-
Started:
June 03, 2022 17:11
-
Completed:
23:39:24
-
Failed:
No.
-
Status:
completed
Events (most recent first):
-
11:19:04
(infos)
++ Calling delete_all on 0 instances...
-
11:19:04
(infos)
++ NUKE: Javascript (0)
-
11:19:04
(infos)
++ NUKE: Link (0)
-
11:19:04
(infos)
++ NUKE: Article (0)
-
11:19:04
(infos)
++ NUKE: Medium (0)
-
11:19:04
(infos)
Removed 0 Identifiers
-
11:19:04
(infos)
++ Calling delete_all on 0 instances...
-
11:19:04
(infos)
++ NUKE: Identifier (0)
-
11:19:04
(infos)
Removed 2038653 Nodeancestors
-
11:13:53
(updates)
Batch 203 (expect 204 batches, maximum 408)...
-
11:13:53
(infos)
Starting (this log message should be replaced shortly)
-
11:13:53
(infos)
++ Batch removal of 2038653 instances...
-
11:13:53
(infos)
++ NUKE: NodeAncestor (2038653)
-
23:39:24
(ends)
Complete
-
23:39:23
(ends)
TOTAL TIME: 3.3d
-
23:39:23
(starts)
TraitBank::Denormalizer.update_resource_vernaculars
-
23:39:23
(starts)
Running
-
23:37:08
(starts)
Resource#fix_native_nodes
-
23:37:08
(starts)
Running
-
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'
-
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 })}
-
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'
-
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'
-
23:36:53
(warns)
FAILED on build_nodes query (MetaData), will re-try once...
-
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'
-
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'
-
23:36:48
(infos)
Importing 128000 rows from publish_metadata_chunk_1.csv
-
23:36:47
(warns)
Found 5552474 rows, will break up into 128000
-
23:36:44
(infos)
adding new metadata
-
23:36:13
(infos)
Importing 128000 rows from publish_traits_chunk_44.csv
-
23:34:37
(infos)
Importing 128000 rows from publish_traits_chunk_43.csv
-
19:59:20
(infos)
Waiting 12900 seconds for the last 'chunk' to be added to neo4j...
-
19:58:00
(warns)
FAILED on build_nodes query (Trait), will re-try once...
-
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.
-
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.
-
19:55:52
(infos)
Importing 128000 rows from publish_traits_chunk_42.csv
-
16:25:48
(infos)
Waiting 12600 seconds for the last 'chunk' to be added to neo4j...
-
16:24:31
(infos)
Importing 128000 rows from publish_traits_chunk_41.csv
-
12:59:26
(infos)
Waiting 12300 seconds for the last 'chunk' to be added to neo4j...
-
12:58:04
(infos)
Importing 128000 rows from publish_traits_chunk_40.csv
-
09:38:00
(infos)
Waiting 12000 seconds for the last 'chunk' to be added to neo4j...
-
09:36:42
(infos)
Importing 128000 rows from publish_traits_chunk_39.csv
-
06:21:38
(infos)
Waiting 11700 seconds for the last 'chunk' to be added to neo4j...
-
06:20:19
(infos)
Importing 128000 rows from publish_traits_chunk_38.csv
-
03:10:15
(infos)
Waiting 11400 seconds for the last 'chunk' to be added to neo4j...
-
03:08:55
(infos)
Importing 128000 rows from publish_traits_chunk_37.csv
-
00:03:51
(infos)
Waiting 11100 seconds for the last 'chunk' to be added to neo4j...
-
00:02:33
(infos)
Importing 128000 rows from publish_traits_chunk_36.csv
-
21:02:29
(infos)
Waiting 10800 seconds for the last 'chunk' to be added to neo4j...
-
21:01:08
(infos)
Importing 128000 rows from publish_traits_chunk_35.csv
