def main(configuration_json, step_to_start_at=0):
f = open(configuration_json,"r")
configuration = json.load(f)
f.close()
i = 0
for vivo_site in configuration["vivo-sites"]:
base_file_name = vivo_site["name"]
current_date_odbc = time.strftime("%Y-%m-%d", time.localtime())
abox_file_name = base_file_name + "_abox_" + current_date_odbc + ".nt"
tbox_file_name = base_file_name + "_tbox_" + current_date_odbc + ".nt"
vivo_site["abox_file_name"] = abox_file_name
vivo_site["tbox_file_name"] = tbox_file_name
if step_to_start_at == 0:
print("Dumping the ontology from '%s' to '%s'" % (vivo_site["site"], os.path.abspath(tbox_file_name)))
extract_rdf_data_from_vivo_site.main(vivo_site["site"], vivo_site["username"], vivo_site["password"],tbox="TBOX", file_name=tbox_file_name, abox=None)
print("Dumping instance data from '%s' to '%s'" % (vivo_site["site"],os.path.abspath(abox_file_name)))
extract_rdf_data_from_vivo_site.main(vivo_site["site"], vivo_site["username"], vivo_site["password"],abox="ABOX", file_name=abox_file_name, tbox=None)
umls_alignment_file_name = abox_file_name + ".umls.nt"
vivo_site["umls_alignment_file_name"] = umls_alignment_file_name
if step_to_start_at <= 1:
print("Aligning research subject area phrases to the UMLS")
umls_alignment.main(abox_file_name, umls_alignment_file_name)
if step_to_start_at <= 2:
print("Building free text index for rdfs:label")
free_text_indices = FreeTextTriples.main(abox_file_name)
else:
free_text_indices = glob.glob(abox_file_name + ".http*")
vivo_site["free_text_indices"] = free_text_indices
i += 1
if step_to_start_at <= 3:
print("Getting CUIS for articles")
pmid_to_cuis.main(abox_file_name, abox_file_name + "." + "pmid2cuis.nt")
else:
pass
vivo_site["pmid2cuis"] = abox_file_name + "." + "pmid2cuis.nt"
pprint.pprint(configuration)
__author__ = 'janos'
import sys
import re
import FreeTextTriples as ftt
if __name__ == "__main__":
if len(sys.argv) >= 3:
ntriples_to_align = sys.argv[1]
alignment_source = sys.argv[2]
ftt.align_ntriples(ntriples_to_align, alignment_source)
if len(sys.argv) > 3:
number_of_words_to_split = 5
number = re.compile("[0-9]+")
properties = []
for arg in sys.argv[3:]:
if number.match(arg):
number_of_words_to_split = int(arg)
else:
properties.append(arg)
if len(properties) == 0:
ftt.align_ntriples(ntriples_to_align, alignment_source, number_of_words_to_split)
else:
ftt.align_ntriples(ntriples_to_align, alignment_source, properties, number_of_words=number_of_words_to_split)
"""
Generates a free text index from an ntriples file.
"""
__author__ = 'Janos G. Hajagos'
import FreeTextTriples
import sys
if __name__ == "__main__":
if len(sys.argv) == 1:
print("""Usage:
python generate_free_text_triples.py reach.nt 'http://www.w3.org/2008/05/skos#prefLabel'""")
else:
if len(sys.argv) == 2:
FreeTextTriples.main(sys.argv[1])
else:
FreeTextTriples.main(sys.argv[1], sys.argv[2:])
__author__ = 'janos'
import sys
import re
import FreeTextTriples as ftt
if __name__ == "__main__":
if len(sys.argv) >= 3:
ntriples_to_align = sys.argv[1]
alignment_source = sys.argv[2]
ftt.align_ntriples(ntriples_to_align, alignment_source)
if len(sys.argv) > 3:
number_of_words_to_split = 5
number = re.compile("[0-9]+")
properties = []
for arg in sys.argv[3:]:
if number.match(arg):
number_of_words_to_split = int(arg)
else:
properties.append(arg)
if len(properties) == 0:
ftt.align_ntriples(ntriples_to_align, alignment_source,
number_of_words_to_split)
else:
ftt.align_ntriples(ntriples_to_align,
alignment_source,
properties,
number_of_words=number_of_words_to_split)
"""
Generates a free text index from an ntriples file.
"""
__author__ = 'Janos G. Hajagos'
import FreeTextTriples
import sys
if __name__ == "__main__":
if len(sys.argv) == 1:
print("""Usage:
python generate_free_text_triples.py reach.nt 'http://www.w3.org/2008/05/skos#prefLabel'"""
)
else:
if len(sys.argv) == 2:
FreeTextTriples.main(sys.argv[1])
else:
FreeTextTriples.main(sys.argv[1], sys.argv[2:])
def test_align_ntriples(self):
align_ntriples = FreeTextTriples.align_ntriples("article_titles.nt","suis_to_align.nt", ["http://purl.org/dc/elements/1.1/title"] )
