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# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
# as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU Affero General Public License for more details.
#
# This program is available from Source Forge: at GeneNetwork Project
# (sourceforge.net/projects/genenetwork/).
#
# Contact Dr. Robert W. Williams at rwilliams@uthsc.edu
#
#
# This module is used by GeneNetwork project (www.genenetwork.org)
from gn2.base.trait import GeneralTrait
from gn2.utility import helper_functions, corr_result_helpers
class SendToBNW:
def __init__(self, start_vars):
trait_db_list = [trait.strip()
for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
trait_samples_list = []
for trait_db in self.trait_list:
trait_1 = trait_db[0]
this_sample_data = trait_1.data
trait1_samples = list(this_sample_data.keys())
trait_samples_list.append(trait1_samples)
shared_samples = list(
set(trait_samples_list[0]).intersection(*trait_samples_list))
self.form_value = "" # ZS: string that is passed to BNW through form
values_list = []
for trait_db in self.trait_list:
this_trait = trait_db[0]
this_sample_data = this_trait.data
trait_vals = []
for sample in this_sample_data:
if sample in shared_samples:
trait_vals.append(this_sample_data[sample].value)
values_list.append(trait_vals)
self.form_value += "_" + str(this_trait.name) + ","
values_list = zip(*values_list)
self.form_value = self.form_value[:-1]
self.form_value += ";"
for row in values_list:
has_none = False
for cell in row:
if not cell:
has_none = True
break
if has_none:
continue
self.form_value += ",".join(str(cell) for cell in row)
self.form_value += ";"
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