def browser(request, index, url, galaxy_url, dataid=0):
""
global FORM_DEFAULTS
# incoming parameters cast into a dictionary
incoming = dict( request.POST.items() )
# alters the incoming parameters based on user interaction
incoming = browserutils.modify_incoming(incoming, FORM_DEFAULTS)
# create the necessary forms
forms = html.Params()
forms.search = formspec.make_form(index.labels)(incoming)
forms.navbar = formspec.NavbarForm()
forms.fitting = formspec.FitForm( incoming )
forms.peaks = formspec.PeakForm( incoming )
# extract the search parameters
params = browserutils.parse_parameters(forms=forms, defaults=formspec.ALL_DEFAULTS)
# run the tool or return an image
if 'runtool' in incoming:
# need to run the tool
# form the url with dictionary substitution
# TODO make parameters names consistent across Galaxy, GeneTrack and script!
strand = 'all' if params.strand=='ALL' else 'two'
mode = 'nolap' if params.smoothing_func =='GK' else 'all'
urlparams = dict(
strand = strand,
exclusion=params.feature_width,
level=int(params.minimum_peak),
mode=mode,
sigma=int(params.sigma),
input=dataid,
method='gauss',
runtool_btn="Execute"
)
url = "%s&%s" % (galaxy_url, urllib.urlencode( urlparams ))
return html.redirect(url)
# creates the multiplot
multi = dataview_multiplot(index=index, params=params, debug=False)
params.image_height = multi.h
# close the data
index.close()
# trigger the occasional cache cleaning
webutil.cache_clean(age=1, chance=10)
# creates a file representation and a name
image_name, image_path = webutil.cache_file(ext='png')
# saves the multiplot
multi.save(image_path)
params.image_name = image_name
return html.template( request=request, name='data-browse.html', forms=forms, params=params, url=url)