FHIR Chat · FHIRServer Tools · pascal

Stream: pascal

Topic: FHIRServer Tools

Jose Costa Teixeira (Nov 25 2019 at 16:15):

I have SCT Intl and the BE extension. Is is easy/possible to put them together and generate the cache for the server?

Jose Costa Teixeira (Nov 25 2019 at 16:16):

do I just merge the two zip file contents (namely the Snapshot) and run it from there?

Grahame Grieve (Nov 25 2019 at 16:16):

in principle, you should load them both. You can combine them but that has special purpose (and is one a special way)

Grahame Grieve (Nov 25 2019 at 16:16):

you need the BE extension as a snap shot

Jose Costa Teixeira (Nov 25 2019 at 16:16):

ok. so i can use both cache files separately?

Grahame Grieve (Nov 25 2019 at 16:17):

yes

Jose Costa Teixeira (Nov 25 2019 at 16:17):

ok thanks, I'll go with that

Grahame Grieve (Nov 25 2019 at 16:17):

here's from my ini:

[terminologies]
icd10=type: icd10; source: C:\ProgramData\fhirserver\icd10.txt
sintl=type: snomed; source: C:\ProgramData\fhirserver\snomed_20190731_intl.cache; default: true
s-usa=type: snomed; source: C:\ProgramData\fhirserver\snomed_20160901_us.cache
s-aus=type: snomed; source: C:\ProgramData\fhirserver\snomed_20161031_au.cache
s-can=type: snomed; source: C:\ProgramData\fhirserver\snomed_20161031_ca.cache

Grahame Grieve (Nov 25 2019 at 16:18):

I should load the be extension on tx.fhir.org too

Jose Costa Teixeira (Nov 25 2019 at 16:25):

pasted image

Jose Costa Teixeira (Nov 25 2019 at 16:26):

am I doing it wrong? Or do I need to add "Belgium" to the editions dropdown (not sure what that will require)

Grahame Grieve (Nov 25 2019 at 16:30):

yes you will need to do that, and figure out what the concept id is (and add it to the documentation at the top of the snomed services class

Jose Costa Teixeira (Nov 25 2019 at 16:38):

I can't find a
FhirServerUtils.dproj

Grahame Grieve (Nov 25 2019 at 16:38):

you shouldn't need to?

Jose Costa Teixeira (Nov 25 2019 at 16:39):

how do I change that form to add Belgium to the dropdown?

Grahame Grieve (Nov 25 2019 at 16:45):

it's part of the main server. just Shift-F12 while the server is the focus

Jose Costa Teixeira (Nov 25 2019 at 16:51):

got it, thanks

Jose Costa Teixeira (Nov 25 2019 at 16:53):

I'll build the tool and try to create the cache in a few hours. thanks again

Jose Costa Teixeira (Dec 05 2019 at 19:58):

I still have the error "unable to resolve status"

Jose Costa Teixeira (Dec 05 2019 at 19:58):

Any idea what I should look at?

Grahame Grieve (Dec 05 2019 at 20:11):

where is this?

Jose Costa Teixeira (Dec 05 2019 at 20:39):

FHIR.Snomed.Importer.TSnomedImporter.ReadConceptsFile
FHIR.Snomed.Importer.TSnomedImporter.ImportSnomed
FHIR.Snomed.Importer.TSnomedImporter.Go
FHIR.Snomed.Importer.importSnomedRF2('C:\HL7\SnomedCT\SnomedCT_BelgiumExtensionRF2_PRODUCTION_20190915T120000Z\Snapshot','C:\HL7\SnomedCT\SnomedCT_BelgiumExtensionRF2_PRODUCTION_20190915T120000Z\cache\snomed-BE.cache','http://snomed.info/sct/11000172109/version/20191205',(FHIR.Server.Manager.TServerManagerForm.sctCallback,$CB782D0))
FHIR.Server.Manager.TServerManagerForm.btnImportSnomedClick($CB16F80)

Jose Costa Teixeira (Dec 05 2019 at 20:39):

concretely, first time it its line 613 on FHIR.Snomed.Importer

Grahame Grieve (Dec 05 2019 at 20:40):

so you should get a concept id

Grahame Grieve (Dec 05 2019 at 20:40):

and the concept id you get should be listed in the concepts file

Jose Costa Teixeira (Dec 05 2019 at 20:41):

(I may be doing something wrong wrt the files that I am importing)

Jose Costa Teixeira (Dec 05 2019 at 20:42):

pasted image

Grahame Grieve (Dec 05 2019 at 20:42):

possible. but does it? the concept id will be in the error message...

Jose Costa Teixeira (Dec 05 2019 at 20:43):

concept ID or status?
the exception line says

ETerminologySetup.create('unable to resolve status: '+inttostr(oConcept.FStatus));

Grahame Grieve (Dec 05 2019 at 20:44):

right so it's 9000...74008. Does that concept exist in the concepts file?

Jose Costa Teixeira (Dec 05 2019 at 20:46):

I'm getting the status, not the ID, right?

Jose Costa Teixeira (Dec 05 2019 at 20:46):

my sct2_Concept_Snapshot_BE1000172_20190915.txt says:

Jose Costa Teixeira (Dec 05 2019 at 20:46):

id  effectiveTime   active  moduleId    definitionStatusId
11000172109 20180315    1   11000172109 900000000000074008
21000172104 20180315    1   11000172109 900000000000074008
31000172101 20180315    1   11000172109 900000000000074008
71000172103 20180315    1   11000172109 900000000000074008
111000172100    20180315    1   11000172109 900000000000074008

Grahame Grieve (Dec 05 2019 at 20:49):

there should also be an entry in the first column for 900000000000074008 somewhere - actually defining the concept

Jose Costa Teixeira (Dec 05 2019 at 20:51):

so you mean the status 9000...74008 is not defined as a concept and this is why it is failing?

Jose Costa Teixeira (Dec 05 2019 at 20:52):

since that one is defined by snomed Intl, I think I'm not feeding the machine with the right files

Grahame Grieve (Dec 05 2019 at 20:52):

you have to feed the full snapshot

Jose Costa Teixeira (Dec 05 2019 at 21:08):

ok so I have the Belgian full, but Belgian full does not mean intl+belgian

Jose Costa Teixeira (Dec 05 2019 at 21:11):

how do I get the really full snapshot? Copy the fiules from intl and be edition into same folder?

Grahame Grieve (Dec 05 2019 at 21:11):

no nothing so simple.

Grahame Grieve (Dec 05 2019 at 21:12):

the belgian download should make it available

Jose Costa Teixeira (Dec 05 2019 at 21:13):

ok I'll read the documentation (when I can find the download link again...)

Jose Costa Teixeira (Dec 05 2019 at 21:14):

got it. will read through

Jose Costa Teixeira (Dec 05 2019 at 21:16):

This is the PRODUCTION Release of the September 2019 SNOMED CT Belgium Extension.
This package is dependent upon the SNOMED CT July 2019 International Edition, and so should be consumed and analysed accordingly.

Jose Costa Teixeira (Dec 05 2019 at 21:16):

and the download for BE is only 10 MB

Grahame Grieve (Dec 05 2019 at 21:17):

well, there's no current way to import that. I don't know if SCT provides tools to create an RF2 version of them combined

Grahame Grieve (Dec 05 2019 at 21:17):

maybe you should ask on #snomed

Jose Costa Teixeira (Dec 05 2019 at 21:18):

Thanks

Jose Costa Teixeira (Dec 05 2019 at 21:24):

(meanwhile I took a shot in the dark and just put the files together and gave it a go. Unless you say it is definitely rubbish, I can abort it. Or I can see what is the result. It is now at 26% and I will do other stuff while this is being processed.)

Jose Costa Teixeira (Dec 05 2019 at 21:30):

ok it aborted saying "Unknown sct lang: nl"

Jose Costa Teixeira (Dec 05 2019 at 21:30):

Is this it?

function readLang(s : String) : byte;
begin
  if (s = 'en') then
    result := 1
  else if (s = 'fr') then
    result := 2
  else
    raise ETerminologyError.create('Unknown SCT Lang "'+s+'"');
end;

Jose Costa Teixeira (Dec 05 2019 at 21:30):

this is FHIR .snomed.services.

Jose Costa Teixeira (Dec 05 2019 at 21:31):

should the nl language be added? if so, which result ? or that needs the code to be added somewhere else?

Grahame Grieve (Dec 05 2019 at 21:43):

well, add it to readLang and codeForLang

Jose Costa Teixeira (Dec 05 2019 at 22:15):

en=1, fr=2,
nl=3?

Grahame Grieve (Dec 05 2019 at 22:16):

y

Grahame Grieve (Dec 05 2019 at 22:16):

and add es = 4 while your're there

Jose Costa Teixeira (Dec 05 2019 at 22:35):

pasted image

Jose Costa Teixeira (Dec 05 2019 at 22:35):

I got this now, probably because I am just putting the files together. Was worth the shot

Grahame Grieve (Dec 05 2019 at 22:41):

yeah you need a tool to mash them together

Richard Ettema (Sep 25 2020 at 21:15):

I'm working on setting up an instance of FHIRServer in my local environment and would like to import the current SNOMED-CT Intl 20200731 version. I'm trying to use the command line import command -snomed-rf2 with -sver but it does not appear to do anything.

Here's my command which immediately returns without any processing:

C:\Program Files\FHIRServer>.\FHIRServer.exe -snomed-rf2 "C:\fhirserver\snomed\SnomedCT_InternationalRF2_PRODUCTION_20200731T120000Z\Snapshot" -sver "http://snomed.info/sct/900000000000207008//version/20200731" -ini ".\fhirserver.ini"
2020-09-25--------------------------------
17:02:59 00:00:00 FHIR Service 1.0.351. Using ini file .\fhirserver.ini with stack dumps on
No -cmd parameter - exiting now

C:\Program Files\FHIRServer>

I also tried looking for the FHIRServer Tools application but cannot find it.

Grahame Grieve (Sep 25 2020 at 21:22):

run it with parameters -cmd manager, and then use the GUI

Richard Ettema (Sep 25 2020 at 21:38):

Thank you.

Last updated: Apr 12 2022 at 19:14 UTC