Harvest for Tasman Sea Species List Created 25 Dec 15:57

Harvesting Log

# Logfile created on 2019-12-25 15:57:22 -0500 by logger.rb/56815
[START] [2019-12-25 15:57:22] logged process
[START] [2019-12-25 15:57:22] create_harvest_instance
[STOP] [2019-12-25 15:57:23] create_harvest_instance
[START] [2019-12-25 15:57:23] fetch_files
[STOP] [2019-12-25 15:57:23] fetch_files
[START] [2019-12-25 15:57:23] validate_each_file
[STOP] [2019-12-25 15:57:26] validate_each_file
[START] [2019-12-25 15:57:26] convert_to_csv
[CMD] [2019-12-25 15:57:26] /usr/bin/sort /app/public/converted_csv/tasman_sea_sp_li_refs_19714.csv > /app/public/converted_csv/tasman_sea_sp_li_refs_19714.csv_sorted
[CMD] [2019-12-25 15:57:26] /usr/bin/sort /app/public/converted_csv/tasman_sea_sp_li_nodes_19715.csv > /app/public/converted_csv/tasman_sea_sp_li_nodes_19715.csv_sorted
[CMD] [2019-12-25 15:57:27] /usr/bin/sort /app/public/converted_csv/tasman_sea_sp_li_occurrences_19716.csv > /app/public/converted_csv/tasman_sea_sp_li_occurrences_19716.csv_sorted
[CMD] [2019-12-25 15:57:27] /usr/bin/sort /app/public/converted_csv/tasman_sea_sp_li_measurements_19717.csv > /app/public/converted_csv/tasman_sea_sp_li_measurements_19717.csv_sorted
[STOP] [2019-12-25 15:57:27] convert_to_csv
[START] [2019-12-25 15:57:27] calculate_delta
[CMD] [2019-12-25 15:57:27] echo "0a" > /app/public/diff/tasman_sea_sp_li_refs_19714.diff
[CMD] [2019-12-25 15:57:27] tail -n +1 /app/public/converted_csv/tasman_sea_sp_li_refs_19714.csv >> /app/public/diff/tasman_sea_sp_li_refs_19714.diff
[CMD] [2019-12-25 15:57:27] echo "." >> /app/public/diff/tasman_sea_sp_li_refs_19714.diff
[CMD] [2019-12-25 15:57:27] echo "0a" > /app/public/diff/tasman_sea_sp_li_nodes_19715.diff
[CMD] [2019-12-25 15:57:28] tail -n +1 /app/public/converted_csv/tasman_sea_sp_li_nodes_19715.csv >> /app/public/diff/tasman_sea_sp_li_nodes_19715.diff
[CMD] [2019-12-25 15:57:28] echo "." >> /app/public/diff/tasman_sea_sp_li_nodes_19715.diff
[CMD] [2019-12-25 15:57:28] echo "0a" > /app/public/diff/tasman_sea_sp_li_occurrences_19716.diff
[CMD] [2019-12-25 15:57:28] tail -n +1 /app/public/converted_csv/tasman_sea_sp_li_occurrences_19716.csv >> /app/public/diff/tasman_sea_sp_li_occurrences_19716.diff
[CMD] [2019-12-25 15:57:28] echo "." >> /app/public/diff/tasman_sea_sp_li_occurrences_19716.diff
[CMD] [2019-12-25 15:57:29] echo "0a" > /app/public/diff/tasman_sea_sp_li_measurements_19717.diff
[CMD] [2019-12-25 15:57:29] tail -n +1 /app/public/converted_csv/tasman_sea_sp_li_measurements_19717.csv >> /app/public/diff/tasman_sea_sp_li_measurements_19717.diff
[CMD] [2019-12-25 15:57:29] echo "." >> /app/public/diff/tasman_sea_sp_li_measurements_19717.diff
[STOP] [2019-12-25 15:57:29] calculate_delta
[START] [2019-12-25 15:57:29] parse_diff_and_store
[INFO] [2019-12-25 15:57:29] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 15:57:29] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 15:57:41] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 15:57:43] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 15:59:05] Storing 2 References
[INFO] [2019-12-25 15:59:05] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 15:59:05] Average Time: 0.0
[INFO] [2019-12-25 15:59:05] Total Time: 1s
[INFO] [2019-12-25 15:59:05] Storing 25473 ScientificNames
[INFO] [2019-12-25 15:59:05] Processing group of 25473 in 26 groups of 1000
[INFO] [2019-12-25 15:59:16] Average Time: 0.407
[INFO] [2019-12-25 15:59:16] Total Time: 11s
[INFO] [2019-12-25 15:59:16] last 3 / first 3: 0.83
[INFO] [2019-12-25 15:59:16] Std.Dev: 0.13784048752090222; Max: 0.87
[INFO] [2019-12-25 15:59:16] Storing 25473 Nodes
[INFO] [2019-12-25 15:59:16] Processing group of 25473 in 26 groups of 1000
[INFO] [2019-12-25 15:59:24] Average Time: 0.31
[INFO] [2019-12-25 15:59:24] Total Time: 9s
[INFO] [2019-12-25 15:59:24] last 3 / first 3: 0.92
[INFO] [2019-12-25 15:59:24] Std.Dev: 0.044721359549995794; Max: 0.39
[INFO] [2019-12-25 15:59:24] Storing 15902 Occurrences
[INFO] [2019-12-25 15:59:24] Processing group of 15902 in 16 groups of 1000
[INFO] [2019-12-25 15:59:26] Average Time: 0.111
[INFO] [2019-12-25 15:59:26] Total Time: 2s
[INFO] [2019-12-25 15:59:26] last 3 / first 3: 0.94
[INFO] [2019-12-25 15:59:26] Std.Dev: 0.0; Max: 0.13
[INFO] [2019-12-25 15:59:26] Storing 31804 TraitsReferences
[INFO] [2019-12-25 15:59:26] Processing group of 31804 in 32 groups of 1000
[INFO] [2019-12-25 15:59:29] Average Time: 0.08
[INFO] [2019-12-25 15:59:29] Total Time: 3s
[INFO] [2019-12-25 15:59:29] last 3 / first 3: 0.68
[INFO] [2019-12-25 15:59:29] Std.Dev: 0.0; Max: 0.16
[INFO] [2019-12-25 15:59:29] Storing 31804 Traits
[INFO] [2019-12-25 15:59:29] Processing group of 31804 in 32 groups of 1000
[INFO] [2019-12-25 15:59:41] Average Time: 0.395
[INFO] [2019-12-25 15:59:41] Total Time: 13s
[INFO] [2019-12-25 15:59:41] last 3 / first 3: 0.75
[INFO] [2019-12-25 15:59:41] Std.Dev: 0.161245154965971; Max: 1.2
[INFO] [2019-12-25 15:59:41] Storing 31755 MetaTraits
[INFO] [2019-12-25 15:59:41] Processing group of 31755 in 32 groups of 1000
[INFO] [2019-12-25 15:59:48] Average Time: 0.2
[INFO] [2019-12-25 15:59:48] Total Time: 7s
[INFO] [2019-12-25 15:59:48] last 3 / first 3: 0.88
[INFO] [2019-12-25 15:59:48] Std.Dev: 0.18708286933869708; Max: 1.2
[STOP] [2019-12-25 15:59:48] parse_diff_and_store
[START] [2019-12-25 15:59:48] resolve_keys
[INFO] [2019-12-25 16:01:08] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 16:01:14] traits to occurrences...
[INFO] [2019-12-25 16:01:22] traits to nodes (through occurrences)...
[INFO] [2019-12-25 16:01:22] Traits to sex term...
[INFO] [2019-12-25 16:01:29] Traits to lifestage term...
[INFO] [2019-12-25 16:01:36] MetaTraits to traits...
[INFO] [2019-12-25 16:01:38] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 16:01:43] Assocs to occurrences...
[INFO] [2019-12-25 16:01:43] Assocs to nodes...
[INFO] [2019-12-25 16:01:43] Assoc to sex term...
[INFO] [2019-12-25 16:01:43] Assoc to lifestage term...
[STOP] [2019-12-25 16:01:43] resolve_keys
[START] [2019-12-25 16:01:43] hold_for_later_1
[STOP] [2019-12-25 16:01:43] hold_for_later_1
[START] [2019-12-25 16:01:43] hold_for_later_2
[STOP] [2019-12-25 16:01:43] hold_for_later_2
[START] [2019-12-25 16:01:43] resolve_missing_parents
[STOP] [2019-12-25 16:02:32] resolve_missing_parents
[START] [2019-12-25 16:02:32] rebuild_nodes
[START] [2019-12-25 16:02:32] Flattener#flatten
[START] [2019-12-25 16:02:32] Flattener#study_resource
[START] [2019-12-25 16:02:32] Flattener#build_ancestry
[STOP] [2019-12-25 16:02:34] Flattener#build_ancestry
[INFO] [2019-12-25 16:02:34] 25473 ancestry keys
[START] [2019-12-25 16:02:34] build_node_ancestors
[INFO] [2019-12-25 16:02:34] old ancestors deleted.
[STOP] [2019-12-25 16:02:54] build_node_ancestors
[START] [2019-12-25 16:02:57] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 16:03:01] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 16:03:01] Flattener#flatten
[STOP] [2019-12-25 16:03:01] rebuild_nodes
[START] [2019-12-25 16:03:01] resolve_missing_media_owners
[STOP] [2019-12-25 16:03:01] resolve_missing_media_owners
[START] [2019-12-25 16:03:01] sanitize_media_verbatims
[STOP] [2019-12-25 16:03:01] sanitize_media_verbatims
[START] [2019-12-25 16:03:01] queue_downloads
[STOP] [2019-12-25 16:03:01] queue_downloads
[START] [2019-12-25 16:03:01] parse_names
[WARN] [2019-12-25 16:03:01] I see 25473 names which still need to be parsed.
[STOP] [2019-12-25 16:03:22] parse_names
[START] [2019-12-25 16:03:22] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 16:03:22] denormalize_canonical_names_to_nodes
[START] [2019-12-25 16:03:22] match_nodes
[START] [2019-12-25 16:03:22] map_all_nodes_to_pages
[STOP] [2019-12-25 17:46:05] map_all_nodes_to_pages
[INFO] [2019-12-25 17:46:05] 1397 Unmatched nodes (of 25473)! That's too many to output. First 10: Scorpaeniformes (#62508732); Hoplichthys mimaseanus (#62530683); Seriola gigas (#62531594); Chrysophrys auratus (#62509379); Fowleria auritus (#62533827); Heteropriacanthus boops (#62518947); Nomeus albula (#62526856); Zenionidae (#62509036); Coloconger giganteus (#62530832); Bathylaconidae (#62523158)
[START] [2019-12-25 17:46:05] update_nodes
[STOP] [2019-12-25 17:46:15] update_nodes
[STOP] [2019-12-25 17:46:15] match_nodes
[START] [2019-12-25 17:46:15] reindex_search
[STOP] [2019-12-25 17:47:38] reindex_search
[START] [2019-12-25 17:47:38] normalize_units
[STOP] [2019-12-25 17:47:38] normalize_units
[START] [2019-12-25 17:47:38] calculate_statistics
[STOP] [2019-12-25 17:47:38] calculate_statistics
[START] [2019-12-25 17:47:38] complete_harvest_instance
[START] [2019-12-25 17:47:38] overall_tsv_creation
[INFO] [2019-12-25 17:47:38] Processing group of 25473 in 3 batches of 10000
[INFO] [2019-12-25 17:49:12] 5252 Traits (unfiltered)...
[INFO] [2019-12-25 17:49:25] 5252 Traits (filtered)...
[INFO] [2019-12-25 17:49:25] 0 Associations (filtered)...
[INFO] [2019-12-25 17:50:15] 26237 metadata added.
[INFO] [2019-12-25 17:50:15] 0 metadata added.
[INFO] [2019-12-25 17:51:57] 6655 Traits (unfiltered)...
[INFO] [2019-12-25 17:52:11] 6655 Traits (filtered)...
[INFO] [2019-12-25 17:52:11] 0 Associations (filtered)...
[INFO] [2019-12-25 17:53:06] 33253 metadata added.
[INFO] [2019-12-25 17:53:06] 0 metadata added.
[INFO] [2019-12-25 17:54:23] 3995 Traits (unfiltered)...
[INFO] [2019-12-25 17:54:37] 3995 Traits (filtered)...
[INFO] [2019-12-25 17:54:37] 0 Associations (filtered)...
[INFO] [2019-12-25 17:55:22] 19971 metadata added.
[INFO] [2019-12-25 17:55:22] 0 metadata added.
[INFO] [2019-12-25 17:55:22] Average Time: 126.097
[INFO] [2019-12-25 17:55:22] Total Time: 7m45s
[STOP] [2019-12-25 17:55:22] overall_tsv_creation
[INFO] [2019-12-25 17:55:22] Done. Check your files:
[INFO] [2019-12-25 17:55:23] (25473 lines) /app/public/data/tasman_sea_sp_li/publish_nodes.tsv
[INFO] [2019-12-25 17:55:23] (135597 lines) /app/public/data/tasman_sea_sp_li/publish_node_ancestors.tsv
[INFO] [2019-12-25 17:55:23] (25473 lines) /app/public/data/tasman_sea_sp_li/publish_scientific_names.tsv
[INFO] [2019-12-25 17:55:23] (15903 lines) /app/public/data/tasman_sea_sp_li/publish_traits.tsv
[INFO] [2019-12-25 17:55:23] (79462 lines) /app/public/data/tasman_sea_sp_li/publish_metadata.tsv
[STOP] [2019-12-25 17:55:23] complete_harvest_instance
[START] [2019-12-25 17:55:23] completed
[STOP] [2019-12-25 17:55:23] completed
[STOP] [2019-12-25 17:55:23] logged process, took 7081.38

Latest Process

25 Dec 15:57 EXITED currently processing 0