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Do not override None with empty string #950

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Merged
jmchilton merged 1 commit into from
Aug 8, 2019
Merged

Do not override None with empty string #950

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9 changes: 5 additions & 4 deletions planemo/galaxy/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -453,7 +453,7 @@ def config_join(*args):
watch_tools="auto",
default_job_shell="/bin/bash", # For conda dependency resolution
tool_data_table_config_path=tool_data_table,
data_manager_config_file=",".join(data_manager_config_paths),
data_manager_config_file=",".join(data_manager_config_paths) or None, # without 'or None' may raise IOError in galaxy (see #946)
integrated_tool_panel_config=("${temp_directory}/"
"integrated_tool_panel_conf.xml"),
migrated_tools_config=empty_tool_conf,
Expand Down Expand Up @@ -1271,9 +1271,10 @@ def _ensure_galaxy_repository_available(ctx, kwds):
def _build_env_for_galaxy(properties, template_args):
env = {}
for key, value in iteritems(properties):
var = "GALAXY_CONFIG_OVERRIDE_%s" % key.upper()
value = _sub(value, template_args)
env[var] = value
if value is not None: # Do not override None with empty string
var = "GALAXY_CONFIG_OVERRIDE_%s" % key.upper()
value = _sub(value, template_args)
env[var] = value
return env


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