            }
        }

        private static async Task ExecuteGetRequest(string address, HttpClient httpClient, CancellationToken cancellationToken)
        {
            using var stream = await httpClient.GetStreamAsync(address, cancellationToken);
            var buffer = new byte[1024];
            int bytesRead;
            while ((bytesRead = stream.Read(buffer, 0, buffer.Length)) > 0)
            {
                // do nothing
            }
        }

        private bool IsFeedReachable(string feed, int timeoutMilliSeconds, int tryCount, bool allowExceptions = true)
        {
            logger.LogInfo($"Checking if NuGet feed '{feed}' is reachable...");

            // Configure the HttpClient to be aware of the Dependabot Proxy, if used.
            HttpClientHandler httpClientHandler = new();
            if (this.dependabotProxy != null)
            {
                httpClientHandler.Proxy = new WebProxy(this.dependabotProxy.Address);

                if (this.dependabotProxy.Certificate != null)
                {
                    httpClientHandler.ServerCertificateCustomValidationCallback = (message, cert, chain, _) =>
                    {
                        if (chain is null || cert is null)
                        {
                            var msg = cert is null && chain is null
                                ? "certificate and chain"
                                : chain is null
                                    ? "chain"
                                    : "certificate";
                            logger.LogWarning($"Dependabot proxy certificate validation failed due to missing {msg}");
                            return false;
                        }
                        chain.ChainPolicy.TrustMode = X509ChainTrustMode.CustomRootTrust;
                        chain.ChainPolicy.CustomTrustStore.Add(this.dependabotProxy.Certificate);
                        return chain.Build(cert);
                    };
                }
            }

            using HttpClient client = new(httpClientHandler);

            for (var i = 0; i < tryCount; i++)
            {
                using var cts = new CancellationTokenSource();
                cts.CancelAfter(timeoutMilliSeconds);
                try
                {
                    ExecuteGetRequest(feed, client, cts.Token).GetAwaiter().GetResult();
                    logger.LogInfo($"Querying NuGet feed '{feed}' succeeded.");
                    return true;
                }
                catch (Exception exc)
                {
                    if (exc is TaskCanceledException tce &&
                        tce.CancellationToken == cts.Token &&
                        cts.Token.IsCancellationRequested)
                    {
                        logger.LogInfo($"Didn't receive answer from NuGet feed '{feed}' in {timeoutMilliSeconds}ms.");
                        timeoutMilliSeconds *= 2;
                        continue;
                    }

                    // We're only interested in timeouts.
                    var start = allowExceptions ? "Considering" : "Not considering";
                    logger.LogInfo($"Querying NuGet feed '{feed}' failed in a timely manner. {start} the feed for use. The reason for the failure: {exc.Message}");
                    return allowExceptions;
                }
            }

            logger.LogWarning($"Didn't receive answer from NuGet feed '{feed}'. Tried it {tryCount} times.");
            return false;
        }

        private (int initialTimeout, int tryCount) GetFeedRequestSettings(bool isFallback)
        {
            int timeoutMilliSeconds = isFallback && int.TryParse(Environment.GetEnvironmentVariable(EnvironmentVariableNames.NugetFeedResponsivenessInitialTimeoutForFallback), out timeoutMilliSeconds)
                ? timeoutMilliSeconds
                : int.TryParse(Environment.GetEnvironmentVariable(EnvironmentVariableNames.NugetFeedResponsivenessInitialTimeout), out timeoutMilliSeconds)
                    ? timeoutMilliSeconds
                    : 1000;
            logger.LogDebug($"Initial timeout for NuGet feed reachability check is {timeoutMilliSeconds}ms.");

            int tryCount = isFallback && int.TryParse(Environment.GetEnvironmentVariable(EnvironmentVariableNames.NugetFeedResponsivenessRequestCountForFallback), out tryCount)
                ? tryCount
                : int.TryParse(Environment.GetEnvironmentVariable(EnvironmentVariableNames.NugetFeedResponsivenessRequestCount), out tryCount)
                    ? tryCount
                    : 4;
            logger.LogDebug($"Number of tries for NuGet feed reachability check is {tryCount}.");

            return (timeoutMilliSeconds, tryCount);
        }

        /// <summary>
        /// Checks that we can connect to all NuGet feeds that are explicitly configured in configuration files
        /// as well as any private package registry feeds that are configured.
        /// </summary>
        /// <param name="explicitFeeds">Outputs the set of explicit feeds.</param>
        /// <param name="allFeeds">Outputs the set of all feeds (explicit and inherited).</param>
        /// <returns>True if all feeds are reachable or false otherwise.</returns>
        private bool CheckFeeds(out HashSet<string> explicitFeeds, out HashSet<string> allFeeds)
        {
            (explicitFeeds, allFeeds) = GetAllFeeds();
            HashSet<string> feedsToCheck = explicitFeeds;

            // If private package registries are configured for C#, then check those
            // in addition to the ones that are configured in `nuget.config` files.
            this.dependabotProxy?.RegistryURLs.ForEach(url => feedsToCheck.Add(url));

            var allFeedsReachable = this.CheckSpecifiedFeeds(feedsToCheck);

            var inheritedFeeds = allFeeds.Except(explicitFeeds).ToHashSet();
            if (inheritedFeeds.Count > 0)
            {
                logger.LogInfo($"Inherited NuGet feeds (not checked for reachability): {string.Join(", ", inheritedFeeds.OrderBy(f => f))}");
                compilationInfoContainer.CompilationInfos.Add(("Inherited NuGet feed count", inheritedFeeds.Count.ToString()));
            }

            return allFeedsReachable;
        }

        /// <summary>
        /// Checks that we can connect to the specified NuGet feeds.
        /// </summary>
        /// <param name="feeds">The set of package feeds to check.</param>
        /// <returns>True if all feeds are reachable or false otherwise.</returns>
        private bool CheckSpecifiedFeeds(HashSet<string> feeds)
        {
            logger.LogInfo("Checking that NuGet feeds are reachable...");

            var excludedFeeds = EnvironmentVariables.GetURLs(EnvironmentVariableNames.ExcludedNugetFeedsFromResponsivenessCheck)
                .ToHashSet();

            if (excludedFeeds.Count > 0)
            {
                logger.LogInfo($"Excluded NuGet feeds from responsiveness check: {string.Join(", ", excludedFeeds.OrderBy(f => f))}");
            }

            var (initialTimeout, tryCount) = GetFeedRequestSettings(isFallback: false);

            var allFeedsReachable = feeds.All(feed => excludedFeeds.Contains(feed) || IsFeedReachable(feed, initialTimeout, tryCount));
            if (!allFeedsReachable)
            {
                logger.LogWarning("Found unreachable NuGet feed in C# analysis with build-mode 'none'. This may cause missing dependencies in the analysis.");
                diagnosticsWriter.AddEntry(new DiagnosticMessage(
                    Language.CSharp,
                    "buildless/unreachable-feed",
                    "Found unreachable NuGet feed in C# analysis with build-mode 'none'",
                    visibility: new DiagnosticMessage.TspVisibility(statusPage: true, cliSummaryTable: true, telemetry: true),
                    markdownMessage: "Found unreachable NuGet feed in C# analysis with build-mode 'none'. This may cause missing dependencies in the analysis.",
                    severity: DiagnosticMessage.TspSeverity.Note
                ));
            }
            compilationInfoContainer.CompilationInfos.Add(("All NuGet feeds reachable", allFeedsReachable ? "1" : "0"));

            return allFeedsReachable;
        }

        private IEnumerable<string> GetFeeds(Func<IList<string>> getNugetFeeds)
        {
            var results = getNugetFeeds();
            var regex = EnabledNugetFeed();
            foreach (var result in results)
            {
                var match = regex.Match(result);
                if (!match.Success)
                {
                    logger.LogError($"Failed to parse feed from '{result}'");
                    continue;
                }

                var url = match.Groups[1].Value;
                if (!url.StartsWith("https://", StringComparison.InvariantCultureIgnoreCase) &&
                    !url.StartsWith("http://", StringComparison.InvariantCultureIgnoreCase))
                {
                    logger.LogInfo($"Skipping feed '{url}' as it is not a valid URL.");
                    continue;
                }

                if (!string.IsNullOrWhiteSpace(url))
                {
                    yield return url;
                }
            }
        }

        private (HashSet<string> explicitFeeds, HashSet<string> allFeeds) GetAllFeeds()
        {
            var nugetConfigs = fileProvider.NugetConfigs;

            // On systems with case-sensitive file systems (for simplicity, we assume that is Linux), the
            // filenames of NuGet configuration files must be named correctly. For compatibility with projects
            // that are typically built on Windows or macOS where this doesn't matter, we accept all variants
            // of `nuget.config` ourselves. However, `dotnet` does not. If we detect that incorrectly-named
            // files are present, we emit a diagnostic to warn the user.
            if (SystemBuildActions.Instance.IsLinux())
            {
                string[] acceptedNugetConfigNames = ["nuget.config", "NuGet.config", "NuGet.Config"];
                var invalidNugetConfigs = nugetConfigs
                    .Where(path => !acceptedNugetConfigNames.Contains(Path.GetFileName(path)));

                if (invalidNugetConfigs.Count() > 0)
                {
                    this.logger.LogWarning(string.Format(
                        "Found incorrectly named NuGet configuration files: {0}",
                        string.Join(", ", invalidNugetConfigs)
                    ));
                    this.diagnosticsWriter.AddEntry(new DiagnosticMessage(
                        Language.CSharp,
                        "buildless/case-sensitive-nuget-config",
                        "Found NuGet configuration files which are not correctly named",
                        visibility: new DiagnosticMessage.TspVisibility(statusPage: true, cliSummaryTable: true, telemetry: true),
                        markdownMessage: string.Format(
                            "On platforms with case-sensitive file systems, NuGet only accepts files with one of the following names: {0}.\n\n" +
                            "CodeQL found the following files while performing an analysis on a platform with a case-sensitive file system:\n\n" +
                            "{1}\n\n" +
                            "To avoid unexpected results, rename these files to match the casing of one of the accepted filenames.",
                            string.Join(", ", acceptedNugetConfigNames),
                            string.Join("\n", invalidNugetConfigs.Select(path => string.Format("- `{0}`", path)))
                        ),
                        severity: DiagnosticMessage.TspSeverity.Warning
                    ));
                }
            }

            // Find feeds that are explicitly configured in the NuGet configuration files that we found.
            var explicitFeeds = nugetConfigs
                .SelectMany(config => GetFeeds(() => dotnet.GetNugetFeeds(config)))
                .ToHashSet();

            if (explicitFeeds.Count > 0)
            {
                logger.LogInfo($"Found {explicitFeeds.Count} NuGet feeds in nuget.config files: {string.Join(", ", explicitFeeds.OrderBy(f => f))}");
            }
            else
            {
                logger.LogDebug("No NuGet feeds found in nuget.config files.");
            }

            // todo: this could be improved.
            HashSet<string>? allFeeds = null;

            if (nugetConfigs.Count > 0)
            {
                // We don't have to get the feeds from each of the folders from below, it would be enought to check the folders that recursively contain the others.
                allFeeds = nugetConfigs
                    .Select(config =>
                    {
                        try
                        {
                            return new FileInfo(config).Directory?.FullName;
                        }
                        catch (Exception exc)
                        {
                            logger.LogWarning($"Failed to get directory of '{config}': {exc}");
                        }
                        return null;
                    })
                    .Where(folder => folder != null)
                    .SelectMany(folder => GetFeeds(() => dotnet.GetNugetFeedsFromFolder(folder!)))
                    .ToHashSet();

                // If we have discovered any explicit feeds, then we also expect these to be in the set of all feeds.
                // Normally, it is a safe assumption to make that `GetNugetFeedsFromFolder` will include the feeds configured
                // in a NuGet configuration file in the given directory. There is one exception: on a system with case-sensitive
                // file systems, we may discover a configuration file such as `Nuget.Config` which is not recognised by `dotnet nuget`.
                // In that case, our call to `GetNugetFeeds` will retrieve the feeds from that file (because it is accepted when
                // provided explicitly as `--configfile` argument), but the call to `GetNugetFeedsFromFolder` will not.
                allFeeds.UnionWith(explicitFeeds);
            }
            else
            {
                // If we haven't found any `nuget.config` files, then obtain a list of feeds from the root source directory.
                allFeeds = GetFeeds(() => dotnet.GetNugetFeedsFromFolder(this.fileProvider.SourceDir.FullName)).ToHashSet();
            }

            logger.LogInfo($"Found {allFeeds.Count} NuGet feeds (with inherited ones) in nuget.config files: {string.Join(", ", allFeeds.OrderBy(f => f))}");

            return (explicitFeeds, allFeeds);
        }

        [GeneratedRegex(@"<TargetFramework>.*</TargetFramework>", RegexOptions.IgnoreCase | RegexOptions.Compiled | RegexOptions.Singleline)]
        private static partial Regex TargetFramework();

        [GeneratedRegex(@"Version=""(\*|\*-\*)""", RegexOptions.IgnoreCase | RegexOptions.Compiled | RegexOptions.Singleline)]
        private static partial Regex PackageReferenceVersion();

        [GeneratedRegex(@"^(.+)\.(\d+\.\d+\.\d+(-(.+))?)$", RegexOptions.IgnoreCase | RegexOptions.Compiled | RegexOptions.Singleline)]
        private static partial Regex LegacyNugetPackage();

        [GeneratedRegex(@"^E\s(.*)$", RegexOptions.IgnoreCase | RegexOptions.Compiled | RegexOptions.Singleline)]
        private static partial Regex EnabledNugetFeed();

        public void Dispose()
        {
            PackageDirectory?.Dispose();
            legacyPackageDirectory?.Dispose();
            missingPackageDirectory?.Dispose();
        }

        /// <summary>
        /// Returns the full path to a temporary directory with the given subfolder name.
        /// </summary>
        private static string ComputeTempDirectoryPath(string subfolderName)
        {
            return Path.Combine(FileUtils.GetTemporaryWorkingDirectory(out _), subfolderName);
        }

        /// <summary>
        /// Computes a unique temporary directory path based on the source directory and the subfolder name.
        /// </summary>
        private static string ComputeTempDirectoryPath(string srcDir, string subfolderName)
        {
            return Path.Combine(FileUtils.GetTemporaryWorkingDirectory(out _), FileUtils.ComputeHash(srcDir), subfolderName);
        }
    }
}