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
|
import logging
import re
import warnings
from contextlib import contextmanager
from time import time
from psycopg2 import Error, ProgrammingError # pylint: disable=import-error
from psycopg2.pool import ThreadedConnectionPool # pylint: disable=import-error
from Orange.data import ContinuousVariable, DiscreteVariable, StringVariable, TimeVariable
from Orange.data.sql.backend.base import Backend, ToSql, BackendError
log = logging.getLogger(__name__)
EXTENSIONS = ('tsm_system_time', 'quantile')
class Psycopg2Backend(Backend):
"""Backend for accessing data stored in a Postgres database
"""
display_name = "PostgreSQL"
connection_pool = None
auto_create_extensions = False
def __init__(self, connection_params):
super().__init__(connection_params)
if self.connection_pool is None:
self._create_connection_pool()
self.missing_extension = []
if self.auto_create_extensions:
self._create_extensions()
def _create_connection_pool(self):
try:
self.connection_pool = ThreadedConnectionPool(
1, 16, **self.connection_params)
except Error as ex:
raise BackendError(str(ex)) from ex
def _create_extensions(self):
for ext in EXTENSIONS:
try:
query = "CREATE EXTENSION IF NOT EXISTS {}".format(ext)
with self.execute_sql_query(query):
pass
except BackendError:
warnings.warn("Database is missing extension {}".format(ext))
self.missing_extension.append(ext)
def create_sql_query(self, table_name, fields, filters=(),
group_by=None, order_by=None,
offset=None, limit=None,
use_time_sample=None):
sql = ["SELECT", ', '.join(fields),
"FROM", table_name]
if use_time_sample is not None:
sql.append("TABLESAMPLE system_time(%i)" % use_time_sample)
if filters:
sql.extend(["WHERE", " AND ".join(filters)])
if group_by is not None:
sql.extend(["GROUP BY", ", ".join(group_by)])
if order_by is not None:
sql.extend(["ORDER BY", ",".join(order_by)])
if offset is not None:
sql.extend(["OFFSET", str(offset)])
if limit is not None:
sql.extend(["LIMIT", str(limit)])
return " ".join(sql)
@contextmanager
def execute_sql_query(self, query, params=None):
connection = self.connection_pool.getconn()
cur = connection.cursor()
try:
utfquery = cur.mogrify(query, params).decode('utf-8')
log.debug("Executing: %s", utfquery)
t = time()
cur.execute(query, params)
yield cur
log.info("%.2f ms: %s", 1000 * (time() - t), utfquery)
except (Error, ProgrammingError) as ex:
raise BackendError(str(ex)) from ex
finally:
connection.commit()
self.connection_pool.putconn(connection)
def quote_identifier(self, name):
return '"%s"' % name
def unquote_identifier(self, quoted_name):
if quoted_name.startswith('"'):
return quoted_name[1:len(quoted_name) - 1]
else:
return quoted_name
def list_tables_query(self, schema=None):
if schema:
schema_clause = "AND n.nspname = '{}'".format(schema)
else:
schema_clause = "AND pg_catalog.pg_table_is_visible(c.oid)"
return """SELECT n.nspname as "Schema",
c.relname AS "Name"
FROM pg_catalog.pg_class c
LEFT JOIN pg_catalog.pg_namespace n ON n.oid = c.relnamespace
WHERE c.relkind IN ('r','v','m','S','f','')
AND n.nspname <> 'pg_catalog'
AND n.nspname <> 'information_schema'
AND n.nspname !~ '^pg_toast'
{}
AND NOT c.relname LIKE '\\_\\_%'
ORDER BY 1,2;""".format(schema_clause)
def n_tables_query(self, schema=None) -> str:
query = "SELECT COUNT(*) FROM information_schema.tables"
if schema:
query += f" WHERE table_schema = '{schema}'"
return query
def create_variable(self, field_name, field_metadata,
type_hints, inspect_table=None):
if field_name in type_hints:
var = type_hints[field_name]
else:
var = self._guess_variable(field_name, field_metadata,
inspect_table)
field_name_q = self.quote_identifier(field_name)
if var.is_continuous:
if isinstance(var, TimeVariable):
var.to_sql = ToSql("extract(epoch from {})"
.format(field_name_q))
else:
var.to_sql = ToSql("({})::double precision"
.format(field_name_q))
else: # discrete or string
var.to_sql = ToSql("({})::text"
.format(field_name_q))
return var
def _guess_variable(self, field_name, field_metadata, inspect_table):
type_code = field_metadata[0]
FLOATISH_TYPES = (700, 701, 1700) # real, float8, numeric
INT_TYPES = (20, 21, 23) # bigint, int, smallint
CHAR_TYPES = (25, 1042, 1043,) # text, char, varchar
BOOLEAN_TYPES = (16,) # bool
DATE_TYPES = (1082, 1114, 1184, ) # date, timestamp, timestamptz
# time, timestamp, timestamptz, timetz
TIME_TYPES = (1083, 1114, 1184, 1266,)
if type_code in FLOATISH_TYPES:
return ContinuousVariable.make(field_name)
if type_code in TIME_TYPES + DATE_TYPES:
tv = TimeVariable.make(field_name)
tv.have_date |= type_code in DATE_TYPES
tv.have_time |= type_code in TIME_TYPES
return tv
if type_code in INT_TYPES: # bigint, int, smallint
if inspect_table:
values = self.get_distinct_values(field_name, inspect_table)
if values:
return DiscreteVariable.make(field_name, values)
return ContinuousVariable.make(field_name)
if type_code in BOOLEAN_TYPES:
return DiscreteVariable.make(field_name, ['false', 'true'])
if type_code in CHAR_TYPES:
if inspect_table:
values = self.get_distinct_values(field_name, inspect_table)
# remove trailing spaces
values = [v.rstrip() for v in values]
if values:
return DiscreteVariable.make(field_name, values)
return StringVariable.make(field_name)
def count_approx(self, query):
sql = "EXPLAIN " + query
with self.execute_sql_query(sql) as cur:
s = ''.join(row[0] for row in cur.fetchall())
return int(re.findall(r'rows=(\d*)', s)[0])
def distinct_values_query(self, field_name: str, table_name: str) -> str:
fields = [self.quote_identifier(field_name)]
return self.create_sql_query(
table_name, fields, group_by=fields, order_by=fields, limit=21
)
def __getstate__(self):
# Drop connection_pool from state as it cannot be pickled
state = dict(self.__dict__)
state.pop('connection_pool', None)
return state
def __setstate__(self, state):
# Create a new connection pool if none exists
self.__dict__.update(state)
if self.connection_pool is None:
self._create_connection_pool()
|
