Hi all, Something very handy for tool developers running functional tests is if the environment variable GALAXY_TEST_NO_CLEANUP is set, run_functional_tests.sh doesn't remove the test output. This is great when debugging why a test is failing.
However, I was having trouble with failures like this: base.twilltestcase: INFO: ## files diff on /mnt/galaxy/galaxy-central/test-data/ecoli.mira4_de_novo.fasta and /tmp/tmpTvyobN/tmpYsEezt/new_files_path_pk7YKe/tmpXr9NYeecoli.mira4_de_novo.fasta lines_diff=0, found diff = 3010 Sadly the temp file here was being deleted - the patch at the end of the email fixes the diff code to respect the configuration setting. Having done that and looked at the preserved file, somehow the wrong output file was being compared to the FASTA output file (it was looking at my log file instead). Because the diff was really between two different files, showing the first forty lines wasn't informative. Instead I've made it show the first 25 and last 25 lines of the diff. I find this a great deal more informative :) Meanwhile this points at a possible bug in the test framework, if anyone wants to attempt to reproduce it I used this version of my MIRA4 wrapper: https://github.com/peterjc/pico_galaxy/commit/3f095eac3f5609b2890440b851029a983fe14a20 $ export GALAXY_TEST_NO_CLEANUP=on $ ./run_functional_tests.sh -id mira_4_0_de_novo ... $ hg summary parent: 13513:f3dc213a5773 tip Backout of 28d43f4. branch: default commit: 7 modified, 229 unknown update: (current) Regards, Peter -- $ hg diff test/base/twilltestcase.py diff -r f3dc213a5773 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Mon Feb 10 22:13:35 2014 -0600 +++ b/test/base/twilltestcase.py Tue Feb 11 14:09:30 2014 +0000 @@ -95,7 +95,10 @@ diff = list( difflib.unified_diff( local_file, history_data, "local_file", "history_data" ) ) diff_lines = get_lines_diff( diff ) if diff_lines > allowed_diff_count: - diff_slice = diff[0:40] + if len(diff) < 60: + diff_slice = diff[0:40] + else: + diff_slice = diff[:25] + ["********\n", "* SNIP *\n", "********\n"] + diff[-25:] #FIXME: This pdf stuff is rather special cased and has not been updated to consider lines_diff #due to unknown desired behavior when used in conjunction with a non-zero lines_diff #PDF forgiveness can probably be handled better by not special casing by __extension__ here @@ -897,7 +900,8 @@ errmsg += str( err ) raise AssertionError( errmsg ) finally: - os.remove( temp_name ) + if 'GALAXY_TEST_NO_CLEANUP' not in os.environ: + os.remove( temp_name ) def __default_dataset_fetcher( self ): def fetcher( hda_id, filename=None ): @@ -971,7 +975,8 @@ errmsg += str( err ) raise AssertionError( errmsg ) finally: - os.remove( temp_name ) + if 'GALAXY_TEST_NO_CLEANUP' not in os.environ: + os.remove( temp_name ) def is_zipped( self, filename ): if not zipfile.is_zipfile( filename ): ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/