@@ -128,17 +128,18 @@ def run_in_config(ctx, config, run=run_galaxy_command, test_data_target_dir=None
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# check if tools created extra files in the file_path all files in the files path
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# - end with '.dat' or
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# - are contained in a directory `dataset_.*_files`
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- for (path , dirs , files ) in os .walk (config .env ["GALAXY_CONFIG_OVERRIDE_FILE_PATH" ]):
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- for name in files :
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- if not (name .endswith (".dat" ) or re .match ('.*/dataset_.*_files$' , path )):
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- extra_files .append (os .path .join (path , name ))
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- if len (extra_files ) > 0 :
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- msg = f"One of the tested tools wrote to Galaxy's files dir: { extra_files } "
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- for i in range (len (structured_data ["tests" ])):
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- structured_data ["tests" ][i ]["data" ]["status" ] = "failure"
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- structured_data ["tests" ][i ]["data" ]["job" ]["stderr" ] += msg
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- error (msg )
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- ec = 1
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+ if os .walk (config .env .get ("GALAXY_CONFIG_OVERRIDE_FILE_PATH" )):
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+ for (path , dirs , files ) in os .walk (config .env .get ("GALAXY_CONFIG_OVERRIDE_FILE_PATH" )):
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+ for name in files :
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+ if not (name .endswith (".dat" ) or re .match ('.*/dataset_.*_files$' , path )):
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+ extra_files .append (os .path .join (path , name ))
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+ if len (extra_files ) > 0 :
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+ msg = f"One of the tested tools wrote to Galaxy's files dir: { extra_files } "
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+ for i in range (len (structured_data ["tests" ])):
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+ structured_data ["tests" ][i ]["data" ]["status" ] = "failure"
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+ structured_data ["tests" ][i ]["data" ]["job" ]["stderr" ] += msg
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+ error (msg )
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+ ec = 1
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return handle_reports_and_summary (
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ctx ,
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structured_data ,
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