diff --git a/app.py b/app.py index 118b7f3..c392ef8 100755 --- a/app.py +++ b/app.py @@ -72,6 +72,8 @@ def object_as_dict(obj): class Chemical(db.Model): query: db.Query id = db.Column(db.Integer, primary_key=True) + standard_grp = db.Column(db.String, nullable=False) + uploaded_by = db.Column(db.String, nullable=False) # all fields after here are included in the database chemical_db_id = db.Column(db.String) library = db.Column(db.String) @@ -89,7 +91,7 @@ class Chemical(db.Model): final_mz = db.Column(db.Float, nullable=False) final_rt = db.Column(db.Float, nullable=False) - final_adduct = db.Column(db.String) + final_adduct = db.Column(db.String, nullable=False) adduct = db.Column(db.String) detected_adducts = db.Column(db.String) adduct_calc_mz = db.Column(db.String) @@ -298,7 +300,7 @@ def batch_add_request(): def cleanup(): return os.remove(filename) # read it as a csv with open(filename, "r") as csvfile: - reader = csv.DictReader(csvfile) + reader = csv.DictReader(csvfile, delimiter="\t") results, error = validate.validate_insertion_csv_fields(reader) if error: cleanup() diff --git a/templates/batchadd.html b/templates/batchadd.html index ecac506..d012923 100644 --- a/templates/batchadd.html +++ b/templates/batchadd.html @@ -5,7 +5,7 @@ Source Code with required type definitions
- +
diff --git a/templates/create_chemical.html b/templates/create_chemical.html index 9749c09..56d1018 100644 --- a/templates/create_chemical.html +++ b/templates/create_chemical.html @@ -2,7 +2,7 @@ {% block content %} {% if id %} -

Editing Chemical {{id}}

+

Editing Chemical {{id}} (* = required)

{% endif %} {% if invalid %}

Invalid Form!

diff --git a/templates/delete_chemical.html b/templates/delete_chemical.html index 36f37eb..149d4eb 100644 --- a/templates/delete_chemical.html +++ b/templates/delete_chemical.html @@ -2,4 +2,4 @@ {% block content %}

Successfully Deleted Chemical with id {{id}}

-{% endblock %} \ No newline at end of file +{% endblock %} diff --git a/validate.py b/validate.py index d7fe253..e5061ee 100755 --- a/validate.py +++ b/validate.py @@ -1,5 +1,4 @@ import csv -from datetime import date """ Required fields when inserting into the database. @@ -14,6 +13,9 @@ _required_fields = [ ("final_mz", "float"), ("final_rt", "float"), + ("final_adduct", "str"), + ("standard_grp", "str"), + ("uploaded_by", "str"), ] @@ -31,7 +33,6 @@ _optional_fields = [ ("inchikey", "str"), ("inchikey14", "str"), - ("final_adduct", "str"), ("adduct", "str"), ("detected_adducts", "str"), ("adduct_calc_mz", "str"),