GPL-985-1 Automated processing on Beckmans: Health Services Laboratories (HSL)

[rl15]

User story

GPL-985	AS representative for LH labs (Alan K) I would like automated processing of surge testing samples from Health Services Laboratories (HSL) (London) to deprecated troublesome Eagle process

Who are the primary contacts for this story Alan K (PAM) Sonia G (PAM) Rich C (ops) James M (ops)

Acceptance criteria To be considered successful the solution must allow:

• [ ] Plate maps standard distributed by Alan to HSL lab lead: https://docs.google.com/document/d/1XC1pwqVTF2uLfyXWzth_cKd-f3B3g1Px8VoauuZ6RW4/edit?usp=sharing
• [ ] Enable read from SFTP share project-heron_hsl (Share is there from 19th April) (check LIMS have read access)
• [ ] Need lab_id: HSLL
• [ ] biomek_labware_class: BIOMEK_LABWARE_CLASS_KINGFISHER ??

Additional context Add any other context or screenshots about the feature request here.

[harrietc52]

support HSL barcodes in Sequencescape for automatic creation through lighthouse workflows (Sentinel and Beckman) The new barcode format to support is: HSLnnnnnn (e.g. HSL123456)

Confirm below values

    {
        "barcode_field": FIELD_RNA_ID,
        "barcode_regex": CENTRE_REGEX_BARCODE,
        "name": "Health Services Laboratories",
        "prefix": "HSL",
        "lab_id_default": "HSL",
        "backups_folder": f"{CENTRE_DIR_BACKUPS}/HSL",
        "sftp_file_regex_unconsolidated_surveillance": f"",
        "sftp_file_regex_consolidated_surveillance": r"^",
        "sftp_file_regex_consolidated_eagle": r"",
        "sftp_root_read": "",
        "file_names_to_ignore": [],
        "biomek_labware_class": BIOMEK_LABWARE_CLASS_KINGFISHER,
    },

Original story from Baracoda sanger/baracoda#111 This story is coupled with SS https://github.com/sanger/sequencescape/issues/3164

[harrietc52]

Answer from Ian K.

1. Yes plan is to have these uploaded to the SFTP with the file name to be that of the plate ID. So “HSLnnnnnn.csv”.
2. Is lab ID distinct from COG UK ID? We are using “HSLL” as COG-UK ID so seems sensible to keep aligned.
3. Will be uploaded to a new folder in the SFTP: /project-heron_hsl

Will need to format this into acceptance criteria for the story.

[rl15]

Expecting to prioritize item for week commencing 3rd May. (From DT4/DT6 meeting discussion)~ 2 weeks of running went live on 20th

[harrietc52]

Deployed to UAT on 27.04.21 Error because project-heron_hsl, which is the sftp_root_read, doesnt exist in the SFTP Redeployed previous version: 1.12.1-develop at 14:15

Assumtion: psd-lims doesnt have access to that folder

[rl15]

Incident Incident [.297620] created to get read access: User psd-lims does not have read permission to sftpsrv.sanger.ac.uk/project-heron_hsl

[rl15]

Incident Incident [.297620] closed - confirmed working