def test_params_form(self):
# -------------------
# VCF file test
# -------------------
self.assertTrue(self.dataset_vcf.is_vcf_file(), "Should be a VCF file")
self.assertTrue(not self.dataset_vcf.is_fastq_file(),
"Should not be FastQ file")
self.assertEqual(self.dataset_vcf.get_file_patterns(),\
GENTB_VCF_FILE_PATTERNS)
pipeline_runner = PipelineScriptRunner(self.dataset_vcf)
script_directory = pipeline_runner.step1_get_script_directory_info()
self.assertTrue(script_directory is not None)
script_command = pipeline_runner.step2_get_script_command(
script_directory)
print script_command
self.assertTrue(script_command is not None)
#if script_command is not NOne:
# pipeline_runner.step3_run_command(script_command)
# -------------------
# FastQ file test
# -------------------
self.assertTrue(not self.dataset_fastq.is_vcf_file(),
"Should NOT be a VCF file")
self.assertTrue(self.dataset_fastq.is_fastq_file(),
"Should be a FastQ file")
self.assertEqual(self.dataset_fastq.get_file_patterns(),\
GENTB_FASTQ_FILE_PATTERNS)
pipeline_runner = PipelineScriptRunner(self.dataset_fastq)
script_directory = pipeline_runner.step1_get_script_directory_info()
self.assertTrue(script_directory is not None)
script_command = pipeline_runner.step2_get_script_command(
script_directory)
print script_command
self.assertTrue(script_command is not None)
def view_single_dataset(request, dataset_md5):
d = get_common_dict(request, 'My Dataset Detail', view_my_datasets=True)
# Not logged in, show login message
#
if not request.user.is_authenticated():
return render_to_response('predict/my_dataset_detail.html',
d,
context_instance=RequestContext(request))
try:
dataset = PredictDataset.objects.get(md5=dataset_md5)
except PredictDataset.DoesNotExist:
raise Http404('PredictDataset not found')
d['dataset'] = dataset
d['dataset_notes'] = PredictDatasetNote.objects.filter(
dataset=dataset).all()
d['script_runs'] = DatasetScriptRun.objects.filter(dataset=dataset).all()
d['tb_user'] = dataset.user
# Pipeline command
(pipeline_command_found, pipeline_command_or_err
) = PipelineScriptRunner.get_pipeline_command(dataset)
d['pipeline_command_found'] = pipeline_command_found
try:
local_directory_contents = os.listdir(dataset.file_directory)
d['local_directory_contents'] = local_directory_contents
except:
d['local_directory_err'] = "Could not list directory contents"
if pipeline_command_found:
d['pipeline_command'] = pipeline_command_or_err
else:
d['pipeline_command_err'] = pipeline_command_or_err
return render_to_response('predict/my_dataset_detail.html',
d,
context_instance=RequestContext(request))
def view_single_dataset(request, dataset_md5):
d = get_common_dict(request, 'My Dataset Detail', view_my_datasets=True)
# Not logged in, show login message
#
if not request.user.is_authenticated():
return render_to_response('predict/my_dataset_detail.html',
d,
context_instance=RequestContext(request))
try:
dataset = PredictDataset.objects.get(md5=dataset_md5)
except PredictDataset.DoesNotExist:
raise Http404('PredictDataset not found')
d['dataset'] = dataset
d['dataset_notes'] = PredictDatasetNote.objects.filter(dataset=dataset).all()
d['script_runs'] = DatasetScriptRun.objects.filter(dataset=dataset).all()
d['tb_user'] = dataset.user
# Pipeline command
(pipeline_command_found, pipeline_command_or_err) = PipelineScriptRunner.get_pipeline_command(dataset)
d['pipeline_command_found'] = pipeline_command_found
try:
local_directory_contents = os.listdir(dataset.file_directory)
d['local_directory_contents'] = local_directory_contents
except:
d['local_directory_err'] = "Could not list directory contents"
if pipeline_command_found:
d['pipeline_command'] = pipeline_command_or_err
else:
d['pipeline_command_err'] = pipeline_command_or_err
return render_to_response('predict/my_dataset_detail.html',
d,
context_instance=RequestContext(request))
def test_params_form(self):
# -------------------
# VCF file test
# -------------------
self.assertTrue(self.dataset_vcf.is_vcf_file(),
"Should be a VCF file")
self.assertTrue(not self.dataset_vcf.is_fastq_file(),
"Should not be FastQ file")
self.assertEqual(self.dataset_vcf.get_file_patterns(),\
GENTB_VCF_FILE_PATTERNS)
pipeline_runner = PipelineScriptRunner(self.dataset_vcf)
script_directory = pipeline_runner.step1_get_script_directory_info()
self.assertTrue(script_directory is not None)
script_command = pipeline_runner.step2_get_script_command(script_directory)
print script_command
self.assertTrue(script_command is not None)
#if script_command is not NOne:
# pipeline_runner.step3_run_command(script_command)
# -------------------
# FastQ file test
# -------------------
self.assertTrue(not self.dataset_fastq.is_vcf_file(),
"Should NOT be a VCF file")
self.assertTrue(self.dataset_fastq.is_fastq_file(),
"Should be a FastQ file")
self.assertEqual(self.dataset_fastq.get_file_patterns(),\
GENTB_FASTQ_FILE_PATTERNS)
pipeline_runner = PipelineScriptRunner(self.dataset_fastq)
script_directory = pipeline_runner.step1_get_script_directory_info()
self.assertTrue(script_directory is not None)
script_command = pipeline_runner.step2_get_script_command(script_directory)
print script_command
self.assertTrue(script_command is not None)
