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
|
"""Views for the genotypes."""
from MySQLdb.cursors import DictCursor
from flask import (flash,
request,
url_for,
redirect,
Blueprint,
render_template,
current_app as app)
from uploader.ui import make_template_renderer
from uploader.oauth2.client import oauth2_post
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.monadic_requests import make_either_error_handler
from uploader.request_checks import with_species, with_population
from uploader.datautils import safe_int, order_by_family, enumerate_sequence
from uploader.population.models import (populations_by_species,
population_by_species_and_id)
from .models import (genotype_markers,
genotype_dataset,
save_new_dataset,
genotype_markers_count,
genocode_by_population)
genotypesbp = Blueprint("genotypes", __name__)
render_template = make_template_renderer("genotypes")
@genotypesbp.route("populations/genotypes", methods=["GET"])
@require_login
def index():
"""Direct entry-point for genotypes."""
with database_connection(app.config["SQL_URI"]) as conn:
if not bool(request.args.get("species_id")):
return render_template("genotypes/index.html",
species=order_by_family(all_species(conn)),
activelink="genotypes")
species = species_by_id(conn, request.args.get("species_id"))
if not bool(species):
flash(f"Could not find species with ID '{request.args.get('species_id')}'!",
"alert-danger")
return redirect(url_for("species.populations.genotypes.index"))
return redirect(url_for("species.populations.genotypes.select_population",
species_id=species["SpeciesId"]))
@genotypesbp.route("/<int:species_id>/populations/genotypes/select-population",
methods=["GET"])
@require_login
@with_species(redirect_uri="species.populations.genotypes.index")
def select_population(species: dict, species_id: int):
"""Select the population under which the genotypes go."""
with database_connection(app.config["SQL_URI"]) as conn:
if not bool(request.args.get("population_id")):
return render_template("genotypes/select-population.html",
species=species,
populations=order_by_family(
populations_by_species(conn, species_id),
order_key="FamilyOrder"),
activelink="genotypes")
population = population_by_species_and_id(
conn, species_id, request.args.get("population_id"))
if not bool(population):
flash("Invalid population selected!", "alert-danger")
return redirect(url_for(
"species.populations.genotypes.select_population",
species_id=species_id))
return redirect(url_for("species.populations.genotypes.list_genotypes",
species_id=species_id,
population_id=population["Id"]))
@genotypesbp.route(
"/<int:species_id>/populations/<int:population_id>/genotypes",
methods=["GET"])
@require_login
@with_population(species_redirect_uri="species.populations.genotypes.index",
redirect_uri="species.populations.genotypes.select_population")
def list_genotypes(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument]
"""List genotype details for species and population."""
with database_connection(app.config["SQL_URI"]) as conn:
return render_template("genotypes/list-genotypes.html",
species=species,
population=population,
genocode=genocode_by_population(
conn, population["Id"]),
total_markers=genotype_markers_count(
conn, species["SpeciesId"]),
dataset=genotype_dataset(conn,
species["SpeciesId"],
population["Id"]),
activelink="list-genotypes")
@genotypesbp.route("/<int:species_id>/genotypes/list-markers", methods=["GET"])
@require_login
@with_species(redirect_uri="species.populations.genotypes.index")
def list_markers(species: dict, **kwargs):# pylint: disable=[unused-argument]
"""List a species' genetic markers."""
with database_connection(app.config["SQL_URI"]) as conn:
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("genotypes/list-markers.html",
species=species,
total_markers=genotype_markers_count(
conn, species["SpeciesId"]),
start_from=start_from,
count=count,
markers=enumerate_sequence(
genotype_markers(conn,
species["SpeciesId"],
offset=start_from,
limit=count),
start=start_from+1),
activelink="list-markers")
@genotypesbp.route(
"/<int:species_id>/populations/<int:population_id>/genotypes/datasets/"
"<int:dataset_id>/view",
methods=["GET"])
@require_login
def view_dataset(species_id: int, population_id: int, dataset_id: int):
"""View details regarding a specific dataset."""
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
if not bool(species):
flash("Invalid species provided!", "alert-danger")
return redirect(url_for("species.populations.genotypes.index"))
population = population_by_species_and_id(
conn, species_id, population_id)
if not bool(population):
flash("Invalid population selected!", "alert-danger")
return redirect(url_for(
"species.populations.genotypes.select_population",
species_id=species_id))
dataset = genotype_dataset(conn, species_id, population_id, dataset_id)
if not bool(dataset):
flash("Could not find such a dataset!", "alert-danger")
return redirect(url_for(
"species.populations.genotypes.list_genotypes",
species_id=species_id,
population_id=population_id))
return render_template("genotypes/view-dataset.html",
species=species,
population=population,
dataset=dataset,
activelink="view-dataset")
@genotypesbp.route(
"/<int:species_id>/populations/<int:population_id>/genotypes/datasets/"
"create",
methods=["GET", "POST"])
@require_login
@with_population(species_redirect_uri="species.populations.genotypes.index",
redirect_uri="species.populations.genotypes.select_population")
def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument]
"""Create a genotype dataset."""
with (database_connection(app.config["SQL_URI"]) as conn,
conn.cursor(cursorclass=DictCursor) as cursor):
if request.method == "GET":
return render_template("genotypes/create-dataset.html",
species=species,
population=population,
activelink="create-dataset")
form = request.form
new_dataset = save_new_dataset(
cursor,
population["Id"],
form["geno-dataset-name"],
form["geno-dataset-fullname"],
form["geno-dataset-shortname"])
def __success__(_success):
flash("Successfully created genotype dataset.", "alert-success")
return redirect(url_for(
"species.populations.genotypes.list_genotypes",
species_id=species["SpeciesId"],
population_id=population["Id"]))
return oauth2_post(
"auth/resource/genotypes/create",
json={
**dict(request.form),
"species_id": species["SpeciesId"],
"population_id": population["Id"],
"dataset_id": new_dataset["Id"],
"dataset_name": form["geno-dataset-name"],
"dataset_fullname": form["geno-dataset-fullname"],
"dataset_shortname": form["geno-dataset-shortname"],
"public": "on"
}
).either(
make_either_error_handler(
"There was an error creating the genotype dataset."),
__success__)
|
