Harvest for Mexico Species List Created 10 Dec 13:17

Stage: completed
Fetched: 10 Dec 13:17
Validated: 10 Dec 13:18
Deltas Created 10 Dec 13:18
Units Normalized: 10 Dec 16:55
Ancestry Built: 10 Dec 13:41
Nodes Matched: 10 Dec 16:51
Names Parsed: 10 Dec 13:42
New Models Stored: 10 Dec 13:32
Indexed: 10 Dec 16:55
Completed: 10 Dec 17:25
Time to Harvest: 4 minutes

Harvesting Log

(203 lines)
# Logfile created on 2019-12-10 13:17:56 -0500 by logger.rb/56815
[START] [2019-12-10 13:17:56] logged process
[START] [2019-12-10 13:17:56] create_harvest_instance
[STOP] [2019-12-10 13:17:56] create_harvest_instance
[START] [2019-12-10 13:17:56] fetch_files
[STOP] [2019-12-10 13:17:56] fetch_files
[START] [2019-12-10 13:17:56] validate_each_file
[STOP] [2019-12-10 13:18:10] validate_each_file
[START] [2019-12-10 13:18:10] convert_to_csv
[CMD] [2019-12-10 13:18:10] /usr/bin/sort /app/public/converted_csv/mexico_sp_list_refs_18902.csv > /app/public/converted_csv/mexico_sp_list_refs_18902.csv_sorted
[CMD] [2019-12-10 13:18:12] /usr/bin/sort /app/public/converted_csv/mexico_sp_list_nodes_18903.csv > /app/public/converted_csv/mexico_sp_list_nodes_18903.csv_sorted
[CMD] [2019-12-10 13:18:13] /usr/bin/sort /app/public/converted_csv/mexico_sp_list_occurrences_18904.csv > /app/public/converted_csv/mexico_sp_list_occurrences_18904.csv_sorted
[CMD] [2019-12-10 13:18:15] /usr/bin/sort /app/public/converted_csv/mexico_sp_list_measurements_18905.csv > /app/public/converted_csv/mexico_sp_list_measurements_18905.csv_sorted
[STOP] [2019-12-10 13:18:17] convert_to_csv
[START] [2019-12-10 13:18:17] calculate_delta
[CMD] [2019-12-10 13:18:17] echo "0a" > /app/public/diff/mexico_sp_list_refs_18902.diff
[CMD] [2019-12-10 13:18:19] tail -n +1 /app/public/converted_csv/mexico_sp_list_refs_18902.csv >> /app/public/diff/mexico_sp_list_refs_18902.diff
[CMD] [2019-12-10 13:18:21] echo "." >> /app/public/diff/mexico_sp_list_refs_18902.diff
[CMD] [2019-12-10 13:18:22] echo "0a" > /app/public/diff/mexico_sp_list_nodes_18903.diff
[CMD] [2019-12-10 13:18:24] tail -n +1 /app/public/converted_csv/mexico_sp_list_nodes_18903.csv >> /app/public/diff/mexico_sp_list_nodes_18903.diff
[CMD] [2019-12-10 13:18:25] echo "." >> /app/public/diff/mexico_sp_list_nodes_18903.diff
[CMD] [2019-12-10 13:18:27] echo "0a" > /app/public/diff/mexico_sp_list_occurrences_18904.diff
[CMD] [2019-12-10 13:18:29] tail -n +1 /app/public/converted_csv/mexico_sp_list_occurrences_18904.csv >> /app/public/diff/mexico_sp_list_occurrences_18904.diff
[CMD] [2019-12-10 13:18:31] echo "." >> /app/public/diff/mexico_sp_list_occurrences_18904.diff
[CMD] [2019-12-10 13:18:33] echo "0a" > /app/public/diff/mexico_sp_list_measurements_18905.diff
[CMD] [2019-12-10 13:18:34] tail -n +1 /app/public/converted_csv/mexico_sp_list_measurements_18905.csv >> /app/public/diff/mexico_sp_list_measurements_18905.diff
[CMD] [2019-12-10 13:18:36] echo "." >> /app/public/diff/mexico_sp_list_measurements_18905.diff
[STOP] [2019-12-10 13:18:38] calculate_delta
[START] [2019-12-10 13:18:38] parse_diff_and_store
[INFO] [2019-12-10 13:18:40] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-10 13:18:41] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-10 13:19:23] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-10 13:19:36] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-10 13:27:57] Storing 2 References
[INFO] [2019-12-10 13:27:57] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-10 13:27:57] Average Time: 0.0
[INFO] [2019-12-10 13:27:57] Total Time: 1s
[INFO] [2019-12-10 13:27:57] Storing 103206 ScientificNames
[INFO] [2019-12-10 13:27:57] Processing group of 103206 in 104 groups of 1000
[INFO] [2019-12-10 13:28:56] Average Time: 0.555
[INFO] [2019-12-10 13:28:56] Total Time: 59s
[INFO] [2019-12-10 13:28:56] last 3 / first 3: 0.9
[INFO] [2019-12-10 13:28:56] Std.Dev: 0.6442049363362563; Max: 4.05
[INFO] [2019-12-10 13:28:56] Storing 103206 Nodes
[INFO] [2019-12-10 13:28:56] Processing group of 103206 in 104 groups of 1000
[INFO] [2019-12-10 13:29:44] Average Time: 0.457
[INFO] [2019-12-10 13:29:44] Total Time: 49s
[INFO] [2019-12-10 13:29:44] last 3 / first 3: 4.15
[INFO] [2019-12-10 13:29:44] Std.Dev: 0.5787918451395113; Max: 4.32
[INFO] [2019-12-10 13:29:44] Storing 80684 Occurrences
[INFO] [2019-12-10 13:29:44] Processing group of 80684 in 81 groups of 1000
[INFO] [2019-12-10 13:29:58] Average Time: 0.177
[INFO] [2019-12-10 13:29:58] Total Time: 15s
[INFO] [2019-12-10 13:29:58] last 3 / first 3: 1.45
[INFO] [2019-12-10 13:29:58] Std.Dev: 0.42544094772365293; Max: 3.95
[INFO] [2019-12-10 13:29:58] Storing 161368 TraitsReferences
[INFO] [2019-12-10 13:29:58] Processing group of 161368 in 162 groups of 1000
[INFO] [2019-12-10 13:30:14] Average Time: 0.094
[INFO] [2019-12-10 13:30:14] Total Time: 17s
[INFO] [2019-12-10 13:30:14] last 3 / first 3: 0.52
[INFO] [2019-12-10 13:30:14] Std.Dev: 0.19493588689617927; Max: 2.51
[INFO] [2019-12-10 13:30:14] Storing 161368 Traits
[INFO] [2019-12-10 13:30:14] Processing group of 161368 in 162 groups of 1000
[INFO] [2019-12-10 13:31:45] Average Time: 0.526
[INFO] [2019-12-10 13:31:45] Total Time: 1m31s
[INFO] [2019-12-10 13:31:45] last 3 / first 3: 0.8
[INFO] [2019-12-10 13:31:45] Std.Dev: 0.8191458966508958; Max: 4.95
[INFO] [2019-12-10 13:31:45] Storing 161156 MetaTraits
[INFO] [2019-12-10 13:31:45] Processing group of 161156 in 162 groups of 1000
[INFO] [2019-12-10 13:32:24] Average Time: 0.24
[INFO] [2019-12-10 13:32:24] Total Time: 40s
[INFO] [2019-12-10 13:32:24] last 3 / first 3: 0.52
[INFO] [2019-12-10 13:32:24] Std.Dev: 0.6496152707564686; Max: 5.0
[STOP] [2019-12-10 13:32:24] parse_diff_and_store
[START] [2019-12-10 13:32:24] resolve_keys
[INFO] [2019-12-10 13:35:35] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-10 13:35:44] traits to occurrences...
[INFO] [2019-12-10 13:35:56] traits to nodes (through occurrences)...
[INFO] [2019-12-10 13:35:58] Traits to sex term...
[INFO] [2019-12-10 13:36:05] Traits to lifestage term...
[INFO] [2019-12-10 13:36:14] MetaTraits to traits...
[INFO] [2019-12-10 13:36:24] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-10 13:36:46] Assocs to occurrences...
[INFO] [2019-12-10 13:36:46] Assocs to nodes...
[INFO] [2019-12-10 13:36:46] Assoc to sex term...
[INFO] [2019-12-10 13:36:46] Assoc to lifestage term...
[STOP] [2019-12-10 13:36:46] resolve_keys
[START] [2019-12-10 13:36:46] hold_for_later_1
[STOP] [2019-12-10 13:36:46] hold_for_later_1
[START] [2019-12-10 13:36:46] hold_for_later_2
[STOP] [2019-12-10 13:36:46] hold_for_later_2
[START] [2019-12-10 13:36:46] resolve_missing_parents
[STOP] [2019-12-10 13:38:56] resolve_missing_parents
[START] [2019-12-10 13:38:56] rebuild_nodes
[START] [2019-12-10 13:38:56] Flattener#flatten
[START] [2019-12-10 13:38:56] Flattener#study_resource
[START] [2019-12-10 13:38:57] Flattener#build_ancestry
[STOP] [2019-12-10 13:39:23] Flattener#build_ancestry
[INFO] [2019-12-10 13:39:23] 103206 ancestry keys
[START] [2019-12-10 13:39:23] build_node_ancestors
[INFO] [2019-12-10 13:39:23] old ancestors deleted.
[STOP] [2019-12-10 13:40:44] build_node_ancestors
[START] [2019-12-10 13:40:50] Flattener#propagate_ancestor_ids
[STOP] [2019-12-10 13:41:15] Flattener#propagate_ancestor_ids
[STOP] [2019-12-10 13:41:15] Flattener#flatten
[STOP] [2019-12-10 13:41:15] rebuild_nodes
[START] [2019-12-10 13:41:15] resolve_missing_media_owners
[STOP] [2019-12-10 13:41:15] resolve_missing_media_owners
[START] [2019-12-10 13:41:15] sanitize_media_verbatims
[STOP] [2019-12-10 13:41:15] sanitize_media_verbatims
[START] [2019-12-10 13:41:15] queue_downloads
[STOP] [2019-12-10 13:41:15] queue_downloads
[START] [2019-12-10 13:41:15] parse_names
[WARN] [2019-12-10 13:41:15] I see 103206 names which still need to be parsed.
[STOP] [2019-12-10 13:42:35] parse_names
[START] [2019-12-10 13:42:35] denormalize_canonical_names_to_nodes
[STOP] [2019-12-10 13:42:37] denormalize_canonical_names_to_nodes
[START] [2019-12-10 13:42:37] match_nodes
[START] [2019-12-10 13:42:37] map_all_nodes_to_pages
[STOP] [2019-12-10 16:51:47] map_all_nodes_to_pages
[INFO] [2019-12-10 16:51:47] 8759 Unmatched nodes (of 103206)! That's too many to output. First 10: Buteo nitida (#60190991); Buteo albicaudatus (#60193976); Buteo plagiata (#60279310); Harpyhaliaetus (#60221559); Asturina plagiata (#60282754); Molothrus oryzivora (#60202790); Contopus borealis (#60194285); Thryothorus pleurostictus (#60188401); Thryothorus sinaloa (#60189579); Thryothorus felix (#60189824)
[START] [2019-12-10 16:51:47] update_nodes
[STOP] [2019-12-10 16:51:48] update_nodes
[STOP] [2019-12-10 16:51:48] match_nodes
[START] [2019-12-10 16:51:48] reindex_search
[STOP] [2019-12-10 16:55:17] reindex_search
[START] [2019-12-10 16:55:17] normalize_units
[STOP] [2019-12-10 16:55:49] normalize_units
[START] [2019-12-10 16:55:49] calculate_statistics
[STOP] [2019-12-10 16:55:49] calculate_statistics
[START] [2019-12-10 16:55:49] complete_harvest_instance
[START] [2019-12-10 16:55:49] overall_tsv_creation
[INFO] [2019-12-10 16:55:50] Processing group of 103206 in 11 batches of 10000
[INFO] [2019-12-10 16:57:20] 6128 Traits (unfiltered)...
[INFO] [2019-12-10 16:57:34] 6128 Traits (filtered)...
[INFO] [2019-12-10 16:57:34] 0 Associations (filtered)...
[INFO] [2019-12-10 16:58:24] 30634 metadata added.
[INFO] [2019-12-10 16:58:24] 0 metadata added.
[INFO] [2019-12-10 16:59:58] 7365 Traits (unfiltered)...
[INFO] [2019-12-10 17:00:11] 7365 Traits (filtered)...
[INFO] [2019-12-10 17:00:11] 0 Associations (filtered)...
[INFO] [2019-12-10 17:01:06] 36818 metadata added.
[INFO] [2019-12-10 17:01:06] 0 metadata added.
[INFO] [2019-12-10 17:02:43] 7721 Traits (unfiltered)...
[INFO] [2019-12-10 17:02:57] 7721 Traits (filtered)...
[INFO] [2019-12-10 17:02:57] 0 Associations (filtered)...
[INFO] [2019-12-10 17:03:53] 38597 metadata added.
[INFO] [2019-12-10 17:03:53] 0 metadata added.
[INFO] [2019-12-10 17:05:30] 7865 Traits (unfiltered)...
[INFO] [2019-12-10 17:05:44] 7865 Traits (filtered)...
[INFO] [2019-12-10 17:05:44] 0 Associations (filtered)...
[INFO] [2019-12-10 17:06:42] 39312 metadata added.
[INFO] [2019-12-10 17:06:42] 0 metadata added.
[INFO] [2019-12-10 17:08:19] 8009 Traits (unfiltered)...
[INFO] [2019-12-10 17:08:32] 8009 Traits (filtered)...
[INFO] [2019-12-10 17:08:33] 0 Associations (filtered)...
[INFO] [2019-12-10 17:09:29] 40034 metadata added.
[INFO] [2019-12-10 17:09:29] 0 metadata added.
[INFO] [2019-12-10 17:11:09] 7929 Traits (unfiltered)...
[INFO] [2019-12-10 17:11:22] 7929 Traits (filtered)...
[INFO] [2019-12-10 17:11:22] 0 Associations (filtered)...
[INFO] [2019-12-10 17:12:19] 39623 metadata added.
[INFO] [2019-12-10 17:12:19] 0 metadata added.
[INFO] [2019-12-10 17:13:55] 7969 Traits (unfiltered)...
[INFO] [2019-12-10 17:14:08] 7969 Traits (filtered)...
[INFO] [2019-12-10 17:14:08] 0 Associations (filtered)...
[INFO] [2019-12-10 17:15:05] 39823 metadata added.
[INFO] [2019-12-10 17:15:05] 0 metadata added.
[INFO] [2019-12-10 17:16:43] 8140 Traits (unfiltered)...
[INFO] [2019-12-10 17:16:57] 8140 Traits (filtered)...
[INFO] [2019-12-10 17:16:57] 0 Associations (filtered)...
[INFO] [2019-12-10 17:17:54] 40675 metadata added.
[INFO] [2019-12-10 17:17:54] 0 metadata added.
[INFO] [2019-12-10 17:19:29] 8244 Traits (unfiltered)...
[INFO] [2019-12-10 17:19:43] 8244 Traits (filtered)...
[INFO] [2019-12-10 17:19:43] 0 Associations (filtered)...
[INFO] [2019-12-10 17:20:39] 41190 metadata added.
[INFO] [2019-12-10 17:20:39] 0 metadata added.
[INFO] [2019-12-10 17:22:15] 8553 Traits (unfiltered)...
[INFO] [2019-12-10 17:22:29] 8553 Traits (filtered)...
[INFO] [2019-12-10 17:22:29] 0 Associations (filtered)...
[INFO] [2019-12-10 17:23:27] 42715 metadata added.
[INFO] [2019-12-10 17:23:27] 0 metadata added.
[INFO] [2019-12-10 17:24:29] 2761 Traits (unfiltered)...
[INFO] [2019-12-10 17:24:43] 2761 Traits (filtered)...
[INFO] [2019-12-10 17:24:43] 0 Associations (filtered)...
[INFO] [2019-12-10 17:25:26] 13787 metadata added.
[INFO] [2019-12-10 17:25:26] 0 metadata added.
[INFO] [2019-12-10 17:25:26] Average Time: 131.852
[INFO] [2019-12-10 17:25:26] Total Time: 29m37s
[INFO] [2019-12-10 17:25:26] last 3 / first 3: 0.94
[INFO] [2019-12-10 17:25:26] Std.Dev: 12.616140455781236; Max: 139.21
[STOP] [2019-12-10 17:25:26] overall_tsv_creation
[INFO] [2019-12-10 17:25:26] Done. Check your files:
[INFO] [2019-12-10 17:25:28] (103206 lines) /app/public/data/mexico_sp_list/publish_nodes.tsv
[INFO] [2019-12-10 17:25:30] (583406 lines) /app/public/data/mexico_sp_list/publish_node_ancestors.tsv
[INFO] [2019-12-10 17:25:31] (103206 lines) /app/public/data/mexico_sp_list/publish_scientific_names.tsv
[INFO] [2019-12-10 17:25:33] (80685 lines) /app/public/data/mexico_sp_list/publish_traits.tsv
[INFO] [2019-12-10 17:25:35] (403209 lines) /app/public/data/mexico_sp_list/publish_metadata.tsv
[STOP] [2019-12-10 17:25:35] complete_harvest_instance
[START] [2019-12-10 17:25:35] completed
[STOP] [2019-12-10 17:25:35] completed
[STOP] [2019-12-10 17:25:35] logged process, took 14859.18

Latest Process