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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.base.trait import retrieve_trait_info
from gn2.utility import helper_functions
from gn2.utility.tools import get_setting
class SendToWebGestalt:
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:
trait_name_list, gene_id_list = gen_gene_id_list(self.trait_list)
self.target_url = "https://www.webgestalt.org/option.php"
id_type = "entrezgene"
self.hidden_vars = {
'gene_list': "\n".join(gene_id_list),
'id_type': "entrezgene",
'ref_set': "genome",
'enriched_database_category': "geneontology",
'enriched_database_name': "Biological_Process",
'sig_method': "fdr",
'sig_value': "0.05",
'enrich_method': "ORA",
'fdr_method': "BH",
'min_num': "2"
}
species = self.trait_list[0][1].group.species
if species == "rat":
self.hidden_vars['organism'] = "rnorvegicus"
elif species == "human":
self.hidden_vars['organism'] = "hsapiens"
elif species == "mouse":
self.hidden_vars['organism'] = "mmusculus"
else:
self.hidden_vars['organism'] = "others"
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,)
)
result = cursor.fetchone()
chip_name = f'{result[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,)
)
result = cursor.fetchone()
if not result:
return "not_microarray"
else:
chip_name = f'{result[0]}_NA'
return chip_name
return chip_name
def gen_gene_id_list(trait_list):
trait_name_list = []
gene_id_list = []
for trait_db in trait_list:
trait = trait_db[0]
trait_name_list.append(trait.name)
retrieve_trait_info(trait, trait.dataset)
gene_id_list.append(str(trait.geneid))
return trait_name_list, gene_id_list
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