..  crate_anon/docs/source/anonymisation/anon_specific.rst

..  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/>.

.. _CRIS: https://pubmed.ncbi.nlm.nih.gov/23842533/
.. _PCMIS: https://www.york.ac.uk/healthsciences/pc-mis/
.. _RiO: https://www.servelec.co.uk/product-range/rio-epr-system/
.. _SystmOne: https://tpp-uk.com/products/


Specific databases
------------------


.. contents::
   :local:


Servelec RiO
~~~~~~~~~~~~


Servelec RiO_ data exports come in several formats, including:

- raw;

- "RCEP": preprocessed by Servelec's RiO CRIS_ Extraction Program.

Individual organizations may process these too. CRATE provides a preprocessor
(:ref:`crate_preprocess_rio <crate_preprocess_rio>`) to convert a RiO database
to a format suitable for anonymisation via CRATE.


PCMIS
~~~~~


There is a specific preprocessing tool for PCMIS_, namely
:ref:`crate_preprocess_pcmis <crate_preprocess_pcmis>`.


TPP SystmOne
~~~~~~~~~~~~


TPP provide a "strategic reporting extract" (SRE) containing SystmOne data.
This contains structured data, but can contain free text too.

The structure of the SRE is good from CRATE's perspective; it does not require
reshaping for anonymisation.

The :ref:`crate_preprocess_systmone <crate_preprocess_systmone>` will index a
SystmOne source database (without which, anonymisation is very slow). It will
also, optionally, create a view to add blurred geographical information, if you
have used the the :ref:`crate_postcodes <crate_postcodes>` tool to import UK
Office for National Statistics geography data into a database.

Use the :ref:`crate_anon_draft_dd <crate_anon_draft_dd>` tool to create a data
dictionary from SystmOne_. CRATE knows something about the structure of a
typical SystmOne database.

NHS numbers, which are `10-digit integers incorporating a checksum
<https://www.datadictionary.nhs.uk/attributes/nhs_number.html>`_, are
represented in our database copy of the SRE by the ``VARCHAR(10)`` data type
(clearly a little suboptimal). It remains OK to use these in your
:ref:`anonymiser config file <anon_config_file>`:

.. code-block:: ini

    sqlatype_mpid = BigInteger
    #
    # Within CPFT, we have some locally created columns with string versions of
    # the primary SystmOne ID, and so forth, so we use:
    #
    # sqlatype_pid = String(100)
    # sqlatype_mpid = String(100)

However, you will see some warnings during config checking.
See :ref:`sqlatype_mpid <anon_config_sqlatype_mpid>`.

When generating a data dictionary, use these settings for your source database:

.. code-block:: ini

    ddgen_omit_by_default = False
    # ... or use "--systemone_include_generic" with crate_anon_draft_dd
    # ... or use True if you want to hand-review everything

    ddgen_per_table_pid_field = IDPatient
    # ... largely cosmetic; improves the warnings if your local database
    # modifications have an odd structure.