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
|
"""The endpoints for the platforms"""
from MySQLdb.cursors import DictCursor
from flask import (
flash,
request,
url_for,
redirect,
Blueprint,
current_app as app)
from uploader.ui import make_template_renderer
from uploader.authorisation import require_login
from uploader.db_utils import database_connection
from uploader.species.models import all_species, species_by_id
from uploader.datautils import safe_int, order_by_family, enumerate_sequence
from .models import (save_new_platform,
platforms_by_species,
species_platforms_count,
platform_by_species_and_id)
platformsbp = Blueprint("platforms", __name__)
render_template = make_template_renderer("platforms")
@platformsbp.route("platforms", methods=["GET"])
@require_login
def index():
"""Entry-point to the platforms feature."""
with database_connection(app.config["SQL_URI"]) as conn:
if not bool(request.args.get("species_id")):
return render_template(
"platforms/index.html",
species=order_by_family(all_species(conn)),
activelink="platforms")
species = species_by_id(conn, request.args["species_id"])
if not bool(species):
flash("No species selected.", "alert-danger")
return redirect(url_for("species.platforms.index"))
return redirect(url_for("species.platforms.list_platforms",
species_id=species["SpeciesId"]))
@platformsbp.route("<int:species_id>/platforms", methods=["GET"])
@require_login
def list_platforms(species_id: int):
"""List all the available genetic sequencing platforms."""
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
if not bool(species):
flash("No species provided.", "alert-danger")
return redirect(url_for("species.platforms.index"))
start_from = max(safe_int(request.args.get("start_from") or 0), 0)
count = safe_int(request.args.get("count") or 20)
return render_template(
"platforms/list-platforms.html",
species=species,
platforms=enumerate_sequence(
platforms_by_species(conn,
species_id,
offset=start_from,
limit=count),
start=start_from+1),
start_from=start_from,
count=count,
total_platforms=species_platforms_count(conn, species_id),
activelink="list-platforms")
@platformsbp.route("<int:species_id>/platforms/create", methods=["GET", "POST"])
@require_login
def create_platform(species_id: int):
"""Create a new genetic sequencing platform."""
with (database_connection(app.config["SQL_URI"]) as conn,
conn.cursor(cursorclass=DictCursor) as cursor):
species = species_by_id(conn, species_id)
if not bool(species):
flash("No species provided.", "alert-danger")
return redirect(url_for("species.platforms.index"))
if request.method == "GET":
return render_template(
"platforms/create-platform.html",
species=species,
activelink="create-platform")
try:
form = request.form
new_platform = save_new_platform(
cursor,
species_id,
form["geo-platform"],
form["platform-name"],
form["platform-shortname"],
form["platform-title"],
form.get("go-tree-value") or None)
except KeyError as _kerr:
flash(f"Required value for field {_kerr.args[0]} was not provided.",
"alert-danger")
return redirect(url_for("species.platforms.create_platform",
species_id=species_id))
except AssertionError as _aerr:
flash(f"Platform with GeoPlatform value of '{form['geo-platform']}'"
f" already exists for species '{species['FullName']}'.",
"alert-danger")
return redirect(url_for("species.platforms.create_platform",
species_id=species_id))
flash("Platform created successfully", "alert-success")
return redirect(url_for("species.platforms.list_platforms",
species_id=species_id))
|
