diff --git a/2-5-23.txt b/2-5-23.txt deleted file mode 100644 index 7046576..0000000 --- a/2-5-23.txt +++ /dev/null @@ -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) diff --git a/entrypoint.sh b/entrypoint.sh index d1a0e81..649159f 100755 --- a/entrypoint.sh +++ b/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 diff --git a/migrations/versions/1a0a82192181_.py b/migrations/versions/1a0a82192181_.py new file mode 100644 index 0000000..da90591 --- /dev/null +++ b/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 ### diff --git a/validate.py b/validate.py index 9378688..e331792 100755 --- a/validate.py +++ b/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"