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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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01:45:35
(ends)
Complete
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01:45:35
(ends)
TOTAL TIME: 12.0h
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01:45:35
(infos)
Removing trait and metadata files
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01:45:35
(infos)
no metadata to add
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01:44:30
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_17.csv
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01:42:39
(warns)
FAILED on build_nodes query (Trait), will re-try once...
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01:42:39
(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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01:42:39
(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_16.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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01:40:48
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_16.csv
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00:20:40
(infos)
Waiting 4800 seconds for the last 'chunk' to be added to neo4j...
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00:19:11
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_15.csv
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23:04:09
(infos)
Waiting 4500 seconds for the last 'chunk' to be added to neo4j...
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23:02:39
(warns)
FAILED on build_nodes query (Trait), will re-try once...
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23:02:39
(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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23:02:39
(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_14.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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23:00:53
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_14.csv
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21:50:50
(infos)
Waiting 4200 seconds for the last 'chunk' to be added to neo4j...
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21:49:49
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_13.csv
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20:44:46
(infos)
Waiting 3900 seconds for the last 'chunk' to be added to neo4j...
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20:43:46
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_12.csv
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19:43:43
(infos)
Waiting 3600 seconds for the last 'chunk' to be added to neo4j...
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19:42:41
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_11.csv
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18:47:39
(infos)
Waiting 3300 seconds for the last 'chunk' to be added to neo4j...
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18:46:38
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_10.csv
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17:56:37
(infos)
Waiting 3000 seconds for the last 'chunk' to be added to neo4j...
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17:55:35
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_9.csv
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17:10:34
(infos)
Waiting 2700 seconds for the last 'chunk' to be added to neo4j...
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17:09:33
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_8.csv
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16:49:32
(infos)
Waiting 1200 seconds for the last 'chunk' to be added to neo4j...
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16:48:32
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_7.csv
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16:31:01
(infos)
Waiting 1050 seconds for the last 'chunk' to be added to neo4j...
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16:29:59
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_6.csv
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16:14:59
(infos)
Waiting 900 seconds for the last 'chunk' to be added to neo4j...
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16:13:56
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_5.csv
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16:01:26
(infos)
Waiting 750 seconds for the last 'chunk' to be added to neo4j...
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16:00:24
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_4.csv
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15:50:23
(infos)
Waiting 600 seconds for the last 'chunk' to be added to neo4j...
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15:49:21
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_3.csv
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15:41:51
(infos)
Waiting 450 seconds for the last 'chunk' to be added to neo4j...
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15:40:48
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_2.csv
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15:35:48
(infos)
Waiting 300 seconds for the last 'chunk' to be added to neo4j...
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15:34:46
(infos)
Importing 128000 rows from new_traits_1645545266_1645721181_chunk_1.csv
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15:34:46
(warns)
Found 2140044 rows, will break up into 128000
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15:34:45
(infos)
adding new traits
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15:34:45
(infos)
removed 2021385 traits
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13:43:29
(infos)
removing traits specified in diff file
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13:43:27
(infos)
Connecting to https://content.eol.org/ ...
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13:43:15
(infos)
Connecting to https://content.eol.org/ ...
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13:43:14
(infos)
polling for trait diff metadata: /resources/532/publish_diffs.json?since=1645622839
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13:43:14
(starts)
#publish_traits = TraitBank::Slurp.load_resource_from_repo
