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"""Views handling ('classical') phenotypes."""
from functools import wraps
from requests.models import Response
from MySQLdb.cursors import DictCursor
from flask import (flash,
request,
url_for,
redirect,
Blueprint,
render_template,
current_app as app)
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 uploader.input_validation import (encode_errors,
decode_errors,
is_valid_representative_name)
from .models import (dataset_by_id,
phenotype_by_id,
phenotypes_count,
save_new_dataset,
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),
start_from=start_at,
count=count,
activelink="view-dataset")
@phenotypesbp.route(
"<int:species_id>/populations/<int:population_id>/phenotypes/datasets"
"/<int:dataset_id>/phenotype/<xref_id>",
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_phenotype(# pylint: disable=[unused-argument]
species: dict,
population: dict,
dataset: dict,
xref_id: int,
**kwargs
):
"""View an individual phenotype from the dataset."""
def __render__(privileges):
return render_template(
"phenotypes/view-phenotype.html",
species=species,
population=population,
dataset=dataset,
phenotype=phenotype_by_id(conn,
species["SpeciesId"],
population["Id"],
dataset["Id"],
xref_id),
privileges=(privileges
### For demo! Do not commit this part
+ ("group:resource:edit-resource",
"group:resource:delete-resource",)
### END: For demo! Do not commit this part
),
activelink="view-phenotype")
def __fail__(error):
if isinstance(error, Response) and error.json() == "No linked resource!":
return __render__(tuple())
return make_either_error_handler(
"There was an error fetching the roles and privileges.")(error)
with database_connection(app.config["SQL_URI"]) as conn:
return oauth2_post(
"/auth/resource/phenotypes/individual/linked-resource",
json={
"species_id": species["SpeciesId"],
"population_id": population["Id"],
"dataset_id": dataset["Id"],
"xref_id": xref_id
}
).then(
lambda resource: tuple(
privilege["privilege_id"] for role in resource["roles"]
for privilege in role["privileges"])
).then(__render__).either(__fail__, lambda resp: resp)
@phenotypesbp.route(
"<int:species_id>/populations/<int:population_id>/phenotypes/datasets/create",
methods=["GET", "POST"])
@require_login
@with_population(
species_redirect_uri="species.populations.phenotypes.index",
redirect_uri="species.populations.phenotypes.select_population")
def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument]
"""Create a new phenotype dataset."""
with (database_connection(app.config["SQL_URI"]) as conn,
conn.cursor(cursorclass=DictCursor) as cursor):
if request.method == "GET":
return render_template("phenotypes/create-dataset.html",
activelink="create-dataset",
species=species,
population=population,
**decode_errors(
request.args.get("error_values", "")))
form = request.form
_errors = tuple()
if not is_valid_representative_name(
(form.get("dataset-name") or "").strip()):
_errors = _errors + (("dataset-name", "Invalid dataset name."),)
if not bool((form.get("dataset-fullname") or "").strip()):
_errors = _errors + (("dataset-fullname",
"You must provide a value for 'Full Name'."),)
if bool(_errors) > 0:
return redirect(url_for(
"species.populations.phenotypes.create_dataset",
species_id=species["SpeciesId"],
population_id=population["Id"],
error_values=encode_errors(_errors, form)))
dataset_shortname = (
form["dataset-shortname"] or form["dataset-name"]).strip()
_pheno_dataset = save_new_dataset(
cursor,
population["Id"],
form["dataset-name"].strip(),
form["dataset-fullname"].strip(),
dataset_shortname)
return redirect(url_for("species.populations.phenotypes.list_datasets",
species_id=species["SpeciesId"],
population_id=population["Id"]))
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