Import Log for Habitat data for microbial organisms

• Started: October 27, 2022 17:05
• Completed: 17:05:24
• Failed: No.
• Status: completed

Events (most recent first):

• 17:05:23 (warns) Trait Publishing failed: At https://eol.org/data/hab_dat_microbi2/publish_traits.tsv @ position 129427 - 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: 'Jaške, K., Barcytė, D., Pánek, T., Ševčíková, T., Eliášová, A., Eliáš, M., 2022. The net-like heterotrophic amoeba Leukarachnion salinum sp. nov. (Ochrophyta, Stramenopiles) has a cryptic plastid. bioRxiv.",https://doi.org/10.1101/2022.04.05.487141,,,,, R1186-PK279499780,52251376,Agolohymena aspidocauda,41ca3b76b9728a384e6dfa1f9aa186e5_1664392380,http://purl.obolibrary.org/obo/RO_0002303,,,,,,http://purl.obolibrary.org/obo/ENVO_00000873,http://purl.obolibrary.org/obo/ENVO_00000873,,,,,,"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:559:in `merge_triple' << /app/lib/trait_bank/slurp.rb:444:in `block in load_csv_where' << /app/lib/trait_bank/slurp.rb:444:in `each' << /app/lib/trait_bank/slurp.rb:444:in `load_csv_where' << /app/lib/trait_bank/slurp.rb:331:in `block (2 levels) in load_csv'
• 17:05:23 (warns) Exception (Neo4j::Driver::Exceptions::DatabaseException) FROM: #merge_triple QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/hab_dat_microbi2/publish_traits.tsv' AS row WITH row WHERE 1=1 MATCH (page:Page { page_id: toInteger(row.page_id) }) MATCH (trait:Trait { eol_pk: row.eol_pk })}
• 17:05:23 (warns) Exception (Neo4j::Driver::Exceptions::DatabaseException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/hab_dat_microbi2/publish_traits.tsv' AS row WITH row WHERE 1=1 MATCH (page:Page { page_id: toInteger(row.page_id) }) MATCH (trait:Trait { eol_pk: row.eol_pk }) MERGE (page)-[:trait]->(trait)} MESSAGE: At https://eol.org/data/hab_dat_microbi2/publish_traits.tsv @ position 129427 - 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: 'Jaške, K., Barcytė, D., Pánek, T., Ševčíková, T., Eliášová, A., Eliáš, M., 2022. The net-like heterotrophic amoeba Leukarachnion salinum sp. nov. (Ochrophyta, Stramenopiles) has a cryptic plastid. bioRxiv.",https://doi.org/10.1101/2022.04.05.487141,,,,, R1186-PK279499780,52251376,Agolohymena aspidocauda,41ca3b76b9728a384e6dfa1f9aa186e5_1664392380,http://purl.obolibrary.org/obo/RO_0002303,,,,,,http://purl.obolibrary.org/obo/ENVO_00000873,http://purl.obolibrary.org/obo/ENVO_00000873,,,,,,"BB'
• 17:05:23 (warns) Exception (Neo4j::Driver::Exceptions::DatabaseException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/hab_dat_microbi2/publish_traits.tsv' 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: At https://eol.org/data/hab_dat_microbi2/publish_traits.tsv @ position 129427 - 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: 'Jaške, K., Barcytė, D., Pánek, T., Ševčíková, T., Eliášová, A., Eliáš, M., 2022. The net-like heterotrophic amoeba Leukarachnion salinum sp. nov. (Ochrophyta, Stramenopiles) has a cryptic plastid. bioRxiv.",https://doi.org/10.1101/2022.04.05.487141,,,,, R1186-PK279499780,52251376,Agolohymena aspidocauda,41ca3b76b9728a384e6dfa1f9aa186e5_1664392380,http://purl.obolibrary.org/obo/RO_0002303,,,,,,http://purl.obolibrary.org/obo/ENVO_00000873,http://purl.obolibrary.org/obo/ENVO_00000873,,,,,,"BB'
• 17:05:23 (warns) FAILED on build_nodes query (Trait), will re-try once...
• 17:05:23 (warns) At https://eol.org/data/hab_dat_microbi2/publish_traits.tsv @ position 129427 - 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: 'Jaške, K., Barcytė, D., Pánek, T., Ševčíková, T., Eliášová, A., Eliáš, M., 2022. The net-like heterotrophic amoeba Leukarachnion salinum sp. nov. (Ochrophyta, Stramenopiles) has a cryptic plastid. bioRxiv.",https://doi.org/10.1101/2022.04.05.487141,,,,, R1186-PK279499780,52251376,Agolohymena aspidocauda,41ca3b76b9728a384e6dfa1f9aa186e5_1664392380,http://purl.obolibrary.org/obo/RO_0002303,,,,,,http://purl.obolibrary.org/obo/ENVO_00000873,http://purl.obolibrary.org/obo/ENVO_00000873,,,,,,"BB'
• 17:05:23 (warns) Exception (Neo4j::Driver::Exceptions::DatabaseException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/hab_dat_microbi2/publish_traits.tsv' 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: At https://eol.org/data/hab_dat_microbi2/publish_traits.tsv @ position 129427 - 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: 'Jaške, K., Barcytė, D., Pánek, T., Ševčíková, T., Eliášová, A., Eliáš, M., 2022. The net-like heterotrophic amoeba Leukarachnion salinum sp. nov. (Ochrophyta, Stramenopiles) has a cryptic plastid. bioRxiv.",https://doi.org/10.1101/2022.04.05.487141,,,,, R1186-PK279499780,52251376,Agolohymena aspidocauda,41ca3b76b9728a384e6dfa1f9aa186e5_1664392380,http://purl.obolibrary.org/obo/RO_0002303,,,,,,http://purl.obolibrary.org/obo/ENVO_00000873,http://purl.obolibrary.org/obo/ENVO_00000873,,,,,,"BB'
• 17:05:23 (warns) Exception (Neo4j::Driver::Exceptions::DatabaseException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/hab_dat_microbi2/publish_traits.tsv' AS row WITH row WHERE 1=1 MERGE (page:Page { page_id: toInteger(row.page_id) })} MESSAGE: At https://eol.org/data/hab_dat_microbi2/publish_traits.tsv @ position 129427 - 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: 'Jaške, K., Barcytė, D., Pánek, T., Ševčíková, T., Eliášová, A., Eliáš, M., 2022. The net-like heterotrophic amoeba Leukarachnion salinum sp. nov. (Ochrophyta, Stramenopiles) has a cryptic plastid. bioRxiv.",https://doi.org/10.1101/2022.04.05.487141,,,,, R1186-PK279499780,52251376,Agolohymena aspidocauda,41ca3b76b9728a384e6dfa1f9aa186e5_1664392380,http://purl.obolibrary.org/obo/RO_0002303,,,,,,http://purl.obolibrary.org/obo/ENVO_00000873,http://purl.obolibrary.org/obo/ENVO_00000873,,,,,,"BB'
• 17:05:23 (warns) FAILED on build_nodes query (Page), will re-try once...
• 17:05:23 (warns) At https://eol.org/data/hab_dat_microbi2/publish_traits.tsv @ position 129427 - 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: 'Jaške, K., Barcytė, D., Pánek, T., Ševčíková, T., Eliášová, A., Eliáš, M., 2022. The net-like heterotrophic amoeba Leukarachnion salinum sp. nov. (Ochrophyta, Stramenopiles) has a cryptic plastid. bioRxiv.",https://doi.org/10.1101/2022.04.05.487141,,,,, R1186-PK279499780,52251376,Agolohymena aspidocauda,41ca3b76b9728a384e6dfa1f9aa186e5_1664392380,http://purl.obolibrary.org/obo/RO_0002303,,,,,,http://purl.obolibrary.org/obo/ENVO_00000873,http://purl.obolibrary.org/obo/ENVO_00000873,,,,,,"BB'
• 17:05:23 (warns) Exception (Neo4j::Driver::Exceptions::DatabaseException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/hab_dat_microbi2/publish_traits.tsv' AS row WITH row WHERE 1=1 MERGE (page:Page { page_id: toInteger(row.page_id) })} MESSAGE: At https://eol.org/data/hab_dat_microbi2/publish_traits.tsv @ position 129427 - 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: 'Jaške, K., Barcytė, D., Pánek, T., Ševčíková, T., Eliášová, A., Eliáš, M., 2022. The net-like heterotrophic amoeba Leukarachnion salinum sp. nov. (Ochrophyta, Stramenopiles) has a cryptic plastid. bioRxiv.",https://doi.org/10.1101/2022.04.05.487141,,,,, R1186-PK279499780,52251376,Agolohymena aspidocauda,41ca3b76b9728a384e6dfa1f9aa186e5_1664392380,http://purl.obolibrary.org/obo/RO_0002303,,,,,,http://purl.obolibrary.org/obo/ENVO_00000873,http://purl.obolibrary.org/obo/ENVO_00000873,,,,,,"BB'
• 17:05:22 (warns) There were NO new pages, skipping...
• 17:05:22 (warns) MISSING https://content.eol.org/data/hab_dat_microbi2/publish_content_sections.tsv [404] (8 bytes); skipping
• 17:05:22 (warns) MISSING https://content.eol.org/data/hab_dat_microbi2/publish_references.tsv [404] (8 bytes); skipping
• 17:05:22 (warns) MISSING https://content.eol.org/data/hab_dat_microbi2/publish_image_info.tsv [404] (8 bytes); skipping
• 17:05:22 (warns) MISSING https://content.eol.org/data/hab_dat_microbi2/publish_attributions.tsv [404] (8 bytes); skipping
• 17:05:21 (warns) MISSING https://content.eol.org/data/hab_dat_microbi2/publish_media.tsv [404] (8 bytes); skipping
• 17:05:21 (warns) MISSING https://content.eol.org/data/hab_dat_microbi2/publish_articles.tsv [404] (8 bytes); skipping
• 17:05:21 (warns) MISSING https://content.eol.org/data/hab_dat_microbi2/publish_vernaculars.tsv [404] (8 bytes); skipping
• 17:05:21 (warns) MISSING https://content.eol.org/data/hab_dat_microbi2/publish_node_ancestors.tsv [404] (8 bytes); skipping
• 17:05:20 (warns) MISSING https://content.eol.org/data/hab_dat_microbi2/publish_identifiers.tsv [404] (8 bytes); skipping
• 17:05:20 (warns) MISSING https://content.eol.org/data/hab_dat_microbi2/publish_bibliographic_citations.tsv [404] (8 bytes); skipping
• 17:05:19 (warns) MISSING https://content.eol.org/data/hab_dat_microbi2/publish_referents.tsv [404] (8 bytes); skipping