Merge branch 'develop' into dsgit1-patch-2

Author: jlubken

setup.py

@@ -3,8 +3,7 @@
 __version__ = "1.1.3"  # update VERSION in constants.py
 __author__ = "Predictive Healthcare @ Penn Medicine"
 
-from os import path
-from setuptools import setup, find_packages, find_namespace_packages
+from setuptools import setup, find_namespace_packages
 
 
 setup(
@@ -24,6 +23,7 @@
     install_requires=[
         "altair",
         "black",
+        "gspread",
         "gunicorn",
         "dash",
         "dash_bootstrap_components",
@@ -33,17 +33,18 @@
         "pyyaml",
         "selenium",
         "streamlit",
+        "gspread",
+        "oauth2client"
     ],
     classifiers=[
         "Programming Language :: Python :: 3",
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
     ],
     python_requires='>=3.7',
-    entry_points = {
+    entry_points={
         'console_scripts': ['penn_chime=penn_chime.cli:main'],
     },
     keywords=[],
     include_package_data=True,
 )
-

src/penn_chime/parameters.py

@@ -19,6 +19,7 @@
 )
 from .validators import (
     Date,
+    GteOne,
     OptionalDate,
     OptionalValue,
     OptionalStrictlyPositive,
@@ -64,7 +65,7 @@ class Disposition(_Disposition):
     @classmethod
     def create(cls, *, days: int, rate: float):
         """Mandate key word arguments."""
-        Positive(key="days", value=days)
+        GteOne(key="days", value=days)
         Rate(key="rate", value=rate)
         return cls(days, rate)
 
@@ -201,7 +202,7 @@ def validate(string):
     (
         "hospitalized_days",
         int,
-        0,
+        1,
         None,
         True,
     ),
@@ -215,7 +216,7 @@ def validate(string):
     (
         "icu_days",
         int,
-        0,
+        1,
         None,
         True,
     ),
@@ -285,7 +286,7 @@ def validate(string):
     (
         "ventilated_days",
         int,
-        0,
+        1,
         None,
         True,
     ),

src/penn_chime/presentation.py

@@ -5,8 +5,10 @@
 
 import altair as alt
 import numpy as np
+import os
+import json
 import pandas as pd
-
+import penn_chime.spreadsheet as sp
 from .constants import (
     CHANGE_DATE,
     DOCS_URL,
@@ -172,6 +174,8 @@ def display_sidebar(st, d: Parameters) -> Parameters:
     # it's kindof like ember or angular if you are familiar with those
 
     st_obj = st.sidebar
+    # used_widget_key = st.get_last_used_widget_key ( )
+
     current_hospitalized_input = NumberInput(
         st_obj,
         "Currently hospitalized COVID-19 patients",
@@ -216,7 +220,11 @@ def display_sidebar(st, d: Parameters) -> Parameters:
         step=1.0,
     )
     hospitalized_pct_input = PercentInput(
-        st_obj, "Hospitalization %(total infections)", value=d.hospitalized.rate,
+        st_obj,
+        "Hospitalization %(total infections)",
+        value=d.hospitalized.rate,
+        min_value=FLOAT_INPUT_MIN,
+        max_value=100.0
     )
     icu_pct_input = PercentInput(st_obj,
         "ICU %(total infections)",
@@ -230,23 +238,23 @@ def display_sidebar(st, d: Parameters) -> Parameters:
     hospitalized_days_input = NumberInput(
         st_obj,
         "Average hospital length of stay (in days)",
-        min_value=0,
+        min_value=1,
         value=d.hospitalized.days,
         step=1,
         format="%i",
     )
     icu_days_input = NumberInput(
         st_obj,
         "Average days in ICU",
-        min_value=0,
+        min_value=1,
         value=d.icu.days,
         step=1,
         format="%i",
     )
     ventilated_days_input = NumberInput(
         st_obj,
         "Average days on ventilator",
-        min_value=0,
+        min_value=1,
         value=d.ventilated.days,
         step=1,
         format="%i",
@@ -268,7 +276,7 @@ def display_sidebar(st, d: Parameters) -> Parameters:
     infectious_days_input = NumberInput(
         st_obj,
         "Infectious days",
-        min_value=0,
+        min_value=1,
         value=d.infectious_days,
         step=1,
         format="%i",
@@ -349,6 +357,8 @@ def display_sidebar(st, d: Parameters) -> Parameters:
         max_y_axis = max_y_axis_input()
 
     current_date = current_date_input()
+    #Subscribe implementation
+    subscribe(st_obj)
 
     return Parameters(
         current_hospitalized=current_hospitalized,
@@ -374,6 +384,66 @@ def display_sidebar(st, d: Parameters) -> Parameters:
             days=ventilated_days),
     )
 
+#Read the environment variables and cteate json key object to use with ServiceAccountCredentials
+def readGoogleApiSecrets():
+    client_secret = {}
+    os.getenv
+    type = os.getenv ('GAPI_CRED_TYPE').strip()
+    print (type)
+    client_secret['type'] = type,
+    client_secret['project_id'] = os.getenv ('GAPI_CRED_PROJECT_ID'),
+    client_secret['private_key_id'] = os.getenv ('GAPI_CRED_PRIVATE_KEY_ID'),
+    client_secret['private_key'] = os.getenv ('GAPI_CRED_PRIVATE_KEY'),
+    client_secret['client_email'] = os.getenv ('GAPI_CRED_CLIENT_EMAIL'),
+    client_secret['client_id'] = os.getenv ('GAPI_CRED_CLIENT_ID'),
+    client_secret['auth_uri'] = os.getenv ('GAPI_CRED_AUTH_URI'),
+    client_secret['token_uri'] = os.getenv ('GAPI_CRED_TOKEN_URI'),
+    client_secret['auth_provider_x509_cert_url'] =  os.getenv ('GAPI_CRED_AUTH_PROVIDER_X509_CERT_URL'),
+    client_secret['client_x509_cert_url'] = os.getenv ('GAPI_CRED_CLIENT_X509_CERT_URI'),
+    json_data = json.dumps (client_secret)
+    print(json_data)
+    return json_data
+
+def readGoogleApiSecretsDict():
+    type = os.getenv ('GAPI_CRED_TYPE')
+    project_id = os.getenv ('GAPI_CRED_PROJECT_ID')
+    private_key_id =  os.getenv ('GAPI_CRED_PRIVATE_KEY_ID')
+    private_key = os.getenv ('GAPI_CRED_PRIVATE_KEY')
+    client_email = os.getenv ('GAPI_CRED_CLIENT_EMAIL')
+    client_id = os.getenv ('GAPI_CRED_CLIENT_ID')
+    auth_uri = os.getenv ('GAPI_CRED_AUTH_URI')
+    token_uri = os.getenv ('GAPI_CRED_TOKEN_URI')
+    auth_provider_x509_cert_url = os.getenv ('GAPI_CRED_AUTH_PROVIDER_X509_CERT_URL')
+    client_x509_cert_url = os.getenv ('GAPI_CRED_CLIENT_X509_CERT_URI')
+
+    secret = {
+        'type' : type,
+        'project_id' : project_id,
+        'private_key_id' : private_key_id,
+        'private_key':private_key,
+        'client_email': client_email,
+        'client_id': client_id,
+        'auth_uri': auth_uri,
+        'token_uri': token_uri,
+        'auth_provider_x509_cert_url':auth_provider_x509_cert_url,
+        'client_x509_cert_url':client_x509_cert_url
+    }
+    return secret
+
+def subscribe(st_obj):
+    st_obj.subheader ("Subscribe")
+    email = st_obj.text_input (label="Enter Email", value="", key="na_lower_1")
+    name = st_obj.text_input (label="Enter Name", value="", key="na_upper_1")
+    affiliation = st_obj.text_input (label="Enter Affiliation", value="", key="na_upper_2")
+    if st_obj.button (label="Submit", key="ta_submit_1"):
+        row = [email, name, affiliation]
+        send_subscription_to_google_sheet(st_obj, row)
+
+def send_subscription_to_google_sheet(st_obj, row):
+    json_secret = readGoogleApiSecretsDict()
+    #print(json_secret)
+    spr = sp.spreadsheet (st_obj, json_secret)
+    spr.writeToSheet("CHIME Form Submissions", row)
 
 def display_footer(st):
     st.subheader("References & Acknowledgements")

src/penn_chime/spreadsheet.py

@@ -0,0 +1,45 @@
+import gspread
+from oauth2client.service_account import ServiceAccountCredentials
+
+class spreadsheet:
+    def __init__(self, st_obj, secret):
+        self.st_obj = st_obj
+        # use creds to create a client to interact with the Google Drive API
+        self.scope = ['https://spreadsheets.google.com/feeds', 'https://www.googleapis.com/auth/drive']
+        #secret = 'client_secret.json'
+        self.creds = ServiceAccountCredentials.from_json(secret)
+        #self.creds = ServiceAccountCredentials.from_json_keyfile_name(secret, self.scope)
+        self.client = gspread.authorize(self.creds)
+
+
+    def createsheet(self, sheetname, header):
+        sheet = None
+        try:
+            self.client.create(sheetname)
+        except Exception as e:
+            print("Caught exception " + e.__str__())
+        try:
+            sheet = self.client.open (sheetname).sheet1
+            index = 0
+            sheet.insert_row (header, index)
+        except Exception as e:
+            print("Caught exception " + e.__str__())
+        return sheet
+
+    def writeToSheet(self, sheetname, row):
+        try:
+            sheet = self.client.open (sheetname).sheet1
+            list_of_hashes = sheet.get_all_records ( )
+            currentrow = sheet.row_count
+            sheet.insert_row (row, currentrow)
+        except Exception as e:
+            print("Caught exception " + e.__str__())
+
+    def getAllRows(self, sheetname):
+        allrows = None
+        try:
+            sheet = self.client.open (sheetname).sheet1
+            allrows = sheet.get_all_records ( )
+        except Exception as e:
+            print("Caught exception " + e.__str__())
+        return allrows

src/penn_chime/validators/__init__.py

@@ -15,6 +15,7 @@
 OptionalStrictlyPositive = ValOptionalBounded(lower_bound=EPSILON)
 StrictlyPositive = ValBounded(lower_bound=EPSILON)
 Positive = ValBounded(lower_bound=-EPSILON)
+GteOne = ValBounded(lower_bound=1)
 Rate = ValRate()
 Date = ValDate()
 OptionalDate = ValOptionalDate()