From 5ced3d8863d36d39a58d74fbf7974511ad2c848c Mon Sep 17 00:00:00 2001 From: riyadesale9 Date: Sat, 19 Oct 2024 19:23:00 -0700 Subject: [PATCH 1/2] added documentation for preview --- docs/getting-started/preview.md | 79 +++++++++++++++++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 docs/getting-started/preview.md diff --git a/docs/getting-started/preview.md b/docs/getting-started/preview.md new file mode 100644 index 0000000..59a81e6 --- /dev/null +++ b/docs/getting-started/preview.md @@ -0,0 +1,79 @@ +# W4H-Preview +## Introduction +This document is for the preview of W4H 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. This toolkit provides the following components: + + +**Dashboard** : An intuitive interface that offers data input forms and visual analytics tools. + +**Notebooks**: A collection of sample Jupyter notebooks that showcase various data analysis techniques. These include Pandas notebook & Pyspark notebooks. + +**Database**: A curated postgres database specifically used in W4H examples, providing real-world data for testing and demonstration purposes. + +## Docker Image +The W4H Toolkit is available as a Docker image, which can be easily pulled from [Docker Hub](https://hub.docker.com/r/uscimsc/w4h). This containerized version includes all the necessary components and dependencies, making it simple to set up and use the toolkit. + +### Pulling the W4H Docker Image +To get started with the W4H Toolkit, follow these steps: +1. Ensure Docker is installed on your system. +2. Open a terminal or command prompt. +3. Pull the W4H Docker image from Docker hub by running the following command: +```bash +docker pull usc-imsc:w4h-toolkit-preview +``` + +### Running the container +Once the image is pulled, run the container using following command: +```bash +docker run -e POSTGRES_DB=postgres -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=postgres -p 8501:8501 -p 5432:5432 -p 8888:8888 --user root -v $(pwd):/app usc-imsc:w4h-toolkit-preview +``` + +## Accessing the Dashboard +After running the container, the dashboard is available at http://localhost:8501/ + +***1. Login*** + +A default account is configured in the preview for the initial testing. Credentials for it are: +``` +username: admin +password: admin +``` + +This dashboard provides the following buttons: ++ ImportHub: It allows to add your database to the dashboard. ++ Input Page : It allows creation of queries for the data by selecting the required database & transforming the data using filters for visualizations. ++ Result Page: It takes you to the result of the query. ++ Query History: You can browse through the history of your visualizations using the Query History Button. ++ Getting Started: It provides a detailed tutorial on how to get started with the preview. + +## Accessing Jupyter Notebooks +To access the Jupyter notebooks in the W4H Toolkit, follow these steps: +1. Navigate to http://localhost:8888 in browser +2. When prompted for authentication, use: +``` +token: admin +``` +3. Once logged in, you'll see the Jupyter notebook interface with access to the /app/notebooks/ directory, which contains the sample notebooks provided by the W4H Toolkit. +4. You can now open existing notebooks or create new ones to work with the W4H datasets. + +## Accessing the Database +The curated postgres database used in the examples can be accessed using tools like pgadmin or psql. +To access the database using pgadmin use the following steps: +1. Download & install [pgadmin](https://www.pgadmin.org/) & launch it. +2. In the pgAdmin dashboard, click on "Add New Server" or right-click on "Servers" in the browser pane and select "Create" > "Server...". +3. In the "Create - Server" dialog, fill in the following details: + + General Tab: + + Name: W4H Database (or any name you prefer) + Connection Tab: + + Host name/address: localhost + Port: 5432 + Maintenance database: postgres + Username: postgres + Password: postgres +4. Save to establish the connection. Once connected, you should see the server appear in the browser pane. +5. To interact with the database: + + Expand the sample database to view its schemas, tables, and other objects. + + Use the Query Tool (accessible via Tools > Query Tool) to run SQL queries. + From 7da6391dea4f71a00eac7f830db45e47ba9b48b6 Mon Sep 17 00:00:00 2001 From: riyadesale9 Date: Sun, 27 Oct 2024 11:14:23 -0700 Subject: [PATCH 2/2] updated as per the comments --- docs/getting-started/preview.md | 47 +++++++++++++++------------------ 1 file changed, 22 insertions(+), 25 deletions(-) diff --git a/docs/getting-started/preview.md b/docs/getting-started/preview.md index 59a81e6..167fe13 100644 --- a/docs/getting-started/preview.md +++ b/docs/getting-started/preview.md @@ -1,36 +1,33 @@ # W4H-Preview -## Introduction -This document is for the preview of W4H 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. This toolkit provides the following components: +This document is for the preview of Wearables for Health (W4H) toolkit. - -**Dashboard** : An intuitive interface that offers data input forms and visual analytics tools. - -**Notebooks**: A collection of sample Jupyter notebooks that showcase various data analysis techniques. These include Pandas notebook & Pyspark notebooks. - -**Database**: A curated postgres database specifically used in W4H examples, providing real-world data for testing and demonstration purposes. - -## Docker Image -The W4H Toolkit is available as a Docker image, which can be easily pulled from [Docker Hub](https://hub.docker.com/r/uscimsc/w4h). This containerized version includes all the necessary components and dependencies, making it simple to set up and use the toolkit. +This Toolkit is available as a Docker image, which can be easily pulled from [Docker Hub](https://hub.docker.com/r/uscimsc/w4h). This containerized version includes all the necessary components and dependencies, making it simple to set up and use the toolkit. ### Pulling the W4H Docker Image To get started with the W4H Toolkit, follow these steps: -1. Ensure Docker is installed on your system. -2. Open a terminal or command prompt. -3. Pull the W4H Docker image from Docker hub by running the following command: +1. Get [Docker](https://docs.docker.com/engine/install/) for your OS. +2. Install Docker engine. +3. Open a terminal or command prompt. +4. Verify Docker installation using: ```bash -docker pull usc-imsc:w4h-toolkit-preview +docker --version ``` - -### Running the container -Once the image is pulled, run the container using following command: +5. Pull the W4H Docker image from Docker hub by running the following command: ```bash -docker run -e POSTGRES_DB=postgres -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=postgres -p 8501:8501 -p 5432:5432 -p 8888:8888 --user root -v $(pwd):/app usc-imsc:w4h-toolkit-preview +docker pull usc-imsc:w4h-toolkit-preview ``` -## Accessing the Dashboard -After running the container, the dashboard is available at http://localhost:8501/ +The W4H toolkit provides the following components: + +**Streamlit Dashboard** : An integrated interface for GeoMTS data extraction, presentation & analysis. It facilitates the analysis of both streaming & stored data. + +**Database supporting GeoMTS**: A postgres database with TimescaleDB for temporal data management, PostGIS for spatial data management & FFT postgres for aggregate queries on time series data. -***1. Login*** +**Notebooks**: A collection of sample Jupyter notebooks that help analyse compliance using Pandas & Pyspark . + + +## Accessing the Dashboard +After running the docker container, the dashboard is available at http://localhost:8501/ A default account is configured in the preview for the initial testing. Credentials for it are: ``` @@ -39,9 +36,9 @@ password: admin ``` This dashboard provides the following buttons: -+ ImportHub: It allows to add your database to the dashboard. ++ ImportHub: The ImportHub allows to integrate offfline datasets into the W4H platform. It aligns the data with GeoMTS schema & automatically maps attributes. + Input Page : It allows creation of queries for the data by selecting the required database & transforming the data using filters for visualizations. -+ Result Page: It takes you to the result of the query. ++ Result Page: It takes you to the result of the query. It provides outlier detection, comparative analysis between different groups of subjects, health insights, etc. + Query History: You can browse through the history of your visualizations using the Query History Button. + Getting Started: It provides a detailed tutorial on how to get started with the preview. @@ -56,7 +53,7 @@ token: admin 4. You can now open existing notebooks or create new ones to work with the W4H datasets. ## Accessing the Database -The curated postgres database used in the examples can be accessed using tools like pgadmin or psql. +The postgres database can be accessed using tools like pgadmin or psql. To access the database using pgadmin use the following steps: 1. Download & install [pgadmin](https://www.pgadmin.org/) & launch it. 2. In the pgAdmin dashboard, click on "Add New Server" or right-click on "Servers" in the browser pane and select "Create" > "Server...".