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
|
"""Views handling ('classical') phenotypes."""
from functools import wraps
from flask import (flash,
request,
url_for,
redirect,
Blueprint,
render_template,
current_app as app)
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.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 (dataset_by_id,
phenotypes_count,
dataset_phenotypes,
datasets_by_population)
phenotypesbp = Blueprint("phenotypes", __name__)
@phenotypesbp.route("/phenotypes", methods=["GET"])
@require_login
def index():
"""Direct entry-point for phenotypes data handling."""
with database_connection(app.config["SQL_URI"]) as conn:
if not bool(request.args.get("species_id")):
return render_template("phenotypes/index.html",
species=order_by_family(all_species(conn)),
activelink="phenotypes")
species = species_by_id(conn, request.args.get("species_id"))
if not bool(species):
flash("No such species!", "alert-danger")
return redirect(url_for("species.populations.phenotypes.index"))
return redirect(url_for("species.populations.phenotypes.select_population",
species_id=species["SpeciesId"]))
@phenotypesbp.route("<int:species_id>/phenotypes/select-population",
methods=["GET"])
@require_login
@with_species(redirect_uri="species.populations.phenotypes.index")
def select_population(species: dict, **kwargs):# pylint: disable=[unused-argument]
"""Select the population for your phenotypes."""
with database_connection(app.config["SQL_URI"]) as conn:
if not bool(request.args.get("population_id")):
return render_template("phenotypes/select-population.html",
species=species,
populations=order_by_family(
populations_by_species(
conn, species["SpeciesId"]),
order_key="FamilyOrder"),
activelink="phenotypes")
population = population_by_species_and_id(
conn, species["SpeciesId"], int(request.args["population_id"]))
if not bool(population):
flash("No such population found!", "alert-danger")
return redirect(url_for(
"species.populations.phenotypes.select_population",
species_id=species["SpeciesId"]))
return redirect(url_for("species.populations.phenotypes.list_datasets",
species_id=species["SpeciesId"],
population_id=population["Id"]))
@phenotypesbp.route(
"<int:species_id>/populations/<int:population_id>/phenotypes/datasets",
methods=["GET"])
@require_login
@with_population(species_redirect_uri="species.populations.phenotypes.index",
redirect_uri="species.populations.phenotypes.select_population")
def list_datasets(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument]
"""List available phenotype datasets."""
with database_connection(app.config["SQL_URI"]) as conn:
return render_template("phenotypes/list-datasets.html",
species=species,
population=population,
datasets=datasets_by_population(
conn,
species["SpeciesId"],
population["Id"]),
activelink="list-datasets")
def with_dataset(
species_redirect_uri: str,
population_redirect_uri: str,
redirect_uri: str
):
"""Ensure the dataset actually exists."""
def __decorator__(func):
@wraps(func)
@with_population(species_redirect_uri, population_redirect_uri)
def __with_dataset__(**kwargs):
try:
_spcid = int(kwargs["species_id"])
_popid = int(kwargs["population_id"])
_dsetid = int(kwargs.get("dataset_id"))
select_dataset_uri = redirect(url_for(
redirect_uri, species_id=_spcid, population_id=_popid))
if not bool(_dsetid):
flash("You need to select a valid 'dataset_id' value.",
"alert-danger")
return select_dataset_uri
with database_connection(app.config["SQL_URI"]) as conn:
dataset = dataset_by_id(conn, _spcid, _popid, _dsetid)
if not bool(dataset):
flash("You must select a valid dataset.",
"alert-danger")
return select_dataset_uri
except ValueError as _verr:
app.logger.debug(
"Exception converting 'dataset_id' to integer: %s",
kwargs.get("dataset_id"),
exc_info=True)
flash("Expected 'dataset_id' value to be an integer."
"alert-danger")
return select_dataset_uri
return func(dataset=dataset, **kwargs)
return __with_dataset__
return __decorator__
@phenotypesbp.route(
"<int:species_id>/populations/<int:population_id>/phenotypes/datasets"
"/<int:dataset_id>/view",
methods=["GET"])
@require_login
@with_dataset(
species_redirect_uri="species.populations.phenotypes.index",
population_redirect_uri="species.populations.phenotypes.select_population",
redirect_uri="species.populations.phenotypes.list_datasets")
def view_dataset(# pylint: disable=[unused-argument]
species: dict, population: dict, dataset: dict, **kwargs):
"""View a specific dataset"""
with database_connection(app.config["SQL_URI"]) as conn:
dataset = dataset_by_id(
conn, species["SpeciesId"], population["Id"], dataset["Id"])
if not bool(dataset):
flash("Could not find such a phenotype dataset!", "alert-danger")
return redirect(url_for(
"species.populations.phenotypes.list_datasets",
species_id=species["SpeciesId"],
population_id=population["Id"]))
start_at = max(safe_int(request.args.get("start_at") or 0), 0)
count = int(request.args.get("count") or 20)
return render_template("phenotypes/view-dataset.html",
species=species,
population=population,
dataset=dataset,
phenotype_count=phenotypes_count(
conn, population["Id"], dataset["Id"]),
phenotypes=enumerate_sequence(
dataset_phenotypes(conn,
population["Id"],
dataset["Id"],
offset=start_at,
limit=count),
start=start_at+1),
activelink="view-dataset")
|
