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Started:
February 25, 2022 07:56
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Completed:
01:45:35
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Failed:
No.
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Status:
completed
Events (most recent first):
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13:43:14
(starts)
Running
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13:38:10
(ends)
Complete
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13:38:10
(ends)
TOTAL TIME: 13.2m
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13:25:16
(infos)
removing traits specified in diff file
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13:25:14
(infos)
Connecting to https://content.eol.org/ ...
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13:24:59
(infos)
Connecting to https://content.eol.org/ ...
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13:24:59
(infos)
polling for trait diff metadata: /resources/532/publish_diffs.json?since=1645622839
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13:24:59
(starts)
#publish_traits = TraitBank::Slurp.load_resource_from_repo
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13:24:59
(starts)
Running
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17:56:21
(ends)
Complete
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17:56:21
(ends)
TOTAL TIME: 10.0h
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17:56:19
(starts)
TraitBank::Denormalizer.update_resource_vernaculars
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17:56:19
(starts)
Running
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17:56:13
(starts)
Resource#fix_native_nodes
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17:56:13
(starts)
Running
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17:56:13
(warns)
Trait Publishing failed: execution expired (Delayed::Worker.max_run_time is only 36000 seconds) FROM /app/lib/trait_bank/slurp.rb:366:in `sleep' << /app/lib/trait_bank/slurp.rb:366:in `block in break_up_large_file' << /app/lib/trait_bank/slurp.rb:357:in `break_up_large_file' << /app/lib/trait_bank/slurp.rb:343:in `break_up_large_files' << /app/lib/trait_bank/slurp.rb:289:in `load_csv' << /app/lib/trait_bank/slurp.rb:612:in `add_traits'
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17:07:38
(infos)
Waiting 4200 seconds for the last 'chunk' to be added to neo4j...
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17:06:19
(warns)
FAILED on build_nodes query (Trait), will re-try once...
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17:06:19
(warns)
The transaction has been terminated. Retry your operation in a new transaction, and you should see a successful result. The transaction has not completed within the specified timeout (dbms.transaction.timeout). You may want to retry with a longer timeout.
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17:06:19
(warns)
Exception (Neo4j::Driver::Exceptions::ClientException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/paleobiology_db/new_traits_1645545266_1645721181_chunk_13.csv' AS row WITH row WHERE 1=1 MERGE (trait:Trait { eol_pk: row.eol_pk })
ON CREATE SET trait.resource_pk = row.resource_pk
ON MATCH SET trait.resource_pk = row.resource_pk
ON CREATE SET trait.source = row.source
ON MATCH SET trait.source = row.source
ON CREATE SET trait.literal = row.literal
ON MATCH SET trait.literal = row.literal
ON CREATE SET trait.measurement = row.measurement
ON MATCH SET trait.measurement = row.measurement
ON CREATE SET trait.scientific_name = row.scientific_name
ON MATCH SET trait.scientific_name = row.scientific_name
ON CREATE SET trait.normal_measurement = row.normal_measurement
ON MATCH SET trait.normal_measurement = row.normal_measurement
ON CREATE SET trait.sample_size = row.sample_size
ON MATCH SET trait.sample_size = row.sample_size
ON CREATE SET trait.citation = row.citation
ON MATCH SET trait.citation = row.citation
ON CREATE SET trait.remarks = row.remarks
ON MATCH SET trait.remarks = row.remarks
ON CREATE SET trait.method = row.method
ON MATCH SET trait.method = row.method} MESSAGE: The transaction has been terminated. Retry your operation in a new transaction, and you should see a successful result. The transaction has not completed within the specified timeout (dbms.transaction.timeout). You may want to retry with a longer timeout.
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17:04:26
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_13.csv
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15:59:25
(infos)
Waiting 3900 seconds for the last 'chunk' to be added to neo4j...
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15:57:58
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_12.csv
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14:57:57
(infos)
Waiting 3600 seconds for the last 'chunk' to be added to neo4j...
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14:56:28
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_11.csv
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14:01:26
(infos)
Waiting 3300 seconds for the last 'chunk' to be added to neo4j...
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13:59:56
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_10.csv
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13:09:55
(infos)
Waiting 3000 seconds for the last 'chunk' to be added to neo4j...
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13:08:33
(warns)
FAILED on build_nodes query (Trait), will re-try once...
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13:08:33
(warns)
The transaction has been terminated. Retry your operation in a new transaction, and you should see a successful result. The transaction has not completed within the specified timeout (dbms.transaction.timeout). You may want to retry with a longer timeout.
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13:08:33
(warns)
Exception (Neo4j::Driver::Exceptions::ClientException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/paleobiology_db/new_traits_1645545266_1645721181_chunk_9.csv' AS row WITH row WHERE 1=1 MERGE (trait:Trait { eol_pk: row.eol_pk })
ON CREATE SET trait.resource_pk = row.resource_pk
ON MATCH SET trait.resource_pk = row.resource_pk
ON CREATE SET trait.source = row.source
ON MATCH SET trait.source = row.source
ON CREATE SET trait.literal = row.literal
ON MATCH SET trait.literal = row.literal
ON CREATE SET trait.measurement = row.measurement
ON MATCH SET trait.measurement = row.measurement
ON CREATE SET trait.scientific_name = row.scientific_name
ON MATCH SET trait.scientific_name = row.scientific_name
ON CREATE SET trait.normal_measurement = row.normal_measurement
ON MATCH SET trait.normal_measurement = row.normal_measurement
ON CREATE SET trait.sample_size = row.sample_size
ON MATCH SET trait.sample_size = row.sample_size
ON CREATE SET trait.citation = row.citation
ON MATCH SET trait.citation = row.citation
ON CREATE SET trait.remarks = row.remarks
ON MATCH SET trait.remarks = row.remarks
ON CREATE SET trait.method = row.method
ON MATCH SET trait.method = row.method} MESSAGE: The transaction has been terminated. Retry your operation in a new transaction, and you should see a successful result. The transaction has not completed within the specified timeout (dbms.transaction.timeout). You may want to retry with a longer timeout.
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13:06:41
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_9.csv
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12:21:39
(infos)
Waiting 2700 seconds for the last 'chunk' to be added to neo4j...
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12:20:10
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_8.csv
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12:00:09
(infos)
Waiting 1200 seconds for the last 'chunk' to be added to neo4j...
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11:58:53
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_7.csv
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11:41:22
(infos)
Waiting 1050 seconds for the last 'chunk' to be added to neo4j...
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11:40:14
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_6.csv
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11:25:13
(infos)
Waiting 900 seconds for the last 'chunk' to be added to neo4j...
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11:23:51
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_5.csv
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11:11:15
(infos)
Waiting 750 seconds for the last 'chunk' to be added to neo4j...
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11:09:56
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_4.csv
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10:59:55
(infos)
Waiting 600 seconds for the last 'chunk' to be added to neo4j...
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10:57:31
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_3.csv
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10:50:01
(infos)
Waiting 450 seconds for the last 'chunk' to be added to neo4j...
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10:48:40
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_2.csv
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10:43:39
(infos)
Waiting 300 seconds for the last 'chunk' to be added to neo4j...
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10:42:28
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_1.csv
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10:42:27
(warns)
Found 2140044 rows, will break up into 128000
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10:42:26
(infos)
adding new traits
