def run(self):
# Read the entire packaging DB in memory for speed.
package_db = parallel.ShardedDB.open(self.input()[0].path).as_dict()
parallel.mapreduce(
parallel.Collection.from_sharded(self.input()[1].path),
mapper=ProductAndPackagingMergingMapper(package_db=package_db),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path,
num_shards=1)
def run(self):
harmonized_db = parallel.ShardedDB.open(self.input()[0].path).as_dict()
json_glob = glob.glob(self.input()[1].path + '/*.json')
parallel.mapreduce(
parallel.Collection.from_glob(json_glob, parallel.JSONLineInput()),
mapper=MaudeAnnotationMapper(harmonized_db=harmonized_db),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path,
num_shards=10,
map_workers=5)
def run(self):
input_dir = self.input().path
for xml_filename in glob.glob('%(input_dir)s/*.xml' % locals()):
parallel.mapreduce(input_collection=parallel.Collection.from_glob(
xml_filename, parallel.XMLDictInput),
mapper=XML2JSONMapper(),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path,
num_shards=1,
map_workers=1)
def run(self):
input_db = self.input()[0].path
harmonized_file = self.input()[1].path
parallel.mapreduce(parallel.Collection.from_sharded(input_db),
mapper=annotate.AnnotateMapper(harmonized_file),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path,
num_shards=4,
map_workers=1)
def run(self):
input_db = self.input()[0].path
harmonized_file = self.input()[1].path
parallel.mapreduce(
parallel.Collection.from_sharded(input_db),
mapper=AnnotateMapper(harmonized_file),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path,
num_shards=1) # TODO: improve the code to avoid having to limit number of shards to one
def run(self):
input_dir = dirname(self.input().path)
for csv_filename in glob.glob('%(input_dir)s/clean-*.csv' % locals()):
parallel.mapreduce(parallel.Collection.from_glob(
csv_filename, parallel.CSVDictLineInput()),
mapper=CSV2JSONMapper(),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path,
num_shards=1,
map_workers=8)
def run(self):
csv2json_db = parallel.ShardedDB.open(self.input()[1].path).as_dict()
parallel.mapreduce(
parallel.Collection.from_glob(self.input()[0].path,
parallel.CSVDictLineInput()),
mapper=RecallDownloaderAndMapper(csv2json_db=csv2json_db),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path,
map_workers=10,
num_shards=10) # Do not hit fda.gov too hard here.
def run(self):
with open(join(EXTRACTED_DIR, 'MarketingStatus_Lookup.txt')) as fin:
rows = (line.split('\t') for line in fin)
doc_lookup = {row[0]: row[1] for row in rows}
parallel.mapreduce(parallel.Collection.from_glob(
join(self.input().path, 'TE.txt'),
parallel.CSVDictLineInput(delimiter='\t')),
mapper=TE2JSONMapper(doc_lookup=doc_lookup),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path)
def run(self):
input_shards = []
input_dir = self.input().path
for xml_filename in glob.glob(input_dir + '/*.xml'):
input_shards.append(xml_filename)
parallel.mapreduce(parallel.Collection.from_list(input_shards),
mapper=XML2JSONMapper(),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path,
num_shards=len(input_shards))
def run(self):
common.shell_cmd('mkdir -p %s', dirname(self.output().path))
input_files = glob.glob(self.input().path + '/*.txt')
parallel.mapreduce(parallel.Collection.from_glob(
input_files,
parallel.CSVDictLineInput(delimiter='|',
quoting=csv.QUOTE_NONE,
escapechar='\\')),
mapper=ClassificationMapper(),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path)
def _run(self):
json_dir = self.input()['data'].path
input_glob = glob.glob(json_dir + '/*.json')
for file_name in input_glob:
logging.info('Running file %s', file_name)
parallel.mapreduce(
parallel.Collection.from_glob(file_name,
parallel.JSONLineInput()),
mapper=index_util.ReloadJSONMapper(config.es_host(),
self.index_name, 'maude'),
reducer=parallel.IdentityReducer(),
output_format=parallel.NullOutput(),
output_prefix='/tmp/loadjson.' + self.index_name)
def test_identity(self):
os.system('rm -rf /tmp/test-identity*')
source_files = ['/tmp/test-identity-%d' % i for i in range(10)]
for f in source_files:
os.system('touch "%s"' % f)
source = parallel.Collection(source_files, parallel.FilenameInput)
parallel.mapreduce(source, parallel.IdentityMapper(),
parallel.IdentityReducer(), '/tmp/test-identity', 2)
results = sorted(list(parallel.ShardedDB.open('/tmp/test-identity/')))
for i in range(10):
key, value = results[i]
assert key == '/tmp/test-identity-%d' % i, results[i]
assert value == ''
def run(self):
input_shards = []
input_dir = self.input().path
for subdir, dirs, files in os.walk(input_dir):
for file in files:
if file.endswith('.xml'):
if not file in NULLIFIED:
input_shards.append(os.path.join(subdir, file))
else:
logging.info("Skipping a nullified case: " + file)
parallel.mapreduce(parallel.Collection.from_list(input_shards),
mapper=XML2JSONMapper(),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path)
def run(self):
applications_db = self.input()[0].path
products_db = self.input()[1].path
applications_docs_db = self.input()[2].path
submissions_db = self.input()[3].path
submissions_property_type_db = self.input()[4].path
marketing_status = self.input()[5].path
te_db = self.input()[6].path
parallel.mapreduce(
parallel.Collection.from_sharded(applications_db),
mapper=MergeAllMapper(applications_db, products_db, applications_docs_db, submissions_db,
submissions_property_type_db, marketing_status, te_db),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path,
map_workers=1,
num_shards=1) # TODO: improve the code to avoid having to limit number of shards to one
def _run(self):
json_dir = self.input()['data'].path
mapper = LoadJSONMapper(config.es_host(),
index_name=self.index_name,
type_name=self.type_name,
docid_key=self.docid_key,
incremental=self.use_checksum)
parallel.mapreduce(parallel.Collection.from_sharded(json_dir),
mapper=mapper,
reducer=parallel.IdentityReducer(),
output_format=parallel.NullOutput(),
map_workers=self.load_json_workers,
output_prefix=config.tmp_dir('%s/load-json' %
self.index_name))
# update metadata index
elasticsearch_requests.update_process_datetime(
config.es_client(), self.index_name,
arrow.utcnow().format('YYYY-MM-DD'))
def run(self):
import sys
import csv
maxInt = sys.maxsize
decrement = True
while decrement:
# decrease the maxInt value by factor 10
# as long as the OverflowError occurs.
decrement = False
try:
csv.field_size_limit(maxInt)
except OverflowError:
maxInt = int(maxInt / 10)
decrement = True
parallel.mapreduce(parallel.Collection.from_glob(
self.input().path, parallel.CSVDictLineInput(delimiter='\t')),
mapper=NDC2JSONMapper(),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path,
num_shards=1)
def run(self):
parallel.mapreduce(parallel.Collection.from_glob(
self.input().path, parallel.CSVDictLineInput()),
mapper=NSDE2JSONMapper(),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path)
def run(self):
mapreduce(Collection.from_sharded(self.input().path),
mapper=Harmonized2OpenFDAMapper(),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path,
num_shards=1)
def run(self):
parallel.mapreduce(
parallel.Collection.from_glob(self.batch, parallel.LineInput),
mapper=SPL2JSONMapper(),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path)
def run(self):
parallel.mapreduce(parallel.Collection.from_glob(
self.input().path, parallel.JSONLineInputUnicode()),
mapper=SubstanceData2JSONMapper(),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path)
def run(self):
parallel.mapreduce(
parallel.Collection.from_sharded(self.input()[1].path),
mapper=UpcMapper(spl_s3_dir=SPL_S3_DIR),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path)
def run(self):
parallel.mapreduce(parallel.Collection.from_sharded(self.input().path),
mapper=CurrentSPLMapper(),
reducer=parallel.IdentityReducer(),
output_prefix=self.output().path)
