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)
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)
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()
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()