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).

lib/galaxy/app.py

@@ -29,7 +29,7 @@ class UniverseApplication( object ):
             db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database
         # Initialize database / check for appropriate schema version
         from galaxy.model.migrate.check import create_or_verify_database
-        create_or_verify_database( db_url, self.config.database_engine_options )
+        create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options )
         # Setup the database engine and ORM
         from galaxy.model import mapping
         self.model = mapping.init( self.config.file_path,

lib/galaxy/eggs/__init__.py

@@ -247,7 +247,7 @@ class Crate( object ):
     Reads the eggs.ini file for use with checking and fetching.
     """
     config_file = os.path.join( galaxy_dir, 'eggs.ini' )
-    def __init__( self, platform=None ):
+    def __init__( self, galaxy_config_file, platform=None ):
         self.eggs = {}
         self.config = CaseSensitiveConfigParser()
         self.repo = None
@@ -256,7 +256,7 @@ class Crate( object ):
         self.py_platform = None
         if platform is not None:
             self.py_platform = platform.split( '-' )[0]
-        self.galaxy_config = GalaxyConfig()
+        self.galaxy_config = GalaxyConfig( galaxy_config_file )
         self.parse()
     def parse( self ):
         self.config.read( Crate.config_file )
@@ -349,12 +349,14 @@ class Crate( object ):
             raise EggNotFetchable( missing )
 
 class GalaxyConfig( object ):
-    config_file = os.path.join( galaxy_dir, "universe_wsgi.ini" )
     always_conditional = ( 'GeneTrack', 'pysam', 'ctypes', 'python_daemon' )
-    def __init__( self ):
-        self.config = ConfigParser.ConfigParser()
-        if self.config.read( GalaxyConfig.config_file ) == []:
-            raise Exception( "error: unable to read Galaxy config from %s" % GalaxyConfig.config_file )
+    def __init__( self, config_file ):
+        if config_file is None:
+            self.config = None
+        else:
+            self.config = ConfigParser.ConfigParser()
+            if self.config.read( config_file ) == []:
+                raise Exception( "error: unable to read Galaxy config from %s" % config_file )
     def check_conditional( self, egg_name ):
         def check_pysam():
             # can't build pysam on solaris < 10
@@ -364,6 +366,10 @@ class GalaxyConfig( object ):
                 if int( minor ) < 10:
                     return False
             return True
+        # If we're using require() we may not have a Galaxy config file, but if
+        # we're using require(), we don't care about conditionals.
+        if self.config is None:
+            return True
         if egg_name == "pysqlite":
             # SQLite is different since it can be specified in two config vars and defaults to True
             try:
@@ -396,7 +402,7 @@ def get_env():
 env = get_env()
 
 def require( req_str ):
-    c = Crate()
+    c = Crate( None )
     req = pkg_resources.Requirement.parse( req_str )
     # TODO: This breaks egg version requirements.  Not currently a problem, but
     # it could become one.

lib/galaxy/eggs/dist.py

@@ -39,10 +39,10 @@ class DistScrambleCrate( ScrambleCrate ):
     Holds eggs with info on how to build them for distribution.
     """
     dist_config_file = os.path.join( galaxy_dir, 'dist-eggs.ini' )
-    def __init__( self, build_on='all' ):
+    def __init__( self, galaxy_config_file, build_on='all' ):
         self.dist_config = CaseSensitiveConfigParser()
         self.build_on = build_on
-        ScrambleCrate.__init__( self )
+        ScrambleCrate.__init__( self, galaxy_config_file )
     def parse( self ):
         self.dist_config.read( DistScrambleCrate.dist_config_file )
         self.hosts = dict( self.dist_config.items( 'hosts' ) )

lib/galaxy/model/migrate/check.py

@@ -20,7 +20,7 @@ dialect_to_egg = {
     "mysql" : "MySQL_python"
 }
 
-def create_or_verify_database( url, engine_options={} ):
+def create_or_verify_database( url, galaxy_config_file, engine_options={} ):
     """
     Check that the database is use-able, possibly creating it if empty (this is
     the only time we automatically create tables, otherwise we force the
@@ -98,8 +98,11 @@ def create_or_verify_database( url, engine_options={} ):
     # Verify that the code and the DB are in sync
     db_schema = schema.ControlledSchema( engine, migrate_repository )
     if migrate_repository.versions.latest != db_schema.version:
-        raise Exception( "Your database has version '%d' but this code expects version '%d'.  Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'."
-                            % ( db_schema.version, migrate_repository.versions.latest ) )
+        config_arg = ''
+        if os.path.abspath( os.path.join( os.getcwd(), 'universe_wsgi.ini' ) ) != galaxy_config_file:
+            config_arg = ' -c %s' % galaxy_config_file.replace( os.path.abspath( os.getcwd() ), '.' )
+        raise Exception( "Your database has version '%d' but this code expects version '%d'.  Please backup your database and then migrate the schema by running 'sh manage_db.sh%s upgrade'."
+                            % ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
     else:
         log.info( "At database version %d" % db_schema.version )
         
@@ -123,4 +126,4 @@ def migrate_to_current_version( engine, schema ):
         finally:
             for message in "".join( sys.stdout.buffer ).split( "\n" ):
                 log.info( message )
-            sys.stdout = old_stdout
+            sys.stdout = old_stdout

run.sh

@@ -32,7 +32,7 @@ for arg in "$@"; do
     [ "$arg" = "--stop-daemon" ] && FETCH_EGGS=0; break
 done
 if [ $FETCH_EGGS -eq 1 ]; then
-    python ./scripts/check_eggs.py quiet
+    python ./scripts/check_eggs.py -q
     if [ $? -ne 0 ]; then
         echo "Some eggs are out of date, attempting to fetch..."
         python ./scripts/fetch_eggs.py

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 )