Bug: hapi-fhir-cli: (1) docs outdated, (2) can't import any terminologies #3276
Comments
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Why ICD10CM source uses a Loinc_2.71_MultiAxialHierarchy_3.5.zip file in the command line. Is it an error? |
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I think it might be a documentation error. I tried with and without, and had an error. I think my colleague may have been able to successfully import all of these, but only if the upload was executed from the same server that the terminology service is running on. I think that in some cases where we were uploading from our local machine, we would receive an error message telling us that we needed to run on the same server. Also, I think the SmileCDR documentation might have some better docs for using the |
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I also tried using the SmileCDR docs to try and find a way to use hapi-fhir-cli successfully. For SNOMED, ICD10CM, and LOINC, only had luck w/ ICD10CM (same as before). I tried doing an extremely simple custom code system (only 2kb, attached), but no luck. Attempt 1 :
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For me, it works the following things: concepts hierarchy Uploading |
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That looks like almost exactly like my setup. Did you include the It said to include like so: {
"resourceType": "CodeSystem",
"url": "https://20.119.216.32:8080/fhir/CodeSystem/2",
"name": "Attempt1",
"description": "I really hope this works",
"status": "active",
"publisher": "TIMS",
"date": "2022-04-21",
"content": "not-present"
}Otherwise my command is exactly the same as yours / basically the same, depending how you look at it. I wonder if it didn't like one of my params, but it didn't give me any error message to indicate that. Maybe it didn't like me assigning my own canonical URL like that. Maybe htat's why it gave me: Can't check at the moment because I'm not on the right PC, but I suppose I'll try changing that. @mcabello-cens Do you have a link to your repo/branch? My fork is only from around December 2021, and I haven't updated it since. Perhaps yours is more recent? |
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@mcabello-cens For uploading custom CSVs the way you did it, I finally got it to work: The problem I had with this particular method of uploading custom CSVs was with my CSVs. Somehow when I saved them from Excel, they somehow became tab-separated instead of comma-separated. There are still issues I'm having with the |
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@mcabello-cens Let me know if you know someone that I should @ on this topic, as nobody else has responded yet. I believe that @ShahimEssaid has located the issue. In a private message, he said:
I think this explains why I'm getting this as my error:
Additional attempts w/ some
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I have run into this exact same problem. The important thing is that the cli and files are accessible within the container. I created a temporary utility container just for this, and uploading of the latest Snomed worked just fine. My dockerfile: and finally load it:
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Heya, just chiming in here: the HAPI-FHIR CLI loader has a hard-coded 10mb limit to uploads, until it decides to use a local file descriptor instead. When it does this, it sends the local file location to the remote server, which in turn fails to resolve it (because it doesnt exist on the remote system). I'll be writing a pull request to provide a CLI argument to increase the maximum size you can send before it attempts to use a local file descriptor instead. |
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That would be great. |
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I was running into the same Problem. In Version 6.4.4 of the hapi-fhir-cli I found a switch to set the max upload filesize adding -s 10GB to the command did the trick and let me upload Loinc-2.73.zip with no problems. |
1. Docs outdated
https://hapifhir.io/hapi-fhir/docs/tools/hapi_fhir_cli.html
1.
The
-fflag should be changed to-v2.
IC10CM:
./hapi-fhir-cli upload-terminology -d Downloads/LOINC_2.54_MULTI-AXIAL_HIERARCHY.zip -d icd10cm_tabular_2021.xml -f dstu3 -t https://localhost:8080/baseDstu3 -u https://hl7.org/fhir/sid/icd-10-cmShould
Downloads/LOINC_2.54_MULTI-AXIAL_HIERARCHY.zipreally be in here?2. Can't import any terminologies
Steps to reproduce the behavior:
makefilemake upload-terminology, which runs commands mentioned in docs.Expected behavior
These code systems / terminologies will be uploaded
Actual behavior
ICD10CM: Succeeds, but doesn't upload any concepts
https://20.119.216.32:8080/fhir/CodeSystem/1?_format=json
{ "resourceType": "CodeSystem", "id": "1", "meta": { "versionId": "1", "lastUpdated": "2022-02-16T23:56:06.161+00:00", "source": "#hoo7Oyh75NdyGFOP" }, "url": "https://hl7.org/fhir/sid/icd-10-cm", "version": "2021", "name": "ICD-10-CM", "status": "active", "content": "not-present" }LOINC
After about 2 minutes, got error:
SNOMED
Environment
Possible causes
Docker:
Could be because using Docker, but the terminology files we're trying to import exist outside the container.
Related issues
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