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Started:
June 24, 2022 09:22
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Completed:
17:30:56
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Failed:
No.
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Status:
completed
Events (most recent first):
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17:30:56
(ends)
Complete
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17:30:56
(ends)
TOTAL TIME: 8.1h
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17:29:31
(starts)
#fix_missing_icons (just to be safe)
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17:29:31
(starts)
Running
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17:29:22
(starts)
#propagate_reference_ids
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17:29:22
(starts)
Running
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17:28:56
(starts)
TraitBank::Denormalizer.update_resource_vernaculars
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17:28:56
(starts)
Running
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17:28:49
(starts)
Resource#fix_native_nodes
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17:28:49
(starts)
Running
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17:28:49
(infos)
Removing /app/tmp/world_reg_mar_sp_content_sections.tsv
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17:28:49
(infos)
Removing /app/tmp/world_reg_mar_sp_references.tsv
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17:28:49
(infos)
Removing /app/tmp/world_reg_mar_sp_image_info.tsv
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17:28:49
(infos)
Removing /app/tmp/world_reg_mar_sp_attributions.tsv
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17:28:48
(infos)
Removing /app/tmp/world_reg_mar_sp_media.tsv
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17:28:48
(infos)
Removing /app/tmp/world_reg_mar_sp_articles.tsv
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17:28:48
(infos)
Removing /app/tmp/world_reg_mar_sp_vernaculars.tsv
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17:28:48
(infos)
Removing /app/tmp/world_reg_mar_sp_node_ancestors.tsv
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17:28:48
(infos)
Removing /app/tmp/world_reg_mar_sp_scientific_names.tsv
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17:28:48
(infos)
Removing /app/tmp/world_reg_mar_sp_identifiers.tsv
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17:28:48
(infos)
Removing /app/tmp/world_reg_mar_sp_bibliographic_citations.tsv
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17:28:48
(infos)
Removing /app/tmp/world_reg_mar_sp_nodes.tsv
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17:28:48
(infos)
Removing /app/tmp/world_reg_mar_sp_referents.tsv
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17:28:48
(infos)
Removing trait and metadata files
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17:28:23
(infos)
Importing 128000 rows from publish_metadata.tsv
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17:28:23
(infos)
adding new metadata
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17:27:13
(infos)
Importing 128000 rows from publish_traits_1642633069_chunk_13.csv
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17:25:19
(infos)
Importing 128000 rows from publish_traits_1642633069_chunk_12.csv
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17:01:18
(infos)
Waiting 24 minutes for the last 'chunk' to be added to neo4j...
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16:59:53
(warns)
FAILED on build_nodes query (Trait), will re-try once...
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16:59:53
(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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16:59:53
(warns)
Exception (Neo4j::Driver::Exceptions::ClientException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/world_reg_mar_sp/publish_traits_1642633069_chunk_11.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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16:58:16
(infos)
Importing 128000 rows from publish_traits_1642633069_chunk_11.csv
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16:36:14
(infos)
Waiting 22 minutes for the last 'chunk' to be added to neo4j...
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16:34:47
(infos)
Importing 128000 rows from publish_traits_1642633069_chunk_10.csv
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16:14:45
(infos)
Waiting 20 minutes for the last 'chunk' to be added to neo4j...
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16:13:16
(infos)
Importing 128000 rows from publish_traits_1642633069_chunk_9.csv
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15:55:15
(infos)
Waiting 18 minutes for the last 'chunk' to be added to neo4j...
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15:53:44
(infos)
Importing 128000 rows from publish_traits_1642633069_chunk_8.csv
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15:37:43
(infos)
Waiting 16 minutes for the last 'chunk' to be added to neo4j...
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15:36:10
(infos)
Importing 128000 rows from publish_traits_1642633069_chunk_7.csv
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15:22:09
(infos)
Waiting 14 minutes for the last 'chunk' to be added to neo4j...
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15:20:38
(infos)
Importing 128000 rows from publish_traits_1642633069_chunk_6.csv
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15:08:37
(infos)
Waiting 12 minutes for the last 'chunk' to be added to neo4j...
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15:07:09
(infos)
Importing 128000 rows from publish_traits_1642633069_chunk_5.csv
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14:57:08
(infos)
Waiting 10 minutes for the last 'chunk' to be added to neo4j...
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14:55:38
(infos)
Importing 128000 rows from publish_traits_1642633069_chunk_4.csv
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14:47:37
(infos)
Waiting 8 minutes for the last 'chunk' to be added to neo4j...
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14:44:22
(infos)
Importing 128000 rows from publish_traits_1642633069_chunk_3.csv
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14:38:21
(infos)
Waiting 6 minutes for the last 'chunk' to be added to neo4j...
