Merge branch 'dev' into bbi-js3

config/galaxy.ini.sample

@@ -211,7 +211,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 #conda_verbose_install_check=False
 # Set to True to instruct Galaxy to install Conda from the web automatically
 # if it cannot find a local copy and conda_exec is not configured.
-#conda_auto_init = True
+#conda_auto_init = False
 
 # File containing the Galaxy Tool Sheds that should be made available to
 # install from in the admin interface (.sample used if default does not exist).

config/reports.ini.sample

@@ -39,12 +39,16 @@ prefix = /reports
 
 # Specifies the factory for the universe WSGI application
 paste.app_factory = galaxy.webapps.reports.buildapp:app_factory
-log_level = DEBUG
+
+# Verbosity of console log messages.  Acceptable values can be found here:
+# https://docs.python.org/2/library/logging.html#logging-levels
+#log_level = DEBUG
 
 # Database connection
-# Galaxy reports are intended for production Galaxy instances, so sqlite is not supported.
-# You may use a SQLAlchemy connection string to specify an external database.
-#database_connection = postgres:///galaxy_test?user=postgres&password=postgres
+# Galaxy reports are intended for production Galaxy instances, so sqlite (and the default value
+# below) is not supported. An SQLAlchemy connection string should be used specify an external
+# database.
+#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
 
 # Where dataset files are saved
 #file_path = database/files
@@ -55,13 +59,6 @@ log_level = DEBUG
 # used for the cache
 #template_cache_path = database/compiled_templates/reports
 
-# Session support (beaker)
-use_beaker_session = True
-session_type = memory
-session_data_dir = %(here)s/database/beaker_sessions
-session_key = galaxysessions
-session_secret = changethisinproduction
-
 # Configuration for debugging middleware
 #debug = False
 

config/tool_shed.ini.sample

@@ -23,23 +23,27 @@ threadpool_kill_thread_limit = 10800
 
 # Specifies the factory for the universe WSGI application
 paste.app_factory = galaxy.webapps.tool_shed.buildapp:app_factory
+
+# Verbosity of console log messages.  Acceptable values can be found here:
+# https://docs.python.org/2/library/logging.html#logging-levels
 #log_level = DEBUG
 
-# Database connection
-database_file = database/community.sqlite
-# You may use a SQLAlchemy connection string to specify
-# an external database instead
-#database_connection = postgres:///community_test?host=/var/run/postgresql
+# By default, the Tool Shed uses a SQLite database at 'database/community.sqlite'.  You
+# may use a SQLAlchemy connection string to specify an external database
+# instead.  This string takes many options which are explained in detail in the
+# config file documentation.
+#database_connection = sqlite:///./database/community.sqlite?isolation_level=IMMEDIATE
 
 # Where the hgweb.config file is stored.
 # The default is the Galaxy installation directory.
 #hgweb_config_dir = None
 
 # Where tool shed repositories are stored.
-file_path = database/community_files
+#file_path = database/community_files
+
 # Temporary storage for additional datasets,
 # this should be shared through the cluster
-new_file_path = database/tmp
+#new_file_path = database/tmp
 
 # File containing old-style genome builds
 #builds_file_path = tool-data/shared/ucsc/builds.txt
@@ -53,13 +57,6 @@ new_file_path = database/tmp
 #   standard).
 #pretty_datetime_format = $locale (UTC)
 
-# Session support (beaker)
-use_beaker_session = True
-session_type = memory
-session_data_dir = %(here)s/database/beaker_sessions
-session_key = galaxysessions
-session_secret = changethisinproduction
-
 # -- Repository and Tool search
 # Using the script located at scripts/build_ts_whoosh_index.py
 # you can generate search index and allow full text API searching over
@@ -94,12 +91,14 @@ session_secret = changethisinproduction
 
 # -- Users and Security
 
-# Galaxy encodes various internal values when these values will be output in
+# The Tool Shed encodes various internal values when these values will be output in
 # some format (for example, in a URL or cookie).  You should set a key to be
 # used by the algorithm that encodes and decodes these values.  It can be any
 # string.  If left unchanged, anyone could construct a cookie that would grant
 # them access to others' sessions.
-id_secret = changethisinproductiontoo
+# One simple way to generate a value for this is with the shell command:
+#   python -c 'import time; print time.time()' | md5sum | cut -f 1 -d ' '
+#id_secret = changethisinproductiontoo
 
 # User authentication can be delegated to an upstream proxy server (usually
 # Apache).  The upstream proxy should set a REMOTE_USER header in the request.
@@ -126,8 +125,11 @@ id_secret = changethisinproductiontoo
 # NEVER enable this on a public site (even test or QA)
 #use_interactive = true
 
-# this should be a comma-separated list of valid Galaxy users
-#admin_users = user1@example.org,user2@example.org
+# Administrative users - set this to a comma-separated list of valid Tool Shed
+# users (email addresses).  These users will have access to the Admin section
+# of the server, and will have access to create users, groups, roles,
+# libraries, and more.
+#admin_users = None
 
 # Force everyone to log in (disable anonymous access)
 #require_login = False

lib/galaxy/auth/providers/ldap_ad.py

@@ -162,12 +162,20 @@ class LDAP(AuthProvider):
 
             l = ldap.initialize(_get_subs(options, 'server', params))
             l.protocol_version = 3
+            bind_password = _get_subs(options, 'bind-password', params)
+            if not bind_password:
+                raise RuntimeError('LDAP authenticate: empty password')
             l.simple_bind_s(_get_subs(
-                options, 'bind-user', params), _get_subs(options, 'bind-password', params))
-            whoami = l.whoami_s()
-            log.debug("LDAP authenticate: whoami is %s", whoami)
-            if whoami is None:
-                raise RuntimeError('LDAP authenticate: anonymous bind')
+                options, 'bind-user', params), bind_password)
+            try:
+                whoami = l.whoami_s()
+            except ldap.PROTOCOL_ERROR:
+                # The "Who am I?" extended operation is not supported by this LDAP server
+                pass
+            else:
+                log.debug("LDAP authenticate: whoami is %s", whoami)
+                if whoami is None:
+                    raise RuntimeError('LDAP authenticate: anonymous bind')
         except Exception:
             log.warning('LDAP authenticate: bind exception', exc_info=True)
             return (failure_mode, '', '')

lib/galaxy/security/validate_user_input.py

@@ -34,7 +34,10 @@ def validate_email( trans, email, user=None, check_dup=True ):
         message = "User with that email already exists."
     #  If the blacklist is not empty filter out the disposable domains.
     elif trans.app.config.blacklist_content is not None:
-        if email.split('@')[1] in trans.app.config.blacklist_content:
+        domain = email.split('@')[1]
+        if len( domain.split('.') ) > 2:
+            domain = ('.').join( domain.split('.')[-2:] )
+        if domain in trans.app.config.blacklist_content:
             message = "Please enter your permanent email address."
     return message
 

lib/galaxy/tools/deps/__init__.py

@@ -22,7 +22,7 @@ EXTRA_CONFIG_KWDS = {
     'conda_debug': None,
     'conda_ensure_channels': 'r,bioconda,iuc',
     'conda_auto_install': False,
-    'conda_auto_init': True,
+    'conda_auto_init': False,
 }
 
 CONFIG_VAL_NOT_FOUND = object()

lib/galaxy/util/postfork.py

@@ -7,8 +7,10 @@ Handle postfork functions under uWSGI
 # uwsgi-managed process.
 try:
     import uwsgi
-    if uwsgi.numproc:
+    if hasattr(uwsgi, "numproc"):
         process_is_uwsgi = True
+    else:
+        process_is_uwsgi = False
 except ImportError:
     # This is not a uwsgi process, or something went horribly wrong.
     process_is_uwsgi = False

lib/galaxy/webapps/tool_shed/config.py

@@ -66,7 +66,7 @@ class Configuration( object ):
         self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root )
         self.cookie_path = kwargs.get( "cookie_path", "/" )
         self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', False ) )
-        self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" )
+        self.id_secret = kwargs.get( "id_secret", "changethisinproductiontoo")
         # Tool stuff
         self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root )
         self.tool_secret = kwargs.get( "tool_secret", "" )