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USC-InfoLab · Jul 21, 2024 · 57f9518 · 57f9518
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diff --git a/.github/workflows/w4h-workflow.yml b/.github/workflows/w4h-workflow.yml
@@ -30,7 +30,7 @@ jobs:
 
       - name: Convert Markdown to HTML
         run: |
-          find . -name '*.md' | while read -r file; do
+          find ./docs -name '*.md' | while read -r file; do
             htmlfile="${file%.md}.html"
             echo "Converting $file to $htmlfile"
             pandoc "$file" -o "$htmlfile" --extract-media .

diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1 @@
+# CONTRIBUTING
diff --git a/LICENSE.html b/LICENSE.html
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 w4h Toolkit
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/README.html b/README.html
diff --git a/README.md b/README.md
@@ -1,2 +1,5 @@
-# w4h-documentation
-End user documentation for the W4H platform
+# W4H Documentation
+
+Documentation for the W4H Toolkit.
+
+[Home](docs/index.md)
diff --git a/docs/getting-started/how_to_start.md b/docs/getting-started/how_to_start.md
@@ -1,6 +1,7 @@
 # Use W4h dashboard to track your patients' health data
 
 ## Introduction
+
 The W4H GeoMTS dashboard is designed to provide visualization and analysis capabilities for GeoMTS data catered specifically for Apple Watch demo purposes.
 
 ## How to play with it

diff --git a/docs/getting-started/other_things.md b/docs/getting-started/other_things.md
@@ -1,4 +1,5 @@
-## Other things:
+# Other things
+
 1. If you want to try how to set up, try in this link: https://labs.play-with-docker.com/
 
 2. There is a 5min video to show how to set up the environment: https://drive.google.com/file/d/1basc9nWQKclpZJgMq-K81KAGihfxkdb2/view?usp=sharing
diff --git a/docs/getting-started/setting_up.md b/docs/getting-started/setting_up.md
@@ -1,13 +1,16 @@
 # Welcome to w4h setting up toturial!
 
 ## Prerequisites
+
 1. In order to install W4H on your server, it is highly recommended to use Docker. This approach helps avoid potential issues related to software version mismatches and environment configurations. Ensure that Docker is running on your server, then execute the following command in your terminal:
+
 > wget https://raw.githubusercontent.com/USC-InfoLab/w4h-integrated-toolkit/jize/docker-compose.yml && docker-compose up --build
 
 2. To set your own database, ensure you have your database service in somewhere, and you know the
 db's host,username,password,database name, and the port it is listening to.
 
 ## Set up
+
 login in with username and password(use "admin" for both username and password in first time)
 
 Then following instruction to set your database

diff --git a/images/choose_exist_db.png → docs/images/choose_exist_db.png b/images/choose_exist_db.png → docs/images/choose_exist_db.png
diff --git a/images/conf.py.example → docs/images/conf.py.example b/images/conf.py.example → docs/images/conf.py.example
diff --git a/images/create_new_db.png → docs/images/create_new_db.png b/images/create_new_db.png → docs/images/create_new_db.png
diff --git a/images/create_success.png → docs/images/create_success.png b/images/create_success.png → docs/images/create_success.png
diff --git a/images/db_config.yaml.example → docs/images/db_config.yaml.example b/images/db_config.yaml.example → docs/images/db_config.yaml.example
diff --git a/images/docker_readme.png → docs/images/docker_readme.png b/images/docker_readme.png → docs/images/docker_readme.png
diff --git a/images/docker_readme2.png → docs/images/docker_readme2.png b/images/docker_readme2.png → docs/images/docker_readme2.png
diff --git a/images/import_page_create.png → docs/images/import_page_create.png b/images/import_page_create.png → docs/images/import_page_create.png
diff --git a/images/input_select_db.png → docs/images/input_select_db.png b/images/input_select_db.png → docs/images/input_select_db.png
diff --git a/images/legacy_synthetic_subject_data.csv → .../images/legacy_synthetic_subject_data.csv b/images/legacy_synthetic_subject_data.csv → .../images/legacy_synthetic_subject_data.csv
diff --git a/images/manage_database_1.png → docs/images/manage_database_1.png b/images/manage_database_1.png → docs/images/manage_database_1.png
diff --git a/images/manage_database_2.png → docs/images/manage_database_2.png b/images/manage_database_2.png → docs/images/manage_database_2.png
diff --git a/images/pgadmin.png → docs/images/pgadmin.png b/images/pgadmin.png → docs/images/pgadmin.png
diff --git a/images/populate_db.png → docs/images/populate_db.png b/images/populate_db.png → docs/images/populate_db.png
diff --git a/images/populate_db_time.png → docs/images/populate_db_time.png b/images/populate_db_time.png → docs/images/populate_db_time.png
diff --git a/images/result_page.png → docs/images/result_page.png b/images/result_page.png → docs/images/result_page.png
diff --git a/images/select_exist_db.png → docs/images/select_exist_db.png b/images/select_exist_db.png → docs/images/select_exist_db.png
diff --git a/images/set_db_name.png → docs/images/set_db_name.png b/images/set_db_name.png → docs/images/set_db_name.png
diff --git a/images/subjects_and_control_group.png → docs/images/subjects_and_control_group.png b/images/subjects_and_control_group.png → docs/images/subjects_and_control_group.png
diff --git a/images/synthetic_subject_data.csv → docs/images/synthetic_subject_data.csv b/images/synthetic_subject_data.csv → docs/images/synthetic_subject_data.csv
diff --git a/images/synthetic_timeseries_data_reduced.csv → ...ges/synthetic_timeseries_data_reduced.csv b/images/synthetic_timeseries_data_reduced.csv → ...ges/synthetic_timeseries_data_reduced.csv
diff --git a/images/upload_subject_csv.png → docs/images/upload_subject_csv.png b/images/upload_subject_csv.png → docs/images/upload_subject_csv.png
diff --git a/images/upload_time_csv.png → docs/images/upload_time_csv.png b/images/upload_time_csv.png → docs/images/upload_time_csv.png
diff --git a/docs/index.md b/docs/index.md
@@ -0,0 +1,47 @@
+# Home
+
+## Introduction 
+
+### What is the W4H Toolkit?
+
+The W4H Toolkit provides an ecosystem of tools health researchers can use to collect, store, query and analyze wearable and EHR data.
+
+### A Progressive Toolkit
+
+W4H Toolkit is an ecosystem that covers most of the common features needed when using wearables in a clinical study or or trial. As studies can have very different requirements, W4H toolkit is designed to be flexible and incrementally adoptable. These are some of the use cases we currently support:
+
+- Collect Fitbit and Garmin data
+- Analyze compliance
+- Transform the data, e.g., to compute energy expenditure
+- Produce data reports for patients in a study
+- Provide approximate queries, e.g., to query the HR of a cohort over an extended period of time
+- Running your data science notebooks on Apache Spark
+- Implementing data workflows using the library to simplify how you interact with wearable data.
+
+Some of these use cases are provided both in notebooks and in dashboard.
+
+## Quick Start
+
+The best way to try the toolkit is to use the Docker container by following the [Quick Start](quick-start.md) that will get you up and running with the dashboard and some sample notebooks in less than 20 minutes.
+
+## Components
+
+The toolkit includes the following components:
+
+- [Dashboard](dashboard/index.md): provides data input forms and visual analytics.
+- [Notebooks](notebooks/index.md): is a collection of sample notebooks that demonstrate include Panda and Spark notebooks.
+- [w4h-datasets](notebooks/): is a collection of datasets used in the W4H examples.
+- [Postgres Extensions](): provides useful extensions to queries data in the W4H database.
+- [Library](w4h-core): core python library of high-level commands to simplify how users interact with wearable data, making the platform more accessible and user-friendly.
+
+## Best Practices
+
+### Production Deployment
+
+## Extra Topics
+
+### Extending the Dashboard
+
+### Using your own Postgres Database
+
+### Contributing
diff --git a/docs/quick-start.md b/docs/quick-start.md
@@ -0,0 +1,18 @@
+# Quick Start
+
+The W4H Toolkit provides an ecosystem of tools to manage and analyze wearable and other EHR data. We have created a Docker container to give you an overview of what's included in the toolkit.
+
+## Starting the Container
+
+You will need to install the `Docker Engine` by following the instructions to [Install Docker Engine](https://docs.docker.com/engine/install/) for your platform.
+
+Once that is done start and type `uscimsc/w4h` in the search bar and select  the `preview` tagged image. After pulling to download the image, run the container by clicking on the “run” icon under “Actions” next to the image name.
+
+![images/](images/docker_readme.png)
+
+## Using the Dashboard
+
+## Using the Sample Notebookes
+
+## Next Steps
+