diff options
Diffstat (limited to 'uploader/genotypes/views.py')
| -rw-r--r-- | uploader/genotypes/views.py | 66 |
1 files changed, 48 insertions, 18 deletions
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index f27671c..c18c330 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -4,11 +4,13 @@ import logging from MySQLdb.cursors import DictCursor from pymonad.either import Left, Right, Either from gn_libs.mysqldb import database_connection +from werkzeug.exceptions import UnsupportedMediaType from flask import (flash, request, jsonify, redirect, Blueprint, + make_response, render_template, current_app as app) @@ -16,17 +18,16 @@ from uploader.flask_extensions import url_for from uploader.ui import make_template_renderer from uploader.oauth2.client import oauth2_post from uploader.authorisation import require_login -from uploader.route_utils import generic_select_population -from uploader.datautils import safe_int, enumerate_sequence -from uploader.species.models import all_species, species_by_id +from uploader.species.models import species_by_id from uploader.monadic_requests import make_either_error_handler from uploader.population.models import population_by_species_and_id -from uploader.request_checks import with_species, with_dataset, with_population +from uploader.request_checks import with_population + from .models import (genotype_markers, + genotype_records, genotype_dataset, save_new_dataset, - genotype_markers_count, genocode_by_population) logger = logging.getLogger(__name__) @@ -40,20 +41,49 @@ render_template = make_template_renderer("genotypes") @require_login @with_population(species_redirect_uri="species.list_species", redirect_uri="species.populations.list_species_populations") -def list_genotypes(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument] - """List genotype details for species and population.""" +def index(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument] + """Entry-point to the genotypes management section.""" 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") + offset = int(request.args.get("start", "0")) + number_of_records = int(request.args.get("count", "10")) + _markers, _total_markers, = genotype_markers( + conn, species["SpeciesId"], population["Id"]) + _genotype_records, _count = genotype_records( + conn, + species["SpeciesId"], + population["Id"], + offset, + number_of_records) + _genotype_records = tuple( + {**_record, "index": _idx} + for _idx, _record + in enumerate(_genotype_records, start=offset+1)) + + ## Order these correctly + _samples = tuple(_genotype_records[0]["data"].keys()) + + if "application/json" in request.headers["Accept"]: + return make_response( + jsonify({ + "genotype_records": _genotype_records, + "total_genotype_records": _count, + "fetched_genotype_records": len(_genotype_records), + "sample_order": _samples + }), 200) + + if "text/html" in request.headers["Accept"]: + return render_template( + "genotypes/index.html", + species=species, + population=population, + genocode=genocode_by_population(conn, population["Id"]), + dataset=genotype_dataset( + conn, species["SpeciesId"], population["Id"]), + genotype_records=_genotype_records, + samples=_samples, + activelink="list-genotypes") + + raise UnsupportedMediaType("This endpoint can only server HTML or JSON") @genotypesbp.route( |