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| author | Frederick Muriuki Muriithi | 2024-01-17 05:02:34 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-01-17 05:39:09 +0300 |
| commit | 4e3f6e51b92d9c56f77452bd4b723323a526bc52 (patch) | |
| tree | c1c2e1ada710352a5f1deafe2f79261973f1d138 | |
| parent | 29e24855d0b223edfbf20bbe5799db7a9e0ad21e (diff) | |
| download | gn-uploader-4e3f6e51b92d9c56f77452bd4b723323a526bc52.tar.gz | |
Enable selecting from existing genotype datasets.
| -rw-r--r-- | qc_app/templates/rqtl2/select-geno-dataset.html | 2 | ||||
| -rw-r--r-- | qc_app/upload/rqtl2.py | 35 |
2 files changed, 34 insertions, 3 deletions
diff --git a/qc_app/templates/rqtl2/select-geno-dataset.html b/qc_app/templates/rqtl2/select-geno-dataset.html index 3487b6e..64f886e 100644 --- a/qc_app/templates/rqtl2/select-geno-dataset.html +++ b/qc_app/templates/rqtl2/select-geno-dataset.html @@ -33,7 +33,7 @@ <legend>Datasets</legend> <label for="select:geno-datasets">Dataset</label> <select id="select:geno-datasets" - name="geno-datasets" + name="geno-dataset-id" required="required" {%if datasets | length == 0%} disabled="disabled" diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py index 146c301..7db005c 100644 --- a/qc_app/upload/rqtl2.py +++ b/qc_app/upload/rqtl2.py @@ -189,6 +189,15 @@ def check_errors(conn, *args, **kwargs) -> Optional[Response]: pgsrc="error"), code=307) + if ("geno-dataset" in args and + not bool(request.form.get("geno-dataset-id"))): + flash("No genotype dataset was provided!", "alert-error alert-rqtl2") + return redirect(url_for("upload.rqtl2.select_geno_dataset", + 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>" @@ -208,7 +217,7 @@ def select_dataset_info(species_id: int, population_id: int): 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")): + if "geno" in cdata and not bool(form.get("geno-dataset-id")): return render_template( "rqtl2/select-geno-dataset.html", species=species_by_id(conn, species_id), @@ -225,7 +234,29 @@ def select_dataset_info(species_id: int, population_id: int): methods=["POST"]) def select_geno_dataset(species_id: int, population_id: int) -> Response: """Select from existing geno datasets.""" - return "IMPLEMENT THIS!!!" + with database_connection(app.config["SQL_URI"]) as conn: + error = check_errors( + conn, "species", "population", "rqtl2_bundle_file", "geno-dataset") + if bool(error): + return error + + geno_dset = geno_dataset_by_species_and_population( + conn, species_id, population_id) + if not bool(geno_dset): + flash("No genotype dataset was provided!", + "alert-error alert-rqtl2") + return redirect(url_for("upload.rqtl2.select_geno_dataset", + species_id=species_id, + population_id=population_id, + pgsrc="error"), + code=307) + + flash("Genotype accepted", "alert-success alert-rqtl2") + return redirect(url_for("upload.rqtl2.select_dataset_info", + species_id=species_id, + population_id=population_id, + pgsrc="upload.rqtl2.select_geno_dataset"), + code=307) @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" "/rqtl2-bundle/create-geno-dataset"), |