# baseURI = d['baseURI']
# cursor.close()
# Setting by hand again for now (!). Base URI not actually used in ind gen as full IRI taken from KB.
vfb_ind = Brain("http://virtualflybrain.org/reports/", "http://purl.obolibrary.org/obo/fbbt/vfb/" + dataset + ".owl") # This sets entity generation to use baseURI from DB.
# vfb_ind = Brain(baseURI, baseURI + dataset + ".owl") # This sets entity generation to use baseURI from DB.
vfb_image = Brain() # Not specifying base as there seems to be a bug that overides full URL specified when adding individuals. Not ideal!
addOboAnnotationProperties(vfb_ind)
#addOboAnnotationProperties(vfb_image)
addVFBAnnotationProperties(vfb_ind)
#vfb_image.addObjectProperty('http://xmlns.com/foaf/0.1/depicts')
#vfb_image.addClass('http://xmlns.com/foaf/0.1/image')
ont_dict = {}
ont_dict['fbbt'] = load_ont(FBBT)
#ont_dict['fbbt'] = load_ont("http://purl.obolibrary.org/obo/fbbt/%s/fbbt-simple.owl" % fbbt_release_version)
ont_dict['fb_feature'] = load_ont("../../owl/fb_features.owl")
#ont_dict['fb_feature'] = load_ont("http://purl.obolibrary.org/obo/fbbt/vfb/fb_features.owl")
ont_dict['vfb_ind'] = vfb_ind
#ont_dict['vfb_image'] = vfb_image # Commenting for now as problems rolling some image files
gen_ind_by_source(nc, ont_dict, dataset)
#add_facts(cursor=conn.cursor(), ont=vfb_ind, source=dataset) # Before turning this on, need to make sure all inds declared first.
vfb_ind.save("../../owl/" + dataset + ".owl")
#vfb_image.save("../../owl/" + dataset + "_image.owl")
vfb_ind.sleep()
ont_dict['fbbt'].sleep()
ont_dict['fb_feature'].sleep()
# baseURI = ''
# for d in dc:
# baseURI = d['baseURI']
# cursor.close()
vfb_ind = Brain('http://www.virtualflybrain.org/owl/', 'http://www.virtualflybrain.org/owl/' + 'flycircuit_plus.owl') # Adding IRI manually for now.
# Setup ontologies
addOboAnnotationProperties(vfb_ind)
addVFBAnnotationProperties(vfb_ind)
ont_dict = {}
ont_dict['vfb_ind']=vfb_ind
ont_dict['fbbt'] = load_ont(FBBT)
#ont_dict['fbbt'] = load_ont("http://purl.obolibrary.org/obo/fbbt/%s/fbbt-simple.owl" % fbbt_release_version)
ont_dict['fb_feature'] = load_ont("../../owl/fb_features.owl")
#ont_dict['fb_feature'] = load_ont("http://purl.obolibrary.org/obo/fbbt/vfb/fb_features.owl")
# Now run all the functions
gen_ind_by_source(nc, ont_dict, dataset)
gen_ind_by_source(nc, ont_dict, "CostaJefferis_v3") # Add v3 clusters
#add_manual_ann(conn.cursor(), vfb_ind)
add_BN_dom_overlap(nc, vfb_ind, ont_dict['fbbt'])
map_to_clusters(nc, vfb_ind)
# Save output file and clean up
vfb_ind.save("../../owl/flycircuit_plus.owl")
#conn.close()
vfb_ind.sleep()
ont_dict['fbbt'].sleep()
ont_dict['fb_feature'].sleep()
if fb['obstat']:
warnings.warn(fb['fbid'] +" " + fb['uc_name'] + " is obsolete ! Not adding to fb_feature.owl.")
else:
if not fb_feature.knowsClass(fb['fbid']): # Only add class if not obsolete.
fb_feature.addClass(fb['fbid'])
tmp = re.sub("<up\>", "[",fb['uc_name'])
uc_name = re.sub("<\/up>", "]", tmp)
fb_feature.label(fb['fbid'], uc_name)
if re.match('FBtp\d+', fb['fbid']):
fb_feature.subClassOf(fb['fbid'], 'SO_0000796')
elif re.match('FBti\d+', fb['fbid']):
fb_feature.subClassOf(fb['fbid'], 'SO_0001218')
elif re.match('FBgn\d+', fb['fbid']):
fb_feature.subClassOf(fb['fbid'], 'SO_0000704')
elif re.match('FBal\d+', fb['fbid']):
fb_feature.subClassOf(fb['fbid'], 'SO_0001023')
else:
warnings.warn("Ignoring this, as doesn't look like an FB feature: %s." % fb['fbid'])
continue
time.sleep(0.1)
# vfb_ms_conn.close()
fb_cursor.close()
fb_pg_conn.close()
fb_feature.save("../../owl/fb_features.owl") # yuk
fb_feature.sleep()
