def testExpectedWarnings(self):
msg = ''
# compare test files (.input and .expected for each)
# N.B. in some cases, python 2 and python 3 will have different output!
for fn in pathmap.all_files(os.path.join('collections', 'warn_err')):
if fn.endswith('.input'):
frag = fn[:-len('.input')]
efn = frag + '.expected'
# check for a python version-specific file, like 'foo.expected-py3'
current_python_version = (sys.version_info > (3, 0)) and 'py3' or 'py2'
versioned_efn = '{f}-{v}'.format(f=efn, v=current_python_version)
if os.path.exists(versioned_efn):
efn = versioned_efn
if os.path.exists(efn):
inp = testing_read_json(fn)
aa = validate_collection(inp)
errors = aa[0]
exp = testing_read_json(efn)
if errors != exp:
ofn = frag + '.output'
testing_write_json(errors, ofn)
msg = "Validation failed to produce expected outcome. Compare {o} and {e}".format(o=ofn, e=efn)
self.assertEqual(exp, errors, msg)
else:
_LOG.warn('Expected output file "{f}" not found'.format(f=efn))
def testExpectedWarnings(self):
msg = ''
# compare test files (.input and .expected for each)
# N.B. in some cases, python 2 and python 3 will have different output!
for fn in pathmap.all_files(os.path.join('collections', 'warn_err')):
if fn.endswith('.input'):
frag = fn[:-len('.input')]
efn = frag + '.expected'
# check for a python version-specific file, like 'foo.expected-py3'
current_python_version = (sys.version_info >
(3, 0)) and 'py3' or 'py2'
versioned_efn = '{f}-{v}'.format(f=efn,
v=current_python_version)
if os.path.exists(versioned_efn):
efn = versioned_efn
if os.path.exists(efn):
inp = testing_read_json(fn)
aa = validate_collection(inp)
errors = aa[0]
exp = testing_read_json(efn)
if errors != exp:
ofn = frag + '.output'
testing_write_json(errors, ofn)
msg = "Validation failed to produce expected outcome. Compare {o} and {e}".format(
o=ofn, e=efn)
self.assertEqual(exp, errors, msg)
else:
_LOG.warn(
'Expected output file "{f}" not found'.format(f=efn))
def _is_valid_collection_json(self, json_repr):
"""Call the primary validator for a quick test"""
collection = self._coerce_json_to_collection(json_repr)
if collection is None:
# invalid JSON, definitely broken
return False
aa = validate_collection(collection)
errors = aa[0]
for e in errors:
_LOG.debug('> invalid JSON: {m}'.format(m=e.encode('utf-8')))
if len(errors) > 0:
return False
return True
def _is_valid_collection_json(self, json_repr):
"""Call the primary validator for a quick test"""
collection = self._coerce_json_to_collection(json_repr)
if collection is None:
# invalid JSON, definitely broken
return False
aa = validate_collection(collection)
errors = aa[0]
for e in errors:
_LOG.debug('> invalid JSON: {m}'.format(m=e.encode('utf-8')))
if len(errors) > 0:
return False
return True
def testValidFilesPass(self):
# just one test file for now
msg = ''
frag = 'collection-good.json'
collection = pathmap.collection_obj(frag)
aa = validate_collection(collection)
errors = aa[0]
for e in errors:
_LOG.debug('unexpected error from {f}: {m}'.format(f=frag, m=UNICODE(e)))
if len(errors) > 0:
ofn = pathmap.collection_source_path(frag + '.output')
testing_write_json(errors, ofn)
msg = "File failed to validate cleanly. See {o}".format(o=ofn)
self.assertEqual(len(errors), 0, msg)
def testValidFilesPass(self):
# just one test file for now
msg = ''
frag = 'collection-good.json'
collection = pathmap.collection_obj(frag)
aa = validate_collection(collection)
errors = aa[0]
for e in errors:
_LOG.debug('unexpected error from {f}: {m}'.format(f=frag,
m=UNICODE(e)))
if len(errors) > 0:
ofn = pathmap.collection_source_path(frag + '.output')
testing_write_json(errors, ofn)
msg = "File failed to validate cleanly. See {o}".format(o=ofn)
self.assertEqual(len(errors), 0, msg)
def testInvalidFilesFail(self):
# just one test file for now
msg = ''
frag = 'collection-incomplete.json'
inp = pathmap.collection_obj(frag)
try:
aa = validate_collection(inp)
if len(aa) > 0:
errors = aa[0]
if len(errors) == 0:
ofn = pathmap.collection_source_path(frag + '.output')
testing_write_json(errors, ofn)
msg = "Failed to reject file. See {o}".format(o=str(msg))
self.assertTrue(False, msg)
except:
pass
def testInvalidFilesFail(self):
# just one test file for now
msg = ''
frag = 'collection-incomplete.json'
inp = pathmap.collection_obj(frag)
try:
aa = validate_collection(inp)
if len(aa) > 0:
errors = aa[0]
if len(errors) == 0:
ofn = pathmap.collection_source_path(frag + '.output')
testing_write_json(errors, ofn)
msg = "Failed to reject file. See {o}".format(o=str(msg))
self.assertTrue(False, msg)
except:
pass
def testCreated(self):
c = get_empty_collection()
aa = validate_collection(c)
errors = aa[0]
self.assertTrue(len(errors) == 0)
from peyotl.collections_store.validation import validate_collection
from peyotl import write_as_json
import sys
# Expecting a lot of lines like pg_2359_4962 for 'pg_2359', 'tree4962'
inp_fn = sys.argv[1]
with open(inp_fn, 'rU') as inp:
lines = []
for line in inp:
line = line.strip()
if (not line) or (line == 'taxonomy'):
continue
assert line.endswith('.tre')
frag = line[:-4]
s = frag.split('_')
study_id, tree_frag = '_'.join(s[:-1]), s[-1]
tree_id = 'tree' + tree_frag
lines.append((study_id, tree_id))
c = get_empty_collection()
d = c['decisions']
for pair in lines:
d.append({'SHA': '',
'decision': 'INCLUDED',
'name': '',
'studyID': pair[0],
'treeID': pair[1]
})
assert not (validate_collection(c)[0])
write_as_json(c, sys.stdout)
def testCreated(self):
c = get_empty_collection()
aa = validate_collection(c)
errors = aa[0]
self.assertTrue(len(errors) == 0)
