def _load_owl(self, owl_file):
if owl_file in self.owl_readers:
self.owl = self.owl_readers[owl_file]
else:
# Retreive owl file for NIDM-Results
# owl_file = os.path.join(RELPATH, 'terms', 'nidm-results.owl')
# check the file exists
assert os.path.exists(owl_file)
# Read owl (turtle) file
owl_path = os.path.dirname(owl_file)
if not "extension" in os.path.dirname(owl_file):
import_files = glob.glob(os.path.join(owl_path, \
os.pardir, os.pardir, "imports", '*.ttl'))
else:
import_files = glob.glob(os.path.join(owl_path, \
os.pardir, os.pardir, os.pardir, os.pardir, "imports", '*.ttl'))
# Main ontology file
import_files += glob.glob(os.path.join(owl_path, \
os.pardir, os.pardir, os.pardir, "terms", '*.owl'))
self.owl = OwlReader(owl_file, import_files)
self.owl_readers[owl_file] = self.owl
def __init__(self,
owl_file,
import_files,
spec_name,
subcomponents=None,
used_by=None,
generated_by=None,
derived_from=None,
attributed_to=None,
prefix=None,
commentable=False,
intro=None):
self.owl = OwlReader(owl_file, import_files)
self.owl.graph.bind('dct', 'http://purl.org/dc/terms/')
self.owl.graph.bind('dicom', 'http://purl.org/nidash/dicom#')
self.owl.graph.bind('nidm', 'http://purl.org/nidash/nidm#')
self.owl.graph.bind('bids', 'http://purl.org/nidash/bids#')
self.owl.graph.bind(
'onli',
'http://neurolog.unice.fr/ontoneurolog/v3.0/instrument.owl#')
self.owl.graph.bind('pato', 'http://purl.obolibrary.org/obo/pato#')
self.owl.graph.bind('prov', 'http://www.w3.org/ns/prov')
self.owl.graph.bind(
'qibo', 'http://www.owl-ontologies.com/Ontology1298855822.owl')
self.owl.graph.bind('sio', 'http://semanticscience.org/resource/')
self.name = spec_name
self.component = self.name.lower().replace("-", "_")
self.section_open = 0
self.already_defined_classes = list()
self.commentable = commentable
self.attributes_done = set()
self.text = ""
self.create_specification(subcomponents, used_by, generated_by,
derived_from, attributed_to, prefix, intro)
def setUp(self):
self.my_execption = ""
owl_file = os.path.join(os.path.dirname(
os.path.dirname(
os.path.realpath(__file__))),
'nidmresults', 'owl',
'nidm-results_130.owl')
self.owl = OwlReader(owl_file)
pwd = os.path.dirname(
os.path.abspath(inspect.getfile(inspect.currentframe())))
# Store test data in a 'data' folder until 'test'
data_dir = os.path.join(pwd, 'data')
if not os.path.exists(data_dir):
os.makedirs(data_dir)
# Collection containing examples of NIDM-Results packs (1.3.0)
req = Request(
"http://neurovault.org/api/collections/2210/nidm_results")
rep = urlopen(req)
response = rep.read()
data = json.loads(response.decode('utf-8'))
# Download the NIDM-Results packs from NeuroVault if not available
# locally
self.packs = list()
for nidm_res in data["results"]:
url = nidm_res["zip_file"]
study = nidm_res["name"]
nidmpack = os.path.join(data_dir, study + ".zip")
if not os.path.isfile(nidmpack):
f = urlopen(url)
print("downloading " + url + " at " + nidmpack)
with open(nidmpack, "wb") as local_file:
local_file.write(f.read())
self.packs.append(nidmpack)
self.packs = glob.glob(os.path.join(data_dir, '*.nidm.zip'))
self.out_dir = os.path.join(data_dir, 'recomputed')
if os.path.isdir(self.out_dir):
shutil.rmtree(self.out_dir)
os.mkdir(self.out_dir)
def __init__(self, owl_file, import_files, spec_name, subcomponents=None,
used_by=None, generated_by=None, derived_from=None,
attributed_to=None, prefix=None, commentable=False,
intro=None):
self.owl = OwlReader(owl_file, import_files)
self.owl.graph.bind('nidm', 'http://purl.org/nidash/nidm#')
self.name = spec_name
self.component = self.name.lower().replace("-", "_")
self.section_open = 0
self.already_defined_classes = list()
self.commentable = commentable
self.attributes_done = set()
self.text = ""
self.create_specification(subcomponents, used_by, generated_by,
derived_from, attributed_to, prefix, intro)
def __init__(self,
nidm_classes,
example_file,
one_file_per_class=False,
owl_file=None,
remove_att=None):
self.nidm_classes = nidm_classes
self.one_file_per_class = one_file_per_class
self.remove_att = remove_att
self.owl = None
if owl_file is None:
import_files = glob.glob(os.path.join(NIDMPATH, "imports",
'*.ttl'))
owl_file = os.path.join(NIDM_TERMS_DIR, 'nidm-results.owl')
self.owl = OwlReader(owl_file, import_files)
if not one_file_per_class:
self.file = example_file
else:
self.dir = example_file
def __init__(self, name, ttl_file, gt_ttl_files, exact_comparison,
version):
self.name = name
self.ttl_file = ttl_file
self.gt_ttl_files = gt_ttl_files
self.exact_comparison = exact_comparison
self.graph = Graph()
print(ttl_file)
self.graph.parse(ttl_file, format='turtle')
# Get NIDM-Results version for each example
self.version = version
if self.version != "dev":
self.gt_ttl_files = [
x.replace(os.path.join("nidm", "nidm"),
os.path.join("nidm_releases", self.version, "nidm"))
for x in self.gt_ttl_files
]
# Owl file corresponding to version
owl_file = os.path.join(
os.path.dirname(os.path.dirname(__file__)), 'owl',
"nidm-results_" + version.replace(".", "") + ".owl")
self.owl_file = owl_file
owl_imports = None
if self.version == "dev":
owl_imports = glob.glob(
os.path.join(os.path.dirname(owl_file), os.pardir, os.pardir,
"imports", '*.ttl'))
self.owl = OwlReader(self.owl_file, owl_imports)
def __init__(self, owl_file):
self.owl = OwlReader(owl_file)
def main(sid, aid, owl_file, template_files, script_files, constants_file):
owl_txt = get_file_text(owl_file)
templates_txt = dict()
for template_file in template_files:
templates_txt[template_file] = get_file_text(template_file)
scripts_txt = dict()
for script_file in script_files:
scripts_txt[script_file] = get_file_text(script_file)
cst_txt = get_file_text(constants_file)
sid_name = sid.split(":")[1]
sid_namespace = sid.split(":")[0]
if sid_namespace == "nidm":
uri = NIDM[sid_name]
pref = "NIDM"
elif sid_namespace == "fsl":
uri = FSL[sid_name]
pref = "FSL"
elif sid_namespace == "spm":
uri = SPM[sid_name]
pref = "SPM"
# If alphanumeric identifier was not defined, find the next available
if aid is None:
before_alnum = sid_namespace + ":" + pref + "_"
# Find all alphanumeric identifiers in the owl file
alphanum_ids = set(re.findall("(" + before_alnum + '\d+)\s+', owl_txt))
# Get identifier number for next alphanumeric identifier
last_id = sorted(list(alphanum_ids))[-1]
new_id_num = int(last_id.replace(before_alnum, "")) + 1
aid = before_alnum + "{0:0>7}".format(new_id_num)
owl = OwlReader
owl = OwlReader(owl_file)
label = owl.get_label(uri).split(":")[1].replace("'", "")
# Replace all occurences of semantic id
owl_txt = owl_txt.replace(sid + " ", aid + " ")
# Replace ids in templates
for tpl, tpl_txt in templates_txt.items():
templates_txt[tpl] = tpl_txt.replace(sid + " ", aid + " ")
for scr, scr_txt in scripts_txt.items():
scripts_txt[scr] = scr_txt.replace('"' + sid + '"', '"' + aid + '"')
new_constant = pref + "_" + \
label.upper().replace(" ", "_").replace("-", "_") + \
" = " + pref + "['"+aid.replace(sid_namespace + ":", "")+"']"
cst_txt = cst_txt.replace("# NIDM constants",
"# NIDM constants\n" + new_constant)
replace_file_txt(owl_file, owl_txt)
replace_file_txt(constants_file, cst_txt)
for tpl, tpl_txt in templates_txt.items():
replace_file_txt(tpl, tpl_txt)
for scr, scr_txt in scripts_txt.items():
replace_file_txt(scr, scr_txt)
