Comments (4)
I've created a report from uat and checked the threads connected and it seems lighthouse uat does not have this issue. It went up from 2 to 3 threads connected, which it is quite smaller than the digits we get in production around 200 threads connected.
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In addition to the reports, we also open connections in the plates/new endpoint (create_plate_from_barcode) in plates_helper.update_mlwh_with_cog_uk_ids.
A preliminary scan of the code suggests that this connection is only opened once per http call, but I believe that the call gets made by lighthouse_ui once per plate in a box. So definitely a candidate for multiple connections.
A quick glance suggests we are calling connection.close() in a finally block.
from lighthouse.
A few things I noted:
- We have a helper method for creating connection engines, but don't use it consistently
- We're manually opening and closing connections, it might be safer to do this via a context manager
- SQL alchemy provides connection pooling: https://docs.sqlalchemy.org/en/13/core/pooling.html I don't think we're accidentally creating 200 pools which we only use once, but it might reduce the number of concurrent connections we have open if opening and closing connections is a little slow. (But it sounds like we're just NOT closing connections)
from lighthouse.
On mail today at 6:55, DBA confirmed all connections are staying below 400 (with a max set of 500). We are not requested to look into it further.
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Related Issues (20)
- DPL-470-1: malformed root_sample_ids that were picked, but are not duplicated in MLWH
- DPL-471-1: malformed root_sample_ids that have duplicates in MLWH, and WERE picked
- DPL-404 As GSU (Alan K) I would like to mark the incorrectly uploaded Randox plate maps with incorrect Root_Sample_IDs as consent withdrawn so that CoTrack reporting will ignore them.
- DPL-469 - Brants Bridge date tested in future HOT 1
- DPL-470 - LSPA date tested in future HOT 1
- DPL-472 - Brants Bridge sent root sample ids in incorrect format
- DPL-473 - Brants Bridge sent ~1500 samples with incorrect RNA ID HOT 1
- DPL-342 Remove report [C=S, V=3]
- DPL-362 As GSU (Alan K) I want to allocate a unique COG-UK ID to all historic Heron samples so that we can use this instead of Root Sample ID within our internal tracking. HOT 10
- DPL-426 Remove updates for MLWH once all samples arrive via RabbitMQ HOT 2
- DPL-429 As developer I want to remove the lighthouse reports generation as is not in use anymore and want to have less code to maintain HOT 1
- DPL-544 Make data consistent between MongoDB, MLWH and Sequencescape
- DPL-614 Missing plate map (Heron)
- DPL-631 [BUG] Incorrect evaluation of must_sequence affects both Box buster and Biosero HOT 1
- DPL-629 Check status of Heron CP plates HOT 1
- DPL-675-2: AROUND SEPTEMBER 2023 -- Remove reports and Sentinel functionality HOT 1
- DPL-717-1: Create a new endpoint for creating entities for Lighthouse deep-well plates in Sequencescape
- DPL-757 As PSD I want to create a first draft design for RVI new project (multipick) that will reflect lims architecture and required components to solve the current list of user requirements obtained.(S=M; C=L) HOT 1
- DPL-776 Investigate a way to identify Heron/RVI samples already in SequenceScape so that we can avoid problems during stamping from deep wells to shallow well plates for RVI.
- DPL-782 Filter samples being imported for deep-well to shallow-well stamping so as to exclude samples already in Sequencescape
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