Upload fails silently for large files

[eboileau]

Is there an existing issue for this?

• I checked the documentation and found no answer
• This bug has not already been reported

A clear and concise description of what the issue is.

This is related to #8 : Data upload (large data) - [ENHANCEMENT].

For large data (how large, what is the limit?), the upload fails silently, i.e. I cannot find any errors in the apache logs (or any other logs). I modified /etc/php/7.4/apache2/php.ini to set all error handling and logging more verbose, specifying the location of a php log e.g. /var/log/php_errors.log, to no avail.

This happens in js/upload_dataset.js in validate_expression. The call to cgi/validate_expression.cgi returns with an error, but filename is not None, so it is as if PHP succeeded. However, the dataset uploader fails to read it because the file is actually not there. Effectively, uploads/files/ does not contain the expression data, but only the metadata.

Output or error messages.

Oops! [Errno 2] Unable to open file (unable to open file: name = '../uploads/files/EGAS00001006374 (1).h5ad', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Anything else?

No response

What browser were you using?

Chrome

[eboileau]

UploadHandler.php does not really log anything, so we had to debug the hard way. Essentially, the problem was the /tmp size/location. I set upload_tmp_dir=/dhart/tmp, on the same file system as the final destination, with enough space /dev/mapper/vgdata-lvdhart 1007G 18G 939G 2% /dhart.

Maybe we should set this up in the install playbook (although this will depend on the actual set-up on the server side), or else make note of it.