From 00b147a6649b8fd1112fa76c573fa78db8e58621 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 14 Nov 2016 12:45:04 -0500
Subject: [PATCH] Bring in updates from galaxy-lib.

---
 lib/galaxy/exceptions/error_codes.py          |  1 +
 lib/galaxy/jobs/metrics/__init__.py           |  1 +
 lib/galaxy/jobs/metrics/collectl/cli.py       |  1 +
 .../jobs/metrics/collectl/subsystems.py       |  1 +
 lib/galaxy/jobs/metrics/instrumenters/core.py |  1 +
 .../jobs/metrics/instrumenters/cpuinfo.py     |  1 +
 lib/galaxy/jobs/metrics/instrumenters/env.py  |  1 +
 .../jobs/metrics/instrumenters/meminfo.py     |  1 +
 lib/galaxy/objectstore/rods.py                |  1 +
 lib/galaxy/tools/cwl/runtime_actions.py       |  1 +
 lib/galaxy/tools/cwl/schema.py                |  1 +
 .../tools/deps/container_resolvers/mulled.py  |  2 +-
 lib/galaxy/tools/deps/containers.py           |  2 +-
 lib/galaxy/tools/deps/mulled/_cli.py          |  1 +
 lib/galaxy/tools/deps/mulled/mulled_build.py  | 22 ++++++++++---------
 .../tools/deps/mulled/mulled_build_channel.py |  4 +++-
 lib/galaxy/tools/deps/resolvers/conda.py      |  2 +-
 lib/galaxy/tools/deps/resolvers/modules.py    |  1 +
 lib/galaxy/tools/parser/output_actions.py     |  1 +
 .../tools/parser/output_collection_def.py     |  1 +
 .../tools/toolbox/lineages/tool_shed.py       |  1 +
 lib/galaxy/tools/toolbox/parser.py            |  1 +
 lib/galaxy/util/__init__.py                   |  5 +++++
 lib/galaxy/util/hash_util.py                  |  1 +
 lib/galaxy/util/object_wrapper.py             |  2 ++
 25 files changed, 43 insertions(+), 14 deletions(-)

diff --git a/lib/galaxy/exceptions/error_codes.py b/lib/galaxy/exceptions/error_codes.py
index e41f0828313..3b6e78a4002 100644
--- a/lib/galaxy/exceptions/error_codes.py
+++ b/lib/galaxy/exceptions/error_codes.py
@@ -40,6 +40,7 @@ def _from_dict(entry):
     message = entry.get("message")
     return (name, ErrorCode(code, message))
 
+
 error_codes_json = resource_string(__name__, 'error_codes.json').decode("UTF-8")
 for entry in loads(error_codes_json):
     name, error_code_obj = _from_dict(entry)
diff --git a/lib/galaxy/jobs/metrics/__init__.py b/lib/galaxy/jobs/metrics/__init__.py
index 87c5fafa54f..a077b25d33a 100644
--- a/lib/galaxy/jobs/metrics/__init__.py
+++ b/lib/galaxy/jobs/metrics/__init__.py
@@ -75,6 +75,7 @@ class NullJobInstrumenter(object):
     def collect_properties(self, job_id, job_directory):
         return {}
 
+
 NULL_JOB_INSTRUMENTER = NullJobInstrumenter()
 
 
diff --git a/lib/galaxy/jobs/metrics/collectl/cli.py b/lib/galaxy/jobs/metrics/collectl/cli.py
index 14dc6d27260..90271d6bee7 100644
--- a/lib/galaxy/jobs/metrics/collectl/cli.py
+++ b/lib/galaxy/jobs/metrics/collectl/cli.py
@@ -137,4 +137,5 @@ class CollectlCli( object ):
         if return_code:
             raise Exception( "Problem running collectl command." )
 
+
 __all__ = ( 'CollectlCli', )
diff --git a/lib/galaxy/jobs/metrics/collectl/subsystems.py b/lib/galaxy/jobs/metrics/collectl/subsystems.py
index 61bb2751069..942c5b36be9 100644
--- a/lib/galaxy/jobs/metrics/collectl/subsystems.py
+++ b/lib/galaxy/jobs/metrics/collectl/subsystems.py
@@ -77,4 +77,5 @@ def get_subsystem( name ):
     """
     return SUBSYSTEM_DICT[ name ]
 
+
 __all__ = ( 'get_subsystem', )
diff --git a/lib/galaxy/jobs/metrics/instrumenters/core.py b/lib/galaxy/jobs/metrics/instrumenters/core.py
index b808cae80f3..ce5534fb901 100644
--- a/lib/galaxy/jobs/metrics/instrumenters/core.py
+++ b/lib/galaxy/jobs/metrics/instrumenters/core.py
@@ -84,4 +84,5 @@ class CorePlugin( InstrumentPlugin ):
             pass
         return value
 
+
 __all__ = ( 'CorePlugin', )
diff --git a/lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py b/lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
index e8f979bda75..1ce31cb2ea6 100644
--- a/lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
+++ b/lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
@@ -60,4 +60,5 @@ class CpuInfoPlugin( InstrumentPlugin ):
     def __instrument_cpuinfo_path( self, job_directory ):
         return self._instrument_file_path( job_directory, "cpuinfo" )
 
+
 __all__ = ( 'CpuInfoPlugin', )
diff --git a/lib/galaxy/jobs/metrics/instrumenters/env.py b/lib/galaxy/jobs/metrics/instrumenters/env.py
index dc5846d386b..762158cc081 100644
--- a/lib/galaxy/jobs/metrics/instrumenters/env.py
+++ b/lib/galaxy/jobs/metrics/instrumenters/env.py
@@ -69,4 +69,5 @@ class EnvPlugin( InstrumentPlugin ):
     def __env_file( self, job_directory ):
         return self._instrument_file_path( job_directory, "vars" )
 
+
 __all__ = ( 'EnvPlugin', )
diff --git a/lib/galaxy/jobs/metrics/instrumenters/meminfo.py b/lib/galaxy/jobs/metrics/instrumenters/meminfo.py
index 49b528f3472..1eac6a69dee 100644
--- a/lib/galaxy/jobs/metrics/instrumenters/meminfo.py
+++ b/lib/galaxy/jobs/metrics/instrumenters/meminfo.py
@@ -62,4 +62,5 @@ class MemInfoPlugin( InstrumentPlugin ):
     def __instrument_meminfo_path( self, job_directory ):
         return self._instrument_file_path( job_directory, "meminfo" )
 
+
 __all__ = ( 'MemInfoPlugin', )
diff --git a/lib/galaxy/objectstore/rods.py b/lib/galaxy/objectstore/rods.py
index dbb14c5e3bb..a6e70e7ed20 100644
--- a/lib/galaxy/objectstore/rods.py
+++ b/lib/galaxy/objectstore/rods.py
@@ -325,6 +325,7 @@ def _rods_strerror( errno ):
                 irods.__rods_strerror_map[ v ] = name
     return irods.__rods_strerror_map.get( errno, 'GALAXY_NO_ERRNO_MAPPING_FOUND' )
 
+
 if irods is not None:
     irods.strerror = _rods_strerror
 
diff --git a/lib/galaxy/tools/cwl/runtime_actions.py b/lib/galaxy/tools/cwl/runtime_actions.py
index 84fe2c6f339..07a4b2c5731 100644
--- a/lib/galaxy/tools/cwl/runtime_actions.py
+++ b/lib/galaxy/tools/cwl/runtime_actions.py
@@ -48,6 +48,7 @@ def handle_outputs(job_directory=None):
             with open(target_path, "w") as f:
                 f.write(json.dumps(output))
 
+
 __all__ = (
     'handle_outputs',
 )
diff --git a/lib/galaxy/tools/cwl/schema.py b/lib/galaxy/tools/cwl/schema.py
index 61065fa5d3f..fb24b784724 100644
--- a/lib/galaxy/tools/cwl/schema.py
+++ b/lib/galaxy/tools/cwl/schema.py
@@ -69,4 +69,5 @@ class SchemaLoader(object):
         )
         return tool
 
+
 schema_loader = SchemaLoader()
diff --git a/lib/galaxy/tools/deps/container_resolvers/mulled.py b/lib/galaxy/tools/deps/container_resolvers/mulled.py
index 3ada6fa08e2..dcf15a020d8 100644
--- a/lib/galaxy/tools/deps/container_resolvers/mulled.py
+++ b/lib/galaxy/tools/deps/container_resolvers/mulled.py
@@ -120,7 +120,7 @@ class MulledContainerResolver(ContainerResolver):
 
     resolver_type = "mulled"
 
-    def __init__(self, app_info=None, namespace="mulled"):
+    def __init__(self, app_info=None, namespace="biocontainers"):
         super(MulledContainerResolver, self).__init__(app_info)
         self.namespace = namespace
 
diff --git a/lib/galaxy/tools/deps/containers.py b/lib/galaxy/tools/deps/containers.py
index fff1989986b..d30349645cd 100644
--- a/lib/galaxy/tools/deps/containers.py
+++ b/lib/galaxy/tools/deps/containers.py
@@ -210,7 +210,7 @@ class ContainerRegistry(object):
         if self.enable_beta_mulled_containers:
             default_resolvers.extend([
                 CachedMulledContainerResolver(self.app_info),
-                MulledContainerResolver(self.app_info, namespace="mulled"),
+                MulledContainerResolver(self.app_info, namespace="biocontainers"),
                 BuildMulledContainerResolver(self.app_info),
             ])
         return default_resolvers
diff --git a/lib/galaxy/tools/deps/mulled/_cli.py b/lib/galaxy/tools/deps/mulled/_cli.py
index 8cf4e6fc1e3..067063d7bba 100644
--- a/lib/galaxy/tools/deps/mulled/_cli.py
+++ b/lib/galaxy/tools/deps/mulled/_cli.py
@@ -14,6 +14,7 @@ def arg_parser(argv, globals):
     )
     return parser
 
+
 __all__ = (
     "arg_parser",
 )
diff --git a/lib/galaxy/tools/deps/mulled/mulled_build.py b/lib/galaxy/tools/deps/mulled/mulled_build.py
index cf55e4e46d1..3a4e1699505 100644
--- a/lib/galaxy/tools/deps/mulled/mulled_build.py
+++ b/lib/galaxy/tools/deps/mulled/mulled_build.py
@@ -14,6 +14,7 @@ import json
 import os
 import string
 import subprocess
+import sys
 from sys import platform as _platform
 
 try:
@@ -49,7 +50,7 @@ def get_tests(args, pkg_path):
     """Extract test cases given a recipe's meta.yaml file."""
     recipes_dir = args.recipes_dir
 
-    tests = ""
+    tests = []
     input_dir = os.path.dirname(os.path.join(recipes_dir, pkg_path))
     recipe_meta = MetaData(input_dir)
 
@@ -59,14 +60,14 @@ def get_tests(args, pkg_path):
 
     if tests_imports or tests_commands:
         if tests_commands:
-            tests = ' && '.join(tests_commands)
-        elif tests_imports and 'python' in requirements:
-            tests = ' && '.join('python -c "import %s"' % imp for imp in tests_imports)
+            tests.append(' && '.join(tests_commands))
+        if tests_imports and 'python' in requirements:
+            tests.append(' && '.join('python -c "import %s"' % imp for imp in tests_imports))
         elif tests_imports and ('perl' in requirements or 'perl-threaded' in requirements):
-            tests = ' && '.join('''perl -e "use %s;"''' % imp for imp in tests_imports)
-        tests = tests.replace('$R ', 'Rscript ')
-    else:
-        pass
+            tests.append(' && '.join('''perl -e "use %s;"''' % imp for imp in tests_imports))
+
+    tests = ' && '.join(tests)
+    tests = tests.replace('$R ', 'Rscript ')
     return tests
 
 
@@ -146,7 +147,8 @@ def mull_targets(
     print(" ".join(involucro_context.build_command(involucro_args)))
     if not dry_run:
         ensure_installed(involucro_context, True)
-        involucro_context.exec_command(involucro_args)
+        return involucro_context.exec_command(involucro_args)
+    return 0
 
 
 def context_from_args(args):
@@ -276,7 +278,7 @@ def main(argv=None):
     parser.add_argument('--test', help='Provide a test command for the container.')
     args = parser.parse_args()
     targets = target_str_to_targets(args.targets)
-    mull_targets(targets, **args_to_mull_targets_kwds(args))
+    sys.exit(mull_targets(targets, **args_to_mull_targets_kwds(args)))
 
 
 __all__ = ("main", )
diff --git a/lib/galaxy/tools/deps/mulled/mulled_build_channel.py b/lib/galaxy/tools/deps/mulled/mulled_build_channel.py
index 272940eed7a..6463d3ea58d 100644
--- a/lib/galaxy/tools/deps/mulled/mulled_build_channel.py
+++ b/lib/galaxy/tools/deps/mulled/mulled_build_channel.py
@@ -19,6 +19,7 @@ See recent changes that would be built with:
 from __future__ import print_function
 
 import os
+import sys
 import time
 
 from ._cli import arg_parser
@@ -40,7 +41,8 @@ def _fetch_repo_data(args):
     if repo_data is None:
         repo_data = "%s-repodata.json" % channel
     if not os.path.exists(repo_data):
-        check_output("wget --quiet https://conda.anaconda.org/%s/linux-64/repodata.json.bz2 -O '%s.bz2' && bzip2 -d '%s.bz2'" % (channel, repo_data, repo_data))
+        platform_tag = 'osx-64' if sys.platform == 'darwin' else 'linux-64'
+        check_output("wget --quiet https://conda.anaconda.org/%s/%s/repodata.json.bz2 -O '%s.bz2' && bzip2 -d '%s.bz2'" % (channel, platform_tag, repo_data, repo_data))
     return repo_data
 
 
diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py
index fd23349cd45..2a1c13f5116 100644
--- a/lib/galaxy/tools/deps/resolvers/conda.py
+++ b/lib/galaxy/tools/deps/resolvers/conda.py
@@ -236,4 +236,4 @@ def _string_as_bool( value ):
     return str( value ).lower() == "true"
 
 
-__all__ = ('CondaDependencyResolver', )
+__all__ = ('CondaDependencyResolver', 'DEFAULT_ENSURE_CHANNELS')
diff --git a/lib/galaxy/tools/deps/resolvers/modules.py b/lib/galaxy/tools/deps/resolvers/modules.py
index be64e6b7489..227abb72a9c 100644
--- a/lib/galaxy/tools/deps/resolvers/modules.py
+++ b/lib/galaxy/tools/deps/resolvers/modules.py
@@ -179,4 +179,5 @@ class ModuleDependency(Dependency):
 def _string_as_bool( value ):
     return str( value ).lower() == "true"
 
+
 __all__ = ('ModuleDependencyResolver', )
diff --git a/lib/galaxy/tools/parser/output_actions.py b/lib/galaxy/tools/parser/output_actions.py
index 750aa2d0efe..2234cd46725 100644
--- a/lib/galaxy/tools/parser/output_actions.py
+++ b/lib/galaxy/tools/parser/output_actions.py
@@ -648,6 +648,7 @@ def compare_re_search( value1, value2 ):
     # checks pattern=value2 in value1
     return bool( re.search( value2, value1 ) )
 
+
 compare_types = {
     'eq': compare_eq,
     'neq': compare_neq,
diff --git a/lib/galaxy/tools/parser/output_collection_def.py b/lib/galaxy/tools/parser/output_collection_def.py
index 1790c89a41e..cd175a2f6cc 100644
--- a/lib/galaxy/tools/parser/output_collection_def.py
+++ b/lib/galaxy/tools/parser/output_collection_def.py
@@ -69,6 +69,7 @@ class DatasetCollectionDescription(object):
         self.sort_key = sort_by
         self.sort_comp = sort_comp
 
+
 DEFAULT_DATASET_COLLECTOR_DESCRIPTION = DatasetCollectionDescription(
     default_dbkey=LEGACY_DEFAULT_DBKEY,
 )
diff --git a/lib/galaxy/tools/toolbox/lineages/tool_shed.py b/lib/galaxy/tools/toolbox/lineages/tool_shed.py
index a2412d12ad3..baeac6fab3e 100644
--- a/lib/galaxy/tools/toolbox/lineages/tool_shed.py
+++ b/lib/galaxy/tools/toolbox/lineages/tool_shed.py
@@ -93,4 +93,5 @@ class ToolShedLineage(ToolLineage):
 def get_installed_tool_version( app, tool_id ):
     return app.tool_version_cache.tool_version_by_tool_id.get(tool_id, None)
 
+
 __all__ = ( "ToolShedLineage", )
diff --git a/lib/galaxy/tools/toolbox/parser.py b/lib/galaxy/tools/toolbox/parser.py
index 8023988d9ba..b81e6421cb6 100644
--- a/lib/galaxy/tools/toolbox/parser.py
+++ b/lib/galaxy/tools/toolbox/parser.py
@@ -151,6 +151,7 @@ def get_toolbox_parser(config_filename):
     else:
         return XmlToolConfSource(config_filename)
 
+
 __all__ = (
     "get_toolbox_parser",
     "ensure_tool_conf_item",
diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index d6dc1863369..90af2b75109 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -447,6 +447,7 @@ def pretty_print_json(json_data, is_json_string=False):
         json_data = json.loads(json_data)
     return json.dumps(json_data, sort_keys=True, indent=4)
 
+
 # characters that are valid
 valid_chars = set(string.ascii_letters + string.digits + " -=_.()/+*^,:?!")
 
@@ -524,6 +525,7 @@ def sanitize_param( value, valid_characters=valid_chars, character_map=mapped_ch
     else:
         raise Exception('Unknown parameter type (%s)' % ( type( value ) ))
 
+
 valid_filename_chars = set( string.ascii_letters + string.digits + '_.' )
 invalid_filenames = [ '', '.', '..' ]
 
@@ -800,6 +802,7 @@ def xml_text(root, name=None):
     # No luck, return empty string
     return ''
 
+
 # asbool implementation pulled from PasteDeploy
 truthy = frozenset(['true', 'yes', 'on', 'y', 't', '1'])
 falsy = frozenset(['false', 'no', 'off', 'n', 'f', '0'])
@@ -1367,6 +1370,7 @@ def safe_str_cmp(a, b):
         rv |= ord(x) ^ ord(y)
     return rv == 0
 
+
 galaxy_root_path = os.path.join(__path__[0], "..", "..", "..")
 
 
@@ -1523,6 +1527,7 @@ class ExecutionTimer(object):
         elapsed = (time.time() - self.begin) * 1000.0
         return "(%0.3f ms)" % elapsed
 
+
 if __name__ == '__main__':
     import doctest
     doctest.testmod(sys.modules[__name__], verbose=False)
diff --git a/lib/galaxy/util/hash_util.py b/lib/galaxy/util/hash_util.py
index 6a84048ba8e..63efe64d100 100644
--- a/lib/galaxy/util/hash_util.py
+++ b/lib/galaxy/util/hash_util.py
@@ -46,4 +46,5 @@ def is_hashable( value ):
         return False
     return True
 
+
 __all__ = ('md5', 'hashlib', 'sha1', 'sha', 'new_secure_hash', 'hmac_new', 'is_hashable')
diff --git a/lib/galaxy/util/object_wrapper.py b/lib/galaxy/util/object_wrapper.py
index 34093082a19..3bcbc299299 100644
--- a/lib/galaxy/util/object_wrapper.py
+++ b/lib/galaxy/util/object_wrapper.py
@@ -487,5 +487,7 @@ def pickle_SafeStringWrapper( safe_object ):
     if isinstance( safe_object, CallableSafeStringWrapper ):
         cls = CallableSafeStringWrapper
     return ( cls, args )
+
+
 copy_reg.pickle( SafeStringWrapper, pickle_SafeStringWrapper, wrap_with_safe_string )
 copy_reg.pickle( CallableSafeStringWrapper, pickle_SafeStringWrapper, wrap_with_safe_string )