[JIT]: just-in-time series computations

.github/workflows/ci.yaml

@@ -106,7 +106,8 @@ jobs:
   image:
     needs: build
     # only on main and dev branch
-    if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/dev'
+    #if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/dev'
+    if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/dev' || github.ref == 'refs/heads/jit_computations'
 
     runs-on: ubuntu-latest
     steps:

deploy.json

@@ -32,14 +32,20 @@
       "match": "^.*\\.(py)$",
       "add-header-comment": true
     },
+    {
+      "type": "move",
+      "src": "src/server/utils",
+      "dst": "[[package]]/server/utils/",
+      "match": "^.*\\.(py)$",
+      "add-header-comment": true
+    },
     {
       "type": "move",
       "src": "src/server/endpoints/covidcast_utils",
       "dst": "[[package]]/server/endpoints/covidcast_utils/",
       "match": "^.*\\.(py)$",
       "add-header-comment": true
     },
-
     "// acquisition - fluview",
     {
       "type": "move",

integrations/acquisition/covidcast/test_csv_uploading.py

@@ -213,8 +213,8 @@ def test_uploading(self):
         "time_value": [20200419],
         "signal": [signal_name],
         "direction": [None]})], axis=1).rename(columns=uploader_column_rename)
-      expected_values_df["missing_value"].iloc[0] = Nans.OTHER
-      expected_values_df["missing_sample_size"].iloc[0] = Nans.NOT_MISSING
+      expected_values_df.loc[0, "missing_value"] = Nans.OTHER
+      expected_values_df.loc[0, "missing_sample_size"] = Nans.NOT_MISSING
       expected_values = expected_values_df.to_dict(orient="records")
       expected_response = {'result': 1, 'epidata': self.apply_lag(expected_values), 'message': 'success'}
 

integrations/acquisition/covidcast/test_db.py

@@ -1,10 +1,11 @@
-import unittest
-
 from delphi_utils import Nans
-from delphi.epidata.acquisition.covidcast.database import Database, CovidcastRow, DBLoadStateException
+
+from delphi.epidata.acquisition.covidcast.database import DBLoadStateException
+from delphi.epidata.acquisition.covidcast.covidcast_row import CovidcastRow
 from delphi.epidata.acquisition.covidcast.test_utils import CovidcastBase
 import delphi.operations.secrets as secrets
 
+
 # all the Nans we use here are just one value, so this is a shortcut to it:
 nmv = Nans.NOT_MISSING.value
 
@@ -31,8 +32,8 @@ def _find_matches_for_row(self, row):
 
     def test_insert_or_update_with_nonempty_load_table(self):
         # make rows
-        a_row = self._make_placeholder_row()[0]
-        another_row = self._make_placeholder_row(time_value=self.DEFAULT_TIME_VALUE+1, issue=self.DEFAULT_ISSUE+1)[0]
+        a_row = CovidcastRow(time_value=20200202)
+        another_row = CovidcastRow(time_value=20200203, issue=20200203)
         # insert one
         self._db.insert_or_update_bulk([a_row])
         # put something into the load table
@@ -61,7 +62,7 @@ def test_id_sync(self):
         latest_view = 'epimetric_latest_v'
 
         # add a data point
-        base_row, _ = self._make_placeholder_row()
+        base_row = CovidcastRow()
         self._insert_rows([base_row])
         # ensure the primary keys match in the latest and history tables
         matches = self._find_matches_for_row(base_row)
@@ -71,7 +72,7 @@ def test_id_sync(self):
         old_pk_id = matches[latest_view][pk_column]
 
         # add a reissue for said data point
-        next_row, _ = self._make_placeholder_row()
+        next_row = CovidcastRow()
         next_row.issue += 1
         self._insert_rows([next_row])
         # ensure the new keys also match

integrations/acquisition/covidcast/test_delete_batch.py

@@ -5,13 +5,10 @@
 import unittest
 from os import path
 
-# third party
-import mysql.connector
-
 # first party
-from delphi_utils import Nans
-from delphi.epidata.acquisition.covidcast.database import Database, CovidcastRow
 import delphi.operations.secrets as secrets
+from delphi.epidata.acquisition.covidcast.database import Database
+from delphi.epidata.acquisition.covidcast.covidcast_row import CovidcastRow
 
 # py3tester coverage target (equivalent to `import *`)
 __test_target__ = 'delphi.epidata.acquisition.covidcast.database'

integrations/client/test_delphi_epidata.py

@@ -1,26 +1,28 @@
 """Integration tests for delphi_epidata.py."""
 
 # standard library
-import unittest
 import time
-from unittest.mock import patch, MagicMock
 from json import JSONDecodeError
+from unittest.mock import MagicMock, patch
 
-# third party
-from aiohttp.client_exceptions import ClientResponseError
-import mysql.connector
+# first party
 import pytest
+from aiohttp.client_exceptions import ClientResponseError
 
-# first party
-from delphi_utils import Nans
-from delphi.epidata.client.delphi_epidata import Epidata
-from delphi.epidata.acquisition.covidcast.database import Database, CovidcastRow
+# third party
+import delphi.operations.secrets as secrets
 from delphi.epidata.acquisition.covidcast.covidcast_meta_cache_updater import main as update_covidcast_meta_cache
+from delphi.epidata.acquisition.covidcast.covidcast_row import CovidcastRow
 from delphi.epidata.acquisition.covidcast.test_utils import CovidcastBase
-import delphi.operations.secrets as secrets
+from delphi.epidata.client.delphi_epidata import Epidata
+from delphi_utils import Nans
+
 
 # py3tester coverage target
 __test_target__ = 'delphi.epidata.client.delphi_epidata'
+# all the Nans we use here are just one value, so this is a shortcut to it:
+nmv = Nans.NOT_MISSING.value
+IGNORE_FIELDS = ["id", "direction_updated_timestamp", "value_updated_timestamp", "source", "time_type", "geo_type"]
 
 def fake_epidata_endpoint(func):
   """This can be used as a decorator to enable a bogus Epidata endpoint to return 404 responses."""
@@ -30,9 +32,6 @@ def wrapper(*args):
     Epidata.BASE_URL = 'http://delphi_web_epidata/epidata/api.php'
   return wrapper
 
-# all the Nans we use here are just one value, so this is a shortcut to it:
-nmv = Nans.NOT_MISSING.value
-
 class DelphiEpidataPythonClientTests(CovidcastBase):
   """Tests the Python client."""
 
@@ -54,12 +53,12 @@ def test_covidcast(self):
 
     # insert placeholder data: three issues of one signal, one issue of another
     rows = [
-      self._make_placeholder_row(issue=self.DEFAULT_ISSUE + i, value=i, lag=i)[0]
+      CovidcastRow(issue=20200202 + i, value=i, lag=i)
       for i in range(3)
     ]
     row_latest_issue = rows[-1]
     rows.append(
-      self._make_placeholder_row(signal="sig2")[0]
+      CovidcastRow(signal="sig2")
     )
     self._insert_rows(rows)
 
@@ -70,10 +69,11 @@ def test_covidcast(self):
       )
 
       expected = [
-        self.expected_from_row(row_latest_issue),
-        self.expected_from_row(rows[-1])
+        row_latest_issue.as_dict(ignore_fields=IGNORE_FIELDS),
+        rows[-1].as_dict(ignore_fields=IGNORE_FIELDS)
       ]
 
+      self.assertEqual(response['epidata'], expected)
       # check result
       self.assertEqual(response, {
         'result': 1,
@@ -89,10 +89,10 @@ def test_covidcast(self):
 
       expected = [{
         rows[0].signal: [
-          self.expected_from_row(row_latest_issue, self.DEFAULT_MINUS + ['signal']),
+          row_latest_issue.as_dict(ignore_fields=IGNORE_FIELDS + ['signal']),
         ],
         rows[-1].signal: [
-          self.expected_from_row(rows[-1], self.DEFAULT_MINUS + ['signal']),
+          rows[-1].as_dict(ignore_fields=IGNORE_FIELDS + ['signal']),
         ],
       }]
 
@@ -109,12 +109,12 @@ def test_covidcast(self):
         **self.params_from_row(rows[0])
       )
 
-      expected = self.expected_from_row(row_latest_issue)
+      expected = [row_latest_issue.as_dict(ignore_fields=IGNORE_FIELDS)]
 
       # check result
       self.assertEqual(response_1, {
         'result': 1,
-        'epidata': [expected],
+        'epidata': expected,
         'message': 'success',
       })
 
@@ -124,13 +124,13 @@ def test_covidcast(self):
         **self.params_from_row(rows[0], as_of=rows[1].issue)
       )
 
-      expected = self.expected_from_row(rows[1])
+      expected = [rows[1].as_dict(ignore_fields=IGNORE_FIELDS)]
 
       # check result
       self.maxDiff=None
       self.assertEqual(response_1a, {
         'result': 1,
-        'epidata': [expected],
+        'epidata': expected,
         'message': 'success',
       })
 
@@ -141,8 +141,8 @@ def test_covidcast(self):
       )
 
       expected = [
-        self.expected_from_row(rows[0]),
-        self.expected_from_row(rows[1])
+        rows[0].as_dict(ignore_fields=IGNORE_FIELDS),
+        rows[1].as_dict(ignore_fields=IGNORE_FIELDS)
       ]
 
       # check result
@@ -158,12 +158,12 @@ def test_covidcast(self):
         **self.params_from_row(rows[0], lag=2)
       )
 
-      expected = self.expected_from_row(row_latest_issue)
+      expected = [row_latest_issue.as_dict(ignore_fields=IGNORE_FIELDS)]
 
       # check result
       self.assertDictEqual(response_3, {
           'result': 1,
-          'epidata': [expected],
+          'epidata': expected,
           'message': 'success',
       })
     with self.subTest(name='long request'):
@@ -223,16 +223,16 @@ def test_geo_value(self):
     # insert placeholder data: three counties, three MSAs
     N = 3
     rows = [
-      self._make_placeholder_row(geo_type="county", geo_value=str(i)*5, value=i)[0]
+      CovidcastRow(geo_type="county", geo_value=str(i)*5, value=i)
       for i in range(N)
     ] + [
-      self._make_placeholder_row(geo_type="msa", geo_value=str(i)*5, value=i*10)[0]
+      CovidcastRow(geo_type="msa", geo_value=str(i)*5, value=i*10)
       for i in range(N)
     ]
     self._insert_rows(rows)
 
     counties = [
-      self.expected_from_row(rows[i]) for i in range(N)
+      rows[i].as_dict(ignore_fields=IGNORE_FIELDS) for i in range(N)
     ]
 
     def fetch(geo):
@@ -241,31 +241,31 @@ def fetch(geo):
       )
 
     # test fetch all
-    r = fetch('*')
-    self.assertEqual(r['message'], 'success')
-    self.assertEqual(r['epidata'], counties)
+    request = fetch('*')
+    self.assertEqual(request['message'], 'success')
+    self.assertEqual(request['epidata'], counties)
     # test fetch a specific region
-    r = fetch('11111')
-    self.assertEqual(r['message'], 'success')
-    self.assertEqual(r['epidata'], [counties[1]])
+    request = fetch('11111')
+    self.assertEqual(request['message'], 'success')
+    self.assertEqual(request['epidata'], [counties[1]])
     # test fetch a specific yet not existing region
-    r = fetch('55555')
-    self.assertEqual(r['message'], 'no results')
+    request = fetch('55555')
+    self.assertEqual(request['message'], 'no results')
     # test fetch a multiple regions
-    r = fetch(['11111', '22222'])
-    self.assertEqual(r['message'], 'success')
-    self.assertEqual(r['epidata'], [counties[1], counties[2]])
+    request = fetch(['11111', '22222'])
+    self.assertEqual(request['message'], 'success')
+    self.assertEqual(request['epidata'], [counties[1], counties[2]])
     # test fetch a multiple regions in another variant
-    r = fetch(['00000', '22222'])
-    self.assertEqual(r['message'], 'success')
-    self.assertEqual(r['epidata'], [counties[0], counties[2]])
+    request = fetch(['00000', '22222'])
+    self.assertEqual(request['message'], 'success')
+    self.assertEqual(request['epidata'], [counties[0], counties[2]])
     # test fetch a multiple regions but one is not existing
-    r = fetch(['11111', '55555'])
-    self.assertEqual(r['message'], 'success')
-    self.assertEqual(r['epidata'], [counties[1]])
+    request = fetch(['11111', '55555'])
+    self.assertEqual(request['message'], 'success')
+    self.assertEqual(request['epidata'], [counties[1]])
     # test fetch a multiple regions but specify no region
-    r = fetch([])
-    self.assertEqual(r['message'], 'no results')
+    request = fetch([])
+    self.assertEqual(request['message'], 'no results')
 
   def test_covidcast_meta(self):
     """Test that the covidcast_meta endpoint returns expected data."""
@@ -275,7 +275,7 @@ def test_covidcast_meta(self):
     # 2nd issue: 1 11 21
     # 3rd issue: 2 12 22
     rows = [
-      self._make_placeholder_row(time_value=self.DEFAULT_TIME_VALUE + t, issue=self.DEFAULT_ISSUE + i, value=t*10 + i)[0]
+      CovidcastRow(time_value=2020_02_02 + t, issue=2020_02_02 + i, value=t*10 + i)
       for i in range(3) for t in range(3)
     ]
     self._insert_rows(rows)
@@ -299,14 +299,14 @@ def test_covidcast_meta(self):
       signal=rows[0].signal,
       time_type=rows[0].time_type,
       geo_type=rows[0].geo_type,
-      min_time=self.DEFAULT_TIME_VALUE,
-      max_time=self.DEFAULT_TIME_VALUE + 2,
+      min_time=2020_02_02,
+      max_time=2020_02_02 + 2,
       num_locations=1,
       min_value=2.,
       mean_value=12.,
       max_value=22.,
       stdev_value=8.1649658, # population stdev, not sample, which is 10.
-      max_issue=self.DEFAULT_ISSUE + 2,
+      max_issue=2020_02_02 + 2,
       min_lag=0,
       max_lag=0, # we didn't set lag when inputting data
     )
@@ -322,10 +322,10 @@ def test_async_epidata(self):
     # insert placeholder data: three counties, three MSAs
     N = 3
     rows = [
-      self._make_placeholder_row(geo_type="county", geo_value=str(i)*5, value=i)[0]
+      CovidcastRow(geo_type="county", geo_value=str(i)*5, value=i)
       for i in range(N)
     ] + [
-      self._make_placeholder_row(geo_type="msa", geo_value=str(i)*5, value=i*10)[0]
+      CovidcastRow(geo_type="msa", geo_value=str(i)*5, value=i*10)
       for i in range(N)
     ]
     self._insert_rows(rows)