Hi Chris,
I am glad that we figured this out. So I am not sure what the best strategy
for datatypes with code dependencies is, we should open a new thread or git
issue and see if someone can help with that.
Thanks,
Sam
On Wed, Dec 14, 2016 at 10:59 AM, Cristel Thomas
wrote:
> Hi again,
> ok, r
Hi again,
ok, ran some more tests - we switched to a new dev server recently and we
were having the issue because of the R/rpy2 thing.
With that taken care of though, we still have files in the dropdown that
shouldn't be there - no more FCS, but .ypnb still show up. I guess this is
because of the
Hey Sam,
thanks, I'll check tomorrow at work but I suspect there might be something
else - I use rpy2 to call R, so that FCS files can be read. As of 2 months
ago there was no efficient way of doing it strictly in python. rpy2 does
not load if R isn't installed on the system (and for this specific
Hey Cris,
Dannon and I figured out, that the problem is that your datatypes are not
loaded properly, due to these two invalid imports:
https://github.com/ImmPortDB/immport-galaxy/blob/release_16.07/lib/galaxy/datatypes/flow.py#L13
Removing them fixes the issue. The error for this is shown in the
Ok, let me look a little bit further then. Can you send me the
corresponding tool xml file and let me know which datatypes appear in the
dropdown list and which of those you would not expect to see? Ideally we
can reproduce it with datatypes available to everyone, so I can test it
locally.
If it's implicit conversion, why does it pick up the FCS bianry format
along with the other text formats?
and why does it get triggered on every single tool instead of just the few
that have the multiple datatypes?
On Mon, Dec 5, 2016 at 12:31 PM, Aysam Guerler
wrote:
> Ok, so this seems to work
Ok, so this seems to work properly, and implicit conversion is the reason
why you see html and text, but not png and pdf files. Currently there is no
option to disable implicit conversion but its an enhancement we can suggest
to be implemented by creating a github issue.
___
there are 8 datatypes, 7 are tabular / text files, one is binary. The
binary format also shows up in the dropdown.
I can send you the datatype specification python code if you'd like, Im not
sure what you need to see.
On Mon, Dec 5, 2016 at 12:01 PM, Aysam Guerler
wrote:
> Thanks for the quick r
Thanks for the quick response. What is the set of datatypes you are
specifying? It is possible that one of the specified datatypes can be
implicitly converted to html and text e.g. a fasta file will be listed even
if only tabular has been specifed as valid datatype. In other words, Galaxy
will impl
Hi Sam,
I'm not sure what tools have multiple datatypes as input on usegalaxy.org
(and my files are still waiting to be uploaded for some reasons.)
I can give you more details though. Those are tools we developed for flow
cytometry with new datatypes. I wonder if the issue is with the fact
Hey Cris,
Thanks for reporting this. I am looking into it. In the meanwhile, I am
wondering if you can reproduce the error on usegalaxy.org? Does it happen
for all tools?
Thanks,
Sam
On Mon, Dec 5, 2016 at 8:47 AM, Cristel Thomas
wrote:
> Hi Galaxy Devs,
>
> We have a few tools with multiple d
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