@openhealth/oht-custom-parser-lib 0.1.19 → 0.2.1

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Files changed (17) hide show
  1. package/dist/index.d.ts +2 -2
  2. package/dist/index.js +5 -1
  3. package/dist/index.js.map +1 -1
  4. package/dist/service/auxiliaryFunctions.service.js +1 -1
  5. package/dist/service/auxiliaryFunctions.service.js.map +1 -1
  6. package/dist/service/errorHandling.service.d.ts +33 -1
  7. package/dist/service/errorHandling.service.js +54 -0
  8. package/dist/service/errorHandling.service.js.map +1 -1
  9. package/dist/service/ohtMeasurementsExtractor.service.js +11 -11
  10. package/dist/service/ohtMeasurementsExtractor.service.js.map +1 -1
  11. package/dist/types/custom-parser.types.d.ts +9 -3
  12. package/dist/types/error.types.d.ts +1 -0
  13. package/dist/types/oht.types.d.ts +3 -2
  14. package/dist/types/oht.types.js +6 -6
  15. package/dist/types/oht.types.js.map +1 -1
  16. package/dist/util-ts/pinoLogger.js.map +1 -1
  17. package/package.json +2 -1
package/dist/index.d.ts CHANGED
@@ -2,9 +2,9 @@ export { postDataImportFileUploadToCore, makeApiCallWithRetry, parseErrorObj } f
2
2
  export { parseExternalPatientId, parseGender, isPatientAgeValid, handleRejection, queryFileUploadsWithFilters, postFileUploadSetStatus } from './service/auxiliaryFunctions.service';
3
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  export { ohtMeasurementsExtractor, checkValueForPlausibleValues, extractReferenceRanges, extractReferenceAnnotation, parseExamValue, getRangeFromPositionAndRegex, extractUnit, extractValueFromGreaterLowerThan } from './service/ohtMeasurementsExtractor.service';
4
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  export { getSlackFileIssueNotificationMessage, sendMessageToSlack } from './service/slackMessages.service';
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- export { aggregateMessages } from './service/errorHandling.service';
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+ export { aggregateMessages, aggregateBiMessages, publishToTopic, generateBIMessages } from './service/errorHandling.service';
6
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  export { LabToOhtContract, LabToOhtMapper, UnknownMeasurementExtraction, ReferenceAsAnnotation, UnitExtraction, RangeExtraction, RangeExtractionResponse, ValueExtraction, unitSynonyms, } from './types/custom-parser.types';
7
- export { AcfBiomarkerRangeAnnotationCheck, AcfBiomarkerGenericDisclaimerLogic, ManualCheck, BiomarkerCompatibility, ReferenceRangeType, AcfReferenceRange, VisualRange, NameAlias, AlternativeUnit, BiomarkerAcf, Biomarker, PipelineStep, DigitizationStatus, MeasurementValueComparator, BiomarkerValueType, DataImportFileUploadStatus, Sex, Digitization, PatientInfo, UnknownMeasurement, Measurement, DataImportFileUpload, MessagePayload, SignedUpload, ReportStyleConfig, LanguageCode, BiomarkerCustomisation, PartnerCustomPanel, ReportDisplaySettings, ReportCustomisation, OHTPartner, } from './types/oht.types';
7
+ export { AcfBiomarkerRangeAnnotationCheck, AcfBiomarkerGenericDisclaimerLogic, ManualCheck, BiomarkerCompatibility, ReferenceRangeType, AcfReferenceRange, VisualRange, NameAlias, AlternativeUnit, BiomarkerAcf, Biomarker, PipelineStep, DigitizationStatus, MeasurementValueComparator, BiomarkerValueType, DataImportFileUploadStatus, Sex, Digitization, PatientInfo, UnknownMeasurement, Measurement, DataImportFileUpload, MessagePayload, SignedUpload, ReportStyleConfig, LanguageCode, BiomarkerCustomisation, PartnerCustomPanel, ReportDisplaySettings, ReportCustomisation, OHTPartner, UploadType, } from './types/oht.types';
8
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  export { ErrorMessage } from './types/error.types';
9
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  export { extractValue, isBiomarkerValueNumerical, isBiomarkerExternalNoVisualRange } from './util-ts/dataUtils';
10
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  export { readFileFromBucket, uploadFileBufferToGCS } from './util-ts/googleStorageUtils';
package/dist/index.js CHANGED
@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
3
3
  return (mod && mod.__esModule) ? mod : { "default": mod };
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
- exports.getLowerThanPatterns = exports.getGreaterThanPatterns = exports.pinoLogger = exports.uploadFileBufferToGCS = exports.readFileFromBucket = exports.isBiomarkerExternalNoVisualRange = exports.isBiomarkerValueNumerical = exports.extractValue = exports.Sex = exports.DataImportFileUploadStatus = exports.BiomarkerValueType = exports.MeasurementValueComparator = exports.DigitizationStatus = exports.PipelineStep = exports.ReferenceRangeType = exports.BiomarkerCompatibility = exports.ManualCheck = exports.AcfBiomarkerGenericDisclaimerLogic = exports.AcfBiomarkerRangeAnnotationCheck = exports.unitSynonyms = exports.aggregateMessages = exports.sendMessageToSlack = exports.getSlackFileIssueNotificationMessage = exports.extractValueFromGreaterLowerThan = exports.extractUnit = exports.getRangeFromPositionAndRegex = exports.parseExamValue = exports.extractReferenceAnnotation = exports.extractReferenceRanges = exports.checkValueForPlausibleValues = exports.ohtMeasurementsExtractor = exports.postFileUploadSetStatus = exports.queryFileUploadsWithFilters = exports.handleRejection = exports.isPatientAgeValid = exports.parseGender = exports.parseExternalPatientId = exports.parseErrorObj = exports.makeApiCallWithRetry = exports.postDataImportFileUploadToCore = void 0;
6
+ exports.getLowerThanPatterns = exports.getGreaterThanPatterns = exports.pinoLogger = exports.uploadFileBufferToGCS = exports.readFileFromBucket = exports.isBiomarkerExternalNoVisualRange = exports.isBiomarkerValueNumerical = exports.extractValue = exports.UploadType = exports.Sex = exports.DataImportFileUploadStatus = exports.BiomarkerValueType = exports.MeasurementValueComparator = exports.DigitizationStatus = exports.PipelineStep = exports.ReferenceRangeType = exports.BiomarkerCompatibility = exports.ManualCheck = exports.AcfBiomarkerGenericDisclaimerLogic = exports.AcfBiomarkerRangeAnnotationCheck = exports.unitSynonyms = exports.generateBIMessages = exports.publishToTopic = exports.aggregateBiMessages = exports.aggregateMessages = exports.sendMessageToSlack = exports.getSlackFileIssueNotificationMessage = exports.extractValueFromGreaterLowerThan = exports.extractUnit = exports.getRangeFromPositionAndRegex = exports.parseExamValue = exports.extractReferenceAnnotation = exports.extractReferenceRanges = exports.checkValueForPlausibleValues = exports.ohtMeasurementsExtractor = exports.postFileUploadSetStatus = exports.queryFileUploadsWithFilters = exports.handleRejection = exports.isPatientAgeValid = exports.parseGender = exports.parseExternalPatientId = exports.parseErrorObj = exports.makeApiCallWithRetry = exports.postDataImportFileUploadToCore = void 0;
7
7
  // ### SERVICES ###
8
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  var reportCreator_service_1 = require("./service/reportCreator.service");
9
9
  Object.defineProperty(exports, "postDataImportFileUploadToCore", { enumerable: true, get: function () { return reportCreator_service_1.postDataImportFileUploadToCore; } });
@@ -30,6 +30,9 @@ Object.defineProperty(exports, "getSlackFileIssueNotificationMessage", { enumera
30
30
  Object.defineProperty(exports, "sendMessageToSlack", { enumerable: true, get: function () { return slackMessages_service_1.sendMessageToSlack; } });
31
31
  var errorHandling_service_1 = require("./service/errorHandling.service");
32
32
  Object.defineProperty(exports, "aggregateMessages", { enumerable: true, get: function () { return errorHandling_service_1.aggregateMessages; } });
33
+ Object.defineProperty(exports, "aggregateBiMessages", { enumerable: true, get: function () { return errorHandling_service_1.aggregateBiMessages; } });
34
+ Object.defineProperty(exports, "publishToTopic", { enumerable: true, get: function () { return errorHandling_service_1.publishToTopic; } });
35
+ Object.defineProperty(exports, "generateBIMessages", { enumerable: true, get: function () { return errorHandling_service_1.generateBIMessages; } });
33
36
  // ### TYPES ###
34
37
  var custom_parser_types_1 = require("./types/custom-parser.types");
35
38
  Object.defineProperty(exports, "unitSynonyms", { enumerable: true, get: function () { return custom_parser_types_1.unitSynonyms; } });
@@ -45,6 +48,7 @@ Object.defineProperty(exports, "MeasurementValueComparator", { enumerable: true,
45
48
  Object.defineProperty(exports, "BiomarkerValueType", { enumerable: true, get: function () { return oht_types_1.BiomarkerValueType; } });
46
49
  Object.defineProperty(exports, "DataImportFileUploadStatus", { enumerable: true, get: function () { return oht_types_1.DataImportFileUploadStatus; } });
47
50
  Object.defineProperty(exports, "Sex", { enumerable: true, get: function () { return oht_types_1.Sex; } });
51
+ Object.defineProperty(exports, "UploadType", { enumerable: true, get: function () { return oht_types_1.UploadType; } });
48
52
  // ### UTIL-TS ###
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  var dataUtils_1 = require("./util-ts/dataUtils");
50
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  Object.defineProperty(exports, "extractValue", { enumerable: true, get: function () { return dataUtils_1.extractValue; } });
package/dist/index.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/dist/service/auxiliaryFunctions.service.js CHANGED
@@ -42,7 +42,7 @@ function handleRejection(parseType, errorMessages) {
42
42
  let rejectedStatus = 'REJECTED';
43
43
  let rejectReason = `Could not parse ${parseType}`;
44
44
  errorMessages.push({
45
- destination: { slack: true, notes: false },
45
+ destination: { slack: true, notes: false, bi: false },
46
46
  message: `File REJECTED, ${parseType} not parsed correctly:`,
47
47
  });
48
48
  return { rejectedStatus, rejectReason };
package/dist/service/auxiliaryFunctions.service.js.map CHANGED
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package/dist/service/errorHandling.service.d.ts CHANGED
@@ -1,2 +1,34 @@
1
1
  import { ErrorMessage } from "../types/error.types";
2
- export declare function aggregateMessages(errorMessages: ErrorMessage[], channel: 'slack' | 'notes'): string;
2
+ export declare function aggregateMessages(errorMessages: ErrorMessage[], channel: 'slack' | 'notes' | 'bi'): string;
3
+ export declare function aggregateBiMessages(errorMessages: ErrorMessage[]): Promise<{
4
+ message: string;
5
+ }[]>;
6
+ export declare function publishToTopic(topic: string, messageBuffer: any, projectId: string): Promise<void>;
7
+ export declare const generateBIMessages: (biMessages: any[], fileUploadId: string, signedUploadId: string, partnerId: string, projectId: string, uuidv4: any, lab: string, timestamp: Date) => {
8
+ envelope: {
9
+ id: any;
10
+ source: string;
11
+ projectId: string;
12
+ type: string;
13
+ version: string;
14
+ timestamp: Date;
15
+ tags: string[];
16
+ };
17
+ payload: {
18
+ content: {
19
+ fileUploadId: string;
20
+ signedUploadId: string;
21
+ message: any;
22
+ labKey: any;
23
+ biomarkerId: any;
24
+ lab: string;
25
+ partnerId: string;
26
+ severity: any;
27
+ };
28
+ metadata: {
29
+ eventType: string;
30
+ sourceSystem: string;
31
+ trackingId: string;
32
+ };
33
+ };
34
+ }[];
package/dist/service/errorHandling.service.js CHANGED
@@ -1,6 +1,10 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.generateBIMessages = void 0;
3
4
  exports.aggregateMessages = aggregateMessages;
5
+ exports.aggregateBiMessages = aggregateBiMessages;
6
+ exports.publishToTopic = publishToTopic;
7
+ const pubsub_1 = require("@google-cloud/pubsub");
4
8
  function aggregateMessages(errorMessages, channel) {
5
9
  const messageMap = errorMessages.filter(({ destination }) => {
6
10
  return destination[channel];
@@ -30,4 +34,54 @@ function aggregateMessages(errorMessages, channel) {
30
34
  })
31
35
  .join('\n');
32
36
  }
37
+ async function aggregateBiMessages(errorMessages) {
38
+ const biMessages = [];
39
+ errorMessages.forEach(({ message, item, destination }) => {
40
+ if (destination.bi) {
41
+ const formattedMessage = message.replace('[PLACEHOLDER]', `[-> ${item}]`);
42
+ biMessages.push({ message: formattedMessage });
43
+ }
44
+ });
45
+ return biMessages;
46
+ }
47
+ async function publishToTopic(topic, messageBuffer, projectId) {
48
+ const pubSubClient = new pubsub_1.PubSub({ projectId });
49
+ await pubSubClient
50
+ .topic(topic)
51
+ .publishMessage({ data: messageBuffer });
52
+ }
53
+ const generateBIMessages = (biMessages, fileUploadId, signedUploadId, partnerId, projectId, uuidv4, lab, timestamp) => {
54
+ return biMessages.map(error => {
55
+ const labKey = error.item?.replace('labKey: ', '').trim();
56
+ return {
57
+ envelope: {
58
+ id: uuidv4,
59
+ source: `${lab} custom-parser`,
60
+ projectId: `${projectId}`,
61
+ type: 'datawarehouse',
62
+ version: '1.0',
63
+ timestamp: timestamp,
64
+ tags: ['warnings', 'custom-parser'],
65
+ },
66
+ payload: {
67
+ content: {
68
+ fileUploadId: fileUploadId,
69
+ signedUploadId: signedUploadId,
70
+ message: error.message ?? '',
71
+ labKey: labKey,
72
+ biomarkerId: error.ohtBmId ?? '',
73
+ lab: `${lab}`,
74
+ partnerId: partnerId,
75
+ severity: error.type ?? 'ERROR',
76
+ },
77
+ metadata: {
78
+ eventType: 'parsing',
79
+ sourceSystem: 'custom-parser',
80
+ trackingId: '',
81
+ },
82
+ },
83
+ };
84
+ });
85
+ };
86
+ exports.generateBIMessages = generateBIMessages;
33
87
  //# sourceMappingURL=errorHandling.service.js.map
package/dist/service/errorHandling.service.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"errorHandling.service.js","sourceRoot":"","sources":["../../service/errorHandling.service.ts"],"names":[],"mappings":";;;AAOA,8CA2BC;AAED,kDAYC;AAGD,wCAKC;AAvDD,iDAA8C;AAM9C,SAAgB,iBAAiB,CAAC,aAA6B,EAAE,OAAiC;IAChG,MAAM,UAAU,GAAe,aAAa,CAAC,MAAM,CAAC,CAAC,EAAC,WAAW,EAAC,EAAC,EAAE;QACnE,OAAO,WAAW,CAAC,OAAO,CAAC,CAAC;IAC9B,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,EAAC,OAAO,EAAE,IAAI,EAAC,EAAE,EAAE;QACjC,IAAI,IAAI,EAAE,CAAC;YACT,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC;gBAClB,GAAG,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC;YACpB,CAAC;YACD,GAAG,CAAC,OAAO,CAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QAC3B,CAAC;aAAM,CAAC;YACN,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC;gBAClB,GAAG,CAAC,OAAO,CAAC,GAAG,IAAI,CAAC;YACtB,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAC;IACb,CAAC,EAAE,EAAgB,CAAC,CAAC;IAErB,OAAO,MAAM,CAAC,OAAO,CAAC,UAAU,CAAC;SAChC,GAAG,CAAC,CAAC,CAAC,OAAO,EAAE,KAAK,CAAC,EAAE,EAAE;QACxB,IAAI,KAAK,EAAE,CAAC;YACV,MAAM,WAAW,GAAG,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,MAAM,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;YAC/D,OAAO,OAAO,CAAC,OAAO,CAAC,eAAe,EAAE,KAAK,WAAW,IAAI,CAAC,CAAC;QAChE,CAAC;aAAM,CAAC;YACN,OAAO,OAAO,CAAC;QACjB,CAAC;IACH,CAAC,CAAC;SACD,IAAI,CAAC,IAAI,CAAC,CAAC;AACd,CAAC;AAEM,KAAK,UAAU,mBAAmB,CAAC,aAA6B;IACrE,MAAM,UAAU,GAA2B,EAAE,CAAC;IAE9C,aAAa,CAAC,OAAO,CAAC,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,WAAW,EAAE,EAAE,EAAE;QACvD,IAAI,WAAW,CAAC,EAAE,EAAE,CAAC;YACnB,MAAM,gBAAgB,GAAG,OAAO,CAAC,OAAO,CAAC,eAAe,EAAE,OAAO,IAAI,GAAG,CAAC,CAAC;YAE1E,UAAU,CAAC,IAAI,CAAC,EAAE,OAAO,EAAE,gBAAgB,EAAC,CAAC,CAAC;QAChD,CAAC;IACH,CAAC,CAAC,CAAC;IAEH,OAAO,UAAU,CAAC;AACpB,CAAC;AAGM,KAAK,UAAU,cAAc,CAAC,KAAa,EAAE,aAAkB,EAAE,SAAiB;IACvF,MAAM,YAAY,GAAG,IAAI,eAAM,CAAC,EAAE,SAAS,EAAE,CAAC,CAAC;IAC7C,MAAM,YAAY;SACf,KAAK,CAAC,KAAK,CAAC;SACZ,cAAc,CAAC,EAAE,IAAI,EAAE,aAAa,EAAE,CAAC,CAAC;AAC/C,CAAC;AAEM,MAAM,kBAAkB,GAAG,CAChC,UAAiB,EACjB,YAAoB,EACpB,cAAsB,EACtB,SAAiB,EACjB,SAAiB,EACjB,MAAW,EACX,GAAW,EACX,SAAe,EACf,EAAE;IACF,OAAO,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE;QAC5B,MAAM,MAAM,GAAG,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,UAAU,EAAE,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;QAC1D,OAAO;YACL,QAAQ,EAAE;gBACR,EAAE,EAAE,MAAM;gBACV,MAAM,EAAE,GAAG,GAAG,gBAAgB;gBAC9B,SAAS,EAAE,GAAG,SAAS,EAAE;gBACzB,IAAI,EAAE,eAAe;gBACrB,OAAO,EAAE,KAAK;gBACd,SAAS,EAAE,SAAS;gBACpB,IAAI,EAAE,CAAC,UAAU,EAAE,eAAe,CAAC;aACpC;YACD,OAAO,EAAE;gBACP,OAAO,EAAE;oBACP,YAAY,EAAE,YAAY;oBAC1B,cAAc,EAAE,cAAc;oBAC9B,OAAO,EAAE,KAAK,CAAC,OAAO,IAAI,EAAE;oBAC5B,MAAM,EAAE,MAAM;oBACd,WAAW,EAAE,KAAK,CAAC,OAAO,IAAI,EAAE;oBAChC,GAAG,EAAE,GAAG,GAAG,EAAE;oBACb,SAAS,EAAE,SAAS;oBACpB,QAAQ,EAAE,KAAK,CAAC,IAAI,IAAI,OAAO;iBAChC;gBACD,QAAQ,EAAE;oBACR,SAAS,EAAE,SAAS;oBACpB,YAAY,EAAE,eAAe;oBAC7B,UAAU,EAAE,EAAE;iBACf;aACF;SACF,CAAC;IACJ,CAAC,CAAC,CAAC;AACL,CAAC,CAAC;AAzCW,QAAA,kBAAkB,sBAyC7B"}
package/dist/service/ohtMeasurementsExtractor.service.js CHANGED
@@ -115,7 +115,7 @@ function extractReferenceRanges(labToOhtMapper, rawData, patientInfo, documentDa
115
115
  // We need a default extraction function for each lab
116
116
  // Here we receive from the custom parser a function inside the RangeExtraction object
117
117
  let rangeExtractionResult = labToOhtMapper?.rangeExtraction?.defaultRangeExtractionFunc
118
- ? labToOhtMapper.rangeExtraction.defaultRangeExtractionFunc(labToOhtMapper, rawData)
118
+ ? labToOhtMapper.rangeExtraction.defaultRangeExtractionFunc(labToOhtMapper, rawData, patientInfo, documentDate)
119
119
  : nullRangeNotParsedCorrectly;
120
120
  if (rangeExtractionResult.isRangeParsedCorrectly) {
121
121
  return rangeExtractionResult;
@@ -176,7 +176,7 @@ function extractValueFromGreaterLowerThan(value) {
176
176
  }
177
177
  function parseExamValue(rawExamObj, valueExtraction, ohtBiomarker) {
178
178
  let value = (0, dataUtils_1.extractValue)(rawExamObj, valueExtraction?.valuePosition);
179
- value = valueExtraction.defaultValueExtractionFunc ? valueExtraction.defaultValueExtractionFunc(value) : value;
179
+ value = valueExtraction?.defaultValueExtractionFunc ? valueExtraction?.defaultValueExtractionFunc(value) : value;
180
180
  // If is parse float nan, the value is alphanumerical
181
181
  const valueType = (0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker)
182
182
  ? oht_types_1.BiomarkerValueType.NUMERICAL
@@ -272,11 +272,11 @@ async function ohtMeasurementsExtractor(labToOhtContract, ohtCoreApiKey) {
272
272
  };
273
273
  // api call to ohtCore to find biomarkers.
274
274
  const biomarkers = await (0, reportCreator_service_1.makeApiCallWithRetry)('post', `${OHT_CORE_URL}/v1/biomarker/biomarkers`, requestData, ohtCoreApiKey);
275
- labToOhtContract.labToOhtList.forEach((labToOhtMapper, idx) => {
275
+ labToOhtContract.labToOhtList.forEach((labToOhtMapper) => {
276
276
  let isMeasurementCorrectlyParsed = true;
277
277
  if (!labToOhtMapper.rawExam) {
278
278
  labToOhtContract.errorMessages.push({
279
- destination: { slack: true, notes: false },
279
+ destination: { slack: true, notes: false, bi: false },
280
280
  message: `Missing rawExam for labKey: ${labToOhtMapper.labKey} filename: ${filename}`,
281
281
  });
282
282
  return;
@@ -287,7 +287,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, ohtCoreApiKey) {
287
287
  if (measurements.some(measurement => measurement.biomarkerId === labToOhtMapper.ohtBmId)) {
288
288
  logger.warn({ labToOhtMapper }, `Biomarker already in measurements array, should investigate, filename: ${filename}`);
289
289
  labToOhtContract.errorMessages.push({
290
- destination: { slack: true, notes: false },
290
+ destination: { slack: true, notes: false, bi: false },
291
291
  message: `Biomarkers Duplicated keys:[PLACEHOLDER]`,
292
292
  item: `bmId:${labToOhtMapper.ohtBmId}, labKey:${labToOhtMapper.labKey}`
293
293
  });
@@ -302,7 +302,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, ohtCoreApiKey) {
302
302
  if (!isUnitParsedCorrectly) {
303
303
  logger.warn({ labToOhtMapper }, `Unit not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
304
304
  labToOhtContract.errorMessages.push({
305
- destination: { slack: true, notes: true },
305
+ destination: { slack: true, notes: true, bi: true },
306
306
  message: `Unit not extracted correctly for:[PLACEHOLDER]`,
307
307
  item: `${bmInfo}`
308
308
  });
@@ -312,7 +312,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, ohtCoreApiKey) {
312
312
  if (!isValueParsedCorrectly) {
313
313
  logger.warn({ labToOhtMapper }, `Value not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
314
314
  labToOhtContract.errorMessages.push({
315
- destination: { slack: true, notes: true },
315
+ destination: { slack: true, notes: true, bi: true },
316
316
  message: `Value not extracted correctly for:[PLACEHOLDER]`,
317
317
  item: `${bmInfo}`
318
318
  });
@@ -324,7 +324,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, ohtCoreApiKey) {
324
324
  if (!isPlausibleValue) {
325
325
  logger.warn({ labToOhtMapper }, `Value [${numberValue} ${unit}] is not plausible for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
326
326
  labToOhtContract.errorMessages.push({
327
- destination: { slack: true, notes: true },
327
+ destination: { slack: true, notes: true, bi: true },
328
328
  message: `Value is not plausible for:[PLACEHOLDER]`,
329
329
  item: `${bmInfo}, value:${numberValue}${unit}`
330
330
  });
@@ -342,7 +342,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, ohtCoreApiKey) {
342
342
  if (!isRangeParsedCorrectly) {
343
343
  logger.warn({ labToOhtMapper }, `Range not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
344
344
  labToOhtContract.errorMessages.push({
345
- destination: { slack: true, notes: true },
345
+ destination: { slack: true, notes: true, bi: true },
346
346
  message: `Range not extracted correctly for:[PLACEHOLDER]`,
347
347
  item: `${bmInfo}`
348
348
  });
@@ -357,7 +357,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, ohtCoreApiKey) {
357
357
  const method = (0, dataUtils_1.extractValue)(rawExamObj, labToOhtMapper.method);
358
358
  let alphaValue = !(0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker) && alphanumericalValue
359
359
  ? alphanumericalValue.trim()
360
- : null;
360
+ : '';
361
361
  // adding unit for alphanumerical values as number.
362
362
  if (!Number.isNaN(parseFloat(alphaValue))) {
363
363
  let originalUnit = (0, dataUtils_1.extractValue)(rawExamObj, labToOhtMapper?.unitExtraction?.unitPosition);
@@ -385,7 +385,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, ohtCoreApiKey) {
385
385
  else {
386
386
  logger.warn(`Created an ungroupedBiomarker for id: ${labToOhtMapper.labKey}, filename: ${filename}`);
387
387
  labToOhtContract.errorMessages.push({
388
- destination: { slack: true, notes: false },
388
+ destination: { slack: true, notes: false, bi: true },
389
389
  message: `Created ungroupedBiomarkers for:[PLACEHOLDER]`,
390
390
  item: `labKey:${labToOhtMapper.labKey}`
391
391
  });
package/dist/service/ohtMeasurementsExtractor.service.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/types/custom-parser.types.d.ts CHANGED
@@ -1,9 +1,15 @@
1
1
  import { ErrorMessage } from "./error.types";
2
- import { PatientInfo } from "./oht.types";
2
+ import { MeasurementValueComparator, PatientInfo } from "./oht.types";
3
3
  export declare const unitSynonyms: Record<string, string>;
4
4
  export interface ValueExtraction {
5
5
  valuePosition?: string;
6
- defaultValueExtractionFunc?: (value: string) => string | null;
6
+ extractionFunc?: (exam: any, labToOhtMapper: LabToOhtMapper) => ValueExtractionResponse;
7
+ defaultValueExtractionFunc?: (value: string) => string | undefined;
8
+ }
9
+ export interface ValueExtractionResponse {
10
+ value: number | string | null;
11
+ comparator: MeasurementValueComparator;
12
+ isValueParsedCorrectly: boolean;
7
13
  }
8
14
  export interface RangeExtractionResponse {
9
15
  from: number | null;
@@ -15,7 +21,7 @@ export interface RangeExtraction {
15
21
  rangePosition?: string;
16
22
  extractionRegex?: RegExp;
17
23
  extractionFunc?: (exam: any, labToOhtMapper: LabToOhtMapper, patientInfo: PatientInfo, documentDate?: Date) => RangeExtractionResponse;
18
- defaultRangeExtractionFunc?: (labToOhtMapper: LabToOhtMapper, exam: any) => RangeExtractionResponse;
24
+ defaultRangeExtractionFunc?: (labToOhtMapper: LabToOhtMapper, exam: any, patientInfo?: PatientInfo, documentDate?: Date) => RangeExtractionResponse;
19
25
  }
20
26
  export interface UnitExtraction {
21
27
  predefinedUnit?: string;
package/dist/types/error.types.d.ts CHANGED
@@ -1,6 +1,7 @@
1
1
  export interface Destination {
2
2
  slack: boolean;
3
3
  notes: boolean;
4
+ bi: boolean;
4
5
  }
5
6
  export interface ErrorMessage {
6
7
  destination: Destination;
package/dist/types/oht.types.d.ts CHANGED
@@ -85,7 +85,7 @@ export type DataImportFileUpload = {
85
85
  fileSizeBytes: number;
86
86
  uploadedByUserId: string;
87
87
  status: DataImportFileUploadStatus;
88
- uploadType: UploadTypes;
88
+ uploadType: UploadType;
89
89
  isArchived: boolean;
90
90
  isDeleted: boolean;
91
91
  lastProcessedByUserId?: string;
@@ -144,6 +144,7 @@ export interface PatientInfo {
144
144
  address?: string;
145
145
  height?: number;
146
146
  weight?: number;
147
+ email?: string;
147
148
  isDigitalizationApproved: boolean;
148
149
  }
149
150
  export type Digitization = {
@@ -158,7 +159,7 @@ export declare enum Sex {
158
159
  FEMALE = "FEMALE",
159
160
  OTHER = "OTHER"
160
161
  }
161
- export declare enum UploadTypes {
162
+ export declare enum UploadType {
162
163
  CLINICAL_ANALYSIS = "CLINICAL_ANALYSIS",
163
164
  OTHER = "OTHER"
164
165
  }
package/dist/types/oht.types.js CHANGED
@@ -1,17 +1,17 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.AcfBiomarkerRangeAnnotationCheck = exports.AcfBiomarkerGenericDisclaimerLogic = exports.ManualCheck = exports.BiomarkerCompatibility = exports.ReferenceRangeType = exports.GoLiveStatus = exports.PipelineStep = exports.DigitizationStatus = exports.MeasurementValueComparator = exports.BiomarkerValueType = exports.DataImportFileUploadStatus = exports.UploadTypes = exports.Sex = void 0;
3
+ exports.AcfBiomarkerRangeAnnotationCheck = exports.AcfBiomarkerGenericDisclaimerLogic = exports.ManualCheck = exports.BiomarkerCompatibility = exports.ReferenceRangeType = exports.GoLiveStatus = exports.PipelineStep = exports.DigitizationStatus = exports.MeasurementValueComparator = exports.BiomarkerValueType = exports.DataImportFileUploadStatus = exports.UploadType = exports.Sex = void 0;
4
4
  var Sex;
5
5
  (function (Sex) {
6
6
  Sex["MALE"] = "MALE";
7
7
  Sex["FEMALE"] = "FEMALE";
8
8
  Sex["OTHER"] = "OTHER";
9
9
  })(Sex || (exports.Sex = Sex = {}));
10
- var UploadTypes;
11
- (function (UploadTypes) {
12
- UploadTypes["CLINICAL_ANALYSIS"] = "CLINICAL_ANALYSIS";
13
- UploadTypes["OTHER"] = "OTHER";
14
- })(UploadTypes || (exports.UploadTypes = UploadTypes = {}));
10
+ var UploadType;
11
+ (function (UploadType) {
12
+ UploadType["CLINICAL_ANALYSIS"] = "CLINICAL_ANALYSIS";
13
+ UploadType["OTHER"] = "OTHER";
14
+ })(UploadType || (exports.UploadType = UploadType = {}));
15
15
  var DataImportFileUploadStatus;
16
16
  (function (DataImportFileUploadStatus) {
17
17
  DataImportFileUploadStatus["UPLOADED"] = "UPLOADED";
package/dist/types/oht.types.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"oht.types.js","sourceRoot":"","sources":["../../types/oht.types.ts"],"names":[],"mappings":";;;AA4KA,IAAY,GAIX;AAJD,WAAY,GAAG;IACb,oBAAa,CAAA;IACb,wBAAiB,CAAA;IACjB,sBAAe,CAAA;AACjB,CAAC,EAJW,GAAG,mBAAH,GAAG,QAId;AAED,IAAY,UAGX;AAHD,WAAY,UAAU;IACpB,qDAAuC,CAAA;IACvC,6BAAe,CAAA;AACjB,CAAC,EAHW,UAAU,0BAAV,UAAU,QAGrB;AAED,IAAY,0BAYX;AAZD,WAAY,0BAA0B;IACpC,mDAAqB,CAAA;IACrB,iDAAmB,CAAA;IACnB,uDAAyB,CAAA;IACzB,uDAAyB,CAAA;IACzB,qDAAuB,CAAA;IACvB,qDAAuB,CAAA;IACvB,6CAAe,CAAA;IACf,iDAAmB,CAAA;IACnB,mDAAqB,CAAA;IACrB,mDAAqB,CAAA;IACrB,2DAA6B,CAAA;AAC/B,CAAC,EAZW,0BAA0B,0CAA1B,0BAA0B,QAYrC;AAED,IAAY,kBAGX;AAHD,WAAY,kBAAkB;IAC5B,uDAAiC,CAAA;IACjC,6CAAuB,CAAA;AACzB,CAAC,EAHW,kBAAkB,kCAAlB,kBAAkB,QAG7B;AAED,IAAY,0BAIX;AAJD,WAAY,0BAA0B;IACpC,6CAAe,CAAA;IACf,2DAA6B,CAAA;IAC7B,qDAAuB,CAAA;AACzB,CAAC,EAJW,0BAA0B,0CAA1B,0BAA0B,QAIrC;AAED,IAAY,kBAOX;AAPD,WAAY,kBAAkB;IAC5B,yCAAmB,CAAA;IACnB,yCAAmB,CAAA;IACnB,+CAAyB,CAAA;IACzB,mCAAa,CAAA;IACb,qCAAe,CAAA;IACf,2CAAqB,CAAA;AACvB,CAAC,EAPW,kBAAkB,kCAAlB,kBAAkB,QAO7B;AAED,IAAY,YASX;AATD,WAAY,YAAY;IACtB,6CAA6B,CAAA;IAC7B,mDAAmC,CAAA;IACnC,yDAAyC,CAAA;IACzC,2DAA2C,CAAA;IAC3C,2DAA2C,CAAA;IAC3C,+DAA+C,CAAA;IAC/C,2DAA2C,CAAA;IAC3C,mDAAmC,CAAA;AACrC,CAAC,EATW,YAAY,4BAAZ,YAAY,QASvB;AA4CD,IAAY,YAIX;AAJD,WAAY,YAAY;IACtB,+BAAe,CAAA;IACf,iCAAiB,CAAA;IACjB,2BAAW,CAAA;AACb,CAAC,EAJW,YAAY,4BAAZ,YAAY,QAIvB;AAsCD,IAAY,kBAIX;AAJD,WAAY,kBAAkB;IAC5B,6CAAuB,CAAA;IACvB,2CAAqB,CAAA;IACrB,uDAAiC,CAAA;AACnC,CAAC,EAJW,kBAAkB,kCAAlB,kBAAkB,QAI7B;AAED,IAAY,sBAOX;AAPD,WAAY,sBAAsB;IAChC,+CAAqB,CAAA;IACrB,+CAAqB,CAAA;IACrB,4EAAkD,CAAA;IAClD,4EAAkD,CAAA;IAClD,4DAAkC,CAAA;IAClC,2CAAiB,CAAA;AACnB,CAAC,EAPW,sBAAsB,sCAAtB,sBAAsB,QAOjC;AAED,IAAY,WAGX;AAHD,WAAY,WAAW;IACrB,wBAAS,CAAA;IACT,sCAAuB,CAAA;AACzB,CAAC,EAHW,WAAW,2BAAX,WAAW,QAGtB;AAED,IAAY,kCAGX;AAHD,WAAY,kCAAkC;IAC5C,6DAAuB,CAAA;IACvB,iEAA2B,CAAA;AAC7B,CAAC,EAHW,kCAAkC,kDAAlC,kCAAkC,QAG7C;AAED,IAAY,gCAMX;AAND,WAAY,gCAAgC;IAC1C,2DAAuB,CAAA;IACvB,6EAAyC,CAAA;IACzC,+EAA2C,CAAA;IAC3C,2FAAuD,CAAA;IACvD,uFAAmD,CAAA;AACrD,CAAC,EANW,gCAAgC,gDAAhC,gCAAgC,QAM3C"}
package/dist/util-ts/pinoLogger.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"pinoLogger.js","sourceRoot":"","sources":["../../util-ts/pinoLogger.ts"],"names":[],"mappings":";;;;;AAAA,gDAAwB;AAOxB,oCAAoC;AACpC,MAAM,cAAc,GAAuB;IACzC,SAAS,EAAE,SAAS;IACpB,OAAO,EAAE,SAAS;IAClB,SAAS,EAAE,OAAO;IAClB,OAAO,EAAE,OAAO;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,MAAM;IACd,MAAM,EAAE,SAAS;IACjB,OAAO,EAAE,OAAO;CACjB,CAAC;AAEF,wCAAwC;AACxC,MAAM,iBAAiB,GAAG;IACxB,UAAU,EAAE,SAAS;IACrB,UAAU,EAAE;QACV,KAAK,CAAC,KAAK,EAAE,MAAM;YACjB,OAAO,EAAE,QAAQ,EAAE,cAAc,CAAC,KAAK,CAAC,IAAI,SAAS,EAAE,KAAK,EAAE,MAAM,EAAE,CAAC;QACzE,CAAC;KACF;IACD,WAAW,EAAE;QACX,KAAK,EAAE,cAAI,CAAC,cAAc,CAAC,GAAG,EAAE,6BAA6B;KAC9D;CACF,CAAC;AAEF,kGAAkG;AAClG,kBAAe,CAAC,sBAA2B,EAAE,EAAe,EAAE;IAC5D,OAAO,IAAA,cAAI,EAAC,EAAE,GAAG,iBAAiB,EAAE,GAAG,mBAAmB,EAAE,CAAC,CAAC;AAChE,CAAC,CAAC"}
1
+ {"version":3,"file":"pinoLogger.js","sourceRoot":"","sources":["../../util-ts/pinoLogger.ts"],"names":[],"mappings":";;;;;AAAA,gDAAwB;AAOxB,oCAAoC;AACpC,MAAM,cAAc,GAAuB;IACzC,SAAS,EAAE,SAAS;IACpB,OAAO,EAAE,SAAS;IAClB,SAAS,EAAE,OAAO;IAClB,OAAO,EAAE,OAAO;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,MAAM;IACd,MAAM,EAAE,SAAS;IACjB,OAAO,EAAE,OAAO;CACjB,CAAC;AAEF,wCAAwC;AACxC,MAAM,iBAAiB,GAAG;IACxB,UAAU,EAAE,SAAS;IACrB,UAAU,EAAE;QACV,KAAK,CAAC,KAAsB,EAAE,MAAW;YACvC,OAAO,EAAE,QAAQ,EAAE,cAAc,CAAC,KAAK,CAAC,IAAI,SAAS,EAAE,KAAK,EAAE,MAAM,EAAE,CAAC;QACzE,CAAC;KACF;IACD,WAAW,EAAE;QACX,KAAK,EAAE,cAAI,CAAC,cAAc,CAAC,GAAG,EAAE,6BAA6B;KAC9D;CACF,CAAC;AAEF,kGAAkG;AAClG,kBAAe,CAAC,sBAA2B,EAAE,EAAe,EAAE;IAC5D,OAAO,IAAA,cAAI,EAAC,EAAE,GAAG,iBAAiB,EAAE,GAAG,mBAAmB,EAAE,CAAC,CAAC;AAChE,CAAC,CAAC"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@openhealth/oht-custom-parser-lib",
3
- "version": "0.1.19",
3
+ "version": "0.2.1",
4
4
  "description": "Shared nodejs lib with with reusable functions",
5
5
  "main": "dist/index.js",
6
6
  "types": "dist/index.d.ts",
@@ -14,6 +14,7 @@
14
14
  "author": "",
15
15
  "license": "ISC",
16
16
  "dependencies": {
17
+ "@google-cloud/pubsub": "^4.10.0",
17
18
  "@google-cloud/storage": "^7.7.0",
18
19
  "axios": "^1.6.7",
19
20
  "bottleneck": "^2.19.5",