Issue after update - temperature + web interface

[bheit]

After updating our cluster yeasterday we are having one (or perhaps two) issues:

1. After running an experiment for a while, the web interface gives this error (presumably after a data update of some sort):

2. If I refresh the page I get the usual pioreactor interface back, but with a bunch of temperature errors:

Log file is attached.

test_2024-09-10-logs-20240603075132.csv

[bheit]

I should add, data logging (including temperature) continues despite this error.

[CamDavidsonPilon]

Thanks for the report. I'll look into this today

[CamDavidsonPilon]

The temperature issue is related to how cold the ambient temperature is. Are you in a particularly chilly room? Normally the Pi warms the ambient air of the Pioreactor to >> 22C, and from the output it looks like the ambient air temperature is less than 22C (we subtract a static 22C from the temp values, and some in the output are negative, hence my inference). Anyways, we can fix that by adjusting the room-temp factor.

The UI error: we are looking into still!

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Edit: or is there an AC unit blowing air near the Pioreactor(s)?

[bheit]

The room is at 19C, so that would explain it. How do I change the room-temp factor? Bryan Heit, Ph.D. Associate Professor, Department of Microbiology & Immunology Western University Health Sciences Addition H320, Dock 15 London, ON, Canada, N6A 5C1 e. ***@***.*** t. 519.661.3407 (x83407) f. 519.661.3499 http://www.phagocytes.ca<http://www.phagocytes.ca/>

…

________________________________ From: Cameron Davidson-Pilon ***@***.***> Sent: Tuesday, September 10, 2024 1:41:38 PM To: Pioreactor/pioreactorui ***@***.***> Cc: Bryan Heit ***@***.***>; Author ***@***.***> Subject: Re: [Pioreactor/pioreactorui] Issue after update - temperature + web interface (Issue #144) The temperature issue is related to how cold the ambient temperature is. Are you in a particularly chilly room? Normally the Pi warms the ambient air of the Pioreactor to >> 22C, and from the output it looks like the ambient air temperature is less than 22C (we subtract a static 22C from the temp values, and some in the output are negative, hence my inference). Anyways, we can fix that by adjusting the room-temp factor. The UI error: we are looking into still! — Reply to this email directly, view it on GitHub<#144 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AW5NL4QWMJ263NTE5LWSBNLZV4VNFAVCNFSM6AAAAABN7AXGZSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBRGU3TONBUGY>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[CamDavidsonPilon]

It's more work than I like, but here's how:

1. SSH into your leader,

2. We'll create a small Python plugin:

   nano .pioreactor/plugins/new_room_temp.py
   

   and paste in the following code:

   from pioreactor.background_jobs.temperature_automation import  TemperatureAutomationJob
   
   def _get_room_temperature2():
      return 19.0
   
   TemperatureAutomationJob._get_room_temperature = staticmethod(_get_room_temperature2)

3. We'll distribute this code to all your workers with:

   pios cp .pioreactor/plugins/new_room_temp.py
   

Or, if you want to just give it to some workers:

pios cp .pioreactor/plugins/new_room_temp.py --units mni01 --units mni02 --units mni03

Moving the default room temp from 22C to 19C should be safe for all Pioreactors though.

[bheit]

Another question for you. For some experiments we want to place the reactors in a walk-in fridge, so we can measure growth at 4C. Should I be setting the default lower for those reactors when we do those experiments? Bryan Heit, Ph.D. Associate Professor, Department of Microbiology & Immunology Co-Director, ***@***.***<http://www.micrographiauwo.ca/> Western University Health Sciences Addition H320, Dock 15 London, ON, Canada, N6A 5C1 e. ***@***.******@***.***> t. 519.661.3407 (x83407) f. 519.661.3499 http://www.phagocytes.ca From: Cameron Davidson-Pilon ***@***.***> Sent: September 10, 2024 2:26 PM To: Pioreactor/pioreactorui ***@***.***> Cc: Bryan Heit ***@***.***>; Author ***@***.***> Subject: Re: [Pioreactor/pioreactorui] Issue after update - temperature + web interface (Issue #144) It's more work than I like, but here's how: 1. SSH into your leader, 2. We'll create a small Python plugin: 3. nano .pioreactor/plugins/new_room_temp.py and paste in the following code: from pioreactor.background_jobs.temperature_automation import TemperatureAutomationJob def _get_room_temperature2(): return 19.0 TemperatureAutomationJob._get_room_temperature = staticmethod(_get_room_temperature2) 1. We'll distribute this code to all your workers with: 5. pios cp .pioreactor/plugins/new_room_temp.py Or, if you want to just give it to some workers: pios cp .pioreactor/plugins/new_room_temp.py --units mni01 --units mni02 --units mni03 Moving the default room temp from 22C to 19C should be safe for all Pioreactors though. — Reply to this email directly, view it on GitHub<#144 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AW5NL4V3ZIU4UILTFARHNETZV42VJAVCNFSM6AAAAABN7AXGZSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBRG4ZDAMRWGE>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[CamDavidsonPilon]

I think it's a good idea, but you might be okay without it. (The temperature inference algorithm for Pioreactor v1.0 fails when the observed temps ~ coded room temperature - it makes the assumption that the Pi heats up the ambient temp - but you would avoid that case. Anyways, it is fine to change that coded room temp parameter to the fridge units.)

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We revamped the algorithm for Pioreactor v1.1s, so they avoid this problem completely. We haven't yet backported the algorithm to v1.0s.