Merge pull request #692 from cmu-delphi/release/delphi-epidata-0.2.9

Release Delphi Epidata 0.2.9

Author: krivard

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.8
+current_version = 0.2.9
 commit = False
 tag = False
 

src/client/delphi_epidata.R

@@ -15,7 +15,7 @@ Epidata <- (function() {
   # API base url
   BASE_URL <- 'https://delphi.cmu.edu/epidata/api.php'
 
-  client_version <- '0.2.8'
+  client_version <- '0.2.9'
 
   # Helper function to cast values and/or ranges to strings
   .listitem <- function(value) {

src/client/delphi_epidata.js

@@ -22,7 +22,7 @@
   }
 })(this, function (exports, fetchImpl, jQuery) {
   const BASE_URL = "https://delphi.cmu.edu/epidata/";
-  const client_version = "0.2.8";
+  const client_version = "0.2.9";
 
   // Helper function to cast values and/or ranges to strings
   function _listitem(value) {

src/client/packaging/npm/package.json

@@ -2,7 +2,7 @@
   "name": "delphi_epidata",
   "description": "Delphi Epidata API Client",
   "authors": "Delphi Group",
-  "version": "0.2.8",
+  "version": "0.2.9",
   "license": "MIT",
   "homepage": "https://github.com/cmu-delphi/delphi-epidata",
   "bugs": {

src/client/packaging/pypi/delphi_epidata/__init__.py

@@ -1,4 +1,4 @@
 from .delphi_epidata import Epidata
 
 name = 'delphi_epidata'
-__version__ = '0.2.8'
+__version__ = '0.2.9'

src/client/packaging/pypi/setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="delphi_epidata",
-    version="0.2.8",
+    version="0.2.9",
     author="David Farrow",
     author_email="[email protected]",
     description="A programmatic interface to Delphi's Epidata API.",

src/server/_config.py

@@ -5,7 +5,7 @@
 
 load_dotenv()
 
-VERSION = "0.2.8"
+VERSION = "0.2.9"
 
 MAX_RESULTS = int(10e6)
 MAX_COMPATIBILITY_RESULTS = int(3650)

src/server/endpoints/covidcast.py

@@ -193,7 +193,10 @@ def handle_trend():
     _verify_argument_time_type_matches(is_day, daily_signals, weekly_signals)
     basis_time_value = extract_date("basis")
     if basis_time_value is None:
-        basis_time_value = shift_time_value(time_value, -7) if is_day else shift_week_value(time_value, -7)
+        base_shift = extract_integer("basis_shift")
+        if base_shift is None:
+            base_shift = 7
+        basis_time_value = shift_time_value(time_value, -1 * base_shift) if is_day else shift_week_value(time_value, -1 * base_shift)
 
     # build query
     q = QueryBuilder("covidcast", "t")
@@ -241,11 +244,10 @@ def handle_trendseries():
 
     time_window, is_day = parse_day_or_week_range_arg("window")
     _verify_argument_time_type_matches(is_day, daily_signals, weekly_signals)
-    basis_shift = extract_integer("basis")
+    basis_shift = extract_integer(("basis", "basis_shift"))
     if basis_shift is None:
         basis_shift = 7
 
-
     # build query
     q = QueryBuilder("covidcast", "t")
 
@@ -369,7 +371,7 @@ def handle_export():
     daily_signals, weekly_signals = count_signal_time_types(source_signal_pairs)
     source_signal_pairs, alias_mapper = create_source_signal_alias_mapper(source_signal_pairs)
     start_day, is_day = parse_day_or_week_arg("start_day", 202001 if weekly_signals > 0 else 20200401)
-    end_day , is_end_day = parse_day_or_week_arg("end_day", 202020 if weekly_signals > 0 else 20200901)
+    end_day, is_end_day = parse_day_or_week_arg("end_day", 202020 if weekly_signals > 0 else 20200901)
     if is_day != is_end_day:
         raise ValidationFailedException("mixing weeks with day arguments")
     _verify_argument_time_type_matches(is_day, daily_signals, weekly_signals)
@@ -380,7 +382,7 @@ def handle_export():
     if geo_values != "*":
         geo_values = geo_values.split(",")
 
-    as_of, is_as_of_day = parse_day_or_week_arg('as_of') if 'as_of' in request.args else (None, is_day)
+    as_of, is_as_of_day = parse_day_or_week_arg("as_of") if "as_of" in request.args else (None, is_day)
     if is_day != is_as_of_day:
         raise ValidationFailedException("mixing weeks with day arguments")
 
@@ -390,7 +392,7 @@ def handle_export():
     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.where_source_signal_pairs("source", "signal", source_signal_pairs)
-    q.where_time_pairs("time_type", "time_value", [TimePair('day' if is_day else 'week', [(start_day, end_day)])])
+    q.where_time_pairs("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)

src/server/endpoints/covidcast_utils/db_signals.csv

@@ -377,16 +377,42 @@ usa-facts,deaths_cumulative_num,TRUE,deaths_7dav_incidence_prop,FALSE,"Confirmed
 usa-facts,deaths_cumulative_num,TRUE,deaths_cumulative_prop,FALSE,"Confirmed COVID Deaths (Cumulative, per 100k people)",TRUE,"Cumulative confirmed COVID deaths, per 100k people",,day,Date,Value,per100k,late,bad,FALSE,FALSE,TRUE,FALSE,FALSE,
 usa-facts,deaths_cumulative_num,TRUE,deaths_incidence_num,TRUE,Confirmed COVID Deaths (Daily new),TRUE,Daily new confirmed COVID deaths,,day,Date,Value,count,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
 usa-facts,deaths_cumulative_num,TRUE,deaths_incidence_prop,FALSE,"Confirmed COVID Deaths (Daily new, per 100k people)",TRUE,"Daily new confirmed COVID deaths, per 100k people",,day,Date,Value,per100k,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
-nchs-mortality,deaths_covid_incidence_num,FALSE,deaths_covid_incidence_num,FALSE,Confirmed or Presumed COVID Deaths (Weekly new),TRUE,Number of weekly new deaths with confirmed or presumed COVID-19 ,National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm)),week,Week,Value,count,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
-nchs-mortality,deaths_covid_incidence_num,TRUE,deaths_covid_incidence_prop,FALSE,"Confirmed or Presumed COVID Deaths (Weekly new, per 100k people)",TRUE,"Number of weekly new deaths with confirmed or presumed COVID-19, per 100k people",,week,Week,Value,per100k,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
-nchs-mortality,deaths_allcause_incidence_num,FALSE,deaths_allcause_incidence_num,FALSE,All Causes Deaths (Weekly new),TRUE,Number of weekly new deaths from all causes,National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm)),week,Week,Value,count,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
-nchs-mortality,deaths_allcause_incidence_num,TRUE,deaths_allcause_incidence_prop,FALSE,"All Causes Deaths (Weekly new, per 100k people)",TRUE,"Number of weekly new deaths from all causes, per 100k people",,week,Week,Value,per100k,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
-nchs-mortality,deaths_flu_incidence_num,FALSE,deaths_flu_incidence_num,FALSE,Influenza Deaths (Weekly new),TRUE,"Number of weekly new deaths involving Influenza and at least one of (Pneumonia, COVID-19)",National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm)),week,Week,Value,count,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
-nchs-mortality,deaths_flu_incidence_num,TRUE,deaths_flu_incidence_prop,FALSE,"Influenza Deaths (Weekly new, per 100k people)",TRUE,"Number of weekly new deaths involving Influenza and at least one of (Pneumonia, COVID-19), per 100k people",,week,Week,Value,per100k,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
-nchs-mortality,deaths_pneumonia_notflu_incidence_num,FALSE,deaths_pneumonia_notflu_incidence_num,FALSE,Pneumonia excl. Influenza Deaths (Weekly new),TRUE,"Number of weekly new deaths involving Pneumonia, excluding Influenza deaths ",National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm)),week,Week,Value,count,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
-nchs-mortality,deaths_pneumonia_notflu_incidence_num,TRUE,deaths_pneumonia_notflu_incidence_prop,FALSE,"Pneumonia excl. Influenza Deaths (Weekly new, per 100k people)",TRUE,"Number of weekly new deaths involving Pneumonia, excluding Influenza deaths, per 100k people",,week,Week,Value,per100k,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
-nchs-mortality,deaths_covid_and_pneumonia_notflu_incidence_num,FALSE,deaths_covid_and_pneumonia_notflu_incidence_num,FALSE,COVID and Pneumonia excl. Influenza Deaths (Weekly new),TRUE,"Number of weekly new deaths involving COVID-19 and Pneumonia, excluding Influenza ",National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm)),week,Week,Value,count,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
-nchs-mortality,deaths_covid_and_pneumonia_notflu_incidence_num,TRUE,deaths_covid_and_pneumonia_notflu_incidence_prop,FALSE,"COVID and Pneumonia excl. Influenza Deaths (Weekly new, per 100k people)",TRUE,"Number of weekly new deaths involving COVID-19 and Pneumonia, excluding Influenza, per 100k people",,week,Week,Value,per100k,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
-nchs-mortality,deaths_pneumonia_or_flu_or_covid_incidence_num,FALSE,deaths_pneumonia_or_flu_or_covid_incidence_num,FALSE,"COVID, Pneumonia or Influenza Deaths (Weekly new)",TRUE,"Number of weekly new deaths involving Pneumonia, Influenza, or COVID-19 ",National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm)),week,Week,Value,count,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
-nchs-mortality,deaths_pneumonia_or_flu_or_covid_incidence_num,TRUE,deaths_pneumonia_or_flu_or_covid_incidence_prop,FALSE,"COVID, Pneumonia or Influenza Deaths (Weekly new, per 100k people)",TRUE,"Number of weekly new deaths involving Pneumonia, Influenza, or COVID-19, per 100k people",,week,Week,Value,per100k,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
-nchs-mortality,deaths_percent_of_expected,FALSE,deaths_percent_of_expected,FALSE,"Percentage of Expected Deaths (Weekly new, per 100k people)",TRUE,Number of weekly new deaths for all causes in 2020 compared to the average number across the same week in 2017–2019 ,,week,Week,Value,percent,late,neutral,FALSE,FALSE,FALSE,FALSE,FALSE,
+nchs-mortality,deaths_covid_incidence_num,FALSE,deaths_covid_incidence_num,FALSE,Confirmed or Presumed COVID Deaths (Weekly new),TRUE,Number of weekly new deaths with confirmed or presumed COVID-19 ,"{short_description}.
+
+National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm))",week,Week,Value,count,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
+nchs-mortality,deaths_covid_incidence_num,TRUE,deaths_covid_incidence_prop,FALSE,"Confirmed or Presumed COVID Deaths (Weekly new, per 100k people)",TRUE,"Number of weekly new deaths with confirmed or presumed COVID-19, per 100k people","{short_description}.
+
+National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm))",week,Week,Value,per100k,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
+nchs-mortality,deaths_allcause_incidence_num,FALSE,deaths_allcause_incidence_num,FALSE,All Causes Deaths (Weekly new),TRUE,Number of weekly new deaths from all causes,"{short_description}.
+
+National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm))",week,Week,Value,count,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
+nchs-mortality,deaths_allcause_incidence_num,TRUE,deaths_allcause_incidence_prop,FALSE,"All Causes Deaths (Weekly new, per 100k people)",TRUE,"Number of weekly new deaths from all causes, per 100k people","{short_description}.
+
+National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm))",week,Week,Value,per100k,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
+nchs-mortality,deaths_flu_incidence_num,FALSE,deaths_flu_incidence_num,FALSE,Influenza Deaths (Weekly new),TRUE,"Number of weekly new deaths involving Influenza and at least one of (Pneumonia, COVID-19)","{short_description}.
+
+National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm))",week,Week,Value,count,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
+nchs-mortality,deaths_flu_incidence_num,TRUE,deaths_flu_incidence_prop,FALSE,"Influenza Deaths (Weekly new, per 100k people)",TRUE,"Number of weekly new deaths involving Influenza and at least one of (Pneumonia, COVID-19), per 100k people","{short_description}.
+
+National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm))",week,Week,Value,per100k,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
+nchs-mortality,deaths_pneumonia_notflu_incidence_num,FALSE,deaths_pneumonia_notflu_incidence_num,FALSE,Pneumonia excl. Influenza Deaths (Weekly new),TRUE,"Number of weekly new deaths involving Pneumonia, excluding Influenza deaths ","{short_description}.
+
+National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm))",week,Week,Value,count,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
+nchs-mortality,deaths_pneumonia_notflu_incidence_num,TRUE,deaths_pneumonia_notflu_incidence_prop,FALSE,"Pneumonia excl. Influenza Deaths (Weekly new, per 100k people)",TRUE,"Number of weekly new deaths involving Pneumonia, excluding Influenza deaths, per 100k people","{short_description}.
+
+National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm))",week,Week,Value,per100k,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
+nchs-mortality,deaths_covid_and_pneumonia_notflu_incidence_num,FALSE,deaths_covid_and_pneumonia_notflu_incidence_num,FALSE,COVID and Pneumonia excl. Influenza Deaths (Weekly new),TRUE,"Number of weekly new deaths involving COVID-19 and Pneumonia, excluding Influenza ","{short_description}.
+
+National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm))",week,Week,Value,count,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
+nchs-mortality,deaths_covid_and_pneumonia_notflu_incidence_num,TRUE,deaths_covid_and_pneumonia_notflu_incidence_prop,FALSE,"COVID and Pneumonia excl. Influenza Deaths (Weekly new, per 100k people)",TRUE,"Number of weekly new deaths involving COVID-19 and Pneumonia, excluding Influenza, per 100k people","{short_description}.
+
+National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm))",week,Week,Value,per100k,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
+nchs-mortality,deaths_pneumonia_or_flu_or_covid_incidence_num,FALSE,deaths_pneumonia_or_flu_or_covid_incidence_num,FALSE,"COVID, Pneumonia or Influenza Deaths (Weekly new)",TRUE,"Number of weekly new deaths involving Pneumonia, Influenza, or COVID-19 ","{short_description}.
+
+National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm))",week,Week,Value,count,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
+nchs-mortality,deaths_pneumonia_or_flu_or_covid_incidence_num,TRUE,deaths_pneumonia_or_flu_or_covid_incidence_prop,FALSE,"COVID, Pneumonia or Influenza Deaths (Weekly new, per 100k people)",TRUE,"Number of weekly new deaths involving Pneumonia, Influenza, or COVID-19, per 100k people","{short_description}.
+
+National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm))",week,Week,Value,per100k,late,bad,FALSE,FALSE,FALSE,FALSE,FALSE,
+nchs-mortality,deaths_percent_of_expected,FALSE,deaths_percent_of_expected,FALSE,Percentage of Expected Deaths,TRUE,Weekly new deaths for all causes in 2020 as a percentage of the average number across the same week in 2017-2019.,"{short_description}.
+
+National provisional death counts is based on death certificate data received and coded by the National Center for Health Statistics ([NCHS](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm))",week,Week,Value,percent,late,neutral,FALSE,FALSE,FALSE,FALSE,FALSE,