Merge pull request #394 from mutalyzer/fix-migrations

Fix data migrations for Reference.source

migrations/versions/33c9465d5a60_reference_source_not_null.py

@@ -59,7 +59,7 @@ def upgrade():
             source = 'lrg'
         elif r.slice_accession:
             source = 'ncbi_slice'
-            data = '{}:{}:{}:{}'.format(r.slice_accession, r.slice_start, r.slice_start, r.slice_orientation)
+            data = '{}:{}:{}:{}'.format(r.slice_accession, r.slice_start, r.slice_stop, r.slice_orientation)
         elif r.download_url:
             source = 'url'
             data = r.download_url

migrations/versions/8ed4dce84496_fix_data_migrations_for_reference_source.py

+"""Fix data migrations for Reference.source
+
+Revision ID: 8ed4dce84496
+Revises: 33c9465d5a60
+Create Date: 2016-06-09 22:38:01.933037
+
+"""
+
+from __future__ import unicode_literals
+
+# revision identifiers, used by Alembic.
+revision = '8ed4dce84496'
+down_revision = u'33c9465d5a60'
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy import sql
+
+
+def upgrade():
+    # We repeat the data migration from migration c92f30c03b62 for sliced
+    # references to correct the error in its original release. Slice start
+    # position was used for both start and stop positions in the new 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('source', sa.Enum('ncbi', 'ncbi_slice', 'lrg', 'url', 'upload', name='reference_source')),
+        sql.column('source_data', sa.String(255)),
+        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')))
+
+    # Get all rows.
+    result = connection.execute(
+        references.select().with_only_columns([
+            references.c.id,
+            references.c.source,
+            references.c.source_data,
+            references.c.slice_accession,
+            references.c.slice_start,
+            references.c.slice_stop,
+            references.c.slice_orientation
+        ]).where(references.c.source == 'ncbi_slice'))
+
+    # Generate parameter values for the UPDATE query below.
+    def update_params(r):
+        data = r.source_data
+        if r.slice_accession:
+            data = '{}:{}:{}:{}'.format(r.slice_accession, r.slice_start, r.slice_stop, r.slice_orientation)
+        return {'r_id': r.id, '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_data` based on existing column values.
+        statement = references.update().where(
+            references.c.id == sql.bindparam('r_id')
+        ).values({'source_data': sql.bindparam('r_source_data')})
+
+        # Execute UPDATE query for fetched rows.
+        connection.execute(statement, [update_params(r) for r in chunk])
+
+
+def downgrade():
+    pass

migrations/versions/c92f30c03b62_add_reference_source.py

@@ -83,7 +83,7 @@ def upgrade():
             source = 'lrg'
         elif r.slice_accession:
             source = 'ncbi_slice'
-            data = '{}:{}:{}:{}'.format(r.slice_accession, r.slice_start, r.slice_start, r.slice_orientation)
+            data = '{}:{}:{}:{}'.format(r.slice_accession, r.slice_start, r.slice_stop, r.slice_orientation)
         elif r.download_url:
             source = 'url'
             data = r.download_url