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-rw-r--r--qc_app/upload/rqtl2.py132
1 files changed, 93 insertions, 39 deletions
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 6ddc83f..3411f98 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -25,7 +25,11 @@ from qc_app.db import (
populations_by_species,
population_by_species_and_id,)
from qc_app.db.datasets import (
- geno_dataset_by_id, geno_dataset_by_species_and_population)
+ geno_dataset_by_id,
+ geno_datasets_by_species_and_population,
+
+ probeset_datasets_by_study,
+ probeset_studies_by_species_and_population)
rqtl2 = Blueprint("rqtl2", __name__)
@@ -199,44 +203,16 @@ def check_errors(conn, *args, **kwargs):
pgsrc="error"),
code=307)
- return None
-
-@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
-
- species = species_by_id(conn, species_id)
- population = population_by_species_and_id(
- conn, species_id, population_id)
- 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-dataset-id")):
- return render_template(
- "rqtl2/select-geno-dataset.html",
- species=species,
- population=population,
- rqtl2_bundle_file=thefile.name,
- datasets=geno_dataset_by_species_and_population(
- conn, species_id, population_id))
-
- geno_dataset = geno_dataset_by_id(
- conn, int(form["geno-dataset-id"]))
+ if ("probe-study-id" in args and
+ not bool(request.form.get("probe-study-id"))):
+ flash("No probeset study was selected!", "alert-error alert-rqtl2")
+ return redirect(url_for("upload.rqtl2.select_probeset_study",
+ species_id=species_id,
+ population_id=population_id,
+ pgsrc="error"),
+ code=307)
- return render_template("rqtl2/summary-info.html",
- species=species,
- population=population,
- geno_dataset=geno_dataset)
+ return None
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
"/rqtl2-bundle/select-geno-dataset"),
@@ -249,7 +225,7 @@ def select_geno_dataset(species_id: int, population_id: int):
if bool(error):
return error
- geno_dset = geno_dataset_by_species_and_population(
+ geno_dset = geno_datasets_by_species_and_population(
conn, species_id, population_id)
if not bool(geno_dset):
flash("No genotype dataset was provided!",
@@ -321,3 +297,81 @@ def create_geno_dataset(species_id: int, population_id: int):
conn, species_id, population_id),
rqtl2_bundle_file=request.form["rqtl2_bundle_file"],
geno_dataset={**new_dataset, "id": cursor.lastrowid})
+
+@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+ "/rqtl2-bundle/select-probeset-study"),
+ methods=["POST"])
+def select_probeset_study(species_id: int, population_id: int):
+ """Select or create a probeset study."""
+ with database_connection(app.config["SQL_URI"]) as conn:
+ error = check_errors(
+ conn, "species", "population", "rqtl2_bundle_file", "geno-dataset",
+ "probe-study-id")
+ if bool(error):
+ return error
+
+ summary_page = redirect(url_for("upload.rqtl2.select_dataset_info",
+ species=species_by_id(conn, species_id),
+ population=population_by_species_and_id(
+ conn, species_id, population_id)),
+ code=307)
+ if not bool(probe_study_by_id(conn, int(request.form["probe-study-id"]))):
+ flash("Invalid study selected!", "alert-error alert-rqtl2")
+ return summary_page
+
+ return summary_page
+
+@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
+
+ species = species_by_id(conn, species_id)
+ population = population_by_species_and_id(
+ conn, species_id, population_id)
+ 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-dataset-id")):
+ return render_template(
+ "rqtl2/select-geno-dataset.html",
+ species=species,
+ population=population,
+ rqtl2_bundle_file=thefile.name,
+ datasets=geno_datasets_by_species_and_population(
+ conn, species_id, population_id))
+ geno_dataset = geno_dataset_by_id(conn, int(form["geno-dataset-id"]))
+
+ if "pheno" in cdata and not bool(form.get("probe-study-id")):
+ return render_template(
+ "rqtl2/select-probeset-study-id.html",
+ species=species,
+ population=population,
+ rqtl2_bundle_file=thefile.name,
+ geno_dataset=geno_dataset,
+ studies=probeset_studies_by_species_and_population(
+ conn, species_id, population_id))
+
+ if "pheno" in cdata and not bool(form.get("probe-dataset-id")):
+ return render_template(
+ "rqtl2/select-probeset-dataset.html",
+ species=species,
+ population=population,
+ rqtl2_bundle_file=thefile.name,
+ geno_dataset=geno_dataset,
+ datasets=probeset_datasets_by_study(
+ conn, int(form["probe-study-id"])))
+
+ return render_template("rqtl2/summary-info.html",
+ species=species,
+ population=population,
+ geno_dataset=geno_dataset)