Incomplete CDM translation #72
Description
The TransformToCDM step seems to be incompatible with one of our test records. Fake patient Aaron Schultz with ResourceId d54661b3-e0b3-bd47-00e7-80de6d12d637 is present in the $export Patient-1.ndjson file, but not in cdm\LocalPatient*.csv file.
cmd /c powershell .\RunAdfCustomActivity.ps1
In fact his record or possibly the one before it (which has a photo) seems to cause the transform to stop transforming patients to csv. We have 4029 fake patients in the ndjson file, but only 3620 make it to the csv file. Record 3621 is the Aaron Schultz patient record in the ndjson file.
Here is the json for Aaron:
{"resourceType":"Patient","id":"d54661b3-e0b3-bd47-00e7-80de6d12d637","meta":{"versionId":"1","lastUpdated":"2021-09-24T13:22:11.896+00:00","profile":["http://standardhealthrecord.org/fhir/StructureDefinition/shr-entity-Patient"]},"text":{"status":"generated","div":"<div xmlns=\"http://www.w3.org/1999/xhtml\">Generated by <a href=\"https://github.com/synthetichealth/synthea\">Synthea</a>.Version identifier: master-branch-latest-2-g1ac455d8\n . Person seed: 4421811931708538165 Population seed: 1624641604004</div>"},"extension":[{"extension":[{"url":"ombCategory","valueCoding":{"system":"urn:oid:2.16.840.1.113883.6.238","code":"2106-3","display":"White"}},{"url":"text","valueString":"White"}],"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-race"},{"extension":[{"url":"ombCategory","valueCoding":{"system":"urn:oid:2.16.840.1.113883.6.238","code":"2186-5","display":"Non Hispanic or Latino"}},{"url":"text","valueString":"Non Hispanic or Latino"}],"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity"},{"url":"http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName","valueString":"Leora789 Pfeffer420"},{"url":"http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex","valueCode":"M"},{"url":"http://hl7.org/fhir/StructureDefinition/patient-birthPlace","valueAddress":{"city":"Lynn","state":"Massachusetts","country":"US"}},{"url":"http://standardhealthrecord.org/fhir/StructureDefinition/shr-actor-FictionalPerson-extension","valueBoolean":true},{"url":"http://standardhealthrecord.org/fhir/StructureDefinition/shr-entity-FathersName-extension","valueHumanName":{"text":"Austin578 Schultz619"}},{"url":"http://standardhealthrecord.org/fhir/StructureDefinition/shr-demographics-SocialSecurityNumber-extension","valueString":"999-82-2338"},{"url":"http://synthetichealth.github.io/synthea/disability-adjusted-life-years","valueDecimal":11.338841186955664},{"url":"http://synthetichealth.github.io/synthea/quality-adjusted-life-years","valueDecimal":59.66115881304434}],"identifier":[{"system":"https://github.com/synthetichealth/synthea","value":"d54661b3-e0b3-bd47-00e7-80de6d12d637"},{"type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"MR","display":"Medical Record Number"}],"text":"Medical Record Number"},"system":"http://hospital.smarthealthit.org","value":"d54661b3-e0b3-bd47-00e7-80de6d12d637"},{"type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"SS","display":"Social Security Number"}],"text":"Social Security Number"},"system":"http://hl7.org/fhir/sid/us-ssn","value":"999-82-2338"},{"type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"DL","display":"Driver's License"}],"text":"Driver's License"},"system":"urn:oid:2.16.840.1.113883.4.3.25","value":"S99925574"},{"type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0203","code":"PPN","display":"Passport Number"}],"text":"Passport Number"},"system":"http://standardhealthrecord.org/fhir/StructureDefinition/passportNumber","value":"X84173412X"}],"name":[{"use":"official","family":"Schultz619","given":["Aaron697"],"prefix":["Mr."]}],"telecom":[{"system":"phone","value":"555-113-3127","use":"home"}],"gender":"male","birthDate":"1949-02-13","address":[{"extension":[{"extension":[{"url":"latitude","valueDecimal":41.708340797966564},{"url":"longitude","valueDecimal":-70.18051732525078}],"url":"http://hl7.org/fhir/StructureDefinition/geolocation"},{"url":"http://hl7.org/fhir/StructureDefinition/geolocationdata"}],"line":["970 Jenkins Byway","1234 Any Street"],"city":"Dennis","state":"MA","country":"US"}],"maritalStatus":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v3-MaritalStatus","code":"M","display":"M"}],"text":"M"},"multipleBirthBoolean":false,"contact":[{"relationship":[{"coding":[{"system":"https://build.fhir.org/ig/HL7/US-Core/StructureDefinition-us-core-patient.html","version":"1.21","code":"mother/sister","display":"this is not really real"}],"text":"Here is Jake his mother sister"}]}],"communication":[{"language":{"coding":[{"system":"urn:ietf:bcp:47","code":"en-US","display":"English"}],"text":"English"}}]}