Error when importing dataset to Rstudio

usegalaxy.eu support
1

Hi everyone, when trying to import a dataset (large .csv file) from my active galaxy history to Rstudio with gx_get(19056) I get the following error:

DEBUG:root:Host IP determined to be b’172.17.0.1\n’
DEBUG:root:TestURL url=https://usegalaxy.eu obj=False
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): usegalaxy.eu:443
DEBUG:urllib3.connectionpool:https://usegalaxy.eu:443 “GET /api/histories?key=###HTTP/1.1” 200 None
DEBUG:root:TestURL url=https://usegalaxy.eu state=success
DEBUG:root:Downloading gx=GalaxyInstance object for Galaxy at https://usegalaxy.eu history=0cd1246fe45a8830 dataset=19056
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): usegalaxy.eu:443
DEBUG:urllib3.connectionpool:https://usegalaxy.eu:443 “GET /api/histories/0cd1246fe45a8830/contents?key=###HTTP/1.1” 200 None
Traceback (most recent call last):
File “/usr/local/bin/get”, line 19, in
results = get( args.id, args.identifier_type, args.history_id )
File “/usr/local/lib/python3.8/dist-packages/galaxy_ie_helpers/init.py”, line 199, in get
datatypes_all.append({ds[identifier_type]: ds[‘extension’] for ds in history})
File “/usr/local/lib/python3.8/dist-packages/galaxy_ie_helpers/init.py”, line 199, in
datatypes_all.append({ds[identifier_type]: ds[‘extension’] for ds in history})
KeyError: ‘extension’

The dataset loads normally in my locally installed Rstudio.
Any suggestions?

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2

Hi @feanor1914

I also noticed a problem with all three of the gx_ commands at both usegalalxy.eu and usegalaxy.org late yesterday, but haven’t had a chance to follow up yet.

Let’s ask the developers if they know what is going on at Gitter. They may post back here or at Gitter, and feel free to join the chat. galaxyproject/dev - Gitter

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Hi @jennaj

Thanks for responding, I forgot to mention that uploading the zipped dataset with the “upload” button in the Rstudio server failed as well returning a “unexpected response from server” message.

4

@jennaj after seeing the people at Gitter saying gx_* worked for them, I tried again (just now) and managed to fetch my data. Not sure if it’s related but before trying again I created a new history with my dataset and a new Rstudio environment. Hope this helps!

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5

Glad worked out! No idea what was wrong originally but seems working on .org and .eu now. Maybe it was a data compression issue for you – or maybe the IE environment got corrupted. But if working now considering it all good.

I was doing something else (and will be doing more today). That involves these same commands. I’ll also use a fresh session.

Thanks for all the followup! :slight_smile:

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