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sourmash_tst_utils.py
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sourmash_tst_utils.py
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"Various utilities used by sourmash tests."
import sys
import os
import tempfile
import shutil
import subprocess
import collections
import pprint
import pkg_resources
from pkg_resources import Requirement, resource_filename, ResolutionError
import traceback
from io import open # pylint: disable=redefined-builtin
try:
from StringIO import StringIO
except ImportError:
from io import StringIO
SIG_FILES = [os.path.join('demo', f) for f in (
"SRR2060939_1.sig", "SRR2060939_2.sig", "SRR2241509_1.sig",
"SRR2255622_1.sig", "SRR453566_1.sig", "SRR453569_1.sig", "SRR453570_1.sig")
]
def scriptpath(scriptname='sourmash'):
"""Return the path to the scripts, in both dev and install situations."""
# note - it doesn't matter what the scriptname is here, as long as
# it's some script present in this version of sourmash.
path = os.path.join(os.path.dirname(__file__), "../")
if os.path.exists(os.path.join(path, scriptname)):
return path
path = os.path.join(os.path.dirname(__file__), "../../EGG-INFO/")
if os.path.exists(os.path.join(path, scriptname)):
return path
for path in os.environ['PATH'].split(':'):
if os.path.exists(os.path.join(path, scriptname)):
return path
def _runscript(scriptname):
"""Find & run a script with exec (i.e. not via os.system or subprocess)."""
namespace = {"__name__": "__main__"}
namespace['sys'] = globals()['sys']
try:
pkg_resources.load_entry_point("sourmash", 'console_scripts', scriptname)()
return 0
except pkg_resources.ResolutionError:
pass
path = scriptpath()
scriptfile = os.path.join(path, scriptname)
if os.path.isfile(scriptfile):
if os.path.isfile(scriptfile):
exec( # pylint: disable=exec-used
compile(open(scriptfile).read(), scriptfile, 'exec'),
namespace)
return 0
return -1
ScriptResults = collections.namedtuple('ScriptResults',
['status', 'out', 'err'])
def runscript(scriptname, args, **kwargs):
"""Run a Python script using exec().
Run the given Python script, with the given args, in the given directory,
using 'exec'. Mimic proper shell functionality with argv, and capture
stdout and stderr.
When using :attr:`fail_ok`=False in tests, specify the expected error.
"""
__tracebackhide__ = True
sysargs = [scriptname]
sysargs.extend(args)
cwd = os.getcwd()
in_directory = kwargs.get('in_directory', cwd)
fail_ok = kwargs.get('fail_ok', False)
try:
status = -1
oldargs = sys.argv
sys.argv = sysargs
oldin = None
if 'stdin_data' in kwargs:
oldin, sys.stdin = sys.stdin, StringIO(kwargs['stdin_data'])
oldout, olderr = sys.stdout, sys.stderr
sys.stdout = StringIO()
sys.stdout.name = "StringIO"
sys.stderr = StringIO()
os.chdir(in_directory)
try:
print('running:', scriptname, 'in:', in_directory, file=oldout)
print('arguments', sysargs, file=oldout)
status = _runscript(scriptname)
except SystemExit as err:
status = err.code
except: # pylint: disable=bare-except
traceback.print_exc(file=sys.stderr)
status = -1
finally:
sys.argv = oldargs
out, err = sys.stdout.getvalue(), sys.stderr.getvalue()
sys.stdout, sys.stderr = oldout, olderr
if oldin:
sys.stdin = oldin
os.chdir(cwd)
if status != 0 and not fail_ok:
print(out)
print(err)
assert False, (status, out, err)
return ScriptResults(status, out, err)
def get_test_data(filename):
filepath = None
try:
filepath = resource_filename(
Requirement.parse("sourmash"), "sourmash/sourmash/test-data/"\
+ filename)
except ResolutionError:
pass
if not filepath or not os.path.isfile(filepath):
filepath = os.path.join(os.path.dirname(__file__), 'test-data',
filename)
return filepath
class TempDirectory(object):
def __init__(self):
self.tempdir = tempfile.mkdtemp(prefix='sourmashtest_')
def __enter__(self):
return self.tempdir
def __exit__(self, exc_type, exc_value, traceback):
try:
shutil.rmtree(self.tempdir, ignore_errors=True)
except OSError:
pass
if exc_type:
return False
class RunnerContext(object):
"""
I am a RunnerContext object from sourmash_tst_utils.
I have methods 'run_sourmash' and 'run', which run Python scripts.
Take a look at my 'location', 'last_command' and 'last_result' attributes!
You can use the 'output' method to build filenames in my temp directory.
"""
def __init__(self, location):
self.location = location
self.last_command = None
self.last_result = None
def run_sourmash(self, *args, **kwargs):
"Run the sourmash script with the given arguments."
kwargs['fail_ok'] = True
if 'in_directory' not in kwargs:
kwargs['in_directory'] = self.location
cmdlist = ['sourmash']
cmdlist.extend(args)
self.last_command = " ".join(cmdlist)
self.last_result = runscript('sourmash', args, **kwargs)
if self.last_result.status:
raise ValueError(self)
return self.last_result
def run(self, scriptname, *args, **kwargs):
"Run a script with the given arguments."
if 'in_directory' not in kwargs:
kwargs['in_directory'] = self.location
self.last_command = " ".join(args)
self.last_result = runscript(scriptname, args, **kwargs)
return self.last_result
def output(self, path):
return os.path.join(self.location, path)
def __str__(self):
s = ""
if self.last_command:
s += "Last command run:\n{}\n".format(repr(self.last_command))
if self.last_result:
s += "\nLAST RESULT:\n"
s += "- exit code: {}\n\n".format(self.last_result.status)
if self.last_result.out:
s += "- stdout:\n---\n{}---\n".format(self.last_result.out)
else:
s += '(no stdout)\n\n'
if self.last_result.err:
s += "- stderr:\n---\n{}---\n".format(self.last_result.err)
else:
s += '(no stderr)\n'
return s
def in_tempdir(fn):
def wrapper(*args, **kwargs):
with TempDirectory() as location:
ctxt = RunnerContext(location)
newargs = [ctxt] + list(args)
return fn(*newargs, **kwargs)
return wrapper
def in_thisdir(fn):
def wrapper(*args, **kwargs):
ctxt = RunnerContext(os.getcwd())
newargs = [ctxt] + list(args)
return fn(*newargs, **kwargs)
return wrapper