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
|
"""Database functions for species."""
from typing import Optional
import MySQLdb as mdb
from MySQLdb.cursors import DictCursor
def all_species(conn: mdb.Connection) -> tuple:
"Retrieve the species from the database."
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
"SELECT Id AS SpeciesId, SpeciesName, LOWER(Name) AS Name, "
"MenuName, FullName, TaxonomyId FROM Species")
return tuple(cursor.fetchall())
return tuple()
def species_by_id(conn: mdb.Connection, speciesid) -> dict:
"Retrieve the species from the database by id."
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
"SELECT Id AS SpeciesId, SpeciesName, LOWER(Name) AS Name, "
"MenuName, FullName, TaxonomyId, Family, FamilyOrderId, OrderId "
"FROM Species WHERE SpeciesId=%s",
(speciesid,))
return cursor.fetchone()
def save_species(conn: mdb.Connection,
common_name: str,
scientific_name: str,
taxon_id: Optional[str] = None) -> int:
"""
Save a new species to the database.
Parameters
----------
conn: A connection to the MariaDB database.
taxon_id: The taxonomy identifier for the new species.
common_name: The species' common name.
scientific_name; The species' scientific name.
"""
genus, species = scientific_name.split(" ")
species = {
"common_name": common_name,
"common_name_lower": common_name.lower(),
"menu_name": f"{common_name} ({genus[0]}. {species.lower()})",
"scientific_name": scientific_name,
"taxon_id": taxon_id
}
with conn.cursor() as cursor:
cursor.execute(
"INSERT INTO Species("
"SpeciesName, Name, MenuName, FullName, TaxonomyId"
") VALUES ("
"%(common_name)s, %(common_name_lower)s, %(menu_name)s, "
"%(scientific_name)s, %(taxon_id)s"
")",
species)
species_id = cursor.lastrowid
cursor.execute("UPDATE Species SET SpeciesId=%s WHERE Id=%s",
(species_id, species_id))
return {
**species,
"species_id": species_id
}
|
