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Map syphilis history to FHIR #8151

Merged
merged 1 commit into from
Oct 3, 2024
Merged

Map syphilis history to FHIR #8151

merged 1 commit into from
Oct 3, 2024

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emyl3
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@emyl3 emyl3 commented Sep 26, 2024

BACKEND PULL REQUEST

Related Issue

Changes Proposed

  • maps syphilis history to FHIR
  • bulk upload results

Additional Information

Testing

  • Use this branch elisa/with-log-8100-fhir-syphilis-aoe to test uploading syphilis results or entering syphilis results individually
    • search in your backend console ZIPZAP to see the shape of the msg

@emyl3 emyl3 force-pushed the elisa/8100-fhir-syphilis-aoe branch 2 times, most recently from c39b723 to 302abfb Compare September 30, 2024 14:03
patient_id,patient_last_name,patient_first_name,patient_middle_name,patient_street,patient_street2,patient_city,patient_state,patient_zip_code,patient_county,patient_phone_number,patient_dob,patient_gender,patient_race,patient_ethnicity,patient_preferred_language,patient_email,accession_number,equipment_model_name,test_performed_code,test_result,order_test_date,specimen_collection_date,testing_lab_specimen_received_date,test_result_date,date_result_released,specimen_type,ordering_provider_id,ordering_provider_last_name,ordering_provider_first_name,ordering_provider_middle_name,ordering_provider_street,ordering_provider_street2,ordering_provider_city,ordering_provider_state,ordering_provider_zip_code,ordering_provider_phone_number,testing_lab_clia,testing_lab_name,testing_lab_street,testing_lab_street2,testing_lab_city,testing_lab_state,testing_lab_zip_code,testing_lab_phone_number,pregnant,employed_in_healthcare,symptomatic_for_disease,illness_onset_date,resident_congregate_setting,residence_type,hospitalized,icu,ordering_facility_name,ordering_facility_street,ordering_facility_street2,ordering_facility_city,ordering_facility_state,ordering_facility_zip_code,ordering_facility_phone_number,comment,test_result_status,test_ordered_code,genders_of_sexual_partners
1234,Doe,Jane,Jingleheimer,123 Main St,Suite 401,Birmingham,AL,35226,Jefferson,205-999-2800,1/20/1962,F,White,Not Hispanic or Latino,Eng,[email protected],123,ID NOW,94534-5,Detected,12/20/2021 14:00,12/20/2021 14:00,12/20/2021 14:00,12/20/2021 14:00,12/20/2021 14:00,Nasal Swab,1013012657,Smith MD,John,Smitty,400 Main Street,Suite 401,Birmingham,AL,35228,205-888-2000,01D1058442,My Urgent Care,400 Main Street,Suite 401,Birmingham,AL,35228,205-888-2000,N,N,N,01/01/1901,N,22232009,N,N,My Urgent Care,400 Main Street,Suite 100,Birmingham,AL,35228,205-888-2000,Test Comment,C,94534-1,"M, F, trans man, TW, nonbinary"
5678,Doe,John,Jingleheimer,333 Elm St,Suite 401,Hoover,AL,35244,Shelby,205-222-2000,11/1/2001,MALE,BLACK OR AFRICAN AMERICAN,NOT HISPANIC OR LATINO,Spa,[email protected],05be96ef-949f-4f46-9c07-2675e8abf412,BD Veritor System for Rapid Detection of SARS-CoV-2*,94558-4,NOT DETECTED,12/21/2021 17:00,12/21/2021 17:00,12/21/2021 17:00,12/21/2021 17:00,12/21/2021 17:00,ANTERIOR NARES SWAB,1013012657,Smith MD,John,Smitty,400 Main Street,Suite 401,Birmingham,AL,35228,205-888-2000,01D1058442,My Urgent Care,400 Main Street,Suite 401,Birmingham,AL,35228,205-888-2000,NO,YES,Y,01/01/2020,Y,HOSTEL,NO,NO,My Urgent Care,400 Main Street,Suite 100,Birmingham,AL,35228,205-888-2000,testy mctesterson,F,94534-2,"Male, NB"
patient_id,patient_last_name,patient_first_name,patient_middle_name,patient_street,patient_street2,patient_city,patient_state,patient_zip_code,patient_county,patient_phone_number,patient_dob,patient_gender,patient_race,patient_ethnicity,patient_preferred_language,patient_email,accession_number,equipment_model_name,test_performed_code,test_result,order_test_date,specimen_collection_date,testing_lab_specimen_received_date,test_result_date,date_result_released,specimen_type,ordering_provider_id,ordering_provider_last_name,ordering_provider_first_name,ordering_provider_middle_name,ordering_provider_street,ordering_provider_street2,ordering_provider_city,ordering_provider_state,ordering_provider_zip_code,ordering_provider_phone_number,testing_lab_clia,testing_lab_name,testing_lab_street,testing_lab_street2,testing_lab_city,testing_lab_state,testing_lab_zip_code,testing_lab_phone_number,pregnant,employed_in_healthcare,symptomatic_for_disease,illness_onset_date,resident_congregate_setting,residence_type,hospitalized,icu,ordering_facility_name,ordering_facility_street,ordering_facility_street2,ordering_facility_city,ordering_facility_state,ordering_facility_zip_code,ordering_facility_phone_number,comment,test_result_status,test_ordered_code,genders_of_sexual_partners,syphilis_history
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⚠️ change here is adding a syphilis_history column that is empty for each of the two rows

@emyl3 emyl3 force-pushed the elisa/8100-fhir-syphilis-aoe branch from 302abfb to 3060e88 Compare September 30, 2024 18:44
@@ -618,6 +618,7 @@ public List<FeedbackMessage> validateIndividualValues() {
testResult, DiseaseService.HIV_NAME, List.of(gendersOfSexualPartners, pregnant)));
}

errors.addAll(validateYesNoAnswer(syphilisHistory));
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⚠️ added validation here for the syphilis_history column

@emyl3 emyl3 marked this pull request as ready for review September 30, 2024 18:58
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sonarcloud bot commented Sep 30, 2024

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@bobbywells52 bobbywells52 left a comment

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🚀 Very clean -- thanks for your work on this!

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@mpbrown mpbrown left a comment

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LGTM! Nice work on this!

@emyl3 emyl3 added this pull request to the merge queue Oct 3, 2024
Merged via the queue into main with commit 3c98da4 Oct 3, 2024
32 checks passed
@emyl3 emyl3 deleted the elisa/8100-fhir-syphilis-aoe branch October 3, 2024 16:50
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[Syphilis] FHIR Mapping for Syphilis AOE data
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