Investigate project backup export from biosoundscape project

[koonchaya]

Original report: https://rfcx.slack.com/archives/C03FD1WD02J/p1718028385095719 @carlybatist

User reported that number of recordings and templates exported from the project didn't match data in the project. Project https://arbimon.org/p/biosoundscape/overview

"When I made a backup of our BioSoundSCape project, the zip did not include the recordings.csv that has the AWS links to recordings. This file is invaluable. Also, it doesn't appear that we got a full list of templates in templates.csv. Maybe this is because there is a lot of data in BioSoundSCape?" This project - https://arbimon.org/p/biosoundscape/overview

Additional information I exported the files from the project and found that the number of recordings and templates didn't match. Export file https://drive.google.com/file/d/1_l2LmgDrn_CIMDx23Bq5JWIlVhmF15A2/view?usp=sharing

[grindarius]

I dug up the logs and found that it's an error at the SQL level. Most statements failed to run when the server is likely at its max. See error images below...

It's an error from legacy, but since our backup system is designed to be fault-tolerant, they can still do an export even if all queries failed. But when the error comes, the next batch won't be queried. So if the first batch fail you will get nothing.

The problem is the query took too long to do so. I guess there are a couple places where we can improve it.

• Index-based pointer on tables that have sortable index.
• Reduce database chunk query to something like 50k but still save the file at 200k rows as normal.

[carlybatist]

@grindarius ok how long do you anticipate it will take to implement these fixes so that we can check if they work in fixing the issue? We need to be able to have large projects work with the backup. And if there is an error where not all rows are going to show up, there needs to be an error message to the user demonstrating that. The user only realized this was a problem when they double-checked the CSVs against the project data.

[antonyharfield]

Reduce database chunk query to something like 50k

That sounds reasonable.

This query is very light because the only ordering is by PK so it shouldn't need to do much to read this data. It more likely failed because there was a lot of db activity at the same time. We could try some exponential backoff: if a query fails then retry in 10 sec, then 20 sec, then 40 sec then 80 sec else fail completely.

If one of the queries fails then I think the whole job should fail -- we don't want to continue and send the user incomplete data.

@carlybatist We are going to need this week to work on some improvements.

[koonchaya]

@antonyharfield @grindarius To find the solution for the job fail case.

[koonchaya]

Email fail status to user and support@rfcx.org/slack

[koonchaya]

Draft email to notify failure export:

Subject: Arbimon project export failed

Hello,

Thanks so much for using Arbimon! We encountered an issue while backing up your project '...'. Our apologies for the inconvenience. Please contact our support team at [contact@arbimon.org] for assistance.

@antonyharfield @carlybatist Can you check if this message need any changes?

[carlybatist]

@koonchaya Tech team would be getting this error notification too right? They should then immediately start looking into it as a support ticket. So I would think the email to the user should be informing them that there was an error and that our team is looking into it and will update them. Noon and I should be auto-cc'd on these emails to users too. So it would be --

Hello,

There was an issue with your project backup of '...'. Our engineering team is looking into this and will update you when we have resolved it. We apologize for the inconvenience and thank you for your patience!

All the best, Arbimon team

[koonchaya]

Ideally, @carlybatist and I would get the email that forwarded from support@rfcx.org. I am not sure about the eng-team will get alert elsewhere.

[carlybatist]

@koonchaya @grindarius what do you expect the timeline for fixing the underlying issue will be?

[koonchaya]

I tested export backup from project https://staging.arbimon.org/p/bci-panama-2018/overview @grindarius here is some feedback

• playlists.csv is empty - there are a lot of playlists in the project (https://staging.arbimon.org/project/bci-panama-2018/audiodata/playlists)

playlists.csv

• pattern_matchings.csv is empty but there are some jobs in the project (https://staging.arbimon.org/project/bci-panama-2018/analysis/patternmatching)

pattern_matchings.csv

• pattern_matching_rois.csv is empty but there should be some rois data

pattern_matching_rois.csv

• recordings.csv is empty but there are 128546 Recordings in the project (https://staging.arbimon.org/project/bci-panama-2018/audiodata/recordings)

recordings.csv

• recording_validations.csv is empty but there are some validations in the project

recording_validations.csv

• rfm_models.csv is empty

rfm_models.csv

• sites.csv is empty

sites.csv

• soundscapes.csv is empty

soundscapes.csv

• species.csv is empty

species.csv

• templates.csv is empty

templates.csv

[koonchaya]

@grindarius

• pattern_matchings.csv has more PM jobs than listed in the project. Test project https://staging.arbimon.org/project/bci-panama-2018/analysis/patternmatching

pattern_matchings.csv

• and I believe the pattern_matching_rois.csv contains the same data as above which are from the PM jobs that not listed in the project.

pattern_matching_rois.csv

• playlists.csv is good but I found there are 2 sites that I could not find in the project playlist.
  • playlist id: 8802 (Test cluster1)
  • playlist id: 8878 (Test playlist not filter)

playlists.csv

• rfm_models.csv contains jobs that are not in the project (not highlighted list in the file = not found in the project)

rfm_models.csv

• rfm_classifications.csv seems to have more data in export than in the project

rfm_classifications_001.csv rfm_classifications_002.csv rfm_classifications_003.csv rfm_classifications_004.csv rfm_classifications_005.csv rfm_classifications_006.csv rfm_classifications_007.csv rfm_classifications_008.csv

• templates.csv contains less species than in the project

templates.csv

[grindarius]

For pattern matchings export, we grab data directly from pattern_matchings table. What you see in the UI are jobs that are joined with the jobs table. But in pattern_matchings table we can get all the jobs from there even some jobs are not related to the jobs table. Same goes for pattern_matching_rois.

For playlists export I did find both playlists inside the export file so it's all good.

For rfm models there are deleted models being exported into the file.

Same goes for rfm classifications, we did not have condition to remove deleted classifications out.

[koonchaya]

@grindarius

• pattern_matchings.csv
  • in project = 6 jobs
  • in export = 50
• rfm_classifications.csv
  • only 3 jobs in the project but there are a lot more models in the export The rest of them are correct

[RatreeOchn]

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