Beispiel #1
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    def test_format_jnlp_file_lines(self):
        """ format_jnlp_file_lines: this converts files into jnlp lines """

        # This can only test the web-based and url listed, since
        # if local, TopiaryExplorer would need to be installed in the same
        # directory on everyones computer
        obs1 = format_jnlp_file_lines(True, 'test', 'test.tep')

        self.assertEqual(''.join(obs1), exp_jnlp_web_url)
Beispiel #2
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 def test_format_jnlp_file_lines(self):
     """ format_jnlp_file_lines: this converts files into jnlp lines """
     
     # This can only test the web-based and url listed, since
     # if local, TopiaryExplorer would need to be installed in the same
     # directory on everyones computer
     obs1 = format_jnlp_file_lines(True,'test','test.tep')
     
     self.assertEqual(''.join(obs1),exp_jnlp_web_url)
Beispiel #3
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def main():
    option_parser, opts, args =\
       parse_command_line_parameters(**script_info)

    # get command line arguments
    otu_table_fp = opts.otu_table_fp
    mapping_fp = opts.mapping_fp
    tree_fp = opts.tree_fp
    output_dir = opts.output_dir
    output_basename = splitext(split(otu_table_fp)[1])[0]
    web_flag = opts.web_flag
    url = opts.url

    # create a generic output folder if not present
    if not output_dir:
        output_dir = 'make_tep_output/'
    create_dir(output_dir)

    # open files for parsing
    otu_table_data = parse_biom_table(open(otu_table_fp, 'U'))
    mapping_lines = open(mapping_fp, 'U')
    tree_lines = open(tree_fp, 'U')
    prefs_dict = {}
    if opts.prefs_file_fp:
        prefs_fp = opts.prefs_file_fp
        # I don't like this eval statement
        prefs_dict = eval(open(prefs_fp, 'U').read())

    # get the tep file lines
    lines = format_tep_file_lines(otu_table_data, mapping_lines, tree_lines,
                                  prefs_dict)

    # write tep file lines if url path not given
    tep_fp = '%s/%s.tep' % (output_dir, output_basename)
    if not url:
        # write tep file
        tepfile = open(tep_fp, 'w')
        tepfile.writelines(lines)
        tepfile.close()

    # get the jnlp file lines
    lines = format_jnlp_file_lines(web_flag, url, tep_fp)

    # write jnlp file
    jnlp_fp = '%s/%s.jnlp' % (output_dir, output_basename)
    jnlpfile = open(jnlp_fp, 'w')
    jnlpfile.writelines(lines)
    jnlpfile.close()
Beispiel #4
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def main():
    option_parser, opts, args =\
       parse_command_line_parameters(**script_info)
    
    # get command line arguments
    otu_table_fp = opts.otu_table_fp
    mapping_fp = opts.mapping_fp
    tree_fp = opts.tree_fp
    output_dir = opts.output_dir
    output_basename = splitext(split(otu_table_fp)[1])[0]
    web_flag = opts.web_flag
    url = opts.url
    
    # create a generic output folder if not present
    if not output_dir:
        output_dir = 'make_tep_output/'
    create_dir(output_dir)    
    
    # open files for parsing
    otu_table_data = parse_biom_table(open(otu_table_fp, 'U'))
    mapping_lines = open(mapping_fp, 'U')    
    tree_lines = open(tree_fp, 'U')
    prefs_dict={}
    if opts.prefs_file_fp:
        prefs_fp = opts.prefs_file_fp
        # I don't like this eval statement
        prefs_dict = eval(open(prefs_fp,'U').read())
    
    # get the tep file lines
    lines = format_tep_file_lines(otu_table_data, mapping_lines, tree_lines, 
                               prefs_dict)
    
    # write tep file lines if url path not given
    tep_fp = '%s/%s.tep' % (output_dir,output_basename)
    if not url:
        # write tep file
        tepfile = open(tep_fp, 'w')
        tepfile.writelines(lines)
        tepfile.close()
    
    # get the jnlp file lines
    lines = format_jnlp_file_lines(web_flag, url, tep_fp)
    
    # write jnlp file
    jnlp_fp = '%s/%s.jnlp' % (output_dir,output_basename)
    jnlpfile = open(jnlp_fp, 'w')
    jnlpfile.writelines(lines)
    jnlpfile.close()