From ecb256ef46a309b893ee44cc74404de577ffcf60 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 5 Mar 2012 12:11:53 -0600
Subject: [PATCH 1/2] Adding db_shell.py that can be used to simplify writing
 command line scripts against the Galaxy model/database layer or to make use
 of Galaxy models in an interactive shell.

---
 scripts/__init__.py |  0
 scripts/db_shell.py | 86 +++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 86 insertions(+)
 create mode 100644 scripts/__init__.py
 create mode 100644 scripts/db_shell.py

diff --git a/scripts/__init__.py b/scripts/__init__.py
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/scripts/db_shell.py b/scripts/db_shell.py
new file mode 100644
index 00000000000..eb02153711b
--- /dev/null
+++ b/scripts/db_shell.py
@@ -0,0 +1,86 @@
+# This script allows easy access to Galaxy's database layer via the
+# Galaxy models. For example:q
+# % python -i scripts/db_shel.py
+# >>> new_user = User("admin@gmail.com")
+# >>> new_user.set_password
+# >>> sa_session.add(new_user)
+# >>> sa_session.commit()
+# >>> sa_session.query(User).all()
+# 
+# You can also use this script as a library, for instance see https://gist.github.com/1979583q
+# TODO: This script overlaps alot wth manage_db.py and create_db.py,
+# these should maybe be refactored to remove duplication.
+import sys, os.path, logging
+
+new_path = [ os.path.join( os.getcwd(), "lib" ) ]
+new_path.extend( sys.path[1:] ) # remove scripts/ from the path
+sys.path = new_path
+
+from galaxy import eggs
+
+import pkg_resources
+pkg_resources.require( "sqlalchemy-migrate" )
+pkg_resources.require( "SQLAlchemy" )
+
+from ConfigParser import SafeConfigParser
+
+log = logging.getLogger( __name__ )
+
+if sys.argv[-1] in [ 'community' ]:
+    # Need to pop the last arg so the command line args will be correct
+    # for sqlalchemy-migrate 
+    webapp = sys.argv.pop()
+    config_file = 'community_wsgi.ini'
+    repo = 'lib/galaxy/webapps/community/model/migrate'
+else:
+    # Poor man's optparse
+    config_file = 'universe_wsgi.ini'
+    if '-c' in sys.argv:
+        pos = sys.argv.index( '-c' )
+        sys.argv.pop(pos)
+        config_file = sys.argv.pop( pos )
+    if not os.path.exists( config_file ):
+        print "Galaxy config file does not exist (hint: use '-c config.ini' for non-standard locations): %s" % config_file
+        sys.exit( 1 )
+    repo = 'lib/galaxy/model/migrate'
+
+cp = SafeConfigParser()
+cp.read( config_file )
+
+if cp.has_option( "app:main", "database_connection" ):
+    db_url = cp.get( "app:main", "database_connection" )
+elif cp.has_option( "app:main", "database_file" ):
+    db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % cp.get( "app:main", "database_file" )
+else:
+    db_url = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE"
+
+dialect_to_egg = {
+    "sqlite" : "pysqlite>=2",
+    "postgres" : "psycopg2",
+    "mysql" : "MySQL_python"
+}
+dialect = ( db_url.split( ':', 1 ) )[0]
+try:
+    egg = dialect_to_egg[dialect]
+    try:
+        pkg_resources.require( egg )
+        log.debug( "%s egg successfully loaded for %s dialect" % ( egg, dialect ) )
+    except:
+        # If the module is in the path elsewhere (i.e. non-egg), it'll still load.
+        log.warning( "%s egg not found, but an attempt will be made to use %s anyway" % ( egg, dialect ) )
+except KeyError:
+    # Let this go, it could possibly work with db's we don't support
+    log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect )
+
+# Setup DB scripting environment 
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from sqlalchemy.exc import *
+
+os.environ['PYTHONINSPECT'] = 'True'
+engine = create_engine(db_url, echo=True)
+db_session = scoped_session( sessionmaker( bind = engine ) )
+from galaxy.model.mapping import context as sa_session
+sa_session.bind = engine
+from galaxy.model import *
+

From de62173affd4862ef432ddd9d2e3edeeb05d8b63 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 5 Mar 2012 15:23:28 -0600
Subject: [PATCH 2/2] Actually we don't want to set that environment variable,
 that make python behave like -i every execution.

---
 scripts/db_shell.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/scripts/db_shell.py b/scripts/db_shell.py
index eb02153711b..c9acde171e1 100644
--- a/scripts/db_shell.py
+++ b/scripts/db_shell.py
@@ -77,7 +77,6 @@ from sqlalchemy import *
 from sqlalchemy.orm import *
 from sqlalchemy.exc import *
 
-os.environ['PYTHONINSPECT'] = 'True'
 engine = create_engine(db_url, echo=True)
 db_session = scoped_session( sessionmaker( bind = engine ) )
 from galaxy.model.mapping import context as sa_session