# -*- coding: utf-8 -*-
#
# Copyright (C) 2012 Alexander Shorin
# All rights reserved.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution.
#
"""
``astm.omnilab.server`` - LabOnline server implementation
----------------------------------------------------------
"""
from astm.server import BaseRecordsDispatcher
from astm.mapping import (
Component, ConstantField, ComponentField, DateTimeField, IntegerField,
SetField, TextField, NotUsedField
)
from .common import (
Header, Terminator, CommonPatient as Patient,
CommonOrder,
CommonResult,
CommonComment,
Sender
)
__all__ = ['RecordsDispatcher',
'Header', 'Patient', 'Order', 'Result', 'Terminator',
'CommentData', 'CompletionDate', 'Instrument', 'Operator',
'Sender', 'Test']
#: Instrument (analyser) information structure.
#:
#: :param _: Reserved. Not used.
#: :type _: None
#:
#: :param rack: Rack number. Length: 5.
#: :type rack: str
#:
#: :param position: Position number. Length: 3.
#: :type position: str
#:
Instrument = Component.build(
TextField(name='_'),
TextField(name='rack', length=5),
TextField(name='position', length=3),
)
#: Test :class:`~astm.mapping.Component` also known as Universal Test ID.
#:
#: :param _: Reserved. Not used.
#: :type _: None
#:
#: :param __: Reserved. Not used.
#: :type __: None
#:
#: :param ___: Reserved. Not used.
#: :type ___: None
#:
#: :param assay_code: Assay code. Required. Length: 20.
#: :type assay_code: str
#:
#: :param assay_name: Assay name. Length: 8.
#: :type assay_name: str
#:
#: :param dilution: Dilution. Length: 10.
#: :type dilution: str
#:
#: :param status: Assay status. Length: 1.
#: :type status: str
#:
#: :param reagent_lot: Reagent lot. Length: 15.
#: :type reagent_lot: str
#:
#: :param reagent_number: Reagent serial number. Length: 5.
#: :type reagent_number: str
#:
#: :param control_lot: Control lot number. Length: 25.
#: :type control_lot: str
#:
#: :param type: Result type value. One of: ``CE``, ``TX``.
#: :type type: str
#:
Test = Component.build(
NotUsedField(name='_'),
NotUsedField(name='__'),
NotUsedField(name='___'),
TextField(name='assay_code', required=True, length=20),
TextField(name='assay_name', length=8),
TextField(name='dilution', length=10),
TextField(name='status', length=1),
TextField(name='reagent_lot', length=15),
TextField(name='reagent_number', length=5),
TextField(name='control_lot', length=25),
SetField(name='type', values=('CE', 'TX'))
)
#: Information about operator that validated results.
#:
#: :param code_on_labonline: Operator code on LabOnline. Length: 12.
#: :type code_on_labonline: str
#:
#: :param code_on_analyzer: Operator code on analyser. Length: 20.
#: :type code_on_analyzer: str
#:
Operator = Component.build(
TextField(name='code_on_labonline', length=12),
TextField(name='code_on_analyzer', length=20),
)
#: Completion date time information.
#:
#: :param labonline: Completion date time on LabOnline.
#: :type labonline: datetime.datetime
#:
#: :param analyzer: Completion date time on analyser.
#: :type analyzer: datetime.datetime
#:
CompletionDate = Component.build(
DateTimeField(name='labonline'),
DateTimeField(name='analyzer'),
)
#: Instrument (analyser) information structure.
#:
#: :param _: Reserved. Not used.
#: :type _: None
#:
#: :param rack: Rack number. Length: 5.
#: :type rack: str
#:
#: :param position: Position number. Length: 3.
#: :type position: str
#:
Instrument = Component.build(
NotUsedField(name='_'),
TextField(name='rack', length=5),
TextField(name='position', length=3),
)
#: Comment control text structure.
#:
CommentData = Component.build(
SetField(name='code', values=('PC', 'RC', 'SC', 'TC',
'CK', 'SE', 'CL', 'TA', 'SS', 'HQ', 'AL', 'PT')),
TextField(name='value'),
TextField(name='field_1'),
TextField(name='field_2'),
TextField(name='field_3'),
TextField(name='field_4'),
TextField(name='field_5'),
)
[docs]class Order(CommonOrder):
"""ASTM order record.
:param type: Record Type ID. Always ``O``.
:type type: str
:param seq: Sequence Number. Required.
:type seq: int
:param sample_id: Sample ID number. Required. Length: 12.
:type sample_id: str
:param instrument: Instrument specimen ID.
:type instrument: :class:`Instrument`
:param test: Test information structure (aka Universal Test ID).
:type test: :class:`Test`
:param priority: Priority flag. Required. Possible values:
- ``S``: stat; -``R``: routine.
:type priority: str
:param created_at: Ordered date and time. Required.
:type created_at: datetime.datetime
:param sampled_at: Specimen collection date and time.
:type sampled_at: datetime.datetime
:param collected_at: Collection end time. Not used.
:type collected_at: None
:param volume: Collection volume. Not used.
:type volume: None
:param collector: Collector ID. Not used.
:type collector: None
:param action_code: Action code. Required. Possible values:
- :const:`None`: normal order result;
- ``Q``: quality control;
:type action_code: str
:param danger_code: Danger code. Not used.
:type danger_code: None
:param clinical_info: Revelant clinical info. Not used.
:type clinical_info: None
:param delivered_at: Date/time specimen received.
:type delivered_at: None
:param biomaterial: Sample material code. Length: 20.
:type biomaterial: str
:param physician: Ordering Physician. Not used.
:type physician: None
:param physician_phone: Physician's phone number. Not used.
:type physician_phone: None
:param user_field_1: An optional field, it will be send back unchanged to
the host along with the result. Length: 20.
:type user_field_1: str
:param user_field_2: An optional field, it will be send back unchanged to
the host along with the result. Length: 1024.
:type user_field_2: str
:param laboratory_field_1: Laboratory field #1. Not used.
:type laboratory_field_1: None
:param laboratory_field_2: Primary tube code. Length: 12.
:type laboratory_field_2: str
:param modified_at: Date and time of last result modification. Not used.
:type modified_at: None
:param instrument_charge: Instrument charge to computer system. Not used.
:type instrument_charge: None
:param instrument_section: Instrument section id. Not used.
:type instrument_section: None
:param report_type: Report type. Always ``F`` which means final order
request.
:type report_type: str
:param reserved: Reserved. Not used.
:type reserved: None
:param location_ward: Location ward of specimen collection. Not used.
:type location_ward: None
:param infection_flag: Nosocomial infection flag. Not used.
:type infection_flag: None
:param specimen_service: Specimen service. Not used.
:type specimen_service: None
:param laboratory: Production laboratory. Not used.
:type laboratory: None
"""
action_code = SetField(values=(None, 'Q'))
instrument = ComponentField(Instrument)
report_type = ConstantField(default='F')
test = ComponentField(Test)
[docs]class Result(CommonResult):
"""ASTM patient record.
:param type: Record Type ID. Always ``R``.
:type type: str
:param seq: Sequence Number. Required.
:type seq: int
:param test: Test information structure (aka Universal Test ID).
:type test: :class:`Test`
:param value: Measurement value. Numeric, coded or free text value
depending on result type. Required. Length: 1024.
:type value: None
:param units: Units. Length: 20.
:type units: str
:param references: Normal reference value interval.
:type references: str
:param abnormal_flag: Result abnormal flag. Possible values:
- ``0``: normal result;
- ``1``: result out of normal values;
- ``2``: result out of attention values;
- ``3``: result out of panic values;
+10 Delta-check;
+1000 Device alarm.
Length: 4.
:type abnormal_flag: str
:param abnormality_nature: Nature of abnormality testing. Possible values:
- ``N``: normal value;
- ``L``: below low normal range;
- ``H``: above high normal range;
- ``LL``: below low critical range;
- ``HH``: above high critical range.
:type abnormality_nature: str
:param status: Result status. ``F`` indicates a final result;
``R`` indicating rerun. Length: 1.
:type status: str
:param normatives_changed_at: Date of changes in instrument normative
values or units. Not used.
:type normatives_changed_at: None
:param operator: Operator ID.
:type operator: :class:`Operator`
:param started_at: When works on test was started on.
:type started_at: datetime.datetime
:param completed_at: When works on test was done.
:type completed_at: datetime.datetime
:param instrument: Instrument ID. Required.
:type instrument: :class:`Instrument`
"""
abnormal_flag = SetField(
field=IntegerField(),
length=4,
values=(0, 1, 2, 3,
10, 11, 12, 13,
1000, 1001, 1002, 1003,
1010, 1011, 1012, 1013))
abnormality_nature = SetField(values=('N', 'L', 'H', 'LL', 'HH'))
completed_at = ComponentField(CompletionDate)
instrument = TextField(length=16)
operator = ComponentField(Operator)
references = TextField()
started_at = DateTimeField(required=True)
status = SetField(values=('F', 'R'))
test = ComponentField(Test)
units = TextField(length=20)
class Comment(CommonComment):
"""ASTM patient record.
:param type: Record Type ID. Always ``C``.
:type type: str
:param seq: Sequence Number. Required.
:type seq: int
:param source: Comment source. Always ``I``.
:type source: str
:param data: Measurement value. Numeric, coded or free text value
depending on result type. Required. Length: 1024.
:type data: :class:`CommentData`
:param ctype: Comment type. Always ``G``.
:type ctype: str
"""
source = ConstantField(default='I')
data = ComponentField(CommentData)
[docs]class RecordsDispatcher(BaseRecordsDispatcher):
"""Omnilab specific records dispatcher. Automatically wraps records by
related mappings."""
def __init__(self, *args, **kwargs):
super(RecordsDispatcher, self).__init__(*args, **kwargs)
self.wrappers = {
'H': Header,
'P': Patient,
'O': Order,
'R': Result,
'C': Comment,
'L': Terminator
}