Merge branch 'master' into Skyline/work/20250126_UpdateLocalizedResxF…

…iles

pwiz_tools/Shared/PanoramaClient/PanoramaClient.cs

@@ -773,7 +773,7 @@ public override PanoramaServer EnsureLogin(PanoramaServer pServer)
         public override void DownloadFile(string fileUrl, string fileName, long fileSize, string realName, IProgressMonitor pm, IProgressStatus progressStatus)
         {
             // TODO: Change this to use IRequestHelper
-            using var wc = new WebClientWithCredentials(ServerUri, Username, Password);
+            using var wc = new LabkeySessionWebClient(new PanoramaServer(ServerUri, Username, Password));
             wc.DownloadProgressChanged += (s, e) =>
             {
                 var progressPercent = e.ProgressPercentage > 0 ? e.ProgressPercentage : -1;
@@ -818,9 +818,10 @@ public override void DownloadFile(string fileUrl, string fileName, long fileSize
 
         public override IRequestHelper GetRequestHelper(bool forPublish = false)
         {
+            var panoramaServer = new PanoramaServer(ServerUri, Username, Password);
             var webClient = forPublish
-                ? new NonStreamBufferingWebClient(ServerUri, Username, Password)
-                : new WebClientWithCredentials(ServerUri, Username, Password);
+                ? new NonStreamBufferingWebClient(panoramaServer)
+                : new LabkeySessionWebClient(panoramaServer);
             return new PanoramaRequestHelper(webClient);
         }
 
@@ -839,7 +840,7 @@ public string DownloadStringAsync(Uri queryUri, CancellationToken cancelToken)
             string data = null;
             Exception error = null;
 
-            using (var webClient = GetWebClientForServer(new PanoramaServer(ServerUri, Username, Password)))
+            using (var webClient = new LabkeySessionWebClient(new PanoramaServer(ServerUri, Username, Password)))
             {
                 bool finishedDownloading = false;
                 webClient.DownloadStringAsync(queryUri);
@@ -861,15 +862,6 @@ public string DownloadStringAsync(Uri queryUri, CancellationToken cancelToken)
                 throw error;
             return data;
         }
-
-        private static WebClient GetWebClientForServer(PanoramaServer server)
-        {
-            return server.HasUserAccount()
-                ? new WebClientWithCredentials(server.URI, server.Username, server.Password)
-                : new UTF8WebClient();// Use anonymous client if we were not given a username and password. Otherwise, request will fail.
-                                      // Prior to LK 24.11 a call that failed authentication would proceed as an unauthenticated user
-
-        }
     }
 
     /// <summary>

pwiz_tools/Shared/PanoramaClient/PanoramaFilePicker.cs

@@ -123,8 +123,7 @@ private static Uri BuildQuery(string server, string folderPath, string queryName
         /// </summary>
         private JToken GetJson(Uri queryUri)
         {
-            using (var requestHelper = new PanoramaRequestHelper(new WebClientWithCredentials(queryUri, FolderBrowser.GetActiveServer().Username,
-                       FolderBrowser.GetActiveServer().Password)))
+            using (var requestHelper = new PanoramaRequestHelper(new LabkeySessionWebClient(FolderBrowser.GetActiveServer())))
             {
                 JToken json = requestHelper.Get(queryUri);
                 return json;

pwiz_tools/Shared/PanoramaClient/PanoramaFolderBrowser.cs

@@ -541,7 +541,7 @@ private void AddWebDavFolders(TreeNode node)
             try
             {
                 query = new Uri(string.Concat(folderInfo.Server.URI, PanoramaUtil.WEBDAV, folderInfo.FolderPath, "?method=json"));
-                using var requestHelper = new PanoramaRequestHelper(new WebClientWithCredentials(query, folderInfo.Server.Username, folderInfo.Server.Password));
+                using var requestHelper = new PanoramaRequestHelper(new LabkeySessionWebClient(folderInfo.Server));
                 JToken json = requestHelper.Get(query);
                 if ((int)json[@"fileCount"] != 0)
                 {

pwiz_tools/Shared/PanoramaClient/PanoramaUtil.cs

@@ -642,37 +642,43 @@ public UTF8WebClient()
         }
     }
 
-    public class WebClientWithCredentials : UTF8WebClient
+    public class LabkeySessionWebClient : UTF8WebClient
     {
         private CookieContainer _cookies = new CookieContainer();
         private string _csrfToken;
         private readonly Uri _serverUri;
 
-        private static string LABKEY_CSRF = @"X-LABKEY-CSRF";
+        private const string LABKEY_CSRF = @"X-LABKEY-CSRF";
 
-        public WebClientWithCredentials(Uri serverUri, string username, string password)
+        public LabkeySessionWebClient(PanoramaServer server)
         {
-            // Add the Authorization header
-            Headers.Add(HttpRequestHeader.Authorization, PanoramaServer.GetBasicAuthHeader(username, password));
-            _serverUri = serverUri;
+            if (server == null)
+            {
+                throw new ArgumentNullException(nameof(server));
+            }
+            // Add the Authorization header only if a username and password is provided. Otherwise, the request will fail.
+            // Prior to LK 24.11 a call that failed authentication would proceed as an unauthenticated user
+            if (server.HasUserAccount())
+            {
+                Headers.Add(HttpRequestHeader.Authorization, server.AuthHeader);
+            }
+
+            _serverUri = server.URI;
         }
 
         protected override WebRequest GetWebRequest(Uri address)
         {
             var request = base.GetWebRequest(address);
-
-            var httpWebRequest = request as HttpWebRequest;
-            if (httpWebRequest != null)
+
+            if (request is HttpWebRequest httpWebRequest)
             {
                 httpWebRequest.CookieContainer = _cookies;
 
-                if (request.Method == PanoramaUtil.FORM_POST)
+                if (request.Method == PanoramaUtil.FORM_POST && !string.IsNullOrEmpty(_csrfToken))
                 {
-                    if (!string.IsNullOrEmpty(_csrfToken))
-                    {
-                        // All POST requests to LabKey Server will be checked for a CSRF token
-                        request.Headers.Add(LABKEY_CSRF, _csrfToken);
-                    }
+                    // All POST requests to LabKey Server will be checked for a CSRF token
+                    request.Headers.Add(LABKEY_CSRF, _csrfToken);
+
                 }
             }
             return request;
@@ -681,8 +687,7 @@ protected override WebRequest GetWebRequest(Uri address)
         protected override WebResponse GetWebResponse(WebRequest request)
         {
             var response = base.GetWebResponse(request);
-            var httpResponse = response as HttpWebResponse;
-            if (httpResponse != null)
+            if (response is HttpWebResponse httpResponse)
             {
                 GetCsrfToken(httpResponse, request.RequestUri);
             }
@@ -742,10 +747,10 @@ public void ClearCsrfToken()
         }
     }
 
-    public class NonStreamBufferingWebClient : WebClientWithCredentials
+    public class NonStreamBufferingWebClient : LabkeySessionWebClient
     {
-        public NonStreamBufferingWebClient(Uri serverUri, string username, string password)
-            : base(serverUri, username, password)
+        public NonStreamBufferingWebClient(PanoramaServer server)
+            : base(server)
         {
         }
 

pwiz_tools/Shared/PanoramaClient/RequestHelper.cs

@@ -195,9 +195,9 @@ private JObject ParseResponse(string response, Uri uri, string messageOnError)
 
     public class PanoramaRequestHelper : AbstractRequestHelper
     {
-        private readonly WebClientWithCredentials _client;
+        private readonly LabkeySessionWebClient _client;
 
-        public PanoramaRequestHelper(WebClientWithCredentials webClient)
+        public PanoramaRequestHelper(LabkeySessionWebClient webClient)
         {
             _client = webClient;
         }

pwiz_tools/Skyline/Controls/Graphs/GraphFullScan.cs

@@ -614,7 +614,7 @@ private void PopulateProperties()
 
                 if (_documentContainer is SkylineWindow stateProvider)
                 {
-                    var chromSet = stateProvider.DocumentUI.Settings.MeasuredResults.Chromatograms.FirstOrDefault(
+                    var chromSet = stateProvider.DocumentUI.Settings.MeasuredResults?.Chromatograms.FirstOrDefault(
                         chrom => chrom.ContainsFile(_msDataFileScanHelper.ScanProvider.DataFilePath));
                     spectrumProperties.ReplicateName = chromSet?.Name;
                     if (_peaks?.Length > 0)

pwiz_tools/Skyline/Executables/AutoQC/AutoQC/PanoramaSettings.cs

@@ -329,8 +329,8 @@ public void PingPanorama()
 
         public void Init()
         {
-            _requestHelper = new PanoramaRequestHelper(new WebClientWithCredentials(_panoramaSettings.PanoramaServerUri,
-                _panoramaSettings.PanoramaUserEmail, _panoramaSettings.PanoramaPassword));
+            _requestHelper = new PanoramaRequestHelper(new LabkeySessionWebClient(new PanoramaServer(_panoramaSettings.PanoramaServerUri,
+                _panoramaSettings.PanoramaUserEmail, _panoramaSettings.PanoramaPassword)));
             _timer = new Timer(e => { PingPanoramaServer(); });
             _timer.Change(TimeSpan.FromSeconds(10), TimeSpan.FromMinutes(5)); // Ping Panorama every 5 minutes.
         }

pwiz_tools/Skyline/Executables/AutoQC/AutoQCTest/PanoramaTest.cs

@@ -113,8 +113,8 @@ private async Task<bool> SuccessfulPanoramaUpload(string uniqueFolder)
             var labKeyQuery = PanoramaUtil.CallNewInterface(panoramaServerUri, "query", $"{uniqueFolder}",
                 "selectRows", "schemaName=targetedms&queryName=runs", true);
             var requestHelper =
-                new PanoramaRequestHelper(new WebClientWithCredentials(panoramaServerUri, TestUtils.PANORAMAWEB_USER,
-                    TestUtils.GetPanoramaWebPassword()));
+                new PanoramaRequestHelper(new LabkeySessionWebClient(new PanoramaServer(panoramaServerUri, TestUtils.PANORAMAWEB_USER,
+                    TestUtils.GetPanoramaWebPassword())));
             var startTime = DateTime.Now.Ticks / TimeSpan.TicksPerMillisecond;
             var x = startTime;
             while (x < startTime + TIMEOUT_80SEC)

pwiz_tools/Skyline/TestConnected/PanoramaClientDownloadTest.cs

@@ -26,6 +26,7 @@
 using pwiz.PanoramaClient;
 using pwiz.Skyline.Alerts;
 using pwiz.Skyline.Properties;
+using pwiz.Skyline.SettingsUI;
 using pwiz.Skyline.ToolsUI;
 using pwiz.Skyline.Util;
 using pwiz.SkylineTestUtil;
@@ -74,8 +75,11 @@ protected override void DoTest()
             // Test viewing webDav browser
             TestWebDav();
 
-            // Test adding a new server to Panorama - Test with and without username and password
+            // Test adding a new server to Panorama
             TestAddServer();
+
+            // Test adding PanoramaWeb as an anonymous server, and downloading a document from Panorama Public.
+            TestWithAnonymousServer();
         }
 
         private void AddPanoramaServers()
@@ -239,7 +243,7 @@ private void TestRenamedFile()
             Assert.IsFalse(File.Exists(path));
         }
 
-        //TODO: Test adding a new server to Panorama - Test with and without username and password 
+        //Test adding a new Panorama server.
         private void TestAddServer()
         {
             var path = TEST_FOLDER;
@@ -258,10 +262,68 @@ private void TestAddServer()
             var remoteDlg = ShowDialog<PanoramaFilePicker>(editItem.OkDialog);
             if (Settings.Default.ServerList != null)
                 Assert.AreEqual(1, Settings.Default.ServerList.Count);
-            RunUI(() => Assert.IsTrue(remoteDlg.IsLoaded));
+            RunUI(() =>
+            {
+                Assert.IsTrue(remoteDlg.IsLoaded);
+                Assert.IsTrue(remoteDlg.FolderBrowser.SelectNode(TEST_FOLDER), "Unable to select folder '{0}'", TEST_FOLDER);
+                Assert.IsTrue(remoteDlg.FolderBrowser.SelectNode(PANORAMA_FOLDER), "Unable to select folder '{0}'", PANORAMA_FOLDER);
+            });
+
             OkDialog(remoteDlg, remoteDlg.Close);
         }
 
+        private void TestWithAnonymousServer()
+        {
+            var toolsOptionsDlg = ShowDialog<ToolOptionsUI>(() => SkylineWindow.ShowToolOptionsUI(ToolOptionsUI.TABS.Panorama));
+
+            // Clear the Panorama server list
+            var editServerListDlg = ShowDialog<EditListDlg<SettingsListBase<Server>, Server>>(toolsOptionsDlg.EditServers);
+            RunUI(editServerListDlg.ResetList);
+
+            // Add PanoramaWeb as an anonymous server
+            var editServerDlg = ShowDialog<EditServerDlg>(editServerListDlg.AddItem);
+            RunUI(() =>
+            {
+                editServerDlg.URL = PANORAMA_WEB;
+                editServerDlg.AnonymousServer = true;
+            });
+            OkDialog(editServerDlg, editServerDlg.OkDialog);
+            OkDialog(editServerListDlg, editServerListDlg.OkDialog);
+            OkDialog(toolsOptionsDlg, toolsOptionsDlg.OkDialog);
+
+            Assert.IsNotNull(Settings.Default.ServerList);
+            Assert.AreEqual(1, Settings.Default.ServerList.Count);
+
+            const string panoramaPublicFolderPath = "Panorama Public/2018/MacLean - Baker IMS";
+            // Document in the "Panorama Public/2018/MacLean - Baker IMS" folder on https://panoramaweb.org that we will download.
+            const string skyDocName = "BSA-Training_2017-09-21_17-59-13.sky.zip";
+            var downloadFilePath = TestContext.GetTestResultsPath(skyDocName);
+            FileEx.SafeDelete(downloadFilePath, true);
+            Assert.IsFalse(File.Exists(downloadFilePath));
+
+            var panoramaFilePickerDlg = ShowDialog<PanoramaFilePicker>(() => SkylineWindow.OpenFromPanorama(downloadFilePath));
+            RunUI(() =>
+            {
+                Assert.IsTrue(panoramaFilePickerDlg.IsLoaded);
+                Assert.IsFalse(panoramaFilePickerDlg.FolderBrowser.SelectNode(TEST_FOLDER),
+                    "Guest user should not be able to see the private folder '{0}'.", TEST_FOLDER);
+
+                foreach (var folder in panoramaPublicFolderPath.Split('/'))
+                {
+                    Assert.IsTrue(panoramaFilePickerDlg.FolderBrowser.SelectNode(folder),
+                        "Guest user should be able to see folder '{0}' in the folder path '{1}'.", folder, panoramaPublicFolderPath);
+                }
+            });
+
+            var doc = SkylineWindow.Document;
+            OkDialog(panoramaFilePickerDlg, () => Assert.IsTrue(panoramaFilePickerDlg.ClickFile(skyDocName), "Unable to select Skyline document {0}", skyDocName));
+            WaitForCondition(() => File.Exists(downloadFilePath));
+            var docLoaded = WaitForDocumentChangeLoaded(doc);
+            AssertEx.IsDocumentState(docLoaded, null, 1, 34, 38, 404);
+            FileEx.SafeDelete(downloadFilePath, true);
+            Assert.IsFalse(File.Exists(downloadFilePath));
+        }
+
         // Test viewing webDav browser
         private void TestWebDav()
         {