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We have users uploading files(content Document) to opportunities. They are able to upload files where the size is greater than 100MB. But salesforce has a heap size limit of 12MB for asynchronous apex. I need to upload these files to AWS s3. I am running into exceeding heap size governor limit when retrieving the file content(contentversion->version Data) which is expected. 1. How can I query chunks of file content using SOQL, so I can upload chunks of 5MB to s3?

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You can't do this in Apex. The most reasonable way to handle this would be to download the file from an external source, such as a web browser, Heroku or AWS EB app, etc, then process the upload from there.

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