public void CanSortGenomes()
{
const int someRidiculouslyHighNumberOfGenomes = 1000;
var genomesListRequest = new ListGenomeRequest()
{
Limit = someRidiculouslyHighNumberOfGenomes, Offset = 0, SortBy = GenomeSortByParameters.SpeciesName, SortDir = SortDirection.Asc
};
var genomesListResponse = Client.ListGenomes(genomesListRequest, null);
Assert.NotNull(genomesListResponse);
var genomeList = genomesListResponse.Response;
string[] genomeSpeciesList =
{
"Arabidopsis thaliana",
"Bacillus Cereus",
"Bos Taurus",
"Escherichia coli",
"H**o sapiens",
"Mus musculus",
"Phix",
"Rattus norvegicus",
"Rhodobacter sphaeroides",
"Saccharomyces cerevisiae",
"Staphylococcus aureus"
};
// this set will only work if we continue to test against the contents of the test db and if that does not change.
Assert.True(genomeList.Items.Length == genomeSpeciesList.Length);
for (int i = 0; i < genomeSpeciesList.Length; i++)
{
Assert.True(genomeList.Items[i].SpeciesName == genomeSpeciesList[i]);
}
}
public void CanListGenomeFileSets()
{
var genomesListRequest = new ListGenomeRequest()
{
Limit = 1000
};
var genomesListResponse = Client.ListGenomes(genomesListRequest, null);
var oneWithFileSets = genomesListResponse.Response.Items.Where(x => x.HrefFileSets != null).FirstOrDefault();
Assert.NotNull(oneWithFileSets);
var fileSets = Client.ListFileSets(new ListGenomeFileSetsRequest(oneWithFileSets), null);
Assert.NotNull(fileSets);
Assert.NotEmpty(fileSets.Response.Items);
var item = fileSets.Response.Items[0];
Assert.NotNull(item.Href);
Assert.NotNull(item.OriginalPath);
Assert.NotNull(item.HrefFiles);
Assert.NotNull(item.Type);
Assert.NotNull(item.Category);
// make sure we can list files
var files = Client.ListFiles(new ListFileSetFilesRequest(item));
Assert.NotNull(files);
Assert.NotNull(files.Response);
Assert.NotEmpty(files.Response.Items);
Assert.NotEmpty(files.Response.Items[0].Name);
}
public void CanListGenomeAnnotationFileSets()
{
var genomesListRequest = new ListGenomeRequest() { Limit = 1000 };
var genomesListResponse = Client.ListGenomes(genomesListRequest, null);
var oneWithFileSets = genomesListResponse.Response.Items.Where(x => x.HrefFileSets != null).FirstOrDefault();
// we know these have annotqations with file sets too
Assert.NotNull(oneWithFileSets);
// this verifies I can list annotations too
var annotations = Client.ListGenomeAnnotations(new ListGenomeAnnotationsRequest(oneWithFileSets));
Assert.NotNull(annotations);
Assert.NotEmpty(annotations.Response.Items);
var annotationWithFileSets = annotations.Response.Items.Where(x => x.HrefFileSets != null).FirstOrDefault();
Assert.NotNull(annotationWithFileSets);
var fileSets = Client.ListFileSets(new ListGenomeAnnotationFileSetsRequest(annotationWithFileSets), null);
Assert.NotNull(fileSets);
Assert.NotEmpty(fileSets.Response.Items);
var item = fileSets.Response.Items[0];
Assert.NotNull(item.Href);
Assert.NotNull(item.OriginalPath);
Assert.NotNull(item.HrefFiles);
Assert.NotNull(item.Source);
Assert.NotNull(item.Version);
// make sure we can list files
var files = Client.ListFiles(new ListFileSetFilesRequest(item));
Assert.NotNull(files);
Assert.NotNull(files.Response);
Assert.NotEmpty(files.Response.Items);
Assert.NotEmpty(files.Response.Items[0].Name);
}
public void CanListGenomeFileSets()
{
var genomesListRequest = new ListGenomeRequest() { Limit = 1000 };
var genomesListResponse = Client.ListGenomes(genomesListRequest, null);
var oneWithFileSets = genomesListResponse.Response.Items.Where(x => x.HrefFileSets != null).FirstOrDefault();
Assert.NotNull(oneWithFileSets);
var fileSets = Client.ListFileSets(new ListGenomeFileSetsRequest(oneWithFileSets), null);
Assert.NotNull(fileSets);
Assert.NotEmpty(fileSets.Response.Items);
var item = fileSets.Response.Items[0];
Assert.NotNull(item.Href);
Assert.NotNull(item.OriginalPath);
Assert.NotNull(item.HrefFiles);
Assert.NotNull(item.Type);
Assert.NotNull(item.Category);
// make sure we can list files
var files = Client.ListFiles(new ListFileSetFilesRequest(item));
Assert.NotNull(files);
Assert.NotNull(files.Response);
Assert.NotEmpty(files.Response.Items);
Assert.NotEmpty(files.Response.Items[0].Name);
}
public void CanSortGenomes()
{
const int someRidiculouslyHighNumberOfGenomes = 1000;
var genomesListRequest = new ListGenomeRequest() { Limit = someRidiculouslyHighNumberOfGenomes, Offset = 0, SortBy = GenomeSortByParameters.SpeciesName, SortDir = SortDirection.Asc };
var genomesListResponse = Client.ListGenomes(genomesListRequest, null);
Assert.NotNull(genomesListResponse);
var genomeList = genomesListResponse.Response;
string[] genomeSpeciesList =
{
"Arabidopsis thaliana",
"Bacillus Cereus",
"Bos Taurus",
"Escherichia coli",
"H**o sapiens",
"Mus musculus",
"Phix",
"Rattus norvegicus",
"Rhodobacter sphaeroides",
"Saccharomyces cerevisiae",
"Staphylococcus aureus"
};
// this set will only work if we continue to test against the contents of the test db and if that does not change.
Assert.True(genomeList.Items.Length == genomeSpeciesList.Length);
for (int i=0; i<genomeSpeciesList.Length; i++)
Assert.True(genomeList.Items[i].SpeciesName == genomeSpeciesList[i]);
}
public static string BuildUrl(this ListGenomeRequest req, string version)
{
var urlWithParameters = AddDefaultQueryParameters(string.Format("{0}/genomes", version), req.Offset,
req.Limit, req.SortDir);
if (req.SortBy.HasValue)
{
urlWithParameters = string.Format("{0}&{1}={2}", urlWithParameters, QueryParameters.SortBy, req.SortBy);
}
return(urlWithParameters);
}
public void CanListGenomeAnnotationFileSets()
{
var genomesListRequest = new ListGenomeRequest()
{
Limit = 1000
};
var genomesListResponse = Client.ListGenomes(genomesListRequest, null);
var oneWithFileSets = genomesListResponse.Response.Items.Where(x => x.HrefFileSets != null).FirstOrDefault();
// we know these have annotqations with file sets too
Assert.NotNull(oneWithFileSets);
// this verifies I can list annotations too
var annotations = Client.ListGenomeAnnotations(new ListGenomeAnnotationsRequest(oneWithFileSets));
Assert.NotNull(annotations);
Assert.NotEmpty(annotations.Response.Items);
var annotationWithFileSets = annotations.Response.Items.Where(x => x.HrefFileSets != null).FirstOrDefault();
Assert.NotNull(annotationWithFileSets);
var fileSets = Client.ListFileSets(new ListGenomeAnnotationFileSetsRequest(annotationWithFileSets), null);
Assert.NotNull(fileSets);
Assert.NotEmpty(fileSets.Response.Items);
var item = fileSets.Response.Items[0];
Assert.NotNull(item.Href);
Assert.NotNull(item.OriginalPath);
Assert.NotNull(item.HrefFiles);
Assert.NotNull(item.Source);
Assert.NotNull(item.Version);
// make sure we can list files
var files = Client.ListFiles(new ListFileSetFilesRequest(item));
Assert.NotNull(files);
Assert.NotNull(files.Response);
Assert.NotEmpty(files.Response.Items);
Assert.NotEmpty(files.Response.Items[0].Name);
}
public Task<ListGenomeResponse> ListGenomesAsync(ListGenomeRequest request, IRequestOptions options)
{
return WebClient.SendAsync<ListGenomeResponse>(HttpMethods.GET, request.BuildUrl(ClientSettings.Version), null, options);
}
public ListGenomeResponse ListGenomes(ListGenomeRequest request, IRequestOptions options = null)
{
return WebClient.Send(request, options);
}
public ListGenomeResponse ListGenomes(ListGenomeRequest request, IRequestOptions options = null)
{
return(WebClient.Send(request, options));
}
public ListGenomeResponse ListGenomes(ListGenomeRequest request, IRequestOptions options = null)
{
return WebClient.Send<ListGenomeResponse>(HttpMethods.GET, request.BuildUrl(ClientSettings.Version), null, options);
}
public ListGenomeResponse ListGenomes(ListGenomeRequest request, IRequestOptions options)
{
return(WebClient.Send <ListGenomeResponse>(HttpMethods.GET, request.BuildUrl(ClientSettings.Version), null, options));
}
