Add error check in get_ext(file_name) function in gdc.py

[arp95]

Hi,

The get_ext(filename) functions splits the filename on '.' and checks for extensions supported by a constant called _SUPPORTED_FILE_TYPES.

There is a case in which if the filename doesnt have any supported format available in the _SUPPORTED_FILE_TYPES array, in that case we are returning the format of the file which is not supported by our code. We should add an error check and return NULL or a default extension supported by _SUPPORTED_FILE_TYPES array incase the filename doesnt have a valid ext supported by our code.

[maryjgoldman]

@jingchunzhu

[Ayoob7]

Hello, I would like to fix the issue with the function, whats the procedure to push my branch ? Thanks in advance.

[yunhailuo]

Thank you for your interests and PR, @Ayoob7 . This issue is a little bit special. The bottom line is it is not a bug but can use some improvements in coding and documentation.

If I remember it correctly, back in the day, GDC has some files named with only UUID which I found not useful to me and decided to rename them while downloading. So if you check the use of get_ext, you would find that they are used for constructing the new filename. Here is why I have this function and how I'd like it to work:

Say we have a file named "uuid.txt.tar.gz", I want to keep all the "txt.tar.gz" part and replace uuid with some meaningful name, say becoming "patient1_cancer.txt.tar.gz" not "patient1_cancer.gz". So get_ext should return "txt.tar.gz". This is important because if you unzip and extract the file, you can and should still have a "txt" extension. This is why I didn't simply keep the last postfix, "gz", but has get_ext to return that joint string. For what @arp95 has mentioned, say txt, tar and gz are not supported. So the filename doesn't have any supported format available, it will return the last postfix, gz, which is not "supported". Yes indeed but it is what I want. I want to get at least the last part rather than nothing because I want an extension no matter what. In another word, get_ext would check filename from left to right and return as soon as it found a recognized extension type and if none of them is recognized it should return the last one so that I have a relevant extension for file renaming rather than nothing. In this sense, I say it is not a bug because it functions as I want.

That being said, this issue can be improved. Either it should not be called "supported" but something else like "recognized" and documented clearly, or the whole file downloading and renaming part should be rewrite. In my opinion, those are directions this issue should go.

I'll close #7 for now but feel free to comment or submit new PR if you have any suggestions. Again, thank you both for your interests.