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-rw-r--r--qc_app/upload/rqtl2.py73
1 files changed, 71 insertions, 2 deletions
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 0eca6ae..e020d5a 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -1,5 +1,6 @@
"""Module to handle uploading of R/qtl2 bundles."""
from pathlib import Path
+from typing import Optional
from zipfile import ZipFile, is_zipfile
from flask import (
@@ -7,6 +8,7 @@ from flask import (
request,
url_for,
redirect,
+ Response,
Blueprint,
render_template,
current_app as app)
@@ -14,14 +16,15 @@ from flask import (
from r_qtl import r_qtl2
from r_qtl.errors import InvalidFormat
-from qc_app.files import save_file
+from qc_app.files import save_file, fullpath
from qc_app.dbinsert import species as all_species
from qc_app.db_utils import with_db_connection, database_connection
from qc_app.db import (
species_by_id,
save_population,
populations_by_species,
- population_by_species_and_id)
+ population_by_species_and_id,
+ geno_dataset_by_species_and_population)
rqtl2 = Blueprint("rqtl2", __name__)
@@ -158,3 +161,69 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
except (InvalidFormat, __RequestError__) as exc:
flash("".join(exc.args), "alert-error alert-danger error-rqtl2")
return this_page_with_errors
+
+def check_errors(conn, *args, **kwargs) -> Optional[Response]:
+ """Check for select errors in the forms and return a page to redirect to."""
+ species_id = kwargs.get("species_id") or request.form.get("species_id")
+ population_id = (kwargs.get("population_id")
+ or request.form.get("population_id"))
+ species = species_by_id(conn, species_id)
+ population = population_by_species_and_id(conn, species_id, population_id)
+
+ if "species" in args and not bool(species):
+ flash("Invalid species!", "alert-error error-rqtl2")
+ return redirect(url_for("upload.rqtl2.select_species"))
+
+ if "population" in args and not bool(population):
+ flash("Invalid Population!", "alert-error error-rqtl2")
+ return redirect(
+ url_for("upload.rqtl2.select_population", pgsrc="error"),
+ code=307)
+
+ if ("rqtl2_bundle_file" in args
+ and not bool(request.form.get("rqtl2_bundle_file"))):
+ flash("There is no file to process.",
+ "alert-error alert-danger error-rqtl2")
+ return redirect(url_for("upload.rqtl2.upload_rqtl2_bundle",
+ species_id=species_id,
+ population_id=population_id,
+ pgsrc="error"),
+ code=307)
+
+ return False
+
+@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+ "/rqtl2-bundle/dataset-info"),
+ methods=["POST"])
+def select_dataset_info(species_id: int, population_id: int):
+ """
+ If `geno` files exist in the R/qtl2 bundle, prompt user to provide the
+ dataset the genotypes belong to.
+ """
+ form = request.form
+ with database_connection(app.config["SQL_URI"]) as conn:
+ error_page = check_errors(conn, "species", "population", "rqtl2_bundle_file")
+ if bool(error_page):
+ return error_page
+
+ thefile = fullpath(form["rqtl2_bundle_file"])
+ with ZipFile(str(thefile), "r") as zfile:
+ cdata = r_qtl2.control_data(zfile)
+ if "geno" in cdata and not bool(form.get("geno_datasetid")):
+ return render_template(
+ "rqtl2/select-geno-dataset.html",
+ species=species_by_id(conn, species_id),
+ population=population_by_species_and_id(
+ conn, species_id, population_id),
+ rqtl2_bundle_file=thefile.name,
+ datasets=geno_dataset_by_species_and_population(
+ conn, species_id, population_id))
+
+ return "All data points collected. Should proceed to launching the job."
+
+@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+ "/rqtl2-bundle/select-geno-dataset"),
+ methods=["POST"])
+def select_geno_dataset(species_id: int, population_id: int) -> Response:
+ """Select from existing geno datasets."""
+ return "IMPLEMENT THIS!!!"