Merge pull request #3 from BrianThomasRoss/dash-app

Push to remote devel

src/chime_dash/README.md

@@ -5,7 +5,7 @@ This directory should provide the interface for a dash app.
 E.g., it contains the actual app which pieces together individual parts which could potentially live on their own.
 This makes it easier to modularize and reuse parts.
 
-![Current interface](interface.png)
+![Current interface](docs/assets/interface.png)
 
 ## Todo
 Plots & callbacks

src/chime_dash/layout/__init__.py → src/chime_dash/app/components/__init__.py

@@ -1,6 +1,6 @@
 """Combines all components
 
-The `sidbar` component cobines all the inputs while other components potentially
+The `sidebar` component combines all the inputs while other components potentially
 have callbacks.
 
 To add or remove components, adjust the `setup`.
@@ -14,13 +14,14 @@
 
 from penn_chime.defaults import Constants
 
-from chime_dash.layout import sidebar
-from chime_dash.layout import header
-from chime_dash.layout import intro
-from chime_dash.layout import additions
-from chime_dash.layout import visualizations
-from chime_dash.layout import definitions
-from chime_dash.layout import footer
+from chime_dash.app.components import sidebar
+from chime_dash.app.components import header
+from chime_dash.app.components import intro
+from chime_dash.app.components import additions
+from chime_dash.app.components import visualizations
+from chime_dash.app.components import definitions
+from chime_dash.app.components import footer
+from chime_dash.app.components import navbar
 
 
 EXTERNAL_STYLESHEETS = [

src/chime_dash/layout/additions.py → src/chime_dash/app/components/additions.py

@@ -13,8 +13,8 @@
 from penn_chime.utils import add_date_column
 from penn_chime.parameters import Parameters
 
-from chime_dash.utils import read_localization_yaml, df_to_html_table
-from chime_dash.plotting import plot_dataframe
+from chime_dash.app.utils.templates import read_localization_yaml, df_to_html_table
+from chime_dash.app.services.plotting import plot_dataframe
 
 
 LOCALIZATION_FILE = "additions.yml"

src/chime_dash/app/components/menu.py

@@ -0,0 +1,41 @@
+"""Initializes dropdown menu
+"""
+import dash_bootstrap_components as dbc
+
+
+def setup ():
+    menu = dbc.DropdownMenu(
+        children=[
+            dbc.DropdownMenuItem(
+                "Penn Medicine",
+                header=True),
+            dbc.DropdownMenuItem(
+                "Predictive Healthcare",
+                href='http://predictivehealthcare.pennmedicine.org/',
+                external_link=True
+            ),
+            dbc.DropdownMenuItem(
+                "Contact Us",
+                href='http://predictivehealthcare.pennmedicine.org/contact/',
+                external_link=True
+            ),
+            dbc.DropdownMenuItem(
+                "User Docs",
+                href="https://code-for-philly.gitbook.io/chime/",
+                external_link=True
+            ),
+            dbc.DropdownMenuItem(
+                "GitHub",
+                href="https://github.com/CodeForPhilly/chime",
+                external_link=True
+            ),
+            dbc.DropdownMenuItem(
+                "Slack",
+                href="https://codeforphilly.org/chat?channel=covid19-chime-penn"
+            )
+        ],
+        in_navbar=True,
+        label="Learn More",
+        color="light"
+    )
+    return menu

src/chime_dash/app/components/navbar.py

@@ -0,0 +1,35 @@
+"""Navigation bar view
+"""
+from typing import List
+from chime_dash.app.static import header
+from chime_dash.app.components import menu
+
+import dash_html_components as html
+import dash_bootstrap_components as dbc
+from dash.development.base_component import ComponentMeta
+
+
+def setup (language: str) -> List[ComponentMeta]:
+    """Initialize the navigation bar
+    """
+    nav = dbc.Navbar(
+        dbc.Container(
+            [
+                html.A(
+                    dbc.Row(
+                        children=[
+                            dbc.Col(header.setup(language)),
+                            dbc.Col(
+                                dbc.NavbarBrand(
+                                    children='Penn Medicine CHIME',
+                                    href='/')
+                            )
+                        ],
+                        align="center",
+                        no_gutters=True,
+                    ),
+                    href='https://www.pennmedicine.org/'),
+                menu.setup()
+            ]
+        ))
+    return nav

src/chime_dash/layout/sidebar.py → src/chime_dash/app/components/sidebar.py

@@ -10,7 +10,7 @@
 from penn_chime.defaults import RateLos, Constants
 from penn_chime.parameters import Parameters
 
-from chime_dash.utils import read_localization_yaml
+from chime_dash.app.utils.templates import read_localization_yaml
 
 LOCALIZATION_FILE = "sidebar.yml"
 

src/chime_dash/layout/visualizations.py → src/chime_dash/app/components/visualizations.py

@@ -13,8 +13,8 @@
 from penn_chime.parameters import Parameters
 
 
-from chime_dash.utils import read_localization_yaml, df_to_html_table
-from chime_dash.plotting import plot_dataframe
+from chime_dash.app.utils.templates import read_localization_yaml, df_to_html_table
+from chime_dash.app.services.plotting import plot_dataframe
 
 LOCALIZATION_FILE = "visualizations.yml"
 

src/chime_dash/app/pages/index.py

@@ -0,0 +1,28 @@
+"""pages/index
+Homepage
+"""
+from typing import List
+
+import dash_html_components as html
+import dash_bootstrap_components as dbc
+from dash.development.base_component import ComponentMeta
+
+from chime_dash.app.components import navbar
+from chime_dash.app.static.homepage import introducing_chime, latest_updates
+
+
+def render (language: str) -> List[ComponentMeta]:
+    """Initializes page
+    """
+    layout = html.Div(
+        [
+            dbc.Row(navbar.setup(language)),
+            dbc.Col(
+                children=introducing_chime('en')
+            ),
+            dbc.Col(
+                children=latest_updates('en')
+            )
+        ]
+    )
+    return layout

src/chime_dash/app/services/__init__.py

@@ -0,0 +1,4 @@
+"""
+app/services
+
+"""

src/chime_dash/layout/definitions.py → src/chime_dash/app/static/definitions.py

@@ -4,7 +4,7 @@
 
 from dash.development.base_component import ComponentMeta
 
-from chime_dash.utils import read_localization_markdown
+from chime_dash.app.utils.templates import read_localization_markdown
 from dash_core_components import Markdown
 
 

src/chime_dash/layout/footer.py → src/chime_dash/app/static/footer.py

@@ -5,7 +5,7 @@
 from dash.development.base_component import ComponentMeta
 from dash_core_components import Markdown
 
-from chime_dash.utils import read_localization_markdown
+from chime_dash.app.utils.templates import read_localization_markdown
 
 LOCALIZATION_FILE = "footer.md"
 

src/chime_dash/layout/header.py → src/chime_dash/app/static/header.py

@@ -5,7 +5,7 @@
 from dash.development.base_component import ComponentMeta
 from dash_html_components import Div, A
 
-from chime_dash.utils import read_localization_yaml
+from chime_dash.app.utils.templates import read_localization_yaml
 
 LOCALIZATION_FILE = "header.yml"
 

src/chime_dash/app/static/homepage.py

@@ -0,0 +1,25 @@
+from typing import List
+
+from dash.development.base_component import ComponentMeta
+from dash_core_components import Markdown
+
+from chime_dash.app.utils.templates import read_localization_markdown
+
+LOCALIZATION_FILE_1 = "chime-intro.md"
+LOCALIZATION_FILE_2 = "latest-updates.md"
+
+
+def introducing_chime (language: str) -> List[ComponentMeta]:
+    """Initializes the header dash html
+    """
+    content = read_localization_markdown(LOCALIZATION_FILE_1, language)
+
+    return [Markdown(content)]
+
+
+def latest_updates (language: str) -> List[ComponentMeta]:
+    """Initializes the header dash html
+    """
+    content = read_localization_markdown(LOCALIZATION_FILE_2, language)
+
+    return [Markdown(content)]

src/chime_dash/layout/intro.py → src/chime_dash/app/static/intro.py

@@ -9,7 +9,7 @@
 from penn_chime.defaults import Constants
 from penn_chime.parameters import Parameters
 
-from chime_dash.utils import read_localization_markdown
+from chime_dash.app.utils.templates import read_localization_markdown
 
 LOCALIZATION_FILE_1 = "intro.md"
 LOCALIZATION_FILE_2 = "tool-details.md"

src/chime_dash/app/templates/en/chime-intro.md

@@ -0,0 +1,30 @@
+# CHIME
+### A Tool for COVID-19 Capacity Planning
+
+As we prepare for the additional demands that the COVID-19 
+outbreak will place on our hospital system, our operational 
+leaders need up-to-date projections of what additional resources 
+will be required. Informed estimates of how many patients will 
+need hospitalization, ICU beds, and mechanical ventilation over 
+the coming days and weeks will be crucial inputs to readiness responses 
+and mitigation strategies.
+
+CHIME allows hospitals to enter information about their population and modify assumptions around the spread and behavior of COVID-19. It then runs a standard SIR model to project the number of new hospital admissions each day, along with the daily hospital census. These projections can then be used to create best- and worst-case scenarios to assist with capacity planning. We’re announcing today that we’re open-sourcing CHIME and making it available to the healthcare community.
+
+While the default parameters are customized and continually updated to reflect the situation at Penn Medicine, CHIME can be adapted for use by any hospital system by modifying parameters to reflect local contexts.
+
+The most impactful parameter in a SIR model is the Doubling Time. This parameter defines how rapidly a disease spreads. Experiences in other geographical contexts suggest that doubling time may range from 3 to 13 days or more, with notable examples:
+
+Wuhan, China: 6 days
+South Korea: 13 days (As of March 14, 2020)
+Italy: 5 days (As of March 14, 2020)
+This value is particularly important because of the exponential nature of the spread of infectious diseases such as COVID-19. This is also why public health officials recommend measures like social distancing and hand washing: the more we can slow down the spread of COVID-19, the lower the peak demand on our healthcare system. Try out our live version of CHIME and see what happens when you modify the Doubling Time parameter. You can also experiment with scenarios involving different levels of incidence severity and average lengths of stay for each severity class.
+
+We’ve put effort into determining good estimates for all model parameters and have set default values accordingly. Some of the default values are based on the current situation in our home region of Philadelphia. If you’re working somewhere outside of the Philadelphia region you can simply modify the following parameters to suit your patient population:
+
+Currently Known Regional Infections
+Currently Hospitalized COVID-19 Patients
+Hospital Market Share (%)
+As local spread progresses, revised estimates can be made for some of the values in CHIME. We will try our best to keep things up to date with the latest research, but if you find an issue with any of the values we are using we’d appreciate your feedback and contributions. We also set up a Slack channel if you’d like to chat with us.
+
+– Penn Predictive Healthcare Team

src/chime_dash/app/templates/en/latest-updates.md

@@ -0,0 +1,37 @@
+# Latest Updates
+
+## [CHIME 0.5.0 released with major updates](http://predictivehealthcare.pennmedicine.org/2020/03/23/admissions_bug_fix.html)
+---
+###### Mar 23, 2020
+
+What was fixed Unfortunately, the COVID-19 crisis forces us to move quickly and one downside 
+of moving quickly is it’s easier to make mistakes. Our latest release of CHIME contains 
+a major bug fix to the way we were calculating daily admissions and census. In the previous 
+version of CHIME, we were not properly accounting for recovered (previously infected) 
+patients in our accounting of newly admitted patients. This was resulting in an undercount 
+of admissions... 
+[Read More >](http://predictivehealthcare.pennmedicine.org/2020/03/23/admissions_bug_fix.html)
+
+## [CHIME comparison with Imperial College COVID-19 Publication](http://predictivehealthcare.pennmedicine.org/2020/03/18/compare-chime.html)
+---
+###### Mar 18, 2020
+
+A few days ago we launched CHIME, a tool for COVID-19 hospital capacity planning. CHIME’s 
+simplified model design and interface enables quick support for hospital planners to assess 
+potential demand for resources over time. It also allows transparent and understandable 
+parameters for our partners to interrogate and modify as more information becomes available.
+The recent paper from Imperial College COVID-19 Response Team gives us a window into 
+another model, set of assumptions, and resulting projections.... 
+[Read More >](http://predictivehealthcare.pennmedicine.org/2020/03/18/compare-chime.html)
+
+## [Announcing CHIME, A tool for COVID-19 capacity planning](http://predictivehealthcare.pennmedicine.org/2020/03/14/accouncing-chime.html)
+---
+###### Mar 14, 2020
+
+As we prepare for the additional demands that the COVID-19 outbreak will place on our hospital 
+system, our operational leaders need up-to-date projections of what additional resources will 
+be required. Informed estimates of how many patients will need hospitalization, ICU beds, 
+and mechanical ventilation over the coming days and weeks will be crucial inputs to readiness 
+responses and mitigation strategies. To this end, the Predictive Healthcare team at 
+Penn Medicine has developed a tool that... 
+[Read More >](http://predictivehealthcare.pennmedicine.org/2020/03/14/accouncing-chime.html)

src/chime_dash/utils.py → src/chime_dash/app/utils/templates.py

@@ -19,15 +19,15 @@ def read_localization_yaml(file: str, language: str) -> Dict[str, Any]:
 
     Arguments:
         file: Name of the section plus `.yml`
-        langage: Localization info
+        language: Localization info
 
     Raises:
         KeyError: If no template for file/language exists.
     """
     file_address = path.join(TEMPLATE_DIR, language, file)
     if not path.exists(file_address):
         raise KeyError(
-            "No template found for langage '{language}' and section '{file}'".format(
+            "No template found for language '{language}' and section '{file}'".format(
                 file=file, language=language
             )
         )
@@ -42,7 +42,7 @@ def read_localization_markdown(file: str, language: str) -> str:
 
     Arguments:
         file: Name of the section plus `.md`
-        langage: Localization info
+        language: Localization info
 
     Raises:
         KeyError: If no template for file/language exists.

src/dash_app.py

@@ -1,11 +1,12 @@
 """Script which launches dash app
 """
 from dash import Dash
+from flask import Flask
 
 from penn_chime.settings import DEFAULTS
 
-from chime_dash.layout import setup, EXTERNAL_STYLESHEETS, EXTERNAL_SCRIPTS
-from chime_dash.layout import CALLBACK_INPUTS, CALLBACK_OUTPUTS, callback_body
+from chime_dash.app.components import setup, EXTERNAL_STYLESHEETS, EXTERNAL_SCRIPTS
+from chime_dash.app.components import CALLBACK_INPUTS, CALLBACK_OUTPUTS, callback_body
 
 LANGUAGE = "en"