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Started:
June 03, 2022 17:11
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Completed:
23:39:24
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Failed:
No.
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Status:
completed
Events (most recent first):
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11:33:19
(warns)
ERROR during delete of 16384 x trait: 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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23:37:03
(warns)
Trait Publishing failed: At https://eol.org/data/Globi/publish_metadata_chunk_1.csv @ position 17349996 - there's a field starting with a quote and whereas it ends that quote there seems to be characters in that field after that ending quote. That isn't supported. This is what I read: 'J. R. E. Jones, . A further ecological study of calcareous streams in the \"BB' 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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23:37:03
(warns)
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_1.csv' AS row WITH row WHERE 1=1
MATCH (metadata:MetaData { eol_pk: row.eol_pk })
MATCH (trait:Trait { eol_pk: row.trait_eol_pk })}
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23:37:03
(warns)
Exception (Neo4j::Driver::Exceptions::DatabaseException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/Globi/publish_metadata_chunk_1.csv' AS row WITH row WHERE 1=1
MATCH (metadata:MetaData { eol_pk: row.eol_pk })
MATCH (trait:Trait { eol_pk: row.trait_eol_pk })
MERGE (trait)-[:metadata]->(metadata)} MESSAGE: At https://eol.org/data/Globi/publish_metadata_chunk_1.csv @ position 17349996 - there's a field starting with a quote and whereas it ends that quote there seems to be characters in that field after that ending quote. That isn't supported. This is what I read: 'J. R. E. Jones, . A further ecological study of calcareous streams in the \"BB'
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23:36:55
(warns)
Exception (Neo4j::Driver::Exceptions::DatabaseException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/Globi/publish_metadata_chunk_1.csv' AS row WITH row WHERE 1=1 MERGE (metadata:MetaData { eol_pk: row.eol_pk })
ON CREATE SET metadata.source = row.source
ON MATCH SET metadata.source = row.source
ON CREATE SET metadata.literal = row.literal
ON MATCH SET metadata.literal = row.literal
ON CREATE SET metadata.measurement = row.measurement
ON MATCH SET metadata.measurement = row.measurement} MESSAGE: At https://eol.org/data/Globi/publish_metadata_chunk_1.csv @ position 17349996 - there's a field starting with a quote and whereas it ends that quote there seems to be characters in that field after that ending quote. That isn't supported. This is what I read: 'J. R. E. Jones, . A further ecological study of calcareous streams in the \"BB'
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23:36:53
(warns)
FAILED on build_nodes query (MetaData), will re-try once...
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23:36:53
(warns)
At https://eol.org/data/Globi/publish_metadata_chunk_1.csv @ position 17349996 - there's a field starting with a quote and whereas it ends that quote there seems to be characters in that field after that ending quote. That isn't supported. This is what I read: 'J. R. E. Jones, . A further ecological study of calcareous streams in the \"BB'
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23:36:51
(warns)
Exception (Neo4j::Driver::Exceptions::DatabaseException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/Globi/publish_metadata_chunk_1.csv' AS row WITH row WHERE 1=1 MERGE (metadata:MetaData { eol_pk: row.eol_pk })
ON CREATE SET metadata.source = row.source
ON MATCH SET metadata.source = row.source
ON CREATE SET metadata.literal = row.literal
ON MATCH SET metadata.literal = row.literal
ON CREATE SET metadata.measurement = row.measurement
ON MATCH SET metadata.measurement = row.measurement} MESSAGE: At https://eol.org/data/Globi/publish_metadata_chunk_1.csv @ position 17349996 - there's a field starting with a quote and whereas it ends that quote there seems to be characters in that field after that ending quote. That isn't supported. This is what I read: 'J. R. E. Jones, . A further ecological study of calcareous streams in the \"BB'
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23:36:47
(warns)
Found 5552474 rows, will break up into 128000
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19:58:00
(warns)
FAILED on build_nodes query (Trait), will re-try once...
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19:58:00
(warns)
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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19:57:59
(warns)
Exception (Neo4j::Driver::Exceptions::ClientException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/Globi/publish_traits_chunk_42.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: 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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17:17:11
(warns)
Found 5552474 rows, will break up into 128000
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17:16:02
(warns)
There were NO new pages, skipping...
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17:15:13
(warns)
MISSING https://content.eol.org/data/Globi/publish_content_sections.tsv [404] (8 bytes); skipping
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17:15:12
(warns)
MISSING https://content.eol.org/data/Globi/publish_references.tsv [404] (8 bytes); skipping
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17:15:12
(warns)
MISSING https://content.eol.org/data/Globi/publish_image_info.tsv [404] (8 bytes); skipping
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17:15:12
(warns)
MISSING https://content.eol.org/data/Globi/publish_attributions.tsv [404] (8 bytes); skipping
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17:15:12
(warns)
MISSING https://content.eol.org/data/Globi/publish_media.tsv [404] (8 bytes); skipping
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17:15:12
(warns)
MISSING https://content.eol.org/data/Globi/publish_articles.tsv [404] (8 bytes); skipping
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17:15:12
(warns)
MISSING https://content.eol.org/data/Globi/publish_vernaculars.tsv [404] (8 bytes); skipping
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17:12:19
(warns)
MISSING https://content.eol.org/data/Globi/publish_identifiers.tsv [404] (8 bytes); skipping
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17:12:19
(warns)
MISSING https://content.eol.org/data/Globi/publish_bibliographic_citations.tsv [404] (8 bytes); skipping
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17:11:52
(warns)
MISSING https://content.eol.org/data/Globi/publish_referents.tsv [404] (8 bytes); skipping
