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
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
|
from __future__ import print_function, division, absolute_import
"""
Results will be returned for each of several trait types: mRNA assays, phenotypes, genotypes, and
(maybe later) genes
For each trait type, the results for each species should be given; for example, have a "Mouse" tab
with the mouse traits in a table inside it
This table will then list each trait, its dataset, and several columns determined by its trait type
(phenotype, genotype, etc)
"""
import sys
sys.path.append("../../..")
import simplejson as json
import sqlalchemy as sa
from sqlalchemy.dialects import mysql
from sqlalchemy.orm import scoped_session, sessionmaker, relationship, backref
from sqlalchemy.orm.exc import NoResultFound
from sqlalchemy.ext.declarative import declarative_base
from BeautifulSoup import UnicodeDammit
import zach_settings as settings
Engine = sa.create_engine(settings.SQLALCHEMY_DATABASE_URI,
#encoding='utf-8',
#client_encoding='utf-8',
#echo="debug",
)
Session = scoped_session(sessionmaker(bind=Engine)) #, extension=VersionedListener()))
#Xsession = Session()
Base = declarative_base(bind=Engine)
Metadata = sa.MetaData()
Metadata.bind = Engine
class ProbeSet(Base):
__tablename__ = 'ProbeSetXRef'
__table_args__ = {'autoload': True}
QuickSearch = sa.Table("QuickSearch", Metadata,
sa.Column('table_name', sa.String(15),
primary_key=True, nullable=False, autoincrement=False), # table that item is inserted from
sa.Column('the_key', sa.String(30),
primary_key=True, nullable=False, autoincrement=False), # key in database table
sa.Column('terms', sa.Text), # terms to compare search string with
#sa.Column('species', sa.Text),
sa.Column('result_fields', sa.Text) # json
)
QuickSearch.drop(Engine, checkfirst=True)
Metadata.create_all(Engine)
#class QuickSearch(Base):
# table_name = Column(String)
# the_key = Column(String)
# terms = Column(String)
#
# def __init__(self, table_name, the_key, terms, category, species, result_fields):
# self.table_name = table_name
# self.the_key = the_key
# self.terms = terms
# self.species = species
# self.category = category
# self.result_fields = json.dumps(sort_keys=True)
def get_unique_terms(trait_type, trait_id):
#if not args:
# return None
if trait_type="ProbeSet":
results = Session.query(
"name",
"symbol",
"description",
"alias"
).from_statement(
"SELECT ProbeSet.Name as name, "
"ProbeSet.Symbol as symbol, "
"ProbeSet.description as description, "
"ProbeSet.alias as alias "
"FROM ProbeSet"
"WHERE ProbeSet.Id = :probeset_id ").params(probeset_id=trait_id).all()
unique = set()
for item in results[0]:
#print("locals:", locals())
if not item:
continue
for token in item.split():
if token.startswith(('(','[')):
token = token[1:]
if token.endswith((')', ']')):
token = token[:-1]
if token.endswith(';'):
token = token[:-1]
if len(token) > 2:
try:
# This hopefully ensures that the token is utf-8
token = token.encode('utf-8')
print(" ->", token)
except UnicodeDecodeError:
print("\n-- UDE \n")
# Can't get it into utf-8, we won't use it
continue
unique.add(token)
print("\nUnique terms are: {}\n".format(unique))
return " ".join(unique)
def main():
conn = Engine.connect()
counter = 0
for ps in page_query(Session.query(ProbeSet)): #all()
values = {}
values['table_name'] = "ProbeSetXRef"
values['the_key'] = json.dumps([ps.ProbeSetId, ps.ProbeSetFreezeId])
values['terms'] = get_unique_terms("ProbeSet", ps.ProbeSetId)
print("terms is:", values['terms'])
#values['species'] = get_species("ProbeSet", ps.Id)
values['result_fields'] = get_result_fields("ProbeSet", ps.ProbeSetId, ps.ProbeSetFreezeId)
ins = QuickSearch.insert().values(**values)
conn.execute(ins)
counter += 1
print("Done:", counter)
def get_species(trait_type, trait_id):
if trait_type == "ProbeSet":
print("Before species query")
results = Session.query("Name").from_statement("SELECT Species.Name "
"FROM ProbeSetXRef, "
"ProbeSetFreeze, "
"ProbeFreeze, "
"InbredSet, "
"Species "
"WHERE ProbeSetXRef.ProbeSetId =:probeset_id and "
"ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and "
"ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and "
"ProbeFreeze.InbredSetId = InbredSet.Id and "
"InbredSet.SpeciesId = Species.Id").params(probeset_id=trait_id).all()
print("After query")
assert len(set([result.Name for result in results])) == 1, "Multiple names?"
print("species is:", results[0].Name)
return results[0].Name
def get_result_fields(trait_type, *args):
if trait_type == "ProbeSet":
print("qs1")
results = Session.query(
"name",
"symbol",
"description",
"chr", "mb",
"genbank_id",
"gene_id",
"chip_id",
"chip_name"
).from_statement(
"SELECT ProbeSet.Name as name, "
"ProbeSet.Symbol as symbol, "
"ProbeSet.description as description, "
"ProbeSet.Chr as chr, "
"ProbeSet.Mb as mb, "
"ProbeSet.GenbankId as genbank_id, "
"ProbeSet.GeneId as gene_id, "
"ProbeSet.ChipId as chip_id, "
"GeneChip.Name as chip_name "
"FROM ProbeSet, GeneChip "
"WHERE ProbeSet.ChipId = GeneChip.Id and "
"ProbeSet.Id = :probeset_id ").params(probeset_id=*args[0], dataset_id=*args[1]).all()
print("qs2")
for result in results:
print(result)
assert len(set(result for result in results)) == 1, "Different results"
print("results are:", results)
result = results[0]
result = row2dict(result)
try:
json_results = json.dumps(result, sort_keys=True)
except UnicodeDecodeError:
print("\n\nTrying to massage unicode\n\n")
#print("result.__dict__ is [{}]: {}".format(type(result.__dict__), result.__dict__))
#resultd = dict(**result.__dict__)
for key, value in result.iteritems():
print(" key is:", key)
print(" value is:", value)
if isinstance(value, basestring):
result[key] = value.decode('utf-8', errors='ignore')
json_results = json.dumps(result, sort_keys=True)
#print("json is: ", json_results)
return json_results
def row2dict(row):
return dict(zip(row.keys(), row)) # http://stackoverflow.com/a/2848519/1175849
#"""http://stackoverflow.com/a/1960546/1175849"""
#d = {}
#for column in row.__table__.columns:
# d[column.name] = getattr(row, column.name)
#
#return d
def page_query(q):
"""http://stackoverflow.com/a/1217947/1175849"""
offset = 0
while True:
r = False
for elem in q.limit(1000).offset(offset):
r = True
yield elem
offset += 1000
if not r:
break
if __name__ == "__main__":
main()
|
