diff options
Diffstat (limited to 'uploader/genotypes')
| -rw-r--r-- | uploader/genotypes/models.py | 15 | ||||
| -rw-r--r-- | uploader/genotypes/views.py | 25 |
2 files changed, 34 insertions, 6 deletions
diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py index 1e09cd3..41270da 100644 --- a/uploader/genotypes/models.py +++ b/uploader/genotypes/models.py @@ -1,14 +1,17 @@ """Functions for handling genotypes.""" +import logging from typing import Optional from functools import reduce from datetime import datetime import MySQLdb as mdb from MySQLdb.cursors import Cursor, DictCursor -from flask import current_app as app from gn_libs.mysqldb import debug_query +logger = logging.getLogger(__name__) + + def genocode_by_population( conn: mdb.Connection, population_id: int) -> tuple[dict, ...]: """Get the allele/genotype codes.""" @@ -62,13 +65,13 @@ def genotype_markers( (species_id, population_id)) _total_records = cursor.fetchone()["total_records"] cursor.execute( - _query_template.replace("%%COLS%%", "gno.*").replace( + _query_template.replace("%%COLS%%", "gno.*, gxr.cM").replace( "%%LIMIT%%", (f"LIMIT {int(limit)} OFFSET {int(offset)}" if bool(limit) and limit >= 0 else "")), (species_id, population_id)) - debug_query(cursor, app.logger) + debug_query(cursor, logger) _records = tuple(dict(row) for row in cursor.fetchall()) return _records, _total_records @@ -107,11 +110,15 @@ def genotype_records( with conn.cursor(cursorclass=DictCursor) as cursor: _markers, _num_records = genotype_markers( conn, species_id, population_id, offset, limit) + if len(_markers) == 0: + return (tuple(), 0) + _genoids = tuple(_marker["Id"] for _marker in _markers) cursor.execute( _query_template.replace( "%%PARAMS_STR%%", ",".join(["%s"] * len(_genoids))), _genoids) + debug_query(cursor, logger) _records: dict[str, dict] = reduce( __organise_geno_records__, cursor.fetchall(), {}) return ( @@ -146,7 +153,7 @@ def genotype_dataset( with conn.cursor(cursorclass=DictCursor) as cursor: cursor.execute(_query, _params) - debug_query(cursor, app.logger) + debug_query(cursor, logger) result = cursor.fetchone() if bool(result): return dict(result) diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index 8c0795d..648b38e 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -22,7 +22,7 @@ from uploader.authorisation import require_login 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_population +from uploader.request_checks import with_dataset, with_population from .models import (genotype_markers, @@ -62,7 +62,8 @@ def index(species: dict, population: dict, **kwargs):# pylint: disable=[unused-a in enumerate(_genotype_records, start=offset+1)) ## Order these correctly - _samples = tuple(_genotype_records[0]["data"].keys()) + _samples = (tuple() if len(_genotype_records) == 0 + else tuple(_genotype_records[0]["data"].keys())) if "application/json" in request.headers["Accept"]: return make_response( @@ -211,3 +212,23 @@ def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable= make_either_error_handler( "There was an error creating the genotype dataset."), __success__) + + +@genotypesbp.route( + "/<int:species_id>/populations/<int:population_id>/genotypes/datasets/" + "<int:dataset_id>/add-records", + methods=["GET", "POST"]) +@require_login +@with_population(species_redirect_uri="species.list_species", + redirect_uri="species.populations.list_species_populations") +@with_dataset(species_redirect_uri="species.list_species", + population_redirect_uri="species.populations.list_species_populations", + redirect_uri="species.populations.genotypes.index", + dataset_by_id=genotype_dataset) +def add_genotype_records(species: dict, population: dict, dataset: dict, **kwargs): + """Add new Genotype records to the dataset.""" + return render_template("genotypes/add-genotypes-records-csv.html", + species=species, + population=population, + dataset=dataset, + activelink="add-genotypes-records") |