nssp pipeline code

Jenkinsfile

@@ -10,7 +10,7 @@
    - TODO: #527 Get this list automatically from python-ci.yml at runtime.
  */
 
-def indicator_list = ["backfill_corrections", "changehc", "claims_hosp", "google_symptoms", "hhs_hosp", "nchs_mortality", "quidel_covidtest", "sir_complainsalot", "doctor_visits", "nwss_wastewater"]
+def indicator_list = ["backfill_corrections", "changehc", "claims_hosp", "google_symptoms", "hhs_hosp", "nchs_mortality", "quidel_covidtest", "sir_complainsalot", "doctor_visits", "nwss_wastewater", "nssp"]
 def build_package_main = [:]
 def build_package_prod = [:]
 def deploy_staging = [:]

_delphi_utils_python/.pylintrc

@@ -19,4 +19,5 @@ attr-rgx=([a-z_][a-z0-9_]*|[a-zA-Z])
 [DESIGN]
 
 # Don't complain about pytest "unused" arguments.
-ignored-argument-names=(_.*|run_as_module)
+ignored-argument-names=(_.*|run_as_module)
+max-line-length=120

_delphi_utils_python/tests/test_weekday.py

@@ -18,24 +18,10 @@ def test_get_params(self):
 
         result = Weekday.get_params(self.TEST_DATA, "den", ["num"], "date", [1], TEST_LOGGER)
         print(result)
-        expected_result = [
-            -0.05993665,
-            -0.0727396,
-            -0.05618517,
-            0.0343405,
-            0.12534997,
-            0.04561813,
-            -2.27669028,
-            -1.89564374,
-            -1.5695407,
-            -1.29838116,
-            -1.08216513,
-            -0.92089259,
-            -0.81456355,
-            -0.76317802,
-            -0.76673598,
-            -0.82523745,
-        ]
+        expected_result = np.array([[-0.05998306, -0.07269935, -0.05603804,  0.03437098,  0.12530953,
+                0.04554737, -2.27674403, -1.89568887, -1.56957556, -1.29840412,
+                -1.08217453, -0.9208868 , -0.81454092, -0.76313691, -0.76667475,
+                -0.82515445]])
         assert np.allclose(result, expected_result)
 
     def test_calc_adjustment_with_zero_parameters(self):
@@ -71,4 +57,4 @@ def test_calc_adjustment(self):
         # The date and "den" column are unchanged by this function
         assert np.allclose(result["num"].values, expected_nums)
         assert np.allclose(result["den"].values, self.TEST_DATA["den"].values)
-        assert np.array_equal(result["date"].values, self.TEST_DATA["date"].values)
+        assert np.array_equal(result["date"].values, self.TEST_DATA["date"].values)

_template_python/.pylintrc

@@ -19,4 +19,5 @@ attr-rgx=[a-z_][a-z0-9_]*
 [DESIGN]
 
 # Don't complain about pytest "unused" arguments.
-ignored-argument-names=(_.*|run_as_module)
+ignored-argument-names=(_.*|run_as_module)
+max-line-length=120

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

@@ -0,0 +1,29 @@
+{
+  "common": {
+    "export_dir": "/common/covidcast/receiving/nssp",
+    "log_filename": "/var/log/indicators/nssp.log",
+    "log_exceptions": false
+  },
+  "indicator": {
+    "wip_signal": true,
+    "static_file_dir": "./static",
+    "socrata_token": "{{ nssp_token }}"
+  },
+  "validation": {
+    "common": {
+      "data_source": "nssp",
+      "api_credentials": "{{ validation_api_key }}",
+      "span_length": 15,
+      "min_expected_lag": {"all": "7"},
+      "max_expected_lag": {"all": "13"},
+      "dry_run": true,
+      "suppressed_errors": []
+    },
+    "static": {
+      "minimum_sample_size": 0,
+      "missing_se_allowed": true,
+      "missing_sample_size_allowed": true
+    },
+    "dynamic": {}
+  }
+}

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

@@ -50,6 +50,10 @@
     "hhs": {
       "max_age":15,
       "maintainers": []
+    },
+    "nssp": {
+      "max_age":13,
+      "maintainers": []
     }
   }
 }

ansible/vars.yaml

@@ -56,6 +56,9 @@ nchs_mortality_token: "{{ vault_cdc_socrata_token }}"
 # NWSS
 nwss_wastewater_token: "{{ vault_cdc_socrata_token }}"
 
+# nssp
+nssp_token: "{{ vault_cdc_socrata_token }}"
+
 # SirCAL
 sir_complainsalot_api_key: "{{ vault_sir_complainsalot_api_key }}"
 sir_complainsalot_slack_token: "{{ vault_sir_complainsalot_slack_token }}"

changehc/.pylintrc

@@ -21,4 +21,5 @@ attr-rgx=[a-z_][a-z0-9_]*
 [DESIGN]
 
 # Don't complain about pytest "unused" arguments.
-ignored-argument-names=(_.*|run_as_module)
+ignored-argument-names=(_.*|run_as_module)
+max-line-length=120

claims_hosp/.pylintrc

@@ -20,4 +20,5 @@ attr-rgx=[a-z_][a-z0-9_]*
 [DESIGN]
 
 # Don't complain about pytest "unused" arguments.
-ignored-argument-names=(_.*|run_as_module)
+ignored-argument-names=(_.*|run_as_module)
+max-line-length=120

doctor_visits/.pylintrc

@@ -6,3 +6,4 @@ min-public-methods=0
 [MESSAGES CONTROL]
 
 disable=R0801, C0200, C0330, E1101, E0611, E1136, C0114, C0116, C0103, R0913, R0914, R0915, W1401, W1202, W1203, W0702
+max-line-length=120

google_symptoms/.pylintrc

@@ -6,3 +6,4 @@ min-public-methods=1
 [MESSAGES CONTROL]
 
 disable=R0801, E1101, E0611, C0114, C0116, C0103, R0913, R0914, W0702, W0707
+max-line-length=120

hhs_hosp/.pylintrc

@@ -20,3 +20,4 @@ attr-rgx=[a-z_][a-z0-9_]*
 
 # Don't complain about pytest "unused" arguments.
 ignored-argument-names=(_.*|run_as_module)
+max-line-length=120

nchs_mortality/.pylintrc

@@ -21,4 +21,5 @@ attr-rgx=[a-z_][a-z0-9_]*
 [DESIGN]
 
 # Don't complain about pytest "unused" arguments.
-ignored-argument-names=(_.*|run_as_module)
+ignored-argument-names=(_.*|run_as_module)
+max-line-length=120

notebooks/.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")