Harvest for Barents Sea Species List Created 22 Dec 20:40

Harvesting Log

# Logfile created on 2019-12-22 20:40:29 -0500 by logger.rb/56815
[START] [2019-12-22 20:40:29] logged process
[START] [2019-12-22 20:40:29] create_harvest_instance
[STOP] [2019-12-22 20:40:29] create_harvest_instance
[START] [2019-12-22 20:40:29] fetch_files
[STOP] [2019-12-22 20:40:29] fetch_files
[START] [2019-12-22 20:40:29] validate_each_file
[STOP] [2019-12-22 20:40:30] validate_each_file
[START] [2019-12-22 20:40:30] convert_to_csv
[CMD] [2019-12-22 20:40:30] /usr/bin/sort /app/public/converted_csv/barents_sea_sp_l_refs_19074.csv > /app/public/converted_csv/barents_sea_sp_l_refs_19074.csv_sorted
[CMD] [2019-12-22 20:40:31] /usr/bin/sort /app/public/converted_csv/barents_sea_sp_l_nodes_19075.csv > /app/public/converted_csv/barents_sea_sp_l_nodes_19075.csv_sorted
[CMD] [2019-12-22 20:40:31] /usr/bin/sort /app/public/converted_csv/barents_sea_sp_l_occurrences_19076.csv > /app/public/converted_csv/barents_sea_sp_l_occurrences_19076.csv_sorted
[CMD] [2019-12-22 20:40:32] /usr/bin/sort /app/public/converted_csv/barents_sea_sp_l_measurements_19077.csv > /app/public/converted_csv/barents_sea_sp_l_measurements_19077.csv_sorted
[STOP] [2019-12-22 20:40:33] convert_to_csv
[START] [2019-12-22 20:40:33] calculate_delta
[CMD] [2019-12-22 20:40:33] echo "0a" > /app/public/diff/barents_sea_sp_l_refs_19074.diff
[CMD] [2019-12-22 20:40:33] tail -n +1 /app/public/converted_csv/barents_sea_sp_l_refs_19074.csv >> /app/public/diff/barents_sea_sp_l_refs_19074.diff
[CMD] [2019-12-22 20:40:34] echo "." >> /app/public/diff/barents_sea_sp_l_refs_19074.diff
[CMD] [2019-12-22 20:40:35] echo "0a" > /app/public/diff/barents_sea_sp_l_nodes_19075.diff
[CMD] [2019-12-22 20:40:35] tail -n +1 /app/public/converted_csv/barents_sea_sp_l_nodes_19075.csv >> /app/public/diff/barents_sea_sp_l_nodes_19075.diff
[CMD] [2019-12-22 20:40:36] echo "." >> /app/public/diff/barents_sea_sp_l_nodes_19075.diff
[CMD] [2019-12-22 20:40:37] echo "0a" > /app/public/diff/barents_sea_sp_l_occurrences_19076.diff
[CMD] [2019-12-22 20:40:37] tail -n +1 /app/public/converted_csv/barents_sea_sp_l_occurrences_19076.csv >> /app/public/diff/barents_sea_sp_l_occurrences_19076.diff
[CMD] [2019-12-22 20:40:38] echo "." >> /app/public/diff/barents_sea_sp_l_occurrences_19076.diff
[CMD] [2019-12-22 20:40:39] echo "0a" > /app/public/diff/barents_sea_sp_l_measurements_19077.diff
[CMD] [2019-12-22 20:40:39] tail -n +1 /app/public/converted_csv/barents_sea_sp_l_measurements_19077.csv >> /app/public/diff/barents_sea_sp_l_measurements_19077.diff
[CMD] [2019-12-22 20:40:40] echo "." >> /app/public/diff/barents_sea_sp_l_measurements_19077.diff
[STOP] [2019-12-22 20:40:41] calculate_delta
[START] [2019-12-22 20:40:41] parse_diff_and_store
[INFO] [2019-12-22 20:40:41] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 20:40:42] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 20:40:44] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 20:40:46] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 20:40:59] Storing 2 References
[INFO] [2019-12-22 20:40:59] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 20:40:59] Average Time: 0.0
[INFO] [2019-12-22 20:40:59] Total Time: 1s
[INFO] [2019-12-22 20:40:59] Storing 4628 ScientificNames
[INFO] [2019-12-22 20:40:59] Processing group of 4628 in 5 groups of 1000
[INFO] [2019-12-22 20:41:01] Average Time: 0.356
[INFO] [2019-12-22 20:41:01] Total Time: 2s
[INFO] [2019-12-22 20:41:01] Storing 4628 Nodes
[INFO] [2019-12-22 20:41:01] Processing group of 4628 in 5 groups of 1000
[INFO] [2019-12-22 20:41:02] Average Time: 0.298
[INFO] [2019-12-22 20:41:02] Total Time: 2s
[INFO] [2019-12-22 20:41:02] Storing 2232 Occurrences
[INFO] [2019-12-22 20:41:02] Processing group of 2232 in 3 groups of 1000
[INFO] [2019-12-22 20:41:03] Average Time: 0.087
[INFO] [2019-12-22 20:41:03] Total Time: 1s
[INFO] [2019-12-22 20:41:03] Storing 4464 TraitsReferences
[INFO] [2019-12-22 20:41:03] Processing group of 4464 in 5 groups of 1000
[INFO] [2019-12-22 20:41:03] Average Time: 0.086
[INFO] [2019-12-22 20:41:03] Total Time: 1s
[INFO] [2019-12-22 20:41:03] Storing 4464 Traits
[INFO] [2019-12-22 20:41:03] Processing group of 4464 in 5 groups of 1000
[INFO] [2019-12-22 20:41:05] Average Time: 0.326
[INFO] [2019-12-22 20:41:05] Total Time: 2s
[INFO] [2019-12-22 20:41:05] Storing 4461 MetaTraits
[INFO] [2019-12-22 20:41:05] Processing group of 4461 in 5 groups of 1000
[INFO] [2019-12-22 20:41:05] Average Time: 0.14
[INFO] [2019-12-22 20:41:05] Total Time: 1s
[STOP] [2019-12-22 20:41:05] parse_diff_and_store
[START] [2019-12-22 20:41:05] resolve_keys
[INFO] [2019-12-22 20:41:26] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 20:41:28] traits to occurrences...
[INFO] [2019-12-22 20:41:29] traits to nodes (through occurrences)...
[INFO] [2019-12-22 20:41:29] Traits to sex term...
[INFO] [2019-12-22 20:41:30] Traits to lifestage term...
[INFO] [2019-12-22 20:41:31] MetaTraits to traits...
[INFO] [2019-12-22 20:41:31] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 20:41:32] Assocs to occurrences...
[INFO] [2019-12-22 20:41:32] Assocs to nodes...
[INFO] [2019-12-22 20:41:32] Assoc to sex term...
[INFO] [2019-12-22 20:41:32] Assoc to lifestage term...
[STOP] [2019-12-22 20:41:32] resolve_keys
[START] [2019-12-22 20:41:32] hold_for_later_1
[STOP] [2019-12-22 20:41:32] hold_for_later_1
[START] [2019-12-22 20:41:32] hold_for_later_2
[STOP] [2019-12-22 20:41:32] hold_for_later_2
[START] [2019-12-22 20:41:32] resolve_missing_parents
[STOP] [2019-12-22 20:41:41] resolve_missing_parents
[START] [2019-12-22 20:41:41] rebuild_nodes
[START] [2019-12-22 20:41:41] Flattener#flatten
[START] [2019-12-22 20:41:41] Flattener#study_resource
[START] [2019-12-22 20:41:41] Flattener#build_ancestry
[STOP] [2019-12-22 20:41:41] Flattener#build_ancestry
[INFO] [2019-12-22 20:41:41] 4628 ancestry keys
[START] [2019-12-22 20:41:41] build_node_ancestors
[INFO] [2019-12-22 20:41:41] old ancestors deleted.
[STOP] [2019-12-22 20:41:43] build_node_ancestors
[START] [2019-12-22 20:41:45] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 20:41:45] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 20:41:45] Flattener#flatten
[STOP] [2019-12-22 20:41:45] rebuild_nodes
[START] [2019-12-22 20:41:45] resolve_missing_media_owners
[STOP] [2019-12-22 20:41:45] resolve_missing_media_owners
[START] [2019-12-22 20:41:45] sanitize_media_verbatims
[STOP] [2019-12-22 20:41:45] sanitize_media_verbatims
[START] [2019-12-22 20:41:45] queue_downloads
[STOP] [2019-12-22 20:41:45] queue_downloads
[START] [2019-12-22 20:41:45] parse_names
[WARN] [2019-12-22 20:41:45] I see 4628 names which still need to be parsed.
[STOP] [2019-12-22 20:41:50] parse_names
[START] [2019-12-22 20:41:50] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 20:41:50] denormalize_canonical_names_to_nodes
[START] [2019-12-22 20:41:50] match_nodes
[START] [2019-12-22 20:41:50] map_all_nodes_to_pages
[STOP] [2019-12-22 20:59:16] map_all_nodes_to_pages
[INFO] [2019-12-22 20:59:16] 93 Unmatched nodes (of 4628)! That's too many to output. First 10: Maxillopoda (#61720961); Metridia lucens (#61720997); Paracalanus parvus (#61722816); Poecilostomatoida (#61721341); Dactylopusia vulgaris (#61724413); Zaus spinatus (#61722852); Harpacticus uniremis (#61722232); Rhizothricidae (#61723884); Cerviniidae (#61723929); Diosaccidae (#61724102)
[START] [2019-12-22 20:59:16] update_nodes
[STOP] [2019-12-22 20:59:17] update_nodes
[STOP] [2019-12-22 20:59:17] match_nodes
[ERR] [2019-12-22 20:59:17] Faraday::TimeoutError
[ERR] [2019-12-22 20:59:17] Net::ReadTimeout
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:130:in `match'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:152:in `match_canonical_in_eol'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:283:in `map_unflagged_node'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:248:in `map_node'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:221:in `map_if_needed'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:189:in `block in map_nodes'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:188:in `map_nodes'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:227:in `block in map_if_needed'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:226:in `map_if_needed'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:189:in `block in map_nodes'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:188:in `map_nodes'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:227:in `block in map_if_needed'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:226:in `map_if_needed'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:189:in `block in map_nodes'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:188:in `map_nodes'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:227:in `block in map_if_needed'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:226:in `map_if_needed'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:189:in `block in map_nodes'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:188:in `map_nodes'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:227:in `block in map_if_needed'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:226:in `map_if_needed'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:189:in `block in map_nodes'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:188:in `map_nodes'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:183:in `block in map_all_nodes_to_pages'
[ERR] [2019-12-22 20:59:17] ../models/logged_process.rb:62:in `enter_group'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:181:in `map_all_nodes_to_pages'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:168:in `block in start'
[ERR] [2019-12-22 20:59:17] ../models/logged_process.rb:19:in `run_step'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:168:in `start'
[ERR] [2019-12-22 20:59:17] ../models/names_matcher.rb:22:in `for_harvest'
[ERR] [2019-12-22 20:59:17] ../models/resource_harvester.rb:608:in `match_nodes'
[ERR] [2019-12-22 20:59:17] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2019-12-22 20:59:17] ../models/logged_process.rb:19:in `run_step'
[ERR] [2019-12-22 20:59:17] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2019-12-22 20:59:17] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2019-12-22 20:59:17] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2019-12-22 20:59:17] ../models/resource.rb:139:in `lock'
[ERR] [2019-12-22 20:59:17] ../models/resource_harvester.rb:72:in `start'
[ERR] [2019-12-22 20:59:17] ../models/resource.rb:223:in `harvest'
[ERR] [2019-12-22 20:59:17] ../models/resource.rb:199:in `re_download_opendata_and_harvest'
[STOP] [2019-12-22 20:59:17] logged process, took 1128.14
[START] [2019-12-22 21:02:00] logged process
[INFO] [2019-12-22 21:02:00] Already completed stage create_harvest_instance, skipping...
[INFO] [2019-12-22 21:02:00] Already completed stage fetch_files, skipping...
[INFO] [2019-12-22 21:02:00] Already completed stage validate_each_file, skipping...
[INFO] [2019-12-22 21:02:00] Already completed stage convert_to_csv, skipping...
[INFO] [2019-12-22 21:02:00] Already completed stage calculate_delta, skipping...
[INFO] [2019-12-22 21:02:00] Already completed stage parse_diff_and_store, skipping...
[INFO] [2019-12-22 21:02:00] Already completed stage resolve_keys, skipping...
[INFO] [2019-12-22 21:02:00] Already completed stage hold_for_later_1, skipping...
[INFO] [2019-12-22 21:02:00] Already completed stage hold_for_later_2, skipping...
[INFO] [2019-12-22 21:02:00] Already completed stage resolve_missing_parents, skipping...
[INFO] [2019-12-22 21:02:00] Already completed stage rebuild_nodes, skipping...
[INFO] [2019-12-22 21:02:00] Already completed stage resolve_missing_media_owners, skipping...
[INFO] [2019-12-22 21:02:00] Already completed stage sanitize_media_verbatims, skipping...
[INFO] [2019-12-22 21:02:00] Already completed stage queue_downloads, skipping...
[INFO] [2019-12-22 21:02:00] Already completed stage parse_names, skipping...
[INFO] [2019-12-22 21:02:00] Already completed stage denormalize_canonical_names_to_nodes, skipping...
[START] [2019-12-22 21:02:00] match_nodes
[START] [2019-12-22 21:02:00] map_all_nodes_to_pages
[STOP] [2019-12-22 21:04:42] map_all_nodes_to_pages
[INFO] [2019-12-22 21:04:42] 150 Unmatched nodes (of 4628)! That's too many to output. First 10: Neoloricata (#61723070); Molpadiida (#61723573); Aspidochirotida (#61724613); Poliometra (#61725005); Poliometra prolixa (#61725004); Callopora smitti (#61724900); Porelloides (#61725391); Phylactella labiata (#61724676); Celleporina incrassata (#61722895); Cellepora canaliculata (#61725023)
[START] [2019-12-22 21:04:42] update_nodes
[STOP] [2019-12-22 21:04:43] update_nodes
[STOP] [2019-12-22 21:04:43] match_nodes
[START] [2019-12-22 21:04:43] reindex_search
[STOP] [2019-12-22 21:04:50] reindex_search
[START] [2019-12-22 21:04:50] normalize_units
[STOP] [2019-12-22 21:04:50] normalize_units
[START] [2019-12-22 21:04:50] calculate_statistics
[STOP] [2019-12-22 21:04:50] calculate_statistics
[START] [2019-12-22 21:04:50] complete_harvest_instance
[START] [2019-12-22 21:04:50] overall_tsv_creation
[INFO] [2019-12-22 21:04:50] Processing group of 4628 in 1 batches of 10000
[INFO] [2019-12-22 21:05:55] 2232 Traits (unfiltered)...
[INFO] [2019-12-22 21:06:08] 2232 Traits (filtered)...
[INFO] [2019-12-22 21:06:08] 0 Associations (filtered)...
[INFO] [2019-12-22 21:06:49] 11157 metadata added.
[INFO] [2019-12-22 21:06:49] 0 metadata added.
[INFO] [2019-12-22 21:06:49] Average Time: 93.45
[INFO] [2019-12-22 21:06:49] Total Time: 1m59s
[STOP] [2019-12-22 21:06:49] overall_tsv_creation
[INFO] [2019-12-22 21:06:49] Done. Check your files:
[INFO] [2019-12-22 21:06:50] (4628 lines) /app/public/data/barents_sea_sp_l/publish_nodes.tsv
[INFO] [2019-12-22 21:06:50] (22819 lines) /app/public/data/barents_sea_sp_l/publish_node_ancestors.tsv
[INFO] [2019-12-22 21:06:51] (4628 lines) /app/public/data/barents_sea_sp_l/publish_scientific_names.tsv
[INFO] [2019-12-22 21:06:51] (2233 lines) /app/public/data/barents_sea_sp_l/publish_traits.tsv
[INFO] [2019-12-22 21:06:52] (11158 lines) /app/public/data/barents_sea_sp_l/publish_metadata.tsv
[STOP] [2019-12-22 21:06:52] complete_harvest_instance
[START] [2019-12-22 21:06:52] completed
[STOP] [2019-12-22 21:06:52] completed
[STOP] [2019-12-22 21:06:52] logged process, took 291.92

Latest Process

22 Dec 21:02 EXITED currently processing 0