diff options
Diffstat (limited to 'qc_app/upload/rqtl2.py')
| -rw-r--r-- | qc_app/upload/rqtl2.py | 44 |
1 files changed, 38 insertions, 6 deletions
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py index 0d80776..fc4e0e8 100644 --- a/qc_app/upload/rqtl2.py +++ b/qc_app/upload/rqtl2.py @@ -172,7 +172,7 @@ def upload_rqtl2_bundle(species_id: int, population_id: int): flash("".join(exc.args), "alert-error alert-rqtl2") return this_page_with_errors -def check_errors(conn, *args, **kwargs): +def check_errors(conn, *args, **kwargs):#pylint: disable=[too-many-return-statements] """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") @@ -208,14 +208,21 @@ def check_errors(conn, *args, **kwargs): pgsrc="error"), code=307) + summary_page = redirect(url_for("upload.rqtl2.select_dataset_info", + species_id=species_id, + population_id=population_id, + pgsrc="error"), + code=307) + 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 summary_page + + if ("probe-dataset-id" in args and + not bool(request.form.get("probe-dataset-id"))): + flash("No probeset dataset was selected!", "alert-error alert-rqtl2") + return summary_page return None @@ -326,6 +333,28 @@ def select_probeset_study(species_id: int, population_id: int): return summary_page @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" + "/rqtl2-bundle/select-probeset-dataset"), + methods=["POST"]) +def select_probeset_dataset(species_id: int, population_id: int): + """Select or create a probeset dataset.""" + with database_connection(app.config["SQL_URI"]) as conn: + error = check_errors( + conn, "species", "population", "rqtl2_bundle_file", "geno-dataset", + "probe-study-id", "probe-dataset-id") + if bool(error): + return error + + summary_page = redirect(url_for("upload.rqtl2.select_dataset_info", + species_id=species_id, + population_id=population_id), + code=307) + if not bool(probeset_study_by_id(conn, int(request.form["probe-study-id"]))): + flash("Invalid dataset selected!", "alert-error alert-rqtl2") + return summary_page + + return summary_page + +@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/create-probeset-study"), methods=["POST"]) def create_probeset_study(species_id: int, population_id: int): @@ -409,6 +438,8 @@ def select_dataset_info(species_id: int, population_id: int): conn, species_id, population_id), platforms=platforms_by_species(conn, species_id), tissues=all_tissues(conn)) + probeset_study = probeset_study_by_id( + conn, int(form["probe-study-id"])) if "pheno" in cdata and not bool(form.get("probe-dataset-id")): return render_template( @@ -417,6 +448,7 @@ def select_dataset_info(species_id: int, population_id: int): population=population, rqtl2_bundle_file=thefile.name, geno_dataset=geno_dataset, + probe_study=probeset_study, datasets=probeset_datasets_by_study( conn, int(form["probe-study-id"]))) |