Merge pull request #22 from senaite/pentra_xlr

Add Horiba Pentra XLR import schema

Author: xispa

.gitignore

@@ -4,3 +4,4 @@
 /astm_messages/
 /test_messages/
 /out/
+.python-version

docs/changelog.rst

@@ -5,6 +5,7 @@ Changelog
 1.0.0 (unreleased)
 ------------------
 
+- #22 Add Horiba Pentra XLR import schema
 - #21 Add Biomérieux MINI VIDAS® import schema
 - #20 Add Abbott Afinion™ 2 Analyzer import schema
 - #19 Add Spotchem™EL SE-1520 import schema

src/senaite/astm/fields.py

@@ -6,6 +6,7 @@
 import datetime
 import decimal
 import inspect
+import json
 import time
 import warnings
 from itertools import islice
@@ -108,6 +109,24 @@ def _set_value(self, value):
         return super(TextField, self)._set_value(value)
 
 
+class JSONListField(Field):
+    """Converts the value into a JSON list
+    """
+    def _set_value(self, value):
+        if not isinstance(value, list):
+            value = [value]
+        value = json.dumps(value)
+        return super(JSONListField, self)._set_value(value)
+
+    def _get_value(self, value, default=None):
+        if default is None:
+            default = []
+        try:
+            return json.loads(value)
+        except (TypeError, ValueError):
+            return default
+
+
 class DateField(Field):
     """Mapping field for storing date/time values.
     """

src/senaite/astm/instruments/horiba_pentra_xlr.py

@@ -0,0 +1,217 @@
+# -*- coding: utf-8 -*-
+
+from senaite.astm import records
+from senaite.astm.fields import ComponentField
+from senaite.astm.fields import DateField
+from senaite.astm.fields import DateTimeField
+from senaite.astm.fields import JSONListField
+from senaite.astm.fields import NotUsedField
+from senaite.astm.fields import SetField
+from senaite.astm.fields import TextField
+from senaite.astm.mapping import Component
+
+VERSION = "1.0.0"
+HEADER_RX = r".*(?<=\|)(LIS|ABX)(?=\|).*"
+
+
+def get_metadata(wrapper):
+    """Additional metadata
+
+    :param wrapper: The wrapper instance
+    :returns: dictionary of additional metadata
+    """
+    return {
+        "version": VERSION,
+        "header_rx": HEADER_RX,
+    }
+
+
+def get_mapping():
+    """Returns the wrappers for this instrument
+    """
+    return {
+        "H": HeaderRecord,
+        "P": PatientRecord,
+        "O": OrderRecord,
+        "R": ResultRecord,
+        "C": CommentRecord,
+        "Q": RequestInformationRecord,
+        "M": ManufacturerInfoRecord,
+        "L": TerminatorRecord,
+    }
+
+
+class HeaderRecord(records.HeaderRecord):
+    """Message Header Record (H)
+    """
+
+    # Note: Although the field comes in as a single value text, we need to nest
+    #       it for senaite.core.astm.consumer.get_sender_name to work properly
+    sender = ComponentField(
+        Component.build(
+            TextField(name="name"),
+        ))
+
+    processing_id = SetField(
+        field=TextField(),
+        # P: Patient message, Q: Quality control message, D: Technician
+        values=("P", "Q", "D"))
+
+    version = TextField()
+
+
+class PatientRecord(records.PatientRecord):
+    """Patient Information Record (P)
+    """
+
+    # Patient Id (Advised on ABX Pentra XL80 for workflow management)
+    laboratory_id = TextField(length=25)
+
+    # format: Name^First name
+    name = ComponentField(
+        Component.build(
+            TextField(name="name"),
+            TextField(name="first_name"),
+        ))
+
+    # format: YYYYMMDD
+    birthdate = DateField()
+
+    # M, F or U
+    sex = SetField(
+        field=TextField(),
+        length=1,
+        values=("M", "F", "U"))
+
+
+class OrderRecord(records.OrderRecord):
+    """Order Record (O)
+    """
+
+    # Note: Field 9.4.3 "Sample ID" for ABX Pentra XL80 and Pentra XLR (Only
+    # from Instrument to Host) is presented as follows:
+    # SampleID^Rack(2 digits max.)^TubePosition(2 digits max.), e.g.
+    # 45264012^02^08
+    sample_id = ComponentField(
+        Component.build(
+            TextField(name="sample_id"),
+            TextField(name="rack"),
+            TextField(name="position"),
+        )
+    )
+
+    # Note: Field 9.4.5 "Universal test ID" must be filled by the parameters
+    # panel requested (CBC or DIF or RET or DIR or CBR):
+    # Refer to Special characteristics for HORIBA Medical data on page 16.).
+    test = ComponentField(
+        Component.build(
+            NotUsedField(name="_"),
+            NotUsedField(name="__"),
+            NotUsedField(name="___"),
+            SetField(
+                name="testname",
+                field=TextField(),
+                values=("CBC", "DIF", "RET", "DIR", "CBR")),
+        ))
+
+    # format: YYYYMMDDHHMMSS
+    sampled_at = DateTimeField()
+
+    # format: YYYYMMDDHHMMSS
+    collected_at = DateTimeField()
+
+    biomaterial = TextField()
+    report_type = SetField(
+        field=TextField(),
+        length=1,
+        values=("F", "C"))  # F: final; C: correction
+
+
+class CommentRecord(records.CommentRecord):
+    """Comment Record (C)
+    """
+    # I: clinical instrument system
+    source = SetField(
+        field=TextField(),
+        length=1,
+        values=("I"))
+
+    # Text (Refer to Table 23 - Analytical alarms, page 18; Table 24 - Analyzer
+    # alarms, page 18; Table 25 - Suspected pathologies, page 18.
+    #
+    # Note: values come in either as a string or a list with variable length.
+    #       Therefore, we simply handle it as a JSON list
+    data = JSONListField()
+
+    # G:Free text
+    # I: Instrument flag comment
+    # L: Comment from host (Patient order) P80 V1.1 and above
+    ctype = SetField(
+        field=TextField(),
+        length=1,
+        values=("G", "I", "L"))
+
+
+class ResultRecord(records.ResultRecord):
+    """Record to transmit analytical data.
+    """
+
+    # Note: Field 10.1.3 "Universal TestID" for ABX Pentra XL80 and Pentra XLR
+    # includes the dilution ratio as follows: ^^^Result name in english^LOINC
+    # code^CDR (CDR=1 or 2 or 3 or 5). Results are returned in between ().
+    test = ComponentField(
+        Component.build(
+            NotUsedField(name='_'),
+            NotUsedField(name='__'),
+            NotUsedField(name='___'),
+            TextField(name='result_name'),
+            TextField(name='loinc_code'),
+            SetField(
+                name="testname",
+                field=TextField(),
+                values=("1", "2", "3", "5")),
+        ))
+
+    value = TextField()
+
+    units = SetField(
+        field=TextField(),
+        length=1,
+        values=("1", "2", "3", "4"))
+
+    abnormal_flag = SetField(
+        field=TextField(),
+        length=2,
+        values=("L", "H", "LL", "HH", ">"))
+
+    # W: suspicion
+    # N: rejected result
+    # F: final result
+    # X: Parameter exceeding the capacity
+    #    (ABX Pentra 80 / ABX Pentra XL80 / Pentra XLR)
+    # M: Value input manually (ABX Pentra XL80 / Pentra XLR)
+    # D: Value obtained by dilution (ABX Pentra XL80 / Pentra XLR)
+    status = SetField(
+        field=TextField(),
+        length=1,
+        values=("W", "N", "F", "X", "M", "D"))
+
+    # Operator Code + Name
+    operator = TextField()
+
+    completed_at = DateTimeField()
+
+
+class RequestInformationRecord(records.RequestInformationRecord):
+    """Request information Record (Q)
+    """
+
+
+class ManufacturerInfoRecord(records.ManufacturerInfoRecord):
+    """Manufacturer Specific Records (M)
+    """
+
+
+class TerminatorRecord(records.TerminatorRecord):
+    """Message Termination Record (L)
+    """

src/senaite/astm/mapping.py

@@ -69,6 +69,7 @@ def build(cls, *a):
         for field in a:
             if field.name is None:
                 raise ValueError('Name is required for ordered fields.')
+            # set the definied fields as class attributes
             setattr(newcls, field.name, field)
             fields.append((field.name, field))
         newcls._fields = fields

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

@@ -1,6 +1,6 @@
 1H|\^&|||ABX|||||||P|E1394-97|2022072712155158
-2P|1||||^|||U56
-3O|1|AUTO_SID1^00^00||^^^DIF|||||||||||Standard||||||||||F68
+2P|1||||Mohale^Rita||19771201|FC9
+3O|1|S1234^00^00||^^^DIF|||202205270000|202205260000|||||||Standard||||||||||F83
 4R|1|^^^WBC^804-5^1|8.5|1||||W||NNE NNEMT||20220727121550E2
 5C|1|I|Alarm_WBC^LMNE-^BASO+^LL^NL^LN^NO^SL1|ID7
 6C|2|I|LARGE IMMATURE CELL^NRBCs|I62