:owl: Snow Owl Terminology Server - production-ready, scalable, supports FHIR R4, FHIR R5, SNOMED CT International and Extensions, LOINC, ICD-10, dm+d, custom code systems and many others
Home Page: https://docs.b2ihealthcare.com/snow-owl/
License: Apache License 2.0
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Running the latest Snowowl 7.x (docker image from today), with ES 6.8.0 in AWS ES.
I got this error while trying to import Snomed:
GET /snowowl/snomed-ct/v3/imports/93b27bc6-2b9f-4b5a-915b-b6a4aa584109 returns:
{"type":"FULL","branchPath":"MAIN","createVersions":true,"codeSystemShortName":"SNOMEDCT","id":"93b27bc6-2b9f-4b5a-915b-b6a4aa584109","status":"FAILED","startDate":"2019-11-19T17:24:42.054+0000","completionDate":"2019-11-19T17:39:20.451+0000"}
Server side logs:
Caused by: org.elasticsearch.client.ResponseException: method [POST], host [https://vpc-es-snowowl-some-path.eu-west-1.es.amazonaws.com], URI [/snomedstore-concept/_bulk?timeout=1m], status line [HTTP/1.1 413 Request Entity Too Large]
{"Message":"Request size exceeded 10485760 bytes"}
Full details:
[2019-11-19T17:24:41.395] INFO eventbus-39 request {"locales":[],"expand":{},"fields":[],"componentIds":"[138875005]","limit":0,"options":{},"operation":"browse","type":"SnomedConceptSearchRequest","branchPath":"MAIN","repositoryId":"snomedStore"}
[2019-11-19T17:24:41.666] INFO eventbus-64 request {"locales":[],"expand":{},"fields":[],"id":"SNOMEDCT","operation":"browse","type":"CodeSystemGetRequest","repositoryId":"snomedStore"}
[2019-11-19T17:24:44.107] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Terminology/sct2_sRefset_OWLExpressionFull_INT_20190131.txt - 93.37 ms
[2019-11-19T17:25:04.759] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Terminology/sct2_StatedRelationship_Full_INT_20190131.txt - 20.65 s
[2019-11-19T17:25:15.334] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Terminology/sct2_Concept_Full_INT_20190131.txt - 10.57 s
[2019-11-19T17:25:15.511] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Terminology/sct2_TextDefinition_Full-en_INT_20190131.txt - 177.0 ms
[2019-11-19T17:27:01.408] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Terminology/sct2_Relationship_Full_INT_20190131.txt - 1.765 min
[2019-11-19T17:27:52.014] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Terminology/sct2_Description_Full-en_INT_20190131.txt - 50.61 s
[2019-11-19T17:27:52.015] WARN eventbus-66 import Unrecognized RF2 file: SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Terminology/sct2_Identifier_Full_INT_20190131.txt
[2019-11-19T17:27:52.015] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Terminology/sct2_Identifier_Full_INT_20190131.txt - 306.1 ?s
[2019-11-19T17:27:55.601] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Refset/Content/der2_cRefset_AssociationFull_INT_20190131.txt - 3.585 s
[2019-11-19T17:28:10.778] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Refset/Content/der2_cRefset_AttributeValueFull_INT_20190131.txt - 15.18 s
[2019-11-19T17:28:11.085] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Refset/Content/der2_Refset_SimpleFull_INT_20190131.txt - 306.5 ms
[2019-11-19T17:29:24.683] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Refset/Language/der2_cRefset_LanguageFull-en_INT_20190131.txt - 1.227 min
[2019-11-19T17:29:30.077] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Refset/Map/der2_iisssccRefset_ExtendedMapFull_INT_20190131.txt - 5.394 s
[2019-11-19T17:29:40.066] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Refset/Map/der2_sRefset_SimpleMapFull_INT_20190131.txt - 9.988 s
[2019-11-19T17:29:40.067] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Refset/Metadata/der2_sssssssRefset_MRCMDomainFull_INT_20190131.txt - 927.7 ?s
[2019-11-19T17:29:40.067] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Refset/Metadata/der2_cRefset_MRCMModuleScopeFull_INT_20190131.txt - 128.5 ?s
[2019-11-19T17:29:40.069] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Refset/Metadata/der2_cissccRefset_MRCMAttributeDomainFull_INT_20190131.txt - 1.044 ms
[2019-11-19T17:29:40.069] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Refset/Metadata/der2_ciRefset_DescriptionTypeFull_INT_20190131.txt - 120.7 ?s
[2019-11-19T17:29:40.070] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Refset/Metadata/der2_ssccRefset_MRCMAttributeRangeFull_INT_20190131.txt - 1.078 ms
[2019-11-19T17:29:40.075] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Refset/Metadata/der2_ssRefset_ModuleDependencyFull_INT_20190131.txt - 4.419 ms
[2019-11-19T17:29:40.075] WARN eventbus-66 import Unrecognized RF2 file: SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Refset/Metadata/der2_cciRefset_RefsetDescriptorFull_INT_20190131.txt
[2019-11-19T17:29:40.075] INFO eventbus-66 import SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z/Full/Refset/Metadata/der2_cciRefset_RefsetDescriptorFull_INT_20190131.txt - 199.8 ?s
[2019-11-19T17:29:41.703] INFO eventbus-66 import Preparing RF2 import took: 4.962 min
[2019-11-19T17:29:41.704] WARN eventbus-66 import Extended Map target field was empty for '80009454-5531-5f78-b7c9-d288f2346d83'
[2019-11-19T17:29:41.704] WARN eventbus-66 import Extended Map target field was empty for '80009454-5531-5f78-b7c9-d288f2346d83'
[2019-11-19T17:29:41.704] WARN eventbus-66 import Extended Map target field was empty for '8002c5db-9038-50fe-8ccc-204a84213674'
[2019-11-19T17:29:41.704] WARN eventbus-66 import Extended Map target field was empty for '8003e488-77eb-5600-b541-7caa2e77503e'
[2019-11-19T17:29:41.704] WARN eventbus-66 import Extended Map target field was empty for '800449ce-37c1-5b0f-9dd5-570a36fc47cd'
[2019-11-19T17:29:41.704] WARN eventbus-66 import Extended Map target field was empty for '800d6fb8-a02f-5d4c-8490-79e922da580e'
[2019-11-19T17:29:41.704] WARN eventbus-66 import Extended Map target field was empty for '800d6fb8-a02f-5d4c-8490-79e922da580e'
[2019-11-19T17:29:41.704] WARN eventbus-66 import Extended Map target field was empty for '800eb8c2-10fc-5c7a-b71a-aa760fb465f8'
[2019-11-19T17:29:41.704] WARN eventbus-66 import Extended Map target field was empty for '800f53ad-bd42-545a-88c2-7ebcd7f354b6'
[2019-11-19T17:29:41.704] WARN eventbus-66 import Extended Map target field was empty for '801046f2-9bd0-5607-88af-c1306f566731'
[2019-11-19T17:29:41.704] WARN eventbus-66 import Extended Map target field was empty for '80111236-0235-55b2-bdf5-9549bf4baea4'
[2019-11-19T17:29:41.704] WARN eventbus-66 import Extended Map target field was empty for '80111236-0235-55b2-bdf5-9549bf4baea4'
[2019-11-19T17:29:41.704] WARN eventbus-66 import Extended Map target field was empty for '801118b2-5a64-5fc1-b47b-cb90df302492'
[2019-11-19T17:29:41.704] WARN eventbus-66 import Extended Map target field was empty for '80112d52-243d-57c4-98d2-d7b3512af59f'
[2019-11-19T17:29:41.704] WARN eventbus-66 import Extended Map target field was empty for '8011dda6-13a6-56e8-b17e-d35a47323d28'
[2019-11-19T17:29:41.704] WARN eventbus-66 import Extended Map target field was empty for '8012f38e-49a5-5d87-8c74-1420b7e4c30c'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '80160259-f2e8-51d1-a507-cf9d0f873a79'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '80161ecc-5c31-5e4e-bf03-b72bf8d32c09'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '8017a655-ac7b-5f34-8545-b82e2b55a1b7'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '8017a72e-701e-538a-9649-df254429b144'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '80197e59-024f-5679-9206-749eee3c5e87'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '80197e59-024f-5679-9206-749eee3c5e87'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '80197e59-024f-5679-9206-749eee3c5e87'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '80197e59-024f-5679-9206-749eee3c5e87'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '801c8c91-d910-5f46-ab56-d581f87b8a44'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '801d8e27-2eef-5c78-b7f5-55d520492da4'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '80214700-023f-5c22-a448-87687dc04593'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '802607b2-a05e-5c5e-9033-8880b8584fde'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '802653ff-9ae8-51be-807b-73af9dad9d71'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '80266cc2-ee20-50f2-ae28-a812495cf9df'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '802cd8af-5702-57de-9b5c-f98ddb037e7b'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '802cd8af-5702-57de-9b5c-f98ddb037e7b'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '802db525-2c8d-5907-a4c6-6662babeedf6'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '802f9230-f038-59e8-b804-c354b10540ae'
[2019-11-19T17:29:41.705] WARN eventbus-66 import Extended Map target field was empty for '803182de-301d-53a4-bab9-94ec816a38c6'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '8031ca9a-f015-573f-b250-4412c9057450'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '803442e9-c4db-57b9-9cd8-a80a798f0f7d'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '803ae809-ad68-5425-b744-44796ce26895'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '803ae809-ad68-5425-b744-44796ce26895'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '803faca9-1745-5161-9a98-8cb7b23d3198'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '8041d5a1-d347-50ae-8ede-bf192569c58c'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '8043fac6-87af-54ba-a946-f716de1b101b'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '8045461b-9c39-5b1f-ba9d-d8eae27269a6'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '804643d3-c3ed-586d-bc99-e778fee9294b'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '80480d7f-7915-588e-9397-bdb873a38a07'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '80481ac4-da43-5882-8a75-3f843919b44e'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '80481ac4-da43-5882-8a75-3f843919b44e'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '804942a9-b822-50f6-afa9-628c36ef7b08'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '804a2304-1ce4-5203-b56a-299471324c05'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '804ba542-190d-5ba8-a3af-c9476722aded'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '804c25b5-cbab-5f17-851c-404378f6ab52'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '804c4959-f213-51c7-b0e8-db5c368feb69'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '804ccbee-d9f2-5ed6-b2e1-ea1a476038b9'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '804e9c2c-6044-59ba-8d98-502614a09b8a'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '8050bea4-dfb1-579c-a821-53fd74b282aa'
[2019-11-19T17:29:41.706] WARN eventbus-66 import Extended Map target field was empty for '8050bea4-dfb1-579c-a821-53fd74b282aa'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '80520877-86d1-5820-aceb-e96fbe9575de'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '8052d01c-05b4-51d8-8720-b2d166b247fb'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '805368bc-59b0-5ff0-9f25-4b29c1e10681'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '805368bc-59b0-5ff0-9f25-4b29c1e10681'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '805395cc-7c79-5d24-9d14-ffc372db9345'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '805aef69-58a0-5890-b456-924730649dc0'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '805d549e-d032-5ceb-9c63-cc3e5257086f'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '805eeb34-572e-5425-8536-21d778c56ada'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '80600c4f-afb4-5dea-a544-9de4f021f7f3'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '8062044e-a5e9-5ef6-b7cb-7325ce5886b3'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '80651b24-dd25-5bff-b03b-1e4a40c297d3'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '8065503e-db9a-523d-9f8a-1fd1989a7140'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '80698369-829d-5a6a-9731-74a742ce3898'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '80698369-829d-5a6a-9731-74a742ce3898'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '80699e8b-f8aa-5aac-baa2-2bf782d5644c'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '806b948c-2c41-561b-ab64-1cd0556b0a69'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '80740729-3eff-5013-99aa-f5e66051942f'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '8074401f-3477-5bab-a48e-b84e7f1a783b'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '8075c84b-e315-5c09-9d60-a921170d28da'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '8075c84b-e315-5c09-9d60-a921170d28da'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '8077ed27-4f95-5a53-ab96-729223870a78'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '8077ed27-4f95-5a53-ab96-729223870a78'
[2019-11-19T17:29:41.707] WARN eventbus-66 import Extended Map target field was empty for '80797fbc-66cb-5d06-ab99-2fb6208f2069'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '80797fbc-66cb-5d06-ab99-2fb6208f2069'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '807c2163-54ef-5a2d-b7e2-e5c2445bb4b9'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '807d17b9-b3ef-5468-96a5-a568978809fb'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '807e12d0-ea86-5e35-967d-50a9bab58d9e'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '807f0c11-6d74-588c-8dc1-a5b26251f678'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '8081611d-8be1-53f3-85ac-58b5e89e244b'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '8081e912-24e3-5647-8f05-73b7eda9f430'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '8081e912-24e3-5647-8f05-73b7eda9f430'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '80854379-b6c2-5e93-b9a1-9428350133c8'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '80854379-b6c2-5e93-b9a1-9428350133c8'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '80867007-7bbf-5400-9689-94e945e9437c'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '80867007-7bbf-5400-9689-94e945e9437c'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '808bba4d-d8a3-5323-936d-a2f251453f21'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '8092e03a-9d8b-522b-b3c7-80c49d28ebd2'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '809544e2-f414-54aa-bc2f-d9c19cc530c5'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '8095bc07-8c68-5326-ab51-012e63b072ef'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '80988aa5-d7bb-5db2-92f6-0756eac7efc1'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '809972d7-a9e5-5389-b135-5c85c64a2be2'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '809b3350-16f6-59c0-872d-c8faaaa70d52'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '809cc936-825c-5272-a62d-0d874044dd36'
[2019-11-19T17:29:41.708] WARN eventbus-66 import Extended Map target field was empty for '809d76b2-fd8c-564c-90de-8bd6b9f959fd'
[2019-11-19T17:29:41.710] INFO eventbus-66 import Validating component consistency in effective time '2002-01-31'
[2019-11-19T17:29:56.684] INFO eventbus-66 import Validating component consistency in effective time '2002-07-31'
[2019-11-19T17:29:59.188] INFO eventbus-66 import Validating component consistency in effective time '2003-01-31'
[2019-11-19T17:30:02.011] INFO eventbus-66 import Validating component consistency in effective time '2003-07-31'
[2019-11-19T17:30:04.173] INFO eventbus-66 import Validating component consistency in effective time '2004-01-31'
[2019-11-19T17:30:05.520] INFO eventbus-66 import Validating component consistency in effective time '2004-07-31'
[2019-11-19T17:30:09.113] INFO eventbus-66 import Validating component consistency in effective time '2005-01-31'
[2019-11-19T17:30:12.349] INFO eventbus-66 import Validating component consistency in effective time '2005-07-31'
[2019-11-19T17:30:14.552] INFO eventbus-66 import Validating component consistency in effective time '2006-01-31'
[2019-11-19T17:30:18.123] INFO eventbus-66 import Validating component consistency in effective time '2006-07-31'
[2019-11-19T17:30:20.461] INFO eventbus-66 import Validating component consistency in effective time '2007-01-31'
[2019-11-19T17:30:25.417] INFO eventbus-66 import Validating component consistency in effective time '2007-07-31'
[2019-11-19T17:30:28.232] INFO eventbus-66 import Validating component consistency in effective time '2008-01-31'
[2019-11-19T17:30:30.592] INFO eventbus-66 import Validating component consistency in effective time '2008-07-31'
[2019-11-19T17:31:11.655] INFO eventbus-66 import Validating component consistency in effective time '2009-01-31'
[2019-11-19T17:31:15.258] INFO eventbus-66 import Validating component consistency in effective time '2009-07-31'
[2019-11-19T17:31:19.220] INFO eventbus-66 import Validating component consistency in effective time '2010-01-31'
[2019-11-19T17:31:22.289] INFO eventbus-66 import Validating component consistency in effective time '2010-07-31'
[2019-11-19T17:31:24.268] INFO eventbus-66 import Validating component consistency in effective time '2011-01-31'
[2019-11-19T17:31:25.845] INFO eventbus-66 import Validating component consistency in effective time '2011-07-31'
[2019-11-19T17:31:27.748] INFO eventbus-66 import Validating component consistency in effective time '2012-01-31'
[2019-11-19T17:31:28.333] INFO eventbus-66 import Validating component consistency in effective time '2012-07-31'
[2019-11-19T17:31:29.123] INFO eventbus-66 import Validating component consistency in effective time '2013-01-31'
[2019-11-19T17:31:30.612] INFO eventbus-66 import Validating component consistency in effective time '2013-07-31'
[2019-11-19T17:31:32.610] INFO eventbus-66 import Validating component consistency in effective time '2014-01-31'
[2019-11-19T17:31:35.711] INFO eventbus-66 import Validating component consistency in effective time '2014-07-31'
[2019-11-19T17:31:45.046] INFO eventbus-66 import Validating component consistency in effective time '2015-01-31'
[2019-11-19T17:31:49.197] INFO eventbus-66 import Validating component consistency in effective time '2015-07-31'
[2019-11-19T17:31:55.230] INFO eventbus-66 import Validating component consistency in effective time '2016-01-31'
[2019-11-19T17:32:00.723] INFO eventbus-66 import Validating component consistency in effective time '2016-07-31'
[2019-11-19T17:32:03.212] INFO eventbus-66 import Validating component consistency in effective time '2017-01-31'
[2019-11-19T17:32:09.833] INFO eventbus-66 import Validating component consistency in effective time '2017-07-31'
[2019-11-19T17:32:24.488] INFO eventbus-66 import Validating component consistency in effective time '2018-01-31'
[2019-11-19T17:32:33.430] INFO eventbus-66 import Validating component consistency in effective time '2018-07-31'
[2019-11-19T17:32:54.026] INFO eventbus-66 import Validating component consistency in effective time '2019-01-31'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '80009454-5531-5f78-b7c9-d288f2346d83'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '80009454-5531-5f78-b7c9-d288f2346d83'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '8002c5db-9038-50fe-8ccc-204a84213674'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '8003e488-77eb-5600-b541-7caa2e77503e'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '800449ce-37c1-5b0f-9dd5-570a36fc47cd'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '800d6fb8-a02f-5d4c-8490-79e922da580e'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '800d6fb8-a02f-5d4c-8490-79e922da580e'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '800eb8c2-10fc-5c7a-b71a-aa760fb465f8'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '800f53ad-bd42-545a-88c2-7ebcd7f354b6'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '801046f2-9bd0-5607-88af-c1306f566731'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '80111236-0235-55b2-bdf5-9549bf4baea4'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '80111236-0235-55b2-bdf5-9549bf4baea4'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '801118b2-5a64-5fc1-b47b-cb90df302492'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '80112d52-243d-57c4-98d2-d7b3512af59f'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '8011dda6-13a6-56e8-b17e-d35a47323d28'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '8012f38e-49a5-5d87-8c74-1420b7e4c30c'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '80160259-f2e8-51d1-a507-cf9d0f873a79'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '80161ecc-5c31-5e4e-bf03-b72bf8d32c09'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '8017a655-ac7b-5f34-8545-b82e2b55a1b7'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '8017a72e-701e-538a-9649-df254429b144'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '80197e59-024f-5679-9206-749eee3c5e87'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '80197e59-024f-5679-9206-749eee3c5e87'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '80197e59-024f-5679-9206-749eee3c5e87'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '80197e59-024f-5679-9206-749eee3c5e87'
[2019-11-19T17:33:19.275] WARN eventbus-66 import Extended Map target field was empty for '801c8c91-d910-5f46-ab56-d581f87b8a44'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '801d8e27-2eef-5c78-b7f5-55d520492da4'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '80214700-023f-5c22-a448-87687dc04593'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '802607b2-a05e-5c5e-9033-8880b8584fde'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '802653ff-9ae8-51be-807b-73af9dad9d71'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '80266cc2-ee20-50f2-ae28-a812495cf9df'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '802cd8af-5702-57de-9b5c-f98ddb037e7b'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '802cd8af-5702-57de-9b5c-f98ddb037e7b'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '802db525-2c8d-5907-a4c6-6662babeedf6'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '802f9230-f038-59e8-b804-c354b10540ae'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '803182de-301d-53a4-bab9-94ec816a38c6'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '8031ca9a-f015-573f-b250-4412c9057450'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '803442e9-c4db-57b9-9cd8-a80a798f0f7d'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '803ae809-ad68-5425-b744-44796ce26895'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '803ae809-ad68-5425-b744-44796ce26895'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '803faca9-1745-5161-9a98-8cb7b23d3198'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '8041d5a1-d347-50ae-8ede-bf192569c58c'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '8043fac6-87af-54ba-a946-f716de1b101b'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '8045461b-9c39-5b1f-ba9d-d8eae27269a6'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '804643d3-c3ed-586d-bc99-e778fee9294b'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '80480d7f-7915-588e-9397-bdb873a38a07'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '80481ac4-da43-5882-8a75-3f843919b44e'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '80481ac4-da43-5882-8a75-3f843919b44e'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '804942a9-b822-50f6-afa9-628c36ef7b08'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '804a2304-1ce4-5203-b56a-299471324c05'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '804ba542-190d-5ba8-a3af-c9476722aded'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '804c25b5-cbab-5f17-851c-404378f6ab52'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '804c4959-f213-51c7-b0e8-db5c368feb69'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '804ccbee-d9f2-5ed6-b2e1-ea1a476038b9'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '804e9c2c-6044-59ba-8d98-502614a09b8a'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '8050bea4-dfb1-579c-a821-53fd74b282aa'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '8050bea4-dfb1-579c-a821-53fd74b282aa'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '80520877-86d1-5820-aceb-e96fbe9575de'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '8052d01c-05b4-51d8-8720-b2d166b247fb'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '805368bc-59b0-5ff0-9f25-4b29c1e10681'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '805368bc-59b0-5ff0-9f25-4b29c1e10681'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '805395cc-7c79-5d24-9d14-ffc372db9345'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '805aef69-58a0-5890-b456-924730649dc0'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '805d549e-d032-5ceb-9c63-cc3e5257086f'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '805eeb34-572e-5425-8536-21d778c56ada'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '80600c4f-afb4-5dea-a544-9de4f021f7f3'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '8062044e-a5e9-5ef6-b7cb-7325ce5886b3'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '80651b24-dd25-5bff-b03b-1e4a40c297d3'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '8065503e-db9a-523d-9f8a-1fd1989a7140'
[2019-11-19T17:33:19.276] WARN eventbus-66 import Extended Map target field was empty for '80698369-829d-5a6a-9731-74a742ce3898'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '80698369-829d-5a6a-9731-74a742ce3898'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '80699e8b-f8aa-5aac-baa2-2bf782d5644c'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '806b948c-2c41-561b-ab64-1cd0556b0a69'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '80740729-3eff-5013-99aa-f5e66051942f'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '8074401f-3477-5bab-a48e-b84e7f1a783b'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '8075c84b-e315-5c09-9d60-a921170d28da'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '8075c84b-e315-5c09-9d60-a921170d28da'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '8077ed27-4f95-5a53-ab96-729223870a78'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '8077ed27-4f95-5a53-ab96-729223870a78'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '80797fbc-66cb-5d06-ab99-2fb6208f2069'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '80797fbc-66cb-5d06-ab99-2fb6208f2069'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '807c2163-54ef-5a2d-b7e2-e5c2445bb4b9'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '807d17b9-b3ef-5468-96a5-a568978809fb'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '807e12d0-ea86-5e35-967d-50a9bab58d9e'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '807f0c11-6d74-588c-8dc1-a5b26251f678'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '8081611d-8be1-53f3-85ac-58b5e89e244b'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '8081e912-24e3-5647-8f05-73b7eda9f430'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '8081e912-24e3-5647-8f05-73b7eda9f430'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '80854379-b6c2-5e93-b9a1-9428350133c8'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '80854379-b6c2-5e93-b9a1-9428350133c8'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '80867007-7bbf-5400-9689-94e945e9437c'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '80867007-7bbf-5400-9689-94e945e9437c'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '808bba4d-d8a3-5323-936d-a2f251453f21'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '8092e03a-9d8b-522b-b3c7-80c49d28ebd2'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '809544e2-f414-54aa-bc2f-d9c19cc530c5'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '8095bc07-8c68-5326-ab51-012e63b072ef'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '80988aa5-d7bb-5db2-92f6-0756eac7efc1'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '809972d7-a9e5-5389-b135-5c85c64a2be2'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '809b3350-16f6-59c0-872d-c8faaaa70d52'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '809cc936-825c-5272-a62d-0d874044dd36'
[2019-11-19T17:33:19.277] WARN eventbus-66 import Extended Map target field was empty for '809d76b2-fd8c-564c-90de-8bd6b9f959fd'
[2019-11-19T17:33:19.277] INFO eventbus-66 import Importing components from 2002-01-31
[2019-11-19T17:33:28.277] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:33:28.331] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:33:28.332] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574184808332
[2019-11-19T17:33:28.335] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:33:30.647] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:33:31.460] WARN pool-5-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:33:31.620] WARN pool-5-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:33:31.804] WARN pool-5-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:33:33.039] INFO pool-5-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:33:33.146] WARN pool-5-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:33:47.533] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574184808332.
[2019-11-19T17:33:47.555] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:33:51.776] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:33:51.836] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:33:51.836] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574184831836
[2019-11-19T17:33:51.840] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:33:54.100] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:33:54.695] WARN pool-6-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:33:54.824] WARN pool-6-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:33:54.977] WARN pool-6-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:33:55.746] INFO pool-6-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:33:55.829] WARN pool-6-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:34:04.619] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574184831836.
[2019-11-19T17:34:04.637] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:34:08.031] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:34:08.074] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:34:08.074] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574184848074
[2019-11-19T17:34:08.077] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:34:10.389] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:34:10.866] INFO pool-7-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:34:10.866] WARN pool-7-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:34:11.223] WARN pool-7-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:34:11.982] WARN pool-7-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:34:12.065] WARN pool-7-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:34:18.946] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574184848074.
[2019-11-19T17:34:18.966] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:34:22.462] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:34:22.501] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:34:22.502] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574184862502
[2019-11-19T17:34:22.505] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:34:25.223] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:34:25.705] INFO pool-8-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:34:25.865] WARN pool-8-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:34:25.905] WARN pool-8-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:34:26.074] WARN pool-8-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:34:26.244] WARN pool-8-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:34:33.090] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574184862502.
[2019-11-19T17:34:33.109] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:34:36.698] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:34:36.761] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:34:36.761] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574184876761
[2019-11-19T17:34:36.766] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:34:38.995] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:34:39.436] INFO pool-9-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:34:39.535] WARN pool-9-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:34:39.800] WARN pool-9-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:34:39.888] WARN pool-9-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:34:40.033] WARN pool-9-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:34:46.519] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574184876761.
[2019-11-19T17:34:46.534] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:34:50.168] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:34:50.206] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:34:50.207] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574184890207
[2019-11-19T17:34:50.212] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:34:52.529] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:34:52.969] INFO pool-10-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:34:53.139] WARN pool-10-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:34:53.312] WARN pool-10-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:34:53.401] WARN pool-10-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:34:53.665] WARN pool-10-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:34:59.577] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574184890207.
[2019-11-19T17:34:59.592] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:35:03.471] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:35:03.514] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:35:03.515] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574184903515
[2019-11-19T17:35:03.519] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:35:06.540] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:35:06.952] INFO pool-11-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:35:07.081] WARN pool-11-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:35:07.221] WARN pool-11-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:35:07.431] WARN pool-11-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:35:07.647] WARN pool-11-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:35:13.534] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574184903515.
[2019-11-19T17:35:13.551] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:35:17.335] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:35:17.372] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:35:17.372] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574184917372
[2019-11-19T17:35:17.376] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:35:19.824] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:35:20.289] INFO pool-12-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:35:20.707] WARN pool-12-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:35:20.732] WARN pool-12-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:35:20.747] WARN pool-12-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:35:20.980] WARN pool-12-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:35:27.259] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574184917372.
[2019-11-19T17:35:27.276] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:35:31.036] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:35:31.073] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:35:31.073] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574184931073
[2019-11-19T17:35:31.076] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:35:33.595] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:35:34.088] INFO pool-13-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:35:34.256] WARN pool-13-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:35:34.440] WARN pool-13-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:35:34.599] WARN pool-13-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:35:34.858] WARN pool-13-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:35:40.744] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574184931073.
[2019-11-19T17:35:40.762] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:35:44.620] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:35:44.656] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:35:44.657] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574184944657
[2019-11-19T17:35:44.661] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:35:47.184] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:35:47.655] INFO pool-14-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:35:47.889] WARN pool-14-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:35:48.087] WARN pool-14-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:35:48.254] WARN pool-14-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:35:48.429] WARN pool-14-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:35:54.730] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574184944657.
[2019-11-19T17:35:54.759] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:35:58.790] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:35:58.826] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:35:58.826] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574184958826
[2019-11-19T17:35:58.830] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:36:01.561] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:36:02.028] INFO pool-15-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:36:02.412] WARN pool-15-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:36:02.664] WARN pool-15-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:36:02.722] WARN pool-15-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:36:02.957] WARN pool-15-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:36:12.488] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574184958826.
[2019-11-19T17:36:12.503] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:36:16.609] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:36:16.660] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:36:16.660] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574184976660
[2019-11-19T17:36:16.664] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:36:19.495] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:36:19.947] INFO pool-16-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:36:20.166] WARN pool-16-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:36:20.369] WARN pool-16-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:36:21.110] WARN pool-16-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:36:21.343] WARN pool-16-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:36:30.176] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574184976660.
[2019-11-19T17:36:30.212] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:36:35.861] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:36:35.898] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:36:35.899] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574184995899
[2019-11-19T17:36:35.902] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:36:38.582] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:36:39.065] INFO pool-17-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:36:39.166] WARN pool-17-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:36:39.505] WARN pool-17-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:36:39.784] WARN pool-17-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:36:40.073] WARN pool-17-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:36:50.960] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574184995899.
[2019-11-19T17:36:50.975] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:36:54.757] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:36:54.794] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:36:54.794] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574185014794
[2019-11-19T17:36:54.797] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:36:57.253] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:36:57.649] INFO pool-18-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:36:57.911] WARN pool-18-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:36:58.034] WARN pool-18-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:36:58.178] WARN pool-18-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:36:58.335] WARN pool-18-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:37:04.559] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574185014794.
[2019-11-19T17:37:04.572] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:37:08.280] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:37:08.317] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:37:08.317] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574185028317
[2019-11-19T17:37:08.321] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:37:10.872] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:37:11.260] INFO pool-19-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:37:11.379] WARN pool-19-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:37:11.518] WARN pool-19-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:37:11.672] WARN pool-19-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:37:11.886] WARN pool-19-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:37:17.584] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574185028317.
[2019-11-19T17:37:17.598] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:37:21.308] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:37:21.348] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:37:21.348] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574185041348
[2019-11-19T17:37:21.351] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:37:23.976] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:37:24.367] INFO pool-20-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:37:24.484] WARN pool-20-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:37:24.554] WARN pool-20-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:37:24.816] WARN pool-20-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:37:25.035] WARN pool-20-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:37:31.032] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574185041348.
[2019-11-19T17:37:31.050] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:37:34.855] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:37:34.891] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:37:34.891] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574185054891
[2019-11-19T17:37:34.894] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:37:37.685] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:37:38.192] INFO pool-21-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:37:38.425] WARN pool-21-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:37:38.486] WARN pool-21-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:37:38.726] WARN pool-21-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:37:38.933] WARN pool-21-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:37:45.003] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574185054891.
[2019-11-19T17:37:45.016] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:37:49.021] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:37:49.054] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:37:49.055] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574185069055
[2019-11-19T17:37:49.057] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:37:51.715] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:37:52.197] INFO pool-22-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:37:52.422] WARN pool-22-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:37:52.586] WARN pool-22-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:37:52.654] WARN pool-22-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:37:52.937] WARN pool-22-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:37:59.210] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574185069055.
[2019-11-19T17:37:59.223] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:38:03.398] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:38:03.442] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:38:03.442] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574185083442
[2019-11-19T17:38:03.446] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:38:06.455] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:38:06.953] INFO pool-23-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:38:07.295] WARN pool-23-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:38:07.359] WARN pool-23-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:38:07.527] WARN pool-23-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:38:07.868] WARN pool-23-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:38:13.852] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574185083442.
[2019-11-19T17:38:13.863] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:38:17.883] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:38:17.919] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:38:17.920] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574185097919
[2019-11-19T17:38:17.922] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:38:20.822] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:38:21.319] INFO pool-24-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:38:21.461] WARN pool-24-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:38:21.817] WARN pool-24-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:38:21.896] WARN pool-24-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:38:22.249] WARN pool-24-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:38:29.220] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574185097919.
[2019-11-19T17:38:29.234] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:38:33.478] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:38:33.513] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:38:33.513] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574185113513
[2019-11-19T17:38:33.516] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:38:36.645] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:38:37.196] INFO pool-25-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:38:37.436] WARN pool-25-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:38:37.700] WARN pool-25-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:38:37.815] WARN pool-25-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:38:38.126] WARN pool-25-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:38:45.050] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574185113513.
[2019-11-19T17:38:45.087] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:38:49.468] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:38:49.506] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:38:49.506] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574185129506
[2019-11-19T17:38:49.510] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:38:52.411] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:38:52.896] INFO pool-26-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:38:52.996] WARN pool-26-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:38:53.386] WARN pool-26-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:38:53.423] WARN pool-26-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:38:53.828] WARN pool-26-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:39:00.627] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574185129506.
[2019-11-19T17:39:00.667] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:39:06.428] INFO eventbus-66 import Pushing changes: Imported components from 2002-01-31
[2019-11-19T17:39:06.464] INFO eventbus-66 lock Lock acquired for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:39:06.465] INFO eventbus-66 repository.snomedStore Persisting changes to MAIN@1574185146465
[2019-11-19T17:39:06.468] INFO eventbus-66 repository.snomedStore Processing changes...
[2019-11-19T17:39:09.414] INFO eventbus-66 repository.snomedStore Processing changes successfully finished.
[2019-11-19T17:39:09.963] INFO pool-27-thread-1 index.snomedstore Updated 1 branch documents with bulk update with script 'commit'
[2019-11-19T17:39:10.061] WARN pool-27-thread-2 index.snomedstore Bulk update with script 'updateRevised' could not be applied to concept documents, no-ops (0), conflicts (0)
[2019-11-19T17:39:10.340] WARN pool-27-thread-1 index.snomedstore Bulk update with script 'updateRevised' could not be applied to relationship documents, no-ops (0), conflicts (0)
[2019-11-19T17:39:10.477] WARN pool-27-thread-3 index.snomedstore Bulk update with script 'updateRevised' could not be applied to description documents, no-ops (0), conflicts (0)
[2019-11-19T17:39:10.879] WARN pool-27-thread-4 index.snomedstore Bulk update with script 'updateRevised' could not be applied to member documents, no-ops (0), conflicts (0)
[2019-11-19T17:39:11.378] ERROR I/O dispatcher 2 index.snomedstore Failed bulk request org.elasticsearch.ElasticsearchStatusException: Unable to parse response body
at org.elasticsearch.client.RestHighLevelClient.parseResponseException(RestHighLevelClient.java:2033)
at org.elasticsearch.client.RestHighLevelClient$1.onFailure(RestHighLevelClient.java:1947)
at org.elasticsearch.client.RestClient$FailureTrackingResponseListener.onDefinitiveFailure(RestClient.java:857)
at org.elasticsearch.client.RestClient$1.completed(RestClient.java:560)
at org.elasticsearch.client.RestClient$1.completed(RestClient.java:537)
at org.apache.http.concurrent.BasicFuture.completed(BasicFuture.java:123)
at org.apache.http.impl.nio.client.DefaultClientExchangeHandlerImpl.responseCompleted(DefaultClientExchangeHandlerImpl.java:181)
at org.apache.http.nio.protocol.HttpAsyncRequestExecutor.processResponse(HttpAsyncRequestExecutor.java:442)
at org.apache.http.nio.protocol.HttpAsyncRequestExecutor.inputReady(HttpAsyncRequestExecutor.java:332)
at org.apache.http.impl.nio.DefaultNHttpClientConnection.consumeInput(DefaultNHttpClientConnection.java:265)
at org.apache.http.impl.nio.client.InternalIODispatch.onInputReady(InternalIODispatch.java:81)
at org.apache.http.impl.nio.client.InternalIODispatch.onInputReady(InternalIODispatch.java:39)
at org.apache.http.impl.nio.reactor.AbstractIODispatch.inputReady(AbstractIODispatch.java:121)
at org.apache.http.impl.nio.reactor.BaseIOReactor.readable(BaseIOReactor.java:162)
at org.apache.http.impl.nio.reactor.AbstractIOReactor.processEvent(AbstractIOReactor.java:337)
at org.apache.http.impl.nio.reactor.AbstractIOReactor.processEvents(AbstractIOReactor.java:315)
at org.apache.http.impl.nio.reactor.AbstractIOReactor.execute(AbstractIOReactor.java:276)
at org.apache.http.impl.nio.reactor.BaseIOReactor.execute(BaseIOReactor.java:104)
at org.apache.http.impl.nio.reactor.AbstractMultiworkerIOReactor$Worker.run(AbstractMultiworkerIOReactor.java:588)
at java.base/java.lang.Thread.run(Thread.java:834)
Suppressed: org.elasticsearch.common.ParsingException: Failed to parse object: expecting field with name [error] but found [Message]
at org.elasticsearch.common.xcontent.XContentParserUtils.ensureFieldName(XContentParserUtils.java:50)
at org.elasticsearch.ElasticsearchException.failureFromXContent(ElasticsearchException.java:605)
at org.elasticsearch.rest.BytesRestResponse.errorFromXContent(BytesRestResponse.java:169)
at org.elasticsearch.client.RestHighLevelClient.parseEntity(RestHighLevelClient.java:2053)
at org.elasticsearch.client.RestHighLevelClient.parseResponseException(RestHighLevelClient.java:2030)
... 19 common frames omitted
Caused by: org.elasticsearch.client.ResponseException: method [POST], host [https://vpc-es-snowowl-some-path.eu-west-1.es.amazonaws.com], URI [/snomedstore-concept/_bulk?timeout=1m], status line [HTTP/1.1 413 Request Entity Too Large]
{"Message":"Request size exceeded 10485760 bytes"}
at org.elasticsearch.client.RestClient$1.completed(RestClient.java:552)
... 16 common frames omitted
[2019-11-19T17:39:17.326] INFO eventbus-66 repository.snomedStore Changes have been successfully persisted to MAIN@1574185146465.
[2019-11-19T17:39:17.346] INFO eventbus-66 lock Lock released for branch 'MAIN' of repository 'snomedStore' (committing changes).
[2019-11-19T17:39:20.450] INFO eventbus-66 request {"type":"SnomedRf2ImportRequest","operation":"import","branchPath":"MAIN","repositoryId":"snomedStore"}
[2019-11-19T17:39:20.451] ERROR eventbus-39 c.b.snowowl.snomed.core.rest.services.SnomedRf2ImportService Error during the import of: 93b27bc6-2b9f-4b5a-915b-b6a4aa584109 com.b2international.snowowl.core.api.SnowowlRuntimeException: java.lang.IllegalArgumentException: Missing component from maps: 236673008
at com.b2international.snowowl.snomed.datastore.request.rf2.SnomedRf2ImportRequest.execute(SnomedRf2ImportRequest.java:126)
at com.b2international.snowowl.snomed.datastore.request.rf2.SnomedRf2ImportRequest.execute(SnomedRf2ImportRequest.java:1)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.datastore.request.RevisionIndexReadRequest.execute(RevisionIndexReadRequest.java:72)
at com.b2international.snowowl.datastore.request.RevisionIndexReadRequest.execute(RevisionIndexReadRequest.java:1)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.datastore.request.BranchRequest.execute(BranchRequest.java:52)
at com.b2international.snowowl.datastore.request.BranchRequest.execute(BranchRequest.java:1)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.datastore.request.IndexReadRequest.lambda$0(IndexReadRequest.java:45)
at com.b2international.index.DefaultIndex.read(DefaultIndex.java:36)
at com.b2international.snowowl.datastore.request.IndexReadRequest.execute(IndexReadRequest.java:43)
at com.b2international.snowowl.datastore.request.IndexReadRequest.execute(IndexReadRequest.java:1)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.datastore.request.RepositoryRequest.execute(RepositoryRequest.java:62)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.core.rate.RateLimitingRequest.execute(RateLimitingRequest.java:50)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.core.authorization.AuthorizedRequest.execute(AuthorizedRequest.java:114)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.core.monitoring.MonitoredRequest.execute(MonitoredRequest.java:47)
at com.b2international.snowowl.core.repository.ApiRequestHandler.handle(ApiRequestHandler.java:67)
at com.b2international.snowowl.core.repository.ApiRequestHandler.handle(ApiRequestHandler.java:1)
at com.b2international.snowowl.internal.eventbus.EventBus$1.run(EventBus.java:163)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.IllegalArgumentException: Missing component from maps: 236673008
at com.b2international.snowowl.snomed.datastore.request.rf2.importer.Rf2TransactionContext.lookup(Rf2TransactionContext.java:172)
at com.b2international.snowowl.snomed.core.store.SnomedRelationshipBuilder.init(SnomedRelationshipBuilder.java:156)
at com.b2international.snowowl.snomed.core.store.SnomedRelationshipBuilder.init(SnomedRelationshipBuilder.java:1)
at com.b2international.snowowl.snomed.datastore.request.rf2.importer.Rf2TransactionContext.add(Rf2TransactionContext.java:290)
at com.b2international.snowowl.snomed.datastore.request.rf2.importer.Rf2EffectiveTimeSlice.doImport(Rf2EffectiveTimeSlice.java:219)
at com.b2international.snowowl.snomed.datastore.request.rf2.SnomedRf2ImportRequest.doImport(SnomedRf2ImportRequest.java:164)
at com.b2international.snowowl.snomed.datastore.request.rf2.SnomedRf2ImportRequest.execute(SnomedRf2ImportRequest.java:121)
... 28 common frames omitted
Trying to use a ConceptMap/$translate endpoint on the following map (obtained by GET /fhir/ConceptMap/snomedStore:MAIN/2019-07-31:446608001 in my SnowOwl runtime)
{
"resourceType": "ConceptMap",
"id": "snomedStore:MAIN/2019-07-31:446608001",
"language": "en-us",
"url": "http://snomed.info/sct/version/20190731",
"identifier": {
"use": "official",
"system": "http://snomed.info/sct/version/20190731",
"value": "446608001"
},
"version": "2019-07-31",
"name": "ICD-O simple map reference set",
"title": "ICD-O simple map reference set",
"status": "active",
"date": "2019-07-31T00:00:00.000+0000",
"group": [
{
"source": "http://snomed.info/sct",
"sourceVersion": "20190731",
"target": "uri://unknown_target_codesystem",
"element": [
{
"code": "173604004",
"display": "Entire interarytenoid notch",
"target": [
{
"code": "C32.0",
"equivalence": "equivalent"
}
]
},
...
The request I use is GET /fhir/ConceptMap/$translate?code=173604004&system=http://snomed.info/sct&targetsystem=uri://unknown_target_codesystem
As an outcome I get
{
"resourceType": "Parameters",
"parameter": [
{
"name": "result",
"valueBoolean": false
},
{
"name": "message",
"valueString": "0 match(es)."
}
]
}
So I suspect, maybe the target codesystems of all SNOMED maps need to be created before SNOMED import takes place to avoid the weird uri://unknown_target_codesystem IRIs?
Still, I would expect the above query to return the mapping (even with weird IRI) ...
Thanks,
Petr
hi! Sorry it's a quick question.
Is latest SnowOwl 7.x version compatible with Elasticsearch 7.1?
We're using AWS Elasticsearch and the latest supported version is currently 7.1.
From inspecting SnowOwl's latest commit it seems to currently require 7.5.2 is that correct? We haven't tried it yet but just wanted to double check with you guys first.
Thanks!
Most of Snow Owl's endpoints return JSON data.
It would be nice to have a pretty query parameter, that pretty prints the output.
Hi,
I would like to be able to view the historical changes to a concept. For example, on date X relationship Y was added. I can't seem to find a feature that provides that functionality. Is it possible to view a concept at a given commit? Also is it possible to be able to see the changes that were made with a commit?
A commit could be a SNOMED delta update or changes done via snow owl.
Thanks,
Josh
Hi Where can we find the api details of LOINC Codes?
I created a relationship that violates one of the Snomed MRCM constraints of range, to test the validation feature:
{"locales":[],"expand":{},"fields":[],"limit":2147483646,"options":{"BRANCH_PATH":"MAIN","WHITELISTED":false,"SORT_BY":[{"field":"ruleId","ascending":true}]},"type":"ValidationIssueSearchRequest"}
[2019-11-28T10:58:45.534] ERROR qtp1700669372-47 com.b2international.snowowl.core.rest.ControllerExceptionMapper Exception during request processing org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'scopedTarget.eventBus': Scope 'request' is not active for the current thread; consider defining a scoped proxy for this bean if you intend to refer to it from a singleton; nested exception is java.lang.IllegalStateException: No thread-bound request found: Are you referring to request attributes outside of an actual web request, or processing a request outside of the originally receiving thread? If you are actually operating within a web request and still receive this message, your code is probably running outside of DispatcherServlet: In this case, use RequestContextListener or RequestContextFilter to expose the current request.
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:365)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
at org.springframework.aop.target.SimpleBeanTargetSource.getTarget(SimpleBeanTargetSource.java:35)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:192)
at com.sun.proxy.$Proxy118.get(Unknown Source)
at com.b2international.snowowl.core.rest.AbstractRestService.getBus(AbstractRestService.java:92)
at com.b2international.snowowl.core.rest.validation.ValidationRestService.lambda$4(ValidationRestService.java:249)
at com.b2international.snowowl.core.events.util.Promise$3.onSuccess(Promise.java:174)
at com.b2international.snowowl.core.events.util.Promise$3.onSuccess(Promise.java:1)
at com.google.common.util.concurrent.Futures$4.run(Futures.java:1135)
at com.google.common.util.concurrent.MoreExecutors$DirectExecutor.execute(MoreExecutors.java:399)
at com.google.common.util.concurrent.AbstractFuture.executeListener(AbstractFuture.java:902)
at com.google.common.util.concurrent.AbstractFuture.complete(AbstractFuture.java:813)
at com.google.common.util.concurrent.AbstractFuture.set(AbstractFuture.java:655)
at com.google.common.util.concurrent.SettableFuture.set(SettableFuture.java:48)
at com.b2international.snowowl.core.events.util.Promise.resolve(Promise.java:235)
at com.b2international.snowowl.core.events.AsyncRequest$1.handle(AsyncRequest.java:52)
at com.b2international.snowowl.core.events.AsyncRequest$1.handle(AsyncRequest.java:1)
at com.b2international.snowowl.internal.eventbus.EventBus$1.run(EventBus.java:163)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.IllegalStateException: No thread-bound request found: Are you referring to request attributes outside of an actual web request, or processing a request outside of the originally receiving thread? If you are actually operating within a web request and still receive this message, your code is probably running outside of DispatcherServlet: In this case, use RequestContextListener or RequestContextFilter to expose the current request.
at org.springframework.web.context.request.RequestContextHolder.currentRequestAttributes(RequestContextHolder.java:131)
at org.springframework.web.context.request.AbstractRequestAttributesScope.get(AbstractRequestAttributesScope.java:42)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:353)
... 23 common frames omitted
[2019-11-28T10:58:45.535] WARN qtp1700669372-47 o.s.w.s.mvc.method.annotation.ExceptionHandlerExceptionResolver Failure in @ExceptionHandler public com.b2international.snowowl.core.rest.RestApiError com.b2international.snowowl.core.rest.ControllerExceptionMapper.handle(java.lang.Exception) org.springframework.web.HttpMediaTypeNotAcceptableException: Could not find acceptable representation
at org.springframework.web.servlet.mvc.method.annotation.AbstractMessageConverterMethodProcessor.writeWithMessageConverters(AbstractMessageConverterMethodProcessor.java:246)
at org.springframework.web.servlet.mvc.method.annotation.RequestResponseBodyMethodProcessor.handleReturnValue(RequestResponseBodyMethodProcessor.java:180)
at org.springframework.web.method.support.HandlerMethodReturnValueHandlerComposite.handleReturnValue(HandlerMethodReturnValueHandlerComposite.java:82)
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:122)
at org.springframework.web.servlet.mvc.method.annotation.ExceptionHandlerExceptionResolver.doResolveHandlerMethodException(ExceptionHandlerExceptionResolver.java:408)
at org.springframework.web.servlet.handler.AbstractHandlerMethodExceptionResolver.doResolveException(AbstractHandlerMethodExceptionResolver.java:61)
at org.springframework.web.servlet.handler.AbstractHandlerExceptionResolver.resolveException(AbstractHandlerExceptionResolver.java:140)
at org.springframework.web.servlet.handler.HandlerExceptionResolverComposite.resolveException(HandlerExceptionResolverComposite.java:79)
at org.springframework.web.servlet.DispatcherServlet.processHandlerException(DispatcherServlet.java:1298)
at org.springframework.web.servlet.DispatcherServlet.processDispatchResult(DispatcherServlet.java:1110)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1056)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:942)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1005)
at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:897)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:687)
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:882)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:873)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1623)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:320)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:116)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:91)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:119)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:84)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:170)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:116)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:102)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:102)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:357)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:270)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1610)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:102)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1610)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:540)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:146)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:257)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1700)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:255)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1345)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:203)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:480)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1667)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:201)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1247)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:144)
at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:194)
at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:152)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
at org.eclipse.jetty.server.Server.handleAsync(Server.java:550)
at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:394)
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:311)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:698)
at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:804)
at java.base/java.lang.Thread.run(Thread.java:834)
[2019-11-28T10:58:45.536] WARN qtp1700669372-47 org.eclipse.jetty.server.HttpChannel /snowowl/admin/validations/validations/27c2551/issues javax.servlet.ServletException: org.springframework.web.util.NestedServletException: Request processing failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'scopedTarget.eventBus': Scope 'request' is not active for the current thread; consider defining a scoped proxy for this bean if you intend to refer to it from a singleton; nested exception is java.lang.IllegalStateException: No thread-bound request found: Are you referring to request attributes outside of an actual web request, or processing a request outside of the originally receiving thread? If you are actually operating within a web request and still receive this message, your code is probably running outside of DispatcherServlet: In this case, use RequestContextListener or RequestContextFilter to expose the current request.
at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:168)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
at org.eclipse.jetty.server.Server.handleAsync(Server.java:550)
at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:394)
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:311)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:698)
at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:804)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: org.springframework.web.util.NestedServletException: Request processing failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'scopedTarget.eventBus': Scope 'request' is not active for the current thread; consider defining a scoped proxy for this bean if you intend to refer to it from a singleton; nested exception is java.lang.IllegalStateException: No thread-bound request found: Are you referring to request attributes outside of an actual web request, or processing a request outside of the originally receiving thread? If you are actually operating within a web request and still receive this message, your code is probably running outside of DispatcherServlet: In this case, use RequestContextListener or RequestContextFilter to expose the current request.
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1013)
at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:897)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:687)
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:882)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:873)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1623)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:320)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:116)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:91)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:119)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:84)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:170)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:116)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:102)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:102)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:357)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:270)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1610)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:102)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1610)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:540)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:146)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:257)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1700)
at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:255)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1345)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:203)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:480)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1667)
at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:201)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1247)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:144)
at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:194)
at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:152)
... 7 common frames omitted
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'scopedTarget.eventBus': Scope 'request' is not active for the current thread; consider defining a scoped proxy for this bean if you intend to refer to it from a singleton; nested exception is java.lang.IllegalStateException: No thread-bound request found: Are you referring to request attributes outside of an actual web request, or processing a request outside of the originally receiving thread? If you are actually operating within a web request and still receive this message, your code is probably running outside of DispatcherServlet: In this case, use RequestContextListener or RequestContextFilter to expose the current request.
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:365)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
at org.springframework.aop.target.SimpleBeanTargetSource.getTarget(SimpleBeanTargetSource.java:35)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:192)
at com.sun.proxy.$Proxy118.get(Unknown Source)
at com.b2international.snowowl.core.rest.AbstractRestService.getBus(AbstractRestService.java:92)
at com.b2international.snowowl.core.rest.validation.ValidationRestService.lambda$4(ValidationRestService.java:249)
at com.b2international.snowowl.core.events.util.Promise$3.onSuccess(Promise.java:174)
at com.b2international.snowowl.core.events.util.Promise$3.onSuccess(Promise.java:1)
at com.google.common.util.concurrent.Futures$4.run(Futures.java:1135)
at com.google.common.util.concurrent.MoreExecutors$DirectExecutor.execute(MoreExecutors.java:399)
at com.google.common.util.concurrent.AbstractFuture.executeListener(AbstractFuture.java:902)
at com.google.common.util.concurrent.AbstractFuture.complete(AbstractFuture.java:813)
at com.google.common.util.concurrent.AbstractFuture.set(AbstractFuture.java:655)
at com.google.common.util.concurrent.SettableFuture.set(SettableFuture.java:48)
at com.b2international.snowowl.core.events.util.Promise.resolve(Promise.java:235)
at com.b2international.snowowl.core.events.AsyncRequest$1.handle(AsyncRequest.java:52)
at com.b2international.snowowl.core.events.AsyncRequest$1.handle(AsyncRequest.java:1)
at com.b2international.snowowl.internal.eventbus.EventBus$1.run(EventBus.java:163)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
... 1 common frames omitted
Caused by: java.lang.IllegalStateException: No thread-bound request found: Are you referring to request attributes outside of an actual web request, or processing a request outside of the originally receiving thread? If you are actually operating within a web request and still receive this message, your code is probably running outside of DispatcherServlet: In this case, use RequestContextListener or RequestContextFilter to expose the current request.
at org.springframework.web.context.request.RequestContextHolder.currentRequestAttributes(RequestContextHolder.java:131)
at org.springframework.web.context.request.AbstractRequestAttributesScope.get(AbstractRequestAttributesScope.java:42)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:353)
... 23 common frames omitted
Hi!
when trying to use swagger ui /snomed-ct/v3/{path}/members and fills path and referenceSet, only the path parameter is taken into account when executing the query.
The curl and path commands shown in swagger also seem to be missing referenceSet parameter.
When fixing the curl command manually, we do get different results:
incorrect curl from swagger=
curl -X GET "https://localhost/snowowl/snomed-ct/v3/MAIN/members" -H "accept: application/json;charset=UTF-8" -H "Accept-Language: en-US;q=0.8,en-GB;q=0.6" -H "authorization: Basic somevalue"
expected correct curl fixed manually:
curl -X GET "https://localhost/snowowl/snomed-ct/v3/MAIN/members?referenceSet=723561005" -H "accept: application/json;charset=UTF-8" -H "Accept-Language: en-US;q=0.8,en-GB;q=0.6" -H "authorization: Basic somevalue"
Hi,
We are trying to use snow owl with a dedicated ES service.
We set the clusterUrl like so:
repository:
host: 0.0.0.0
port: 2036
index:
socketTimeout: 60000
clusterUrl: "http://terminology-elasticsearch-client:9200"
We were able to CURL this internal URL (http://terminology-elasticsearch-client:9200) from the snow owl container. But we see this in the logs:
ES REST client is connecting to 'http://127.0.0.1:9200', connect timeout: 1000 ms, socket timeout: 60000 ms.
What are we missing?
Does the ES service has default credentials and it's falling back to the localhost url?
Best Regards
My problem relates to importing an initial SNOMED CT RF2 distribution. The sequence of steps I took were
• I downloaded a distribution – “uk_sct2cl_28.0.0_20191001000001.zip”
This contains 2 subdirectories
SnomedCT_InternationalRF2_PRODUCTION_20180731T120000Z
SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z
I attempted to import the zip file as is but the import process returned a 500 error of “Something went wrong during the processing of your request”
I unzipped the zip file and zipped up the individual subfolders, so that each had Delta, Snapshot and Full folders
• I created an import context using POST /snomed-ct/v3/imports and extracted the location header value
curl -X POST "http://localhost:8000/snowowl/snomed-ct/v3/imports" -H "accept: /" -H "authorization: Basic c25vd293bDpzbm93b3ds" -H "Content-Type: application/json;charset=UTF-8" -d "{ "branchPath": "MAIN", "createVersions": true, "type": "FULL"}"
response:
cache-control: no-cache, no-store, max-age=0, must-revalidate content-length: 0 expires: 0 location: http://localhost:8000/snowowl/snomed-ct/v3/imports/f5da278e-d931-422b-9ba6-30959414e438 pragma: no-cache server: Jetty(9.4.18.v20190429) x-content-type-options: nosniff x-frame-options: DENY x-xss-protection: 1; mode=block
• I started an import using POST /snomed-ct/v3/imports/{importId}/archive
curl -X POST "http://localhost:8000/snowowl/snomed-ct/v3/imports/f5da278e-d931-422b-9ba6-30959414e438/archive" -H "accept: /" -H "authorization: Basic c25vd293bDpzbm93b3ds" -H "Content-Type: multipart/form-data" -F file=@SnomedCT_UKClinicalRF2_PRODUCTION_20191001T000001Z.zip
• I queried the import run details using GET /snomed-ct/v3/imports/{importId}
curl -X GET "http://localhost:8000/snowowl/snomed-ct/v3/imports/f5da278e-d931-422b-9ba6-30959414e438" -H "accept: application/json;charset=UTF-8" -H "authorization: Basic c25vd293bDpzbm93b3ds"
response:
{"type":"FULL","branchPath":"MAIN","createVersions":true,"codeSystemShortName":"SNOMEDCT","id":"378146e8-2598-485b-a75c-93dd01470bcb","status":"RUNNING","startDate":"2020-01-16T09:33:12.383+0000"}
• After a few hours I re-ran the above step
curl -X GET "http://localhost:8000/snowowl/snomed-ct/v3/imports/f5da278e-d931-422b-9ba6-30959414e438" -H "accept: application/json;charset=UTF-8" -H "authorization: Basic c25vd293bDpzbm93b3ds"
{"type":"FULL","branchPath":"MAIN","createVersions":true,"codeSystemShortName":"SNOMEDCT","id":"/f5da278e-d931-422b-9ba6-30959414e438","status":"FAILED","startDate":"2020-01-16T09:33:12.383+0000","completionDate":"2020-01-16T11:48:02.322+0000"}
How can I resolve the FAILED status, or understand why the import failed?
I got the following error when trying to start Snow-owl 7.x:
[2019-11-19T11:49:15.714] ERROR Container: a8a4fc02-d3f8-4644-aa62-880362697eb5 snowowl Couldn't execute bulk updates com.b2international.index.IndexException: Couldn't execute bulk updates
at com.b2international.index.es.EsDocumentWriter.commit(EsDocumentWriter.java:153)
at com.b2international.snowowl.datastore.remotejobs.RemoteJobTracker.lambda$0(RemoteJobTracker.java:121)
at com.b2international.index.DefaultIndex.write(DefaultIndex.java:47)
at com.b2international.snowowl.datastore.remotejobs.RemoteJobTracker.<init>(RemoteJobTracker.java:111)
at com.b2international.snowowl.core.repository.RepositoryPlugin.initializeJobSupport(RepositoryPlugin.java:232)
at com.b2international.snowowl.core.repository.RepositoryPlugin.run(RepositoryPlugin.java:221)
at com.b2international.snowowl.core.setup.Plugins.run(Plugins.java:74)
at com.b2international.snowowl.core.SnowOwl.run(SnowOwl.java:292)
at com.b2international.snowowl.core.SnowOwl.run(SnowOwl.java:267)
at com.b2international.snowowl.core.SnowOwl.run(SnowOwl.java:255)
at com.b2international.snowowl.server.product.SnowOwlServerActivator.start(SnowOwlServerActivator.java:51)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:842)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:834)
at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:791)
at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:1013)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:365)
at org.eclipse.osgi.container.Module.doStart(Module.java:598)
at org.eclipse.osgi.container.Module.start(Module.java:462)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel$1.run(ModuleContainer.java:1820)
at org.eclipse.osgi.internal.framework.EquinoxContainerAdaptor$2$1.execute(EquinoxContainerAdaptor.java:150)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1813)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1770)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.doContainerStartLevel(ModuleContainer.java:1735)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1661)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1)
at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:234)
at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:345)
Caused by: java.util.concurrent.ExecutionException: ElasticsearchStatusException[Unable to parse response body]; nested: ResponseException[method [GET], host [https://vpc-es-some-path.eu-west-1.es.amazonaws.com], URI [/_settings?master_timeout=30s&ignore_throttled=false&ignore_unavailable=false&expand_wildcards=open%2Cclosed&allow_no_indices=true], status line [HTTP/1.1 401 Unauthorized]
{"Message":"Your request: '/_settings' is not allowed."}]; nested: ResponseException[method [GET], host [https://vpc-es-some-path.eu-west-1.es.amazonaws.com], URI [/_settings?master_timeout=30s&ignore_throttled=false&ignore_unavailable=false&expand_wildcards=open%2Cclosed&allow_no_indices=true], status line [HTTP/1.1 401 Unauthorized]
{"Message":"Your request: '/_settings' is not allowed."}];
at com.google.common.util.concurrent.AbstractFuture.getDoneValue(AbstractFuture.java:502)
at com.google.common.util.concurrent.AbstractFuture.get(AbstractFuture.java:461)
at com.google.common.util.concurrent.AbstractFuture$TrustedFuture.get(AbstractFuture.java:78)
at com.b2international.index.es.EsDocumentWriter.commit(EsDocumentWriter.java:150)
... 28 common frames omitted
Caused by: org.elasticsearch.ElasticsearchStatusException: Unable to parse response body
at org.elasticsearch.client.RestHighLevelClient.parseResponseException(RestHighLevelClient.java:2033)
at org.elasticsearch.client.RestHighLevelClient.internalPerformRequest(RestHighLevelClient.java:1777)
at org.elasticsearch.client.RestHighLevelClient.performRequest(RestHighLevelClient.java:1734)
at org.elasticsearch.client.RestHighLevelClient.performRequestAndParseEntity(RestHighLevelClient.java:1696)
at org.elasticsearch.client.IndicesClient.getSettings(IndicesClient.java:858)
at com.b2international.index.es.client.http.IndicesHttpClient.settings(IndicesHttpClient.java:116)
at com.b2international.index.es.client.EsClientBase.checkClusterSettings(EsClientBase.java:145)
at com.b2international.index.es.client.EsClientBase$ExpiringMemoizingSupplier.get(EsClientBase.java:207)
at com.b2international.index.es.client.EsClientBase$ExpiringMemoizingSupplier.lambda$1(EsClientBase.java:224)
at net.jodah.failsafe.Functions.lambda$get$0(Functions.java:47)
at net.jodah.failsafe.RetryPolicyExecutor.lambda$supply$0(RetryPolicyExecutor.java:62)
at net.jodah.failsafe.Execution.executeSync(Execution.java:129)
at net.jodah.failsafe.FailsafeExecutor.call(FailsafeExecutor.java:376)
at net.jodah.failsafe.FailsafeExecutor.get(FailsafeExecutor.java:67)
at com.b2international.index.es.client.EsClientBase.waitFor(EsClientBase.java:173)
at com.b2international.index.es.client.EsClientBase$ExpiringMemoizingSupplier.waitUntilValue(EsClientBase.java:221)
at com.b2international.index.es.client.EsClientBase.isIndexReadOnly(EsClientBase.java:156)
at com.b2international.index.es.client.EsClientBase.status(EsClientBase.java:84)
at com.b2international.index.es.client.EsClientBase.checkHealthy(EsClientBase.java:104)
at com.b2international.index.es.client.http.EsHttpClient.updateByQuery(EsHttpClient.java:159)
at com.b2international.index.es.admin.EsIndexAdmin.bulkIndexByScroll(EsIndexAdmin.java:556)
at com.b2international.index.es.admin.EsIndexAdmin.bulkUpdate(EsIndexAdmin.java:531)
at com.b2international.index.es.EsDocumentWriter.lambda$1(EsDocumentWriter.java:143)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at com.google.common.util.concurrent.TrustedListenableFutureTask$TrustedFutureInterruptibleTask.runInterruptibly(TrustedListenableFutureTask.java:111)
at com.google.common.util.concurrent.InterruptibleTask.run(InterruptibleTask.java:58)
at com.google.common.util.concurrent.TrustedListenableFutureTask.run(TrustedListenableFutureTask.java:75)
at com.google.common.util.concurrent.MoreExecutors$DirectExecutorService.execute(MoreExecutors.java:260)
at java.base/java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:118)
at com.google.common.util.concurrent.AbstractListeningExecutorService.submit(AbstractListeningExecutorService.java:56)
at com.b2international.index.es.EsDocumentWriter.commit(EsDocumentWriter.java:143)
... 28 common frames omitted
Suppressed: org.elasticsearch.common.ParsingException: Failed to parse object: expecting field with name [error] but found [Message]
at org.elasticsearch.common.xcontent.XContentParserUtils.ensureFieldName(XContentParserUtils.java:50)
at org.elasticsearch.ElasticsearchException.failureFromXContent(ElasticsearchException.java:605)
at org.elasticsearch.rest.BytesRestResponse.errorFromXContent(BytesRestResponse.java:169)
at org.elasticsearch.client.RestHighLevelClient.parseEntity(RestHighLevelClient.java:2053)
at org.elasticsearch.client.RestHighLevelClient.parseResponseException(RestHighLevelClient.java:2030)
... 58 common frames omitted
Caused by: org.elasticsearch.client.ResponseException: method [GET], host [https://vpc-es-some-path.eu-west-1.es.amazonaws.com], URI [/_settings?master_timeout=30s&ignore_throttled=false&ignore_unavailable=false&expand_wildcards=open%2Cclosed&allow_no_indices=true], status line [HTTP/1.1 401 Unauthorized]
{"Message":"Your request: '/_settings' is not allowed."}
Could it be that Snow-owl hits a restricted api?
I am wondering if using /_all/_settings (instead of /_settings) could be a possible alternative?
While playing around with the FHIR API (using the GET endpoints only) I suddenly started getting timeout responses. This then turned into the whole application being unable to load. After restarting the pods the other endpoints were working, but all FHIR ones throw this exception, on each call:
Exception in thread "Remote job cleanup" com.b2international.index.IndexException: Failed to execute index write
[2019-12-24T14:06:16.043] ERROR qtp1714099025-77 com.b2international.snowowl.core.rest.ControllerExceptionMapper Exception during request processing org.springframework.web.context.request.async.AsyncRequestTimeoutException: null
at org.springframework.web.context.request.async.TimeoutDeferredResultProcessingInterceptor.handleTimeout(TimeoutDeferredResultProcessingInterceptor.java:42)
at org.springframework.web.context.request.async.DeferredResultInterceptorChain.triggerAfterTimeout(DeferredResultInterceptorChain.java:79)
at org.springframework.web.context.request.async.WebAsyncManager.lambda$startDeferredResultProcessing$5(WebAsyncManager.java:427)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1540)
at org.springframework.web.context.request.async.StandardServletAsyncWebRequest.onTimeout(StandardServletAsyncWebRequest.java:150)
at org.eclipse.jetty.server.HttpChannelState$2.run(HttpChannelState.java:610)
at org.eclipse.jetty.server.handler.ContextHandler.handle(ContextHandler.java:1436)
at org.eclipse.jetty.server.HttpChannelState.runInContext(HttpChannelState.java:1135)
at org.eclipse.jetty.server.HttpChannelState.onTimeout(HttpChannelState.java:631)
at org.eclipse.jetty.server.AsyncContextEvent.lambda$run$0(AsyncContextEvent.java:164)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:698)
at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:804)
at java.base/java.lang.Thread.run(Thread.java:834)
at com.b2international.index.DefaultIndex.write(DefaultIndex.java:51)
at com.b2international.snowowl.datastore.remotejobs.RemoteJobTracker$CleanUpTask.run(RemoteJobTracker.java:73)
at java.base/java.util.TimerThread.mainLoop(Timer.java:556)
at java.base/java.util.TimerThread.run(Timer.java:506)
Caused by: java.io.IOException: listener timeout after waiting for [30000] ms
at org.elasticsearch.client.RestClient$SyncResponseListener.get(RestClient.java:912)
at org.elasticsearch.client.RestClient.performRequest(RestClient.java:233)
at org.elasticsearch.client.RestHighLevelClient.internalPerformRequest(RestHighLevelClient.java:1764)
at org.elasticsearch.client.RestHighLevelClient.performRequest(RestHighLevelClient.java:1734)
at org.elasticsearch.client.RestHighLevelClient.performRequestAndParseEntity(RestHighLevelClient.java:1696)
at org.elasticsearch.client.RestHighLevelClientExt.clearScroll(RestHighLevelClientExt.java:61)
at com.b2international.index.es.client.http.EsHttpClient.clearScroll(EsHttpClient.java:153)
at com.b2international.index.es.EsDocumentSearcher.search(EsDocumentSearcher.java:216)
at com.b2international.snowowl.datastore.remotejobs.RemoteJobTracker$CleanUpTask.lambda$0(RemoteJobTracker.java:74)
at com.b2international.index.DefaultIndex.write(DefaultIndex.java:47)
... 3 more
Now, I have no way of fixing that because it seems like the restart even doesn't do it.
I am not sure if this is something intentional but I wouldn't expect a cleanup/maintenance job should kill the whole app.
Any advice how to recover from this? Should deleting the index, somehow, fix it or would that make things worst?
I tried to
{
"parent": "MAIN",
"name": "SNOMEDCT-UK"
}
{
"oid": "1",
"branchPath": "MAIN/SNOMEDCT-UK",
"extensionOf": "SNOMEDCT",
"name": "SNOMED CT UK Clinical Edition",
"organizationLink": "http://digital.nhs.uk",
"primaryLanguage": "ENG",
"repositoryUuid": "snomedStore",
"citation": "SNOMED CT UK Clinical Edition",
"iconPath": "icons/snomed.png",
"shortName": "SNOMEDCT-UK",
"terminologyId": "com.b2international.snowowl.terminology.snomedctuk"
}
Cannot spot any exception inside, but there are some ERRORs of not found mappings.
Any idea would be appreciated.
Cheers,
Petr
Hi,
I'm working with @psiotwo and exploring the branching and version control capabilities of Snow Owl. I am doing a test whereby I create a new branch, make a change and then merge that change with the original branch.
Here is what I've got so far:
/snowowl/snomed-ct/v3/branches:curl -X POST "http://X:8080/snowowl/snomed-ct/v3/branches" -H "accept: application/json;charset=UTF-8" -H "authorization: Basic X" -H "Content-Type: application/json" -d "{ \"parent\": \"MAIN\", \"name\": \"test-1\", \"metadata\": { }}"
/snowowl/snomed-ct/v3/MAIN%2Ftest-1/concepts/449752001:curl -X DELETE "http://X:8080/snowowl/snomed-ct/v3/MAIN%2Ftest-1/concepts/449752001?force=true" -H "accept: */*" -H "authorization: Basic X"
Now if I compare the two branches using /snowowl/snomed-ct/v3/compare:
curl -X POST "http://X:8080/snowowl/snomed-ct/v3/compare" -H "accept: application/json;charset=UTF-8" -H "authorization: Basic X" -H "Content-Type: application/json;charset=UTF-8" -d "{ \"baseBranch\": \"MAIN\", \"compareBranch\": \"MAIN/test-1\", \"limit\": 0}"
It shows no changes:
{
"baseBranch": "MAIN",
"compareBranch": "MAIN/test-1",
"compareHeadTimestamp": 1573640436578,
"newComponents": [],
"changedComponents": [],
"deletedComponents": [],
"totalNew": 0,
"totalChanged": 0,
"totalDeleted": 0
}
Do I need to commit the change before I can see changes? What am I missing?
When trying to compile and use Snow Owl with OpenJDK 13/AdoptJDK 13 it throws the following exception during REST API initialization:
ASM ClassReader failed to parse class file - probably due to a new Java class file version that isn't supported yet: file [C:\dev\snow-owl-7x\git\snow-owl\core\com.b2international.snowowl.core.rest\target\classes\com\b2international\snowowl\core\rest\AbstractRestService.class]; nested exception is java.lang.IllegalArgumentException: Unsupported class file major version 57
at org.springframework.core.type.classreading.SimpleMetadataReader.<init>(SimpleMetadataReader.java:57)
at org.springframework.core.type.classreading.SimpleMetadataReaderFactory.getMetadataReader(SimpleMetadataReaderFactory.java:103)
at org.springframework.core.type.classreading.CachingMetadataReaderFactory.getMetadataReader(CachingMetadataReaderFactory.java:123)
at org.springframework.context.annotation.ClassPathScanningCandidateComponentProvider.scanCandidateComponents(ClassPathScanningCandidateComponentProvider.java:430)
... 97 common frames omitted
Caused by: java.lang.IllegalArgumentException: Unsupported class file major version 57
at org.springframework.asm.ClassReader.<init>(ClassReader.java:184)
at org.springframework.asm.ClassReader.<init>(ClassReader.java:166)
at org.springframework.asm.ClassReader.<init>(ClassReader.java:152)
at org.springframework.asm.ClassReader.<init>(ClassReader.java:273)
at org.springframework.core.type.classreading.SimpleMetadataReader.<init>(SimpleMetadataReader.java:54)
... 100 common frames omitted
To fix the issue, Spring needs to be upgraded to 5.2.x, see here:
https://github.com/spring-projects/spring-framework/wiki/Spring-Framework-Versions
Hi,
I see you have two identityProviders at the moment. Do you have it as a goal somewhere on your roadmap to support OAuth?
From what I am seeing and I think adding it wouldn't be as straightforward as just adding a new plugin because you use internal/custom jwt creator and validator in the identity plugin so it looks like adding new provider would require changing this and essentially create a slightly diff version, which is not ideal.
Thanks
After an import failure (cf #438), is it rolled-back like in a transactional database, or is there some manual cleaning to do to remove part of the data imported successfully in Elasticsearch?
Hi,
I'm investigating Snow Owl's support of SNOMED ECL (Expression Constraint Language). In the frontpage readme it states that you support ECL 1.3.
It also looks like the best way of querying using ECL is using the /snomed-ct/v3/{path}/concepts endpoint with the ecl parameter.
How is the ECL executed? What engine or reasoner does it use? Are all ECL 1.3 operations fully supported?
Thanks,
Josh
I am interested to find out what would be the best way to import non-SNOMED terminologies to SnowOwl, either existing ones (e.g. LOINC), or custom ones. What would be the entry point in source code for developing a custom store for other terminologies?
Good Morning,
I am getting the following issue with branch merging in SnowOwl 7.x.
Starting from an empty index, I imported Snomed-International in the MAIN branch.
I then imported Snomed-UK (snapshot) into MAIN/2018-07-31 (a sub-branch of Snomed-International).
I then created an "empty" branch A starting from MAIN/2018-07-31: the new branch path is MAIN/2018-07-31/A
Now since I want to use branch A to have visibility and create concepts that may refer to both Snomed-UK and Snomed-International concepts, I tried to merge Snomed-UK branch into branch A.
(Would that be a reasonable expectation? Or possible scenario?)
After the merge, I still have the job in RUNNING status if I query GET /snowowl/admin/jobs, and Elasticsearch index "locks-lock" contains two synchronizing changes (one for source and destination branches involved in the merge). This prevents me for further merge into the branch A: I wish to also import and merge Snomed-US snapshot and merge it into A, but a GET /snowowl/snomed-ct/v3/merges/{id} returns a status failed with "Could not acquire requested lock(s)."
Is this a bug? How to make SnowOwl "finish" the merge and have the destination branch unlocked for subsequent merges?
Thanks!
Hi,
I currently have a branching model of:
MAIN is SNOMED INT (January 2019)MAIN/SNOMEDCT-UK is the UK edition extensionMAIN/SNOMEDCT-UK/BABYLON-UK is the Babylon extension to the UK editionAfter updating SNOMED INT using the latest July 2019 delta using the /snomed-ct/v3/imports endpoint MAIN has the latest content in it.
To make the latest content available to the other branches presumably the best way would be to rebase them using the /snomed-ct/v3/merges. If I rebase MAIN/SNOMEDCT-UK will MAIN/SNOMEDCT-UK/BABYLON-UK also be rebased? What's the best way of doing it?
Hi,
after running latest docker image 7.x, I can only see NoOpReasoner in the list of /snomed-ct/v3/reasoners. Is classification supported in OSS version? If so, how to plug e.g. ElkReasoner in?
Thanks,
Petr
Would be great to expose capability statement on /metadata endpoint (TerminologyCapabilities), as specified in http://hl7.org/fhir/http.html.
Hi,
Ive started a merge process using POST /snomed-ct/v3/merges and then when I check the status using GET /snomed-ct/v3/merges/{id} its says the merge status is "SCHEDULED" and the scheduledDate is just the time I query GET /snomed-ct/v3/merges/{id}. What does "SCHEDULED" mean and how do I get the merge to start?
Hi,
I was looking at the documentation and the code and iI have a hard time figuring out how to upload new ConceptMaps, CodeSystems and ValueSets.
Theoretically it should be possible to server all these :
For the CodeSystems there's an admin API and from what I understand requires to create a separate branch, repository, the code system and the import the data through the commands in the readme. Is this correct?
I also am not completely clear on is how this then gets served by the FHIR API?
In the commercial version you have LOINC and few others, are those separate branches that then the FHIR API pulls when GETting the codeSystems? Doesn’t that make them essentially extensions and you said the lookup from an extension is something you are adding now?
Also how does the upload of ValueSets and ConceptMaps works at the moment and would there be a REST API for this?
Those are a lot of questions fired at once sorry, hopefully it's clear enough though.
Thanks
The current implementation of the effectiveTime filter (REST API) does not allow users to filter for Unpublished content.
The underlying Java API actually allows this via the
SnomedSearchRequestBuilder.filterByEffectiveTime(long)
method, but the REST API endpoints are calling the
SnomedSearchRequestBuilder.filterByEffectiveTime(String)
which does not allow unset effective time values to be used.
It would be great to support both the -1 and Unpublished values in that filter.
DELTA export of an extension on a branch is working:
{ "branchPath" : "MAIN/TEST", "extensionOnly": true, "moduleIds" : [ "10000001000242103" ], "type": "DELTA" }
but for FULL/SNAPSHOT the export files are generated with empty content.
The three generated exports:
https://filebin.net/i7j6h6d40hsovbwe
Hi,
running GET /snowowl/fhir/ConceptMap ends up with
"resourceType": "OperationOutcome",
"issue": [
{
"severity": "error",
"code": "exception",
"diagnostics": "Something went wrong during the processing of your request. Exception: null",
"details": {
"text": "Bad Syntax in %s",
"coding": [
{
"code": "msg_bad_syntax",
"system": "http://hl7.org/fhir/operation-outcome",
"display": "Bad Syntax in %s"
}
]
},
"location": [],
"expression": []
}
]
}```
What is in: SNOMED-CT intl 20190731, SNOMED-CT UK 20190601, LOINC-SNOMED mappings 2017
Log here - https://pastebin.com/5uhyTL6K.
Any idea would be appreciated.
Petr
hi! I understand /snowowl/admin/info endpoint is the preferred health check endpoint as described in https://docs.b2i.sg/snow-owl/index/explore/check-status
While trying to deploy snowowl in kubernetes, I am struggling configuring kubernetes health configuration, since snowowl returns a HTTP 401 Missing authorization token when called without authentication. I am referring to readinessProbe defined here: https://kubernetes.io/docs/tasks/configure-pod-container/configure-liveness-readiness-startup-probes/
Could it be possible to have a non restricted endpoint for such simple usage? I would basically need a very simple endpoint that returns 200 when the application is ready to receive traffic, or other error code otherwise.
Thank you!
Some detail of my test with docker image b2ihealthcare/snow-owl-oss:7.x
curl --verbose http://localhost:8080/snowowl/admin/info
* About to connect() to localhost port 8080 (#0)
* Trying 127.0.0.1...
* Connected to localhost (127.0.0.1) port 8080 (#0)
> GET /snowowl/admin/info HTTP/1.1
> User-Agent: curl/7.29.0
> Host: localhost:8080
> Accept: */*
>
< HTTP/1.1 401 Unauthorized
< X-Content-Type-Options: nosniff
< X-XSS-Protection: 1; mode=block
< Cache-Control: no-cache, no-store, max-age=0, must-revalidate
< Pragma: no-cache
< Expires: 0
< X-Frame-Options: DENY
< Content-Type: application/json;charset=utf-8
< X-Content-Type-Options: nosniff
< Transfer-Encoding: chunked
< Server: Jetty(9.4.18.v20190429)
<
* Connection #0 to host localhost left intact
{"status":401,"code":0,"message":"Missing authorization token","developerMessage":"Missing authorization token","errorCode":0,"statusCode":401}
Affected is the file snowowl.bat of the windows release from https://github.com/b2ihealthcare/snow-owl/releases/download/v7.1.0/snow-owl-oss-7.1.0.zip
the CONFIG_AREA is set by
set CONFIG_AREA=%KERNEL_HOME%/work
to 'Volume:\path_to_folder\snowowl_folder \work'
what leads to the error:
"<title>Invalid Configuration Location</title>The configuration area at ''Volume:\path_to_folder\snowowl_folder \work' could not be created. Please choose a writable location using the '-configuration' command line option."
The correct path must be without blank:
set CONFIG_AREA=Volume:\path_to_folder\snowowl_folder\work
I am calling the following endpoints but I am getting confusing results
GET /snomed-ct/v3/{path}/members - Retrieve reference set members from a branch
GET /snomed-ct/v3/{path}/refsets - Retrieve Reference Sets from a branch
Using the Swagger UI,
http://localhost:8000/snowowl/snomed-ct/v3/MAIN/members returns 50 out of a potential 10067083 records.
http://localhost:8000/snowowl/snomed-ct/v3/MAIN/refsets?limit=50 returns 0 records.
Why 0 records? I get the same from my own code so I am wondering if there are any other required parameters. If so, could you give some detail on what they are and what kind of values I should use?
When GETting a previously POSTed export, e.g.
{{SERVER}}/snowowl/snomed-ct/v3/exports/1bbc27b5-a63a-4c27-8f70-c53b837a1045
most of the time the expected response is obtained
{ "type": "DELTA", "branchPath": "MAIN/TEST", "namespaceId": "INT", "moduleIds": [ "10000001000242103" ], "includeUnpublished": false, "codeSystemShortName": "SNOMEDCT", "extensionOnly": true, "acceptLanguage": "en-US,en-GB", "id": "1bbc27b5-a63a-4c27-8f70-c53b837a1045" }
But randomly also this response often occurs:
{ "status": 404, "code": 0, "message": "Export run with identifier '1bbc27b5-a63a-4c27-8f70-c53b837a1045' could not be found.", "developerMessage": "The requested instance resource (id = '1bbc27b5-a63a-4c27-8f70-c53b837a1045', type = 'Export run') does not exist and/or not yet created.", "errorCode": 0, "statusCode": 404 }
Trying the GET request multiple times gets either the first or the second each time.
What is the most recent version of Elasticsearch supported by SnowOwl?
Would a 6.5 version work as an example? (that's the one we have at the moment in our cluster so I just want to make sure).
What about the latest stable version? 7.4.x https://www.elastic.co/guide/en/elasticsearch/reference/current/es-release-notes.html
Thanks!
Hi,
When trying to review (so I can then merge) two branches I get the following error:
Cannot create review for source 'MAIN/X' and target 'MAIN/Y', because there is no relation between them.
I did the following steps:
Is this the desired behaviour or a bug?
I have two branches - one contains a SNOMED CT International, snapshot 2018-07-31, the other SNOMED CT UK extension, snapshot 2019-06-01. The latter is derived from the former. When looking up a SNOMED CT UK concept I correctly find it in the latter and not in the former:
/snomed-ct/v3/MAIN/2018-07-31/SNOMEDCT-UK-2019-06-01/concepts/1019581000000105
gives 200, while
/snomed-ct/v3/MAIN/2018-07-31/concepts/1019581000000105
gives 404.
However, when comparing these two branches using /snomed-ct/v3/compare
{
"compareBranch": "MAIN/2018-07-31/SNOMEDCT-UK-2019-06-01",
"baseBranch": "MAIN/2018-07-31",
"limit" : 1
}
I get an empty diff:
{
"baseBranch": "MAIN/2018-07-31/BABYLON",
"compareBranch": "MAIN/2018-07-31/SNOMEDCT-UK-2019-06-01",
"compareHeadTimestamp": 1580912379100,
"newComponents": [],
"changedComponents": [],
"deletedComponents": [],
"totalNew": 0,
"totalChanged": 0,
"totalDeleted": 0
}
I was expecting to see the UK concepts (e.g. the mentioned 1019581000000105) in the diff. Is it a bug or do I miss something? (tried to consult https://docs.b2i.sg/snow-owl/api/snomed/compare, but maybe I misunderstood the logic of this operation.)
Thanks
Petr
Hi!
I have deployed 2 instances of SnowOwl behind a loadbalancer and called the loadbalancer endpoint to import a file.
At the end of the process, it seems like only one of the two instances of SnowOwl knows about the importId value: one instance returns a HTTP 404 and the other one returns the expected result:
instance 1:
{"status":404,"code":0,"message":"SNOMED CT import configuration with identifier 'aeb488d8-b6c5-4354-8306-fe98a4a7ead2' could not be found.","developerMessage":"The requested instance resource (id = 'aeb488d8-b6c5-4354-8306-fe98a4a7ead2', type = 'SNOMED CT import configuration') does not exist and/or not yet created.","errorCode":0,"statusCode":404}
instance 2:
{"type":"FULL","branchPath":"MAIN/SNOMEDCT-UK","createVersions":true,"codeSystemShortName":"SNOMEDCT","id":"aeb488d8-b6c5-4354-8306-fe98a4a7ead2","status":"COMPLETED","startDate":"2020-01-17T14:47:58.549+0000","completionDate":"2020-01-17T15:23:24.453+0000"}
Calling the loadbalancer:
It randomly returns the result above for either instance 1 or for instance 2.
This makes it difficult for a client code to handle real error or adapt to it, and the probability of getting the false-positive 404 increases with the number of instances behind the loadbalancer.
Could storing the import status object in storage (ES) instead of in memory be a possible solution?
Hi,
How do you resolve branch merging conflicts? For example, I am attempting to merge two branches MAIN/test-1 and MAIN/test-1/test-2. I get the following results from GET /snomed-ct/v3/merges/{id}:
{
"id": "691edea0-e3af-4d40-9f21-5fc2412ddc1b",
"source": "MAIN/test-1/test-2",
"target": "MAIN/test-1",
"status": "CONFLICTS",
"scheduledDate": "2019-12-17T13:08:55.618+0000",
"startDate": "2019-12-17T13:08:55.618+0000",
"endDate": "2019-12-17T13:08:55.670+0000",
"conflicts": [
{
"componentId": "91000242116",
"componentType": "description",
"conflictingAttributes": [
{
"property": "term",
"value": "Special Invitation to participate in clinical trial change 2. test-2",
"oldValue": "Special Invitation to participate in clinical trial (finding)"
}
],
"type": "CONFLICTING_CHANGE",
"message": "description with ID '91000242116' has a conflict of type 'CONFLICTING_CHANGE' on target branch, conflicting attributes are: [term -> old value: Special Invitation to participate in clinical trial (finding), value: Special Invitation to participate in clinical trial change 2. test-2]."
}
]
}
What are the next steps I need to do to resolve the conflicts?
Hello,
a question on search, my scenario is searching labels (descriptions) of concepts, filtering by ancestors (my ideal response should contain description/label matched and its concept_id):
/snomed-ct/v3/{path}/concepts/search supports filtering by ancestors, but the response doesn't show what terms were actually matched. Is this something that can be added in the response, by using Lucene's highlights for example?/snomed-ct/v3/{path}/descriptions/search returns the matched labels (although with different results from the concept endpoint, on same inputs) but I don't know whether it's possible to filter by concept's ancestorDo you have any plans in one of these two directions?
Thanks!
After successful import of SNOMED Intl FULL (20190131 release), and then I wanted to get the change history for a concept (incl. relationships where from/to is the chosen concept and descriptions of that concept). Currently the only option seems to me to use the /commits API to get all the commits related to the concept, e.g.:
/snomed-ct/v3/commits?affectedComponentId=61462000
This results in a list of commits, containing e.g.
{
"id": "7ca1c4da-a045-4f7c-a6e0-f632d5243b06",
"branch": "MAIN",
"author": "System",
"comment": "Imported components from 2015-01-31",
"timestamp": 1574255944125
},
Since the commit wraps the whole import, getting its details by
/snomed-ct/v3/commits/7ca1c4da-a045-4f7c-a6e0-f632d5243b06?expand=details()
results in a huge output which also takes a minute or more to get. Unless I missed some parameter for this call that would allow me to filter by concept SCTID on the server side (in that case I would first get the current descriptions and relationships for the concept and then get their details across all the commits).
Any hint how to use the API efficiently for imported SNOMED components would be appreciated!
Hi,
when trying to POST to refset/members, after a few subsequent posts the import fails with the the following exception.
What would be the canonical way to create a SIMPLE_MAP refset and add members to it?
Thanks,
Petr
[2019-12-10T16:11:14.743] ERROR qtp329654759-46 com.b2international.snowowl.core.rest.ControllerExceptionMapper Exception during request processing com.b2international.snowowl.core.api.SnowowlRuntimeException: java.lang.IllegalArgumentException: expected one element but was: <DatastoreLockIndexEntry{id=371, userId=snowowl, description=committing changes, parentDescription=<<root>>, repositoryId=snomedStore, branchPath=MAIN/SNOMEDCT-UK/BABYLON-97d972f8-4118-4b92-89a9-e9cf59a9cb11}, DatastoreLockIndexEntry{id=418, userId=snowowl, description=committing changes, parentDescription=<<root>>, repositoryId=snomedStore, branchPath=MAIN/SNOMEDCT-UK/BABYLON-97d972f8-4118-4b92-89a9-e9cf59a9cb11}>
at com.b2international.snowowl.datastore.request.TransactionalRequest.execute(TransactionalRequest.java:66)
at com.b2international.snowowl.datastore.request.TransactionalRequest.execute(TransactionalRequest.java:1)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.datastore.request.RevisionIndexReadRequest.lambda$0(RevisionIndexReadRequest.java:64)
at com.b2international.index.revision.DefaultRevisionIndex.lambda$0(DefaultRevisionIndex.java:112)
at com.b2international.index.DefaultIndex.read(DefaultIndex.java:36)
at com.b2international.index.revision.DefaultRevisionIndex.read(DefaultRevisionIndex.java:112)
at com.b2international.index.revision.DefaultRevisionIndex.read(DefaultRevisionIndex.java:106)
at com.b2international.snowowl.datastore.request.RevisionIndexReadRequest.execute(RevisionIndexReadRequest.java:62)
at com.b2international.snowowl.datastore.request.RevisionIndexReadRequest.execute(RevisionIndexReadRequest.java:1)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.datastore.request.BranchRequest.execute(BranchRequest.java:52)
at com.b2international.snowowl.datastore.request.BranchRequest.execute(BranchRequest.java:1)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.datastore.request.IndexReadRequest.lambda$0(IndexReadRequest.java:45)
at com.b2international.index.DefaultIndex.read(DefaultIndex.java:36)
at com.b2international.snowowl.datastore.request.IndexReadRequest.execute(IndexReadRequest.java:43)
at com.b2international.snowowl.datastore.request.IndexReadRequest.execute(IndexReadRequest.java:1)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.datastore.request.HealthCheckingRequest.execute(HealthCheckingRequest.java:47)
at com.b2international.snowowl.datastore.request.HealthCheckingRequest.execute(HealthCheckingRequest.java:1)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.datastore.request.RepositoryRequest.execute(RepositoryRequest.java:62)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.core.rate.RateLimitingRequest.execute(RateLimitingRequest.java:50)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.core.authorization.AuthorizedRequest.execute(AuthorizedRequest.java:114)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.core.monitoring.MonitoredRequest.execute(MonitoredRequest.java:47)
at com.b2international.snowowl.core.repository.ApiRequestHandler.handle(ApiRequestHandler.java:67)
at com.b2international.snowowl.core.repository.ApiRequestHandler.handle(ApiRequestHandler.java:1)
at com.b2international.snowowl.internal.eventbus.EventBus$1.run(EventBus.java:163)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.IllegalArgumentException: expected one element but was: <DatastoreLockIndexEntry{id=371, userId=snowowl, description=committing changes, parentDescription=<<root>>, repositoryId=snomedStore, branchPath=MAIN/SNOMEDCT-UK/BABYLON-97d972f8-4118-4b92-89a9-e9cf59a9cb11}, DatastoreLockIndexEntry{id=418, userId=snowowl, description=committing changes, parentDescription=<<root>>, repositoryId=snomedStore, branchPath=MAIN/SNOMEDCT-UK/BABYLON-97d972f8-4118-4b92-89a9-e9cf59a9cb11}>
at com.google.common.collect.Iterators.getOnlyElement(Iterators.java:322)
at com.google.common.collect.Iterators.getOnlyElement(Iterators.java:335)
at com.google.common.collect.Iterables.getOnlyElement(Iterables.java:277)
at com.b2international.snowowl.datastore.oplock.DatastoreOperationLockManager.getOrCreateLock(DatastoreOperationLockManager.java:297)
at com.b2international.snowowl.datastore.oplock.DatastoreOperationLockManager.unlock(DatastoreOperationLockManager.java:149)
at com.b2international.snowowl.datastore.oplock.DatastoreOperationLockManager.unlock(DatastoreOperationLockManager.java:125)
at com.b2international.snowowl.core.repository.RepositoryTransactionContext.commit(RepositoryTransactionContext.java:252)
at com.b2international.snowowl.datastore.request.TransactionalRequest.commit(TransactionalRequest.java:75)
at com.b2international.snowowl.datastore.request.TransactionalRequest.execute(TransactionalRequest.java:62)
... 36 common frames omitted
I am trying to create a new concept. Steps I have taken:
Successfully imported SNOMED CT Intl 20190131 and SNOMED UK 20180131
Created a custom branch as a child of SNOMED CT Intl
POST /snowowl/snomed-ct/v3/branches
{
"parent": "MAIN",
"name": "TEST"
}
/snowowl/cis/login{
"username": "snowowl",
"password": "snowowl"
}
POST /snowowl/cis/authenticate - and I obtained the token which I use in the subsequent requests
Generate and publish an identifier - I am using a fake namespace 1009999.
POST /snowowl/cis/sct/generate?token=XYZ,
PUT /snowowl/cis/sct/publish?token=XYZ,
Create a fresh concept POST `/snowowl/snomed-ct/v3/MAIN/TEST/concepts. The ids 11009999102, 21009999106, 31009999108, 41009999101 were generated and published in point 5.
"active": true,
"commitComment": "First concept first commit message",
"defaultModuleId": "900000000000207008",
"descriptions": [
{
"acceptability": {
"900000000000509007": "PREFERRED",
"900000000000508004": "PREFERRED"
},
"active": true,
"caseSignificance": "ENTIRE_TERM_CASE_SENSITIVE",
"conceptId": "11009999102",
"id": "41009999101",
"languageCode": "en",
"moduleId": "900000000000207008",
"namespaceId": "1009999",
"term": "First Concept - PT",
"typeId": "900000000000013009"
},
{
"acceptability": {
"900000000000509007": "PREFERRED",
"900000000000508004": "PREFERRED"
},
"active": true,
"caseSignificance": "ENTIRE_TERM_CASE_SENSITIVE",
"conceptId": "11009999102",
"id": "31009999108",
"languageCode": "en",
"moduleId": "900000000000207008",
"namespaceId": "1009999",
"term": "First Concept - FSN",
"typeId": "900000000000003001"
}
],
"relationships" : [
{
"active": true,
"id": "21009999106",
"moduleId": "900000000000207008",
"namespaceId": "1009999",
"destinationId":"138875005",
"typeId": "116680003"
}
],
"id": "11009999102",
"moduleId": "900000000000207008",
"namespaceId": "1009999"
}
As an output I get
"status": 400,
"code": 0,
"message": "Cannot register 1 component IDs because they are not available, reserved, or already assigned.",
"developerMessage": "Input representation syntax or validation errors. Check input values.",
"errorCode": 0,
"statusCode": 400,
"11009999102": "Published"
}
The log is silent - after concept creation request it outputs just
[2019-11-18T15:22:25.416] INFO eventbus-128 request {"commitComment":"First concept first commit message","next":{"active":true,"moduleId":"900000000000207008","operation":"browse","type":"SnomedConceptCreateRequest"},"type":"TransactionalRequest","branchPath":"MAIN/TEST","repositoryId":"snomedStore"} ```
What I am missing?
Thanks,
Petr
Hi,
I was testing the $lookup endpoint and wanted to search for a concept in a snomed extension(the UK one) thinking the format should be [snomed-base-uri]/[extension-module-id] and passing the code of the concept. However, this does not work, not out of the box with the current setup.
I had a quick look at the code and seems like the path is build mainly based on the version as branch of the main codesystem, could not find where the extension module is used besides being verified.
Can you please provide any guidelines how is this supposed to work?
Thanks
when trying to start a validation in /admin/validations endpoint, with a sub-branch under MAIN, I get a stacktrace linking to:
but it works when I ask with branch value being MAIN. I suspect because it's the branch associated with the code system I am using.
Is there a way to validate the data in a sub-branch? That would be an interesting scenario IMHO
https://docs.b2i.sg/snow-owl/index-1/index-1/elasticsearch details how to set the value of Elasticsearch cluster URL with repository.index.clusterUrl in snowowl.yml file.
I was wondering about setting it at runtime, maybe via an environment variable or a property, instead of hardcoding the value?
Is there a way to override configuration properties in snowowl.yml by runtime parameters?
(I basically would like to avoid re-building the docker image when I change the Elasticsearch URL in snowowl.yml)
Thanks!
Trying an import from an empty server, I got this in server side:
[2020-01-16T17:32:32.185] ERROR eventbus-64 c.b.snowowl.snomed.core.rest.services.SnomedRf2ImportService Error during the import of: 825351e7-efdd-4e5d-a4ba-121f705616cc com.b2international.snowowl.core.api.SnowowlRuntimeException: com.b2international.snowowl.core.api.SnowowlRuntimeException: Couldn't execute query: listener timeout after waiting for [30000] ms
at com.b2international.snowowl.snomed.datastore.request.rf2.SnomedRf2ImportRequest.execute(SnomedRf2ImportRequest.java:126)
at com.b2international.snowowl.snomed.datastore.request.rf2.SnomedRf2ImportRequest.execute(SnomedRf2ImportRequest.java:1)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.datastore.request.RevisionIndexReadRequest.execute(RevisionIndexReadRequest.java:72)
at com.b2international.snowowl.datastore.request.RevisionIndexReadRequest.execute(RevisionIndexReadRequest.java:1)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.datastore.request.BranchRequest.execute(BranchRequest.java:52)
at com.b2international.snowowl.datastore.request.BranchRequest.execute(BranchRequest.java:1)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.datastore.request.IndexReadRequest.lambda$0(IndexReadRequest.java:45)
at com.b2international.index.DefaultIndex.read(DefaultIndex.java:36)
at com.b2international.snowowl.datastore.request.IndexReadRequest.execute(IndexReadRequest.java:43)
at com.b2international.snowowl.datastore.request.IndexReadRequest.execute(IndexReadRequest.java:1)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.datastore.request.RepositoryRequest.execute(RepositoryRequest.java:62)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.core.rate.RateLimitingRequest.execute(RateLimitingRequest.java:50)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.core.authorization.AuthorizedRequest.execute(AuthorizedRequest.java:114)
at com.b2international.snowowl.core.events.DelegatingRequest.next(DelegatingRequest.java:72)
at com.b2international.snowowl.core.monitoring.MonitoredRequest.execute(MonitoredRequest.java:47)
at com.b2international.snowowl.core.repository.ApiRequestHandler.handle(ApiRequestHandler.java:67)
at com.b2international.snowowl.core.repository.ApiRequestHandler.handle(ApiRequestHandler.java:1)
at com.b2international.snowowl.internal.eventbus.EventBus$1.run(EventBus.java:163)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: com.b2international.snowowl.core.api.SnowowlRuntimeException: Couldn't execute query: listener timeout after waiting for [30000] ms
at com.b2international.snowowl.core.repository.RepositoryTransactionContext.commit(RepositoryTransactionContext.java:250)
at com.b2international.snowowl.snomed.datastore.request.rf2.importer.Rf2TransactionContext.commit(Rf2TransactionContext.java:121)
at com.b2international.snowowl.snomed.datastore.request.rf2.importer.Rf2EffectiveTimeSlice.doImport(Rf2EffectiveTimeSlice.java:233)
at com.b2international.snowowl.snomed.datastore.request.rf2.SnomedRf2ImportRequest.doImport(SnomedRf2ImportRequest.java:164)
at com.b2international.snowowl.snomed.datastore.request.rf2.SnomedRf2ImportRequest.execute(SnomedRf2ImportRequest.java:121)
... 28 common frames omitted
Caused by: com.b2international.index.IndexException: Couldn't execute query: listener timeout after waiting for [30000] ms
at com.b2international.index.es.EsDocumentSearcher.search(EsDocumentSearcher.java:190)
at com.b2international.index.revision.DefaultRevisionSearcher.search(DefaultRevisionSearcher.java:107)
at com.b2international.snowowl.snomed.datastore.index.change.ConceptChangeProcessor.process(ConceptChangeProcessor.java:156)
at com.b2international.snowowl.datastore.index.BaseRepositoryPreCommitHook.doProcess(BaseRepositoryPreCommitHook.java:100)
at com.b2international.snowowl.datastore.index.BaseRepositoryPreCommitHook.updateDocuments(BaseRepositoryPreCommitHook.java:92)
at com.b2international.snowowl.datastore.index.BaseRepositoryPreCommitHook.lambda$0(BaseRepositoryPreCommitHook.java:46)
at com.b2international.index.revision.DefaultRevisionIndex.lambda$0(DefaultRevisionIndex.java:112)
at com.b2international.index.DefaultIndex.read(DefaultIndex.java:36)
at com.b2international.index.revision.DefaultRevisionIndex.read(DefaultRevisionIndex.java:112)
at com.b2international.index.revision.DefaultRevisionIndex.read(DefaultRevisionIndex.java:106)
at com.b2international.index.revision.StagingArea.read(StagingArea.java:125)
at com.b2international.snowowl.datastore.index.BaseRepositoryPreCommitHook.run(BaseRepositoryPreCommitHook.java:45)
at com.b2international.index.revision.StagingArea.lambda$12(StagingArea.java:206)
Sorry for poor formatting, the important part is: listener timeout after waiting for [30000] ms probably returned by Elasticsearch. I did a quick dive in the code + googling..and found socket time configuration in ES client could be in cause.
I will retry increasing the socket timeout in SnowOwl ES client configuration to 60s instead of 30s, but I read some comments online that it is better to change the cient code and send smaller chunks. I am using an Elasticsearch serviced by AWS.
The file I am importing is SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z.zip
Hi,
The GET /fhir/ConceptMap endpoint always times-out and ends up returning 504 after approximately 59.20something - 59.30something seconds of waiting.
So, after noticing this I cancelled a request and this led to around 16 exceptions like the one below right off the bat.
com.b2international.snowowl.core.rest.ControllerExceptionMapper Exception during request processing org.springframework.web.context.request.async.AsyncRequestTimeoutException: null
at org.springframework.web.context.request.async.TimeoutDeferredResultProcessingInterceptor.handleTimeout(TimeoutDeferredResultProcessingInterceptor.java:42)
at org.springframework.web.context.request.async.DeferredResultInterceptorChain.triggerAfterTimeout(DeferredResultInterceptorChain.java:79)
at org.springframework.web.context.request.async.WebAsyncManager.lambda$startDeferredResultProcessing$5(WebAsyncManager.java:427)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1540)
at org.springframework.web.context.request.async.StandardServletAsyncWebRequest.onTimeout(StandardServletAsyncWebRequest.java:150)
at org.eclipse.jetty.server.HttpChannelState$2.run(HttpChannelState.java:610)
at org.eclipse.jetty.server.handler.ContextHandler.handle(ContextHandler.java:1436)
at org.eclipse.jetty.server.HttpChannelState.runInContext(HttpChannelState.java:1135)
at org.eclipse.jetty.server.HttpChannelState.onTimeout(HttpChannelState.java:631)
at org.eclipse.jetty.server.AsyncContextEvent.lambda$run$0(AsyncContextEvent.java:164)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:698)
at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:804)
at java.base/java.lang.Thread.run(Thread.java:834)
It's also not just these 16 exceptions but they continue to be thrown on each other request and the other requests start returning 504 as well.
This continues basically until the application dies, or essentially it becomes unresponsive, the kube readiness probe fails and it appears as not running but there is no other exception besides the above.
Regards
Hey B2ihealthcare team,
We are trying to quickly load the SNOMED CT resources into snow-owl version 7 (retrieved using this https://docs.b2i.sg/snow-owl/index/installation) for testing purposes. According to the documentation (https://github.com/b2ihealthcare/snow-owl/blob/7.x/documentation/src/main/markdown/configuration_reference.md) there should be a way to turn of indexing. At part "Component Identifier Configuration" there is a setting with name "source" which can have two possible values: INDEX and MEMORY. The MEMORY setting is not an acceptable configuration so we are wondering if there is another way to achieve this. Could you help us with this issue?
Thanks in advance!
PS: Do you already have a docker file for snow-owl?
Hi,
I created a custom refset with a single SNOMED code in the MAIN/2018-07-31 branch (where I have SNOMED International 2018-07-31 imported).
I am able to see the refset through the GET ValueSet endpoint (see listing below):
{ "resourceType": "ValueSet", "id": "snomedStore:MAIN/2018-07-31:3741000242102", "language": "en-us", "url": "http://snomed.info/sct/version/20180731", "identifier": { "use": "official", "system": "http://snomed.info/sct/version/20180731", "value": "3741000242102" }, "version": "2018-07-31", "name": "Stanford Sleepiness Scale 2", "title": "Stanford Sleepiness Scale 2", "status": "active", "date": "2018-07-31T00:00:00.000+0000", "compose": [ { "include": [ { "system": "http://snomed.info/sct", "concept": [], "filter": [ { "property": "expression", "value": "^3741000242102", "op": "=" } ], "valueSet": [] } ], "exclude": [] } ] }
But when I try to use ValueSet/$validate-code with code=248220008, system=http://snomed.info/sct, I struggle to invent the correct value for the 'url' and 'version' parameter. I tried
But either ends with 500 "Query part is missing for value set code validation"
Could you help me understand how to run the $validate-code endpoint?
Thanks
Petr
I'm getting this error after runing ./bin/snowowl.sh while trying to install snow-owl 7.1.0 from the binary. I downloaded, unarchived the tar.gz.
Any hints?
snow-owl-oss-7.1.0.201909021539$ ./bin/snowowl.sh
~/opt/snow-owl-oss-7.1.0.201909021539 ~/opt/snow-owl-oss-7.1.0.201909021539
Java HotSpot(TM) 64-Bit Server VM warning: Option UseConcMarkSweepGC was deprecated in version 9.0 and will likely be removed in a future release.
[2019-10-27T22:50:55.356] ERROR Container: d19684d1-91bf-4ad2-8cf3-5e27b28ac3c5 snowowl com/b2international/index/revision/Hooks$PreCommitHook java.lang.NoClassDefFoundError: com/b2international/index/revision/Hooks$PreCommitHook
at java.base/java.lang.Class.getDeclaredConstructors0(Native Method)
at java.base/java.lang.Class.privateGetDeclaredConstructors(Class.java:3142)
at java.base/java.lang.Class.getConstructor0(Class.java:3347)
at java.base/java.lang.Class.newInstance(Class.java:571)
at com.b2international.commons.extension.ClassPathScanner.lambda$4(ClassPathScanner.java:156)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:177)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:177)
at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1654)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:913)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:578)
at com.b2international.commons.extension.ClassPathScanner.instantiate(ClassPathScanner.java:162)
at com.b2international.commons.extension.ClassPathScanner.getComponentsBySuperclass(ClassPathScanner.java:147)
at com.b2international.snowowl.core.SnowOwl.<init>(SnowOwl.java:108)
at com.b2international.snowowl.core.SnowOwl.create(SnowOwl.java:188)
at com.b2international.snowowl.server.product.ServerProductActivator.start(ServerProductActivator.java:50)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:842)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:552)
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:834)
at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:791)
at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:1013)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:365)
at org.eclipse.osgi.container.Module.doStart(Module.java:598)
at org.eclipse.osgi.container.Module.start(Module.java:462)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel$1.run(ModuleContainer.java:1820)
at org.eclipse.osgi.internal.framework.EquinoxContainerAdaptor$2$1.execute(EquinoxContainerAdaptor.java:150)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1813)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1770)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.doContainerStartLevel(ModuleContainer.java:1735)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1661)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1)
at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:234)
at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:345)
Caused by: java.lang.ClassNotFoundException: An error occurred while automatically activating bundle com.b2international.index (11).
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:126)
at org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:570)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:330)
at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:396)
at org.eclipse.osgi.internal.loader.sources.SingleSourcePackage.loadClass(SingleSourcePackage.java:41)
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:470)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:423)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:415)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:155)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
... 37 common frames omitted
Caused by: org.osgi.framework.BundleException: Exception in com.b2international.index.Activator.start() of bundle com.b2international.index.
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:863)
at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:791)
at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:1013)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:365)
at org.eclipse.osgi.container.Module.doStart(Module.java:598)
at org.eclipse.osgi.container.Module.start(Module.java:462)
at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:493)
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:117)
... 46 common frames omitted
Caused by: java.lang.RuntimeException: java.lang.NoSuchFieldException: modifiers
at com.b2international.index.Activator.withTccl(Activator.java:113)
at com.b2international.index.Activator.start(Activator.java:63)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:842)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:552)
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:834)
... 53 common frames omitted
Caused by: java.lang.NoSuchFieldException: modifiers
at java.base/java.lang.Class.getDeclaredField(Class.java:2416)
at com.b2international.index.Activator.lambda$0(Activator.java:76)
at com.b2international.index.Activator.withTccl(Activator.java:110)
... 58 common frames omitted
Hi,
tried to get all SNOMED refsets from SnowOwl and ended up with running GET /snowowl/snomed-ct/v3/MAIN/refsets?limit=10 (also tried /snowowl/snomed-ct/v3/MAIN/900000000000455006/refsets?limit=10) - both return 500 (stacktrace https://pastebin.com/RhnazQvp).
Petr
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Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
Microsoft
Open source projects and samples from Microsoft.
Google
Google ❤️ Open Source for everyone.
Alibaba
Alibaba Open Source for everyone
D3
Data-Driven Documents codes.
Tencent
China tencent open source team.