From 8d3c2569eaa5c669ccb5af51d684dfb1f245ea86 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 22 Sep 2014 19:14:12 -0400
Subject: [PATCH] Fix ORM scripts for 42f677bab2e4880b62758614fcb2c7dc27013788.
 Updating common Python module used by ORM scripts
 (create_db.sh/migrate_db.sh/db_shell.py) to allow the same configuration via
 enviornment variables as well. Thanks to Bjoern for the bug report/feature
 request.

---
 lib/galaxy/config.py            | 16 ++++---------
 lib/galaxy/model/orm/scripts.py | 14 +++++------
 lib/galaxy/util/properties.py   | 41 +++++++++++++++++++++++++++++++++
 3 files changed, 52 insertions(+), 19 deletions(-)
 create mode 100644 lib/galaxy/util/properties.py

diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index 571bf3e8557..bea6d458c7e 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -13,6 +13,7 @@ import logging.config
 import ConfigParser
 from datetime import timedelta
 from galaxy.web.formatting import expand_pretty_datetime_format
+from galaxy.util.properties import load_app_properties
 from galaxy.util import string_as_bool
 from galaxy.util import listify
 from galaxy.util.dbkeys import GenomeBuilds
@@ -20,9 +21,6 @@ from galaxy import eggs
 
 log = logging.getLogger( __name__ )
 
-CONFIG_DEFAULT_PREFIX = "GALAXY_CONFIG_"
-CONFIG_OVERRIDE_PREFIX = "GALAXY_CONFIG_OVERRIDE_"
-
 
 def resolve_path( path, root ):
     """If 'path' is relative make absolute by prepending 'root'"""
@@ -39,15 +37,9 @@ class Configuration( object ):
     deprecated_options = ( 'database_file', )
 
     def __init__( self, **kwargs ):
-        for key in os.environ:
-            if key.startswith( CONFIG_OVERRIDE_PREFIX ):
-                config_key = key[ len( CONFIG_OVERRIDE_PREFIX ): ].lower()
-                kwargs[ config_key ] = os.environ[ key ]
-            elif key.startswith( CONFIG_DEFAULT_PREFIX ):
-                config_key = key[ len( CONFIG_DEFAULT_PREFIX ): ].lower()
-                if config_key not in kwargs:
-                    kwargs[ config_key ] = os.environ[ key ]
-
+        kwargs = load_app_properties(
+            kwds=kwargs
+        )
         self.config_dict = kwargs
         self.root = kwargs.get( 'root_dir', '.' )
 
diff --git a/lib/galaxy/model/orm/scripts.py b/lib/galaxy/model/orm/scripts.py
index 0b399ac87fa..a05b161fd45 100644
--- a/lib/galaxy/model/orm/scripts.py
+++ b/lib/galaxy/model/orm/scripts.py
@@ -3,7 +3,6 @@ Code to support database helper scripts (create_db.py, manage_db.py, etc...).
 """
 import logging
 import os.path
-from ConfigParser import SafeConfigParser
 
 from galaxy import eggs
 
@@ -12,6 +11,7 @@ eggs.require( "Tempita" )
 eggs.require( "SQLAlchemy" )
 eggs.require( "sqlalchemy_migrate" )
 
+from galaxy.util.properties import load_app_properties
 from galaxy.model.orm import dialect_to_egg
 
 import pkg_resources
@@ -112,13 +112,13 @@ def get_config( argv, cwd=None ):
     if cwd:
         config_file = os.path.join( cwd, config_file )
 
-    cp = SafeConfigParser()
-    cp.read( config_file )
+    properties = load_app_properties( ini_file=config_file )
 
-    if cp.has_option( "app:main", "%sdatabase_connection" % config_prefix):
-        db_url = cp.get( "app:main", "%sdatabase_connection" % config_prefix )
-    elif cp.has_option( "app:main", "%sdatabase_file" % config_prefix ):
-        db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % cp.get( "app:main", "database_file" )
+    if ("%sdatabase_connection" % config_prefix) in properties:
+        db_url = properties[ "%sdatabase_connection" % config_prefix ]
+    elif ("%sdatabase_file" % config_prefix) in properties:
+        database_file = properties[ "%sdatabase_file" % config_prefix ]
+        db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % database_file
     else:
         db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % default_sqlite_file
 
diff --git a/lib/galaxy/util/properties.py b/lib/galaxy/util/properties.py
new file mode 100644
index 00000000000..1dad1130bed
--- /dev/null
+++ b/lib/galaxy/util/properties.py
@@ -0,0 +1,41 @@
+""" Module used to blend ini, environment, and explicit dictionary properties
+to determine application configuration. Some hard coded defaults for Galaxy but
+this should be reusable by tool shed and pulsar as well.
+"""
+import os
+import os.path
+
+
+def load_app_properties(
+    kwds={},
+    ini_file=None,
+    ini_section="app:main",
+    config_prefix="GALAXY_CONFIG_"
+):
+    properties = kwds.copy() if kwds else {}
+    if ini_file:
+        defaults = {
+            'here': os.path.dirname(os.path.abspath(ini_file)),
+            '__file__': os.path.abspath(ini_file)
+        }
+        # Mimic the way loadwsgi loads configuration files - needed for
+        # correctness given the very specific ways interpolation is handled.
+        from galaxy.util.pastescript.loadwsgi import NicerConfigParser
+        parser = NicerConfigParser(ini_file, defaults=defaults)
+        parser.optionxform = str  # Don't lower-case keys
+        with open(ini_file) as f:
+            parser.read_file(f)
+
+        properties.update( dict( parser.items( ini_section ) ) )
+
+    override_prefix = "%sOVERRIDE_" % config_prefix
+    for key in os.environ:
+        if key.startswith( override_prefix ):
+            config_key = key[ len( override_prefix ): ].lower()
+            properties[ config_key ] = os.environ[ key ]
+        elif key.startswith( config_prefix ):
+            config_key = key[ len( config_prefix ): ].lower()
+            if config_key not in properties:
+                properties[ config_key ] = os.environ[ key ]
+
+    return properties