We do have pretty old code, so I applied your patches.
One minor problem, in multi_upload tool "Dataset Name" is ignored, just picks
the first file name. Do we need to update upoald.py or multi_upload.xml?
From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John Chilton
Sent: Friday, 31 May 2013 5:50 AM
To: Khassapov, Alex (CSIRO IM&T, Clayton)
Cc: Burdett, Neil (ICT Centre, Herston - RBWH); <galaxy-...@bx.psu.edu>
Subject: Re: Multi File upload api
Alex, if I am not mistaken you guys are using a fairly old version of the
multiple file dataset code. I think on the server side you would need to apply
the following three changesets to update the library backend to support the
creation of multifile datasets (I guess if you are doing path pasting only the
first changeset is really needed):
If your version of Galaxy is likewise pretty old you will need pull request 123
Once those are in place updating example_watch_folder.py should be pretty
doable (Hagai Cohen had it working at some point):
1) You will need to replace:
data['upload_option'] = 'upload_paths'
data['upload_option'] = 'upload_paths_multifile'
2) You will need to specify a name (e.g. add something like:
data['NAME'] = os.path.basename(fullpath))
3) Multiple file datasets do not support data['ext'] = 'auto', so you will need
to specify an explicit format there (the script will hopefully be able to
determine this from the inputs).
The most updated version of the multiple file dataset stuff
https://bitbucket.org/msiappdev/galaxy-extras/ paired with the most updated
version of blend4j (https://github.com/jmchilton/blend4j) are compatible and if
you do enough digging can provide insights on how to create multiple file
datasets via the API (library path pastes, library server directory uploads,
and history uploads).
Hope this helps,
On Thu, May 30, 2013 at 1:40 AM, <alex.khassa...@csiro.au> wrote:
> Hi John,
> Can you please have a look at Neil's question.
> Thank you,
> From: Burdett, Neil (ICT Centre, Herston - RBWH)
> Sent: Thursday, 30 May 2013 4:30 PM
> To: Khassapov, Alex (CSIRO IM&T, Clayton)
> Subject: Multi File upload api
> Hi Alex,
> The file "galaxy-dist/scripts/api/example_watch_folder.py"
> allows us to watch a folder then upload files that arrive in a
> specified input folder into the database and history.
> Can you ask your friend (who implemented the multi file upload tool),
> what changes are necessary to this file so we can upload multiple
> files as we do from the GUI. I assume he would know quite quickly what
> to do and hopefully quite simple....
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