1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
|
"""Script that generates the data for the main dropdown menus on the home page
Writes out data as /static/new/javascript/dataset_menu_structure.json
It needs to be run manually when database has been changed.
"""
# 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 Drs. Robert W. Williams
# at rwilliams@uthsc.edu
#
#
#
# This module is used by GeneNetwork project (www.genenetwork.org)
from __future__ import print_function, division
import sys
sys.path.insert(0, "..")
import MySQLdb
import simplejson as json
from pprint import pformat as pf
from base import webqtlConfig
# build MySql database connection
Con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,
host=webqtlConfig.MYSQL_SERVER,
user=webqtlConfig.DB_USER,
passwd=webqtlConfig.DB_PASSWD)
Cursor = Con.cursor()
def get_species():
"""Build species list"""
Cursor.execute("select Name, MenuName from Species order by OrderId")
species = list(Cursor.fetchall())
return species
def get_groups(species):
"""Build groups list"""
groups = {}
for species_name, _species_full_name in species:
Cursor.execute("""select InbredSet.Name, InbredSet.FullName from InbredSet,
Species,
ProbeFreeze, GenoFreeze, PublishFreeze where Species.Name = %s
and InbredSet.SpeciesId = Species.Id and InbredSet.Name != 'BXD300' and
(PublishFreeze.InbredSetId = InbredSet.Id
or GenoFreeze.InbredSetId = InbredSet.Id
or ProbeFreeze.InbredSetId = InbredSet.Id)
group by InbredSet.Name
order by InbredSet.Name""", (species_name))
groups[species_name] = list(Cursor.fetchall())
return groups
def get_types(groups):
"""Build types list"""
types = {}
for species, group_dict in groups.iteritems():
types[species] = {}
for group_name, _group_full_name in group_dict:
# make group an alias to shorten the code
types[species][group_name] = [("Phenotypes", "Phenotypes"), ("Genotypes", "Genotypes")]
types[species][group_name] += build_types(species, group_name)
return types
def build_types(species, group):
"""Fetches tissues
Gets the tissues with data for this species/group
(all types except phenotype/genotype are tissues)
"""
Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA')
from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species
where Species.Name = %s and Species.Id = InbredSet.SpeciesId and
InbredSet.Name = %s and
ProbeFreeze.TissueId = Tissue.Id and
ProbeFreeze.InbredSetId = InbredSet.Id and
ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
ProbeSetFreeze.public > %s
order by Tissue.Name""", (species, group, webqtlConfig.PUBLICTHRESH))
return Cursor.fetchall()
def get_datasets(types):
"""Build datasets list"""
datasets = {}
for species, group_dict in types.iteritems():
datasets[species] = {}
for group, type_list in group_dict.iteritems():
datasets[species][group] = {}
for type_name, _type_full_name in type_list:
datasets[species][group][type_name] = build_datasets(species, group, type_name)
return datasets
def build_datasets(species, group, type_name):
"""Gets dataset names from database"""
dataset_text = dataset_value = None
if type_name == "Phenotypes":
dataset_value = "%sPublish" % group
if group == 'MDP':
dataset_text = "Mouse Phenome Database"
else:
dataset_text = "%s Published Phenotypes" % group
elif type_name == "Genotypes":
dataset_value = "%sGeno" % group
dataset_text = "%s Genotypes" % group
if dataset_value:
return [(dataset_value, dataset_text)]
else:
Cursor.execute("""select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from
ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where
Species.Name = %s and Species.Id = InbredSet.SpeciesId and
InbredSet.Name = %s and
ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = %s
and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId =
InbredSet.Id and ProbeSetFreeze.public > %s order by
ProbeSetFreeze.CreateTime desc""", (
species, group, type_name, webqtlConfig.PUBLICTHRESH))
return Cursor.fetchall()
def main():
"""Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
species = get_species()
groups = get_groups(species)
types = get_types(groups)
datasets = get_datasets(types)
species.append(('All Species', 'All Species'))
groups['All Species'] = [('All Groups', 'All Groups')]
types['All Species'] = {}
types['All Species']['All Groups'] = [('Phenotypes', 'Phenotypes')]
datasets['All Species'] = {}
datasets['All Species']['All Groups'] = {}
datasets['All Species']['All Groups']['Phenotypes'] = [('All Phenotypes','All Phenotypes')]
data = dict(species=species,
groups=groups,
types=types,
datasets=datasets,
)
output_file = """../wqflask/static/new/javascript/dataset_menu_structure.json"""
with open(output_file, 'w') as fh:
json.dump(data, fh, indent=" ", sort_keys=True)
print("\nWrote file to:", output_file)
def _test_it():
"""Used for internal testing only"""
types = build_types("Mouse", "BXD")
print("build_types:", pf(types))
datasets = build_datasets("Mouse", "BXD", "Hippocampus")
print("build_datasets:", pf(datasets))
if __name__ == '__main__':
main()
|
