migrations work properly

2-5-23.txt

@@ -1,12 +0,0 @@
-# Changes to Make
-
-- Show how to make a network request in R to the server
-- Version Control (what date a compound was added)
-  - createdAt, but configurable. DONE
-  - Compare the database to the list of compunds and you only want compounds
-    from that date or before? DONE
-
-- Emphasizing Local? - Accessible through a url. DONE, all fields accessible.
-
-- Shiny app
-  - Permissions System (revoke, access API keys)

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,

entrypoint.sh

@@ -2,7 +2,6 @@
 
 set -x
 
-#flask db upgrade
-./initialize_db.py
-#gunicorn -b 0.0.0.0:5000 'app.__init__.create_app()' --chdir /app
+cd /app || exit
+flask db upgrade
 gunicorn -b 0.0.0.0:5000 app:app --chdir /app

migrations/versions/1a0a82192181_.py

@@ -0,0 +1,56 @@
+"""empty message
+
+Revision ID: 1a0a82192181
+Revises: 7e9528cf1416
+Create Date: 2023-04-11 19:01:00.565936
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '1a0a82192181'
+down_revision = '7e9528cf1416'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('chemical', schema=None) as batch_op:
+        batch_op.add_column(sa.Column('person_name', sa.String(), nullable=False))
+        batch_op.add_column(sa.Column('standard_grp', sa.String(), nullable=False))
+        batch_op.add_column(sa.Column('metabolite_name', sa.String(), nullable=False))
+        batch_op.alter_column('inchikey',
+               existing_type=sa.VARCHAR(),
+               nullable=False)
+        batch_op.alter_column('final_adduct',
+               existing_type=sa.VARCHAR(),
+               nullable=False)
+        batch_op.alter_column('msms_detected',
+               existing_type=sa.BOOLEAN(),
+               nullable=False)
+        batch_op.drop_column('name')
+
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('chemical', schema=None) as batch_op:
+        batch_op.add_column(sa.Column('name', sa.VARCHAR(), nullable=False))
+        batch_op.alter_column('msms_detected',
+               existing_type=sa.BOOLEAN(),
+               nullable=True)
+        batch_op.alter_column('final_adduct',
+               existing_type=sa.VARCHAR(),
+               nullable=True)
+        batch_op.alter_column('inchikey',
+               existing_type=sa.VARCHAR(),
+               nullable=True)
+        batch_op.drop_column('metabolite_name')
+        batch_op.drop_column('standard_grp')
+        batch_op.drop_column('person_name')
+
+    # ### end Alembic commands ###

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"},

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"

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>,

templates/batchadd.html

@@ -5,8 +5,8 @@
 <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"> Input file (tab delimited text file) </label>
-    <input type="file" name="csv">
+    <label for="input"> Input file (tab delimited text file) </label>
+    <input type="file" name="input">
     <input type="submit" value="Submit">
 </form>
 

templates/batchquery.html

@@ -5,8 +5,8 @@
 <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>
-    <input type="file" name="csv">
+    <label for="input">Input (tab-delimited text file): </label>
+    <input type="file" name="input">
     <input type="submit" value="Submit">
 </form>
 

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"),
 ]