MoNA Offline and some local databases not working

[schymane]

As posted via MetFrag feedback, now moving to issue as requested by @sneumann, so far we've noticed:

• MoNA Offline Exact scores = 0, even for stock standard spectra in MassBank that always work
• Local versions of YMDB and HMDB are not working (error fetching candidates)
• Local versions of PubChemLite for Exposomics seem to work
• Server version of HMDB (and others) seem to work

[sneumann]

I can confirm the local HMDB and YMDB, logs show

10:04:25.658 ERROR de.ipbhalle.metfraglib.database.LocalCSVDatabase - Error: No Identifier column defined.

and indeed the following local databases are empty, so likely a container build issue:

-rw-r--r-- 1 root root         0 Jan 30 09:41 CompTox_07March19_WWMetaData.csv
-rw-r--r-- 1 root root         0 Jan 30 09:43 Zebrafish_13Nov2019_Beta.csv
-rw-r--r-- 1 root root         0 Jan 30 09:45 EColiMDB_11Nov2019.csv
-rw-r--r-- 1 root root         0 Jan 30 09:47 YMDB2_17Sept2019.csv
-rw-r--r-- 1 root root         0 Jan 30 09:49 WormJam_10Sept19.csv
-rw-r--r-- 1 root root         0 Jan 30 09:51 HMDB4_23Aug19.csv

[sneumann]

The spectral-library failure is a local deployment issue. Since last year there is the new option to add custom spectral libraries into a directory. If that is empty, none is used. If there is no directory, the default embedded MoNA is used. Currently, I have an empty directory there. Need to change that.

[sneumann]

The Spectral library issue was fixed in default helm installations in https://github.com/ipb-halle/ipb-charts-public/commit/f1ad00f0e5f87cd12115bc0175fa15429a8b80bd

[schymane]

We can confirm that the patches seem to be working well on Beta ;-)

[schymane]

OK so the plot thickens ... today, we have multiple users on MetFragBeta and for some MetFragBeta retrieves candidates from YMDB .. and for others ... we get Error fetching candidates. They only get candidates from the HMDB server DB (not the local one). Do we have multiple MetFragBeta's? We are still testing the MS/MS (MoNA) scores for those who fail to get YMDB candidates...

[schymane]

OK it appears we still get MoNA scores even for those who have Error fetching candidates for YMDB. Not tested on as many instances as the candidates yet ...

[schymane]

@sneumann has confirmed there were multiple MetFragBeta instances with different versions (which explains our observations), fixing this is WiP ... (thanks @sneumann ;-) )

[schymane]

We still have some versions of MetFragBeta giving Error fetching candidates from YMDB for students ... but both Beta and the main website seem to work fine for me so far (at least wrt YMDB and MoNA)! ;-) (how does it know who is the teacher?! ;-) )

[schymane]

Seems everything worked like a charm today, so closing this now - thanks for your help updating things this week @sneumann 👍