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Started:
April 16, 2024 17:41
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Completed:
10:05:13
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Failed:
No.
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Status:
completed
Events (most recent first):
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10:05:13
(ends)
resource.rb:225:in `publish'> fast.rb:177:in `by_resource'> Complete
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10:05:13
(ends)
resource.rb:225:in `publish'> fast.rb:176:in `by_resource'> TOTAL TIME: 16.4h
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10:05:11
(starts)
resource.rb:225:in `publish'> fast.rb:163:in `by_resource'> TraitBank::Denormalizer.update_resource_vernaculars
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10:05:11
(starts)
resource.rb:225:in `publish'> fast.rb:163:in `by_resource'> Running
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10:04:43
(starts)
resource.rb:225:in `publish'> fast.rb:161:in `by_resource'> Resource#fix_native_nodes
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10:04:43
(starts)
resource.rb:225:in `publish'> fast.rb:161:in `by_resource'> Running
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10:04:43
(warns)
resource.rb:225:in `publish'> fast.rb:207:in `rescue in publish_traits_with_cleanup'> Trait Publishing failed: At https://eol.org/data/Globi/publish_metadata_chunk_21.csv @ position 17010961 - Missing end for quote (") which started on line 64578 FROM /gems/ruby/2.7.0/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:533:in `merge_triple' << /app/lib/trait_bank/slurp.rb:418:in `block in load_csv_where' << /app/lib/trait_bank/slurp.rb:418:in `each' << /app/lib/trait_bank/slurp.rb:418:in `load_csv_where' << /app/lib/trait_bank/slurp.rb:296:in `block (2 levels) in load_csv'
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10:04:43
(warns)
each.rb:9:in `each'> slurp.rb:535:in `rescue in merge_triple'> Exception (Neo4j::Driver::Exceptions::DatabaseException) FROM: #merge_triple QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/Globi/publish_metadata_chunk_21.csv' AS row WITH row WHERE (row.sex IS NOT NULL AND TRIM(row.sex) <> '')
MATCH (metadata:MetaData { eol_pk: row.eol_pk })
MATCH (sex:Term { uri: row.sex })}
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10:04:43
(warns)
each.rb:9:in `each'> slurp.rb:571:in `rescue in autocommit_query'> Exception (Neo4j::Driver::Exceptions::DatabaseException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/Globi/publish_metadata_chunk_21.csv' AS row WITH row WHERE (row.sex IS NOT NULL AND TRIM(row.sex) <> '')
MATCH (metadata:MetaData { eol_pk: row.eol_pk })
MATCH (sex:Term { uri: row.sex })
MERGE (metadata)-[:sex_term]->(sex)} MESSAGE: At https://eol.org/data/Globi/publish_metadata_chunk_21.csv @ position 17010961 - Missing end for quote (") which started on line 64578
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10:04:24
(infos)
each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_21.csv
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09:34:18
(infos)
each.rb:9:in `each'> slurp.rb:329:in `block in break_up_large_file'> Waiting 30 minutes for the part 21 of 24 to be added to neo4j.
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09:34:18
(infos)
each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 2560000
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09:33:28
(infos)
each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_20.csv
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09:03:23
(infos)
each.rb:9:in `each'> slurp.rb:329:in `block in break_up_large_file'> Waiting 30 minutes for the part 20 of 24 to be added to neo4j.
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09:03:23
(infos)
each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 2432000
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09:02:33
(infos)
each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_19.csv
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08:32:27
(infos)
each.rb:9:in `each'> slurp.rb:329:in `block in break_up_large_file'> Waiting 30 minutes for the part 19 of 24 to be added to neo4j.
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08:32:27
(infos)
each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 2304000
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08:31:38
(infos)
each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_18.csv
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08:01:31
(infos)
each.rb:9:in `each'> slurp.rb:329:in `block in break_up_large_file'> Waiting 30 minutes for the part 18 of 24 to be added to neo4j.
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08:01:31
(infos)
each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 2176000
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08:00:42
(infos)
each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_17.csv
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07:30:37
(infos)
each.rb:9:in `each'> slurp.rb:329:in `block in break_up_large_file'> Waiting 30 minutes for the part 17 of 24 to be added to neo4j.
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07:30:37
(infos)
each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 2048000
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07:29:46
(infos)
each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_16.csv
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06:59:41
(infos)
each.rb:9:in `each'> slurp.rb:329:in `block in break_up_large_file'> Waiting 30 minutes for the part 16 of 24 to be added to neo4j.
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06:59:41
(infos)
each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 1920000
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06:58:53
(infos)
each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_15.csv
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06:28:48
(infos)
each.rb:9:in `each'> slurp.rb:329:in `block in break_up_large_file'> Waiting 30 minutes for the part 15 of 24 to be added to neo4j.
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06:28:48
(infos)
each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 1792000
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06:28:01
(infos)
each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_14.csv
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05:59:56
(infos)
each.rb:9:in `each'> slurp.rb:329:in `block in break_up_large_file'> Waiting 28 minutes for the part 14 of 24 to be added to neo4j.
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05:59:56
(infos)
each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 1664000
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05:59:10
(infos)
each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_13.csv
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05:33:06
(infos)
each.rb:9:in `each'> slurp.rb:329:in `block in break_up_large_file'> Waiting 26 minutes for the part 13 of 24 to be added to neo4j.
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05:33:06
(infos)
each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 1536000
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05:32:17
(infos)
each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_12.csv
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05:08:13
(infos)
each.rb:9:in `each'> slurp.rb:329:in `block in break_up_large_file'> Waiting 24 minutes for the part 12 of 24 to be added to neo4j.
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05:08:13
(infos)
each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 1408000
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05:07:25
(infos)
each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_11.csv
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04:45:22
(infos)
each.rb:9:in `each'> slurp.rb:329:in `block in break_up_large_file'> Waiting 22 minutes for the part 11 of 24 to be added to neo4j.
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04:45:22
(infos)
each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 1280000
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04:44:36
(infos)
each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_10.csv
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04:24:33
(infos)
each.rb:9:in `each'> slurp.rb:329:in `block in break_up_large_file'> Waiting 20 minutes for the part 10 of 24 to be added to neo4j.
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04:24:33
(infos)
each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 1152000
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04:23:45
(infos)
each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_9.csv
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04:05:43
(infos)
each.rb:9:in `each'> slurp.rb:329:in `block in break_up_large_file'> Waiting 18 minutes for the part 9 of 24 to be added to neo4j.
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04:05:43
(infos)
each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 1024000
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04:04:55
(infos)
each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_8.csv
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03:48:53
(infos)
each.rb:9:in `each'> slurp.rb:329:in `block in break_up_large_file'> Waiting 16 minutes for the part 8 of 24 to be added to neo4j.
