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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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10:04:43
(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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02:49:04
(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
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21:03:55
(warns)
each.rb:9:in `each'> slurp.rb:289:in `rescue in block (2 levels) in load_csv'> ...re-trying.
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20:58:55
(warns)
each.rb:9:in `each'> slurp.rb:285:in `rescue in block (2 levels) in load_csv'> FAILED on build_nodes query (Trait), will re-try 3 times after 5 minute pause (the site may be too busy to serve the CSV to Neo4j)...
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20:58:55
(warns)
each.rb:9:in `each'> slurp.rb:284:in `rescue in block (2 levels) in load_csv'> Couldn't load the external resource at: https://eol.org/data/Globi/publish_traits_chunk_12.csv
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20:58:55
(warns)
each.rb:9:in `each'> slurp.rb:571:in `rescue in autocommit_query'> Exception (Neo4j::Driver::Exceptions::ClientException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/Globi/publish_traits_chunk_12.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: Couldn't load the external resource at: https://eol.org/data/Globi/publish_traits_chunk_12.csv
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19:28:28
(warns)
each.rb:9:in `each'> slurp.rb:289:in `rescue in block (2 levels) in load_csv'> ...re-trying.
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19:23:28
(warns)
each.rb:9:in `each'> slurp.rb:285:in `rescue in block (2 levels) in load_csv'> FAILED on build_nodes query (Page), will re-try 2 times after 5 minute pause (the site may be too busy to serve the CSV to Neo4j)...
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19:23:28
(warns)
each.rb:9:in `each'> slurp.rb:284:in `rescue in block (2 levels) in load_csv'> Couldn't load the external resource at: https://eol.org/data/Globi/publish_traits_chunk_8.csv
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19:23:28
(warns)
each.rb:9:in `each'> slurp.rb:571:in `rescue in autocommit_query'> Exception (Neo4j::Driver::Exceptions::ClientException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/Globi/publish_traits_chunk_8.csv' AS row WITH row WHERE 1=1 MERGE (page:Page { page_id: toInteger(row.page_id) })} MESSAGE: Couldn't load the external resource at: https://eol.org/data/Globi/publish_traits_chunk_8.csv
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19:23:26
(warns)
each.rb:9:in `each'> slurp.rb:289:in `rescue in block (2 levels) in load_csv'> ...re-trying.
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19:18:26
(warns)
each.rb:9:in `each'> slurp.rb:285:in `rescue in block (2 levels) in load_csv'> FAILED on build_nodes query (Page), will re-try 3 times after 5 minute pause (the site may be too busy to serve the CSV to Neo4j)...
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19:18:26
(warns)
each.rb:9:in `each'> slurp.rb:284:in `rescue in block (2 levels) in load_csv'> Couldn't load the external resource at: https://eol.org/data/Globi/publish_traits_chunk_8.csv
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19:18:26
(warns)
each.rb:9:in `each'> slurp.rb:571:in `rescue in autocommit_query'> Exception (Neo4j::Driver::Exceptions::ClientException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/Globi/publish_traits_chunk_8.csv' AS row WITH row WHERE 1=1 MERGE (page:Page { page_id: toInteger(row.page_id) })} MESSAGE: Couldn't load the external resource at: https://eol.org/data/Globi/publish_traits_chunk_8.csv
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17:58:04
(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
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17:57:30
(warns)
slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:114:in `log_warn'> Took 23 seconds.
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17:57:07
(warns)
slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:114:in `log_warn'> USING wget TO RETRIEVE FULL FILE...
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17:57:07
(warns)
slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:114:in `log_warn'> TRUNCATED RESPONSE! Got 266253535 bytes out of 747585637 from https://content.eol.org/data/Globi/publish_metadata.tsv
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17:56:17
(warns)
slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:114:in `log_warn'> Took 30 seconds.
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17:55:47
(warns)
slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:114:in `log_warn'> USING wget TO RETRIEVE FULL FILE...
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17:55:47
(warns)
slurp.rb:20:in `load_resource_from_repo'> content_server_connection.rb:114:in `log_warn'> TRUNCATED RESPONSE! Got 115170663 bytes out of 949928114 from https://content.eol.org/data/Globi/publish_traits.tsv
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17:55:44
(warns)
fast.rb:155:in `by_resource'> page_creator.rb:22:in `by_node_pks'> There were NO new pages, skipping...
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17:54:19
(warns)
fast.rb:246:in `grab_file'> content_server_connection.rb:114:in `log_warn'> MISSING https://content.eol.org/data/Globi/publish_content_sections.tsv [404] (8 bytes); skipping
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17:54:19
(warns)
fast.rb:246:in `grab_file'> content_server_connection.rb:114:in `log_warn'> MISSING https://content.eol.org/data/Globi/publish_references.tsv [404] (8 bytes); skipping
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17:54:19
(warns)
fast.rb:246:in `grab_file'> content_server_connection.rb:114:in `log_warn'> MISSING https://content.eol.org/data/Globi/publish_image_info.tsv [404] (8 bytes); skipping
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17:54:19
(warns)
fast.rb:246:in `grab_file'> content_server_connection.rb:114:in `log_warn'> MISSING https://content.eol.org/data/Globi/publish_attributions.tsv [404] (8 bytes); skipping
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17:54:19
(warns)
fast.rb:246:in `grab_file'> content_server_connection.rb:114:in `log_warn'> MISSING https://content.eol.org/data/Globi/publish_media.tsv [404] (8 bytes); skipping
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17:54:19
(warns)
fast.rb:246:in `grab_file'> content_server_connection.rb:114:in `log_warn'> MISSING https://content.eol.org/data/Globi/publish_articles.tsv [404] (8 bytes); skipping
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17:54:19
(warns)
fast.rb:246:in `grab_file'> content_server_connection.rb:114:in `log_warn'> MISSING https://content.eol.org/data/Globi/publish_vernaculars.tsv [404] (8 bytes); skipping
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17:48:19
(warns)
fast.rb:246:in `grab_file'> content_server_connection.rb:114:in `log_warn'> Took 7 seconds.
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17:48:12
(warns)
fast.rb:246:in `grab_file'> content_server_connection.rb:114:in `log_warn'> USING wget TO RETRIEVE FULL FILE...
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17:48:12
(warns)
fast.rb:246:in `grab_file'> content_server_connection.rb:114:in `log_warn'> TRUNCATED RESPONSE! Got 149064000 bytes out of 255228025 from https://content.eol.org/data/Globi/publish_node_ancestors.tsv
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17:47:01
(warns)
fast.rb:246:in `grab_file'> content_server_connection.rb:114:in `log_warn'> MISSING https://content.eol.org/data/Globi/publish_identifiers.tsv [404] (8 bytes); skipping
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17:47:01
(warns)
fast.rb:246:in `grab_file'> content_server_connection.rb:114:in `log_warn'> MISSING https://content.eol.org/data/Globi/publish_bibliographic_citations.tsv [404] (8 bytes); skipping
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17:46:01
(warns)
fast.rb:246:in `grab_file'> content_server_connection.rb:114:in `log_warn'> MISSING https://content.eol.org/data/Globi/publish_referents.tsv [404] (8 bytes); skipping
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17:45:57
(warns)
resource.rb:225:in `publish'> fast.rb:143:in `by_resource'> All existing content has been destroyed for the resource.
