3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a0880211749b/ Changeset: a0880211749b Branch: next-stable User: saketkc Date: 2014-09-25 06:10:51+00:00 Summary: Update tool_list to reflect recent change in use of envirnoment variables tool_list.py now makese use of GALAXY_TEST_TOOL_CONF and exits throwing an appropriate error Affected #: 1 file diff -r 5296d69134bddeb11246c70347d83c6073da646f -r a0880211749b1f65c4fa78f9c121fa2234decc67 tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -1,9 +1,15 @@ -import os,sys +import os +import sys #--------read tool_conf.xml to get all the tool xml file names----------- onoff = 1 tool_list = [] -for line in open("tool_conf.xml", "r"): +tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'config/tool_conf.xml' ) +if not os.path.isfile(tool_conf_file): + sys.stderr.write( "Tool config file not found: {}\n".format(tool_conf_file) ) + sys.exit(1) + +for line in open(tool_conf_file, "r"): if line.find("<!--") != -1: onoff = 0 if line.find("file") != -1 and onoff==1: https://bitbucket.org/galaxy/galaxy-central/commits/f3284eb7ec21/ Changeset: f3284eb7ec21 Branch: next-stable User: jmchilton Date: 2014-09-25 13:00:38+00:00 Summary: Fixes to tool_list.py for legacy configurations and modified tool confs. Now uses roughly the same order of precedence as Galaxy proper's config. Affected #: 1 file diff -r a0880211749b1f65c4fa78f9c121fa2234decc67 -r f3284eb7ec210d50a3e9f2c0d393cffcb24894da tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -4,8 +4,15 @@ #--------read tool_conf.xml to get all the tool xml file names----------- onoff = 1 tool_list = [] -tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'config/tool_conf.xml' ) -if not os.path.isfile(tool_conf_file): +tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', None ) + +if tool_conf_file is None: + for possible_tool_file in [ 'config/tool_conf.xml', 'tool_conf.xml', 'config/tool_conf.xml.sample' ]: + tool_conf_file = possible_tool_file + if os.path.isfile( possible_tool_file ): + break + +if tool_conf_file is None or not os.path.isfile(tool_conf_file): sys.stderr.write( "Tool config file not found: {}\n".format(tool_conf_file) ) sys.exit(1) https://bitbucket.org/galaxy/galaxy-central/commits/1db1d66229db/ Changeset: 1db1d66229db User: jmchilton Date: 2014-09-25 13:03:21+00:00 Summary: Merge latest next-stable. Affected #: 1 file diff -r bcd98385d0af97c1dd5d4ba7944da49ff28158e1 -r 1db1d66229db79f633f70b6f5b52d339cdb2dbb4 tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -4,8 +4,15 @@ #--------read tool_conf.xml to get all the tool xml file names----------- onoff = 1 tool_list = [] -tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'config/tool_conf.xml' ) -if not os.path.isfile(tool_conf_file): +tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', None ) + +if tool_conf_file is None: + for possible_tool_file in [ 'config/tool_conf.xml', 'tool_conf.xml', 'config/tool_conf.xml.sample' ]: + tool_conf_file = possible_tool_file + if os.path.isfile( possible_tool_file ): + break + +if tool_conf_file is None or not os.path.isfile(tool_conf_file): sys.stderr.write( "Tool config file not found: {}\n".format(tool_conf_file) ) sys.exit(1) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.