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Viewing changes to tests/test_workflow/test_util.py

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-06-17 18:28:26 UTC
  • mfrom: (9.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20130617182826-376az5ad080a0sfe
Tags: 1.7.0+dfsg-1
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tests/test_workflow/test_util.py
 
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#!/usr/bin/env python
 
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# File created on 30 Mar 2010
 
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from __future__ import division
 
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__author__ = "Greg Caporaso"
 
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__copyright__ = "Copyright 2011, The QIIME Project"
 
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__credits__ = ["Greg Caporaso", "Kyle Bittinger", "Jai Ram Rideout"]
 
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__license__ = "GPL"
 
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__version__ = "1.7.0"
 
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__maintainer__ = "Greg Caporaso"
 
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__email__ = "gregcaporaso@gmail.com"
 
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__status__ = "Release"
 
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from shutil import rmtree
 
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from glob import glob
 
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from os.path import exists, join, getsize
 
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from cogent.util.unit_test import TestCase, main
 
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from cogent.util.misc import remove_files
 
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from qiime.util import (load_qiime_config,
 
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                        get_tmp_filename,
 
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                        get_qiime_temp_dir,
 
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                        create_dir)
 
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from qiime.parse import parse_qiime_parameters
 
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from qiime.test import (initiate_timeout,
 
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                        disable_timeout,
 
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                        get_test_data_fps)
 
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from qiime.workflow.util import (call_commands_serially,
 
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                                 no_status_updates,
 
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                                 WorkflowError)
 
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from qiime.workflow.downstream import run_beta_diversity_through_plots
 
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class WorkflowTests(TestCase):
 
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    def setUp(self):
 
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        """ """
 
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        self.test_data = get_test_data_fps()
 
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        self.files_to_remove = []
 
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        self.dirs_to_remove = []
 
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        # Create example output directory
 
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        tmp_dir = get_qiime_temp_dir()
 
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        self.test_out = get_tmp_filename(tmp_dir=tmp_dir,
 
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                                         prefix='core_qiime_analyses_test_',
 
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                                         suffix='',
 
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                                         result_constructor=str)
 
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        self.dirs_to_remove.append(self.test_out)
 
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        create_dir(self.test_out)
 
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        self.qiime_config = load_qiime_config()
 
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        self.params = parse_qiime_parameters({})
 
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        initiate_timeout(60)
 
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    def tearDown(self):
 
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        """ """
 
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        disable_timeout()
 
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        remove_files(self.files_to_remove)
 
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        # remove directories last, so we don't get errors
 
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        # trying to remove files which may be in the directories
 
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        for d in self.dirs_to_remove:
 
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            if exists(d):
 
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                rmtree(d)
 
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    def test_unsupported_options_handled_nicely(self):
 
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        """WorkflowError raised on unsupported option """
 
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        self.params['beta_diversity'] = {'blah':"something-broken"}
 
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        self.assertRaises(WorkflowError,
 
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                          run_beta_diversity_through_plots,
 
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                          self.test_data['biom'][0], 
 
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                          self.test_data['map'][0],
 
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                          self.test_out, 
 
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                          call_commands_serially,
 
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                          self.params,
 
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                          self.qiime_config,
 
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                          tree_fp=self.test_data['tree'][0],
 
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                          parallel=False, 
 
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                          status_update_callback=no_status_updates)
 
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        # Check that the log file is created and has size > 0
 
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        log_fp = glob(join(self.test_out,'log*.txt'))[0]
 
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        self.assertTrue(getsize(log_fp) > 0)
 
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if __name__ == "__main__":
 
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    main()