コード例 #1
0
def copy_support_files(file_path):
    """Copy the support files to a named destination 

    file_path: path where you want the support files to be copied to

    Will raise EmperorSupportFilesError if a problem is found whilst trying to
    copy the files.
    """
    file_path = join(file_path, 'emperor_required_resources')

    if not exists(file_path):
        makedirs(file_path)

    # shutil.copytree does not provide an easy way to copy the contents of a
    # directory into another existing directory, hence the system call.
    # use double quotes for the paths to escape any invalid chracter(s)/spaces
    cmd = 'cp -R "%s/"* "%s"' % (get_emperor_support_files_dir(),
                                 abspath(file_path))
    cmd_o, cmd_e, cmd_r = qcli_system_call(cmd)

    if cmd_e:
        raise EmperorSupportFilesError, "Error found whilst trying to copy " +\
            "the support files:\n%s\n Could not execute: %s" % (cmd_e, cmd)

    return
コード例 #2
0
ファイル: util.py プロジェクト: jairideout/emperor
def copy_support_files(file_path):
    """Copy the support files to a named destination 

    file_path: path where you want the support files to be copied to

    Will raise EmperorSupportFilesError if a problem is found whilst trying to
    copy the files.
    """
    file_path = join(file_path, 'emperor_required_resources')

    if not exists(file_path):
        makedirs(file_path)

    # shutil.copytree does not provide an easy way to copy the contents of a
    # directory into another existing directory, hence the system call.
    # use double quotes for the paths to escape any invalid chracter(s)/spaces
    cmd = 'cp -R "%s/"* "%s"' % (get_emperor_support_files_dir(),
        abspath(file_path))
    cmd_o, cmd_e, cmd_r = qcli_system_call(cmd)

    if cmd_e:
        raise EmperorSupportFilesError, "Error found whilst trying to copy " +\
            "the support files:\n%s\n Could not execute: %s" % (cmd_e, cmd)

    return
コード例 #3
0
def main():
    option_parser, opts, args =\
       parse_command_line_parameters(**script_info)
    
    Query_collection=[] 
    rank_collection=[]
    Query_dict=defaultdict(list)
    temp_dir_name=tempfile.mkdtemp(prefix='root_')
    level=0
    for root,dirs,files in os.walk(opts.input_HMM_fp):
        print root
        #print dirs
        #print files
        #print ".................."
        path_to_db=os.path.join(root,'db')
        path_to_result=os.path.join(root,'result.out')
        if level==0:
            stdout,stderr,return_value = qcli_system_call('hmmscan '+path_to_db+' '+opts.input_query_fp+' > '+path_to_result)
            if return_value != 0:
                print 'Stdout:\n%s\nStderr:%s\n' % (stdout,stderr)
                exit(1)
            HMM_result=open(path_to_result,'U')
            HMM_choice_list,HMM_Query_list,HMM_choice_list_with_ID=search_HMM(HMM_result)
            create_temp_test_seq_file(temp_dir_name,HMM_choice_list_with_ID,open(opts.input_query_fp,'U'))
            rank_collection.extend(HMM_choice_list)
            Query_collection.extend(HMM_Query_list)
            for Query_ID, rank in HMM_choice_list_with_ID:
                Query_dict[Query_ID].append(rank)
        else:
            if os.path.basename(root) in rank_collection:
                path_to_test_seq=os.path.join(temp_dir_name,os.path.basename(root)+'.fasta')
                stdout,stderr,return_value = qcli_system_call('hmmscan '+path_to_db+' '+path_to_test_seq+' > '+path_to_result)
                if return_value != 0:
                    print 'Stdout:\n%s\nStderr:%s\n' % (stdout,stderr)
                    exit(1)
                HMM_result=open(path_to_result,'U')
                HMM_choice_list,HMM_Query_list,HMM_choice_list_with_ID=search_HMM(HMM_result)
                create_temp_test_seq_file(temp_dir_name,HMM_choice_list_with_ID,open(path_to_test_seq,'U'))
                rank_collection.extend(HMM_choice_list)
                for Query_ID, rank in HMM_choice_list_with_ID:
                    Query_dict[Query_ID].append(rank)
        level+=1
    shutil.rmtree(temp_dir_name)
    taxonomy_assignment_to_query_seq(Query_dict,Query_collection)
コード例 #4
0
ファイル: util.py プロジェクト: jairideout/emperor
def get_emperor_library_version():
    """Get Emperor version and the git SHA + current branch (if applicable)"""
    emperor_dir = get_emperor_project_dir()
    emperor_version = emperor_library_version

    # more information could be retrieved following this pattern
    sha_cmd = 'git --git-dir %s/.git rev-parse HEAD' % (emperor_dir)
    sha_o, sha_e, sha_r = qcli_system_call(sha_cmd)
    git_sha = sha_o.strip()

    branch_cmd = 'git --git-dir %s/.git rev-parse --abbrev-ref HEAD' %\
        (emperor_dir)
    branch_o, branch_e, branch_r = qcli_system_call(branch_cmd)
    git_branch = branch_o.strip()

    # validate the output from both command calls
    if is_valid_git_refname(git_branch) and is_valid_git_sha1(git_sha):
        return '%s, %s@%s' % (emperor_version, git_branch, git_sha[0:7])
    else:
        return '%s' % emperor_version
コード例 #5
0
def get_emperor_library_version():
    """Get Emperor version and the git SHA + current branch (if applicable)"""
    emperor_dir = get_emperor_project_dir()
    emperor_version = emperor_library_version

    # more information could be retrieved following this pattern
    sha_cmd = 'git --git-dir %s/.git rev-parse HEAD' % (emperor_dir)
    sha_o, sha_e, sha_r = qcli_system_call(sha_cmd)
    git_sha = sha_o.strip()

    branch_cmd = 'git --git-dir %s/.git rev-parse --abbrev-ref HEAD' %\
        (emperor_dir)
    branch_o, branch_e, branch_r = qcli_system_call(branch_cmd)
    git_branch = branch_o.strip()

    # validate the output from both command calls
    if is_valid_git_refname(git_branch) and is_valid_git_sha1(git_sha):
        return '%s, %s@%s' % (emperor_version, git_branch, git_sha[0:7])
    else:
        return '%s' % emperor_version
コード例 #6
0
ファイル: test.py プロジェクト: douginator2000/pyqi
def run_script_usage_tests(test_data_dir,
                           scripts_dir,
                           working_dir,
                           verbose=False,
                           tests=None,
                           failure_log_fp=None,
                           force_overwrite=False,
                           timeout=60):
    """ Test script_usage examples when test data is present in test_data_dir

        Returns a result summary string and the number of script usage
        examples (i.e. commands) that failed.
    """
    # process input filepaths and directories
    test_data_dir = abspath(test_data_dir)
    working_dir = join(working_dir,'script_usage_tests')
    if force_overwrite and exists(working_dir):
        rmtree(working_dir)
    if failure_log_fp != None:
        failure_log_fp = abspath(failure_log_fp)

    if tests == None:
        tests = [split(d)[1] for d in sorted(glob('%s/*' % test_data_dir)) if isdir(d)]
    
    if verbose:
        print 'Tests to run:\n %s' % ' '.join(tests)
    
    addsitedir(scripts_dir)
    
    failed_tests = []
    warnings = []
    total_tests = 0
    for test in tests:
        
        # import the usage examples - this is possible because we added 
        # scripts_dir to the PYTHONPATH above
        script_fn = '%s/%s.py' % (scripts_dir,test)
        script = __import__(test)
        usage_examples = script.script_info['script_usage']
        
        if verbose:
            print 'Testing %d usage examples from: %s' % (len(usage_examples),script_fn)
        
        # init the test environment
        test_input_dir = '%s/%s' % (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('$PWD',getcwd()),ignore_errors=True)
            remove_files([e.replace('$PWD',getcwd())],error_on_missing=False)
        
        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,
            
            timed_out = False
            initiate_timeout(timeout)
            try:
                stdout, stderr, return_value = qcli_system_call(cmd)
            except TimeExceededError:
                timed_out = True
            else:
                disable_timeout()
            
            total_tests += 1
            if timed_out:
                # Add a string instead of return_value - if fail_tests ever ends
                # up being returned from this function we'll want to code this as 
                # an int for consistency in the return value type.
                failed_tests.append((cmd, "", "", "None, time exceeded"))
                if verbose: print ": Timed out"
            elif return_value != 0:
                failed_tests.append((cmd, stdout, stderr, return_value))
                if verbose: print ": Failed"
            else:
                pass
                if verbose: print ": Pass"
        
        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 script interface tests passed.\n')
        else:
            i = 1
            for cmd, stdout, stderr, return_value in failed_tests:
                failure_log_f.write('**Failed test %d:\n%s\n\nReturn value: %s\n\nStdout:\n%s\n\nStderr:\n%s\n\n' % (i,cmd,str(return_value), stdout, stderr))
                i += 1
        failure_log_f.close()
    
    
    if warnings:
        print 'Warnings:'
        for warning in warnings:
            print ' ' + warning
        print ''
    
    result_summary = 'Ran %d commands to test %d scripts. %d of these commands failed.' % (total_tests,len(tests),len(failed_tests))
    if len(failed_tests) > 0:
        failed_scripts = set([split(e[0].split()[0])[1] for e in failed_tests])
        result_summary += '\nFailed scripts were: %s' % " ".join(failed_scripts)
    if failure_log_fp:
        result_summary += "\nFailures are summarized in %s" % failure_log_fp
    
    rmtree(working_dir)
    
    return result_summary, len(failed_tests)
コード例 #7
0
ファイル: all_tests.py プロジェクト: ranjit58/emperor
def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)

    unittest_glob = opts.unittest_glob
    temp_filepath = opts.temp_filepath
    script_usage_tests = opts.script_usage_tests
    suppress_unit_tests = opts.suppress_unit_tests
    suppress_script_usage_tests = opts.suppress_script_usage_tests
    suppress_javascript_unit_tests = opts.suppress_javascript_unit_tests

    # since the test data is in the tests folder just add scripts_test_data
    emperor_test_data_dir = join(abspath(dirname(__file__)),
        'scripts_test_data/')

    # offer the option for the user to pass the scripts dir from the command
    # line since there is no other way to get the scripts dir. If not provided
    # the base structure of the repository will be assumed. Note that for both
    # cases we are using absolute paths, to avoid unwanted failures.
    if opts.emperor_scripts_dir is None:
        emperor_scripts_dir = abspath(join(get_emperor_project_dir(),
            'scripts/'))

        # let's try to guess cases for qiime-deploy type of installs
        if get_emperor_project_dir().endswith('/lib'):
            emperor_scripts_dir = abspath(join(get_emperor_project_dir()[:-3],
                'scripts/'))

    else:
        emperor_scripts_dir = abspath(opts.emperor_scripts_dir)

    # make a sanity check
    if (suppress_unit_tests and suppress_script_usage_tests and
        suppress_javascript_unit_tests):
        option_parser.error("All tests have been suppresed. Nothing to run.")

    test_dir = abspath(dirname(__file__))

    unittest_good_pattern = re.compile('OK\s*$')
    application_not_found_pattern = re.compile('ApplicationNotFoundError')
    python_name = 'python'
    bad_tests = []
    missing_application_tests = []

    # Run through all of Emperor's unit tests, and keep track of any files which
    # fail unit tests, note that these are the unit tests only
    if not suppress_unit_tests:
        unittest_names = []
        if not unittest_glob:
            for root, dirs, files in walk(test_dir):
                for name in files:
                    if name.startswith('test_') and name.endswith('.py'):
                        unittest_names.append(join(root,name))
        else:
            for fp in glob(unittest_glob):
                fn = split(fp)[1]
                if fn.startswith('test_') and fn.endswith('.py'):
                    unittest_names.append(abspath(fp))

        unittest_names.sort()

        for unittest_name in unittest_names:
            print "Testing %s:\n" % unittest_name
            command = '%s %s -v' % (python_name, unittest_name)
            stdout, stderr, return_value = qcli_system_call(command)
            print stderr
            if not unittest_good_pattern.search(stderr):
                if application_not_found_pattern.search(stderr):
                    missing_application_tests.append(unittest_name)
                else:
                    bad_tests.append(unittest_name)

    script_usage_failures = 0

    # choose to run some of the script usage tests or all the available ones
    if not suppress_script_usage_tests and exists(emperor_test_data_dir) and\
        exists(emperor_scripts_dir):
        if script_usage_tests != None:
            script_tests = script_usage_tests.split(',')
        else:
            script_tests = None

        initial_working_directory = getcwd()

        # Run the script usage testing functionality; note that depending on the
        # module where this was imported, the name of the arguments will change
        # that's the reason why I added the name of the arguments in here
        script_usage_result_summary, script_usage_failures = \
            run_script_usage_tests( emperor_test_data_dir,  # test_data_dir
                                    emperor_scripts_dir,    # scripts_dir
                                    temp_filepath,          # working_dir
                                    True,                   # verbose
                                    script_tests,           # tests
                                    None,                   # failure_log_fp
                                    False)                  # force_overwrite

        # running script usage tests breaks the current working directory
        chdir(initial_working_directory)

    if not suppress_javascript_unit_tests:
        runner = join(test_dir, 'javascript_tests', 'runner.js')
        index = join(test_dir, 'javascript_tests', 'index.html')

        o, e, r = qcli_system_call('phantomjs %s %s' % (runner, index))

        if o:
            print o
        if e:
            print e

        # if all the tests passed
        javascript_tests_passed = True if r == 0 else False
    else:
        javascript_tests_passed = True


    print "==============\nResult summary\n=============="

    if not suppress_unit_tests:
        print "\nUnit test result summary\n------------------------\n"
        if bad_tests:
            print "\nFailed the following unit tests.\n%s" %'\n'.join(bad_tests)
    
        if missing_application_tests:
            print "\nFailed the following unit tests, in part or whole due "+\
                "to missing external applications.\nDepending on the Emperor "+\
                "features you plan to use, this may not be critical.\n%s"\
                % '\n'.join(missing_application_tests)
        
        if not(missing_application_tests or bad_tests):
            print "\nAll unit tests passed.\n"

    if not suppress_script_usage_tests:
        if exists(emperor_test_data_dir) and exists(emperor_scripts_dir):
            print "\nScript usage test result summary"+\
                "\n--------------------------------\n"
            print script_usage_result_summary
        else:
            print ("\nCould not run script usage tests.\nThe Emperor scripts "
                "directory could not be automatically located, try supplying "
                " it manually using the --emperor_scripts_dir option.")

    if not suppress_javascript_unit_tests:
        print ('\nJavaScript unit tests result summary\n'
               '------------------------------------\n')
        if javascript_tests_passed:
            print 'All JavaScript unit tests passed.\n'
        else:
            print 'JavaScript unit tests failed, check the summary above.'

    # In case there were no failures of any type, exit with a return code of 0
    return_code = 1
    if (len(bad_tests) == 0 and len(missing_application_tests) == 0 and
        script_usage_failures == 0 and javascript_tests_passed):
        return_code = 0

    return return_code
コード例 #8
0
ファイル: all_tests.py プロジェクト: jacksonchen/emperor
def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)

    unittest_glob = opts.unittest_glob
    temp_filepath = opts.temp_filepath
    script_usage_tests = opts.script_usage_tests
    suppress_unit_tests = opts.suppress_unit_tests
    suppress_script_usage_tests = opts.suppress_script_usage_tests

    # since the test data is in the tests folder just add scripts_test_data
    emperor_test_data_dir = join(abspath(dirname(__file__)),
                                 'scripts_test_data/')

    # offer the option for the user to pass the scripts dir from the command
    # line since there is no other way to get the scripts dir. If not provided
    # the base structure of the repository will be assumed. Note that for both
    # cases we are using absolute paths, to avoid unwanted failures.
    if opts.emperor_scripts_dir is None:
        emperor_scripts_dir = abspath(
            join(get_emperor_project_dir(), 'scripts/'))

        # let's try to guess cases for qiime-deploy type of installs
        if get_emperor_project_dir().endswith('/lib'):
            emperor_scripts_dir = abspath(
                join(get_emperor_project_dir()[:-3], 'scripts/'))

    else:
        emperor_scripts_dir = abspath(opts.emperor_scripts_dir)

    # make a sanity check
    if (suppress_unit_tests and suppress_script_usage_tests):
        option_parser.error("All tests have been suppresed. Nothing to run.")

    test_dir = abspath(dirname(__file__))

    unittest_good_pattern = re.compile('OK\s*$')
    application_not_found_pattern = re.compile('ApplicationNotFoundError')
    python_name = 'python'
    bad_tests = []
    missing_application_tests = []

    # Run through all of Emperor's unit tests, and keep track of any files which
    # fail unit tests, note that these are the unit tests only
    if not suppress_unit_tests:
        unittest_names = []
        if not unittest_glob:
            for root, dirs, files in walk(test_dir):
                for name in files:
                    if name.startswith('test_') and name.endswith('.py'):
                        unittest_names.append(join(root, name))
        else:
            for fp in glob(unittest_glob):
                fn = split(fp)[1]
                if fn.startswith('test_') and fn.endswith('.py'):
                    unittest_names.append(abspath(fp))

        unittest_names.sort()

        for unittest_name in unittest_names:
            print "Testing %s:\n" % unittest_name
            command = '%s %s -v' % (python_name, unittest_name)
            stdout, stderr, return_value = qcli_system_call(command)
            print stderr
            if not unittest_good_pattern.search(stderr):
                if application_not_found_pattern.search(stderr):
                    missing_application_tests.append(unittest_name)
                else:
                    bad_tests.append(unittest_name)

    script_usage_failures = 0

    # choose to run some of the script usage tests or all the available ones
    if not suppress_script_usage_tests and exists(emperor_test_data_dir) and\
        exists(emperor_scripts_dir):
        if script_usage_tests != None:
            script_tests = script_usage_tests.split(',')
        else:
            script_tests = None
        # Run the script usage testing functionality; note that depending on the
        # module where this was imported, the name of the arguments will change
        # that's the reason why I added the name of the arguments in here
        script_usage_result_summary, script_usage_failures = \
            run_script_usage_tests( emperor_test_data_dir,  # test_data_dir
                                    emperor_scripts_dir,    # scripts_dir
                                    temp_filepath,          # working_dir
                                    True,                   # verbose
                                    script_tests,           # tests
                                    None,                   # failure_log_fp
                                    False)                  # force_overwrite

    print "==============\nResult summary\n=============="

    if not suppress_unit_tests:
        print "\nUnit test result summary\n------------------------\n"
        if bad_tests:
            print "\nFailed the following unit tests.\n%s" % '\n'.join(
                bad_tests)

        if missing_application_tests:
            print "\nFailed the following unit tests, in part or whole due "+\
                "to missing external applications.\nDepending on the Emperor "+\
                "features you plan to use, this may not be critical.\n%s"\
                % '\n'.join(missing_application_tests)

        if not (missing_application_tests or bad_tests):
            print "\nAll unit tests passed.\n\n"

    if not suppress_script_usage_tests:
        if exists(emperor_test_data_dir) and exists(emperor_scripts_dir):
            print "\nScript usage test result summary"+\
                "\n------------------------------------\n"
            print script_usage_result_summary
        else:
            print(
                "\nCould not run script usage tests.\nThe Emperor scripts "
                "directory could not be automatically located, try supplying "
                " it manually using the --emperor_scripts_dir option.")

    # In case there were no failures of any type, exit with a return code of 0
    return_code = 1
    if (len(bad_tests) == 0 and len(missing_application_tests) == 0
            and script_usage_failures == 0):
        return_code = 0

    return return_code
コード例 #9
0
ファイル: all_tests.py プロジェクト: wangjs/ili
def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)

    unittest_glob = opts.unittest_glob
    temp_filepath = opts.temp_filepath
    script_usage_tests = opts.script_usage_tests
    suppress_unit_tests = opts.suppress_unit_tests
    suppress_script_usage_tests = opts.suppress_script_usage_tests
    suppress_javascript_unit_tests = opts.suppress_javascript_unit_tests

    # since the test data is in the tests folder just add scripts_test_data
    ili_test_data_dir = join(abspath(dirname(__file__)), 'scripts_test_data/')

    # offer the option for the user to pass the scripts dir from the command
    # line since there is no other way to get the scripts dir. If not provided
    # the base structure of the repository will be assumed. Note that for both
    # cases we are using absolute paths, to avoid unwanted failures.
    if opts.ili_scripts_dir is None:
        ili_scripts_dir = abspath(join(get_ili_project_dir(), 'scripts/'))
    else:
        ili_scripts_dir = abspath(opts.ili_scripts_dir)

    # make a sanity check
    if (suppress_unit_tests and suppress_script_usage_tests
            and suppress_javascript_unit_tests):
        option_parser.error("All tests have been suppresed. Nothing to run.")

    test_dir = abspath(dirname(__file__))

    unittest_good_pattern = re.compile('OK\s*$')
    application_not_found_pattern = re.compile('ApplicationNotFoundError')
    python_name = 'python'
    bad_tests = []
    missing_application_tests = []

    # Run through all of ili's unit tests, and keep track of any files
    # which fail unit tests, note that these are the unit tests only
    if not suppress_unit_tests:
        unittest_names = []
        if not unittest_glob:
            for root, dirs, files in walk(test_dir):
                for name in files:
                    if name.startswith('test_') and name.endswith('.py'):
                        unittest_names.append(join(root, name))
        else:
            for fp in glob(unittest_glob):
                fn = split(fp)[1]
                if fn.startswith('test_') and fn.endswith('.py'):
                    unittest_names.append(abspath(fp))

        unittest_names.sort()

        for unittest_name in unittest_names:
            print "Testing %s:\n" % unittest_name
            command = '%s %s -v' % (python_name, unittest_name)
            stdout, stderr, return_value = qcli_system_call(command)
            print stderr
            if not unittest_good_pattern.search(stderr):
                if application_not_found_pattern.search(stderr):
                    missing_application_tests.append(unittest_name)
                else:
                    bad_tests.append(unittest_name)

    script_usage_failures = 0

    # choose to run some of the script usage tests or all the available ones
    if (not suppress_script_usage_tests and exists(ili_test_data_dir)
            and exists(ili_scripts_dir)):
        if script_usage_tests is not None:
            script_tests = script_usage_tests.split(',')
        else:
            script_tests = None

        initial_working_directory = getcwd()

        # Run the script usage testing functionality; note that depending on
        # the module where this was imported, the name of the arguments will
        # change that's the reason why I added the name of the arguments in
        # here
        script_usage_result_summary, script_usage_failures = \
            run_script_usage_tests(ili_test_data_dir,      # test_data_dir
                                   ili_scripts_dir,        # scripts_dir
                                   temp_filepath,          # working_dir
                                   True,                   # verbose
                                   script_tests,           # tests
                                   None,                   # failure_log_fp
                                   False)                  # force_overwrite

        # running script usage tests breaks the current working directory
        chdir(initial_working_directory)

    if not suppress_javascript_unit_tests:
        runner = join(test_dir, 'javascript_tests', 'runner.js')
        index = join(test_dir, 'javascript_tests', 'index.html')

        o, e, r = qcli_system_call('phantomjs %s %s' % (runner, index))

        if o:
            print o
        if e:
            print e

        # if all the tests passed
        javascript_tests_passed = True if r == 0 else False
    else:
        javascript_tests_passed = True

    print "==============\nResult summary\n=============="

    if not suppress_unit_tests:
        print "\nUnit test result summary\n------------------------\n"
        if bad_tests:
            print("\nFailed the following unit tests.\n%s" %
                  '\n'.join(bad_tests))

        if missing_application_tests:
            print(
                "\nFailed the following unit tests, in part or whole due "
                "to missing external applications.\nDepending on the "
                "ili features you plan to use, this may not be "
                "critical.\n%s" % '\n'.join(missing_application_tests))

        if not (missing_application_tests or bad_tests):
            print "\nAll unit tests passed.\n"

    if not suppress_script_usage_tests:
        if exists(ili_test_data_dir) and exists(ili_scripts_dir):
            print(
                "\nScript usage test result summary"
                "\n--------------------------------\n")
            print script_usage_result_summary
        else:
            print(
                "\nCould not run script usage tests.\nThe ili scripts "
                "directory could not be automatically located, try "
                "supplying it manually using the --ili_scripts_dir "
                "option.")

    if not suppress_javascript_unit_tests:
        print(
            '\nJavaScript unit tests result summary\n'
            '------------------------------------\n')
        if javascript_tests_passed:
            print 'All JavaScript unit tests passed.\n'
        else:
            print 'JavaScript unit tests failed, check the summary above.'

    # In case there were no failures of any type, exit with a return code of 0
    return_code = 1
    if (len(bad_tests) == 0 and len(missing_application_tests) == 0
            and script_usage_failures == 0 and javascript_tests_passed):
        return_code = 0

    return return_code