def generate_csa(result_pk, monitor_pk=None):
result = models.Results.objects.get(pk=result_pk)
report_dir = result.get_report_dir()
raw_data_dir = result.experiment.expDir
try:
monitor = models.FileMonitor.objects.get(pk=monitor_pk)
except models.FileMonitor.DoesNotExist:
monitor = models.FileMonitor()
monitor.tags = "generate_csa"
csa_file_name = "csa_{0:04d}.zip".format(int(result_pk))
monitor.status = "Generating"
monitor.local_dir = report_dir
monitor.name = csa_file_name
monitor.save()
# Generate report PDF file.
# This will create a file named report.pdf in results directory
makePDF.write_report_pdf(result_pk)
csa_path = makeCSA.makeCSA(report_dir, raw_data_dir, monitor.name)
digest_hex, digest_64, size = md5_stats_file(csa_path)
monitor.md5sum = digest_hex
monitor.size = size
monitor.status = "Generated"
monitor.save()
def export_upload_report(request):
try:
report_pk = int(request.POST.get("report"))
except ValueError:
raise Http404("'{0}' is not a valid report ID".format(report_pk))
path = request.POST.get("file_path")
report = get_object_or_404(models.Results, pk=report_pk)
root = report.get_report_dir()
full_path = os.path.join(root, path)
if not os.path.exists(full_path):
raise Http404("'{0}' does not exist as a file in report {1}".format(
path, report_pk))
tag = "report/{0}/".format(report_pk)
monitor = models.FileMonitor(
local_dir=os.path.dirname(full_path),
name=os.path.basename(full_path),
tags="upload," + tag,
status="Queued",
)
monitor.save()
result = export_upload_file.delay(monitor.id)
monitor.celery_task_id = result.task_id
monitor.save()
return redirect("list_export_uploads", tag="")
def getReady(self, zip_location):
'''
Create a publisher and a monitor, also copy the panel archive under test
into a temp folder, which ampliseq_zip_upload can do whatever it wants with.
'''
monitor = models.FileMonitor()
monitor.name = "fake_fixed_design.zip"
monitor.url = "fake_url"
monitor.celery_task_id = "fake_celery_task_id"
monitor.created = datetime.datetime.now()
monitor.updated = datetime.datetime.now()
monitor.save()
self.temp_intial_dir = tempfile.mkdtemp()
self.full_path = os.path.join(self.temp_intial_dir,
'fake_fixed_panel.zip')
shutil.copy(zip_location, self.full_path)
def report_support_upload(request):
form = SupportUploadForm(request.POST)
# check for existing support upload
data = {
"created": False,
}
account = models.RemoteAccount.objects.get(
remote_resource="support.iontorrent")
if not account.has_access():
data["error"] = "invalid_auth"
if not form.is_valid():
data["error"] = "invalid_form"
data["form_errors"] = form.errors
if "error" not in data:
result_pk = form.cleaned_data['result']
support_upload = models.SupportUpload.objects.filter(
result=result_pk).order_by('-id').first()
if not support_upload:
data["created"] = True
support_upload = models.SupportUpload(
account=account,
result_id=result_pk,
user=request.user,
local_status="Preparing",
contact_email=form.cleaned_data['contact_email'],
description=form.cleaned_data['description'])
support_upload.save()
async_result = AsyncResult(support_upload.celery_task_id)
if (not support_upload.celery_task_id
or async_result.status in celery.states.READY_STATES):
if not support_upload.file:
monitor = models.FileMonitor()
monitor.save()
support_upload.file = monitor
support_upload.save()
support_upload.file.status = "Queued",
support_upload.file.tags = "support_upload,generate_csa"
support_upload.file.save()
generate = generate_csa.s(result_pk, support_upload.file.pk)
errback = filemonitor_errback.s(support_upload.file.pk)
gen_result = generate.apply_async(link_error=errback)
support_upload.file.celery_task_id = gen_result.task_id
auth_result = check_authentication.delay(support_upload.pk)
upload_result = check_and_upload.apply_async(
(support_upload.pk, auth_result.task_id, gen_result.task_id),
countdown=1)
support_upload.celery_task_id = upload_result.task_id
support_upload.save()
resource = SupportUploadResource()
uri = resource.get_resource_uri(support_upload)
data["resource_uri"] = uri
# make CSA
# check auth
# start upload task
# respond with support upload object for JS polling
return HttpResponse(json.dumps(data, indent=4, sort_keys=True),
mimetype='application/json')