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
|
"""Handle db interactions for platforms."""
from typing import Optional
import MySQLdb as mdb
from MySQLdb.cursors import Cursor, DictCursor
def platforms_by_species(
conn: mdb.Connection,
speciesid: int,
offset: int = 0,
limit: Optional[int] = None
) -> tuple[dict, ...]:
"""Retrieve platforms by the species"""
_query = ("SELECT * FROM GeneChip WHERE SpeciesId=%s "
"ORDER BY GeneChipName ASC")
if bool(limit) and limit > 0:# type: ignore[operator]
_query = f"{_query} LIMIT {limit} OFFSET {offset}"
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(_query, (speciesid,))
return tuple(dict(row) for row in cursor.fetchall())
def species_platforms_count(conn: mdb.Connection, species_id: int) -> int:
"""Get the number of platforms in the database for a particular species."""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
"SELECT COUNT(GeneChipName) AS count FROM GeneChip "
"WHERE SpeciesId=%s",
(species_id,))
return int(cursor.fetchone()["count"])
def platform_by_id(conn: mdb.Connection, platformid: int) -> Optional[dict]:
"""Retrieve a platform by its ID"""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute("SELECT * FROM GeneChip WHERE Id=%s",
(platformid,))
result = cursor.fetchone()
if bool(result):
return dict(result)
return None
def platform_by_species_and_id(
conn: mdb.Connection, species_id: int, platformid: int
) -> Optional[dict]:
"""Retrieve a platform by its species and ID"""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute("SELECT * FROM GeneChip WHERE SpeciesId=%s AND Id=%s",
(species_id, platformid))
result = cursor.fetchone()#pylint: disable=[duplicate-code]
if bool(result):
return dict(result)
return None
def save_new_platform(# pylint: disable=[too-many-arguments]
cursor: Cursor,
species_id: int,
geo_platform: str,
platform_name: str,
platform_shortname: str,
platform_title: str,
go_tree_value: Optional[str]
) -> dict:
"""Save a new platform to the database."""
params = {
"species_id": species_id,
"GeoPlatform": geo_platform,
"GeneChipName": platform_name,
"Name": platform_shortname,
"Title": platform_title,
"GO_tree_value": go_tree_value
}
cursor.execute("SELECT SpeciesId, GeoPlatform FROM GeneChip")
assert (species_id, geo_platform) not in (
(row["SpeciesId"], row["GeoPlatform"]) for row in cursor.fetchall())
cursor.execute(
"INSERT INTO "
"GeneChip(SpeciesId, GeneChipName, Name, GeoPlatform, Title, GO_tree_value) "
"VALUES("
"%(species_id)s, %(GeneChipName)s, %(Name)s, %(GeoPlatform)s, "
"%(Title)s, %(GO_tree_value)s"
")",
params)
new_id = cursor.lastrowid
cursor.execute("UPDATE GeneChip SET GeneChipId=%s WHERE Id=%s",
(new_id, new_id))
return {
**params,
"Id": new_id,
"GeneChipId": new_id
}
|
