Merge pull request #4994 from natefoo/non-mule-changes

Changes made while working on uWSGI mules that don't belong in the mules PR

lib/galaxy/objectstore/__init__.py

@@ -22,9 +22,11 @@ from galaxy.exceptions import ObjectInvalid, ObjectNotFound
 from galaxy.util import (
     directory_hash_id,
     force_symlink,
+    umask_fix_perms,
+)
+from galaxy.util.path import (
     safe_makedirs,
     safe_relpath,
-    umask_fix_perms,
 )
 from galaxy.util.odict import odict
 from galaxy.util.sleeper import Sleeper

lib/galaxy/objectstore/azure_blob.py

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

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

lib/galaxy/util/__init__.py

@@ -862,13 +862,25 @@ def string_as_bool_or_none(string):
 
 def listify(item, do_strip=False):
     """
-    Make a single item a single item list, or return a list if passed a
-    list.  Passing a None returns an empty list.
+    Make a single item a single item list.
+
+    If *item* is a string, it is split on comma (``,``) characters to produce the list. Optionally, if *do_strip* is
+    true, any extra whitespace around the split items is stripped.
+
+    If *item* is a list it is returned unchanged. If *item* is a tuple, it is converted to a list and returned. If
+    *item* evaluates to False, an empty list is returned.
+
+    :type  item:        object
+    :param item:        object to make a list from
+    :type  do_strip:    bool
+    :param do_strip:    strip whitespaces from around split items, if set to ``True``
+    :rtype:             list
+    :returns:           The input as a list
     """
     if not item:
         return []
-    elif isinstance(item, list):
-        return item
+    elif isinstance(item, list) or isinstance(item, tuple):
+        return list(item)
     elif isinstance(item, string_types) and item.count(','):
         if do_strip:
             return [token.strip() for token in item.split(',')]

lib/galaxy/util/script.py

@@ -0,0 +1,57 @@
+"""Utilities for Galaxy scripts
+"""
+import argparse
+import os
+import sys
+
+from galaxy.util.properties import find_config_file, load_app_properties
+
+DESCRIPTION = None
+ACTIONS = None
+ARGUMENTS = None
+DEFAULT_ACTION = None
+
+
+def main_factory(description=None, actions=None, arguments=None, default_action=None):
+    global DESCRIPTION, ACTIONS, ARGUMENTS, DEFAULT_ACTION
+    DESCRIPTION = description
+    ACTIONS = actions or {}
+    ARGUMENTS = arguments or []
+    DEFAULT_ACTION = default_action
+    return main
+
+
+def main(argv=None):
+    """Entry point for conversion process."""
+    if argv is None:
+        argv = sys.argv[1:]
+    args = _arg_parser().parse_args(argv)
+    kwargs = _app_properties(args)
+    action = args.action
+    action_func = ACTIONS[action]
+    action_func(args, kwargs)
+
+
+def _app_properties(args):
+    # FIXME: you can use galaxy.util.path.extensions for this
+    config_file = args.config_file or find_config_file(args.app)
+    app_properties = load_app_properties(config_file=config_file, config_section=args.config_section)
+    return app_properties
+
+
+def _arg_parser():
+    parser = argparse.ArgumentParser(description=DESCRIPTION)
+    parser.add_argument('action', metavar='ACTION', type=str,
+                        choices=ACTIONS.keys(),
+                        default=DEFAULT_ACTION,
+                        nargs='?' if DEFAULT_ACTION is not None else None,
+                        help='action to perform')
+    parser.add_argument("-c", "--config-file",
+                        default=os.environ.get('GALAXY_CONFIG_FILE', None))
+    parser.add_argument("--config-section",
+                        default=os.environ.get('GALAXY_CONFIG_SECTION', None))
+    parser.add_argument("--app",
+                        default=os.environ.get('GALAXY_APP', 'galaxy'))
+    for argument in ARGUMENTS:
+        parser.add_argument(*argument[0], **argument[1])
+    return parser

lib/tool_shed/capsule/capsule_manager.py

@@ -12,8 +12,9 @@ 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, safe_relpath
+from galaxy.util import asbool, build_url, CHUNK_SIZE
 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

scripts/manage_tool_dependencies.py

@@ -1,4 +1,3 @@
-import argparse
 import os.path
 import sys
 
@@ -11,43 +10,16 @@ from galaxy.config import (
     parse_dependency_options,
 )
 from galaxy.tools.deps import CachedDependencyManager, DependencyManager, NullDependencyManager
-from galaxy.util.properties import find_config_file, load_app_properties
+from galaxy.util.script import main_factory
 
 DESCRIPTION = "Script to manage tool dependencies (with focus on a Conda environments)."
 
 
-def main(argv=None):
-    """Entry point for conversion process."""
-    if argv is None:
-        argv = sys.argv[1:]
-    args = _arg_parser().parse_args(argv)
-    action = args.action
-    action_func = ACTIONS[action]
-    action_func(args)
-
-
-def _init_if_needed(args):
-    kwargs = _app_properties(args)
-
+def _init_if_needed(args, kwargs):
     # If conda_auto_init is set, simply building the Conda resolver will call handle installation.
     _build_dependency_manager_no_config(kwargs)
 
 
-def _app_properties(args):
-    config_file = find_config_file("config/galaxy.ini", "universe_wsgi.ini", args.config_file)
-    app_properties = load_app_properties(ini_file=config_file)
-    return app_properties
-
-
-def _arg_parser():
-    parser = argparse.ArgumentParser(description=DESCRIPTION)
-    parser.add_argument('action', metavar='ACTION', type=str,
-                        choices=ACTIONS.keys(),
-                        help='action to perform')
-    parser.add_argument("-c", "--config-file", default=None)
-    return parser
-
-
 def _build_dependency_manager_no_config(kwargs):
     """Simplified variant of build_dependency_manager from galaxy.tools.deps.
 
@@ -84,4 +56,5 @@ ACTIONS = {
 
 
 if __name__ == '__main__':
+    main = main_factory(description=DESCRIPTION, actions=ACTIONS)
     main()