def run(self):
# AERS_SGML_2007q4.ZIP has files in sqml
filenames = []
for input in self.input():
sgml_path = '/s[gq]ml/*.SGM'
xml_path = '/[Xx][Mm][Ll]/*.xml'
logging.info('Checking for inputs in: %s', input.path)
filenames.extend(glob.glob(input.path + sgml_path))
filenames.extend(glob.glob(input.path + xml_path))
assert len(filenames) > 0, 'No files to process for quarter? %s' % self.quarter
input_shards = []
for filename in filenames:
if 'test' in filename.lower():
continue
logging.info('Adding input file to pool: %s', filename)
input_shards.append(filename)
report_counts = parallel.mapreduce(
parallel.Collection.from_list(input_shards),
xml_to_json.ExtractSafetyReportsMapper(),
xml_to_json.MergeSafetyReportsReducer(),
self.output().path,
num_shards=16)
combined_counts = collections.defaultdict(int)
for rc in report_counts:
for timestamp, count in rc.iteritems():
combined_counts[timestamp] += count
print '----REPORT COUNTS----'
for timestamp, count in sorted(combined_counts.items()):
print '>> ', timestamp, count
def run(self):
logging.info('Pipelining...')
# AERS_SGML_2007q4.ZIP has files in sqml
sgml_path = '/AERS_SGML_*/s[gq]ml/*.SGM'
xml_path = '/FAERS_XML*/[Xx][Mm][Ll]/*.xml'
filenames = glob.glob(self.input().path + sgml_path)
filenames.extend(glob.glob(self.input().path + xml_path))
input_shards = []
for filename in filenames:
if 'test' in filename.lower():
continue
logging.info('Adding input file to pool: %s', filename)
input_shards.append(filename)
report_counts = parallel.mapreduce(
parallel.Collection.from_list(input_shards),
xml_to_json.ExtractSafetyReportsMapper(),
xml_to_json.MergeSafetyReportsReducer(),
self.output().path, 10)
combined_counts = collections.defaultdict(int)
for rc in report_counts:
for timestamp, count in rc.iteritems():
combined_counts[timestamp] += count
print '----REPORT COUNTS----'
for timestamp, count in sorted(combined_counts.items()):
print '>> ', timestamp, count
