Granting the Site Collection Administrator Permission in SharePoint Online
This high level permission is required because SharePoint Online currently does not offer lower level permissions that allow to crawl site collection content. The root site collection administrator permission is needed by the SharePoint auto discovery mechanism that the Coveo connector uses for operations such as detecting refreshed and deleted folders and crawling.
Grant the administrator permission using SharePoint Online admin center
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Access SharePoint Online administration center (https://your_domain-admin.sharepoint.com).
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Click Manage site collections.
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In the navigation panel on left, click Site Collections.
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In the panel on the right, under Site Collections, select one or more site collections you want to crawl.
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In the tool bar, click Owners, and then Manage Administrators.
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Add the crawling account to the list of Site Collection Administrators.
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Click OK.
What's Next?
CES 7.0.7914+ (October 2015) Assign the admin role to your crawling account in Office 365 (see Assigning admin roles in Office 365).