def idba(request):
response_dict = dict(settings.TEMPLATE_ARGS_BY_DEFAULT)
response_dict.update(get_report_response_dict(os.path.join(settings.IDBA_DIRPATH)))
response_dict['hide_date'] = True
response_dict['data_set'] = {
'title': 'E. coli, single-cell',
}
return render_to_response('examples/idba.html', response_dict)
def example(request):
response_dict = dict(settings.TEMPLATE_ARGS_BY_DEFAULT)
response_dict.update(get_report_response_dict(settings.EXAMPLE_DIRPATH))
response_dict['title'] = response_dict['caption'] = 'Sample report'
response_dict['hide_date'] = True
response_dict['data_set'] = {
'title': 'E. coli, single-cell',
}
return render_to_response('report.html', response_dict)
def common_view(dir_name, caption, slug_name, download_fname, template_dir_name=None,
html_template_name=None, data_set_name=None, title=None):
template_dir_name = 'examples/' + (template_dir_name or dir_name)
html_template_name = html_template_name or slug_name
if download_fname:
download_fpath = os.path.join(settings.FILES_DOWNLOADS_DIRPATH, download_fname)
if os.path.exists(download_fpath):
# if download_fname[-4:] == '.zip':
# mimetype = 'application/zip'
# else:
# mimetype = 'application/force-download'
# f = FileWrapper(fpath)
# response = HttpResponse(mimetype=mimetype)
# response['Content-Disposition'] = 'attachment; filename=%s' % download_fname
# response['X-Sendfile'] = download_fpath
# response['Content-Length'] = 100
# return response
wrapper = FileWrapper(open(download_fpath, 'r'))
content_type = mimetypes.guess_type(download_fpath)[0]
response = HttpResponse(wrapper, content_type=content_type)
response['Content-Length'] = os.path.getsize(download_fpath)
response['Content-Disposition'] = 'attachment; filename=' + smart_str(download_fname)
return response
else:
raise Http404('File %s does not exist' % download_fname)
else:
response_dict = dict(settings.TEMPLATE_ARGS_BY_DEFAULT)
report_dict = get_report_response_dict(
os.path.join(settings.FILES_DIRPATH, dir_name, slug_name))
response_dict.update(report_dict)
response_dict['caption'] = caption
response_dict['title'] = title
response_dict['hide_date'] = True
response_dict['download_link'] = slug_name + '_quast_report.zip'
response_dict['download_text'] = download_text
response_dict['data_set'] = {
'title': data_set_name,
}
return render_to_response(template_dir_name + html_template_name + '.html', response_dict)
def common_view(dir_name, caption, slug_name, download_fname):
if download_fname:
download_fpath = os.path.join(settings.FILES_DOWNLOADS_DIRPATH, slug_name, download_fname)
if os.path.exists(download_fpath):
# if download_fname[-4:] == '.zip':
# mimetype = 'application/zip'
# else:
# mimetype = 'application/force-download'
# f = FileWrapper(fpath)
# response = HttpResponse(mimetype=mimetype)
# response['Content-Disposition'] = 'attachment; filename=%s' % download_fname
# response['X-Sendfile'] = download_fpath
# response['Content-Length'] = 100
# return response
wrapper = FileWrapper(open(download_fpath, 'r'))
content_type = mimetypes.guess_type(download_fpath)[0]
response = HttpResponse(wrapper, content_type=content_type)
response['Content-Length'] = os.path.getsize(download_fpath)
response['Content-Disposition'] = 'attachment; filename=' + smart_str(download_fname)
return response
else:
raise Http404('File %s does not exist' % download_fname)
else:
response_dict = settings.TEMPLATE_ARGS_BY_DEFAULT
report_dict = get_report_response_dict(
os.path.join(settings.PAPER_DIRPATH, slug_name),
caption,
link=slug_name + '_quast_report.zip'
)
response_dict.update(report_dict)
response_dict['download'] = True
# response_dict['download_link'] = slug_name + '_quast_report.zip'
response_dict['download_text'] = download_text
return render_to_response(dir_name + slug_name + '.html', response_dict)
def report_view(dir_name, caption, slug_name, template_dir_name=None,
html_template_name=None, data_set_name=None, title=None):
template_dir_name = 'examples/' + (template_dir_name or dir_name)
html_template_name = html_template_name or slug_name
response_dict = dict(settings.TEMPLATE_ARGS_BY_DEFAULT)
report_dict = get_report_response_dict(os.path.join(settings.FILES_DIRPATH, dir_name, slug_name))
response_dict.update(report_dict)
response_dict['caption'] = caption
response_dict['title'] = title
response_dict['hide_date'] = True
response_dict['download_link'] = slug_name + '_quast_report.zip'
response_dict['download_text'] = download_text
response_dict['download'] = True
response_dict['data_set'] = {
'title': data_set_name,
}
return render_to_response(template_dir_name + html_template_name + '.html', response_dict)
def index_view(us, response_dict, request):
# Evaluation
if request.method == 'POST':
log_msg = 'Somebody posted a form:'
for k, v in request.POST.items():
if k == 'contigs:':
log_msg += '\n\t%s' % k
for contig in v.split('\n'):
log_msg += '\n\t\t%s' % contig
else:
log_msg += '\n\t%s:\t%s' % (str(k), str(v))
# mailer.info(log_msg)
form = DataSetForm(us, request.POST)
report_id = form.data.get('report_id')
if not report_id:
logger.error('data_set_form.data.get(\'report_id\') is None')
return HttpResponseBadRequest('No report_id in form')
try:
qs = QuastSession.objects.get(report_id=report_id)
except QuastSession.DoesNotExist:
logger.error('QuastSession with report_id=%s does not exist' % report_id)
return HttpResponseBadRequest('No quast session with report_id=%s' % report_id)
else:
#TODO: Temporary, used because user_session was always deleted when registering a user
if not qs.user_session:
qs.user_session = us
#TODO: End of temporary
# Contigs fnames from this form
# contigs_in_form = data_set_form.data.get('contigs')
#
# split = contigs_in_form.split('\r\n')
# if len(split) == 1:
# split = contigs_in_form.split('\n')
# if len(split) == 1:
# logger.error('No contigs fnames got from "data_set_form.contigs": the value got is %s', str(contigs_in_form))
# return HttpResponseBadRequest("Error: no contigs loaded")
# contigs_fnames = split[:-1]
if form.is_valid():
qs.submitted = True
qs.min_contig = form.cleaned_data['min_contig']
qs.scaffolds = form.cleaned_data['scaffolds']
qs.eukaryotic = form.cleaned_data['domain'] == 'True'
qs.estimated_ref_size = form.cleaned_data['estimated_ref_size']
qs.find_genes = form.cleaned_data['find_genes']
qs.data_set = get_data_set(request, form, us, default_name=qs.report_id)
us.set_min_contig(qs.min_contig)
us.set_scaffolds(qs.scaffolds)
us.set_eukaryotic(qs.eukaryotic)
us.set_estimated_ref_size(qs.estimated_ref_size)
us.set_find_genes(qs.find_genes)
us.set_default_data_set(qs.data_set)
us.save()
qs.comment = form.cleaned_data.get('comment')
qs.caption = form.cleaned_data.get('caption')
qs.generate_link()
qs.save()
logger.info('quast_app.views.index.POST: '
'caption = %s, link = %s, data set = %s, '
'min_contig = %d, scaffolds = %r, eukaryotic = %r, find_genes = %r',
qs.caption, qs.get_report_html_link(), qs.data_set.name if qs.data_set else '<unknown>',
qs.min_contig, qs.scaffolds, qs.eukaryotic, qs.find_genes)
# Starting Quast
start_quast_session(us, qs)
# return HttpResponseRedirect(reverse('True}))
request.session['after_evaluation'] = True
# return redirect('quast_app.views.index')
return HttpResponseRedirect(reverse("quast_app.views.index"))
# return redirect('quast_app.views.report', link=quast_session.link)
else:
logger.info('quast_app.views.index.POST: form invalid, errors are: = %s', str(form.errors.items()))
elif request.method == 'GET':
# min_contig = request.session.get('min_contig') or qconfig.min_contig
# scaffolds = request.session.get('scaffolds') or False
# eukaryotic = request.session.get('eukaryotic') or False
# estimated_ref_size = request.session.get('estimated_ref_size') or None
# find_genes = request.session.get('find_genes') or False
qs = QuastSession.create(us)
form = DataSetForm(us, initial={
'report_id': qs.report_id,
'name_selected': qs.data_set.name if qs.data_set else None,
'min_contig': qs.min_contig,
'scaffolds': qs.scaffolds,
'domain': qs.eukaryotic,
'estimated_ref_size': qs.estimated_ref_size,
'find_genes': qs.find_genes,
})
response_dict['report_id'] = qs.report_id
# Default data set for this user
# if user_session.get_default_data_set():
# default_data_set_name = user_session.get_default_data_set().name
# else:
# default_data_set_name = request.session.get('default_data_set_name') or ''
# if default_data_set_name:
# try:
# default_data_set = DataSet.objects.get(name=default_data_set_name)
# user_session.set_default_data_set(default_data_set)
# except DataSet.DoesNotExist:
# pass
#
# form.set_default_data_set_name(default_data_set_name)
else:
logger.warn('Request method is %s' % request.method)
return HttpResponseBadRequest("GET and POST are only supported here")
# uploaded_contigs_fnames = [c_f.fname for c_f in user_session.contigsfile_set.all()]
response_dict.update({
'csrf_token': get_token(request),
'contigs_fnames': [],
'contig_max_size_mb': settings.CONTIG_MAX_SIZE_MB,
'qs_form': form,
'email': us.get_email(),
'session_key': us.session_key,
'is_authorized': us.user is not None,
})
# REPORTS
response_dict.update(get_reports_response_dict(
us,
after_evaluation=request.session.get('after_evaluation', False),
limit=settings.REPORTS_SHOW_LIMIT))
request.session['after_evaluation'] = False
# EXAMPLE
response_dict.update(get_report_response_dict(settings.EXAMPLE_DIRPATH))
response_dict['hide_date'] = True
response_dict['data_set'] = {
'title': 'E. coli, single-cell',
}
return render_to_response(
'index.html',
response_dict,
context_instance=RequestContext(request))
