skip invalid files in runGdal

[itati01]

This pull request fixes the issue #93. If files are empty or otherwise corrupt and checkIntegrity == True (default), they will be silently skipped to avoid an error message in getSds.

[fdetsch]

Sorry for the delay. Can you maybe reproduce why getHdf()'s integrity check, which is being run directly before the code you inserted, does not capture that? I believe capturing corrupted .hdf files in there would be a slightly more stringent approach.

[itati01]

Just tested it again with tileH=18 and tileV=4.

• with my previous download folder: getHDF is reporting that a file is corrupt and starts re-downloading it, which fails.
• new download folder only for GF files. The remote connection fails. In /tmp/.../MOD16A2GF.006, there is an empty file 2014.07.28/MOD16A2GF.A2014209.h18v04.006.2020010011028.hdf.

The fact that there is a corrupt (empty) file after a failed download is causing the issue in runGdal. However, it might be more appropriate to address it in getHDF() or even in ModisFileDownloader(). Actually, I don't know which process created but not removed the empty temp file (curl? wget?). Interestingly, it remains only for the last date.

[fdetsch]

Alright, thanks for having another look into this and issuing a PR. Seems like your solution should be the safest way to capture this for now.