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111 lines
3.9 KiB
Python
111 lines
3.9 KiB
Python
import os
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from base.twilltestcase import TwillTestCase
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class UcscTests(TwillTestCase):
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def test_00_first(self): # will run first due to its name
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"""Clearing history"""
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self.clear_history()
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# def test_Biomart_Uniprot(self):
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# """Connection to Biomart"""
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# #All this test does, is check to see if biomart is accessible through Galaxy. A dataset is never retrieved or checked.
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#
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# # some button indices are hardcoded (twill limitation)
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# self.run_tool('biomart')
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#
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# self.submit_form(form='mainform', button='get_count_button',
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# dataBase='default____UNIPROT PROTOTYPE 4-5 (EBI)', dataset='uniprot'
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# )
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#
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# #self.submit_form(form='settings', button='stage_filter',
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# # database='UNIPROTPROTOTYPE4-5(EBI)__default', dataset='uniprot'
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# #)
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#
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# #self.submit_form(form='settings', button=6,
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# # uniprot_collection_start=1, uniprot_collection_end=1,
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# # uniprot_component_start=1000, uniprot_component_end=2000
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# #)
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#
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# #self.submit_form(form='settings', button=5,
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# # outtype='Features', outformat='tsv'
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# #)
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#
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# #self.check_data('biomart_uniprot.dat')
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# def test_UCSC_interface(self):
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# """Diffing first page of UCSC proxy."""
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# # hgsid needs to be set or else we get a different one every time.
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# self.go2myurl("http://www.genome.ucsc.edu/cgi-bin/hgTables?org=Human&db=hg18&hgsid=84962660&hgta_doMainPage=1")
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# current_file = self.get_fname('new_ucsc_proxy_page.dat')
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# diff_file = self.get_fname('ucsc_proxy_page.dat')
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#
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# currentpage = self.last_page()
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# file(current_file, 'wb').write(currentpage)
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#
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# try:
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# self.diff( current_file, diff_file )
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# os.remove( current_file )
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# except AssertionError, err:
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# raise AssertionError( "UCSC Page has changed:\n" + str( err ) )
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#
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# # Note that execution will not reach this if there is an
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# # error. This is intended so that the new ucsc page will be
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# # stored and can be easily checked by hand and updated.
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# def test_UCSC_bed(self):
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# """Getting bed files from UCSC"""
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#
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# self.clear_history()
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#
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# # in range
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# self.run_tool('ucsc_proxy')
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# params = dict(
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# hgta_regionType="range",
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# hgta_outputType="primaryTable",
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# )
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# self.submit_form(1, button="hgta_doTopSubmit", **params)
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#
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# # encode
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# self.run_tool('ucsc_proxy')
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# params = dict(
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# hgta_regionType="encode",
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# hgta_outputType="primaryTable",
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# )
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# self.submit_form(1, button="hgta_doTopSubmit", **params)
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#
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# self.wait()
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#
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# self.check_data('ucsc_proxy_range.dat', hid=1)
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# self.check_data('ucsc_proxy_encode.dat', hid=2)
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# We probably will not move this to main
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#def test_hbvar(self):
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# """Getting hybrid gene mutations from HbVar"""
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# #self.load_cookies("hbvar_cookie.txt")
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# self.clear_history()
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# self.run_tool('hbvar')
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# params = dict(
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# htyp="any hybrid gene",
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# )
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# self.submit_form(form=1, button="Submit Query", **params)
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# params = dict(
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# display_format="galaxy",
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# )
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# self.submit_form(form=1, button="Go", **params)
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# params = dict(
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# build="hg17",
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# )
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# self.submit_form(form=1, button="ok", **params);
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# """
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# TODO: Currently fails when using sqlite, although successful when
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# using Postgres. Upgrading our version of sqlite may fix this, but
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# confirmation is required.
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# """
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# self.check_data('hbvar_hybrid_genes.dat')
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