Release covidcast-indicators 0.3.5

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.4
+current_version = 0.3.5
 commit = True
 message = chore: bump covidcast-indicators to {new_version}
 tag = False

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

@@ -28,7 +28,9 @@
         "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

@@ -141,7 +141,7 @@
       "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", "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"]
       ]

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.

dsew_community_profile/params.json.template

@@ -11,7 +11,11 @@
     "export_signals": [
       "confirmed covid-19 admissions",
       "total",
-      "positivity"
+      "positivity",
+      "doses administered",
+      "booster doses administered",
+      "fully vaccinated",
+      "booster dose since"
     ]
   },
   "validation": {
@@ -34,7 +38,9 @@
         "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"
       ]
     }
   }

dsew_community_profile/tests/test_pull.py

@@ -16,43 +16,49 @@
 class TestPull:
     def test_DatasetTimes(self):
         examples = [
-            example(DatasetTimes("xyzzy", date(2021, 10, 30), date(2021, 10, 20), date(2021, 10, 22)),
-                    DatasetTimes("xyzzy", date(2021, 10, 30), date(2021, 10, 20), date(2021, 10, 22))),
+            example(DatasetTimes("xyzzy", date(2021, 10, 30), date(2021, 10, 20), date(2021, 10, 22), date(2021, 10, 23), date(2021, 10, 24)),
+                    DatasetTimes("xyzzy", date(2021, 10, 30), date(2021, 10, 20), date(2021, 10, 22), date(2021, 10, 23), date(2021, 10, 24))),
         ]
         for ex in examples:
             assert ex.given == ex.expected, "Equality"
 
-        dt = DatasetTimes("xyzzy", date(2021, 10, 30), date(2021, 10, 20), date(2021, 10, 22))
+        dt = DatasetTimes("xyzzy", date(2021, 10, 30), date(2021, 10, 20), date(2021, 10, 22), date(2021, 10, 23), date(2021, 10, 24))
         assert dt["positivity"] == date(2021, 10, 30), "positivity"
         assert dt["total"] == date(2021, 10, 20), "total"
         assert dt["confirmed covid-19 admissions"] == date(2021, 10, 22), "confirmed covid-19 admissions"
+        assert dt["doses administered"] == date(2021, 10, 24), "doses administered"
+        assert dt["fully vaccinated"] == date(2021, 10, 23), "fully vaccinated"
         with pytest.raises(ValueError):
             dt["xyzzy"]
 
     def test_DatasetTimes_from_header(self):
         examples = [
             example("TESTING: LAST WEEK (October 24-30, Test Volume October 20-26)",
-                    DatasetTimes("last", date(2021, 10, 30), date(2021, 10, 26), None)),
+                    DatasetTimes("last", date(2021, 10, 30), date(2021, 10, 26), None, None, None)),
             example("TESTING: PREVIOUS WEEK (October 24-30, Test Volume October 20-26)",
-                    DatasetTimes("previous", date(2021, 10, 30), date(2021, 10, 26), None)),
+                    DatasetTimes("previous", date(2021, 10, 30), date(2021, 10, 26), None, None, None)),
             example("TESTING: LAST WEEK (October 24-November 30, Test Volume October 20-26)",
-                    DatasetTimes("last", date(2021, 11, 30), date(2021, 10, 26), None)),
+                    DatasetTimes("last", date(2021, 11, 30), date(2021, 10, 26), None, None, None)),
             example("VIRAL (RT-PCR) LAB TESTING: LAST WEEK (June 7-13, Test Volume June 3-9 )",
-                    DatasetTimes("last", date(2021, 6, 13), date(2021, 6, 9), None)),
+                    DatasetTimes("last", date(2021, 6, 13), date(2021, 6, 9), None, None, None)),
             example("VIRAL (RT-PCR) LAB TESTING: LAST WEEK (March 7-13)",
-                    DatasetTimes("last", date(2021, 3, 13), date(2021, 3, 13), None)),
+                    DatasetTimes("last", date(2021, 3, 13), date(2021, 3, 13), None, None, None)),
             example("HOSPITAL UTILIZATION: LAST WEEK (June 2-8)",
-                    DatasetTimes("last", None, None, date(2021, 6, 8))),
+                    DatasetTimes("last", None, None, date(2021, 6, 8), None, None)),
             example("HOSPITAL UTILIZATION: LAST WEEK (June 28-July 8)",
-                    DatasetTimes("last", None, None, date(2021, 7, 8)))
+                    DatasetTimes("last", None, None, date(2021, 7, 8), None, None)),
+            example("COVID-19 VACCINATION DATA: CUMULATIVE (January 25)",
+                    DatasetTimes("", None, None, None, date(2021, 1, 25), None)),
+            example("COVID-19 VACCINATION DATA: LAST WEEK (January 25-31)",
+                    DatasetTimes("last", None, None,  None, None, date(2021, 1, 25)))
         ]
         for ex in examples:
             assert DatasetTimes.from_header(ex.given, date(2021, 12, 31)) == ex.expected, ex.given
 
         # test year boundary
         examples = [
             example("TESTING: LAST WEEK (October 24-30, Test Volume October 20-26)",
-                    DatasetTimes("last", date(2020, 10, 30), date(2020, 10, 26), None)),
+                    DatasetTimes("last", date(2020, 10, 30), date(2020, 10, 26), None, None, None)),
         ]
         for ex in examples:
             assert DatasetTimes.from_header(ex.given, date(2021, 1, 1)) == ex.expected, ex.given
@@ -78,6 +84,12 @@ def test_Dataset_skip_overheader(self):
             example("HOSPITAL UTILIZATION: CHANGE FROM PREVIOUS WEEK",
                     True),
             example("HOSPITAL UTILIZATION: DEMOGRAPHIC DATA",
+                    True),
+            example("COVID-19 VACCINATION DATA: CUMULATIVE (January 25)",
+                    False),
+            example("COVID-19 VACCINATION DATA: LAST WEEK (January 25-31)",
+                    False),
+            example("COVID-19 VACCINATION DATA: DEMOGRAPHIC DATA",
                     True)
         ]
         for ex in examples:

facebook/delphiFacebook/R/responses.R

@@ -648,7 +648,7 @@ create_complete_responses <- function(input_data, county_crosswalk, params)
     "I6_1", "I6_2", "I6_3", "I6_4", "I6_5", "I6_6", "I6_7", "I6_8",
     "I7", "K1", "K2", "V11a", "V12a", "V15a", "V15b", "V16", "V3a", # added in Wave 11
     "V1alt", "B13a", "V15c", "P1", "P2", "P3", "P4", "P5", "P6", # added in experimental Wave 12
-    "C17b", "V17_1", "V17_2", "V2b", "V2c", "V2d", # added in Wave 13
+    "C17b", "V17_month", "V17_year", "V2b", "V2c", "V2d", # added in Wave 13
 
     "raceethnicity", "token", "wave", "w12_treatment", "module", "UserLanguage",
     "zip5" # temporarily; we'll filter by this column later and then drop it before writing

sir_complainsalot/params.json.template

@@ -140,7 +140,7 @@
       "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", "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"]
       ]