1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/b762062399b3/
changeset: b762062399b3
user: greg
date: 2012-06-12 21:09:39
summary: Migration script to alter the tool_dependency.version database table column type to Text.
affected #: 2 files
diff -r 9a3ab5009e8e70596a07283e3611661410f92c4d -r b762062399b3cab0a4139dc3fcd33f30945e49ac lib/galaxy/model/mapping.py
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -397,7 +397,7 @@
Column( "tool_shed_repository_id", Integer, ForeignKey( "tool_shed_repository.id" ), index=True, nullable=False ),
Column( "installed_changeset_revision", TrimmedString( 255 ) ),
Column( "name", TrimmedString( 255 ) ),
- Column( "version", TrimmedString( 40 ) ),
+ Column( "version", Text ),
Column( "type", TrimmedString( 40 ) ),
Column( "uninstalled", Boolean, default=False ) )
diff -r 9a3ab5009e8e70596a07283e3611661410f92c4d -r b762062399b3cab0a4139dc3fcd33f30945e49ac lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
@@ -0,0 +1,53 @@
+"""
+Migration script to alter the type of the tool_dependency.version column from TrimmedString(40) to Text.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+def upgrade():
+ print __doc__
+ metadata.reflect()
+ ToolDependency_table = Table( "tool_dependency", metadata, autoload=True )
+ # Change the tool_dependency table's version column from TrimmedString to Text.
+ if migrate_engine.name == 'postgres':
+ cmd = "ALTER TABLE tool_dependency ALTER COLUMN version TYPE Text;"
+ elif migrate_engine.name == 'mysql':
+ cmd = "ALTER TABLE tool_dependency MODIFY COLUMN version Text;"
+ else:
+ # We don't have to do anything for sqlite tables. From the sqlite documentation at http://sqlite.org/datatype3.html:
+ # 1.0 Storage Classes and Datatypes
+ # Each value stored in an SQLite database (or manipulated by the database engine) has one of the following storage classes:
+ # NULL. The value is a NULL value.
+ # INTEGER. The value is a signed integer, stored in 1, 2, 3, 4, 6, or 8 bytes depending on the magnitude of the value.
+ # REAL. The value is a floating point value, stored as an 8-byte IEEE floating point number.
+ # TEXT. The value is a text string, stored using the database encoding (UTF-8, UTF-16BE or UTF-16LE).
+ # BLOB. The value is a blob of data, stored exactly as it was input.
+ cmd = None
+ if cmd:
+ try:
+ db_session.execute( cmd )
+ except Exception, e:
+ log.debug( "Altering tool_dependency.version column from TrimmedString(40) to Text failed: %s" % str( e ) )
+def downgrade():
+ # Not necessary to change column type Text to TrimmedString(40).
+ pass
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/9a3ab5009e8e/
changeset: 9a3ab5009e8e
user: dan
date: 2012-06-12 20:12:46
summary: Allow OpenID to work when require_login is set to True.
affected #: 1 file
diff -r 36c540d788c3842b37c4ab5e522afd612ea8bd80 -r 9a3ab5009e8e70596a07283e3611661410f92c4d lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -435,6 +435,9 @@
url_for( controller='user', action='manage_user_info' ),
url_for( controller='user', action='set_default_permissions' ),
url_for( controller='user', action='reset_password' ),
+ url_for( controller='user', action='openid_auth' ),
+ url_for( controller='user', action='openid_process' ),
+ url_for( controller='user', action='openid_associate' ),
url_for( controller='library', action='browse' ),
url_for( controller='history', action='list' ),
url_for( controller='dataset', action='list' )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/17302ca3be4e/
changeset: 17302ca3be4e
user: jgoecks
date: 2012-06-11 21:22:51
summary: Put myExperiment URL in config's Beta features location.
affected #: 1 file
diff -r 0f32c2fc37cdc2959c86d2fdb0debe9a4c66282b -r 17302ca3be4e7b3d987733ea6e61982f9520996d universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -527,6 +527,9 @@
# be used for each "Set at Runtime" input, independent of others in the Workflow
#enable_unique_workflow_defaults = False
+# The URL to the myExperiment instance being used (omit scheme but include port)
+#myexperiment_url = www.myexperiment.org:80
+
# Enable Galaxy's "Upload via FTP" interface. You'll need to install and
# configure an FTP server (we've used ProFTPd since it can use Galaxy's
# database for authentication) and set the following two options.
@@ -681,9 +684,6 @@
#pbs_stage_path =
#pbs_dataset_server =
-# The URL to the myExperiment instance being used (omit scheme but include port)
-myexperiment_url = www.myexperiment.org:80
-
# This option allows users to see the full path of datasets via the "View
# Details" option in the history. Administrators can always see this.
#expose_dataset_path = False
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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