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Horta error for LVV #5

Closed freshpomelo closed 4 years ago

freshpomelo commented 4 years ago

Hi everyone,

I've succeeded to display the 2d image for tiff octree in LVV.

But when I tried to "Navigate to This location in Horta (channel 1)", the error message displayed as below:

horta

The tiff data folder is:

tree

The steps I imported the octree data are:

WX20200304-233219@2x ATMS1

Any advices would be greatly appreciated! Thanks a lot in advance.

krokicki commented 4 years ago

Please check the server-side logs for JADE and JACS and investigate the root cause of the error. You can do this using ./manage.sh or docker service logs.

freshpomelo commented 4 years ago

Hi Konrad,

Thank you very much for your response.

The log for jacs_jade-master_1 is

2020-03-04_15:38:52.245 [XNIO-1 task-39] INFO  o.j.j.rest.MasterStorageResource - Count storage records filtered with: org.janelia.jacsstorage.model.jacsstorage.JacsBundle@468fe194[entityRefId=JacsBundle#,name=<null>,path=/jade1/local,storageFormat=<null>,storageVolumeId=<null>,linkedPath=<null>]
2020-03-04_15:38:52.246 [XNIO-1 task-39] INFO  o.j.j.rest.MasterStorageResource - List storage records filtered with: org.janelia.jacsstorage.model.jacsstorage.JacsBundle@468fe194[entityRefId=JacsBundle#,name=<null>,path=/jade1/local,storageFormat=<null>,storageVolumeId=<null>,linkedPath=<null>] / org.janelia.jacsstorage.datarequest.PageRequest@42b07d9d[firstPageOffset=0,pageNumber=0,pageSize=0,sortCriteria=<null>]
2020-03-04_15:38:52.252 [XNIO-1 task-39] INFO  o.j.j.app.JAXMasterStorageApp - 172.22.0.4 unknown unknown '' GET http://jade-master:8080/jacsstorage/master_api/v1/storage ?storagePath=%2Fjade1%2Flocal status=200 response_bytes=60 rt=0.031 tp=0.015 'Jersey/2.29.1 (HttpUrlConnection 1.8.0_232)'
2020-03-04_15:38:52.316 [XNIO-1 task-40] INFO  o.j.j.rest.StorageVolumesResource - List storage volumes filtered with: org.janelia.jacsstorage.datarequest.StorageQuery@70d7987e[id=<null>,shared=false,localToAnyAgent=false,dataStoragePath=/jade1/local,accessibleOnAgent=<null>,storageAgentIds=<null>,storageAgentURLs=<null>,storageName=<null>,storageVirtualPath=<null>,storageTags=[],minAvailableSpaceInBytes=<null>]
2020-03-04_15:38:52.326 [XNIO-1 task-40] INFO  o.j.j.s.d.DistributedStorageVolumeManager - Accessed method: DistributedStorageVolumeManager.findVolumes with {arg0=org.janelia.jacsstorage.datarequest.StorageQuery@70d7987e[id=<null>,shared=false,localToAnyAgent=false,dataStoragePath=/jade1/local,accessibleOnAgent=<null>,storageAgentIds=<null>,storageAgentURLs=<null>,storageName=<null>,storageVirtualPath=<null>,storageTags=[],minAvailableSpaceInBytes=<null>]}  - 10.0859 ms
2020-03-04_15:38:52.330 [XNIO-1 task-40] INFO  o.j.j.app.JAXMasterStorageApp - 172.22.0.4 unknown unknown '' GET http://jade-master:8080/jacsstorage/master_api/v1/storage_volumes ?dataStoragePath=%2Fjade1%2Flocal status=200 response_bytes=610 rt=0.019 tp=0.248 'Jersey/2.29.1 (HttpUrlConnection 1.8.0_232)'
2020-03-04_15:38:56.597 [XNIO-1 task-41] INFO  o.j.j.rest.StorageVolumesResource - List storage volumes filtered with: org.janelia.jacsstorage.datarequest.StorageQuery@2cdf52fc[id=<null>,shared=false,localToAnyAgent=false,dataStoragePath=/jade1/local,accessibleOnAgent=<null>,storageAgentIds=<null>,storageAgentURLs=<null>,storageName=<null>,storageVirtualPath=<null>,storageTags=[],minAvailableSpaceInBytes=<null>]
2020-03-04_15:38:56.600 [XNIO-1 task-41] INFO  o.j.j.s.d.DistributedStorageVolumeManager - Accessed method: DistributedStorageVolumeManager.findVolumes with {arg0=org.janelia.jacsstorage.datarequest.StorageQuery@2cdf52fc[id=<null>,shared=false,localToAnyAgent=false,dataStoragePath=/jade1/local,accessibleOnAgent=<null>,storageAgentIds=<null>,storageAgentURLs=<null>,storageName=<null>,storageVirtualPath=<null>,storageTags=[],minAvailableSpaceInBytes=<null>]}  - 3.0909 ms
2020-03-04_15:38:56.603 [XNIO-1 task-41] INFO  o.j.j.app.JAXMasterStorageApp - 172.22.0.15 youmin youmin 'Workstation' GET http://dulabyoumin-mac.local/jacsstorage/master_api/v1/storage_volumes ?dataStoragePath=%2Fjade1%2Flocal status=200 response_bytes=610 rt=0.010 tp=0.462 'Jersey/2.21 (HttpUrlConnection 1.8.0_231)'
2020-03-04_15:38:56.624 [XNIO-1 task-42] INFO  o.j.j.rest.StorageVolumesResource - List storage volumes filtered with: org.janelia.jacsstorage.datarequest.StorageQuery@742ecccf[id=<null>,shared=false,localToAnyAgent=false,dataStoragePath=/jade1/local,accessibleOnAgent=<null>,storageAgentIds=<null>,storageAgentURLs=<null>,storageName=<null>,storageVirtualPath=<null>,storageTags=[],minAvailableSpaceInBytes=<null>]
2020-03-04_15:38:56.631 [XNIO-1 task-42] INFO  o.j.j.s.d.DistributedStorageVolumeManager - Accessed method: DistributedStorageVolumeManager.findVolumes with {arg0=org.janelia.jacsstorage.datarequest.StorageQuery@742ecccf[id=<null>,shared=false,localToAnyAgent=false,dataStoragePath=/jade1/local,accessibleOnAgent=<null>,storageAgentIds=<null>,storageAgentURLs=<null>,storageName=<null>,storageVirtualPath=<null>,storageTags=[],minAvailableSpaceInBytes=<null>]}  - 6.5274 ms
2020-03-04_15:38:56.632 [XNIO-1 task-42] INFO  o.j.j.app.JAXMasterStorageApp - 172.22.0.15 youmin youmin 'Workstation' GET http://dulabyoumin-mac.local/jacsstorage/master_api/v1/storage_volumes ?dataStoragePath=%2Fjade1%2Flocal status=200 response_bytes=610 rt=0.010 tp=0.452 'Jersey/2.21 (HttpUrlConnection 1.8.0_231)'

And the log for jacs-sync is:

2020-03-04_15:38:49.307 [XNIO-1 task-154] INFO  o.j.j.r.s.v.d.AuthResource [service=] [rootService=] - Authenticate(youmin)
2020-03-04_15:38:49.485 [XNIO-1 task-154] INFO  o.janelia.jacs2.app.JAXSyncAppConfig [service=] [rootService=] - 172.22.0.15 youmin youmin 'Workstation' POST http://dulabyoumin-mac.local/api/rest-v2/auth/authenticate  status=200 response_bytes=253 rt=0.08 tp=0.010 'Jersey/2.21 (HttpUrlConnection 1.8.0_231)'
2020-03-04_15:38:49.584 [XNIO-1 task-155] INFO  o.janelia.jacs2.app.JAXSyncAppConfig [service=] [rootService=] - 172.22.0.15 youmin youmin 'Workstation' GET http://dulabyoumin-mac.local/api/rest-v2/data/user/getorcreate ?subjectKey=user%3Ayoumin status=200 response_bytes=408 rt=0.18 tp=0.174 'Jersey/2.21 (HttpUrlConnection 1.8.0_231)'
2020-03-04_15:38:49.675 [XNIO-1 task-156] INFO  o.janelia.jacs2.app.JAXSyncAppConfig [service=] [rootService=] - 172.22.0.15 youmin youmin 'Workstation' GET http://dulabyoumin-mac.local/api/rest-v2/data/workspaces ?subjectKey=user%3Ayoumin status=200 response_bytes=1446 rt=0.19 tp=0.589 'Jersey/2.21 (HttpUrlConnection 1.8.0_231)'
2020-03-04_15:38:49.715 [XNIO-1 task-157] INFO  o.janelia.jacs2.app.JAXSyncAppConfig [service=] [rootService=] - 172.22.0.15 youmin youmin 'Workstation' POST http://dulabyoumin-mac.local/api/rest-v2/data/domainobject/details  status=200 response_bytes=448 rt=0.19 tp=0.181 'Jersey/2.21 (HttpUrlConnection 1.8.0_231)' {"subjectKey":"user:youmin","references":null,"objectIds":[2775097842258149380],"ordering":null,"objectType":"TmSample","propertyName":null,"propertyValue":null,"domainObject":null,"objectList":null,"preference":null}
2020-03-04_15:38:49.760 [XNIO-1 task-159] INFO  o.janelia.jacs2.app.JAXSyncAppConfig [service=] [rootService=] - 172.22.0.15 youmin youmin 'Workstation' GET http://dulabyoumin-mac.local/api/rest-v2/data/ontology ?subjectKey=user%3Ayoumin status=200 response_bytes=2 rt=0.09 tp=0.002 'Jersey/2.21 (HttpUrlConnection 1.8.0_231)'
2020-03-04_15:38:49.768 [XNIO-1 task-158] INFO  o.janelia.jacs2.app.JAXSyncAppConfig [service=] [rootService=] - 172.22.0.15 youmin youmin 'Workstation' POST http://dulabyoumin-mac.local/api/rest-v2/data/domainobject/details  status=200 response_bytes=348 rt=0.26 tp=0.107 'Jersey/2.21 (HttpUrlConnection 1.8.0_231)' {"subjectKey":"user:youmin","references":["TreeNode#2775092829590913028"],"objectIds":null,"ordering":null,"objectType":null,"propertyName":null,"propertyValue":null,"domainObject":null,"objectList":null,"preference":null}
2020-03-04_15:38:49.945 [XNIO-1 task-160] INFO  o.janelia.jacs2.app.JAXSyncAppConfig [service=] [rootService=] - 172.22.0.15 youmin youmin 'Workstation' POST http://dulabyoumin-mac.local/api/rest-v2/data/domainobject/details  status=200 response_bytes=463 rt=0.08 tp=0.459 'Jersey/2.21 (HttpUrlConnection 1.8.0_231)' {"subjectKey":"user:youmin","references":["TmSample#2775096990126571524"],"objectIds":null,"ordering":null,"objectType":null,"propertyName":null,"propertyValue":null,"domainObject":null,"objectList":null,"preference":null}
2020-03-04_15:38:49.972 [XNIO-1 task-161] INFO  o.janelia.jacs2.app.JAXSyncAppConfig [service=] [rootService=] - 172.22.0.15 youmin youmin 'Workstation' POST http://dulabyoumin-mac.local/api/rest-v2/data/annotation/details  status=200 response_bytes=2 rt=0.08 tp=0.002 'Jersey/2.21 (HttpUrlConnection 1.8.0_231)' {"subjectKey":"user:youmin","references":["TmSample#2775096990126571524","TmSample#2775097842258149380"],"objectIds":null,"ordering":null,"objectType":null,"propertyName":null,"propertyValue":null,"domainObject":null,"objectList":null,"preference":null}
2020-03-04_15:38:49.991 [XNIO-1 task-162] INFO  o.janelia.jacs2.app.JAXSyncAppConfig [service=] [rootService=] - 172.22.0.15 youmin youmin 'Workstation' GET http://dulabyoumin-mac.local/api/rest-v2/data/user/preferences ?subjectKey=user%3Ayoumin status=200 response_bytes=2 rt=0.08 tp=0.002 'Jersey/2.21 (HttpUrlConnection 1.8.0_231)'
2020-03-04_15:38:52.339 [XNIO-1 task-163] INFO  o.j.j.d.s.DataStorageLocationFactory [service=] [rootService=] - Create JADE volume location with URLs http://dulabyoumin-mac.local:9881/jacsstorage/agent_api/v1, http://dulabyoumin-mac.local:9881/jacsstorage/agent_api/v1/agent_storage/storage_volume/2748132569525522445 and volume path local
2020-03-04_15:38:52.905 [XNIO-1 task-163] INFO  o.j.r.JADEBasedRenderedVolumeLocation [service=] [rootService=] - Read tile info for default.0.tif in 192 ms
2020-03-04_15:38:52.908 [XNIO-1 task-163] INFO  o.janelia.jacs2.app.JAXSyncAppConfig [service=] [rootService=] - 172.22.0.15 youmin youmin 'Workstation' GET http://dulabyoumin-mac.local/api/rest-v2/mouselight/samples/2775097842258149380/volume_info  status=200 response_bytes=591 rt=0.84 tp=0.006 'Jakarta Commons-HttpClient/3.1'
2020-03-04_15:38:53.365 [XNIO-1 task-164] INFO  o.janelia.jacs2.app.JAXSyncAppConfig [service=] [rootService=] - 172.22.0.15 youmin youmin 'Workstation' GET http://dulabyoumin-mac.local/api/rest-v2/data/domainobject/class ?subjectKey=user%3Ayoumin&domainClass=org.janelia.model.domain.tiledMicroscope.TmReviewTask status=200 response_bytes=2 rt=0.07 tp=0.002 'Jersey/2.21 (HttpUrlConnection 1.8.0_231)'
cgoina commented 4 years ago

do you have the logs from jade agent - those may be the relevant ones since the agent is responsible for actually retrieving the files. The master only "assigns" the job or return the appropriate agent that can handle the data

freshpomelo commented 4 years ago

Hi Cristian, Thank you very much for your response.

The log for jacs_jade-agent1_1 is:

2020-03-04_15:38:52.451 [XNIO-1 task-341] INFO  o.j.j.s.l.LocalStorageVolumeManager - Accessed method: LocalStorageVolumeManager.getVolumeById with {arg0=2748132569525522445}  - 19.0884 ms
2020-03-04_15:38:52.472 [XNIO-1 task-341] INFO  o.j.j.helper.StorageResourceHelper - /data/jacsstorage/samples/local/transform.txt file size is: 70
2020-03-04_15:38:52.504 [XNIO-1 task-341] INFO  o.j.j.app.JAXAgentStorageApp - 172.22.0.1 unknown unknown '' GET http://dulabyoumin-mac.local:9881/jacsstorage/agent_api/v1/agent_storage/storage_volume/2748132569525522445/data_content/local/transform.txt  status=200 response_bytes=70 rt=0.093 tp=0.006 'Jersey/2.29.1 (HttpUrlConnection 1.8.0_232)'
2020-03-04_15:38:52.672 [XNIO-1 task-342] INFO  o.j.j.s.l.LocalStorageVolumeManager - Accessed method: LocalStorageVolumeManager.getVolumeById with {arg0=2748132569525522445}  - 5.0788 ms
2020-03-04_15:38:52.711 [XNIO-1 task-342] INFO  o.j.j.app.JAXAgentStorageApp - 172.22.0.1 unknown unknown '' GET http://dulabyoumin-mac.local:9881/jacsstorage/agent_api/v1/agent_storage/storage_volume/2748132569525522445/list/local ?depth=1 status=200 response_bytes=8195 rt=0.048 tp=1.269 'Jersey/2.29.1 (HttpUrlConnection 1.8.0_232)'
2020-03-04_15:38:52.776 [XNIO-1 task-343] INFO  o.j.j.s.l.LocalStorageVolumeManager - Accessed method: LocalStorageVolumeManager.getVolumeById with {arg0=2748132569525522445}  - 6.7884 ms
2020-03-04_15:38:52.901 [XNIO-1 task-343] INFO  o.j.j.app.JAXAgentStorageApp - 172.22.0.1 unknown unknown '' GET http://dulabyoumin-mac.local:9881/jacsstorage/agent_api/v1/agent_storage/storage_volume/2748132569525522445/data_info/local/default.0.tif  status=200 response_bytes=63 rt=0.140 tp=0.004 'Jersey/2.29.1 (HttpUrlConnection 1.8.0_232)'
krokicki commented 4 years ago

We cannot reproduce this issue, and there's nothing in the logs indicating what the problem might be. Maybe the KTX path was not populated correctly on the TmSample object because it was inaccessible at sample creation time?