###############################################################################
### MAIN ######################################################################
###############################################################################
if __name__ == '__main__':
# Create store
from cubicweb.dataimport import SQLGenObjectStore
store = SQLGenObjectStore(session)
sqlgen_store = True
root_dir = osp.abspath(sys.argv[4])
subjects_dir = osp.join(root_dir, 'subjects')
genetics_dir = osp.join(root_dir, 'genetics')
### Study #################################################################
study = import_study(data_dir=root_dir)
study = store.create_entity('Study', **study)
### Initialize questionnaire ##############################################
one_subject = glob.glob('%s/*' % subjects_dir)[0]
questionnaire, questions = import_questionnaire(one_subject)
questionnaire = store.create_entity('Questionnaire', **questionnaire)
questions_id = {}
for question in questions:
question['questionnaire'] = questionnaire.eid
question = store.create_entity('Question', **question)
questions_id[question.text] = question.eid
### Initialize genetics ####################################################
# Chromosomes
chrs = import_chromosomes(os.path.join(genetics_dir, 'chromosomes.json'))
chr_map = {}
### BODYLOCATION ##############################################################
###############################################################################
""" This come from the following sparql request on dbpedia.org
prefix dbpedia-owl:<http://dbpedia.org/ontology/>
prefix dbpprop:<http://dbpedia.org/property/>
select distinct ?u, ?t, ?n, ?a where
{?u a dbpedia-owl:AnatomicalStructure.
?u dbpprop:name ?t.
OPTIONAL{?u dbpprop:meshnumber ?n.
?u dbpedia-owl:abstract ?a.
FILTER (lang(?a)="en")}
FILTER (lang(?t)="en")}"""
reader = ucsvreader(open(osp.join(HERE, 'bodylocation.csv')), separator='\t')
for identifier, name, mesh, descr in reader:
store.create_entity('BodyLocation', identifier=identifier,
name=name, mesh_id=mesh, description=descr)
###############################################################################
### DISEASE ###################################################################
###############################################################################
"""This come from the following sparql request on dbpedia.org
prefix dbpedia-owl:<http://dbpedia.org/ontology/>
prefix dbpprop:<http://dbpedia.org/property/>
select distinct ?u, ?t, ?n, ?d, ?a where
{?u a dbpedia-owl:Disease.
?u dbpedia-owl:meshId ?n.
?u dbpedia-owl:icd10 ?d.
?u dbpedia-owl:abstract ?a.
?u rdfs:label ?t.
help="Json file of snps")
(options, args) = parser.parse_args(__args__)
store = SQLGenObjectStore(session)
###############################################################################
### GENETICS DATA #############################################################
###############################################################################
platform = None
if options.chromosomes:
chrs = import_chromosomes(options.chromosomes)
chr_map = {}
for _chr in chrs:
print 'chr', _chr['name']
_chr = store.create_entity('Chromosome', **_chr)
chr_map.setdefault(_chr['name'], _chr.eid)
store.flush()
if options.genes:
genes = import_genes(options.chromosomes, options.genes)
for gene in genes:
print 'gene', gene['name'], gene['chromosome']
gene['chromosome'] = chr_map[gene['chromosome']]
gene = store.create_entity('Gene', **gene)
store.flush()
if options.snps:
snps = import_snps(options.chromosomes, options.snps)
snp_eids = []
for ind, snp in enumerate(snps):
print 'snp', snp['rs_id']
snp['chromosome'] = chr_map[snp['chromosome']]
import sys
import os.path as osp
import glob
import nibabel as nb
from cubicweb.dataimport import SQLGenObjectStore as Store
from cubes.brainomics.importers.helpers import get_image_info
if __name__ == '__main__':
base_path = osp.abspath(sys.argv[4])
store = Store(session)
global_study = store.create_entity('Study', data_filepath=unicode(base_path), name = u'mindboggle',
description=u'''The Mindboggle-101 dataset includes manually labeled anatomical regions for 101 healthy subjects. The manually edited cortical labels follow sulcus landmarks according to the Desikan-Killiany-Tourville (DKT) protocol. See http://www.frontiersin.org/Brain_Imaging_Methods/10.3389/fnins.2012.00171/full “101 labeled brain images and a consistent human cortical labeling protocol”
Arno Klein, Jason Tourville. Frontiers in Brain Imaging Methods. 6:171. DOI: 10.3389/fnins.2012.00171
and http://mindboggle.info/data.html''')
for study_path in ('Extra-18_volumes', 'MMRR-21_volumes', 'NKI-RS-22_volume',
'NKI-TRT-20_volumes', 'OASIS-TRT-20_volumes'):
full_study_path = osp.join(base_path, study_path)
if not osp.exists(full_study_path):
print '%s does not exist, skip it' % full_study_path
continue
# Create study
count_subject = 0
study = store.create_entity('Study', data_filepath=unicode(full_study_path),
name = unicode(study_path))
for subject_path in glob.iglob(osp.join(full_study_path,'*')):
subject_id = subject_path.split('/')[-1]
print '--->', subject_id
subject = store.create_entity('Subject', identifier=unicode(subject_id),
import sys
import os.path as osp
import glob
import nibabel as nb
from cubicweb.dataimport import SQLGenObjectStore as Store
from cubes.brainomics.importers.helpers import get_image_info
if __name__ == '__main__':
base_path = osp.abspath(sys.argv[4])
store = Store(session)
count_all_subject = 0
global_study = store.create_entity('Study', data_filepath=unicode(base_path), name = u'openfmri',
description=u'''OpenfMRI.org is a project dedicated to the free and open sharing of functional magnetic resonance imaging (fMRI) datasets, including raw data. See http://openfmri.org/''')
# All studies
for study_path in glob.iglob(osp.join(base_path,'*/')):
study_id = study_path[:-1].split('/')[-1]
print '--->', study_id
# XXX use True metadata for studies, P.I. ...
study = store.create_entity('Study', data_filepath=unicode(osp.abspath(study_path)),
name = u'openfmri-%s' % study_id, keywords='openfmri')
# Device
device_path = osp.join(study_path, 'scan_key.txt')
device_eid = None
if osp.exists(device_path):
device = open(device_path).readline()
if device.strip():
device = store.create_entity('Device', name=unicode(device.strip()),
model=unicode(device.strip()))