Problem loading Loinc_2.72 #511
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Thank you for reporting this bug. The errors in the first upload are caused by Snowstorm attempting to expand value sets as they are imported in an attempt to validate them. This does not always work well because some value sets refer to other nested value sets that are not yet imported. I intend to remove this validation so that the first import completes cleanly. It looks like the error in the second upload may also be caused by an issue with that validation. I will look into this. |
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Hi. Thanks in advance. |
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This will not be fixed quickly. I estimate the end of July. |
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The tech team, who are in charge of the Snowstorm release schedule, plan to make a public release at the start of August and another at the end of September. @FJGL how pressing are your timelines for this fix? Creating a fix release in the SnowstormX project could be a short term workaround. |
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Hi.
Don´t worry.. We will wait for the September Release.
Sorry for the late reply.
Regards.
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Hi. Thanks. |
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A Snowstorm version 9.0.0 release candidate has been created in the release-candidate branch including the LOINC package loading fixes. The release candidate will go through the usual testing and is scheduled to be deployed to our production environments on the 27th September. This release has breaking changes because it requires JDK 17 (Snowstorm previously required JDK 11). You have the option of testing the release candidate directly by checking out the |
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We have built the release candidate 9.0.0 and it now successfully loads the Loinc_2.72 distribution without errors in the log the first or subsequent times, but it does not load the last version of LOINC 2.76. 2023-09-21 08:08:33.25 [main] ERROR c.u.f.c.UploadTerminologyCommand Received the following response: We assume it's because of the comment in using-the-fhir-api.md: "N.B. The new filename since Loinc 2.73 doesn't work yet." Any idea when versions of Loinc later than 2.72 can be used? TIA |
Any news about the deployment?. Has everything gone well or will be necessary a bugfix 9.0.1 ? Just to have an estimate of the release date of the Release Candidate. Regards. |
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I have just published SnowstormX 9.0.1 with the fix for loading LOINC 2.73 and above. Please let us know if this works for you and we will get this change into a future Snowstorm release. |
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Hello. Yes, it works! and we are very interested in having that change included in the next Snowstorm release. We have loaded Loinc versions 2.74 and 2.76 in a clean Elasticsearch installation without problems. Just for the sake of completeness if we load version 2.72 there is an exception: ERROR c.u.f.c.UploadTerminologyCommand Received the following response: We understand that it is no longer compatible with Loinc versions < 2.73. EDIT: But... We have detected a problem because we need to perform the upload remotely and it fails with an exception related to the maximum size of a JSON request. .\hapi-fhir-cli upload-terminology -s 1GB -d Loinc_2.76.zip -v r4 -t http://192.168.0.26:8888/snowstorm/fhir -u http://loinc.org c.u.f.c.UploadTerminologyCommand Adding ZIP file: Loinc_2.76.zip ERROR c.u.f.c.UploadTerminologyCommand Received the following response: ERROR ca.uhn.fhir.cli.App Error during execution: |
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@FJGL what version of the hapi-fhir-cli tool you are using? This is my output: |
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@kaicode The version is just that:
To reproduce the issue yo must try with a "remote" file: .\hapi-fhir-cli upload-terminology -s 1GB -d Loinc_2.76.zip -v r4 -t http://192.168.0.26:8888/snowstorm/fhir -u http://loinc.org/ instead of a local reference: hapi-fhir-cli upload-terminology -d Loinc_2.76.zip -v r4 -t http://localhost:8080/fhir -u http://loinc.org We have investigated the issue amd it seems that is a problem with the HAPI-FHIR version 6.6.2 included with snowstorm-x that is resolved with the 6.8.5 release or later, We have tested it successfully by rebuilding Snowstorm-X 9.0.1 with the HAPI-FHIR dependencies updated to 6.8.5. However, we are unsure of the impact of this on the rest of the FHIR functionality. |
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@FJGL thank you for debugging this and finding a fix that should work. |
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This is fixed in Snowstorm version 10.2.1, released today: |
Hi.
We are in the process of testing this new feature of 8.1.0 of loading LOINC files using the hapi-fhir-cli
https://github.com/IHTSDO/snowstorm/blob/master/docs/using-the-fhir-api.md#loinc
The first import works, except for a few valuesets not found, but after that succesful upload, it fails on every next try to reload the same file with an elasticsearch exception:
SNOWSTORM: 8.1.0
ELASTICSEARCH: 7.17.10 (clean installation, same with 7.17.8)
FIRST UPLOAD
SECOND UPLOAD
The exception at client side
all shards failedis a bit misleading, because the real error in the snowstorm spring.log seems that is supressedfailed to create query: maxClauseCount is set to 1024:The text was updated successfully, but these errors were encountered: