Merge pull request #15 from eipm/develop

v1.0.0

.gitignore

@@ -162,3 +162,8 @@ cython_debug/
 #.idea/
 
 src/.deployment
+src/backup
+css/backup
+
+transformation
+data

CITATION.cff

@@ -18,6 +18,19 @@ authors:
     given-names: Jeff
     affiliation: Weill Cornell Medicine (WCM)
     orcid: 'https://orcid.org/0009-0006-0366-5050'
+  - family-names: Bevers
+    given-names: Isaac
+    affiliation: Massachusetts Institute of Technology (MIT)
+    orcid: 'https://orcid.org/0009-0002-0074-0087'
+  - family-names: Gallois
+    given-names: Hortense
+    affiliation: Simon Fraser University
+  - family-names: Bernier
+    given-names: Alexander
+    affiliation: McGill University
+  - family-names: Bensoussan
+    given-names: Yaël
+    affiliation: University of South Florida  
   - family-names: Bensoussan
     given-names: Yaël
     affiliation: University of South Florida

README.md

@@ -2,14 +2,14 @@
 
 Docs for the Bridge2AI Voice Project.
 
-[![Github](https://img.shields.io/badge/github-0.4.0-green?style=flat&logo=github)](https://github.com/eipm/bridge2ai-docs) [![Python 3.11.5](https://img.shields.io/badge/python-3.12.0-blue.svg)](https://www.python.org/downloads/release/python-3120/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)  [![DOI](https://zenodo.org/badge/860006845.svg)](https://zenodo.org/doi/10.5281/zenodo.13834653)
+[![Github](https://img.shields.io/badge/github-1.0.0-green?style=flat&logo=github)](https://github.com/eipm/bridge2ai-docs) [![Python 3.11.5](https://img.shields.io/badge/python-3.12.0-blue.svg)](https://www.python.org/downloads/release/python-3120/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)  [![DOI](https://zenodo.org/badge/860006845.svg)](https://zenodo.org/doi/10.5281/zenodo.13834653)
 
 
 ## 🤝 License
 See [LICENSE](./LICENSE)
 
 ## 📚 How to Cite
-> Sigaras, A., Zisimopoulos, P., Tang, J., Bensoussan, Y., Ghosh, S. S., Rameau, A., Powell, M. E., Belisle-Pipon, J.-C., Ravitsky, V., Johnson, A., Elemento, O., Dorr, D., … Bridge2AI-Voice. (2024). eipm/bridge2ai-docs. Zenodo. [https://zenodo.org/doi/10.5281/zenodo.13834653](https://zenodo.org/doi/10.5281/zenodo.13834653)
+> Sigaras, A., Zisimopoulos, P., Tang, J., Bevers, I., Gallois, H., Bernier, A., Bensoussan, Y., Ghosh, S. S., Rameau, A., Powell, M. E., Belisle-Pipon, J.-C., Ravitsky, V., Johnson, A., Elemento, O., Dorr, D., … Bridge2AI-Voice. (2024). eipm/bridge2ai-docs. Zenodo. [https://zenodo.org/doi/10.5281/zenodo.13834653](https://zenodo.org/doi/10.5281/zenodo.13834653)
 
 ## Prerequisites
 

css/dashboard.css

@@ -0,0 +1,113 @@
+[data-testid="stDecoration"] {
+    display: none;
+}
+
+[data-testid="stAppDeployButton"]{
+    display: none;
+}
+
+[data-testid="stBaseButton-headerNoPadding"] {
+    display: none;
+}
+
+img[data-testid="stLogo"] {
+    margin-top: -16px;
+    margin-left: -20px;
+    height: 3.5rem;
+}
+
+/* Set the font size for the tab headers */ 
+button[data-baseweb="tab"] > div[data-testid="stMarkdownContainer"] > p {
+    font-size: 18px;
+    white-space: wrap;
+    word-break: normal;
+    align-items: flex-start;
+}
+
+.stTabs [data-baseweb="tab-highlight"] {
+    border-bottom: 4px solid rgb(255, 75, 75);
+    color: black;
+}
+
+.stTabs [data-baseweb="tab-list"] > button[data-baseweb="tab"] {
+    display: flex;
+    align-items: flex-start;
+}
+
+/* Reduce white space on top */
+.block-container {
+    padding-top: 2rem;
+}
+
+/* Sticky footer */
+footer {
+    position: fixed;
+    bottom: 0;
+    left: 0;
+    width: 100%;
+    background: linear-gradient(90deg, #d3d3d3, #f0f0f0);
+    color: black;
+    display: flex;
+    height: 30px;
+    justify-content: center;
+    padding: 4px;
+    z-index: 1000;
+    font-size: smaller;
+}
+
+@media screen and (max-width: 1278px) {
+    .stTabs [data-baseweb="tab-list"] {
+        padding-bottom: 25px;
+    }
+}
+
+/* set border for plots */
+.js-plotly-plot {
+    background-color: white;
+    border: 2px solid #d3d3d3;
+    border-radius: 5px;
+    margin-right: -5px;
+    margin-bottom: -5px;
+    padding: 0;
+    box-shadow: 0 4px 12px rgba(0, 0, 0, 0.1);
+}
+
+[data-testid="stMetric"] {
+    border: 2px solid #d3d3d3;
+    margin-right: -5px;
+    margin-bottom: -5px;
+    border-radius: 5px;
+    box-shadow: 0 4px 12px rgba(0, 0, 0, 0.1);
+    background-color: white;
+}
+
+/* set text and metri in columns to center */
+.stMetric > div, [data-testid="stMetricLabel"] {
+    color: black;
+    display: flex;
+    justify-content: center;
+    align-items: center;
+    text-align: center;
+}
+
+.js-plotly-plot .plotly .modebar-btn {
+    font-size: 14px;
+    padding: 0;
+    margin: 0;
+}
+
+.js-plotly-plot .plotly .modebar {
+    top: -1px;
+    right: 0;
+    left: auto;
+    width: 48px;
+}
+
+.legendtext {
+    transform: translateX(-10px);
+}
+
+/* set weight font for plotly title */
+.gtitle tspan {
+    font-weight: 500 !important;
+}

src/dashboard.py

@@ -1,114 +1,57 @@
 import streamlit as st
-import pandas as pd
-import numpy as np
-import plotly.express as px
-
-custom_style = """
-<style>
-
-[data-testid="stDecoration"] {
-	display: none;
-}
-
-/* Hide the Streamlit hamburger menu */
-#MainMenu {visibility: hidden;}
-
-/* Set the font size for the tab headers */ 
-.stTabs [data-baseweb="tab-list"] button [data-testid="stMarkdownContainer"] p {
-    font-size: 18px;
-}
-
-/* Reduce white space on top */
-.block-container {
-    padding-top: 2rem;
-    # padding-left: 5px;
-    # padding-right: 5px;
-    # padding-bottom: 0;
-    # margin-left: 0;
-    # margin-right: 0;
-}
-
-/* Sticky footer */
-footer {
-    position: fixed;
-    bottom: 0;
-    left: 0;
-    width: 100%;
-    background-color: #f1f1f1;
-    display: flex;
-    height: 30px;
-    justify-content: center;
-    padding: 4px;
-    z-index: 1000;
-    font-size: smaller;
-}
-
-</style>
-"""
-
-def coming_soon_message(tab_name):
-        # Your Streamlit application code
-    st.title('Bridge2AI Voice Dashboard')
-    st.write(f"{tab_name} - Coming soon!")
-
-    # Add an image to the page
-    image_path = "images/Wave.png"  # Replace with your image file name
-    st.image(image_path, caption='', use_column_width=True)
-
-def about_page(tab_name):
-    coming_soon_message(tab_name)
-
-def healthsheet_page(tab_name):
-    coming_soon_message(tab_name)
-
-def study_dashboard_page(tab_name):
-    coming_soon_message(tab_name)
-
-def study_metadata_page(tab_name):
-    coming_soon_message(tab_name)
-
-def dataset_metadata_page(tab_name):
-    coming_soon_message(tab_name)
-
-def dataset_structure_preview_page(tab_name):
-    coming_soon_message(tab_name)
-
-def dataset_quality_dashboard_page(tab_name):
-    coming_soon_message(tab_name)
-
-def dataset_uses_page(tab_name):
-    coming_soon_message(tab_name)
-
-def create_tabs(tabs_func):
-    tab_names = list(tabs_func.keys())
-    tabs = st.tabs(tab_names)
-    for tab, name in zip(tabs, tab_names):
-        with tab:
-            tabs_func[name](name)
+from tabs.about import about_page
+from tabs.healthsheet import healthsheet_page
+from tabs.study_dashboard import study_dashboard_page
+from tabs.study_metadata import study_metadata_page
+from tabs.dataset_metadata import dataset_metadata_page
+from tabs.dataset_structure_preview import dataset_structure_preview_page
+from tabs.dataset_quality_dashboard import dataset_quality_dashboard_page
+from tabs.dataset_uses import dataset_uses_page
 
 def config_page(version):         
     st.set_page_config(
         page_title="Bridge2AI Voice Dashboard",
         page_icon="images/B2AI Logo.ico",
         layout="wide")
 
-    st.markdown(custom_style, unsafe_allow_html=True)
+    # Add the CSS file
+    with open("css/dashboard.css") as f:
+        st.markdown(f"<style>{f.read()}</style>", unsafe_allow_html=True)
+
+    st.logo("images/B2AI Logo.png", )
 
     # Add the footer
     footer = f"""
     <footer>
        © Weill Cornell Medicine | Version {version} &nbsp;|&nbsp;
-       <a href="https://weill.cornell.edu/notice-privacy-practices" target="_blank" style="color: black">Privacy Policy</a> &nbsp;|&nbsp; 
-       <a href="https://weill.cornell.edu/weill-cornell-medicine-web-terms-use" target="_blank" style="color: black">Terms of Use</a>
+       <a href="https://weill.cornell.edu/notice-privacy-practices" target="_blank">Privacy Policy</a> &nbsp;|&nbsp; 
+       <a href="https://weill.cornell.edu/weill-cornell-medicine-web-terms-use" target="_blank">Terms of Use</a>
     </footer>
     """
     st.markdown(footer, unsafe_allow_html=True)
 
+def create_tabs(tabs_func):
+    tab_names = list(tabs_func.keys())
+    tabs = st.tabs(tab_names)
+    for tab, name in zip(tabs, tab_names):
+        with tab:
+            tabs_func[name](name)
 
 def main():  
-    # Define the version variable
-    version = "0.4.0"
+    # Current version of the app
+    version = "1.0.0"
     # Map tab names to functions
+    # In this dictionary, the key is the tab name and the value is the function that will be called when the tab is selected
+    # The function is defined in the respective file
+    # about_page() is defined in tabs/about.py
+    # healthsheet_page() is defined in tabs/healthsheet.py
+    # study_dashboard_page() is defined in tabs/study_dashboard.py
+    # study_metadata_page() is defined in tabs/study_metadata.py
+    # dataset_metadata_page() is defined in tabs/dataset_metadata.py
+    # dataset_structure_preview_page() is defined in tabs/dataset_structure_preview.py
+    # dataset_quality_dashboard_page() is defined in tabs/dataset_quality_dashboard.py
+    # dataset_uses_page() is defined in tabs/dataset_uses.py
+
     tab_functions = {
         "About": about_page,
         "Healthsheet": healthsheet_page,
@@ -126,5 +69,4 @@ def main():
     create_tabs(tab_functions)
 
 if __name__ == "__main__":
-
-    main()
+    main()

src/tabs/about.py

@@ -0,0 +1,5 @@
+import streamlit as st
+from tabs.utils import coming_soon_message
+
+def about_page(tab_name):
+    coming_soon_message(tab_name)

src/tabs/dataset_metadata.py

@@ -0,0 +1,6 @@
+import streamlit as st
+from tabs.utils import coming_soon_message
+
+# Define the content of the Dataset Metadata page
+def dataset_metadata_page(tab_name):
+    coming_soon_message(tab_name)

src/tabs/dataset_quality_dashboard.py

@@ -0,0 +1,6 @@
+import streamlit as st
+from tabs.utils import coming_soon_message
+
+# Define the content of the Dataset Quality Dashboard page
+def dataset_quality_dashboard_page(tab_name):
+    coming_soon_message(tab_name)

src/tabs/dataset_structure_preview.py

@@ -0,0 +1,6 @@
+import streamlit as st
+from tabs.utils import coming_soon_message
+
+# Define the content of the Dataset Structure Preview page
+def dataset_structure_preview_page(tab_name):
+    coming_soon_message(tab_name)

src/tabs/dataset_uses.py

@@ -0,0 +1,6 @@
+import streamlit as st
+from tabs.utils import coming_soon_message
+
+# Define the content of the Dataset Uses page
+def dataset_uses_page(tab_name):
+    coming_soon_message(tab_name)

src/tabs/healthsheet.py

@@ -0,0 +1,6 @@
+import streamlit as st
+from tabs.utils import coming_soon_message
+
+# Define the content of the Health Sheet page
+def healthsheet_page(tab_name):
+    coming_soon_message(tab_name)