Merge branch 'develop' into develop

Author: jlubken

.github/workflows/pythonapp.yml

@@ -43,7 +43,7 @@ jobs:
         python -m pytest
     - name: Run App
       run: |
-        streamlit run src/app.py &
+        PARAMETERS=./defaults/cypress.cfg streamlit run src/app.py &
     - name: Cypress
       uses: cypress-io/github-action@v1
       with:

Dockerfile

@@ -1,16 +1,13 @@
 FROM python:3.7.7-slim-buster
-RUN mkdir /app
+ENV PARAMETERS=./defaults/webapp.cfg
 WORKDIR /app
 COPY README.md .
 COPY setup.cfg .
 COPY setup.py .
-COPY requirements.txt .
-# Creating an empty src dir is a (hopefully) temporary hack to improve layer caching and speed up image builds
-# todo fix once the Pipfile, setup.py, requirements.txt, pyprojec.toml build/dist story is figured out
-RUN mkdir src && pip install -q .
 COPY .streamlit .streamlit
-COPY settings.cfg .
+COPY defaults defaults
 COPY src src
+RUN pip install -q .
 
 CMD ["streamlit", "run", "src/app.py"]
 

Dockerfile.dash

@@ -4,11 +4,14 @@ WORKDIR /code
 
 ARG PORT
 ENV PORT $PORT
+ENV PARAMETERS=./defaults/webapp.cfg
 
-COPY requirements.txt requirements.txt
-RUN pip install -r requirements.txt
-
+COPY README.md .
+COPY setup.py .
+COPY setup.cfg .
 COPY src src 
+COPY defaults ./src/defaults
+RUN pip install -q .
 
 # EXPOSE $PORT 
 

settings.cfg renamed to defaults/cli.cfg

@@ -1,13 +1,14 @@
---current-hospitalized 14
+--current-hospitalized 69
 --doubling-time 4.0
 --hospitalized-days 7
 --hospitalized-rate 0.025
 --icu-days 9
 --icu-rate 0.0075
 --infectious-days 14
---market_share 0.15
---n-days 60
---population 4119405
+--market-share 0.15
+--n-days 100
+--population 3600000
+--recovered 0
 --relative-contact-rate 0.3
 --ventilated-days 10
 --ventilated-rate 0.005

defaults/cypress.cfg

@@ -0,0 +1,15 @@
+--current-hospitalized 69
+--date-first-hospitalized 2020-03-07
+--doubling-time 4.0
+--hospitalized-days 7
+--hospitalized-rate 0.025
+--icu-days 9
+--icu-rate 0.0075
+--infectious-days 14
+--market-share 0.15
+--n-days 100
+--population 3600000
+--recovered 0
+--relative-contact-rate 0.3
+--ventilated-days 10
+--ventilated-rate 0.005

defaults/readme.txt

@@ -0,0 +1,3 @@
+Webapps need default values for both date_first_hosptalized and doubling_time. The ui overrides one of them.
+
+CLI needs either date_first_hospitalized xor doubling_time.

defaults/webapp.cfg

@@ -0,0 +1,15 @@
+--current-hospitalized 69
+--date-first-hospitalized 2020-03-07
+--doubling-time 4.0
+--hospitalized-days 7
+--hospitalized-rate 0.025
+--icu-days 9
+--icu-rate 0.0075
+--infectious-days 14
+--market-share 0.15
+--n-days 100
+--population 3600000
+--recovered 0
+--relative-contact-rate 0.3
+--ventilated-days 10
+--ventilated-rate 0.005

k8s/app.yaml

@@ -27,10 +27,52 @@ spec:
       containers:
       - image: docker.pkg.github.com/codeforphilly/chime/penn-chime:1.1.2
         name: chime
+        env:
+          - name: GAPI_CRED_TYPE
+            valueFrom:
+              secretKeyRef:
+                name: google-api-creds
+                key: type
+          - name: GAPI_CRED_PROJECT_ID
+            valueFrom:
+              secretKeyRef:
+                name: google-api-creds
+                key: project_id
+          - name: GAPI_CRED_PRIVATE_KEY_ID
+            valueFrom:
+              secretKeyRef:
+                name: google-api-creds
+                key: private_key_id
+          - name: GAPI_CRED_PRIVATE_KEY
+            valueFrom:
+              secretKeyRef:
+                name: google-api-creds
+                key: private_key
+          - name: GAPI_CRED_CLIENT_EMAIL
+            valueFrom:
+              secretKeyRef:
+                name: google-api-creds
+                key: client_email
+          - name: GAPI_CRED_CLIENT_ID
+            valueFrom:
+              secretKeyRef:
+                name: google-api-creds
+                key: client_id
+          - name: GAPI_CRED_AUTH_PROVIDER_X509_CERT_URL
+            valueFrom:
+              secretKeyRef:
+                name: google-api-creds
+                key: auth_provider_x509_cert_url
+          - name: GAPI_CRED_CLIENT_X509_CERT_URL
+            valueFrom:
+              secretKeyRef:
+                name: google-api-creds
+                key: client_x509_cert_url
         ports:
         - containerPort: 8000
           name: http
           protocol: TCP
+          
       imagePullSecrets:
       - name: regcred
 

setup.py

@@ -1,6 +1,6 @@
 """Setup file for chime
 """
-__version__ = "1.1.2"  # update VERSION in constants.py
+__version__ = "1.1.3"  # update VERSION in constants.py
 __author__ = "Predictive Healthcare @ Penn Medicine"
 
 from os import path
@@ -33,6 +33,8 @@
         "pyyaml",
         "selenium",
         "streamlit",
+        "gspread",
+        "oauth2client"
     ],
     classifiers=[
         "Programming Language :: Python :: 3",

src/app.py

@@ -1,16 +1,18 @@
 """App."""
 
+import os
+
 import altair as alt  # type: ignore
 import streamlit as st  # type: ignore
 
+from penn_chime.parameters import Parameters
 from penn_chime.presentation import (
     display_download_link,
     display_footer,
     display_header,
     display_sidebar,
     hide_menu_style,
 )
-from penn_chime.settings import get_defaults
 from penn_chime.models import SimSirModel
 from penn_chime.charts import (
     build_admits_chart,
@@ -26,7 +28,7 @@
 # In dev, this should be shown
 st.markdown(hide_menu_style, unsafe_allow_html=True)
 
-d = get_defaults()
+d = Parameters.create(os.environ, [])
 p = display_sidebar(st, d)
 m = SimSirModel(p)
 
@@ -36,7 +38,7 @@
 st.markdown("Projected number of **daily** COVID-19 admissions. \n\n _NOTE: Now including estimates of prior admissions for comparison._")
 admits_chart = build_admits_chart(alt=alt, admits_floor_df=m.admits_floor_df, max_y_axis=p.max_y_axis)
 st.altair_chart(admits_chart, use_container_width=True)
-st.markdown(build_descriptions(chart=admits_chart, labels=p.labels, suffix=" Admissions"))
+st.markdown(build_descriptions(chart=admits_chart, labels=p.labels, prefix="admits_", suffix=" Admissions"))
 display_download_link(
     st,
     filename=f"{p.current_date}_projected_admits.csv",
@@ -58,7 +60,7 @@
 st.markdown("Projected **census** of COVID-19 patients, accounting for arrivals and discharges \n\n _NOTE: Now including estimates of prior census for comparison._")
 census_chart = build_census_chart(alt=alt, census_floor_df=m.census_floor_df, max_y_axis=p.max_y_axis)
 st.altair_chart(census_chart, use_container_width=True)
-st.markdown(build_descriptions(chart=census_chart, labels=p.labels, suffix=" Census"))
+st.markdown(build_descriptions(chart=census_chart, labels=p.labels, prefix="census_", suffix=" Census"))
 display_download_link(
     st,
     filename=f"{p.current_date}_projected_census.csv",