def _to_python(self, value, state=None):
if isinstance(value, cgi.FieldStorage):
factory = ExperimentMetadataObjectFactory()
try:
plate = factory.parse_plate(None, infile=value.file)
return plate
except Exception, e:
raise formencode.Invalid("Could not read file", value, state)
def from_plate(self, id=None):
if not id:
abort(404)
plate = Session.query(Plate).get(id)
if not plate:
abort(404)
# ignore possibility of reprocess config for now
storage = QLStorageSource(config)
path = storage.plate_path(plate)
factory = ExperimentMetadataObjectFactory()
qlp = factory.parse_plate(path)
c.wells = qlp.analyzed_wells
c.original_source = plate.name
c.plate_template_id = None
c.plate_setup_id = None
c.id = id
return self.__display(rowcol_order=qlp.acquisition_order)
def preview(self):
template = os.path.basename(request.params.get('template'))
# this is hacky, should be QLTStorageSource
qlt_path = "%s/%s" % (config['qlb.setup_template_store'], template)
factory = ExperimentMetadataObjectFactory()
qlp = factory.parse_plate(qlt_path)
c.wells = qlp.analyzed_wells
c.original_source = None
c.plate_template_id = None
c.plate_setup_id = None
c.id = None
# this is ugly
c.assay_field = {'value': '', 'options': [('','')]}
c.class_decorator = lambda well: ''
c.re_field = fl.instock_enzyme_field()
c.form = h.LiteralForm(
value = {'rowcol_order': str(ROWCOL_ORDER_ROW)},
option = {'rowcol_order': [(ROWCOL_ORDER_ROW, 'By Row (Left->Right)')]}
)
c.preview_mode = True
return render('/template/design.html')