Issue with Delta import of Snomed Uk #699

cristinacivili-work · 2020-10-21T16:25:52Z

cristinacivili-work
Oct 21, 2020

Hello,

We are having some issues with the import of a Delta Snomed Uk update.

This is our structure:

MAIN/2018-07-31/SNOMEDCT-UK/2019-06-01 is our most recent branch
SNOMEDCT2_28.0.0_20191001000001 is the oldest Snomed Uk update we need to import.

Our steps are the following:

create a branch 2019-10-01 with parent MAIN/2018-07-31/SNOMEDCT-UK/
import archive SNOMEDCT2_28.0.0_20191001000001 into MAIN/2018-07-31/SNOMEDCT-UK/ 2019-10-01
check the import commit on the branch and, if the import succeeds, merge MAIN/2018-07-31/SNOMEDCT-UK/2019-06-01 into MAIN/2018-07-31/SNOMEDCT-UK/ 2019-10-01

The problem is that, with archive SNOMEDCT2_28.0.0_20191001000001, the import doesn't produce any commit on the branch. There are no errors in the log, except for a few unrecognized snomed ids, and the import apparently succeeds, but the branch is just empty.

We have tried with other archives and it works perfectly fine, but we need this one first.

Any suggestion on what we could be doing wrong or anything we can check?

Thanks,
Cristina

Answered by cmark

Dec 17, 2020

Hi @cristinacivili-work,

FYI: The latest version has an improved RF2 import API, where you will be able to run the import process in dryRun mode, where only the validation phase is going to be executed and the actual import will be skipped. The response object should also contain information about potential import file defects and aid you in locating and resolving them.

Let us know what you think.

Cheers,
Mark

View full answer

cmark · 2020-10-22T08:08:37Z

cmark
Oct 22, 2020
Maintainer

Hi @cristinacivili-work,

Could you please send us some relevant logs from Snow Owl to aid the investigation?
What kind of content you have imported and on which branch in your Snow Owl instance?
Is the SNOMEDCT2_28.0.0_20191001000001 an official UK Clinical RF2 archive?

Usually, the import produces no commit because of the following two reasons:

There is nothing to actually commit, because you already have all the data imported on the branch.
There are structural (inconsistent file structure, invalid IDs, etc.) validation errors that prevent importing the selected RF2 data

Thank you,
Mark

0 replies

cristinacivili-work · 2020-10-22T08:56:11Z

cristinacivili-work
Oct 22, 2020
Author

Hi Mark,
thank you for your reply.

SNOMEDCT2_28.0.0_20191001000001 an official UK Clinical RF2 (Delta only) archive.
Our installation is in sync with releases up to June 2019, and this is the first Delta we need to import to update our data.

The current content is in branch MAIN/2018-07-31/SNOMEDCT-UK/2019-06-01 while the import attempt was in branch MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01

By manually looking at the archive files, it looks like there are at least a few new concepts to import in that release, so I think it is unlikely that there is nothing to commit. But there were some error messages, so your second option may explain the issue.

Please find below the logs of the import attempt.

Oct 21, 2020 @ 15:30:32.286	[2020-10-21 14:30:32.286] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  index.jobs - Updated 1 job documents with bulk update with script 'withDone' 

Oct 21, 2020 @ 15:30:32.265	[2020-10-21 14:30:32.265] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  lock - Lock released for branch 'MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01' of repository 'snomedStore' (importing release file content). 

Oct 21, 2020 @ 15:30:32.253	[2020-10-21 14:30:32.252] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] ERROR import - Component refers to a non-existing description with id '1916701000000112' in effective time '2019-10-01' 

Oct 21, 2020 @ 15:30:32.253	[2020-10-21 14:30:32.252] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] ERROR import - Component refers to a non-existing description with id '1916711000000114' in effective time '2019-10-01' 

Oct 21, 2020 @ 15:30:32.253	[2020-10-21 14:30:32.252] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] ERROR import - Component refers to a non-existing description with id '1916691000000112' in effective time '2019-10-01' 

Oct 21, 2020 @ 15:30:32.252	[2020-10-21 14:30:32.252] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] ERROR import - Component refers to a non-existing description with id '1916681000000110' in effective time '2019-10-01' 

Oct 21, 2020 @ 15:30:32.252	[2020-10-21 14:30:32.252] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] ERROR import - Component refers to a non-existing description with id '1916721000000115' in effective time '2019-10-01' 

Oct 21, 2020 @ 15:30:06.663	[2020-10-21 14:30:06.663] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - Validating component consistency in effective time '2019-09-19' 

Oct 21, 2020 @ 15:30:06.663	[2020-10-21 14:30:06.662] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - Preparing RF2 import took: 9.111 s 

Oct 21, 2020 @ 15:30:06.663	[2020-10-21 14:30:06.663] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - Validating component consistency in effective time '2019-10-01' 

Oct 21, 2020 @ 15:30:06.578	[2020-10-21 14:30:06.578] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Terminology/sct2_sRefset_OwlExpressionDelta_GB1000000_20191001.txt - 67.17 μs 

Oct 21, 2020 @ 15:30:06.578	[2020-10-21 14:30:06.578] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Terminology/sct2_TextDefinition_Delta-en_GB1000000_20191001.txt - 67.81 μs 

Oct 21, 2020 @ 15:30:06.578	[2020-10-21 14:30:06.578] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Terminology/sct2_StatedRelationship_Delta_GB1000000_20191001.txt - 73.15 μs 

Oct 21, 2020 @ 15:30:06.578	[2020-10-21 14:30:06.578] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Terminology/sct2_Relationship_Delta_GB1000000_20191001.txt - 6.573 ms 

Oct 21, 2020 @ 15:30:06.571	[2020-10-21 14:30:06.571] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Terminology/sct2_Description_Delta-en_GB1000000_20191001.txt - 5.163 ms 

Oct 21, 2020 @ 15:30:06.571	[2020-10-21 14:30:06.571] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Terminology/sct2_Identifier_Delta_GB1000000_20191001.txt - 109.3 μs 

Oct 21, 2020 @ 15:30:06.571	[2020-10-21 14:30:06.571] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] WARN  import - Unrecognized RF2 file: SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Terminology/sct2_Identifier_Delta_GB1000000_20191001.txt 

Oct 21, 2020 @ 15:30:06.566	[2020-10-21 14:30:06.565] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Terminology/sct2_Concept_Delta_GB1000000_20191001.txt - 1.438 ms 

Oct 21, 2020 @ 15:30:06.564	[2020-10-21 14:30:06.564] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Refset/Metadata/der2_sssssssRefset_MRCMDomainDelta_GB1000000_20191001.txt - 72.75 μs 

Oct 21, 2020 @ 15:30:06.564	[2020-10-21 14:30:06.564] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Refset/Metadata/der2_ssRefset_ModuleDependencyDelta_GB1000000_20191001.txt - 1.038 ms 

Oct 21, 2020 @ 15:30:06.563	[2020-10-21 14:30:06.563] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Refset/Metadata/der2_ssccRefset_MRCMAttributeRangeDelta_GB1000000_20191001.txt - 52.88 μs 

Oct 21, 2020 @ 15:30:06.563	[2020-10-21 14:30:06.562] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Refset/Metadata/der2_cRefset_MRCMModuleScopeDelta_GB1000000_20191001.txt - 53.11 μs 

Oct 21, 2020 @ 15:30:06.562	[2020-10-21 14:30:06.562] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Refset/Metadata/der2_cissccRefset_MRCMAttributeDomainDelta_GB1000000_20191001.txt - 54.41 μs 

Oct 21, 2020 @ 15:30:06.562	[2020-10-21 14:30:06.562] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] WARN  import - Unrecognized RF2 file: SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Refset/Metadata/der2_cciRefset_RefsetDescriptorDelta_GB1000000_20191001.txt 

Oct 21, 2020 @ 15:30:06.562	[2020-10-21 14:30:06.562] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Refset/Metadata/der2_ciRefset_DescriptionTypeDelta_GB1000000_20191001.txt - 56.91 μs 

Oct 21, 2020 @ 15:30:06.562	[2020-10-21 14:30:06.562] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Refset/Metadata/der2_cciRefset_RefsetDescriptorDelta_GB1000000_20191001.txt - 146.0 μs 

Oct 21, 2020 @ 15:30:06.562	[2020-10-21 14:30:06.562] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Refset/Map/der2_iissscRefset_ComplexMapDelta_GB1000000_20191001.txt - 169.6 μs 

Oct 21, 2020 @ 15:30:06.562	[2020-10-21 14:30:06.562] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Refset/Map/der2_sRefset_SimpleMapDelta_GB1000000_20191001.txt - 55.88 μs 

Oct 21, 2020 @ 15:30:06.561	[2020-10-21 14:30:06.561] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Refset/Map/der2_iisssciRefset_ExtendedMapDelta_GB1000000_20191001.txt - 881.8 ms 

Oct 21, 2020 @ 15:30:05.679	[2020-10-21 14:30:05.679] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Refset/Language/der2_cRefset_LanguageDelta-en_GB1000000_20191001.txt - 59.14 ms 

Oct 21, 2020 @ 15:30:05.679	[2020-10-21 14:30:05.679] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Refset/Map/der2_iisssccRefset_ExtendedMapDelta_GB1000000_20191001.txt - 103.1 μs 

Oct 21, 2020 @ 15:30:05.620	[2020-10-21 14:30:05.620] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Refset/Content/der2_Refset_SimpleDelta_GB1000000_20191001.txt - 8.060 s 

Oct 21, 2020 @ 15:29:57.560	[2020-10-21 14:29:57.560] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Refset/Content/der2_cRefset_AttributeValueDelta_GB1000000_20191001.txt - 1.858 ms 

Oct 21, 2020 @ 15:29:57.558	[2020-10-21 14:29:57.558] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z/Delta/Refset/Content/der2_cRefset_AssociationDelta_GB1000000_20191001.txt - 1.004 ms 

Oct 21, 2020 @ 15:29:57.557	[2020-10-21 14:29:57.556] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Terminology/sct2_StatedRelationship_Delta_INT_20181031.txt - 61.57 μs 

Oct 21, 2020 @ 15:29:57.557	[2020-10-21 14:29:57.557] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Terminology/sct2_TextDefinition_Delta-en_INT_20181031.txt - 65.65 μs 

Oct 21, 2020 @ 15:29:57.556	[2020-10-21 14:29:57.556] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Terminology/sct2_sRefset_OWLOntologyDelta_INT_20181031.txt - 50.80 μs 

Oct 21, 2020 @ 15:29:57.556	[2020-10-21 14:29:57.556] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] WARN  import - Unrecognized RF2 file: SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Terminology/sct2_Identifier_Delta_INT_20181031.txt 

Oct 21, 2020 @ 15:29:57.556	[2020-10-21 14:29:57.556] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Terminology/sct2_Relationship_Delta_INT_20181031.txt - 62.22 μs 

Oct 21, 2020 @ 15:29:57.556	[2020-10-21 14:29:57.556] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Terminology/sct2_sRefset_OWLAxiomDelta_INT_20181031.txt - 54.77 μs 

Oct 21, 2020 @ 15:29:57.556	[2020-10-21 14:29:57.556] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Terminology/sct2_Identifier_Delta_INT_20181031.txt - 115.1 μs 

Oct 21, 2020 @ 15:29:57.555	[2020-10-21 14:29:57.555] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Refset/Metadata/der2_ssccRefset_MRCMAttributeRangeDelta_INT_20181031.txt - 57.12 μs 

Oct 21, 2020 @ 15:29:57.555	[2020-10-21 14:29:57.555] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Refset/Metadata/der2_ssRefset_ModuleDependencyDelta_INT_20181031.txt - 57.40 μs 

Oct 21, 2020 @ 15:29:57.555	[2020-10-21 14:29:57.555] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Terminology/sct2_Description_Delta-en_INT_20181031.txt - 53.13 μs 

Oct 21, 2020 @ 15:29:57.555	[2020-10-21 14:29:57.555] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Terminology/sct2_Concept_Delta_INT_20181031.txt - 69.70 μs 

Oct 21, 2020 @ 15:29:57.555	[2020-10-21 14:29:57.555] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Refset/Metadata/der2_sssssssRefset_MRCMDomainDelta_INT_20181031.txt - 64.42 μs 

Oct 21, 2020 @ 15:29:57.554	[2020-10-21 14:29:57.554] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Refset/Map/der2_sRefset_SimpleMapDelta_INT_20181031.txt - 56.15 μs 

Oct 21, 2020 @ 15:29:57.554	[2020-10-21 14:29:57.554] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Refset/Metadata/der2_cciRefset_RefsetDescriptorDelta_INT_20181031.txt - 91.65 μs 

Oct 21, 2020 @ 15:29:57.554	[2020-10-21 14:29:57.554] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] WARN  import - Unrecognized RF2 file: SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Refset/Metadata/der2_cciRefset_RefsetDescriptorDelta_INT_20181031.txt 

Oct 21, 2020 @ 15:29:57.554	[2020-10-21 14:29:57.554] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Refset/Metadata/der2_cissccRefset_MRCMAttributeDomainDelta_INT_20181031.txt - 57.23 μs 

Oct 21, 2020 @ 15:29:57.554	[2020-10-21 14:29:57.554] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Refset/Metadata/der2_ciRefset_DescriptionTypeDelta_INT_20181031.txt - 59.68 μs 

Oct 21, 2020 @ 15:29:57.554	[2020-10-21 14:29:57.554] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Refset/Metadata/der2_cRefset_MRCMModuleScopeDelta_INT_20181031.txt - 74.92 μs 

Oct 21, 2020 @ 15:29:57.553	[2020-10-21 14:29:57.553] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Refset/Content/der2_Refset_SimpleDelta_INT_20181031.txt - 68.95 μs 

Oct 21, 2020 @ 15:29:57.553	[2020-10-21 14:29:57.553] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Refset/Map/der2_iisssccRefset_ExtendedMapDelta_INT_20181031.txt - 73.34 μs 

Oct 21, 2020 @ 15:29:57.553	[2020-10-21 14:29:57.553] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Refset/Content/der2_cRefset_AttributeValueDelta_INT_20181031.txt - 85.35 μs 

Oct 21, 2020 @ 15:29:57.553	[2020-10-21 14:29:57.553] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Refset/Language/der2_cRefset_LanguageDelta-en_INT_20181031.txt - 59.70 μs 

Oct 21, 2020 @ 15:29:57.553	[2020-10-21 14:29:57.552] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  import - SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z/Delta/Refset/Content/der2_cRefset_AssociationDelta_INT_20181031.txt - 170.0 μs 

Oct 21, 2020 @ 15:29:57.534	[2020-10-21 14:29:57.533] [Worker-1: snomed-import-MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01] INFO  lock - Lock acquired for branch 'MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01' of repository 'snomedStore' (importing release file content).

Thanks,
Cristina

0 replies

cmark · 2020-10-22T17:35:48Z

cmark
Oct 22, 2020
Maintainer

Hi @cristinacivili-work,

That is the source of the issue then.
The branch 2019-10-01 does not have any UK content, neither on that branch directly nor on the parent branches.
I would expect the UK content to be present on the SNOMEDCT-UK branch and the 2019-06-01 branch an "empty" version branch. By empty I mean like a Git tag, a reference to a point where the UK content represents the 2019-06-01 version.

If the data lives on the SNOMEDCT-UK branch, then feel free to import it onto that branch with the createVersion boolean flag set to true. That will implicitly create all necessary version branches (based on the effective time values in the source file) during import, so in the end the 2019-10-01 should be available, and should have all the data from the input RF2 delta file loaded properly.

Hint: The Extension management documentation has very descriptive images and scenarios to help you understand Snow Owl's branching/versioning features and how an extension can be represented in Snow Owl.

I hope this clarifies your question, let me know if you have any further.

Cheers,
Mark

0 replies

cristinacivili-work · 2020-10-23T14:42:02Z

cristinacivili-work
Oct 23, 2020
Author

Hi @cmark,
thank you very much for the explanation, I was finally able to import the archive by importing directly into MAIN/2018-07-31/SNOMEDCT-UK.
In order to do so, however, I also had to amend manually the archive by removing the IDs that were causing validation errors. This operation is very time consuming and error prone. Is there a way to configure the import so that the validation errors won't block the process and the rows containing "bad IDs" will just be ignored?

Alternatively, do you have any plan of exposing the import validation as a separate endpoint?
That could be very useful for automating the kind of cleanup that I did manually.

Thanks,
Cristina

0 replies

cmark · 2020-10-25T15:15:09Z

cmark
Oct 25, 2020
Maintainer

Hi @cristinacivili-work,

Yes, I understand hacking the RF2 file is not the best solution when it comes to importing it without errors into Snow Owl.
So far, we have used internal tools and other scripts to modify the content of an RF2 archive to make it importable into Snow Owl, but that is unfortunately cannot be open sourced yet.
At the moment, there is no way to filter out components that reference missing content (or ignore the validation issue), because that might break something in the long run (especially when it comes to core SNOMED CT components).
I see two possible enhancements here:

Allow the import to filter out/ignore non-metadata reference set members (like mappings and simple type members). This is a common scenario we deal with with our internal tools and it would be a great addition to the open-source RF2 import feature set.
Expose an RF2 archive validator endpoint that can validate the incoming package against the currently stored content.

Let us know if you have any further issues with RF2 imports.

Thank you for your feedback and ideas,
Mark

0 replies

cristinacivili-work · 2020-10-29T15:52:50Z

cristinacivili-work
Oct 29, 2020
Author

Hi @cmark,
thanks again for your help.

I was able to make progress with the delta updates, but I'm now stuck with one specific archive.
It's the Delta Snomed UK Release of May 2020 (here https://isd.digital.nhs.uk/trud3/user/authenticated/group/0/pack/26/subpack/104/releases).

I am getting a lot of validation errors referring to missing IDs contained in the file der2_cRefset_CareRecordElementDelta_GB_20200513.txt.
After several attempt of fixing the file manually, I attempted to import the archive without that file. Unfortunately I'm now experiencing a different issue: the import fails because it detect an already existing MAIN/2018-07-31/SNOMEDCT-UK/2020-05-01 branch, which I believe is created by the import itself.

I wanted to check if you tried to use this archive and if you run into the same issues.

Thanks,
Cristina

0 replies

cmark · 2020-11-22T09:19:14Z

cmark
Nov 22, 2020
Maintainer

Hi @cristinacivili-work,

I'm happy to hear you were able to make progress.

Yes, UK RefSets often refer content from another extension, especially if the member is coming from the UK EDITION.
There are two ways to resolve such errors:

Remove those lines from the RF2 archive: in case you don't need that content, feel free to remove it, to help you identify lines like that we have made a small change to allow the importer to run in dryRun mode, just validate the archive against the current data and skip the import phase. See the branch here: https://github.com/b2ihealthcare/snow-owl/tree/feature/SO-4483-support-dry-run-rf2-import
Import the required content first or merge the required content with the RF2 archive you have, resulting in a single RF2 import file and import that. There is a tool that might be helpful in such cases: https://github.com/b2ihealthcare/rf2-d2

Yes, we are maintaining servers with all the UK data up to the most recent releases (both 2020-08-05 and 2020-10-28) and we have identified those issues as well and in order to import them, we had to fix them first in the RF2 archive.

I hope this helps and as always feel free to reach us if you run into any issues.

Cheers,
Mark

0 replies

cmark · 2020-12-17T09:58:10Z

cmark
Dec 17, 2020
Maintainer

Hi @cristinacivili-work,

FYI: The latest version has an improved RF2 import API, where you will be able to run the import process in dryRun mode, where only the validation phase is going to be executed and the actual import will be skipped. The response object should also contain information about potential import file defects and aid you in locating and resolving them.

Let us know what you think.

Cheers,
Mark

0 replies

cristinacivili-work · 2021-01-08T11:04:09Z

cristinacivili-work
Jan 8, 2021
Author

Thank you for letting me know Mark.
I haven't had the chance to try it yet, but I'll do. it soon.
It sounds like a great addition to the API.

0 replies

cristinacivili-work · 2021-01-20T11:05:35Z

cristinacivili-work
Jan 20, 2021
Author

Hi @cmark,
I finally had the chance to try the new dry run feature and it has been really helpful to identify and get rid of some of the import error I was getting.

I have now a slightly different question, still related to the imports.

Assume I have my Snomed UK in a branch like this MAIN/2018-07-31/SNOMED-UK.
After loading the last June delta release I have MAIN/2018-07-31/SNOMED-UK/2020-06-01. After that, Snomed Uk switches to the 2019 international release, but if I load the August Delta using the path MAIN/2018-07-31/SNOMED-UK I wrongly get the import in MAIN/2018-07-31/SNOMED-UK/2020-08-05 while I was expecting MAIN/2019-07-31/SNOMED-UK/2020-08-05.

What would be the right approach here?
Would creating an empty branch MAIN/2019-07-31, moving SNOMED-UK code system under that and using MAIN/2019-07-31/SNOMED-UK as import path work?

Again, thanks for your help! :)

3 replies

cmark Jan 20, 2021
Maintainer

Hi @cristinacivili-work,

Thank you for trying out the new dryRun feature.

The easiest solution to your problem is to import the UK CL 2020-08-05 Snapshot RF2 directly onto the MAIN/2019-07-31 version branch, which has been automatically created during the INT RF2 import.
If you don't have the International Edition RF2 data up to at least the required UK CL dependency version, then you have to import that first directly to MAIN as a Delta RF2.
If you have it then the MAIN/2019-07-31 branch should be available if you have imported the International RF2 with createVersions enabled and from a Full Release.

I hope this solves your problem, let us know if you have any further questions.

Cheers,
Mark

cristinacivili-work Jan 20, 2021
Author

Thank you so much Mark, it makes totally sense.
I was missing the intermediate step of the International update before attempting the august UK import.

Cheers

cmark Jan 22, 2021
Maintainer

Glad to hear that. Let us know if you have any further questions.

cristinacivili-work · 2021-01-25T11:40:10Z

cristinacivili-work
Jan 25, 2021
Author

Good morning Mark,
unfortunately I'm still having some issues with importing the August 2020 Snomed CT Uk archive.

So, to recall, currently we have MAIN/2018-07-31/SNOMEDCT-UK/2019-06-01 and we start a series of delta updates from there.

What I do:

Delta updates for Snomed UK using MAIN/2018-07-31/SNOMEDCT-UK as path. These are 6 updates from October 2019 to June 2020, which succeed and create the expected branch. With these we reach MAIN/2018-07-31/SNOMEDCT-UK/2020-06-10.
The next update requires 2019 International release, so I proceed with the Delta updates for Snomed International using MAIN as path. These succeed and create MAIN/2019-07-31.
Now I create the branch MAIN/2019-07-31/SNOMEDCT-UK, perform a merge with source=MAIN/2018-07-31/SNOMEDCT-UK and target = MAIN/2019-07-31/SNOMEDCT-UK and update the code system path for SNOMEDCT-UK to the newer branch.
Now I resume the Snomed Uk updates and attempt to import the August 2020 release in MAIN/2019-07-31/SNOMEDCT-UK. The dry run reveals more than 17k errors, basically no code mentioned in the archive seems to be recognized, as if I was attempting to import in an empty branch. I must mention that If I try the dry run on MAIN/2018-07-31/SNOMEDCT-UK, for comparison, as I expect the branch to be equals at this point, I only get around 3K, which sounds more reasonable.

Do you see something wrong in the above steps that would cause this to happen?

I should mention, I also tried to merge the latest uk branch - MAIN/2018-07-31/SNOMEDCT-UK/2020-06-10 directly into MAIN/2019-07-31/SNOMEDCT-UK, but the result is still the same (i.e., 17k errors).

Cheers,

Cristina

1 reply

cmark Jan 26, 2021
Maintainer

Hi @cristinacivili-work,

The steps look ok to me.
A couple of questions that might help resolve this issue:

Which version of Snow Owl are you using?
Are you sure the merge process completes without any issues? Did you use the new squash=false option?
When you say Import X UK Release, you import a Delta or Snapshot?
What happens if you perform a single UK concept request from both branches? Do you get the expected concept object back?

Thanks,
Mark

cristinacivili-work · 2021-01-27T09:37:48Z

cristinacivili-work
Jan 27, 2021
Author

Hi @cmark ,
thanks again for helping!

we are using version 7.14.0
the merge process status appear as COMPLETED, however it takes a very small amount of time considering the amount of data it should be merging. I'm not using squash= false, I'm just passing the source and target branch when merging. Should I try that?
I'm always importing deltas, both for the international and the UK release.
Attempt to retrieve a single UK concept that exists in MAIN/2018-07-31/SNOMEDCT-UK failed in MAIN/2019-07-31/SNOMEDCT-UK after the merge. So the merge appears to be the problem.

Cheers,
Cristina

1 reply

cmark Jan 28, 2021
Maintainer

Hi @cristinacivili-work,

Okay, then could you please try to use 7.14.3 and the squash=false option?
That contains a branch visibility query fix and a few performance-related fixes.
Do you have anything in the log files that indicate that the merge has failed for any reason?

Cheers,
Mark

cristinacivili-work · 2021-01-29T09:37:09Z

cristinacivili-work
Jan 29, 2021
Author

Hi Mark,
I didn't see anything indicating a merge failure in the logs.
I will try to update to the latest version and redo all the steps and merge with squash=false.

Thanks again,
Cristina

0 replies

cristinacivili-work · 2021-02-01T18:35:57Z

cristinacivili-work
Feb 1, 2021
Author

Hi @cmark,
I updated and tried again today, but the process still seems to be faulty.

At the point in which i merge with "source": "MAIN/2018-07-31/SNOMEDCT-UK", "target": "MAIN/2019-07-31/SNOMEDCT-UK" and "squash": false, I can now see UK concepts in both branches, but I cannot see Snomed International concepts.

More precisely, assume I try to lookup international concept XYZ, I can see it in MAIN/2018-07-31/SNOMEDCT-UK, I can see it in MAIN/2019-07-31, but I cannot see it in MAIN/2019-07-31/SNOMEDCT-UK, where I get an error 500.

The following attempts at imports fail again due to many references to international codes that cannot be found.

The merge status is completed and not log indicates any failure. In this case the issue seems to be the child branch is not inheriting the parent branch concepts as expected.

Any idea what may be going on?

Cheers,

Cristina

1 reply

cmark Feb 8, 2021
Maintainer

Hi @cristinacivili-work,

Could you please send us the 500 error from your log? It might help us identify the root cause.

Thank you,
Mark

cristinacivili-work · 2021-03-26T11:28:43Z

cristinacivili-work
Mar 26, 2021
Author

Hi @cmark,
apologies for reopening this old thread, I've been working on other things for a while.

The issue with the merge seems to be resolved, but I still cannot do a clean import of the August 2020 Uk release.

I now have MAIN/2018-07-31/SNOMEDCT-UK and MAIN/2019-07-31/SNOMEDCT-UK, which have exactly the same number of concepts, and have updated the dependency of SNOMEDCT-UK to the 2019 branch.

I want to import the August Delta, dependent on the 2019 release, and the following happens:

If I import in MAIN/2018-07-31/SNOMEDCT-UK it succeeds and creates MAIN/2018-07-31/SNOMEDCT-UK/2020-08-05, but this is not the expected branch.
If I import in MAIN/2019-07-31/SNOMEDCT-UK, as it should be, the dryRun finds around 30K errors (the number seem to be inconsistent at every attempt).

Of course we could keep importing everything into the 2018 branch, but this would result in a wrong branching structure going forward.

Do you have any other suggestions of what could be causing the issue?

Cheers,
Cristina

9 replies

cmark Mar 29, 2021
Maintainer

Thanks, that looks good.

The next one is to check whether the component 781062007 is visible. Could you please send me the responses to the following request?

GET /snomed-ct/v3/MAIN/2018-07-31/concepts/781062007
GET /snomed-ct/v3/MAIN/2019-01-31/concepts/781062007
GET /snomed-ct/v3/MAIN/2019-07-31/concepts/781062007
GET /snomed-ct/v3/SNOMEDCT/concepts/781062007
GET /snomed-ct/v3/SNOMEDCT-UK/concepts/781062007

Also could you please send me the version list for the SNOMEDCT-UK CodeSystem?
GET /admin/codesystems/SNOMEDCT-UK/versions

Cheers,
Mark

cristinacivili-work Mar 29, 2021
Author

Ah, this is interesting:

GET /snomed-ct/v3/MAIN/2018-07-31/concepts/781062007

{
    "id": "781062007",
    "released": true,
    "active": true,
    "effectiveTime": "20190131",
    "moduleId": "900000000000207008",
    "iconId": "medicinal_product_form",
    "definitionStatus": {
        "id": "900000000000073002"
    },
    "subclassDefinitionStatus": "NON_DISJOINT_SUBCLASSES",
    "ancestorIds": [
        "-1",
        "11783005",
        "138875005",
        "350102001",
        "354035004",
        "373873005",
        "440131009",
        "763087004",
        "763158003",
        "763760008",
        "777075006",
        "10363601000001109",
        "10363701000001104"
    ],
    "parentIds": [
        "776796004",
        "781061000"
    ],
    "statedAncestorIds": [
        "-1",
        "138875005",
        "373873005"
    ],
    "statedParentIds": [
        "763158003"
    ],
    "definitionStatusId": "900000000000073002"
}

GET /snomed-ct/v3/MAIN/2019-01-31/concepts/781062007 --> As above

GET /snomed-ct/v3/MAIN/2019-07-31/concepts/781062007 --> Back to the 500

{
    "status": 500,
    "code": 0,
    "message": "Something went wrong during the processing of your request.",
    "errorCode": 0,
    "statusCode": 500
}

Logs

Mar 29, 2021 @ 17:03:54.409 | at com.b2international.snowowl.internal.eventbus.EventBus$1.run(EventBus.java:164) |  
-- | -- | --

  |   | Mar 29, 2021 @ 17:03:54.409 | at com.b2international.snowowl.core.repository.ApiRequestHandler.handle(ApiRequestHandler.java:68) |  

  |   | Mar 29, 2021 @ 17:03:54.409 | at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) |  

  |   | Mar 29, 2021 @ 17:03:54.409 | at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:75) |  

  |   | Mar 29, 2021 @ 17:03:54.409 | at com.b2international.snowowl.core.request.HealthCheckingRequest.execute(HealthCheckingRequest.java:1) |  

  |   | Mar 29, 2021 @ 17:03:54.408 | at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:75) |  

  |   | Mar 29, 2021 @ 17:03:54.408 | at com.b2international.index.revision.DefaultRevisionIndex.lambda$0(DefaultRevisionIndex.java:113) |  

  |   | Mar 29, 2021 @ 17:03:54.408 | java.lang.IllegalStateException: Multiple documents found for '781062007'. |  

  |   | Mar 29, 2021 @ 17:03:54.407 | at com.b2international.snowowl.core.authorization.AuthorizedRequest.execute(AuthorizedRequest.java:123) |  

  |   | Mar 29, 2021 @ 17:03:54.407 | at com.b2international.snowowl.core.monitoring.MonitoredRequest.execute(MonitoredRequest.java:52) |  

  |   | Mar 29, 2021 @ 17:03:54.407 | at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:75) |  

  |   | Mar 29, 2021 @ 17:03:54.407 | at com.b2international.snowowl.core.repository.ApiRequestHandler.handle(ApiRequestHandler.java:1)

GET /snomed-ct/v3/SNOMEDCT/concepts/781062007 --> Correct response as above

GET /snomed-ct/v3/SNOMEDCT-UK/concepts/781062007 --> 500 Error

Finally, for `GET /snomed-ct/v3/SNOMEDCT-UK/concepts/781062007

{
    "items": [
        {
            "importDate": "2020-07-27T18:52:26.753+0000",
            "effectiveDate": "20190601",
            "lastModificationDate": "1970-01-01T00:00:00.000+0000",
            "description": "created on import",
            "version": "2019-06-01",
            "path": "MAIN/2018-07-31/SNOMEDCT-UK/2019-06-01",
            "uri": "SNOMEDCT-UK/2019-06-01"
        },
        {
            "importDate": "2021-02-12T16:16:36.614+0000",
            "effectiveDate": "20190919",
            "lastModificationDate": "1970-01-01T00:00:00.000+0000",
            "description": "",
            "version": "2019-09-19",
            "path": "MAIN/2018-07-31/SNOMEDCT-UK/2019-09-19",
            "uri": "SNOMEDCT-UK/2019-09-19"
        },
        {
            "importDate": "2021-02-12T16:21:37.892+0000",
            "effectiveDate": "20191001",
            "lastModificationDate": "1970-01-01T00:00:00.000+0000",
            "description": "",
            "version": "2019-10-01",
            "path": "MAIN/2018-07-31/SNOMEDCT-UK/2019-10-01",
            "uri": "SNOMEDCT-UK/2019-10-01"
        },
        {
            "importDate": "2021-02-12T16:23:40.388+0000",
            "effectiveDate": "20200204",
            "lastModificationDate": "1970-01-01T00:00:00.000+0000",
            "description": "",
            "version": "2020-02-04",
            "path": "MAIN/2018-07-31/SNOMEDCT-UK/2020-02-04",
            "uri": "SNOMEDCT-UK/2020-02-04"
        },
        {
            "importDate": "2021-02-12T16:36:18.112+0000",
            "effectiveDate": "20200401",
            "lastModificationDate": "1970-01-01T00:00:00.000+0000",
            "description": "",
            "version": "2020-04-01",
            "path": "MAIN/2018-07-31/SNOMEDCT-UK/2020-04-01",
            "uri": "SNOMEDCT-UK/2020-04-01"
        },
        {
            "importDate": "2021-02-12T16:37:44.597+0000",
            "effectiveDate": "20200415",
            "lastModificationDate": "1970-01-01T00:00:00.000+0000",
            "description": "",
            "version": "2020-04-15",
            "path": "MAIN/2018-07-31/SNOMEDCT-UK/2020-04-15",
            "uri": "SNOMEDCT-UK/2020-04-15"
        },
        {
            "importDate": "2021-02-12T16:47:20.660+0000",
            "effectiveDate": "20200501",
            "lastModificationDate": "1970-01-01T00:00:00.000+0000",
            "description": "",
            "version": "2020-05-01",
            "path": "MAIN/2018-07-31/SNOMEDCT-UK/2020-05-01",
            "uri": "SNOMEDCT-UK/2020-05-01"
        },
        {
            "importDate": "2021-02-12T16:51:37.368+0000",
            "effectiveDate": "20200501",
            "lastModificationDate": "1970-01-01T00:00:00.000+0000",
            "description": "",
            "version": "2020-05-01",
            "path": "MAIN/2018-07-31/SNOMEDCT-UK/2020-05-01",
            "uri": "SNOMEDCT-UK/2020-05-01"
        },
        {
            "importDate": "2021-02-12T16:37:49.316+0000",
            "effectiveDate": "20200501",
            "lastModificationDate": "1970-01-01T00:00:00.000+0000",
            "description": "",
            "version": "2020-05-01",
            "path": "MAIN/2018-07-31/SNOMEDCT-UK/2020-05-01",
            "uri": "SNOMEDCT-UK/2020-05-01"
        },
        {
            "importDate": "2021-02-12T17:01:06.507+0000",
            "effectiveDate": "20200513",
            "lastModificationDate": "1970-01-01T00:00:00.000+0000",
            "description": "",
            "version": "2020-05-13",
            "path": "MAIN/2018-07-31/SNOMEDCT-UK/2020-05-13",
            "uri": "SNOMEDCT-UK/2020-05-13"
        },
        {
            "importDate": "2021-02-12T17:03:15.195+0000",
            "effectiveDate": "20200610",
            "lastModificationDate": "1970-01-01T00:00:00.000+0000",
            "description": "",
            "version": "2020-06-10",
            "path": "MAIN/2018-07-31/SNOMEDCT-UK/2020-06-10",
            "uri": "SNOMEDCT-UK/2020-06-10"
        }
    ],
    "searchAfter": "AoJwwNjhzfICQQ==",
    "limit": 2147483646,
    "total": 11
}

Cheers,
Cristina

cmark Mar 29, 2021
Maintainer

Hmm, something happened during the Import of International 2019-07-31 Delta, because both MAIN/2019-07-31 and MAIN/2019-07-31/SNOMEDCT-UK suffer from the same issue.

The multiple documents issue means that for a single logical component there is more than one physical actual index document in the Elasticsearch index. This should not happen under normal circumstances, as the system ensures revision document uniqueness through transactions.
There were a few bugs related to sync issues we have found in the past couple of months and resolved them successfully. This might be one of the few rare occurrences of the issue.

To fix you have two options:

Start from scratch (this is the easiest). If you have all the data exported to RF2 format, then you can easily start from scratch by replaying the codesystem create/import requests in chronological order (you could even import the entire SNOMED CT International Edition of 2021-01-31 if you want).
Collect and fix all the affected concepts either manually or using a groovy script (we are about to release a CLI command for this very feature actually, so we can even create a groovy script for it in the coming days)

One more vote besides the "start from scratch" option is that in the list of versions for SNOMEDCT-UK there are multiple documents found with the same version/effectiveTime. This is a bug in the RF2 importer which is actually going to be fixed in the upcoming 7.17.0 release. Importing the same RF2 content twice does not produce any content change but produces a duplicate version entry which is incorrect and should not happen.

Let me know if this helps or you need any further clarification to make the best decision.

Cheers,
Mark

cristinacivili-work Apr 12, 2021
Author

Thank you Mark,
I managed to do the update at last! 👍
What worked was updating the International via Deltas, and importing the latest UK snapshot under the 2020-07-31 branch, as I understood that the problem with duplicates was restricted to the UK branches.
I really appreciated your help with this, keep up the good work.

Cheers,
Cristina

cmark Apr 12, 2021
Maintainer

Thank you Cristina :)
Glad to hear you've managed to import the latest UK Snapshot.
Feel free to contact us here if you run into any other issues.

Issue with Delta import of Snomed Uk #699

cristinacivili-work Oct 21, 2020

Replies: 15 comments · 15 replies

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