def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if exists(opts.output_dir):
# don't overwrite existing output directory - make the user provide a
# different name or move/delete the existing directory since it may
# have taken a while to create.
option_parser.error("Output directory (%s) already exists. "
"Won't overwrite." % opts.output_dir)
personal_ids = opts.personal_ids
if personal_ids is not None:
personal_ids = opts.personal_ids.split(',')
individual_titles = opts.individual_titles.split(',')
if opts.print_only:
command_handler = print_commands
else:
command_handler = call_commands_serially
if opts.verbose:
status_update_callback = print_to_stdout
else:
status_update_callback = no_status_updates
create_personal_results(opts.output_dir,
opts.mapping_fp,
opts.coord_fname,
opts.collated_dir,
opts.otu_table_fp,
opts.prefs_fp,
opts.personal_id_column,
personal_ids,
opts.column_title,
individual_titles,
opts.category_to_split,
opts.time_series_category,
rarefaction_depth=opts.rarefaction_depth,
alpha=opts.alpha,
rep_set_fp=opts.rep_set_fp,
parameter_fp=opts.parameter_fp,
body_site_rarefied_otu_table_dir=opts.body_site_rarefied_otu_table_dir,
retain_raw_data=opts.retain_raw_data,
suppress_alpha_rarefaction=opts.suppress_alpha_rarefaction,
suppress_beta_diversity=opts.suppress_beta_diversity,
suppress_taxa_summary_plots=opts.suppress_taxa_summary_plots,
suppress_alpha_diversity_boxplots=opts.suppress_alpha_diversity_boxplots,
suppress_otu_category_significance=opts.suppress_otu_category_significance,
command_handler=command_handler,
status_update_callback=status_update_callback)
def test_create_personal_results_print_only(self):
"""Test running workflow, but only printing the commands."""
# Save stdout and replace it with something that will capture the print
# statement. Note: this code was taken from here:
# http://stackoverflow.com/questions/4219717/how-to-assert-output-
# with-nosetest-unittest-in-python/4220278#4220278
saved_stdout = sys.stdout
try:
out = StringIO()
sys.stdout = out
obs = create_personal_results(self.output_dir, self.mapping_fp,
self.coord_fp, self.rarefaction_dir, self.otu_table_fp,
self.prefs_fp, 'PersonalID', rarefaction_depth=10,
command_handler=print_commands)
obs_output = out.getvalue().strip()
finally:
sys.stdout = saved_stdout
exp = set(['NAU123/time_series', 'NAU123/beta_diversity',
'NAU789/beta_diversity', 'NAU789/otu_category_significance',
'NAU789/alpha_rarefaction', 'NAU456/time_series',
'NAU123/alpha_rarefaction', 'NAU456/adiv_boxplots',
'NAU456/otu_category_significance', 'NAU123/adiv_boxplots',
'NAU123/otu_category_significance', 'NAU789/adiv_boxplots',
'NAU789/time_series', 'NAU456/alpha_rarefaction',
'NAU456/beta_diversity'])
fps = []
for fp in obs:
fps.append(join(basename(dirname(fp)), basename(fp)))
# Order is not guaranteed.
fps = set(fps)
self.assertEqual(fps, exp)
def test_create_personal_results_suppress_all(self):
"""Test running workflow with all output types suppressed."""
# No output directories should be created under each personal ID
# directory. We should only end up with a log file, support_files
# directory, directories for each personal ID, and an index.html file
# in each.
exp_personal_ids = ['NAU123', 'NAU456', 'NAU789']
obs = create_personal_results(self.output_dir, self.mapping_fp,
self.coord_fp, self.rarefaction_dir, self.otu_table_fp,
self.prefs_fp, 'PersonalID',
suppress_alpha_rarefaction=True,
suppress_beta_diversity=True,
suppress_taxa_summary_plots=True,
suppress_alpha_diversity_boxplots=True,
suppress_otu_category_significance=True)
self.assertEqual(obs, [])
num_logs = len(glob(join(self.output_dir, 'log_*.txt')))
self.assertEqual(num_logs, 1)
support_files_exist = isdir(join(self.output_dir, 'support_files'))
self.assertTrue(support_files_exist)
for personal_id in exp_personal_ids:
personal_dir_exists = isdir(join(self.output_dir, personal_id))
self.assertTrue(personal_dir_exists)
personal_files = map(basename,
glob(join(self.output_dir, personal_id, '*')))
self.assertEqual(personal_files, ['index.html'])