Hello Dr. Davidson,
Responses inline.
On Wed, Nov 20, 2013 at 11:13 AM, Robert Davidson
bobbledavid...@yahoo.co.uk wrote:
Hi all,
I recently tried uploading an couple of xml files to my local Galaxy
installation using the standard ‘Upload File (version 1.1.3)’ tool. For some
files this produced the error: The uploaded file contains inappropriate HTML
content.
Given the files had been created by the same automated code and contained
the same tags etc, I couldn't understand why one would produce this error
and the other not.
Finally tracking down the function check_html() in
galaxy-dist/lib/galaxy/datatypes/checkers.py, I discovered that my use of
the tag metabolite had flagged up as a likely META tag and produced the
warning/failed upload.
The reason this did not happen in every case is that check_html only reads
the first 100 lines of the file and depending upon how many samples were in
my dataset, my metabolite tag could appear before or after this cutoff.
I've solved the problem by changing my xml tag names but my question is:
a) why does check_html only read up to line 100?
My guess is that this results from a desire to not process every line
of multi-gigabyte FASTQ files on each upload - this would be very
costly.
https://bitbucket.org/galaxy/galaxy-central/commits/35cc1687eb7b348811bf9e4f6e9d4374b00b6f09
I have reworked the code so that there is now a HTML_CHECK_LINES
variable at this top of this file - you can simply set that to None to
process all lines in your Galaxy distribution. My hope is this check
is largely a bonus check, this content is actually locked down when
feeding the data out - indeed if you try to upload a file with html
content after line 100, Galaxy still serves it out as plain text. If
you (or anyone) does discover a way to circumvent this and produce say
a cross-site scripting attack - please contact galaxy-b...@bx.psu.edu
or myself right away and the problem will hopefully be addressed
promptly.
b) would it be possible to change the regular expressions in check_html so
that e.g. meta ... would be found but e.g. metaxxx ... would not?
I have pushed out an update that does exactly this. Sorry for the inconvenience.
https://bitbucket.org/galaxy/galaxy-central/commits/583c64d963d41c7e38f76e2be23531b160ec972f
Both of these updates should be included in the next galaxy-dist
(probably still a over a month away).
Thanks for the e-mail and thanks for using Galaxy.
-John
Thanks for reading.
Rob
Dr Robert L Davidson
NERC Metabolomics Facility
School of Biosciences
University of Birmingham
Edgbaston, UK
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