From d402ac1cad1a76f9fc3a7e533fa71fe2d184e629 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Tue, 4 Feb 2014 22:38:54 +0100
Subject: [PATCH] Use Alembic for database migrations
---
migrations/README | 1 +
migrations/alembic.ini | 54 +++++++++++++
migrations/env.py | 76 +++++++++++++++++++
migrations/script.py.mako | 22 ++++++
.../versions/ea660b66f26_initial_schema.py | 22 ++++++
mutalyzer/db/models.py | 14 ----
mutalyzer/entrypoints/admin.py | 50 ++++++++++++
requirements.txt | 1 +
8 files changed, 226 insertions(+), 14 deletions(-)
create mode 100644 migrations/README
create mode 100644 migrations/alembic.ini
create mode 100644 migrations/env.py
create mode 100644 migrations/script.py.mako
create mode 100644 migrations/versions/ea660b66f26_initial_schema.py
diff --git a/migrations/README b/migrations/README
new file mode 100644
index 00000000..98e4f9c4
--- /dev/null
+++ b/migrations/README
@@ -0,0 +1 @@
+Generic single-database configuration.
\ No newline at end of file
diff --git a/migrations/alembic.ini b/migrations/alembic.ini
new file mode 100644
index 00000000..f82bd39d
--- /dev/null
+++ b/migrations/alembic.ini
@@ -0,0 +1,54 @@
+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+script_location = %(here)s
+
+# template used to generate migration files
+# file_template = %%(rev)s_%%(slug)s
+
+# max length of characters to apply to the
+# "slug" field
+#truncate_slug_length = 40
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+sqlalchemy.url = driver://user:pass@localhost/dbname
+
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S
diff --git a/migrations/env.py b/migrations/env.py
new file mode 100644
index 00000000..015e56e8
--- /dev/null
+++ b/migrations/env.py
@@ -0,0 +1,76 @@
+from __future__ import with_statement
+from alembic import context
+from sqlalchemy import engine_from_config, pool
+from logging.config import fileConfig
+
+from mutalyzer import db
+from mutalyzer.config import settings
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+fileConfig(config.config_file_name)
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+# from myapp import mymodel
+# target_metadata = mymodel.Base.metadata
+target_metadata = db.Base.metadata
+
+# other values from the config, defined by the needs of env.py,
+# can be acquired:
+# my_important_option = config.get_main_option("my_important_option")
+# ... etc.
+
+def run_migrations_offline():
+ """Run migrations in 'offline' mode.
+
+ This configures the context with just a URL
+ and not an Engine, though an Engine is acceptable
+ here as well. By skipping the Engine creation
+ we don't even need a DBAPI to be available.
+
+ Calls to context.execute() here emit the given string to the
+ script output.
+
+ """
+ url = config.get_main_option("sqlalchemy.url")
+ context.configure(url=url)
+
+ with context.begin_transaction():
+ context.run_migrations()
+
+def run_migrations_online():
+ """Run migrations in 'online' mode.
+
+ In this scenario we need to create an Engine
+ and associate a connection with the context.
+
+ """
+ alembic_config = config.get_section(config.config_ini_section)
+ alembic_config['sqlalchemy.url'] = settings.DATABASE_URI
+
+ engine = engine_from_config(
+ alembic_config,
+ prefix='sqlalchemy.',
+ poolclass=pool.NullPool)
+
+ connection = engine.connect()
+ context.configure(
+ connection=connection,
+ target_metadata=target_metadata
+ )
+
+ try:
+ with context.begin_transaction():
+ context.run_migrations()
+ finally:
+ connection.close()
+
+if context.is_offline_mode():
+ run_migrations_offline()
+else:
+ run_migrations_online()
diff --git a/migrations/script.py.mako b/migrations/script.py.mako
new file mode 100644
index 00000000..95702017
--- /dev/null
+++ b/migrations/script.py.mako
@@ -0,0 +1,22 @@
+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision}
+Create Date: ${create_date}
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = ${repr(up_revision)}
+down_revision = ${repr(down_revision)}
+
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
+
+def upgrade():
+ ${upgrades if upgrades else "pass"}
+
+
+def downgrade():
+ ${downgrades if downgrades else "pass"}
diff --git a/migrations/versions/ea660b66f26_initial_schema.py b/migrations/versions/ea660b66f26_initial_schema.py
new file mode 100644
index 00000000..d0d474ed
--- /dev/null
+++ b/migrations/versions/ea660b66f26_initial_schema.py
@@ -0,0 +1,22 @@
+"""initial schema
+
+Revision ID: ea660b66f26
+Revises: None
+Create Date: 2014-02-04 18:38:28.416032
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = 'ea660b66f26'
+down_revision = None
+
+from alembic import op
+import sqlalchemy as sa
+
+
+def upgrade():
+ pass
+
+
+def downgrade():
+ pass
diff --git a/mutalyzer/db/models.py b/mutalyzer/db/models.py
index 4e61087c..4c54beb8 100644
--- a/mutalyzer/db/models.py
+++ b/mutalyzer/db/models.py
@@ -499,17 +499,3 @@ Index('transcript_mapping_transcript',
TranscriptMapping.gene, TranscriptMapping.transcript,
TranscriptMapping.chromosome_id,
unique=True)
-
-
-def create_all():
- db.Base.metadata.drop_all(db.session.get_bind())
- db.Base.metadata.create_all(db.session.get_bind())
- db.session.commit()
-
- # Todo: Use alembic.
-
- # if using alembic:
- #from alembic.config import Config
- #from alembic import command
- #alembic_cfg = Config("alembic.ini")
- #command.stamp(alembic_cfg, "head")
diff --git a/mutalyzer/entrypoints/admin.py b/mutalyzer/entrypoints/admin.py
index a8217bef..7fbf7171 100644
--- a/mutalyzer/entrypoints/admin.py
+++ b/mutalyzer/entrypoints/admin.py
@@ -3,13 +3,27 @@ Command line interface to Mutalyzer administrative tools.
"""
+# Todo: Group subcommands to subsubcommands. For example:
+#
+# mutalyzer-admin announcement unset
+#
+# instead of
+#
+# mutalyzer-admin unset-announcement
+
+
import argparse
import json
+import os
+import alembic.command
+import alembic.config
+from alembic.migration import MigrationContext
from sqlalchemy.exc import IntegrityError
from sqlalchemy.orm.exc import NoResultFound
from .. import announce
+from .. import db
from ..db import session
from ..db.models import Assembly, Chromosome
from .. import mapping
@@ -128,6 +142,28 @@ def unset_announcement():
announce.unset_announcement()
+def setup_database(alembic_config_path=None, destructive=False):
+ """
+ Setup database tables (if they do not yet exist).
+ """
+ if alembic_config_path and not os.path.isfile(alembic_config_path):
+ raise UserError('Cannot find Alembic configuration: %s'
+ % alembic_config_path)
+
+ if destructive:
+ db.Base.metadata.drop_all(db.session.get_bind())
+
+ db.Base.metadata.create_all(db.session.get_bind())
+
+ if alembic_config_path:
+ context = MigrationContext.configure(db.session.connection())
+ if destructive or context.get_current_revision() is None:
+ alembic_config = alembic.config.Config(alembic_config_path)
+ alembic.command.stamp(alembic_config, 'head')
+
+ db.session.commit()
+
+
def main():
"""
Command-line interface to Mutalyzer administrative tools.
@@ -226,6 +262,20 @@ def main():
description=unset_announcement.__doc__.split('\n\n')[0])
p.set_defaults(func=unset_announcement)
+ p = subparsers.add_parser(
+ 'setup-database', help='setup database',
+ description=setup_database.__doc__.split('\n\n')[0],
+ epilog='If Alembic config is given (--alembic-config), this also '
+ 'prepares the database for future migrations with Alembic '
+ '(recommended).')
+ p.add_argument(
+ '--destructive', dest='destructive', action='store_true',
+ help='delete any existing tables and data')
+ p.add_argument(
+ '-c', '--alembic-config', metavar='ALEMBIC_CONFIG',
+ dest='alembic_config_path', help='path to Alembic configuration file')
+ p.set_defaults(func=setup_database)
+
args = parser.parse_args()
try:
diff --git a/requirements.txt b/requirements.txt
index 9ff2792d..c5872b7c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -18,3 +18,4 @@ SQLAlchemy==0.9.1
redis==2.8.0
mockredispy==2.8.0.2
mock==1.0.1
+alembic==0.6.2
--
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