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"""Reference.source NOT NULL
Revision ID: 33c9465d5a60
Revises: c92f30c03b62
Create Date: 2016-06-09 15:20:44.734913
"""
from __future__ import unicode_literals
# revision identifiers, used by Alembic.
revision = '33c9465d5a60'
down_revision = u'c92f30c03b62'
from alembic import op
import sqlalchemy as sa
from sqlalchemy import sql
def upgrade():
# We repeat the data migration from migration c92f30c03b62, so we're sure
# there are no NULL values left in the source column.
connection = op.get_bind()
# Inline table definition we can use in this migration.
references = sql.table(
'references',
sql.column('id', sa.Integer()),
sql.column('accession', sa.String(20)),
sql.column('source', sa.Enum('ncbi', 'ncbi_slice', 'lrg', 'url', 'upload', name='reference_source')),
sql.column('source_data', sa.String(255)),
sql.column('geninfo_identifier', sa.String(13)),
sql.column('slice_accession', sa.String(20)),
sql.column('slice_start', sa.Integer()),
sql.column('slice_stop', sa.Integer()),
sql.column('slice_orientation', sa.Enum('forward', 'reverse', name='slice_orientation')),
sql.column('download_url', sa.String(255)))
# Get all rows.
result = connection.execute(
references.select().with_only_columns([
references.c.id,
references.c.accession,
references.c.source,
references.c.source_data,
references.c.geninfo_identifier,
references.c.slice_accession,
references.c.slice_start,
references.c.slice_stop,
references.c.slice_orientation,
references.c.download_url]))
# Generate parameter values for the UPDATE query below.
def update_params(r):
data = None
if r.source:
source = r.source
data = r.source_data
if r.accession.startswith('LRG_'):
source = 'lrg'
elif r.slice_accession:
source = 'ncbi_slice'
data = '{}:{}:{}:{}'.format(r.slice_accession, r.slice_start, r.slice_stop, r.slice_orientation)
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elif r.download_url:
source = 'url'
data = r.download_url
elif r.geninfo_identifier:
source = 'ncbi'
else:
source = 'upload'
return {'r_id': r.id, 'r_source': source, 'r_source_data': data}
# Process a few rows at a time, since they will be read in memory.
while True:
chunk = result.fetchmany(1000)
if not chunk:
break
# Populate `source` and `source_data` based on existing column values.
statement = references.update().where(
references.c.id == sql.bindparam('r_id')
).values({'source': sql.bindparam('r_source'),
'source_data': sql.bindparam('r_source_data')})
# Execute UPDATE query for fetched rows.
connection.execute(statement, [update_params(r) for r in chunk])
# Unfortunately, SQLite doesn't support adding the NOT NULL constraint on
# an existing column. We use batch_alter_table to workaround this.
with op.batch_alter_table('references') as batch_op:
batch_op.alter_column('source', nullable=False, existing_type=sa.Enum(
'ncbi', 'ncbi_slice', 'lrg', 'url', 'upload', name='reference_source'))
def downgrade():
### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('references') as batch_op:
batch_op.alter_column('source', nullable=True, existing_type=sa.Enum(
'ncbi', 'ncbi_slice', 'lrg', 'url', 'upload', name='reference_source'))
### end Alembic commands ###