Harvest for Indonesia Species List Created 10 Dec 11:09

Harvesting Log

# Logfile created on 2019-12-10 11:09:14 -0500 by logger.rb/56815
[START] [2019-12-10 11:09:14] logged process
[START] [2019-12-10 11:09:14] create_harvest_instance
[STOP] [2019-12-10 11:09:14] create_harvest_instance
[START] [2019-12-10 11:09:14] fetch_files
[STOP] [2019-12-10 11:09:14] fetch_files
[START] [2019-12-10 11:09:14] validate_each_file
[STOP] [2019-12-10 11:09:30] validate_each_file
[START] [2019-12-10 11:09:30] convert_to_csv
[CMD] [2019-12-10 11:09:30] /usr/bin/sort /app/public/converted_csv/indonesia_sp_lis_refs_18894.csv > /app/public/converted_csv/indonesia_sp_lis_refs_18894.csv_sorted
[CMD] [2019-12-10 11:09:31] /usr/bin/sort /app/public/converted_csv/indonesia_sp_lis_nodes_18895.csv > /app/public/converted_csv/indonesia_sp_lis_nodes_18895.csv_sorted
[CMD] [2019-12-10 11:09:33] /usr/bin/sort /app/public/converted_csv/indonesia_sp_lis_occurrences_18896.csv > /app/public/converted_csv/indonesia_sp_lis_occurrences_18896.csv_sorted
[CMD] [2019-12-10 11:09:35] /usr/bin/sort /app/public/converted_csv/indonesia_sp_lis_measurements_18897.csv > /app/public/converted_csv/indonesia_sp_lis_measurements_18897.csv_sorted
[STOP] [2019-12-10 11:09:36] convert_to_csv
[START] [2019-12-10 11:09:36] calculate_delta
[CMD] [2019-12-10 11:09:36] echo "0a" > /app/public/diff/indonesia_sp_lis_refs_18894.diff
[CMD] [2019-12-10 11:09:38] tail -n +1 /app/public/converted_csv/indonesia_sp_lis_refs_18894.csv >> /app/public/diff/indonesia_sp_lis_refs_18894.diff
[CMD] [2019-12-10 11:09:40] echo "." >> /app/public/diff/indonesia_sp_lis_refs_18894.diff
[CMD] [2019-12-10 11:09:41] echo "0a" > /app/public/diff/indonesia_sp_lis_nodes_18895.diff
[CMD] [2019-12-10 11:09:43] tail -n +1 /app/public/converted_csv/indonesia_sp_lis_nodes_18895.csv >> /app/public/diff/indonesia_sp_lis_nodes_18895.diff
[CMD] [2019-12-10 11:09:45] echo "." >> /app/public/diff/indonesia_sp_lis_nodes_18895.diff
[CMD] [2019-12-10 11:09:46] echo "0a" > /app/public/diff/indonesia_sp_lis_occurrences_18896.diff
[CMD] [2019-12-10 11:09:48] tail -n +1 /app/public/converted_csv/indonesia_sp_lis_occurrences_18896.csv >> /app/public/diff/indonesia_sp_lis_occurrences_18896.diff
[CMD] [2019-12-10 11:09:50] echo "." >> /app/public/diff/indonesia_sp_lis_occurrences_18896.diff
[CMD] [2019-12-10 11:09:52] echo "0a" > /app/public/diff/indonesia_sp_lis_measurements_18897.diff
[CMD] [2019-12-10 11:09:53] tail -n +1 /app/public/converted_csv/indonesia_sp_lis_measurements_18897.csv >> /app/public/diff/indonesia_sp_lis_measurements_18897.diff
[CMD] [2019-12-10 11:09:55] echo "." >> /app/public/diff/indonesia_sp_lis_measurements_18897.diff
[STOP] [2019-12-10 11:09:57] calculate_delta
[START] [2019-12-10 11:09:57] parse_diff_and_store
[INFO] [2019-12-10 11:09:58] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-10 11:10:00] Loading nodes diff file into memory (true lines)...
[WARN] [2019-12-10 11:10:12] Filtered Scientific Name `Huechys  fusca` to `Huechys fusca`
[INFO] [2019-12-10 11:10:23] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-10 11:10:30] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-10 11:14:30] Storing 2 References
[INFO] [2019-12-10 11:14:30] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-10 11:14:30] Average Time: 0.0
[INFO] [2019-12-10 11:14:30] Total Time: 1s
[INFO] [2019-12-10 11:14:30] Storing 54832 ScientificNames
[INFO] [2019-12-10 11:14:30] Processing group of 54832 in 55 groups of 1000
[INFO] [2019-12-10 11:14:52] Average Time: 0.402
[INFO] [2019-12-10 11:14:52] Total Time: 23s
[INFO] [2019-12-10 11:14:52] last 3 / first 3: 0.95
[INFO] [2019-12-10 11:14:52] Std.Dev: 0.11832159566199232; Max: 0.93
[INFO] [2019-12-10 11:14:52] Storing 54832 Nodes
[INFO] [2019-12-10 11:14:52] Processing group of 54832 in 55 groups of 1000
[INFO] [2019-12-10 11:15:13] Average Time: 0.382
[INFO] [2019-12-10 11:15:13] Total Time: 22s
[INFO] [2019-12-10 11:15:13] last 3 / first 3: 1.0
[INFO] [2019-12-10 11:15:13] Std.Dev: 0.3209361307176242; Max: 2.25
[INFO] [2019-12-10 11:15:13] Storing 40731 Occurrences
[INFO] [2019-12-10 11:15:13] Processing group of 40731 in 41 groups of 1000
[INFO] [2019-12-10 11:15:18] Average Time: 0.108
[INFO] [2019-12-10 11:15:18] Total Time: 5s
[INFO] [2019-12-10 11:15:18] last 3 / first 3: 0.79
[INFO] [2019-12-10 11:15:18] Std.Dev: 0.0; Max: 0.19
[INFO] [2019-12-10 11:15:18] Storing 81462 TraitsReferences
[INFO] [2019-12-10 11:15:18] Processing group of 81462 in 82 groups of 1000
[INFO] [2019-12-10 11:15:25] Average Time: 0.078
[INFO] [2019-12-10 11:15:25] Total Time: 7s
[INFO] [2019-12-10 11:15:25] last 3 / first 3: 1.07
[INFO] [2019-12-10 11:15:25] Std.Dev: 0.03162277660168379; Max: 0.2
[INFO] [2019-12-10 11:15:25] Storing 81462 Traits
[INFO] [2019-12-10 11:15:25] Processing group of 81462 in 82 groups of 1000
[INFO] [2019-12-10 11:15:55] Average Time: 0.36
[INFO] [2019-12-10 11:15:55] Total Time: 30s
[INFO] [2019-12-10 11:15:55] last 3 / first 3: 0.3
[INFO] [2019-12-10 11:15:55] Std.Dev: 0.24289915602982237; Max: 1.99
[INFO] [2019-12-10 11:15:55] Storing 81399 MetaTraits
[INFO] [2019-12-10 11:15:55] Processing group of 81399 in 82 groups of 1000
[INFO] [2019-12-10 11:16:10] Average Time: 0.187
[INFO] [2019-12-10 11:16:10] Total Time: 16s
[INFO] [2019-12-10 11:16:10] last 3 / first 3: 0.76
[INFO] [2019-12-10 11:16:10] Std.Dev: 0.3872983346207417; Max: 2.68
[STOP] [2019-12-10 11:16:10] parse_diff_and_store
[START] [2019-12-10 11:16:10] resolve_keys
[INFO] [2019-12-10 11:18:34] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-10 11:18:42] traits to occurrences...
[INFO] [2019-12-10 11:18:50] traits to nodes (through occurrences)...
[INFO] [2019-12-10 11:18:51] Traits to sex term...
[INFO] [2019-12-10 11:18:57] Traits to lifestage term...
[INFO] [2019-12-10 11:19:04] MetaTraits to traits...
[INFO] [2019-12-10 11:19:09] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-10 11:19:20] Assocs to occurrences...
[INFO] [2019-12-10 11:19:20] Assocs to nodes...
[INFO] [2019-12-10 11:19:20] Assoc to sex term...
[INFO] [2019-12-10 11:19:20] Assoc to lifestage term...
[STOP] [2019-12-10 11:19:20] resolve_keys
[START] [2019-12-10 11:19:20] hold_for_later_1
[STOP] [2019-12-10 11:19:20] hold_for_later_1
[START] [2019-12-10 11:19:20] hold_for_later_2
[STOP] [2019-12-10 11:19:20] hold_for_later_2
[START] [2019-12-10 11:19:20] resolve_missing_parents
[STOP] [2019-12-10 11:20:42] resolve_missing_parents
[START] [2019-12-10 11:20:42] rebuild_nodes
[START] [2019-12-10 11:20:42] Flattener#flatten
[START] [2019-12-10 11:20:42] Flattener#study_resource
[START] [2019-12-10 11:20:42] Flattener#build_ancestry
[STOP] [2019-12-10 11:20:51] Flattener#build_ancestry
[INFO] [2019-12-10 11:20:51] 54832 ancestry keys
[START] [2019-12-10 11:20:51] build_node_ancestors
[INFO] [2019-12-10 11:20:51] old ancestors deleted.
[STOP] [2019-12-10 11:21:35] build_node_ancestors
[START] [2019-12-10 11:21:36] Flattener#propagate_ancestor_ids
[STOP] [2019-12-10 11:21:44] Flattener#propagate_ancestor_ids
[STOP] [2019-12-10 11:21:44] Flattener#flatten
[STOP] [2019-12-10 11:21:44] rebuild_nodes
[START] [2019-12-10 11:21:44] resolve_missing_media_owners
[STOP] [2019-12-10 11:21:44] resolve_missing_media_owners
[START] [2019-12-10 11:21:44] sanitize_media_verbatims
[STOP] [2019-12-10 11:21:44] sanitize_media_verbatims
[START] [2019-12-10 11:21:44] queue_downloads
[STOP] [2019-12-10 11:21:44] queue_downloads
[START] [2019-12-10 11:21:44] parse_names
[WARN] [2019-12-10 11:21:44] I see 54832 names which still need to be parsed.
[STOP] [2019-12-10 11:22:26] parse_names
[START] [2019-12-10 11:22:26] denormalize_canonical_names_to_nodes
[STOP] [2019-12-10 11:22:26] denormalize_canonical_names_to_nodes
[START] [2019-12-10 11:22:26] match_nodes
[START] [2019-12-10 11:22:27] map_all_nodes_to_pages
[STOP] [2019-12-10 12:56:29] map_all_nodes_to_pages
[INFO] [2019-12-10 12:56:29] 3516 Unmatched nodes (of 54832)! That's too many to output. First 10: Stenomys (#60135659); Mayermys (#60164872); Tadarida plicata (#60168160); Homo erectus (#60139868); Homo floresiensis (#60142136); Homo palaeojavanicus (#60144602); Homo modjokertensis (#60167075); Erinaceomorpha (#60134086); Hippopotamus antiquus (#60169038); Prionailurus viverrina (#60160356)
[START] [2019-12-10 12:56:29] update_nodes
[STOP] [2019-12-10 12:56:48] update_nodes
[STOP] [2019-12-10 12:56:48] match_nodes
[START] [2019-12-10 12:56:48] reindex_search
[STOP] [2019-12-10 12:58:40] reindex_search
[START] [2019-12-10 12:58:40] normalize_units
[STOP] [2019-12-10 12:58:40] normalize_units
[START] [2019-12-10 12:58:40] calculate_statistics
[STOP] [2019-12-10 12:58:41] calculate_statistics
[START] [2019-12-10 12:58:41] complete_harvest_instance
[START] [2019-12-10 12:58:41] overall_tsv_creation
[INFO] [2019-12-10 12:58:41] Processing group of 54832 in 6 batches of 10000
[INFO] [2019-12-10 13:00:23] 6181 Traits (unfiltered)...
[INFO] [2019-12-10 13:00:37] 6181 Traits (filtered)...
[INFO] [2019-12-10 13:00:37] 0 Associations (filtered)...
[INFO] [2019-12-10 13:01:28] 30901 metadata added.
[INFO] [2019-12-10 13:01:28] 0 metadata added.
[INFO] [2019-12-10 13:03:03] 7177 Traits (unfiltered)...
[INFO] [2019-12-10 13:03:17] 7177 Traits (filtered)...
[INFO] [2019-12-10 13:03:17] 0 Associations (filtered)...
[INFO] [2019-12-10 13:04:10] 35878 metadata added.
[INFO] [2019-12-10 13:04:10] 0 metadata added.
[INFO] [2019-12-10 13:05:51] 7524 Traits (unfiltered)...
[INFO] [2019-12-10 13:06:04] 7524 Traits (filtered)...
[INFO] [2019-12-10 13:06:04] 0 Associations (filtered)...
[INFO] [2019-12-10 13:07:00] 37611 metadata added.
[INFO] [2019-12-10 13:07:00] 0 metadata added.
[INFO] [2019-12-10 13:08:36] 7743 Traits (unfiltered)...
[INFO] [2019-12-10 13:08:50] 7743 Traits (filtered)...
[INFO] [2019-12-10 13:08:50] 0 Associations (filtered)...
[INFO] [2019-12-10 13:09:46] 38706 metadata added.
[INFO] [2019-12-10 13:09:46] 0 metadata added.
[INFO] [2019-12-10 13:11:22] 8081 Traits (unfiltered)...
[INFO] [2019-12-10 13:11:36] 8081 Traits (filtered)...
[INFO] [2019-12-10 13:11:36] 0 Associations (filtered)...
[INFO] [2019-12-10 13:12:32] 40383 metadata added.
[INFO] [2019-12-10 13:12:32] 0 metadata added.
[INFO] [2019-12-10 13:13:43] 4025 Traits (unfiltered)...
[INFO] [2019-12-10 13:13:56] 4025 Traits (filtered)...
[INFO] [2019-12-10 13:13:56] 0 Associations (filtered)...
[INFO] [2019-12-10 13:14:41] 20113 metadata added.
[INFO] [2019-12-10 13:14:41] 0 metadata added.
[INFO] [2019-12-10 13:14:41] Average Time: 128.518
[INFO] [2019-12-10 13:14:41] Total Time: 16m1s
[STOP] [2019-12-10 13:14:41] overall_tsv_creation
[INFO] [2019-12-10 13:14:41] Done. Check your files:
[INFO] [2019-12-10 13:14:43] (54832 lines) /app/public/data/indonesia_sp_lis/publish_nodes.tsv
[INFO] [2019-12-10 13:14:45] (307665 lines) /app/public/data/indonesia_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-12-10 13:14:46] (54832 lines) /app/public/data/indonesia_sp_lis/publish_scientific_names.tsv
[INFO] [2019-12-10 13:14:48] (40732 lines) /app/public/data/indonesia_sp_lis/publish_traits.tsv
[INFO] [2019-12-10 13:14:50] (203593 lines) /app/public/data/indonesia_sp_lis/publish_metadata.tsv
[STOP] [2019-12-10 13:14:50] complete_harvest_instance
[START] [2019-12-10 13:14:50] completed
[STOP] [2019-12-10 13:14:50] completed
[STOP] [2019-12-10 13:14:50] logged process, took 7536.1

Latest Process

10 Dec 11:09 EXITED currently processing 0