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Merge pull request #21 from senaite/mini-vidas
Add Biomérieux MINI VIDAS® import schema
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‎docs/changelog.rst

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1.0.0 (unreleased)
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------------------
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- #21 Add Biomérieux MINI VIDAS® import schema
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- #20 Add Abbott Afinion™ 2 Analyzer import schema
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- #19 Add Spotchem™EL SE-1520 import schema
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- #18 Add Siemens' DCA Vantage® Analyzer import schema

‎src/senaite/astm/adapters/__init__.py

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# -*- coding: utf-8 -*-
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from senaite.astm.adapters import biomerieux # noqa: F401
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from senaite.astm.adapters import spotchem # noqa: F401

‎src/senaite/astm/adapters/biomerieux/__init__.py

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# -*- coding: utf-8 -*-
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from . import mini_vidas # noqa: F401

‎src/senaite/astm/adapters/biomerieux/mini_vidas.py

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# -*- coding: utf-8 -*-
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import re
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from datetime import datetime
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from senaite.astm import adapter_registry
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from senaite.astm import utils
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from senaite.astm.constants import ENQ
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from senaite.astm.constants import EOT
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from senaite.astm.constants import NAK
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from senaite.astm.interfaces import IDataHandler
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from senaite.astm.utils import f
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from senaite.astm.utils import u
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from zope.interface import implementer
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RX = (
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rb"\x02" # Start of the message
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rb"(?:\x1emt(?P<mt>[^|]*))?" # Message Type (mt)
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rb"(?:\|\x1epi(?P<pi>[^|]*))?" # Patient Identifier (pi)
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rb"(?:\|\x1epn(?P<pn>[^|]*))?" # Patient Name (pn)
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rb"(?:\|\x1epb(?P<pb>[^|]*))?" # Patient Birthdate (pb)
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rb"(?:\|\x1eps(?P<ps>[^|]*))?" # Patient Sex (ps)
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rb"(?:\|\x1eso(?P<so>[^|]*))?" # Sample Origin (so)
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rb"(?:\|\x1esi(?P<si>[^|]*))?" # Specimen separator (si)
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rb"(?:\|\x1eci(?P<ci>[^|]*))?" # Sample Identifier (ci)
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rb"(?:\|\x1ert(?P<rt>[^|]*))?" # Short assay name (rt)
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rb"(?:\|\x1ern(?P<rn>[^|]*))?" # Long assay name (rn)
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rb"(?:\|\x1ett(?P<tt>[^|]*))?" # Test completion time (tt)
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rb"(?:\|\x1etd(?P<td>[^|]*))?" # Test completion date (td)
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rb"(?:\|\x1eql(?P<ql>[^|]*))?" # Qualitative Result (ql)
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rb"(?:\|\x1eqn(?P<qn>[^|]*))?" # Quantitative Result (qn)
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rb"(?:\|\x1ey3(?P<y3>[^|]*))?" # Unit associated with qn (y3)
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rb"(?:\|\x1eqd(?P<qd>[^|]*))?" # Dilution (qd)
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rb"(?:\|\x1enc(?P<nc>[^|]*))?" # Vidas flags (nc)
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rb"(?:\|\x1eid(?P<id>[^|]*))?" # Instrument ID (id)
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rb"(?:\|\x1esn(?P<sn>[^|]*))?" # Serial Number (sn)
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rb"(?:\|\x1em4(?P<m4>[^|]*))?" # Technologist (m4)
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rb"(?:\|\x1d(?P<checksum>[a-fA-F0-9]{2}))$" # Checksum
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)
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@implementer(IDataHandler)
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class DataHandler:
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"""Custom data handler for Biomérieux miniVidas
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We receive from this instrument a non valid ASTM message that need to be
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handled differntly
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"""
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def __init__(self, protocol, data):
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self.protocol = protocol
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self.data = data
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def can_handle(self):
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return re.match(RX, self.data) is not None
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def to_timestamp(self, date, time):
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"""Make a timestamp from the date and time
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"""
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dt = datetime.now()
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if date:
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dt = datetime.strptime(u(date), '%m/%d/%y')
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if time:
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t = datetime.strptime(u(time), '%H:%M').time()
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dt = datetime.combine(dt, t)
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return dt.strftime("%Y%m%d%H%M%S")
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def handle_data(self):
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"""Create a valid ASTM message of the received data
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1. Create a static header record
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2. Create a results record with the given data
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3. Create a termination record
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"""
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parts = re.match(RX, self.data)
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if not parts:
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return NAK
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# initialize the communication if we're not already in transfer state
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# Note: This is mainly a test fixture for the simulator
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if not self.protocol.in_transfer_state:
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self.protocol.on_enq(ENQ)
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data = {}
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for k, v in parts.groupdict().items():
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data[k] = u(v) if v else ""
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# convert date and time to a timestamp
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date = data.get("td")
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time = data.get("tt")
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data["ts"] = self.to_timestamp(date, time)
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frames = [
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f("1H|\\^&|||miniVidas^biomerieux^1.0.0|||||||||{ts}{CR}{ETX}",
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**data),
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f("2P|1|||{pi}|{pn}||{pb}|{ps}||||||||||||||||||||||||||{CR}{ETX}",
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**data),
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f("3O|1|{ci}||{rn}||||||||||||||||||{ts}||||||||{CR}{ETX}",
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**data),
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f("4R|1|{rt}|{qn}|||{nc}||{ql}||{m4}||{ts}|{CR}{ETX}",
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**data),
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f("5L|1|N{CR}{ETX}"),
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]
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messages = []
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for frame in frames:
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cs = utils.make_checksum(frame)
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messages.append(
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f("{STX}{frame}{cs}{CRLF}", frame=u(frame), cs=u(cs)))
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# fill in the full message
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self.protocol.messages = messages
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# end the communicaiton
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self.protocol.on_eot(EOT)
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# register the adapter
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adapter_registry.registerAdapter(
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DataHandler,
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required=(object, object),
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provided=IDataHandler,
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name="mini_vidas",
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)

‎src/senaite/astm/adapters/spotchem/se1520.py

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DataHandler,
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required=(object, object),
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provided=IDataHandler,
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name="spotchem_se1520",
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)

‎src/senaite/astm/codec.py

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frame, cs = frame_cs[:-2], frame_cs[-2:]
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# validate the checksum
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ccs = make_checksum(frame)
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assert cs == ccs, "Checksum failure: expected %r, got %r" % (cs, ccs)
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assert cs.upper() == ccs, "Checksum wrong: expected %r, got %r" % (cs, ccs)
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seq, records = decode_frame(frame, encoding)
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return seq, records, cs.decode()
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‎src/senaite/astm/instruments/biomerieux_mini_vidas.py

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# -*- coding: utf-8 -*-
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from senaite.astm import records
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from senaite.astm.fields import ComponentField, DateField
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from senaite.astm.fields import DateTimeField
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from senaite.astm.fields import TextField
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from senaite.astm.mapping import Component
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VERSION = "1.0.0"
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# Supports Biomérieux miniVidas
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HEADER_RX = r".*miniVidas\^"
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def get_metadata(wrapper):
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"""Additional metadata
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:param wrapper: The wrapper instance
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:returns: dictionary of additional metadata
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"""
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return {
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"version": VERSION,
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"header_rx": HEADER_RX,
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}
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def get_mapping():
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"""Returns the wrappers for this instrument
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"""
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return {
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"H": HeaderRecord,
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"P": PatientRecord,
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"O": OrderRecord,
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"R": ResultRecord,
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"L": TerminatorRecord,
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}
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class HeaderRecord(records.HeaderRecord):
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"""Message Header Record (H)
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"""
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sender = ComponentField(
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Component.build(
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TextField(name="name"),
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TextField(name="manufacturer", default="Biomerieux"),
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TextField(name="version"),
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))
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timestamp = DateTimeField()
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class PatientRecord(records.PatientRecord):
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"""Patient Information Record (P)
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This record is used to transfer patient information to the analyzer (test
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order messages) or to the host (result messages).
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"""
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name = TextField()
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birthdate = DateField()
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sex = TextField()
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class OrderRecord(records.OrderRecord):
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sample_id = TextField()
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test = TextField()
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reported_at = DateTimeField()
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class ResultRecord(records.ResultRecord):
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"""Record to transmit analytical data.
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"""
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test = TextField()
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value = TextField()
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status = TextField()
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completed_at = DateTimeField()
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class TerminatorRecord(records.TerminatorRecord):
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"""Message Termination Record (L)
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"""

‎src/senaite/astm/protocol.py

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"""Process incoming data
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"""
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# lookup custom multi-adapter to handle the data
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adapter = adapter_registry.queryMultiAdapter(
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(self, data), IDataHandler)
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if adapter and adapter.can_handle():
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return adapter.handle_data()
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adapters = adapter_registry.getAdapters((self, data), IDataHandler)
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for name, adapter in adapters:
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if adapter and adapter.can_handle():
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return adapter.handle_data()
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response = None
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if data.startswith(ENQ):

‎src/senaite/astm/tests/base.py

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from senaite.astm.constants import ACK
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from senaite.astm.constants import ENQ
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# Ignore invalid ASTM files that are handled by and adapter (see PR #19)
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IGNORE_INSTRUMENT_FILES = [
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"spotchem_el.txt" # Not valid ASTM (see PR #19)
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"spotchem_el.txt",
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"mini_vidas.txt",
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]
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‎src/senaite/astm/tests/data/mini_vidas.txt

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mtrsl|pi|pn|si|ciZ1G021SCR|rtHBCT|rnAnti-HBc Total II|tt18:35|td10/25/24|qlPositif|qn0.05|b0

‎src/senaite/astm/tests/data/mini_vidas_mock.txt

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1H|\\^&|||miniVidas^biomerieux^1.0.0|||||||||2024102518350058
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2P|1||||test_patient|||||||||||||||||||||||||||||4F
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3O|1|Z1G021SCR||Anti-HBc Total II||||||||||||||||||20241025183500||||||||D5
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4R|1|HBCT|0.05|||||Positif||||20241025183500|96
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5L|1|N08

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