LabKey API - ESP Integration

GTAC-MGI / GTAC-ESP-LIMS

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LabKey API - ESP Integration #455

Closed billtell closed 1 month ago

billtell commented 3 months ago

Integrate the functions developed in #428 into LabKey.py

The goal is to have sample ingest in both Seq and SC possible through the API

billtell commented 2 months ago

Sending Samples a second time

Found existing plate: RowId: 860, Location: TESTING_FREEZER / Shelf2 / Column1 / rjUv4Q
row ids: [50557, 50558, 50559]
Error adding samples to storage: 400: Position (1, 1) is already occupied.

This is a ServerContextError : 400 error

billtell commented 2 months ago

Created a testing workflow chain LabKey API Testing for Seq Lab Testing Only adding samples to TESTING_FREEZER

billtell commented 2 months ago

To Deploy:

[x] Switch back to illumina project from testing
[x] Remove Testing workflow chain
[x] Check if Sample already exists before making it. -A lot of samples will be registered and not placed in storage. Could lead to a lot of duplicates.
[x] Set sample_responses = sample_api.query.insert_rows("samples", "Test-Sample", samples, audit_behavior=AuditBehavior.DETAILED, audit_user_comment="Creating sample via python API") to "Sample"
[x] Make sure file export still works with extra spaces
[x] Clean up print statements

billtell commented 2 months ago

Example Report print statements

New Samples

Existing Samples in same location

Existing Samples put in more than 1 plate location

billtell commented 2 months ago

[x] LabKey Storage View column added to park LabKey Storage View hyperlink

billtell commented 2 months ago

[x] Fix the SR lookup bug
[x] Hide Sample Name and Pool Name by default, remove onrender = unnecessary
[ ] Bulk edit missing SRs from file with revised lookup function