Merge.

config/reports_wsgi.ini.sample

@@ -64,10 +64,10 @@ mailing_join_addr = galaxy-user-join@bx.psu.edu
 use_new_layout = true
 
 # Serving static files (needed if running standalone)
-static_enabled = True
-static_cache_time = 360
-static_dir = %(here)s/static/
-static_images_dir = %(here)s/static/images
-static_favicon_dir = %(here)s/static/favicon.ico
-static_scripts_dir = %(here)s/static/scripts/
-static_style_dir = %(here)s/static/june_2007_style/blue
+# static_enabled = True
+# static_cache_time = 360
+# static_dir = %(here)s/static/
+# static_images_dir = %(here)s/static/images
+# static_favicon_dir = %(here)s/static/favicon.ico
+# static_scripts_dir = %(here)s/static/scripts/
+# static_style_dir = %(here)s/static/june_2007_style/blue

eggs.ini

@@ -73,7 +73,7 @@ WebOb = 0.8.5
 wsgiref = 0.1.2
 Babel = 1.3
 wchartype = 0.1
-Whoosh = 2.5.7
+Whoosh = 2.4.1
 ; fluent_logger = 0.3.3
 raven = 3.1.8
 

lib/galaxy/util/__init__.py

@@ -371,7 +371,7 @@ def pretty_print_time_interval( time = False, precise = False ):
                 if second_diff < 86400:
                     return str(second_diff / 3600) + " hours ago"
         if day_diff == 1:
-            return "Yesterday"
+            return "yesterday"
         if day_diff < 7:
             return str( day_diff ) + " days ago"
         if day_diff < 31:
@@ -381,16 +381,16 @@ def pretty_print_time_interval( time = False, precise = False ):
         return str( day_diff / 365 ) + " years ago"
     else:
         if day_diff == 0:
-            return "Today"
+            return "today"
         if day_diff == 1:
-            return "Yesterday"
+            return "yesterday"
         if day_diff < 7:
-            return "this week"
+            return "less than a week"
         if day_diff < 31:
-            return "this month"
+            return "less than a month"
         if day_diff < 365:
-            return "this year"
-        return str( day_diff / 365 ) + " years ago"
+            return "less than a year"
+        return "a few years ago"
 
 
 def pretty_print_json(json_data, is_json_string=False):

lib/galaxy/web/framework/webapp.py

@@ -814,3 +814,26 @@ class GalaxyWebTransaction( base.DefaultWebTransaction,
         template = Template( source=template_string,
                              searchList=[context or kwargs, dict(caller=self)] )
         return str(template)
+
+
+def build_url_map( app, global_conf, local_conf ):
+    from paste.urlmap import URLMap
+    from galaxy.web.framework.middleware.static import CacheableStaticURLParser as Static
+    urlmap = URLMap()
+    # Merge the global and local configurations
+    conf = global_conf.copy()
+    conf.update(local_conf)
+    # Get cache time in seconds
+    cache_time = conf.get( "static_cache_time", None )
+    if cache_time is not None:
+        cache_time = int( cache_time )
+    # Send to dynamic app by default
+    urlmap["/"] = app
+    # Define static mappings from config
+    urlmap["/static"] = Static( conf.get( "static_dir", "./static/" ), cache_time )
+    urlmap["/images"] = Static( conf.get( "static_images_dir", "./static/images" ), cache_time )
+    urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir", "./static/scripts/" ), cache_time )
+    urlmap["/static/style"] = Static( conf.get( "static_style_dir", "./static/style/blue" ), cache_time )
+    urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir", "./static/favicon.ico" ), cache_time )
+    urlmap["/robots.txt"] = Static( conf.get( "static_robots_txt", "./static/robots.txt" ), cache_time )
+    return urlmap, cache_time

lib/galaxy/webapps/galaxy/api/provenance.py

@@ -52,15 +52,21 @@ class BaseProvenanceController( BaseAPIController ):
             if item.copied_from_library_dataset_dataset_association:
                 item = item.copied_from_library_dataset_dataset_association
             job = item.creating_job
-            return {
-                "id": trans.security.encode_id(item.id),
-                "uuid": ( lambda uuid: str( uuid ) if uuid else None )( item.dataset.uuid),
-                "job_id": trans.security.encode_id( job.id ),
-                "tool_id": job.tool_id,
-                "parameters": self._get_job_record(trans, job, follow),
-                "stderr": job.stderr,
-                "stdout": job.stdout,
-            }
+            if job is not None:
+                return {
+                    "id": trans.security.encode_id(item.id),
+                    "uuid": ( lambda uuid: str( uuid ) if uuid else None )( item.dataset.uuid),
+                    "job_id": trans.security.encode_id( job.id ),
+                    "tool_id": job.tool_id,
+                    "parameters": self._get_job_record(trans, job, follow),
+                    "stderr": job.stderr,
+                    "stdout": job.stdout,
+                }
+            else:
+                return {
+                    "id": trans.security.encode_id(item.id),
+                    "uuid": ( lambda uuid: str( uuid ) if uuid else None )( item.dataset.uuid)
+                }
         return None
 
     def _get_job_record(self, trans, job, follow):

lib/galaxy/webapps/galaxy/buildapp.py

@@ -610,26 +610,8 @@ def wrap_in_middleware( app, global_conf, **local_conf ):
     return app
 
 def wrap_in_static( app, global_conf, plugin_frameworks=None, **local_conf ):
-    from paste.urlmap import URLMap
     from galaxy.web.framework.middleware.static import CacheableStaticURLParser as Static
-    urlmap = URLMap()
-    # Merge the global and local configurations
-    conf = global_conf.copy()
-    conf.update(local_conf)
-    # Get cache time in seconds
-    cache_time = conf.get( "static_cache_time", None )
-    if cache_time is not None:
-        cache_time = int( cache_time )
-    # Send to dynamic app by default
-    urlmap["/"] = app
-    # Define static mappings from config
-    urlmap["/static"] = Static( conf.get( "static_dir", "./static/" ), cache_time )
-    urlmap["/images"] = Static( conf.get( "static_images_dir", "./static/images" ), cache_time )
-    urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir", "./static/scripts/" ), cache_time )
-    urlmap["/static/style"] = Static( conf.get( "static_style_dir", "./static/style/blue" ), cache_time )
-    urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir", "./static/favicon.ico" ), cache_time )
-    urlmap["/robots.txt"] = Static( conf.get( "static_robots_txt", "./static/robots.txt" ), cache_time )
-
+    urlmap, cache_time = galaxy.web.framework.webapp.build_url_map( app, global_conf, local_conf )
     # wrap any static dirs for plugins
     plugin_frameworks = plugin_frameworks or []
     for framework in plugin_frameworks:

lib/galaxy/webapps/reports/buildapp.py

@@ -62,7 +62,7 @@ def app_factory( global_conf, **kwargs ):
     # Wrap the webapp in some useful middleware
     if kwargs.get( 'middleware', True ):
         webapp = wrap_in_middleware( webapp, global_conf, **kwargs )
-    if kwargs.get( 'static_enabled', True ):
+    if asbool( kwargs.get( 'static_enabled', True ) ):
         webapp = wrap_in_static( webapp, global_conf, **kwargs )
     # Close any pooled database connections before forking
     try:
@@ -135,25 +135,7 @@ def wrap_in_middleware( app, global_conf, **local_conf ):
     return app
 
 def wrap_in_static( app, global_conf, **local_conf ):
-    from paste.urlmap import URLMap
-    from galaxy.web.framework.middleware.static import CacheableStaticURLParser as Static
-    urlmap = URLMap()
-    # Merge the global and local configurations
-    conf = global_conf.copy()
-    conf.update(local_conf)
-    # Get cache time in seconds
-    cache_time = conf.get( "static_cache_time", None )
-    if cache_time is not None:
-        cache_time = int( cache_time )
-    # Send to dynamic app by default
-    urlmap["/"] = app
-    # Define static mappings from config
-    urlmap["/static"] = Static( conf.get( "static_dir" ), cache_time )
-    urlmap["/images"] = Static( conf.get( "static_images_dir" ), cache_time )
-    urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir" ), cache_time )
-    urlmap["/static/style"] = Static( conf.get( "static_style_dir" ), cache_time )
-    urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir" ), cache_time )
-    # URL mapper becomes the root webapp
+    urlmap, _ = galaxy.web.framework.webapp.build_url_map( app, global_conf, local_conf )
     return urlmap
 
 def build_template_error_formatters():

lib/galaxy/webapps/tool_shed/buildapp.py

@@ -134,7 +134,7 @@ def app_factory( global_conf, **kwargs ):
     # Wrap the webapp in some useful middleware
     if kwargs.get( 'middleware', True ):
         webapp = wrap_in_middleware( webapp, global_conf, **kwargs )
-    if kwargs.get( 'static_enabled', True ):
+    if asbool( kwargs.get( 'static_enabled', True ) ):
         webapp = wrap_in_static( webapp, global_conf, **kwargs )
     # Close any pooled database connections before forking
     try:
@@ -227,26 +227,7 @@ def wrap_in_middleware( app, global_conf, **local_conf ):
     return app
 
 def wrap_in_static( app, global_conf, **local_conf ):
-    from paste.urlmap import URLMap
-    from galaxy.web.framework.middleware.static import CacheableStaticURLParser as Static
-    urlmap = URLMap()
-    # Merge the global and local configurations
-    conf = global_conf.copy()
-    conf.update(local_conf)
-    # Get cache time in seconds
-    cache_time = conf.get( "static_cache_time", None )
-    if cache_time is not None:
-        cache_time = int( cache_time )
-    # Send to dynamic app by default
-    urlmap["/"] = app
-    # Define static mappings from config
-    urlmap["/static"] = Static( conf.get( "static_dir", "./static/" ), cache_time )
-    urlmap["/images"] = Static( conf.get( "static_images_dir", "./static/images" ), cache_time )
-    urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir", "./static/scripts/" ), cache_time )
-    urlmap["/static/style"] = Static( conf.get( "static_style_dir", "./static/style/blue" ), cache_time )
-    urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir", "./static/favicon.ico" ), cache_time )
-    urlmap["/robots.txt"] = Static( conf.get( "static_robots_txt", "./static/robots.txt" ), cache_time )
-    # URL mapper becomes the root webapp
+    urlmap, _ = galaxy.web.framework.webapp.build_url_map( app, global_conf, local_conf )
     return urlmap
 
 def build_template_error_formatters():

lib/galaxy/webapps/tool_shed/search/repo_search.py

@@ -45,7 +45,7 @@ class RepoWeighting( scoring.BM25F ):
     use_final = True
 
     def final( self, searcher, docnum, score ):
-        log.debug('score before: ' +  str(score) )
+        # log.debug('score before: ' +  str(score) )
         
         # Arbitrary for now
         reasonable_hits = 100.0
@@ -59,15 +59,15 @@ class RepoWeighting( scoring.BM25F ):
         if times_downloaded == 0:
             times_downloaded = 1
         popularity_modifier = ( times_downloaded / reasonable_hits )
-        log.debug('popularity_modifier: ' +  str(popularity_modifier) )
+        # log.debug('popularity_modifier: ' +  str(popularity_modifier) )
 
         cert_modifier = 2 if searcher.stored_fields( docnum )[ "approved" ] == 'yes' else 1
-        log.debug('cert_modifier: ' +  str(cert_modifier) )
+        # log.debug('cert_modifier: ' +  str(cert_modifier) )
 
         # Adjust the computed score for this document by the popularity
         # and by the certification level.
         final_score = score * popularity_modifier * cert_modifier
-        log.debug('score after: ' +  str( final_score ) )
+        # log.debug('score after: ' +  str( final_score ) )
         return final_score
 
 
@@ -108,16 +108,14 @@ class RepoSearch( object ):
                         'remote_repository_url',
                         'repo_owner_username' ], schema = schema )
 
-                    # user_query = parser.parse( search_term )
                     user_query = parser.parse( '*' + search_term + '*' )
-
-                    # hits = searcher.search( user_query, terms = True )
                     hits = searcher.search_page( user_query, page, pagelen = 10, terms = True )
+
                     log.debug( 'searching for: #' +  str( search_term ) )
                     log.debug( 'total hits: ' +  str( len( hits ) ) )
                     log.debug( 'scored hits: ' + str( hits.scored_length() ) )
                     results = {}
-                    results[ 'total_results'] = str( hits.scored_length() )
+                    results[ 'total_results'] = str( len( hits ) )
                     results[ 'hits' ] = []
                     for hit in hits:
                         hit_dict = {}

scripts/update_shed_config_path.py

@@ -0,0 +1,80 @@
+import os
+import argparse
+import ConfigParser
+import sys
+new_path = [ os.path.join( os.getcwd(), "lib" ) ]
+new_path.extend( sys.path[1:] )
+sys.path = new_path
+
+import logging
+import galaxy.model.tool_shed_install
+import galaxy.model.tool_shed_install.mapping as mapping
+from galaxy.model.orm import *
+from galaxy import eggs
+eggs.require('sqlalchemy')
+import sqlalchemy
+
+def main( opts, session, model ):
+    '''
+    Find all tool shed repositories with the bad path and update with the correct path.
+    '''
+    for row in session.query( model.ToolShedRepository ).all():
+        if 'shed_config_filename' in row.metadata:
+            if row.metadata['shed_config_filename'] == opts.bad_filename:
+                row.metadata['shed_config_filename'] = opts.good_filename
+                session.add( row )
+                session.flush()
+    return 0
+
+def create_database( config_file ):
+    parser = ConfigParser.SafeConfigParser()
+    parser.read( config_file )
+    # Determine which database connection to use.
+    database_connection = parser.get( 'app:main', 'install_database_connection' )
+    if database_connection is None:
+        database_connection = parser.get( 'app:main', 'database_connection' )
+    if database_connection is None:
+        database_connection = 'sqlite:///%s' % parser.get( 'app:main', 'database_file' )
+    if database_connection is None:
+        print 'Unable to determine correct database connection.'
+        exit(1)
+
+    '''Initialize the database file.'''
+    dialect_to_egg = {
+        "sqlite" : "pysqlite>=2",
+        "postgres" : "psycopg2",
+        "postgresql" : "psycopg2",
+        "mysql" : "MySQL_python"
+    }
+    dialect = ( database_connection.split( ':', 1 ) )[0]
+    try:
+        egg = dialect_to_egg[ dialect ]
+        try:
+            eggs.require( egg )
+            print( "%s egg successfully loaded for %s dialect" % ( egg, dialect ) )
+        except:
+            # If the module is in the path elsewhere (i.e. non-egg), it'll still load.
+            print( "%s egg not found, but an attempt will be made to use %s anyway" % ( egg, dialect ) )
+    except KeyError:
+        # Let this go, it could possibly work with db's we don't support.
+        print( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect )
+
+    # Initialize the database connection.
+    engine = create_engine( database_connection )
+    meta = MetaData( bind=engine )
+    install_session = Session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) )
+    model = mapping.init( database_connection )
+    return install_session, model
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument( '--config_file', dest='config_file', required=True, help="The path to your Galaxy configuration .ini file." )
+    parser.add_argument( '--from', dest='bad_filename', required=True, help="The old, invalid path to the shed_tool_conf.xml or migrated_tools_conf.xml file." )
+    parser.add_argument( '--to', dest='good_filename', required=True, help="The updated path to the shed_tool_conf.xml or migrated_tools_conf.xml file." )
+    parser.add_argument( '--force', dest='force', action='store_true', help="Use this flag to set the new path even if the file does not (yet) exist there." )
+    opts = parser.parse_args()
+    if not os.path.exists( opts.good_filename ) and not opts.force:
+        print 'The file %s does not exist, use the --force option to proceed.' % opts.good_filename
+        exit(1)
+    session, model = create_database( opts.config_file )
+    exit( main( opts, session, model ) )