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the problem is, the dataset has over a million rows and distribute from 2002 to present and all over different countries. Is there a way to avoid download MODIS raw file to local, while directly extracting the spectra during the download?
Unfortunately, there is no easy way to do that without downloading the original files.
One method that I used may help a little. You can find all the MODIS L1 and L2 files that matches the date and time (+- time differences that you prefer). Then use wget to download all the files, and subtract the corresponding lat/lon by writing a little python script or using SeaDAS pixel extraction function. Make sure the date and time you used to find matched files have no duplicates, otherwise you'll download the same MODIS file multiple times.