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
|
"""Module to handle uploading of R/qtl2 bundles."""
from pathlib import Path
from zipfile import ZipFile, is_zipfile
from flask import (
flash,
request,
url_for,
redirect,
Blueprint,
render_template,
current_app as app)
from r_qtl import r_qtl2
from r_qtl.errors import InvalidFormat
from qc_app.files import save_file
from qc_app.dbinsert import species as all_species
from qc_app.db_utils import with_db_connection, database_connection
from qc_app.db import (
species_by_id,
save_population,
populations_by_species,
population_by_species_and_id)
rqtl2 = Blueprint("rqtl2", __name__)
@rqtl2.route("/", methods=["GET", "POST"])
@rqtl2.route("/select-species", methods=["POST"])
def select_species():
"""Select the species."""
if request.method == "GET":
return render_template("rqtl2/index.html", species=with_db_connection(all_species))
species_id = request.form.get("species_id")
species = with_db_connection(
lambda conn: species_by_id(conn, species_id))
if bool(species):
return redirect(url_for(
"upload.rqtl2.select_population", species_id=species_id))
flash("Invalid species or no species selected!", "alert-error error-rqtl2")
return redirect(url_for("upload.rqtl2.select_species"))
@rqtl2.route("/upload/species/<int:species_id>/select-population",
methods=["GET", "POST"])
def select_population(species_id: int):
"""Select/Create the population to organise data under."""
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
if not bool(species):
flash("Invalid species selected!", "alert-error error-rqtl2")
return redirect(url_for("upload.rqtl2.select_species"))
if request.method == "GET":
return render_template(
"rqtl2/select-population.html",
species=species,
populations=populations_by_species(conn, species_id))
population = population_by_species_and_id(
conn, species["SpeciesId"], request.form.get("inbredset_id"))
if not bool(population):
flash("Invalid Population!", "alert-error error-rqtl2")
return redirect(
url_for("upload.rqtl2.select_population", pgsrc="error"),
code=307)
return redirect(url_for("upload.rqtl2.upload_rqtl2_bundle",
species_id=species["SpeciesId"],
population_id=population["InbredSetId"]))
@rqtl2.route("/upload/species/<int:species_id>/create-population",
methods=["POST"])
def create_population(species_id: int):
"""Create a new population for the given species."""
population_page = redirect(url_for("upload.rqtl2.select_population"))
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
population_name = request.form.get("inbredset_name", "").strip()
population_fullname = request.form.get("inbredset_fullname", "").strip()
if not bool(species):
flash("Invalid species!", "alert-error error-rqtl2")
return redirect(url_for("upload.rqtl2.select_species"))
if not bool(population_name):
flash("Invalid Population Name!", "alert-error error-rqtl2")
return population_page
if not bool(population_fullname):
flash("Invalid Population Full Name!", "alert-error error-rqtl2")
return population_page
new_population = save_population(conn, {
"SpeciesId": species["SpeciesId"],
"Name": population_name,
"InbredSetName": population_fullname,
"FullName": population_fullname,
"Family": request.form.get("inbredset_family") or None,
"Description": request.form.get("description") or None
})
flash("Population created successfully.", "alert-success")
return redirect(
url_for("upload.rqtl2.upload_rqtl2_bundle",
population_id=new_population["population_id"],
pgsrc="create-population"),
code=307)
class __RequestError__(Exception): #pylint: disable=[invalid-name]
"""Internal class to avoid pylint's `too-many-return-statements` error."""
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
"/rqtl2-bundle"),
methods=["GET", "POST"])
def upload_rqtl2_bundle(species_id: int, population_id: int):
"""Allow upload of R/qtl2 bundle."""
this_page_with_errors = redirect(url_for("upload.rqtl2.upload_rqtl2_bundle",
species_id=species_id,
population_id=population_id,
pgsrc="error"),
code=307)
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
population = population_by_species_and_id(
conn, species["SpeciesId"], population_id)
if not bool(species):
flash("Invalid species!", "alert-error error-rqtl2")
return redirect(url_for("upload.rqtl2.select_species"))
if not bool(population):
flash("Invalid Population!", "alert-error error-rqtl2")
return redirect(
url_for("upload.rqtl2.select_population", pgsrc="error"),
code=307)
if request.method == "GET" or (
request.method == "POST"
and bool(request.args.get("pgsrc"))):
return render_template("rqtl2/upload-rqtl2-bundle.html",
species=species,
population=population)
if not bool(request.files.get("rqtl2_bundle")):
raise __RequestError__("No R/qtl2 zip bundle provided.")
the_file = save_file(
request.files["rqtl2_bundle"], Path(app.config["UPLOAD_FOLDER"]))
if not bool(the_file):
raise __RequestError__("Please provide a valid R/qtl2 zip bundle.")
if not is_zipfile(str(the_file)):
raise __RequestError__("Invalid file! Expected a zip file.")
try:
with ZipFile(str(the_file), "r") as zfile:
r_qtl2.validate_bundle(zfile)
return "WOULD PROCESS THE BUNDLE..."
except (InvalidFormat, __RequestError__) as exc:
flash("".join(exc.args), "alert-error alert-danger error-rqtl2")
return this_page_with_errors
|
