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1
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Examining issue #2 from UCSB
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2
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FROM UCSB identifiers missing xml_documents or xml_revisions
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3
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4
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doi:10.6073/AA/knb-lter-gce.144.3
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5
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doi:10.6073/AA/knb-lter-gce.172.3
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6
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doi:10.6073/AA/knb-lter-gce.170.1
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7
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doi:10.6073/AA/knb-lter-gce.178.1
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8
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doi:10.6073/AA/knb-lter-gce.181.2
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9
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doi:10.6073/AA/knb-lter-gce.57.14
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10
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doi:10.6073/AA/knb-lter-gce.50.5
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11
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doi:10.6073/AA/knb-lter-gce.66.3
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12
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doi:10.6073/AA/knb-lter-gce.83.5
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13
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doi:10.6073/AA/knb-lter-gce.71.12
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14
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doi:10.6073/AA/knb-lter-gce.80.6
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15
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doi:10.6073/AA/knb-lter-gce.87.4
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16
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doi:10.6073/AA/knb-lter-gce.87.5
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17
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doi:10.6073/AA/knb-lter-gce.97.4
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18
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doi:10.6073/AA/knb-lter-gce.8.3
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19
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doi:10.6073/AA/knb-lter-kbs.35.6
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20
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doi:10.6073/AA/knb-lter-kbs.38.2
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21
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doi:10.6073/AA/knb-lter-kbs.39.2
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22
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(18 rows)
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23
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24
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looking at doi:10.6073/AA/knb-lter-gce.144.3
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25
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cd /var/log/dataone/synchronize/
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26
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grep -P 'doi\:10\.6073\/AA\/knb\-lter\-gce\.144\.3' *
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27
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28
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FROM UCSB (CREATED)
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29
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cn-synchronization.log.15:[ INFO] 2012-06-26 13:12:01,716 (SyncObjectTask:call:207) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 received
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30
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cn-synchronization.log.15:[ INFO] 2012-06-26 13:12:01,716 (TransferObjectTask:call:114) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Locking task of attempt 1
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31
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cn-synchronization.log.15:[ INFO] 2012-06-26 13:12:01,857 (TransferObjectTask:call:120) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Processing task
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32
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cn-synchronization.log.15:[ INFO] 2012-06-26 13:12:02,271 (TransferObjectTask:retrieveSystemMetadata:250) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Retrieved SystemMetadata Identifier:doi:10.6073/AA/knb-lter-gce.144.3 from node urn:node:LTER for ObjectInfo Identifier doi:10.6073/AA/knb-lter-gce.144.3
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33
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cn-synchronization.log.15:[ INFO] 2012-06-26 13:12:02,271 (TransferObjectTask:call:123) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Writing task
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34
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cn-synchronization.log.15:[ INFO] 2012-06-26 13:12:02,271 (TransferObjectTask:write:376) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Getting sysMeta from CN
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35
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cn-synchronization.log.15:[ INFO] 2012-06-26 13:12:02,438 (TransferObjectTask:write:396) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Create from Exception
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36
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cn-synchronization.log.15:[ INFO] 2012-06-26 13:12:02,852 (SyncObjectTask:call:180) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3Waiting for the future :(5): since 2012-06-26T13:12:01.716+00:00
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37
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cn-synchronization.log.15:[ INFO] 2012-06-26 13:12:03,144 (TransferObjectTask:createObject:535) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Creating Object
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38
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cn-synchronization.log.15:[ INFO] 2012-06-26 13:12:05,488 (SyncObjectTask:call:180) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3Waiting for the future :(5): since 2012-06-26T13:12:01.716+00:00
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39
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cn-synchronization.log.15:[ INFO] 2012-06-26 13:12:07,658 (SyncObjectTask:call:180) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3Waiting for the future :(5): since 2012-06-26T13:12:01.716+00:00
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40
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cn-synchronization.log.15:[ INFO] 2012-06-26 13:12:11,065 (TransferObjectTask:createObject:538) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Created Object
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41
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cn-synchronization.log.15:[ INFO] 2012-06-26 13:12:20,056 (SyncObjectTask:call:149) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Returned from the Future :5:
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42
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43
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FROM ORC (UPDATED)
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44
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cn-synchronization.log.6:[ INFO] 2012-06-30 04:13:58,705 (SyncObjectTask:call:207) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 received
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45
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cn-synchronization.log.6:[ INFO] 2012-06-30 04:14:25,604 (SyncObjectTask:call:207) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 received
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46
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cn-synchronization.log.6:[ INFO] 2012-06-30 04:14:25,607 (TransferObjectTask:call:114) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Locking task of attempt 1
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47
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cn-synchronization.log.6:[ INFO] 2012-06-30 04:14:25,886 (TransferObjectTask:call:120) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Processing task
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48
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cn-synchronization.log.6:[ INFO] 2012-06-30 04:14:26,313 (SyncObjectTask:call:180) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3Waiting for the future :(4): since 2012-06-30T04:14:25.604+00:00
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49
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cn-synchronization.log.6:[ INFO] 2012-06-30 04:14:26,494 (TransferObjectTask:retrieveSystemMetadata:250) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Retrieved SystemMetadata Identifier:doi:10.6073/AA/knb-lter-gce.144.3 from node urn:node:LTER for ObjectInfo Identifier doi:10.6073/AA/knb-lter-gce.144.3
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50
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cn-synchronization.log.6:[ INFO] 2012-06-30 04:14:26,494 (TransferObjectTask:call:123) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Writing task
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51
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cn-synchronization.log.6:[ INFO] 2012-06-30 04:14:26,494 (TransferObjectTask:write:376) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Getting sysMeta from CN
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52
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cn-synchronization.log.6:[ INFO] 2012-06-30 04:14:26,567 (TransferObjectTask:write:398) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Pid Exists. Must be an Update
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53
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cn-synchronization.log.6:[ INFO] 2012-06-30 04:14:26,638 (TransferObjectTask:write:419) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Update sysMeta because checksum is same
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54
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cn-synchronization.log.6:[ INFO] 2012-06-30 04:14:26,708 (TransferObjectTask:updateSystemMetadata:579) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Update Archived
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55
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cn-synchronization.log.6:[ INFO] 2012-06-30 04:14:36,521 (TransferObjectTask:auditReplicaSystemMetadata:636) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 auditReplicaSystemMetadata
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56
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cn-synchronization.log.6:[ INFO] 2012-06-30 04:14:37,756 (TransferObjectTask:updateSystemMetadata:583) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Updated Archived
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57
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cn-synchronization.log.6:[ INFO] 2012-06-30 04:15:10,771 (SyncObjectTask:call:149) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Returned from the Future :4:
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58
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59
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FROM UCSB (updated again?)
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60
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cn-synchronization.log.13:[ INFO] 2012-06-30 04:12:33,056 (SyncObjectTask:call:207) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 received
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61
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cn-synchronization.log.12:[ INFO] 2012-07-01 21:12:06,054 (SyncObjectTask:call:207) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 received
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62
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cn-synchronization.log.12:[ INFO] 2012-07-01 21:12:06,093 (TransferObjectTask:call:114) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Locking task of attempt 1
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63
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cn-synchronization.log.12:[ INFO] 2012-07-01 21:12:06,119 (TransferObjectTask:call:120) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Processing task
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64
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cn-synchronization.log.12:[ INFO] 2012-07-01 21:12:06,608 (TransferObjectTask:retrieveSystemMetadata:250) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Retrieved SystemMetadata Identifier:doi:10.6073/AA/knb-lter-gce.144.3 from node urn:node:LTER for ObjectInfo Identifier doi:10.6073/AA/knb-lter-gce.144.3
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65
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cn-synchronization.log.12:[ INFO] 2012-07-01 21:12:06,609 (TransferObjectTask:call:123) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Writing task
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66
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cn-synchronization.log.12:[ INFO] 2012-07-01 21:12:06,609 (TransferObjectTask:write:376) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Getting sysMeta from CN
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67
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cn-synchronization.log.12:[ INFO] 2012-07-01 21:12:06,619 (SyncObjectTask:call:180) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3Waiting for the future :(2): since 2012-07-01T21:12:06.054+00:00
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68
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cn-synchronization.log.12:[ INFO] 2012-07-01 21:12:06,636 (TransferObjectTask:write:398) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Pid Exists. Must be an Update
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69
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cn-synchronization.log.12:[ INFO] 2012-07-01 21:12:06,662 (TransferObjectTask:write:419) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Update sysMeta because checksum is same
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70
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cn-synchronization.log.12:[ INFO] 2012-07-01 21:12:06,712 (SyncObjectTask:call:149) Task-urn:node:LTER-doi:10.6073/AA/knb-lter-gce.144.3 Returned from the Future :2:
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71
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72
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73
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Next, look at tables and metacat logs to determine the cause and extent of the error.
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74
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75
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TRYING:
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76
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doi:10.6073/AA/knb-lter-gce.144.3
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77
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78
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su postgres -c "psql -d metacat -c \"select * from identifier where guid = 'doi:10.6073/AA/knb-lter-gce.144.3'\""
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79
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guid | docid | rev
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80
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-----------------------------------+-----------------------------+-----
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81
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doi:10.6073/AA/knb-lter-gce.144.3 | autogen.2012062606120365006 | 1
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82
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83
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su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062606120365006' and rev= 1\"" 0 on UCSB, 1 on UNM, 1 on ORC
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84
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85
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revisionid | docid | rootnodeid | docname | doctype | user_owner | user_updated | server_location | rev | date_created | date_updated | public_access | catalog_id
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86
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------------+-----------------------------+------------+---------+------------------------------------+---------------------------------------+--------------+-----------------+-----+--------------+--------------+---------------+------------
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87
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2650 | autogen.2012062606120365006 | 23138109 | eml | eml://ecoinformatics.org/eml-2.0.0 | CN=urn:node:CNUCSB1,DC=dataone,DC=org | | 2 | 1 | 2012-06-26 | 2012-06-26 | 0 | 24
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88
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(1 row)
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89
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90
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/var/metacat/logs# grep -P 'autogen\.2012062606120365006' replicate.log*
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91
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92
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replicate.log.53:knb 2012-06-30T04:17:33: [ERROR]: ReplicationService.handleForceReplicateDeleteRequest - error: Problem deleting xml query result for docid autogen.2012062606120365006 : XMLQueryresultAccess.deleteXMLQueryresulForDoc - SQL error when deletingxml query result for doc id: autogen.2012062606120365006:Backend start-up failed: FATAL: connection limit exceeded for non-superusers.
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93
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94
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TRYING:
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95
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doi:10.6073/AA/knb-lter-gce.172.3
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96
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autogen.2012062606221626752
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97
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su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062606221626752' and rev= 1\"" 0 on UCSB, 1 on UNM, 1 on ORC
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98
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grep -P '\[ERROR\].+?autogen\.2012062606221626752' replicate.log*
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99
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100
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no reason given for failure
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101
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102
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TRYING:
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103
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doi:10.6073/AA/knb-lter-gce.170.1
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104
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su postgres -c "psql -d metacat -c \"select * from identifier where guid = 'doi:10.6073/AA/knb-lter-gce.170.1'\""
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105
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doi:10.6073/AA/knb-lter-gce.170.1 | autogen.2012062606222580668 | 1
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106
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107
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su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062606222580668' and rev= 1\"" 0 on UCSB, 1 on UNM, 1 on ORC
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108
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grep -P '\[ERROR\].+?autogen\.2012062606222580668' replicate.log*
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109
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replicate.log.52:knb 2012-07-03T00:04:27: [ERROR]: ReplicationHandler.handleSingleXMLDocument - Failed to write doc autogen.2012062606222580668.1 into db because The file you are trying to write already exists in metacat. Please update your version number.
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110
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111
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TRYING:
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112
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doi:10.6073/AA/knb-lter-gce.178.1
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113
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su postgres -c "psql -d metacat -c \"select * from identifier where guid = 'doi:10.6073/AA/knb-lter-gce.178.1'\""
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114
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doi:10.6073/AA/knb-lter-gce.178.1 | autogen.2012062606252741934 | 1
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115
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116
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su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062606252741934' and rev= 1\"" 0 on UCSB, 1 on UNM, 1 on ORC
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117
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grep -P '\[ERROR\].+?autogen\.2012062606252741934' replicate.log*
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118
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119
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no reason for failure
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120
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121
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TRYING:
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122
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su postgres -c "psql -d metacat -c \"select * from identifier where guid = 'doi:10.6073/AA/knb-lter-gce.181.2'\""
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123
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doi:10.6073/AA/knb-lter-gce.181.2 | autogen.2012062606250182948 | 1
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124
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su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062606250182948'\"" 0 on UCSB, 1 on UNM, 1 on ORC
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125
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grep -P '\[ERROR\].+?autogen.2012062606250182948' replicate.log*
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126
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replicate.log.51:knb 2012-07-04T01:03:11: [ERROR]: ReplicationHandler.handleSingleXMLDocument - Failed to write doc autogen.2012062606250182948.1 into db because The file you are trying to write already exists in metacat. Please update your version number.
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127
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128
|
TRYING:
|
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129
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su postgres -c "psql -d metacat -c \"select * from identifier where guid = 'doi:10.6073/AA/knb-lter-gce.57.14'\""
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130
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doi:10.6073/AA/knb-lter-gce.57.14 | autogen.2012062607340591517 | 1
|
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131
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su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062607340591517'\"" 0 on UCSB, 1 on UNM, 1 on ORC
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132
|
|
|
133
|
TRYING:
|
|
134
|
su postgres -c "psql -d metacat -c \"select * from identifier where guid = 'doi:10.6073/AA/knb-lter-gce.50.5'\""
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135
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doi:10.6073/AA/knb-lter-gce.50.5 | autogen.2012062607353935542 | 1
|
|
136
|
su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062607353935542'\"" 0 on UCSB, 1 on UNM, 1 on ORC
|
|
137
|
|
|
138
|
TRYING:
|
|
139
|
su postgres -c "psql -d metacat -c \"select * from identifier where guid = 'doi:10.6073/AA/knb-lter-gce.66.3'\""
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140
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doi:10.6073/AA/knb-lter-gce.66.3 | autogen.2012062607395066141 | 1
|
|
141
|
su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062607395066141'\"" 0 on UCSB, 1 on UNM, 1 on ORC
|
|
142
|
|
|
143
|
TRYING:
|
|
144
|
su postgres -c "psql -d metacat -c \"select * from identifier where guid = 'doi:10.6073/AA/knb-lter-gce.83.5'\""
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145
|
doi:10.6073/AA/knb-lter-gce.83.5 | autogen.2012062607482200460 | 1
|
|
146
|
su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062607482200460'\"" 0 on UCSB, 1 on UNM, 1 on ORC
|
|
147
|
|
|
148
|
TRYING:
|
|
149
|
su postgres -c "psql -d metacat -c \"select * from identifier where guid = 'doi:10.6073/AA/knb-lter-gce.71.12'\""
|
|
150
|
doi:10.6073/AA/knb-lter-gce.71.12 | autogen.2012062607482390661 | 1
|
|
151
|
su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062607482390661'\"" 0 on UCSB, 1 on UNM, 1 on ORC
|
|
152
|
|
|
153
|
TRYING:
|
|
154
|
su postgres -c "psql -d metacat -c \"select * from identifier where guid = 'doi:10.6073/AA/knb-lter-gce.80.6'\""
|
|
155
|
doi:10.6073/AA/knb-lter-gce.80.6 | autogen.2012062607511917641 | 1
|
|
156
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su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062607511917641'\"" 0 on UCSB, 1 on UNM, 1 on ORC
|
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157
|
|
|
158
|
TRYING:
|
|
159
|
su postgres -c "psql -d metacat -c \"select * from identifier where guid = 'doi:10.6073/AA/knb-lter-gce.87.4'\""
|
|
160
|
doi:10.6073/AA/knb-lter-gce.87.4 | autogen.2012062607512667245 | 1
|
|
161
|
su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062607512667245'\"" 0 on UCSB, 1 on UNM, 1 on ORC
|
|
162
|
|
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163
|
TRYING:
|
|
164
|
su postgres -c "psql -d metacat -c \"select * from identifier where guid = 'doi:10.6073/AA/knb-lter-gce.87.5'\""
|
|
165
|
doi:10.6073/AA/knb-lter-gce.87.5 | autogen.2012062607511486800 | 1
|
|
166
|
su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062607511486800'\"" 0 on UCSB, 1 on UNM, 1 on ORC
|
|
167
|
|
|
168
|
TRYING:
|
|
169
|
su postgres -c "psql -d metacat -c \"select * from identifier where guid = 'doi:10.6073/AA/knb-lter-gce.97.4'\""
|
|
170
|
doi:10.6073/AA/knb-lter-gce.97.4 | autogen.2012062607550210306 | 1
|
|
171
|
su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062607550210306'\"" 0 on UCSB, 1 on UNM, 1 on ORC
|
|
172
|
|
|
173
|
TRYING:
|
|
174
|
su postgres -c "psql -d metacat -c \"select * from identifier where guid = 'doi:10.6073/AA/knb-lter-gce.8.3'\""
|
|
175
|
doi:10.6073/AA/knb-lter-gce.8.3 | autogen.2012062610185537952 | 1
|
|
176
|
su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062610185537952'\"" 0 on UCSB, 1 on UNM, 1 on ORC
|
|
177
|
|
|
178
|
TRYING:
|
|
179
|
su postgres -c "psql -d metacat -c \"select * from identifier where guid = 'doi:10.6073/AA/knb-lter-kbs.35.6'\""
|
|
180
|
doi:10.6073/AA/knb-lter-kbs.35.6 | autogen.2012062921413143003 | 1
|
|
181
|
su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062921413143003'\"" 0 on UCSB, 1 on UNM, 1 on ORC
|
|
182
|
|
|
183
|
TRYING:
|
|
184
|
su postgres -c "psql -d metacat -c \"select * from identifier where guid = 'doi:10.6073/AA/knb-lter-kbs.38.2'\""
|
|
185
|
doi:10.6073/AA/knb-lter-kbs.38.2 | autogen.2012062921414116209 | 1
|
|
186
|
su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062921414116209'\"" 0 on UCSB, 1 on UNM, 1 on ORC
|
|
187
|
|
|
188
|
TRYING:
|
|
189
|
su postgres -c "psql -d metacat -c \"select * from identifier where guid = 'doi:10.6073/AA/knb-lter-kbs.39.2'\""
|
|
190
|
doi:10.6073/AA/knb-lter-kbs.39.2 | autogen.2012062921414281310 | 1
|
|
191
|
su postgres -c "psql -d metacat -c \"select * from xml_revisions where docid='autogen.2012062921414281310'\"" 0 on UCSB, 1 on UNM, 1 on ORC
|
|
192
|
|
|
193
|
|
