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);
}
private IEnumerable <RemoteItem> ListItems(ChorusUrl chorusUrl, ChorusContents chorusContents)
{
IEnumerable <RemoteItem> items = new RemoteItem[0];
if (null != chorusContents.experiments)
{
items = items.Concat(chorusContents.experiments.Select(experiment =>
new RemoteItem(chorusUrl.SetExperimentId(experiment.id).AddPathPart(experiment.GetName()),
experiment.GetName(), DataSourceUtil.FOLDER_TYPE, null, 0)));
}
if (null != chorusContents.files)
{
items = items.Concat(chorusContents.files.Select(
file =>
{
ChorusUrl fileUrl = (ChorusUrl)chorusUrl.SetFileId(file.id)
.AddPathPart(file.GetName())
.ChangeRunStartTime(file.GetAcquisitionDateTime())
.ChangeModifiedTime(file.GetModifiedDateTime());
return(new RemoteItem(fileUrl, file.GetName(),
GetFileType(file), file.GetModifiedDateTime(), file.fileSizeBytes));
}
));
}
if (null != chorusContents.projects)
{
items = items.Concat(chorusContents.projects.Select(project =>
new RemoteItem(chorusUrl.SetProjectId(project.id).AddPathPart(project.GetName()),
project.GetName(), DataSourceUtil.FOLDER_TYPE, null, project.GetSize())));
}
return(items);
}
public ChromatogramGeneratorTask(ChromTaskList chromTaskList, ChorusAccount chorusAccount, ChorusUrl chorusUrl,
ChromatogramRequestDocument chromatogramRequestDocument)
{
ChromTaskList = chromTaskList;
ChorusAccount = chorusAccount;
ChorusUrl = chorusUrl;
ChromatogramRequestDocument = chromatogramRequestDocument;
}
public ChromatogramRequestProvider(SrmDocument srmDocument, ChorusUrl chorusUrl, IRetentionTimePredictor retentionTimePredictor, bool firstPass)
{
_srmDocument = srmDocument;
_chorusUrl = chorusUrl;
_retentionTimePredictor = retentionTimePredictor;
_firstPass = firstPass;
// Create a SpectrumFilter without an IRetentionTimeProvider in order to get the list of ChromKeys that we will eventually provide.
SpectrumFilter spectrumFilter = new SpectrumFilter(_srmDocument, _chorusUrl, null, 0);
_chromKeys = ImmutableList.ValueOf(ListChromKeys(GetChromatogramRequestDocument(spectrumFilter)));
}
public MsDataSpectrum[] GetSpectra(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 ChorusScanProvider(string docFilePath, ChorusUrl chorusUrl, ChromSource source, IList <float> times,
TransitionFullScanInfo[] transitions)
{
ChorusUrl = chorusUrl;
DocFilePath = docFilePath;
DataFilePath = chorusUrl;
Source = source;
Times = times;
Transitions = transitions;
ChorusAccount chorusAccount = ChorusUrl.FindChorusAccount(Settings.Default.RemoteAccountList);
_chorusSession = new ChorusSession(chorusAccount);
}
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, false);
var chromCacheFile = rawData.ChromCacheFiles[0];
rawData.ChromCacheFiles = new[]
{
chromCacheFile.ChangeFilePath(chorusUrl)
};
return new ChromatogramCache(string.Empty, rawData,
new ChromatogramGeneratorTask.MemoryPooledStream(memoryStream));
}));
}
public ChromTaskList(Action checkCancelledAction, SrmDocument srmDocument, ChorusAccount chorusAccount, ChorusUrl chorusUrl, IEnumerable <ChromatogramRequestDocument> chromatogramRequestDocuments)
{
SrmDocument = srmDocument;
ChorusSession = new ChorusSession(chorusAccount);
_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>();
}
protected bool Equals(ChorusUrl other)
{
return(base.Equals(other) && ProjectId == other.ProjectId && ExperimentId == other.ExperimentId &&
FileId == other.FileId && RunStartTime.Equals(other.RunStartTime));
}