BatchValidateChecksumsTask fails to read MD5 sum file in dev environment - Githubissues

bihealth / sodar-server

SODAR: System for Omics Data Access and Retrieval

https://github.com/bihealth/sodar-server

MIT License

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BatchValidateChecksumsTask fails to read MD5 sum file in dev environment #2022

Closed mikkonie closed 1 month ago

mikkonie commented 1 month ago

At some point during the iRODS 4.3 and python-irodsclient upgrade, landing zone moving and validation in dev fails with the following error:

Failed to move landing zone files: BatchValidateChecksumsTask failed: Could not connect to specified host and port: irods:1247 (Unable to read checksum file "xxx.md5")

Some facts:

The iRODS server is up and responding normally
The file exists and has the expected content
The rodsuser who uploaded the file can iget the file just fine.

What is suspicious is the irods:1247 URL there. Could this be another case of the redirecting "feature" introduced in python-irodsclient v1.1.9?

Update: Yes, of course it was that. So the solution right now is:

Add 127.0.0.1 irods into /etc/hosts
Add a note about this in the docs together with irods-test (already there)
Upgrade to python-irodsbackend v2.1.1 once it's out, as that will fix the default redirect problem

mikkonie commented 1 month ago

Documentation updated. Closing this issue, but it will be properly fixed by #2023.