def testUploadNIDMZip(self):
for name, info in self.files.items():
zip_file = open(info['file'], 'rb')
post_dict = {
'name': name,
'description': '{0} upload test'.format(name),
'collection': self.coll.pk,
}
fname = os.path.basename(info['file'])
file_dict = {
'zip_file': SimpleUploadedFile(fname, zip_file.read())}
form = NIDMResultsForm(post_dict, file_dict)
self.assertTrue(form.is_valid())
nidm = form.save()
self.assertEquals(len(nidm.nidmresultstatisticmap_set.all()),
info['num_statmaps'])
map_type = info['output_row']['type'][0]
map_img = nidm.nidmresultstatisticmap_set.filter(
map_type=map_type).first()
self.assertEquals(map_img.name, info['output_row']['name'])
def test_adding_nidm(self):
zip_file = open(os.path.join(self.test_path,'test_data/nidm/fsl.nidm.zip'), 'rb')
post_dict = {
'name': 'fsl_nidm',
'description':'{0} upload test'.format('fsl_nidm'),
'collection':self.Collection1.pk}
fname = os.path.basename(os.path.join(self.test_path,'test_data/nidm/fsl.nidm.zip'))
file_dict = {'zip_file': SimpleUploadedFile(fname, zip_file.read())}
zip_file.close()
form = NIDMResultsForm(post_dict, file_dict)
# Transforms should be generated synchronously
nidm = form.save()
images_processing = count_processing_comparisons()
print "\nTesting Counter - added nidm result ###"
# And when we count, there should be 0 still processing
print "%s images processing [should be 0]" %(images_processing)
assert_equal(images_processing,0)
# We should have 2 images total, so 1 comparison
total_comparisons = count_existing_comparisons()
assert_equal(total_comparisons,1)
# Make sure comparisons were calculated
number_comparisons = len(Comparison.objects.all())
print "\n %s comparisons exist after adding NIDM [should not be 0]" %(number_comparisons)
assert_equal(number_comparisons>0,True)
def test_adding_nidm(self):
Image2 = StatisticMap(name='Image2', collection=self.Collection1, file='beta_0001.nii.gz', map_type="Other")
Image2.file = SimpleUploadedFile('beta_0001.nii.gz', file(os.path.join(self.test_path,'test_data/statmaps/beta_0001.nii.gz')).read())
Image2.save()
zip_file = open(os.path.join(self.test_path,'test_data/nidm/spm_example.nidm.zip'), 'rb')
post_dict = {
'name': 'spm_nidm',
'description':'{0} upload test'.format('spm_example'),
'collection':self.Collection2.pk}
fname = os.path.basename(os.path.join(self.test_path,'test_data/nidm/spm_example.nidm.zip'))
file_dict = {'zip_file': SimpleUploadedFile(fname, zip_file.read())}
zip_file.close()
form = NIDMResultsForm(post_dict, file_dict)
# Transforms should be generated synchronously
nidm = form.save()
print "\nTesting Counter - added nidm result ###"
# We should have 2 images total, so 1 comparison
total_comparisons = count_existing_comparisons(Image2.pk)
self.assertEqual(total_comparisons,1)
#Let's add a single subject map - this should not trigger a comparison
Image2ss = StatisticMap(name='Image2 - single subject', collection=self.Collection3, file='beta_0001.nii.gz', map_type="Other", analysis_level='S')
Image2ss.file = SimpleUploadedFile('beta_0001.nii.gz', file(os.path.join(self.test_path,'test_data/statmaps/beta_0001.nii.gz')).read())
Image2ss.save()
total_comparisons = count_existing_comparisons(Image2ss.pk)
self.assertEqual(total_comparisons,0)
# Make sure comparisons were calculated
number_comparisons = len(Comparison.objects.all())
print "\n %s comparisons exist after adding NIDM `[should not be 0]" %(number_comparisons)
self.assertEqual(number_comparisons>0,True)
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 test_adding_nidm(self):
Image2 = StatisticMap(name='Image2',
collection=self.Collection1,
file='beta_0001.nii.gz',
map_type="Other")
Image2.file = SimpleUploadedFile(
'beta_0001.nii.gz',
file(
os.path.join(self.test_path,
'test_data/statmaps/beta_0001.nii.gz')).read())
Image2.save()
zip_file = open(
os.path.join(self.test_path,
'test_data/nidm/spm_example.nidm.zip'), 'rb')
post_dict = {
'name': 'spm_nidm',
'description': '{0} upload test'.format('spm_example'),
'collection': self.Collection2.pk
}
fname = os.path.basename(
os.path.join(self.test_path,
'test_data/nidm/spm_example.nidm.zip'))
file_dict = {'zip_file': SimpleUploadedFile(fname, zip_file.read())}
zip_file.close()
form = NIDMResultsForm(post_dict, file_dict)
# Transforms should be generated synchronously
nidm = form.save()
print "\nTesting Counter - added nidm result ###"
# We should have 2 images total, so 1 comparison
total_comparisons = count_existing_comparisons(Image2.pk)
self.assertEqual(total_comparisons, 1)
#Let's add a single subject map - this should not trigger a comparison
Image2ss = StatisticMap(name='Image2 - single subject',
collection=self.Collection3,
file='beta_0001.nii.gz',
map_type="Other",
analysis_level='S')
Image2ss.file = SimpleUploadedFile(
'beta_0001.nii.gz',
file(
os.path.join(self.test_path,
'test_data/statmaps/beta_0001.nii.gz')).read())
Image2ss.save()
total_comparisons = count_existing_comparisons(Image2ss.pk)
self.assertEqual(total_comparisons, 0)
# Make sure comparisons were calculated
number_comparisons = len(Comparison.objects.all())
print "\n %s comparisons exist after adding NIDM `[should not be 0]" % (
number_comparisons)
self.assertEqual(number_comparisons > 0, True)
def save_nidm_form(zip_file, collection, name=None):
if name == None:
name = "fsl_nidm"
zip_file_obj = open(zip_file, "rb")
post_dict = {"name": name, "description": "{0} upload test".format("fsl_nidm"), "collection": collection.pk}
fname = os.path.basename(zip_file)
file_dict = {"zip_file": SimpleUploadedFile(fname, zip_file_obj.read())}
zip_file_obj.close()
form = NIDMResultsForm(post_dict, file_dict)
return form.save()
def save_nidm_form(zip_file,collection,name=None):
if name == None:
name = "fsl_nidm"
zip_file_obj = open(zip_file, 'rb')
post_dict = {'name': name,
'description':'{0} upload test'.format('fsl_nidm'),
'collection':collection.pk}
fname = os.path.basename(zip_file)
file_dict = {'zip_file': SimpleUploadedFile(fname, zip_file_obj.read())}
zip_file_obj.close()
form = NIDMResultsForm(post_dict, file_dict)
return form.save()
def save_nidm_form(zip_file,collection,name=None):
if name == None:
name = "fsl_nidm"
zip_file_obj = open(zip_file, 'rb')
post_dict = {'name': name,
'description':'{0} upload test'.format('fsl_nidm'),
'collection':collection.pk}
fname = os.path.basename(zip_file)
file_dict = {'zip_file': SimpleUploadedFile(fname, zip_file_obj.read())}
zip_file_obj.close()
form = NIDMResultsForm(post_dict, file_dict)
return form.save()
def testDownloadCollection_NIDM_results(self):
collection = Collection(owner=self.user, name="Collection2")
collection.save()
# Upload NIMDResult zip file
zip_file = open(
os.path.join(TEST_PATH, 'test_data/nidm/auditory.nidm.zip'), 'rb')
post_dict = {
'name': 'auditory',
'description': '{0} upload test'.format('spm_auditory_v1.2.0'),
'collection': collection.pk,
}
fname = os.path.basename(
os.path.join(TEST_PATH, 'test_data/nidm/auditory.nidm.zip'))
file_dict = {'zip_file': SimpleUploadedFile(fname, zip_file.read())}
form = NIDMResultsForm(post_dict, file_dict)
form.save()
# Upload Statistic Map
image = save_statmap_form(image_path=os.path.join(
TEST_PATH, 'test_data/statmaps/all.nii.gz'),
collection=collection,
image_name="all.nii.gz")
factory = RequestFactory()
self.client.login(username=self.user)
request = factory.get('/collections/%s/download' % collection.pk,
{'format': 'img.zip'})
request.user = self.user
response = download_collection(request, str(collection.pk))
self.assertTrue(response.streaming_content)
self.assertEqual(response.status_code, 200)
self.assertEqual(response.get('Content-Disposition'),
"attachment; filename=" + collection.name + ".zip")
zf = zipfile.ZipFile(io.BytesIO(''.join(response.streaming_content)))
self.assertEqual(len(zf.filelist), 2) # 1 NIDMResult, 1 Statmap
self.assertIsNone(zf.testzip())
self.assertIn("Collection2/all.nii.gz", zf.namelist())
self.assertIn("Collection2/auditory.nidm.zip", zf.namelist())
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
fslnidm = FSLtoNIDMExporter(feat_dir=root, version="1.2.0")
fslnidm.parse()
info['nidm_file'] = fslnidm.export()
# confirm results path and existence
self.assertTrue(os.path.exists(info['nidm_file']))
# test upload nidm
for fname, info in self.testfiles.items():
zname = os.path.basename(info['nidm_file'])
post_dict = {
'name': zname,
'description': '{0} upload test'.format(zname),
'collection': self.coll.pk,
}
file_dict = {'zip_file': SimpleUploadedFile(zname, open(info['nidm_file'],'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 testDownloadCollection_NIDM_results(self):
collection = Collection(owner=self.user, name="Collection2")
collection.save()
# Upload NIMDResult zip file
zip_file = open(os.path.join(TEST_PATH, 'test_data/nidm/auditory.nidm.zip'), 'rb')
post_dict = {
'name': 'auditory',
'description': '{0} upload test'.format('spm_auditory_v1.2.0'),
'collection': collection.pk,
}
fname = os.path.basename(os.path.join(TEST_PATH, 'test_data/nidm/auditory.nidm.zip'))
file_dict = {
'zip_file': SimpleUploadedFile(fname, zip_file.read())}
form = NIDMResultsForm(post_dict, file_dict)
form.save()
# Upload Statistic Map
image = save_statmap_form(image_path=os.path.join(TEST_PATH, 'test_data/statmaps/all.nii.gz'),
collection=collection,
image_name="all.nii.gz")
factory = RequestFactory()
self.client.login(username=self.user)
request = factory.get('/collections/%s/download' % collection.pk, {'format': 'img.zip'})
request.user = self.user
response = download_collection(request, str(collection.pk))
self.assertTrue(response.streaming_content)
self.assertEqual(response.status_code, 200)
self.assertEqual(response.get('Content-Disposition'), "attachment; filename=" + collection.name + ".zip")
zf = zipfile.ZipFile(io.BytesIO(''.join(response.streaming_content)))
self.assertEqual(len(zf.filelist),2) # 1 NIDMResult, 1 Statmap
self.assertIsNone(zf.testzip())
self.assertIn("Collection2/all.nii.gz", zf.namelist())
self.assertIn("Collection2/auditory.nidm.zip", zf.namelist())
def view_nidm_results(request, collection_cid, nidm_name):
collection = get_collection(collection_cid,request)
nidmr = get_object_or_404(NIDMResults, collection=collection,name=nidm_name)
if request.method == "POST":
if not request.user.has_perm("statmaps.change_nidmresults", nidmr):
return HttpResponseForbidden()
form = NIDMResultsForm(request.POST, request.FILES, instance=nidmr)
if form.is_valid():
instance = form.save(commit=False)
instance.save()
form.save_nidm()
form.save_m2m()
return HttpResponseRedirect(collection.get_absolute_url())
else:
if owner_or_contrib(request,collection):
form = NIDMResultsForm(instance=nidmr)
else:
form = NIDMViewForm(instance=nidmr)
# Generate viewer for nidm result
nidm_files = [nidmr.ttl_file.path.encode("utf-8")]
standard_brain = "/static/images/MNI152.nii.gz"
# We will remove these scripts
remove_resources = ["BOOTSTRAPCSS","ROBOTOFONT"]
# We will remove these columns
columns_to_remove = ["statmap_location","statmap",
"statmap_type","coordinate_id"]
html_snippet = generate(nidm_files,
base_image=standard_brain,
remove_scripts=remove_resources,
columns_to_remove=columns_to_remove,
template_choice="embed")
context = {"form": form,"nidm_viewer":html_snippet}
return render(request, "statmaps/edit_nidm_results.html", context)
def view_nidm_results(request, collection_cid, nidm_name):
collection = get_collection(collection_cid,request)
try:
nidmr = NIDMResults.objects.get(collection=collection,name=nidm_name)
except NIDMResults.DoesNotExist:
return Http404("This NIDM Result was not found.")
if request.method == "POST":
if not owner_or_contrib(request,collection):
return HttpResponseForbidden()
form = NIDMResultsForm(request.POST, request.FILES, instance=nidmr)
if form.is_valid():
instance = form.save(commit=False)
instance.save()
form.save_nidm()
form.save_m2m()
return HttpResponseRedirect(collection.get_absolute_url())
else:
if owner_or_contrib(request,collection):
form = NIDMResultsForm(instance=nidmr)
else:
form = NIDMViewForm(instance=nidmr)
context = {"form": form}
return render(request, "statmaps/edit_nidm_results.html.haml", context)
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']))
def view_nidm_results(request, collection_cid, nidm_name):
collection = get_collection(collection_cid, request)
try:
nidmr = NIDMResults.objects.get(collection=collection, name=nidm_name)
except NIDMResults.DoesNotExist:
return Http404("This NIDM Result was not found.")
if request.method == "POST":
if not owner_or_contrib(request, collection):
return HttpResponseForbidden()
form = NIDMResultsForm(request.POST, request.FILES, instance=nidmr)
if form.is_valid():
instance = form.save(commit=False)
instance.save()
form.save_nidm()
form.save_m2m()
return HttpResponseRedirect(collection.get_absolute_url())
else:
if owner_or_contrib(request, collection):
form = NIDMResultsForm(instance=nidmr)
else:
form = NIDMViewForm(instance=nidmr)
context = {"form": form}
return render(request, "statmaps/edit_nidm_results.html.haml", context)