public void doAlignmentTest1()
{
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var deconToolsResultFile = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_targetedFeatures.txt");
var importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile);
var repo = importer.Import();
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
aligner.Execute(run);
float testScan = 6005;
var testNET1 = run.NetAlignmentInfo.GetNETValueForScan((int)testScan);
//note - this is Multialign's
Assert.AreEqual(0.3253423m, (decimal)testNET1);
}
public void ExportNET_andMass_AlignmentDataTest1()
{
var exportNETFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedNETAlignmentInfo1.txt");
var exportMassFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedMassAlignmentInfo1.txt");
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var deconToolsResultFile = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_targetedFeatures.txt");
var importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile);
var repo = importer.Import();
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
aligner.Execute(run);
var exporter = new NETAlignmentInfoToTextExporter(exportNETFilename);
exporter.ExportAlignmentInfo(run.AlignmentInfo);
var massInfoexporter = new MassAlignmentInfoToTextExporter(exportMassFilename);
massInfoexporter.ExportAlignmentInfo(run.AlignmentInfo);
}
public override TargetCollection GetRuntimeBuildList( )
{
TargetCollection sc = new TargetCollection();
sc.Add(@"awscalculobuquesgranelero", "dll");
return(sc);
}
public void AddNewTargetNullName()
{
project.LoadXml(ProjectContentSeveralTargets);
TargetCollection targets = project.Targets;
targets.AddNewTarget(null);
}
public void WithInputs(TargetCollection targets, List <int> inputsReceived)
{
"Given a target with inputs 1 and 2"
.x(() => Ensure(ref targets).Add(CreateTarget("default", new[] { 1, 2 }, input => Ensure(ref inputsReceived).Add(input))));
"When I run the target"
.x(() => targets.RunAsync(new List <string>(), default, default, default));
public void NotExistentDependencies(TargetCollection targets, TestConsole console, bool anyRan, Exception exception)
{
"Given a target"
.x(() => Ensure(ref targets).Add(CreateTarget("first", () => anyRan = true)));
"And a second target which depends on the first target and a non-existent target"
.x(() => targets.Add(CreateTarget("second", new[] { "first", "non-existing" }, () => anyRan = true)));
"And a third target which depends on the second target and another non-existent target"
.x(() => targets.Add(CreateTarget("third", new[] { "second", "also-non-existing" }, () => anyRan = true)));
"When I run the third target"
.x(async() => exception = await Record.ExceptionAsync(() => targets.RunAsync(new List <string> {
"third"
}, console = new TestConsole())));
"Then the operation fails"
.x(() => Assert.NotNull(exception));
"And I am told that the first non-existent target could not be found"
.x(() => Assert.Contains("non-existing, required by second", exception.Message));
"And I am told that the second non-existent target could not be found"
.x(() => Assert.Contains("also-non-existing, required by third", exception.Message));
"And the other targets are not run"
.x(() => Assert.False(anyRan));
}
public void RemoveTargetFromImport()
{
Project p = GetProjectThatImportsAnotherProject(null, null);
TargetCollection targets = p.Targets;
targets.RemoveTarget(GetSpecificTargetFromProject(p, "t2"));
}
bool DoLast()
{
if (Last <= 0)
{
return(false);
}
Skip = (int)(TargetCollection.Count(_Query) - Skip - Last);
First = Last;
if (Skip >= 0)
{
return(false);
}
First += Skip;
if (First <= 0)
{
if (Count)
{
WriteObject(0);
}
return(true);
}
Skip = 0;
return(false);
}
public override TargetCollection GetRuntimeBuildList( )
{
TargetCollection sc = new TargetCollection();
sc.Add(@"awscalculartanqueros", "dll");
return(sc);
}
public override TargetCollection GetRuntimeBuildList( )
{
TargetCollection sc = new TargetCollection();
sc.Add(@"awscalcularportavehiculosrorosoap", "dll");
return(sc);
}
public void Validate()
{
CosmosAccount.Validate();
StorageAccount.Validate();
SourceCollection.Validate();
TargetCollection.Validate();
}
public void ExistsWhenTargetDoesNotExist()
{
project.LoadXml(ProjectContentSeveralTargets);
TargetCollection targets = project.Targets;
Assertion.AssertEquals(false, targets.Exists("tNot"));
}
public void IsSynchronizedDefault()
{
project.LoadXml(ProjectContentSeveralTargets);
TargetCollection targets = project.Targets;
Assertion.AssertEquals(false, targets.IsSynchronized);
}
public void CountWithNoTargets()
{
project.LoadXml(ProjectContentNoTargets);
TargetCollection targets = project.Targets;
Assertion.AssertEquals(0, targets.Count);
}
public void ExistsWhenTargetExists()
{
project.LoadXml(ProjectContentSeveralTargets);
TargetCollection targets = project.Targets;
Assertion.AssertEquals(true, targets.Exists("t2"));
}
public void CountWithImportedTargets()
{
string importProjectContents = @"
<Project xmlns='http://schemas.microsoft.com/developer/msbuild/2003'>
<Target Name='t2'>
<Message Text='imported.t2.task' />
</Target>
<Target Name='t3' />
</Project>
";
string projectContents = @"
<Project xmlns='http://schemas.microsoft.com/developer/msbuild/2003'>
<Target Name='t1'>
<Message Text='parent.t1.task' />
</Target>
<Import Project='import.proj' />
</Project>
";
Project p = GetProjectThatImportsAnotherProject(importProjectContents, projectContents);
TargetCollection targets = p.Targets;
Assertion.AssertEquals(3, targets.Count);
}
public void NestedDependencies(TargetCollection targets, TestConsole console, List <string> ran)
{
"Given a target"
.x(() => Ensure(ref targets).Add(CreateTarget("first", () => Ensure(ref ran).Add("first"))));
"And a second target which depends on the first target"
.x(() => targets.Add(CreateTarget("second", new[] { "first" }, () => Ensure(ref ran).Add("second"))));
"And a third target which depends on the second target"
.x(() => targets.Add(CreateTarget("third", new[] { "second" }, () => Ensure(ref ran).Add("third"))));
"When I run the third target"
.x(() => targets.RunAsync(new List <string> {
"third"
}, console = new TestConsole()));
"Then all targets are run"
.x(() => Assert.Equal(3, ran.Count));
"And the first target is run first"
.x(() => Assert.Equal("first", ran[0]));
"And the second target is run second"
.x(() => Assert.Equal("second", ran[1]));
"And the third target is run third"
.x(() => Assert.Equal("third", ran[2]));
}
public void DependencyOrderWhenParallelAndSkipping(
TargetCollection targets,
TestConsole console,
int clock,
int buildStartTime,
int test1StartTime,
int test2StartTime)
{
"Given a target that takes a long time to start up"
.x(() => Ensure(ref targets).Add(CreateTarget(
"build",
() => {
Thread.Sleep(TimeSpan.FromSeconds(1)); // a weak way to encourage the tests to run first
buildStartTime = Interlocked.Increment(ref clock);
})));
"And a second target which depends on the first target"
.x(() => targets.Add(CreateTarget("test1", new[] { "build" }, () => test1StartTime = Interlocked.Increment(ref clock))));
"And a third target which depends on the first target"
.x(() => targets.Add(CreateTarget("test2", new[] { "build" }, () => test2StartTime = Interlocked.Increment(ref clock))));
"When I run all the targets with parallelism, skipping dependencies"
.x(() => targets.RunAsync(new List <string> {
"--parallel", "--skip-dependencies", "test1", "test2", "build"
}, console = new TestConsole()));
"Then the first target is run first"
.x(() => Assert.Equal(1, buildStartTime));
"And the other targets are run later"
.x(() => Assert.Equal(5, test1StartTime + test2StartTime));
}
public void CopyToSimple()
{
project.LoadXml(ProjectContentSeveralTargets);
TargetCollection targets = project.Targets;
object[] array = new object[targets.Count];
targets.CopyTo(array, 0);
List <string> listOfTargets = new List <string>();
foreach (Target t in array)
{
listOfTargets.Add(t.Name);
}
// This originates in a hashtable, whose ordering is undefined
// and indeed changes in CLR4
listOfTargets.Sort();
Assertion.AssertEquals(targets["t1"].Name, listOfTargets[0]);
Assertion.AssertEquals(targets["t2"].Name, listOfTargets[1]);
Assertion.AssertEquals(targets["t3"].Name, listOfTargets[2]);
Assertion.AssertEquals(targets["t4"].Name, listOfTargets[3]);
Assertion.AssertEquals(targets["t5"].Name, listOfTargets[4]);
}
public void ExistsOfImportedTarget()
{
Project p = GetProjectThatImportsAnotherProject(null, null);
TargetCollection targets = p.Targets;
Assertion.AssertEquals(true, targets.Exists("t4"));
}
public void CopyToNull()
{
project.LoadXml(ProjectContentSeveralTargets);
TargetCollection targets = project.Targets;
targets.CopyTo(null, 0);
}
public void ExistsWhenImportedTargetAndParentTargetHaveSameName()
{
string importProjectContents = @"
<Project xmlns='http://schemas.microsoft.com/developer/msbuild/2003'>
<Target Name='t1'>
<Message Text='imported.t2.task' />
</Target>
</Project>
";
string parentProjectContents = @"
<Project xmlns='http://schemas.microsoft.com/developer/msbuild/2003'>
<Target Name='t1'>
<Message Text='parent.t1.task' />
</Target>
<Target Name='t2' />
<Import Project='import.proj' />
</Project>
";
Project p = GetProjectThatImportsAnotherProject(importProjectContents, parentProjectContents);
TargetCollection targets = p.Targets;
Assertion.AssertEquals(true, targets.Exists("t1"));
}
public void CountMany()
{
project.LoadXml(ProjectContentSeveralTargets);
TargetCollection targets = project.Targets;
Assertion.AssertEquals(5, targets.Count);
}
public void AddNewTargetEmptyStringName()
{
project.LoadXml(ProjectContentSeveralTargets);
TargetCollection targets = project.Targets;
targets.AddNewTarget(String.Empty);
}
public override TargetCollection GetRuntimeBuildList( )
{
TargetCollection sc = new TargetCollection();
sc.Add(@"home", "dll");
return(sc);
}
public void cannotFindMassTag_test1()
{
//
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 26523;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 1 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var workflow = new BasicTargetedWorkflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult;
Assert.IsNull(result.IsotopicProfile);
Assert.IsNull(result.ScanSet);
Assert.IsNull(result.ChromPeakSelected);
Assert.IsTrue(result.FailedResult);
Assert.AreEqual(DeconTools.Backend.Globals.TargetedResultFailureType.ChrompeakNotFoundWithinTolerances, result.FailureType);
}
void DoDistinct()
{
foreach (var it in TargetCollection.Distinct(Distinct, _Query))
{
WriteObject(Actor.ToObject(it));
}
}
public void AddNewTargetSpecialCharacterName()
{
project.LoadXml(ProjectContentSeveralTargets);
TargetCollection targets = project.Targets;
targets.AddNewTarget("%24%40%3b%5c%25");
}
public override TargetCollection GetRuntimeBuildList( )
{
TargetCollection sc = new TargetCollection();
sc.Add(@"wwpbaseobjects\seclogin", "dll");
return(sc);
}
public void RemoveTargetNull()
{
project.LoadXml(ProjectContentSeveralTargets);
TargetCollection targets = project.Targets;
targets.RemoveTarget(null);
}
static Backup()
{
if (!File.Exists("targets.json"))
targets = new TargetCollection();
else
targets = TargetCollection.FromJSON(File.ReadAllText("targets.json"));
}
/// <summary>
/// Returns a collection of named targets specified in the configuration.
/// </summary>
/// <returns>A <see cref="TargetCollection"/> object that contains a list of named targets.</returns>
/// <remarks>
/// Unnamed targets (such as those wrapped by other targets) are not returned.
/// </remarks>
public TargetCollection GetConfiguredNamedTargets()
{
TargetCollection tc = new TargetCollection();
foreach (Target t in _targets.Values)
{
tc.Add(t);
}
return tc;
}
