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I’ve been contemplating a similar scenario for a while, using a RaspberryPi instead of an Arduino, and have come up with the following options to get the data from the tracking device to the webserver:
· Sockets - Seems to be the most efficient, but are more complex to use. http://en.wikipedia.org/wiki/Network_socket
· HTTP – Relatively easy to use, but it requires the ability to perform native HTTP requests on the Arduino? If this is possible, it should be simple to send that CSV file line-by-line, to your PHP webpage, one HTTP request at a time, using a “GET”, “POST” or even “PUT”. http://en.wikipedia.org/wiki/Hypertext_Transfer_Protocol
· Web Sockets – Typically used by a web browser, BUT is can also be used by any component supposing this functionality. If such a component existed for the Arduino, then this option would be my initial choice during the POC, which could later be converted to “conventional” sockets. http://en.wikipedia.org/wiki/WebSocket
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I don't know how comfortable you are with JavaScript (or whether this suggestion might have value), but perhaps you should consider:
Using Node.js (with some framework like Express on top of it) on the server-side to deal with the "blocking" issues. Although you could do this in just about any language, there should be literally tons of tutorials for Node/Express and you may even stumble across a few for a unique hardware solution like yours.