small schema changes

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()

templates/batchadd.html

@@ -5,7 +5,7 @@
 <a href="https://git.junickim.me/junikimm717/walker-database/raw/master/validate.py"> Source Code with required type definitions </a>
 
 <form method="post" enctype="multipart/form-data">
-    <label for="csv">CSV: </label>
+    <label for="csv"> Input file (tab delimited text file) </label>
     <input type="file" name="csv">
     <input type="submit" value="Submit">
 </form>

templates/create_chemical.html

@@ -2,7 +2,7 @@
 
 {% block content %}
 {% if id %}
-<h2>Editing Chemical {{id}}</h2>
+<h2>Editing Chemical {{id}} (* = required)</h2>
 {% endif %}
 {% if invalid %}
 <p style="color: red;">Invalid Form!</p>

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"),