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#!/usr/bin/env python
#file test_plot_taxa_summary.py
__author__ = "Jesse Stombaugh"
__copyright__ = "Copyright 2011, The QIIME Project" #consider project name
__credits__ = ["Jesse Stombaugh","Julia Goodrich"] #remember to add yourself
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
__status__ = "Release"
import matplotlib
from matplotlib import use
use('Agg',warn=False)
from numpy import array
from os.path import exists
from StringIO import StringIO
from cogent.util.unit_test import TestCase, main
from os import remove, mkdir, removedirs,listdir
from qiime.plot_taxa_summary import (make_pie_chart,make_img_name,
get_counts,write_html_file,
make_HTML_table,get_fracs, make_all_charts,
make_area_bar_chart,make_legend)
class TopLevelTests(TestCase):
"""Tests of top-level functions"""
def setUp(self):
"""define some top-level data"""
self.props={"title": "Class: from 3 categories"}
self.prefs = {'1':{'column':'1'}}
self.counts1 = [(1,"a;b;c","a<br>b<br>c"),(3,"d;e;f","d<br>e<br>f"),
(4,"a;g;h","a<br>g<br>h"),(2,"d;e;i","d<br>e<br>i")]
self.sample_ids=['14FC041','14FC042','14FC043','14FC044']
self.taxa=["a;b;c", "d;e;i", "d;e;f", "a;g;h"]
self.lines_parsed = (['14FC041','14FC042','14FC043','14FC044'],\
['a;b;c','d;e;f','a;g;h',"d;e;i"],\
[['0.1','0.3','0.2'],['0','0.2','0.1'],\
['0.4','0','0.3'],['0.5','0','0.1']])
self.fracs = [("a;b;c",1.0/10),("d;e;f",3.0/10),
("a;g;h",4.0/10),("d;e;i",2.0/10)]
self.colors=['#0000ff', '#00ff00', '#ff0000', '#00ffff']
self.area_fracs=[[0.1,0.3,0.2],[0.0,0.2,0.1],\
[0.4,0.0,0.3],[0.5,0.0,0.1]]
self.color_prefs={"a;b;c": 'blue1', "d;e;i": 'red1', "d;e;f": 'blue2', \
"a;g;h": 'red2'}
self.dpi=80
self.plot_width=12
self.plot_height=6
self.bar_width=1
self.generate_image_type='pdf'
self._paths_to_clean_up = []
self._dirs_to_clean_up = []
self.dir_path = "/tmp/qiimewebfiles/"
#make the webfile directory
try:
mkdir(self.dir_path)
except OSError:
pass
#make the charts directory
try:
mkdir("/tmp/qiimewebfiles/charts")
except OSError:
pass
#define directory to clean up
self._dirs_to_clean_up = ["/tmp/qiimewebfiles/charts"]
def tearDown(self):
map(remove,self._paths_to_clean_up)
map(removedirs,self._dirs_to_clean_up)
def test_make_legend(self):
"""make_legend create a legend image given an array of ids and
colors"""
fpath='/tmp/qiimewebfiles/area.pdf'
filename1='/tmp/qiimewebfiles/area_legend.pdf'
obs=make_legend(self.sample_ids,self.colors,self.plot_width,\
self.plot_height,'black','white',fpath,\
self.generate_image_type,self.dpi)
self.assertTrue(exists(filename1),'The png file was not created in \
the appropriate location')
self._paths_to_clean_up = [filename1]
def test_get_counts(self):
"""get_counts should gets all the counts for an input file"""
#test the pie charts
img_data = get_counts("Phylum",['14FC041','14FC042','14FC043'],5,\
"/tmp/qiimewebfiles/",1,self.lines_parsed,\
self.prefs,self.color_prefs,'black','white',\
'pie',self.generate_image_type,self.plot_width,\
self.plot_height,self.bar_width,self.dpi,\
'file.txt',0,'categorical',False,False)
self.assertEqual(len(img_data), 8)
#test the area charts
img_data = get_counts("Phylum",['14FC041','14FC042','14FC043'],5,\
"/tmp/qiimewebfiles/",1,self.lines_parsed,\
self.prefs,self.color_prefs,'black','white',\
'area',self.generate_image_type,self.plot_width,\
self.plot_height,self.bar_width,self.dpi,\
'file.txt',0,'categorical',False,False)
self.assertEqual(len(img_data), 2)
#test the area charts
img_data = get_counts("Phylum",['14FC041','14FC042','14FC043'],5,\
"/tmp/qiimewebfiles/",1,self.lines_parsed,\
self.prefs,self.color_prefs,'black','white',\
'bar',self.generate_image_type,self.plot_width,\
self.plot_height,self.bar_width,self.dpi,\
'file.txt',0,'categorical',False,False)
self.assertEqual(len(img_data), 2)
#clean up files generated
self._paths_to_clean_up = ["/tmp/qiimewebfiles/charts/"+f \
for f in listdir("/tmp/qiimewebfiles/charts")]
def test_get_fracs(self):
""""get_fracs should Return fractions for matplotlib chart"""
#test the pie charts
exp_all_counts=[DATA_HTML%("4",(4.0/10)*100,'a<br>g','h', 'h',"a;g;h"),\
DATA_HTML%('3',(3.0/10)*100,'d<br>e','f', 'f',"d;e;f"),\
DATA_HTML%('2',(2.0/10)*100,'d<br>e','i', 'i',"d;e;i"),\
DATA_HTML%('1',(1.0/10)*100,'a<br>b','c', 'c',"a;b;c")]
fracs_labels_other,fracs_labels,all_counts, other_cat, red,other_frac \
= get_fracs(self.counts1,5,10,'pie')
self.assertEqual(fracs_labels_other,[("a;b;c",1.0/10),("a;g;h",4.0/10),\
("d;e;f",3.0/10),("d;e;i",2.0/10)])
self.assertEqual(fracs_labels,[])
self.assertEqual(all_counts,exp_all_counts)
self.assertEqual(other_cat,0)
self.assertEqual(red,10)
self.assertEqual(other_frac,0)
fracs_labels_other,fracs_labels,all_counts, other_cat, red,other_frac \
= get_fracs(self.counts1,3,10,'pie')
self.assertEqual(fracs_labels_other,[("a;g;h",4.0/10),("d;e;f",3.0/10)])
self.assertEqual(fracs_labels,[("a;g;h",4.0/7),("d;e;f",3.0/7)])
self.assertEqual(all_counts,exp_all_counts)
self.assertEqual(other_cat,2)
self.assertEqual(red,7)
self.assertEqual(other_frac,3.0/10)
#test the area charts
exp_all_counts=['4', '3', '2', '1']
fracs_labels_other,fracs_labels,all_counts, other_cat, red,other_frac \
= get_fracs(self.counts1,5,10,'area')
self.assertEqual(fracs_labels_other,[("a;b;c",1.0/10),("a;g;h",4.0/10),\
("d;e;f",3.0/10),("d;e;i",2.0/10)])
self.assertEqual(fracs_labels,[])
self.assertEqual(all_counts,exp_all_counts)
self.assertEqual(other_cat,0)
self.assertEqual(red,10)
self.assertEqual(other_frac,0)
fracs_labels_other,fracs_labels,all_counts, other_cat, red,other_frac \
= get_fracs(self.counts1,3,10,'area')
self.assertEqual(fracs_labels_other,[("a;g;h",4.0/10),("d;e;f",3.0/10),\
('d;e;i',2.0/10)])
self.assertEqual(fracs_labels,[("a;g;h",8.0/18),("d;e;f",6.0/18)])
self.assertEqual(all_counts,exp_all_counts)
self.assertEqual(other_cat,2)
self.assertEqual(red,9)
self.assertEqual(other_frac,3.0/10)
#test bar charts
exp_all_counts=['4', '3', '2', '1']
fracs_labels_other,fracs_labels,all_counts, other_cat, red,other_frac \
= get_fracs(self.counts1,5,10,'bar')
self.assertEqual(fracs_labels_other,[("a;b;c",1.0/10),("a;g;h",4.0/10),\
("d;e;f",3.0/10),("d;e;i",2.0/10)])
self.assertEqual(fracs_labels,[])
self.assertEqual(all_counts,exp_all_counts)
self.assertEqual(other_cat,0)
self.assertEqual(red,10)
self.assertEqual(other_frac,0)
fracs_labels_other,fracs_labels,all_counts, other_cat, red,other_frac \
= get_fracs(self.counts1,3,10,'bar')
self.assertEqual(fracs_labels_other,[("a;g;h",4.0/10),("d;e;f",3.0/10),\
('d;e;i',2.0/10)])
self.assertEqual(fracs_labels,[("a;g;h",8.0/18),("d;e;f",6.0/18)])
self.assertEqual(all_counts,exp_all_counts)
self.assertEqual(other_cat,2)
self.assertEqual(red,9)
self.assertEqual(other_frac,3.0/10)
self._paths_to_clean_up = ["/tmp/qiimewebfiles/charts/"+f \
for f in listdir("/tmp/qiimewebfiles/charts")]
def test_make_HTML_table(self):
"""make_HTML_table should Make HTML tables for one set charts"""
#test pie charts
fracs_labels_other,fracs_labels,all_counts,other_cat,red,other_frac = \
get_fracs(self.counts1,5,10,'pie')
img_data = make_HTML_table("Phylum",other_frac,10,red,other_cat,\
fracs_labels_other,fracs_labels,\
self.dir_path,all_counts,1,self.prefs,\
self.color_prefs,'black','white','pie',\
'Test1',\
self.generate_image_type,self.plot_width,\
self.plot_height,self.bar_width,self.dpi,0,\
'categorical',False,False)
self.assertEqual(len(img_data),2)
#test area charts
fracs_labels_other,fracs_labels,all_counts,other_cat,red,other_frac = \
get_fracs(self.counts1,5,10,'area')
img_data = make_HTML_table("Phylum",other_frac,10,red,other_cat,\
fracs_labels_other,fracs_labels,\
self.dir_path,all_counts,1,self.prefs,\
self.color_prefs,'black','white','pie',\
'Test1',\
self.generate_image_type,self.plot_width,\
self.plot_height,self.bar_width,self.dpi,0,\
'categorical',False,False)
self.assertEqual(len(img_data),2)
#test bar charts
fracs_labels_other,fracs_labels,all_counts,other_cat,red,other_frac = \
get_fracs(self.counts1,5,10,'bar')
img_data = make_HTML_table("Phylum",other_frac,10,red,other_cat,\
fracs_labels_other,fracs_labels,\
self.dir_path,all_counts,1,self.prefs,\
self.color_prefs,'black','white','pie',\
'Test1',\
self.generate_image_type,self.plot_width,\
self.plot_height,self.bar_width,self.dpi,0,\
'categorical',False,False)
self.assertEqual(len(img_data),2)
self._paths_to_clean_up = ["/tmp/qiimewebfiles/charts/"+f \
for f in listdir("/tmp/qiimewebfiles/charts")]
def test_make_pie_chart(self):
"""make_pie_chart should create HTML source and pdfs for pie_charts"""
filename1='/tmp/qiimewebfiles/charts/pie_chart.png'
filename2='/tmp/qiimewebfiles/charts/pie_chart_legend.pdf'
filename3='/tmp/qiimewebfiles/charts/pie_chart.pdf'
obs1,obs2,obs3,obs4=make_pie_chart(self.fracs,self.dir_path,1,\
self.prefs,self.color_prefs, "black","white",\
self.generate_image_type,self.plot_width,\
self.plot_height,self.bar_width,self.dpi,False,\
file_prefix="pie_chart",\
props=self.props)
self.assertTrue(exists(filename1),'The png file was not created in \
the appropriate location')
self.assertTrue(exists(filename2),'The eps file was not created in \
the appropriate location')
self.assertTrue(exists(filename3),'The pdf file was not created in \
the appropriate location')
self._paths_to_clean_up = ["/tmp/qiimewebfiles/charts/"+f \
for f in listdir("/tmp/qiimewebfiles/charts")]
def test_make_area_bar_chart(self):
"""make_area_bar_chart should create HTML source and pdfs for area
and bar charts"""
# following is a list of files being generated
filename1='/tmp/qiimewebfiles/charts/area_chart.png'
filename2='/tmp/qiimewebfiles/charts/area_chart_legend.pdf'
filename3='/tmp/qiimewebfiles/charts/area_chart.pdf'
filename4='/tmp/qiimewebfiles/charts/bar_chart.png'
filename5='/tmp/qiimewebfiles/charts/bar_chart_legend.pdf'
filename6='/tmp/qiimewebfiles/charts/bar_chart.pdf'
#test area chart
obs1,obs2,obs3,obs4=make_area_bar_chart(self.sample_ids,\
self.area_fracs,\
self.taxa,self.dir_path,1,self.prefs,\
self.color_prefs,"black","white","area",\
self.generate_image_type,self.plot_width,\
self.plot_height,self.bar_width,\
self.dpi,0,'categorical',False,False,\
"area_chart")
self.assertTrue(exists(filename1),'The png file was not created in \
the appropriate location')
self.assertTrue(exists(filename2),'The eps file was not created in \
the appropriate location')
self.assertTrue(exists(filename3),'The pdf file was not created in \
the appropriate location')
#test bar chart
obs1,obs2,obs3,obs4=make_area_bar_chart(self.sample_ids,\
self.area_fracs,\
self.taxa,self.dir_path,1,self.prefs,\
self.color_prefs,"black","white","bar",\
self.generate_image_type,self.plot_width,\
self.plot_height,self.bar_width,self.dpi,\
0,'categorical',False,False,"bar_chart",\
self.props)
self.assertTrue(exists(filename4),'The png file was not created in \
the appropriate location')
self.assertTrue(exists(filename5),'The eps file was not created in \
the appropriate location')
self.assertTrue(exists(filename6),'The pdf file was not created in \
the appropriate location')
self._paths_to_clean_up = ["/tmp/qiimewebfiles/charts/"+f \
for f in listdir("/tmp/qiimewebfiles/charts")]
def test_write_html_file(self):
"Write html and make sure it gets cleaned up"""
filename1='/tmp/test.html'
self._paths_to_clean_up = [filename1]
write_html_file('Test','/tmp/test.html')
self.assertTrue(exists(filename1),'The file was not created in \
the appropriate location')
self._paths_to_clean_up = [filename1]
#expected results for the unit testing
DATA_HTML = """<tr class=normal><td>%s</td> <td nowrap>%.2f%%</td>\
<td class="normal" ><a onmouseover="return overlib('<b>Taxonomy:</b><br>%s<br>\
<a href=javascript:gg(\\'%s\\');>%s</a> ',STICKY,MOUSEOFF,RIGHT);" \
onmouseout="return nd();">%s</a></td></tr>"""
#run tests if called from command line
if __name__ == "__main__":
main()
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