Merge pull request #63 from mcode/add-all-extractors

Adding remaining CSV extractors from the MEF
mcode · May 10, 2023 · 97a554e · 97a554e
2 parents 9e5dfed + 48dddf3
commit 97a554e
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Showing 7 changed files with 47 additions and 3 deletions.
diff --git a/src/ICARECSVClient.js b/src/ICARECSVClient.js
@@ -1,10 +1,16 @@
 const {
   BaseClient,
+  CSVAdverseEventExtractor,
   CSVCancerDiseaseStatusExtractor,
+  CSVCancerRelatedMedicationAdministrationExtractor,
+  CSVCancerRelatedMedicationRequestExtractor,
+  CSVClinicalTrialInformationExtractor,
   CSVConditionExtractor,
   CSVCTCAdverseEventExtractor,
-  CSVClinicalTrialInformationExtractor,
+  CSVObservationExtractor,
   CSVPatientExtractor,
+  CSVProcedureExtractor,
+  CSVStagingExtractor,
   CSVTreatmentPlanChangeExtractor,
   sortExtractors,
 } = require('mcode-extraction-framework');
@@ -14,11 +20,17 @@ class ICARECSVClient extends BaseClient {
   constructor({ extractors, commonExtractorArgs }) {
     super();
     this.registerExtractors(
+      CSVAdverseEventExtractor,
       CSVCancerDiseaseStatusExtractor,
-      CSVConditionExtractor,
+      CSVCancerRelatedMedicationAdministrationExtractor,
+      CSVCancerRelatedMedicationRequestExtractor,
       CSVClinicalTrialInformationExtractor,
+      CSVConditionExtractor,
       CSVCTCAdverseEventExtractor,
+      CSVObservationExtractor,
       CSVPatientExtractor,
+      CSVProcedureExtractor,
+      CSVStagingExtractor,
       CSVTreatmentPlanChangeExtractor,
     );
     // Store the extractors defined by the configuration file as local state
@@ -28,10 +40,15 @@ class ICARECSVClient extends BaseClient {
       { type: 'CSVPatientExtractor', dependencies: [] },
       { type: 'CSVConditionExtractor', dependencies: ['CSVPatientExtractor'] },
       { type: 'CSVCancerDiseaseStatusExtractor', dependencies: ['CSVPatientExtractor'] },
-      { type: 'CSVCTCAdverseEventExtractor', dependencies: ['CSVPatientExtractor'] },
       { type: 'CSVClinicalTrialInformationExtractor', dependencies: ['CSVPatientExtractor'] },
       { type: 'CSVTreatmentPlanChangeExtractor', dependencies: ['CSVPatientExtractor'] },
       { type: 'CSVStagingExtractor', dependencies: ['CSVPatientExtractor'] },
+      { type: 'CSVCancerRelatedMedicationAdministrationExtractor', dependencies: ['CSVPatientExtractor'] },
+      { type: 'CSVCancerRelatedMedicationRequestExtractor', dependencies: ['CSVPatientExtractor'] },
+      { type: 'CSVProcedureExtractor', dependencies: ['CSVPatientExtractor'] },
+      { type: 'CSVObservationExtractor', dependencies: ['CSVPatientExtractor'] },
+      { type: 'CSVAdverseEventExtractor', dependencies: ['CSVPatientExtractor'] },
+      { type: 'CSVCTCAdverseEventExtractor', dependencies: ['CSVPatientExtractor'] },
     ];
     // Sort extractors based on order and dependencies
     this.extractorConfig = sortExtractors(this.extractorConfig, dependencyInfo);

diff --git a/test/sample-client-data/adverse-event-information.csv b/test/sample-client-data/adverse-event-information.csv
@@ -0,0 +1,4 @@
+mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventDisplayText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,severity,actuality,studyId,effectiveDate,recordedDate
+123,adverseEventId-1,109006,code-system,Anxiety disorder of childhood OR adolescence,procedure-id,Procedure,serious,http://terminology.hl7.org/CodeSystem/adverse-event-seriousness,Serious,product-use-error|product-quality|wrong-rate,http://terminology.hl7.org/CodeSystem/adverse-event-category|http://snomed.info/sct|http://terminology.hl7.org/CodeSystem/adverse-event-category,Product Use Error|Product Quality|Wrong Rate,severe,actual,researchId-1,12-09-1994,12-09-1994
+456,adverseEventId-2,134006,http://snomed.info/sct,Decreased hair growth,medicationId-1,Medication,non-serious,http://terminology.hl7.org/CodeSystem/adverse-event-seriousness,Non-serious,product-quality|wrong-rate,http://terminology.hl7.org/CodeSystem/adverse-event-category|,Product Quality|,mild,potential,researchId-2,12-10-1995,12-10-1995
+789,adverseEventId-3,150003,,,,,,,,product-use-error,,,,,,12-09-1994,
diff --git a/test/sample-client-data/cancer-related-medication-administration-information.csv b/test/sample-client-data/cancer-related-medication-administration-information.csv
@@ -0,0 +1,4 @@
+mrn,medicationId,code,codeSystem,displayText,startDate,endDate,treatmentReasonCode,treatmentReasonCodeSystem,treatmentReasonDisplayText,treatmentIntent,status
+123,medicationId-1,10760,http://www.nlm.nih.gov/research/umls/rxnorm,Triamcinolone Oral Paste,2020-01-01,2020-07-05,999000,http://snomed.info/sct,Mixed islet cell and exocrine adenocarcinoma,373808002,on-hold
+456,medicationId-2,91318,http://www.nlm.nih.gov/research/umls/rxnorm,Coal Tar Topical Solution,2020-02-17,2020-08-13,915007,http://snomed.info/sct,Malignant melanoma in junctional nevus,373808002,completed
+789,medicationId-3,91833,http://www.nlm.nih.gov/research/umls/rxnorm,Vitamin K1 Injectable Solution [Aquamephyton],2020-01-12,2020-10-01,900006,http://snomed.info/sct,Mucin-producing adenocarcinoma,363676003,stopped
diff --git a/test/sample-client-data/cancer-related-medication-request-information.csv b/test/sample-client-data/cancer-related-medication-request-information.csv
@@ -0,0 +1,4 @@
+mrn,requestId,code,codeSystem,displayText,treatmentReasonCode,treatmentReasonCodeSystem,treatmentReasonDisplayText,procedureIntent,status,intent,authoredOn,requesterId
+123,requestId-1,10760,http://www.nlm.nih.gov/research/umls/rxnorm,Triamcinolone Oral Paste,999000,http://snomed.info/sct,Mixed islet cell and exocrine adenocarcinoma,373808002,active,order,2020-01-01,requester-1
+456,requestId-2,91318,http://www.nlm.nih.gov/research/umls/rxnorm,Coal Tar Topical Solution,915007,http://snomed.info/sct,Malignant melanoma in junctional nevus,373808002,on-hold,proposal,2019-02-02,requester-2
+789,requestId-3,91833,http://www.nlm.nih.gov/research/umls/rxnorm,Vitamin K1 Injectable Solution [Aquamephyton],900006,http://snomed.info/sct,Mucin-producing adenocarcinoma,363676003,cancelled,plan,2021-06-12,requester-3
diff --git a/test/sample-client-data/observation-information.csv b/test/sample-client-data/observation-information.csv
@@ -0,0 +1,4 @@
+mrn,observationId,status,code,codeSystem,displayName,value,valueCodeSystem,effectiveDate,bodySite,laterality
+123,observation-id-1,final,1695-6,http://loinc.org,,10828004,http://snomed.info/sct,2020-01-02,251007,66459002
+456,observation-id-2,final,8302-2,http://loinc.org,Body height,66.89 [in_i],,2020-01-02,251007,66459002
+789,observation-id-3,final,29463-7,http://loinc.org,Body Weight,185 [lb_av],,2020-01-02,251007,66459002
diff --git a/test/sample-client-data/procedure-information.csv b/test/sample-client-data/procedure-information.csv
@@ -0,0 +1,5 @@
+mrn,procedureId,conditionId,status,code,codeSystem,displayName,reasonCode,reasonCodeSystem,reasonDisplayName,effectiveDate,bodySite,laterality,treatmentIntent
+123,procedure-id-1,condition-id-1,completed,152198000,http://snomed.info/sct,Brachytherapy (procedure),363346000,http://snomed.info/sct,Malignant tumor,2020-01-01,41224006,51440002,373808002
+456,procedure-id-2,condition-id-2,in-progress,174337000,http://snomed.info/sct,Destruction of lesion,363346000,http://snomed.info/sct,Malignant tumor,2020-01-12,41224006,51440002,373808002
+789,procedure-id-3,condition-id-3,completed,172043006,http://snomed.info/sct,Total mastectomy,363346000,http://snomed.info/sct,Malignant tumor,2020-06-30,41224006,51440002,373808002
+789,procedure-id-4,condition-id-3,in-progress,10611004,http://snomed.info/sct,Teleradiotherapy protons (procedure),363346000,http://snomed.info/sct,Malignant tumor,2020-01-12,41224006,51440002,373808002
diff --git a/test/sample-client-data/staging-information.csv b/test/sample-client-data/staging-information.csv
@@ -0,0 +1,6 @@
+mrn,conditionId,stageGroup,t,n,m,type,stagingSystem,stagingCodeSystem,effectiveDate
+123,conditionId-1,3C,cT3,cN3,cM0,Clinical,C146985,http://ncimeta.nci.nih.gov,2020-01-01
+456,conditionId-2,3C,cT3,cN3,cM0,Clinical,443830009,http://snomed.info/sct,2020-01-01
+789,conditionId-3,3C,,cN3,cM0,Clinical,444256004,http://snomed.info/sct,2020-01-02
+789,conditionId-3,3C,cT3,,cM0,Clinical,,,2020-01-03
+789,conditionId-3,3C,cT3,cN3,,Clinical,258235000,http://snomed.info/sct,2020-01-04