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Started:
June 03, 2022 15:26
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Completed:
15:56:55
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Failed:
No.
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Status:
completed
Events (most recent first):
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16:35:34
(infos)
++ NUKE: Medium (0)
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16:35:34
(infos)
Removed 0 Identifiers
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16:35:34
(infos)
++ Calling delete_all on 0 instances...
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16:35:34
(infos)
++ NUKE: Identifier (0)
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16:35:34
(infos)
Removed 2038653 Nodeancestors
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16:32:34
(updates)
Batch 203 (expect 204 batches, maximum 408)...
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16:32:34
(infos)
Starting (this log message should be replaced shortly)
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16:32:34
(infos)
++ Batch removal of 2038653 instances...
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16:32:34
(infos)
++ NUKE: NodeAncestor (2038653)
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15:56:55
(ends)
Complete
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15:56:55
(ends)
TOTAL TIME: 30.0m
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15:56:55
(starts)
TraitBank::Denormalizer.update_resource_vernaculars
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15:56:55
(starts)
Running
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15:56:48
(starts)
Resource#fix_native_nodes
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15:56:48
(starts)
Running
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15:56:48
(warns)
Trait Publishing failed: 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. FROM /usr/local/bundle/bundler/gems/neo4j-ruby-driver-fe5438fb945d/ffi/neo4j/driver/internal/handlers/response_handler.rb:38:in `check_summary_failure' << /app/lib/trait_bank/slurp.rb:562:in `merge_triple' << /app/lib/trait_bank/slurp.rb:447:in `block in load_csv_where' << /app/lib/trait_bank/slurp.rb:447:in `each' << /app/lib/trait_bank/slurp.rb:447:in `load_csv_where' << /app/lib/trait_bank/slurp.rb:331:in `block (2 levels) in load_csv'
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15:56:48
(warns)
Exception (Neo4j::Driver::Exceptions::ClientException) FROM: #merge_triple QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/Globi/publish_traits_chunk_2.csv' AS row WITH row WHERE (row.object_page_id IS NOT NULL AND TRIM(row.object_page_id) <> '')
MATCH (trait:Trait { eol_pk: row.eol_pk })
MATCH (object_page:Page { page_id: toInteger(row.object_page_id) })}
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15:56:48
(warns)
Exception (Neo4j::Driver::Exceptions::ClientException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/Globi/publish_traits_chunk_2.csv' AS row WITH row WHERE (row.object_page_id IS NOT NULL AND TRIM(row.object_page_id) <> '')
MATCH (trait:Trait { eol_pk: row.eol_pk })
MATCH (object_page:Page { page_id: toInteger(row.object_page_id) })
MERGE (trait)-[:object_page]->(object_page)} 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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15:54:25
(infos)
Importing 128000 rows from publish_traits_chunk_2.csv
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15:49:24
(infos)
Waiting 300 seconds for the last 'chunk' to be added to neo4j...
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15:48:08
(infos)
Importing 128000 rows from publish_traits_chunk_1.csv
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15:48:07
(warns)
Found 5552474 rows, will break up into 128000
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15:48:02
(infos)
adding new traits
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15:39:51
(infos)
removing all traits
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15:39:21
(infos)
Connecting to https://content.eol.org/ ...
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15:38:42
(infos)
Connecting to https://content.eol.org/ ...
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15:38:40
(infos)
polling for trait diff metadata: /resources/20/publish_diffs.json
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15:38:40
(starts)
#publish_traits = TraitBank::Slurp.load_resource_from_repo
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15:38:40
(starts)
Running
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15:38:40
(warns)
There were NO new pages, skipping...
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15:37:51
(starts)
create_new_pages
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15:37:48
(starts)
PageCreator
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15:37:48
(starts)
Running
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15:37:48
(starts)
restoring vernacular preferences...
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15:37:48
(starts)
Running
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15:37:48
(warns)
MISSING https://content.eol.org/data/Globi/publish_content_sections.tsv [404] (8 bytes); skipping
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15:37:48
(infos)
Connecting to https://content.eol.org/ ...
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15:37:48
(starts)
#grab_file content_sections.tsv
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15:37:48
(starts)
Running
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15:37:48
(starts)
#import_and_prop_ids ContentSection
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15:37:48
(starts)
Running
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15:37:48
(warns)
MISSING https://content.eol.org/data/Globi/publish_references.tsv [404] (8 bytes); skipping
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15:37:48
(infos)
Connecting to https://content.eol.org/ ...
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15:37:48
(starts)
#grab_file references.tsv
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15:37:48
(starts)
Running
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15:37:48
(starts)
#import_and_prop_ids Reference
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15:37:48
(starts)
Running
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15:37:48
(warns)
MISSING https://content.eol.org/data/Globi/publish_image_info.tsv [404] (8 bytes); skipping
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15:37:48
(infos)
Connecting to https://content.eol.org/ ...
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15:37:48
(starts)
#grab_file image_info.tsv
