14.3.24. crate_anon.crateweb.consent.lookup_systmone

crate_anon/crateweb/consent/lookup_systmone.py

Copyright (C) 2015, University of Cambridge, Department of Psychiatry. Created by Rudolf Cardinal (rnc1001@cam.ac.uk).

This file is part of CRATE.

CRATE is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

CRATE is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with CRATE. If not, see <https://www.gnu.org/licenses/>.

Functions to look up patient details from a TPP SystmOne Strategic Reporting Extract (SRE) database, or at least its CPFT equivalent.

class crate_anon.crateweb.consent.lookup_systmone.ResearchSNOMED[source]

SNOMED codes used for the CPFT Research Database in SystmOne.

Verify at https://termbrowser.nhs.uk/.

crate_anon.crateweb.consent.lookup_systmone.gen_opt_out_pids_mpids_cpft_systmone() → Generator[Tuple[str, str], None, None][source]

Generates PID/MPID pairs from all patients opting out entirely from the CPFT Research Database, from a CPFT SystmOne database.

Note: this is the CPFT Research Database opt-out, not the NHS National Data Opt-Out. The latter applies to NHS Act s251 work, and is in SRNDOptOutPreference [marked as “future” in the SRE details?] or, in CPFT’s copy, S1_Patient.NationalDataOptOut.

Yields:

s1_patient_id, nhs_number for each patient opting out, in string format

PRESUMPTION: that if some “un-opts out”, their row here is deleted. There is a DateEvent column, but no codes for reversing the decision.

SELECT DISTINCT SNOMEDCode, SNOMEDText, CTV3Code, CTV3Text
FROM S1_ClinicalOutcome_ConsentResearch_OptOutCheck

Returns the latest CPFT consent mode for a patient, from a CPFT SystmOne database.

Parameters:

  • nhs_number – NHS number

  • decisions – list of human-readable decisions; will be modified

Returns:

a crate_anon.crateweb.consent.models.ConsentMode, or None

crate_anon.crateweb.consent.lookup_systmone.lookup_cpft_systmone(lookup: PatientLookup, decisions: List[str], secret_decisions: List[str]) → None[source]

Look up patient details from a TPP SystmOne Strategic Reporting Extract (SRE) database.

Parameters:

  • lookup – a crate_anon.crateweb.consent.models.PatientLookup

  • decisions – list of human-readable decisions; will be modified

  • secret_decisions – list of human-readable decisions containing secret (identifiable) information; will be modified