Merge branch 'release_19.09' into release_20.01

lib/galaxy/jobs/runners/util/cli/shell/local.py

@@ -34,6 +34,8 @@ class LocalShell(BaseShellExec):
     True
     >>> exec_result.stdout.strip() == u'Hello World'
     True
+    >>> exec_result.returncode
+    0
     >>> exec_result = exec_python("import time; time.sleep(10)", timeout=1, timeout_check_interval=.1)
     >>> exec_result.stdout == u''
     True
@@ -63,6 +65,8 @@ class LocalShell(BaseShellExec):
             kill_pg(p.pid)
             return Bunch(stdout=u'', stderr=TIMEOUT_ERROR_MESSAGE, returncode=TIMEOUT_RETURN_CODE)
         outf.seek(0)
+        # Need to poll once to establish return code
+        p.poll()
         return Bunch(stdout=_read_str(outf), stderr=_read_str(p.stderr), returncode=p.returncode)
 
 

lib/galaxy/managers/users.py

@@ -106,12 +106,7 @@ class UserManager(base.ModelManager, deletable.PurgableManagerMixin):
             # TODO:?? flush needed for permissions below? If not, make optional
         except exc.IntegrityError as db_err:
             raise exceptions.Conflict(str(db_err))
-        # can throw an sqlalx.IntegrityError if username not unique
-        self.app.security_agent.create_private_user_role(user)
-        # We set default user permissions, before we log in and set the default history permissions
-        if hasattr(self.app.config, "new_user_dataset_access_role_default_private"):
-            permissions = self.app.config.new_user_dataset_access_role_default_private
-            self.app.security_agent.user_set_default_permissions(user, default_access_private=permissions)
+        self.app.security_agent.create_user_role(user, self.app)
         return user
 
     def delete(self, user, flush=True):

lib/galaxy/model/security.py

@@ -656,6 +656,18 @@ class GalaxyRBACAgent(RBACAgent):
         self.sa_session.flush()
         return assoc
 
+    def create_user_role(self, user, app):
+        # Create private user role if necessary
+        if not self.get_private_user_role(user):
+            self.create_private_user_role(user)
+        # Create default user permissions if necessary
+        if not user.default_permissions:
+            if hasattr(app.config, "new_user_dataset_access_role_default_private"):
+                permissions = app.config.new_user_dataset_access_role_default_private
+                self.user_set_default_permissions(user, default_access_private=permissions)
+            else:
+                self.user_set_default_permissions(user, history=True, dataset=True)
+
     def create_private_user_role(self, user):
         # Create private role
         role = self.model.Role(name=user.email, description='Private Role for ' + user.email, type=self.model.Role.types.PRIVATE)

lib/galaxy/web/framework/webapp.py

@@ -714,6 +714,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
            - add the disk usage of the current session to the user's total disk usage
         """
         self.user_checks(user)
+        self.app.security_agent.create_user_role(user, self.app)
         # Set the previous session
         prev_galaxy_session = self.galaxy_session
         prev_galaxy_session.is_valid = False

packages/tool_util/HISTORY.rst

@@ -6,7 +6,13 @@ History
 .. to_doc
 
 ---------------------
-19.9.1.dev0
+19.9.2.dev0
+---------------------
+
+
+
+---------------------
+19.9.1 (2019-12-28)
 ---------------------
 
 

packages/tool_util/galaxy/project_galaxy_tool_util.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '19.9.1.dev0'
+__version__ = '19.9.2.dev0'
 
 PROJECT_NAME = "galaxy-tool-util"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"