Diagnosis CSVs Upload

Hi, If I want a clean slate, do I need to manually delete all existing diagnosis-related concept information from openMRS before uploading the three diagnosis-related csv files? Thanks Andrew

What do you mean by clean state ? Is it only diagnosis clean state or complete clean state ?

If it is just diagnosis concepts, then You can retire the concepts. Please don’t delete.

Yes, by clean slate I meant removing existing diagnoses (retiring, as you mentioned) and uploading my own data sets using the three csv files necessary. Thanks for the reply.

Okay, so I retired all the diagnosis concepts in openMRS. I downloaded the 3 diagnosis-related csv files and populated them with new data. I then went to Bahmni Admin and uploaded these 3 files as instructed in the Bahmni documentation. Each uploadsproduced an error:

The error file generated for diagnosis_concepts.csv appears to contain all the entries of the original csv file.

Any pointers? Andrew

@andys, Yes the Error file will contain all the entries of the original csv file but the extra information will be the error messages at the end of row. Please check the last column in the csv file. Can you also share it once?

Thanks for the reply. Each cell in the last column of the file contains the word “concept”.

Can you share the Error file? And openmrs logs from /var/log/openmrs/openmrs.log related to import/upload aswell.

Error file: Diagnosis_concepts_2016-12-01_08_29_34.err.txt (86.3 KB)

Log File: (renamed as .txt for upload): openmrslog.txt (2.6 MB)

The error is “Concept reference source not found” The exception is as below

org.openmrs.api.APIException: Concept reference source not found
at org.bahmni.module.referencedata.labconcepts.service.impl.ReferenceDataConceptReferenceTermServiceImpl.throwExceptionIfExists(ReferenceDataConceptReferenceTermServiceImpl.java:86)
at org.bahmni.module.referencedata.labconcepts.service.impl.ReferenceDataConceptReferenceTermServiceImpl.validate(ReferenceDataConceptReferenceTermServiceImpl.java:80)
at org.bahmni.module.referencedata.labconcepts.service.impl.ReferenceDataConceptReferenceTermServiceImpl.getConceptReferenceTerm(ReferenceDataConceptReferenceTermServiceImpl.java:24)
at org.bahmni.module.referencedata.labconcepts.service.impl.ReferenceDataConceptReferenceTermServiceImpl.getConceptMap(ReferenceDataConceptReferenceTermServiceImpl.java:32)
at org.bahmni.module.referencedata.labconcepts.service.impl.ReferenceDataConceptServiceImpl.clearAndAddConceptMappings(ReferenceDataConceptServiceImpl.java:94)
at org.bahmni.module.referencedata.labconcepts.service.impl.ReferenceDataConceptServiceImpl.getConcept(ReferenceDataConceptServiceImpl.java:84)
at org.bahmni.module.referencedata.labconcepts.service.impl.ReferenceDataConceptServiceImpl.saveConcept(ReferenceDataConceptServiceImpl.java:49)
at org.bahmni.module.admin.csv.persister.ConceptPersister.persist(ConceptPersister.java:34)
at org.bahmni.module.admin.csv.persister.ConceptPersister.persist(ConceptPersister.java:13)
at org.bahmni.module.admin.csv.persister.DatabasePersister.persist(DatabasePersister.java:25)
at org.bahmni.csv.MigrationCallable.call(StageCallable.java:46)
at org.bahmni.csv.MigrationCallable.call(StageCallable.java:32)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

The Diagnosis concepts are not uploading because the Diagnosis Reference terms are not uploaded. Please share your Diagnosis Reference terms, Concepts, Concept-sets csv files in csv format only. Text format is adding all spaces making it difficult to read it.

I tried to upload csv files, but the platform does not accept this format, which is why I used .txt files.

Can you use File Dropper to share?

Diagnosis Concept SetsDiagnosis_concept_sets.txt (13.3 KB) Diagnosis ConceptsDiagnosis_concepts.txt (61.6 KB) Diagnosis Reference TermsDiagnosis_Reference_Terms.txt (43.5 KB)

Will Dropbox work for you?

1 Like

Yes Dropbox works for me.

Looks like you missed column header name Code in this file. Can you please check the Diagnosis Reference terms sample file.

Ah, the heading of the column :slight_smile: - not sure how that happened - it’s always something simple, thanks.

Now I get the error in Error File Concept reference source ICD-10-WHO does not exists.

Can you check if ICD-10-WHO in Concept Sources list at /openmrs/admin/concepts/conceptSource.list.

Apologies for curtailing this conversation so abruptly.

Thanks, the WHO concept was there, but in a different format (ICD 10 - WHO as opposed to ICD-10-WHO).

So I managed to resolve the Diagnostic Terms csv and I have managed to upload the concepts csv without any errors. However, I am still stuck when uploading Diagnosis Concept Set Sets file which I tried to upload using the Concepts option. I get the error “No Column found in the csv file. datatype”

I believe that there is an error on page: https://bahmni.atlassian.net/wiki/display/BAH/Diagnosis+Data of the Documentation.

Create and upload the Diagnosis concept sets. While uploading, choose the option for Concepts (should read Concept Set I think) Sample file: Diagnosis_concept_sets.csv

@andys, Yes… Thank you for pointing out. Are you able to get the Diagnosis_concept_sets.csv import work now? I have fixed the mistake in Documentation.