#!/usr/bin/env python
#unit tests for format.py
from __future__ import division

__author__ = "Rob Knight"
__copyright__ = "Copyright 2011, The QIIME Project" #consider project name
__credits__ = ["Rob Knight","Jeremy Widmann","Jens Reeder", "Daniel McDonald",
               "Jai Ram Rideout", "Jose Antonio Navas Molina"]
#remember to add yourself if you make changes
__license__ = "GPL"
__version__ = "1.8.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"

import json
from os import remove
from string import digits
from numpy import array, nan
from cogent.util.misc import remove_files
from cogent.util.unit_test import TestCase, main
from cogent.parse.fasta import MinimalFastaParser
from qiime.util import (get_tmp_filename, get_qiime_library_version,
        DistanceMatrix, MetadataMap)
from qiime.parse import fields_to_dict, parse_mapping_file
from qiime.format import (format_distance_matrix, format_otu_table,
    format_coords, build_prefs_string, format_matrix, format_map_file,
    format_histograms, write_Fasta_from_name_seq_pairs, 
    format_unifrac_sample_mapping,format_otu_map,write_otu_map, 
    format_summarize_taxa, write_summarize_taxa, 
    format_add_taxa_summary_mapping, write_add_taxa_summary_mapping,
    format_taxa_summary, format_correlation_vector,
    format_correlation_info, format_qiime_parameters,
    format_p_value_for_num_iters, format_mapping_file, illumina_data_to_fastq,
    format_biom_table, format_mapping_html_data, format_te_prefs, 
    format_tep_file_lines, format_jnlp_file_lines, format_anosim_results,
    format_best_results, format_permanova_results, format_fastq_record,
    format_histograms_two_bins)
from qiime.stats import Anosim, Best, Permanova
from biom.parse import parse_biom_table, parse_classic_table_to_rich_table
from biom.table import SparseTaxonTable
from StringIO import StringIO

class TopLevelTests(TestCase):
    """Tests of top-level module functions."""
    
    def setUp(self):
        self.otu_map1 = [('0',['seq1','seq2','seq5']),
                         ('1',['seq3','seq4']),
                         ('2',['seq6','seq7','seq8'])]
        self.tmp_fp1 = get_tmp_filename(prefix='FormatTests_',suffix='.txt')
        self.tmp_fp2 = get_tmp_filename(prefix='FormatTests_',suffix='.txt')
        self.files_to_remove = []

        self.taxa_summary = [[('a','b','c'),0,1,2],
                             [('d','e','f'),3,4,5]]
        self.taxa_header = ['Taxon','foo','bar','foobar']
       
        self.add_taxa_summary = {'s1':[1,2],'s2':[3,4]}
        self.add_taxa_header = ['sample_id','foo','bar']
        self.add_taxa_order = [('a','b','c'),('d','e','f')]
        self.add_taxa_mapping = [['s1','something1','something2'],
                                 ['s2','something3','something4'],
                                 ['s3','something5','something6']]
        self.biom1 = parse_biom_table(biom1.split('\n'))
        
        self.expected_formatted_html_no_errors_warnings =\
         expected_formatted_html_no_errors_warnings
        self.expected_formatted_html_errors =\
         expected_formatted_html_errors
        self.expected_formatted_html_warnings =\
         expected_formatted_html_warnings
        self.expected_formatted_html_data_nonloc_error =\
         expected_formatted_html_data_nonloc_error

        # For testing formatting of correlation vectors.
        self.corr_vec1 = [('S1', 'T1', 0.7777777777, 0, 0, 0, 0, (0.5, 1.0))]
        self.corr_vec2 = [('S1', 'T1', 0.7777777777, 0, 0, 0, 0, (0.5, 1.0)),
                          ('S2', 'T2', 0.1, 0.05, 0.15, 0.04, 0.12,
                           (-0.1, 0.2)),
                          ('S3', 'T3', 100.68, 0.9, 1, 1, 1, (-0.4, -0.2))]
        self.corr_vec3 = [('S1', 'T1', 0.7777777777, 0, 0, 0, 0, (None, None))]

        # For testing statistical method formatters.
        self.overview_dm = DistanceMatrix.parseDistanceMatrix(
                overview_dm_lines)
        self.overview_map = MetadataMap.parseMetadataMap(overview_map_lines)

        self.soils_dm = DistanceMatrix.parseDistanceMatrix(soils_dm_lines)
        self.soils_map = MetadataMap.parseMetadataMap(soils_map_lines)

        self.anosim_overview = Anosim(self.overview_map, self.overview_dm,
                                      'Treatment')
        self.permanova_overview = Permanova(self.overview_map,
                                            self.overview_dm, 'Treatment')
        self.best_overview = Best(self.overview_dm, self.overview_map, ['DOB'])
        self.best_88_soils = Best(self.soils_dm, self.soils_map,
                ['TOT_ORG_CARB', 'SILT_CLAY', 'ELEVATION',
                 'SOIL_MOISTURE_DEFICIT', 'CARB_NITRO_RATIO',
                 'ANNUAL_SEASON_TEMP', 'ANNUAL_SEASON_PRECPT', 'PH',
                 'CMIN_RATE', 'LONGITUDE', 'LATITUDE'])

    def tearDown(self):
        remove_files(self.files_to_remove)

    def remove_nums(self, text):
        """Removes all digits from the given string.

        Returns the string will all digits removed. Useful for testing strings
        for equality in unit tests where you don't care about numeric values,
        or if some values are random.

        This code was taken from http://bytes.com/topic/python/answers/
            850562-finding-all-numbers-string-replacing

        Arguments:
            text - the string to remove digits from
        """
        return text.translate(None, digits)
    
    def test_format_biom_table(self):
        """ Formatting of BIOM table correctly includes "generated-by" information 
        """
        generated_by = "QIIME " + get_qiime_library_version()
        self.assertTrue(generated_by in format_biom_table(self.biom1))

    def test_format_mapping_file(self):
        """ format_mapping file should match expected result"""
        headers = ['SampleID','col1','col0','Description']
        samples =\
         [['bsample','v1_3','v0_3','d1'],['asample','aval','another','d2']]
        comments = ['this goes after headers','this too']
        self.assertEqual(format_mapping_file(headers,samples,comments),
         example_mapping_file)
        # need file or stringIO for roundtrip test
        # roundtrip = parse_mapping_file(format_mapping_file(headers,samples,comments))
        # self.assertEqual(roundtrip, [headers,samples,comments])

    def test_format_p_value_for_num_iters(self):
        """ format_p_value_for_num_iters functions as expected """
        self.assertEqual(\
         format_p_value_for_num_iters(0.119123123123,100),"0.12")
        self.assertEqual(\
         format_p_value_for_num_iters(0.119123123123,250),"0.12")
        self.assertEqual(\
         format_p_value_for_num_iters(0.119123123123,1000),"0.119")
        # test num_iters too low still returns a string (this can
        # be the last step of a long process, so we don't want to fail)
        self.assertEqual(\
         format_p_value_for_num_iters(0.119123123123,9),
         "Too few iters to compute p-value (num_iters=9)")
        self.assertEqual(\
         format_p_value_for_num_iters(0.119123123123,1),
         "Too few iters to compute p-value (num_iters=1)")
        self.assertEqual(\
         format_p_value_for_num_iters(0.119123123123,0),
         "Too few iters to compute p-value (num_iters=0)")

    def test_format_summarize_taxa(self):
        """format_summarize_taxa functions as expected"""
        # Classic format.
        exp = '\n'.join(['Taxon\tfoo\tbar\tfoobar',
                         'a;b;c\t0\t1\t2',
                         'd;e;f\t3\t4\t5\n'])
        obs = ''.join(list(format_summarize_taxa(self.taxa_summary,
                                                 self.taxa_header)))
        self.assertEqual(obs, exp)

        # BIOM format. Test by converting our expected output to a biom table
        # and comparing that to our observed table.
        exp = parse_classic_table_to_rich_table(exp.split('\n'), None, None,
                                                None, SparseTaxonTable)
        obs = ''.join(list(format_summarize_taxa(self.taxa_summary,
                                                 self.taxa_header,
                                                 file_format='biom')))
        obs = parse_biom_table(obs)
        self.assertEqual(obs, exp)

        # Bad file_format argument.
        with self.assertRaises(ValueError):
            list(format_summarize_taxa(self.taxa_summary, self.taxa_header,
                 file_format='foo'))

    def test_write_summarize_taxa(self):
        """write_summarize_taxa functions as expected"""
        # Classic format.
        write_summarize_taxa(self.taxa_summary, self.taxa_header, self.tmp_fp1)
        obs = open(self.tmp_fp1).read()
        exp = '\n'.join(['Taxon\tfoo\tbar\tfoobar',
                         'a;b;c\t0\t1\t2',
                         'd;e;f\t3\t4\t5\n'])
        self.assertEqual(obs,exp)
        self.files_to_remove.append(self.tmp_fp1)

        # BIOM format.
        write_summarize_taxa(self.taxa_summary, self.taxa_header, self.tmp_fp2,
                             file_format='biom')
        exp = parse_classic_table_to_rich_table(exp.split('\n'), None, None,
                                                None, SparseTaxonTable)
        obs = open(self.tmp_fp2).read()
        obs = parse_biom_table(obs)
        self.assertEqual(obs, exp)
        self.files_to_remove.append(self.tmp_fp2)

    def test_write_summarize_taxa_transposed_output(self):
        """write_summarize_taxa_transposed_output functions as expected"""
        # Classic format.
        write_summarize_taxa(self.taxa_summary, self.taxa_header, self.tmp_fp1, transposed_output=True)
        obs = open(self.tmp_fp1).read()
        exp = '\n'.join(['SampleID\ta;b;c\td;e;f',
                         'foo\t0\t3\nbar\t1\t4',
                         'foobar\t2\t5\n'])
        self.assertEqual(obs,exp)
        self.files_to_remove.append(self.tmp_fp1)

        # BIOM format.
        write_summarize_taxa(self.taxa_summary, self.taxa_header, self.tmp_fp2,
                             transposed_output=True, file_format='biom')
        exp = parse_classic_table_to_rich_table(exp.split('\n'), None, None,
                                                None, SparseTaxonTable)
        obs = open(self.tmp_fp2).read()
        obs = parse_biom_table(obs)
        self.assertEqual(obs, exp)
        self.files_to_remove.append(self.tmp_fp2)

    def test_format_add_taxa_summary_mapping(self):
        """format_add_taxa_summary_mapping functions as expected"""
        exp = '\n'.join(['#sample_id\tfoo\tbar\ta;b;c\td;e;f',
                         's1\tsomething1\tsomething2\t1\t2',
                         's2\tsomething3\tsomething4\t3\t4\n'])
        tmp = format_add_taxa_summary_mapping(self.add_taxa_summary,\
                                              self.add_taxa_order,\
                                              self.add_taxa_mapping, \
                                              self.add_taxa_header)
        obs = ''.join(list(tmp))
        self.assertEqual(obs,exp)

    def test_format_taxa_summary(self):
        """Test formatting a taxa summary works correctly."""
        # More than one sample.
        taxa_summary = (['Even7','Even8'], ['Eukarya'], array([[1.0, 1.0]]))
        exp = 'Taxon\tEven7\tEven8\nEukarya\t1.0\t1.0\n'
        obs = format_taxa_summary(taxa_summary)
        self.assertEqual(obs, exp)

        # More than one taxon.
        taxa_summary = (['Expected'], ['Eukarya', 'Bacteria', 'Archaea'],
                        array([[0.5], [0.6], [0.4]]))
        exp = 'Taxon\tExpected\nEukarya\t0.5\nBacteria\t0.6\nArchaea\t0.4\n'
        obs = format_taxa_summary(taxa_summary)
        self.assertEqual(obs, exp)

    def test_format_correlation_vector(self):
        """Test formatting correlation vector works correctly."""
        # One row, zero permutations.
        exp = 'Sample ID\tSample ID\tCorrelation coefficient\t' + \
              'Parametric p-value\tParametric p-value ' + \
              '(Bonferroni-corrected)\tNonparametric p-value\t' + \
              'Nonparametric p-value (Bonferroni-corrected)\t' + \
              'CI (lower)\tCI (upper)\nS1\tT1\t0.7778\t0.0000\t' + \
              '0.0000\tN/A\tN/A\t0.5000\t1.0000\n'
        obs = format_correlation_vector(self.corr_vec1, 0)
        self.assertEqual(obs, exp)

        # Undefined confidence interval.
        exp = 'Sample ID\tSample ID\tCorrelation coefficient\t' + \
              'Parametric p-value\tParametric p-value ' + \
              '(Bonferroni-corrected)\tNonparametric p-value\t' + \
              'Nonparametric p-value (Bonferroni-corrected)\t' + \
              'CI (lower)\tCI (upper)\nS1\tT1\t0.7778\t0.0000\t' + \
              '0.0000\tN/A\tN/A\tN/A\tN/A\n'
        obs = format_correlation_vector(self.corr_vec3, 0)
        self.assertEqual(obs, exp)

        # Multiple rows, 999 permutations.
        exp = 'Sample ID\tSample ID\tCorrelation coefficient\t' + \
              'Parametric p-value\tParametric p-value ' + \
              '(Bonferroni-corrected)\tNonparametric p-value\t' + \
              'Nonparametric p-value (Bonferroni-corrected)\t' + \
              'CI (lower)\tCI (upper)\nS1\tT1\t0.7778\t0.0000\t' + \
              '0.0000\t0.000\t0.000\t0.5000\t1.0000\nS2\tT2\t0.1000\t' + \
              '0.0500\t0.1500\t0.040\t0.120\t-0.1000\t0.2000\nS3\tT3\t' + \
              '100.6800\t0.9000\t1.0000\t1.000\t1.000\t-0.4000\t-0.2000\n'
        obs = format_correlation_vector(self.corr_vec2, 999)
        self.assertEqual(obs, exp)

    def test_format_correlation_vector_with_header(self):
        """Test formatting correlation vector with a header works correctly."""
        exp = '#foo\nSample ID\tSample ID\tCorrelation coefficient\t' + \
              'Parametric p-value\tParametric p-value ' + \
              '(Bonferroni-corrected)\tNonparametric p-value\t' + \
              'Nonparametric p-value (Bonferroni-corrected)\t' + \
              'CI (lower)\tCI (upper)\nS1\tT1\t0.7778\t0.0000\t' + \
              '0.0000\tN/A\tN/A\t0.5000\t1.0000\n'
        obs = format_correlation_vector(self.corr_vec1, 0, '#foo')
        self.assertEqual(obs, exp)

    def test_format_correlation_vector_small_num_permutations(self):
        """Test formatting corr vector with small num of permutations."""
        exp = 'Sample ID\tSample ID\tCorrelation coefficient\t' + \
              'Parametric p-value\tParametric p-value ' + \
              '(Bonferroni-corrected)\tNonparametric p-value\t' + \
              'Nonparametric p-value (Bonferroni-corrected)\t' + \
              'CI (lower)\tCI (upper)\nS1\tT1\t0.7778\t0.0000\t' + \
              '0.0000\tToo few iters to compute p-value (num_iters=2)\t' + \
              'Too few iters to compute p-value (num_iters=2)\t' + \
              '0.5000\t1.0000\n'
        obs = format_correlation_vector(self.corr_vec1, 2)
        self.assertEqual(obs, exp)

    def test_format_correlation_info(self):
        """Test formatting correlation information with valid input."""
        # With 999 permutations.
        exp = 'Correlation coefficient\tParametric p-value\tNonparametric ' + \
              'p-value\tCI (lower)\tCI (upper)\n0.7778\t0.0000\t' + \
              '0.000\t0.0000\t1.0000\n'
        obs = format_correlation_info(0.7778, 0, 0, (0, 1), 999)
        self.assertEqual(obs, exp)

        # With 0 permutations.
        exp = 'Correlation coefficient\tParametric p-value\tNonparametric ' + \
              'p-value\tCI (lower)\tCI (upper)\n0.7778\t0.0000\t' + \
              'N/A\t0.0000\t1.0000\n'
        obs = format_correlation_info(0.7778, 0, 0, (0, 1), 0)
        self.assertEqual(obs, exp)

        # With a small number of permutations.
        exp = 'Correlation coefficient\tParametric p-value\tNonparametric ' + \
              'p-value\tCI (lower)\tCI (upper)\n0.7778\t0.0000\t' + \
              'Too few iters to compute p-value (num_iters=1)\t' + \
              '0.0000\t1.0000\n'
        obs = format_correlation_info(0.7778, 0, 0, (0, 1), 1)
        self.assertEqual(obs, exp)

        # With undefined confidence interval.
        exp = 'Correlation coefficient\tParametric p-value\tNonparametric ' + \
              'p-value\tCI (lower)\tCI (upper)\n0.7778\t0.0000\t' + \
              'N/A\tN/A\tN/A\n'
        obs = format_correlation_info(0.7778, 0, 0, (None, None), 0)
        self.assertEqual(obs, exp)

    def test_format_correlation_info_with_header(self):
        """Test formatting correlation information with header."""
        exp = '# Some comment...\nCorrelation coefficient\t' + \
              'Parametric p-value\tNonparametric ' + \
              'p-value\tCI (lower)\tCI (upper)\n0.7778\t0.0000\t' + \
              '0.000\t0.0000\t1.0000\n'
        obs = format_correlation_info(0.7778, 0, 0, (0, 1), 999,
                                      '# Some comment...')
        self.assertEqual(obs, exp)

    def test_format_qiime_parameters(self):
        """format_qiime_parameters: returns lines in qiime_parameters format"""
        params = {'pick_otus':
                    {'similarity':'0.94','otu_picking_method':'cdhit'},
                 'assign_taxonomy':
                    {'use_rdp':None}}
        obs = format_qiime_parameters(params)
        exp = ["#QIIME parameters",
               "assign_taxonomy:use_rdp\tTrue",
               "pick_otus:otu_picking_method\tcdhit",
               "pick_otus:similarity\t0.94"]
        self.assertEqual(obs, exp)

    def test_write_add_taxa_summary_mapping(self):
        """write_add_taxa_summary_mapping functions as expected"""
        write_add_taxa_summary_mapping(self.add_taxa_summary,\
                                       self.add_taxa_order,\
                                       self.add_taxa_mapping,\
                                       self.add_taxa_header,\
                                       self.tmp_fp1)
        obs = open(self.tmp_fp1).read()
        exp = '\n'.join(['#sample_id\tfoo\tbar\ta;b;c\td;e;f',
                         's1\tsomething1\tsomething2\t1\t2',
                         's2\tsomething3\tsomething4\t3\t4\n'])
        self.assertEqual(obs, exp)
        self.files_to_remove.append(self.tmp_fp1)

    def test_format_otu_map(self):
        """format_otu_map functions as expected """
        actual = list(format_otu_map(self.otu_map1,''))
        actual.sort()
        expected = ['0\tseq1\tseq2\tseq5\n',
                    '1\tseq3\tseq4\n',
                    '2\tseq6\tseq7\tseq8\n']
        expected.sort()
        self.assertEqual(actual,expected)
        
    def test_write_otu_map(self):
        """write_otu_map functions as expected """
        write_otu_map(self.otu_map1,self.tmp_fp1)
        actual = fields_to_dict(open(self.tmp_fp1))
        self.files_to_remove.append(self.tmp_fp1)
        self.assertEqual(actual,dict(self.otu_map1))
        
        
    def test_write_otu_map_prefix(self):
        """write_otu_map functions as expected w otu prefix """
        write_otu_map(self.otu_map1,self.tmp_fp1,'my.otu.')
        actual = fields_to_dict(open(self.tmp_fp1))
        self.files_to_remove.append(self.tmp_fp1)
        
        exp = {'my.otu.0':['seq1','seq2','seq5'],
               'my.otu.1':['seq3','seq4'],
               'my.otu.2':['seq6','seq7','seq8']}
        self.assertEqual(actual,exp)
        
    
    def test_format_otu_map_prefix(self):
        """format_otu_map functions as expected w prefix"""
        actual = list(format_otu_map(self.otu_map1,'my.otu.'))
        actual.sort()
        expected = ['my.otu.0\tseq1\tseq2\tseq5\n',
                    'my.otu.1\tseq3\tseq4\n',
                    'my.otu.2\tseq6\tseq7\tseq8\n']
        expected.sort()
        self.assertEqual(actual,expected)
    
    def test_format_otu_map_error_on_bad_prefix(self):
        """format_otu_map functions as expected with bad prefix char"""
        self.assertRaises(ValueError,list,
                          format_otu_map(self.otu_map1,'my_otu_'))

    def test_format_distance_matrix(self):
        """format_distance_matrix should return tab-delimited dist mat"""
        a = array([[1,2,3],[4,5,6],[7,8,9]])
        labels = [11,22,33]
        res = format_distance_matrix(labels, a)
        self.assertEqual(res, 
            '\t11\t22\t33\n11\t1\t2\t3\n22\t4\t5\t6\n33\t7\t8\t9')
        self.assertRaises(ValueError, format_distance_matrix, labels[:2], a)

    def test_format_matrix(self):
        """format_matrix should return tab-delimited mat"""
        a = [[1,2,3], [4,5,6], [7,8,9]]
        row_labels = ['a','b','c']
        col_labels = [11,22,33]
        res = format_matrix(a, row_labels, col_labels)
        
        #test as list
        self.assertEqual(res, 
            '\t11\t22\t33\na\t1\t2\t3\nb\t4\t5\t6\nc\t7\t8\t9')
        self.assertRaises(ValueError, format_matrix, a, row_labels[:2], col_labels)
        self.assertRaises(ValueError, format_matrix, None, row_labels, col_labels)

        #tes as array
        a = array(a)
        self.assertEqual(res, 
                         '\t11\t22\t33\na\t1\t2\t3\nb\t4\t5\t6\nc\t7\t8\t9')
        self.assertRaises(ValueError, format_matrix, a, row_labels[:2], col_labels)
        self.assertRaises(ValueError, format_matrix, None, row_labels, col_labels)

    def assertEqualOtuTable(self,obs,exp):
        """ """
        obs = json.loads(obs)
        exp = json.loads(exp)
        for e in ['generated_by','date']:
            del obs[e]
            del exp[e]
        self.assertEqual(obs,exp)

    def test_format_otu_table(self):
        """format_otu_table should return biom-formatted string"""
        a = array([[1,2,3],
                   [4,5,2718281828459045]])
        samples = ['a','b','c']
        otus = [1,2]
        taxa = ['Bacteria','Archaea']
        res = format_otu_table(samples, otus, a)
        # confirm that parsing the res gives us a valid biom file with 
        # expected observation and sample ids
        t = parse_biom_table(res.split('\n'))
        self.assertEqual(t.ObservationIds,('1','2'))
        self.assertEqual(t.SampleIds,('a','b','c'))

    def test_format_coords(self):
        """format_coords should return tab-delimited table of coords"""
        a = array([[1,2,3],[4,5,6],[7,8,9]])
        header = list('abc')
        eigvals = [2,4,6]
        pct_var = [3,2,1]
        res = format_coords(header, a, eigvals, pct_var)
        self.assertEqual(res, "pc vector number\t1\t2\t3\na\t1\t2\t3\nb\t4\t5\t6\nc\t7\t8\t9\n\n\neigvals\t2\t4\t6\n% variation explained\t3\t2\t1")
    
    def test_build_prefs_string(self):
        """build_prefs_string should return a properly formatted prefs string.
        """
        #Try with correctly formatted color_by_string
        mapping_headers_to_use='First,Second'
        background_color='black'
        monte_carlo_dist=10
        otu_ids=['Root;Bacteria']
        headers=['First','Second']
        ball_size=2.5
        arrow_head_color='red'
        arrow_line_color='white'
        exp_string = \
        """{\n'background_color':'black',\n\n'sample_coloring':\n\t{\n\t\t'First':\n\t\t{\n\t\t\t'column':'First',\n\t\t\t'colors':(('red',(0,100,100)),('blue',(240,100,100)))\n\t\t},\n\t\t'Second':\n\t\t{\n\t\t\t'column':'Second',\n\t\t\t'colors':(('red',(0,100,100)),('blue',(240,100,100)))\n\t\t}\n\t},\n'MONTE_CARLO_GROUP_DISTANCES':\n\t{\n\t\t'First': 10,\n\t\t'Second': 10\n\t},\n'FIELDS':\n\t[\n\t\t'Second',\n\t\t'First'\n\t],\n'taxonomy_coloring':\n\t{\n\t\t'Level_1':\n\t\t{\n\t\t\t'column':'1',\n\t\t\t'colors':\n\t\t\t{\n\t\t\t\t'Root;Bacteria':('red0',(0,100,100))\n\t\t\t}\n\t\t}\n\t},\n'ball_scale':'2.500000',\n'arrow_line_color':'white',\n'arrow_head_color':'red'\n}"""
        obs_string = build_prefs_string(mapping_headers_to_use, \
                                    background_color, monte_carlo_dist, headers,
                                    otu_ids, ball_size, arrow_line_color,
                                    arrow_head_color)
        
        self.assertEqual(obs_string,exp_string)
        
    def test_format_map_file(self):
        """format_map_file should produce correct result"""
        
        desc_key = "Description"
        sample_id = "SampleID"
        headers = ['SampleID', 'a', 'Description', 'b']
        id_map = {'x':{'a':3,'b':4}, 'y':{'a':5,'b':6}}
        desc_map = {'x':'sample x','y':'sample y'}
        run_desc = 'run desc'
        self.assertEqual(format_map_file(headers, id_map, desc_key, sample_id,\
         desc_map, run_desc),
"""#SampleID\ta\tb\tDescription
#run desc
x\t3\t4\tsample x
y\t5\t6\tsample y""")

    def test_format_histograms(self):
        """format_histograms should print histograms correctly"""
        self.assertEqual(format_histograms(array([0,1,0,2,2,3]),
         array([2,1,0,2,0,0]), array([0,0,0,2,0,1]),
         array([100,110,120,130,140,150,160])),
            """# bins raw sequence lengths, length of sequences that pass quality filters before processing, and lengths of sequences that pass quality filters post processing.\nLength\tRaw\tBefore\tAfter\n100\t0\t2\t0\n110\t1\t1\t0\n120\t0\t0\t0\n130\t2\t2\t2\n140\t2\t0\t0\n150\t3\t0\t1""")

    def test_format_histograms_two_bins(self):
        """format_histograms_two_bins should print histograms correctly """
        self.assertEqual(format_histograms_two_bins(array([0,1,0,2,2,3]),
         array([2,1,0,2,0,0]), array([100,110,120,130,140,150,160])), 
         """Length\tBefore\tAfter\n100\t0\t2\n110\t1\t1\n120\t0\t0\n130\t2\t2\n140\t2\t0\n150\t3\t0""")

        
    def test_write_Fasta_from_name_seqs_pairs(self):
        """write_Fasta_from_name_seqs_pairs write proper FASTA string."""
        
        seqs = [('1',"AAA"),('2',"CCCCC"),('3',"GGGG")]

        #None fh raises Error
        self.assertRaises(ValueError, write_Fasta_from_name_seq_pairs,seqs,None)

        tmp_filename = get_tmp_filename(prefix="test_write_Fasta", suffix=".fna")
        fh = open(tmp_filename,"w")
        write_Fasta_from_name_seq_pairs(seqs,fh)
        fh.close()
        actual_seqs = list(MinimalFastaParser(open(tmp_filename,"U")))
        remove(tmp_filename)
        
        self.assertEqual(actual_seqs, seqs)

    def test_format_unifrac_sample_mapping(self):
        """format sample mapping works
        """
        a = [[1,0,0], [0,2,4], [7,0,9.0]]
        otu_ids = ['OTUa','OTUb','OTUc']
        sample_ids = ['Sa','Sb','Sc']
        result = format_unifrac_sample_mapping(sample_ids, otu_ids, a)
        self.assertEqual(result, ['OTUa\tSa\t1', 'OTUb\tSb\t2', 'OTUb\tSc\t4', 'OTUc\tSa\t7', 'OTUc\tSc\t9.0'])
        
    def test_illumina_data_to_fastq(self):
        """illumina_data_to_fastq functions as expected """
        in1 = ("M10","68","1","1","28680","29475","0","1","AACGAAAGGCAGTTTTGGAAGTAGGCGAATTAGGGTAACGCATATAGGATGCTAATACAACGTGAATGAAGTACTGCATCTATGTCACCAGCTTATTACAGCAGCTTGTCATACATGGCCGTACAGGAAACACACATCATAGCATCACACG.","BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB","0")
        expected = """@M10_68:1:1:28680:29475#0/1\nAACGAAAGGCAGTTTTGGAAGTAGGCGAATTAGGGTAACGCATATAGGATGCTAATACAACGTGAATGAAGTACTGCATCTATGTCACCAGCTTATTACAGCAGCTTGTCATACATGGCCGTACAGGAAACACACATCATAGCATCACACGN\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB""", 0
        
        self.assertEqual(illumina_data_to_fastq(in1),expected)

        expected12 = """@M10_68:1:1:28680:29475#0/1\nAACGAAAGGCAG\n+\nBBBBBBBBBBBB""", 0
        self.assertEqual(illumina_data_to_fastq(in1,number_of_bases=12),expected12)
        
        # different value in the pass filter field
        in2 = ("M10","68","1","1","28680","29475","0","1","AACGAAAGGCAGTTTTGGAAGTAGGCGAATTAGGGTAACGCATATAGGATGCTAATACAACGTGAATGAAGTACTGCATCTATGTCACCAGCTTATTACAGCAGCTTGTCATACATGGCCGTACAGGAAACACACATCATAGCATCACACG.","BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB","1")
        expected = """@M10_68:1:1:28680:29475#0/1\nAACGAAAGGCAGTTTTGGAAGTAGGCGAATTAGGGTAACGCATATAGGATGCTAATACAACGTGAATGAAGTACTGCATCTATGTCACCAGCTTATTACAGCAGCTTGTCATACATGGCCGTACAGGAAACACACATCATAGCATCACACGN\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB""", 1
        
        self.assertEqual(illumina_data_to_fastq(in2),expected)
        
    def test_illumina_data_to_fastq_no_pass_filter_field(self):
        """illumina_data_to_fastq functions as expected with no pass filter field"""
        in1 = ("M10","68","1","1","28680","29475","0","1","AACGAAAGGCAGTTTTGGAAGTAGGCGAATTAGGGTAACGCATATAGGATGCTAATACAACGTGAATGAAGTACTGCATCTATGTCACCAGCTTATTACAGCAGCTTGTCATACATGGCCGTACAGGAAACACACATCATAGCATCACACG.","BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB")
        expected = """@M10_68:1:1:28680:29475#0/1\nAACGAAAGGCAGTTTTGGAAGTAGGCGAATTAGGGTAACGCATATAGGATGCTAATACAACGTGAATGAAGTACTGCATCTATGTCACCAGCTTATTACAGCAGCTTGTCATACATGGCCGTACAGGAAACACACATCATAGCATCACACGN\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB""", 2
        
        self.assertEqual(illumina_data_to_fastq(in1),expected)
        
    def test_format_mapping_html_data(self):
        """ Properly formats html string for mapping file errors/warnings """
        
        header = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence',
         'Description']
        mapping_data = [['Sample1','AACCGGTT','ACATATT','Desc_1'],
                        ['Sample2','CCAATTGG','ACATATT','Desc_2']
                       ]
        errors = []
        warnings = []
        
        # no errors or warnings, shouldn't get any popup mouseover data
        
        actual_formatted_html_data = format_mapping_html_data(header,
         mapping_data, errors, warnings)
         
        self.assertEqual(actual_formatted_html_data,
         self.expected_formatted_html_no_errors_warnings)
         
    def test_format_mapping_html_data_errors(self):
        """ Properly formats html string for mapping file errors/warnings """
        
        header = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence',
         'Description']
        mapping_data = [['Sample1','AACCGGTT','ACATATT','Desc_1'],
                        ['Sample2','CCAATTGG','ACATATT','Desc_2']
                       ]
        errors = ['problem1\t1,2']
        warnings = []
        
        # Should create a an error popup in the right location
        
        actual_formatted_html_data = format_mapping_html_data(header,
         mapping_data, errors, warnings)
         
        self.assertEqual(actual_formatted_html_data,
         self.expected_formatted_html_errors)
         
    def test_format_mapping_html_data_warnings(self):
        """ Properly formats html string for mapping file errors/warnings """
        
        header = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence',
         'Description']
        mapping_data = [['Sample1','AACCGGTT','ACATATT','Desc_1'],
                        ['Sample2','CCAATTGG','ACATATT','Desc_2']
                       ]
        errors = []
        warnings = ['warning1\t2,2']
        
        # Should create a an warning popup in the right location
        
        actual_formatted_html_data = format_mapping_html_data(header,
         mapping_data, errors, warnings)
         
         
        self.assertEqual(actual_formatted_html_data,
         self.expected_formatted_html_warnings)

    def test_format_mapping_html_data_non_location_error(self):
        """ Properly formats html string for mapping file errors/warnings """
        
        header = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence',
         'Description']
        mapping_data = [['Sample1','AACCGGTT','ACATATT','Desc_1'],
                        ['Sample2','CCAATTGG','ACATATT','Desc_2']
                       ]
        errors = ['error1\t-1,-1']
        warnings = []
        
        # Should list errors with location -1,-1 outside of table
        
        actual_formatted_html_data = format_mapping_html_data(header,
         mapping_data, errors, warnings)
         
        
        self.assertEqual(actual_formatted_html_data,
         self.expected_formatted_html_data_nonloc_error)
    
    def test_format_te_prefs(self):
        """ format_te_prefs: this takes a prefs file and generates te lines """
        
        # define variables
        prefs_dict1 = {'sample_coloring': {'TEST1': {'column': 'TEST1', 
            'colors': (('red', (0, 100, 100)), ('blue', (240, 100, 100)))}}}
        prefs_dict2 = {'sample_coloring': {'TEST1': {'column': 'TEST1', 
            'colors': {'Sample1':'red1','Sample2':'blue1'}}}}

        # list expected results
        exp_lines1 = ['0,100,100,\n', '240,100,100,\n', '>defaultTEST1:TEST1\n']
        exp_lines2 = ['Sample1:0,100,100,\n', 'Sample2:240,100,100,\n', 
                      '>defaultTEST1:TEST1\n']
        
        obs_lines1 = format_te_prefs(prefs_dict1)
        self.assertEqual(obs_lines1,exp_lines1)

        obs_lines2 = format_te_prefs(prefs_dict2)
        self.assertEqual(obs_lines1,exp_lines1)

    
    def test_format_tep_file_lines(self):
        """ format_tep_file_lines: this converts files into tep lines """
        
        # set variables
        prefs_dict1 = {'sample_coloring': {'TEST1': {'column': 'TEST1', 
            'colors': (('red', (0, 100, 100)), ('blue', (240, 100, 100)))}}}
        test_biom2 = parse_biom_table(biom2)
        
        # test with prefs file
        exp1 = ['>>tre\n', "['(tax1:0.00000043418318065054,((tax2:0.01932550067944402081,tax3:0.08910446960529855298):0.00000043418318065054,tax4:0.17394765077611337722):0.00000043418318065054,tax5:0.00000043418318065054):0.0;']", '\n', '>>otm\n#OTU ID\tOTU Metadata\n', u'tax1\tk__Bacteria;p__Proteobacteria;', '\n', u'tax2\tk__Bacteria;p__Cyanobacteria;', '\n', '>>osm\n', '# Constructed from biom file\n#OTU ID\tsam1\tsam2\tConsensus Lineage\ntax1\t7.0\t4.0\tk__Bacteria;p__Proteobacteria\ntax2\t1.0\t2.0\tk__Bacteria;p__Cyanobacteria', '\n>>sam\n', "['#SampleID\\tcol1\\tcol0\\tDescription', 'sam1\\tv1_3\\tv0_3\\td1', 'sam2\\taval\\tanother\\td2']", '\n>>pre\n', '0,100,100,\n', '240,100,100,\n', '>defaultTEST1:TEST1\n']
        obs1 = format_tep_file_lines(test_biom2, 
                             StringIO(example_mapping_file2.split('\n')), 
                             StringIO(example_tree.split('\n')), 
                             prefs_dict1)
        
        self.assertEqual(obs1,exp1)
        
        # test without prefs file
        exp2 = ['>>tre\n', "['(tax1:0.00000043418318065054,((tax2:0.01932550067944402081,tax3:0.08910446960529855298):0.00000043418318065054,tax4:0.17394765077611337722):0.00000043418318065054,tax5:0.00000043418318065054):0.0;']", '\n', '>>otm\n#OTU ID\tOTU Metadata\n', u'tax1\tk__Bacteria;p__Proteobacteria;', '\n', u'tax2\tk__Bacteria;p__Cyanobacteria;', '\n', '>>osm\n', '# Constructed from biom file\n#OTU ID\tsam1\tsam2\tConsensus Lineage\ntax1\t7.0\t4.0\tk__Bacteria;p__Proteobacteria\ntax2\t1.0\t2.0\tk__Bacteria;p__Cyanobacteria', '\n>>sam\n', "['#SampleID\\tcol1\\tcol0\\tDescription', 'sam1\\tv1_3\\tv0_3\\td1', 'sam2\\taval\\tanother\\td2']"]
        obs2 = format_tep_file_lines(test_biom2, 
                             StringIO(example_mapping_file2.split('\n')), 
                             StringIO(example_tree.split('\n')), 
                             {})
        
        self.assertEqual(obs2,exp2)
        
        
    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_anosim_results(self):
        """Test formatting results of ANOSIM."""
        exp = 'Method name\tR statistic\tp-value\tNumber of permutations\n' + \
              'ANOSIM\t.\t.\t\n'
        obs = format_anosim_results(self.anosim_overview(999))
        self.assertEqual(self.remove_nums(obs), exp)

        exp = 'Method name\tR statistic\tp-value\tNumber of permutations\n' + \
              'ANOSIM\t.\tToo few iters to compute p-value (num_iters=)\t\n'
        obs = format_anosim_results(self.anosim_overview(0))
        self.assertEqual(self.remove_nums(obs), exp)

    def test_format_permanova_results(self):
        """Test formatting results of PERMANOVA."""
        exp = 'Method name\tPseudo-F statistic\tp-value\tNumber of ' + \
              'permutations\nPERMANOVA\t.\t.\t\n'
        obs = format_permanova_results(self.permanova_overview(999))
        self.assertEqual(self.remove_nums(obs), exp)

        exp = 'Method name\tPseudo-F statistic\tp-value\tNumber of ' + \
              'permutations\nPERMANOVA\t.\tToo few iters to compute ' + \
              'p-value (num_iters=)\t\n'
        obs = format_permanova_results(self.permanova_overview(0))
        self.assertEqual(self.remove_nums(obs), exp)

    def test_format_best_results(self):
        """Test formatting results of BEST."""
        # Single category.
        exp = 'Method name\tNumber of categories\tCategories\t' + \
              'rho statistics\nBEST\t\tDOB = \t(., \'\')\n'
        obs = format_best_results(self.best_overview(999))
        self.assertEqual(self.remove_nums(obs), exp)

        # Multiple categories.
        obs = format_best_results(self.best_88_soils(0))
        self.assertEqual(self.remove_nums(obs), exp_best_88_soils)
        
    def test_format_fastq_record(self):
        """ Returns fastq record in the correct format """
        
        label = "test_label"
        seq = "AATTCCGG"
        qual = "12345678"
        
        actual_lines = format_fastq_record(label, seq, qual)
        expected_lines = '@test_label\nAATTCCGG\n+\n12345678\n'
        
        self.assertEqual(actual_lines, expected_lines)


example_mapping_file = """#SampleID\tcol1\tcol0\tDescription
#this goes after headers
#this too
bsample\tv1_3\tv0_3\td1
asample\taval\tanother\td2"""

expected_formatted_html_no_errors_warnings = """<html>
<head>

<script type="text/javascript" src="./overlib.js"></script>
</head>
<body bgcolor="white"> <h1>No errors or warnings detected.<br></h1><h1>Mapping file error and warning details.</h1>
Notes for interpreting this report:
<ul>
    <li>Errors will be listed in red, warnings in yellow.  
    <li>Mouse over an error or warning in a cell for more details.
    <li>Errors in the header row may mask other errors, so these should be corrected first.
    <li>Modifications to your mapping file to fix certain issues may result in different errors. You should run <tt>validate_mapping_file.py</tt> until no errors (nor warnings, ideally) are found.
</ul>
<p>
Some general rules about formatting mapping files (see <a href="http://qiime.org/documentation/file_formats.html#metadata-mapping-files">here</a> for additional details):
<ul> 
    <li>Header characters should only contain alphanumeric and <tt>_</tt> characters only.
    <li>Valid characters for SampleID fields are alphanumeric and <tt>.</tt> only.<br>
    <li>Other fields allow alphanumeric and <tt>+-%./ :,;_</tt> characters.
</ul>
General issues with your mapping file (i.e., those that do not pertain to a particular cell) will be listed here, if any:<table border="1" cellspacing="0" cellpadding="7"><tr></tr></table><br>
<table border="2" cellspacing="0" cellpadding="5">

<tr></tr>
<tr>
<th>SampleID</th><th>BarcodeSequence</th><th>LinkerPrimerSequence</th><th>Description</th>
</tr>

<tr>
<tr><th><tt>Sample1</tt></th><th><tt>AACCGGTT</tt></th><th><tt>ACATATT</tt></th><th><tt>Desc_1</tt></th></tr><tr><th><tt>Sample2</tt></th><th><tt>CCAATTGG</tt></th><th><tt>ACATATT</tt></th><th><tt>Desc_2</tt></th></tr>
</tr>
</table>

</body>
</html>"""

expected_formatted_html_errors = """<html>
<head>

<script type="text/javascript" src="./overlib.js"></script>
</head>
<body bgcolor="white"> <h1>Mapping file error and warning details.</h1>
Notes for interpreting this report:
<ul>
    <li>Errors will be listed in red, warnings in yellow.  
    <li>Mouse over an error or warning in a cell for more details.
    <li>Errors in the header row may mask other errors, so these should be corrected first.
    <li>Modifications to your mapping file to fix certain issues may result in different errors. You should run <tt>validate_mapping_file.py</tt> until no errors (nor warnings, ideally) are found.
</ul>
<p>
Some general rules about formatting mapping files (see <a href="http://qiime.org/documentation/file_formats.html#metadata-mapping-files">here</a> for additional details):
<ul> 
    <li>Header characters should only contain alphanumeric and <tt>_</tt> characters only.
    <li>Valid characters for SampleID fields are alphanumeric and <tt>.</tt> only.<br>
    <li>Other fields allow alphanumeric and <tt>+-%./ :,;_</tt> characters.
</ul>
General issues with your mapping file (i.e., those that do not pertain to a particular cell) will be listed here, if any:<table border="1" cellspacing="0" cellpadding="7"><tr></tr></table><br>
<table border="2" cellspacing="0" cellpadding="5">

<tr></tr>
<tr>
<th>SampleID</th><th>BarcodeSequence</th><th>LinkerPrimerSequence</th><th>Description</th>
</tr>

<tr>
<tr><th><tt>Sample1</tt></th><th><tt>AACCGGTT</tt></th><th bgcolor=red><a href="javascript:void(0);" onmouseover="return overlib('problem1<br>Location (SampleID,Header Field)<br>Sample1,LinkerPrimerSequence');" onmouseout="return nd();"><font color=white><tt>ACATATT</tt></a></th><th><tt>Desc_1</tt></th></tr><tr><th><tt>Sample2</tt></th><th><tt>CCAATTGG</tt></th><th><tt>ACATATT</tt></th><th><tt>Desc_2</tt></th></tr>
</tr>
</table>

</body>
</html>"""

expected_formatted_html_warnings = """<html>
<head>

<script type="text/javascript" src="./overlib.js"></script>
</head>
<body bgcolor="white"> <h1>Mapping file error and warning details.</h1>
Notes for interpreting this report:
<ul>
    <li>Errors will be listed in red, warnings in yellow.  
    <li>Mouse over an error or warning in a cell for more details.
    <li>Errors in the header row may mask other errors, so these should be corrected first.
    <li>Modifications to your mapping file to fix certain issues may result in different errors. You should run <tt>validate_mapping_file.py</tt> until no errors (nor warnings, ideally) are found.
</ul>
<p>
Some general rules about formatting mapping files (see <a href="http://qiime.org/documentation/file_formats.html#metadata-mapping-files">here</a> for additional details):
<ul> 
    <li>Header characters should only contain alphanumeric and <tt>_</tt> characters only.
    <li>Valid characters for SampleID fields are alphanumeric and <tt>.</tt> only.<br>
    <li>Other fields allow alphanumeric and <tt>+-%./ :,;_</tt> characters.
</ul>
General issues with your mapping file (i.e., those that do not pertain to a particular cell) will be listed here, if any:<table border="1" cellspacing="0" cellpadding="7"><tr></tr></table><br>
<table border="2" cellspacing="0" cellpadding="5">

<tr></tr>
<tr>
<th>SampleID</th><th>BarcodeSequence</th><th>LinkerPrimerSequence</th><th>Description</th>
</tr>

<tr>
<tr><th><tt>Sample1</tt></th><th><tt>AACCGGTT</tt></th><th><tt>ACATATT</tt></th><th><tt>Desc_1</tt></th></tr><tr><th><tt>Sample2</tt></th><th><tt>CCAATTGG</tt></th><th bgcolor=yellow><a href="javascript:void(0);" onmouseover="return overlib('warning1<br>Location (SampleID,Header Field)<br>Sample2,LinkerPrimerSequence');" onmouseout="return nd();"><font color=black><tt>ACATATT</tt></a></th><th><tt>Desc_2</tt></th></tr>
</tr>
</table>

</body>
</html>"""

expected_formatted_html_data_nonloc_error = """<html>
<head>

<script type="text/javascript" src="./overlib.js"></script>
</head>
<body bgcolor="white"> <h1>Mapping file error and warning details.</h1>
Notes for interpreting this report:
<ul>
    <li>Errors will be listed in red, warnings in yellow.  
    <li>Mouse over an error or warning in a cell for more details.
    <li>Errors in the header row may mask other errors, so these should be corrected first.
    <li>Modifications to your mapping file to fix certain issues may result in different errors. You should run <tt>validate_mapping_file.py</tt> until no errors (nor warnings, ideally) are found.
</ul>
<p>
Some general rules about formatting mapping files (see <a href="http://qiime.org/documentation/file_formats.html#metadata-mapping-files">here</a> for additional details):
<ul> 
    <li>Header characters should only contain alphanumeric and <tt>_</tt> characters only.
    <li>Valid characters for SampleID fields are alphanumeric and <tt>.</tt> only.<br>
    <li>Other fields allow alphanumeric and <tt>+-%./ :,;_</tt> characters.
</ul>
General issues with your mapping file (i.e., those that do not pertain to a particular cell) will be listed here, if any:<table border="1" cellspacing="0" cellpadding="7"><tr><td bgcolor="red"><font color="white">error1<font color="black"></td></tr></table><br>
<table border="2" cellspacing="0" cellpadding="5">

<tr></tr>
<tr>
<th>SampleID</th><th>BarcodeSequence</th><th>LinkerPrimerSequence</th><th>Description</th>
</tr>

<tr>
<tr><th><tt>Sample1</tt></th><th><tt>AACCGGTT</tt></th><th><tt>ACATATT</tt></th><th><tt>Desc_1</tt></th></tr><tr><th><tt>Sample2</tt></th><th><tt>CCAATTGG</tt></th><th><tt>ACATATT</tt></th><th><tt>Desc_2</tt></th></tr>
</tr>
</table>

</body>
</html>"""

biom1 = """{"rows": [{"id": "tax1", "metadata": {}}, {"id": "tax2", "metadata": {}}, {"id": "tax3", "metadata": {}}, {"id": "tax4", "metadata": {}}, {"id": "endbigtaxon", "metadata": {}}, {"id": "tax6", "metadata": {}}, {"id": "tax7", "metadata": {}}, {"id": "tax8", "metadata": {}}, {"id": "tax9", "metadata": {}}], "format": "Biological Observation Matrix 0.9.0-dev", "data": [[0, 0, 7.0], [0, 1, 4.0], [0, 2, 2.0], [0, 3, 1.0], [1, 0, 1.0], [1, 1, 2.0], [1, 2, 4.0], [1, 3, 7.0], [1, 4, 8.0], [1, 5, 7.0], [1, 6, 4.0], [1, 7, 2.0], [1, 8, 1.0], [2, 5, 1.0], [2, 6, 2.0], [2, 7, 4.0], [2, 8, 7.0], [2, 9, 8.0], [2, 10, 7.0], [2, 11, 4.0], [2, 12, 2.0], [2, 13, 1.0], [3, 10, 1.0], [3, 11, 2.0], [3, 12, 4.0], [3, 13, 7.0], [3, 14, 8.0], [3, 15, 7.0], [3, 16, 4.0], [3, 17, 2.0], [3, 18, 1.0], [4, 15, 1.0], [4, 16, 2.0], [4, 17, 4.0], [4, 18, 7.0], [5, 1, 1.0], [5, 2, 1.0], [6, 6, 2.0], [6, 7, 1.0], [7, 11, 3.0], [7, 12, 1.0], [8, 16, 4.0], [8, 17, 1.0]], "columns": [{"id": "sam1", "metadata": null}, {"id": "sam2", "metadata": null}, {"id": "sam3", "metadata": null}, {"id": "sam4", "metadata": null}, {"id": "sam5", "metadata": null}, {"id": "sam6", "metadata": null}, {"id": "sam7", "metadata": null}, {"id": "sam8", "metadata": null}, {"id": "sam9", "metadata": null}, {"id": "sam_middle", "metadata": null}, {"id": "sam11", "metadata": null}, {"id": "sam12", "metadata": null}, {"id": "sam13", "metadata": null}, {"id": "sam14", "metadata": null}, {"id": "sam15", "metadata": null}, {"id": "sam16", "metadata": null}, {"id": "sam17", "metadata": null}, {"id": "sam18", "metadata": null}, {"id": "sam19", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2520", "matrix_type": "sparse", "shape": [9, 19], "format_url": "http://biom-format.org", "date": "2011-12-20T19:03:28.130403", "type": "OTU table", "id": null, "matrix_element_type": "float"}"""

biom2 = """{"rows": [{"id": "tax1", "metadata": {"taxonomy":["k__Bacteria", "p__Proteobacteria"]}}, {"id": "tax2", "metadata": {"taxonomy":["k__Bacteria", "p__Cyanobacteria"]}}], "format": "Biological Observation Matrix 0.9.0-dev", "data": [[0, 0, 7.0], [0, 1, 4.0],  [1, 0, 1.0], [1, 1, 2.0]], "columns": [{"id": "sam1", "metadata": null}, {"id": "sam2", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2520", "matrix_type": "sparse", "shape": [2, 2], "format_url": "http://biom-format.org", "date": "2011-12-20T19:03:28.130403", "type": "OTU table", "id": null, "matrix_element_type": "float"}"""

example_tree = """(tax1:0.00000043418318065054,((tax2:0.01932550067944402081,tax3:0.08910446960529855298):0.00000043418318065054,tax4:0.17394765077611337722):0.00000043418318065054,tax5:0.00000043418318065054):0.0;"""
example_mapping_file2 = """#SampleID\tcol1\tcol0\tDescription
sam1\tv1_3\tv0_3\td1
sam2\taval\tanother\td2"""

exp_jnlp_web_url="""
<?xml version="1.0" encoding="utf-8"?>

<jnlp codebase="http://topiaryexplorer.sourceforge.net/app/">
    
    <information>
    <title>TopiaryExplorer</title>
    <vendor>University of Colorado</vendor>
    <description>TopiaryExplorer</description>

    <offline-allowed/>

    </information>

    <security>
        <all-permissions/>
    </security>

    <resources>
        <j2se version="1.6+" initial-heap-size="500M" max-heap-size="2000m" />

        <jar href="topiaryexplorer1.0.jar" />
        <jar href="lib/core.jar" />
        <jar href="lib/itext.jar" />
        <jar href="lib/pdf.jar" />
        <jar href="lib/ojdbc14.jar" />
        <jar href="lib/opengl.jar" />
        <jar href="lib/mysql-connector-java-5.1.10-bin.jar" />
        <jar href="lib/javaws.jar" />
        <jar href="lib/classes12.jar" />
        <jar href="lib/jogl.jar" />
        <jar href="lib/guava-r09.jar" />
    </resources>

    <application-desc main-class="topiaryexplorer.TopiaryExplorer">
    <argument>test</argument>
    </application-desc>
</jnlp>
"""

overview_dm_lines = ["\tPC.354\tPC.355\tPC.356\tPC.481\tPC.593\
                      \tPC.607\tPC.634\tPC.635\tPC.636",
                      "PC.354\t0.0\t0.595483768391\t0.618074717633\
                      \t0.582763100909\t0.566949022108\
                      \t0.714717232268\t0.772001731764\
                      \t0.690237118413\t0.740681707488",
                      "PC.355\t0.595483768391\t0.0\t0.581427669668\
                      \t0.613726772383\t0.65945132763\
                      \t0.745176523638\t0.733836123821\
                      \t0.720305073505\t0.680785600439",
                      "PC.356\t0.618074717633\t0.581427669668\t0.0\
                      \t0.672149021573\t0.699416863323\
                      \t0.71405573754\t0.759178215168\
                      \t0.689701276341\t0.725100672826",
                      "PC.481\t0.582763100909\t0.613726772383\
                      \t0.672149021573\t0.0\t0.64756120797\
                      \t0.666018240373\t0.66532968784\
                      \t0.650464714994\t0.632524644216",
                      "PC.593\t0.566949022108\t0.65945132763\
                      \t0.699416863323\t0.64756120797\t0.0\
                      \t0.703720200713\t0.748240937349\
                      \t0.73416971958\t0.727154987937",
                      "PC.607\t0.714717232268\t0.745176523638\
                      \t0.71405573754\t0.666018240373\
                      \t0.703720200713\t0.0\t0.707316869557\
                      \t0.636288883818\t0.699880573956",
                      "PC.634\t0.772001731764\t0.733836123821\
                      \t0.759178215168\t0.66532968784\
                      \t0.748240937349\t0.707316869557\t0.0\
                      \t0.565875193399\t0.560605525642",
                      "PC.635\t0.690237118413\t0.720305073505\
                      \t0.689701276341\t0.650464714994\
                      \t0.73416971958\t0.636288883818\
                      \t0.565875193399\t0.0\t0.575788039321",
                      "PC.636\t0.740681707488\t0.680785600439\
                      \t0.725100672826\t0.632524644216\
                      \t0.727154987937\t0.699880573956\
                      \t0.560605525642\t0.575788039321\t0.0"]

overview_map_lines = ["#SampleID\tBarcodeSequence\tTreatment\tDOB",
                      "PC.354\tAGCACGAGCCTA\tControl\t20061218",
                      "PC.355\tAACTCGTCGATG\tControl\t20061218",
                      "PC.356\tACAGACCACTCA\tControl\t20061126",
                      "PC.481\tACCAGCGACTAG\tControl\t20070314",
                      "PC.593\tAGCAGCACTTGT\tControl\t20071210",
                      "PC.607\tAACTGTGCGTAC\tFast\t20071112",
                      "PC.634\tACAGAGTCGGCT\tFast\t20080116",
                      "PC.635\tACCGCAGAGTCA\tFast\t20080116",
                      "PC.636\tACGGTGAGTGTC\tFast\t20080116"]

soils_dm_lines = ["\tMT2.141698\tCA1.141704\tBB2.141659\t"
"CO2.141657\tTL3.141709\tSN3.141650", "MT2.141698\t0.0\t"
"0.623818643706\t0.750015427505\t0.585201193913\t0.729023583672\t"
"0.622135587669", "CA1.141704\t0.623818643706\t0.0\t0.774881224555"
"\t0.649822398416\t0.777203137034\t0.629507320436", "BB2.141659\t"
"0.750015427505\t0.774881224555\t0.0\t0.688845424001\t0.567470311282"
"\t0.721707516043", "CO2.141657\t0.585201193913\t0.649822398416\t"
"0.688845424001\t0.0\t0.658853575764\t0.661223617505", "TL3.141709\t"
"0.729023583672\t0.777203137034\t0.567470311282\t0.658853575764\t0.0\t"
"0.711173405838", "SN3.141650\t0.622135587669\t0.629507320436\t"
"0.721707516043\t0.661223617505\t0.711173405838\t0.0"]

soils_map_lines = ["#SampleId\tTOT_ORG_CARB\tSILT_CLAY\t"
"ELEVATION\tSOIL_MOISTURE_DEFICIT\tCARB_NITRO_RATIO\t"
"ANNUAL_SEASON_TEMP\tANNUAL_SEASON_PRECPT\tPH\tCMIN_RATE\tLONGITUDE\t"
"LATITUDE", "MT2.141698\t39.1\t35\t1000\t70\t23.087\t7\t450\t6.66\t"
"19.7\t-114\t46.8", "CA1.141704\t16.7\t73\t2003\t198\t13\t10.3\t400\t"
"7.27\t2.276\t-111.7666667\t36.05", "BB2.141659\t52.2\t44\t400\t-680\t"
"21.4\t6.1\t1200\t4.6\t2.223\t-68.1\t44.86666667", "CO2.141657\t18.1\t"
"24\t2400\t104\t31.8\t6.1\t350\t5.68\t9.223\t-105.3333333\t"
"40.58333333", "TL3.141709\t53.9\t52\t894\t-212\t24.6\t-9.3\t400\t"
"4.23\t16.456\t-149.5833333\t68.63333333", "SN3.141650\t16.6\t20\t"
"3000\t-252\t13.9\t3.6\t600\t5.74\t6.289\t-118.1666667\t36.45"]

exp_best_88_soils = """Method name\tNumber of categories\tCategories\trho statistics
BEST\t\tTOT_ORG_CARB = , SILT_CLAY = , ELEVATION = , SOIL_MOISTURE_DEFICIT = , CARB_NITRO_RATIO = , ANNUAL_SEASON_TEMP = , ANNUAL_SEASON_PRECPT = , PH = , CMIN_RATE = , LONGITUDE = , LATITUDE = \t(., ''), (., ','), (., ',,'), (., ',,,'), (., ',,,,'), (., ',,,,,'), (., ',,,,,,'), (., ',,,,,,,'), (., ',,,,,,,,'), (., ',,,,,,,,,'), (., ',,,,,,,,,,')
"""


#run unit tests if run from command-line
if __name__ == '__main__':
    main()