public static void CanGetProject(IBaseSpaceClient client, string[] includeStrings = null)
{
var project = CreateRandomTestProject(client);
ListProjectsResponse listProjectResponse = client.ListProjects(new ListProjectsRequest() { Limit = 1, Offset = 0, Name = project.Name });
Assert.True(listProjectResponse.Response.Items.Length == 1);
var compactProject = listProjectResponse.Response.Items[0];
Assert.True(project.Id == compactProject.Id);
Assert.True(project.Name == compactProject.Name);
var getProjRequest = new GetProjectRequest(compactProject.Id);
if (includeStrings != null && includeStrings.Length > 0)
getProjRequest.Include = includeStrings;
var getProjectResponse = client.GetProject(new GetProjectRequest(compactProject.Id) { Include = new[] { ProjectIncludes.PERMISSIONS } });
var retrievedProject = getProjectResponse.Response;
Assert.True(project.Id == retrievedProject.Id);
Assert.True(project.Name == retrievedProject.Name);
Assert.True(project.HrefAppResults == retrievedProject.HrefAppResults);
Assert.True(project.HrefBaseSpaceUI == retrievedProject.HrefBaseSpaceUI);
Assert.True(project.HrefSamples == retrievedProject.HrefSamples);
if (includeStrings != null && includeStrings.Length > 0)
Assert.NotNull(retrievedProject.Permissions);
}
public static AppResult CreateRandomTestAppResult(IBaseSpaceClient client, Project project)
{
var appResultName = CreateRandomTestAppResultName();
var response = client.CreateAppResult(new CreateAppResultRequest(project.Id, appResultName));
Assert.NotNull(response);
Assert.NotNull(response.Response);
var appResult = response.Response;
Assert.NotNull(appResult);
Assert.True(appResult.Name.Contains(appResultName));
return appResult;
}
internal static AppSession CreateTestAppSession(IBaseSpaceClient client)
{
var project = TestHelpers.CreateRandomTestProject(client);
var appResult = TestHelpers.CreateRandomTestAppResult(client, project);
var appSessionCompact = appResult.AppSession;
Assert.NotNull(appSessionCompact);
var appSessionResponse = client.GetAppSession(new GetAppSessionRequest(appSessionCompact.Id));
Assert.NotNull(appSessionResponse);
var appSession = appSessionResponse.Response;
Assert.NotNull(appSession);
return appSession;
}
public static Project CreateRandomTestProject(IBaseSpaceClient client, string projectName = null)
{
projectName = projectName ?? CreateRandomTestProjectName();
var response = client.CreateProject(new CreateProjectRequest(projectName));
Assert.NotNull(response);
Assert.NotNull(response.ResponseStatus);
Assert.Null(response.ResponseStatus.ErrorCode);
Assert.NotNull(response.Response);
var project = response.Response;
Assert.NotNull(project);
Assert.True(project.Name.Contains(projectName));
return project;
}
internal static AppResult CreateRandomTestAppResult(IBaseSpaceClient client, Project project)
{
var appResultName = CreateRandomTestAppResultName();
var response = client.CreateAppResult(new PostAppResultRequest(project.Id, appResultName));
Assert.NotNull(response);
Assert.NotNull(response.ResponseStatus);
Assert.Null(response.ResponseStatus.ErrorCode);
Assert.NotNull(response.Response);
var appResult = response.Response;
Assert.NotNull(appResult);
Assert.True(appResult.Name.Contains(appResultName));
return(appResult);
}
public static Project CreateRandomTestProject(IBaseSpaceClient client, string projectName = null)
{
projectName = projectName ?? CreateRandomTestProjectName();
var response = client.CreateProject(new PostProjectRequest(projectName));
Assert.NotNull(response);
Assert.NotNull(response.ResponseStatus);
Assert.Null(response.ResponseStatus.ErrorCode);
Assert.NotNull(response.Response);
var project = response.Response;
Assert.NotNull(project);
Assert.True(project.Name.Contains(projectName));
return(project);
}
internal static Sample CreateRandomTestSample(IBaseSpaceClient client, Project project)
{
/*
var sampleName = TestHelpers.CreateRandomTestSampleName();
var response = client.CreateSample(new PostSampleRequest(sampleName));
Assert.NotNull(response);
Assert.NotNull(response.ResponseStatus);
Assert.Null(response.ResponseStatus.ErrorCode);
Assert.NotNull(response.Response);
var project = response.Response;
Assert.NotNull(project);
Assert.True(project.Name.Contains(sampleName));
return project;
*/
return null;
}
internal static Sample CreateRandomTestSample(IBaseSpaceClient client, Project project)
{
/*
* var sampleName = TestHelpers.CreateRandomTestSampleName();
* var response = client.CreateSample(new PostSampleRequest(sampleName));
* Assert.NotNull(response);
* Assert.NotNull(response.ResponseStatus);
* Assert.Null(response.ResponseStatus.ErrorCode);
*
* Assert.NotNull(response.Response);
* var project = response.Response;
* Assert.NotNull(project);
* Assert.True(project.Name.Contains(sampleName));
* return project;
*/
return(null);
}
public static void CanGetProject(IBaseSpaceClient client, string[] includeStrings = null)
{
var project = CreateRandomTestProject(client);
ListProjectsResponse listProjectResponse = client.ListProjects(new ListProjectsRequest()
{
Limit = 1, Offset = 0, Name = project.Name
});
Assert.True(listProjectResponse.Response.Items.Length == 1);
var compactProject = listProjectResponse.Response.Items[0];
Assert.True(project.Id == compactProject.Id);
Assert.True(project.Name == compactProject.Name);
var getProjRequest = new GetProjectRequest(compactProject.Id);
if (includeStrings != null && includeStrings.Length > 0)
{
getProjRequest.Include = includeStrings;
}
var getProjectResponse = client.GetProject(new GetProjectRequest(compactProject.Id)
{
Include = new[] { ProjectIncludes.PERMISSIONS }
});
var retrievedProject = getProjectResponse.Response;
Assert.True(project.Id == retrievedProject.Id);
Assert.True(project.Name == retrievedProject.Name);
Assert.True(project.HrefAppResults == retrievedProject.HrefAppResults);
Assert.True(project.HrefBaseSpaceUI == retrievedProject.HrefBaseSpaceUI);
Assert.True(project.HrefSamples == retrievedProject.HrefSamples);
if (includeStrings != null && includeStrings.Length > 0)
{
Assert.NotNull(retrievedProject.Permissions);
}
}
public static void CanGetUserProjectsFirstPage(IBaseSpaceClient client, string[] includeStrings = null)
{
var getListProjsRequest = new ListProjectsRequest();
if (includeStrings != null && includeStrings.Length > 0)
getListProjsRequest.Include = includeStrings;
ListProjectsResponse response = client.ListProjects(getListProjsRequest);
Assert.NotNull(response);
Assert.True(response.Response.TotalCount > 0); //make sure account has at least 1 for access token
ProjectCompact projectResult = response.Response.Items[0];
Assert.NotNull(projectResult);
Assert.NotEmpty(projectResult.Id);
Assert.NotEmpty(projectResult.Name);
Assert.NotSame(projectResult.Id, projectResult.Name);
Assert.True(projectResult.DateCreated > new DateTime(2009, 1, 1));
if (includeStrings != null && includeStrings.Length > 0)
Assert.NotNull(projectResult.Permissions);
}
internal static RunCompact[] ListReadyRuns(IBaseSpaceClient client)
{
var plannedRuns = client.ListRuns(new ListRunsRequest() {Statuses="Ready"});
return plannedRuns.Response.Items;
}
internal static void MarkRunAsReadyToSequence(IBaseSpaceClient client, string plannedRunId)
{
client.PlannedRunReadyRequest(new PlannedRunReadyRequest(plannedRunId, true));
Assert.Equal(ListReadyRuns(client).Where(r => r.Id == plannedRunId).Count(), 1);
}
internal static BiologicalSample CreateBiologicalSample(IBaseSpaceClient client, string sampleId=null, string sampleName=null, string nucleicAcid=null)
{
var sample = string.Format("sample_SDK_Test_{0}", StringHelpers.RandomAlphanumericString(5));
var biologicalSample = client.CreateBiologicalSample(new CreateBiologicalSampleRequest(sampleId ?? sample, sampleName ?? sample, nucleicAcid ?? "DNA"));
Assert.NotNull(biologicalSample.Response);
return biologicalSample.Response;
}
internal static LibraryContainer CreateContainerLibraries(IBaseSpaceClient client, int libraryCount)
{
var prepKitIndex = "1";
var originalLibraryCount = libraryCount;
var container = CreateLibraryContainer(client);
var libraryRequests = new List<SampleLibraryRequest>();
var containerPositions = CreateContainerPositions();
int containerPositionIndex = 0;
var project = CreateRandomTestProject(client);
var libraryPrep = GetLibraryPrepKit(client, prepKitIndex);
while (libraryCount > 0)
{
var libraryRequest = new SampleLibraryRequest()
{
BiologicalSampleId = CreateBiologicalSample(client).Id,
Index1SequenceId = libraryPrep.Index1Sequences.ElementAt(containerPositionIndex).Id,
Position = containerPositions[containerPositionIndex],
ProjectId = project.Id
};
libraryRequests.Add(libraryRequest);
libraryCount--;
containerPositionIndex++;
}
client.CreateOrUpdateContainerLibraries(new CreateOrUpdateContainerLibrariesRequest(libraryRequests, container.Id));
var sampleLibraries = GetSampleLibrariesInContainer(client, container.Id);
Assert.Equal(sampleLibraries.Count(), originalLibraryCount);
Assert.Equal(sampleLibraries.FirstOrDefault().BiologicalSample.Id, libraryRequests.FirstOrDefault().BiologicalSampleId);
return container;
}
internal static LibraryContainer CreateLibraryContainer(IBaseSpaceClient client, string libraryPrepId=null, string userContainerId=null, string containerType=null, bool indexByWell=true)
{
libraryPrepId = libraryPrepId ?? "1";
userContainerId = userContainerId ?? string.Format("container-sdk-{0}", StringHelpers.RandomAlphanumericString(5));
containerType = containerType ?? "Plate96";
indexByWell = indexByWell ? indexByWell : false;
var libraryContainer = client.CreateLibraryContainer(new CreateLibraryContainerRequest(libraryPrepId, userContainerId, containerType, indexByWell));
var response = libraryContainer.Response ;
Assert.NotNull(response);
Assert.Equal(response.UserContainerId, userContainerId);
return response;
}
internal static LibraryPool CreateLibraryPoolWithMapping(IBaseSpaceClient client, IEnumerable<string>libraryIds, string userPoolId = null)
{
userPoolId = string.Format("pool-sdk-{0}", StringHelpers.RandomAlphanumericString(5)) ?? userPoolId;
var libraryPool = client.CreateLibraryPool(new CreateLibraryPoolRequest(userPoolId, libraryIds)).Response;
Assert.NotNull(libraryPool);
//client.UpdatePoolToLibraryMapping(new UpdatePoolToLibraryMappingRequest(libraryPool.Id, libraryIds));
return libraryPool;
}
internal static PlannedRun CreatePlannedRun(IBaseSpaceClient client, IEnumerable<PlannedRunPoolMapping> poolMappings, int numCyclesRead1, string name=null,
string platformName=null, string analysisWorkFlowType=null)
{
var plannedRun = client.CreatePlannedRun(new CreatePlannedRunRequest(
poolMappings,
numCyclesRead1,
name ?? string.Format("Run-SDK-{0}", StringHelpers.RandomAlphanumericString(5)),
platformName ?? "NextSeq",
analysisWorkFlowType ?? "HiSeqFastQ",
"None"
)).Response;
Assert.NotNull(plannedRun);
return plannedRun;
}
internal static void MarkRunAsReadyToSequence(IBaseSpaceClient client, string plannedRunId)
{
client.PlannedRunReadyRequest(new PlannedRunReadyRequest(plannedRunId, true));
Assert.Equal(ListReadyRuns(client).Where(r => r.Id == plannedRunId).Count(), 1);
}
internal static LibraryPrepKit GetLibraryPrepKit(IBaseSpaceClient client, string libraryPrepKitId)
{
var libraryPrepKit = client.GetLibraryPrepKit(new GetLibraryPrepKitIdRequest(libraryPrepKitId));
Assert.NotNull(libraryPrepKit.Response);
return libraryPrepKit.Response;
}
internal static SampleLibrary[] GetSampleLibrariesInContainer(IBaseSpaceClient client, string containerId)
{
var sampleLibraries = client.GetContainerToLibraryMapping(new GetContainerToLibraryMappingRequest(containerId));
var response = sampleLibraries.Response;
Assert.NotNull(response);
Assert.Equal(response.Items.FirstOrDefault().Container.Id, containerId);
return response.Items;
}
