Import Log for Global Biotic Interactions

Started: April 16, 2024 17:41
Completed: 10:05:13.000
Failed: No.
Status: completed

Events (most recent first):

show warnings (38)

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10:05:13.000 (ends) resource.rb:225:in `publish'> fast.rb:177:in `by_resource'> Complete
10:05:13.000 (ends) resource.rb:225:in `publish'> fast.rb:176:in `by_resource'> TOTAL TIME: 16.4h
10:05:11.000 (starts) resource.rb:225:in `publish'> fast.rb:163:in `by_resource'> TraitBank::Denormalizer.update_resource_vernaculars
10:05:11.000 (starts) resource.rb:225:in `publish'> fast.rb:163:in `by_resource'> Running
10:04:43.000 (starts) resource.rb:225:in `publish'> fast.rb:161:in `by_resource'> Resource#fix_native_nodes
10:04:43.000 (starts) resource.rb:225:in `publish'> fast.rb:161:in `by_resource'> Running
10:04:43.000 (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'
10:04:43.000 (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 })}
10:04:43.000 (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
10:04:24.000 (infos) each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_21.csv
09:34:18.000 (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.
09:34:18.000 (infos) each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 2560000
09:33:28.000 (infos) each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_20.csv
09:03:23.000 (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.
09:03:23.000 (infos) each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 2432000
09:02:33.000 (infos) each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_19.csv
08:32:27.000 (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.
08:32:27.000 (infos) each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 2304000
08:31:38.000 (infos) each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_18.csv
08:01:31.000 (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.
08:01:31.000 (infos) each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 2176000
08:00:42.000 (infos) each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_17.csv
07:30:37.000 (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.
07:30:37.000 (infos) each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 2048000
07:29:46.000 (infos) each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_16.csv
06:59:41.000 (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.
06:59:41.000 (infos) each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 1920000
06:58:53.000 (infos) each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_15.csv
06:28:48.000 (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.
06:28:48.000 (infos) each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 1792000
06:28:01.000 (infos) each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_14.csv
05:59:56.000 (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.
05:59:56.000 (infos) each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 1664000
05:59:10.000 (infos) each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_13.csv
05:33:06.000 (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.
05:33:06.000 (infos) each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 1536000
05:32:17.000 (infos) each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_12.csv
05:08:13.000 (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.
05:08:13.000 (infos) each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 1408000
05:07:25.000 (infos) each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_11.csv
04:45:22.000 (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.
04:45:22.000 (infos) each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 1280000
04:44:36.000 (infos) each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_10.csv
04:24:33.000 (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.
04:24:33.000 (infos) each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 1152000
04:23:45.000 (infos) each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_9.csv
04:05:43.000 (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.
04:05:43.000 (infos) each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 2980194; Traits: 2979072; MetaData: 1024000
04:04:55.000 (infos) each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_8.csv
03:48:53.000 (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.

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