George's Stuff (25/06/2020)

Owned by George Swinnerton
Last updated: Jun 25, 2020
2 min read

SPEAK / SPEAK2

See R:\0 Information Governance\Data sharing agreements (DSAs)\DSAs\Current DSAs\DSA47 Hamilton_SPEAK_Bristol Uni

Currently this has involved tracing a cohort and providing the address / death data so Alex can write to the SPEAK patients to see if they want to participate in SPEAK2. Some are from Scotland/NI so could not be traced.

I believe there is also going to be a request for UKRR followup data for the SPEAK patients. This is described in the DSA.

The various files are under Q:\Data Sets\2017-04 SPEAK

"Quick" Data Loading

RR-SQL-Test has been restored with a copy of Live.

All DMs need to be added to whatever group gives them access to the Test database in Validation/Editor.

The RR_VALIDATION_LOG table shows which files have been loaded into a particular database. It would be worth doing a periodic comparison between the two to make sure any file that is loaded on to Live has also been loaded onto Test.

RR_No files must NOT be issued from the Test database.

UKRR Editor and Q100

A fixed version is in:

R:\Registry_Utils\Test\Editor\1.1.16b

I shall do "proper" 1.1.16 releases of Editor/Validation when I've come back.


NHS England ('Old' Monthly Process)

I should be back in time for this to be run.

If I'm not then the Validation in -

R:\Registry_Utils\Validation\1.1.14j

Needs to be used (and NOT the latest version) as that had already been modified with a draft of the new extract.

NHS England ('New' Monthly Process)

I'll run this when I get back.

If not look in -

sql_runner/browse/jobs/regular/nhs_england

sql_runner/browse/jobs/regular/nhs_england_studyid


PHE England

See https://bitbucket.renalregistry.nhs.uk/projects/COV/repos/phe_extract/browse (NOTE - The code is in a branch).

ukrr_trace.py is used to make a Tracing file.

phe_extract.py is used to produce the list of NHS Numbers. It also uses the Tracing file as input.

phe_merge.py is used to produce the Q100 UKRR dataset. It also uses the Tracing file, however given the time taken by PHE for matching you may want to generate a fresh one.

Covid Bi-Weekly

See:

https://bitbucket.renalregistry.nhs.uk/projects/COV/repos/ukrdc_extract/browse

data_extract.py is used to produce the extract and needs modifying to point at the current traced Covid file, as well as a new output directory. There are flags to control which bits of data are output.

Because of the growth in the number of results it may be difficult to run this to completion remotely due to the VPN time limits.

As an alternative to running this Anna may ask specifically about a couple of patients.

Do -

SELECT
    patientid as nhsno,
    fromtime,
    totime,
    admitreasoncode as treatment_modality
FROM
	patientnumber A
LEFT JOIN
	treatment B ON A.pid = B.pid
WHERE
	A.patientid in ('111111111', '222222222')
ORDER BY
	patientid,
	fromtime

NHS BT Q100

See Q100 Branch in https://bitbucket.renalregistry.nhs.uk/projects/RR/repos/rr_ukt_import/browse?at=refs%2Fheads%2Fq100