public void TestVennDiagram()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string result1Path = @"C:\cygwin\home\kims336\Data\QCShewQE\NoMod_NTT1.tsv";
const string result2Path = @"C:\cygwin\home\kims336\Data\QCShewQE\Ic_NTT1_Test\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28_IcTda.tsv";
if (!File.Exists(result1Path))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, result1Path);
}
if (!File.Exists(result2Path))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, result2Path);
}
const double pepQValueThreshold = 0.01;
var result1 = new TsvFileParser(result1Path);
var result2 = new TsvFileParser(result2Path);
var vennDiagram = new VennDiagram<string>(result1.GetPeptides(pepQValueThreshold),
result2.GetPeptides(pepQValueThreshold));
var intersectionPeptides = vennDiagram.Intersection;
Console.WriteLine(vennDiagram.Set1 + " " + vennDiagram.Set2);
Console.WriteLine(vennDiagram.Set1 + " " + vennDiagram.Intersection + " " + vennDiagram.Set2Only);
}
public void GenerateVennDiagrams()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// DIA
const string dir = @"H:\Research\EDRN\Ic\DIA_Replicate";
const string rep1 = dir + @"\EDRN_Serum_07_DIA_1_01_13Nov13_Samwise_13-07-28_IcTda.tsv";
//const string rep2 = dir + @"\EDRN_Serum_07_DIA_1_02_13Nov13_Samwise_13-07-28_IcTda.tsv";
//const string rep3 = dir + @"\EDRN_Serum_07_DIA_1_03_13Nov13_Samwise_13-07-28_IcTda.tsv";
const string rep4 = dir + @"\EDRN_Serum_07_DIA_1_04_13Nov13_Samwise_13-07-28_IcTda.tsv";
//const string rep5 = dir + @"\EDRN_Serum_07_DIA_1_05_18Nov13_Samwise_13-07-28_IcTda.tsv";
const string resultPath1 = rep1;
const string resultPath2 = rep4;
var result1 = new TsvFileParser(resultPath1);
var result2 = new TsvFileParser(resultPath2);
const double pepQValueThreshold = 0.01;
var vennDiagram = new VennDiagram <string>(result1.GetPeptidesAboveQValueThreshold(pepQValueThreshold),
result2.GetPeptidesAboveQValueThreshold(pepQValueThreshold));
Console.WriteLine("{0}\t{1}\t{2}",
vennDiagram.Set1Only.Count, // + vennDiagram.Intersection.Count,
vennDiagram.Intersection.Count,
vennDiagram.Set2Only.Count //+ vennDiagram.Intersection.Count
);
}
public static Diff DiffGenericObjects(IEnumerable <object> pastObjects, IEnumerable <object> currentObjects, DiffConfig diffConfig = null, bool useExistingHash = false)
{
BH.Engine.Reflection.Compute.RecordNote("This diffing method cannot track modified objects between different revisions." +
"\nIt will simply return the objects that appear exclusively in the past set, in the following set, and in both." +
$"\nConsider using '{nameof(DiffWithCustomId)}', '{nameof(DiffWithFragmentId)}' or '{nameof(DiffRevisions)}' if this feature is needed.");
// Set configurations if diffConfig is null. Clone it for immutability in the UI.
DiffConfig diffConfigCopy = diffConfig == null ? new DiffConfig() : (DiffConfig)diffConfig.DeepClone();
// Clone objects for immutability in the UI.
List <object> pastObjects_cloned = BH.Engine.Base.Query.DeepClone(pastObjects).ToList();
List <object> currentObjects_cloned = BH.Engine.Base.Query.DeepClone(currentObjects).ToList();
if (!useExistingHash)
{
// Clean any existing hash fragment.
// This ensures the hash will be re-computed within this method using the provided DiffConfig.
pastObjects_cloned.OfType <IBHoMObject>().ToList().ForEach(o => o.Fragments.Remove(typeof(HashFragment)));
currentObjects_cloned.OfType <IBHoMObject>().ToList().ForEach(o => o.Fragments.Remove(typeof(HashFragment)));
}
// Compute the "Diffing" by means of a VennDiagram.
// Hashes are computed in the DiffingHashComparer, once per each object (the hash is stored in a hashFragment).
VennDiagram <object> vd = Engine.Data.Create.VennDiagram(pastObjects_cloned, currentObjects_cloned, new DiffingHashComparer <object>(diffConfigCopy, true));
return(new Diff(vd.OnlySet2, vd.OnlySet1, null, diffConfigCopy, null, vd.Intersection));
}
public void TestVennDiagram()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const string result1Path = @"C:\cygwin\home\kims336\Data\QCShewQE\NoMod_NTT1.tsv";
const string result2Path = @"C:\cygwin\home\kims336\Data\QCShewQE\Ic_NTT1_Test\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28_IcTda.tsv";
if (!File.Exists(result1Path))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, result1Path);
}
if (!File.Exists(result2Path))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, result2Path);
}
const double pepQValueThreshold = 0.01;
var result1 = new TsvFileParser(result1Path);
var result2 = new TsvFileParser(result2Path);
var vennDiagram = new VennDiagram <string>(result1.GetPeptides(pepQValueThreshold),
result2.GetPeptides(pepQValueThreshold));
var intersectionPeptides = vennDiagram.Intersection;
Console.WriteLine(vennDiagram.Set1 + " " + vennDiagram.Set2);
Console.WriteLine(vennDiagram.Set1 + " " + vennDiagram.Intersection + " " + vennDiagram.Set2Only);
}
public void GenerateVennDiagrams()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// DIA
const string dir = @"H:\Research\EDRN\Ic\DIA_Replicate";
const string rep1 = dir + @"\EDRN_Serum_07_DIA_1_01_13Nov13_Samwise_13-07-28_IcTda.tsv";
//const string rep2 = dir + @"\EDRN_Serum_07_DIA_1_02_13Nov13_Samwise_13-07-28_IcTda.tsv";
//const string rep3 = dir + @"\EDRN_Serum_07_DIA_1_03_13Nov13_Samwise_13-07-28_IcTda.tsv";
const string rep4 = dir + @"\EDRN_Serum_07_DIA_1_04_13Nov13_Samwise_13-07-28_IcTda.tsv";
//const string rep5 = dir + @"\EDRN_Serum_07_DIA_1_05_18Nov13_Samwise_13-07-28_IcTda.tsv";
const string resultPath1 = rep1;
const string resultPath2 = rep4;
var result1 = new TsvFileParser(resultPath1);
var result2 = new TsvFileParser(resultPath2);
const double pepQValueThreshold = 0.01;
var vennDiagram = new VennDiagram<string>(result1.GetPeptidesAboveQValueThreshold(pepQValueThreshold),
result2.GetPeptidesAboveQValueThreshold(pepQValueThreshold));
Console.WriteLine("{0}\t{1}\t{2}",
vennDiagram.Set1Only.Count, // + vennDiagram.Intersection.Count,
vennDiagram.Intersection.Count,
vennDiagram.Set2Only.Count //+ vennDiagram.Intersection.Count
);
}
/***************************************************/
/**** Public Methods ****/
/***************************************************/
public static VennDiagram <T> VennDiagram <T>(IEnumerable <T> set1, IEnumerable <T> set2, IEqualityComparer <T> comparer) //where T : BH.oM.Base.IBHoMObject
{
VennDiagram <T> diagram = new VennDiagram <T>();
foreach (T a in set1)
{
bool found = false;
foreach (T b in set2)
{
//Check if object exists
if (comparer.Equals(a, b))
{
diagram.Intersection.Add(new Tuple <T, T>(a, b));
found = true;
break;
}
}
if (!found)
{
diagram.OnlySet1.Add(a);
}
}
diagram.OnlySet2 = set2.Except(diagram.Intersection.Select(x => x.Item2)).ToList();
return(diagram);
}
public static string VennDiagramTest()
{
int[] data = new int[] { 100, 80, 60, 30, 30, 30, 10 };
VennDiagram vennDiagram = new VennDiagram(150, 150);
vennDiagram.SetTitle("Venn Diagram");
vennDiagram.SetData(data);
return(vennDiagram.GetUrl());
}
// Note: setAssignedId is currently not exposed as an option
// -- waiting for Adapter refactoring LVL 04 to expose a new CRUDconfig input for the Push
// CRUDconfig will become available to all CRUD methods
protected bool CreateAnyObject(List <IObject> objects, bool setAssignedId = true)
{
/// Create the objects
List <SpeckleObject> objs_serialized = SpeckleCore.Converter.Serialise(objects);
SpeckleLayer.ObjectCount += objects.Count();
SpeckleStream.Objects.AddRange(objs_serialized);
/// Assign any other property to the objects before sending them
var objList = objects.ToList();
int i = 0;
foreach (var o in SpeckleStream.Objects)
{
IBHoMObject bhomObj = objList[i] as IBHoMObject;
if (bhomObj != null)
{
SpeckleStream.Objects[i].Name = string.IsNullOrEmpty(bhomObj.Name) ? bhomObj.GetType().ToString() : bhomObj.Name;
//SpeckleStream.Objects[i].Type = string.IsNullOrEmpty(bhomObj.Name) ? bhomObj.GetType().ToString() : bhomObj.Name;
}
i++;
}
/// Send the objects
var updateResponse = SpeckleClient.StreamUpdateAsync(SpeckleStreamId, SpeckleStream).Result;
SpeckleClient.BroadcastMessage("stream", SpeckleStreamId, new { eventType = "update-global" });
/// Read the IBHoMobjects as exported in speckle
/// so we can assign the Speckle-generated id into the BHoMobjects
if (setAssignedId)
{
ResponseObject response = SpeckleClient.StreamGetObjectsAsync(SpeckleStreamId, "").Result;
List <IBHoMObject> bHoMObjects_inSpeckle = new List <IBHoMObject>();
IEnumerable <IBHoMObject> iBhomObjsInSpeckle = BH.Engine.Speckle.Convert.ToBHoM(response, true);
VennDiagram <IBHoMObject> correspondenceDiagram = Engine.Data.Create.VennDiagram(objects.Where(o => o as IBHoMObject != null).Cast <IBHoMObject>(), iBhomObjsInSpeckle, new IBHoMGUIDComparer());
if (correspondenceDiagram.Intersection.Count != objects.Count())
{
var gna = 0;
//Engine.Reflection.Compute.RecordError("Push failed.\nNumber of objects created in Speckle do not correspond to the number of objects pushed.");
//return false;
}
correspondenceDiagram.Intersection.ForEach(o => o.Item1.CustomData[AdapterId] = o.Item2.CustomData[AdapterId]);
}
return(true);
}
public void CompareRtFusion()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Fusion
const string qeDdaResult = @"D:\Research\Data\UW\Fusion\DDA_Summary.tsv";
const string qeDiaResult = @"D:\Research\Data\UW\Fusion\DIA_Summary.tsv";
const string specFileDda = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618.raw";
var ddaReader = new XCaliburReader(specFileDda);
const string specFileDia = @"D:\Research\Data\UW\Fusion\WT_D_DIA_130412091220.raw";
var diaReader = new XCaliburReader(specFileDia);
const string resultPath1 = qeDdaResult;
const string resultPath2 = qeDiaResult;
var result1 = new TsvFileParser(resultPath1);
var result2 = new TsvFileParser(resultPath2);
const double pepQValueThreshold = 0.01;
var vennDiagram = new VennDiagram <string>(result1.GetPeptides(pepQValueThreshold),
result2.GetPeptides(pepQValueThreshold));
var intersectionPeptides = vennDiagram.Intersection;
var result1Peptides = result1.GetData("Peptide");
var result1ScanNums = result1.GetData("ScanNum");
var result2Peptides = result2.GetData("Peptide");
var result2ScanNums = result2.GetData("ScanNum");
Console.WriteLine("Peptide\tScanNum1\tScanNum2\tRt1\tRt2");
foreach (var peptide in intersectionPeptides)
{
var index1 = result1Peptides.IndexOf(peptide);
var index2 = result2Peptides.IndexOf(peptide);
var scanNum1 = Convert.ToInt32(result1ScanNums[index1]);
var scanNum2 = Convert.ToInt32(result2ScanNums[index2]);
var reader1 = ddaReader;
var reader2 = diaReader;
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", peptide.Replace("C+57.021", "C"), scanNum1, scanNum2, reader1.RtFromScanNum(scanNum1), reader2.RtFromScanNum(scanNum2));
}
}
public static Output <List <IBHoMObject>, List <IBHoMObject>, List <IBHoMObject>, List <IBHoMObject> > Diffing(IEnumerable <IBHoMObject> setA, IEnumerable <IBHoMObject> setB, DiffConfig diffConfig = null)
{
Stream streamA = BH.Engine.Diffing.Create.Stream(setA, diffConfig, "");
Stream streamB = BH.Engine.Diffing.Create.Stream(setB, diffConfig, "");
VennDiagram <IBHoMObject> diagram = Engine.Data.Create.VennDiagram(streamA.Objects, streamB.Objects, new HashFragmComparer <IBHoMObject>());
return(new Output <List <IBHoMObject>, List <IBHoMObject>, List <IBHoMObject>, List <IBHoMObject> >
{
Item1 = diagram.OnlySet1,
Item2 = diagram.Intersection.Select(tuple => tuple.Item1).ToList(),
Item3 = diagram.Intersection.Select(tuple => tuple.Item2).ToList(),
Item4 = diagram.OnlySet2,
});
}
public static Output <List <IBHoMObject>, List <IBHoMObject>, List <IBHoMObject>, List <IBHoMObject> > Diffing(IEnumerable <IBHoMObject> setA, IEnumerable <IBHoMObject> setB, List <string> exceptions = null, bool useDefaultExceptions = true)
{
Stream streamA = BH.Engine.Diffing.Create.Stream(setA, null);
Stream streamB = BH.Engine.Diffing.Create.Stream(setB, null);
VennDiagram <IBHoMObject> diagram = Engine.Data.Create.VennDiagram(streamA.Objects, streamB.Objects, new HashFragmComparer <IBHoMObject>());
return(new Output <List <IBHoMObject>, List <IBHoMObject>, List <IBHoMObject>, List <IBHoMObject> >
{
Item1 = diagram.OnlySet1,
Item2 = diagram.Intersection.Select(tuple => tuple.Item1).ToList(),
Item3 = diagram.Intersection.Select(tuple => tuple.Item2).ToList(),
Item4 = diagram.OnlySet2,
});
}
public void GenerateVennDiagramsPeMmr()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// No PE-MMR
//const string noPeMmr = @"D:\Research\Data\PEMMR\iTRAQ_N33T34_10ug_100cm_300min_C2_061213.tsv";
// PE-MMR Scan based FDR
//const string scanBasedPeMmr = @"D:\Research\Data\PEMMR\NewSpectra\iTRAQ_N33T34_10ug_100cm_300min_C2_061213_MX_PEMMR_UMCID_ScanFDR.tsv";
// UMC based FDR
const string umcBasedPeMmr = @"D:\Research\Data\PEMMR\NewSpectra\iTRAQ_N33T34_10ug_100cm_300min_C2_061213_MX_PEMMR_UMCID_UMCFDR.tsv";
// IPA
const string ipa = @"D:\Research\Data\PEMMR\Ox\IPA_Summary_TargetOnly.tsv";
const string resultPath1 = umcBasedPeMmr;
const string resultPath2 = ipa;
var result1 = new TsvFileParser(resultPath1);
var result2 = new TsvFileParser(resultPath2);
const double pepQValueThreshold = 0.01;
var vennDiagram = new VennDiagram <string>(result1.GetPeptides(pepQValueThreshold),
result2.GetPeptides(pepQValueThreshold));
Console.WriteLine("{0}\t{1}\t{2}",
vennDiagram.Set1Only.Count + vennDiagram.Intersection.Count,
vennDiagram.Intersection.Count,
vennDiagram.Set2Only.Count + vennDiagram.Intersection.Count);
Console.WriteLine("{0}\t{1}\t{2}",
vennDiagram.Set1Only.Count,
vennDiagram.Intersection.Count,
vennDiagram.Set2Only.Count);
foreach (var peptide in vennDiagram.Set2Only)
{
Console.WriteLine(peptide);
var peptides = result2.GetData("Peptide");
}
}
// Computes the diffing for IEnumerable<object>.
// For BHoMObjects, it assumes that they all have a HashFragment assigned (like when they have been passed through a Revision).
// For non-BHoMObjects, it performs the VennDiagram comparision with a HashComparer.
// Results for BHoMObjects and non are concatenated.
private static Diff DiffRevisionObjects(IEnumerable <object> pastRevisionObjs, IEnumerable <object> followingRevisionObjs, DiffConfig diffConfig = null)
{
// Set configurations if diffConfig is null. Clone it for immutability in the UI.
DiffConfig diffConfigCopy = diffConfig == null ? new DiffConfig() : diffConfig.DeepClone() as DiffConfig;
// Dispatch the objects in BHoMObjects and generic objects.
IEnumerable <IBHoMObject> prevObjs_BHoM = pastRevisionObjs.OfType <IBHoMObject>();
IEnumerable <IBHoMObject> currObjs_BHoM = followingRevisionObjs.OfType <IBHoMObject>();
// If all objects are bhomobjects, just call the appropriate method
if (pastRevisionObjs.Count() != 0 && pastRevisionObjs.Count() == prevObjs_BHoM.Count() && followingRevisionObjs.Count() == currObjs_BHoM.Count())
{
return(DiffRevisionObjects(prevObjs_BHoM, currObjs_BHoM, diffConfigCopy));
}
IEnumerable <object> prevObjs_nonBHoM = pastRevisionObjs.Where(o => !(o is IBHoMObject));
IEnumerable <object> currObjs_nonBHoM = followingRevisionObjs.Where(o => !(o is IBHoMObject));
// Compute the specific Diffing for the BHoMObjects.
Diff diff = Compute.DiffRevisionObjects(prevObjs_BHoM, currObjs_BHoM, diffConfigCopy);
// Compute the generic Diffing for the other objects.
// This is left to the VennDiagram with a HashComparer.
VennDiagram <object> vd = Engine.Data.Create.VennDiagram(prevObjs_nonBHoM, currObjs_nonBHoM, new DiffingHashComparer <object>(diffConfig));
// Concatenate the results of the two diffing operations.
List <object> allPrevObjs = new List <object>();
List <object> allCurrObjs = new List <object>();
List <object> allUnchangedObjs = new List <object>();
allCurrObjs.AddRange(diff.AddedObjects);
allCurrObjs.AddRange(vd.OnlySet1);
allPrevObjs.AddRange(diff.RemovedObjects);
allPrevObjs.AddRange(vd.OnlySet2);
// Create the final, actual diff.
Diff finalDiff = new Diff(allCurrObjs, allPrevObjs, diff.ModifiedObjects, diffConfigCopy, diff.ModifiedPropsPerObject, diff.UnchangedObjects);
return(finalDiff);
}
public void GenerateVennDiagrams()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
// DIA
const string dir = @"H:\Research\DDAPlus\NTT2";
//const string dda1 = dir + @"\20140701_yeast_DDA_01_IcTda.tsv";
//const string dda2 = dir + @"\20140701_yeast_DDA_02_2_IcTda.tsv";
const string ddaPlus1 = dir + @"\20140701_yeast_DDAp_binCharge_01_IcTda.tsv";
const string ddaPlus2 = dir + @"\20140701_yeast_DDAp_binCharge_02_IcTda.tsv";
const string resultPath1 = ddaPlus1;
const string resultPath2 = ddaPlus2;
if (!File.Exists(resultPath1))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultPath1);
}
if (!File.Exists(resultPath2))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultPath2);
}
var result1 = new TsvFileParser(resultPath1);
var result2 = new TsvFileParser(resultPath2);
const double pepQValueThreshold = 0.01;
var vennDiagram = new VennDiagram <string>(result1.GetPeptidesAboveQValueThreshold(pepQValueThreshold),
result2.GetPeptidesAboveQValueThreshold(pepQValueThreshold));
Console.WriteLine("{0}\t{1}\t{2}",
vennDiagram.Set1Only.Count, // + vennDiagram.Intersection.Count,
vennDiagram.Intersection.Count,
vennDiagram.Set2Only.Count //+ vennDiagram.Intersection.Count
);
}
private static void VennDiagramExamples()
{
Console.WriteLine("**Venn Diagram Examples**");
// Generate some random data of integers
Console.WriteLine("Generating Random Values");
int numberofsets = 5;
int maxvalue = 100;
int maxitems = 50;
Random ran = new Random(135121321);
VennSet <int>[] sets = new VennSet <int> [numberofsets];
for (int i = 0; i < numberofsets; i++)
{
sets[i] = new VennSet <int>(string.Format("Set {0}", i));
for (int j = 0; j < maxitems; j++)
{
sets[i].Add(ran.Next(maxvalue));
}
}
// Create diagram
VennDiagram <int> diagram = VennDiagram <int> .CreateDiagram(sets);
}
public void GenerateVennDiagrams()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Fusion
//const string fusionMsgfResult = @"D:\Research\Data\UW\Fusion\MSGFPlusResults\TI2.tsv";
const string fusionDdaResult = @"D:\Research\Data\UW\Fusion\DDA_Summary.tsv";
//const string fusionDiaResult = @"D:\Research\Data\UW\Fusion\DIA_Summary.tsv";
// Q-Exactive
//const string qeDdaMsGfResult = @"D:\Research\Data\UW\QExactive\82593_lv_mcx_DDA.tsv";
//const string qeDdaResult = @"D:\Research\Data\UW\QExactive\DDA_All_Summary.tsv";
//const string qeDiaResult = @"D:\Research\Data\UW\QExactive\DIA_All_Summary.tsv";
// PE-MMR
//const string pemmrQeDia = @"D:\Research\Data\UW\PEMMR\QE\allFDR.tsv";
const string pemmrFusionDda = @"D:\Research\Data\UW\PEMMR\Fusion\WT_D_DDA_130412065618_MX_PEMMR.tsv";
//const string pemmrFusionDia = @"D:\Research\Data\UW\PEMMR\Fusion\WT_D_DIA_130412091220_MX_PEMMR.tsv";
const string resultPath1 = pemmrFusionDda;
const string resultPath2 = fusionDdaResult;
var result1 = new TsvFileParser(resultPath1);
var result2 = new TsvFileParser(resultPath2);
const double pepQValueThreshold = 0.01;
var vennDiagram = new VennDiagram <string>(result1.GetPeptides(pepQValueThreshold),
result2.GetPeptides(pepQValueThreshold));
Console.WriteLine("{0}\t{1}\t{2}",
vennDiagram.Set1Only.Count + vennDiagram.Intersection.Count,
vennDiagram.Intersection.Count,
vennDiagram.Set2Only.Count + vennDiagram.Intersection.Count);
}
/***************************************************/
/**** Private Methods ****/
/***************************************************/
private static TestResult RunOneSet(IBHoMAdapter adapter, string setName, List <IBHoMObject> objects, IRequest request, IEqualityComparer <IBHoMObject> comparer, bool resetModelBetweenRuns)
{
if (adapter == null)
{
return(new TestResult {
Description = "PushPullCompare", Message = "Adapter is null, could not preform test", Status = oM.Test.TestStatus.Error
});
}
TestResult setResult = new TestResult {
Description = $"PushPullCompare: Adapter: {adapter.GetType().Name}, test set: {setName}.", ID = adapter.GetType().Name + ":" + setName
};
bool success = true;
//CalculateObjectHashes
objects = objects.SetHashFragment();
//Start up an empty model
if (resetModelBetweenRuns)
{
adapter.Execute(new NewModel());
}
List <IBHoMObject> pushedObjects = new List <IBHoMObject>();
List <IBHoMObject> pulledObjects = new List <IBHoMObject>();
BH.oM.Base.ComparisonConfig config = Engine.Test.Create.DefaultTestComparisonConfig();
config.PropertyExceptions.Add("CustomData");
config.TypeExceptions.Add(typeof(HashFragment));
//Push objects
try
{
Engine.Base.Compute.ClearCurrentEvents();
pushedObjects = adapter.Push(objects).Cast <IBHoMObject>().ToList();
success &= pushedObjects.Count == objects.Count;
}
catch (Exception e)
{
Engine.Base.Compute.RecordError(e.Message);
setResult.Message = "The adapter crashed trying to push the objects.";
setResult.Status = oM.Test.TestStatus.Error;
return(setResult);
}
finally
{
setResult.Information.AddRange(Engine.Base.Query.CurrentEvents().Select(x => x.ToEventMessage()));
}
if (pushedObjects.Count != objects.Count)
{
setResult.Information.AddRange(objects.Where(x => !pushedObjects.Any(y => x.Name == y.Name)).Select(x => TestFailedResult(x, "Object could not be pushed.")));
}
//Pull objects
try
{
Engine.Base.Compute.ClearCurrentEvents();
pulledObjects = adapter.Pull(request).Cast <IBHoMObject>().ToList();
success &= pulledObjects.Count == pushedObjects.Count;
}
catch (Exception e)
{
Engine.Base.Compute.RecordError(e.Message);
setResult.Message = "The adapter crashed trying to pull the objects.";
setResult.Status = oM.Test.TestStatus.Error;
return(setResult);
}
finally
{
setResult.Information.AddRange(Engine.Base.Query.CurrentEvents().Select(x => x.ToEventMessage()));
}
//Compare pushed and pulled objects
VennDiagram <IBHoMObject> diagram = Engine.Data.Create.VennDiagram(pushedObjects, pulledObjects, comparer);
foreach (Tuple <IBHoMObject, IBHoMObject> pair in diagram.Intersection)
{
setResult.Information.Add(ComparePushedAndPulledObject(pair.Item1, pair.Item2, config));
}
setResult.Information.AddRange(diagram.OnlySet1.Select(x => TestFailedResult(x, "Unable to compare the object.")));
//Close the model
if (resetModelBetweenRuns)
{
adapter.Execute(new Close {
SaveBeforeClose = false
});
}
//Clear events
Engine.Base.Compute.ClearCurrentEvents();
setResult.Status = setResult.Information.OfType <TestResult>().MostSevereStatus();
if (setResult.Status == oM.Test.TestStatus.Error)
{
setResult.Message = "Errors where raised trying to run the test";
}
else if (setResult.Status == oM.Test.TestStatus.Pass)
{
setResult.Message = "All objects were successfully pushed, pulled and compared without any differences.";
}
else
{
setResult.Message = "All objects were successfully pushed and pulled, but some differences were found.";
}
return(setResult);
}
public void GenerateVennDiagrams()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// DIA
const string dir = @"H:\Research\DDAPlus\NTT2";
//const string dda1 = dir + @"\20140701_yeast_DDA_01_IcTda.tsv";
//const string dda2 = dir + @"\20140701_yeast_DDA_02_2_IcTda.tsv";
const string ddaPlus1 = dir + @"\20140701_yeast_DDAp_binCharge_01_IcTda.tsv";
const string ddaPlus2 = dir + @"\20140701_yeast_DDAp_binCharge_02_IcTda.tsv";
const string resultPath1 = ddaPlus1;
const string resultPath2 = ddaPlus2;
if (!File.Exists(resultPath1))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultPath1);
}
if (!File.Exists(resultPath2))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultPath2);
}
var result1 = new TsvFileParser(resultPath1);
var result2 = new TsvFileParser(resultPath2);
const double pepQValueThreshold = 0.01;
var vennDiagram = new VennDiagram<string>(result1.GetPeptidesAboveQValueThreshold(pepQValueThreshold),
result2.GetPeptidesAboveQValueThreshold(pepQValueThreshold));
Console.WriteLine("{0}\t{1}\t{2}",
vennDiagram.Set1Only.Count, // + vennDiagram.Intersection.Count,
vennDiagram.Intersection.Count,
vennDiagram.Set2Only.Count //+ vennDiagram.Intersection.Count
);
}
public void CompareRt()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Q-Exactive
//const string qeDdaResult = @"D:\Research\Data\UW\QExactive\DDA_All_Summary.tsv";
//const string qeDiaResult = @"D:\Research\Data\UW\QExactive\DIA_All_Summary.tsv";
// Fusion
const string qeDdaResult = @"D:\Research\Data\UW\Fusion\DDA_Summary.tsv";
const string qeDiaResult = @"D:\Research\Data\UW\Fusion\DIA_Summary.tsv";
const string specFileDda = @"D:\Research\Data\UW\QExactive\82593_lv_mcx_DDA.raw";
var ddaReader = new XCaliburReader(specFileDda);
var specFileToReader = new Dictionary <string, XCaliburReader>();
var specFilesDia = Directory.GetFiles(@"D:\Research\Data\UW\QExactive\", "*_DIA_*.raw");
foreach (var specFile in specFilesDia)
{
var specFileNoExt = Path.GetFileNameWithoutExtension(specFile);
if (specFileNoExt == null)
{
continue;
}
var reader = new XCaliburReader(specFile);
specFileToReader.Add(specFileNoExt, reader);
}
const string resultPath1 = qeDdaResult;
const string resultPath2 = qeDiaResult;
var result1 = new TsvFileParser(resultPath1);
var result2 = new TsvFileParser(resultPath2);
const double pepQValueThreshold = 0.01;
var vennDiagram = new VennDiagram <string>(result1.GetPeptides(pepQValueThreshold),
result2.GetPeptides(pepQValueThreshold));
var intersectionPeptides = vennDiagram.Intersection;
var result1Peptides = result1.GetData("Peptide");
var result1ScanNums = result1.GetData("ScanNum");
var result2Peptides = result2.GetData("Peptide");
var result2ScanNums = result2.GetData("ScanNum");
var result2SpecFile = result2.GetData("#SpecFile");
Console.WriteLine("Peptide\tScanNum1\tScanNum2\tRt1\tRt2");
foreach (var peptide in intersectionPeptides)
{
var index1 = result1Peptides.IndexOf(peptide);
var index2 = result2Peptides.IndexOf(peptide);
var scanNum1 = Convert.ToInt32(result1ScanNums[index1]);
var scanNum2 = Convert.ToInt32(result2ScanNums[index2]);
var diaFile = Path.GetFileNameWithoutExtension(result2SpecFile[index2]);
var reader1 = ddaReader;
var reader2 = specFileToReader[diaFile];
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", peptide.Replace("C+57.021", "C"), scanNum1, scanNum2, reader1.RtFromScanNum(scanNum1), reader2.RtFromScanNum(scanNum2));
}
}
public void GenerateVennDiagrams()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Fusion
//const string fusionMsgfResult = @"D:\Research\Data\UW\Fusion\MSGFPlusResults\TI2.tsv";
const string fusionDdaResult = @"D:\Research\Data\UW\Fusion\DDA_Summary.tsv";
//const string fusionDiaResult = @"D:\Research\Data\UW\Fusion\DIA_Summary.tsv";
// Q-Exactive
//const string qeDdaMsGfResult = @"D:\Research\Data\UW\QExactive\82593_lv_mcx_DDA.tsv";
//const string qeDdaResult = @"D:\Research\Data\UW\QExactive\DDA_All_Summary.tsv";
//const string qeDiaResult = @"D:\Research\Data\UW\QExactive\DIA_All_Summary.tsv";
// PE-MMR
//const string pemmrQeDia = @"D:\Research\Data\UW\PEMMR\QE\allFDR.tsv";
const string pemmrFusionDda = @"D:\Research\Data\UW\PEMMR\Fusion\WT_D_DDA_130412065618_MX_PEMMR.tsv";
//const string pemmrFusionDia = @"D:\Research\Data\UW\PEMMR\Fusion\WT_D_DIA_130412091220_MX_PEMMR.tsv";
const string resultPath1 = pemmrFusionDda;
const string resultPath2 = fusionDdaResult;
var result1 = new TsvFileParser(resultPath1);
var result2 = new TsvFileParser(resultPath2);
const double pepQValueThreshold = 0.01;
var vennDiagram = new VennDiagram<string>(result1.GetPeptides(pepQValueThreshold),
result2.GetPeptides(pepQValueThreshold));
Console.WriteLine("{0}\t{1}\t{2}",
vennDiagram.Set1Only.Count + vennDiagram.Intersection.Count,
vennDiagram.Intersection.Count,
vennDiagram.Set2Only.Count + vennDiagram.Intersection.Count);
}
/***************************************************/
public static int Count <T>(this VennDiagram <T> diagram)
{
return(diagram.Intersection.Count + diagram.OnlySet1.Count + diagram.OnlySet2.Count);
}
public void GenerateVennDiagramsPeMmr()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// No PE-MMR
//const string noPeMmr = @"D:\Research\Data\PEMMR\iTRAQ_N33T34_10ug_100cm_300min_C2_061213.tsv";
// PE-MMR Scan based FDR
//const string scanBasedPeMmr = @"D:\Research\Data\PEMMR\NewSpectra\iTRAQ_N33T34_10ug_100cm_300min_C2_061213_MX_PEMMR_UMCID_ScanFDR.tsv";
// UMC based FDR
const string umcBasedPeMmr = @"D:\Research\Data\PEMMR\NewSpectra\iTRAQ_N33T34_10ug_100cm_300min_C2_061213_MX_PEMMR_UMCID_UMCFDR.tsv";
// IPA
const string ipa = @"D:\Research\Data\PEMMR\Ox\IPA_Summary_TargetOnly.tsv";
const string resultPath1 = umcBasedPeMmr;
const string resultPath2 = ipa;
var result1 = new TsvFileParser(resultPath1);
var result2 = new TsvFileParser(resultPath2);
const double pepQValueThreshold = 0.01;
var vennDiagram = new VennDiagram<string>(result1.GetPeptides(pepQValueThreshold),
result2.GetPeptides(pepQValueThreshold));
Console.WriteLine("{0}\t{1}\t{2}",
vennDiagram.Set1Only.Count + vennDiagram.Intersection.Count,
vennDiagram.Intersection.Count,
vennDiagram.Set2Only.Count + vennDiagram.Intersection.Count);
Console.WriteLine("{0}\t{1}\t{2}",
vennDiagram.Set1Only.Count,
vennDiagram.Intersection.Count,
vennDiagram.Set2Only.Count);
foreach (var peptide in vennDiagram.Set2Only)
{
Console.WriteLine(peptide);
var peptides = result2.GetData("Peptide");
}
}
public void CompareRtFusion()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Fusion
const string qeDdaResult = @"D:\Research\Data\UW\Fusion\DDA_Summary.tsv";
const string qeDiaResult = @"D:\Research\Data\UW\Fusion\DIA_Summary.tsv";
const string specFileDda = @"D:\Research\Data\UW\Fusion\WT_D_DDA_130412065618.raw";
var ddaReader = new XCaliburReader(specFileDda);
const string specFileDia = @"D:\Research\Data\UW\Fusion\WT_D_DIA_130412091220.raw";
var diaReader = new XCaliburReader(specFileDia);
const string resultPath1 = qeDdaResult;
const string resultPath2 = qeDiaResult;
var result1 = new TsvFileParser(resultPath1);
var result2 = new TsvFileParser(resultPath2);
const double pepQValueThreshold = 0.01;
var vennDiagram = new VennDiagram<string>(result1.GetPeptides(pepQValueThreshold),
result2.GetPeptides(pepQValueThreshold));
var intersectionPeptides = vennDiagram.Intersection;
var result1Peptides = result1.GetData("Peptide");
var result1ScanNums = result1.GetData("ScanNum");
var result2Peptides = result2.GetData("Peptide");
var result2ScanNums = result2.GetData("ScanNum");
Console.WriteLine("Peptide\tScanNum1\tScanNum2\tRt1\tRt2");
foreach (var peptide in intersectionPeptides)
{
var index1 = result1Peptides.IndexOf(peptide);
var index2 = result2Peptides.IndexOf(peptide);
var scanNum1 = Convert.ToInt32(result1ScanNums[index1]);
var scanNum2 = Convert.ToInt32(result2ScanNums[index2]);
var reader1 = ddaReader;
var reader2 = diaReader;
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", peptide.Replace("C+57.021", "C"), scanNum1, scanNum2, reader1.RtFromScanNum(scanNum1), reader2.RtFromScanNum(scanNum2));
}
}
public void CompareRt()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Q-Exactive
//const string qeDdaResult = @"D:\Research\Data\UW\QExactive\DDA_All_Summary.tsv";
//const string qeDiaResult = @"D:\Research\Data\UW\QExactive\DIA_All_Summary.tsv";
// Fusion
const string qeDdaResult = @"D:\Research\Data\UW\Fusion\DDA_Summary.tsv";
const string qeDiaResult = @"D:\Research\Data\UW\Fusion\DIA_Summary.tsv";
const string specFileDda = @"D:\Research\Data\UW\QExactive\82593_lv_mcx_DDA.raw";
var ddaReader = new XCaliburReader(specFileDda);
var specFileToReader = new Dictionary<string, XCaliburReader>();
var specFilesDia = Directory.GetFiles(@"D:\Research\Data\UW\QExactive\", "*_DIA_*.raw");
foreach (var specFile in specFilesDia)
{
var specFileNoExt = Path.GetFileNameWithoutExtension(specFile);
if (specFileNoExt == null) continue;
var reader = new XCaliburReader(specFile);
specFileToReader.Add(specFileNoExt, reader);
}
const string resultPath1 = qeDdaResult;
const string resultPath2 = qeDiaResult;
var result1 = new TsvFileParser(resultPath1);
var result2 = new TsvFileParser(resultPath2);
const double pepQValueThreshold = 0.01;
var vennDiagram = new VennDiagram<string>(result1.GetPeptides(pepQValueThreshold),
result2.GetPeptides(pepQValueThreshold));
var intersectionPeptides = vennDiagram.Intersection;
var result1Peptides = result1.GetData("Peptide");
var result1ScanNums = result1.GetData("ScanNum");
var result2Peptides = result2.GetData("Peptide");
var result2ScanNums = result2.GetData("ScanNum");
var result2SpecFile = result2.GetData("#SpecFile");
Console.WriteLine("Peptide\tScanNum1\tScanNum2\tRt1\tRt2");
foreach (var peptide in intersectionPeptides)
{
var index1 = result1Peptides.IndexOf(peptide);
var index2 = result2Peptides.IndexOf(peptide);
var scanNum1 = Convert.ToInt32(result1ScanNums[index1]);
var scanNum2 = Convert.ToInt32(result2ScanNums[index2]);
var diaFile = Path.GetFileNameWithoutExtension(result2SpecFile[index2]);
var reader1 = ddaReader;
var reader2 = specFileToReader[diaFile];
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", peptide.Replace("C+57.021", "C"), scanNum1, scanNum2, reader1.RtFromScanNum(scanNum1), reader2.RtFromScanNum(scanNum2));
}
}
/// This method is actually useless --
/// written assuming IBHoMObjects had static GUID (instead they are re-instantiated at any modification).
private bool DiffingByBHoMGuid(List <IObject> objectsToBePushed, out List <IObject> objectsCreated)
{
objectsCreated = new List <IObject>();
List <IObject> objectsToBeCreated = new List <IObject>();
// Dispatch objects to be pushed
List <IBHoMObject> bhomObjectsToBePushed = null;
List <IObject> iObjectsToBePushed = null;
BH.Engine.Speckle.Query.DispatchBHoMObjects(objectsToBePushed, out bhomObjectsToBePushed, out iObjectsToBePushed);
// Receive and dispatch objects already in speckle
ResponseObject response = SpeckleClient.StreamGetObjectsAsync(SpeckleStreamId, "").Result;
List <IBHoMObject> bhomObjectsInSpeckle = null;
List <IObject> iObjectsInSpeckle = null;
List <object> reminderObjectsInSpeckle = null;
BH.Engine.Speckle.Convert.ToBHoM(response, out bhomObjectsInSpeckle, out iObjectsInSpeckle, out reminderObjectsInSpeckle, false);
// If speckle doesn't contain anything, push everything
if (response.Resources.Count == 0)
{
objectsToBeCreated = bhomObjectsToBePushed.Concat(iObjectsToBePushed).ToList();
if (CreateAnyObject(objectsToBeCreated))
{
objectsCreated = objectsToBeCreated;
}
return(true);
}
// Diffing for IBHoMObjects
VennDiagram <IBHoMObject> guidDiagram = Engine.Data.Create.VennDiagram(objectsToBePushed.Where(o => o as IBHoMObject != null).Cast <IBHoMObject>(), bhomObjectsInSpeckle, new IBHoMGUIDComparer());
List <IBHoMObject> newObjects = guidDiagram.OnlySet1.ToList(); // Not having a counterpart in the Speckle Server
List <IBHoMObject> toBeDeleted = guidDiagram.OnlySet2.ToList(); // Objects in the Speckle server that do not exist anymore locally. Just not push them.
List <IBHoMObject> toBeDiffedByProperty = guidDiagram.Intersection.Select(o => o.Item1).ToList(); // Objects that already exist on the Speckle Server, based on their BHoM GUID.
// // - Insert code here for toBeDiffedByProperty to use custom comparers to diff by property.
// At the moment, not having any custom comparer, the toBeDiffedByProperty are all just re-created (like assuming they've all changed, even if they didn't).
objectsToBeCreated = newObjects.Concat(toBeDiffedByProperty).Concat(objectsToBePushed.Where(o => o as IBHoMObject == null)).ToList();
if (objectsToBeCreated.Count == 0)
{
BH.Engine.Reflection.Compute.RecordNote("Speckle already contains every BHoM currently being pushed. They have not been pushed.");
}
// IObjects always have to be recreated as they have no GUID
List <int> objectsToPushHashes = new List <int>();
objectsToPushHashes = objectsToBePushed.Select(o => o.ToString().GetHashCode()).ToList();
foreach (var o in iObjectsToBePushed) //.Concat(reminderObjectsInSpeckle)
{
if (!objectsToPushHashes.Any(hash => hash == o.ToString().GetHashCode()))
{
objectsToBeCreated.Add(o);
}
}
if (CreateAnyObject(objectsToBeCreated))
{
objectsCreated = objectsToBeCreated;
}
return(true);
}
