def testFEAT_NIDM(self):
# test feat parsing
for fname, info in self.testfiles.items():
info['found_feat'] = False
for root, dirs, files in os.walk(info['dir']):
if detect_feat_directory(root):
print 'Found FEAT directory at {}.'.format(root)
info['found_feat'] = True
try:
fslnidm = FSLtoNIDMExporter(feat_dir=root, version="0.2.0")
fslnidm.parse()
export_dir = fslnidm.export()
ttl_file = os.path.join(export_dir,'nidm.ttl')
except:
print("Unable to parse the FEAT directory: \n{0}.".format(get_traceback()))
# confirm results path and existence
self.assertTrue(os.path.exists(export_dir))
self.assertEquals(os.path.join(info['dir'],info['export_dir']),export_dir)
# incomplete ttl = failure in processing
self.assertGreaterEqual(os.path.getsize(ttl_file),info['ttl_fsize'])
# test upload nidm
for fname, info in self.testfiles.items():
nidm_zpath = os.path.join(self.tmpdir,'{}.nidm.zip'.format(fname.replace('.zip','')))
nidm_zip = zipfile.ZipFile(nidm_zpath, 'w')
for root, dirs, files in os.walk(os.path.join(info['dir'],info['export_dir'])):
for nfile in files:
nidm_zip.write(os.path.join(root, nfile))
nidm_zip.close()
zname = os.path.basename(nidm_zip.filename)
post_dict = {
'name': zname,
'description':'{0} upload test'.format(zname),
'collection':self.coll.pk,
}
file_dict = {'zip_file': SimpleUploadedFile(zname, open(nidm_zpath,'r').read())}
form = NIDMResultsForm(post_dict, file_dict)
# validate NIDM Results
self.assertEqual(form.errors, {})
nidm = form.save()
statmaps = nidm.nidmresultstatisticmap_set.all()
self.assertEquals(len(statmaps),info['num_statmaps'])
map_types = [v.map_type for v in statmaps]
self.assertEquals(sorted(map_types), sorted(info['map_types']))
names = [v.name for v in statmaps]
self.assertEquals(sorted(names), sorted(info['names']))
def testFEAT_NIDM(self):
# test feat parsing
for fname, info in self.testfiles.items():
info['found_feat'] = False
for root, dirs, files in os.walk(info['dir']):
if detect_feat_directory(root):
print 'Found FEAT directory at {}.'.format(root)
info['found_feat'] = True
try:
fslnidm = FSLtoNIDMExporter(feat_dir=root,
version="0.2.0")
fslnidm.parse()
export_dir = fslnidm.export()
ttl_file = os.path.join(export_dir, 'nidm.ttl')
except:
print("Unable to parse the FEAT directory: \n{0}.".
format(get_traceback()))
# confirm results path and existence
self.assertTrue(os.path.exists(export_dir))
self.assertEquals(
os.path.join(info['dir'], info['export_dir']),
export_dir)
# incomplete ttl = failure in processing
self.assertEquals(os.path.getsize(ttl_file),
info['ttl_fsize'])
# test upload nidm
for fname, info in self.testfiles.items():
nidm_zpath = os.path.join(
self.tmpdir, '{}.nidm.zip'.format(fname.replace('.zip', '')))
nidm_zip = zipfile.ZipFile(nidm_zpath, 'w')
for root, dirs, files in os.walk(
os.path.join(info['dir'], info['export_dir'])):
for nfile in files:
nidm_zip.write(os.path.join(root, nfile))
nidm_zip.close()
zname = os.path.basename(nidm_zip.filename)
post_dict = {
'name': zname,
'description': '{0} upload test'.format(zname),
'collection': self.coll.pk,
}
file_dict = {
'zip_file': SimpleUploadedFile(zname,
open(nidm_zpath, 'r').read())
}
form = NIDMResultsForm(post_dict, file_dict)
# validate NIDM Results
self.assertTrue(form.is_valid())
nidm = form.save()
statmaps = nidm.nidmresultstatisticmap_set.all()
self.assertEquals(len(statmaps), info['num_statmaps'])
map_types = [v.map_type for v in statmaps]
self.assertEquals(sorted(map_types), sorted(info['map_types']))
names = [v.name for v in statmaps]
self.assertEquals(sorted(names), sorted(info['names']))
if __name__ == '__main__':
feat_dirs_path = raw_input("Enter location of test data:") or '/vagrant/FEAT'
find = 0
parse = 0
fail = 0
for root, dirs, files in os.walk(feat_dirs_path, topdown=False):
if detect_feat_directory(root):
if '.files' in dirs:
call(["rm", "-rf",os.path.join(root,'.files')])
tmpdir = tempfile.mkdtemp()
feat_dir = os.path.join(tmpdir,os.path.basename(root))
shutil.copytree(root, feat_dir)
print 'found feat directory at {0}'.format(root)
print 'testing {0}'.format(feat_dir)
find += 1
try:
fslnidm = FSLtoNIDMExporter(feat_dir=feat_dir, version="0.2.0")
fslnidm.parse()
export_dir = fslnidm.export()
parse += 1
except:
fail += 1
print("Unable to parse the FEAT directory: \n{0}.".format(get_traceback()))
finally:
print 'ttl length: {}'.format(os.path.getsize(os.path.join(export_dir,'nidm.ttl')))
shutil.rmtree(tmpdir)
print 'found {0} FEAT dirs, {1} successfully processed, {2} failures.'.format(find,parse,fail)
find = 0
parse = 0
fail = 0
for root, dirs, files in os.walk(feat_dirs_path, topdown=False):
if detect_feat_directory(root):
if '.files' in dirs:
call(["rm", "-rf", os.path.join(root, '.files')])
tmpdir = tempfile.mkdtemp()
feat_dir = os.path.join(tmpdir, os.path.basename(root))
shutil.copytree(root, feat_dir)
print 'found feat directory at {0}'.format(root)
print 'testing {0}'.format(feat_dir)
find += 1
try:
fslnidm = FSLtoNIDMExporter(feat_dir=feat_dir, version="0.2.0")
fslnidm.parse()
export_dir = fslnidm.export()
parse += 1
except:
fail += 1
print("Unable to parse the FEAT directory: \n{0}.".format(
get_traceback()))
finally:
print 'ttl length: {}'.format(
os.path.getsize(os.path.join(export_dir, 'nidm.ttl')))
shutil.rmtree(tmpdir)
print 'found {0} FEAT dirs, {1} successfully processed, {2} failures.'.format(
find, parse, fail)
