Merge pull request #573 from CodeForPhilly/ppe

- Adds Personal Protective Equipment (PPE) Model with downloadable tool

Author: BrianThomasRoss

.github/workflows/pythonapp.yml

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

Dockerfile

@@ -1,4 +1,5 @@
 FROM python:3.7.7-slim-buster
+ENV ASSETS=./defaults/assets/
 ENV PARAMETERS=./defaults/webapp.cfg
 ENV PORT=8000
 WORKDIR /app
@@ -11,4 +12,5 @@ COPY defaults defaults
 COPY src src
 COPY st_app.py st_app.py
 RUN pip install -q .
+
 CMD STREAMLIT_SERVER_PORT=$PORT streamlit run st_app.py

Procfile

@@ -1 +1 @@
-web: PARAMETERS=defaults/webapp.cfg STREAMLIT_SERVER_PORT=$PORT streamlit run st_app.py
+web: PARAMETERS=./defaults/webapp.cfg ASSETS=./defaults/assets STREAMLIT_SERVER_PORT=$PORT streamlit run st_app.py

defaults/assets/PPE_Calculator_for_COVID-19.xlsx

@@ -46,12 +46,14 @@ pip install streamlit
 ## Run the Streamlit Web App
 
 ```bash
+ASSETS=./defaults/assets \
 PARAMETERS=-./defaults/webapp.cfg streamlit run st_app.py
 ```
 
 ## Run the Command Line Interface
 
 ```bash
+ASSETS=./defaults/assets \
 PARAMETERS=./defaults/cli.cfg penn_chime
 ```
 
@@ -66,6 +68,7 @@ penn_chime --help
 If you want a different set of default parameters, you may use your own configuration file.
 
 ```bash
+ASSETS=./defaults/assets \
 PARAMETERS=./defaults/yours.cfg streamlit run st_app.py
 ```
 
@@ -77,7 +80,9 @@ Be sure to include `--mitigation-date` in the file if social distancing was impl
 If you need to run the application on a different port than the default (8000), you can set an environment variable.
 
 ```bash
-STREAMLIT_SERVER_PORT=1234 PARAMETERS=./defaults/webapp.cfg streamlit run st_app.py
+ASSETS=./defaults/assets \
+STREAMLIT_SERVER_PORT=1234 \
+PARAMETERS=./defaults/webapp.cfg streamlit run st_app.py
 ```
 
 ## Project Layout

defaults/assets/PPE_Screenshot.jpg

@@ -2,4 +2,4 @@ build:
   docker:
     web: Dockerfile
   config: 
-    PORT: ${PORT}
+    PORT: ${PORT}

defaults/assets/PPE_Screenshot_Interface_v0.png

@@ -6,17 +6,21 @@
 from .model.parameters import Parameters
 from .model.sir import Sir
 
+
 def run(argv):
+    """Eun cli."""
     p = Parameters.create(os.environ, argv[1:])
     m = Sir(p)
 
     for df, name in (
         (m.sim_sir_w_date_df, "sim_sir_w_date"),
         (m.admits_df, "projected_admits"),
         (m.census_df, "projected_census"),
+        (m.ppe_df, 'ppe_data')
     ):
         df.to_csv(f"{p.current_date}_{name}.csv")
 
+
 def main():
     """Main."""
     run(sys.argv)

defaults/assets/PPE_Screenshot_Output_v0.png

@@ -3,6 +3,7 @@ en:
   app-new-admissions-text: "Projected number of **daily** COVID-19 admissions."
   app-admitted-patients-title: "Admitted Patients (Census)"
   app-admitted-patients-text: "Projected **census** of COVID-19 patients, accounting for arrivals and discharges."
+  app-PPE-title: "Personal Protective Equipment (PPE) Calculator"
   app-SIR-title: "Susceptible, Infected, and Recovered"
   app-SIR-text: "The number of susceptible, infected, and recovered individuals in the hospital catchment region at any given moment"
   charts-date: "Date"

docs/contributing/app-dev.md

@@ -0,0 +1,14 @@
+"""Personal Protective Equipment."""
+
+import os
+from typing import Dict
+
+
+class PPE:
+
+    def __init__(self, env: Dict[str, str]):
+        """__init__."""
+        self.assets = assets = env['ASSETS']
+        self.filename = filename = "PPE_Calculator_for_COVID-19.xlsx"
+        self.src = os.path.join(assets, filename)
+        self.screenshot = os.path.join(assets, 'PPE_Screenshot.jpg')

heroku.yml

@@ -174,6 +174,15 @@ def __init__(self, p: Parameters):
             'census_icu': self.raw['census_icu'],
             'census_ventilated': self.raw['census_ventilated'],
         })
+        self.ppe_df = pd.DataFrame(data={
+            'day': self.raw['day'],
+            'date': self.raw['date'],
+            'census_hospitalized': self.raw['census_hospitalized'],
+            'census_icu': self.raw['census_icu'],
+            'census_ventilated': self.raw['census_ventilated'],
+            'admits_hospitalized': self.raw['admits_hospitalized'],
+        })
+        self.ppe_df = self.ppe_df[self.ppe_df['day']>=0]
 
         logger.info('len(np.arange(-i_day, n_days+1)): %s', len(np.arange(-self.i_day, p.n_days+1)))
         logger.info('len(raw_df): %s', len(self.raw_df))

src/penn_chime/cli.py

@@ -6,7 +6,7 @@
 
 
 def dataframe_to_base64(df: pd.DataFrame) -> str:
-    """Converts a dataframe to a base64-encoded CSV representation of that data.
+    """Converts a dataframe into csv base64-encoded data.
 
     This is useful for building datauris for use to download the data in the browser.
 
@@ -16,3 +16,9 @@ def dataframe_to_base64(df: pd.DataFrame) -> str:
     csv = df.to_csv(index=False)
     b64 = b64encode(csv.encode()).decode()
     return b64
+
+
+def excel_to_base64(filename: str) -> str:
+    """Converts an excel document into base64-encoded data."""
+    with open(filename, 'rb') as fin:
+        return b64encode(fin.read()).decode()

src/penn_chime/locales/en.yml

@@ -2,9 +2,9 @@
 
 import os
 
-import altair as alt  # type: ignore
-import streamlit as st  # type: ignore
-import i18n  # type: ignore
+import altair as alt
+import streamlit as st
+import i18n
 
 i18n.set('filename_format', '{locale}.{format}')
 i18n.set('locale', 'en')
@@ -13,13 +13,15 @@
 
 from ..model.parameters import Parameters
 from ..model.sir import Sir
+from ..model.ppe import PPE
 from .charts import (
     build_admits_chart,
     build_census_chart,
     build_sim_sir_w_date_chart,
 )
 from .st_display import (
     display_download_link,
+    display_excel_download_link,
     display_footer,
     display_header,
     display_sidebar,
@@ -35,6 +37,8 @@ def main():
     st.markdown(hide_menu_style, unsafe_allow_html=True)
 
     d = Parameters.create(os.environ, [])
+    ppe = PPE(os.environ)
+
     p = display_sidebar(st, d)
     m = Sir(p)
 
@@ -62,6 +66,29 @@ def main():
         df=m.census_df,
     )
 
+    st.subheader(i18n.t("app-PPE-title"))
+    display_excel_download_link(st, ppe.filename, ppe.src)
+    display_download_link(
+        st,
+        p,
+        filename=f"{p.current_date}_projected_census_for_ppe_calculator.csv",
+        df=m.ppe_df,
+    )
+
+    if st.checkbox("Show a screenshot of the tool"):
+        st.image(
+            image=ppe.screenshot,
+            width=600,
+            format='JPEG',
+        )
+    st.markdown("""
+        Refer to our <a href="{link_to_docs}">user documentation for instructions on how to use the tool</a>.
+    """.format(
+            link_to_docs="https://code-for-philly.gitbook.io/chime/ppe-calculator",
+        ),
+        unsafe_allow_html=True
+    )
+
     st.subheader(i18n.t("app-SIR-title"))
     st.markdown(i18n.t("app-SIR-text"))
     sim_sir_w_date_chart = build_sim_sir_w_date_chart(alt=alt, sim_sir_w_date_floor_df=m.sim_sir_w_date_floor_df)

src/penn_chime/model/ppe.py

@@ -3,8 +3,10 @@
 import os
 import json
 
+from logging import INFO, basicConfig, getLogger
 import pandas as pd
 import i18n
+from sys import stdout
 
 from ..constants import (
     CHANGE_DATE,
@@ -15,9 +17,21 @@
     VERSION,
 )
 from ..model.parameters import Parameters, Disposition
-from ..utils import dataframe_to_base64
+from ..utils import (
+    dataframe_to_base64,
+    excel_to_base64,
+)
 from .spreadsheet import spreadsheet
 
+
+basicConfig(
+    level=INFO,
+    format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
+    stream=stdout,
+)
+logger = getLogger(__name__)
+
+
 hide_menu_style = """
         <style>
         #MainMenu {visibility: hidden;}
@@ -448,7 +462,6 @@ def display_footer(st):
     )
     st.markdown(i18n.t("presentation-copyright"))
 
-
 def display_download_link(st, p, filename: str, df: pd.DataFrame):
     csv = dataframe_to_base64(df.rename(p.labels, axis=1))
     st.markdown(
@@ -457,3 +470,13 @@ def display_download_link(st, p, filename: str, df: pd.DataFrame):
         ),
         unsafe_allow_html=True,
     )
+
+def display_excel_download_link(st, filename: str, src: str):
+    excel = excel_to_base64(src)
+    st.markdown("""
+        Download the PPE Calculator here: <a download="{filename}" href="data:file/xlsx;base64,{excel}">{filename}</a>.
+    """.format(
+            excel=excel, filename=filename
+        ),
+        unsafe_allow_html=True,
+    )