Harvest for Jonkers et al 1997 Created 16 Jun 09:07

Harvesting Log

# Logfile created on 2020-06-16 08:48:04 -0400 by logger.rb/v1.4.2
[INFO] [2020-06-16 08:48:04] ## HARVEST: type = -harvest
[START] [2020-06-16 08:48:05] logged process
[START] [2020-06-16 08:48:05] create_harvest_instance
[STOP] [2020-06-16 08:48:06] create_harvest_instance
[START] [2020-06-16 08:48:06] fetch_files
[STOP] [2020-06-16 08:48:06] fetch_files
[START] [2020-06-16 08:48:06] validate_each_file
[STOP] [2020-06-16 08:48:06] validate_each_file
[ERR] [2020-06-16 08:48:06] Exceptions::ColumnUnmatched
[ERR] [2020-06-16 08:48:06] TOO MANY COLUMNS: nodes: ,
[ERR] [2020-06-16 08:48:06] ../models/resource_harvester.rb:138:in `block in validate_each_file'
[ERR] [2020-06-16 08:48:06] ../models/resource_harvester.rb:666:in `block in each_format'
[ERR] [2020-06-16 08:48:06] ../models/resource_harvester.rb:651:in `each_format'
[ERR] [2020-06-16 08:48:06] ../models/resource_harvester.rb:132:in `validate_each_file'
[ERR] [2020-06-16 08:48:06] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2020-06-16 08:48:06] ../models/logged_process.rb:19:in `run_step'
[ERR] [2020-06-16 08:48:06] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2020-06-16 08:48:06] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2020-06-16 08:48:06] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2020-06-16 08:48:06] ../models/resource.rb:151:in `lock'
[ERR] [2020-06-16 08:48:06] ../models/resource_harvester.rb:72:in `start'
[ERR] [2020-06-16 08:48:06] ../models/resource.rb:232:in `harvest'
[ERR] [2020-06-16 08:48:06] bin/rails:4:in `require'
[ERR] [2020-06-16 08:48:06] bin/rails:4:in `<main>'
[STOP] [2020-06-16 08:48:06] logged process, took 1.15
[INFO] [2020-06-16 08:51:40] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-06-16 08:51:44] ## remove_type: ScientificName
[INFO] [2020-06-16 08:51:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 08:51:44] [08:51:44.578] Removed 0 Scientificnames
[INFO] [2020-06-16 08:51:44] ## remove_type: Vernacular
[INFO] [2020-06-16 08:51:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 08:51:44] [08:51:44.581] Removed 0 Vernaculars
[INFO] [2020-06-16 08:51:44] ## remove_type: Article
[INFO] [2020-06-16 08:51:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 08:51:44] [08:51:44.584] Removed 0 Articles
[INFO] [2020-06-16 08:51:44] ## remove_type: Medium
[INFO] [2020-06-16 08:51:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 08:51:44] [08:51:44.588] Removed 0 Media
[INFO] [2020-06-16 08:51:44] ## remove_type: Trait
[INFO] [2020-06-16 08:51:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 08:51:44] [08:51:44.591] Removed 0 Traits
[INFO] [2020-06-16 08:51:44] ## remove_type: MetaTrait
[INFO] [2020-06-16 08:51:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 08:51:44] [08:51:44.600] Removed 0 Metatraits
[INFO] [2020-06-16 08:51:44] ## remove_type: OccurrenceMetadatum
[INFO] [2020-06-16 08:51:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 08:51:44] [08:51:44.602] Removed 0 Occurrencemetadata
[INFO] [2020-06-16 08:51:44] ## remove_type: Assoc
[INFO] [2020-06-16 08:51:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 08:51:44] [08:51:44.605] Removed 0 Assocs
[INFO] [2020-06-16 08:51:44] ## remove_type: MetaAssoc
[INFO] [2020-06-16 08:51:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 08:51:44] [08:51:44.608] Removed 0 Metaassocs
[INFO] [2020-06-16 08:51:44] ## remove_type: Identifier
[INFO] [2020-06-16 08:51:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 08:51:44] [08:51:44.627] Removed 0 Identifiers
[INFO] [2020-06-16 08:51:44] ## remove_type: Reference
[INFO] [2020-06-16 08:51:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 08:51:44] [08:51:44.630] Removed 0 References
[INFO] [2020-06-16 08:51:44] ## remove_type: Node
[INFO] [2020-06-16 08:51:44] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 08:51:44] [08:51:44.685] Removed 0 Nodes
[START] [2020-06-16 08:51:45] logged process
[START] [2020-06-16 08:51:45] Creating resource from OpenData
[START] [2020-06-16 08:51:45] logged process
[START] [2020-06-16 08:51:45] Parse meta.xml file and create formats with fields
[STOP] [2020-06-16 08:51:45] Parse meta.xml file and create formats with fields
[STOP] [2020-06-16 08:51:45] Creating resource from OpenData
[START] [2020-06-16 08:51:45] logged process
[START] [2020-06-16 08:51:45] create_harvest_instance
[STOP] [2020-06-16 08:51:46] create_harvest_instance
[START] [2020-06-16 08:51:46] fetch_files
[STOP] [2020-06-16 08:51:46] fetch_files
[START] [2020-06-16 08:51:46] validate_each_file
[STOP] [2020-06-16 08:51:46] validate_each_file
[START] [2020-06-16 08:51:46] convert_to_csv
[CMD] [2020-06-16 08:51:46] /usr/bin/sort /app/public/converted_csv/jonkers_et_al_jo_nodes_21238.csv > /app/public/converted_csv/jonkers_et_al_jo_nodes_21238.csv_sorted
[CMD] [2020-06-16 08:51:46] /usr/bin/sort /app/public/converted_csv/jonkers_et_al_jo_occurrences_21239.csv > /app/public/converted_csv/jonkers_et_al_jo_occurrences_21239.csv_sorted
[CMD] [2020-06-16 08:51:46] /usr/bin/sort /app/public/converted_csv/jonkers_et_al_jo_measurements_21240.csv > /app/public/converted_csv/jonkers_et_al_jo_measurements_21240.csv_sorted
[STOP] [2020-06-16 08:51:46] convert_to_csv
[START] [2020-06-16 08:51:46] calculate_delta
[CMD] [2020-06-16 08:51:46] echo "0a" > /app/public/diff/jonkers_et_al_jo_nodes_21238.diff
[CMD] [2020-06-16 08:51:46] tail -n +1 /app/public/converted_csv/jonkers_et_al_jo_nodes_21238.csv >> /app/public/diff/jonkers_et_al_jo_nodes_21238.diff
[CMD] [2020-06-16 08:51:46] echo "." >> /app/public/diff/jonkers_et_al_jo_nodes_21238.diff
[CMD] [2020-06-16 08:51:46] echo "0a" > /app/public/diff/jonkers_et_al_jo_occurrences_21239.diff
[CMD] [2020-06-16 08:51:46] tail -n +1 /app/public/converted_csv/jonkers_et_al_jo_occurrences_21239.csv >> /app/public/diff/jonkers_et_al_jo_occurrences_21239.diff
[CMD] [2020-06-16 08:51:46] echo "." >> /app/public/diff/jonkers_et_al_jo_occurrences_21239.diff
[CMD] [2020-06-16 08:51:46] echo "0a" > /app/public/diff/jonkers_et_al_jo_measurements_21240.diff
[CMD] [2020-06-16 08:51:46] tail -n +1 /app/public/converted_csv/jonkers_et_al_jo_measurements_21240.csv >> /app/public/diff/jonkers_et_al_jo_measurements_21240.diff
[CMD] [2020-06-16 08:51:46] echo "." >> /app/public/diff/jonkers_et_al_jo_measurements_21240.diff
[STOP] [2020-06-16 08:51:46] calculate_delta
[START] [2020-06-16 08:51:46] parse_diff_and_store
[INFO] [2020-06-16 08:51:46] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-16 08:51:46] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-16 08:51:46] Loading measurements diff file into memory (true lines)...
[INFO] [2020-06-16 08:51:46] Storing 20 ScientificNames
[INFO] [2020-06-16 08:51:46] Processing group of 20 in 1 groups of 1000
[INFO] [2020-06-16 08:51:46] Average Time: 0.01
[INFO] [2020-06-16 08:51:46] Total Time: 1s
[INFO] [2020-06-16 08:51:46] Storing 20 Nodes
[INFO] [2020-06-16 08:51:46] Processing group of 20 in 1 groups of 1000
[INFO] [2020-06-16 08:51:46] Average Time: 0.01
[INFO] [2020-06-16 08:51:46] Total Time: 1s
[INFO] [2020-06-16 08:51:46] Storing 8 Occurrences
[INFO] [2020-06-16 08:51:46] Processing group of 8 in 1 groups of 1000
[INFO] [2020-06-16 08:51:46] Average Time: 0.0
[INFO] [2020-06-16 08:51:46] Total Time: 1s
[INFO] [2020-06-16 08:51:46] Storing 24 Traits
[INFO] [2020-06-16 08:51:46] Processing group of 24 in 1 groups of 1000
[INFO] [2020-06-16 08:51:46] Average Time: 0.01
[INFO] [2020-06-16 08:51:46] Total Time: 1s
[INFO] [2020-06-16 08:51:46] Storing 16 MetaTraits
[INFO] [2020-06-16 08:51:46] Processing group of 16 in 1 groups of 1000
[INFO] [2020-06-16 08:51:46] Average Time: 0.02
[INFO] [2020-06-16 08:51:46] Total Time: 1s
[STOP] [2020-06-16 08:51:46] parse_diff_and_store
[START] [2020-06-16 08:51:46] resolve_keys
[INFO] [2020-06-16 08:51:54] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-16 08:51:54] traits to occurrences...
[INFO] [2020-06-16 08:51:54] traits to nodes (through occurrences)...
[INFO] [2020-06-16 08:51:54] Traits to sex term...
[INFO] [2020-06-16 08:51:54] Traits to lifestage term...
[INFO] [2020-06-16 08:51:54] MetaTraits to traits...
[INFO] [2020-06-16 08:51:54] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-16 08:51:54] Assocs to occurrences...
[INFO] [2020-06-16 08:51:54] Assocs to nodes...
[INFO] [2020-06-16 08:51:54] Assoc to sex term...
[INFO] [2020-06-16 08:51:54] Assoc to lifestage term...
[STOP] [2020-06-16 08:51:54] resolve_keys
[START] [2020-06-16 08:51:54] hold_for_later_1
[STOP] [2020-06-16 08:51:54] hold_for_later_1
[START] [2020-06-16 08:51:54] hold_for_later_2
[STOP] [2020-06-16 08:51:54] hold_for_later_2
[START] [2020-06-16 08:51:54] resolve_missing_parents
[STOP] [2020-06-16 08:51:54] resolve_missing_parents
[START] [2020-06-16 08:51:54] rebuild_nodes
[START] [2020-06-16 08:51:54] Flattener#flatten
[START] [2020-06-16 08:51:54] Flattener#study_resource
[START] [2020-06-16 08:51:54] Flattener#build_ancestry
[STOP] [2020-06-16 08:51:54] Flattener#build_ancestry
[INFO] [2020-06-16 08:51:54] 20 ancestry keys
[START] [2020-06-16 08:51:54] build_node_ancestors
[INFO] [2020-06-16 08:51:54] old ancestors deleted.
[STOP] [2020-06-16 08:51:54] build_node_ancestors
[START] [2020-06-16 08:51:54] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 08:51:54] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 08:51:54] Flattener#flatten
[STOP] [2020-06-16 08:51:54] rebuild_nodes
[START] [2020-06-16 08:51:54] resolve_missing_media_owners
[STOP] [2020-06-16 08:51:54] resolve_missing_media_owners
[START] [2020-06-16 08:51:54] sanitize_media_verbatims
[STOP] [2020-06-16 08:51:54] sanitize_media_verbatims
[START] [2020-06-16 08:51:54] queue_downloads
[STOP] [2020-06-16 08:51:54] queue_downloads
[START] [2020-06-16 08:51:54] parse_names
[WARN] [2020-06-16 08:51:54] I see 20 names which still need to be parsed.
[STOP] [2020-06-16 08:51:55] parse_names
[START] [2020-06-16 08:51:55] denormalize_canonical_names_to_nodes
[STOP] [2020-06-16 08:51:55] denormalize_canonical_names_to_nodes
[START] [2020-06-16 08:51:55] match_nodes
[START] [2020-06-16 08:51:55] map_all_nodes_to_pages
[STOP] [2020-06-16 08:52:14] map_all_nodes_to_pages
[INFO] [2020-06-16 08:52:14] ZERO unmatched nodes (of 20)! Nicely done.
[START] [2020-06-16 08:52:14] update_nodes
[STOP] [2020-06-16 08:52:14] update_nodes
[STOP] [2020-06-16 08:52:14] match_nodes
[START] [2020-06-16 08:52:14] reindex_search
[STOP] [2020-06-16 08:52:15] reindex_search
[START] [2020-06-16 08:52:15] normalize_units
[STOP] [2020-06-16 08:52:15] normalize_units
[START] [2020-06-16 08:52:15] calculate_statistics
[STOP] [2020-06-16 08:52:15] calculate_statistics
[START] [2020-06-16 08:52:15] complete_harvest_instance
[START] [2020-06-16 08:52:15] overall_tsv_creation
[INFO] [2020-06-16 08:52:15] Processing group of 20 in 1 batches of 10000
[INFO] [2020-06-16 08:54:11] 8 Traits (unfiltered)...
[INFO] [2020-06-16 08:54:24] 8 Traits (filtered)...
[INFO] [2020-06-16 08:54:24] 0 Associations (filtered)...
[INFO] [2020-06-16 08:55:02] 24 metadata added.
[INFO] [2020-06-16 08:55:02] 0 metadata added.
[INFO] [2020-06-16 08:55:02] Average Time: 74.08
[INFO] [2020-06-16 08:55:02] Total Time: 2m48s
[STOP] [2020-06-16 08:55:02] overall_tsv_creation
[INFO] [2020-06-16 08:55:02] Done. Check your files:
[INFO] [2020-06-16 08:55:02] (20 lines) /app/public/data/jonkers_et_al_jo/publish_nodes.tsv
[INFO] [2020-06-16 08:55:02] (31 lines) /app/public/data/jonkers_et_al_jo/publish_node_ancestors.tsv
[INFO] [2020-06-16 08:55:02] (20 lines) /app/public/data/jonkers_et_al_jo/publish_scientific_names.tsv
[INFO] [2020-06-16 08:55:02] (9 lines) /app/public/data/jonkers_et_al_jo/publish_traits.tsv
[INFO] [2020-06-16 08:55:02] (25 lines) /app/public/data/jonkers_et_al_jo/publish_metadata.tsv
[STOP] [2020-06-16 08:55:02] complete_harvest_instance
[START] [2020-06-16 08:55:02] completed
[STOP] [2020-06-16 08:55:02] completed
[STOP] [2020-06-16 08:55:02] logged process, took 197.62
[INFO] [2020-06-16 09:07:00] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-06-16 09:07:01] ## remove_type: ScientificName
[INFO] [2020-06-16 09:07:01] ++ Calling delete_all on 20 instances...
[INFO] [2020-06-16 09:07:01] [09:07:01.896] Removed 20 Scientificnames
[INFO] [2020-06-16 09:07:01] ## remove_type: Vernacular
[INFO] [2020-06-16 09:07:01] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:07:01] [09:07:01.899] Removed 0 Vernaculars
[INFO] [2020-06-16 09:07:01] ## remove_type: Article
[INFO] [2020-06-16 09:07:01] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:07:01] [09:07:01.903] Removed 0 Articles
[INFO] [2020-06-16 09:07:01] ## remove_type: Medium
[INFO] [2020-06-16 09:07:01] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:07:01] [09:07:01.907] Removed 0 Media
[INFO] [2020-06-16 09:07:01] ## remove_type: Trait
[INFO] [2020-06-16 09:07:01] ++ Calling delete_all on 24 instances...
[INFO] [2020-06-16 09:07:01] [09:07:01.913] Removed 24 Traits
[INFO] [2020-06-16 09:07:01] ## remove_type: MetaTrait
[INFO] [2020-06-16 09:07:01] ++ Calling delete_all on 16 instances...
[INFO] [2020-06-16 09:07:01] [09:07:01.917] Removed 16 Metatraits
[INFO] [2020-06-16 09:07:01] ## remove_type: OccurrenceMetadatum
[INFO] [2020-06-16 09:07:01] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:07:01] [09:07:01.920] Removed 0 Occurrencemetadata
[INFO] [2020-06-16 09:07:01] ## remove_type: Assoc
[INFO] [2020-06-16 09:07:01] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:07:01] [09:07:01.923] Removed 0 Assocs
[INFO] [2020-06-16 09:07:01] ## remove_type: MetaAssoc
[INFO] [2020-06-16 09:07:01] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:07:01] [09:07:01.926] Removed 0 Metaassocs
[INFO] [2020-06-16 09:07:01] ## remove_type: Identifier
[INFO] [2020-06-16 09:07:01] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:07:01] [09:07:01.929] Removed 0 Identifiers
[INFO] [2020-06-16 09:07:01] ## remove_type: Reference
[INFO] [2020-06-16 09:07:01] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:07:01] [09:07:01.932] Removed 0 References
[INFO] [2020-06-16 09:07:01] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:01] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:02] Starting batch with ID 80097669...
[INFO] [2020-06-16 09:07:03] Starting batch with ID 80097670...
[INFO] [2020-06-16 09:07:03] Starting batch with ID 80097672...
[INFO] [2020-06-16 09:07:03] Starting batch with ID 80097672...
[INFO] [2020-06-16 09:07:03] Starting batch with ID 80097672...
[INFO] [2020-06-16 09:07:04] ## remove_type: Node
[INFO] [2020-06-16 09:07:04] ++ Calling delete_all on 20 instances...
[INFO] [2020-06-16 09:07:04] [09:07:04.229] Removed 20 Nodes
[START] [2020-06-16 09:07:04] logged process
[START] [2020-06-16 09:07:04] Creating resource from OpenData
[START] [2020-06-16 09:07:04] logged process
[START] [2020-06-16 09:07:04] Parse meta.xml file and create formats with fields
[STOP] [2020-06-16 09:07:04] Parse meta.xml file and create formats with fields
[STOP] [2020-06-16 09:07:04] Creating resource from OpenData
[START] [2020-06-16 09:07:04] logged process
[START] [2020-06-16 09:07:04] create_harvest_instance
[STOP] [2020-06-16 09:07:05] create_harvest_instance
[START] [2020-06-16 09:07:05] fetch_files
[STOP] [2020-06-16 09:07:05] fetch_files
[START] [2020-06-16 09:07:05] validate_each_file
[STOP] [2020-06-16 09:07:06] validate_each_file
[START] [2020-06-16 09:07:06] convert_to_csv
[CMD] [2020-06-16 09:07:06] /usr/bin/sort /app/public/converted_csv/jonkers_et_al_jo_nodes_21256.csv > /app/public/converted_csv/jonkers_et_al_jo_nodes_21256.csv_sorted
[CMD] [2020-06-16 09:07:06] /usr/bin/sort /app/public/converted_csv/jonkers_et_al_jo_occurrences_21257.csv > /app/public/converted_csv/jonkers_et_al_jo_occurrences_21257.csv_sorted
[CMD] [2020-06-16 09:07:06] /usr/bin/sort /app/public/converted_csv/jonkers_et_al_jo_measurements_21258.csv > /app/public/converted_csv/jonkers_et_al_jo_measurements_21258.csv_sorted
[STOP] [2020-06-16 09:07:06] convert_to_csv
[START] [2020-06-16 09:07:06] calculate_delta
[CMD] [2020-06-16 09:07:06] echo "0a" > /app/public/diff/jonkers_et_al_jo_nodes_21256.diff
[CMD] [2020-06-16 09:07:06] tail -n +1 /app/public/converted_csv/jonkers_et_al_jo_nodes_21256.csv >> /app/public/diff/jonkers_et_al_jo_nodes_21256.diff
[CMD] [2020-06-16 09:07:06] echo "." >> /app/public/diff/jonkers_et_al_jo_nodes_21256.diff
[CMD] [2020-06-16 09:07:06] echo "0a" > /app/public/diff/jonkers_et_al_jo_occurrences_21257.diff
[CMD] [2020-06-16 09:07:06] tail -n +1 /app/public/converted_csv/jonkers_et_al_jo_occurrences_21257.csv >> /app/public/diff/jonkers_et_al_jo_occurrences_21257.diff
[CMD] [2020-06-16 09:07:06] echo "." >> /app/public/diff/jonkers_et_al_jo_occurrences_21257.diff
[CMD] [2020-06-16 09:07:06] echo "0a" > /app/public/diff/jonkers_et_al_jo_measurements_21258.diff
[CMD] [2020-06-16 09:07:06] tail -n +1 /app/public/converted_csv/jonkers_et_al_jo_measurements_21258.csv >> /app/public/diff/jonkers_et_al_jo_measurements_21258.diff
[CMD] [2020-06-16 09:07:06] echo "." >> /app/public/diff/jonkers_et_al_jo_measurements_21258.diff
[STOP] [2020-06-16 09:07:06] calculate_delta
[START] [2020-06-16 09:07:06] parse_diff_and_store
[INFO] [2020-06-16 09:07:06] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-16 09:07:06] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-16 09:07:06] Loading measurements diff file into memory (true lines)...
[INFO] [2020-06-16 09:07:06] Storing 20 ScientificNames
[INFO] [2020-06-16 09:07:06] Processing group of 20 in 1 groups of 1000
[INFO] [2020-06-16 09:07:06] Average Time: 0.01
[INFO] [2020-06-16 09:07:06] Total Time: 1s
[INFO] [2020-06-16 09:07:06] Storing 20 Nodes
[INFO] [2020-06-16 09:07:06] Processing group of 20 in 1 groups of 1000
[INFO] [2020-06-16 09:07:06] Average Time: 0.01
[INFO] [2020-06-16 09:07:06] Total Time: 1s
[INFO] [2020-06-16 09:07:06] Storing 8 Occurrences
[INFO] [2020-06-16 09:07:06] Processing group of 8 in 1 groups of 1000
[INFO] [2020-06-16 09:07:06] Average Time: 0.0
[INFO] [2020-06-16 09:07:06] Total Time: 1s
[INFO] [2020-06-16 09:07:06] Storing 24 Traits
[INFO] [2020-06-16 09:07:06] Processing group of 24 in 1 groups of 1000
[INFO] [2020-06-16 09:07:06] Average Time: 0.01
[INFO] [2020-06-16 09:07:06] Total Time: 1s
[INFO] [2020-06-16 09:07:06] Storing 32 MetaTraits
[INFO] [2020-06-16 09:07:06] Processing group of 32 in 1 groups of 1000
[INFO] [2020-06-16 09:07:06] Average Time: 0.0
[INFO] [2020-06-16 09:07:06] Total Time: 1s
[STOP] [2020-06-16 09:07:06] parse_diff_and_store
[START] [2020-06-16 09:07:06] resolve_keys
[INFO] [2020-06-16 09:07:13] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-16 09:07:13] traits to occurrences...
[INFO] [2020-06-16 09:07:13] traits to nodes (through occurrences)...
[INFO] [2020-06-16 09:07:13] Traits to sex term...
[INFO] [2020-06-16 09:07:13] Traits to lifestage term...
[INFO] [2020-06-16 09:07:13] MetaTraits to traits...
[INFO] [2020-06-16 09:07:13] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-16 09:07:13] Assocs to occurrences...
[INFO] [2020-06-16 09:07:13] Assocs to nodes...
[INFO] [2020-06-16 09:07:13] Assoc to sex term...
[INFO] [2020-06-16 09:07:13] Assoc to lifestage term...
[STOP] [2020-06-16 09:07:13] resolve_keys
[START] [2020-06-16 09:07:13] hold_for_later_1
[STOP] [2020-06-16 09:07:13] hold_for_later_1
[START] [2020-06-16 09:07:13] hold_for_later_2
[STOP] [2020-06-16 09:07:13] hold_for_later_2
[START] [2020-06-16 09:07:13] resolve_missing_parents
[STOP] [2020-06-16 09:07:13] resolve_missing_parents
[START] [2020-06-16 09:07:13] rebuild_nodes
[START] [2020-06-16 09:07:13] Flattener#flatten
[START] [2020-06-16 09:07:13] Flattener#study_resource
[START] [2020-06-16 09:07:13] Flattener#build_ancestry
[STOP] [2020-06-16 09:07:13] Flattener#build_ancestry
[INFO] [2020-06-16 09:07:13] 20 ancestry keys
[START] [2020-06-16 09:07:13] build_node_ancestors
[INFO] [2020-06-16 09:07:13] old ancestors deleted.
[STOP] [2020-06-16 09:07:13] build_node_ancestors
[START] [2020-06-16 09:07:13] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 09:07:13] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 09:07:13] Flattener#flatten
[STOP] [2020-06-16 09:07:13] rebuild_nodes
[START] [2020-06-16 09:07:13] resolve_missing_media_owners
[STOP] [2020-06-16 09:07:13] resolve_missing_media_owners
[START] [2020-06-16 09:07:13] sanitize_media_verbatims
[STOP] [2020-06-16 09:07:13] sanitize_media_verbatims
[START] [2020-06-16 09:07:13] queue_downloads
[STOP] [2020-06-16 09:07:13] queue_downloads
[START] [2020-06-16 09:07:13] parse_names
[WARN] [2020-06-16 09:07:13] I see 20 names which still need to be parsed.
[STOP] [2020-06-16 09:07:14] parse_names
[START] [2020-06-16 09:07:14] denormalize_canonical_names_to_nodes
[STOP] [2020-06-16 09:07:14] denormalize_canonical_names_to_nodes
[START] [2020-06-16 09:07:14] match_nodes
[START] [2020-06-16 09:07:14] map_all_nodes_to_pages
[STOP] [2020-06-16 09:07:15] map_all_nodes_to_pages
[INFO] [2020-06-16 09:07:15] ZERO unmatched nodes (of 20)! Nicely done.
[START] [2020-06-16 09:07:15] update_nodes
[STOP] [2020-06-16 09:07:15] update_nodes
[STOP] [2020-06-16 09:07:15] match_nodes
[START] [2020-06-16 09:07:15] reindex_search
[STOP] [2020-06-16 09:07:15] reindex_search
[START] [2020-06-16 09:07:15] normalize_units
[STOP] [2020-06-16 09:07:15] normalize_units
[START] [2020-06-16 09:07:15] calculate_statistics
[STOP] [2020-06-16 09:07:15] calculate_statistics
[START] [2020-06-16 09:07:15] complete_harvest_instance
[START] [2020-06-16 09:07:15] overall_tsv_creation
[INFO] [2020-06-16 09:07:15] Processing group of 20 in 1 batches of 10000
[INFO] [2020-06-16 09:08:05] 8 Traits (unfiltered)...
[INFO] [2020-06-16 09:08:18] 8 Traits (filtered)...
[INFO] [2020-06-16 09:08:18] 0 Associations (filtered)...
[INFO] [2020-06-16 09:08:56] 40 metadata added.
[INFO] [2020-06-16 09:08:56] 0 metadata added.
[INFO] [2020-06-16 09:08:56] Average Time: 72.43
[INFO] [2020-06-16 09:08:56] Total Time: 1m41s
[STOP] [2020-06-16 09:08:56] overall_tsv_creation
[INFO] [2020-06-16 09:08:56] Done. Check your files:
[INFO] [2020-06-16 09:08:56] (20 lines) /app/public/data/jonkers_et_al_jo/publish_nodes.tsv
[INFO] [2020-06-16 09:08:56] (31 lines) /app/public/data/jonkers_et_al_jo/publish_node_ancestors.tsv
[INFO] [2020-06-16 09:08:56] (20 lines) /app/public/data/jonkers_et_al_jo/publish_scientific_names.tsv
[INFO] [2020-06-16 09:08:56] (9 lines) /app/public/data/jonkers_et_al_jo/publish_traits.tsv
[INFO] [2020-06-16 09:08:56] (41 lines) /app/public/data/jonkers_et_al_jo/publish_metadata.tsv
[STOP] [2020-06-16 09:08:56] complete_harvest_instance
[START] [2020-06-16 09:08:56] completed
[STOP] [2020-06-16 09:08:56] completed
[STOP] [2020-06-16 09:08:56] logged process, took 111.28

Latest Process

16 Jun 09:07 EXITED currently processing 0