private Uri GetContentsUri(ChorusAccount chorusAccount, ChorusUrl chorusUrl)
{
if (chorusUrl.FileId.HasValue)
{
return(null);
}
if (chorusUrl.ExperimentId.HasValue)
{
return(new Uri(chorusUrl.ServerUrl + "/skyline/api/contents/experiments/" + chorusUrl.ExperimentId + "/files")); // Not L10N
}
if (chorusUrl.ProjectId.HasValue)
{
return(new Uri(chorusUrl.ServerUrl + "/skyline/api/contents/projects/" + chorusUrl.ProjectId + "/experiments")); // Not L10N
}
if (!chorusUrl.GetPathParts().Any())
{
return(null);
}
string topLevelName = chorusUrl.GetPathParts().First();
TopLevelContents topLevelContents = TOP_LEVEL_ITEMS.FirstOrDefault(item => item.Name.Equals(topLevelName));
if (null != topLevelContents)
{
return(new Uri(chorusUrl.ServerUrl + "/skyline/api/contents" + topLevelContents.ContentsPath)); // Not L10N
}
return(null);
}
public void Login(ChorusAccount chorusAccount, CookieContainer cookieContainer)
{
var webRequest = (HttpWebRequest)WebRequest.Create(new Uri(chorusAccount.ServerUrl + "/j_spring_security_check")); // Not L10N
// ReSharper disable NonLocalizedString
webRequest.ContentType = "application/x-www-form-urlencoded";
webRequest.Method = "POST";
webRequest.CookieContainer = cookieContainer;
string postData = "j_username="******"&j_password="******"login.html")); // Not L10N
if (!loginSuccessful)
{
throw new ChorusServerException(Resources.ChorusSession_Login_Unable_to_log_in___Username_or_password_is_incorrect_);
}
}
private void FetchAndStoreContents(ChorusAccount chorusAccount, Uri requestUri)
{
ChorusContents contents = new ChorusContents();
var key = new RequestKey(chorusAccount, requestUri);
try
{
StoreContentsResponse(key, new ChorusContentsResponse(FetchContents(chorusAccount, requestUri), true));
}
catch (Exception exception)
{
ChorusServerException chorusException = exception as ChorusServerException;
// ReSharper disable once ConvertIfStatementToNullCoalescingExpression
if (null == chorusException)
{
chorusException = new ChorusServerException(
Resources.ChorusSession_FetchContents_There_was_an_error_communicating_with_the_server__
+ exception.Message, exception);
}
StoreContentsResponse(key, new ChorusContentsResponse(contents, true)
{
ChorusException = chorusException,
});
}
finally
{
lock (_lock)
{
_fetchRequests.Remove(key);
}
}
}
public bool AsyncFetchContents(ChorusAccount chorusAccount, ChorusUrl chorusUrl, out ChorusServerException chorusException)
{
Uri requestUri = GetContentsUri(chorusAccount, chorusUrl);
if (null == requestUri)
{
chorusException = null;
return(true);
}
RequestKey requestKey = new RequestKey(chorusAccount, requestUri);
lock (_lock)
{
ChorusContentsResponse chorusContentsResponse;
if (_chorusContentsByServerUrl.TryGetValue(requestKey, out chorusContentsResponse))
{
chorusException = chorusContentsResponse.ChorusException;
return(chorusContentsResponse.IsComplete);
}
chorusException = null;
if (!_fetchRequests.Add(requestKey))
{
return(false);
}
}
ActionUtil.RunAsync(() => FetchAndStoreContents(chorusAccount, requestUri), "Fetch from Chorus"); // Not L10N
return(false);
}
public MsDataSpectrum[] GetMsDataFileSpectraWithCommonRetentionTime(int dataFileSpectrumStartIndex)
{
double precursor = Transitions.Select(transition => transition.PrecursorMz).FirstOrDefault();
ChorusAccount chorusAccount = ChorusUrl.FindChorusAccount(Settings.Default.ChorusAccountList);
return(_chorusSession.GetSpectra(chorusAccount, ChorusUrl, Source, precursor, dataFileSpectrumStartIndex));
}
public ChromatogramGeneratorTask(ChromTaskList chromTaskList, ChorusAccount chorusAccount, ChorusUrl chorusUrl,
ChromatogramRequestDocument chromatogramRequestDocument)
{
ChromTaskList = chromTaskList;
ChorusAccount = chorusAccount;
ChorusUrl = chorusUrl;
ChromatogramRequestDocument = chromatogramRequestDocument;
}
public void AddAuthHeader(ChorusAccount chorusAccount, HttpWebRequest webRequest)
{
if (null != chorusAccount)
{
// ReSharper disable NonLocalizedString
byte[] authBytes = Encoding.UTF8.GetBytes(chorusAccount.Username + ':' + chorusAccount.Password);
var authHeader = "Basic " + Convert.ToBase64String(authBytes);
// ReSharper restore NonLocalizedString
webRequest.Headers.Add(HttpRequestHeader.Authorization, authHeader);
}
}
public MsDataSpectrum[] GetSpectra(ChorusAccount chorusAccount, ChorusUrl chorusUrl, ChromSource source,
SignedMz precursor, int scanId)
{
string strSource;
int msLevel = 1;
// ReSharper disable NonLocalizedString
switch (source)
{
case ChromSource.ms1:
strSource = "ms1";
break;
case ChromSource.sim:
strSource = "sim";
break;
case ChromSource.fragment:
strSource = "ms2";
msLevel = 2;
break;
default:
throw new ArgumentException("Unknown source " + source);
}
string strUri = string.Format(CultureInfo.InvariantCulture,
"{0}/skyline/api/chroextract-drift/file/{1}/source/{2}/precursor/{3}/{4}",
chorusUrl.ServerUrl,
chorusUrl.FileId,
strSource,
precursor.RawValue, // This will be a negative value for negative ion mode data
scanId);
// ReSharper restore NonLocalizedString
var webRequest = (HttpWebRequest)WebRequest.Create(new Uri(strUri));
AddAuthHeader(chorusAccount, webRequest);
return(SendRequest(webRequest, response =>
{
string strResponse = string.Empty;
var responseStream = response.GetResponseStream();
if (null != responseStream)
{
var streamReader = new StreamReader(responseStream);
strResponse = streamReader.ReadToEnd();
}
JObject jObject = JsonConvert.DeserializeObject <JObject>(strResponse);
JArray array = (JArray)jObject["results"]; // Not L10N
return array.OfType <JObject>().Select(obj => GetSpectrumFromJObject(obj, msLevel)).ToArray();
}));
}
public ChromatogramCache GenerateChromatograms(ChorusAccount chorusAccount,
ChorusUrl chorusUrl,
ChromatogramRequestDocument chromatogramRequestDocument)
{
var webRequest = (HttpWebRequest)WebRequest.Create(chorusUrl.GetChromExtractionUri());
AddAuthHeader(chorusAccount, webRequest);
webRequest.Method = "POST"; // Not L10N
var xmlSerializer = new XmlSerializer(typeof(ChromatogramRequestDocument));
xmlSerializer.Serialize(webRequest.GetRequestStream(), chromatogramRequestDocument);
webRequest.GetRequestStream().Close();
return(SendRequest(webRequest, response =>
{
MemoryStream memoryStream = new MemoryStream();
var responseStream = response.GetResponseStream();
if (responseStream != null)
{
byte[] buffer = new byte[65536];
int count;
while ((count = responseStream.Read(buffer, 0, buffer.Length)) != 0)
{
memoryStream.Write(buffer, 0, count);
}
}
if (0 == memoryStream.Length)
{
if (response.StatusCode != HttpStatusCode.OK)
{
throw new IOException(string.Format("Empty response: status = {0}", response.StatusCode)); // Not L10N
}
Debug.WriteLine("Zero byte response"); // Not L10N
return null;
}
ChromatogramCache.RawData rawData;
ChromatogramCache.LoadStructs(memoryStream, out rawData);
var chromCacheFile = rawData.ChromCacheFiles[0];
rawData.ChromCacheFiles = new[]
{
new ChromCachedFile(chorusUrl, chromCacheFile.Flags, chromCacheFile.FileWriteTime,
chromCacheFile.RunStartTime, chromCacheFile.MaxRetentionTime, chromCacheFile.MaxIntensity,
chromCacheFile.InstrumentInfoList),
};
return new ChromatogramCache(string.Empty, rawData,
new ChromatogramGeneratorTask.MemoryPooledStream(memoryStream));
}));
}
public ChorusContents FetchContents(ChorusAccount chorusAccount, Uri uri)
{
HttpWebRequest webRequest = (HttpWebRequest)WebRequest.Create(uri); // Not L10N
AddAuthHeader(chorusAccount, webRequest);
return(SendRequest(webRequest, webResponse =>
{
string strResponse = string.Empty;
var responseStream = webResponse.GetResponseStream();
if (responseStream != null)
{
var streamReader = new StreamReader(responseStream);
strResponse = streamReader.ReadToEnd();
}
var chorusContents = JsonConvert.DeserializeObject <ChorusContents>(strResponse);
return chorusContents;
}));
}
public ChromTaskList(Action checkCancelledAction, SrmDocument srmDocument, ChorusAccount chorusAccount, ChorusUrl chorusUrl, IEnumerable <ChromatogramRequestDocument> chromatogramRequestDocuments)
{
SrmDocument = srmDocument;
ChorusSession = new ChorusSession();
_checkCancelledAction = checkCancelledAction;
_chromatogramGeneratorTasks = new List <ChromatogramGeneratorTask>();
_chromKeys = new Dictionary <ChromKey, ChromatogramGeneratorTask>();
foreach (var chunk in chromatogramRequestDocuments)
{
ChromatogramGeneratorTask task = new ChromatogramGeneratorTask(this, chorusAccount, chorusUrl, chunk);
_chromatogramGeneratorTasks.Add(task);
foreach (ChromKey chromKey in ListChromKeys(chunk))
{
_chromKeys[chromKey] = task;
}
}
_executingTasks = new HashSet <ChromatogramGeneratorTask>();
}
public void RetryFetchContents(ChorusAccount chorusAccount, ChorusUrl chorusUrl)
{
Uri requestUri = GetContentsUri(chorusAccount, chorusUrl);
if (null == requestUri)
{
return;
}
RequestKey requestKey = new RequestKey(chorusAccount, requestUri);
lock (_lock)
{
if (_fetchRequests.Contains(requestKey))
{
return;
}
_chorusContentsByServerUrl.Remove(requestKey);
ChorusServerException exceptionIgnore;
AsyncFetchContents(chorusAccount, chorusUrl, out exceptionIgnore);
}
}
public IEnumerable <ChorusItem> ListContents(ChorusAccount chorusAccount, ChorusUrl chorusUrl)
{
if (!chorusUrl.GetPathParts().Any())
{
return(TOP_LEVEL_ITEMS.Select(
item => new ChorusItem(chorusUrl.AddPathPart(item.Name), item.Label, DataSourceUtil.FOLDER_TYPE, null, 0)));
}
Uri requestUri = GetContentsUri(chorusAccount, chorusUrl);
ChorusContents contents;
var key = new RequestKey(chorusAccount, requestUri);
lock (_lock)
{
ChorusContentsResponse chorusContentsResponse;
if (!_chorusContentsByServerUrl.TryGetValue(key, out chorusContentsResponse))
{
return(new ChorusItem[0]);
}
contents = chorusContentsResponse.Data;
}
return(ListItems(chorusUrl, contents));
}
public RequestKey(ChorusAccount chorusAccount, Uri requestUri) : this()
{
ChorusAccount = chorusAccount;
RequestUri = requestUri;
}
private ChorusAccount(ChorusAccount chorusAccount)
{
ServerUrl = chorusAccount.ServerUrl;
Username = chorusAccount.Username;
Password = chorusAccount.Password;
}
private bool Equals(ChorusAccount other)
{
return(string.Equals(Username, other.Username) &&
string.Equals(Password, other.Password) &&
Equals(ServerUrl, other.ServerUrl));
}
