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I wanted to post to @Clive comment on How can I quickly re-save all users on my site? and ask about how to do this for fields in a field collection but couldn't because I've never posted to this site before so I had to ask a new question. He provided the following code to run as a php script in VBO on all users:

$items = field_get_items('user', $entity, 'field_name'); 
if (empty($items)) { 
   $entity->field_name[LANGUAGE_NONE][0]['value'] = 1; 
}
user_save($entity);

This solution works great for a single field of a user. I need a similar solution for setting default field values in a field collection after importing users.

I migrated 6000+ users and have set default values for fields in a field collection after the fact that don't show up unless I re-save a user account. I want to bulk re-save all 6000+ users so that the default field collection fields are saved and are visible. It's almost identical to the original question except the field is not just a singular field associated with the entity -- the field(s) in question are part of a field collection. How do I access the fields from my default field collection to then force re-save of users?

Is the proper way to access field data through entity_metadata_wrapper? If this is the case, how do I get/set the values of fields in a field collection that I want to associate with users using this wrapping class?

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This finally worked for me -- may it save someone hours of headaches:

// load the user
$userwrapper = entity_metadata_wrapper('user', $entity);
// apparently you have to create the field collection entity
$fieldCollection = entity_create('field_collection_item', array('field_name' => 'field_yourCollectionName'));
// attach your field collection to the user
$fieldCollection->setHostEntity('user', $entity);
// set the value of one of your fields in your field collection - in my case it's a boolean
$userwrapper->get('field_yourCollectionName')->field_fieldNameInYourCollection->set(0);
// save the entity
$userwrapper->save();
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