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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.wqflask.database import database_connection
from gn2.utility import helper_functions
from gn2.utility.tools import get_setting
class SendToGeneWeaver:
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)
self.chip_name = test_chip(self.trait_list)
self.wrong_input = "False"
if self.chip_name == "mixed" or self.chip_name == "not_microarray" or '_NA' in self.chip_name:
self.wrong_input = "True"
else:
species = self.trait_list[0][1].group.species
if species == "rat":
species_name = "Rattus norvegicus"
elif species == "human":
species_name = "Homo sapiens"
elif species == "mouse":
species_name = "Mus musculus"
else:
species_name = ""
trait_name_list = get_trait_name_list(self.trait_list)
self.hidden_vars = {
'client': "genenetwork",
'species': species_name,
'idtype': self.chip_name,
'list': ",".join(trait_name_list),
}
def get_trait_name_list(trait_list):
name_list = []
for trait_db in trait_list:
name_list.append(trait_db[0].name)
return name_list
def test_chip(trait_list):
final_chip_name = ""
with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
for trait_db in trait_list:
dataset = trait_db[1]
cursor.execute(
"SELECT GeneChip.GO_tree_value "
"FROM GeneChip, ProbeFreeze, ProbeSetFreeze "
"WHERE GeneChip.Id = ProbeFreeze.ChipId "
"AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
"AND ProbeSetFreeze.Name = %s",
(dataset.name,)
)
if result := cursor.fetchone():
chip_name = result[0]
if chip_name:
if chip_name != final_chip_name:
if final_chip_name:
return "mixed"
else:
final_chip_name = chip_name
else:
pass
else:
cursor.execute(
"SELECT GeneChip.Name "
"FROM GeneChip, ProbeFreeze, ProbeSetFreeze "
"WHERE GeneChip.Id = ProbeFreeze.ChipId "
"AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
"AND ProbeSetFreeze.Name = %s",
(dataset.name,)
)
chip_name = f'{cursor.fetchone()[0]}_NA'
return chip_name
else:
cursor.execute(
"SELECT GeneChip.Name FROM GeneChip, "
"ProbeFreeze, ProbeSetFreeze WHERE "
"GeneChip.Id = ProbeFreeze.ChipId "
"AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
"AND ProbeSetFreeze.Name = %s",
(dataset.name,)
)
if result := cursor.fetchone():
chip_name = f'{result[0]}_NA'
return chip_name
return "not_microarray"
return chip_name
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