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#!/usr/bin/env python
#
# Copyright 2014 by Leighton Pritchard. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tests for online functionality of the KGML modules."""
# Builtins
from __future__ import with_statement
import os
import unittest
import requires_internet
requires_internet.check()
# Biopython
from Bio.Graphics.ColorSpiral import ColorSpiral
# Do we have ReportLab? Raise error if not present.
from Bio import MissingExternalDependencyError
try:
from reportlab.pdfgen.canvas import Canvas
from reportlab.lib.pagesizes import A4
except ImportError:
raise MissingExternalDependencyError(
"Install reportlab if you want to use Bio.Graphics.")
# Do we have PIL?
try:
from PIL import Image
except ImportError:
raise MissingExternalDependencyError(
"Install Pillow or its predecessor PIL (Python Imaging Library) "
"if you want to use bitmaps from KGML.")
# Biopython Bio.KEGG.KGML
from Bio.KEGG.KGML.KGML_parser import read
from Bio.Graphics.KGML_vis import KGMLCanvas
# test_KGML_graphics module
from test_KGML_graphics import PathwayData
__docformat__ = "restructuredtext en"
class KGMLPathwayOnlineTest(unittest.TestCase):
"""Import XML file and write KGML - online tests.
Import metabolic maps from a local .xml KGML file, and from
the KEGG site, and write valid KGML output for each
"""
def setUp(self):
# Does our output directory exist? If not, create it
if not os.path.isdir('KEGG'):
os.mkdir('KEGG')
# Define some data to work with as a list of tuples:
# (infilename, outfilename, (entry_count, ortholog_count,
# compound_count, map_counts), pathway_image,
# show_image_map)
self.data = [
PathwayData("01100", (3628, 1726, 1746, 149)),
PathwayData("03070", (81, 72, 8, 1), True),
]
def test_render_KGML_import_map(self):
"""Basic rendering of KGML: use imported imagemap
Uses the URL indicated in the .xml file.
This test may fail if the imagemap is not available (e.g. if
there is not a web connection), and may look odd if the remote
imagemap has changed since the local KGML file was downloaded.
"""
# We test rendering of the original KEGG KGML using imported files
for p in self.data:
with open(p.infilename, 'rU') as f:
pathway = read(f)
kgml_map = KGMLCanvas(pathway, import_imagemap=True)
kgml_map.draw(p.output_stem + '_importmap.pdf')
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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