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Posted to issues@airavata.apache.org by "Marcus Christie (Jira)" <ji...@apache.org> on 2019/11/20 21:53:00 UTC
[jira] [Comment Edited] (AIRAVATA-3268) BUG: The input file name
cannot be changed using value field content in application interface
[ https://issues.apache.org/jira/browse/AIRAVATA-3268?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16978768#comment-16978768 ]
Marcus Christie edited comment on AIRAVATA-3268 at 11/20/19 9:52 PM:
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Getting this error in API server after the openjdk 11 upgrade:
{noformat}
2019-11-20 21:45:48,381 [pool-9-thread-14] ERROR o.a.t.server.TThreadPoolServer - Thrift error occurred during process
ing of message.
org.apache.thrift.protocol.TProtocolException: Required field 'overridebyAiravata' is unset! Struct:ComputeResourcePref
erence(computeResourceId:bridges.psc.edu_8bfb9e14-e0ad-44b6-a4d0-5c2b28fdffa0, overridebyAiravata:true, loginUserName:g
communi, preferredJobSubmissionProtocol:SSH, preferredDataMovementProtocol:SCP, preferredBatchQueue:RM, scratchLocation
:/home/gcommuni/scratch/seagrid_workdirs, allocationProjectNumber:ch87lmp, resourceSpecificCredentialStoreToken:7cd5828
8-c013-462b-b091-530d0ca1ebad, usageReportingGatewayId:seagrid.org, qualityOfService:, reservation:, reservationStartTi
me:1483552965000, reservationEndTime:1483552965000)
at org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference.validate(ComputeResourcePrefer
ence.java:1627)
at org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference$ComputeResourcePreferenceStand
ardScheme.write(ComputeResourcePreference.java:1827)
at org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference$ComputeResourcePreferenceStand
ardScheme.write(ComputeResourcePreference.java:1657)
at org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference.write(ComputeResourcePreferenc
e.java:1455)
at org.apache.airavata.model.appcatalog.gatewayprofile.GatewayResourceProfile$GatewayResourceProfileStandardSch
eme.write(GatewayResourceProfile.java:882)
at org.apache.airavata.model.appcatalog.gatewayprofile.GatewayResourceProfile$GatewayResourceProfileStandardSch
eme.write(GatewayResourceProfile.java:768)
at org.apache.airavata.model.appcatalog.gatewayprofile.GatewayResourceProfile.write(GatewayResourceProfile.java
:668)
at org.apache.airavata.registry.api.RegistryService$getGatewayResourceProfile_result$getGatewayResourceProfile_
resultStandardScheme.write(RegistryService.java)
at org.apache.airavata.registry.api.RegistryService$getGatewayResourceProfile_result$getGatewayResourceProfile_
resultStandardScheme.write(RegistryService.java)
at org.apache.airavata.registry.api.RegistryService$getGatewayResourceProfile_result.write(RegistryService.java
)
at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:55)
at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
2019-11-20 21:45:48,381 [pool-9-thread-14] WARN o.a.t.t.TIOStreamTransport - Error closing output stream.
java.net.SocketException: Socket closed
at java.base/java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:113)
at java.base/java.net.SocketOutputStream.write(SocketOutputStream.java:150)
at java.base/java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:81)
at java.base/java.io.BufferedOutputStream.flush(BufferedOutputStream.java:142)
at java.base/java.io.FilterOutputStream.close(FilterOutputStream.java:182)
at org.apache.thrift.transport.TIOStreamTransport.close(TIOStreamTransport.java:110)
at org.apache.thrift.transport.TSocket.close(TSocket.java:235)
at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:303)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
{noformat}
It is complaining that overridebyAiravata isn't set ({{Required field 'overridebyAiravata' is unset!}}), but it clearly is ({{Struct:ComputeResourcePreference(computeResourceId:bridges.psc.edu_8bfb9e14-e0ad-44b6-a4d0-5c2b28fdffa0, overridebyAiravata:true, ....}}).
was (Author: marcuschristie):
Getting this error in API server after the openjdk 11 upgrade:
{noformat}
2019-11-20 21:45:48,381 [pool-9-thread-14] ERROR o.a.t.server.TThreadPoolServer - Thrift error occurred during process
ing of message.
org.apache.thrift.protocol.TProtocolException: Required field 'overridebyAiravata' is unset! Struct:ComputeResourcePref
erence(computeResourceId:bridges.psc.edu_8bfb9e14-e0ad-44b6-a4d0-5c2b28fdffa0, overridebyAiravata:true, loginUserName:g
communi, preferredJobSubmissionProtocol:SSH, preferredDataMovementProtocol:SCP, preferredBatchQueue:RM, scratchLocation
:/home/gcommuni/scratch/seagrid_workdirs, allocationProjectNumber:ch87lmp, resourceSpecificCredentialStoreToken:7cd5828
8-c013-462b-b091-530d0ca1ebad, usageReportingGatewayId:seagrid.org, qualityOfService:, reservation:, reservationStartTi
me:1483552965000, reservationEndTime:1483552965000)
at org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference.validate(ComputeResourcePrefer
ence.java:1627)
at org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference$ComputeResourcePreferenceStand
ardScheme.write(ComputeResourcePreference.java:1827)
at org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference$ComputeResourcePreferenceStand
ardScheme.write(ComputeResourcePreference.java:1657)
at org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference.write(ComputeResourcePreferenc
e.java:1455)
at org.apache.airavata.model.appcatalog.gatewayprofile.GatewayResourceProfile$GatewayResourceProfileStandardSch
eme.write(GatewayResourceProfile.java:882)
at org.apache.airavata.model.appcatalog.gatewayprofile.GatewayResourceProfile$GatewayResourceProfileStandardSch
eme.write(GatewayResourceProfile.java:768)
at org.apache.airavata.model.appcatalog.gatewayprofile.GatewayResourceProfile.write(GatewayResourceProfile.java
:668)
at org.apache.airavata.registry.api.RegistryService$getGatewayResourceProfile_result$getGatewayResourceProfile_
resultStandardScheme.write(RegistryService.java)
at org.apache.airavata.registry.api.RegistryService$getGatewayResourceProfile_result$getGatewayResourceProfile_
resultStandardScheme.write(RegistryService.java)
at org.apache.airavata.registry.api.RegistryService$getGatewayResourceProfile_result.write(RegistryService.java
)
at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:55)
at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
2019-11-20 21:45:48,381 [pool-9-thread-14] WARN o.a.t.t.TIOStreamTransport - Error closing output stream.
java.net.SocketException: Socket closed
at java.base/java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:113)
at java.base/java.net.SocketOutputStream.write(SocketOutputStream.java:150)
at java.base/java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:81)
at java.base/java.io.BufferedOutputStream.flush(BufferedOutputStream.java:142)
at java.base/java.io.FilterOutputStream.close(FilterOutputStream.java:182)
at org.apache.thrift.transport.TIOStreamTransport.close(TIOStreamTransport.java:110)
at org.apache.thrift.transport.TSocket.close(TSocket.java:235)
at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:303)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
{noformat}
It is complaining that overridebyAiravata isn't set ({{Required field 'overridebyAiravata' is unset!}}), but it clearly is ({{Struct:ComputeResourcePref
erence(computeResourceId:bridges.psc.edu_8bfb9e14-e0ad-44b6-a4d0-5c2b28fdffa0, overridebyAiravata:true, ....}}).
> BUG: The input file name cannot be changed using value field content in application interface
> ---------------------------------------------------------------------------------------------
>
> Key: AIRAVATA-3268
> URL: https://issues.apache.org/jira/browse/AIRAVATA-3268
> Project: Airavata
> Issue Type: Sub-task
> Components: Django Portal
> Affects Versions: 0.18
> Reporter: Eroma
> Assignee: Marcus Christie
> Priority: Critical
> Fix For: 0.19
>
>
> 1. When creating application inputs in Interface tab user can have the uploading file name changed to the value given in "Value" field.
> 2. This new assigned name will be the one that get added to the job script as well as the name of the file when the file is in the compute resource working directory.
> h5. TODO
> - [x] model/db changes
> - [x] db migration script to copy input.value to input.overrideFilename
> - [ ] Django frontend changes
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