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Another fix for galaxy.ini being conditionally existent.

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Update scripts/check_eggs.py and scripts/fetch_eggs.py with logic to find the correct config file. These files should be refactored so they can share some of this code the way I refactored the database management scripts I guess.
This commit is contained in:
John Chilton
2014-10-03 01:34:42 -04:00
parent d7208e7f8c
commit 01a9e91f39
2 changed files with 32 additions and 13 deletions
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scripts/check_eggs.py
+16 -6
View File
@@ -10,12 +10,22 @@ import os, sys, logging
from optparse import OptionParser
parser = OptionParser()
parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)', default='config/galaxy.ini' )
parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)', default=None )
parser.add_option( '-q', '--quiet', dest='quiet', action="store_true", help='Quiet (no output, only set return code)', default=False )
( options, args ) = parser.parse_args()
if not os.path.exists( options.config ):
print "Config file does not exist (see 'python %s --help'): %s" % ( sys.argv[0], options.config )
config_set = True
config = options.config
if config is None:
config_set = False
for name in ['config/galaxy.ini', 'universe_wsgi.ini', 'config/galaxy.ini.sample']:
if os.path.exists(name):
config = name
break
if not os.path.exists( config ):
print "Config file does not exist (see 'python %s --help'): %s" % ( sys.argv[0], config )
sys.exit( 1 )
root = logging.getLogger()
@@ -23,15 +33,15 @@ root.setLevel( 10 )
root.addHandler( logging.StreamHandler( sys.stdout ) )
config_arg = ''
if options.config != 'config/galaxy.ini':
config_arg = '-c %s' % options.config
if config_set:
config_arg = '-c %s' % config
lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) )
sys.path.append( lib )
from galaxy.eggs import Crate
c = Crate( options.config )
c = Crate( config )
if c.config_missing:
if not options.quiet:
print "Some of your Galaxy eggs are out of date. Please update them"
scripts/fetch_eggs.py
+16 -7
View File
@@ -9,13 +9,22 @@ import os, sys, logging
from optparse import OptionParser
parser = OptionParser()
parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)', default='config/galaxy.ini' )
parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (config/galaxy.ini)', default=None )
parser.add_option( '-e', '--egg-name', dest='egg_name', help='Egg name (as defined in eggs.ini) to fetch, or "all" for all eggs, even those not needed by your configuration' )
parser.add_option( '-p', '--platform', dest='platform', help='Fetch for a specific platform (by default, eggs are fetched for *this* platform' )
( options, args ) = parser.parse_args()
if not os.path.exists( options.config ):
print "Config file does not exist (see 'python %s --help'): %s" % ( sys.argv[0], options.config )
config_set = True
config = options.config
if config is None:
config_set = False
for name in ['config/galaxy.ini', 'universe_wsgi.ini', 'config/galaxy.ini.sample']:
if os.path.exists(name):
config = name
break
if not os.path.exists( config ):
print "Config file does not exist (see 'python %s --help'): %s" % ( sys.argv[0], config )
sys.exit( 1 )
root = logging.getLogger()
@@ -29,9 +38,9 @@ from galaxy.eggs import Crate, EggNotFetchable
import pkg_resources
if options.platform:
c = Crate( options.config, platform = options.platform )
c = Crate( config, platform = options.platform )
else:
c = Crate( options.config )
c = Crate( config )
try:
if not options.egg_name:
c.resolve() # Only fetch eggs required by the config
@@ -49,8 +58,8 @@ try:
print "%s %s is installed at %s" % ( dist.project_name, dist.version, dist.location )
except EggNotFetchable, e:
config_arg = ''
if options.config != 'config/galaxy.ini':
config_arg = '-c %s ' % options.config
if config_set:
config_arg = '-c %s ' % config
try:
assert options.egg_name != 'all'
egg = e.eggs[0]