From 4b2bf122b627d4dfbd87e9491cbf97755f40a9bf Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 3 Jan 2018 11:26:04 +0100 Subject: [PATCH] fix for microbial import tool There seems to be no UnvalidatedValue class anymore. So I removed these checks which seems to make the tool functional again. Note that there is one more instance of such a check in the Galaxy sources (in tools/parameters/basic.py). I guess this can also be removed? --- tools/data_source/microbial_import_code.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/tools/data_source/microbial_import_code.py b/tools/data_source/microbial_import_code.py index f9f53b6427a..7db3f0e07fb 100644 --- a/tools/data_source/microbial_import_code.py +++ b/tools/data_source/microbial_import_code.py @@ -101,11 +101,6 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr # if not (kingdom or group or org): if not (kingdom or org): print("Parameters are not available.") - # workflow passes galaxy.tools.parameters.basic.UnvalidatedValue instead of values - if isinstance(kingdom, tools.parameters.basic.UnvalidatedValue): - kingdom = kingdom.value - if isinstance(org, tools.parameters.basic.UnvalidatedValue): - org = org.value GALAXY_DATA_INDEX_DIR = app.config.tool_data_path microbe_info = load_microbial_data(GALAXY_DATA_INDEX_DIR, sep='\t')