def import_by_url(self, url):
# TODO: replace with chain
# http://docs.celeryproject.org/en/latest/userguide/tasks.html#task-synchronous-subtasks
parsed_url = urlparse.urlparse(url)
file_name = parsed_url.path.split('/')[-1]
temp_file_path = os.path.join(get_temp_dir(), file_name)
try:
# TODO: refactor download_file to take file handle instead
# of path
download_file(url, temp_file_path)
except RuntimeError as exc:
error_msg = "Problem downloading ISA-Tab file from: " + url
logger.error("%s. %s", error_msg, exc)
return {
"success": False,
"message": error_msg
}
return {
"success": True,
"message": "File imported.",
"data": {
"temp_file_path": temp_file_path
}
}
def import_by_url(self, url):
# TODO: replace with chain
# http://docs.celeryproject.org/en/latest/userguide/tasks.html#task-synchronous-subtasks
parsed_url = urlparse.urlparse(url)
file_name = parsed_url.path.split('/')[-1]
temp_file_path = os.path.join(get_temp_dir(), file_name)
try:
# TODO: refactor download_file to take file handle instead
# of path
download_file(url, temp_file_path)
except DownloadError as e:
error_msg = "Problem downloading ISA-Tab file from: " + url
logger.error("%s. %s", (error_msg, e))
return {
"success": False,
"message": error_msg
}
return {
"success": True,
"message": "File imported.",
"data": {
"temp_file_path": temp_file_path
}
}
def post(self, request, *args, **kwargs):
form = ImportISATabFileForm(request.POST, request.FILES)
if form.is_valid():
f = form.cleaned_data['isa_tab_file']
url = form.cleaned_data['isa_tab_url']
logger.debug("ISA-Tab URL: %s", url)
context = RequestContext(request, {'form': form})
if url:
# TODO: replace with chain
# http://docs.celeryproject.org/en/latest/userguide/tasks.html#task-synchronous-subtasks
u = urlparse(url)
file_name = u.path.split('/')[-1]
temp_file_path = os.path.join(get_temp_dir(), file_name)
try:
# TODO: refactor download_file to take file handle instead
# of path
download_file(url, temp_file_path)
except DownloadError as e:
logger.error("Problem downloading ISA-Tab file. %s", e)
error = "Problem downloading ISA-Tab file from: " + url
context = RequestContext(request,
{'form': form, 'error': error})
return render_to_response(self.template_name,
context_instance=context)
else:
temp_file_path = os.path.join(get_temp_dir(), f.name)
try:
handle_uploaded_file(f, temp_file_path)
except IOError as e:
error_msg = "Error writing ISA-Tab file to disk."
error_msg += " IOError: %s, file name: %s, error: %s"
logger.error(error_msg, e.errno, e.filename, e.strerror)
error = "Error writing ISA-Tab file to disk"
context = RequestContext(request,
{'form': form, 'error': error})
return render_to_response(self.template_name,
context_instance=context)
logger.debug("Temp file name: '%s'", temp_file_path)
dataset_uuid = (parse_isatab.delay(
request.user.username,
False,
temp_file_path
).get())[0]
# TODO: exception handling (OSError)
os.unlink(temp_file_path)
if dataset_uuid:
# TODO: redirect to the list of analysis samples for the given
# UUID
return HttpResponseRedirect(
reverse(self.success_view_name, args=(dataset_uuid,)))
else:
error = 'Problem parsing ISA-Tab file'
context = RequestContext(request,
{'form': form, 'error': error})
return render_to_response(self.template_name,
context_instance=context)
else: # submitted form is not valid
context = RequestContext(request, {'form': form})
return render_to_response(self.template_name,
context_instance=context)
def get(self, request, *args, **kwargs):
# a workaround for automatic ISA archive import after logging in
try:
url_from_cookie = request.COOKIES[self.isa_tab_cookie_name]
except KeyError:
logger.info("ISA-Tab URL was not provided")
form = ImportISATabFileForm()
context = RequestContext(request, {'form': form})
return render_to_response(self.template_name,
context_instance=context)
form = ImportISATabFileForm({'isa_tab_url': url_from_cookie})
if form.is_valid():
url = form.cleaned_data['isa_tab_url']
else:
context = RequestContext(request, {'form': form})
response = render_to_response(self.template_name,
context_instance=context)
response.delete_cookie(self.isa_tab_cookie_name)
return response
u = urlparse.urlparse(url)
file_name = u.path.split('/')[-1]
temp_file_path = os.path.join(get_temp_dir(), file_name)
try:
# TODO: refactor download_file to take file handle instead of path
download_file(url, temp_file_path)
except DownloadError as e:
logger.error("Problem downloading ISA-Tab file. %s", e)
error = "Problem downloading ISA-Tab file from: '{}'".format(url)
context = RequestContext(request, {'form': form, 'error': error})
response = render_to_response(self.template_name,
context_instance=context)
response.delete_cookie(self.isa_tab_cookie_name)
return response
logger.debug("Temp file name: '%s'", temp_file_path)
dataset_uuid = parse_isatab.delay(request.user.username, False,
temp_file_path).get()[0]
# TODO: exception handling
os.unlink(temp_file_path)
if dataset_uuid:
if 'ajax' in kwargs and kwargs['ajax']:
return HttpResponse(
json.dumps({'new_data_set_uuid': dataset_uuid}),
'application/json'
)
else:
response = HttpResponseRedirect(
reverse(self.success_view_name, args=(dataset_uuid,)))
response.delete_cookie(self.isa_tab_cookie_name)
return response
else:
error = "Problem parsing ISA-Tab file"
context = RequestContext(request, {'form': form, 'error': error})
response = render_to_response(self.template_name,
context_instance=context)
response.delete_cookie(self.isa_tab_cookie_name)
return response
def get(self, request, *args, **kwargs):
# a workaround for automatic ISA archive import after logging in
try:
url_from_cookie = request.COOKIES[self.isa_tab_cookie_name]
except KeyError:
logger.info("ISA-Tab URL was not provided")
form = ImportISATabFileForm()
context = RequestContext(request, {'form': form})
return render_to_response(self.template_name,
context_instance=context)
form = ImportISATabFileForm({'isa_tab_url': url_from_cookie})
if form.is_valid():
url = form.cleaned_data['isa_tab_url']
else:
context = RequestContext(request, {'form': form})
response = render_to_response(self.template_name,
context_instance=context)
response.delete_cookie(self.isa_tab_cookie_name)
return response
u = urlparse.urlparse(url)
file_name = u.path.split('/')[-1]
temp_file_path = os.path.join(get_temp_dir(), file_name)
try:
# TODO: refactor download_file to take file handle instead of path
download_file(url, temp_file_path)
except DownloadError as e:
logger.error("Problem downloading ISA-Tab file. %s", e)
error = "Problem downloading ISA-Tab file from: '{}'".format(url)
context = RequestContext(request, {'form': form, 'error': error})
response = render_to_response(self.template_name,
context_instance=context)
response.delete_cookie(self.isa_tab_cookie_name)
return response
logger.debug("Temp file name: '%s'", temp_file_path)
dataset_uuid = parse_isatab.delay(request.user.username, False,
temp_file_path).get()[0]
# TODO: exception handling
os.unlink(temp_file_path)
if dataset_uuid:
if 'ajax' in kwargs and kwargs['ajax']:
return HttpResponse(
json.dumps({'new_data_set_uuid': dataset_uuid}),
'application/json')
else:
response = HttpResponseRedirect(
reverse(self.success_view_name, args=(dataset_uuid, )))
response.delete_cookie(self.isa_tab_cookie_name)
return response
else:
error = "Problem parsing ISA-Tab file"
context = RequestContext(request, {'form': form, 'error': error})
response = render_to_response(self.template_name,
context_instance=context)
response.delete_cookie(self.isa_tab_cookie_name)
return response
def import_by_url(url):
# TODO: replace with chain
# http://docs.celeryproject.org/en/latest/userguide/tasks.html#task-synchronous-subtasks
parsed_url = urlparse.urlparse(url)
file_name = parsed_url.path.split('/')[-1]
temp_file_path = os.path.join(tempfile.gettempdir(), file_name)
try:
# TODO: refactor download_file to take file handle instead
# of path
download_file(url, temp_file_path)
except RuntimeError as exc:
error_msg = "Problem downloading ISA-Tab file from: " + url
logger.error("%s. %s", error_msg, exc)
return _error_message(error_msg)
return _success_message(temp_file_path)
def get(self, request, *args, **kwargs):
# a workaround for automatic ISA archive import after logging in
try:
url_from_cookie = request.COOKIES[self.isa_tab_cookie_name]
except KeyError:
logger.info("ISA-Tab URL was not provided")
form = ImportISATabFileForm()
context = RequestContext(request, {'form': form})
return render_to_response(self.template_name,
context_instance=context)
form = ImportISATabFileForm({'isa_tab_url': url_from_cookie})
if form.is_valid():
url = form.cleaned_data['isa_tab_url']
else:
context = RequestContext(request, {'form': form})
response = render_to_response(self.template_name,
context_instance=context)
response.delete_cookie(self.isa_tab_cookie_name)
return response
u = urlparse.urlparse(url)
file_name = u.path.split('/')[-1]
temp_file_path = os.path.join(get_temp_dir(), file_name)
try:
# TODO: refactor download_file to take file handle instead of path
download_file(url, temp_file_path)
except RuntimeError as exc:
logger.error("Problem downloading ISA-Tab file. %s", exc)
error = "Problem downloading ISA-Tab file from: '{}'".format(url)
context = RequestContext(request, {'form': form, 'error': error})
response = render_to_response(self.template_name,
context_instance=context)
response.delete_cookie(self.isa_tab_cookie_name)
return response
logger.debug("Temp file name: '%s'", temp_file_path)
try:
dataset_uuid = parse_isatab(
request.user.username,
False,
temp_file_path
)
except ParserException as e:
error_message = "{} {}".format(
PARSER_ERROR_MESSAGE,
e.message
)
logger.error(error_message)
return HttpResponseBadRequest(error_message)
except Exception as e:
error_message = "{} {}".format(
PARSER_UNEXPECTED_ERROR_MESSAGE,
traceback.format_exc(e)
)
logger.error(error_message)
return HttpResponseBadRequest(
PARSER_UNEXPECTED_ERROR_MESSAGE +
e.message
)
try:
os.unlink(temp_file_path)
except OSError as exc:
logger.error("Couldn't unlink ISATab's `temp_file_path`: %s %s",
temp_file_path, exc)
if dataset_uuid:
if 'ajax' in kwargs and kwargs['ajax']:
return JsonResponse({'new_data_set_uuid': dataset_uuid})
else:
response = HttpResponseRedirect(
reverse(self.success_view_name, args=(dataset_uuid,)))
response.delete_cookie(self.isa_tab_cookie_name)
return response
else:
error = "Problem parsing ISA-Tab file"
context = RequestContext(request, {'form': form, 'error': error})
response = render_to_response(self.template_name,
context_instance=context)
response.delete_cookie(self.isa_tab_cookie_name)
return response
def get(self, request, *args, **kwargs):
# a workaround for automatic ISA archive import after logging in
try:
url_from_cookie = request.COOKIES[self.isa_tab_cookie_name]
except KeyError:
logger.info("ISA-Tab URL was not provided")
form = ImportISATabFileForm()
context = RequestContext(request, {'form': form})
return render_to_response(self.template_name,
context_instance=context)
form = ImportISATabFileForm({'isa_tab_url': url_from_cookie})
if form.is_valid():
url = form.cleaned_data['isa_tab_url']
else:
context = RequestContext(request, {'form': form})
response = render_to_response(self.template_name,
context_instance=context)
response.delete_cookie(self.isa_tab_cookie_name)
return response
u = urlparse.urlparse(url)
file_name = u.path.split('/')[-1]
temp_file_path = os.path.join(tempfile.gettempdir(), file_name)
try:
# TODO: refactor download_file to take file handle instead of path
download_file(url, temp_file_path)
except RuntimeError as exc:
logger.error("Problem downloading ISA-Tab file. %s", exc)
error = "Problem downloading ISA-Tab file from: '{}'".format(url)
context = RequestContext(request, {'form': form, 'error': error})
response = render_to_response(self.template_name,
context_instance=context)
response.delete_cookie(self.isa_tab_cookie_name)
return response
logger.debug("Temp file name: '%s'", temp_file_path)
try:
dataset_uuid = parse_isatab(
request.user.username,
False,
temp_file_path
)
except ParserException as e:
error_message = "{} {}".format(
PARSER_ERROR_MESSAGE,
e.message
)
logger.error(error_message)
return HttpResponseBadRequest(error_message)
except Exception as e:
error_message = "{} {}".format(
PARSER_UNEXPECTED_ERROR_MESSAGE,
traceback.format_exc(e)
)
logger.error(error_message)
return HttpResponseBadRequest(
PARSER_UNEXPECTED_ERROR_MESSAGE +
e.message
)
try:
os.unlink(temp_file_path)
except OSError as exc:
logger.error("Couldn't unlink ISATab's `temp_file_path`: %s %s",
temp_file_path, exc)
if dataset_uuid:
if 'ajax' in kwargs and kwargs['ajax']:
return JsonResponse({'new_data_set_uuid': dataset_uuid})
else:
response = HttpResponseRedirect(
reverse(self.success_view_name, args=(dataset_uuid,)))
response.delete_cookie(self.isa_tab_cookie_name)
return response
else:
error = "Problem parsing ISA-Tab file"
context = RequestContext(request, {'form': form, 'error': error})
response = render_to_response(self.template_name,
context_instance=context)
response.delete_cookie(self.isa_tab_cookie_name)
return response