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Merged
dnicolalde merged 10 commits into from
Jun 23, 2026
Merged

Switch to new hematology analyzer format #969

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b3e8377
Update hematology parser with new tests and updated JS
LeviCameron1 Apr 28, 2026
2a634a3
Add new tests to results
LeviCameron1 Apr 28, 2026
2f2a710
Update results query to extend to 4 digits
LeviCameron1 Apr 30, 2026
76a586b
Update results input field for hematology results to capture up to 4 …
LeviCameron1 Apr 30, 2026
8382938
Remove runId from pivot query which was added during testing
LeviCameron1 May 4, 2026
105e62f
Update results query to extend to 4 digits
LeviCameron1 Apr 30, 2026
154fa06
Remove runId from pivot query which was added during testing
LeviCameron1 May 4, 2026
58e5e08
Use Martys suggestion for updating the pivot query
LeviCameron1 May 6, 2026
e431f1c
Remove extra whitespace causing issues in file format
LeviCameron1 May 26, 2026
00acf60
Move NRBC# test to ABS calculations
LeviCameron1 Jun 10, 2026
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2 changes: 1 addition & 1 deletion WNPRC_EHR/resources/queries/study/hematologyAbsCount.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ ON (
)

WHERE
b.testId IN ('NE', 'LY', 'MN', 'EO', 'BS', 'BANDS', 'METAMYELO', 'MYELO', 'TP', 'RETICULO', 'PRO MYELO', 'ATYP', 'OTHER')
b.testId IN ('NE', 'LY', 'MN', 'EO', 'BS', 'BANDS', 'METAMYELO', 'MYELO', 'TP', 'RETICULO', 'PRO MYELO', 'ATYP', 'OTHER', 'NRBC')
and b.qcstate.publicdata = true
and b2.qcstate.publicdata = true
and b2.id is not null
Expand Down
70 changes: 34 additions & 36 deletions WNPRC_EHR/resources/queries/study/hematologyPivot.sql
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Original file line number Diff line number Diff line change
@@ -1,39 +1,37 @@

SELECT
b.id,
b.date,
b.testId,
group_concat(b.result) as results
b.id,
COALESCE(cpr.date, max(b.date)) as date,
b.testId,
group_concat(b.result) as results

FROM (SELECT
b.id,
b.date,
b.testId,
coalesce(b.taskid, b.parentid, b.runId) as runId,
b.resultoorindicator,
CASE
WHEN b.result IS NULL THEN b.qualresult
ELSE CAST(TRUNCATE(ROUND(CAST(b.result AS NUMERIC), 2), 2) AS VARCHAR)
END as result

FROM study."Hematology Results" b

WHERE testId IN ('WBC', 'RBC', 'HGB', 'HCT', 'MCV', 'MCH','MCHC', 'RDW', 'PLT', 'MPV','PCV','NE','LY','MN','EO','BS','BANDS','METAMYELO','MYELO','TP','RETICULO', 'PRO MYELO', 'ATYP', 'OTHER')
and b.qcstate.publicdata = true

UNION ALL

SELECT
b.id,
b.date,
b.testId,
coalesce(b.taskid, b.parentid) as runId,
b.percentoorindicator,
CAST(TRUNCATE(ROUND(CAST(b.result AS NUMERIC), 2), 2) AS VARCHAR),
FROM study.hematologyAbsCount b

) b

GROUP BY b.id, b.date, b.runId, b.testId
PIVOT results BY testId IN ('WBC', 'RBC', 'HGB', 'HCT', 'MCV', 'MCH','MCHC', 'RDW', 'PLT', 'MPV','PCV','NE','NE-ABS','LY','LY-ABS','MN','MN-ABS','EO','EO-ABS','BS','BS-ABS','BANDS','BANDS-ABS','METAMYELO','MYELO','TP','RETICULO', 'PRO MYELO', 'ATYP', 'OTHER')

b.id,
b.date,
b.testId,
coalesce(b.taskid, b.parentid, b.runId) as runId,
b.resultoorindicator,
CASE
WHEN b.result IS NULL THEN b.qualresult
ELSE CAST(CAST(ROUND(CAST(b.result AS NUMERIC), 4) AS DOUBLE) AS VARCHAR)
END as result
FROM study."Hematology Results" b

WHERE testId IN ('WBC', 'RBC', 'HGB', 'HCT', 'MCV', 'MCH','MCHC', 'RDW','RDW-SD', 'RDW-CV', 'PLT', 'MPV','PCV','NE','LY','MN','EO','BS','BANDS','METAMYELO','MYELO','TP','RETICULO', 'RETIC-AB', 'IRF', 'NRBC', 'NRBC-ABS', 'RETIC HGB', 'IPF', 'PDW', 'P-LCR', 'PCT', 'LFR', 'MFR', 'HFR', 'PRO MYELO', 'ATYP', 'OTHER')
and b.qcstate.publicdata = true

UNION ALL

SELECT
b.id,
b.date,
b.testId,
coalesce(b.taskid, b.parentid) as runId,
b.percentoorindicator,
CAST(CAST(ROUND(CAST(b.result AS NUMERIC), 2) AS DOUBLE) AS VARCHAR) AS result
FROM study.hematologyAbsCount b

) b
LEFT JOIN study.clinpathRuns cpr ON b.runId = cpr.objectId

GROUP BY b.id, b.runId, b.testId, cpr.date
PIVOT results BY testId IN ('WBC', 'RBC', 'HGB', 'HCT', 'MCV', 'MCH','MCHC', 'RDW','RDW-SD', 'RDW-CV', 'PLT', 'MPV','PCV','NE','NE-ABS','LY','LY-ABS','MN','MN-ABS','EO','EO-ABS','BS','BS-ABS','BANDS','BANDS-ABS','METAMYELO','MYELO','PRO MYELO', 'ATYP', 'OTHER', 'TP','RETICULO', 'RETIC-AB', 'IRF', 'NRBC', 'NRBC-ABS', 'RETIC HGB', 'IPF', 'PDW', 'P-LCR', 'PCT', 'LFR', 'MFR', 'HFR')
267 changes: 138 additions & 129 deletions WNPRC_EHR/resources/web/ehr/ext3/ExtContainers.js
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -939,161 +939,171 @@ EHR.ext.HematologyExcelWin = Ext.extend(Ext.Panel, {
this.processData(data);
},
processData: function(data){
var skippedRows = [];
var runsStore = Ext.StoreMgr.get("study||Clinpath Runs||||");
var unitStore = Ext.StoreMgr.get("ehr_lookups||hematology_tests||testid||testid");

var result;
var tests;
var row1;
var row2;
var toAdd = [];

if(!data.length || !data[0].length){
if (!Array.isArray(data) || !data.length || !data[0]?.length) {
alert('Something went wrong processing the file');
console.log(data)
return;
}

data = data[0][0].split(/D1U/i);
const cleanData = data[0][0].replace(/\s+/g, ' ').trim(); // remove extra whitespace

Ext.each(data, function(row, idx){
if(!row.match(/D2U/i))
return;

row = row.split(/D2U/i);

row1 = row[0];
row2 = row[1];
row1 = row1.replace(/\s+/g, '');
row2 = row2.split(/\s+/);
row2 = row2.slice(2, row2.length-1);
row2 = row2.join('');

result = {};
tests = {};
const formattedObjData = {};
const regex = /(\.D[A-Z0-9]+U)\s+(.*?)(?=\.\D[A-Z0-9]+U|$)/gs;
let match;
while ((match = regex.exec(cleanData)) !== null) {
const key = match[1];
const value = match[2].trim();
const animalId = value.substring(25, 31).toLowerCase();
if(!formattedObjData[animalId]){
formattedObjData[animalId] = {};
}
formattedObjData[animalId][key] = value;
}
const skippedRows = [];
const toAdd = [];

//result.animalId = row1[2].substr(0,6);
result.animalId = row1.substring(27,33);
result.animalId = result.animalId.toLowerCase();
// CONFIGURABLE: Define where to start extracting substrings from D2U and D6U
const headerConfig = {
".D2U": 31, // "XN-10^854650000000017000 cj2795" (0-30) (31 length)
".D6U": 137, // remove header plus 106 "reserved"
// Example: D2U starts with "XN-10^... cj2795", skip header, then parse fixed fields
};

var requestNumber = runsStore.find('Id',result.animalId)
var record = runsStore.getAt(requestNumber);
Object.entries(formattedObjData).forEach(([animalId, rawTests]) => {
if (!rawTests[".D2U"] || !rawTests[".D6U"]) {
alert("Failed to parse formatted data (missing .D1U/.D2U...) for ", animalId);
return;
}
const d2uRaw = rawTests[".D2U"];
const d6uRaw = rawTests[".D6U"];
// Remove headers

const d2u = d2uRaw.slice(headerConfig[".D2U"]);
const d6u = d6uRaw.slice(headerConfig[".D6U"]);

/* These tests were based on the standard definitions revision 7 and 12. The ones initially provided (revision 12) seems to be incorrect given
* our current output. To best understand this data refer to revision 7.
*/

/*
"Reserved" Definition: “0”s or " "(space) are set to this parameter to fill the specified number of characters.
Reserved should be "0" characters but this doesn't seem to be the actual case, it looks like it is a mix
of "0" and " " (space). Because of this it can cause issues with CoolTerm because CoolTerm trims whitespace,
which is needed to correctly guess some values.
*/

const tests = {
WBC: d2u.substring(0, 6),
RBC: d2u.substring(6, 11),
HGB: d2u.substring(11, 16),
HCT: d2u.substring(16, 21),
MCV: d2u.substring(21, 26),
MCH: d2u.substring(26, 31),
MCHC: d2u.substring(31, 36),
PLT: d2u.substring(36, 41),
LY: d2u.substring(41, 46),
MN: d2u.substring(46, 51),
NE: d2u.substring(51, 56),
EO: d2u.substring(56, 61),
BS: d2u.substring(61, 66),
"RDW-CV": d2u.substring(95, 101),
"RDW-SD": d2u.substring(101, 106),
MPV: d2u.substring(106, 111),
RETICULO: d2u.substring(121, 126),
IRF: d2u.substring(131, 136),
NRBC: d2u.substring(157, 162),
'RETIC-AB': d2u.substring(179, 185),
'RETIC HGB': d2u.substring(185, 190),
IPF: d2u.substring(190, 195),
// Start D6U Tests
PDW: d6u.substring(0, 5),
"P-LCR": d6u.substring(10, 15),
LFR: d6u.substring(30, 35),
MFR: d6u.substring(35, 40),
HFR: d6u.substring(40, 45),
PCT: d6u.substring(45, 50),
};

// Lookup run record
const requestNumber = runsStore.find('Id', animalId);
const record = runsStore.getAt(requestNumber);
let collectionDate;
//Getting the collection time from the request itself, if it matches animalId
if(requestNumber!= -1 && result.animalId == record.get('Id')){
if(requestNumber !== -1 && animalId === record.get('Id')){

var collectionDate = record.get('date');
collectionDate = record.get('date');
}

//result.sequenceNo = row1[1].substr(20,4);
//result.date = new Date(row1[2].substr(6,4), row1[2].substr(10,2)-1, row1[2].substr(12,2));
//result.date = new Date(row1.substr(33,4), row1.substr(37,2)-1, row1.substr(39,2));
result.date= new Date(collectionDate);

if(!result.animalId || runsStore.find('Id', result.animalId)==-1){
if(!animalId || runsStore.find('Id', animalId)===-1){
//alert('ID: '+result.animalId+' not found in Clinpath Runs section. Records will not be added');
skippedRows.push('Not found in Clinpath Runs: '+result.animalId);
skippedRows.push('Not found in Clinpath Runs: ' + animalId);
console.log("Skip Row", animalId);
return;
}

tests['WBC'] = row2.substring(6, 12);
tests['RBC'] = row2.substring(12, 17);
tests['HGB'] = row2.substring(17, 22);
tests['HCT'] = row2.substring(22, 27);
tests['MCV'] = row2.substring(27, 32);
tests['MCH'] = row2.substring(32, 37);
tests['MCHC'] = row2.substring(37, 42);
tests['PLT'] = row2.substring(42, 47);
//tests['LYMPH%'] = row2.substring(47, 52);
tests['LY'] = row2.substring(47, 52);

//tests['MONO%'] = row2.substring(52, 57);
tests['MN'] = row2.substring(52, 57);

//tests['SEG%'] = row2.substring(57, 62);
tests['NE'] = row2.substring(57, 62);

//tests['EOSIN%'] = row2.substring(62, 67);
tests['EO'] = row2.substring(62, 67);

//tests['BASO%'] = row2.substring(67, 72);
tests['BS'] = row2.substring(67, 72);

//tests['LYMPH#'] = row2.substring(72, 78);
//tests['MONO#'] = row2.substring(78, 84);
//tests['SEG#'] = row2.substring(84, 90);
//tests['EOSIN#'] = row2.substring(90, 96);
//tests['BASO#'] = row2.substring(96, 102);
//tests['RDW'] = row2.substring(102, 107);
tests['RDW-CV'] = row2.substring(102, 107);
tests['RDW-SD'] = row2.substring(107, 112);
//tests['PDW'] = row2.substring(112, 117);
tests['MPV'] = row2.substring(117, 122);
//tests['P-LCR'] = row2.substring(122, 127);


var value;
for(var test in tests){
var origVal = tests[test];
value = tests[test];
const result = {
animalId,
date: new Date(collectionDate),
};

if (value.match(/^00(\d){4}$/)) {
tests[test] = value.substring(2,5) / 100;
}
//note: at the moment WBC is the only test with 6 chars, so this test is possibly redundant
else if (value.match(/^0(\d){4,}$/) && test=='WBC') {
tests[test] = value.substring(1,5) / 100;
}
else if (value.match(/^0\d{4}$/)){
if (test=='RBC') {
tests[test] = value.substring(1,4) / 100;
}
else if (test=='PLT') {
tests[test] = value.substring(1,4) / 1; //convert to number
}
else {
tests[test] = value.substring(1,4) / 10;

/*
Rules: Define the test and how many digits from the right the decimal should appear in the string.
It does not matter how many initial digits are in the string (WBC has 6 while RBC has 5).
The majority of tests are 1 decimal, so that is the default. If the test does not exist within rules
specifically it will use the default.
Ex.
Rule: 2
RBC: 000.00
WBRC: 0000.00
*/
const rules = {
WBC: 2,
'NRBC#': 2,
RBC: 2,
RETICULO: 2,
'RETIC-AB': 4,
PLT: 0,
PCT: 2,
_default: 1
};

for(var test in tests){
const decimal = (test in rules) ? rules[test] : rules['_default'];
const value = tests[test];

const data = value.slice(0, -1);

const number = parseInt(data);

// Convert to string to easily manipulate decimal placement
let numberStr = number.toString();

// If decimal is 0, no decimal point needed
if (decimal === 0) {
tests[test] = number;
} else {
// If we need to add a decimal point
if (numberStr.length <= decimal) {
// If number is shorter than decimal places, pad with zeros
numberStr = '0'.repeat(decimal - numberStr.length) + numberStr;
tests[test] = parseFloat('0.' + numberStr);
} else {
// Insert decimal point at the correct position from the right
const decimalIndex = numberStr.length - decimal;
const formatted = numberStr.slice(0, decimalIndex) + '.' + numberStr.slice(decimalIndex);
tests[test] = parseFloat(formatted);
}
}
else if (test=='PLT') {
tests[test] = value.substring(0,4);
}

//NOTE: the following is a possible replacement for the logic above
//it attempts to more clearly define how the parsing works
//so far as i can tell, specific tests return different sets of decimals
//and there is no clear way to determine decimal number without knowing the test name
// if(value.match(/^(\d){5,6}$/)){
// //we drop the last digit in all cases
// value = value.substr(0, value.length-1);
//
// var decimals = 1;
// //WBC is output as 10^1/uL, but reported at 10^3/ul
// //RBC is output as 10^4/ul, but reported at 10^6/ul
// if(test=='WBC' || test=='RBC')
// decimals = 2;
// if(test=='PLT')
// decimals = 0;
//
// value = value / Math.pow(10, decimals);
//
// value = Ext4.util.Format.round(value, decimals);
// }
// else {
// //alert('Value: '+value+' is not a number');
// return;
// }
//
// if(value != tests[test]){
// console.log('error: '+test+'/'+tests[test]+'/'+value+'/'+decimals);
// }

//find units
var idx = unitStore.find('testid', test);
var units = null;
var sortOrder = null;
if(idx!=-1){
if(idx !== -1){
units = unitStore.getAt(idx).get('units');
sortOrder = unitStore.getAt(idx).get('sort_order');
}
Expand All @@ -1112,8 +1122,7 @@ EHR.ext.HematologyExcelWin = Ext.extend(Ext.Panel, {
sortOrder: sortOrder
});
}

}, this);
});

if(toAdd.length){
toAdd.sort(function(a, b){
Expand Down
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