diff options
| -rw-r--r-- | uploader/expression_data/dbinsert.py | 63 |
1 files changed, 32 insertions, 31 deletions
diff --git a/uploader/expression_data/dbinsert.py b/uploader/expression_data/dbinsert.py index e746944..32ca359 100644 --- a/uploader/expression_data/dbinsert.py +++ b/uploader/expression_data/dbinsert.py @@ -319,37 +319,38 @@ def selected_keys(original: dict, keys: tuple) -> dict: @require_login def final_confirmation(): "Preview the data before triggering entry into the database" - form = request.form - try: - assert form.get("filename"), "filename" - assert form.get("filetype"), "filetype" - assert form.get("species"), "species" - assert form.get("genechipid"), "platform" - assert form.get("studyid"), "study" - assert form.get("datasetid"), "dataset" - - speciesid = form["species"] - genechipid = form["genechipid"] - studyid = form["studyid"] - datasetid=form["datasetid"] - return render_template( - "final_confirmation.html", filename=form["filename"], - filetype=form["filetype"], totallines=form["totallines"], - species=speciesid, genechipid=genechipid, studyid=studyid, - datasetid=datasetid, the_species=selected_keys( - with_db_connection(lambda conn: species_by_id(conn, speciesid)), - ("SpeciesName", "Name", "MenuName")), - platform=selected_keys( - platform_by_species_and_id(speciesid, genechipid), - ("GeneChipName", "Name", "GeoPlatform", "Title", "GO_tree_value")), - study=selected_keys( - study_by_id(studyid), ("Name", "FullName", "ShortName")), - dataset=selected_keys( - dataset_by_id(datasetid), - ("AvgMethodName", "Name", "Name2", "FullName", "ShortName", - "DataScale"))) - except AssertionError as aserr: - return render_error(f"Missing data: {aserr.args[0]}") + with database_connection(app.config["SQL_URI"]) as conn: + form = request.form + try: + assert form.get("filename"), "filename" + assert form.get("filetype"), "filetype" + assert form.get("species"), "species" + assert form.get("genechipid"), "platform" + assert form.get("studyid"), "study" + assert form.get("datasetid"), "dataset" + + speciesid = form["species"] + genechipid = form["genechipid"] + studyid = form["studyid"] + datasetid=form["datasetid"] + return render_template( + "final_confirmation.html", filename=form["filename"], + filetype=form["filetype"], totallines=form["totallines"], + species=speciesid, genechipid=genechipid, studyid=studyid, + datasetid=datasetid, the_species=selected_keys( + with_db_connection(lambda conn: species_by_id(conn, speciesid)), + ("SpeciesName", "Name", "MenuName")), + platform=selected_keys( + platform_by_species_and_id(conn, speciesid, genechipid), + ("GeneChipName", "Name", "GeoPlatform", "Title", "GO_tree_value")), + study=selected_keys( + study_by_id(studyid), ("Name", "FullName", "ShortName")), + dataset=selected_keys( + dataset_by_id(datasetid), + ("AvgMethodName", "Name", "Name2", "FullName", "ShortName", + "DataScale"))) + except AssertionError as aserr: + return render_error(f"Missing data: {aserr.args[0]}") @dbinsertbp.route("/insert-data", methods=["POST"]) @require_login |