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JaneliaSciComp / jacs-cm

JACS Configuration Management
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Import Imagery #8

Closed SupermeLC closed 4 years ago

SupermeLC commented 4 years ago

Hi, I load the image as the Janelia Workstation User Manual.pdf "Image Octree Data Format". The Host1 status is as follow: image

My transform.txt is as follow:

ox: 128
oy: 128
oz: 128
sx: 200.0
sy: 200.0
sz: 200.0
nl: 2

The tree of folder is as follow:

image

the image .tif is 128 , 128 , 128 (8bit). But I still cannot import the images from the client: image The error is :

org.janelia.workstation.core.api.exceptions.RemoteServiceException: Remote service returned InboundJaxrsResponse{context=ClientResponse{method=PUT, uri=https://xx.xx.xx.xx/SCSW/JACS2SyncServices/v2/mouselight/data/sample?subjectKey=user%3Aroot, status=500, reason=Internal Server Error}} response
    at org.janelia.workstation.core.api.http.RESTClientBase.checkBadResponse(RESTClientBase.java:26)
    at org.janelia.workstation.gui.large_volume_viewer.api.TiledMicroscopeRestClient.create(TiledMicroscopeRestClient.java:137)
    at org.janelia.workstation.gui.large_volume_viewer.api.TiledMicroscopeDomainMgr.save(TiledMicroscopeDomainMgr.java:116)
    at org.janelia.workstation.gui.large_volume_viewer.action.SaveTiledMicroscopeSampleAction$1.doStuff(SaveTiledMicroscopeSampleAction.java:63)
    at org.janelia.workstation.core.workers.SimpleWorker.createResult(SimpleWorker.java:14)
    at org.janelia.workstation.core.workers.SimpleWorker.createResult(SimpleWorker.java:10)
    at org.janelia.workstation.core.workers.ResultWorker.doInBackground(ResultWorker.java:50)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
[catch] at java.lang.Thread.run(Unknown Source)

Hoping for your reply! Liu

krokicki commented 4 years ago

Hi Liu, Can you please post the error on the server side using this command: docker service logs jacs_jacs-sync There's no need to post the entire log, just whatever is logged when you try to import the sample. Thanks, Konrad

SupermeLC commented 4 years ago

Hi Konrad, The output of docker service logs jacs_jacs-sync is:

jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    | 2019-10-26_14:47:54.032 [XNIO-1 task-11] INFO  o.j.j.r.s.v.d.TmSampleResource [service=] [rootService=] - Creating new TmSample test with path /jade1/test
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    | 2019-10-26_14:47:54.113 [XNIO-1 task-11] INFO  o.j.j.d.s.DataStorageLocationFactory [service=] [rootService=] - Create JADE volume location with URLs http://csdl-neutu:9881/jacsstorage/agent_api/v1, http://csdl-neutu:9881/jacsstorage/agent_api/v1/agent_storage/storage_volume/2727932710805835845 and volume path test
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    | 2019-10-26_14:47:54.114 [XNIO-1 task-11] INFO  o.j.j.r.s.v.d.TmSampleResource [service=] [rootService=] - Reading transform.txt from http://csdl-neutu:9881/jacsstorage/agent_api/v1/agent_storage/storage_volume/2727932710805835845/test/
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    | 2019-10-26_14:47:54.152 [XNIO-1 task-11] INFO  o.j.j.r.s.v.d.TmSampleResource [service=] [rootService=] - Found 2 levels in octree
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    | 2019-10-26_14:47:54.152 [XNIO-1 task-11] INFO  o.j.j.r.s.v.d.TmSampleResource [service=] [rootService=] - KTX data path not provided for test. Attempting to find it relative to the octree...
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    | 2019-10-26_14:47:54.207 [XNIO-1 task-11] INFO  o.j.j.d.s.DataStorageLocationFactory [service=] [rootService=] - Create JADE volume location with URLs http://csdl-neutu:9881/jacsstorage/agent_api/v1, http://csdl-neutu:9881/jacsstorage/agent_api/v1/agent_storage/storage_volume/2727932710805835845 and volume path test/ktx
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    | 2019-10-26_14:47:54.208 [XNIO-1 task-11] INFO  o.j.j.r.s.v.d.TmSampleResource [service=] [rootService=] - RAW data path not provided for test. Attempting to read it from the tilebase.cache.yml...
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    | 2019-10-26_14:47:54.236 [XNIO-1 task-11] ERROR o.j.j.r.IllegalStateRequestHandler [service=] [rootService=] - Invalid state exception
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    | java.lang.IllegalStateException: java.lang.IllegalStateException: Subject does not have a default workspace: user:root
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.janelia.model.access.domain.dao.mongo.TmSampleMongoDao.createTmSample(TmSampleMongoDao.java:39)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.janelia.model.access.domain.dao.searchables.TmSampleSearchableDao.createTmSample(TmSampleSearchableDao.java:27)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.janelia.jacs2.rest.sync.v2.dataresources.TmSampleResource.createTmSample(TmSampleResource.java:322)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.janelia.jacs2.rest.sync.v2.dataresources.TmSampleResource$Proxy$_$$_WeldClientProxy.createTmSample(Unknown Source)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at java.lang.reflect.Method.invoke(Method.java:498)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory.lambda$static$0(ResourceMethodInvocationHandlerFactory.java:52)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:124)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:167)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:176)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:79)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:469)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:391)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:80)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:253)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.internal.Errors$1.call(Errors.java:248)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.internal.Errors$1.call(Errors.java:244)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.internal.Errors.process(Errors.java:292)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.internal.Errors.process(Errors.java:274)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.internal.Errors.process(Errors.java:244)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:265)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:232)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:679)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:392)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:346)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:365)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:318)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:205)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.servlet.handlers.ServletHandler.handleRequest(ServletHandler.java:74)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.servlet.handlers.security.ServletSecurityRoleHandler.handleRequest(ServletSecurityRoleHandler.java:62)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.servlet.handlers.ServletChain$1.handleRequest(ServletChain.java:68)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.servlet.handlers.ServletDispatchingHandler.handleRequest(ServletDispatchingHandler.java:36)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.servlet.handlers.security.SSLInformationAssociationHandler.handleRequest(SSLInformationAssociationHandler.java:132)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.servlet.handlers.security.ServletAuthenticationCallHandler.handleRequest(ServletAuthenticationCallHandler.java:57)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.security.handlers.AbstractConfidentialityHandler.handleRequest(AbstractConfidentialityHandler.java:46)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.servlet.handlers.security.ServletConfidentialityConstraintHandler.handleRequest(ServletConfidentialityConstraintHandler.java:64)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.security.handlers.AuthenticationMechanismsHandler.handleRequest(AuthenticationMechanismsHandler.java:60)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.servlet.handlers.security.CachedAuthenticatedSessionHandler.handleRequest(CachedAuthenticatedSessionHandler.java:77)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.security.handlers.AbstractSecurityContextAssociationHandler.handleRequest(AbstractSecurityContextAssociationHandler.java:43)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.servlet.handlers.ServletInitialHandler.handleFirstRequest(ServletInitialHandler.java:292)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.servlet.handlers.ServletInitialHandler.access$100(ServletInitialHandler.java:81)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.servlet.handlers.ServletInitialHandler$2.call(ServletInitialHandler.java:138)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.servlet.handlers.ServletInitialHandler$2.call(ServletInitialHandler.java:135)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.servlet.core.ServletRequestContextThreadSetupAction$1.call(ServletRequestContextThreadSetupAction.java:48)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.servlet.core.ContextClassLoaderSetupAction$1.call(ContextClassLoaderSetupAction.java:43)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.servlet.handlers.ServletInitialHandler.dispatchRequest(ServletInitialHandler.java:272)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.servlet.handlers.ServletInitialHandler.access$000(ServletInitialHandler.java:81)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.servlet.handlers.ServletInitialHandler$1.handleRequest(ServletInitialHandler.java:104)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.server.Connectors.executeRootHandler(Connectors.java:364)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at io.undertow.server.HttpServerExchange$1.run(HttpServerExchange.java:830)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at java.lang.Thread.run(Thread.java:748)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    | Caused by: java.lang.IllegalStateException: Subject does not have a default workspace: user:root
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.janelia.model.access.domain.DomainDAO.getOrCreateDefaultTreeNodeFolder(DomainDAO.java:1779)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   at org.janelia.model.access.domain.dao.mongo.TmSampleMongoDao.createTmSample(TmSampleMongoDao.java:35)
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    |   ... 57 common frames omitted
jacs_jacs-sync.1.i6gml2stqbc7@csdl-neutu    | 2019-10-26_14:47:54.238 [XNIO-1 task-11] INFO  o.janelia.jacs2.app.JAXSyncAppConfig [service=] [rootService=] - 10.0.6.4 root root 'Workstation' PUT http://csdl-neutu/api/rest-v2/mouselight/data/sample ?subjectKey=user%3Aroot status=500 response_bytes=104 rt=0.13 tp=0.004 'Jersey/2.21 (Apache HttpClient 4.5)' {"subjectKey":"user:root","references":null,"objectIds":null,"ordering":null,"objectType":null,"propertyName":null,"propertyValue":null,"domainObject":{"class":"org.janelia.model.domain.tiledMicroscope.TmSample","name":"test","ownerKey":null,"readers":[],"writers":[],"creationDate":null,"updatedDate":null,"micronToVoxMatrix":null,"voxToMicronMatrix":null,"origin":null,"scaling":null,"numImageryLevels":null,"files":{"LargeVolumeOctree":"/jade1/test"},"filesystemSync":true,"filepath":null,"_id":null},"objectL... truncated ...

Liu

krokicki commented 4 years ago

That's intentional (though it should have a better error message). The root user cannot create samples. You should create a real user and then create the sample.