Undo changes unrelated to uWSGI mule work

lib/galaxy/objectstore/__init__.py

@@ -23,10 +23,10 @@ from galaxy.util import (
     directory_hash_id,
     force_symlink,
     safe_makedirs,
+    safe_relpath,
     umask_fix_perms,
 )
 from galaxy.util.odict import odict
-from galaxy.util.path import safe_relpath
 from galaxy.util.sleeper import Sleeper
 
 NO_SESSION_ERROR_MESSAGE = "Attempted to 'create' object store entity in configuration with no database session present."

lib/galaxy/objectstore/azure_blob.py

@@ -11,8 +11,7 @@ import time
 from datetime import datetime
 
 from galaxy.exceptions import ObjectInvalid, ObjectNotFound
-from galaxy.util import directory_hash_id, umask_fix_perms
-from galaxy.util.path import safe_relpath
+from galaxy.util import directory_hash_id, safe_relpath, umask_fix_perms
 from galaxy.util.sleeper import Sleeper
 from ..objectstore import convert_bytes, ObjectStore
 

lib/galaxy/objectstore/pithos.py

@@ -8,9 +8,9 @@ import shutil
 from galaxy.exceptions import ObjectInvalid, ObjectNotFound
 from galaxy.util import (
     directory_hash_id,
+    safe_relpath,
     umask_fix_perms,
 )
-from galaxy.util.path import safe_relpath
 from ..objectstore import ObjectStore
 
 try:

lib/galaxy/objectstore/rods.py

@@ -13,7 +13,7 @@ from posixpath import dirname as path_dirname
 from posixpath import join as path_join
 
 from galaxy.exceptions import ObjectInvalid, ObjectNotFound
-from galaxy.util.path import safe_relpath
+from galaxy.util import safe_relpath
 
 from ..objectstore import DiskObjectStore, local_extra_dirs
 

lib/galaxy/objectstore/s3.py

@@ -22,11 +22,11 @@ except ImportError:
 from galaxy.exceptions import ObjectInvalid, ObjectNotFound
 from galaxy.util import (
     directory_hash_id,
+    safe_relpath,
     string_as_bool,
     umask_fix_perms,
     which,
 )
-from galaxy.util.path import safe_relpath
 from galaxy.util.sleeper import Sleeper
 
 from .s3_multipart_upload import multipart_upload

lib/galaxy/tools/toolbox/base.py

@@ -2,7 +2,6 @@ import logging
 import os
 import string
 import time
-from errno import ENOENT
 from xml.etree.ElementTree import ParseError
 
 from markupsafe import escape
@@ -545,7 +544,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin, object):
             concrete_path = os.path.join(tool_path, path)
             if not os.path.exists(concrete_path):
                 # This is a lot faster than attempting to load a non-existing tool
-                raise IOError(ENOENT, os.strerror(ENOENT))
+                raise IOError
             tool_shed_repository = None
             can_load_into_panel_dict = True
 
@@ -586,8 +585,8 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin, object):
             labels = item.labels
             if labels is not None:
                 tool.labels = labels
-        except (IOError, OSError) as exc:
-            log.error("Error reading tool configuration file from path '%s': %s", path, exc)
+        except IOError:
+            log.error("Error reading tool configuration file from path: %s" % path)
         except Exception:
             log.exception("Error reading tool from path: %s", path)
 

lib/galaxy/util/__init__.py

@@ -860,21 +860,17 @@ def string_as_bool_or_none(string):
         return False
 
 
-def listify(item, do_strip=None, strip=False, split=True):
+def listify(item, do_strip=False):
     """
     Make a single item a single item list, or return a list if passed a
-    list.  Splits strings on commas unless split=False, strips whitespace
-    from around comma-split elements if strip=True.  Passing a None returns
-    an empty list.  Passing a tuple returns the tuple.
+    list.  Passing a None returns an empty list.
     """
-    if do_strip is not None and strip is False:
-        strip = do_strip
     if not item:
         return []
-    elif isinstance(item, list) or isinstance(item, tuple):
+    elif isinstance(item, list):
         return item
-    elif split and isinstance(item, string_types) and item.count(','):
-        if strip:
+    elif isinstance(item, string_types) and item.count(','):
+        if do_strip:
             return [token.strip() for token in item.split(',')]
         else:
             return item.split(',')

lib/tool_shed/capsule/capsule_manager.py

@@ -12,9 +12,8 @@ from sqlalchemy import and_, false
 
 import tool_shed.repository_types.util as rt_util
 from galaxy import web
-from galaxy.util import asbool, build_url, CHUNK_SIZE
+from galaxy.util import asbool, build_url, CHUNK_SIZE, safe_relpath
 from galaxy.util.odict import odict
-from galaxy.util.path import safe_relpath
 from tool_shed.dependencies import attribute_handlers
 from tool_shed.dependencies.repository.relation_builder import RelationBuilder
 from tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager import RepositoryDependencyInstallManager