I have the same remark regarding zip files: there should be an easy way to configure a file type as a “non-standard zip”: a zipped file that Galaxy just leaves untouched instead of unzipping it and passing the first file. For now I had to make 2 changes:
1- In datatypes_conf.xml : add the type extension for your type (in my case mscfileset):
<datatype extension="mscfileset" type="galaxy.datatypes.data:Data" mimetype="application/zip" display_in_upload="true"/>
2- In the tools/data_source/upload.py code add something like the following marked in red below:
I think it should be possible to adjust the upload.py code in a generic way (see “ if is_zipped : “ block).
Regards,
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Siemen Henk Sikkema
Sent: donderdag 15 december 2011 11:14
To: Peter Cock
Cc: Greg Von Kuster; galaxy-dev@bx.psu.edu
Subject: Re: [galaxy-dev] Excel upload problems
Hi All,
Thanks for the responses! I just got around to trying the solution by Joe Cruz. This did the trick for xls files, so that's the good news! The slightly less good news is that the same does not hold for xlsx files. Those files are pure zip files containing lots of internal xml stuff. Even when following the suggested procedure, Galaxy insists that it knows how to handle those files: by unpacking them and returning the first file from the zip (in this case a pretty useless xml file).
On a more general note, having to do these tricks can restrict sharing of new tools a bit in my opinion. It would be great if there would be an easy way to tell Galaxy: "leave files of this type as is, I can handle it" :P
Siemen
On Thu, Dec 8, 2011 at 10:18 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
> On Fri, Dec 9, 2011 at 3:35 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
>>
>> P.S. Why do you call your class XIs, surely Excel would be
>> clearer?
I've only just realised Xls is title case xls (as in the extension),
I read it at the title case of xis (which made no sense). I still
think using Excel as the class name would be clearer.
On Thu, Dec 8, 2011 at 9:01 PM, Ross <ross.lazarus@gmail.com> wrote:
> +1
> I'd agree that calling it excel is suitably wry - because it doesn't IMHO.
> Please name the new binary datatype something other than xls because
> many (of my) tools create outputs with that extension and it's a
> subclass of tabular here - the .xls extension fools excel into loading
> them automagically.
I don't entirely agree with your logic, but I would agree that
as the format name it would be consistent with most of the
other Galaxy formats to go for a longer name (e.g. "excel")
over a short 3 letter extension (here "xls").
However, does this matter for the extension that Galaxy
gives on downloading the dataset, or is that all done via
the mime type? We want it to be easy for people to
download an Excel file from Galaxy and open it, which
means getting the extension right under Windows.
Peter