.. crate_anon/docs/source/anonymisation/data_dictionary.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 . .. _data_dictionary: 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. .. _crate_anon_draft_dd: Drafting a data dictionary ~~~~~~~~~~~~~~~~~~~~~~~~~~ Once you have edited your :ref:`anonymiser config file ` to point to your source database, you can generate a **draft data dictionary** like this: .. code-block:: bash 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: .. literalinclude:: _crate_anon_draft_dd.txt :language: none 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. - There is a special row type for **table comments**, in which the fieldnames are blank. That is, just the database and table names are specified, with a comment (but no other flags). src_db ^^^^^^ *String.* This column specifies the source database, using a name that matches one from the ``source_databases`` list in the config file. src_table ^^^^^^^^^ *String.* This column specifies the table name in the source database. src_field ^^^^^^^^^ *String.* This column specifies the field (column) name in the source database. src_datatype ^^^^^^^^^^^^ *String.* This column gives the source column's SQL data type (e.g. `INT`, `VARCHAR(50)`). .. _dd_src_flags: 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 :ref:`source_hash_fieldname ` variable; it is of type ``VARCHAR`` and its length is determined by the :ref:`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, (a) 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. (b) 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 :ref:`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 :ref:`allow_no_patient_info ` is set. ``M`` | **MASTER PID.** | Master ID (e.g. NHS number). (a) The first such value encountered for any patient will be recorded as their MPID. (b) If the field is not omitted, it will be hashed with the MPID hasher. You cannot specify another :ref:`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 :ref:`optout_col_values ` config setting, that patient will be opted out entirely from the anonymised database. ``R`` | **REQUIRED SCRUBBER.** | If this field is a :ref:`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.) =========== =================================================================== .. _dd_scrub_src: 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 :ref:`decision `), are automatically hashed with the "primary" PID hasher, allowing you to link connected records in the research database. You cannot specify another :ref:`alter_method `. ======================= ======================================================= .. _dd_scrub_method: 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. =========================== =================================================== .. _dd_decision: 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. 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']`` exclusion_values ^^^^^^^^^^^^^^^^ *String.* As for ``inclusion_values``, but the row is excluded if the field's value is in the exclusion_values list. .. _dd_alter_method: 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 .. code-block:: none 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 ``&`` to ``&`` and ``<`` to ``<`` ``html_untag`` HTML tags are removed, e.g. from ``see link`` 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: .. code-block:: none filename_to_text,skip_if_extract_fails,scrub or: .. code-block:: none html_untag,html_unescape,scrub dest_table ^^^^^^^^^^ *String.* Table name in the destination database. dest_field ^^^^^^^^^^ *String.* Field (column) name in the destination database. dest_datatype ^^^^^^^^^^^^^ *String.* Default: none. SQL data type in the destination database. If omitted, the source SQL data type is translated appropriately. 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. =========== =================================================================== 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. comment ^^^^^^^ *String.* Field (column) comment, stored in the destination database. 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. .. code-block:: none 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.