@openhealth/oht-custom-parser-lib 0.5.57 → 0.5.58
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/service/auxiliaryFunctions.service.js +3 -2
- package/dist/service/auxiliaryFunctions.service.js.map +1 -1
- package/dist/service/fileUploadErrorHandler.service.js +2 -0
- package/dist/service/fileUploadErrorHandler.service.js.map +1 -1
- package/dist/service/parsingErrorService.service.js +19 -16
- package/dist/service/parsingErrorService.service.js.map +1 -1
- package/dist/types/error.types.d.ts +8 -7
- package/dist/types/error.types.js +10 -0
- package/dist/types/error.types.js.map +1 -1
- package/dist/types/oht.types.d.ts +2 -0
- package/dist/types/oht.types.js +2 -0
- package/dist/types/oht.types.js.map +1 -1
- package/dist/util-ts/sensitivePaths.js +5 -2
- package/dist/util-ts/sensitivePaths.js.map +1 -1
- package/package.json +1 -1
- package/dist/service/ohtAgnosticMeasurementsExtractor.service.d.ts +0 -59
- package/dist/service/ohtAgnosticMeasurementsExtractor.service.js +0 -603
- package/dist/service/ohtAgnosticMeasurementsExtractor.service.js.map +0 -1
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@@ -135,7 +135,7 @@ function handleRejection(parseType, notifySlack = true, notifyNotes = false, not
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rejectReason = oht_types_1.RejectReason.INVALID_DATA_NO_BIOMARKER_DATA;
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}
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const errorType = resolveRejectionParsingErrorType(lowerParseType, rejectReason);
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-
const messageSuffix = errorType === error_types_1.ParsingErrorType.
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138
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+
const messageSuffix = errorType === error_types_1.ParsingErrorType.REJECTED_UNKNOWN
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? `File rejected: ${parseType} parsing failed. Reason: ${rejectReason}`
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: String(rejectReason);
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parsingErrorService_service_1.parsingErrorService.record(errorType, {
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@@ -171,7 +171,8 @@ function resolveRejectionParsingErrorType(lowerParseType, rejectReason) {
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if (rejectReason === oht_types_1.RejectReason.NO_IN_PANEL_BIOMARKER) {
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return error_types_1.ParsingErrorType.REJECTED_NO_BIOMARKERS;
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}
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-
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+
processingLogger_service_1.processingLogger.logError(`resolveRejectionParsingErrorType: unrecognized parseType="${lowerParseType}", rejectReason="${rejectReason}" — falling back to REJECTED_UNKNOWN`);
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175
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+
return error_types_1.ParsingErrorType.REJECTED_UNKNOWN;
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}
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async function queryFileUploadsWithFilters(filters, ohtCoreApiKey) {
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const OHT_CORE_URL = process.env.OHT_CORE_URL;
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"auxiliaryFunctions.service.js","sourceRoot":"","sources":["../../service/auxiliaryFunctions.service.ts"],"names":[],"mappings":";;;;;
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1
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+
{"version":3,"file":"auxiliaryFunctions.service.js","sourceRoot":"","sources":["../../service/auxiliaryFunctions.service.ts"],"names":[],"mappings":";;;;;AAiWE,wDAAsB;AACtB,kCAAW;AACX,8CAAiB;AACjB,sCAAa;AACb,0CAAe;AACf,kEAA2B;AAC3B,0DAAuB;AACvB,sEAA6B;AAxW/B,2DAAmC;AACnC,kDAAyD;AACzD,yEAA8D;AAC9D,+EAAoE;AACpE,sDAAwD;AACxD,kDAA+M;AAC/M,kDAA0B;AAC1B,uFAA+D;AAC/D,2DAAmC;AAInC,eAAK,CAAC,MAAM,CAAC,2BAAiB,CAAC,CAAC;AAChC,eAAK,CAAC,MAAM,CAAC,aAAG,CAAC,CAAC;AAElB,MAAM,YAAY,GAAG,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC;AAE9C,SAAS,aAAa,CAAC,YAAmB,EAAE,gBAAuB;IAC/D,IAAI,CAAC,gBAAgB,IAAI,CAAC,YAAY;QAAE,OAAO,IAAI,CAAC;IAEpD,2DAA2D;IAC3D,MAAM,OAAO,GAAG,IAAA,gBAAM,EAAC,YAAY,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;IACpD,MAAM,SAAS,GAAG,IAAA,gBAAM,EAAC,gBAAgB,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;IAE1D,OAAO,OAAO,CAAC,IAAI,CAAC,SAAS,EAAE,OAAO,CAAC,CAAC;AAC5C,CAAC;AAED,SAAS,iBAAiB,CAAC,YAAmB,EAAE,gBAAuB;IACnE,MAAM,UAAU,GAAG,aAAa,CAAC,YAAY,EAAE,gBAAgB,CAAC,CAAC;IAEjE,IAAI,UAAU,KAAK,IAAI,EAAE,CAAC;QACtB,OAAO,KAAK,CAAC;IACjB,CAAC;IAED,OAAO,UAAU,IAAI,EAAE,IAAI,UAAU,IAAI,GAAG,CAAC;AACjD,CAAC;AAED,SAAS,sBAAsB,CAAC,iBAA0B;IACtD,OAAO,iBAAiB,KAAK,SAAS,IAAI,iBAAiB,CAAC,MAAM,GAAG,CAAC,CAAC;AAC3E,CAAC;AAED,SAAS,WAAW,CAAC,aAAsB;IACvC,MAAM,MAAM,GAAG,aAAa,EAAE,WAAW,EAAE,CAAC;IAE5C,QAAQ,MAAM,EAAE,CAAC;QACb,KAAK,GAAG,CAAC;QACT,KAAK,WAAW,CAAC;QACjB,KAAK,MAAM;YACP,OAAO,EAAE,GAAG,EAAE,eAAG,CAAC,IAAI,EAAE,uBAAuB,EAAE,IAAI,EAAE,CAAC;QAC5D,KAAK,GAAG,CAAC;QACT,KAAK,UAAU,CAAC;QAChB,KAAK,QAAQ;YACT,OAAO,EAAE,GAAG,EAAE,eAAG,CAAC,MAAM,EAAE,uBAAuB,EAAE,IAAI,EAAE,CAAC;QAC9D;YACI,OAAO,EAAE,GAAG,EAAE,eAAG,CAAC,KAAK,EAAE,uBAAuB,EAAE,KAAK,EAAE,CAAC;IAClE,CAAC;AACL,CAAC;AAED;;;GAGG;AACH,SAAS,eAAe,CACtB,SAAiB,EACjB,cAAuB,IAAI,EAC3B,cAAuB,KAAK,EAC5B,WAAoB,KAAK;IAEvB,MAAM,cAAc,GAAG,UAAU,CAAC;IAClC,MAAM,cAAc,GAAG,SAAS,CAAC,WAAW,EAAE,CAAC;IAE/C,0DAA0D;IAC1D,IAAI,YAA0B,CAAC;IAE/B,kEAAkE;IAClE,IAAI,cAAc,KAAK,YAAY,IAAI,cAAc,KAAK,aAAa,EAAE,CAAC;QACtE,YAAY,GAAG,wBAAY,CAAC,eAAe,CAAC;IAChD,CAAC;SACI,IAAI,cAAc,KAAK,mBAAmB,IAAI,cAAc,KAAK,qBAAqB,IAAI,cAAc,KAAK,oBAAoB,EAAE,CAAC;QACrI,YAAY,GAAG,wBAAY,CAAC,2BAA2B,CAAC;IAC5D,CAAC;SACI,IAAI,cAAc,KAAK,YAAY,IAAI,cAAc,KAAK,aAAa,EAAE,CAAC;QAC3E,YAAY,GAAG,wBAAY,CAAC,mBAAmB,CAAC;IACpD,CAAC;SACI,IAAI,cAAc,CAAC,QAAQ,CAAC,WAAW,CAAC,IAAI,cAAc,CAAC,QAAQ,CAAC,YAAY,CAAC,IAAI,cAAc,CAAC,QAAQ,CAAC,mBAAmB,CAAC,EAAE,CAAC;QACrI,YAAY,GAAG,wBAAY,CAAC,yBAAyB,CAAC;IAC1D,CAAC;SACI,IAAI,cAAc,CAAC,QAAQ,CAAC,YAAY,CAAC,IAAI,cAAc,CAAC,QAAQ,CAAC,cAAc,CAAC,IAAI,cAAc,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC;QAC/H,YAAY,GAAG,wBAAY,CAAC,oBAAoB,CAAC;IACrD,CAAC;IACD,sEAAsE;IACtE,yDAAyD;SACpD,IAAI,cAAc,CAAC,QAAQ,CAAC,UAAU,CAAC;QACxC,CAAC,cAAc,CAAC,QAAQ,CAAC,KAAK,CAAC,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,SAAS,CAAC,IAAI,cAAc,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE,CAAC;QACnH,YAAY,GAAG,wBAAY,CAAC,eAAe,CAAC;IAChD,CAAC;IACD,oDAAoD;SAC/C,IAAI,cAAc,CAAC,QAAQ,CAAC,WAAW,CAAC;QACpC,CAAC,cAAc,CAAC,QAAQ,CAAC,MAAM,CAAC,IAAI,cAAc,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC;QAC5E,YAAY,GAAG,wBAAY,CAAC,iBAAiB,CAAC;IAClD,CAAC;IACD,uBAAuB;SAClB,IAAI,cAAc,CAAC,QAAQ,CAAC,eAAe,CAAC;QACxC,cAAc,CAAC,QAAQ,CAAC,aAAa,CAAC;QACtC,cAAc,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;QAC1C,YAAY,GAAG,wBAAY,CAAC,iBAAiB,CAAC;IAClD,CAAC;IACD,0BAA0B;SACrB,IAAI,cAAc,CAAC,QAAQ,CAAC,UAAU,CAAC;QACnC,cAAc,CAAC,QAAQ,CAAC,sBAAsB,CAAC,EAAE,CAAC;QACvD,YAAY,GAAG,wBAAY,CAAC,sBAAsB,CAAC;IACvD,CAAC;IACD,2EAA2E;SACtE,IAAI,cAAc,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE,CAAC;QAC5C,YAAY,GAAG,wBAAY,CAAC,qBAAqB,CAAC;IACtD,CAAC;IACD,iCAAiC;SAC5B,IAAI,cAAc,CAAC,QAAQ,CAAC,MAAM,CAAC;QAC/B,cAAc,CAAC,QAAQ,CAAC,YAAY,CAAC;QACrC,cAAc,CAAC,QAAQ,CAAC,cAAc,CAAC,EAAE,CAAC;QAC/C,YAAY,GAAG,wBAAY,CAAC,eAAe,CAAC;IAChD,CAAC;IACD,sCAAsC;SACjC,IAAI,cAAc,CAAC,QAAQ,CAAC,aAAa,CAAC;QACtC,cAAc,CAAC,QAAQ,CAAC,QAAQ,CAAC;QACjC,cAAc,CAAC,QAAQ,CAAC,eAAe,CAAC,EAAE,CAAC;QAChD,YAAY,GAAG,wBAAY,CAAC,kBAAkB,CAAC;IACnD,CAAC;IACD,mBAAmB;SACd,IAAI,cAAc,CAAC,QAAQ,CAAC,aAAa,CAAC;QACtC,cAAc,CAAC,QAAQ,CAAC,eAAe,CAAC;QACxC,cAAc,CAAC,QAAQ,CAAC,cAAc,CAAC,EAAE,CAAC;QAC/C,YAAY,GAAG,wBAAY,CAAC,gBAAgB,CAAC;IACjD,CAAC;IACD,yBAAyB;SACpB,IAAI,cAAc,CAAC,QAAQ,CAAC,cAAc,CAAC;QACvC,cAAc,CAAC,QAAQ,CAAC,iBAAiB,CAAC,EAAE,CAAC;QAClD,YAAY,GAAG,wBAAY,CAAC,sBAAsB,CAAC;IACvD,CAAC;IACD,+CAA+C;SAC1C,CAAC;QACF,YAAY,GAAG,wBAAY,CAAC,8BAA8B,CAAC;IAC/D,CAAC;IAED,MAAM,SAAS,GAAG,gCAAgC,CAAC,cAAc,EAAE,YAAY,CAAC,CAAC;IACjF,MAAM,aAAa,GACjB,SAAS,KAAK,8BAAgB,CAAC,gBAAgB;QAC7C,CAAC,CAAC,kBAAkB,SAAS,4BAA4B,YAAY,EAAE;QACvE,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,CAAC;IAC3B,iDAAmB,CAAC,MAAM,CACxB,SAAS,EACT;QACE,aAAa;QACb,YAAY;KACb,EACD,EAAE,WAAW,EAAE,WAAW,EAAE,QAAQ,EAAE,CACvC,CAAC;IAEF,OAAO,EAAE,cAAc,EAAE,YAAY,EAAE,CAAC;AAC5C,CAAC;AAED,SAAS,gCAAgC,CACvC,cAAsB,EACtB,YAA0B;IAE1B,IAAI,cAAc,KAAK,YAAY,IAAI,cAAc,KAAK,aAAa,EAAE,CAAC;QACxE,OAAO,8BAAgB,CAAC,yBAAyB,CAAC;IACpD,CAAC;IACD,IACE,cAAc,KAAK,mBAAmB;QACtC,cAAc,KAAK,qBAAqB;QACxC,cAAc,KAAK,oBAAoB,EACvC,CAAC;QACD,OAAO,8BAAgB,CAAC,2BAA2B,CAAC;IACtD,CAAC;IACD,IAAI,cAAc,KAAK,YAAY,IAAI,cAAc,KAAK,aAAa,EAAE,CAAC;QACxE,OAAO,8BAAgB,CAAC,4BAA4B,CAAC;IACvD,CAAC;IACD,IAAI,cAAc,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE,CAAC;QACzC,OAAO,8BAAgB,CAAC,sBAAs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@@ -83,6 +83,8 @@ function extractFormattedRejectReason(rejectReason, fieldName, errorMessage) {
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return `${baseRejectReason} - Missing '${fieldName}'`;
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case oht_types_1.RejectReason.INVALID_DATA_NO_BIOMARKER_DATA:
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return `${baseRejectReason} - Invalid '${fieldName}'`;
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case oht_types_1.RejectReason.DUPLICATE_FIELD_VALUE:
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return `${baseRejectReason} - '${fieldName}' contains multiple values`;
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default:
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return `${baseRejectReason} - Issue with '${fieldName}'`;
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88
90
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"fileUploadErrorHandler.service.js","sourceRoot":"","sources":["../../service/fileUploadErrorHandler.service.ts"],"names":[],"mappings":";;;;;;AAyDA,kEAQC;AAKD,
|
|
1
|
+
{"version":3,"file":"fileUploadErrorHandler.service.js","sourceRoot":"","sources":["../../service/fileUploadErrorHandler.service.ts"],"names":[],"mappings":";;;;;;AAyDA,kEAQC;AAKD,oEA0CC;AAoBD,wDAsDC;AAKD,kCAkKC;AAjWD,kDAK4B;AAC5B,mEAAmG;AACnG,6EAGsC;AACtC,kDAAoD;AACpD,yEAA8D;AAC9D,sDAAkE;AAClE,kDAA0B;AAC1B,2DAAmC;AAEnC,eAAK,CAAC,MAAM,CAAC,aAAG,CAAC,CAAC;AAElB;;;GAGG;AACU,QAAA,0BAA0B,GAAG,qBAA8B,CAAC;AAEzE;;;;GAIG;AACH,SAAS,qBAAqB,CAAC,KAAY;IACzC,OAAO,KAAK,CAAC,IAAI,KAAK,kCAA0B,CAAC;AACnD,CAAC;AAED;;;GAGG;AACH,MAAa,eAAgB,SAAQ,KAAK;IAIxC,YACE,OAAe,EACf,YAA0B,EAC1B,SAAkB;QAElB,KAAK,CAAC,OAAO,CAAC,CAAC;QACf,IAAI,CAAC,IAAI,GAAG,iBAAiB,CAAC;QAC9B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAC;QACjC,IAAI,CAAC,SAAS,GAAG,SAAS,CAAC;IAC7B,CAAC;CACF;AAdD,0CAcC;AAED;;GAEG;AACH,SAAgB,2BAA2B,CACzC,YAAsC,EACtC,mBAAmC;IAEnC,IAAI,CAAC,YAAY,IAAI,mBAAmB,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACtD,OAAO,IAAI,CAAC;IACd,CAAC;IACD,OAAO,CAAC,mBAAmB,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC;AACrD,CAAC;AAED;;GAEG;AACH,SAAgB,4BAA4B,CAC1C,YAA0B,EAC1B,SAAkB,EAClB,YAAqB;IAErB,MAAM,gBAAgB,GAAG,MAAM,CAAC,YAAY,CAAC,CAAC;IAE9C,IAAI,YAAY,KAAK,wBAAY,CAAC,mBAAmB,IAAI,YAAY,EAAE,CAAC;QACtE,MAAM,cAAc,GAAG,YAAY,CAAC,KAAK,CAAC,gEAAgE,CAAC,CAAC;QAC5G,IAAI,cAAc,EAAE,CAAC;YACnB,MAAM,cAAc,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC;YACzC,MAAM,cAAc,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC;YACzC,MAAM,SAAS,GAAG,SAAS,CAAC,CAAC,CAAC,SAAS,SAAS,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;YACzD,OAAO,sBAAsB,SAAS,eAAe,cAAc,eAAe,cAAc,GAAG,CAAC;QACtG,CAAC;IACH,CAAC;IAED,IAAI,SAAS,EAAE,CAAC;QACd,QAAQ,YAAY,EAAE,CAAC;YACrB,KAAK,wBAAY,CAAC,eAAe;gBAC/B,IAAI,SAAS,KAAK,YAAY,EAAE,CAAC;oBAC/B,OAAO,kCAAkC,SAAS,4CAA4C,CAAC;gBACjG,CAAC;gBACD,OAAO,GAAG,gBAAgB,0BAA0B,SAAS,GAAG,CAAC;YACnE,KAAK,wBAAY,CAAC,iBAAiB;gBACjC,OAAO,GAAG,gBAAgB,eAAe,SAAS,GAAG,CAAC;YACxD,KAAK,wBAAY,CAAC,oBAAoB;gBACpC,OAAO,GAAG,gBAAgB,eAAe,SAAS,GAAG,CAAC;YACxD,KAAK,wBAAY,CAAC,2BAA2B;gBAC3C,OAAO,GAAG,gBAAgB,eAAe,SAAS,GAAG,CAAC;YACxD,KAAK,wBAAY,CAAC,mBAAmB;gBACnC,OAAO,GAAG,gBAAgB,eAAe,SAAS,GAAG,CAAC;YACxD,KAAK,wBAAY,CAAC,8BAA8B;gBAC9C,OAAO,GAAG,gBAAgB,eAAe,SAAS,GAAG,CAAC;YACxD,KAAK,wBAAY,CAAC,qBAAqB;gBACrC,OAAO,GAAG,gBAAgB,OAAO,SAAS,4BAA4B,CAAC;YACzE;gBACE,OAAO,GAAG,gBAAgB,kBAAkB,SAAS,GAAG,CAAC;QAC7D,CAAC;IACH,CAAC;IAED,OAAO,gBAAgB,CAAC;AAC1B,CAAC;AAED,SAAS,2BAA2B,CAAC,UAA8B,EAAE,YAAoB;IACvF,MAAM,YAAY,GAAG,YAAY,CAAC,WAAW,EAAE,CAAC;IAChD,MAAM,UAAU,GAAG,UAAU,KAAK,GAAG;QACnC,YAAY,CAAC,QAAQ,CAAC,iBAAiB,CAAC;QACxC,YAAY,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;IAE/B,IAAI,CAAC,UAAU;QAAE,OAAO,KAAK,CAAC;IAE9B,MAAM,8BAA8B,GAAG,YAAY,CAAC,QAAQ,CAAC,WAAW,CAAC;QACvE,CAAC,YAAY,CAAC,QAAQ,CAAC,SAAS,CAAC;QACjC,CAAC,YAAY,CAAC,QAAQ,CAAC,UAAU,CAAC,CAAC;IAErC,OAAO,CAAC,8BAA8B,CAAC;AACzC,CAAC;AAED;;GAEG;AACH,SAAgB,sBAAsB,CACpC,KAAY,EACZ,YAAoB,EACpB,UAAmB;IAEnB,IAAI,2BAA2B,CAAC,UAAU,EAAE,YAAY,CAAC,EAAE,CAAC;QAC1D,OAAO,wBAAY,CAAC,eAAe,CAAC;IACtC,CAAC;IAED,MAAM,eAAe,GAAG,KAAK,YAAY,eAAe,IAAI,cAAc,IAAI,KAAK,CAAC;IACpF,IAAI,eAAe,EAAE,CAAC;QACpB,MAAM,YAAY,GAAI,KAAa,CAAC,YAAY,CAAC;QACjD,IAAI,YAAY,KAAK,SAAS,IAAI,YAAY,KAAK,IAAI,IAAI,YAAY,KAAK,EAAE,EAAE,CAAC;YAC/E,OAAO,YAA4B,CAAC;QACtC,CAAC;IACH,CAAC;IAED,MAAM,YAAY,GAAG,YAAY,CAAC,WAAW,EAAE,CAAC;IAEhD,IAAI,YAAY,CAAC,QAAQ,CAAC,qBAAqB,CAAC,IAAI,YAAY,CAAC,QAAQ,CAAC,gBAAgB,CAAC,IAAI,YAAY,CAAC,QAAQ,CAAC,iBAAiB,CAAC,EAAE,CAAC;QACxI,OAAO,wBAAY,CAAC,mBAAmB,CAAC;IAC1C,CAAC;IACD,IAAI,YAAY,CAAC,QAAQ,CAAC,cAAc,CAAC,IAAI,YAAY,CAAC,QAAQ,CAAC,eAAe,CAAC,IAAI,YAAY,CAAC,QAAQ,CAAC,iBAAiB,CAAC,EAAE,CAAC;QAChI,OAAO,wBAAY,CAAC,8BAA8B,CAAC;IACrD,CAAC;IACD,IAAI,YAAY,CAAC,QAAQ,CAAC,eAAe,CAAC,IAAI,YAAY,CAAC,QAAQ,CAAC,aAAa,CAAC,EAAE,CAAC;QACnF,OAAO,wBAAY,CAAC,iBAAiB,CAAC;IACxC,CAAC;IACD,IAAI,YAAY,CAAC,QAAQ,CAAC,UAAU,CAAC,IAAI,CAAC,YAAY,CAAC,QAAQ,CAAC,KAAK,CAAC,IAAI,YAAY,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC;QAC5G,OAAO,wBAAY,CAAC,eAAe,CAAC;IACtC,CAAC;IACD,IAAI,YAAY,CAAC,QAAQ,CAAC,UAAU,CAAC,IAAI,YAAY,CAAC,QAAQ,CAAC,sBAAsB,CAAC,EAAE,CAAC;QACvF,OAAO,wBAAY,CAAC,sBAAsB,CAAC;IAC7C,CAAC;IACD,IAAI,YAAY,CAAC,QAAQ,CAAC,aAAa,CAAC,IAAI,YAAY,CAAC,QAAQ,CAAC,eAAe,CAAC,EAAE,CAAC;QACnF,OAAO,wBAAY,CAAC,gBAAgB,CAAC;IACvC,CAAC;IACD,IAAI,YAAY,CAAC,QAAQ,CAAC,mBAAmB,CAAC,IAAI,YAAY,CAAC,QAAQ,CAAC,SAAS,CAAC,IAAI,YAAY,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE,CAAC;QACpH,OAAO,wBAAY,CAAC,iBAAiB,CAAC;IACxC,CAAC;IACD,IAAI,YAAY,CAAC,QAAQ,CAAC,cAAc,CAAC,IAAI,YAAY,CAAC,QAAQ,CAAC,YAAY,CAAC,IAAI,YAAY,CAAC,QAAQ,CAAC,cAAc,CAAC,EAAE,CAAC;QAC1H,OAAO,wBAAY,CAAC,eAAe,CAAC;IACtC,CAAC;IACD,IAAI,YAAY,CAAC,QAAQ,CAAC,iBAAiB,CAAC,IAAI,YAAY,CAAC,QAAQ,CAAC,cAAc,CAAC,EAAE,CAAC;QACtF,OAAO,wBAAY,CAAC,sBAAsB,CAAC;IAC7C,CAAC;IACD,IAAI,YAAY,CAAC,QAAQ,CAAC,0BAA0B,CAAC,IAAI,YAAY,CAAC,QAAQ,CAAC,oBAAoB,CAAC,EAAE,CAAC;QACrG,OAAO,wBAAY,CAAC,2BAA2B,CAAC;IAClD,CAAC;IACD,IAAI,YAAY,CAAC,QAAQ,CAAC,aAAa,CAAC,IAAI,YAAY,CAAC,QAAQ,CAAC,eAAe,CAAC,EAAE,CAAC;QACnF,OAAO,wBAAY,CAAC,kBAAkB,CAAC;IACzC,CAAC;IAED,OAAO,wBAAY,CAAC,kBAAkB,CAAC;AACzC,CAAC;AAED;;GAEG;AACI,KAAK,UAAU,WAAW,CAC/B,KAAY,EACZ,QAAgB,EAChB,MAAc,EACd,QAAgB,EAChB,YAAqB,EACrB,WAAoB,EACpB,sBAAsC,EAAE;IAExC,MAAM,YAAY,GAAG,IAAA,wBAAa,EAAC,KAAY,CAAQ,CAAC;IACxD,MAAM,YAAY,GAAI,YAAoB,CAAC,YAAY,CAAC;IACxD,MAAM,UAAU,GAAI,YAAoB,CAAC,MAAM,CAAC;IAChD,MAAM,eAAe,GAAI,KAAa,CAAC,QAAQ,EAAE,MAAM,CAAC;IACxD,MAAM,eAAe,GAAG,UAAU,IAAI,eAAe,CAAC;IAEtD,MAAM,YAAY,GAAG,YAAY;QAC/B,CAAC,CAAC,GAAG,KAAK,CAAC,OAAO,gBAAgB,IAAI,CAAC,SAAS,CAAC,YAAY,CAAC,EAAE;QAChE,CAAC,CAAC,KAAK,CAAC,OAAO,IAAI,wBAAwB,CAAC;IAE9C,MAAM,gBAAgB,GAAG,eAAe,KAAK,GAAG;QAC9C,YAAY,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;QAC/C,YAAoB,CAAC,MAAM,EAAE,GAAG,EAAE,QAAQ,CAAC,YAAY,CAAC,CAAC;IAC5D,MAAM,YAAY,GAAG,gBAAgB;QACnC,CAAC,CAAC,wBAAY,CAAC,eAAe;QAC9B,CAAC,CAAC,wBAAY,CAAC,mBAAmB,CAAC;IAErC,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC;IACzC,MAAM,YAAY,GAAG,sBAAsB,CAAC,KAAK,EAAE,YAAY,EAAE,eAAe,CAAC,CAAC;IAElF,IAAI,SAA6B,CAAC;IAClC,IAAI,KAAK,YAAY,eAAe,EAAE,CAAC;QACrC,SAAS,GAAG,KAAK,CAAC,SAAS,CAAC;IAC9B,CAAC;SAAM,IAAI,qBAAqB,CAAC,KAAK,CAAC,EAAE,CAAC;QACxC,MAAM,IAAI,GAAI,KAAgC,CAAC,SAAS,EAAE,IAAI,EAAE,CAAC;QACjE,SAAS,GAAG,IAAI,IAAI,SAAS,CAAC;IAChC,CAAC;SAAM,IAAI,eAAe,KAAK,GAAG,IAAI,YAAY,KAAK,wBAAY,CAAC,eAAe,EAAE,CAAC;QACpF,SAAS,GAAG,YAAY,CAAC;IAC3B,CAAC;IAED,MAAM,qBAAqB,GAAG,4BAA4B,CAAC,YAAY,EAAE,SAAS,EAAE,YAAY,CAAC,CAAC;IAElG,wEAAwE;IACxE,wFAAwF;IACxF,MAAM,wBAAwB,GAC5B,CAAC,KAAK,YAAY,eAAe,IAAI,qBAAqB,CAAC,KAAK,CAAC,CAAC;QAClE,CAAE,YAAY,KAAK,wBAAY,CAAC,8BAA8B;YAC5D,YAAY,KAAK,wBAAY,CAAC,oBAAoB;YAClD,YAAY,KAAK,wBAAY,CAAC,iBAAiB;YAC/C,YAAY,KAAK,wBAAY,CAAC,2BAA2B;YACzD,YAAY,KAAK,wBAAY,CAAC,mBAAmB;YACjD,YAAY,KAAK,wBAAY,CAAC,yBAAyB;YACvD,wGAAwG;YACxG,CAAC,YAAY,KAAK,wBAAY,CAAC,eAAe,IAAI,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC;IAE3E,MAAM,YAAY,GAAG,2CAAgB,CAAC,QAAQ,EAAE,CAAC,YAAY,CAAC;IAC9D,IAAI,CAAC,YAAY,EAAE,CAAC;QAClB,MAAM,mBAAmB,GAAG,IAAI,KAAK,CAAC,IAAA,6BAAe,EAAC,uBAAS,CAAC,+BAA+B,CAAC,CAAC,CAAC;QAClG,2CAAgB,CAAC,QAAQ,CAAC,mBAAmB,EAAE,gBAAgB,EAAE;YAC/D,YAAY,EAAE,MAAM,CAAC,wBAAY,CAAC,iCAAiC,CAAC;YACpE,SAAS,EAAE,uBAAS,CAAC,+BAA+B;SACrD,CAAC,CAAC;QACH,2CAAgB,CAAC,QAAQ,CAAC,2CAA2C,EAAE,mBAAmB,EAAE;YAC1F,UAAU,EAAE,uBAAS,CAAC,+BAA+B;YACrD,cAAc,EAAE,YAAY;YAC5B,YAAY,EAAE,WAAW;SAC1B,CAAC,CAAC;QACH,MAAM,mBAAmB,CAAC;IAC5B,CAAC;IAED,IAAI,CAAC;QACH,2CAAgB,CAAC,QAAQ,CAAC,KAAK,EAAE,gBAAgB,EAAE;YACjD,YAAY,EAAE,qBAAqB;YACnC,SAAS,EAAE,uBAAS,CAAC,wBAAwB;SAC9C,CAAC,CAAC;QAEH,MAAM,OAAO,GAAG,GAAG,QAAQ,6BAA6B,YAAY,EAAE,CAAC;QACvE,MAAM,SAAS,GAAG,2BAA2B,CAAC,YAAY,EAAE,mBAAmB,CAAC,CAAC;QAEjF,MAAM,SAAS,GAAG,SAAS,CAAC,CAAC,CAAC,gBAAgB,SAAS,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;QACjE,MAAM,YAAY,GAAG,IAAA,4DAAoC,EACvD,0CAA0C;YAC1C,YAAY,SAAS,KAAK,YAAY,IAAI;YAC1C,oBAAoB,qBAAqB,GAAG,SAAS,IAAI;YACzD,aAAa,QAAQ,MAAM;YAC3B,cAAc,WAAW,IAAI,SAAS,IAAI;YAC1C,uBAAuB,YAAY,MAAM;YACzC,CAAC,YAAY,CAAC,CAAC,CAAC,iBAAiB,YAAY,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,EACzD,oBAAoB,WAAW,IAAI,iBAAiB,EAAE,EACtD,OAAO,CACR,CAAC;QAEF,MAAM,CAAC,WAAW,EAAE,YAAY,CAAC,GAAG,MAAM,OAAO,CAAC,UAAU,CAAC;YAC3D,SAAS,CAAC,CAAC,CAAC,IAAA,0CAAkB,EAAC,YAAY,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,OAAO,EAAE;YAChE,IAAA,oDAAuB,EACrB;gBACE,MAAM,EAAE,sCAA0B,CAAC,QAAQ;gBAC3C,GAAG,CAAC,wBAAwB,IAAI,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC;gBACrD,cAAc,EAAE;oBACd,MAAM,EAAE,8BAAkB,CAAC,KAAK;oBAChC,YAAY,EAAE,YAAY;oBAC1B,gBAAgB,EAAE,qBAAqB;oBACvC,SAAS,EAAE,eAAK,CAAC,GAAG,EAAE,CAAC,WAAW,EAAE;iBACP;gBAC/B,GAAG,CAAC,qBAAqB,IAAI,EAAE,YAAY,EAAE,qBAAqB,EAAE,CAAC;aACtE,EACD,YAAY,EACZ,QAAQ,EACR,MAAM,CACP;SACF,CAAC,CAAC;QAEH,IAAI,WAAW,CAAC,MAAM,KAAK,UAAU,EAAE,CAAC;YACtC,2CAAgB,CAAC,UAAU,CAAC,2BAA2B,EAAE,2BAA2B,EAAE;gBACpF,WAAW,EAAE,2BAA2B;gBACxC,eAAe,EAAE,gBAAgB;gBACjC,eAAe,EAAE,UAAU;gBAC3B,WAAW,EAAE,uBAAS,CAAC,mBAAmB;gBAC1C,IAAI,EAAE;oBACJ,UAAU,EAAE,uBAAS,CAAC,mBAAmB;oBACzC,cAAc,EAAE,YAAY;oBAC5B,WAAW,EAAE,IAAA,wBAAa,EAAC,WAAW,CAAC,MAAa,CAAC;iBACtD;aACF,CAAC,CAAC;QACL,CAAC;QAED,IAAI,YAAY,CAAC,MAAM,KAAK,UAAU,EAAE,CAAC;YACvC,MAAM,kBAAkB,GAAG,IAAA,wBAAa,EAAC,YAAY,CAAC,MAAa,CAAQ,CAAC;YAC5E,MAAM,kBAAkB,GAAG,kBAAkB,CAAC,YAAY,CAAC;YAC3D,2CAAgB,CAAC,QAAQ,CACvB,wCAAwC,kBAAkB,CAAC,OAAO,GAAG,kBAAkB,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,SAAS,CAAC,kBAAkB,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,EAAE,EAC3I,SAAS,EACT;gBACE,UAAU,EAAE,uBAAS,CAAC,2BAA2B;gBACjD,cAAc,EAAE,YAAY;gBAC5B,YAAY,EAAE,kBAAkB;aACjC,CACF,CAAC;QACJ,CAAC;IAEH,CAAC;IAAC,OAAO,oBAAoB,EAAE,CAAC;QAC9B,MAAM,gBAAgB,GACpB,oBAAoB,YAAY,KAAK;YACnC,CAAC,CAAC,oBAAoB,CAAC,OAAO;YAC9B,CAAC,CAAC,MAAM,CAAC,oBAAoB,CAAC,CAAC;QAEnC,MAAM,aAAa,GAAG,oBAAoB,YAAY,KAAK;YACzD,CAAC,CAAC,oBAAoB;YACtB,CAAC,CAAC,IAAI,KAAK,CAAC,MAAM,CAAC,oBAAoB,CAAC,CAAC,CAAC;QAC5C,2CAAgB,CAAC,QAAQ,CAAC,aAAa,EAAE,wBAAwB,EAAE;YACjE,YAAY,EAAE,MAAM,CAAC,wBAAY,CAAC,iCAAiC,CAAC;YACpE,SAAS,EAAE,uBAAS,CAAC,sBAAsB;SAC5C,CAAC,CAAC;QACH,2CAAgB,CAAC,QAAQ,CAAC,0BAA0B,gBAAgB,EAAE,EAAE,aAAa,EAAE;YACrF,UAAU,EAAE,uBAAS,CAAC,sBAAsB;YAC5C,YAAY,EAAE,WAAW;YACzB,cAAc,EAAE,YAAY;YAC5B,mBAAmB,EAAE,SAAS;YAC9B,cAAc,EAAE,gBAAgB;SACjC,CAAC,CAAC;QAEH,MAAM,KAAK,CAAC;IACd,CAAC;AACH,CAAC"}
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|
@@ -31,14 +31,9 @@ function maxParsingErrorSeverity(a, b) {
|
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|
31
31
|
}
|
|
32
32
|
function getMutableState() {
|
|
33
33
|
const requestId = (0, processingLogger_service_1.getCurrentRequestId)();
|
|
34
|
-
if (requestId == null)
|
|
35
|
-
return
|
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36
|
-
|
|
37
|
-
const state = parsingErrorStateRegistry.get(requestId);
|
|
38
|
-
if (state === undefined) {
|
|
39
|
-
return createEmptyParsingErrorState();
|
|
40
|
-
}
|
|
41
|
-
return state;
|
|
34
|
+
if (requestId == null)
|
|
35
|
+
return null;
|
|
36
|
+
return parsingErrorStateRegistry.get(requestId) ?? null;
|
|
42
37
|
}
|
|
43
38
|
/** Maps a LocalParsingError to a single processingLogger call (severity → warning/error). */
|
|
44
39
|
function syncToProcessingLogger(localError) {
|
|
@@ -111,19 +106,24 @@ class ParsingErrorService {
|
|
|
111
106
|
originalExam: details?.originalExam,
|
|
112
107
|
timestamp: new Date(),
|
|
113
108
|
};
|
|
114
|
-
getMutableState()
|
|
109
|
+
const state = getMutableState();
|
|
110
|
+
if (state === null) {
|
|
111
|
+
processingLogger_service_1.processingLogger.logError('parsingErrorService.record() called outside request scope — Layer 1/2 skipped', undefined, { errorType });
|
|
112
|
+
return localError;
|
|
113
|
+
}
|
|
114
|
+
state.localErrors.push(localError);
|
|
115
115
|
syncToProcessingLogger(localError);
|
|
116
116
|
return localError;
|
|
117
117
|
}
|
|
118
118
|
getLocalErrors() {
|
|
119
|
-
return [...getMutableState()
|
|
119
|
+
return [...(getMutableState()?.localErrors ?? [])];
|
|
120
120
|
}
|
|
121
121
|
// --- Layer 1 outputs (not persisted to Core) ---
|
|
122
122
|
getAggregatedNotes() {
|
|
123
|
-
return (0, errorHandling_service_1.aggregateMessages)(localErrorsToErrorMessages(getMutableState()
|
|
123
|
+
return (0, errorHandling_service_1.aggregateMessages)(localErrorsToErrorMessages(getMutableState()?.localErrors ?? [], 'notes'), 'notes');
|
|
124
124
|
}
|
|
125
125
|
getAggregatedSlack() {
|
|
126
|
-
return (0, errorHandling_service_1.aggregateMessages)(localErrorsToErrorMessages(getMutableState()
|
|
126
|
+
return (0, errorHandling_service_1.aggregateMessages)(localErrorsToErrorMessages(getMutableState()?.localErrors ?? [], 'slack'), 'slack');
|
|
127
127
|
}
|
|
128
128
|
async sendSlackIfNeeded(ohapiUrl, partnerName, fileUploadId) {
|
|
129
129
|
const slackText = this.getAggregatedSlack();
|
|
@@ -132,7 +132,8 @@ class ParsingErrorService {
|
|
|
132
132
|
}
|
|
133
133
|
const fileUrl = `${ohapiUrl}/data-import/file-uploads/${fileUploadId}`;
|
|
134
134
|
const slackMsg = (0, slackMessages_service_1.getSlackFileIssueNotificationMessage)(slackText, `AgnosticParser [${partnerName}]`, fileUrl);
|
|
135
|
-
|
|
135
|
+
const messageBlock = slackMsg.blocks[3];
|
|
136
|
+
if (messageBlock?.text?.text?.trim()) {
|
|
136
137
|
await (0, slackMessages_service_1.sendMessageToSlack)(slackMsg);
|
|
137
138
|
}
|
|
138
139
|
}
|
|
@@ -142,7 +143,7 @@ class ParsingErrorService {
|
|
|
142
143
|
* Technical message → occurrence snapshot; clientMessage → profile message.
|
|
143
144
|
*/
|
|
144
145
|
buildCorePayloads(ctx) {
|
|
145
|
-
const localErrors = getMutableState()
|
|
146
|
+
const localErrors = getMutableState()?.localErrors ?? [];
|
|
146
147
|
if (localErrors.length === 0) {
|
|
147
148
|
return [];
|
|
148
149
|
}
|
|
@@ -203,7 +204,7 @@ class ParsingErrorService {
|
|
|
203
204
|
*/
|
|
204
205
|
async flushToCoreSafe() {
|
|
205
206
|
const state = getMutableState();
|
|
206
|
-
if (state.localErrors.length === 0) {
|
|
207
|
+
if (!state || state.localErrors.length === 0) {
|
|
207
208
|
return;
|
|
208
209
|
}
|
|
209
210
|
const loggerState = processingLogger_service_1.processingLogger.getState();
|
|
@@ -235,7 +236,9 @@ class ParsingErrorService {
|
|
|
235
236
|
}
|
|
236
237
|
}
|
|
237
238
|
clear() {
|
|
238
|
-
getMutableState()
|
|
239
|
+
const state = getMutableState();
|
|
240
|
+
if (state)
|
|
241
|
+
state.localErrors.length = 0;
|
|
239
242
|
}
|
|
240
243
|
}
|
|
241
244
|
exports.parsingErrorService = new ParsingErrorService();
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"parsingErrorService.service.js","sourceRoot":"","sources":["../../service/parsingErrorService.service.ts"],"names":[],"mappings":";;;
|
|
1
|
+
{"version":3,"file":"parsingErrorService.service.js","sourceRoot":"","sources":["../../service/parsingErrorService.service.ts"],"names":[],"mappings":";;;AAuUA,oEAIC;AAED,sEAEC;AA/UD;;;;;;;GAOG;AACH,sDAY8B;AAC9B,oDAA2E;AAC3E,yEAKoC;AAEpC,mEAA4D;AAC5D,mEAGiC;AAMjC,8EAA8E;AAC9E,MAAM,yBAAyB,GAAG,IAAI,GAAG,EAA6B,CAAC;AAEvE,SAAS,4BAA4B;IACnC,OAAO,EAAE,WAAW,EAAE,EAAE,EAAE,CAAC;AAC7B,CAAC;AAED,MAAM,aAAa,GAAyC;IAC1D,OAAO,EAAE,CAAC;IACV,KAAK,EAAE,CAAC;IACR,QAAQ,EAAE,CAAC;CACZ,CAAC;AAEF,SAAS,uBAAuB,CAC9B,CAAuB,EACvB,CAAuB;IAEvB,OAAO,aAAa,CAAC,CAAC,CAAC,IAAI,aAAa,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;AACtD,CAAC;AAED,SAAS,eAAe;IACtB,MAAM,SAAS,GAAG,IAAA,8CAAmB,GAAE,CAAC;IACxC,IAAI,SAAS,IAAI,IAAI;QAAE,OAAO,IAAI,CAAC;IACnC,OAAO,yBAAyB,CAAC,GAAG,CAAC,SAAS,CAAC,IAAI,IAAI,CAAC;AAC1D,CAAC;AAED,6FAA6F;AAC7F,SAAS,sBAAsB,CAAC,UAA6B;IAC3D,MAAM,OAAO,GAAG,mCAAqB,CAAC,UAAU,CAAC,SAAS,CAAC,CAAC;IAC5D,IAAI,UAAU,CAAC,QAAQ,KAAK,UAAU,EAAE,CAAC;QACvC,MAAM,YAAY,GAAG,UAAU,CAAC,YAAY,IAAI,OAAO,CAAC,YAAY,CAAC;QACrE,2CAAgB,CAAC,QAAQ,CAAC,IAAI,KAAK,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,UAAU,CAAC,YAAY,EAAE;YAChF,YAAY;YACZ,SAAS,EAAE,UAAU,CAAC,SAAS;SAChC,CAAC,CAAC;QACH,OAAO;IACT,CAAC;IAED,MAAM,eAAe,GAAG,UAAU,CAAC,QAAQ,KAAK,OAAO,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,MAAM,CAAC;IAC9E,2CAAgB,CAAC,UAAU,CAAC,UAAU,CAAC,OAAO,EAAE,UAAU,CAAC,YAAY,EAAE;QACvE,WAAW,EAAE,OAAO,CAAC,WAAW,IAAI,eAAe;QACnD,eAAe,EAAE,OAAO,CAAC,eAAe,IAAI,SAAS;QACrD,eAAe;QACf,IAAI,EAAE,UAAU,CAAC,UAAU;QAC3B,WAAW,EAAE,UAAU,CAAC,SAAS;KAClC,CAAC,CAAC;AACL,CAAC;AAED,iFAAiF;AACjF,SAAS,0BAA0B,CACjC,WAAgC,EAChC,OAAiC;IAEjC,OAAO,WAAW;SACf,MAAM,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,YAAY,CAAC,OAAO,CAAC,CAAC;SAC9C,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC;QACf,WAAW,EAAE,KAAK,CAAC,YAAY;QAC/B,OAAO,EAAE,KAAK,CAAC,OAAO;QACtB,IAAI,EAAE,KAAK,CAAC,IAAI;KACjB,CAAC,CAAC,CAAC;AACR,CAAC;AAED,MAAM,mBAAmB;IACvB,wEAAwE;IACxE,gBAAgB,CAAC,SAAiB;QAChC,yBAAyB,CAAC,GAAG,CAAC,SAAS,EAAE,4BAA4B,EAAE,CAAC,CAAC;IAC3E,CAAC;IAED,iBAAiB,CAAC,SAAiB;QACjC,yBAAyB,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC;IAC9C,CAAC;IAED;;;OAGG;IACH,MAAM,CACJ,SAA2B,EAC3B,OAAmC,EACnC,OAAmC;QAEnC,MAAM,OAAO,GAAG,mCAAqB,CAAC,SAAS,CAAC,CAAC;QACjD,MAAM,QAAQ,GAAG,OAAO,EAAE,QAAQ,IAAI,OAAO,CAAC,QAAQ,CAAC;QACvD,MAAM,YAAY,GAAG,OAAO,EAAE,YAAY,IAAI,OAAO,CAAC,YAAY,CAAC;QACnE,MAAM,UAAU,GAAG,IAAA,2CAA6B,EAAC,OAAO,CAAC,UAAU,EAAE,OAAO,CAAC,CAAC;QAC9E,MAAM,OAAO,GAAG,IAAA,sCAAwB,EAAC,OAAO,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;QACnE,MAAM,YAAY,GAAG,OAAO,EAAE,YAAY,IAAI,OAAO,CAAC,YAAY,CAAC;QAEnE,MAAM,YAAY,GAAgB;YAChC,KAAK,EAAE,OAAO,EAAE,WAAW,IAAI,OAAO,EAAE,YAAY,EAAE,KAAK,IAAI,OAAO,CAAC,YAAY,CAAC,KAAK;YACzF,KAAK,EAAE,OAAO,EAAE,WAAW,IAAI,OAAO,EAAE,YAAY,EAAE,KAAK,IAAI,OAAO,CAAC,YAAY,CAAC,KAAK;YACzF,EAAE,EAAE,OAAO,EAAE,QAAQ,IAAI,OAAO,EAAE,YAAY,EAAE,EAAE,IAAI,OAAO,CAAC,YAAY,CAAC,EAAE;SAC9E,CAAC;QAEF,MAAM,UAAU,GAAsB;YACpC,SAAS;YACT,QAAQ;YACR,OAAO;YACP,aAAa,EAAE,OAAO,CAAC,aAAa;YACpC,YAAY;YACZ,UAAU;YACV,IAAI,EAAE,OAAO,EAAE,IAAI;YACnB,YAAY;YACZ,YAAY;YACZ,WAAW,EAAE,OAAO,EAAE,WAAW;YACjC,aAAa,EAAE,OAAO,EAAE,aAAa;YACrC,UAAU,EAAE,OAAO,EAAE,UAAU;YAC/B,OAAO,EAAE,OAAO,EAAE,OAAO;YACzB,YAAY,EAAE,OAAO,EAAE,YAAY;YACnC,SAAS,EAAE,IAAI,IAAI,EAAE;SACtB,CAAC;QAEF,MAAM,KAAK,GAAG,eAAe,EAAE,CAAC;QAChC,IAAI,KAAK,KAAK,IAAI,EAAE,CAAC;YACnB,2CAAgB,CAAC,QAAQ,CACvB,+EAA+E,EAC/E,SAAS,EACT,EAAE,SAAS,EAAE,CACd,CAAC;YACF,OAAO,UAAU,CAAC;QACpB,CAAC;QAED,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;QACnC,sBAAsB,CAAC,UAAU,CAAC,CAAC;QACnC,OAAO,UAAU,CAAC;IACpB,CAAC;IAED,cAAc;QACZ,OAAO,CAAC,GAAG,CAAC,eAAe,EAAE,EAAE,WAAW,IAAI,EAAE,CAAC,CAAC,CAAC;IACrD,CAAC;IAED,kDAAkD;IAElD,kBAAkB;QAChB,OAAO,IAAA,yCAAiB,EAAC,0BAA0B,CAAC,eAAe,EAAE,EAAE,WAAW,IAAI,EAAE,EAAE,OAAO,CAAC,EAAE,OAAO,CAAC,CAAC;IAC/G,CAAC;IAED,kBAAkB;QAChB,OAAO,IAAA,yCAAiB,EAAC,0BAA0B,CAAC,eAAe,EAAE,EAAE,WAAW,IAAI,EAAE,EAAE,OAAO,CAAC,EAAE,OAAO,CAAC,CAAC;IAC/G,CAAC;IAED,KAAK,CAAC,iBAAiB,CAAC,QAAgB,EAAE,WAAmB,EAAE,YAAoB;QACjF,MAAM,SAAS,GAAG,IAAI,CAAC,kBAAkB,EAAE,CAAC;QAC5C,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,EAAE,CAAC;YACtB,OAAO;QACT,CAAC;QAED,MAAM,OAAO,GAAG,GAAG,QAAQ,6BAA6B,YAAY,EAAE,CAAC;QACvE,MAAM,QAAQ,GAAG,IAAA,4DAAoC,EACnD,SAAS,EACT,mBAAmB,WAAW,GAAG,EACjC,OAAO,CACR,CAAC;QACF,MAAM,YAAY,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;QACxC,IAAI,YAAY,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE,CAAC;YACrC,MAAM,IAAA,0CAAkB,EAAC,QAAQ,CAAC,CAAC;QACrC,CAAC;IACH,CAAC;IAED,kEAAkE;IAElE;;;OAGG;IACH,iBAAiB,CAAC,GAAsB;QACtC,MAAM,WAAW,GAAG,eAAe,EAAE,EAAE,WAAW,IAAI,EAAE,CAAC;QACzD,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,OAAO,EAAE,CAAC;QACZ,CAAC;QAED,MAAM,MAAM,GAAG,IAAI,GAAG,EAA+B,CAAC;QACtD,KAAK,MAAM,KAAK,IAAI,WAAW,EAAE,CAAC;YAChC,MAAM,GAAG,GAAG,GAAG,KAAK,CAAC,SAAS,KAAK,KAAK,CAAC,UAAU,EAAE,CAAC;YACtD,MAAM,KAAK,GAAG,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;YAC9B,IAAI,KAAK,EAAE,CAAC;gBACV,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;YACpB,CAAC;iBAAM,CAAC;gBACN,MAAM,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC;YAC3B,CAAC;QACH,CAAC;QAED,MAAM,YAAY,GAAG,GAAG,CAAC,YAAY,IAAI,0BAA0B,CAAC;QACpE,MAAM,QAAQ,GAA0B,EAAE,CAAC;QAE3C,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,MAAM,EAAE,EAAE,CAAC;YACpC,MAAM,cAAc,GAAG,KAAK,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;YAC/C,MAAM,QAAQ,GAAG,KAAK,CAAC,MAAM,CAC3B,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,uBAAuB,CAAC,GAAG,EAAE,KAAK,CAAC,QAAQ,CAAC,EAC5D,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,CAClB,CAAC;YACF,MAAM,SAAS,GAAqC,KAAK,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC;gBACxE,sBAAsB,EAAE,YAAY;gBACpC,OAAO,EAAE,KAAK,CAAC,OAAO;gBACtB,YAAY,EAAE,KAAK,CAAC,YAAY;gBAChC,QAAQ,EAAE,KAAK,CAAC,QAAQ;gBACxB,YAAY,EAAE,KAAK,CAAC,YAAY,IAAI,IAAI;gBACxC,UAAU,EAAE,KAAK,CAAC,UAAU;gBAC5B,UAAU,EAAE,KAAK,CAAC,SAAS,CAAC,WAAW,EAAE;aAC1C,CAAC,CAAC,CAAC;YAEJ,MAAM,OAAO,GAAwB;gBACnC,UAAU,EAAE,cAAc,CAAC,UAAU;gBACrC,SAAS,EAAE,cAAc,CAAC,SAAS;gBACnC,QAAQ;gBACR,OAAO,EAAE,cAAc,CAAC,aAAa;gBACrC,YAAY,EAAE,cAAc,CAAC,YAAY;gBACzC,YAAY,EAAE,cAAc,CAAC,YAAY,IAAI,IAAI;gBACjD,WAAW,EAAE,cAAc,CAAC,WAAW;gBACvC,aAAa,EAAE,cAAc,CAAC,aAAa;gBAC3C,UAAU,EAAE,cAAc,CAAC,UAAU;gBACrC,OAAO,EAAE,cAAc,CAAC,OAAO;gBAC/B,YAAY,EAAE,cAAc,CAAC,YAAY;gBACzC,MAAM,EAAE,gBAAgB;gBACxB,gBAAgB,EAAE,GAAG,CAAC,gBAAgB;aACvC,CAAC;YAEF,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBACvB,OAAO,CAAC,UAAU,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC;YACpC,CAAC;iBAAM,CAAC;gBACN,OAAO,CAAC,WAAW,GAAG,SAAS,CAAC;gBAChC,OAAO,CAAC,gBAAgB,GAAG,KAAK,CAAC,MAAM,CAAC;YAC1C,CAAC;YAED,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;QACzB,CAAC;QAED,OAAO,QAAQ,CAAC;IAClB,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,eAAe;QACnB,MAAM,KAAK,GAAG,eAAe,EAAE,CAAC;QAChC,IAAI,CAAC,KAAK,IAAI,KAAK,CAAC,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7C,OAAO;QACT,CAAC;QAED,MAAM,WAAW,GAAG,2CAAgB,CAAC,QAAQ,EAAE,CAAC;QAChD,MAAM,SAAS,GAAG,WAAW,CAAC,SAAS,CAAC;QACxC,MAAM,SAAS,GAAG,WAAW,CAAC,SAAS,IAAI,KAAK,CAAC;QACjD,IAAI,CAAC,SAAS,IAAI,SAAS,EAAE,CAAC;YAC5B,OAAO;QACT,CAAC;QAED,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,gCAAgC,CAAC;QAC5D,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,2CAAgB,CAAC,QAAQ,CACvB,gFAAgF,EAChF,SAAS,EACT,EAAE,UAAU,EAAE,SAAS,EAAE,CAC1B,CAAC;YACF,OAAO;QACT,CAAC;QAED,MAAM,GAAG,GAAsB;YAC7B,YAAY,EAAE,WAAW,CAAC,YAAY;YACtC,SAAS;YACT,gBAAgB,EAAE,WAAW,CAAC,gBAAgB;YAC9C,SAAS;SACV,CAAC;QAEF,IAAI,CAAC;YACH,MAAM,QAAQ,GAAG,IAAI,CAAC,iBAAiB,CAAC,GAAG,CAAC,CAAC;YAC7C,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBAC1B,OAAO;YACT,CAAC;YACD,MAAM,IAAA,+CAAmC,EAAC,SAAS,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAC;QACzE,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,2CAAgB,CAAC,QAAQ,CACvB,gDAAgD,EAChD,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,EAC1C,EAAE,UAAU,EAAE,SAAS,EAAE,CAC1B,CAAC;QACJ,CAAC;IACH,CAAC;IAED,KAAK;QACH,MAAM,KAAK,GAAG,eAAe,EAAE,CAAC;QAChC,IAAI,KAAK;YAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;IAC1C,CAAC;CACF;AAEY,QAAA,mBAAmB,GAAG,IAAI,mBAAmB,EAAE,CAAC;AAE7D,oEAAoE;AACpE,SAAgB,4BAA4B,CAAC,OAA0B;IACrE,MAAM,SAAS,GAAG,IAAA,kDAAuB,EAAC,OAAO,CAAC,CAAC;IACnD,2BAAmB,CAAC,gBAAgB,CAAC,SAAS,CAAC,CAAC;IAChD,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,SAAgB,6BAA6B,CAAC,SAAiB;IAC7D,2BAAmB,CAAC,iBAAiB,CAAC,SAAS,CAAC,CAAC;AACnD,CAAC"}
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import { RejectReason } from './oht.types';
|
|
1
|
+
import { OhtExam, OriginalExam, RejectReason } from './oht.types';
|
|
2
2
|
export type ParsingWarningCategory = 'patient_data' | 'mapping' | 'measurements' | 'ingestion' | 'infrastructure' | 'general';
|
|
3
3
|
export interface Destination {
|
|
4
4
|
slack: boolean;
|
|
@@ -24,6 +24,7 @@ export declare enum ParsingErrorType {
|
|
|
24
24
|
REJECTED_UNDERAGE_PATIENT = "REJECTED_UNDERAGE_PATIENT",
|
|
25
25
|
REJECTED_MISSING_PATIENT_ID = "REJECTED_MISSING_PATIENT_ID",
|
|
26
26
|
REJECTED_MISSING_PATIENT_SEX = "REJECTED_MISSING_PATIENT_SEX",
|
|
27
|
+
REJECTED_UNKNOWN = "REJECTED_UNKNOWN",
|
|
27
28
|
FATAL_VALIDATION = "FATAL_VALIDATION",
|
|
28
29
|
FATAL_NORMALIZATION = "FATAL_NORMALIZATION",
|
|
29
30
|
FATAL_FILE_IO = "FATAL_FILE_IO",
|
|
@@ -54,8 +55,8 @@ export interface LocalParsingError {
|
|
|
54
55
|
biomarkerId?: number;
|
|
55
56
|
biomarkerName?: string;
|
|
56
57
|
errorTrace?: Record<string, unknown>;
|
|
57
|
-
ohtExam?:
|
|
58
|
-
originalExam?:
|
|
58
|
+
ohtExam?: OhtExam;
|
|
59
|
+
originalExam?: OriginalExam;
|
|
59
60
|
timestamp: Date;
|
|
60
61
|
}
|
|
61
62
|
export interface ParsingErrorOccurrenceSnapshot {
|
|
@@ -77,8 +78,8 @@ export interface ErrorProfilePayload {
|
|
|
77
78
|
biomarkerId?: number;
|
|
78
79
|
biomarkerName?: string;
|
|
79
80
|
errorTrace?: Record<string, unknown>;
|
|
80
|
-
ohtExam?:
|
|
81
|
-
originalExam?:
|
|
81
|
+
ohtExam?: OhtExam;
|
|
82
|
+
originalExam?: OriginalExam;
|
|
82
83
|
source: string;
|
|
83
84
|
uploadedByUserId?: string;
|
|
84
85
|
occurrence?: ParsingErrorOccurrenceSnapshot;
|
|
@@ -95,8 +96,8 @@ export interface RecordParsingErrorDetails {
|
|
|
95
96
|
biomarkerId?: number;
|
|
96
97
|
biomarkerName?: string;
|
|
97
98
|
errorTrace?: Record<string, unknown>;
|
|
98
|
-
ohtExam?:
|
|
99
|
-
originalExam?:
|
|
99
|
+
ohtExam?: OhtExam;
|
|
100
|
+
originalExam?: OriginalExam;
|
|
100
101
|
destinations?: Partial<Destination>;
|
|
101
102
|
severity?: ParsingErrorSeverity;
|
|
102
103
|
}
|
|
@@ -25,6 +25,7 @@ var ParsingErrorType;
|
|
|
25
25
|
ParsingErrorType["REJECTED_UNDERAGE_PATIENT"] = "REJECTED_UNDERAGE_PATIENT";
|
|
26
26
|
ParsingErrorType["REJECTED_MISSING_PATIENT_ID"] = "REJECTED_MISSING_PATIENT_ID";
|
|
27
27
|
ParsingErrorType["REJECTED_MISSING_PATIENT_SEX"] = "REJECTED_MISSING_PATIENT_SEX";
|
|
28
|
+
ParsingErrorType["REJECTED_UNKNOWN"] = "REJECTED_UNKNOWN";
|
|
28
29
|
ParsingErrorType["FATAL_VALIDATION"] = "FATAL_VALIDATION";
|
|
29
30
|
ParsingErrorType["FATAL_NORMALIZATION"] = "FATAL_NORMALIZATION";
|
|
30
31
|
ParsingErrorType["FATAL_FILE_IO"] = "FATAL_FILE_IO";
|
|
@@ -188,6 +189,15 @@ exports.PARSING_ERROR_CATALOG = {
|
|
|
188
189
|
destinations: { slack: true, notes: false, bi: false },
|
|
189
190
|
pipelineStep: 'create_report_with_patient',
|
|
190
191
|
},
|
|
192
|
+
[ParsingErrorType.REJECTED_UNKNOWN]: {
|
|
193
|
+
severity: 'critical',
|
|
194
|
+
message: 'File rejected: unknown reason.',
|
|
195
|
+
clientMessage: 'Processing could not be completed. Please try again or contact support.',
|
|
196
|
+
contextKey: 'custom:rejectedUnknown',
|
|
197
|
+
rejectReason: oht_types_1.RejectReason.PROCESSING_COULD_NOT_BE_COMPLETED,
|
|
198
|
+
destinations: { slack: false, notes: true, bi: false },
|
|
199
|
+
pipelineStep: 'create_report_with_patient',
|
|
200
|
+
},
|
|
191
201
|
[ParsingErrorType.FATAL_VALIDATION]: {
|
|
192
202
|
severity: 'critical',
|
|
193
203
|
message: 'Validation failed:',
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
|
@@ -381,6 +381,8 @@ export declare enum RejectReason {
|
|
|
381
381
|
INCOMPLETE_DATA = "Incomplete Data (ie. missing units)",
|
|
382
382
|
NOT_AN_OFFICIAL_REPORT = "Not An Official Report",
|
|
383
383
|
INVALID_DATA_FORMAT = "Invalid Data Format [expected: {expectedFormat}, received: {receivedFormat}]",
|
|
384
|
+
/** Scalar metadata/patient field contains multiple values (e.g. multi-patient/batch source file). */
|
|
385
|
+
DUPLICATE_FIELD_VALUE = "Duplicated field value",
|
|
384
386
|
/** File could not be parsed or content is invalid (client-facing, no system detail). */
|
|
385
387
|
INVALID_FILE_CONTENT = "Invalid file content or format",
|
|
386
388
|
/** Generic client-facing message for internal/system failures. Do not expose system details. */
|
package/dist/types/oht.types.js
CHANGED
|
@@ -74,6 +74,8 @@ var RejectReason;
|
|
|
74
74
|
RejectReason["INCOMPLETE_DATA"] = "Incomplete Data (ie. missing units)";
|
|
75
75
|
RejectReason["NOT_AN_OFFICIAL_REPORT"] = "Not An Official Report";
|
|
76
76
|
RejectReason["INVALID_DATA_FORMAT"] = "Invalid Data Format [expected: {expectedFormat}, received: {receivedFormat}]";
|
|
77
|
+
/** Scalar metadata/patient field contains multiple values (e.g. multi-patient/batch source file). */
|
|
78
|
+
RejectReason["DUPLICATE_FIELD_VALUE"] = "Duplicated field value";
|
|
77
79
|
/** File could not be parsed or content is invalid (client-facing, no system detail). */
|
|
78
80
|
RejectReason["INVALID_FILE_CONTENT"] = "Invalid file content or format";
|
|
79
81
|
/** Generic client-facing message for internal/system failures. Do not expose system details. */
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"oht.types.js","sourceRoot":"","sources":["../../types/oht.types.ts"],"names":[],"mappings":";;;AAiWA,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;AAED,IAAY,
|
|
1
|
+
{"version":3,"file":"oht.types.js","sourceRoot":"","sources":["../../types/oht.types.ts"],"names":[],"mappings":";;;AAiWA,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;AAED,IAAY,YAsBX;AAtBD,WAAY,YAAY;IACtB,mFAAmE,CAAA;IACnE,uDAAuC,CAAA;IACvC,+DAA+C,CAAA;IAC/C,mDAAmC,CAAA;IACnC,iEAAiD,CAAA;IACjD,uDAAuC,CAAA;IACvC,uDAAuC,CAAA;IACvC,6DAA6C,CAAA;IAC7C,2EAA2D,CAAA;IAC3D,2DAA2C,CAAA;IAC3C,uEAAuD,CAAA;IACvD,yDAAyC,CAAA;IACzC,uEAAuD,CAAA;IACvD,iEAAiD,CAAA;IACjD,oHAAoG,CAAA;IACpG,qGAAqG;IACrG,gEAAgD,CAAA;IAChD,wFAAwF;IACxF,uEAAuD,CAAA;IACvD,gGAAgG;IAChG,6HAA6G,CAAA;AAC/G,CAAC,EAtBW,YAAY,4BAAZ,YAAY,QAsBvB;AA0CD,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"}
|
|
@@ -47,7 +47,8 @@ const sensitivePrefixes = [
|
|
|
47
47
|
'patient',
|
|
48
48
|
'patientInfo',
|
|
49
49
|
'error.config',
|
|
50
|
-
'error.config.data'
|
|
50
|
+
'error.config.data',
|
|
51
|
+
'warning_data',
|
|
51
52
|
];
|
|
52
53
|
const sensitiveKeys = [
|
|
53
54
|
// Personal Info
|
|
@@ -95,8 +96,10 @@ const sensitiveKeys = [
|
|
|
95
96
|
// General IDs
|
|
96
97
|
'id',
|
|
97
98
|
'externalId',
|
|
98
|
-
// Document
|
|
99
|
+
// Document History
|
|
99
100
|
'action',
|
|
101
|
+
// Healthcare Data
|
|
102
|
+
'exam',
|
|
100
103
|
];
|
|
101
104
|
/**
|
|
102
105
|
* Returns dot-notated paths of sensitive fields for use with Pino's `redact.paths`.
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"sensitivePaths.js","sourceRoot":"","sources":["../../util-ts/sensitivePaths.ts"],"names":[],"mappings":";AAAA,kFAAkF;;;
|
|
1
|
+
{"version":3,"file":"sensitivePaths.js","sourceRoot":"","sources":["../../util-ts/sensitivePaths.ts"],"names":[],"mappings":";AAAA,kFAAkF;;;AAqL/C,8CAAiB;AAnLpD,MAAM,iBAAiB,GAAG;IACxB,EAAE;IACF,aAAa;IACb,kBAAkB;IAClB,sBAAsB;IACtB,kBAAkB;IAClB,0BAA0B;IAC1B,wBAAwB;IACxB,yBAAyB;IACzB,sBAAsB;IACtB,kCAAkC;IAClC,6BAA6B;IAC7B,wBAAwB;IACxB,6BAA6B;IAC7B,iBAAiB;IACjB,iBAAiB;IACjB,kBAAkB;IAClB,eAAe;IACf,2BAA2B;IAC3B,0BAA0B;IAC1B,sBAAsB;IACtB,sBAAsB;IACtB,kCAAkC;IAClC,UAAU;IACV,MAAM;IACN,aAAa;IACb,kBAAkB;IAClB,8BAA8B;IAC9B,cAAc;IACd,WAAW;IACX,uBAAuB;IACvB,kBAAkB;IAClB,QAAQ;IACR,aAAa;IACb,yBAAyB;IACzB,UAAU;IACV,qBAAqB;IACrB,kBAAkB;IAClB,YAAY;IACZ,wBAAwB;IACxB,aAAa;IACb,SAAS;IACT,aAAa;IACb,cAAc;IACd,mBAAmB;IACnB,cAAc;CACf,CAAC;AAEF,MAAM,aAAa,GAAG;IACpB,gBAAgB;IAChB,KAAK;IACL,eAAe;IACf,WAAW;IACX,WAAW;IACX,WAAW;IACX,UAAU;IACV,YAAY;IACZ,UAAU;IACV,OAAO;IACP,OAAO;IACP,SAAS;IACT,KAAK;IACL,QAAQ;IACR,MAAM;IAEN,gBAAgB;IAChB,UAAU;IACV,qBAAqB;IACrB,kBAAkB;IAClB,mBAAmB;IACnB,aAAa;IAEb,YAAY;IACZ,QAAQ;IACR,kBAAkB;IAClB,uBAAuB;IACvB,YAAY;IACZ,WAAW;IACX,YAAY;IACZ,OAAO;IACP,cAAc;IAEd,4BAA4B;IAC5B,QAAQ;IACR,eAAe;IACf,eAAe;IACf,OAAO;IACP,UAAU;IACV,SAAS;IACT,SAAS;IAET,+BAA+B;IAC/B,QAAQ;IACR,QAAQ;IACR,KAAK;IAEL,cAAc;IACd,IAAI;IACJ,YAAY;IAEZ,mBAAmB;IACnB,QAAQ;IAER,kBAAkB;IAClB,MAAM;CACP,CAAC;AACF;;;GAGG;AACH,SAAS,iBAAiB;IACxB,OAAO,iBAAiB,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,CACxC,aAAa,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,MAAM,IAAI,GAAG,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAC9D,CAAC;AACJ,CAAC;AAKD;;;GAGG;AACH,MAAM,wBAAwB,GAAG,CAAC,KAAsB,EAAmB,EAAE;IAC3E,IAAI,KAAK,IAAI,IAAI;QAAE,OAAO,KAAK,CAAC;IAEhC,MAAM,aAAa,GAAG,CAAC,GAAY,EAAqB,EAAE,CACxD,MAAM,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,iBAAiB,CAAC;IAE5D,MAAM,QAAQ,GAAG,CAAC,KAAgB,EAAa,EAAE;QAC/C,IAAI,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;YACzB,OAAO,KAAK,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;QAC7B,CAAC;QAED,IAAI,aAAa,CAAC,KAAK,CAAC,EAAE,CAAC;YACzB,OAAO,MAAM,CAAC,WAAW,CACvB,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE;gBACvC,IAAI,aAAa,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;oBAChC,OAAO,CAAC,GAAG,EAAE,YAAY,CAAC,CAAC;gBAC7B,CAAC;gBAED,IAAI,OAAO,GAAG,KAAK,QAAQ,EAAE,CAAC;oBAC5B,IAAI,CAAC;wBACH,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;wBAC/B,IAAI,OAAO,MAAM,KAAK,QAAQ,IAAI,MAAM,KAAK,IAAI,EAAE,CAAC;4BAClD,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;wBACjD,CAAC;oBACH,CAAC;oBAAC,MAAM,CAAC;wBACP,oBAAoB;oBACtB,CAAC;oBACD,OAAO,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC;gBACpB,CAAC;gBAED,IAAI,aAAa,CAAC,GAAG,CAAC,IAAI,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;oBAC7C,OAAO,CAAC,GAAG,EAAE,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC;gBAC9B,CAAC;gBAED,OAAO,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC;YACpB,CAAC,CAAC,CACH,CAAC;QACJ,CAAC;QAED,OAAO,KAAK,CAAC;IACf,CAAC,CAAC;IAEF,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;QAC9B,IAAI,CAAC;YACH,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC;YACjC,MAAM,SAAS,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC;YACnC,OAAO,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,CAAC;QACnC,CAAC;QAAC,MAAM,CAAC;YACP,OAAO,KAAK,CAAC;QACf,CAAC;IACH,CAAC;IAED,OAAO,QAAQ,CAAC,KAAmB,CAAe,CAAC;AACrD,CAAC,CAAC;AAGO,4DAAwB"}
|
package/package.json
CHANGED
|
@@ -1,59 +0,0 @@
|
|
|
1
|
-
import { LabToOhtContract, LabToOhtMapper, RangeExtractionResponse, SynonymUnit, UnknownUnits, TransformationRulesChains } from "../types/custom-parser.types";
|
|
2
|
-
import { Biomarker, BiomarkerValueType, Measurement, MeasurementValueComparator, PatientInfo, UnknownMeasurement, Exam } from "../types/oht.types";
|
|
3
|
-
/**
|
|
4
|
-
* Extracts unit from rawData (OhtExam object)
|
|
5
|
-
* @param rawData - OhtExam object (not a JSON string)
|
|
6
|
-
* @param ohtBiomarker - Biomarker information
|
|
7
|
-
* @param synonymUnits - Synonym units for unit resolution
|
|
8
|
-
* @param partnerId - Partner ID for synonym resolution
|
|
9
|
-
*/
|
|
10
|
-
declare function agnosticExtractUnit(rawData: any, ohtBiomarker: Biomarker, synonymUnits?: SynonymUnit[] | null, partnerId?: string | null | undefined): {
|
|
11
|
-
unit: string;
|
|
12
|
-
isUnitParsedCorrectly: boolean;
|
|
13
|
-
originalUnit: string;
|
|
14
|
-
isArbitraryUnit: boolean;
|
|
15
|
-
unknownUnit: string;
|
|
16
|
-
};
|
|
17
|
-
/**
|
|
18
|
-
* Extracts reference annotation from rawExam (OhtExam object)
|
|
19
|
-
* @param labToOhtMapper - Lab to OHT mapper configuration
|
|
20
|
-
* @param rawExam - OhtExam object (not a JSON string)
|
|
21
|
-
* @param patientInfo - Patient information
|
|
22
|
-
* @param documentDate - Document date
|
|
23
|
-
* @param exams - Array of exams for appended mappings
|
|
24
|
-
*/
|
|
25
|
-
declare function agnosticExtractReferenceAnnotation(labToOhtMapper: LabToOhtMapper, rawExam: any, patientInfo: PatientInfo, documentDate?: Date, exams?: Exam[]): string;
|
|
26
|
-
/**
|
|
27
|
-
* Extracts reference ranges from rawData (OhtExam object)
|
|
28
|
-
* Always uses parseRange function from extractionUtils for range extraction
|
|
29
|
-
*/
|
|
30
|
-
declare function agnosticExtractReferenceRanges(labToOhtMapper: LabToOhtMapper, rawData: any, patientInfo: PatientInfo, documentDate?: Date): RangeExtractionResponse;
|
|
31
|
-
declare function agnosticExtractValueFromGreaterLowerThan(value: string): {
|
|
32
|
-
extractedValue: number | null;
|
|
33
|
-
extractedValueComparator: MeasurementValueComparator | null;
|
|
34
|
-
valueParsedCorrectly: boolean;
|
|
35
|
-
};
|
|
36
|
-
/**
|
|
37
|
-
* Parses exam value from rawExamObj (OhtExam object)
|
|
38
|
-
* Now uses value directly from ohtExam
|
|
39
|
-
*/
|
|
40
|
-
declare function agnosticParseExamValue(rawExamObj: any, ohtBiomarker: Biomarker): {
|
|
41
|
-
valueType: BiomarkerValueType;
|
|
42
|
-
alphanumericalValue: string | null;
|
|
43
|
-
numberValue: number | null;
|
|
44
|
-
valueComparator: MeasurementValueComparator;
|
|
45
|
-
isValueParsedCorrectly: boolean;
|
|
46
|
-
};
|
|
47
|
-
declare function agnosticCheckValueForPlausibleValues(labToOhtMapper: LabToOhtMapper, ohtBiomarker: Biomarker, unit: string, value: number, isUnitParsedCorrectly: boolean): boolean;
|
|
48
|
-
type ApplyTransformationRulesResult = {
|
|
49
|
-
transformedExams: Exam[];
|
|
50
|
-
applicationErrorMessages: string[];
|
|
51
|
-
};
|
|
52
|
-
declare function ohtAgnosticMeasurementsExtractor(labToOhtContract: LabToOhtContract, exams: Exam[], transformationRules: TransformationRulesChains, ohtCoreApiKey: string, partnerId?: string | null | undefined): Promise<{
|
|
53
|
-
measurements: Measurement[];
|
|
54
|
-
unknownMeasurements: UnknownMeasurement[];
|
|
55
|
-
unknownUnits: UnknownUnits[];
|
|
56
|
-
isReportCorrectlyParsed: boolean;
|
|
57
|
-
transformationRulesErrors: string[];
|
|
58
|
-
}>;
|
|
59
|
-
export { ApplyTransformationRulesResult, ohtAgnosticMeasurementsExtractor, agnosticCheckValueForPlausibleValues, agnosticExtractReferenceRanges, agnosticExtractReferenceAnnotation, agnosticParseExamValue, agnosticExtractUnit, agnosticExtractValueFromGreaterLowerThan };
|
|
@@ -1,603 +0,0 @@
|
|
|
1
|
-
"use strict";
|
|
2
|
-
var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
3
|
-
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
|
-
};
|
|
5
|
-
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
|
-
exports.ohtAgnosticMeasurementsExtractor = ohtAgnosticMeasurementsExtractor;
|
|
7
|
-
exports.agnosticCheckValueForPlausibleValues = agnosticCheckValueForPlausibleValues;
|
|
8
|
-
exports.agnosticExtractReferenceRanges = agnosticExtractReferenceRanges;
|
|
9
|
-
exports.agnosticExtractReferenceAnnotation = agnosticExtractReferenceAnnotation;
|
|
10
|
-
exports.agnosticParseExamValue = agnosticParseExamValue;
|
|
11
|
-
exports.agnosticExtractUnit = agnosticExtractUnit;
|
|
12
|
-
exports.agnosticExtractValueFromGreaterLowerThan = agnosticExtractValueFromGreaterLowerThan;
|
|
13
|
-
const dataUtils_1 = require("../util-ts/dataUtils");
|
|
14
|
-
const regexUtils_1 = require("../util-ts/regexUtils");
|
|
15
|
-
const extractionUtils_1 = require("../util-ts/extractionUtils");
|
|
16
|
-
const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
|
|
17
|
-
const apiUtils_1 = require("../util-ts/apiUtils");
|
|
18
|
-
const oht_types_1 = require("../types/oht.types");
|
|
19
|
-
const transformationRules_service_1 = require("./transformationRules.service");
|
|
20
|
-
const auxiliaryFunctions_service_1 = require("./auxiliaryFunctions.service");
|
|
21
|
-
const logger = (0, pinoLogger_1.default)();
|
|
22
|
-
const OHT_CORE_URL = process.env.OHT_CORE_URL;
|
|
23
|
-
let filename = '';
|
|
24
|
-
/**
|
|
25
|
-
* Extracts unit from rawData (OhtExam object)
|
|
26
|
-
* @param rawData - OhtExam object (not a JSON string)
|
|
27
|
-
* @param ohtBiomarker - Biomarker information
|
|
28
|
-
* @param synonymUnits - Synonym units for unit resolution
|
|
29
|
-
* @param partnerId - Partner ID for synonym resolution
|
|
30
|
-
*/
|
|
31
|
-
function agnosticExtractUnit(rawData, ohtBiomarker, synonymUnits = null, partnerId = null) {
|
|
32
|
-
if (!(0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker)) {
|
|
33
|
-
return { unit: "None", isUnitParsedCorrectly: true, originalUnit: "", isArbitraryUnit: false, unknownUnit: '' };
|
|
34
|
-
}
|
|
35
|
-
const isArbitraryUnit = ohtBiomarker.acf.standardUnitArbUnitLogic === 'default';
|
|
36
|
-
let originalUnit = '';
|
|
37
|
-
// Use unit directly from ohtExam
|
|
38
|
-
const unit = rawData?.unit ?? '';
|
|
39
|
-
let unitLowerCase = unit?.toLowerCase();
|
|
40
|
-
unitLowerCase = unitLowerCase?.replaceAll(/ /g, '') ?? '';
|
|
41
|
-
const standardUnit = ohtBiomarker.acf.standardUnit;
|
|
42
|
-
const allBmOhtUnits = [
|
|
43
|
-
standardUnit?.toLowerCase(),
|
|
44
|
-
...ohtBiomarker.acf?.alternativeUnits
|
|
45
|
-
?.map((bmAlternative) => bmAlternative.name.toLowerCase()) ?? []
|
|
46
|
-
];
|
|
47
|
-
// If the biomarker uses an arbitrary unit, return standard unit and set the original unit as the unit extracted from the data
|
|
48
|
-
if (isArbitraryUnit) {
|
|
49
|
-
originalUnit = unit;
|
|
50
|
-
return { unit: standardUnit, isUnitParsedCorrectly: true, originalUnit: originalUnit, isArbitraryUnit: isArbitraryUnit, unknownUnit: '' };
|
|
51
|
-
}
|
|
52
|
-
// First test if the biomarker has the unit explicit in the 'unity' field
|
|
53
|
-
const allUnitContainsJsonUnit = allBmOhtUnits.includes(unitLowerCase);
|
|
54
|
-
if (unitLowerCase?.length > 0 && allUnitContainsJsonUnit) {
|
|
55
|
-
// Find the original case version from standardUnit or alternativeUnits
|
|
56
|
-
let matchedUnit = standardUnit?.toLowerCase().replaceAll(/ /g, '') === unitLowerCase
|
|
57
|
-
? standardUnit?.replaceAll(/ /g, '')
|
|
58
|
-
: ohtBiomarker.acf?.alternativeUnits?.find((bmAlternative) => bmAlternative.name.toLowerCase().replaceAll(/ /g, '') === unitLowerCase)?.name?.replaceAll(/ /g, '');
|
|
59
|
-
// Fallback to original unit if no match found (shouldn't happen, but safety check)
|
|
60
|
-
matchedUnit = matchedUnit || unit?.replaceAll(/ /g, '');
|
|
61
|
-
return {
|
|
62
|
-
unit: matchedUnit,
|
|
63
|
-
isUnitParsedCorrectly: true,
|
|
64
|
-
originalUnit: originalUnit,
|
|
65
|
-
isArbitraryUnit: isArbitraryUnit,
|
|
66
|
-
unknownUnit: ''
|
|
67
|
-
};
|
|
68
|
-
}
|
|
69
|
-
// Check if there are any Synonym configured
|
|
70
|
-
if (unitLowerCase?.length > 0) {
|
|
71
|
-
let resolvedUnit = null;
|
|
72
|
-
if (synonymUnits && synonymUnits.length > 0) {
|
|
73
|
-
const resolved = (0, dataUtils_1.resolveUnitFromSynonyms)(unitLowerCase, ohtBiomarker.id, partnerId, synonymUnits);
|
|
74
|
-
if (resolved.found && resolved.targetUnit) {
|
|
75
|
-
resolvedUnit = resolved.targetUnit;
|
|
76
|
-
}
|
|
77
|
-
}
|
|
78
|
-
if (resolvedUnit) {
|
|
79
|
-
const allUnitContainsJsonUnitSynonyms = allBmOhtUnits.includes(resolvedUnit.toLowerCase());
|
|
80
|
-
if (allUnitContainsJsonUnitSynonyms) {
|
|
81
|
-
return { unit: resolvedUnit, isUnitParsedCorrectly: true, originalUnit: originalUnit, isArbitraryUnit: isArbitraryUnit, unknownUnit: '' };
|
|
82
|
-
}
|
|
83
|
-
}
|
|
84
|
-
}
|
|
85
|
-
// if the unit didnt match any of the cases, add the unit to an unknownUnit list
|
|
86
|
-
return { unit: '', isUnitParsedCorrectly: false, originalUnit: '', isArbitraryUnit: false, unknownUnit: unit };
|
|
87
|
-
}
|
|
88
|
-
/**
|
|
89
|
-
* Extracts reference annotation from rawExam (OhtExam object)
|
|
90
|
-
* @param labToOhtMapper - Lab to OHT mapper configuration
|
|
91
|
-
* @param rawExam - OhtExam object (not a JSON string)
|
|
92
|
-
* @param patientInfo - Patient information
|
|
93
|
-
* @param documentDate - Document date
|
|
94
|
-
* @param exams - Array of exams for appended mappings
|
|
95
|
-
*/
|
|
96
|
-
function agnosticExtractReferenceAnnotation(labToOhtMapper, rawExam, patientInfo, documentDate, exams) {
|
|
97
|
-
let annotation = '';
|
|
98
|
-
// if it is an appended mapping, add the extracted values to annotation
|
|
99
|
-
if (labToOhtMapper?.annotationConfig?.enabled) {
|
|
100
|
-
const appendedResult = (0, dataUtils_1.processAppendedMappings)(exams, labToOhtMapper.annotationConfig.labKeys, filename, {
|
|
101
|
-
maxLength: labToOhtMapper.annotationConfig.maxLength,
|
|
102
|
-
fallbackValue: labToOhtMapper.annotationConfig.fallbackValue,
|
|
103
|
-
separator: labToOhtMapper.annotationConfig.separator
|
|
104
|
-
});
|
|
105
|
-
if (appendedResult.text?.length) {
|
|
106
|
-
annotation += appendedResult.text;
|
|
107
|
-
}
|
|
108
|
-
}
|
|
109
|
-
// Use annotation directly from ohtExam
|
|
110
|
-
const extractedReference = rawExam?.annotation ?? '';
|
|
111
|
-
if (extractedReference?.length) {
|
|
112
|
-
annotation += annotation ? `\n${extractedReference}` : extractedReference;
|
|
113
|
-
}
|
|
114
|
-
return annotation || undefined;
|
|
115
|
-
}
|
|
116
|
-
/**
|
|
117
|
-
* Extracts reference ranges from rawData (OhtExam object)
|
|
118
|
-
* Always uses parseRange function from extractionUtils for range extraction
|
|
119
|
-
*/
|
|
120
|
-
function agnosticExtractReferenceRanges(labToOhtMapper, rawData, patientInfo, documentDate) {
|
|
121
|
-
const nullRangeNotParsedCorrectly = { from: null, to: null, isRangeParsedCorrectly: false };
|
|
122
|
-
const nullRangeParsedCorrectly = { from: null, to: null, isRangeParsedCorrectly: true };
|
|
123
|
-
// if internalRange return null, but is parsed correctly
|
|
124
|
-
if (labToOhtMapper?.rangeExtraction?.useInternalRange) {
|
|
125
|
-
return nullRangeParsedCorrectly;
|
|
126
|
-
}
|
|
127
|
-
// Always use parseRange function from extractionUtils
|
|
128
|
-
const rangeExtractionResult = (0, extractionUtils_1.parseRange)(rawData, labToOhtMapper, patientInfo);
|
|
129
|
-
if (rangeExtractionResult.isRangeParsedCorrectly) {
|
|
130
|
-
return rangeExtractionResult;
|
|
131
|
-
}
|
|
132
|
-
return nullRangeNotParsedCorrectly;
|
|
133
|
-
}
|
|
134
|
-
function agnosticExtractValueFromGreaterLowerThan(value) {
|
|
135
|
-
// Checks first if any greater than pattern is present
|
|
136
|
-
const greaterThanPatterns = (0, regexUtils_1.getGreaterThanPatterns)();
|
|
137
|
-
const lowerThanPatterns = (0, regexUtils_1.getLowerThanPatterns)();
|
|
138
|
-
value = value.toLowerCase();
|
|
139
|
-
for (const pattern of greaterThanPatterns) {
|
|
140
|
-
const match = pattern.exec(value);
|
|
141
|
-
if (match) {
|
|
142
|
-
const value = parseFloat(match?.[1].replaceAll(',', '.'));
|
|
143
|
-
const valueComparator = oht_types_1.MeasurementValueComparator.GREATER_THAN;
|
|
144
|
-
return {
|
|
145
|
-
extractedValue: value,
|
|
146
|
-
extractedValueComparator: valueComparator,
|
|
147
|
-
valueParsedCorrectly: !Number.isNaN(value)
|
|
148
|
-
};
|
|
149
|
-
}
|
|
150
|
-
}
|
|
151
|
-
// Checks if any lower than pattern is present
|
|
152
|
-
for (const pattern of lowerThanPatterns) {
|
|
153
|
-
const match = pattern.exec(value);
|
|
154
|
-
if (match) {
|
|
155
|
-
const value = parseFloat(match?.[1].replaceAll(',', '.'));
|
|
156
|
-
const valueComparator = oht_types_1.MeasurementValueComparator.LESS_THAN;
|
|
157
|
-
return {
|
|
158
|
-
extractedValue: value,
|
|
159
|
-
extractedValueComparator: valueComparator,
|
|
160
|
-
valueParsedCorrectly: !Number.isNaN(value)
|
|
161
|
-
};
|
|
162
|
-
}
|
|
163
|
-
}
|
|
164
|
-
// If no pattern is found, return the value as is and the comparator as EQUAL and isValueParsedCorrectly as false
|
|
165
|
-
return { extractedValue: null, extractedValueComparator: null, valueParsedCorrectly: false };
|
|
166
|
-
}
|
|
167
|
-
/**
|
|
168
|
-
* Parses exam value from rawExamObj (OhtExam object)
|
|
169
|
-
* Now uses value directly from ohtExam
|
|
170
|
-
*/
|
|
171
|
-
function agnosticParseExamValue(rawExamObj, ohtBiomarker) {
|
|
172
|
-
// Use value directly from ohtExam
|
|
173
|
-
let value = rawExamObj?.value ?? '';
|
|
174
|
-
// Normalize to string for parseFloat
|
|
175
|
-
if (value != null) {
|
|
176
|
-
value = String(value);
|
|
177
|
-
}
|
|
178
|
-
else {
|
|
179
|
-
value = '';
|
|
180
|
-
}
|
|
181
|
-
// If is parse float nan, the value is alphanumerical
|
|
182
|
-
const valueType = (0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker)
|
|
183
|
-
? oht_types_1.BiomarkerValueType.NUMERICAL
|
|
184
|
-
: oht_types_1.BiomarkerValueType.ALPHANUMERICAL;
|
|
185
|
-
let alphanumericalValue = Number.isNaN(parseFloat(value))
|
|
186
|
-
? value
|
|
187
|
-
: null;
|
|
188
|
-
if (valueType === oht_types_1.BiomarkerValueType.ALPHANUMERICAL
|
|
189
|
-
&& !Number.isNaN(parseFloat(value))) {
|
|
190
|
-
// convert numberValue to string
|
|
191
|
-
alphanumericalValue = value.toString();
|
|
192
|
-
}
|
|
193
|
-
if (valueType === oht_types_1.BiomarkerValueType.NUMERICAL
|
|
194
|
-
&& Number.isNaN(parseFloat(value))) {
|
|
195
|
-
// convert numberValue to string
|
|
196
|
-
const { extractedValue, extractedValueComparator, valueParsedCorrectly } = agnosticExtractValueFromGreaterLowerThan(value);
|
|
197
|
-
return {
|
|
198
|
-
valueType,
|
|
199
|
-
alphanumericalValue,
|
|
200
|
-
numberValue: extractedValue,
|
|
201
|
-
valueComparator: extractedValueComparator ?? oht_types_1.MeasurementValueComparator.EQUAL,
|
|
202
|
-
isValueParsedCorrectly: valueParsedCorrectly
|
|
203
|
-
};
|
|
204
|
-
}
|
|
205
|
-
if (valueType === 'NUMERICAL') {
|
|
206
|
-
return {
|
|
207
|
-
valueType,
|
|
208
|
-
alphanumericalValue,
|
|
209
|
-
numberValue: parseFloat(value),
|
|
210
|
-
valueComparator: oht_types_1.MeasurementValueComparator.EQUAL,
|
|
211
|
-
isValueParsedCorrectly: !Number.isNaN(parseFloat(value))
|
|
212
|
-
};
|
|
213
|
-
}
|
|
214
|
-
if (valueType === 'ALPHANUMERICAL') {
|
|
215
|
-
return {
|
|
216
|
-
valueType,
|
|
217
|
-
alphanumericalValue,
|
|
218
|
-
numberValue: parseFloat(value),
|
|
219
|
-
valueComparator: oht_types_1.MeasurementValueComparator.EQUAL,
|
|
220
|
-
isValueParsedCorrectly: Boolean(alphanumericalValue)
|
|
221
|
-
};
|
|
222
|
-
}
|
|
223
|
-
return {
|
|
224
|
-
valueType,
|
|
225
|
-
alphanumericalValue,
|
|
226
|
-
numberValue: null,
|
|
227
|
-
valueComparator: oht_types_1.MeasurementValueComparator.EQUAL,
|
|
228
|
-
isValueParsedCorrectly: false
|
|
229
|
-
};
|
|
230
|
-
}
|
|
231
|
-
function agnosticCheckValueForPlausibleValues(labToOhtMapper, ohtBiomarker, unit, value, isUnitParsedCorrectly) {
|
|
232
|
-
if (!(0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker) && isUnitParsedCorrectly) {
|
|
233
|
-
return true;
|
|
234
|
-
}
|
|
235
|
-
const standardUnit = ohtBiomarker.acf.standardUnit;
|
|
236
|
-
const plausibleLowerValue = ohtBiomarker.acf.plausibilityRangeCheck;
|
|
237
|
-
const plausibleUpperValue = ohtBiomarker.acf.plausibilityRangeCheckHigh;
|
|
238
|
-
const biomarkerStdValueDecimals = ohtBiomarker.acf?.displayDecimals ?? 2;
|
|
239
|
-
if (unit !== standardUnit) {
|
|
240
|
-
const alternativeUnit = (Array.isArray(ohtBiomarker.acf?.alternativeUnits)
|
|
241
|
-
? ohtBiomarker.acf?.alternativeUnits
|
|
242
|
-
: [])?.find((altUnit) => altUnit.name === unit);
|
|
243
|
-
if (alternativeUnit) {
|
|
244
|
-
const conversionFactor = alternativeUnit.conversionFactor;
|
|
245
|
-
value = +(value * conversionFactor).toFixed(biomarkerStdValueDecimals);
|
|
246
|
-
}
|
|
247
|
-
}
|
|
248
|
-
const isPlausibleValue = value >= plausibleLowerValue && value <= plausibleUpperValue;
|
|
249
|
-
// Log if the value is not plausible
|
|
250
|
-
if (!isPlausibleValue) {
|
|
251
|
-
logger.warn({ labToOhtMapper, value, standardUnit, plausibleLowerValue, plausibleUpperValue, filename }, `Value "${value} ${standardUnit}" not plausible "${plausibleLowerValue} to ${plausibleUpperValue}" for "${labToOhtMapper.ohtBmId}" | "${labToOhtMapper.ohtExam.labKey}", filename: ${filename}`);
|
|
252
|
-
}
|
|
253
|
-
return isPlausibleValue;
|
|
254
|
-
}
|
|
255
|
-
/**
|
|
256
|
-
* Apply transformation rules to exams
|
|
257
|
-
* This function applies transformation rules chain to each exam, passing all exams as context
|
|
258
|
-
*
|
|
259
|
-
* @param exams - Array of original exam objects
|
|
260
|
-
* @param transformationRules - Mapping of labKey to transformation rule chains
|
|
261
|
-
* @param labToOhtContract - The contract containing patient info and other context
|
|
262
|
-
* @returns Promise<Exam[]> - Array of transformed exams
|
|
263
|
-
*/
|
|
264
|
-
async function applyTransformationRulesToExams(exams, transformationRules, patientInfo, documentDate) {
|
|
265
|
-
if (transformationRules.size === 0) {
|
|
266
|
-
return {
|
|
267
|
-
transformedExams: exams,
|
|
268
|
-
applicationErrorMessages: []
|
|
269
|
-
};
|
|
270
|
-
}
|
|
271
|
-
const transformedExams = [];
|
|
272
|
-
// Prepare context for transformation rules
|
|
273
|
-
const reportContext = {
|
|
274
|
-
patient: {
|
|
275
|
-
sex: patientInfo.sex,
|
|
276
|
-
birthdate: patientInfo.birthdate,
|
|
277
|
-
age: (0, auxiliaryFunctions_service_1.getPatientAge)(documentDate, patientInfo.birthdate),
|
|
278
|
-
}
|
|
279
|
-
};
|
|
280
|
-
// Prepare the OHT exam data
|
|
281
|
-
const ohtReport = {
|
|
282
|
-
exams: exams.map(e => e.ohtExam),
|
|
283
|
-
};
|
|
284
|
-
logger.info({ examsCount: exams.length, chainsCount: transformationRules.size, filename }, 'Applying transformation rules to exams...');
|
|
285
|
-
let labKeysWithRulesCount = 0;
|
|
286
|
-
let transformedLabKeysCount = 0;
|
|
287
|
-
const applicationErrorMessages = [];
|
|
288
|
-
for (const exam of exams) {
|
|
289
|
-
const labKey = exam.ohtExam.labKey;
|
|
290
|
-
const rulesChain = transformationRules.get(labKey);
|
|
291
|
-
if (!rulesChain || rulesChain.length === 0) {
|
|
292
|
-
transformedExams.push(exam);
|
|
293
|
-
continue;
|
|
294
|
-
}
|
|
295
|
-
labKeysWithRulesCount++;
|
|
296
|
-
try {
|
|
297
|
-
const result = await (0, transformationRules_service_1.applyRules)(rulesChain, exam.ohtExam, {
|
|
298
|
-
ohtReportJson: ohtReport,
|
|
299
|
-
contextJson: reportContext,
|
|
300
|
-
});
|
|
301
|
-
if (result.errors.length > 0) {
|
|
302
|
-
logger.warn({ labKey, errors: result.errors, filename }, 'Errors applying transformation rule(s) for labKey.');
|
|
303
|
-
applicationErrorMessages.push(`${labKey}: ${result.errors.map(e => `(rule ID ${e.ruleId}) ${e.error}`).join('; ')}`);
|
|
304
|
-
}
|
|
305
|
-
else {
|
|
306
|
-
if (result.appliedRules.length > 0) {
|
|
307
|
-
transformedLabKeysCount++;
|
|
308
|
-
}
|
|
309
|
-
logger.info({ labKey, appliedRules: result.appliedRules.length, filename }, 'Done applying transformation rule(s) for labKey.');
|
|
310
|
-
// Add the transformed exam to the result array only if there are no errors in the chain
|
|
311
|
-
transformedExams.push({
|
|
312
|
-
ohtExam: result.data,
|
|
313
|
-
originalExam: exam.originalExam
|
|
314
|
-
});
|
|
315
|
-
}
|
|
316
|
-
}
|
|
317
|
-
catch (error) {
|
|
318
|
-
logger.error({ labKey, error, filename }, 'Failed to apply transformation rules for labKey.');
|
|
319
|
-
applicationErrorMessages.push(`${labKey}: Unhandled error occurred.`);
|
|
320
|
-
}
|
|
321
|
-
}
|
|
322
|
-
logger.info({
|
|
323
|
-
filename,
|
|
324
|
-
examsCount: exams.length,
|
|
325
|
-
chainsCount: transformationRules.size,
|
|
326
|
-
transformedLabKeysCount,
|
|
327
|
-
labKeysWithRulesCount,
|
|
328
|
-
}, 'Done applying the transformation rules to exams.');
|
|
329
|
-
return {
|
|
330
|
-
transformedExams,
|
|
331
|
-
applicationErrorMessages
|
|
332
|
-
};
|
|
333
|
-
}
|
|
334
|
-
async function ohtAgnosticMeasurementsExtractor(labToOhtContract, exams, transformationRules, ohtCoreApiKey, partnerId) {
|
|
335
|
-
filename = labToOhtContract.sourceFilename;
|
|
336
|
-
const measurements = [];
|
|
337
|
-
const unknownMeasurements = [];
|
|
338
|
-
const unknownUnits = [];
|
|
339
|
-
let isReportCorrectlyParsed = true;
|
|
340
|
-
let transformationRulesErrors = [];
|
|
341
|
-
// Apply transformation rules to all exams
|
|
342
|
-
let transformedExamsResult = { transformedExams: [], applicationErrorMessages: [] };
|
|
343
|
-
try {
|
|
344
|
-
transformedExamsResult = await applyTransformationRulesToExams(exams, transformationRules, labToOhtContract.patientInfo, labToOhtContract.documentDate);
|
|
345
|
-
}
|
|
346
|
-
catch (error) {
|
|
347
|
-
logger.error({ error, filename }, 'Unhandled error while applying transformation rules to exams.');
|
|
348
|
-
labToOhtContract.errorMessages.push({
|
|
349
|
-
destination: { slack: true, notes: true, bi: false },
|
|
350
|
-
message: `Failed applying the transformation rules for filename ${filename}. ${error instanceof Error ? error.message : error}`,
|
|
351
|
-
});
|
|
352
|
-
}
|
|
353
|
-
if (transformedExamsResult.applicationErrorMessages.length > 0) {
|
|
354
|
-
transformationRulesErrors = transformedExamsResult.applicationErrorMessages;
|
|
355
|
-
labToOhtContract.errorMessages.push({
|
|
356
|
-
destination: { slack: false, notes: true, bi: false },
|
|
357
|
-
message: `Failed applying some transformation rules:\n${transformedExamsResult.applicationErrorMessages.map((e) => ` - ${e}`).join("\n\n")}`,
|
|
358
|
-
});
|
|
359
|
-
}
|
|
360
|
-
const transformedExams = transformedExamsResult.transformedExams;
|
|
361
|
-
const transformedExamsMap = transformedExams.reduce((map, exam) => map.set(exam.ohtExam.labKey, exam), new Map());
|
|
362
|
-
const allPossibleOHTBmIds = [];
|
|
363
|
-
[
|
|
364
|
-
...Object.values(labToOhtContract.labToOhtList)
|
|
365
|
-
].forEach(labToOhtMapper => {
|
|
366
|
-
if (labToOhtMapper.ohtBmId) {
|
|
367
|
-
allPossibleOHTBmIds.push(labToOhtMapper.ohtBmId);
|
|
368
|
-
}
|
|
369
|
-
});
|
|
370
|
-
// data to request api
|
|
371
|
-
const requestData = {
|
|
372
|
-
"biomarkerIds": allPossibleOHTBmIds,
|
|
373
|
-
"page": 1,
|
|
374
|
-
"pageSize": allPossibleOHTBmIds.length
|
|
375
|
-
};
|
|
376
|
-
// api call to ohtCore to find biomarkers.
|
|
377
|
-
const biomarkers = await (0, apiUtils_1.makeApiCallWithRetry)('post', `${OHT_CORE_URL}/v1/biomarker/biomarkers`, requestData, ohtCoreApiKey);
|
|
378
|
-
// Fetch synonym units from API if enabled
|
|
379
|
-
let synonymUnits = null;
|
|
380
|
-
if (partnerId) {
|
|
381
|
-
synonymUnits = await (0, dataUtils_1.fetchSynonymUnits)(partnerId, ohtCoreApiKey);
|
|
382
|
-
// If API fetch failed or returned empty, set to null to use hardcoded fallback
|
|
383
|
-
if (synonymUnits.length === 0) {
|
|
384
|
-
synonymUnits = null;
|
|
385
|
-
}
|
|
386
|
-
}
|
|
387
|
-
labToOhtContract.labToOhtList.forEach((labToOhtMapper) => {
|
|
388
|
-
let isMeasurementCorrectlyParsed = true;
|
|
389
|
-
if (!labToOhtMapper.ohtExam) {
|
|
390
|
-
labToOhtContract.errorMessages.push({
|
|
391
|
-
destination: { slack: true, notes: false, bi: false },
|
|
392
|
-
message: `Missing ohtExam for labKey: ${labToOhtMapper.ohtExam?.labKey || 'unknown'} filename: ${filename}`,
|
|
393
|
-
});
|
|
394
|
-
return;
|
|
395
|
-
}
|
|
396
|
-
// Get the transformed exam for this labKey, or use the original ohtExam
|
|
397
|
-
const transformedExam = transformedExamsMap.get(labToOhtMapper.ohtExam.labKey);
|
|
398
|
-
const examObj = transformedExam ? transformedExam.ohtExam : labToOhtMapper.ohtExam;
|
|
399
|
-
if (labToOhtMapper?.ohtBmId && labToOhtMapper?.ohtBmId !== -1) {
|
|
400
|
-
// if BM is already in measurements, continue to the next one
|
|
401
|
-
if (measurements.some(measurement => measurement.biomarkerId === labToOhtMapper.ohtBmId)) {
|
|
402
|
-
logger.warn({ labToOhtMapper }, `Biomarker already in measurements array, should investigate, filename: ${filename}`);
|
|
403
|
-
labToOhtContract.errorMessages.push({
|
|
404
|
-
destination: { slack: false, notes: false, bi: true },
|
|
405
|
-
message: `Biomarkers Duplicated keys:[PLACEHOLDER]`,
|
|
406
|
-
item: `bmId:${labToOhtMapper.ohtBmId}, labKey:${examObj.labKey}`
|
|
407
|
-
});
|
|
408
|
-
return;
|
|
409
|
-
}
|
|
410
|
-
const ohtBiomarker = biomarkers?.data?.items.find((bm) => bm.id === labToOhtMapper.ohtBmId);
|
|
411
|
-
// Used for error messages
|
|
412
|
-
const bmInfo = ohtBiomarker?.acf?.shortName ?
|
|
413
|
-
`name:${ohtBiomarker.acf.shortName}, bmId:${labToOhtMapper.ohtBmId}, labKey:${examObj.labKey}` :
|
|
414
|
-
`bmId:${labToOhtMapper.ohtBmId}, labKey:${examObj.labKey}`;
|
|
415
|
-
const { unit, isUnitParsedCorrectly, originalUnit, isArbitraryUnit, unknownUnit } = agnosticExtractUnit(examObj, ohtBiomarker, synonymUnits, partnerId);
|
|
416
|
-
if (unknownUnit.length > 0) {
|
|
417
|
-
unknownUnits.push({
|
|
418
|
-
biomarkerId: ohtBiomarker.id,
|
|
419
|
-
unit: unknownUnit,
|
|
420
|
-
partnerId: partnerId,
|
|
421
|
-
labKey: examObj.labKey,
|
|
422
|
-
ohtExam: labToOhtMapper.ohtExam,
|
|
423
|
-
originalExam: labToOhtMapper.originalExam,
|
|
424
|
-
biomarkerName: examObj.mnemonic || '',
|
|
425
|
-
dataImportFileUploadId: null, // is null it will be set later in the structParser.service.ts
|
|
426
|
-
});
|
|
427
|
-
}
|
|
428
|
-
if (!isUnitParsedCorrectly) {
|
|
429
|
-
logger.warn({ labToOhtMapper }, `Unit not extracted correctly for "${labToOhtMapper.ohtBmId}|${examObj.labKey}", filename: ${filename}`);
|
|
430
|
-
labToOhtContract.errorMessages.push({
|
|
431
|
-
destination: { slack: true, notes: true, bi: true },
|
|
432
|
-
message: `Unit not extracted correctly for:[PLACEHOLDER]`,
|
|
433
|
-
item: `${bmInfo}`
|
|
434
|
-
});
|
|
435
|
-
isMeasurementCorrectlyParsed = false;
|
|
436
|
-
}
|
|
437
|
-
let { valueType, alphanumericalValue, numberValue, valueComparator, isValueParsedCorrectly } = agnosticParseExamValue(examObj, ohtBiomarker);
|
|
438
|
-
if (!isValueParsedCorrectly) {
|
|
439
|
-
logger.warn({ labToOhtMapper }, `Value not extracted correctly for "${labToOhtMapper.ohtBmId}|${examObj.labKey}", filename: ${filename}`);
|
|
440
|
-
labToOhtContract.errorMessages.push({
|
|
441
|
-
destination: { slack: true, notes: true, bi: true },
|
|
442
|
-
message: `Value not extracted correctly for:[PLACEHOLDER]`,
|
|
443
|
-
item: `${bmInfo}`
|
|
444
|
-
});
|
|
445
|
-
isMeasurementCorrectlyParsed = false;
|
|
446
|
-
}
|
|
447
|
-
if ((0, dataUtils_1.isNumericalWithoutValidResult)(valueType, numberValue, alphanumericalValue)) {
|
|
448
|
-
const alphanumericalValueTrimmed = alphanumericalValue?.trim() ?? '';
|
|
449
|
-
const unknownMeasurement = {
|
|
450
|
-
labKey: examObj.labKey,
|
|
451
|
-
biomarkerName: examObj.description ?? '',
|
|
452
|
-
value: alphanumericalValueTrimmed,
|
|
453
|
-
unit: unit ?? '',
|
|
454
|
-
annotation: examObj.annotation ?? '',
|
|
455
|
-
dataOrigin: [{
|
|
456
|
-
itemExtracted: 'measurement',
|
|
457
|
-
method: 'custom-parser',
|
|
458
|
-
methodVersion: 'oht-custom-parser-lib',
|
|
459
|
-
path: 'exams',
|
|
460
|
-
}],
|
|
461
|
-
originalName: examObj.examName ?? '',
|
|
462
|
-
originalExam: {
|
|
463
|
-
contentType: 'application/json',
|
|
464
|
-
exam: JSON.stringify(examObj)
|
|
465
|
-
},
|
|
466
|
-
ohtExam: examObj
|
|
467
|
-
};
|
|
468
|
-
unknownMeasurements.push(unknownMeasurement);
|
|
469
|
-
return;
|
|
470
|
-
}
|
|
471
|
-
// Check if the value is plausible
|
|
472
|
-
if (isValueParsedCorrectly && valueType === 'NUMERICAL') {
|
|
473
|
-
const isPlausibleValue = numberValue !== null && agnosticCheckValueForPlausibleValues(labToOhtMapper, ohtBiomarker, unit, numberValue, isUnitParsedCorrectly);
|
|
474
|
-
if (!isPlausibleValue) {
|
|
475
|
-
logger.warn({ labToOhtMapper }, `Value [${numberValue} ${unit}] is not plausible for "${labToOhtMapper.ohtBmId}|${examObj.labKey}", filename: ${filename}`);
|
|
476
|
-
labToOhtContract.errorMessages.push({
|
|
477
|
-
destination: { slack: true, notes: true, bi: true },
|
|
478
|
-
message: `Value is not plausible for:[PLACEHOLDER]`,
|
|
479
|
-
item: `${bmInfo}, value:${numberValue}${unit}`
|
|
480
|
-
});
|
|
481
|
-
isMeasurementCorrectlyParsed = false;
|
|
482
|
-
}
|
|
483
|
-
}
|
|
484
|
-
let from = null, to = null;
|
|
485
|
-
let isRangeParsedCorrectly = true;
|
|
486
|
-
// If the biomarker is numerical, extract the reference range
|
|
487
|
-
if ((0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker)) {
|
|
488
|
-
const extractedRange = agnosticExtractReferenceRanges(labToOhtMapper, examObj, labToOhtContract.patientInfo, labToOhtContract.documentDate);
|
|
489
|
-
from = extractedRange.from ?? null;
|
|
490
|
-
to = extractedRange.to ?? null;
|
|
491
|
-
isRangeParsedCorrectly = extractedRange.isRangeParsedCorrectly;
|
|
492
|
-
if (!isRangeParsedCorrectly) {
|
|
493
|
-
logger.warn({ labToOhtMapper }, `Range not extracted correctly for "${labToOhtMapper.ohtBmId}|${examObj.labKey}", filename: ${filename}`);
|
|
494
|
-
labToOhtContract.errorMessages.push({
|
|
495
|
-
destination: { slack: true, notes: true, bi: true },
|
|
496
|
-
message: `Range not extracted correctly for:[PLACEHOLDER]`,
|
|
497
|
-
item: `${bmInfo}`
|
|
498
|
-
});
|
|
499
|
-
isMeasurementCorrectlyParsed = false;
|
|
500
|
-
}
|
|
501
|
-
}
|
|
502
|
-
let extractedAnnotation;
|
|
503
|
-
if (labToOhtMapper?.referenceAsAnnotation?.use || labToOhtMapper?.annotationConfig?.enabled) {
|
|
504
|
-
extractedAnnotation = agnosticExtractReferenceAnnotation(labToOhtMapper, examObj, labToOhtContract.patientInfo, labToOhtContract.documentDate, transformedExams);
|
|
505
|
-
}
|
|
506
|
-
// Use material and method directly from ohtExam
|
|
507
|
-
const material = examObj?.material ?? '';
|
|
508
|
-
const method = examObj?.method ?? '';
|
|
509
|
-
let alphaValue = !(0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker) && alphanumericalValue
|
|
510
|
-
? alphanumericalValue.trim()
|
|
511
|
-
: '';
|
|
512
|
-
// adding unit for alphanumerical values as number.
|
|
513
|
-
if (!Number.isNaN(parseFloat(alphaValue))) {
|
|
514
|
-
// Use unit directly from ohtExam
|
|
515
|
-
let originalUnit = examObj?.unit ?? '';
|
|
516
|
-
originalUnit = originalUnit?.replaceAll(/ /g, '') ?? '';
|
|
517
|
-
alphaValue = alphaValue && unit?.length > 0 ? `${alphaValue} ${originalUnit}`.trim() : alphaValue;
|
|
518
|
-
}
|
|
519
|
-
// adding dates for measurements in ISO 8601 format
|
|
520
|
-
const collectionDate = examObj.collectionDate ? new Date(examObj.collectionDate).toISOString() : null;
|
|
521
|
-
const effectiveDate = examObj.effectiveDate ? new Date(examObj.effectiveDate).toISOString() : null;
|
|
522
|
-
const examCollectionDate = examObj.examCollectionDate ? new Date(examObj.examCollectionDate).toISOString() : null;
|
|
523
|
-
const examEffectiveDate = examObj.examEffectiveDate ? new Date(examObj.examEffectiveDate).toISOString() : null;
|
|
524
|
-
// add original name for document search
|
|
525
|
-
const originalName = examObj.examName ?? '';
|
|
526
|
-
let measurement = {
|
|
527
|
-
biomarkerId: ohtBiomarker.id,
|
|
528
|
-
valueType,
|
|
529
|
-
value: (0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker) ? numberValue : null,
|
|
530
|
-
alphanumericValue: alphaValue,
|
|
531
|
-
rangeAnnotation: extractedAnnotation ? extractedAnnotation : null,
|
|
532
|
-
showVisualisationIfAnnotated: false, // TODO: WHAT SHOULD BE THE DEFAULT VALUE?
|
|
533
|
-
comparator: valueComparator ?? oht_types_1.MeasurementValueComparator.EQUAL,
|
|
534
|
-
minNormalValue: from,
|
|
535
|
-
maxNormalValue: to,
|
|
536
|
-
unit,
|
|
537
|
-
originalUnit,
|
|
538
|
-
isArbitraryUnit,
|
|
539
|
-
material,
|
|
540
|
-
method,
|
|
541
|
-
isDigitalizationApproved: isMeasurementCorrectlyParsed,
|
|
542
|
-
isManualChecked: isMeasurementCorrectlyParsed,
|
|
543
|
-
collectionDate: collectionDate,
|
|
544
|
-
effectiveDate: effectiveDate,
|
|
545
|
-
examCollectionDate: examCollectionDate,
|
|
546
|
-
examEffectiveDate: examEffectiveDate,
|
|
547
|
-
originalName: originalName,
|
|
548
|
-
};
|
|
549
|
-
measurements.push(measurement);
|
|
550
|
-
}
|
|
551
|
-
else {
|
|
552
|
-
const labKey = examObj.labKey;
|
|
553
|
-
logger.warn(`Created an ungroupedBiomarker for id: ${labKey}, filename: ${filename}`);
|
|
554
|
-
labToOhtContract.errorMessages.push({
|
|
555
|
-
destination: { slack: false, notes: false, bi: true },
|
|
556
|
-
message: `Created ungroupedBiomarkers for:[PLACEHOLDER]`,
|
|
557
|
-
item: `labKey:${labKey}`
|
|
558
|
-
});
|
|
559
|
-
const biomarkerName = labToOhtMapper?.unknownMeasurement?.biomarkerName ?? '';
|
|
560
|
-
const value = labToOhtMapper?.unknownMeasurement?.value ?? '';
|
|
561
|
-
const unit = labToOhtMapper?.unknownMeasurement?.unit ?? '';
|
|
562
|
-
const annotation = labToOhtMapper?.unknownMeasurement?.annotation ?? '';
|
|
563
|
-
const originalName = labToOhtMapper?.unknownMeasurement?.originalName ?? '';
|
|
564
|
-
const originalExam = labToOhtMapper?.unknownMeasurement?.originalExam
|
|
565
|
-
? {
|
|
566
|
-
contentType: typeof labToOhtMapper.unknownMeasurement.originalExam.contentType === 'string'
|
|
567
|
-
? labToOhtMapper.unknownMeasurement.originalExam.contentType
|
|
568
|
-
: '',
|
|
569
|
-
exam: typeof labToOhtMapper.unknownMeasurement.originalExam.exam === 'string'
|
|
570
|
-
? labToOhtMapper.unknownMeasurement.originalExam.exam
|
|
571
|
-
: String(labToOhtMapper.unknownMeasurement.originalExam.exam || '')
|
|
572
|
-
}
|
|
573
|
-
: { contentType: '', exam: '' };
|
|
574
|
-
const ohtExam = labToOhtMapper?.unknownMeasurement?.ohtExam
|
|
575
|
-
? labToOhtMapper.unknownMeasurement.ohtExam
|
|
576
|
-
: { labKey: '', value: '', unit: '', collectionDate: '', documentDate: '', description: '', mnemonic: '', examName: '', range: [], annotation: '' };
|
|
577
|
-
const dataOrigin = labToOhtMapper?.unknownMeasurement?.dataOrigin
|
|
578
|
-
? [labToOhtMapper?.unknownMeasurement?.dataOrigin]
|
|
579
|
-
: [{ path: '' }];
|
|
580
|
-
const unknownMeasurement = {
|
|
581
|
-
labKey: labKey,
|
|
582
|
-
biomarkerName: biomarkerName,
|
|
583
|
-
value: value,
|
|
584
|
-
unit: unit,
|
|
585
|
-
annotation: annotation,
|
|
586
|
-
dataOrigin: dataOrigin,
|
|
587
|
-
originalName: originalName,
|
|
588
|
-
originalExam: originalExam,
|
|
589
|
-
ohtExam: ohtExam
|
|
590
|
-
};
|
|
591
|
-
unknownMeasurements.push(unknownMeasurement);
|
|
592
|
-
}
|
|
593
|
-
isReportCorrectlyParsed = isReportCorrectlyParsed && isMeasurementCorrectlyParsed;
|
|
594
|
-
});
|
|
595
|
-
return {
|
|
596
|
-
measurements,
|
|
597
|
-
unknownMeasurements,
|
|
598
|
-
unknownUnits,
|
|
599
|
-
isReportCorrectlyParsed,
|
|
600
|
-
transformationRulesErrors,
|
|
601
|
-
};
|
|
602
|
-
}
|
|
603
|
-
//# sourceMappingURL=ohtAgnosticMeasurementsExtractor.service.js.map
|
|
@@ -1 +0,0 @@
|
|
|
1
|
-
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