1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/da3aece419ca/ changeset: da3aece419ca user: greg date: 2013-03-18 15:24:03 summary: Rename community_wsgi.ini.sample to be tool_shed_wsgi.ini.sample, run_community.sh to run_tool_shed.sh, and fix references to these files in the code. affected #: 8 files

diff -r 6be1fed44bf65402f11d2bd4b576fa76941f1393 -r da3aece419ca2940c4a8a3a059e3bfe25a98098b community_wsgi.ini.sample --- a/community_wsgi.ini.sample +++ /dev/null @@ -1,98 +0,0 @@ -# ---- HTTP Server ---------------------------------------------------------- - -[server:main] - -use = egg:Paste#http -port = 9009 - -# The address on which to listen. By default, only listen to localhost (the tool shed will not -# be accessible over the network). Use '0.0.0.0' to listen on all available network interfaces. -#host = 0.0.0.0 -host = 127.0.0.1 - -use_threadpool = true -threadpool_workers = 10 - -# ---- Galaxy Webapps Community Interface ------------------------------------------------- - -[app:main] - -# Specifies the factory for the universe WSGI application -paste.app_factory = galaxy.webapps.tool_shed.buildapp:app_factory -log_level = DEBUG - -# Database connection -database_file = database/community.sqlite -# You may use a SQLAlchemy connection string to specify an external database instead -#database_connection = postgres:///community_test?host=/var/run/postgresql - -# Where the hgweb.config file is stored. The default is the Galaxy installation directory. -#hgweb_config_dir = None - -# Where dataset files are saved -file_path = database/community_files -# Temporary storage for additional datasets, this should be shared through the cluster -new_file_path = database/tmp - -# Session support (beaker) -use_beaker_session = True -session_type = memory -session_data_dir = %(here)s/database/beaker_sessions -session_key = galaxysessions -session_secret = changethisinproduction - -# -- Users and Security - -# Galaxy encodes various internal values when these values will be output in -# some format (for example, in a URL or cookie). You should set a key to be -# used by the algorithm that encodes and decodes these values. It can be any -# string. If left unchanged, anyone could construct a cookie that would grant -# them access to others' sessions. -id_secret = changethisinproductiontoo - -# User authentication can be delegated to an upstream proxy server (usually -# Apache). The upstream proxy should set a REMOTE_USER header in the request. -# Enabling remote user disables regular logins. For more information, see: -# http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy -#use_remote_user = False - -# Configuration for debugging middleware -debug = true -use_lint = false - -# NEVER enable this on a public site (even test or QA) -# use_interactive = true - -# this should be a comma-separated list of valid Galaxy users -#admin_users = user1@example.org,user2@example.org - -# Force everyone to log in (disable anonymous access) -require_login = False - -# path to sendmail -sendmail_path = /usr/sbin/sendmail - -# For use by email messages sent from the tool shed -#smtp_server = smtp.your_tool_shed_server -#email_from = your_tool_shed_email@server - -# The URL linked by the "Support" link in the "Help" menu. -#support_url = http://wiki.g2.bx.psu.edu/Support - -# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) -## use_heartbeat = True - -# Profiling middleware (cProfile based) -## use_profile = True - -# Use the new iframe / javascript based layout -use_new_layout = true - -# Serving static files (needed if running standalone) -static_enabled = True -static_cache_time = 360 -static_dir = %(here)s/static/ -static_images_dir = %(here)s/static/images -static_favicon_dir = %(here)s/static/favicon.ico -static_scripts_dir = %(here)s/static/scripts/ -static_style_dir = %(here)s/static/june_2007_style/blue

diff -r 6be1fed44bf65402f11d2bd4b576fa76941f1393 -r da3aece419ca2940c4a8a3a059e3bfe25a98098b run_community.sh --- a/run_community.sh +++ /dev/null @@ -1,37 +0,0 @@ -#!/bin/sh - -cd `dirname $0` - -SAMPLES=" - community_wsgi.ini.sample - datatypes_conf.xml.sample - external_service_types_conf.xml.sample - migrated_tools_conf.xml.sample - reports_wsgi.ini.sample - shed_tool_conf.xml.sample - tool_conf.xml.sample - shed_tool_data_table_conf.xml.sample - tool_data_table_conf.xml.sample - tool_sheds_conf.xml.sample - openid_conf.xml.sample - universe_wsgi.ini.sample - tool-data/shared/ncbi/builds.txt.sample - tool-data/shared/ensembl/builds.txt.sample - tool-data/shared/ucsc/builds.txt.sample - tool-data/shared/ucsc/publicbuilds.txt.sample - tool-data/shared/igv/igv_build_sites.txt.sample - tool-data/shared/rviewer/rviewer_build_sites.txt.sample - tool-data/*.sample - static/welcome.html.sample -" - -# Create any missing config/location files -for sample in $SAMPLES; do - file=`echo $sample | sed -e 's/.sample$//'` - if [ ! -f "$file" -a -f "$sample" ]; then - echo "Initializing $file from `basename $sample`" - cp $sample $file - fi -done - -python ./scripts/paster.py serve community_wsgi.ini --pid-file=community_webapp.pid --log-file=community_webapp.log $@

diff -r 6be1fed44bf65402f11d2bd4b576fa76941f1393 -r da3aece419ca2940c4a8a3a059e3bfe25a98098b run_tool_shed.sh --- /dev/null +++ b/run_tool_shed.sh @@ -0,0 +1,37 @@ +#!/bin/sh + +cd `dirname $0` + +SAMPLES=" + tool_shed_wsgi.ini.sample + datatypes_conf.xml.sample + external_service_types_conf.xml.sample + migrated_tools_conf.xml.sample + reports_wsgi.ini.sample + shed_tool_conf.xml.sample + tool_conf.xml.sample + shed_tool_data_table_conf.xml.sample + tool_data_table_conf.xml.sample + tool_sheds_conf.xml.sample + openid_conf.xml.sample + universe_wsgi.ini.sample + tool-data/shared/ncbi/builds.txt.sample + tool-data/shared/ensembl/builds.txt.sample + tool-data/shared/ucsc/builds.txt.sample + tool-data/shared/ucsc/publicbuilds.txt.sample + tool-data/shared/igv/igv_build_sites.txt.sample + tool-data/shared/rviewer/rviewer_build_sites.txt.sample + tool-data/*.sample + static/welcome.html.sample +" + +# Create any missing config/location files +for sample in $SAMPLES; do + file=`echo $sample | sed -e 's/.sample$//'` + if [ ! -f "$file" -a -f "$sample" ]; then + echo "Initializing $file from `basename $sample`" + cp $sample $file + fi +done + +python ./scripts/paster.py serve tool_shed_wsgi.ini --pid-file=tool_shed_webapp.pid --log-file=tool_shed_webapp.log $@

diff -r 6be1fed44bf65402f11d2bd4b576fa76941f1393 -r da3aece419ca2940c4a8a3a059e3bfe25a98098b scripts/db_shell.py --- a/scripts/db_shell.py +++ b/scripts/db_shell.py @@ -30,7 +30,7 @@ # 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' + config_file = 'tool_shed_wsgi.ini' repo = 'lib/galaxy/webapps/tool_shed/model/migrate' else: # Poor man's optparse

diff -r 6be1fed44bf65402f11d2bd4b576fa76941f1393 -r da3aece419ca2940c4a8a3a059e3bfe25a98098b scripts/manage_db.py --- a/scripts/manage_db.py +++ b/scripts/manage_db.py @@ -18,7 +18,7 @@ # 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' + config_file = 'tool_shed_wsgi.ini' repo = 'lib/galaxy/webapps/tool_shed/model/migrate' else: # Poor man's optparse

diff -r 6be1fed44bf65402f11d2bd4b576fa76941f1393 -r da3aece419ca2940c4a8a3a059e3bfe25a98098b scripts/tool_shed/migrate_tools_to_repositories.py --- a/scripts/tool_shed/migrate_tools_to_repositories.py +++ b/scripts/tool_shed/migrate_tools_to_repositories.py @@ -10,7 +10,7 @@

0. This script must be run on a repo updated to changeset: 5621:4618be57481b

-1. Before running this script, make sure the following config setting is set in community_wsgi.ini +1. Before running this script, make sure the following config setting is set in tool_shed_wsgi.ini

# Enable next-gen tool shed features enable_next_gen_tool_shed = True @@ -262,7 +262,7 @@ print " " print "##########################################" print "%s - Migrating current tool archives to new tool repositories" % now - # community_wsgi.ini file + # tool_shed_wsgi.ini file ini_file = sys.argv[1] conf_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} ) conf_parser.read( ini_file )

diff -r 6be1fed44bf65402f11d2bd4b576fa76941f1393 -r da3aece419ca2940c4a8a3a059e3bfe25a98098b test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -175,7 +175,7 @@ os.environ[ 'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF' ] = shed_tool_data_table_conf_file # ---- Build Tool Shed Application -------------------------------------------------- toolshedapp = None - global_conf = { '__file__' : 'community_wsgi.ini.sample' } + global_conf = { '__file__' : 'tool_shed_wsgi.ini.sample' } # if not toolshed_database_connection.startswith( 'sqlite://' ): # kwargs[ 'database_engine_option_max_overflow' ] = '20' if tool_dependency_dir is not None:

diff -r 6be1fed44bf65402f11d2bd4b576fa76941f1393 -r da3aece419ca2940c4a8a3a059e3bfe25a98098b tool_shed_wsgi.ini.sample --- /dev/null +++ b/tool_shed_wsgi.ini.sample @@ -0,0 +1,98 @@ +# ---- HTTP Server ---------------------------------------------------------- + +[server:main] + +use = egg:Paste#http +port = 9009 + +# The address on which to listen. By default, only listen to localhost (the tool shed will not +# be accessible over the network). Use '0.0.0.0' to listen on all available network interfaces. +#host = 0.0.0.0 +host = 127.0.0.1 + +use_threadpool = true +threadpool_workers = 10 + +# ---- Galaxy Webapps Community Interface ------------------------------------------------- + +[app:main] + +# Specifies the factory for the universe WSGI application +paste.app_factory = galaxy.webapps.tool_shed.buildapp:app_factory +log_level = DEBUG + +# Database connection +database_file = database/community.sqlite +# You may use a SQLAlchemy connection string to specify an external database instead +#database_connection = postgres:///community_test?host=/var/run/postgresql + +# Where the hgweb.config file is stored. The default is the Galaxy installation directory. +#hgweb_config_dir = None + +# Where dataset files are saved +file_path = database/community_files +# Temporary storage for additional datasets, this should be shared through the cluster +new_file_path = database/tmp + +# Session support (beaker) +use_beaker_session = True +session_type = memory +session_data_dir = %(here)s/database/beaker_sessions +session_key = galaxysessions +session_secret = changethisinproduction + +# -- Users and Security + +# Galaxy encodes various internal values when these values will be output in +# some format (for example, in a URL or cookie). You should set a key to be +# used by the algorithm that encodes and decodes these values. It can be any +# string. If left unchanged, anyone could construct a cookie that would grant +# them access to others' sessions. +id_secret = changethisinproductiontoo + +# User authentication can be delegated to an upstream proxy server (usually +# Apache). The upstream proxy should set a REMOTE_USER header in the request. +# Enabling remote user disables regular logins. For more information, see: +# http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy +#use_remote_user = False + +# Configuration for debugging middleware +debug = true +use_lint = false + +# NEVER enable this on a public site (even test or QA) +# use_interactive = true + +# this should be a comma-separated list of valid Galaxy users +#admin_users = user1@example.org,user2@example.org + +# Force everyone to log in (disable anonymous access) +require_login = False + +# path to sendmail +sendmail_path = /usr/sbin/sendmail + +# For use by email messages sent from the tool shed +#smtp_server = smtp.your_tool_shed_server +#email_from = your_tool_shed_email@server + +# The URL linked by the "Support" link in the "Help" menu. +#support_url = http://wiki.g2.bx.psu.edu/Support + +# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) +## use_heartbeat = True + +# Profiling middleware (cProfile based) +## use_profile = True + +# Use the new iframe / javascript based layout +use_new_layout = true + +# Serving static files (needed if running standalone) +static_enabled = True +static_cache_time = 360 +static_dir = %(here)s/static/ +static_images_dir = %(here)s/static/images +static_favicon_dir = %(here)s/static/favicon.ico +static_scripts_dir = %(here)s/static/scripts/ +static_style_dir = %(here)s/static/june_2007_style/blue

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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