biocompute-objects / biocompute-objects/portal_userdb

504 Gateway Timeout Error

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Dominant language
JavaScript
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Description

**Describe the bug**
There appears to be a server-side or network timeout

**To Reproduce**
Steps to reproduce the behavior:
This error occured when I was creating BCOs on the GlyGen Dev server using the following command:

`$ python3 create-bco.py -t XXX -f bco_templates/dicty_proteoform_glycosylation_sites_tablemaker.json`

*redacted my token for security purposes.

The "create-bco.py" script essentially takes any BCO created on the GlyGen Dev Server (in this case: dicty_proteoform_glycosylation_sites_tablemaker.json) and generates a GlyGen BCO (prefix: GLY). This worked fine a few times and then gave a 504 error.

**Expected behavior**
Typically, I get a success message that the BCO was created w/ the BCO ID. Instead I get the following message:

```
/usr/local/lib/python3.9/site-packages/urllib3/connectionpool.py:1064: InsecureRequestWarning: Unverified HTTPS request is being made to host 'biocomputeobject.org'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#ssl-warnings warnings.warn( { "status": "ERROR", "code": 504 }
```

**Screenshots**
If applicable, add screenshots to help explain your problem.

**Desktop (please complete the following information):**
- OS: Macbook
- Browser GlyGen Dev Server
- Version N/A

**Additional context**
This was working fine for the first few BCOs I created and then stopped working suddenly.

Contributor guide

Open the contributing guide

Research direction

Start by running create-bco.py with the stated bco_templates/dicty_proteoform_glycosylation_sites_tablemaker.json input against the GlyGen Dev Server, then trace the request that returns the 504 response. Done means the cause of the intermittent timeout is identified and the command again returns a created BCO ID.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
api, backend
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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