Harvest for South Korea Species List Created 16 Oct 01:42

Stage: completed
Fetched: 16 Oct 01:42
Validated: 16 Oct 01:42
Deltas Created 16 Oct 01:42
Units Normalized: 16 Oct 01:50
Ancestry Built: 16 Oct 01:43
Nodes Matched: 16 Oct 01:50
Names Parsed: 16 Oct 01:43
New Models Stored: 16 Oct 01:42
Indexed: 16 Oct 01:50
Completed: 16 Oct 01:52
Time to Harvest: less than a minute
Harvesting Log

(150 lines)
# Logfile created on 2019-10-16 01:42:02 -0400 by logger.rb/56815
[START] [2019-10-16 01:42:02] logged process
[START] [2019-10-16 01:42:02] create_harvest_instance
[STOP] [2019-10-16 01:42:03] create_harvest_instance
[START] [2019-10-16 01:42:03] fetch_files
[STOP] [2019-10-16 01:42:03] fetch_files
[START] [2019-10-16 01:42:03] validate_each_file
[STOP] [2019-10-16 01:42:04] validate_each_file
[START] [2019-10-16 01:42:04] convert_to_csv
[CMD] [2019-10-16 01:42:04] /usr/bin/sort /app/public/converted_csv/s_korea_sp_list_refs_17293.csv > /app/public/converted_csv/s_korea_sp_list_refs_17293.csv_sorted
[CMD] [2019-10-16 01:42:04] /usr/bin/sort /app/public/converted_csv/s_korea_sp_list_nodes_17294.csv > /app/public/converted_csv/s_korea_sp_list_nodes_17294.csv_sorted
[CMD] [2019-10-16 01:42:05] /usr/bin/sort /app/public/converted_csv/s_korea_sp_list_occurrences_17295.csv > /app/public/converted_csv/s_korea_sp_list_occurrences_17295.csv_sorted
[CMD] [2019-10-16 01:42:05] /usr/bin/sort /app/public/converted_csv/s_korea_sp_list_measurements_17296.csv > /app/public/converted_csv/s_korea_sp_list_measurements_17296.csv_sorted
[STOP] [2019-10-16 01:42:05] convert_to_csv
[START] [2019-10-16 01:42:05] calculate_delta
[CMD] [2019-10-16 01:42:05] echo "0a" > /app/public/diff/s_korea_sp_list_refs_17293.diff
[CMD] [2019-10-16 01:42:05] tail -n +1 /app/public/converted_csv/s_korea_sp_list_refs_17293.csv >> /app/public/diff/s_korea_sp_list_refs_17293.diff
[CMD] [2019-10-16 01:42:06] echo "." >> /app/public/diff/s_korea_sp_list_refs_17293.diff
[CMD] [2019-10-16 01:42:06] echo "0a" > /app/public/diff/s_korea_sp_list_nodes_17294.diff
[CMD] [2019-10-16 01:42:06] tail -n +1 /app/public/converted_csv/s_korea_sp_list_nodes_17294.csv >> /app/public/diff/s_korea_sp_list_nodes_17294.diff
[CMD] [2019-10-16 01:42:07] echo "." >> /app/public/diff/s_korea_sp_list_nodes_17294.diff
[CMD] [2019-10-16 01:42:07] echo "0a" > /app/public/diff/s_korea_sp_list_occurrences_17295.diff
[CMD] [2019-10-16 01:42:07] tail -n +1 /app/public/converted_csv/s_korea_sp_list_occurrences_17295.csv >> /app/public/diff/s_korea_sp_list_occurrences_17295.diff
[CMD] [2019-10-16 01:42:07] echo "." >> /app/public/diff/s_korea_sp_list_occurrences_17295.diff
[CMD] [2019-10-16 01:42:08] echo "0a" > /app/public/diff/s_korea_sp_list_measurements_17296.diff
[CMD] [2019-10-16 01:42:08] tail -n +1 /app/public/converted_csv/s_korea_sp_list_measurements_17296.csv >> /app/public/diff/s_korea_sp_list_measurements_17296.diff
[CMD] [2019-10-16 01:42:08] echo "." >> /app/public/diff/s_korea_sp_list_measurements_17296.diff
[STOP] [2019-10-16 01:42:09] calculate_delta
[START] [2019-10-16 01:42:09] parse_diff_and_store
[INFO] [2019-10-16 01:42:09] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 01:42:09] Loading nodes diff file into memory (true lines)...
[WARN] [2019-10-16 01:42:10] Filtered Scientific Name `Orosanga  japonicus` to `Orosanga japonicus`
[INFO] [2019-10-16 01:42:12] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 01:42:13] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 01:42:34] Storing 2 References
[INFO] [2019-10-16 01:42:34] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 01:42:34] Average Time: 0.0
[INFO] [2019-10-16 01:42:34] Total Time: 1s
[INFO] [2019-10-16 01:42:34] Storing 6924 ScientificNames
[INFO] [2019-10-16 01:42:34] Processing group of 6924 in 7 groups of 1000
[INFO] [2019-10-16 01:42:37] Average Time: 0.373
[INFO] [2019-10-16 01:42:37] Total Time: 3s
[INFO] [2019-10-16 01:42:37] last 3 / first 3: 0.85
[INFO] [2019-10-16 01:42:37] Std.Dev: 0.03162277660168379; Max: 0.42
[INFO] [2019-10-16 01:42:37] Storing 6924 Nodes
[INFO] [2019-10-16 01:42:37] Processing group of 6924 in 7 groups of 1000
[INFO] [2019-10-16 01:42:40] Average Time: 0.37
[INFO] [2019-10-16 01:42:40] Total Time: 3s
[INFO] [2019-10-16 01:42:40] last 3 / first 3: 0.76
[INFO] [2019-10-16 01:42:40] Std.Dev: 0.10488088481701516; Max: 0.6
[INFO] [2019-10-16 01:42:40] Storing 3374 Occurrences
[INFO] [2019-10-16 01:42:40] Processing group of 3374 in 4 groups of 1000
[INFO] [2019-10-16 01:42:40] Average Time: 0.095
[INFO] [2019-10-16 01:42:40] Total Time: 1s
[INFO] [2019-10-16 01:42:40] Storing 7460 TraitsReferences
[INFO] [2019-10-16 01:42:40] Processing group of 7460 in 8 groups of 1000
[INFO] [2019-10-16 01:42:41] Average Time: 0.084
[INFO] [2019-10-16 01:42:41] Total Time: 1s
[INFO] [2019-10-16 01:42:41] last 3 / first 3: 0.71
[INFO] [2019-10-16 01:42:41] Std.Dev: 0.03162277660168379; Max: 0.16
[INFO] [2019-10-16 01:42:41] Storing 7459 Traits
[INFO] [2019-10-16 01:42:41] Processing group of 7459 in 8 groups of 1000
[INFO] [2019-10-16 01:42:43] Average Time: 0.304
[INFO] [2019-10-16 01:42:43] Total Time: 3s
[INFO] [2019-10-16 01:42:43] last 3 / first 3: 0.74
[INFO] [2019-10-16 01:42:43] Std.Dev: 0.08366600265340755; Max: 0.45
[INFO] [2019-10-16 01:42:43] Storing 7450 MetaTraits
[INFO] [2019-10-16 01:42:43] Processing group of 7450 in 8 groups of 1000
[INFO] [2019-10-16 01:42:44] Average Time: 0.11
[INFO] [2019-10-16 01:42:44] Total Time: 1s
[INFO] [2019-10-16 01:42:44] last 3 / first 3: 0.74
[INFO] [2019-10-16 01:42:44] Std.Dev: 0.03162277660168379; Max: 0.15
[STOP] [2019-10-16 01:42:44] parse_diff_and_store
[START] [2019-10-16 01:42:44] resolve_keys
[INFO] [2019-10-16 01:43:13] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 01:43:15] traits to occurrences...
[INFO] [2019-10-16 01:43:18] traits to nodes (through occurrences)...
[INFO] [2019-10-16 01:43:19] Traits to sex term...
[INFO] [2019-10-16 01:43:21] Traits to lifestage term...
[INFO] [2019-10-16 01:43:24] MetaTraits to traits...
[INFO] [2019-10-16 01:43:25] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 01:43:26] Assocs to occurrences...
[INFO] [2019-10-16 01:43:26] Assocs to nodes...
[INFO] [2019-10-16 01:43:26] Assoc to sex term...
[INFO] [2019-10-16 01:43:26] Assoc to lifestage term...
[STOP] [2019-10-16 01:43:26] resolve_keys
[START] [2019-10-16 01:43:26] hold_for_later_1
[STOP] [2019-10-16 01:43:26] hold_for_later_1
[START] [2019-10-16 01:43:26] hold_for_later_2
[STOP] [2019-10-16 01:43:26] hold_for_later_2
[START] [2019-10-16 01:43:26] resolve_missing_parents
[STOP] [2019-10-16 01:43:39] resolve_missing_parents
[START] [2019-10-16 01:43:39] rebuild_nodes
[START] [2019-10-16 01:43:39] Flattener#flatten
[START] [2019-10-16 01:43:39] Flattener#study_resource
[START] [2019-10-16 01:43:39] Flattener#build_ancestry
[STOP] [2019-10-16 01:43:39] Flattener#build_ancestry
[INFO] [2019-10-16 01:43:39] 6924 ancestry keys
[START] [2019-10-16 01:43:39] build_node_ancestors
[INFO] [2019-10-16 01:43:39] old ancestors deleted.
[STOP] [2019-10-16 01:43:41] build_node_ancestors
[START] [2019-10-16 01:43:42] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 01:43:42] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 01:43:42] Flattener#flatten
[STOP] [2019-10-16 01:43:42] rebuild_nodes
[START] [2019-10-16 01:43:42] resolve_missing_media_owners
[STOP] [2019-10-16 01:43:42] resolve_missing_media_owners
[START] [2019-10-16 01:43:42] sanitize_media_verbatims
[STOP] [2019-10-16 01:43:42] sanitize_media_verbatims
[START] [2019-10-16 01:43:42] queue_downloads
[STOP] [2019-10-16 01:43:42] queue_downloads
[START] [2019-10-16 01:43:42] parse_names
[WARN] [2019-10-16 01:43:42] I see 6924 names which still need to be parsed.
[STOP] [2019-10-16 01:43:48] parse_names
[START] [2019-10-16 01:43:48] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 01:43:48] denormalize_canonical_names_to_nodes
[START] [2019-10-16 01:43:48] match_nodes
[START] [2019-10-16 01:43:48] map_all_nodes_to_pages
[STOP] [2019-10-16 01:50:07] map_all_nodes_to_pages
[INFO] [2019-10-16 01:50:07] 496 Unmatched nodes (of 6924)! That's too many to output. First 10: Anas clypeata (#52033970); Anas strepera (#52033982); Anas formosa (#52034059); Anas falcata (#52034065); Anas penelope (#52034113); Anas querquedula (#52034501); Chen (#52034620); Chen caerulescens (#52034619); Pseudomonas syringae (#52033929); Passer rutilans (#52035804)
[START] [2019-10-16 01:50:07] update_nodes
[STOP] [2019-10-16 01:50:09] update_nodes
[STOP] [2019-10-16 01:50:09] match_nodes
[START] [2019-10-16 01:50:09] reindex_search
[STOP] [2019-10-16 01:50:24] reindex_search
[START] [2019-10-16 01:50:24] normalize_units
[STOP] [2019-10-16 01:50:25] normalize_units
[START] [2019-10-16 01:50:25] calculate_statistics
[STOP] [2019-10-16 01:50:25] calculate_statistics
[START] [2019-10-16 01:50:25] complete_harvest_instance
[START] [2019-10-16 01:50:25] overall_tsv_creation
[INFO] [2019-10-16 01:50:25] Processing group of 6924 in 1 batches of 10000
[INFO] [2019-10-16 01:51:39] 3374 Traits (unfiltered)...
[INFO] [2019-10-16 01:51:53] 3374 Traits (filtered)...
[INFO] [2019-10-16 01:51:53] 0 Associations (filtered)...
[INFO] [2019-10-16 01:52:38] 16861 metadata added.
[INFO] [2019-10-16 01:52:38] 0 metadata added.
[INFO] [2019-10-16 01:52:39] Average Time: 108.33
[INFO] [2019-10-16 01:52:39] Total Time: 2m14s
[STOP] [2019-10-16 01:52:39] overall_tsv_creation
[INFO] [2019-10-16 01:52:39] Done. Check your files:
[INFO] [2019-10-16 01:52:39] (6924 lines) /app/public/data/s_korea_sp_list/publish_nodes.tsv
[INFO] [2019-10-16 01:52:39] (16026 lines) /app/public/data/s_korea_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-16 01:52:39] (6924 lines) /app/public/data/s_korea_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-16 01:52:40] (3375 lines) /app/public/data/s_korea_sp_list/publish_traits.tsv
[INFO] [2019-10-16 01:52:40] (16862 lines) /app/public/data/s_korea_sp_list/publish_metadata.tsv
[STOP] [2019-10-16 01:52:40] complete_harvest_instance
[START] [2019-10-16 01:52:40] completed
[STOP] [2019-10-16 01:52:40] completed
[STOP] [2019-10-16 01:52:40] logged process, took 637.98
Latest Process

16 Oct 01:42 EXITED currently processing 0