diff --git a/__init__.py b/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/app.py b/app.py
index c392ef8..af0b1ca 100755
--- a/app.py
+++ b/app.py
@@ -11,13 +11,16 @@ from flask_migrate import Migrate
from uuid import uuid4
import csv
import validate
+import secrets
+from dotenv import load_dotenv
+load_dotenv()
# from datetime import date
app = Flask(__name__)
app.config["SQLALCHEMY_DATABASE_URI"] = "sqlite:///project.db"
-app.secret_key = '98d31240f9fbe14c8083586db49c19c3a8d3f726'
+app.secret_key = os.getenv('SECRET_KEY', secrets.token_hex(16))
db: SQLAlchemy = SQLAlchemy()
migrate = Migrate()
db.init_app(app)
@@ -72,20 +75,20 @@ def object_as_dict(obj):
class Chemical(db.Model):
query: db.Query
id = db.Column(db.Integer, primary_key=True)
+ person_name = db.Column(db.String, nullable=False)
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)
# important fields
- name = db.Column(db.String, nullable=False)
+ metabolite_name = db.Column(db.String, nullable=False)
formula = db.Column(db.String, nullable=False)
mass = db.Column(db.Float, nullable=False)
pubchem_cid = db.Column(db.Integer)
pubmed_refcount = db.Column(db.Integer)
standard_class = db.Column(db.String)
- inchikey = db.Column(db.String)
+ inchikey = db.Column(db.String, nullable=False)
inchikey14 = db.Column(db.String)
final_mz = db.Column(db.Float, nullable=False)
@@ -95,7 +98,7 @@ class Chemical(db.Model):
adduct = db.Column(db.String)
detected_adducts = db.Column(db.String)
adduct_calc_mz = db.Column(db.String)
- msms_detected = db.Column(db.Boolean)
+ msms_detected = db.Column(db.Boolean, nullable=False)
msms_purity = db.Column(db.Float)
# serialized into datetime.date
@@ -275,7 +278,7 @@ def search_api():
data = []
for x in result:
data.append({"url": url_for("chemical_view", id=x.id),
- "name": x.name, "mz": x.final_mz, "rt": x.final_rt})
+ "name": x.metabolite_name, "mz": x.final_mz, "rt": x.final_rt})
return jsonify(data)
@@ -289,10 +292,10 @@ def batch_add_request():
if not session.get('admin'):
abort(403)
if request.method == "POST":
- if "csv" not in request.files or request.files["csv"].filename == '':
+ if "input" not in request.files or request.files["input"].filename == '':
return render_template("batchadd.html", invalid="Blank file included")
# save the file to RAM
- file = request.files["csv"]
+ file = request.files["input"]
os.makedirs("/tmp/walkerdb", exist_ok=True)
filename = os.path.join("/tmp/walkerdb", str(uuid4()))
file.save(filename)
@@ -320,10 +323,10 @@ def batch_query_request():
if not session.get('admin'):
abort(403)
if request.method == "POST":
- if "csv" not in request.files or request.files["csv"].filename == '':
+ if "input" not in request.files or request.files["input"].filename == '':
return render_template("batchadd.html", invalid="Blank file included")
# save the file to RAM
- file = request.files["csv"]
+ file = request.files["input"]
os.makedirs("/tmp/walkerdb", exist_ok=True)
filename = os.path.join("/tmp/walkerdb", str(uuid4()))
file.save(filename)
@@ -331,7 +334,7 @@ def batch_query_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")
queries, error = validate.validate_query_csv_fields(reader)
if error:
cleanup()
@@ -351,7 +354,7 @@ def batch_query_request():
hits = []
for x in result:
hits.append({"url": url_for("chemical_view", id=x.id),
- "name": x.name, "mz": x.final_mz, "rt": x.final_rt})
+ "name": x.metabolite_name, "mz": x.final_mz, "rt": x.final_rt})
data.append(dict(
query=query,
hits=hits,
diff --git a/poetry.lock b/poetry.lock
index 1a67079..143dd23 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -278,6 +278,17 @@ category = "dev"
optional = false
python-versions = ">=3.6"
+[[package]]
+name = "python-dotenv"
+version = "1.0.0"
+description = "Read key-value pairs from a .env file and set them as environment variables"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+
+[package.extras]
+cli = ["click (>=5.0)"]
+
[[package]]
name = "six"
version = "1.16.0"
@@ -473,7 +484,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-co
[metadata]
lock-version = "1.1"
python-versions = "^3.9"
-content-hash = "8595ab65ac1a098228335d1c012a7f266cea9014f71af835581a10debdf36230"
+content-hash = "29c910c8ad182165233a27e0d14ba7a56f9bc8393e7ab8f081767bfa0a470dc9"
[metadata.files]
alembic = [
@@ -663,6 +674,10 @@ pycodestyle = [
{file = "pycodestyle-2.10.0-py2.py3-none-any.whl", hash = "sha256:8a4eaf0d0495c7395bdab3589ac2db602797d76207242c17d470186815706610"},
{file = "pycodestyle-2.10.0.tar.gz", hash = "sha256:347187bdb476329d98f695c213d7295a846d1152ff4fe9bacb8a9590b8ee7053"},
]
+python-dotenv = [
+ {file = "python-dotenv-1.0.0.tar.gz", hash = "sha256:a8df96034aae6d2d50a4ebe8216326c61c3eb64836776504fcca410e5937a3ba"},
+ {file = "python_dotenv-1.0.0-py3-none-any.whl", hash = "sha256:f5971a9226b701070a4bf2c38c89e5a3f0d64de8debda981d1db98583009122a"},
+]
six = []
sqlalchemy = [
{file = "SQLAlchemy-1.4.46-cp27-cp27m-macosx_10_14_x86_64.whl", hash = "sha256:7001f16a9a8e06488c3c7154827c48455d1c1507d7228d43e781afbc8ceccf6d"},
diff --git a/pyproject.toml b/pyproject.toml
index 4b32abb..c85452d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,6 +15,7 @@ wtforms-alchemy = "^0.18.0"
flask-wtf = "^1.0.1"
gunicorn = "^20.1.0"
Flask-Migrate = "^4.0.4"
+python-dotenv = "^1.0.0"
[tool.poetry.dev-dependencies]
autopep8 = "^2.0.1"
diff --git a/templates/admin.html b/templates/admin.html
index ecd3ab7..0645cfb 100644
--- a/templates/admin.html
+++ b/templates/admin.html
@@ -53,8 +53,9 @@ session.post(baseurl + "/admin/login", {"username": (username), "password": (pas
fields = {
"chemical_db_id": <db id from another database>,
"library": (library, is a string),
+ "person_name": (name of person who uploaded, string)
# name, formula, and mass are required fields!
- "name": (name of the chemical, is a string),
+ "metabolite_name": (name of the chemical, is a string),
"formula": (molecular formula, is a string),
"mass": (monoisotopic mass, is a float),
"pubchem_cid": <string>,
diff --git a/templates/batchadd.html b/templates/batchadd.html
index d012923..652ce50 100644
--- a/templates/batchadd.html
+++ b/templates/batchadd.html
@@ -5,8 +5,8 @@
Source Code with required type definitions
diff --git a/templates/batchquery.html b/templates/batchquery.html
index edc958e..b7a20be 100644
--- a/templates/batchquery.html
+++ b/templates/batchquery.html
@@ -5,8 +5,8 @@
Source Code with required type definitions
diff --git a/validate.py b/validate.py
index e5061ee..9378688 100755
--- a/validate.py
+++ b/validate.py
@@ -6,8 +6,9 @@ Required fields when inserting into the database.
_required_fields = [
# the "str" type means that this field can be any valid string.
- ("name", "str"),
+ ("metabolite_name", "str"),
("formula", "str"),
+ ("person_name", "str"),
# any field labeled a "float" needs to have a value in decimal notation.
("mass", "float"),
@@ -15,7 +16,9 @@ _required_fields = [
("final_rt", "float"),
("final_adduct", "str"),
("standard_grp", "str"),
- ("uploaded_by", "str"),
+ ("person_name", "str"),
+ ("msms_detected", "yesno"), # Value can either be "Yes" or "No"
+ ("inchikey", "str"),
]
@@ -30,13 +33,11 @@ _optional_fields = [
("pubchem_cid", "int"), # Only integers are permitted.
("pubmed_refcount", "int"),
("standard_class", "str"),
- ("inchikey", "str"),
("inchikey14", "str"),
("adduct", "str"),
("detected_adducts", "str"),
("adduct_calc_mz", "str"),
- ("msms_detected", "yesno"), # Value can either be "Yes" or "No"
("msms_purity", "float"),
]
@@ -89,6 +90,7 @@ def validate_insertion_csv_fields(reader: csv.DictReader) -> tuple[list[dict], s
chemicals: list[dict] = []
for row in reader:
chemical = {}
+ print("row", row)
for field, t in _required_fields:
if field not in row:
return [], f"Required field \"{field}\" not present in csv"