#!/usr/bin/env python
"""
camcops_server/cc_modules/cc_simpleobjects.py
===============================================================================
Copyright (C) 2012, University of Cambridge, Department of Psychiatry.
Created by Rudolf Cardinal (rnc1001@cam.ac.uk).
This file is part of CamCOPS.
CamCOPS 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.
CamCOPS 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 CamCOPS. If not, see <https://www.gnu.org/licenses/>.
===============================================================================
**Simple struct-like classes.**
"""
import copy
from typing import List, TYPE_CHECKING
from pendulum import Date
from cardinal_pythonlib.datetimefunc import format_datetime
from cardinal_pythonlib.reprfunc import auto_repr
from camcops_server.cc_modules.cc_constants import DateFormat
if TYPE_CHECKING:
from camcops_server.cc_modules.cc_request import CamcopsRequest
# Prefer classes to collections.namedtuple; both support type checking but
# classes support better parameter checking (and refactoring) via PyCharm.
# =============================================================================
# IdNumReference
# =============================================================================
[docs]class IdNumReference(object):
"""
A simple way of referring to an ID number.
It's not stored in the database -- it's just an object to be passed around
that encapsulates ``which_idnum`` and ``idnum_value``.
As an example, suppose our administrator has defined ID type
(``which_idnum``) 7 to be "NHS number". Then if a patient has NHS number
9999999999, we might represent this ID of theirs as
``IdNumReference(which_idnum=7, idnum_value=9999999999)``.
"""
[docs] def __init__(self, which_idnum: int, idnum_value: int) -> None:
self.which_idnum = which_idnum
self.idnum_value = idnum_value
def __str__(self) -> str:
return f"idnum{self.which_idnum}={self.idnum_value}"
def __repr__(self) -> str:
return auto_repr(self)
def is_valid(self) -> bool:
return (
self.which_idnum is not None
and self.which_idnum > 0
and self.idnum_value is not None
and self.idnum_value > 0
)
def __eq__(self, other: "IdNumReference") -> bool:
if not isinstance(other, IdNumReference):
return False
return (
self.which_idnum == other.which_idnum
and self.idnum_value == other.idnum_value
)
def description(self, req: "CamcopsRequest") -> str:
if not self.is_valid():
return "[invalid_IdNumReference]"
return f"{req.get_id_shortdesc(self.which_idnum)} = {self.idnum_value}"
# =============================================================================
# HL7PatientIdentifier
# =============================================================================
# noinspection PyShadowingBuiltins
[docs]class HL7PatientIdentifier(object):
"""
Represents a patient identifier for the HL7 protocol.
"""
[docs] def __init__(
self, pid: str, id_type: str, assigning_authority: str
) -> None:
self.pid = pid
# ... called "pid" not "id" as type checker sometimes thinks "id" must
# be integer, as in Python's id(object).
self.id_type = id_type
self.assigning_authority = assigning_authority
# =============================================================================
# BarePatientInfo
# =============================================================================
[docs]class BarePatientInfo(object):
"""
Represents information about a patient using a simple object with no
connection to a database.
In some situations we avoid using
:class:`camcops_server.cc_modules.cc_patient.Patient`: specifically, when
we would otherwise have to deal with mutual dependency problems and the use
of the database (prior to full database initialization).
"""
[docs] def __init__(
self,
forename: str = None,
surname: str = None,
sex: str = None,
dob: Date = None,
address: str = None,
email: str = None,
gp: str = None,
otherdetails: str = None,
idnum_definitions: List[IdNumReference] = None,
) -> None:
self.forename = forename
self.surname = surname
self.sex = sex
self.dob = dob
self.address = address
self.email = email
self.gp = gp
self.otherdetails = otherdetails
self.idnum_definitions = (
idnum_definitions or []
) # type: List[IdNumReference]
def __str__(self) -> str:
return (
"Patient(forename={f!r}, surname={sur!r}, sex={sex!r}, DOB={dob}, "
"address={a!r}, email={email!r}, gp={gp!r}, otherdetails={o!r}, "
"idnums={i})".format(
f=self.forename,
sur=self.surname,
sex=self.sex,
dob=format_datetime(self.dob, DateFormat.ISO8601_DATE_ONLY),
a=self.address,
email=self.email,
gp=self.gp,
o=self.otherdetails,
i="[{}]".format(
", ".join(str(idnum) for idnum in self.idnum_definitions)
),
)
)
def __repr__(self) -> str:
return auto_repr(self)
[docs] def add_idnum(self, idref: IdNumReference) -> None:
"""
Adds an ID number. No checks in relation to what's already present.
Args:
idref: a :class:`IdNumReference`
"""
self.idnum_definitions.append(idref)
def __eq__(self, other: "BarePatientInfo") -> bool:
"""
Do all data elements match those of ``other``?
"""
if not isinstance(other, BarePatientInfo):
return False
return (
self.forename == other.forename
and self.surname == other.surname
and self.sex == other.sex
and self.dob == other.dob
and self.address == other.address
and self.email == other.email
and self.gp == other.gp
and self.otherdetails == other.otherdetails
and self.idnum_definitions == other.idnum_definitions
)
# =============================================================================
# Raw XML value
# =============================================================================
[docs]class XmlSimpleValue(object):
"""
Represents XML lowest-level items. See functions in ``cc_xml.py``.
"""
[docs] def __init__(self, value) -> None:
self.value = value
# =============================================================================
# TaskExportOptions
# =============================================================================
[docs]class TaskExportOptions(object):
"""
Information-holding object for options controlling XML and other
representations of tasks.
"""
[docs] def __init__(
self,
db_patient_id_per_row: bool = False,
db_make_all_tables_even_empty: bool = False,
db_include_summaries: bool = False,
include_blobs: bool = False,
xml_include_ancillary: bool = False,
xml_include_calculated: bool = False,
xml_include_comments: bool = True,
xml_include_patient: bool = False,
xml_include_plain_columns: bool = False,
xml_include_snomed: bool = False,
xml_skip_fields: List[str] = None,
xml_sort_by_name: bool = True,
xml_with_header_comments: bool = False,
) -> None:
"""
Args:
db_patient_id_per_row:
generates an anonymisation staging database -- that is, a
database with patient IDs in every row of every table, suitable
for feeding into an anonymisation system like CRATE
(https://doi.org/10.1186%2Fs12911-017-0437-1).
db_make_all_tables_even_empty:
create all tables, even empty ones
include_blobs:
include binary large objects (BLOBs) (applies to several export
formats)
xml_include_ancillary:
include ancillary tables as well as the main?
xml_include_calculated:
include fields calculated by the task
xml_include_comments:
include comments in XML?
xml_include_patient:
include patient details?
xml_include_plain_columns:
include the base columns
xml_include_snomed:
include SNOMED-CT codes, if available?
xml_skip_fields:
fieldnames to skip
xml_sort_by_name:
sort by field/attribute names?
xml_with_header_comments:
include header-style comments?
"""
self.db_patient_id_in_each_row = db_patient_id_per_row
self.db_make_all_tables_even_empty = db_make_all_tables_even_empty
self.db_include_summaries = db_include_summaries
self.include_blobs = include_blobs
self.xml_include_ancillary = xml_include_ancillary
self.xml_include_calculated = xml_include_calculated
self.xml_include_comments = xml_include_comments
self.xml_include_patient = xml_include_patient
self.xml_include_plain_columns = xml_include_plain_columns
self.xml_include_snomed = xml_include_snomed
self.xml_skip_fields = xml_skip_fields or [] # type: List[str]
self.xml_sort_by_name = xml_sort_by_name
self.xml_with_header_comments = xml_with_header_comments
[docs] def clone(self) -> "TaskExportOptions":
"""
Returns a copy of this object.
"""
return copy.copy(self)