diff options
Diffstat (limited to 'uploader/genotypes')
| -rw-r--r-- | uploader/genotypes/models.py | 24 | ||||
| -rw-r--r-- | uploader/genotypes/views.py | 178 |
2 files changed, 90 insertions, 112 deletions
diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py index 4c3e634..34d2cfe 100644 --- a/uploader/genotypes/models.py +++ b/uploader/genotypes/models.py @@ -31,16 +31,28 @@ def genotype_markers( species_id: int, offset: int = 0, limit: Optional[int] = None -) -> tuple[dict, ...]: +) -> tuple[tuple[dict, ...], int]: """Retrieve markers from the database.""" - _query = "SELECT * FROM Geno WHERE SpeciesId=%s" - if bool(limit) and limit > 0:# type: ignore[operator] - _query = _query + f" LIMIT {limit} OFFSET {offset}" + _query_template = ( + "SELECT %%COLS%% FROM Geno AS gno " + "WHERE gno.SpeciesId=%s " + "%%LIMIT%%") with conn.cursor(cursorclass=DictCursor) as cursor: - cursor.execute(_query, (species_id,)) + cursor.execute( + _query_template.replace("%%LIMIT%%", "").replace( + "%%COLS%%", "COUNT(gno.Id) AS total_records"), + (species_id,)) + _total_records = cursor.fetchone()["total_records"] + cursor.execute( + _query_template.replace("%%COLS%%", "gno.*").replace( + "%%LIMIT%%", + (f"LIMIT {int(limit)} OFFSET {int(offset)}" + if bool(limit) and limit > 0 + else "")), + (species_id,)) debug_query(cursor, app.logger) - return tuple(dict(row) for row in cursor.fetchall()) + return tuple(dict(row) for row in cursor.fetchall()), _total_records def genotype_dataset( diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index 0433420..f27671c 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -1,23 +1,27 @@ """Views for the genotypes.""" +import logging + from MySQLdb.cursors import DictCursor +from pymonad.either import Left, Right, Either from gn_libs.mysqldb import database_connection from flask import (flash, request, - url_for, + jsonify, redirect, Blueprint, render_template, current_app as app) +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.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.population.models import population_by_species_and_id +from uploader.request_checks import with_species, with_dataset, with_population from .models import (genotype_markers, genotype_dataset, @@ -25,61 +29,17 @@ from .models import (genotype_markers, genotype_markers_count, genocode_by_population) +logger = logging.getLogger(__name__) 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") +@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.""" with database_connection(app.config["SQL_URI"]) as conn: @@ -97,34 +57,31 @@ def list_genotypes(species: dict, population: dict, **kwargs):# pylint: disable= @genotypesbp.route( - "/<int:species_id>/populations/<int:population_id>/genotypes/list-markers", + "/<int:species_id>/populations/<int:population_id>/genotypes/<int:dataset_id>/list-markers", methods=["GET"]) @require_login -@with_population(species_redirect_uri="species.populations.genotypes.index", - redirect_uri="species.populations.genotypes.select_population") -def list_markers( - species: dict, - population: dict, - **kwargs -):# pylint: disable=[unused-argument] - """List a species' genetic markers.""" +@with_species(redirect_uri="species.populations.genotypes.list_genotypes") +def list_markers(species: dict, **_kwargs): + """List the markers that exist for this species.""" + args = request.args + offset = int(args.get("start") or 0) 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, - population=population, - 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") + markers, total_records = genotype_markers( + conn, + species["SpeciesId"], + offset=offset, + limit=int(args.get("length") or 0)) + return jsonify({ + **({"draw": int(args.get("draw"))} + if bool(args.get("draw") or False) + else {}), + "recordsTotal": total_records, + "recordsFiltered": len(markers), + "markers": tuple({**marker, "index": idx} + for idx, marker in + enumerate(markers, start=offset+1)) + }) + @genotypesbp.route( "/<int:species_id>/populations/<int:population_id>/genotypes/datasets/" @@ -137,14 +94,14 @@ def view_dataset(species_id: int, population_id: int, dataset_id: int): 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")) + return redirect(url_for("species.list_species")) 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.populations.list_species_populations", species_id=species_id)) dataset = genotype_dataset(conn, species_id, population_id, dataset_id) @@ -167,25 +124,32 @@ def view_dataset(species_id: int, population_id: int, dataset_id: int): "create", methods=["GET", "POST"]) @require_login -@with_population(species_redirect_uri="species.populations.genotypes.index", - redirect_uri="species.populations.genotypes.select_population") +@with_population(species_redirect_uri="species.list_species", + redirect_uri="species.populations.list_species_populations") def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument] """Create a genotype dataset.""" + if request.method == "GET": + return render_template("genotypes/create-dataset.html", + species=species, + population=population, + activelink="create-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 __save_dataset__() -> Either: + form = request.form + try: + return Right(save_new_dataset( + cursor, + population["Id"], + form["geno-dataset-name"], + form["geno-dataset-fullname"], + form["geno-dataset-shortname"])) + except Exception: + msg = "Error adding new Genotype dataset to database." + logger.error(msg, exc_info=True) + return Left(Exception(msg)) def __success__(_success): flash("Successfully created genotype dataset.", "alert-success") @@ -194,18 +158,20 @@ def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable= 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" - } + return __save_dataset__().then( + lambda new_dataset: 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": new_dataset["Name"], + "dataset_fullname": new_dataset["FullName"], + "dataset_shortname": new_dataset["ShortName"], + "public": "on" + } + ) ).either( make_either_error_handler( "There was an error creating the genotype dataset."), |