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CONTRIBUTING.html

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LICENSE.html

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README.html

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+<h1 id="w4h-documentation">w4h-documentation</h1>
+<p>End user documentation for the W4H platform</p>

docs/datasets/management.html

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+

docs/datasets/sampling.html

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docs/docker/Readme.html

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+<h1 id="docker-getting-started-guide">Docker Getting Started Guide</h1>
+<h2 id="installation">Installation</h2>
+<p>Docker is available for Linux, Mac, and Windows. Install the appropriate version of Docker Desktop from <a href="https://www.docker.com/products/docker-desktop">here</a>.</p>
+<h2 id="installing-the-image-in-docker-desktop">Installing the Image in Docker Desktop</h2>
+<ol type="1">
+<li>Start the Docker Desktop application.</li>
+<li>In Docker Desktop, search for <code>uscimsc/w4h</code> and select the preview-tagged image.</li>
+<li>Click “pull” to download the image.</li>
+</ol>
+<h2 id="starting-the-container">Starting the Container</h2>
+<h3 id="running-the-container-from-docker-desktop">Running the Container from Docker Desktop</h3>
+<p>When you load an image into memory, it becomes a running container. To run a container in Docker Desktop:Click on the “run” icon under “Actions” next to the image name. <span class="image">alt text</span> Click on “Optional Settings” and fill in the form as follows: <span class="image">alt text</span> Finally, click the “Run” button to start the container.</p>
+<h3 id="running-the-container-from-the-command-line-as-a-background-process">Running the Container from the Command Line as a Background Process</h3>
+<p>Alternatively, you can run a Docker image from the CLI, which is the preferred method for running Docker images.</p>
+<p><strong>NOTE:</strong> To use the Docker Command Line Interface (CLI) you may need to add <code>$HOME/.docker/bin</code> to your PATH (see note under Settings &gt; Advanced in docker desktop).</p>
+<p>When you start the container for the first time, docker will “pull” the image from Docker Hub and place a copy on your system.</p>
+<p>To start the container as a background process, execute:</p>
+<div class="sourceCode" id="cb1"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true"></a><span class="ex">docker</span> run -p 5432:5432 -e POSTGRES_DB=admin -e POSTGRES_USER=admin -e POSTGRES_PASSWORD=admin -e hostname=db -dp 8501:8501 -p 8888:8888 --name w4h uscimsc/w4h:preview</span></code></pre></div>
+<h3 id="running-the-container-from-the-command-line-in-verbose-mode">Running the Container from the Command Line in Verbose Mode</h3>
+<p>To start the container in verbose mode, execute in a terminal:</p>
+<div class="sourceCode" id="cb2"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true"></a><span class="ex">docker</span> run -p 5432:5432 -e POSTGRES_DB=admin -e POSTGRES_USER=admin -e POSTGRES_PASSWORD=admin -e hostname=db -p 8501:8501 -p 8888:8888 --name w4h uscimsc/w4h:preview</span></code></pre></div>
+<p>The following is the truncated output:</p>
+<div class="sourceCode" id="cb3"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true"></a><span class="ex">docker</span> run -p 5432:5432 -e POSTGRES_USER=admin -e POSTGRES_DB=admin -e POSTGRES_PASSWORD=admin -e hostname=db -p 8501:8501 uscimsc/w4h:sample</span>
+<span id="cb3-2"><a href="#cb3-2" aria-hidden="true"></a><span class="ex">Unable</span> to find image <span class="st">&#39;uscimsc/w4h:sample&#39;</span> locally</span>
+<span id="cb3-3"><a href="#cb3-3" aria-hidden="true"></a><span class="ex">sample</span>: Pulling from uscimsc/w4h</span>
+<span id="cb3-4"><a href="#cb3-4" aria-hidden="true"></a><span class="ex">09f376ebb190</span>: Already exists</span>
+<span id="cb3-5"><a href="#cb3-5" aria-hidden="true"></a><span class="ex">276709cbedc1</span>: Already exists</span>
+<span id="cb3-6"><a href="#cb3-6" aria-hidden="true"></a><span class="ex">e5c23cad8c0c</span>: Already exists</span>
+<span id="cb3-7"><a href="#cb3-7" aria-hidden="true"></a><span class="ex">a56c5f373d66</span>: Already exists</span>
+<span id="cb3-8"><a href="#cb3-8" aria-hidden="true"></a><span class="ex">52a924435656</span>: Already exists</span>
+<span id="cb3-9"><a href="#cb3-9" aria-hidden="true"></a><span class="ex">44287a1b4544</span>: Pull complete</span>
+<span id="cb3-10"><a href="#cb3-10" aria-hidden="true"></a><span class="ex">faeff104f7d4</span>: Pull complete</span>
+<span id="cb3-11"><a href="#cb3-11" aria-hidden="true"></a><span class="ex">8348408b99d4</span>: Pull complete</span>
+<span id="cb3-12"><a href="#cb3-12" aria-hidden="true"></a><span class="ex">42f17385f3e6</span>: Pull complete</span>
+<span id="cb3-13"><a href="#cb3-13" aria-hidden="true"></a><span class="ex">f664f8d57e6f</span>: Pull complete</span>
+<span id="cb3-14"><a href="#cb3-14" aria-hidden="true"></a><span class="ex">fc8b5d5b936d</span>: Pull complete</span>
+<span id="cb3-15"><a href="#cb3-15" aria-hidden="true"></a><span class="ex">f0f33a64bd6a</span>: Pull complete</span>
+<span id="cb3-16"><a href="#cb3-16" aria-hidden="true"></a><span class="ex">d0ecff9210b4</span>: Pull complete</span>
+<span id="cb3-17"><a href="#cb3-17" aria-hidden="true"></a><span class="ex">fc27e1e5de2b</span>: Pull complete</span>
+<span id="cb3-18"><a href="#cb3-18" aria-hidden="true"></a><span class="ex">4a3bc7281b03</span>: Pull complete</span>
+<span id="cb3-19"><a href="#cb3-19" aria-hidden="true"></a><span class="ex">Digest</span>: sha256:6475ddd657e2264751081ee7567367455deb876975ad3e862dbf2446a27d0eb0</span>
+<span id="cb3-20"><a href="#cb3-20" aria-hidden="true"></a><span class="ex">Status</span>: Downloaded newer image for uscimsc/w4h:sample</span>
+<span id="cb3-21"><a href="#cb3-21" aria-hidden="true"></a><span class="ex">WARNING</span>: The requested image<span class="st">&#39;s platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested</span></span>
+<span id="cb3-22"><a href="#cb3-22" aria-hidden="true"></a><span class="st">Starting PostgreSQL 15 database server: main.</span></span>
+<span id="cb3-23"><a href="#cb3-23" aria-hidden="true"></a><span class="st">...</span></span>
+<span id="cb3-24"><a href="#cb3-24" aria-hidden="true"></a><span class="st">Collecting usage statistics. To deactivate, set browser.gatherUsageStats to False.</span></span>
+<span id="cb3-25"><a href="#cb3-25" aria-hidden="true"></a></span>
+<span id="cb3-26"><a href="#cb3-26" aria-hidden="true"></a><span class="st"> * Serving Flask app &#39;</span>stream_sim<span class="st">&#39; (lazy loading)</span></span>
+<span id="cb3-27"><a href="#cb3-27" aria-hidden="true"></a><span class="st"> * Environment: production</span></span>
+<span id="cb3-28"><a href="#cb3-28" aria-hidden="true"></a><span class="st">   WARNING: This is a development server. Do not use it in a production deployment.</span></span>
+<span id="cb3-29"><a href="#cb3-29" aria-hidden="true"></a><span class="st">   Use a production WSGI server instead.</span></span>
+<span id="cb3-30"><a href="#cb3-30" aria-hidden="true"></a><span class="st"> * Debug mode: off</span></span>
+<span id="cb3-31"><a href="#cb3-31" aria-hidden="true"></a><span class="st">WARNING: This is a development server. Do not use it in a production deployment. Use a production WSGI server instead.</span></span>
+<span id="cb3-32"><a href="#cb3-32" aria-hidden="true"></a><span class="st"> * Running on http://127.0.0.1:9977</span></span>
+<span id="cb3-33"><a href="#cb3-33" aria-hidden="true"></a><span class="st">Press CTRL+C to quit</span></span>
+<span id="cb3-34"><a href="#cb3-34" aria-hidden="true"></a></span>
+<span id="cb3-35"><a href="#cb3-35" aria-hidden="true"></a><span class="st">  You can now view your Streamlit app in your browser.</span></span>
+<span id="cb3-36"><a href="#cb3-36" aria-hidden="true"></a></span>
+<span id="cb3-37"><a href="#cb3-37" aria-hidden="true"></a><span class="st">  Network URL: http://172.17.0.2:8501</span></span>
+<span id="cb3-38"><a href="#cb3-38" aria-hidden="true"></a><span class="st">  External URL: http://64.98.216.199:8501</span></span></code></pre></div>
+<p>You can reach the dashboard at http://localhost:8501. ## Container Management</p>
+<h3 id="show-all-running-containers">Show All Running Containers</h3>
+<p>To show all currently running containers on your system, execute:</p>
+<div class="sourceCode" id="cb4"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true"></a><span class="ex">docker</span> ps</span></code></pre></div>
+<p>The following is an example output:</p>
+<div class="sourceCode" id="cb5"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true"></a><span class="ex">CONTAINER</span> ID   IMAGE                COMMAND                  CREATED        STATUS        PORTS                                            NAMES</span>
+<span id="cb5-2"><a href="#cb5-2" aria-hidden="true"></a><span class="ex">8e1812539aa6</span>   uscimsc/w4h:sample   <span class="st">&quot;./inituser_and_star…&quot;</span>   23 hours ago   Up 23 hours   0.0.0.0:5432-<span class="op">&gt;</span>5432/tcp, 0.0.0.0:8501-<span class="op">&gt;</span>8501/tcp   kind_cohen</span></code></pre></div>
+<h3 id="show-all-stopped-containers">Show All Stopped Containers</h3>
+<p>To show all stopped containers on your system, execute:</p>
+<div class="sourceCode" id="cb6"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true"></a><span class="ex">docker</span> ps -filter <span class="st">&quot;status=exited&quot;</span></span></code></pre></div>
+<p>The following is an example output:</p>
+<div class="sourceCode" id="cb7"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true"></a><span class="ex">CONTAINER</span> ID   IMAGE                COMMAND                  CREATED        STATUS        PORTS                                            NAMES</span>
+<span id="cb7-2"><a href="#cb7-2" aria-hidden="true"></a><span class="ex">8e1812539aa6</span>   uscimsc/w4h:sample   <span class="st">&quot;./inituser_and_star…&quot;</span>   23 hours ago   Up 23 hours   0.0.0.0:5432-<span class="op">&gt;</span>5432/tcp, 0.0.0.0:8501-<span class="op">&gt;</span>8501/tcp   kind_cohen</span></code></pre></div>
+<h3 id="stopping-the-container">Stopping the Container</h3>
+<p>To stop a running container, execute:</p>
+<div class="sourceCode" id="cb8"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true"></a><span class="ex">docker</span> stop <span class="op">&lt;</span>container id<span class="op">&gt;</span></span></code></pre></div>
+<h3 id="starting-a-stopped-container">Starting a Stopped Container</h3>
+<p>To restart a stopped container, execute:</p>
+<div class="sourceCode" id="cb9"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true"></a><span class="ex">docker</span> start <span class="op">&lt;</span>container id<span class="op">&gt;</span></span></code></pre></div>
+<h3 id="removing-a-container">Removing a Container</h3>
+<p>To remove a Docker container from your system, execute:</p>
+<div class="sourceCode" id="cb10"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true"></a><span class="ex">docker</span> rm <span class="op">&lt;</span>container id<span class="op">&gt;</span></span></code></pre></div>
+<h3 id="starting-a-shell-on-a-running-container">Starting a Shell on a Running Container</h3>
+<p>To open a shell session on a running container, execute:</p>
+<div class="sourceCode" id="cb11"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true"></a><span class="ex">docker</span> exec -it <span class="op">&lt;</span>container ID<span class="op">&gt;</span> sh</span></code></pre></div>
+<h2 id="image-management">Image Management</h2>
+<h3 id="show-all-images-in-local-repository">Show All Images in Local Repository</h3>
+<p>To see all images on your local system, execute:</p>
+<div class="sourceCode" id="cb12"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true"></a><span class="ex">docker</span> images</span></code></pre></div>
+<p>The following is an example of the output:</p>
+<div class="sourceCode" id="cb13"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true"></a><span class="ex">REPOSITORY</span>    TAG       IMAGE ID       CREATED        SIZE</span>
+<span id="cb13-2"><a href="#cb13-2" aria-hidden="true"></a><span class="ex">uscimsc/w4h</span>   sample    9b5e51e6d1b8   25 hours ago   1.66GB</span></code></pre></div>
+<h3 id="remove-image-from-local-repository">Remove Image from Local Repository</h3>
+<p>To remove an image from your system, run:</p>
+<div class="sourceCode" id="cb14"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true"></a><span class="ex">docker</span> rmi <span class="op">&lt;</span>image name<span class="op">&gt;</span></span></code></pre></div>
+<h2 id="how-to-login-dashboard">How to login dashboard</h2>
+<p>Then access <code>http://{your_server_ip}:8501/</code> to see the dashboard.</p>
+<p>username: admin passward: admin</p>
+<p>more details please check <a href="https://github.com/USC-InfoLab/w4h-documentation/blob/main/docs/getting-started/how_to_start.md">Use W4h dashboard to track your patients’ health data</a></p>

docs/docker/configuration.html

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+

docs/docker/deploy.html

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+

docs/getting-started/how_to_start.html

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+<h1 id="use-w4h-dashboard-to-track-your-patients-health-data">Use W4h dashboard to track your patients’ health data</h1>
+<h2 id="introduction">Introduction</h2>
+<p>The W4H GeoMTS dashboard is designed to provide visualization and analysis capabilities for GeoMTS data catered specifically for Apple Watch demo purposes.</p>
+<h2 id="how-to-play-with-it">How to play with it</h2>
+<ol start="0" type="1">
+<li><p><strong>Log in</strong><br />
+We have provided a default account for you to test the system. In the future, w4h will be polished to support multiple users and password management. The default account is: &gt; username: admin<br />
+password: admin</p></li>
+<li><p><strong>Create/Manage your database instance in your DB server:</strong><br />
+At this moment, you should have read the Setting up tutorial and set up your database server. If you already have data in proper format in your database, you can skip this step.<br />
+Click the “import page” button on the left side of the dashboard, you will see a page like this:<br />
+<span class="image">import_page_create</span></p>
+<p>Let’s start from creating a new database instance:<br />
+First, Select “Create new W4H database instance”<br />
+<span class="image">create_new_db</span></p>
+<p>Second, type in the name of database you want to make, and click “create”. In this case we name it “test2” <span class="image">import_page_create</span> If it’s created successfully, you will see a message like this:<br />
+<span class="image">import_page_create</span></p>
+<p>Third, select “Choose existing W4H database instance”<br />
+<span class="image">import_page_create</span> Select the database you just created<br />
+<span class="image">import_page_create</span></p>
+<p>For the Following step, if you need some test file, try to download here:<br />
+<a href="./../../images/synthetic_subject_data.csv">synthetic_subject_data.csv</a></p>
+<p><a href="./../../images/synthetic_timeseries_data_reduced.csv">synthetic_timeseries_data_reduced.csv</a></p>
+<p>Fourth, Upload your subjects csv file, and check “Populate subject table name”. <span class="image">import_page_create</span> After making sure corresponding Column are all correct, click “Populate database” at the bottom.<br />
+<span class="image">import_page_create</span></p>
+<p>Fifth, upload your time series csv file<br />
+<span class="image">import_page_create</span> After making sure corresponding Column are all correct, click “Populate database” at the bottom.<br />
+<span class="image">import_page_create</span></p>
+<p>(Optional)Sixth, open your DB management tool, such as PgAdmin4, and check if the data is populated correctly.<br />
+<span class="image">import_page_create</span></p></li>
+<li><p><strong>choose your db in the input page, then setup it!</strong></p>
+<p>choose your db in the input page<br />
+<span class="image">import_page_create</span></p>
+<p>select the subjects and control group you want to check<br />
+<span class="image">import_page_create</span></p>
+<p>select if you want to simulate the data click “show result”</p></li>
+<li><p><strong>check the result page</strong><br />
+You are there!<br />
+<span class="image">import_page_create</span></p></li>
+</ol>

docs/getting-started/other_things.html

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+<h2 id="other-things">Other things:</h2>
+<ol type="1">
+<li><p>If you want to try how to set up, try in this link: https://labs.play-with-docker.com/</p></li>
+<li><p>There is a 5min video to show how to set up the environment: https://drive.google.com/file/d/1basc9nWQKclpZJgMq-K81KAGihfxkdb2/view?usp=sharing</p></li>
+</ol>

docs/getting-started/setting_up.html

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+<h1 id="welcome-to-w4h-setting-up-toturial">Welcome to w4h setting up toturial!</h1>
+<h2 id="prerequisites">Prerequisites</h2>
+<ol type="1">
+<li><p>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: &gt; wget https://raw.githubusercontent.com/USC-InfoLab/w4h-integrated-toolkit/jize/docker-compose.yml &amp;&amp; docker-compose up –build</p></li>
+<li><p>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.</p></li>
+</ol>
+<h2 id="set-up">Set up</h2>
+<p>login in with username and password(use “admin” for both username and password in first time)</p>
+<p>Then following instruction to set your database <span class="image">import_page_create</span> <span class="image">import_page_create</span></p>

docs/notebooks/examples/example1.html

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docs/notebooks/examples/example2.html

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docs/notebooks/overview.html

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+