def __init__(self, field_weightings={}, kill_threshold=None,
match_threshold=None):
self.doctors = db.query(Doctor).all()
self.field_weightings = self.DEFAULT_FIELD_WEIGHTINGS
self.field_weightings.update(field_weightings)
self.match_threshold = match_threshold or self.DEFAULT_MATCH_THRESHOLD
self.kill_threshold = kill_threshold or self.DEFAULT_KILL_THRESHOLD
self.metrics = MetricsRegistry()
guaranteed_metrics(self.metrics)
def main():
global metricsRegistry
metricsRegistry = MetricsRegistry()
#timer = metricsRegistry.timer("post_calls")
#print((str(metricsRegistry._get_timer_metrics("post_calls"))))
loop = uvloop.new_event_loop()
asyncio.set_event_loop(loop)
app = Application()
app.listen(options.port)
asyncio.get_event_loop().run_forever()
def setup_registry(self, registry=None):
""" Setup the Metric Reporter with the given registry(s) """
if not registry:
self.registry = [MetricsRegistry(), ]
else:
if not isinstance(registry, (tuple, list)):
registry = [registry, ]
self.registry = []
for reg in registry:
if not isinstance(reg, (MetricsRegistry, RegexRegistry)):
raise GoblinMetricsException(
"%s is not an instance of pyformance.MetricsRegistry" +
" or pyformance.RegexRegistry")
self.registry.append(reg)
def __init__(self, filename):
self.metrics = MetricsRegistry()
self.field_sets = {
'cpt': set(),
'description': set(),
'price': set(),
'modifier': set(),
'all': set(),
}
print filename.split('.')[0]
self._custom_mapping = CUSTOM_COLUMN_MAPPING.get(filename.split('.')[0])
if filename:
self._input = open(settings.PARSED_FILES_PATH + '/' + filename)
self._output = open(settings.EXTRACTED_FILES_PATH + '/' + '.extracted.'.join(filename.split('.')), 'w')
def fetch_docs(base_path, es_host, es_index, es_query=None, limit=-1):
exp_name = "fetch_docs"
exp_path = f"{base_path}/{exp_name}"
os.makedirs(exp_path, exist_ok=True)
run = mlflow.start_run(experiment_id=get_or_create_experiment_id(exp_name))
docs_path = f"{exp_path}/{run.run_info.run_uuid}"
registry = MetricsRegistry()
mlflow_reporter = MlflowReporter(registry=registry,
active_run=run,
reporting_interval=10)
mlflow_reporter.start()
influx_reporter = InfluxReporter(registry=registry,
reporting_interval=10,
autocreate_database=True)
influx_reporter.start()
try:
mlflow.log_param("docs_path", docs_path)
mlflow.log_param("es_host", es_host)
mlflow.log_param("es_index", es_index)
mlflow.log_param("es_query", es_query)
_write_docs(
_get_docs_scrolled(registry, es_host, es_index, es_query, limit),
docs_path)
influx_reporter.report_now()
mlflow_reporter.report_now()
mlflow.end_run()
except Exception as e:
mlflow.end_run("FAILED")
raise e
finally:
influx_reporter.stop()
mlflow_reporter.stop()
return run
def reset_metrics():
pyformance.set_global_registry(MetricsRegistry())
class RequestHandler(Resource):
# isLeaf is a way of indicate whether the object
# has child nodes
isLeaf = True
# run server then go to: http://localhost:8001/?world_size=n
# n being a number of your choice
def render_GET(self, request):
counter = metricsRegistry.counter("hello_called").inc()
world_size = request.args["world_size"][0]
histogram = metricsRegistry.histogram("world_size")
histogram.add(int(world_size))
request.setResponseCode(200)
return str(metricsRegistry._get_histogram_metrics("world_size"))
if __name__ == '__main__':
# Load up twisted web
global metricsRegistry
metricsRegistry = MetricsRegistry()
try:
resource = RequestHandler()
factory = Site(resource)
reactor.listenTCP(8001, factory)
reactor.run()
except Exception as e:
print(e)
class DedupManager(object):
"""
a wrapper on RecordDeduper:
- memoizes doctors list
- handles variations in field weightings and thresholds
- handles stats reporting
"""
DEFAULT_FIELD_WEIGHTINGS = {
"last_name": [50, 'ratio', 0.7],
"first_name": [10, 'ratio', 0.8],
"middle_name": [20, 'ratio', 0.8],
"birth_year": [10, 'exact', None],
"graduation_year": [10, 'exact', None],
"degree": [5, 'ratio', 0.8],
"school": [3, 'ratio', 0.3],
"street_address": [1, 'ratio', 0.6],
"city": [1, 'ratio', 0.9],
"state_code": [1, 'ratio', 0.8],
"zip_code": [1, 'ratio', 0.8],
"phone_number": [0, 'ratio', 0.3],
}
DEFAULT_MATCH_THRESHOLD = 1
DEFAULT_KILL_THRESHOLD = -5
def __init__(self, field_weightings={}, kill_threshold=None,
match_threshold=None):
self.doctors = db.query(Doctor).all()
self.field_weightings = self.DEFAULT_FIELD_WEIGHTINGS
self.field_weightings.update(field_weightings)
self.match_threshold = match_threshold or self.DEFAULT_MATCH_THRESHOLD
self.kill_threshold = kill_threshold or self.DEFAULT_KILL_THRESHOLD
self.metrics = MetricsRegistry()
guaranteed_metrics(self.metrics)
def dedup(self, record):
record_deduper = RecordDeduper(record, self.doctors, self.field_weightings,
self.kill_threshold, self.match_threshold, self.metrics)
new, doctor = record_deduper.run()
if new: self.doctors.append(doctor)
#METRICS
if record["is_dup"]:
self.metrics.counter('is_dup').inc()
else:
self.metrics.counter('not_dup').inc()
self.metrics.counter('records').inc()
if new:
self.metrics.counter('new').inc()
if record["is_dup"]:
self.metrics.counter('false_negative').inc()
else:
self.metrics.counter('true_negative').inc()
else:
self.metrics.counter('match').inc()
if not record["is_dup"]:
self.metrics.counter('true_positive').inc()
else:
self.metrics.counter('false_positive').inc()
import asyncio
import concurrent.futures
import requests
import os
from pyformance import counter, count_calls
from pyformance.registry import MetricsRegistry
import signalfx.pyformance
registry = MetricsRegistry()
counter = registry.counter("http_requests_sent")
token = ''
if 'SF_TOKEN' not in os.environ:
token = os.environ['SF_TOKEN']
sfx = signalfx.pyformance.SignalFxReporter(token=os.environ['SF_TOKEN'],
reporting_interval=1,
registry=registry)
sfx.start()
async def main():
with concurrent.futures.ThreadPoolExecutor(max_workers=20) as executor:
target = 'http://localhost:8901'
if 'TARGET_ADDRESS' in os.environ:
target = os.environ['TARGET_ADDRESS']
print('Sending data to ..', target)
Send a POST request::
curl -d "foo=bar&bin=baz" http://localhost
"""
from http.server import BaseHTTPRequestHandler, HTTPServer
import socketserver
from pyformance import counter, count_calls #, timer
from pyformance.registry import MetricsRegistry
#from pyformance.reporters import ConsoleReporter
import signalfx.pyformance
import os
import socket
import sys
registry = MetricsRegistry()
counter = registry.counter("http_get_requests")
#timer = registry.timer("time_calls")
default_dimensions = {'containerId': socket.gethostname()}
class S(BaseHTTPRequestHandler):
def _set_headers(self):
self.send_response(200)
self.send_header('Content-type', 'text/html')
self.end_headers()
@count_calls
def do_GET(self):
#with timer.time():
self._set_headers()
class Extractor(object):
def __init__(self, filename):
self.metrics = MetricsRegistry()
self.field_sets = {
'cpt': set(),
'description': set(),
'price': set(),
'modifier': set(),
'all': set(),
}
print filename.split('.')[0]
self._custom_mapping = CUSTOM_COLUMN_MAPPING.get(filename.split('.')[0])
if filename:
self._input = open(settings.PARSED_FILES_PATH + '/' + filename)
self._output = open(settings.EXTRACTED_FILES_PATH + '/' + '.extracted.'.join(filename.split('.')), 'w')
def extract(self):
for line in self._input:
if len(line) < 2:
continue
item = simplejson.loads(line, use_decimal=True)
# add all field names to all field set
self.field_sets['all'].update(item['contents'].keys())
price, descriptions, cpt, modifier = self._process_item(item)
item['output'] = {
'price': price,
'cpt': cpt,
'descriptions': descriptions,
'modifier': modifier
}
self._output.write(simplejson.dumps(item, use_decimal=True) + '\n')
# Write item metrics
self.metrics.counter('lines').inc()
if price:
self.metrics.counter('prices').inc()
self.field_sets['price'].add(price.keys()[0])
if cpt:
self.metrics.counter('cpts').inc()
self.field_sets['cpt'].add(cpt.keys()[0])
if modifier:
self.metrics.counter('modifiers').inc()
self.field_sets['modifier'].add(modifier.keys()[0])
if descriptions:
self.metrics.counter('descriptions').inc()
self.field_sets['description'].update([d.keys()[0] for d in descriptions])
if cpt and price:
self.metrics.counter('coded_lines').inc()
GLOBAL_METRICS.counter('coded_lines').inc()
if descriptions and price:
self.metrics.counter('desc_lines').inc()
GLOBAL_METRICS.counter('desc_lines').inc()
GLOBAL_METRICS.counter('lines').inc()
GLOBAL_METRICS.counter('hospitals').inc()
if self.metrics.counter('cpts').get_count() > 500:
GLOBAL_METRICS.counter('500_hosp').inc()
def _process_item(self, item):
contents = dict([(k,v) for k,v in item['contents'].items() if v or v == 0])
price = self._find_price(contents)
descriptions = self._find_descriptions(contents)
cpt = self._find_cpt(contents, descriptions)
modifier = self._find_modifier(contents, cpt)
return (price, descriptions, cpt, modifier)
def _find_price(self, contents):
if self._custom_mapping and self._custom_mapping['price']:
return dict((k, v) for k, v in contents.iteritems() if k == self._custom_mapping['price'])
else:
matches = []
for column, value in contents.iteritems():
new = self._is_price(column, value)
if new:
matches.append(new)
if not matches:
return None
elif len(matches) == 1:
return matches[0]
else:
return self._resolve_multiple_price_matches(matches)
def _resolve_multiple_price_matches(self, matches):
if all([match.values()[0] == 0 for match in matches]):
return matches[0]
matches = [match for match in matches if match.values()[0] > 0]
if len(matches) == 1:
return matches[0]
price_only = [match for match in matches if 'price' in match.keys()[0].lower()]
if price_only:
matches = price_only
if len(matches) == 1:
return matches[0]
return sorted(matches, key=lambda d: d.values()[0])[-1]
def _is_price(self, column, value):
# check column
if not any([re.search(regex, column, re.I) for regex in PRICE_REGEXES]):
return False
if any([re.search(regex, column, re.I) for regex in PRICE_REGEXES_NEG + TRASH]):
return False
# check and clean value
search = re.findall(r'\b(\d[\d\.]{0,9})\b', unicode(value), re.I)
if search:
fl = float(search[0])
if fl < 500000:
return {column: fl}
else:
return False
else:
return False
def _find_descriptions(self, contents):
matches = []
for column, value in contents.iteritems():
new = self._is_description(column, value)
if new:
matches.append(new)
return matches
def _is_description(self, column, value):
# check column
if not any([re.search(regex, column, re.I) for regex in DESC_REGEXES]):
return False
if any([re.search(regex, column, re.I) for regex in DESC_REGEXES_NEG + TRASH]):
return False
# check and clean value
if not re.search(r'^\s*[\w\.\$]+\s*$', unicode(value)):
return {column: value}
else:
return False
def _find_cpt(self, contents, descriptions):
if self._custom_mapping and self._custom_mapping['cpt']:
return dict((k, v) for k, v in contents.iteritems() if k == self._custom_mapping['cpt'])
good_columns = [column for column in contents.keys() if self._is_cpt_column(column)]
if len(good_columns) > 1:
good_columns = [column for column in good_columns if re.search('cpt|hcpcs', column, re.I)]
matches = []
for column in good_columns:
clean_value = self._get_cpt_value(contents[column])
if clean_value:
matches.append({column: clean_value})
if len(matches) > 1:
matches = matches[:1]
if not matches:
matches.extend(self._cpt_from_descriptions(descriptions))
return matches and matches[0] or None
def _is_cpt_column(self, column):
if not any([re.search(regex, column, re.I) for regex in CPT_REGEXES]):
return False
elif any([re.search(regex, column, re.I) for regex in CPT_REGEXES_NEG + TRASH]):
return False
else:
return True
def _get_cpt_value(self, value):
search = re.findall(r'\b((?:\w\d{3}\w)(?:[- ]\w\w)*)\b', unicode(value), re.UNICODE)
if search and search[0][:5] in CPT_CODES_LIST:
return search[0]
else:
return False
def _cpt_from_descriptions(self, descriptions):
matches = []
for desc_dict in descriptions:
column, desc = desc_dict.items()[0]
cpts = re.findall('cpt.{0,7}(\w\d{3}\w)', unicode(desc), re.I)
if cpts:
matches.append({'From desc: ' + column: cpts[0]})
return matches
def _find_modifier(self, contents, cpt):
matches = []
for column, value in contents.iteritems():
new = self._is_modifier(column, value)
if new:
matches.append(new)
if not matches and cpt:
from_cpt = self._modifier_from_cpt(cpt)
from_cpt and matches.append(from_cpt)
if len(matches) > 1:
raise Exception('Found multiple modifiers %s: %s' % (contents, matches))
return matches and matches[0] or None
def _is_modifier(self, column, value):
# check column
if not any([re.search(regex, column, re.I) for regex in MODIFIER_REGEXES]):
return False
if any([re.search(regex, column, re.I) for regex in MODIFIER_REGEXES_NEG + TRASH]):
return False
# check and clean value
search = re.findall(r'\b(?:\w\d{3}\w)[- ](\w\w)\b', unicode(value), re.U)
if search and search[0] in ['22', '23', '24', '25', '26', '32', '33', '47', '50', '51', '52', '53', '54', '55', '56', '57', '58', '59', '62', '63', '66', '76', '77', '78', '79', '80', '81', '82', '90', '91', '92', '99', 'P1', 'P2', 'P3', 'P4', 'P5', 'P6', '25', '27', '50', '52', '58', '59', '73', '74', '76', '77', '78', '79', '91', 'E1', 'E2', 'E3', 'E4', 'F1', 'F2', 'F4', 'F5', 'F6', 'F7', 'F8', 'F9', 'FA', 'GG', 'GH', 'LC', 'LD', 'LT', 'QM', 'QN', 'RC', 'RT', 'T1', 'T2', 'T4', 'T5', 'T6', 'T7', 'T8', 'T9','TA']:
return {column: search[0]}
else:
return False
def _modifier_from_cpt(self, cpt):
column, value = cpt.items()[0]
search = re.findall(r'\b(?:\w\d{3}\w)-(\w\w)\b', unicode(value), re.U)
if search:
return {'From cpt: ' + column: search[0]}
else:
return None
