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)

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 ###

validate.py

@@ -90,7 +90,6 @@ 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"