nuVistA/htdocs/reportparser.mjs

function isEqualArray(a, b) {
	if(a.length == b.length) {
		for(var i = a.length - 1; i >= 0; --i) if(a[i] != b[i]) return false;
		return true;
	} else return false;
}

export function lab_parse(data) {
	data = data.join('\n');
	if(data == '\nNo Data Found') return [];
	return data.split('\n===============================================================================\n \n').map(lab_parse1).filter(x => x);
}

export function lab_reparse_results(reports) {
	var res = [], report, result;
	for(var i = 0; i < reports.length; ++i) {
		if((report = reports[i]).hasOwnProperty('results')) {
			report = Object.assign({}, report);
			var results = report.results;
			delete report.results;
			if(report.hasOwnProperty('comment')) delete report.comment;
			for(var j = 0; j < results.length; ++j) res.push(result = Object.assign({}, report, results[j]));
		}
	}
	return res;
}

function lab_parse1(data) {
	if(data.startsWith('\n')) return lab_parse1default(data);
	if(data.startsWith('                            ---- MICROBIOLOGY ----\n')) return lab_parse1microbiology(data);
	if(data.startsWith('Performing Lab Sites\n')) return null;
}

function lab_parse1default(data) {
	var res = {}, m, x, line;
	if(m = data.match(/^Report Released Date\/Time: (.*)/m)) res.time_released = new Date(m[1]);	// 'Aug 24, 2022@07:15'
	if(m = data.match(/^Provider: (.*)/m)) res.practitioner = m[1];	// 'BARGNES,VINCENT HARRY III'
	if(m = data.match(/^  Specimen: (.*?)\.\s*(.*)/m)) {
		res.specimen = m[1];	// 'SERUM'
		res.accession = m[2];	// 'CH 0800 6706'
	}
	if(m = data.match(/^    Specimen Collection Date: (.*)/m)) res.time_collected = new Date(m[1]);	// 'Aug 24, 2022'
	data = data.split('\n      Test name                Result    units      Ref.   range   Site Code\n')[1].split('\n');
	var results = res.results = [];
	for(var i = 0; i < data.length; ++i) {
		if((line = data[i]).startsWith('Comment: ')) {
			res.comment = data.slice(i).join('\n').substring(9);
			break;
		} else if(line.startsWith('      Eval: ')) {
			if(results.length > 0) {
				x = results[results.length - 1];
				if(x.comment) x.comment.push(line.substring(12));
				else x.comment = [line.substring(12)];
			} else console.log('DANGLING:', line);
		} else if((line.startsWith('COVID-19 SCR (CEPHEID-RAPID)')) && (m = line.substring(28).match(/^(?<value>.*?)(?: (?<flag>L\*|L|H\*|H))?\s+(?:(?<unit>.{10}) (?<range>.{16}) \[(?<site>\d+)\])?$/))) {
			if((m.groups.range) && (m.groups.range.startsWith('Ref: '))) m.groups.range = m.groups.range.substring(5);
			results.push(x = m.groups);
			for(var k in x) if(x[k]) x[k] = x[k] ? x[k].replace(/^\s+|\s+$/g, '') : undefined;
			x.name = 'COVID-19 SCR (CEPHEID-RAPID)';
		} else if(m = line.match(/^\b(?<name>.*?)\s{2,}(?<value>.*?)(?: (?<flag>L\*|L|H\*|H))?\s+(?:(?<unit>.{10}) (?<range>.{16}) \[(?<site>\d+)\])?$/)) {
			if((m.groups.range) && (m.groups.range.startsWith('Ref: '))) m.groups.range = m.groups.range.substring(5);
			results.push(x = m.groups);
			for(var k in x) if(x[k]) x[k] = x[k] ? x[k].replace(/^\s+|\s+$/g, '') : undefined;
		} else if(line.startsWith('                                                                    [')) {
			if(results.length > 0) results[results.length - 1].site = line.split('[')[1].split(']')[0]
			else console.log('DANGLING:', line);
		} else if(line.startsWith('                                                   ')) {
			if(results.length > 0) {
				x = results[results.length - 1];
				if(line.endsWith(']')) {
					x.range = line.split('[')[0].replace(/^\s+|\s+$/g, '');
					x.site = line.split('[')[1].split(']')[0];
				} else x.range = line.replace(/^\s+|\s+$/g, '');
			} else console.log('DANGLING:', line);
		} else console.log('INVALID:', line);
	}
	for(var i = results.length - 1; i >= 0; --i) {
		results[(x = results[i]).name] = x;
		if(x.comment) x.comment = x.comment.join('\n');
	}
	if((res.accession.startsWith('HE ')) && ((results.hasOwnProperty('SEGS')) || (results.hasOwnProperty('BANDS')))) {
		results.push(results['NEUTROPHIL%'] = {
			name: 'NEUTROPHIL%', unit: '%', range: '42.2 - 75.2',
			value: x = (results.hasOwnProperty('SEGS') ? +results.SEGS.value : 0) + (results.hasOwnProperty('BANDS') ? +results.BANDS.value : 0),
			flag: (x < 42.2 ? 'L' : x > 75.2 ? 'H' : undefined)
		});
		results.push(results['NEUTROPHIL#'] = {
			name: 'NEUTROPHIL#', unit: 'K/cmm', range: '1.4 - 6.5',
			value: +(x = 0.01*x*results.WBC.value).toFixed(3),
			flag: (x < 1.4 ? 'L' : x > 6.5 ? 'H' : undefined)
		});
	}
	return res;
}

function lab_parse1microbiology(data) {
	var res = {}, lines = data.split('\n'), line, m;
	var idx_body = lines.indexOf('                                                                               ');
	for(var i = 0; i < lines.length; ++i) {
		line = lines[i];
		if(line.startsWith('Accession [UID]: ')) {
			if(m = line.match(/^Accession \[UID\]: (?<accession>.*?) \[(?<accession_uid>\d+)\]/)) {	// 'BCUL 22 819 [3922000819]'
				res.accession = m.groups.accession;
				res.accession_uid = m.groups.accession_uid;
			}
			if(m = line.match(/Received: (.*)$/)) res.time_received = new Date(m[1]);	// 'Aug 01, 2022@11:57'
		} else if(line.startsWith('Collection sample: ')) {
			res.sample = line.substring(0, 39).substring(19).replace(/^\s+|\s+$/g, '');
			res.time_collected = new Date(line.substring(39).split('Collection date: ')[1].replace(/^\s+|\s+$/g, ''));
		} else if(line.startsWith('Site/Specimen: ')) {
			res.specimen = line.substring(15).replace(/^\s+|\s+$/g, '');
		} else if(line.startsWith('Provider: ')) {
			res.practitioner = line.substring(10).replace(/^\s+|\s+$/g, '');
		} else if(line.startsWith('Comment on specimen:')) {
			res.comment = lines.slice(i, idx_body).join('\n').substring(20).replace(/^\s+|\s+$/g, '');
			break
		}
	}
	var idx_footer = lines.indexOf('=--=--=--=--=--=--=--=--=--=--=--=--=--=--=--=--=--=--=--=--=--=--=--=--=--=--')
	if(idx_footer > idx_body) {
		res.body = lines.slice(idx_body, idx_footer).join('\n').replace(/^\s+|\s+$/g, '');
		res.footer = lines.slice(idx_footer + 1).join('\n').replace(/^\s+|\s+$/g, '');
	} else res.body = lines.slice(idx_body).join('\n').replace(/^\s+|\s+$/g, '');
	return res;
}

export function measurement_parse(data) {
	var extras = [];
	var res = data.map(function(row) {
		if(row.charAt(0) != ' ') {
			var res = {}, idx = 0, value, m;
			res.measurement_ien = row.substring(0, idx = row.indexOf('^'));
			if(res.measurement_ien == '0') return;	// '0^NO VITALS/MEASUREMENTS  ENTERED WITHIN THIS PERIOD'
			res.datetime = new Date(row.substring(idx + 1, idx = row.indexOf('   ', idx)));
			res.name = row.substring(idx + 3, idx = row.indexOf(':   ', idx));
			value = row.substring(idx + 4, idx = row.indexOf(' _', idx));
			res.user = row.substring(idx + 2);
			m = value.match(/^(?:(.*?)(?: (\S+))?)(\*)?(?: \((?:(.*?)(?: (\S+))?)\))?\s*$/);
			res.value = m[4] ? m[4] : m[1];
			res.unit = m[4] ? m[5] : m[2];
			res.flag = m[3];
			res.value_american = m[4] ? m[1] : m[4];
			res.unit_american = m[4] ? m[2] : m[5];
			if(res.value.charAt(res.value.length - 1) == '%') {
				res.unit = '%';
				res.value = res.value.substring(0, res.value.length - 1);
			}
			if(res.name == 'B/P') {
				var bpsplit = res.value.split('/');
				extras.push({...res, name: 'SBP', range: '90 - 120', unit: 'mmHg', value: bpsplit[0] });
				extras.push({...res,  name: 'DBP', range: '60 - 80', unit: 'mmHg', value: bpsplit[1] });
			}
			return res;
		}
	}).filter(x => x);
	res.push(...extras);
	return res;
}