Harvest for Norwegian Sea Species List Created 25 Dec 08:47

Stage: completed
Fetched: 25 Dec 08:47
Validated: 25 Dec 08:47
Deltas Created 25 Dec 08:47
Units Normalized: 25 Dec 08:51
Ancestry Built: 25 Dec 08:47
Nodes Matched: 25 Dec 08:51
Names Parsed: 25 Dec 08:47
New Models Stored: 25 Dec 08:47
Indexed: 25 Dec 08:51
Completed: 25 Dec 08:53
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-25 08:47:12 -0500 by logger.rb/56815
[START] [2019-12-25 08:47:12] logged process
[START] [2019-12-25 08:47:12] create_harvest_instance
[STOP] [2019-12-25 08:47:12] create_harvest_instance
[START] [2019-12-25 08:47:12] fetch_files
[STOP] [2019-12-25 08:47:12] fetch_files
[START] [2019-12-25 08:47:12] validate_each_file
[STOP] [2019-12-25 08:47:12] validate_each_file
[START] [2019-12-25 08:47:12] convert_to_csv
[CMD] [2019-12-25 08:47:12] /usr/bin/sort /app/public/converted_csv/norwegian_sea_sp_refs_19570.csv > /app/public/converted_csv/norwegian_sea_sp_refs_19570.csv_sorted
[CMD] [2019-12-25 08:47:13] /usr/bin/sort /app/public/converted_csv/norwegian_sea_sp_nodes_19571.csv > /app/public/converted_csv/norwegian_sea_sp_nodes_19571.csv_sorted
[CMD] [2019-12-25 08:47:14] /usr/bin/sort /app/public/converted_csv/norwegian_sea_sp_occurrences_19572.csv > /app/public/converted_csv/norwegian_sea_sp_occurrences_19572.csv_sorted
[CMD] [2019-12-25 08:47:14] /usr/bin/sort /app/public/converted_csv/norwegian_sea_sp_measurements_19573.csv > /app/public/converted_csv/norwegian_sea_sp_measurements_19573.csv_sorted
[STOP] [2019-12-25 08:47:15] convert_to_csv
[START] [2019-12-25 08:47:15] calculate_delta
[CMD] [2019-12-25 08:47:15] echo "0a" > /app/public/diff/norwegian_sea_sp_refs_19570.diff
[CMD] [2019-12-25 08:47:16] tail -n +1 /app/public/converted_csv/norwegian_sea_sp_refs_19570.csv >> /app/public/diff/norwegian_sea_sp_refs_19570.diff
[CMD] [2019-12-25 08:47:16] echo "." >> /app/public/diff/norwegian_sea_sp_refs_19570.diff
[CMD] [2019-12-25 08:47:17] echo "0a" > /app/public/diff/norwegian_sea_sp_nodes_19571.diff
[CMD] [2019-12-25 08:47:18] tail -n +1 /app/public/converted_csv/norwegian_sea_sp_nodes_19571.csv >> /app/public/diff/norwegian_sea_sp_nodes_19571.diff
[CMD] [2019-12-25 08:47:18] echo "." >> /app/public/diff/norwegian_sea_sp_nodes_19571.diff
[CMD] [2019-12-25 08:47:19] echo "0a" > /app/public/diff/norwegian_sea_sp_occurrences_19572.diff
[CMD] [2019-12-25 08:47:20] tail -n +1 /app/public/converted_csv/norwegian_sea_sp_occurrences_19572.csv >> /app/public/diff/norwegian_sea_sp_occurrences_19572.diff
[CMD] [2019-12-25 08:47:20] echo "." >> /app/public/diff/norwegian_sea_sp_occurrences_19572.diff
[CMD] [2019-12-25 08:47:21] echo "0a" > /app/public/diff/norwegian_sea_sp_measurements_19573.diff
[CMD] [2019-12-25 08:47:22] tail -n +1 /app/public/converted_csv/norwegian_sea_sp_measurements_19573.csv >> /app/public/diff/norwegian_sea_sp_measurements_19573.diff
[CMD] [2019-12-25 08:47:23] echo "." >> /app/public/diff/norwegian_sea_sp_measurements_19573.diff
[STOP] [2019-12-25 08:47:23] calculate_delta
[START] [2019-12-25 08:47:23] parse_diff_and_store
[INFO] [2019-12-25 08:47:24] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 08:47:25] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 08:47:26] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 08:47:26] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 08:47:29] Storing 2 References
[INFO] [2019-12-25 08:47:29] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 08:47:29] Average Time: 0.0
[INFO] [2019-12-25 08:47:29] Total Time: 1s
[INFO] [2019-12-25 08:47:29] Storing 1072 ScientificNames
[INFO] [2019-12-25 08:47:29] Processing group of 1072 in 2 groups of 1000
[INFO] [2019-12-25 08:47:30] Average Time: 0.26
[INFO] [2019-12-25 08:47:30] Total Time: 1s
[INFO] [2019-12-25 08:47:30] Storing 1072 Nodes
[INFO] [2019-12-25 08:47:30] Processing group of 1072 in 2 groups of 1000
[INFO] [2019-12-25 08:47:30] Average Time: 0.24
[INFO] [2019-12-25 08:47:30] Total Time: 1s
[INFO] [2019-12-25 08:47:30] Storing 452 Occurrences
[INFO] [2019-12-25 08:47:30] Processing group of 452 in 1 groups of 1000
[INFO] [2019-12-25 08:47:30] Average Time: 0.07
[INFO] [2019-12-25 08:47:30] Total Time: 1s
[INFO] [2019-12-25 08:47:30] Storing 904 TraitsReferences
[INFO] [2019-12-25 08:47:30] Processing group of 904 in 1 groups of 1000
[INFO] [2019-12-25 08:47:30] Average Time: 0.14
[INFO] [2019-12-25 08:47:30] Total Time: 1s
[INFO] [2019-12-25 08:47:30] Storing 904 Traits
[INFO] [2019-12-25 08:47:30] Processing group of 904 in 1 groups of 1000
[INFO] [2019-12-25 08:47:31] Average Time: 0.5
[INFO] [2019-12-25 08:47:31] Total Time: 1s
[INFO] [2019-12-25 08:47:31] Storing 903 MetaTraits
[INFO] [2019-12-25 08:47:31] Processing group of 903 in 1 groups of 1000
[INFO] [2019-12-25 08:47:31] Average Time: 0.16
[INFO] [2019-12-25 08:47:31] Total Time: 1s
[STOP] [2019-12-25 08:47:31] parse_diff_and_store
[START] [2019-12-25 08:47:31] resolve_keys
[INFO] [2019-12-25 08:47:38] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 08:47:38] traits to occurrences...
[INFO] [2019-12-25 08:47:39] traits to nodes (through occurrences)...
[INFO] [2019-12-25 08:47:39] Traits to sex term...
[INFO] [2019-12-25 08:47:39] Traits to lifestage term...
[INFO] [2019-12-25 08:47:40] MetaTraits to traits...
[INFO] [2019-12-25 08:47:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 08:47:40] Assocs to occurrences...
[INFO] [2019-12-25 08:47:40] Assocs to nodes...
[INFO] [2019-12-25 08:47:40] Assoc to sex term...
[INFO] [2019-12-25 08:47:40] Assoc to lifestage term...
[STOP] [2019-12-25 08:47:40] resolve_keys
[START] [2019-12-25 08:47:40] hold_for_later_1
[STOP] [2019-12-25 08:47:40] hold_for_later_1
[START] [2019-12-25 08:47:40] hold_for_later_2
[STOP] [2019-12-25 08:47:40] hold_for_later_2
[START] [2019-12-25 08:47:40] resolve_missing_parents
[STOP] [2019-12-25 08:47:41] resolve_missing_parents
[START] [2019-12-25 08:47:41] rebuild_nodes
[START] [2019-12-25 08:47:41] Flattener#flatten
[START] [2019-12-25 08:47:41] Flattener#study_resource
[START] [2019-12-25 08:47:41] Flattener#build_ancestry
[STOP] [2019-12-25 08:47:41] Flattener#build_ancestry
[INFO] [2019-12-25 08:47:41] 1072 ancestry keys
[START] [2019-12-25 08:47:41] build_node_ancestors
[INFO] [2019-12-25 08:47:41] old ancestors deleted.
[STOP] [2019-12-25 08:47:41] build_node_ancestors
[START] [2019-12-25 08:47:42] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 08:47:42] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 08:47:42] Flattener#flatten
[STOP] [2019-12-25 08:47:42] rebuild_nodes
[START] [2019-12-25 08:47:42] resolve_missing_media_owners
[STOP] [2019-12-25 08:47:42] resolve_missing_media_owners
[START] [2019-12-25 08:47:42] sanitize_media_verbatims
[STOP] [2019-12-25 08:47:42] sanitize_media_verbatims
[START] [2019-12-25 08:47:42] queue_downloads
[STOP] [2019-12-25 08:47:42] queue_downloads
[START] [2019-12-25 08:47:42] parse_names
[WARN] [2019-12-25 08:47:42] I see 1072 names which still need to be parsed.
[STOP] [2019-12-25 08:47:44] parse_names
[START] [2019-12-25 08:47:44] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 08:47:44] denormalize_canonical_names_to_nodes
[START] [2019-12-25 08:47:44] match_nodes
[START] [2019-12-25 08:47:44] map_all_nodes_to_pages
[STOP] [2019-12-25 08:51:33] map_all_nodes_to_pages
[INFO] [2019-12-25 08:51:33] 125 Unmatched nodes (of 1072)! That's too many to output. First 10: Gasterosteiformes (#62395381); Anas querquedula (#62396204); Anas clypeata (#62396224); Maxillopoda (#62395249); Poecilostomatoida (#62395270); Harpacticus uniremis (#62395492); Dermatomyzon nigripes (#62395964); Hansenocarididae (#62396039); Hansenocaris (#62396038); Hansenocaris itoi (#62396037)
[START] [2019-12-25 08:51:33] update_nodes
[STOP] [2019-12-25 08:51:34] update_nodes
[STOP] [2019-12-25 08:51:34] match_nodes
[START] [2019-12-25 08:51:34] reindex_search
[STOP] [2019-12-25 08:51:37] reindex_search
[START] [2019-12-25 08:51:37] normalize_units
[STOP] [2019-12-25 08:51:37] normalize_units
[START] [2019-12-25 08:51:37] calculate_statistics
[STOP] [2019-12-25 08:51:37] calculate_statistics
[START] [2019-12-25 08:51:37] complete_harvest_instance
[START] [2019-12-25 08:51:37] overall_tsv_creation
[INFO] [2019-12-25 08:51:37] Processing group of 1072 in 1 batches of 10000
[INFO] [2019-12-25 08:52:28] 452 Traits (unfiltered)...
[INFO] [2019-12-25 08:52:41] 452 Traits (filtered)...
[INFO] [2019-12-25 08:52:41] 0 Associations (filtered)...
[INFO] [2019-12-25 08:53:19] 2259 metadata added.
[INFO] [2019-12-25 08:53:19] 0 metadata added.
[INFO] [2019-12-25 08:53:19] Average Time: 77.72
[INFO] [2019-12-25 08:53:19] Total Time: 1m43s
[STOP] [2019-12-25 08:53:19] overall_tsv_creation
[INFO] [2019-12-25 08:53:19] Done. Check your files:
[INFO] [2019-12-25 08:53:20] (1072 lines) /app/public/data/norwegian_sea_sp/publish_nodes.tsv
[INFO] [2019-12-25 08:53:21] (4673 lines) /app/public/data/norwegian_sea_sp/publish_node_ancestors.tsv
[INFO] [2019-12-25 08:53:21] (1072 lines) /app/public/data/norwegian_sea_sp/publish_scientific_names.tsv
[INFO] [2019-12-25 08:53:22] (453 lines) /app/public/data/norwegian_sea_sp/publish_traits.tsv
[INFO] [2019-12-25 08:53:22] (2260 lines) /app/public/data/norwegian_sea_sp/publish_metadata.tsv
[STOP] [2019-12-25 08:53:23] complete_harvest_instance
[START] [2019-12-25 08:53:23] completed
[STOP] [2019-12-25 08:53:23] completed
[STOP] [2019-12-25 08:53:23] logged process, took 371.01
Latest Process

25 Dec 08:47 EXITED currently processing 0