mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-25 00:12:08 +08:00
82 lines
2.8 KiB
Python
82 lines
2.8 KiB
Python
import os
|
|
from base.twilltestcase import TwillTestCase
|
|
|
|
class UcscTests(TwillTestCase):
|
|
|
|
def test_00_first(self): # will run first due to its name
|
|
"""Clearing history"""
|
|
self.clear_history()
|
|
|
|
def test_Biomart_Uniprot(self):
|
|
"""Connection to Biomart"""
|
|
#All this test does, is check to see if biomart is accessible through Galaxy. A dataset is never retrieved or checked.
|
|
|
|
# some button indices are hardcoded (twill limitation)
|
|
self.run_tool('biomart')
|
|
|
|
self.submit_form(form='mainform', button='get_count_button',
|
|
dataBase='default____UNIPROT PROTOTYPE 4-5 (EBI)', dataset='uniprot'
|
|
)
|
|
|
|
#self.submit_form(form='settings', button='stage_filter',
|
|
# database='UNIPROTPROTOTYPE4-5(EBI)__default', dataset='uniprot'
|
|
#)
|
|
|
|
#self.submit_form(form='settings', button=6,
|
|
# uniprot_collection_start=1, uniprot_collection_end=1,
|
|
# uniprot_component_start=1000, uniprot_component_end=2000
|
|
#)
|
|
|
|
#self.submit_form(form='settings', button=5,
|
|
# outtype='Features', outformat='tsv'
|
|
#)
|
|
|
|
#self.check_data('biomart_uniprot.dat')
|
|
|
|
def test_UCSC_interface(self):
|
|
"""Diffing first page of UCSC proxy."""
|
|
# hgsid needs to be set or else we get a different one every time.
|
|
self.go2myurl("http://www.genome.ucsc.edu/cgi-bin/hgTables?org=Human&db=hg18&hgsid=84962660&hgta_doMainPage=1")
|
|
current_file = self.get_fname('new_ucsc_proxy_page.dat')
|
|
diff_file = self.get_fname('ucsc_proxy_page.dat')
|
|
|
|
currentpage = self.last_page()
|
|
file(current_file, 'wb').write(currentpage)
|
|
|
|
try:
|
|
self.diff( current_file, diff_file )
|
|
except AssertionError, err:
|
|
raise AssertionError( "UCSC Page has changed:\n" + str( err ) )
|
|
|
|
# Note that execution will not reach this if there is an
|
|
# error. This is intended so that the new ucsc page will be
|
|
# stored and can be easily checked by hand and updated.
|
|
os.remove( current_file )
|
|
|
|
def test_UCSC_bed(self):
|
|
"""Getting bed files from UCSC"""
|
|
|
|
self.clear_history()
|
|
|
|
# in range
|
|
self.run_tool('ucsc_proxy')
|
|
params = dict(
|
|
hgta_regionType="range",
|
|
hgta_outputType="primaryTable",
|
|
)
|
|
self.submit_form(1, button="hgta_doTopSubmit", **params)
|
|
|
|
# encode
|
|
self.run_tool('ucsc_proxy')
|
|
params = dict(
|
|
hgta_regionType="encode",
|
|
hgta_outputType="primaryTable",
|
|
)
|
|
self.submit_form(1, button="hgta_doTopSubmit", **params)
|
|
|
|
self.wait()
|
|
|
|
self.check_data('ucsc_proxy_range.dat', hid=1)
|
|
self.check_data('ucsc_proxy_encode.dat', hid=2)
|
|
|