def update_analysis_append_samples(request, analysis_id):
if request.method == 'POST':
form = webforms.DataUploadForm(request.POST, request.FILES)
if form.is_valid():
time_stamp = helper_functions.get_time_stamp()
data_file_path = helper_functions.save_uploaded_file(form.cleaned_data['data_file'], time_stamp, output_file_name = constants.data_file_name)
data_file_sha1sum = helper_functions.get_sha1sum(data_file_path)
# just send the data file
server_request = {'request': 'append_samples_to_analysis',
'analysis_id': analysis_id,
'data_file_path': data_file_path}
server_response = server(server_request)
if server_response['response'] == 'OK':
return HttpResponse(get_template("simple.tmpl").render(Context({'content': "Your request is being processed."})))
else:
return HttpResponse(get_template("simple.tmpl").render(Context({'content': "something happened. has no clue. seriously :("})))
else:
return HttpResponse(get_template("error.tmpl").render(Context({'content': "Form wasn't valid :( Please click 'back' button of your browser and re-submit the form."})))
else:
form = webforms.DataUploadForm()
tmpl = "data_upload_form.tmpl"
return HttpResponse(get_template(tmpl).render(Context({'form': form, 'analysis_id': analysis_id})))
def exec_env(request):
if request.method == 'POST':
form = webforms.EnvUploadForm(request.POST, request.FILES)
if form.is_valid():
job_description = form.cleaned_data['job_description']
time_stamp = helper_functions.get_time_stamp()
data_file_path = helper_functions.save_uploaded_file(form.cleaned_data['env_file'], time_stamp, output_file_name = constants.data_file_name)
data_file_sha1sum = helper_functions.get_sha1sum(data_file_path)
server_request = {'request': 'status'}
server_response = server(server_request)
if data_file_sha1sum in server_response['running_analyses']:
#error we already have it lan
tmpl = get_template("simple.tmpl")
return HttpResponse(tmpl.render(Context({'content': "Your ENV file is still being analyzed"})))
elif data_file_sha1sum in server_response['done_analyses']:
tmpl = get_template("simple.tmpl")
return HttpResponse(tmpl.render(Context({'content': "It seems we already have this ENV file analyzed"})))
# TODO: check validity of the file here..
server_request = {'request': 'exec_env',
'job_description': job_description,
'data_file_path': data_file_path,
'data_file_sha1sum': data_file_sha1sum}
server_response = server(server_request)
if server_response['response'] == 'OK':
return HttpResponse(get_template("simple.tmpl").render(Context({'content': "Your ENV file is being processed. This is your process id: %s" % server_response['process_id']})))
else:
return HttpResponse(get_template("simple.tmpl").render(Context({'content': "something happened"})))
else:
form = webforms.EnvUploadForm()
return HttpResponse(get_template("env_upload_form.tmpl").render(Context({'form': form})))
def new_analysis(request, analysis_type):
if request.method == 'POST':
#import pdb; pdb.set_trace()
if analysis_type == "rdp":
form = webforms.FastaUploadForm(request.POST, request.FILES)
if analysis_type == "qpcr":
form = webforms.QpcrUploadForm(request.POST, request.FILES)
if analysis_type == "env":
form = webforms.EnvUploadForm(request.POST, request.FILES)
if analysis_type == "blast":
form = webforms.BlastUploadForm(request.POST, request.FILES)
if analysis_type == "vamps":
form = webforms.VampsUploadForm(request.POST, request.FILES)
if form.is_valid():
job_description = form.cleaned_data['job_description']
time_stamp = helper_functions.get_time_stamp()
if len(request.FILES) == 1:
data_file_path = helper_functions.save_uploaded_file(
form.cleaned_data['data_file'],
time_stamp, output_file_name = constants.data_file_name)
elif len(request.FILES) > 1:
files = [request.FILES[f] for f in request.FILES.keys() if
f.startswith("data_file")]
data_file_path = cat(files)
data_file_sha1sum = helper_functions.get_sha1sum(data_file_path)
server_request = {'request': 'status'}
server_response = server(server_request)
if data_file_sha1sum in server_response['running_analyses']:
return HttpResponse(get_template("simple.tmpl").render(Context({'content': "This data file is still being analyzed"})))
elif data_file_sha1sum in server_response['done_analyses']:
return HttpResponse(get_template("simple.tmpl").render(Context({'content': "This data file has already been analyzed. The analysis id is "+str(data_file_sha1sum)})))
# TODO: check validity of the file here..
#standard request dict for all analyses.
server_request = {'request': 'exec_analysis',
'analysis_type': analysis_type,
'job_description': job_description,
'data_file_path': data_file_path,
'data_file_sha1sum': data_file_sha1sum}
#update server request with special options for certain analysis types
#if your module needs information not contained in a standard request,
#(say phase of the moon or something), add it here in a tuple of
#(name, function) where name is the name attribute in the form, and
#the function converts the raw value or cleaned_data into
#whatever it needs to be
special_options = [("seperator",str),
("qa_mode", int),
("db_name",str),
("threshold",float),
("codes_primers",list),
("homopolymer_length",int),
("threshold_dict",dict)]
for opt in special_options:
if form.cleaned_data.get(opt[0]):
server_request[opt[0]] = opt[1](form.cleaned_data[opt[0]])
server_response = server(server_request)
if server_response['response'] == 'OK':
return HttpResponse(get_template("simple.tmpl").render(Context({'content': "Your request is being processed. This is your process id: %s" % server_response['process_id']})))
else:
return HttpResponse(get_template("simple.tmpl").render(Context({'content': "Server error:"+str(server_response.get("exception"))})))
else:
return HttpResponse(get_template(templates[analysis_type]).render(
Context({"form":form})))
else:
if analysis_type == "rdp":
form = webforms.FastaUploadForm()
tmpl = "fasta_upload_form.tmpl"
elif analysis_type == "qpcr":
form = webforms.QpcrUploadForm()
tmpl = "qpcr_upload_form.tmpl"
elif analysis_type == "env":
form = webforms.EnvUploadForm()
tmpl = "env_upload_form.tmpl"
elif analysis_type == 'blast':
form = webforms.BlastUploadForm()
tmpl = "blast_upload_form.tmpl"
elif analysis_type == "vamps":
form = webforms.EnvUploadForm()
tmpl = "vamps_upload_form.tmpl"
return HttpResponse(get_template(tmpl).render(Context({'form': form})))