Hi Peter, Thanks for the help.
I managed to do what I wanted by subclassing the Html datatype, defining it as composite and overriding _archive_composite_dataset to link to the pre-packaged zip file. Defining it as composite was necessary as "html" seems to be treated specially in display_data() and added manually to the composite_types list. Best, Renato Quoting Peter Cock on 17-07-2014 20:19: > Hi Renato, > > You probably need to look at overriding the display_data method > in your subclass, see here for a simple example to render a > binary composte file type as a simple text caption: > > https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatypes/blast.py > > You can also override _archive_main_file to change the name of > he default main HTML file generated, or _archive_composite_dataset > for full control - but these are not really intended as public interfaces. > > (I did play with this a while back, but right now I forget which > branch this was on...) > > Peter > > On Thu, Jul 17, 2014 at 6:53 PM, Renato Alves <rjal...@igc.gulbenkian.pt> > wrote: >> Hi all, >> >> >> TLDR - Last 2 lines of this email >> >> >> Some time ago we created a wrapper script for breseq, a tool that >> generates a friendly HTML report of mutations. >> >> This was a perfect match for Galaxy given that we could simply set the >> "summary.html" file to be displayed using Galaxy's HTML datatype and >> place all extra media files in $htmlfile.files_path. >> >> However the friendliness quickly became a pain with large datasets. The >> size of the "files_path" folder quickly grew to over 500MB if multiple >> references are used. Still this was not the biggest problem since the >> size is spread over lots of tiny HTML files which work fine in Galaxy's >> preview. >> >> The real nasty hit us when we found that with the HTML format Galaxy >> does on-the-fly compression of the whole folder if a user clicks the >> "download" button. Needless to say most of the time users end up getting >> a server time-out and we get lots of broken pipes on the logs. >> >> An additional complication of the HTML format is that only the size of >> the primary html file is taken into account. So most users didn't >> understand why a 10KB file would cause so much pain to download and why >> was their quota being taken for no apparent reason. >> >> >> So after this we got stuck with 2 alternatives: >> >> 1) Customize the HTML datatype to do /a priori/ zipping instead of >> on-the-fly. Provide this pre-zipped file if users click on the download >> button. Fix the HTML datatype to display the correct size of the full >> dataset. >> >> 2) Provide 2 outputs, the usual HTML file output and an additional >> "complete report" which is a pre-packaged zip file generated by the wrapper. >> >> >> After spending quite some time browsing the existing documentation and >> trying to make sense of the code we gave up on 1). >> Looking at datatype class definitions, in particular HTML and the class >> hierarchy, we couldn't even figure out how the "files_path" mechanism >> worked. Documentation or lack thereof didn't help either. >> Knowing what methods are mandatory and what, when and how are they >> called would be a major help. >> >> So we jumped on 2). Getting the pre-packaged zip was quick and easy. We >> had to create a zip datatype but the existing Binary class worked fine: >> >> <datatype extension="zip" type="galaxy.datatypes.binary:Binary" >> mimetype="application/zip" subclass="True" /> >> >> The second part of the problem was to disable the HTML "download" link. >> And now we are back into customizing the HTML datatype... >> >> >> >> So long story short, if I want to customize what happens when a user >> clicks the download link of a given format, which methods should I be >> looking at? >> >> Can you think of any alternative (better) way to solve the original problem? >> >> >> Thanks, >> Renato >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/
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