6.4. Data dictionary (DD)

The data dictionary is a catalogue of tables and columns (fields) in a source database (typically containing identifiable data). It tells CRATE how to transform the data into a de-identified destination database.

The data dictionary is a spreadsheet-style file: a tab-separated values (TSV) file, OpenOffice Spreadsheet (ODS) file, or Microsoft Excel XLSX (OpenXML, Excel 2007+) file.

It has a single header row, and columns as defined below.

6.4.1. Drafting a data dictionary

Once you have edited your anonymiser config file to point to your source database, you can generate a draft data dictionary like this:

crate_anon_draft_dd --output mydd.xlsx

Now edit the data dictionary as required. (And then edit your config file so it points to the data dictionary you have created.)

Full options for this tool are:

usage: crate_anon_draft_dd [-h] [--config CONFIG] [--verbose] [--incremental]
                           [--skip_dd_check] [--output OUTPUT]
                           [--explicit_dest_datatype] [--systmone]
                           [--systmone_context {tpp_sre,cpft_dw}]
                           [--systmone_sre_spec SYSTMONE_SRE_SPEC]
                           [--systmone_append_comments]
                           [--systmone_include_generic]
                           [--systmone_allow_unprefixed_tables]
                           [--systmone_alter_loaded_rows]

Draft a data dictionary for the anonymiser. (CRATE version 0.19.4, 2022-05-24.
Created by Rudolf Cardinal.)

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Config file (overriding environment variable
                        CRATE_ANON_CONFIG). Note that the config file has
                        several options governing the automatic generation of
                        data dictionaries. (default: None)
  --verbose, -v         Be verbose (default: False)
  --incremental         Drafts an INCREMENTAL draft data dictionary
                        (containing fields in the database that aren't in the
                        existing data dictionary referred to by the config
                        file). (default: False)
  --skip_dd_check       Skip validity check (against the source database) for
                        the data dictionary. (default: False)
  --output OUTPUT       File for output; use '-' for stdout. (default: -)
  --explicit_dest_datatype
                        (Primarily for debugging.) CRATE will convert the
                        source column data type (e.g. INTEGER, FLOAT,
                        VARCHAR(25)) to a datatype for the destination
                        database, sometimes with modifications. However, this
                        is usually implicit: the draft data dictionary doesn't
                        show these data types unless they require
                        modification. Use this option to make them all
                        explicit. (default: False)
  --systmone            Modify the data dictionary for SystmOne. CRATE knows
                        about some of the standard SystmOne data structure and
                        can read a database and customize the data dictionary
                        for SystmOne. (default: False)

SystmOne options (for when --systmone is used):
  --systmone_context {tpp_sre,cpft_dw}
                        Context of the SystmOne database that you are reading.
                        [tpp_sre: TPP Strategic Reporting Extract // cpft_dw:
                        CPFT Data Warehouse] (default: cpft_dw)
  --systmone_sre_spec SYSTMONE_SRE_SPEC
                        SystmOne Strategic Reporting Extract (SRE)
                        specification CSV filename (from TPP, containing
                        table/field comments). (default: None)
  --systmone_append_comments
                        Append to comments, rather than replacing them.
                        (default: False)
  --systmone_include_generic
                        Include all 'generic' fields, overriding preferences
                        set via the config file options. (default: False)
  --systmone_allow_unprefixed_tables
                        Permit tables that don't start with the expected
                        prefix (which is e.g. 'SR' for the TPP SRE context,
                        'S1_' for the CPFT Data Warehouse context). May add
                        helpful content, but you may get odd tables and views.
                        (default: False)
  --systmone_alter_loaded_rows
                        (For --incremental.) Alter rows that were loaded from
                        disk (not read from a database)? The default is to
                        leave such rows untouched. (default: False)

6.4.2. Columns in the data dictionary

  • The DD columns can be in any order as long as the header row matches the data, and the column headings include the headings shown here.

  • In TSV format, lines beginning with a hash (#) are treated as comments and ignored, as are blank lines.

6.4.2.1. src_db

String.

This column specifies the source database, using a name that matches one from the source_databases list in the config file.

6.4.2.2. src_table

String.

This column specifies the table name in the source database.

6.4.2.3. src_field

String.

This column specifies the field (column) name in the source database.

6.4.2.4. src_datatype

String.

This column gives the source column’s SQL data type (e.g. INT, VARCHAR(50)).

6.4.2.5. src_flags

String.

This field can be blank or can contain a string made up of one or more characters. The characters have the following meanings:

Character

Meaning

K

PK.
This field is the primary key (PK) for the table it’s in.

N

NOT NULL.
This field should be set to NOT NULL in the destination.
  • Primary key columns are usually NOT NULL. It is in principle possible to have a NULL primary key but this is extremely rare and not usually sensible.

  • Primary PID columns (see below) are set to NOT NULL automatically by CRATE.

  • NOT NULL status might not seem to matter for a read-only research database, but having the correct NOT NULL status is required by some database engines (e.g. SQL Server) for full-text indexing of other fields (see below).

H

ADD SOURCE HASH.
Add source hash of the record, for incremental updates?
  • This flag may only be set for source PK (K) fields (which cannot then be omitted in the destination, and which require the index=U setting, so that a unique index is created for this field).

  • If set, an additional column (field) is added to the destination table. This extra column’s name is the value of the config’s source_hash_fieldname variable; it is of type VARCHAR and its length is determined by the hash_method option. This field will contain a hash of the contents of the source record (specifically, a hash of a composite of all fields that are not omitted, OR contain scrubbing information as determined by scrub_src).

  • This table is then capable of incremental updates.

C

CONSTANT.
Record contents are constant (will not change) for a given PK.
  • An alternative to H. Can’t be used with it.

  • The flag can be set only on src_pk fields, which can’t be omitted in the destination, and which have the same index requirements as the H flag.

  • If set, no hash is added to the destination, but the destination contents are assumed to exist and not to have changed.

  • Be CAUTIOUS with this flag, i.e. certain that the contents will not change.

  • Intended for very data-intensive fields, such as BLOB fields containing binary documents, where hashing would be quite slow over many gigabytes of data.

  • Does not imply that the whole table cannot change!

A

ADDITION ONLY.
Marks an addition-only table. It is assumed that records can only be added to this table, not deleted.
  • The field is permitted only for PK (K) fields.

P

PRIMARY PID.
Primary patient ID field. If set,
  1. This field will be used to link records for the same patient across all tables. It must therefore be present, and marked in the data dictionary, for ALL tables that contain patient-identifiable information.

  2. If the field is not omitted: the field will be hashed as the primary ID (database patient primary key) in the destination, and a transient research ID (TRID) also added. You cannot specify another alter_method.

*

DEFINES PRIMARY PIDS.
This field defines primary PIDs. If set, this row will be used to search for all patient IDs, and will define them for this database. Only those patients will be processed (for all tables containing patient info). Typically, this flag is applied to a SINGLE field in a SINGLE table, usually the principal patient registration/demographics table. CRATE will warn you if there is more than one such field, and will raise an error if there are none, unless allow_no_patient_info is set.

M

MASTER PID.
Master ID (e.g. NHS number).
  1. The first such value encountered for any patient will be recorded as their MPID.

  2. If the field is not omitted, it will be hashed with the MPID hasher. You cannot specify another alter_method.

!

OPT OUT.
This field is used to mark that the patient wishes to opt out entirely. It must be in a table that also has a primary patient ID field (because that’s the ID that will be omitted). If the opt-out field contains a value that’s defined in the optout_col_values config setting, that patient will be opted out entirely from the anonymised database.

R

REQUIRED SCRUBBER.
If this field is a scrub_src field (see below), and this flag is set, then at least one non-NULL value for this field must be present for each patient, or no information will be processed for this patient. (Typical use: where you have a master patient index separate from the patient name table, and data might have been brought across partially, so there are some missing names. In this situation, text might go unscrubbed because the names are missing. Setting this flag for the name field will prevent this.)

6.4.2.6. scrub_src

String.

One of the following values, or blank:

Value

Meaning

patient

Contains patient-identifiable information that must be removed from scrub_in fields.

thirdparty

Contains identifiable information about a carer, family member, or other third party, which must be removed from scrub_in fields.

thirdparty_xref_pid

This field is a patient identifier for ANOTHER patient (such as a relative). The scrubber should recursively include THAT patient’s identifying information as third-party information for THIS patient.

Fields marked thus, if included in the destination database (see decision), are automatically hashed with the “primary” PID hasher, allowing you to link connected records in the research database. You cannot specify another alter_method.

6.4.2.7. scrub_method

String.

Applicable to scrub_src fields, this column determines the manner in which this field should be treated for scrubbing. It must be one of the following values (or blank):

Value

Meaning

words

Treat as a set of textual words. This is the default for all textual fields (e.g. CHAR, VARCHAR, TEXT). Typically used for names: for example, “John Smith” will scrub both “John” and “Smith” separately. Also OK for e-mail addresses.

phrase

Treat as a textual phrase (a sequence of words to be replaced only when they occur in sequence). Any superfluous whitespace at the start/end, or between words, is ignored. Typically used for address components: for example, “5 Tree Avenue” will not scrub “tree” or “avenue” by themselves, but this phrase will be scrubbed.

phrase_unless_numeric

If the value is numeric, ignore it. Otherwise, treat it as phrase. For example, if you have an address field that is meant to be “building number” (e.g. “5”) but someone might put a name (e.g. “Seaview”) or an address line (e.g. “5 Tree Road”), this will remove the more complex pieces of information but will ignore “5” (preserving e.g. “haloperidol 5 mg” elsewhere).

number

Treat as a number. This is the default for all numeric fields (e.g. INTEGER, FLOAT). If you have a phone number in a text field, use this method; it will be scrubbed regardless of spacing/punctuation.

code

Treat as an alphanumeric code. Suited to postcodes. Very like the numeric method, but permits non-digits.

date

Treat as a date, and scrub any recognizable representations of that date. This is the default for all DATE/DATETIME fields.

6.4.2.8. decision

String.

One of the following two values:

Value

Meaning

OMIT

Omit the field from the output entirely.

include

Include it.

This is case sensitive, for safety.

6.4.2.9. inclusion_values

String.

Either blank, or an expression that evaluates to a Python iterable (e.g. list or tuple) with Python’s ast.literal_eval() function (see https://docs.python.org/3.4/library/ast.html).

  • If this is not blank/None, then it serves as a ROW INCLUSION LIST – the source row will only be processed if the field’s value is one of the inclusion values.

  • It applies to the raw value from the database (before any transformation via alter_method).

  • This is not applied to scrub_src fields (which contribute to the scrubber regardless).

  • Note that [None] is a list with one member, None, whereas None is equivalent to leaving the field blank.

Examples:

  • [None, 0]

  • [True, 1, 'yes', 'true', 'Yes', 'True']

6.4.2.10. exclusion_values

String.

As for inclusion_values, but the row is excluded if the field’s value is in the exclusion_values list.

6.4.2.11. alter_method

String.

Manner in which to alter the data. Blank, or a comma-separated list of one or more of the following. (You should replace aspects in capitals with appropriate values.)

Component

Meaning

scrub

Scrub in. Applies to text fields only. The field will have its contents anonymised (using information from other fields). Use this for any text field that end users might store free-text comments in.

truncate_date

Truncate this date to the first of the month. Applicable to text or date-as-text fields.

binary_to_text=EXTFIELDNAME

Convert a binary field (e.g. `VARBINARY`, `BLOB`) to text (e.g. `LONGTEXT`). Insert your chosen field name in place of EXTFIELDNAME. The binary data is taken to be the representation of a document. The field must be in the same source table, must contain the file extension (e.g. 'pdf', '.pdf') or a filename with that extension (e.g. '/some/path/mything.pdf'), so that the anonymiser knows how to treat the binary data to extract text from it.

filename_to_text

As for the binary-to-text option, but the field contains a full filename (the contents of which is converted to text), rather than containing binary data directly.

filename_format_to_text=FMT

A more powerful way of specifying a filename that can be created using data from this table. Replace FMT with an unquoted Python str.format() string; see https://docs.python.org/3.4/library/stdtypes.html#str.format. The dictionary passed to format() is created from all fields in the row.

Using an example from RiO: if your ClientDocuments table contains a ClientID column (with a value like 999999) and a Path column (with a value like appointment_letter.pdf), and you know that the actual file will then be found at C:\some\path\999999\docs\appointment_letter.pdf, then you can specify this with

filename_format_to_text=C:\some\path\{ClientID}\docs\{Path}

You probably want to apply this alter_method to the Path column in this example, though that’s not mandatory.

skip_if_extract_fails

If one of the text extraction methods is specified, and this flag is also specified, then the data row will be skipped if text extraction fails (rather than inserted with a NULL value for the text). This is helpful, for example, if your text-processing pipeline breaks; the option prevents rows being created erroneously with NULL text values, so that a subsequent incremental update will fix the problems once you’ve fixed your text extraction tools.

html_unescape

HTML encoding is removed, e.g. convert &amp; to & and &lt; to <

html_untag

HTML tags are removed, e.g. from <a href="http://somewhere">see link</a> to see link

hash=HASH_CONFIG_SECTION

Hash this field, using the hasher specified in the config file section that you name.

You can specify multiple options separated by commas.

Not all are compatible (e.g. scrubbing is for text; date truncation is for dates).

If there’s more than one, text extraction from BLOBs/files is performed first. After that, they are executed in sequence. (The position of the skip-if-text-extraction-fails flag is immaterial.)

A typical combination might be:

filename_to_text,skip_if_extract_fails,scrub

or:

html_untag,html_unescape,scrub

6.4.2.12. dest_table

String.

Table name in the destination database.

6.4.2.13. dest_field

String.

Field (column) name in the destination database.

6.4.2.14. dest_datatype

String. Default: none.

SQL data type in the destination database.

If omitted, the source SQL data type is translated appropriately.

6.4.2.15. index

String.

One of:

Value

Meaning

(blank)

No index.

I

Create a normal index on the destination field.

U

Create a unique index on the destination field.

F

Create a FULLTEXT index, for rapid searching within long text fields. Only applicable to one field per table.

  • Some database engines (e.g. Microsoft SQL Server) require a NOT NULL column with a unique index (i.e. effectively a slightly more restricted primary key) to be present in the same table before it will permit a FULLTEXT index.

6.4.2.16. indexlen

Integer. Default: none.

Can be blank. If not, sets the prefix length of the index. This is mandatory in MySQL if you apply a normal (+/- unique) index to a TEXT or BLOB field. It is not required for FULLTEXT indexes.

6.4.2.17. comment

String.

Field (column) comment, stored in the destination database.

6.4.3. Minimal data dictionary example

This illustrates a data dictionary for a fictional database.

Some more specialist columns (inclusion_values, exclusion_values) are not shown for clarity.

src_db  src_table  src_field    src_datatype  src_flags  scrub_src  scrub_method  decision  alter_method            dest_table  dest_field  dest_datatype  index  indexlen  comment
------- ---------- ------------ ------------- ---------- ---------- ------------- --------- ----------------------- ----------- ----------- -------------- ------ --------- ----------------------------------------------------

# The source table "patients" defines our patients.
# This is also a primary source of information that is used to build our scrubbers.
# Most information shouldn't come through to the destination database, but some (e.g. DOB) is helpful in a truncated form.
# This table also includes our master opt-out switch.

mydb    patients   patientnum   INTEGER(11)   K*H        patient    number        OMIT                                                                                      Local patient ID (PID); will be replaced by RID+TRID
mydb    patients   nhsnum       INTEGER(11)   M          patient    number        OMIT                                                                                      NHS number (MPID); will be replaced by MRID
mydb    patients   dob          DATE                     patient    date          include   truncate_date           patients    dob         DATE                            Date of birth (truncated to first of month)
mydb    patients   dod          DATE                                              include                           patients    dod         DATE                            Date of death, or NULL if alive
mydb    patients   forename     VARCHAR(255)             patient    words         OMIT
mydb    patients   surname      VARCHAR(255)             patient    words         OMIT
mydb    patients   telephone    VARCHAR(255)             patient    number        OMIT                                                                                      A phone number.
mydb    patients   opt_out_anon BIT           !

# The "addresses" table gives (potentially several) addresses per patient.

mydb    addresses  pk           INTEGER(11)   KH                                  include                           addresses   pk          INTEGER(11)     U               Arbitrary address PK.
mydb    addresses  patientnum   INTEGER(11)   P                                   OMIT
mydb    addresses  from_date    DATE                                              include                           addresses   from_date                   I
mydb    addresses  to_date      DATE                                              include                           addresses   to_date                     I
mydb    addresses  line1        VARCHAR(255)             patient    phrase        OMIT
mydb    addresses  line2        VARCHAR(255)             patient    phrase        OMIT
mydb    addresses  line3        VARCHAR(255)             patient    phrase        OMIT
mydb    addresses  line4        VARCHAR(255)             patient    phrase        OMIT
mydb    addresses  line5        VARCHAR(255)             patient    phrase        OMIT
mydb    addresses  postcode     VARCHAR(10)              patient    code          OMIT                                                                                      UK postcode.
mydb    addresses  lsoa         VARCHAR(10)                                       include                           addresses   lsoa                                        Lower Super Output Area, added by CRATE preprocessor (calculated from postcode).
mydb    addresses  imd          INTEGER                                           include                           addresses   imd                                         UK Index of Multiple Deprivation, added by CRATE preprocessor.

# The "relatives" table gives us some third-party information to add to our scrubbers.

mydb    relatives  pk           INTEGER(11)   KH                                  OMIT
mydb    relatives  patientnum   INTEGER(11)   P                                   OMIT
mydb    relatives  relationship VARCHAR(255)                                      OMIT
mydb    relatives  forename     VARCHAR(255)             thirdparty words         OMIT
mydb    relatives  surname      VARCHAR(255)             thirdparty words         OMIT

# The "notes" table contains simple text that needs scrubbing.

mydb    notes      pk           INTEGER(11)   KH                                  include                           notes       pk          INTEGER(11)      U
mydb    notes      patientnum   INTEGER(11)   P                                   OMIT                                                                                      Patient ID will be replaced by RID+TRID
mydb    notes      when         DATETIME                                          include                           notes       when        DATETIME         I
mydb    notes      note         VARCHAR(MAX)                                      include   scrub                   notes       note        LONGTEXT                        Gives the scrubbed note.

# The "documents" table uses filenames to refer to binary documents on disk, which need scrubbing.
# (If binary documents won't change once added, you might want to set the "C" flag on "doc_id", instead of "H", for efficiency.)

mydb    documents  doc_id       INTEGER(11)   KH                                  include                           documents   doc_id      INTEGER(11)      U              Document PK
mydb    documents  patientnum   INTEGER(11)   P                                   OMIT                                                                                      Patient ID will be replaced by RID+TRID
mydb    documents  when_added   DATETIME                                          include                           documents   when_added  DATETIME         I
mydb    documents  filename     VARCHAR(255)                                      include   filename_to_text,scrub  documents   contents    LONGTEXT         F              Becomes scrubbed document contents with FULLTEXT index.

Todo

Check minimal data dictionary example works.