Hey Dannon,
Thanks for pointing that out! I missed it. I am now connecting to the remote database. I ran "sh manage_db.sh upgrade" and it upgraded from schema 114 to 118 without error messages. I then ran "sh ./scripts/migrate_tools/0010_tools.sh install_dependencies" and received the following error:
Traceback (most recent call last): File "./scripts/migrate_tools/migrate_tools.py", line 21, in app = MigrateToolsApplication( sys.argv[ 1 ] ) File "/localdata1/galaxy/glxmaint/src/lib/tool_shed/galaxy_install/migrate/common.py", line 59, in __init__ install_dependencies=install_dependencies ) File "/localdata1/galaxy/glxmaint/src/lib/tool_shed/galaxy_install/install_manager.py", line 122, in __init__ is_repository_dependency=is_repository_dependency ) File "/localdata1/galaxy/glxmaint/src/lib/tool_shed/galaxy_install/install_manager.py", line 506, in install_repository is_repository_dependency=is_repository_dependency ) File "/localdata1/galaxy/glxmaint/src/lib/tool_shed/galaxy_install/install_manager.py", line 345, in handle_repository_contents guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config ) File "/localdata1/galaxy/glxmaint/src/lib/tool_shed/galaxy_install/install_manager.py", line 253, in get_guid tool = self.toolbox.load_tool( full_path ) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", line 671, in load_tool return ToolClass( config_file, root, self.app, guid=guid, repository_id=repository_id, **kwds ) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", line 1045, in __init__ self.parse( root, guid=guid ) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", line 1260, in parse self.parse_inputs( root ) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", line 1351, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", line 1655, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", line 1723, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", line 1679, in parse_input_elem group.inputs = self.parse_input_elem( elem, enctypes, context ) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", line 1751, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/__init__.py", line 1764, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/parameters/basic.py", line 215, in build return parameter_types[param_type]( tool, param ) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/parameters/basic.py", line 1566, in __init__ ToolParameter.__init__( self, tool, elem ) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/parameters/basic.py", line 54, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/parameters/validation.py", line 283, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/localdata1/galaxy/glxmaint/src/lib/galaxy/tools/data/__init__.py", line 35, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes'
I fixed this by adding the appropriate entries to tool_data_table_conf.xml. I then reran the migrate_tools command successfully. However, now my "history_dataset_association" table in the database was blown away at some point. The table is now completely empty. Have you ever seen this before?
Thanks, Eric ________________________________ From: Dannon Baker [dannon.baker@gmail.com] Sent: Tuesday, May 27, 2014 7:40 AM To: Paniagua, Eric Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host
Hey Eric,
It looks like you have connection info for both tcp/ip connections and unix sockets in the connection strings. If you're logging in using "psql -h wigserv5.cshl.eduhttp://wigserv5.cshl.edu <snip>", then you only want the tcp/ip connection info. Drop the ?host=tmp off the third option you listed and I think you'll be up and running, so:
postgresql://glxeric:XXXXX@wigserv5.cshl.edu:5432/glxerichttp://glxeric:XXXXX@wigserv5.cshl.edu:5432/glxeric
-Dannon
On Sat, May 24, 2014 at 1:49 AM, Paniagua, Eric <epaniagu@cshl.edumailto:epaniagu@cshl.edu> wrote: Dear Galaxy Developers,
I've been banging my head against this one for a few days now.
I have two Galaxy instances. One resides on a server called "genomics", which also hosts the corresponding PostgreSQL installation. The second also resides on "genomics", but its database is hosted on "wigserv5".
Based on the tests I just ran and code I just read, sqlalchemy (not Galaxy) is ignoring the hostname/port part of the database_connection string. For reference, the connection strings I've tried are:
postgresql://glxeric:XXXXX@/glxeric?host=/tmp postgresql://glxeric:XXXXX@wigserv5.cshl.edu/glxeric?host=/tmphttp://glxeric:XXXXX@wigserv5.cshl.edu/glxeric?host=/tmp postgresql://glxeric:XXXXX@wigserv5.cshl.edu:5432/glxeric?host=/tmphttp://glxeric:XXXXX@wigserv5.cshl.edu:5432/glxeric?host=/tmp postgresql://glxeric:XXXXX@adgdgdfdflkhjfdhfkl/glxeric?host=/tmp
All of these appear to result in Galaxy connecting to the PostgreSQL installation on genomics, as determined by Galaxy schema version discrepancies and other constraints. With each connection string, Galaxy starts up normally. I force database activity by browsing saved histories. It works every time. By all appearances, the second Galaxy instance is using the PostgreSQL database hosted on "genomics", not on "wigserv5".
All databases and roles exist, and the databases are populated.
When I comment out the "database_connection" line in universe_wsgi.ini, I get errors arising from the later configuration of PostgreSQL-specific Galaxy options, as expected.
I can connect to the database server on "wigserv5" using "psql -h wigserv5.cshl.eduhttp://wigserv5.cshl.edu -d glxeric -U glxeric" from the server "genomics".
Have you ever observed this behavior from Galaxy or sqlalchemy?
Thanks, Eric
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