Harvest for White Sea Species List Created 25 Dec 17:55

Stage: completed
Fetched: 25 Dec 17:55
Validated: 25 Dec 17:55
Deltas Created 25 Dec 17:55
Units Normalized: 25 Dec 18:00
Ancestry Built: 25 Dec 17:55
Nodes Matched: 25 Dec 18:00
Names Parsed: 25 Dec 17:55
New Models Stored: 25 Dec 17:55
Indexed: 25 Dec 18:00
Completed: 25 Dec 18:01
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-25 17:55:28 -0500 by logger.rb/56815
[START] [2019-12-25 17:55:28] logged process
[START] [2019-12-25 17:55:28] create_harvest_instance
[STOP] [2019-12-25 17:55:28] create_harvest_instance
[START] [2019-12-25 17:55:28] fetch_files
[STOP] [2019-12-25 17:55:28] fetch_files
[START] [2019-12-25 17:55:28] validate_each_file
[STOP] [2019-12-25 17:55:29] validate_each_file
[START] [2019-12-25 17:55:29] convert_to_csv
[CMD] [2019-12-25 17:55:29] /usr/bin/sort /app/public/converted_csv/white_sea_sp_lis_refs_19738.csv > /app/public/converted_csv/white_sea_sp_lis_refs_19738.csv_sorted
[CMD] [2019-12-25 17:55:29] /usr/bin/sort /app/public/converted_csv/white_sea_sp_lis_nodes_19739.csv > /app/public/converted_csv/white_sea_sp_lis_nodes_19739.csv_sorted
[CMD] [2019-12-25 17:55:29] /usr/bin/sort /app/public/converted_csv/white_sea_sp_lis_occurrences_19740.csv > /app/public/converted_csv/white_sea_sp_lis_occurrences_19740.csv_sorted
[CMD] [2019-12-25 17:55:29] /usr/bin/sort /app/public/converted_csv/white_sea_sp_lis_measurements_19741.csv > /app/public/converted_csv/white_sea_sp_lis_measurements_19741.csv_sorted
[STOP] [2019-12-25 17:55:29] convert_to_csv
[START] [2019-12-25 17:55:29] calculate_delta
[CMD] [2019-12-25 17:55:29] echo "0a" > /app/public/diff/white_sea_sp_lis_refs_19738.diff
[CMD] [2019-12-25 17:55:29] tail -n +1 /app/public/converted_csv/white_sea_sp_lis_refs_19738.csv >> /app/public/diff/white_sea_sp_lis_refs_19738.diff
[CMD] [2019-12-25 17:55:30] echo "." >> /app/public/diff/white_sea_sp_lis_refs_19738.diff
[CMD] [2019-12-25 17:55:30] echo "0a" > /app/public/diff/white_sea_sp_lis_nodes_19739.diff
[CMD] [2019-12-25 17:55:30] tail -n +1 /app/public/converted_csv/white_sea_sp_lis_nodes_19739.csv >> /app/public/diff/white_sea_sp_lis_nodes_19739.diff
[CMD] [2019-12-25 17:55:30] echo "." >> /app/public/diff/white_sea_sp_lis_nodes_19739.diff
[CMD] [2019-12-25 17:55:30] echo "0a" > /app/public/diff/white_sea_sp_lis_occurrences_19740.diff
[CMD] [2019-12-25 17:55:31] tail -n +1 /app/public/converted_csv/white_sea_sp_lis_occurrences_19740.csv >> /app/public/diff/white_sea_sp_lis_occurrences_19740.diff
[CMD] [2019-12-25 17:55:31] echo "." >> /app/public/diff/white_sea_sp_lis_occurrences_19740.diff
[CMD] [2019-12-25 17:55:31] echo "0a" > /app/public/diff/white_sea_sp_lis_measurements_19741.diff
[CMD] [2019-12-25 17:55:31] tail -n +1 /app/public/converted_csv/white_sea_sp_lis_measurements_19741.csv >> /app/public/diff/white_sea_sp_lis_measurements_19741.diff
[CMD] [2019-12-25 17:55:31] echo "." >> /app/public/diff/white_sea_sp_lis_measurements_19741.diff
[STOP] [2019-12-25 17:55:31] calculate_delta
[START] [2019-12-25 17:55:31] parse_diff_and_store
[INFO] [2019-12-25 17:55:32] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 17:55:32] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 17:55:32] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 17:55:33] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 17:55:35] Storing 2 References
[INFO] [2019-12-25 17:55:35] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 17:55:35] Average Time: 0.0
[INFO] [2019-12-25 17:55:35] Total Time: 1s
[INFO] [2019-12-25 17:55:35] Storing 1051 ScientificNames
[INFO] [2019-12-25 17:55:35] Processing group of 1051 in 2 groups of 1000
[INFO] [2019-12-25 17:55:36] Average Time: 0.235
[INFO] [2019-12-25 17:55:36] Total Time: 1s
[INFO] [2019-12-25 17:55:36] Storing 1051 Nodes
[INFO] [2019-12-25 17:55:36] Processing group of 1051 in 2 groups of 1000
[INFO] [2019-12-25 17:55:36] Average Time: 0.19
[INFO] [2019-12-25 17:55:36] Total Time: 1s
[INFO] [2019-12-25 17:55:36] Storing 452 Occurrences
[INFO] [2019-12-25 17:55:36] Processing group of 452 in 1 groups of 1000
[INFO] [2019-12-25 17:55:36] Average Time: 0.07
[INFO] [2019-12-25 17:55:36] Total Time: 1s
[INFO] [2019-12-25 17:55:36] Storing 904 TraitsReferences
[INFO] [2019-12-25 17:55:36] Processing group of 904 in 1 groups of 1000
[INFO] [2019-12-25 17:55:36] Average Time: 0.16
[INFO] [2019-12-25 17:55:36] Total Time: 1s
[INFO] [2019-12-25 17:55:36] Storing 904 Traits
[INFO] [2019-12-25 17:55:36] Processing group of 904 in 1 groups of 1000
[INFO] [2019-12-25 17:55:39] Average Time: 2.78
[INFO] [2019-12-25 17:55:39] Total Time: 3s
[INFO] [2019-12-25 17:55:39] Storing 903 MetaTraits
[INFO] [2019-12-25 17:55:39] Processing group of 903 in 1 groups of 1000
[INFO] [2019-12-25 17:55:39] Average Time: 0.29
[INFO] [2019-12-25 17:55:39] Total Time: 1s
[STOP] [2019-12-25 17:55:39] parse_diff_and_store
[START] [2019-12-25 17:55:39] resolve_keys
[INFO] [2019-12-25 17:55:46] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 17:55:47] traits to occurrences...
[INFO] [2019-12-25 17:55:47] traits to nodes (through occurrences)...
[INFO] [2019-12-25 17:55:47] Traits to sex term...
[INFO] [2019-12-25 17:55:48] Traits to lifestage term...
[INFO] [2019-12-25 17:55:48] MetaTraits to traits...
[INFO] [2019-12-25 17:55:48] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 17:55:48] Assocs to occurrences...
[INFO] [2019-12-25 17:55:48] Assocs to nodes...
[INFO] [2019-12-25 17:55:48] Assoc to sex term...
[INFO] [2019-12-25 17:55:48] Assoc to lifestage term...
[STOP] [2019-12-25 17:55:48] resolve_keys
[START] [2019-12-25 17:55:48] hold_for_later_1
[STOP] [2019-12-25 17:55:48] hold_for_later_1
[START] [2019-12-25 17:55:48] hold_for_later_2
[STOP] [2019-12-25 17:55:48] hold_for_later_2
[START] [2019-12-25 17:55:48] resolve_missing_parents
[STOP] [2019-12-25 17:55:49] resolve_missing_parents
[START] [2019-12-25 17:55:49] rebuild_nodes
[START] [2019-12-25 17:55:49] Flattener#flatten
[START] [2019-12-25 17:55:49] Flattener#study_resource
[START] [2019-12-25 17:55:49] Flattener#build_ancestry
[STOP] [2019-12-25 17:55:49] Flattener#build_ancestry
[INFO] [2019-12-25 17:55:49] 1051 ancestry keys
[START] [2019-12-25 17:55:49] build_node_ancestors
[INFO] [2019-12-25 17:55:49] old ancestors deleted.
[STOP] [2019-12-25 17:55:50] build_node_ancestors
[START] [2019-12-25 17:55:50] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 17:55:50] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 17:55:50] Flattener#flatten
[STOP] [2019-12-25 17:55:50] rebuild_nodes
[START] [2019-12-25 17:55:50] resolve_missing_media_owners
[STOP] [2019-12-25 17:55:50] resolve_missing_media_owners
[START] [2019-12-25 17:55:50] sanitize_media_verbatims
[STOP] [2019-12-25 17:55:50] sanitize_media_verbatims
[START] [2019-12-25 17:55:50] queue_downloads
[STOP] [2019-12-25 17:55:50] queue_downloads
[START] [2019-12-25 17:55:50] parse_names
[WARN] [2019-12-25 17:55:50] I see 1051 names which still need to be parsed.
[STOP] [2019-12-25 17:55:52] parse_names
[START] [2019-12-25 17:55:52] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 17:55:52] denormalize_canonical_names_to_nodes
[START] [2019-12-25 17:55:52] match_nodes
[START] [2019-12-25 17:55:52] map_all_nodes_to_pages
[STOP] [2019-12-25 18:00:12] map_all_nodes_to_pages
[INFO] [2019-12-25 18:00:12] 118 Unmatched nodes (of 1051)! That's too many to output. First 10: Gasterosteiformes (#62552166); Philomachus (#62552764); Philomachus pugnax (#62552763); Anas clypeata (#62552814); Anas querquedula (#62553026); Maxillopoda (#62552030); Metridia lucens (#62552891); Poecilostomatoida (#62552051); Harpacticus uniremis (#62552276); Hansenocarididae (#62552806)
[START] [2019-12-25 18:00:12] update_nodes
[STOP] [2019-12-25 18:00:13] update_nodes
[STOP] [2019-12-25 18:00:13] match_nodes
[START] [2019-12-25 18:00:13] reindex_search
[STOP] [2019-12-25 18:00:15] reindex_search
[START] [2019-12-25 18:00:15] normalize_units
[STOP] [2019-12-25 18:00:15] normalize_units
[START] [2019-12-25 18:00:15] calculate_statistics
[STOP] [2019-12-25 18:00:15] calculate_statistics
[START] [2019-12-25 18:00:15] complete_harvest_instance
[START] [2019-12-25 18:00:15] overall_tsv_creation
[INFO] [2019-12-25 18:00:15] Processing group of 1051 in 1 batches of 10000
[INFO] [2019-12-25 18:01:05] 452 Traits (unfiltered)...
[INFO] [2019-12-25 18:01:18] 452 Traits (filtered)...
[INFO] [2019-12-25 18:01:18] 0 Associations (filtered)...
[INFO] [2019-12-25 18:01:58] 2259 metadata added.
[INFO] [2019-12-25 18:01:58] 0 metadata added.
[INFO] [2019-12-25 18:01:58] Average Time: 79.75
[INFO] [2019-12-25 18:01:58] Total Time: 1m43s
[STOP] [2019-12-25 18:01:58] overall_tsv_creation
[INFO] [2019-12-25 18:01:58] Done. Check your files:
[INFO] [2019-12-25 18:01:58] (1051 lines) /app/public/data/white_sea_sp_lis/publish_nodes.tsv
[INFO] [2019-12-25 18:01:58] (4534 lines) /app/public/data/white_sea_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-12-25 18:01:58] (1051 lines) /app/public/data/white_sea_sp_lis/publish_scientific_names.tsv
[INFO] [2019-12-25 18:01:58] (453 lines) /app/public/data/white_sea_sp_lis/publish_traits.tsv
[INFO] [2019-12-25 18:01:59] (2260 lines) /app/public/data/white_sea_sp_lis/publish_metadata.tsv
[STOP] [2019-12-25 18:01:59] complete_harvest_instance
[START] [2019-12-25 18:01:59] completed
[STOP] [2019-12-25 18:01:59] completed
[STOP] [2019-12-25 18:01:59] logged process, took 390.89
Latest Process

25 Dec 17:55 EXITED currently processing 0