Stage:
completed
Fetched:
23 Dec 10:51
Validated:
23 Dec 10:51
Deltas Created
23 Dec 10:51
Units Normalized:
23 Dec 18:01
Ancestry Built:
23 Dec 11:12
Nodes Matched:
23 Dec 17:55
Names Parsed:
23 Dec 11:13
New Models Stored:
23 Dec 11:04
Indexed:
23 Dec 18:01
Completed:
23 Dec 18:30
Time to Harvest:
8 minutes
Harvesting Log
(198 lines)
# Logfile created on 2019-12-23 10:51:25 -0500 by logger.rb/56815
[START] [2019-12-23 10:51:25] logged process
[START] [2019-12-23 10:51:25] create_harvest_instance
[STOP] [2019-12-23 10:51:26] create_harvest_instance
[START] [2019-12-23 10:51:26] fetch_files
[STOP] [2019-12-23 10:51:26] fetch_files
[START] [2019-12-23 10:51:26] validate_each_file
[STOP] [2019-12-23 10:51:40] validate_each_file
[START] [2019-12-23 10:51:40] convert_to_csv
[CMD] [2019-12-23 10:51:40] /usr/bin/sort /app/public/converted_csv/Indian_Ocean_Spe_refs_19386.csv > /app/public/converted_csv/Indian_Ocean_Spe_refs_19386.csv_sorted
[CMD] [2019-12-23 10:51:40] /usr/bin/sort /app/public/converted_csv/Indian_Ocean_Spe_nodes_19387.csv > /app/public/converted_csv/Indian_Ocean_Spe_nodes_19387.csv_sorted
[CMD] [2019-12-23 10:51:40] /usr/bin/sort /app/public/converted_csv/Indian_Ocean_Spe_occurrences_19388.csv > /app/public/converted_csv/Indian_Ocean_Spe_occurrences_19388.csv_sorted
[CMD] [2019-12-23 10:51:40] /usr/bin/sort /app/public/converted_csv/Indian_Ocean_Spe_measurements_19389.csv > /app/public/converted_csv/Indian_Ocean_Spe_measurements_19389.csv_sorted
[STOP] [2019-12-23 10:51:41] convert_to_csv
[START] [2019-12-23 10:51:41] calculate_delta
[CMD] [2019-12-23 10:51:41] echo "0a" > /app/public/diff/Indian_Ocean_Spe_refs_19386.diff
[CMD] [2019-12-23 10:51:41] tail -n +1 /app/public/converted_csv/Indian_Ocean_Spe_refs_19386.csv >> /app/public/diff/Indian_Ocean_Spe_refs_19386.diff
[CMD] [2019-12-23 10:51:41] echo "." >> /app/public/diff/Indian_Ocean_Spe_refs_19386.diff
[CMD] [2019-12-23 10:51:41] echo "0a" > /app/public/diff/Indian_Ocean_Spe_nodes_19387.diff
[CMD] [2019-12-23 10:51:41] tail -n +1 /app/public/converted_csv/Indian_Ocean_Spe_nodes_19387.csv >> /app/public/diff/Indian_Ocean_Spe_nodes_19387.diff
[CMD] [2019-12-23 10:51:41] echo "." >> /app/public/diff/Indian_Ocean_Spe_nodes_19387.diff
[CMD] [2019-12-23 10:51:41] echo "0a" > /app/public/diff/Indian_Ocean_Spe_occurrences_19388.diff
[CMD] [2019-12-23 10:51:41] tail -n +1 /app/public/converted_csv/Indian_Ocean_Spe_occurrences_19388.csv >> /app/public/diff/Indian_Ocean_Spe_occurrences_19388.diff
[CMD] [2019-12-23 10:51:41] echo "." >> /app/public/diff/Indian_Ocean_Spe_occurrences_19388.diff
[CMD] [2019-12-23 10:51:41] echo "0a" > /app/public/diff/Indian_Ocean_Spe_measurements_19389.diff
[CMD] [2019-12-23 10:51:41] tail -n +1 /app/public/converted_csv/Indian_Ocean_Spe_measurements_19389.csv >> /app/public/diff/Indian_Ocean_Spe_measurements_19389.diff
[CMD] [2019-12-23 10:51:41] echo "." >> /app/public/diff/Indian_Ocean_Spe_measurements_19389.diff
[STOP] [2019-12-23 10:51:42] calculate_delta
[START] [2019-12-23 10:51:42] parse_diff_and_store
[INFO] [2019-12-23 10:51:42] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 10:51:42] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 10:52:21] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 10:52:32] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 10:59:54] Storing 2 References
[INFO] [2019-12-23 10:59:54] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 10:59:54] Average Time: 0.0
[INFO] [2019-12-23 10:59:54] Total Time: 1s
[INFO] [2019-12-23 10:59:54] Storing 96922 ScientificNames
[INFO] [2019-12-23 10:59:54] Processing group of 96922 in 97 groups of 1000
[INFO] [2019-12-23 11:00:55] Average Time: 0.618
[INFO] [2019-12-23 11:00:55] Total Time: 1m1s
[INFO] [2019-12-23 11:00:55] last 3 / first 3: 3.39
[INFO] [2019-12-23 11:00:55] Std.Dev: 0.7529940238806679; Max: 4.44
[INFO] [2019-12-23 11:00:55] Storing 96922 Nodes
[INFO] [2019-12-23 11:00:55] Processing group of 96922 in 97 groups of 1000
[INFO] [2019-12-23 11:01:38] Average Time: 0.448
[INFO] [2019-12-23 11:01:38] Total Time: 44s
[INFO] [2019-12-23 11:01:38] last 3 / first 3: 1.66
[INFO] [2019-12-23 11:01:38] Std.Dev: 0.5049752469181039; Max: 4.46
[INFO] [2019-12-23 11:01:38] Storing 72118 Occurrences
[INFO] [2019-12-23 11:01:38] Processing group of 72118 in 73 groups of 1000
[INFO] [2019-12-23 11:01:57] Average Time: 0.252
[INFO] [2019-12-23 11:01:57] Total Time: 19s
[INFO] [2019-12-23 11:01:57] last 3 / first 3: 1.21
[INFO] [2019-12-23 11:01:57] Std.Dev: 0.5941380311005179; Max: 4.42
[INFO] [2019-12-23 11:01:57] Storing 144236 TraitsReferences
[INFO] [2019-12-23 11:01:57] Processing group of 144236 in 145 groups of 1000
[INFO] [2019-12-23 11:02:12] Average Time: 0.099
[INFO] [2019-12-23 11:02:12] Total Time: 16s
[INFO] [2019-12-23 11:02:12] last 3 / first 3: 0.53
[INFO] [2019-12-23 11:02:12] Std.Dev: 0.19748417658131498; Max: 2.42
[INFO] [2019-12-23 11:02:12] Storing 144236 Traits
[INFO] [2019-12-23 11:02:12] Processing group of 144236 in 145 groups of 1000
[INFO] [2019-12-23 11:03:38] Average Time: 0.589
[INFO] [2019-12-23 11:03:38] Total Time: 1m26s
[INFO] [2019-12-23 11:03:38] last 3 / first 3: 0.82
[INFO] [2019-12-23 11:03:38] Std.Dev: 0.9570788891204319; Max: 4.99
[INFO] [2019-12-23 11:03:38] Storing 144118 MetaTraits
[INFO] [2019-12-23 11:03:38] Processing group of 144118 in 145 groups of 1000
[INFO] [2019-12-23 11:04:15] Average Time: 0.252
[INFO] [2019-12-23 11:04:15] Total Time: 37s
[INFO] [2019-12-23 11:04:15] last 3 / first 3: 0.63
[INFO] [2019-12-23 11:04:15] Std.Dev: 0.68044103344816; Max: 5.01
[STOP] [2019-12-23 11:04:15] parse_diff_and_store
[START] [2019-12-23 11:04:15] resolve_keys
[INFO] [2019-12-23 11:07:06] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 11:07:16] traits to occurrences...
[INFO] [2019-12-23 11:07:26] traits to nodes (through occurrences)...
[INFO] [2019-12-23 11:07:28] Traits to sex term...
[INFO] [2019-12-23 11:07:35] Traits to lifestage term...
[INFO] [2019-12-23 11:07:43] MetaTraits to traits...
[INFO] [2019-12-23 11:07:52] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 11:08:11] Assocs to occurrences...
[INFO] [2019-12-23 11:08:11] Assocs to nodes...
[INFO] [2019-12-23 11:08:11] Assoc to sex term...
[INFO] [2019-12-23 11:08:11] Assoc to lifestage term...
[STOP] [2019-12-23 11:08:11] resolve_keys
[START] [2019-12-23 11:08:11] hold_for_later_1
[STOP] [2019-12-23 11:08:11] hold_for_later_1
[START] [2019-12-23 11:08:12] hold_for_later_2
[STOP] [2019-12-23 11:08:12] hold_for_later_2
[START] [2019-12-23 11:08:12] resolve_missing_parents
[STOP] [2019-12-23 11:10:01] resolve_missing_parents
[START] [2019-12-23 11:10:01] rebuild_nodes
[START] [2019-12-23 11:10:01] Flattener#flatten
[START] [2019-12-23 11:10:01] Flattener#study_resource
[START] [2019-12-23 11:10:01] Flattener#build_ancestry
[STOP] [2019-12-23 11:10:26] Flattener#build_ancestry
[INFO] [2019-12-23 11:10:26] 96922 ancestry keys
[START] [2019-12-23 11:10:26] build_node_ancestors
[INFO] [2019-12-23 11:10:26] old ancestors deleted.
[STOP] [2019-12-23 11:11:41] build_node_ancestors
[START] [2019-12-23 11:11:44] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 11:12:08] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 11:12:08] Flattener#flatten
[STOP] [2019-12-23 11:12:08] rebuild_nodes
[START] [2019-12-23 11:12:08] resolve_missing_media_owners
[STOP] [2019-12-23 11:12:08] resolve_missing_media_owners
[START] [2019-12-23 11:12:08] sanitize_media_verbatims
[STOP] [2019-12-23 11:12:08] sanitize_media_verbatims
[START] [2019-12-23 11:12:08] queue_downloads
[STOP] [2019-12-23 11:12:08] queue_downloads
[START] [2019-12-23 11:12:08] parse_names
[WARN] [2019-12-23 11:12:08] I see 96922 names which still need to be parsed.
[STOP] [2019-12-23 11:13:21] parse_names
[START] [2019-12-23 11:13:21] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 11:13:22] denormalize_canonical_names_to_nodes
[START] [2019-12-23 11:13:22] match_nodes
[START] [2019-12-23 11:13:23] map_all_nodes_to_pages
[STOP] [2019-12-23 17:55:18] map_all_nodes_to_pages
[INFO] [2019-12-23 17:55:18] 6295 Unmatched nodes (of 96922)! That's too many to output. First 10: Johnius fuscolineata (#62036874); Johnius parva (#62045625); Pennahia argentatus (#62021187); Chrysoblephus pugicephalus (#62040879); Spondyliosoma microlepis (#62035804); Pagellus bellotti (#62066329); Dentex japonica (#62068170); Chrysophrys auratus (#61991655); Scomberoides sancti-petri (#62041839); Trachinotus umhlangae (#62038728)
[START] [2019-12-23 17:55:18] update_nodes
[STOP] [2019-12-23 17:55:58] update_nodes
[STOP] [2019-12-23 17:55:58] match_nodes
[START] [2019-12-23 17:55:58] reindex_search
[STOP] [2019-12-23 18:01:51] reindex_search
[START] [2019-12-23 18:01:51] normalize_units
[STOP] [2019-12-23 18:01:51] normalize_units
[START] [2019-12-23 18:01:51] calculate_statistics
[STOP] [2019-12-23 18:01:52] calculate_statistics
[START] [2019-12-23 18:01:52] complete_harvest_instance
[START] [2019-12-23 18:01:52] overall_tsv_creation
[INFO] [2019-12-23 18:01:52] Processing group of 96922 in 10 batches of 10000
[INFO] [2019-12-23 18:03:27] 5704 Traits (unfiltered)...
[INFO] [2019-12-23 18:03:40] 5704 Traits (filtered)...
[INFO] [2019-12-23 18:03:40] 0 Associations (filtered)...
[INFO] [2019-12-23 18:04:31] 28509 metadata added.
[INFO] [2019-12-23 18:04:31] 0 metadata added.
[INFO] [2019-12-23 18:06:08] 6700 Traits (unfiltered)...
[INFO] [2019-12-23 18:06:23] 6700 Traits (filtered)...
[INFO] [2019-12-23 18:06:23] 0 Associations (filtered)...
[INFO] [2019-12-23 18:07:19] 33495 metadata added.
[INFO] [2019-12-23 18:07:19] 0 metadata added.
[INFO] [2019-12-23 18:08:58] 7224 Traits (unfiltered)...
[INFO] [2019-12-23 18:09:11] 7224 Traits (filtered)...
[INFO] [2019-12-23 18:09:11] 0 Associations (filtered)...
[INFO] [2019-12-23 18:10:08] 36108 metadata added.
[INFO] [2019-12-23 18:10:08] 0 metadata added.
[INFO] [2019-12-23 18:11:45] 7482 Traits (unfiltered)...
[INFO] [2019-12-23 18:11:59] 7482 Traits (filtered)...
[INFO] [2019-12-23 18:11:59] 0 Associations (filtered)...
[INFO] [2019-12-23 18:13:03] 37401 metadata added.
[INFO] [2019-12-23 18:13:03] 0 metadata added.
[INFO] [2019-12-23 18:14:49] 7672 Traits (unfiltered)...
[INFO] [2019-12-23 18:15:03] 7672 Traits (filtered)...
[INFO] [2019-12-23 18:15:03] 0 Associations (filtered)...
[INFO] [2019-12-23 18:16:01] 38348 metadata added.
[INFO] [2019-12-23 18:16:01] 0 metadata added.
[INFO] [2019-12-23 18:17:42] 7755 Traits (unfiltered)...
[INFO] [2019-12-23 18:17:56] 7755 Traits (filtered)...
[INFO] [2019-12-23 18:17:56] 0 Associations (filtered)...
[INFO] [2019-12-23 18:18:54] 38760 metadata added.
[INFO] [2019-12-23 18:18:54] 0 metadata added.
[INFO] [2019-12-23 18:20:35] 7767 Traits (unfiltered)...
[INFO] [2019-12-23 18:20:48] 7767 Traits (filtered)...
[INFO] [2019-12-23 18:20:48] 0 Associations (filtered)...
[INFO] [2019-12-23 18:21:47] 38825 metadata added.
[INFO] [2019-12-23 18:21:47] 0 metadata added.
[INFO] [2019-12-23 18:23:30] 7945 Traits (unfiltered)...
[INFO] [2019-12-23 18:23:43] 7945 Traits (filtered)...
[INFO] [2019-12-23 18:23:43] 0 Associations (filtered)...
[INFO] [2019-12-23 18:24:42] 39709 metadata added.
[INFO] [2019-12-23 18:24:42] 0 metadata added.
[INFO] [2019-12-23 18:26:25] 8190 Traits (unfiltered)...
[INFO] [2019-12-23 18:26:39] 8190 Traits (filtered)...
[INFO] [2019-12-23 18:26:39] 0 Associations (filtered)...
[INFO] [2019-12-23 18:27:42] 40932 metadata added.
[INFO] [2019-12-23 18:27:42] 0 metadata added.
[INFO] [2019-12-23 18:29:17] 5679 Traits (unfiltered)...
[INFO] [2019-12-23 18:29:31] 5679 Traits (filtered)...
[INFO] [2019-12-23 18:29:31] 0 Associations (filtered)...
[INFO] [2019-12-23 18:30:25] 28385 metadata added.
[INFO] [2019-12-23 18:30:25] 0 metadata added.
[INFO] [2019-12-23 18:30:25] Average Time: 138.801
[INFO] [2019-12-23 18:30:25] Total Time: 28m34s
[INFO] [2019-12-23 18:30:25] last 3 / first 3: 1.01
[INFO] [2019-12-23 18:30:25] Std.Dev: 7.04719802474714; Max: 145.43
[STOP] [2019-12-23 18:30:25] overall_tsv_creation
[INFO] [2019-12-23 18:30:25] Done. Check your files:
[INFO] [2019-12-23 18:30:26] (96922 lines) /app/public/data/Indian_Ocean_Spe/publish_nodes.tsv
[INFO] [2019-12-23 18:30:26] (544339 lines) /app/public/data/Indian_Ocean_Spe/publish_node_ancestors.tsv
[INFO] [2019-12-23 18:30:26] (96922 lines) /app/public/data/Indian_Ocean_Spe/publish_scientific_names.tsv
[INFO] [2019-12-23 18:30:26] (72119 lines) /app/public/data/Indian_Ocean_Spe/publish_traits.tsv
[INFO] [2019-12-23 18:30:26] (360473 lines) /app/public/data/Indian_Ocean_Spe/publish_metadata.tsv
[STOP] [2019-12-23 18:30:26] complete_harvest_instance
[START] [2019-12-23 18:30:26] completed
[STOP] [2019-12-23 18:30:26] completed
[STOP] [2019-12-23 18:30:26] logged process, took 27541.09
Latest Process