14.1.21. crate_anon.anonymise.researcher_report

crate_anon/anonymise/researcher_report.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/>.

Produce a researcher-oriented report about a destination database.

class crate_anon.anonymise.researcher_report.Default[source]

Default values.

class crate_anon.anonymise.researcher_report.ResearcherReportConfig(output_filename: str, anonconfig: crate_anon.anonymise.config.Config = None, base_font_size: str = '11pt', db_name: str = None, db_url: str = None, debug_pdf: bool = False, max_distinct_values: int = 20, max_value_length: int = 50, header_footer_spacing_mm: int = 3, margin_left_right: str = '15mm', margin_top_bottom: str = '18mm', page_size: str = 'A4', orientation: str = 'landscape', show_counts: bool = True, show_url: bool = True, show_values: bool = True, skip_values_if_too_many: bool = False, use_dd: bool = True, echo: bool = False)[source]
__init__(output_filename: str, anonconfig: Config | None = None, base_font_size: str = '11pt', db_name: str | None = None, db_url: str | None = None, debug_pdf: bool = False, max_distinct_values: int = 20, max_value_length: int = 50, header_footer_spacing_mm: int = 3, margin_left_right: str = '15mm', margin_top_bottom: str = '18mm', page_size: str = 'A4', orientation: str = 'landscape', show_counts: bool = True, show_url: bool = True, show_values: bool = True, skip_values_if_too_many: bool = False, use_dd: bool = True, echo: bool = False) → None
get_annotation_when_no_ddr_found(col_name: str) → str[source]

Returns best-guess CRATE annotation information when no data dictionary row is available.

Parameters:

col_name – Column name.

get_db_engine_type() → str[source]

Returns the engine type (e.g. mysql).

get_db_name() → str[source]

Returns a short database name used for titles.

safe_db_url_if_selected() → str[source]

Sanitised version of the database URL, or a blank string if not enabled.

wkhtmltopdf_options() → Dict[str, str | None][source]

Returns wkhtmltopdf options for the current setup.

class crate_anon.anonymise.researcher_report.Templates[source]

Template filenames, within TEMPLATE_DIR.

crate_anon.anonymise.researcher_report.get_values_summary(column: Column, reportcfg: ResearcherReportConfig, ddr: DataDictionaryRow | None = None) → str[source]

Return a textual summary of values in a column (from a de-identified database).

Parameters:

  • column – SQLAlchemy Column object to summarize. (It knows its own Table.)

  • reportcfg – ResearcherReportConfig object, governing the report.

  • ddr – Corresponding CRATE DataDictionaryRow, if there is one.

crate_anon.anonymise.researcher_report.literal(value: Any, max_length: int = 50, truncated_suffix: str = '…') → str[source]

Returns a rough-and-ready SQL literal, intended for human viewing only. Truncates long strings at a given length.

  • Some duplication from within cardinal_pythonlib.sqlalchemy.dump.get_literal_query.

  • Dates/times are NOT enclosed in quotes here.

crate_anon.anonymise.researcher_report.main() → None[source]

Command-line entry point.

crate_anon.anonymise.researcher_report.mk_comment(reportcfg: ResearcherReportConfig, column: Column, ddr: DataDictionaryRow | None = None) → str[source]

Return a comment. For databases that don’t support comments, we’ll want the CRATE DD one (unless that’s been disabled). For databases that do, we don’t want duplication.

crate_anon.anonymise.researcher_report.mk_researcher_report_html(reportcfg: ResearcherReportConfig) → Tuple[str, str, str][source]

Produces a researcher-oriented report about a destination database, as HTML.

Parameters:

reportcfg – ResearcherReportConfig object, governing the report.

Returns:

header_html, html, footer_html

Return type:

tuple

crate_anon.anonymise.researcher_report.mk_researcher_report_pdf(reportcfg: ResearcherReportConfig) → bool[source]

Produces a researcher-oriented report about a destination database, as a PDF.

Parameters:

reportcfg – ResearcherReportConfig object, governing the report.

Returns:

success

crate_anon.anonymise.researcher_report.mk_table_html(table_name: str, reportcfg: ResearcherReportConfig) → str[source]

Returns HTML for the per-table aspects of the report.

Parameters:

  • table_name – Table to process.

  • reportcfg – ResearcherReportConfig object, governing the report.

Returns:

HTML as a string.

crate_anon.anonymise.researcher_report.sorter(x: Any) → Tuple[bool, Any][source]

Used for sorting values that may be None/NULL. Remember that False < True, so this puts None values lowest (first in a default sort).

crate_anon.anonymise.researcher_report.template(filename: str) → str[source]

Returns a filename from our specific template directory.