def harmonization_extract_worker(args): filename = args[0] name_queue = args[1] try: tree = extract.parse_xml(filename) harmonized = {} harmonized['spl_set_id'] = extract.extract_set_id(tree) harmonized['id'] = extract.extract_id(tree) harmonized['spl_version'] = extract.extract_version_number(tree) harmonized['is_original_packager'] = extract.is_original_packager(tree) harmonized['ProductNDCs'] = extract.extract_product_ndcs(tree) harmonized['OriginalPackagerProductNDSs'] = \ extract.extract_original_packager_product_ndcs(tree) harmonized['PackageNDCs'] = extract.extract_package_ndcs(tree) name_queue.put(harmonized) except Exception as inst: print filename + 'has a problem' print inst
def _extract(self, filename): ''' Moving this code from the `spl_harmonization` file, since it is the only part of that file that is needed now that we have converted to a map reduction.` ''' try: tree = extract.parse_xml(filename) harmonized = {} harmonized['spl_set_id'] = spl.extract.extract_set_id(tree) harmonized['id'] = spl.extract.extract_id(tree) harmonized['spl_version'] = spl.extract.extract_version_number(tree) harmonized['is_original_packager'] = \ spl.extract.is_original_packager(tree) harmonized['spl_product_ndc'] = spl.extract.extract_product_ndcs(tree) harmonized['original_packager_product_ndc'] = \ spl.extract.extract_original_packager_product_ndcs(tree) harmonized['package_ndc'] = spl.extract.extract_package_ndcs(tree) return harmonized except: logging.warn('ERROR processing SPL data: %s', filename) return None
def harmonization_extract_worker(args): filename = args[0] name_queue = args[1] try: tree = extract.parse_xml(filename) harmonized = {} unii_list = [] intermediate = [] harmonized['unii'] = extract_unii.extract_unii(tree) harmonized['set_id'] = extract_unii.extract_set_id(tree) harmonized['name'] = extract_unii.extract_unii_name(tree) # zipping together two arrays, since they came from the same xpath locations # these are the NUI codes and their respective names # we might be able to get the names from somewhere else and avoid the zip intermediate = zip(extract_unii.extract_unii_other_code(tree), extract_unii.extract_unii_other_name(tree)) header = ['number', 'name'] harmonized['va'] = [dict(zip(header, s)) for s in intermediate] unii_list.append(harmonized) name_queue.put(unii_list) except Exception as inst: print filename + 'has a problem' print inst
def setUp(self): self.tree = extract_spl.parse_xml(os.path.dirname(__file__) + "/data/METHOXSALEN.xml")
def setUp(self): self.tree = extract_spl.parse_xml(os.path.dirname(__file__) + '/data/METHOXSALEN.xml')
def setUp(self): self.tree = extract.parse_xml(data_filename('lipitor-orig.xml'))
def setUp(self): self.tree = extract.parse_xml(data_filename('no-title.xml'))
def setUp(self): self.tree = extract.parse_xml(data_filename('cough.xml'))
def setUp(self): self.tree = extract.parse_xml(data_filename('humira.xml'))