ported the core functionality to qiime.

script_usage_tests.py

@@ -12,25 +12,20 @@
 __status__ = "Development"
 
 
-from os.path import isdir, split, join, abspath
-from os import chdir, getcwd
-from shutil import copytree, rmtree
-from glob import glob
-from site import addsitedir
-from sys import path
-from cogent.util.misc import remove_files
+
 from qiime.util import (parse_command_line_parameters,
-                        make_option,
-                        load_qiime_config,
-                        qiime_system_call)
+                        make_option, load_qiime_config)
+from qiime.test import run_script_usage_tests
 
 
 qiime_config = load_qiime_config()
 
 script_info = {}
 script_info['brief_description'] = ""
 script_info['script_description'] = ""
-script_info['script_usage'] = [("","","")]
+script_info['script_usage'] = []
+script_info['script_usage'].append(("Run a subset of the interface tests in verbose mode","Run interface tests for the add_taxa.py and make_otu_table.py scripts. This illustrates how to run from the qiime_test_dir directory.","%prog -i $PWD/ -l $HOME/qime_script_tests.log -t add_taxa,make_otu_table -v"))
+script_info['script_usage'].append(("Run all of the interface tests","Run all script interface tests.  This illustrates how to run from the qiime_test_dir directory.","%prog -i $PWD/ -l $HOME/all_qime_script_tests.log"))
 script_info['output_description']= ""
 script_info['required_options'] = [
  make_option('-i','--qiime_test_data_dir',type="existing_dirpath",
@@ -50,99 +45,16 @@
 ]
 script_info['version'] = __version__
 
-def run_script_usage_tests(qiime_test_data_dir,
-                           qiime_scripts_dir,
-                           working_dir,
-                           verbose=False,
-                           tests=None,
-                           failure_log_fp=None):
-    if tests == None:
-        tests = [split(d)[1] for d in glob('%s/*' % qiime_test_data_dir) if isdir(d)]
-    else:
-        tests = tests.split(',')
-
-    if verbose:
-        print 'Tests to run:\n %s' % ' '.join(tests)
-
-    addsitedir(qiime_scripts_dir)
-
-    failed_tests = []
-    warnings = []
-    total_tests = 0
-    for test in tests:
-
-        # import the usage examples - this is possible because we added 
-        # qiime_scripts_dir to the PYTHONPATH above
-        script_fn = '%s/%s.py' % (qiime_scripts_dir,test)
-        script = __import__(test)
-        usage_examples = script.script_info['script_usage']
-
-        if verbose:
-            print 'Testing %d usage examples from: %s.py' % (len(usage_examples),script_fn)
-
-        # init the test environment
-        test_input_dir = '%s/%s' % (qiime_test_data_dir,test)
-        test_working_dir = '%s/%s' % (working_dir,test)
-        copytree(test_input_dir,test_working_dir)
-        chdir(test_working_dir)
-
-        # remove pre-exisitng output files if any
-        try:
-            script_usage_output_to_remove = script.script_info['script_usage_output_to_remove']
-        except KeyError:
-            script_usage_output_to_remove = []
-        for e in script_usage_output_to_remove:
-            rmtree(e.replace('$PWD',getcwd()),ignore_errors=True)
-
-        if verbose:
-            print ' Running tests in: %s' % getcwd()
-            print ' Tests:'
-
-        for usage_example in usage_examples:
-            if '%prog' not in usage_example[2]:
-                warnings.append('%s usage examples do not all use %%prog to represent the command name. You may not be running the version of the command that you think you are!' % test)
-            cmd = usage_example[2].replace('%prog',script_fn)
-            if verbose:
-                print '  %s' % cmd
-            stdout, stderr, return_value = qiime_system_call(cmd)
-            total_tests += 1
-            if return_value != 0:
-                failed_tests.append((cmd, stdout, stderr, return_value))
-
-        if verbose:
-            print ''
-
-    if failure_log_fp:
-        failure_log_f = open(failure_log_fp,'w')
-        if len(failed_tests) == 0:
-            failure_log_f.write('All tests passed.')
-        else:
-            i = 0
-            for cmd, stdout, stderr, return_value in failed_tests:
-                failure_log_f.write('**Failed test %d:\n%s\n\nReturn value: %d\n\nStdout:\n%s\n\nStderr:\n%s\n\n' % (i,cmd,return_value, stdout, stderr))
-        failure_log_f.close()
-
-
-    if warnings:
-        print 'Warnings:'
-        for warning in warnings:
-            print ' ' + warning
-        print ''
-
-    print 'Ran %d commands to test %d scripts. %d of these commands failed. Failures are summarized in %s.' % (total_tests,len(tests),len(failed_tests),failure_log_fp)
-
-    rmtree(working_dir)
-
 def main():
     option_parser, opts, args =\
        parse_command_line_parameters(**script_info)
 
-    qiime_test_data_dir = abspath(opts.qiime_test_data_dir)
+    qiime_test_data_dir = opts.qiime_test_data_dir
     qiime_scripts_dir = opts.qiime_scripts_dir
-    working_dir = join(opts.working_dir,'script_usage_tests')
+    working_dir = opts.working_dir
     verbose = opts.verbose
     tests = opts.tests
-    failure_log_fp = abspath(opts.failure_log_fp)
+    failure_log_fp = opts.failure_log_fp
 
     run_script_usage_tests(qiime_test_data_dir,
                            qiime_scripts_dir,