Merge branch 'main' into krivard/refactor-archiver-tests

Author: krivard

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.2
+current_version = 0.3.6
 commit = True
 message = chore: bump covidcast-indicators to {new_version}
 tag = False

_delphi_utils_python/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.1
+current_version = 0.3.2
 commit = True
 message = chore: bump delphi_utils to {new_version}
 tag = False

_delphi_utils_python/delphi_utils/__init__.py

@@ -15,4 +15,4 @@
 from .nancodes import Nans
 from .weekday import Weekday
 
-__version__ = "0.3.1"
+__version__ = "0.3.2"

_delphi_utils_python/setup.py

@@ -26,7 +26,7 @@
 
 setup(
     name="delphi_utils",
-    version="0.3.1",
+    version="0.3.2",
     description="Shared Utility Functions for Indicators",
     long_description=long_description,
     long_description_content_type="text/markdown",

_delphi_utils_python/tests/test_archive.py

@@ -290,18 +290,13 @@ def test_diff_and_filter_exports(self, tmp_path):
     "aws_secret_access_key": "FAKE_TEST_SECRET_ACCESS_KEY",
 }
 
-@pytest.fixture(scope="function")
-def s3_client():
-    with mock_s3():
-        yield Session(**AWS_CREDENTIALS).client("s3")
-
-
 class TestS3ArchiveDiffer(ArchiveDifferTestlike):
     bucket_name = "test-bucket"
     indicator_prefix = "test"
 
     @mock_s3
-    def test_update_cache(self, tmp_path, s3_client):
+    def test_update_cache(self, tmp_path):
+        s3_client = Session(**AWS_CREDENTIALS).client("s3")
         cache_dir, export_dir = self.set_up(tmp_path)
 
         csv1 = CSVS["mod_2_del_3_add_4"].before
@@ -336,7 +331,8 @@ def test_update_cache(self, tmp_path, s3_client):
         assert set(listdir(cache_dir)) == {"csv1.csv", "csv2.csv"}
 
     @mock_s3
-    def test_archive_exports(self, tmp_path, s3_client):
+    def test_archive_exports(self, tmp_path):
+        s3_client = Session(**AWS_CREDENTIALS).client("s3")
         cache_dir, export_dir = self.set_up(tmp_path)
 
         csv1 = CSVS["mod_2_del_3_add_4"].before
@@ -364,7 +360,8 @@ def test_archive_exports(self, tmp_path, s3_client):
         assert_frame_equal(pd.read_csv(body, dtype=CSV_DTYPES), csv1)
 
     @mock_s3
-    def test_run(self, tmp_path, s3_client):
+    def test_run(self, tmp_path):
+        s3_client = Session(**AWS_CREDENTIALS).client("s3")
         cache_dir, export_dir = self.set_up(tmp_path)
 
         s3_client.create_bucket(Bucket=self.bucket_name)

ansible/templates/dsew_community_profile-params-prod.json.j2

@@ -6,7 +6,13 @@
   "indicator": {
     "input_cache": "./input_cache",
     "reports": "new",
-    "export_signals": ["confirmed covid-19 admissions"]
+    "export_signals": [
+      "confirmed covid-19 admissions",
+      "doses administered",
+      "booster doses administered",
+      "fully vaccinated",
+      "booster dose since"
+    ]
   },
   "validation": {
     "common": {
@@ -28,7 +34,9 @@
         "naats_total_7dav",
         "naats_positivity_7dav",
         "confirmed_admissions_covid_1d_prop_7dav",
-        "confirmed_admissions_covid_1d_7dav"
+        "confirmed_admissions_covid_1d_7dav",
+        "doses_admin_7dav",
+        "booster_doses_admin_7dav"
       ]
     }
   }

ansible/templates/sir_complainsalot-params-prod.json.j2

@@ -92,6 +92,7 @@
         ["smoothed_vaccine_barrier_travel_tried", "msa"], ["smoothed_wvaccine_barrier_travel_tried", "msa"],
         ["smoothed_vaccine_barrier_type_tried", "msa"], ["smoothed_wvaccine_barrier_type_tried", "msa"],
         ["smoothed_try_vaccinate_1m", "hrr"], ["smoothed_wtry_vaccinate_1m", "hrr"],
+        ["smoothed_try_vaccinate_1m", "msa"], ["smoothed_wtry_vaccinate_1m", "msa"],
         ["smoothed_dontneed_reason_dont_spend_time", "hrr"], ["smoothed_wdontneed_reason_dont_spend_time", "hrr"],
         ["smoothed_dontneed_reason_had_covid", "hrr"], ["smoothed_wdontneed_reason_had_covid", "hrr"],
         ["smoothed_dontneed_reason_not_beneficial", "hrr"], ["smoothed_wdontneed_reason_not_beneficial", "hrr"],
@@ -137,7 +138,13 @@
     "quidel": {
       "max_age":6,
       "maintainers": ["U01AP8GSWG3","U01069KCRS7"],
-      "retired-signals": ["raw_pct_negative","smoothed_pct_negative","raw_tests_per_device","smoothed_tests_per_device"]
+      "retired-signals": [
+        "raw_pct_negative","smoothed_pct_negative","raw_tests_per_device","smoothed_tests_per_device",
+        ["covid_ag_raw_pct_positive_age_0_4", "hrr"], ["covid_ag_raw_pct_positive_age_0_4", "msa"],
+        ["covid_ag_raw_pct_positive_age_5_17", "hrr"], ["covid_ag_raw_pct_positive_age_5_17", "msa"],
+        ["covid_ag_raw_pct_positive_age_50_64", "hrr"], ["covid_ag_raw_pct_positive_age_50_64", "msa"],
+        ["covid_ag_raw_pct_positive_age_65plus", "hrr"], ["covid_ag_raw_pct_positive_age_65plus", "msa"]
+      ]
     },
     "nchs-mortality": {
       "max_age":16,

dsew_community_profile/delphi_dsew_community_profile/constants.py

@@ -51,22 +51,50 @@ class Transform:
     "total": {
         "is_rate" : False,
         "api_name": "naats_total_7dav",
-        "make_prop": False
+        "make_prop": False,
+        "cumulative" : False
     },
     "positivity": {
         "is_rate" : True,
         "api_name": "naats_positivity_7dav",
-        "make_prop": False
+        "make_prop": False,
+        "cumulative" : False
     },
     "confirmed covid-19 admissions": {
         "is_rate" : False,
         "api_name": "confirmed_admissions_covid_1d_7dav",
         "make_prop": True,
-        "api_prop_name": "confirmed_admissions_covid_1d_prop_7dav"
+        "api_prop_name": "confirmed_admissions_covid_1d_prop_7dav",
+        "cumulative" : False
+    },
+    "fully vaccinated": {
+        "is_rate" : False,
+        "api_name": "people_full_vaccinated",
+        "make_prop": False,
+        "cumulative" : True
+    },
+    "booster dose since": {
+        "is_rate" : False,
+        "api_name": "people_booster_doses",
+        "make_prop": False,
+        "cumulative" : True
+    },
+    "booster doses administered": {
+        "is_rate" : False,
+        "api_name": "booster_doses_admin_7dav",
+        "make_prop": False,
+        "cumulative" : False
+    },
+    "doses administered": {
+        "is_rate" : False,
+        "api_name": "doses_admin_7dav",
+        "make_prop": False,
+        "cumulative" : False
     }
 }
 
-COUNTS_7D_SIGNALS = {key for key, value in SIGNALS.items() if not value["is_rate"]}
+COUNTS_7D_SIGNALS = {key for key, value in SIGNALS.items() \
+                        if not((value["is_rate"]) or (value["cumulative"]))}
 
 def make_signal_name(key, is_prop=False):
     """Convert a signal key to the corresponding signal name for the API.