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:
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.
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.
This error is still presenting, and is an issue on the server. Let’s ask the EU admins again for help, Hi @wm75 – I can still reproduce this, any status updates you can share?
There are two common error classes, and other situations possible!
Busy server, or some server issue
Gateway Time-out
If you see this under the Job Details inside the Standard Error Logs (stderr), then you are impacted. Find this using the i-icon, or navigate through the eye or pencil icon and tab into the Details.
Usage error: naming conflict
Exception: Naming Conflict. You do not have write permission on this organism.
If instead you find this in the stderr logs, create your own dedicated browser with a unique organism name. The portion of the logs about permissions can be ignored as on the public servers shared browsers will usually be restricted for general users.
The issue right now is that with a novel name, the Error 1 timeout issue is presenting and that is what we are hoping to resolve in this topic.
Pending clarification: organism naming “rules”
Someone mentioned that the “fasta needs to be same as the organism name” and I don’t think that is needed. Instead, all the files are pulled in under whatever name was used. Maybe @wm75 can clarify how to use the tool a the EU server, beyond what the GTN tutorial is explaining.
Not registered at all!
Do you need to register? Do this with the tool Register Account with Apollo → link at the EU server.
You should have already created your Galaxy account first → how-to.
Let’s revisit from here, and hopefully we can get it resolved!
The issue right now is that with a novel name, the Error 1 timeout issue is presenting and that is what we are hoping to resolve in this topic.