[Spike] Bulk Upload specimen types getting remapped.

[DanielSass]

From ReportStream:

For specimen_type . When you enter this snomed code 258607008 in the CSV upload, we get this code 87100004 in the FHIR bundle

After a quick look through the code it's not immediately clear why this would be happening. I do believe we will try to find device information from our DB to fill in missing optional data, but I don't believe we should be overwriting data that has been passed in.

Investigate and if the fix is simple, contribute it to the PR for the parent issue: https://github.com/CDCgov/prime-simplereport/pull/8627

[DanielSass]

87100004 is the "unknown collection location code" could indicate a default value is overriding a provided value

[mehansen]

Fwiw I tested this locally and couldn't reproduce it. This is what the specimen looks like in json:

{
  "resourceType" : "Specimen",
  "id" : "f2c2d463-f3ab-4cda-9151-981afb5f1e82",
  "identifier" : [ {
    "value" : "a9961ef3-d653-4f93-a8aa-74643478497e"
  } ],
  "type" : {
    "coding" : [ {
      "system" : "http://snomed.info/sct",
      "code" : "258607008"
    } ]
  },
  "receivedTime" : "2021-12-20T14:00:00-05:00",
  "collection" : {
    "collectedDateTime" : "2021-12-20T14:00:00-05:00",
    "bodySite" : {
      "coding" : [ {
        "system" : "http://snomed.info/sct",
        "code" : "87100004"
      } ],
      "text" : "Topography unknown (body structure)"
    }
  }
}

the default value is there for the collection site but it's not overwriting the original value

[arinkulshi-skylight]

So based on what Victor is saying in the thread, as long as we eventually transition our CovidPipeline to UP we should be good? So would it make sense to close this ticket for now?

[mehansen]

So based on what Victor is saying in the thread, as long as we eventually transition our CovidPipeline to UP we should be good? So would it make sense to close this ticket for now?

Unsure since it sounds like Victor is still verifying based on this message? But we could always reopen if he has anything further for us to do

[arinkulshi-skylight]

Ok! Sounds good I'll close the PR for now and keep the ticket in Blocked until we hear otherwise. Thanks Merethe!

[DanielSass]

from victor on RS

Yeah, the issue with specimen_type is that we're not getting specimen_source_site_code from you in the CP, but we are getting it in the UP. The CP has some mappings to populate it when it's blank and so that causes that value to be different between the two. I remember talking to Chris about this and we said we can move forward with the value we're getting from you in the UP because we don't know if the mappings we have in the Covid pipeline are accurate.