diff options
Diffstat (limited to 'qc_app/upload/rqtl2.py')
| -rw-r--r-- | qc_app/upload/rqtl2.py | 65 |
1 files changed, 63 insertions, 2 deletions
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py index fc4e0e8..0b446ac 100644 --- a/qc_app/upload/rqtl2.py +++ b/qc_app/upload/rqtl2.py @@ -22,6 +22,7 @@ from qc_app.db_utils import with_db_connection, database_connection from qc_app.db.tissues import all_tissues, tissue_by_id from qc_app.db.platforms import platform_by_id, platforms_by_species +from qc_app.db.averaging import averaging_methods, averaging_method_by_id from qc_app.db import ( species_by_id, save_population, @@ -33,6 +34,7 @@ from qc_app.db.datasets import ( probeset_study_by_id, probeset_create_study, + probeset_create_dataset, probeset_datasets_by_study, probeset_studies_by_species_and_population) @@ -349,7 +351,7 @@ def select_probeset_dataset(species_id: int, population_id: int): 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") + flash("Invalid study selected!", "alert-error alert-rqtl2") return summary_page return summary_page @@ -398,6 +400,64 @@ def create_probeset_study(species_id: int, population_id: int): study=study) @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" + "/rqtl2-bundle/create-probeset-dataset"), + methods=["POST"]) +def create_probeset_dataset(species_id: int, population_id: int):#pylint: disable=[too-many-return-statements] + """Create a new 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") + if bool(error): + return error + + form = request.form + summary_page = redirect(url_for("upload.rqtl2.select_dataset_info", + species_id=species_id, + population_id=population_id), + code=307) + if not bool(form.get("averageid")): + flash("Averaging method not selected!", "alert-error alert-rqtl2") + return summary_page + if not bool(form.get("datasetname")): + flash("Dataset name not provided!", "alert-error alert-rqtl2") + return summary_page + if not bool(form.get("datasetfullname")): + flash("Dataset full name not provided!", "alert-error alert-rqtl2") + return summary_page + + study = probeset_study_by_id(conn, int(form["probe-study-id"])) + if not bool(study): + flash("Invalid ProbeSet study provided!", "alert-error alert-rqtl2") + return summary_page + + avgmethod = averaging_method_by_id(conn, int(form["averageid"])) + if not bool(avgmethod): + flash("Invalid averaging method provided!", "alert-error alert-rqtl2") + return summary_page + + dset = probeset_create_dataset(conn, + int(form["probe-study-id"]), + int(form["averageid"]), + form["datasetname"], + form["datasetfullname"], + form["datasetshortname"], + form["datasetpublic"] == "on", + form.get("datasetdatascale", "log2")) + return render_template( + "rqtl2/create-probe-dataset-success.html", + species=species_by_id(conn, species_id), + population=population_by_species_and_id( + conn, species_id, population_id), + rqtl2_bundle_file=request.form["rqtl2_bundle_file"], + geno_dataset=geno_dataset_by_id( + conn, + int(request.form["geno-dataset-id"])), + study=study, + avgmethod=avgmethod, + dataset=dset) + +@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): @@ -450,7 +510,8 @@ def select_dataset_info(species_id: int, population_id: int): geno_dataset=geno_dataset, probe_study=probeset_study, datasets=probeset_datasets_by_study( - conn, int(form["probe-study-id"]))) + conn, int(form["probe-study-id"])), + avgmethods=averaging_methods(conn)) return render_template("rqtl2/summary-info.html", species=species, |