diff options
Diffstat (limited to 'qc_app')
| -rw-r--r-- | qc_app/templates/rqtl2/select-geno-dataset.html | 4 | ||||
| -rw-r--r-- | qc_app/upload/rqtl2.py | 62 |
2 files changed, 32 insertions, 34 deletions
diff --git a/qc_app/templates/rqtl2/select-geno-dataset.html b/qc_app/templates/rqtl2/select-geno-dataset.html index 069ae98..438cb3f 100644 --- a/qc_app/templates/rqtl2/select-geno-dataset.html +++ b/qc_app/templates/rqtl2/select-geno-dataset.html @@ -27,7 +27,7 @@ <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> - {{flash_messages("error-rqtl2")}} + {{flash_messages("error-rqtl2-select-geno-dataset")}} <fieldset> <legend>Datasets</legend> @@ -72,7 +72,7 @@ <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" /> - {{flash_messages("error-rqtl2")}} + {{flash_messages("error-rqtl2-create-geno-dataset")}} <fieldset> <label for="txt:dataset-name">Name</label> diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py index 810e031..f36a3a6 100644 --- a/qc_app/upload/rqtl2.py +++ b/qc_app/upload/rqtl2.py @@ -60,7 +60,7 @@ def select_species(): if bool(species): return redirect(url_for( "upload.rqtl2.select_population", species_id=species_id)) - flash("Invalid species or no species selected!", "alert-error alert-rqtl2") + flash("Invalid species or no species selected!", "alert-error error-rqtl2") return redirect(url_for("upload.rqtl2.select_species")) @rqtl2.route("/upload/species/<int:species_id>/select-population", @@ -70,7 +70,7 @@ def select_population(species_id: int): with database_connection(app.config["SQL_URI"]) as conn: species = species_by_id(conn, species_id) if not bool(species): - flash("Invalid species selected!", "alert-error alert-rqtl2") + flash("Invalid species selected!", "alert-error error-rqtl2") return redirect(url_for("upload.rqtl2.select_species")) if request.method == "GET": @@ -82,7 +82,7 @@ def select_population(species_id: int): population = population_by_species_and_id( conn, species["SpeciesId"], request.form.get("inbredset_id")) if not bool(population): - flash("Invalid Population!", "alert-error alert-rqtl2") + flash("Invalid Population!", "alert-error error-rqtl2") return redirect( url_for("upload.rqtl2.select_population", pgsrc="error"), code=307) @@ -102,13 +102,13 @@ def create_population(species_id: int): population_name = request.form.get("inbredset_name", "").strip() population_fullname = request.form.get("inbredset_fullname", "").strip() if not bool(species): - flash("Invalid species!", "alert-error alert-rqtl2") + flash("Invalid species!", "alert-error error-rqtl2") return redirect(url_for("upload.rqtl2.select_species")) if not bool(population_name): - flash("Invalid Population Name!", "alert-error alert-rqtl2") + flash("Invalid Population Name!", "alert-error error-rqtl2") return population_page if not bool(population_fullname): - flash("Invalid Population Full Name!", "alert-error alert-rqtl2") + flash("Invalid Population Full Name!", "alert-error error-rqtl2") return population_page new_population = save_population(conn, { "SpeciesId": species["SpeciesId"], @@ -146,10 +146,10 @@ def upload_rqtl2_bundle(species_id: int, population_id: int): population = population_by_species_and_id( conn, species["SpeciesId"], population_id) if not bool(species): - flash("Invalid species!", "alert-error alert-rqtl2") + flash("Invalid species!", "alert-error error-rqtl2") return redirect(url_for("upload.rqtl2.select_species")) if not bool(population): - flash("Invalid Population!", "alert-error alert-rqtl2") + flash("Invalid Population!", "alert-error error-rqtl2") return redirect( url_for("upload.rqtl2.select_population", pgsrc="error"), code=307) @@ -180,7 +180,7 @@ def upload_rqtl2_bundle(species_id: int, population_id: int): population=population, rqtl2_bundle_file=the_file.name)#type: ignore[union-attr] except (InvalidFormat, __RequestError__) as exc: - flash("".join(exc.args), "alert-error alert-rqtl2") + flash("".join(exc.args), "alert-error error-rqtl2") return this_page_with_errors def check_errors(conn, *args, **kwargs):#pylint: disable=[too-many-return-statements] @@ -192,18 +192,18 @@ def check_errors(conn, *args, **kwargs):#pylint: disable=[too-many-return-statem population = population_by_species_and_id(conn, species_id, population_id) if "species" in args and not bool(species): - flash("Invalid species!", "alert-error alert-rqtl2") + 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 alert-rqtl2") + 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-rqtl2") + flash("There is no file to process.", "alert-error error-rqtl2") return redirect(url_for("upload.rqtl2.upload_rqtl2_bundle", species_id=species_id, population_id=population_id, @@ -212,7 +212,7 @@ def check_errors(conn, *args, **kwargs):#pylint: disable=[too-many-return-statem if ("geno-dataset" in args and not bool(request.form.get("geno-dataset-id"))): - flash("No genotype dataset was provided!", "alert-error alert-rqtl2") + flash("No genotype dataset was provided!", "alert-error error-rqtl2") return redirect(url_for("upload.rqtl2.select_geno_dataset", species_id=species_id, population_id=population_id, @@ -227,12 +227,12 @@ def check_errors(conn, *args, **kwargs):#pylint: disable=[too-many-return-statem 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") + flash("No probeset study was selected!", "alert-error error-rqtl2") 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") + flash("No probeset dataset was selected!", "alert-error error-rqtl2") return summary_page return None @@ -252,14 +252,14 @@ def select_geno_dataset(species_id: int, population_id: int): conn, species_id, population_id) if not bool(geno_dset): flash("No genotype dataset was provided!", - "alert-error alert-rqtl2") + "alert-error error-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") + flash("Genotype accepted", "alert-success error-rqtl2") return redirect(url_for("upload.rqtl2.select_dataset_info", species_id=species_id, population_id=population_id, @@ -281,17 +281,15 @@ def create_geno_dataset(species_id: int, population_id: int): population_id=population_id, pgsrc="error"), code=307) + errorclasses = "alert-error error-rqtl2 error-rqtl2-create-geno-dataset" if not bool(request.form.get("dataset-name")): - flash("You must provide the dataset name", - "alert-error alert-rqtl2") + flash("You must provide the dataset name", errorclasses) return sgeno_page if not bool(request.form.get("dataset-fullname")): - flash("You must provide the dataset full name", - "alert-error alert-rqtl2") + flash("You must provide the dataset full name", errorclasses) return sgeno_page if not bool(request.form.get("dataset-shortname")): - flash("You must provide the dataset short name", - "alert-error alert-rqtl2") + flash("You must provide the dataset short name", errorclasses) return sgeno_page public = 2 if request.form.get("dataset-public") == "on" else 0 @@ -338,7 +336,7 @@ def select_probeset_study(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 study selected!", "alert-error alert-rqtl2") + flash("Invalid study selected!", "alert-error error-rqtl2") return summary_page return summary_page @@ -360,7 +358,7 @@ 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 study selected!", "alert-error alert-rqtl2") + flash("Invalid study selected!", "alert-error error-rqtl2") return summary_page return summary_page @@ -385,12 +383,12 @@ def create_probeset_study(species_id: int, population_id: int): if not (bool(form.get("platformid")) and bool(platform_by_id(conn, int(form["platformid"])))): - flash("Invalid platform selected.", "alert-error alert-rqtl2") + flash("Invalid platform selected.", "alert-error error-rqtl2") return select_study_page if not (bool(form.get("tissueid")) and bool(tissue_by_id(conn, int(form["tissueid"])))): - flash("Invalid tissue selected.", "alert-error alert-rqtl2") + flash("Invalid tissue selected.", "alert-error error-rqtl2") return select_study_page study = probeset_create_study( @@ -426,23 +424,23 @@ def create_probeset_dataset(species_id: int, population_id: int):#pylint: disabl population_id=population_id), code=307) if not bool(form.get("averageid")): - flash("Averaging method not selected!", "alert-error alert-rqtl2") + flash("Averaging method not selected!", "alert-error error-rqtl2") return summary_page if not bool(form.get("datasetname")): - flash("Dataset name not provided!", "alert-error alert-rqtl2") + flash("Dataset name not provided!", "alert-error error-rqtl2") return summary_page if not bool(form.get("datasetfullname")): - flash("Dataset full name not provided!", "alert-error alert-rqtl2") + flash("Dataset full name not provided!", "alert-error error-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") + flash("Invalid ProbeSet study provided!", "alert-error error-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") + flash("Invalid averaging method provided!", "alert-error error-rqtl2") return summary_page dset = probeset_create_dataset(conn, |