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|
#!/usr/bin/env python
#
# suite of cogent package unit tests.
# run suite by executing this file
#
import doctest, cogent.util.unit_test as unittest, sys, os
from cogent.util.misc import app_path
__author__ = "Peter Maxwell and Gavin Huttley"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Peter Maxwell", "Gavin Huttley", "Rob Knight",
"Hau Ying", "Helen Lindsay", "Jeremy Widmann",
"Sandra Smit", "Greg Caporaso", "Matthew Wakefield"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
def my_import(name):
"""Imports a module, possibly qualified with periods. Returns the module.
__import__ only imports the top-level module.
Recipe from python documentation at:
http://www.python.org/doc/2.4/lib/built-in-funcs.html
"""
mod = __import__(name)
components = name.split('.')
for comp in components[1:]:
mod = getattr(mod, comp)
return mod
def module_present(modules):
"""returns True if dependencies present"""
if type(modules) == str:
modules = [modules]
try:
for module in modules:
mod = __import__(module)
except ImportError:
return False
return True
def suite():
modules_to_test = [
'test_recalculation.rst',
'test_phylo',
'test_dictarray.rst',
'test_align.test_align',
'test_align.test_algorithm',
'test_align.test_weights.test_methods',
'test_align.test_weights.test_util',
'test_app.test_parameters',
'test_app.test_util',
'test_cluster.test_goodness_of_fit',
'test_cluster.test_metric_scaling',
'test_cluster.test_approximate_mds',
'test_cluster.test_procrustes',
'test_cluster.test_UPGMA',
'test_cluster.test_nmds',
'test_core.test_alphabet',
'test_core.test_alignment',
'test_core.test_annotation',
'test_core.test_bitvector',
'test_core.test_core_standalone',
'test_core.test_features.rst',
'test_core.test_entity',
'test_core.test_genetic_code',
'test_core.test_info',
'test_core.test_location',
'test_core.test_maps',
'test_core.test_moltype',
'test_core.test_profile',
'test_core.test_seq_aln_integration',
'test_core.test_sequence',
'test_core.test_tree',
'test_core.test_usage',
'test_data.test_molecular_weight',
'test_evolve.test_best_likelihood',
'test_evolve.test_bootstrap',
'test_evolve.test_coevolution',
'test_evolve.test_models',
'test_evolve.test_motifchange',
'test_evolve.test_substitution_model',
'test_evolve.test_scale_rules',
'test_evolve.test_likelihood_function',
'test_evolve.test_newq',
'test_evolve.test_pairwise_distance',
'test_evolve.test_parameter_controller',
'test_format.test_bedgraph',
'test_format.test_fasta',
'test_format.test_mage',
'test_format.test_pdb_color',
'test_format.test_xyzrn',
'test_maths.test_fit_function',
'test_maths.test_geometry',
'test_maths.test_matrix_logarithm',
'test_maths.test_period',
'test_maths.test_matrix.test_distance',
'test_maths.test_spatial.test_ckd3',
'test_maths.test_stats.test_alpha_diversity',
'test_maths.test_stats.test_distribution',
'test_maths.test_stats.test_histogram',
'test_maths.test_stats.test_information_criteria',
'test_maths.test_stats.test_period',
'test_maths.test_stats.test_special',
'test_maths.test_stats.test_test',
'test_maths.test_stats.test_ks',
'test_maths.test_stats.test_rarefaction',
'test_maths.test_stats.test_util',
'test_maths.test_stats.test_cai.test_adaptor',
'test_maths.test_stats.test_cai.test_get_by_cai',
'test_maths.test_stats.test_cai.test_util',
'test_maths.test_optimisers',
'test_maths.test_distance_transform',
'test_maths.test_unifrac.test_fast_tree',
'test_maths.test_unifrac.test_fast_unifrac',
'test_motif.test_util',
'test_parse.test_aaindex',
'test_parse.test_agilent_microarray',
'test_parse.test_binary_sff',
'test_parse.test_blast',
'test_parse.test_bowtie',
'test_parse.test_bpseq',
'test_parse.test_cigar',
'test_parse.test_clustal',
'test_parse.test_column',
'test_parse.test_comrna',
'test_parse.test_consan',
'test_parse.test_cove',
'test_parse.test_ct',
'test_parse.test_cut',
'test_parse.test_cutg',
'test_parse.test_dialign',
'test_parse.test_ebi',
'test_parse.test_fasta',
'test_parse.test_fastq',
'test_parse.test_gbseq',
'test_parse.test_gibbs',
'test_parse.test_genbank',
'test_parse.test_gff',
'test_parse.test_greengenes',
'test_parse.test_ilm',
'test_parse.test_illumina_sequence',
'test_parse.test_locuslink',
'test_parse.test_mage',
'test_parse.test_meme',
'test_parse.test_msms',
'test_parse.test_ncbi_taxonomy',
'test_parse.test_nexus',
'test_parse.test_nupack',
'test_parse.test_pdb',
'test_parse.test_psl',
'test_parse.test_structure',
'test_parse.test_pamlmatrix',
'test_parse.test_phylip',
'test_parse.test_pknotsrg',
'test_parse.test_rdb',
'test_parse.test_record',
'test_parse.test_record_finder',
'test_parse.test_rfam',
'test_parse.test_rnaalifold',
'test_parse.test_rna_fold',
'test_parse.test_rnaview',
'test_parse.test_rnaforester',
'test_parse.test_sprinzl',
'test_parse.test_tinyseq',
'test_parse.test_tree',
'test_parse.test_unigene',
'test_seqsim.test_analysis',
'test_seqsim.test_birth_death',
'test_seqsim.test_markov',
'test_seqsim.test_microarray',
'test_seqsim.test_microarray_normalize',
'test_seqsim.test_randomization',
'test_seqsim.test_searchpath',
'test_seqsim.test_sequence_generators',
'test_seqsim.test_tree',
'test_seqsim.test_usage',
'test_struct.test_knots',
'test_struct.test_pairs_util',
'test_struct.test_rna2d',
'test_struct.test_asa',
'test_struct.test_contact',
'test_struct.test_annotation',
'test_struct.test_selection',
'test_struct.test_manipulation',
'test_util.test_unit_test',
'test_util.test_array',
'test_util.test_dict2d',
'test_util.test_misc',
'test_util.test_organizer',
'test_util.test_recode_alignment',
'test_util.test_table.rst',
'test_util.test_transform',
]
try:
import matplotlib
except:
print >> sys.stderr, "No matplotlib so not running test_draw.py"
else:
modules_to_test.append('test_draw')
modules_to_test.append('test_draw.test_distribution_plots')
#Try importing modules for app controllers
apps = [('formatdb', 'test_formatdb'),
('blastall', 'test_blast'),
('blat', 'test_blat'),
('bwa', 'test_bwa'),
('carnac', 'test_carnac'),
('clearcut', 'test_clearcut'),
('clustalw', 'test_clustalw'),
('cmalign', 'test_infernal'),
('cmfinder.pl', 'test_cmfinder'),
('comrna', 'test_comrna'),
('contrafold', 'test_contrafold'),
('covea', 'test_cove'),
('dialign2-2', 'test_dialign'),
('dynalign', 'test_dynalign'),
('FastTree', 'test_fasttree'),
('foldalign', 'test_foldalign'),
('guppy', 'test_guppy'),
('ilm', 'test_ilm'),
('knetfold.pl', 'test_knetfold'),
('mafft', 'test_mafft'),
('mfold', 'test_mfold'),
('mothur', 'test_mothur'),
('muscle', 'test_muscle_v38'),
('msms', 'test_msms'),
('ParsInsert', 'test_parsinsert'),
('pplacer', 'test_pplacer'),
('rdp_classifier-2.2.jar', 'test_rdp_classifier'),
('rdp_classifier-2.0.jar', 'test_rdp_classifier20'),
('Fold.out', 'test_nupack'),
('findphyl', 'test_pfold'),
('pknotsRG-1.2-i386-linux-static', 'test_pknotsrg'),
('RNAalifold', 'test_rnaalifold'),
('rnaview', 'test_rnaview'),
('RNAfold', 'test_vienna_package'),
('raxmlHPC', 'test_raxml_v730'),
('rtax', 'test_rtax'),
('sfold.X86_64.LINUX', 'test_sfold'),
('stride', 'test_stride'),
('hybrid-ss-min', 'test_unafold'),
('cd-hit', 'test_cd_hit'),
('calculate_likelihood', 'test_gctmpca'),
('sfffile', 'test_sfffile'),
('sffinfo', 'test_sffinfo'),
('uclust','test_uclust'),
('usearch','test_usearch')
]
for app, test_name in apps:
should_run_test = False
if app_path(app):
should_run_test = True
elif app.startswith('rdp_classifier') and os.environ.get('RDP_JAR_PATH'):
# This is ugly, but because this is a jar file, it won't be in
# $PATH -- we require users to set an environment variable to
# point to the location of this jar file, so we test for that.
# My new version of app_path can be applied to do smarter checks,
# but will involve some re-write of how we check whether tests can
# be run. -Greg
if app == os.path.basename(os.environ.get('RDP_JAR_PATH')):
should_run_test = True
if should_run_test:
modules_to_test.append('test_app.' + test_name)
else:
print >> sys.stderr, "Can't find %s executable: skipping test" % app
if app_path('muscle'):
modules_to_test.append('test_format.test_pdb_color')
# we now toggle the db tests, based on an environment flag
if int(os.environ.get('TEST_DB', 0)):
db_tests = ['test_db.test_ncbi', 'test_db.test_pdb',
'test_db.test_rfam', 'test_db.test_util']
# we check for an environment flag for ENSEMBL
# we expect this to have the username and account for a localhost
# installation of the Ensembl MySQL databases
if 'ENSEMBL_ACCOUNT' in os.environ:
# check for cogent.db.ensembl dependencies
test_ensembl = True
for module in ['MySQLdb', 'sqlalchemy']:
if not module_present(module):
test_ensembl = False
print >> sys.stderr, \
"Module '%s' not present: skipping test" % module
if test_ensembl:
db_tests += ['test_db.test_ensembl.test_assembly',
'test_db.test_ensembl.test_database',
'test_db.test_ensembl.test_compara',
'test_db.test_ensembl.test_genome',
'test_db.test_ensembl.test_host',
'test_db.test_ensembl.test_metazoa',
'test_db.test_ensembl.test_species',
'test_db.test_ensembl.test_feature_level']
else:
print >> sys.stderr, "Environment variable ENSEMBL_ACCOUNT not "\
"set: skipping db.ensembl tests"
for db_test in db_tests:
modules_to_test.append(db_test)
else:
print >> sys.stderr, \
"Environment variable TEST_DB=1 not set: skipping db tests"
assert sys.version_info >= (2, 6)
alltests = unittest.TestSuite()
for module in modules_to_test:
if module.endswith('.rst'):
module = os.path.join(*module.split(".")[:-1]) + ".rst"
test = doctest.DocFileSuite(module, optionflags=
doctest.REPORT_ONLY_FIRST_FAILURE |
doctest.ELLIPSIS)
else:
test = unittest.findTestCases(my_import(module))
alltests.addTest(test)
return alltests
class BoobyTrappedStream(object):
def __init__(self, output):
self.output = output
def write(self, text):
self.output.write(text)
raise RuntimeError, "Output not allowed in tests"
def flush(self):
pass
def isatty(self):
return False
if __name__ == '__main__':
if '--debug' in sys.argv:
s = suite()
s.debug()
else:
orig = sys.stdout
if '--output-ok' in sys.argv:
sys.argv.remove('--output-ok')
else:
sys.stdout = BoobyTrappedStream(orig)
try:
unittest.main(defaultTest='suite', argv=sys.argv)
finally:
sys.stdout = orig
|
