Apollo Create or Update Organism error

usegalaxy.eu support
,
1

hey
i had problem with tool “create or update organisme” that used for apollo
i tried to change the name of the organism also i found that the name sould be like the fasta name but the same error and when the tool faild i need to change to another name or the tool shows another issue. any solution thank u.
"`INFO:root:curl https://usegalaxy.eu/apollo_api/user/loadUsers -H ‘Content-Type: application/json’ -d ‘{“userId”: “a.oua@edu.umi.ac.ma”, “username”: “XXXXXXXXX”, “password”: “XXXXXXXXX”}’
INFO:main:Determining if add or update required
INFO:root:curl https://usegalaxy.eu/apollo_api/organism/findAllOrganisms -H ‘Content-Type: application/json’ -d ‘{“organism”: “artegeSNAP101 (gx121028)”, “username”: “XXXXXXXXX”, “password”: “XXXXXXXXX”}’
INFO:main: Adding Organism
INFO:root:curl https://usegalaxy.eu/apollo_api/organism/addOrganism -H ‘Content-Type: application/json’ -d ‘{“commonName”: “artegeSNAP101 (gx121028)”, “directory”: “/data/dnb01/apollo/196815973”, “publicMode”: false, “genus”: “Artemisia”, “species”: “ifranensis”, “username”: “XXXXXXXXX”, “password”: “XXXXXXXXX”}’
Traceback (most recent call last):
File “/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/9e7b8c7185ad/apollo_create_or_update/create_or_update_organism.py”, line 215, in
data = wa.organisms.add_organism(
File “/usr/local/tools/_conda/envs/mulled-v1-6e30e94176c826cd507c7589aec34fbb1f15b9501101942752ee5cacfab9ba49/lib/python3.9/site-packages/decorator.py”, line 232, in fun
return caller(func, *(extras + args), **kw)
File “/usr/local/tools/_conda/envs/mulled-v1-6e30e94176c826cd507c7589aec34fbb1f15b9501101942752ee5cacfab9ba49/lib/python3.9/site-packages/apollo/decorators.py”, line 8, in raise_error_decorator
r = fn(*args, **kwargs)
File “/usr/local/tools/_conda/envs/mulled-v1-6e30e94176c826cd507c7589aec34fbb1f15b9501101942752ee5cacfab9ba49/lib/python3.9/site-packages/apollo/organisms/init.py”, line 66, in add_organism
response = self.post(‘addOrganism’, data)
File “/usr/local/tools/_conda/envs/mulled-v1-6e30e94176c826cd507c7589aec34fbb1f15b9501101942752ee5cacfab9ba49/lib/python3.9/site-packages/apollo/client.py”, line 82, in post
raise Exception(“Unexpected response from apollo %s: %s” %
Exception: Unexpected response from apollo 504:

504 Gateway Time-out

504 Gateway Time-out

nginx/1.20.1 `"
2

Welcome @trso

The timeout message can be temporary. Have you tried again?

If you still need help, would you please either set your history to a shared state then post the link back here, or you can screenshot everything on the Job Details view (with any input datasets expanded to show the peek view). We can help to double check the parameters. Part of your message is explaining a type of mismatched data entry.

How to do this is in this topic:

Thanks and let’s start there! :slight_smile:

XREF → Hands-on: Refining Genome Annotations with Apollo (prokaryotes) / Refining Genome Annotations with Apollo (prokaryotes) / Genome Annotation

3

Thank u @jennaj for replaying
yes i already tried today again, but i got the same error
this is the link of my shared history

4

Hi @trso

Thanks for sharing the history! The problem is on the EU server from what I can tell. I also had a test case fail.

Let’s ask one of the EU administrators for help. Hi @wm75 – the tool is reporting timeout issues. All ok? Another example job → Galaxy based on this tutorial.

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