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<span class="md-nav__icon md-icon"></span>
|
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Empatica
|
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</label>
|
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
|
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<a href="../../datastreams/empatica-zip/" class="md-nav__link">
|
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empatica_zip
|
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</a>
|
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</li>
|
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<li class="md-nav__item">
|
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<a href="../../datastreams/mandatory-empatica-format/" class="md-nav__link">
|
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Mandatory Empatica Format
|
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</a>
|
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</li>
|
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</ul>
|
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</nav>
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</li>
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<li class="md-nav__item">
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<a href="../../datastreams/add-new-data-streams/" class="md-nav__link">
|
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Add New Data Streams
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</a>
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</li>
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</ul>
|
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</nav>
|
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</li>
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
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<input class="md-nav__toggle md-toggle" data-md-toggle="__nav_4" type="checkbox" id="__nav_4" >
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<label class="md-nav__link" for="__nav_4">
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Behavioral Features
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" aria-label="Behavioral Features" data-md-level="1">
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<label class="md-nav__title" for="__nav_4">
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<span class="md-nav__icon md-icon"></span>
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Behavioral Features
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../../features/feature-introduction/" class="md-nav__link">
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Introduction
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</a>
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</li>
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<li class="md-nav__item md-nav__item--nested">
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<input class="md-nav__toggle md-toggle" data-md-toggle="__nav_4_2" type="checkbox" id="__nav_4_2" >
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<label class="md-nav__link" for="__nav_4_2">
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Phone
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<span class="md-nav__icon md-icon"></span>
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</label>
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<nav class="md-nav" aria-label="Phone" data-md-level="2">
|
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<label class="md-nav__title" for="__nav_4_2">
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<span class="md-nav__icon md-icon"></span>
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Phone
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</label>
|
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../../features/phone-accelerometer/" class="md-nav__link">
|
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Phone Accelerometer
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</a>
|
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</li>
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<li class="md-nav__item">
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<a href="../../features/phone-activity-recognition/" class="md-nav__link">
|
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Phone Activity Recognition
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</a>
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</li>
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<li class="md-nav__item">
|
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<a href="../../features/phone-applications-crashes/" class="md-nav__link">
|
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Phone Applications Crashes
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</a>
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</li>
|
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<li class="md-nav__item">
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<a href="../../features/phone-applications-foreground/" class="md-nav__link">
|
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Phone Applications Foreground
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</a>
|
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</li>
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<li class="md-nav__item">
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<a href="../../features/phone-applications-notifications/" class="md-nav__link">
|
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Phone Applications Notifications
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</a>
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</li>
|
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<li class="md-nav__item">
|
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<a href="../../features/phone-battery/" class="md-nav__link">
|
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Phone Battery
|
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</a>
|
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</li>
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<li class="md-nav__item">
|
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<a href="../../features/phone-bluetooth/" class="md-nav__link">
|
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Phone Bluetooth
|
|
</a>
|
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</li>
|
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<li class="md-nav__item">
|
|
<a href="../../features/phone-calls/" class="md-nav__link">
|
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Phone Calls
|
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</a>
|
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</li>
|
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<li class="md-nav__item">
|
|
<a href="../../features/phone-conversation/" class="md-nav__link">
|
|
Phone Conversation
|
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</a>
|
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</li>
|
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|
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<li class="md-nav__item">
|
|
<a href="../../features/phone-data-yield/" class="md-nav__link">
|
|
Phone Data Yield
|
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</a>
|
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</li>
|
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|
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<li class="md-nav__item">
|
|
<a href="../../features/phone-keyboard/" class="md-nav__link">
|
|
Phone Keyboard
|
|
</a>
|
|
</li>
|
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|
|
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|
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<li class="md-nav__item">
|
|
<a href="../../features/phone-light/" class="md-nav__link">
|
|
Phone Light
|
|
</a>
|
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</li>
|
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|
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<li class="md-nav__item">
|
|
<a href="../../features/phone-locations/" class="md-nav__link">
|
|
Phone Locations
|
|
</a>
|
|
</li>
|
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|
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|
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<li class="md-nav__item">
|
|
<a href="../../features/phone-log/" class="md-nav__link">
|
|
Phone Log
|
|
</a>
|
|
</li>
|
|
|
|
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|
|
<li class="md-nav__item">
|
|
<a href="../../features/phone-messages/" class="md-nav__link">
|
|
Phone Messages
|
|
</a>
|
|
</li>
|
|
|
|
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|
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<li class="md-nav__item">
|
|
<a href="../../features/phone-screen/" class="md-nav__link">
|
|
Phone Screen
|
|
</a>
|
|
</li>
|
|
|
|
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|
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|
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|
|
<li class="md-nav__item">
|
|
<a href="../../features/phone-wifi-connected/" class="md-nav__link">
|
|
Phone WiFI Connected
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
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|
|
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|
|
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|
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|
|
<li class="md-nav__item">
|
|
<a href="../../features/phone-wifi-visible/" class="md-nav__link">
|
|
Phone WiFI Visible
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
</ul>
|
|
</nav>
|
|
</li>
|
|
|
|
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|
|
|
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|
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|
|
|
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|
|
<li class="md-nav__item md-nav__item--nested">
|
|
|
|
|
|
<input class="md-nav__toggle md-toggle" data-md-toggle="__nav_4_3" type="checkbox" id="__nav_4_3" >
|
|
|
|
|
|
|
|
|
|
<label class="md-nav__link" for="__nav_4_3">
|
|
Fitbit
|
|
<span class="md-nav__icon md-icon"></span>
|
|
</label>
|
|
|
|
<nav class="md-nav" aria-label="Fitbit" data-md-level="2">
|
|
<label class="md-nav__title" for="__nav_4_3">
|
|
<span class="md-nav__icon md-icon"></span>
|
|
Fitbit
|
|
</label>
|
|
<ul class="md-nav__list" data-md-scrollfix>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../features/fitbit-calories-intraday/" class="md-nav__link">
|
|
Fitbit Calories Intraday
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../features/fitbit-data-yield/" class="md-nav__link">
|
|
Fitbit Data Yield
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../features/fitbit-heartrate-summary/" class="md-nav__link">
|
|
Fitbit Heart Rate Summary
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
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|
|
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|
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|
|
<li class="md-nav__item">
|
|
<a href="../../features/fitbit-heartrate-intraday/" class="md-nav__link">
|
|
Fitbit Heart Rate Intraday
|
|
</a>
|
|
</li>
|
|
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|
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|
|
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|
|
<li class="md-nav__item">
|
|
<a href="../../features/fitbit-sleep-summary/" class="md-nav__link">
|
|
Fitbit Sleep Summary
|
|
</a>
|
|
</li>
|
|
|
|
|
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|
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|
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|
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|
|
<li class="md-nav__item">
|
|
<a href="../../features/fitbit-sleep-intraday/" class="md-nav__link">
|
|
Fitbit Sleep Intraday
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../features/fitbit-steps-summary/" class="md-nav__link">
|
|
Fitbit Steps Summary
|
|
</a>
|
|
</li>
|
|
|
|
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|
|
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|
|
|
|
|
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|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../features/fitbit-steps-intraday/" class="md-nav__link">
|
|
Fitbit Steps Intraday
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
</ul>
|
|
</nav>
|
|
</li>
|
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|
|
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|
|
|
|
|
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|
|
<li class="md-nav__item md-nav__item--nested">
|
|
|
|
|
|
<input class="md-nav__toggle md-toggle" data-md-toggle="__nav_4_4" type="checkbox" id="__nav_4_4" >
|
|
|
|
|
|
|
|
|
|
<label class="md-nav__link" for="__nav_4_4">
|
|
Empatica
|
|
<span class="md-nav__icon md-icon"></span>
|
|
</label>
|
|
|
|
<nav class="md-nav" aria-label="Empatica" data-md-level="2">
|
|
<label class="md-nav__title" for="__nav_4_4">
|
|
<span class="md-nav__icon md-icon"></span>
|
|
Empatica
|
|
</label>
|
|
<ul class="md-nav__list" data-md-scrollfix>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../features/empatica-accelerometer/" class="md-nav__link">
|
|
Empatica Accelerometer
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../features/empatica-heartrate/" class="md-nav__link">
|
|
Empatica Heart Rate
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../features/empatica-temperature/" class="md-nav__link">
|
|
Empatica Temperature
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../features/empatica-electrodermal-activity/" class="md-nav__link">
|
|
Empatica Electrodermal Activity
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../features/empatica-blood-volume-pulse/" class="md-nav__link">
|
|
Empatica Blood Volume Pulse
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../features/empatica-inter-beat-interval/" class="md-nav__link">
|
|
Empatica Inter Beat Interval
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../features/empatica-tags/" class="md-nav__link">
|
|
Empatica Tags
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
</ul>
|
|
</nav>
|
|
</li>
|
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|
|
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|
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|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../features/add-new-features/" class="md-nav__link">
|
|
Add New Features
|
|
</a>
|
|
</li>
|
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|
|
|
|
|
|
|
|
</ul>
|
|
</nav>
|
|
</li>
|
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|
|
|
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|
|
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
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|
<input class="md-nav__toggle md-toggle" data-md-toggle="__nav_5" type="checkbox" id="__nav_5" >
|
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|
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|
|
|
|
<label class="md-nav__link" for="__nav_5">
|
|
Visualizations
|
|
<span class="md-nav__icon md-icon"></span>
|
|
</label>
|
|
|
|
<nav class="md-nav" aria-label="Visualizations" data-md-level="1">
|
|
<label class="md-nav__title" for="__nav_5">
|
|
<span class="md-nav__icon md-icon"></span>
|
|
Visualizations
|
|
</label>
|
|
<ul class="md-nav__list" data-md-scrollfix>
|
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|
|
|
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|
|
|
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|
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|
|
<li class="md-nav__item">
|
|
<a href="../../visualizations/data-quality-visualizations/" class="md-nav__link">
|
|
Data Quality
|
|
</a>
|
|
</li>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../visualizations/feature-visualizations/" class="md-nav__link">
|
|
Features
|
|
</a>
|
|
</li>
|
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|
|
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</ul>
|
|
</nav>
|
|
</li>
|
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|
|
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
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|
|
<input class="md-nav__toggle md-toggle" data-md-toggle="__nav_6" type="checkbox" id="__nav_6" >
|
|
|
|
|
|
|
|
|
|
<label class="md-nav__link" for="__nav_6">
|
|
Analysis Workflows
|
|
<span class="md-nav__icon md-icon"></span>
|
|
</label>
|
|
|
|
<nav class="md-nav" aria-label="Analysis Workflows" data-md-level="1">
|
|
<label class="md-nav__title" for="__nav_6">
|
|
<span class="md-nav__icon md-icon"></span>
|
|
Analysis Workflows
|
|
</label>
|
|
<ul class="md-nav__list" data-md-scrollfix>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<li class="md-nav__item">
|
|
<a href="../../workflow-examples/analysis/" class="md-nav__link">
|
|
Complete Example
|
|
</a>
|
|
</li>
|
|
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<h1 id="validation-schema-of-configyaml">Validation schema of <code>config.yaml</code><a class="headerlink" href="#validation-schema-of-configyaml" title="Permanent link">¶</a></h1>
|
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<div class="admonition hint">
|
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<p class="admonition-title">Why do we need to validate the <code>config.yaml</code>?</p>
|
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<p>Most of the key/values in the <code>config.yaml</code> are constrained to a set of possible values or types. For example <code>[TIME_SEGMENTS][TYPE]</code> can only be one of <code>["FREQUENCY", "PERIODIC", "EVENT"]</code>, and <code>[TIMEZONE]</code> has to be a string. </p>
|
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<p>We should show the user an error if that’s not the case. We could validate this in Python or R but since we reuse scripts and keys in multiple places, tracking these validations can be time consuming and get out of control. Thus, we do these validations through a schema and check that schema before RAPIDS starts processing any data so the user can see the error right away.</p>
|
|
<p>Keep in mind these validations can only cover certain base cases. Some validations that require more complex logic should still be done in the respective script. For example, we can check that a CSV file path actually ends in <code>.csv</code> but we can only check that the file actually exists in a Python script.</p>
|
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</div>
|
|
<p>The structure and values of the <code>config.yaml</code> file are validated using a YAML schema stored in <code>tools/config.schema.yaml</code>. Each key in <code>config.yaml</code>, for example <code>PIDS</code>, has a corresponding entry in the schema where we can validate its type, possible values, required properties, min and max values, among other things. </p>
|
|
<p>The <code>config.yaml</code> is validated against the schema every time RAPIDS runs (see the top of the <code>Snakefile</code>):</p>
|
|
<div class="highlight"><pre><span></span><code><span class="n">validate</span><span class="p">(</span><span class="n">config</span><span class="p">,</span> <span class="s2">"tools/config.schema.yaml"</span><span class="p">)</span>
|
|
</code></pre></div>
|
|
<h2 id="structure-of-the-schema">Structure of the schema<a class="headerlink" href="#structure-of-the-schema" title="Permanent link">¶</a></h2>
|
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<p>The schema has three main sections <code>required</code>, <code>definitions</code>, and <code>properties</code>. All of them are just nested key/value YAML pairs, where the value can be a primitive type (<code>integer</code>, <code>string</code>, <code>boolean</code>, <code>number</code>) or can be another key/value pair (<code>object</code>).</p>
|
|
<h3 id="required">required<a class="headerlink" href="#required" title="Permanent link">¶</a></h3>
|
|
<p><code>required</code> lists <code>properties</code> that should be present in the <code>config.yaml</code>. We will almost always add every <code>config.yaml</code> key to this list (meaning that the user cannot delete any of those keys like <code>TIMEZONE</code> or <code>PIDS</code>). </p>
|
|
<h3 id="definitions">definitions<a class="headerlink" href="#definitions" title="Permanent link">¶</a></h3>
|
|
<p><code>definitions</code> lists key/values that are common to different <code>properties</code> so we can reuse them. You can define a key/value under <code>definitions</code> and use <code>$ref</code> to refer to it in any <code>property</code>. </p>
|
|
<p>For example, every sensor like <code>[PHONE_ACCELEROMETER]</code> has one or more providers like <code>RAPIDS</code> and <code>PANDA</code>, these providers have some common properties like the <code>COMPUTE</code> flag or the <code>SRC_SCRIPT</code> string. Therefore we define a shared provider “template” that is used by every provider and extended with properties exclusive to each one of them. For example:</p>
|
|
<div class="tabbed-set" data-tabs="1:2"><input checked="checked" id="__tabbed_1_1" name="__tabbed_1" type="radio" /><label for="__tabbed_1_1">provider definition (template)</label><div class="tabbed-content">
|
|
<p>The <code>PROVIDER</code> definition will be used later on different <code>properties</code>.</p>
|
|
<div class="highlight"><pre><span></span><code><span class="nt">PROVIDER</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">object</span>
|
|
<span class="nt">required</span><span class="p">:</span> <span class="p p-Indicator">[</span><span class="nv">COMPUTE</span><span class="p p-Indicator">,</span> <span class="nv">SRC_SCRIPT</span><span class="p p-Indicator">,</span> <span class="nv">FEATURES</span><span class="p p-Indicator">]</span>
|
|
<span class="nt">properties</span><span class="p">:</span>
|
|
<span class="nt">COMPUTE</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">boolean</span>
|
|
<span class="nt">FEATURES</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="p p-Indicator">[</span><span class="nv">array</span><span class="p p-Indicator">,</span> <span class="nv">object</span><span class="p p-Indicator">]</span>
|
|
<span class="nt">SRC_SCRIPT</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">string</span>
|
|
<span class="nt">pattern</span><span class="p">:</span> <span class="s">"^.*\\.(py|R)$"</span>
|
|
</code></pre></div>
|
|
</div>
|
|
<input id="__tabbed_1_2" name="__tabbed_1" type="radio" /><label for="__tabbed_1_2">provider reusing and extending the template</label><div class="tabbed-content">
|
|
<p>Notice that <code>RAPIDS</code> (a provider) uses and extends the <code>PROVIDER</code> template in this example. The <code>FEATURES</code> key is overriding the <code>FEATURES</code> key from the <code>#/definitions/PROVIDER</code> template but is keeping the validation for <code>COMPUTE</code>, and <code>SRC_SCRIPT</code>. For more details about reusing properties, go to this <a href="http://json-schema.org/understanding-json-schema/structuring.html#reuse">link</a></p>
|
|
<div class="highlight"><pre><span></span><code><span class="nt">PHONE_ACCELEROMETER</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">object</span>
|
|
<span class="l l-Scalar l-Scalar-Plain"># .. other properties</span>
|
|
<span class="nt">PROVIDERS</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="p p-Indicator">[</span><span class="s">"null"</span><span class="p p-Indicator">,</span> <span class="nv">object</span><span class="p p-Indicator">]</span>
|
|
<span class="nt">properties</span><span class="p">:</span>
|
|
<span class="nt">RAPIDS</span><span class="p">:</span>
|
|
<span class="nt">allOf</span><span class="p">:</span>
|
|
<span class="hll"> <span class="p p-Indicator">-</span> <span class="nt">$ref</span><span class="p">:</span> <span class="s">"#/definitions/PROVIDER"</span>
|
|
</span><span class="hll"> <span class="p p-Indicator">-</span> <span class="nt">properties</span><span class="p">:</span>
|
|
</span> <span class="nt">FEATURES</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">array</span>
|
|
<span class="nt">uniqueItems</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">True</span>
|
|
<span class="nt">items</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">string</span>
|
|
<span class="nt">enum</span><span class="p">:</span> <span class="p p-Indicator">[</span><span class="s">"maxmagnitude"</span><span class="p p-Indicator">,</span> <span class="s">"minmagnitude"</span><span class="p p-Indicator">,</span> <span class="s">"avgmagnitude"</span><span class="p p-Indicator">,</span> <span class="s">"medianmagnitude"</span><span class="p p-Indicator">,</span> <span class="s">"stdmagnitude"</span><span class="p p-Indicator">]</span>
|
|
</code></pre></div>
|
|
</div>
|
|
</div>
|
|
<h3 id="properties">properties<a class="headerlink" href="#properties" title="Permanent link">¶</a></h3>
|
|
<p><code>properties</code> are nested key/values that describe the different components of our <code>config.yaml</code> file. Values can be of one or more primitive types like <code>string</code>, <code>number</code>, <code>array</code>, <code>boolean</code> and <code>null</code>. Values can also be another key/value pair (of type <code>object</code>) that are similar to a dictionary in Python.</p>
|
|
<p>For example, the following property validates the <code>PIDS</code> of our <code>config.yaml</code>. It checks that <code>PIDS</code> is an <code>array</code> with unique items of type <code>string</code>.</p>
|
|
<div class="highlight"><pre><span></span><code><span class="nt">PIDS</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">array</span>
|
|
<span class="nt">uniqueItems</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">True</span>
|
|
<span class="nt">items</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">string</span>
|
|
</code></pre></div>
|
|
<h2 id="modifying-the-schema">Modifying the schema<a class="headerlink" href="#modifying-the-schema" title="Permanent link">¶</a></h2>
|
|
<div class="admonition hint">
|
|
<p class="admonition-title">Validating the <code>config.yaml</code> during development</p>
|
|
<p>If you updated the schema and want to check the <code>config.yaml</code> is compliant, you can run the command <code>snakemake --list-params-changes</code>. You will see <code>Building DAG of jobs...</code> if there are no problems or an error message otherwise (try setting any <code>COMPUTE</code> flag to a string like <code>test</code> instead of <code>False/True</code>).</p>
|
|
<p>You can use this command without having to configure RAPIDS to process any participants or sensors.</p>
|
|
</div>
|
|
<p>You can validate different aspects of each key/value in our <code>config.yaml</code> file:</p>
|
|
<div class="tabbed-set" data-tabs="2:5"><input checked="checked" id="__tabbed_2_1" name="__tabbed_2" type="radio" /><label for="__tabbed_2_1">number/integer</label><div class="tabbed-content">
|
|
<p>Including min and max values
|
|
<div class="highlight"><pre><span></span><code><span class="nt">MINUTE_RATIO_THRESHOLD_FOR_VALID_YIELDED_HOURS</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">number</span>
|
|
<span class="nt">minimum</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">0</span>
|
|
<span class="nt">maximum</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">1</span>
|
|
|
|
<span class="nt">FUSED_RESAMPLED_CONSECUTIVE_THRESHOLD</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">integer</span>
|
|
<span class="nt">exclusiveMinimum</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">0</span>
|
|
</code></pre></div></p>
|
|
</div>
|
|
<input id="__tabbed_2_2" name="__tabbed_2" type="radio" /><label for="__tabbed_2_2">string</label><div class="tabbed-content">
|
|
<p>Including valid values (<code>enum</code>)
|
|
<div class="highlight"><pre><span></span><code><span class="nt">items</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">string</span>
|
|
<span class="nt">enum</span><span class="p">:</span> <span class="p p-Indicator">[</span><span class="s">"count"</span><span class="p p-Indicator">,</span> <span class="s">"maxlux"</span><span class="p p-Indicator">,</span> <span class="s">"minlux"</span><span class="p p-Indicator">,</span> <span class="s">"avglux"</span><span class="p p-Indicator">,</span> <span class="s">"medianlux"</span><span class="p p-Indicator">,</span> <span class="s">"stdlux"</span><span class="p p-Indicator">]</span>
|
|
</code></pre></div></p>
|
|
</div>
|
|
<input id="__tabbed_2_3" name="__tabbed_2" type="radio" /><label for="__tabbed_2_3">boolean</label><div class="tabbed-content">
|
|
<div class="highlight"><pre><span></span><code><span class="nt">MINUTES_DATA_USED</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">boolean</span>
|
|
</code></pre></div>
|
|
</div>
|
|
<input id="__tabbed_2_4" name="__tabbed_2" type="radio" /><label for="__tabbed_2_4">array</label><div class="tabbed-content">
|
|
<p>Including whether or not it should have unique values, the type of the array’s elements (<code>strings</code>, <code>numbers</code>) and valid values (<code>enum</code>).
|
|
<div class="highlight"><pre><span></span><code><span class="nt">MESSAGES_TYPES</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">array</span>
|
|
<span class="nt">uniqueItems</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">True</span>
|
|
<span class="nt">items</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">string</span>
|
|
<span class="nt">enum</span><span class="p">:</span> <span class="p p-Indicator">[</span><span class="s">"received"</span><span class="p p-Indicator">,</span> <span class="s">"sent"</span><span class="p p-Indicator">]</span>
|
|
</code></pre></div></p>
|
|
</div>
|
|
<input id="__tabbed_2_5" name="__tabbed_2" type="radio" /><label for="__tabbed_2_5">object</label><div class="tabbed-content">
|
|
<p><code>PARENT</code> is an object that has two properties. <code>KID1</code> is one of those properties that are, in turn, another object that will reuse the <code>"#/definitions/PROVIDER"</code> <code>definition</code> <strong>AND</strong> also include (extend) two extra properties <code>GRAND_KID1</code> of type <code>array</code> and <code>GRAND_KID2</code> of type <code>number</code>. <code>KID2</code> is another property of <code>PARENT</code> of type <code>boolean</code>.</p>
|
|
<p>The schema validation looks like this
|
|
<div class="highlight"><pre><span></span><code><span class="nt">PARENT</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">object</span>
|
|
<span class="nt">properties</span><span class="p">:</span>
|
|
<span class="nt">KID1</span><span class="p">:</span>
|
|
<span class="nt">allOf</span><span class="p">:</span>
|
|
<span class="p p-Indicator">-</span> <span class="nt">$ref</span><span class="p">:</span> <span class="s">"#/definitions/PROVIDER"</span>
|
|
<span class="p p-Indicator">-</span> <span class="nt">properties</span><span class="p">:</span>
|
|
<span class="nt">GRAND_KID1</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">array</span>
|
|
<span class="nt">uniqueItems</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">True</span>
|
|
<span class="nt">GRAND_KID2</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">number</span>
|
|
<span class="nt">KID2</span><span class="p">:</span>
|
|
<span class="nt">type</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">boolean</span>
|
|
</code></pre></div></p>
|
|
<p>The <code>config.yaml</code> key that the previous schema validates looks like this:
|
|
<div class="highlight"><pre><span></span><code><span class="nt">PARENT</span><span class="p">:</span>
|
|
<span class="nt">KID1</span><span class="p">:</span>
|
|
<span class="c1"># These four come from the `PROVIDER` definition (template)</span>
|
|
<span class="nt">COMPUTE</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">False</span>
|
|
<span class="nt">FEATURES</span><span class="p">:</span> <span class="p p-Indicator">[</span><span class="nv">x</span><span class="p p-Indicator">,</span> <span class="nv">y</span><span class="p p-Indicator">]</span> <span class="c1"># an array</span>
|
|
<span class="nt">SRC_SCRIPT</span><span class="p">:</span> <span class="s">"a</span><span class="nv"> </span><span class="s">path</span><span class="nv"> </span><span class="s">to</span><span class="nv"> </span><span class="s">a</span><span class="nv"> </span><span class="s">py</span><span class="nv"> </span><span class="s">or</span><span class="nv"> </span><span class="s">R</span><span class="nv"> </span><span class="s">script"</span>
|
|
|
|
<span class="c1"># This two come from the extension</span>
|
|
<span class="nt">GRAND_KID1</span><span class="p">:</span> <span class="p p-Indicator">[</span><span class="nv">a</span><span class="p p-Indicator">,</span> <span class="nv">b</span><span class="p p-Indicator">]</span> <span class="c1"># an array</span>
|
|
<span class="nt">GRAND_KID2</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">5.1</span> <span class="c1"># an number</span>
|
|
<span class=" -Error"> </span><span class="nt">KID2</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">True</span> <span class="c1"># a boolean</span>
|
|
</code></pre></div></p>
|
|
</div>
|
|
</div>
|
|
<h2 id="verifying-the-schema-is-correct">Verifying the schema is correct<a class="headerlink" href="#verifying-the-schema-is-correct" title="Permanent link">¶</a></h2>
|
|
<p>We recommend that before you start modifying the schema you modify the <code>config.yaml</code> key that you want to validate with an invalid value. For example, if you want to validate that <code>COMPUTE</code> is boolean, you set <code>COMPUTE: 123</code>. Then create your validation, run <code>snakemake --list-params-changes</code> and make sure your validation fails (123 is not <code>boolean</code>), and then set the key to the correct value. In other words, make sure it’s broken first so that you know that your validation works.</p>
|
|
<div class="admonition warning">
|
|
<p class="admonition-title">Warning</p>
|
|
<p><strong>Be careful</strong>. You can check that the schema <code>config.schema.yaml</code> has a valid format by running <code>python tools/check_schema.py</code>. You will see this message if its structure is correct: <code>Schema is OK</code>. However, we don’t have a way to detect typos, for example <code>allOf</code> will work but <code>allOF</code> won’t (capital <code>F</code>) and it won’t show any error. That’s why we recommend to start with an invalid key/value in your <code>config.yaml</code> so that you can be sure the schema validation finds the problem.</p>
|
|
</div>
|
|
<h2 id="useful-resources">Useful resources<a class="headerlink" href="#useful-resources" title="Permanent link">¶</a></h2>
|
|
<p>Read the following links to learn more about what we can validate with schemas. They are based on <code>JSON</code> instead of <code>YAML</code> schemas but the same concepts apply.</p>
|
|
<ul>
|
|
<li><a href="http://json-schema.org/understanding-json-schema/index.html">Understanding JSON Schemas</a></li>
|
|
<li><a href="https://tools.ietf.org/html/draft-handrews-json-schema-01">Specification of the JSON schema we use</a></li>
|
|
</ul>
|
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