def _verify_outputs( self, testdef, history, jobs, shed_tool_id, data_list, data_collection_list, galaxy_interactor ):
assert len(jobs) == 1, "Test framework logic error, somehow tool test resulted in more than one job."
job = jobs[ 0 ]
maxseconds = testdef.maxseconds
if testdef.num_outputs is not None:
expected = testdef.num_outputs
actual = len( data_list )
if expected != actual:
messaage_template = "Incorrect number of outputs - expected %d, found %s."
message = messaage_template % ( expected, actual )
raise Exception( message )
found_exceptions = []
def register_exception(e):
if not found_exceptions:
# Only print this stuff out once.
for stream in ['stdout', 'stderr']:
if stream in job_stdio:
print >>sys.stderr, self._format_stream( job_stdio[ stream ], stream=stream, format=True )
found_exceptions.append(e)
if testdef.expect_failure:
if testdef.outputs:
raise Exception("Cannot specify outputs in a test expecting failure.")
# Wait for the job to complete and register expections if the final
# status was not what test was expecting.
job_failed = False
try:
galaxy_interactor.wait_for_job( job[ 'id' ], history, maxseconds )
except Exception as e:
job_failed = True
if not testdef.expect_failure:
found_exceptions.append(e)
job_stdio = galaxy_interactor.get_job_stdio( job[ 'id' ] )
if not job_failed and testdef.expect_failure:
error = AssertionError("Expected job to fail but Galaxy indicated the job successfully completed.")
register_exception(error)
expect_exit_code = testdef.expect_exit_code
if expect_exit_code is not None:
exit_code = job_stdio["exit_code"]
if str(expect_exit_code) != str(exit_code):
error = AssertionError("Expected job to complete with exit code %s, found %s" % (expect_exit_code, exit_code))
register_exception(error)
for output_index, output_tuple in enumerate(testdef.outputs):
# Get the correct hid
name, outfile, attributes = output_tuple
output_testdef = bunch.Bunch( name=name, outfile=outfile, attributes=attributes )
try:
output_data = data_list[ name ]
except (TypeError, KeyError):
# Legacy - fall back on ordered data list access if data_list is
# just a list (case with twill variant or if output changes its
# name).
if hasattr(data_list, "values"):
output_data = data_list.values()[ output_index ]
else:
output_data = data_list[ len(data_list) - len(testdef.outputs) + output_index ]
self.assertTrue( output_data is not None )
try:
galaxy_interactor.verify_output( history, jobs, output_data, output_testdef=output_testdef, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
except Exception as e:
register_exception(e)
other_checks = {
"command_line": "Command produced by the job",
"stdout": "Standard output of the job",
"stderr": "Standard error of the job",
}
for what, description in other_checks.items():
if getattr( testdef, what, None ) is not None:
try:
data = job_stdio[what]
verify_assertions( data, getattr( testdef, what ) )
except AssertionError, err:
errmsg = '%s different than expected\n' % description
errmsg += str( err )
register_exception( AssertionError( errmsg ) )
def _verify_outputs(self, testdef, history, jobs, shed_tool_id, data_list,
data_collection_list, galaxy_interactor):
assert len(
jobs
) == 1, "Test framework logic error, somehow tool test resulted in more than one job."
job = jobs[0]
maxseconds = testdef.maxseconds
if testdef.num_outputs is not None:
expected = testdef.num_outputs
actual = len(data_list)
if expected != actual:
messaage_template = "Incorrect number of outputs - expected %d, found %s."
message = messaage_template % (expected, actual)
raise Exception(message)
found_exceptions = []
def register_exception(e):
if not found_exceptions:
# Only print this stuff out once.
for stream in ['stdout', 'stderr']:
if stream in job_stdio:
print >> sys.stderr, self._format_stream(
job_stdio[stream], stream=stream, format=True)
found_exceptions.append(e)
if testdef.expect_failure:
if testdef.outputs:
raise Exception(
"Cannot specify outputs in a test expecting failure.")
# Wait for the job to complete and register expections if the final
# status was not what test was expecting.
job_failed = False
try:
galaxy_interactor.wait_for_job(job['id'], history, maxseconds)
except Exception as e:
job_failed = True
if not testdef.expect_failure:
found_exceptions.append(e)
job_stdio = galaxy_interactor.get_job_stdio(job['id'])
if not job_failed and testdef.expect_failure:
error = AssertionError(
"Expected job to fail but Galaxy indicated the job successfully completed."
)
register_exception(error)
expect_exit_code = testdef.expect_exit_code
if expect_exit_code is not None:
exit_code = job_stdio["exit_code"]
if str(expect_exit_code) != str(exit_code):
error = AssertionError(
"Expected job to complete with exit code %s, found %s" %
(expect_exit_code, exit_code))
register_exception(error)
for output_index, output_tuple in enumerate(testdef.outputs):
# Get the correct hid
name, outfile, attributes = output_tuple
output_testdef = bunch.Bunch(name=name,
outfile=outfile,
attributes=attributes)
try:
output_data = data_list[name]
except (TypeError, KeyError):
# Legacy - fall back on ordered data list access if data_list is
# just a list (case with twill variant or if output changes its
# name).
if hasattr(data_list, "values"):
output_data = data_list.values()[output_index]
else:
output_data = data_list[len(data_list) -
len(testdef.outputs) +
output_index]
self.assertTrue(output_data is not None)
try:
galaxy_interactor.verify_output(history,
jobs,
output_data,
output_testdef=output_testdef,
shed_tool_id=shed_tool_id,
maxseconds=maxseconds)
except Exception as e:
register_exception(e)
other_checks = {
"command_line": "Command produced by the job",
"stdout": "Standard output of the job",
"stderr": "Standard error of the job",
}
for what, description in other_checks.items():
if getattr(testdef, what, None) is not None:
try:
data = job_stdio[what]
verify_assertions(data, getattr(testdef, what))
except AssertionError, err:
errmsg = '%s different than expected\n' % description
errmsg += str(err)
register_exception(AssertionError(errmsg))