Comments (4)
Test this by running the positives report from lighthouse ui, and making sure the contents of the 'LIMS submission' column is correct:
- It should say 'Yes' for any samples that have been cherrypicked the Sentinel way ('cherrypick_layout_set' event)
- It should say 'Yes' for any samples that have been cherrypicked the Beckman way ('lh_beckman_cp_destination_created' event)
- It should say 'No' for other samples
from lighthouse.
Joins on sample UUID. Looks for the Beckman destination plate creation event type for a specific sample
SELECT mlwh_sample.description AS `root_sample_id`, mlwh_lh_sample.plate_barcode AS `plate_barcode`,
mlwh_sample.phenotype AS `Result_lower`, mlwh_lh_sample.coordinate AS `coordinate`
FROM mlwhd_mlwarehouse_devdata.sample AS mlwh_sample
JOIN mlwhd_mlwarehouse_devdata.lighthouse_sample AS mlwh_lh_sample ON (mlwh_sample.uuid_sample_lims = mlwh_lh_sample.lh_sample_uuid)
JOIN mlwhd_mlwh_events_proddata.subjects AS mlwh_events_subjects ON (mlwh_events_subjects.uuid = UNHEX(REPLACE(mlwh_lh_sample.lh_sample_uuid, "-", "")))
JOIN mlwhd_mlwh_events_proddata.roles AS mlwh_events_roles ON (mlwh_events_roles.subject_id = mlwh_events_subjects.id)
JOIN mlwhd_mlwh_events_proddata.events AS mlwh_events_events ON (mlwh_events_events.id = mlwh_events_roles.event_id)
JOIN mlwhd_mlwh_events_proddata.event_types AS mlwh_events_event_types ON (mlwh_events_event_types.id = mlwh_events_events.event_type_id)
-- f" WHERE mlwh_sample.description IN %(root_sample_ids)s"
-- f" AND mlwh_lh_sample.plate_barcode IN %(plate_barcodes)s"
AND mlwh_events_event_types.key = "lh_beckman_cp_destination_created"
GROUP BY mlwh_sample.description, mlwh_lh_sample.plate_barcode, mlwh_sample.phenotype, mlwh_lh_sample.coordinate;
from lighthouse.
Do we need to back populate the lh_sample_uuid
in the lighthouse_samples table, as 19/22 million records do not have a lh_sample_uuid
value, therefore the JOIN may not work as intended? Could some how the combo key root_sample_id / rna_id / result
be used to identify the correct sample uuid
from lighthouse.
Do we need to back populate the
lh_sample_uuid
in the lighthouse_samples table, as 19/22 million records do not have alh_sample_uuid
value, therefore the JOIN may not work as intended? Could some how the combo keyroot_sample_id / rna_id / result
be used to identify the correct sample uuid
Crawler's update_mlwh_and_dart_with_legacy_samples
migration should handle this. It needs to be run before a sample can be added to DART (be processed by the Beckman workflow), and gives samples lh_sample_uuid
s
from lighthouse.
Related Issues (20)
- 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
- DPL-821 [RVI] Cherry-picking LSW-96 Stock plates using the existing Tecan systems HOT 4
- DPL-670-4 Pass a Lighthouse specific API key to Sequencescape calls HOT 3
- DPL-840 Populate missing sample fields in MLWH and consequently in CoTrack
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from lighthouse.