type hints work again; organize imports

Organize imports by stdlib, 3rd party, 1st party per PEP8.

csv_load.py

@@ -1,10 +1,13 @@
 from collections import defaultdict
 from csv import DictReader
 from datetime import datetime
+from typing import Dict
+
+from sqlalchemy import func, MetaData, Table, Column  # type: ignore
+from sqlalchemy.types import String  # type: ignore
+
 from etl_tasks import DBAccessTask
 from param_val import StrParam, IntParam
-from sqlalchemy import func, MetaData, Table, Column
-from sqlalchemy.types import String
 
 import logging
 import sqlalchemy as sqla
@@ -34,17 +37,18 @@ def run(self) -> None:
         self.setStatus()
 
     def load(self) -> None:
-        def sz(l, chunk=16):
+        def sz(l: int, chunk: int=16) -> int:
             return max(chunk, chunk * ((l + chunk - 1) // chunk))
 
         db = self._dbtarget().engine
         schema = MetaData()
         l = list()
 
-        with open(self.csvname) as fin:
+        with open(self.csvname) as fin:  # ISSUE: ambient
             dr = DictReader(fin)
 
-            mcl = defaultdict(int)
+            Dict  # for tools that don't see type: comments.
+            mcl = defaultdict(int)  # type: Dict[str, int]
             for row in dr:
                 l.append(row)
                 for col in dr.fieldnames:

eventlog.py

@@ -74,7 +74,8 @@ def __init__(self, logger: logging.Logger, event: JSONObject,
         List  # let flake8 know we're using it
 
     def __repr__(self) -> str:
-        return '%s(%s, %s)' % (self.__class__.__name__, self.name, self.event)
+        # typeshed doesn't know that LoggerAdapter has .name?
+        return '%s(%s, %s)' % (self.__class__.__name__, self.name, self.event)  # type: ignore
 
     def process(self, msg: str, kwargs: KWArgs) -> Tuple[str, KWArgs]:
         extra = dict(kwargs.get('extra', {}),

i2p_tasks.py

@@ -1,14 +1,17 @@
 """i2p_tasks -- Luigi CDM task support.
 """
 
+from typing import List
+
+import luigi
+from sqlalchemy.engine import RowProxy
+from sqlalchemy.exc import DatabaseError
+
 from csv_load import LoadCSV
 from etl_tasks import SqlScriptTask
 from param_val import IntParam
 from script_lib import Script
-from sql_syntax import Environment
-from sqlalchemy.engine import RowProxy
-from sqlalchemy.exc import DatabaseError
-from typing import List
+from sql_syntax import Environment, Params
 
 
 class CDMScriptTask(SqlScriptTask):
@@ -24,63 +27,63 @@ def variables(self) -> Environment:
 class condition(CDMScriptTask):
     script = Script.condition
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [encounter()]
 
 
 class death(CDMScriptTask):
     script = Script.death
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [demographic()]
 
 
 class death_cause(CDMScriptTask):
     script = Script.death_cause
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [pcornet_init()]
 
 
 class demographic(CDMScriptTask):
     script = Script.demographic
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [pcornet_init()]
 
 
 class diagnosis(CDMScriptTask):
     script = Script.diagnosis
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [encounter()]
 
 
 class dispensing(CDMScriptTask):
     script = Script.dispensing
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [encounter()]
 
 
 class encounter(CDMScriptTask):
     script = Script.encounter
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [demographic()]
 
 
 class enrollment(CDMScriptTask):
     script = Script.enrollment
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [pcornet_init()]
 
 
 class harvest(CDMScriptTask):
     script = Script.harvest
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [condition(), death(), death_cause(), diagnosis(), dispensing(), enrollment(),
                 lab_result_cm(), med_admin(), obs_clin(), obs_gen(), pcornet_trial(),
                 prescribing(), pro_cm(), procedures(), provider(), vital()]
@@ -89,14 +92,14 @@ def requires(self):
 class lab_result_cm(CDMScriptTask):
     script = Script.lab_result_cm
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [encounter()]
 
 
 class med_admin(CDMScriptTask):
     script = Script.med_admin
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [pcornet_init()]
 
 
@@ -126,7 +129,8 @@ def results(self) -> List[RowProxy]:
                       chunk_num <= :chunk_max)
                order by chunk_num
              '''
-            params = dict(chunk_max=self.patient_chunk_max, chunk_qty=self.patient_chunks)
+            Params
+            params = dict(chunk_max=self.patient_chunk_max, chunk_qty=self.patient_chunks)  # type: Params
 
             try:
                 return lc.execute(q, params=params).fetchall()
@@ -137,42 +141,42 @@ def results(self) -> List[RowProxy]:
 class pcornet_init(CDMScriptTask):
     script = Script.pcornet_init
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [loadLabNormal(), loadHarvestLocal()]
 
 
 class pcornet_loader(CDMScriptTask):
     script = Script.pcornet_loader
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [harvest()]
 
 
 class pcornet_trial(CDMScriptTask):
     script = Script.pcornet_trial
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [pcornet_init()]
 
 
 class prescribing(CDMScriptTask):
     script = Script.prescribing
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [encounter()]
 
 
 class pro_cm(CDMScriptTask):
     script = Script.pro_cm
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [pcornet_init()]
 
 
 class procedures(CDMScriptTask):
     script = Script.procedures
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [encounter()]
 
 
@@ -183,7 +187,7 @@ class provider(CDMScriptTask):
 class vital(CDMScriptTask):
     script = Script.vital
 
-    def requires(self):
+    def requires(self) -> List[luigi.Task]:
         return [encounter()]