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Task #8091

Mysterious sync failure of an eml object from the GOA node

Added by Jing Tao over 4 years ago. Updated over 4 years ago.

Status:
In Progress
Priority:
Normal
Assignee:
Category:
dataone-cn-os-core
Target version:
Start date:
2017-05-05
Due date:
% Done:

30%

Milestone:
None
Product Version:
*
Story Points:
Sprint:

Description

Matt reported an eml object which is in a package wasn't indexed on production cns but it was indexed on the mn:
https://goa.nceas.ucsb.edu/#view/urn:uuid:3249ada0-afe3-4dd6-875e-0f7928a4c171

It turned out that the object hadn't been synchronized to cns.

I looked at the cn-synchornizaztion.log:
[ INFO] 2017-05-05 17:37:18,104 (V2TransferObjectTask:call:234) Task-urn:node:GOA-urn:uuid:3249ada0-afe3-4dd6-875e-0f7928a4c171 - Unlocked Pid.
[ERROR] 2017-05-05 17:37:18,104 (V2TransferObjectTask:call:269) Task-urn:node:GOA-urn:uuid:3249ada0-afe3-4dd6-875e-0f7928a4c171 - UnrecoverableException: urn:uuid:3249ada0-afe3-4dd6-875e-0f7928a4c171 cn.createObject failed
org.dataone.cn.batch.exceptions.UnrecoverableException: urn:uuid:3249ada0-afe3-4dd6-875e-0f7928a4c171 cn.createObject failed
at org.dataone.cn.batch.synchronization.tasks.V2TransferObjectTask.createObject(V2TransferObjectTask.java:808)
at org.dataone.cn.batch.synchronization.tasks.V2TransferObjectTask.processNewObject(V2TransferObjectTask.java:493)
at org.dataone.cn.batch.synchronization.tasks.V2TransferObjectTask.processTask(V2TransferObjectTask.java:426)
at org.dataone.cn.batch.synchronization.tasks.V2TransferObjectTask.call(V2TransferObjectTask.java:211)
at org.dataone.cn.batch.synchronization.tasks.V2TransferObjectTask.call(V2TransferObjectTask.java:113)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
[ WARN] 2017-05-05 17:37:18,106 (SyncFailedTask:submitSynchronizationFailed:116) Task-urn:node:GOA-urn:uuid:3249ada0-afe3-4dd6-875e-0f7928a4c171 - SynchronizationFailed: detail code: 6001 id:urn:uuid:3249ada0-afe3-4dd6-875e-0f7928a4c171 nodeId:urn:node:CNUCSB1 description:Synchronization task of [PID::] urn:uuid:3249ada0-afe3-4dd6-875e-0f7928a4c171 [::PID] failed. Cause: ServiceFailure: Task-urn:node:GOA-urn:uuid:3249ada0-afe3-4dd6-875e-0f7928a4c171 - null
[ INFO] 2017-05-05 17:37:18,149 (V2TransferObjectTask:call:294) Task-urn:node:GOA-urn:uuid:3249ada0-afe3-4dd6-875e-0f7928a4c171 - exiting with callState: FAILED

I also looked at the metacat.log there is not much information either:
metacat 20170505-18:01:17: [ERROR]: D1ResourceHandler: Serializing exception with code 500: null [edu.ucsb.nceas.metacat.restservice.D1ResourceHandler:serializeException:456]
metacat 20170505-18:01:17: [WARN]: Could not check docid for revision: urn:uuid:3249ada0-afe3-4dd6-875e-0f7928a4c171 [edu.ucsb.nceas.metacat.EventLog:getReport:291]
edu.ucsb.nceas.metacat.McdbDocNotFoundException: the requested docid 'urn:uuid:3249ada0-afe3-4dd6-875e-0f7928a4c171' does not exist

metacat 20170505-18:01:17: [ERROR]: D1ResourceHandler: Serializing exception with code 404: No record found for: urn:uuid:3249ada0-afe3-4dd6-875e-0f7928a4c171. [edu.ucsb.nceas.metacat.restservice.D1ResourceHandler:serializeException:456]

I asked Peter to uploaded the package into sandbox and the eml object couldn't be sync either.
https://mn-sandbox-ucsb-1.test.dataone.org/knb/d1/mn/v2/query/solr/?q=id:%22urn:uuid:7b45e981-505b-42b1-b598-936da6277ae9%22
https://cn-sandbox.test.dataone.org/cn/v2/meta/urn:uuid:7b45e981-505b-42b1-b598-936da6277ae9


Related issues

Related to Infrastructure - Bug #8229: cn.creates failing with "413: Request Entity Too Large" thrown from apache Closed 2017-12-18

History

#1 Updated by Jing Tao over 4 years ago

  • Assignee set to Jing Tao
  • Category set to Metacat

#2 Updated by Jing Tao over 4 years ago

We have a similar syc failure from ebird:
https://redmine.dataone.org/issues/8054

#3 Updated by Jing Tao over 4 years ago

[ INFO] 2017-05-05 23:19:12,921 (SyncObjectTask:executeTransferObjectTask:219) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 received
[ INFO] 2017-05-05 23:19:12,922 (SyncObjectTask:executeTransferObjectTask:236) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 submitted for execution
[DEBUG] 2017-05-05 23:19:12,922 (SyncObjectTask:call:164) ActiveCount: 1 Pool size 1 Max Pool Size 100
[ INFO] 2017-05-05 23:19:12,922 (V2TransferObjectTask:call:202) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 - Locking task, attempt 1
[ INFO] 2017-05-05 23:19:12,987 (V2TransferObjectTask:call:207) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 - Processing SyncObject
[ INFO] 2017-05-05 23:19:13,509 (V2TransferObjectTask:retrieveMNSystemMetadata:315) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 - Retrieved SystemMetadata Identifier:urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 from node urn:node:mnDemo6 for ObjectInfo Identifier urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23
[DEBUG] 2017-05-05 23:19:13,509 (V2TransferObjectTask:call:209) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 MN system metadata retrieved...
[DEBUG] 2017-05-05 23:19:13,509 (V2TransferObjectTask:processTask:410) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 entering processTask...
[DEBUG] 2017-05-05 23:19:13,509 (V2TransferObjectTask:validateSeriesId:579) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 entering validateSeriesId...
[DEBUG] 2017-05-05 23:19:13,509 (V2TransferObjectTask:resolve:685) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 entering resolve...
[DEBUG] 2017-05-05 23:19:13,824 (V2TransferObjectTask:resolve:695) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 PID urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 does not exist on the CN.
[DEBUG] 2017-05-05 23:19:13,824 (V2TransferObjectTask:processNewObject:462) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 entering processNewObject...
[DEBUG] 2017-05-05 23:19:13,899 (V2TransferObjectTask:processNewObject:475) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 Pid is not reserved by anyone.
[DEBUG] 2017-05-05 23:19:13,899 (V2TransferObjectTask:populateInitialReplicaList:511) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 entering populateInitialReplicaList
[DEBUG] 2017-05-05 23:19:13,900 (V2TransferObjectTask:populateInitialReplicaList:526) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 Included replica for original MN
[DEBUG] 2017-05-05 23:19:13,900 (V2TransferObjectTask:populateInitialReplicaList:530) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 Get Object Format
[DEBUG] 2017-05-05 23:19:13,933 (V2TransferObjectTask:populateInitialReplicaList:542) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 Added CN as replica because formatType METADATA is not DATA
[ INFO] 2017-05-05 23:19:13,933 (V2TransferObjectTask:createObject:727) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 - Start CreateObject
[ INFO] 2017-05-05 23:19:13,936 (SystemMetadataValidator:schemaValidateSystemMetadata:70) Entering schemaValidateSysMeta method...
[DEBUG] 2017-05-05 23:19:13,937 (V2TransferObjectTask:validateChecksum:835) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 entering validateChecksum...
[DEBUG] 2017-05-05 23:19:13,975 (V2TransferObjectTask:createObject:758) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 getting ScienceMetadata
[DEBUG] 2017-05-05 23:19:14,016 (V2TransferObjectTask:createObject:795) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 Calling CNCreate...
[ INFO] 2017-05-05 23:19:14,055 (V2TransferObjectTask:call:234) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 - Unlocked Pid.
[ERROR] 2017-05-05 23:19:14,056 (V2TransferObjectTask:call:269) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 - UnrecoverableException: urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 cn.createObject failed
org.dataone.cn.batch.exceptions.UnrecoverableException: urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 cn.createObject failed
at org.dataone.cn.batch.synchronization.tasks.V2TransferObjectTask.createObject(V2TransferObjectTask.java:813)
at org.dataone.cn.batch.synchronization.tasks.V2TransferObjectTask.processNewObject(V2TransferObjectTask.java:491)
at org.dataone.cn.batch.synchronization.tasks.V2TransferObjectTask.processTask(V2TransferObjectTask.java:424)
at org.dataone.cn.batch.synchronization.tasks.V2TransferObjectTask.call(V2TransferObjectTask.java:211)
at org.dataone.cn.batch.synchronization.tasks.V2TransferObjectTask.call(V2TransferObjectTask.java:113)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
[ WARN] 2017-05-05 23:19:14,057 (SyncFailedTask:submitSynchronizationFailed:116) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 - SynchronizationFailed: detail code: 6001 id:urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 nodeId:urn:node:cnDevUCSB1 description:Synchronization task of [PID::] urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 [::PID] failed. Cause: ServiceFailure: Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 - null
[ INFO] 2017-05-05 23:19:14,075 (V2TransferObjectTask:call:293) Task-urn:node:mnDemo6-urn:uuid:cfe74e5e-d1f9-4fd9-851a-c0d846d15c23 - exiting with callState: FAILED

From the above log, the method failed at this line:
d1Identifier = nodeCommunications.getCnCore().create(session, d1Identifier, sciMetaStream,
systemMetadata);

But the problem is I can't see something like this at the metacat log:
HTTP Verb: POST
metacat 20170505-22:51:12: [INFO]: D1RestServlet.doPost - HTTP Verb: POST [edu.ucsb.nceas.metacat.restservice.D1RestServlet:doPost:84]
original pathInfo: /object
metacat 20170505-22:51:12: [INFO]: D1HttpRequest.getPathInfo - the orignial pathInfo: /object [edu.ucsb.nceas.metacat.restservice.D1HttpRequest:getPathInfo:59]
original requestURI: /metacat/d1/cn/v2/object

So the CN.create wasn't called!

#4 Updated by Jing Tao over 4 years ago

  • Status changed from New to In Progress
  • Category changed from Metacat to dataone-cn-os-core
  • % Done changed from 0 to 30

Finally I found the issue - in the apache error log I saw this error:
[Sat May 06 03:23:43.208704 2017] [ssl:error] [pid 31763:tid 140386760611584] [client 128.111.54.78:54623] AH02018: request body exceeds maximum size (131072) for SSL buffer
[Sat May 06 03:23:43.208817 2017] [ssl:error] [pid 31763:tid 140386760611584] [client 128.111.54.78:54623] AH02257: could not buffer message body to allow SSL renegotiation to proceed

When I added the directive on the cn-ssl.conf:

SSLRenegBufferSize 100000000

After I reloaded the configuration, it worked.

#5 Updated by Jing Tao over 4 years ago

  • Target version set to CCI-2.4.0

#6 Updated by Jing Tao over 4 years ago

Dave just pointed out we may use the http 1.1 header named "Excpect". This header essentially says "I've got a huge payload, but before I send it please let me know if you can handle it". This gives the endpoints time to renegotiate the client certificate before the payload is sent.

http://stackoverflow.com/questions/14281628/ssl-renegotiation-with-client-certificate-causes-server-buffer-overflow

#7 Updated by Jing Tao over 4 years ago

Chris pointed a relative ticket:
https://redmine.dataone.org/issues/2693

#8 Updated by Rob Nahf almost 4 years ago

  • Related to Bug #8229: cn.creates failing with "413: Request Entity Too Large" thrown from apache added

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