Import Log for Global Biotic Interactions

Started: April 16, 2024 13:22
Completed: 17:08:49
Failed: 17:08:49
Status: stopped

Events (most recent first):

show warnings (32)

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16:39:50 (infos) fast.rb:334:in `publish_traits'> slurp.rb:36:in `load_resource_from_repo'> Removing trait and metadata files
16:39:50 (infos) fast.rb:334:in `publish_traits'> slurp.rb:353:in `log_node_count'> Nodes: 0; Traits: 0; MetaData: 0
16:39:46 (infos) fast.rb:334:in `publish_traits'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata.tsv
16:39:46 (infos) fast.rb:334:in `publish_traits'> slurp.rb:594:in `add_metadata'> adding new metadata
16:39:46 (infos) fast.rb:334:in `publish_traits'> slurp.rb:353:in `log_node_count'> Nodes: 0; Traits: 0; MetaData: 0
16:34:46 (infos) fast.rb:334:in `publish_traits'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_traits.tsv
16:34:46 (infos) fast.rb:334:in `publish_traits'> slurp.rb:584:in `add_traits'> adding new traits
16:34:46 (infos) fast.rb:334:in `publish_traits'> slurp.rb:613:in `remove_traits'> not removing any traits
16:34:46 (warns) slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:112:in `log_warn'> MISSING https://content.eol.org/data/Globi/publish_metadata.tsv [502] (5 bytes); skipping
16:34:46 (infos) slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:104:in `log_info'> Connecting to https://content.eol.org/ ...
16:34:46 (infos) slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:104:in `log_info'> /data/Globi/publish_traits.tsv: Scheme missing.
16:34:46 (warns) slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:112:in `log_warn'> USING wget TO RETRIEVE FULL FILE...
16:34:46 (warns) slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:112:in `log_warn'> TRUNCATED RESPONSE! Got 470950975 bytes out of 949928114 from https://content.eol.org/data/Globi/publish_traits.tsv
16:34:08 (infos) slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:104:in `log_info'> Connecting to https://content.eol.org/ ...
16:34:07 (infos) slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:104:in `log_info'> polling for trait diff metadata: /resources/20/publish_diffs.json
16:34:07 (starts) (pry):2:in `__pry__'> fast.rb:202:in `publish_traits_with_cleanup'> #publish_traits = TraitBank::Slurp.load_resource_from_repo
16:34:07 (starts) (pry):2:in `__pry__'> fast.rb:202:in `publish_traits_with_cleanup'> Running
16:34:07 (starts) (pry):2:in `__pry__'> fast.rb:186:in `traits_by_resource'> Publishing::Fast.traits_by_resource
16:34:07 (starts) (pry):2:in `__pry__'> fast.rb:186:in `traits_by_resource'> Running
16:26:21 (ends) (pry):2:in `__pry__'> fast.rb:195:in `traits_by_resource'> Complete
16:26:21 (ends) (pry):2:in `__pry__'> fast.rb:194:in `traits_by_resource'> TOTAL TIME: 24.31585785s
16:26:21 (warns) (pry):2:in `__pry__'> fast.rb:207:in `rescue in publish_traits_with_cleanup'> Trait Publishing failed: undefined local variable or method `debugger' for #<TraitBank::Slurp:0x0000557141b0cfe0> FROM /app/lib/trait_bank/slurp.rb:277:in `block in load_csv' << /app/lib/trait_bank/slurp.rb:307:in `break_up_large_files' << /app/lib/trait_bank/slurp.rb:274:in `load_csv' << /app/lib/trait_bank/slurp.rb:585:in `add_traits' << /app/lib/trait_bank/slurp.rb:30:in `load_resource_from_repo' << /app/app/models/publishing/fast.rb:334:in `publish_traits'
16:26:21 (infos) fast.rb:334:in `publish_traits'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_traits.tsv
16:26:20 (infos) fast.rb:334:in `publish_traits'> slurp.rb:584:in `add_traits'> adding new traits
16:26:20 (infos) fast.rb:334:in `publish_traits'> slurp.rb:613:in `remove_traits'> not removing any traits
16:26:19 (infos) slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:104:in `log_info'> /data/Globi/publish_metadata.tsv: Scheme missing.
16:26:19 (warns) slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:112:in `log_warn'> USING wget TO RETRIEVE FULL FILE...
16:26:19 (warns) slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:112:in `log_warn'> TRUNCATED RESPONSE! Got 393712287 bytes out of 747585637 from https://content.eol.org/data/Globi/publish_metadata.tsv
16:26:06 (infos) slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:104:in `log_info'> Connecting to https://content.eol.org/ ...
16:26:06 (infos) slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:104:in `log_info'> /data/Globi/publish_traits.tsv: Scheme missing.
16:26:05 (warns) slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:112:in `log_warn'> USING wget TO RETRIEVE FULL FILE...
16:26:05 (warns) slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:112:in `log_warn'> TRUNCATED RESPONSE! Got 128302575 bytes out of 949928114 from https://content.eol.org/data/Globi/publish_traits.tsv
16:25:59 (infos) slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:104:in `log_info'> Connecting to https://content.eol.org/ ...
16:25:58 (infos) slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:104:in `log_info'> polling for trait diff metadata: /resources/20/publish_diffs.json
16:25:58 (starts) (pry):2:in `__pry__'> fast.rb:202:in `publish_traits_with_cleanup'> #publish_traits = TraitBank::Slurp.load_resource_from_repo
16:25:58 (starts) (pry):2:in `__pry__'> fast.rb:202:in `publish_traits_with_cleanup'> Running
16:25:58 (starts) (pry):2:in `__pry__'> fast.rb:186:in `traits_by_resource'> Publishing::Fast.traits_by_resource
16:25:58 (starts) (pry):2:in `__pry__'> fast.rb:186:in `traits_by_resource'> Running
13:49:32 (ends) resource.rb:225:in `publish'> fast.rb:177:in `ensure in by_resource'> Complete
13:49:32 (ends) resource.rb:225:in `publish'> fast.rb:176:in `ensure in by_resource'> TOTAL TIME: 26.9m
13:46:28 (infos) each.rb:9:in `each'> slurp.rb:329:in `block in break_up_large_file'> Waiting 6 minutes for the part 3 of 24 to be added to neo4j.
13:46:28 (infos) each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 0; Traits: 0; MetaData: 0
13:46:02 (infos) each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_2.csv
13:42:01 (infos) each.rb:9:in `each'> slurp.rb:329:in `block in break_up_large_file'> Waiting 4 minutes for the part 2 of 24 to be added to neo4j.
13:42:01 (infos) each.rb:9:in `each'> slurp.rb:351:in `log_node_count'> Nodes: 0; Traits: 0; MetaData: 0
13:41:34 (infos) each.rb:9:in `each'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_metadata_chunk_1.csv
13:41:34 (warns) fast.rb:334:in `publish_traits'> slurp.rb:308:in `break_up_large_files'> Found 2980195 rows, will break up into 24 of 128000
13:41:33 (infos) fast.rb:334:in `publish_traits'> slurp.rb:592:in `add_metadata'> adding new metadata
13:41:33 (infos) fast.rb:334:in `publish_traits'> slurp.rb:351:in `log_node_count'> Nodes: 0; Traits: 0; MetaData: 0
13:41:30 (infos) fast.rb:334:in `publish_traits'> slurp.rb:275:in `block in load_csv'> Importing 128000 rows from publish_traits.tsv

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