def testComposeLocalUrlGenomeAttributesNonAscii(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('galaxy:/12345abc',
genome=u'hg18ø',
attributes=OrderedDict([('one', 'yes')])))
gSuite.addTrack(
GSuiteTrack('file:/path/to/file2',
genome='hg19',
attributes=OrderedDict([('two', u'nø')])))
gSuite.addTrack(
GSuiteTrack(
HbGSuiteTrack.generateURI(trackName=[u'track', u'nøme']),
genome='hg38',
attributes=OrderedDict([('two', 'yes')])))
gSuite.setCustomHeader('my header', u'bø!')
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: local\n' \
'##file format: unknown\n' \
'##track type: unknown\n' \
'##genome: multiple\n' \
'##my header: b%C3%B8!\n' \
'###uri\ttitle\tfile_format\tgenome\tone\ttwo\n' \
'galaxy:/12345abc\t12345abc\tunknown\thg18%C3%B8\tyes\t.\n' \
'file:/path/to/file2\tfile2\tunknown\thg19\t.\tn%C3%B8\n' \
'hb:/track/n%C3%B8me\tn%C3%B8me\tpreprocessed\thg38\t.\tyes\n'
self.assertEquals(targetOutput, output)
def testFullCompose(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('ftp://server.somewhere.com/path/to/file1.bed',
title='Track',
attributes=OrderedDict([('cell', 'k562'),
('antibody', 'cMyb')])))
gSuite.addTrack(
GSuiteTrack('http://server.other.com/path/to/file2.bed',
title='Track2',
attributes=OrderedDict([('cell', 'GM12878'),
('antibody', 'cMyc')])))
gSuite.addTrack(
GSuiteTrack('https://server.other.com/path/to/file3.bed',
attributes=OrderedDict([('cell', 'GM12878'),
('antibody', 'cMyb')])))
gSuite.addTrack(
GSuiteTrack('rsync://server.other.com/path/to/file4;wig',
title='Track4',
attributes=OrderedDict([('cell', 'NHFL')])))
gSuite.addTrack(GSuiteTrack('hb:/track/name/hierarchy', title='Track'))
gSuite.addTrack(
GSuiteTrack('galaxy:/ad123dd12fg;btrack?track=track:name',
title='Track',
attributes=OrderedDict([('cell', 'k562'),
('antibody', 'cMyb')])))
gSuite.addTrack(
GSuiteTrack('file:/path/to/file.btrack?track=track:name',
title='Track name7',
attributes=OrderedDict([('antibody', 'cMyb'),
('extra', 'yes')])))
gSuite.setGenomeOfAllTracks('hg18')
gSuite.setCustomHeader('My header', 'Some value')
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: multiple\n' \
'##file format: multiple\n' \
'##track type: unknown\n' \
'##genome: hg18\n' \
'##my header: Some value\n' \
'###uri\ttitle\tfile_format\tcell\tantibody\textra\n' \
'ftp://server.somewhere.com/path/to/file1.bed\tTrack\tprimary\tk562\tcMyb\t.\n' \
'http://server.other.com/path/to/file2.bed\tTrack2\tprimary\tGM12878\tcMyc\t.\n' \
'https://server.other.com/path/to/file3.bed\tfile3.bed\tprimary\tGM12878\tcMyb\t.\n' \
'rsync://server.other.com/path/to/file4;wig\tTrack4\tprimary\tNHFL\t.\t.\n' \
'hb:/track/name/hierarchy\tTrack (2)\tpreprocessed\t.\t.\t.\n' \
'galaxy:/ad123dd12fg;btrack?track=track%3Aname\tTrack (3)\tpreprocessed\tk562\tcMyb\t.\n' \
'file:/path/to/file.btrack?track=track%3Aname\tTrack name7\tpreprocessed\t.\tcMyb\tyes\n'
self.assertEquals(targetOutput, output)
def testCustomHeaders(self):
gSuite = GSuite(customHeaders=OrderedDict([('My Header', 'My value')]))
self.assertEqual(OrderedDict([('my header', 'My value')]),
gSuite.customHeaders)
self.assertEqual('My value', gSuite.getCustomHeader('my header'))
self.assertEqual(None, gSuite.getCustomHeader('wrong header'))
gSuite.customHeaders = OrderedDict([('My New Header', 'My new value')])
gSuite.setCustomHeader('my_second_header', 'My other value')
self.assertEqual('My other value',
gSuite.getCustomHeader('my_second_header'))
self.assertEqual(['my new header', 'my_second_header'],
gSuite.customHeaders.keys())
self.assertEqual(['My new value', 'My other value'],
gSuite.customHeaders.values())
with self.assertRaises(AttributeError):
gSuite.my_new_header
self.assertEqual('My other value', gSuite.my_second_header)
with self.assertRaises(ArgumentValueError):
gSuite.customHeaders = OrderedDict([('a', 'value'),
('A', 'other value')])
