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Started:
February 25, 2022 07:56
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Completed:
01:45:35.000
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Failed:
No.
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Status:
completed
Events (most recent first):
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01:42:39.000
(warns)
FAILED on build_nodes query (Trait), will re-try once...
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01:42:39.000
(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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01:42:39.000
(warns)
Exception (Neo4j::Driver::Exceptions::ClientException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/paleobiology_db/new_traits_1645545266_1645721181_chunk_16.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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23:02:39.000
(warns)
FAILED on build_nodes query (Trait), will re-try once...
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23:02:39.000
(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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23:02:39.000
(warns)
Exception (Neo4j::Driver::Exceptions::ClientException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/paleobiology_db/new_traits_1645545266_1645721181_chunk_14.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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15:34:46.000
(warns)
Found 2140044 rows, will break up into 128000
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17:56:13.000
(warns)
Trait Publishing failed: execution expired (Delayed::Worker.max_run_time is only 36000 seconds) FROM /app/lib/trait_bank/slurp.rb:366:in `sleep' << /app/lib/trait_bank/slurp.rb:366:in `block in break_up_large_file' << /app/lib/trait_bank/slurp.rb:357:in `break_up_large_file' << /app/lib/trait_bank/slurp.rb:343:in `break_up_large_files' << /app/lib/trait_bank/slurp.rb:289:in `load_csv' << /app/lib/trait_bank/slurp.rb:612:in `add_traits'
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17:06:19.000
(warns)
FAILED on build_nodes query (Trait), will re-try once...
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17:06:19.000
(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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17:06:19.000
(warns)
Exception (Neo4j::Driver::Exceptions::ClientException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/paleobiology_db/new_traits_1645545266_1645721181_chunk_13.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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13:08:33.000
(warns)
FAILED on build_nodes query (Trait), will re-try once...
-
13:08:33.000
(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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13:08:33.000
(warns)
Exception (Neo4j::Driver::Exceptions::ClientException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/paleobiology_db/new_traits_1645545266_1645721181_chunk_9.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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10:42:27.000
(warns)
Found 2140044 rows, will break up into 128000
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08:09:30.000
(warns)
Skipping reindexing. You should reindex soon.
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08:07:50.000
(warns)
MULTIPLE matching names for VernacularPreference.find(62519) (chipmunk), using first.
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08:07:50.000
(warns)
MULTIPLE matching names for VernacularPreference.find(62486) (Redtail tegus), using first.
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08:07:50.000
(warns)
Missing matching name for VernacularPreference.find(36843) (plains zebra)
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08:07:50.000
(warns)
MULTIPLE matching names for VernacularPreference.find(5894) (burrowing toad), using first.
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08:07:49.000
(warns)
MISSING https://content.eol.org/data/paleobiology_db/publish_content_sections.tsv [404] (8 bytes); skipping
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08:07:49.000
(warns)
MISSING https://content.eol.org/data/paleobiology_db/publish_references.tsv [404] (8 bytes); skipping
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08:07:49.000
(warns)
MISSING https://content.eol.org/data/paleobiology_db/publish_image_info.tsv [404] (8 bytes); skipping
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08:07:49.000
(warns)
MISSING https://content.eol.org/data/paleobiology_db/publish_attributions.tsv [404] (8 bytes); skipping
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08:07:49.000
(warns)
MISSING https://content.eol.org/data/paleobiology_db/publish_media.tsv [404] (8 bytes); skipping
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08:07:49.000
(warns)
MISSING https://content.eol.org/data/paleobiology_db/publish_articles.tsv [404] (8 bytes); skipping
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08:04:21.000
(warns)
MISSING https://content.eol.org/data/paleobiology_db/publish_identifiers.tsv [404] (8 bytes); skipping
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08:04:21.000
(warns)
MISSING https://content.eol.org/data/paleobiology_db/publish_bibliographic_citations.tsv [404] (8 bytes); skipping
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08:03:33.000
(warns)
MISSING https://content.eol.org/data/paleobiology_db/publish_referents.tsv [404] (8 bytes); skipping
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08:03:31.000
(warns)
All existing content has been destroyed for the resource.
