API server code health pass - misc. refactors

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
 

src/server/_params.py

@@ -7,7 +7,7 @@
 
 
 from ._exceptions import ValidationFailedException
-from .utils import days_in_range, weeks_in_range, guess_time_value_is_day, guess_time_value_is_week, TimeValues, days_to_ranges, weeks_to_ranges
+from .utils import days_in_range, weeks_in_range, guess_time_value_is_day, guess_time_value_is_week, IntRange, TimeValues, days_to_ranges, weeks_to_ranges
 
 
 def _parse_common_multi_arg(key: str) -> List[Tuple[str, Union[bool, Sequence[str]]]]:
@@ -140,7 +140,7 @@ def to_ranges(self):
         return TimePair(self.time_type, days_to_ranges(self.time_values))
 
 
-def _verify_range(start: int, end: int) -> Union[int, Tuple[int, int]]:
+def _verify_range(start: int, end: int) -> IntRange:
     if start == end:
         # the first and last numbers are the same, just treat it as a singe value
         return start
@@ -151,7 +151,7 @@ def _verify_range(start: int, end: int) -> Union[int, Tuple[int, int]]:
     raise ValidationFailedException(f"the given range {start}-{end} is inverted")
 
 
-def parse_week_value(time_value: str) -> Union[int, Tuple[int, int]]:
+def parse_week_value(time_value: str) -> IntRange:
     count_dashes = time_value.count("-")
     msg = f"{time_value} does not match a known format YYYYWW or YYYYWW-YYYYWW"
 
@@ -171,7 +171,7 @@ def parse_week_value(time_value: str) -> Union[int, Tuple[int, int]]:
     raise ValidationFailedException(msg)
 
 
-def parse_day_value(time_value: str) -> Union[int, Tuple[int, int]]:
+def parse_day_value(time_value: str) -> IntRange:
     count_dashes = time_value.count("-")
     msg = f"{time_value} does not match a known format YYYYMMDD, YYYY-MM-DD, YYYYMMDD-YYYYMMDD, or YYYY-MM-DD--YYYY-MM-DD"
 

src/server/_query.py

@@ -20,7 +20,7 @@
 from ._exceptions import DatabaseErrorException
 from ._validate import extract_strings
 from ._params import GeoPair, SourceSignalPair, TimePair
-from .utils import time_values_to_ranges, TimeValues
+from .utils import time_values_to_ranges, IntRange, TimeValues
 
 
 def date_string(value: int) -> str:
@@ -34,7 +34,7 @@ def date_string(value: int) -> str:
 
 def to_condition(
     field: str,
-    value: Union[str, Tuple[int, int], int],
+    value: Union[str, IntRange],
     param_key: str,
     params: Dict[str, Any],
     formatter=lambda x: x,
@@ -50,7 +50,7 @@ def to_condition(
 
 def filter_values(
     field: str,
-    values: Optional[Sequence[Union[str, Tuple[int, int], int]]],
+    values: Optional[Sequence[Union[str, IntRange]]],
     param_key: str,
     params: Dict[str, Any],
     formatter=lambda x: x,
@@ -75,7 +75,7 @@ def filter_strings(
 
 def filter_integers(
     field: str,
-    values: Optional[Sequence[Union[Tuple[int, int], int]]],
+    values: Optional[Sequence[IntRange]],
     param_key: str,
     params: Dict[str, Any],
 ):
@@ -399,7 +399,7 @@ def _fq_field(self, field: str) -> str:
     def where_integers(
         self,
         field: str,
-        values: Optional[Sequence[Union[Tuple[int, int], int]]],
+        values: Optional[Sequence[IntRange]],
         param_key: Optional[str] = None,
     ) -> "QueryBuilder":
         fq_field = self._fq_field(field)
@@ -466,25 +466,41 @@ def where_time_pair(
         )
         return self
 
+    def apply_lag_filter(self, history_table: str, lag: Optional[int]):
+        if lag is not None:
+            self.retable(history_table)
+            # history_table has full spectrum of lag values to search from whereas the latest_table does not
+            self.where(lag=lag)
+        return self
+
+    def apply_issues_filter(self, history_table: str, issues: Optional[TimeValues]):
+        if issues:
+            self.retable(history_table)
+            self.where_integers("issue", issues)
+        return self
+
+    def apply_as_of_filter(self, history_table: str, as_of: Optional[int]):
+        if as_of is not None:
+            self.retable(history_table)
+            sub_condition_asof = "(issue <= :as_of)"
+            self.params["as_of"] = as_of
+            sub_fields = "max(issue) max_issue, time_type, time_value, `source`, `signal`, geo_type, geo_value"
+            sub_group = "time_type, time_value, `source`, `signal`, geo_type, geo_value"
+            alias = self.alias
+            sub_condition = f"x.max_issue = {alias}.issue AND x.time_type = {alias}.time_type AND x.time_value = {alias}.time_value AND x.source = {alias}.source AND x.signal = {alias}.signal AND x.geo_type = {alias}.geo_type AND x.geo_value = {alias}.geo_value"
+            self.subquery = f"JOIN (SELECT {sub_fields} FROM {self.table} WHERE {self.conditions_clause} AND {sub_condition_asof} GROUP BY {sub_group}) x ON {sub_condition}"
+        return self
+
     def set_fields(self, *fields: Iterable[str]) -> "QueryBuilder":
         self.fields = [f"{self.alias}.{field}" for field_list in fields for field in field_list]
         return self
 
-    def set_order(self, *args: str, **kwargs: Union[str, bool]) -> "QueryBuilder":
+    def set_sort_order(self, *args: str):
         """
         sets the order for the given fields (as key word arguments), True = ASC, False = DESC
         """
 
-        def to_asc(v: Union[str, bool]) -> str:
-            if v is True:
-                return "ASC"
-            elif v is False:
-                return "DESC"
-            return cast(str, v)
-
-        args_order = [f"{self.alias}.{k} ASC" for k in args]
-        kw_order = [f"{self.alias}.{k} {to_asc(v)}" for k, v in kwargs.items()]
-        self.order = args_order + kw_order
+        self.order = [f"{self.alias}.{k} ASC" for k in args]
         return self
 
     def with_max_issue(self, *args: str) -> "QueryBuilder":

src/server/_validate.py

@@ -3,7 +3,7 @@
 from flask import request
 
 from ._exceptions import UnAuthenticatedException, ValidationFailedException
-from .utils import TimeValues
+from .utils import IntRange, TimeValues
 
 
 def resolve_auth_token() -> Optional[str]:
@@ -84,9 +84,6 @@ def extract_strings(key: Union[str, Sequence[str]]) -> Optional[List[str]]:
     return [v for vs in s for v in vs.split(",")]
 
 
-IntRange = Union[Tuple[int, int], int]
-
-
 def extract_integer(key: Union[str, Sequence[str]]) -> Optional[int]:
     s = _extract_value(key)
     if not s:

src/server/endpoints/covid_hosp_facility.py

@@ -139,7 +139,7 @@ def handle():
     q.set_fields(fields_string, fields_int, fields_float)
 
     # basic query info
-    q.set_order("collection_week", "hospital_pk", "publication_date")
+    q.set_sort_order("collection_week", "hospital_pk", "publication_date")
 
     # build the filter
     q.where_integers("collection_week", collection_weeks)

src/server/endpoints/covid_hosp_facility_lookup.py

@@ -33,7 +33,7 @@ def handle():
         ]
     )
     # basic query info
-    q.set_order("hospital_pk")
+    q.set_sort_order("hospital_pk")
     # build the filter
     # these are all fast because the table has indexes on each of these fields
     if state:

src/server/endpoints/covid_hosp_state_timeseries.py

@@ -145,7 +145,7 @@ def handle():
     ]
 
     q.set_fields(fields_string, fields_int, fields_float)
-    q.set_order("date", "state", "issue")
+    q.set_sort_order("date", "state", "issue")
 
     # build the filter
     q.where_integers("date", dates)

src/server/endpoints/covidcast.py

@@ -91,28 +91,6 @@ def parse_time_pairs() -> TimePair:
     return parse_time_arg()
 
 
-def _handle_lag_issues_as_of(q: QueryBuilder, issues: Optional[TimeValues] = None, lag: Optional[int] = None, as_of: Optional[int] = None):
-    if issues:
-        q.retable(history_table)
-        q.where_integers("issue", issues)
-    elif lag is not None:
-        q.retable(history_table)
-        # history_table has full spectrum of lag values to search from whereas the latest_table does not
-        q.where(lag=lag)
-    elif as_of is not None:
-        # fetch the most recent issue as of a certain date (not to be confused w/ plain-old "most recent issue"
-        q.retable(history_table)
-        sub_condition_asof = "(issue <= :as_of)"
-        q.params["as_of"] = as_of
-        sub_fields = "max(issue) max_issue, time_type, time_value, `source`, `signal`, geo_type, geo_value"
-        sub_group = "time_type, time_value, `source`, `signal`, geo_type, geo_value"
-        sub_condition = f"x.max_issue = {q.alias}.issue AND x.time_type = {q.alias}.time_type AND x.time_value = {q.alias}.time_value AND x.source = {q.alias}.source AND x.signal = {q.alias}.signal AND x.geo_type = {q.alias}.geo_type AND x.geo_value = {q.alias}.geo_value"
-        q.subquery = f"JOIN (SELECT {sub_fields} FROM {q.table} WHERE {q.conditions_clause} AND {sub_condition_asof} GROUP BY {sub_group}) x ON {sub_condition}"
-    else:
-        # else we are using the (standard/default) `latest_table`, to fetch the most recent issue quickly
-        pass
-
-
 @bp.route("/", methods=("GET", "POST"))
 def handle():
     source_signal_pairs = parse_source_signal_pairs()
@@ -132,11 +110,11 @@ def handle():
     fields_float = ["value", "stderr", "sample_size"]
     is_compatibility = is_compatibility_mode()
     if is_compatibility:
-        q.set_order("signal", "time_value", "geo_value", "issue")
+        q.set_sort_order("signal", "time_value", "geo_value", "issue")
     else:
         # transfer also the new detail columns
         fields_string.extend(["source", "geo_type", "time_type"])
-        q.set_order("source", "signal", "time_type", "time_value", "geo_type", "geo_value", "issue")
+        q.set_sort_order("source", "signal", "time_type", "time_value", "geo_type", "geo_value", "issue")
     q.set_fields(fields_string, fields_int, fields_float)
 
     # basic query info
@@ -147,7 +125,9 @@ def handle():
     q.where_geo_pairs("geo_type", "geo_value", geo_pairs)
     q.where_time_pair("time_type", "time_value", time_pair)
 
-    _handle_lag_issues_as_of(q, issues, lag, as_of)
+    q.apply_issues_filter(history_table, issues)
+    q.apply_lag_filter(history_table, lag)
+    q.apply_as_of_filter(history_table, as_of)
 
     def transform_row(row, proxy):
         if is_compatibility or not alias_mapper or "source" not in row:
@@ -195,15 +175,12 @@ def handle_trend():
     fields_int = ["time_value"]
     fields_float = ["value"]
     q.set_fields(fields_string, fields_int, fields_float)
-    q.set_order("geo_type", "geo_value", "source", "signal", "time_value")
+    q.set_sort_order("geo_type", "geo_value", "source", "signal", "time_value")
 
     q.where_source_signal_pairs("source", "signal", source_signal_pairs)
     q.where_geo_pairs("geo_type", "geo_value", geo_pairs)
     q.where_time_pair("time_type", "time_value", time_window)
 
-    # fetch most recent issue fast
-    _handle_lag_issues_as_of(q, None, None, None)
-
     p = create_printer()
 
     def gen(rows):
@@ -246,15 +223,12 @@ def handle_trendseries():
     fields_int = ["time_value"]
     fields_float = ["value"]
     q.set_fields(fields_string, fields_int, fields_float)
-    q.set_order("geo_type", "geo_value", "source", "signal", "time_value")
+    q.set_sort_order("geo_type", "geo_value", "source", "signal", "time_value")
 
     q.where_source_signal_pairs("source", "signal", source_signal_pairs)
     q.where_geo_pairs("geo_type", "geo_value", geo_pairs)
     q.where_time_pair("time_type", "time_value", time_window)
 
-    # fetch most recent issue fast
-    _handle_lag_issues_as_of(q, None, None, None)
-
     p = create_printer()
 
     shifter = lambda x: shift_day_value(x, -basis_shift)
@@ -303,7 +277,7 @@ def handle_correlation():
     fields_int = ["time_value"]
     fields_float = ["value"]
     q.set_fields(fields_string, fields_int, fields_float)
-    q.set_order("geo_type", "geo_value", "source", "signal", "time_value")
+    q.set_sort_order("geo_type", "geo_value", "source", "signal", "time_value")
 
     q.where_source_signal_pairs(
         "source",
@@ -381,12 +355,12 @@ def handle_export():
     q = QueryBuilder(latest_table, "t")
 
     q.set_fields(["geo_value", "signal", "time_value", "issue", "lag", "value", "stderr", "sample_size", "geo_type", "source"], [], [])
-    q.set_order("time_value", "geo_value")
+    q.set_sort_order("time_value", "geo_value")
     q.where_source_signal_pairs("source", "signal", source_signal_pairs)
     q.where_time_pair("time_type", "time_value", TimePair("day" if is_day else "week", [(start_day, end_day)]))
     q.where_geo_pairs("geo_type", "geo_value", [GeoPair(geo_type, True if geo_values == "*" else geo_values)])
 
-    _handle_lag_issues_as_of(q, None, None, as_of)
+    q.apply_as_of_filter(history_table, as_of)
 
     format_date = time_value_to_iso if is_day else lambda x: time_value_to_week(x).cdcformat()
     # tag as_of in filename, if it was specified
@@ -459,16 +433,13 @@ def handle_backfill():
     fields_int = ["time_value", "issue"]
     fields_float = ["value", "sample_size"]
     # sort by time value and issue asc
-    q.set_order(time_value=True, issue=True)
+    q.set_sort_order("time_value", "issue")
     q.set_fields(fields_string, fields_int, fields_float, ["is_latest_issue"])
 
     q.where_source_signal_pairs("source", "signal", source_signal_pairs)
     q.where_geo_pairs("geo_type", "geo_value", [geo_pair])
     q.where_time_pair("time_type", "time_value", time_pair)
 
-    # no restriction of issues or dates since we want all issues
-    # _handle_lag_issues_as_of(q, issues, lag, as_of)
-
     p = create_printer()
 
     def find_anchor_row(rows: List[Dict[str, Any]], issue: int) -> Optional[Dict[str, Any]]:
@@ -642,9 +613,7 @@ def handle_coverage():
     q.where_source_signal_pairs("source", "signal", source_signal_pairs)
     q.where_time_pair("time_type", "time_value", time_window)
     q.group_by = "c.source, c.signal, c.time_value"
-    q.set_order("source", "signal", "time_value")
-
-    _handle_lag_issues_as_of(q, None, None, None)
+    q.set_sort_order("source", "signal", "time_value")
 
     def transform_row(row, proxy):
         if not alias_mapper or "source" not in row:

src/server/endpoints/covidcast_utils/model.py

@@ -236,11 +236,6 @@ def _load_data_signals(sources: List[DataSource]):
         data_signals_by_key[(source.db_source, d.signal)] = d
 
 
-
-def get_related_signals(signal: DataSignal) -> List[DataSignal]:
-    return [s for s in data_signals if s != signal and s.signal_basename == signal.signal_basename]
-
-
 def count_signal_time_types(source_signals: List[SourceSignalPair]) -> Tuple[int, int]:
     """
     count the number of signals in this query for each time type

src/server/endpoints/dengue_nowcast.py

@@ -22,7 +22,7 @@ def handle():
     fields_float = ["value", "std"]
     q.set_fields(fields_string, fields_int, fields_float)
 
-    q.set_order("epiweek", "location")
+    q.set_sort_order("epiweek", "location")
 
     # build the filter
     q.where_strings("location", locations)

src/server/endpoints/dengue_sensors.py

@@ -26,7 +26,7 @@ def handle():
     fields_float = ["value"]
     q.set_fields(fields_string, fields_int, fields_float)
 
-    q.set_order('epiweek', 'name', 'location')
+    q.set_sort_order('epiweek', 'name', 'location')
 
     q.where_strings('name', names)
     q.where_strings('location', locations)