Remove hardcoding of universe_wsgi.ini, fixes issue #358 (except for the sample cleanup scripts which, as samples, are expected to be modified by the site anyway).

scripts/check_eggs.py

@@ -3,27 +3,35 @@
 usage: check_eggs.py
 """
 import os, sys, logging
+from optparse import OptionParser
+
+parser = OptionParser()
+parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default='universe_wsgi.ini' )
+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 )
+    sys.exit( 1 )
 
 root = logging.getLogger()
 root.setLevel( 10 )
 root.addHandler( logging.StreamHandler( sys.stdout ) )
 
+config_arg = ''
+if options.config != 'universe_wsgi.ini':
+    config_arg = '-c %s' % options.config
+
 lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) )
 sys.path.append( lib )
 
-try:
-    assert sys.argv[1] == 'quiet'
-    quiet = True
-except:
-    quiet = False
-
 from galaxy.eggs import Crate
 
-c = Crate()
+c = Crate( options.config )
 if c.config_missing:
-    if not quiet:
+    if not options.quiet:
         print "Some of your Galaxy eggs are out of date.  Please update them"
         print "by running:"
-        print "  python scripts/fetch_eggs.py"
+        print "  python scripts/fetch_eggs.py %s" % config_arg
     sys.exit( 1 )
 sys.exit( 0 )

scripts/dist-scramble.py

@@ -1,11 +1,10 @@
-"""
-usage: dist-scramble.py <egg_name> [platform]
-  egg_name - The egg to scramble (as defined in eggs.ini)
-  platform - The platform to scramble on (as defined in
-             dist-eggs.ini).  Leave blank for all.
-             Platform-inspecific eggs ignore this argument.
-"""
 import os, sys, logging
+from optparse import OptionParser
+
+parser = OptionParser()
+parser.add_option( '-e', '--egg-name', dest='egg_name', help='Egg name (as defined in eggs.ini) to scramble (required)' )
+parser.add_option( '-p', '--platform', dest='platform', help='Scramble for a specific platform (by default, eggs are scrambled for all platforms, see dist-eggs.ini for platform names)' )
+( options, args ) = parser.parse_args()
 
 root = logging.getLogger()
 root.setLevel( 10 )
@@ -17,18 +16,20 @@ sys.path.append( lib )
 from galaxy.eggs.dist import DistScrambleCrate, ScrambleFailure
 from galaxy.eggs import EggNotFetchable
 
-if len( sys.argv ) > 3 or len( sys.argv ) < 2:
-    print __doc__
+if not options.egg_name:
+    print "ERROR: You must specify an egg to scramble (-e)"
+    parser.print_help()
     sys.exit( 1 )
-elif len( sys.argv ) == 3:
-    c = DistScrambleCrate( sys.argv[2] )
+
+if options.platform:
+    c = DistScrambleCrate( None, options.platform )
 else:
-    c = DistScrambleCrate()
+    c = DistScrambleCrate( None )
 
 try:
-    eggs = c[sys.argv[1]]
+    eggs = c[options.egg_name]
 except:
-    print "error: %s not in eggs.ini" % sys.argv[1]
+    print "ERROR: %s not in eggs.ini" % options.egg_name
     sys.exit( 1 )
 failed = []
 for egg in eggs:

scripts/fetch_eggs.py

@@ -1,15 +1,15 @@
-"""
-usage: fetch_eggs.py [egg_name] [platform]
-    With no arguments, fetches all eggs necessary according to the
-    settings in universe_wsgi.ini.
-  egg_name - Fetch only this egg (as defined in eggs.ini) or 'all' for
-    all eggs (even those not required by your settings).
-  platform - Fetch eggs for a specific platform (if not provided, fetch
-    eggs for *this* platform).  Useful for fetching eggs for cluster
-    nodes which are of a different architecture than the head node.
-    Platform name can be determined with the get_platforms.py script.
-"""
 import os, sys, logging
+from optparse import OptionParser
+
+parser = OptionParser()
+parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default='universe_wsgi.ini' )
+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 )
+    sys.exit( 1 )
 
 root = logging.getLogger()
 root.setLevel( 10 )
@@ -21,18 +21,18 @@ sys.path.append( lib )
 from galaxy.eggs import Crate, EggNotFetchable
 import pkg_resources
 
+if options.platform:
+    c = Crate( options.config, platform = options.platform )
+else:
+    c = Crate( options.config )
 try:
-    c = Crate( platform = sys.argv[2] )
-except:
-    c = Crate()
-try:
-    if len( sys.argv ) == 1:
+    if not options.egg_name:
         c.resolve() # Only fetch eggs required by the config
-    elif sys.argv[1] == 'all':
+    elif options.egg_name == 'all':
         c.resolve( all=True ) # Fetch everything
     else:
         # Fetch a specific egg
-        name = sys.argv[1]
+        name = options.egg_name
         try:
             egg = c[name]
         except:
@@ -41,12 +41,15 @@ try:
         dist = egg.resolve()[0]
         print "%s %s is installed at %s" % ( dist.project_name, dist.version, dist.location )
 except EggNotFetchable, e:
+    config_arg = ''
+    if options.config != 'universe_wsgi.ini':
+        config_arg = '-c %s ' % options.config
     try:
-        assert sys.argv[1] != 'all'
+        assert options.egg_name != 'all'
         egg = e.eggs[0]
         print "%s %s couldn't be downloaded automatically.  You can try" % ( egg.name, egg.version )
         print "building it by hand with:"
-        print "  python scripts/scramble.py %s"
+        print "  python scripts/scramble.py %s-e %s" % ( config_arg, egg.name )
     except ( AssertionError, IndexError ):
         print "One or more of the python eggs necessary to run Galaxy couldn't be"
         print "downloaded automatically.  You can try building them by hand (all"
@@ -54,6 +57,6 @@ except EggNotFetchable, e:
         print "  python scripts/scramble.py"
         print "Or individually:"
         for egg in e.eggs:
-            print "  python scripts/scramble.py %s" % egg.name
+            print "  python scripts/scramble.py %s-e %s" % ( config_arg, egg.name )
     sys.exit( 1 )
 sys.exit( 0 )

scripts/manage_db.py

@@ -21,7 +21,15 @@ if sys.argv[-1] in [ 'community' ]:
     config_file = 'community_wsgi.ini'
     repo = 'lib/galaxy/webapps/community/model/migrate'
 else:
+    # Poor man's optparse
     config_file = 'universe_wsgi.ini'
+    if '-c' in sys.argv:
+        pos = sys.argv.index( '-c' )
+        sys.argv.pop(pos)
+        config_file = sys.argv.pop( pos )
+    if not os.path.exists( config_file ):
+        print "Galaxy config file does not exist (hint: use '-c config.ini' for non-standard locations): %s" % config_file
+        sys.exit( 1 )
     repo = 'lib/galaxy/model/migrate'
 
 cp = SafeConfigParser()

scripts/scramble.py

@@ -1,11 +1,14 @@
-"""
-usage: scramble.py [egg_name]
-    With no arguments, scrambles all eggs necessary according to the
-    settings in universe_wsgi.ini.
-  egg_name - Scramble only this egg (as defined in eggs.ini) or 'all'
-    for all eggs (even those not required by your settings).
-"""
 import os, sys, logging
+from optparse import OptionParser
+
+parser = OptionParser()
+parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default='universe_wsgi.ini' )
+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' )
+( 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 )
+    sys.exit( 1 )
 
 root = logging.getLogger()
 root.setLevel( 10 )
@@ -16,22 +19,25 @@ sys.path.append( lib )
 
 from galaxy.eggs.scramble import ScrambleCrate, ScrambleFailure, EggNotFetchable
 
-c = ScrambleCrate()
+c = ScrambleCrate( options.config )
 
 try:
-    if len( sys.argv ) == 1:
+    if not options.egg_name:
         eggs = c.scramble()
-    elif sys.argv[1] == 'all':
+    elif options.egg_name == 'all':
         c.scramble( all=True )
     else:
         # Scramble a specific egg
-        name = sys.argv[1]
+        name = options.egg_name
         try:
             egg = c[name]
         except:
             print "error: %s not in eggs.ini" % name
             sys.exit( 1 )
         for dependency in egg.dependencies:
+            config_arg = ''
+            if options.config != 'universe_wsgi.ini':
+                config_arg = '-c %s' % options.config
             print "Checking %s dependency: %s" % ( egg.name, dependency )
             try:
                 c[dependency].require()
@@ -39,7 +45,7 @@ try:
                 degg = e.eggs[0]
                 print "%s build dependency %s %s couldn't be downloaded" % ( egg.name, degg.name, degg.version )
                 print "automatically.  You can try building it by hand with:"
-                print "  python scripts/scramble.py %s" % degg.name
+                print "  python scripts/scramble.py %s-e %s" % ( config_agr, degg.name )
                 sys.exit( 1 )
         egg.scramble()
         sys.exit( 0 )