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 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)
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 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']))
