[WIP] API server code health pass

docs/api/covidcast.md

@@ -158,7 +158,7 @@ require knowing when we last confirmed an unchanged value, please get in touch.
 | Field | Description | Type |
 | --- | --- | --- |
 | `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
-| `epidata` | list of results, 1 per geo/time pair | array of objects |
+| `epidata` | list of results, 1 per geo/time filter | array of objects |
 | `epidata[].source` | selected `data_source` | string |
 | `epidata[].signal` | selected `signal` | string |
 | `epidata[].geo_type` | selected `geo_type` | string |

docs/api/covidcast_meta.md

@@ -26,7 +26,7 @@ None required.
 | Field                     | Description                                                         | Type             |
 |---------------------------|---------------------------------------------------------------------|------------------|
 | `result`                  | result code: 1 = success, 2 = too many results, -2 = no results     | integer          |
-| `epidata`                 | list of results, one per name/geo_type pair                         | array of objects |
+| `epidata`                 | list of results, one per name/geo_type filter                       | array of objects |
 | `epidata[].data_source`   | data source                                                         | string           |
 | `epidata[].signal`        | signal name                                                         | string           |
 | `epidata[].time_type`     | temporal resolution of the signal (e.g., `day`, `week`)             | string           |

integrations/server/test_covidcast_endpoints.py

@@ -53,7 +53,7 @@ def test_basic(self):
             self.assertEqual(out["result"], -1)
 
         with self.subTest("simple"):
-            out = self._fetch("/", signal=first.signal_pair(), geo=first.geo_pair(), time="day:*")
+            out = self._fetch("/", signal=first.signal_filter(), geo=first.geo_filter(), time="day:*")
             self.assertEqual(len(out["epidata"]), len(rows))
 
     def test_trend(self):
@@ -66,7 +66,7 @@ def test_trend(self):
         ref = rows[num_rows // 2]
         self._insert_rows(rows)
 
-        out = self._fetch("/trend", signal=first.signal_pair(), geo=first.geo_pair(), date=last.time_value, window="20200401-20201212", basis=ref.time_value)
+        out = self._fetch("/trend", signal=first.signal_filter(), geo=first.geo_filter(), date=last.time_value, window="20200401-20201212", basis=ref.time_value)
 
         self.assertEqual(out["result"], 1)
         self.assertEqual(len(out["epidata"]), 1)
@@ -99,7 +99,7 @@ def test_trendseries(self):
         last = rows[-1]
         self._insert_rows(rows)
 
-        out = self._fetch("/trendseries", signal=first.signal_pair(), geo=first.geo_pair(), date=last.time_value, window="20200401-20200410", basis=1)
+        out = self._fetch("/trendseries", signal=first.signal_filter(), geo=first.geo_filter(), date=last.time_value, window="20200401-20200410", basis=1)
 
         self.assertEqual(out["result"], 1)
         self.assertEqual(len(out["epidata"]), 3)
@@ -167,7 +167,7 @@ def test_correlation(self):
         self._insert_rows(other_rows)
         max_lag = 3
 
-        out = self._fetch("/correlation", reference=first.signal_pair(), others=other.signal_pair(), geo=first.geo_pair(), window="20200401-20201212", lag=max_lag)
+        out = self._fetch("/correlation", reference=first.signal_filter(), others=other.signal_filter(), geo=first.geo_filter(), window="20200401-20201212", lag=max_lag)
         self.assertEqual(out["result"], 1)
         df = pd.DataFrame(out["epidata"])
         self.assertEqual(len(df), max_lag * 2 + 1)  # -...0...+
@@ -191,7 +191,7 @@ def test_csv(self):
 
         response = requests.get(
             f"{BASE_URL}/csv",
-            params=dict(signal=first.signal_pair(), start_day="2020-04-01", end_day="2020-12-12", geo_type=first.geo_type),
+            params=dict(signal=first.signal_filter(), start_day="2020-04-01", end_day="2020-12-12", geo_type=first.geo_type),
         )
         response.raise_for_status()
         out = response.text
@@ -209,7 +209,7 @@ def test_backfill(self):
         self._insert_rows([*issue_0, *issue_1, *last_issue])
         first = issue_0[0]
 
-        out = self._fetch("/backfill", signal=first.signal_pair(), geo=first.geo_pair(), time="day:20200401-20201212", anchor_lag=3)
+        out = self._fetch("/backfill", signal=first.signal_filter(), geo=first.geo_filter(), time="day:20200401-20201212", anchor_lag=3)
         self.assertEqual(out["result"], 1)
         df = pd.DataFrame(out["epidata"])
         self.assertEqual(len(df), 3 * num_rows)  # num issues
@@ -277,17 +277,17 @@ def test_coverage(self):
         first = rows[0]
 
         with self.subTest("default"):
-            out = self._fetch("/coverage", signal=first.signal_pair(), geo_type=first.geo_type, latest=dates[-1], format="json")
+            out = self._fetch("/coverage", signal=first.signal_filter(), geo_type=first.geo_type, latest=dates[-1], format="json")
             self.assertEqual(len(out), len(num_geos_per_date))
             self.assertEqual([o["time_value"] for o in out], dates)
             self.assertEqual([o["count"] for o in out], num_geos_per_date)
 
         with self.subTest("specify window"):
-            out = self._fetch("/coverage", signal=first.signal_pair(), geo_type=first.geo_type, window=f"{dates[0]}-{dates[1]}", format="json")
+            out = self._fetch("/coverage", signal=first.signal_filter(), geo_type=first.geo_type, window=f"{dates[0]}-{dates[1]}", format="json")
             self.assertEqual(len(out), 2)
             self.assertEqual([o["time_value"] for o in out], dates[:2])
             self.assertEqual([o["count"] for o in out], num_geos_per_date[:2])
 
         with self.subTest("invalid geo_type"):
-            out = self._fetch("/coverage", signal=first.signal_pair(), geo_type="doesnt_exist", format="json")
+            out = self._fetch("/coverage", signal=first.signal_filter(), geo_type="doesnt_exist", format="json")
             self.assertEqual(len(out), 0)

src/acquisition/covidcast/covidcast_meta_cache_updater.py

@@ -15,7 +15,7 @@ def get_argument_parser():
 
   parser = argparse.ArgumentParser()
   parser.add_argument("--log_file", help="filename for log output")
-  parser.add_argument("--num_threads", type=int, help="number of worker threads to spawn for processing source/signal pairs")
+  parser.add_argument("--num_threads", type=int, help="number of worker threads to spawn for processing source/signal filters")
   return parser
 
 

src/acquisition/covidcast/database.py

@@ -60,10 +60,10 @@ def __init__(self, source, signal, time_type, geo_type, time_value, geo_value, v
     self.issue = issue
     self.lag = lag
 
-  def signal_pair(self):
+  def signal_filter(self):
     return f"{self.source}:{self.signal}"
 
-  def geo_pair(self):
+  def geo_filter(self):
     return f"{self.geo_type}:{self.geo_value}"
 
 
@@ -551,7 +551,7 @@ def worker():
       try:
         while True:
           (source, signal) = srcsigs.get_nowait() # this will throw the Empty caught below
-          logger.info("starting pair", thread=name, pair=f"({source}, {signal})")
+          logger.info("starting filter", thread=name, filter=f"({source}, {signal})")
           w_cursor.execute(inner_sql, (source, signal))
           with meta_lock:
             meta.extend(list(

src/server/_common.py

@@ -2,15 +2,16 @@
 import time
 
 from flask import Flask, g, request
-from sqlalchemy import event
-from sqlalchemy.engine import Connection
+from sqlalchemy import create_engine, event
+from sqlalchemy.engine import Connection, Engine
 from werkzeug.local import LocalProxy
 
 from .utils.logger import get_structured_logger
-from ._config import SECRET
-from ._db import engine
+from ._config import SECRET, SQLALCHEMY_DATABASE_URI, SQLALCHEMY_ENGINE_OPTIONS
 from ._exceptions import DatabaseErrorException, EpiDataException
 
+engine: Engine = create_engine(SQLALCHEMY_DATABASE_URI, **SQLALCHEMY_ENGINE_OPTIONS)
+
 app = Flask("EpiData", static_url_path="")
 app.config["SECRET"] = SECRET