Harvest for South Africa Species List Created 15 Oct 20:40

Harvesting Log

# Logfile created on 2019-10-15 20:40:07 -0400 by logger.rb/56815
[START] [2019-10-15 20:40:07] logged process
[START] [2019-10-15 20:40:07] create_harvest_instance
[STOP] [2019-10-15 20:40:08] create_harvest_instance
[START] [2019-10-15 20:40:08] fetch_files
[STOP] [2019-10-15 20:40:08] fetch_files
[START] [2019-10-15 20:40:08] validate_each_file
[STOP] [2019-10-15 20:40:16] validate_each_file
[START] [2019-10-15 20:40:16] convert_to_csv
[CMD] [2019-10-15 20:40:16] /usr/bin/sort /app/public/converted_csv/s_africa_sp_list_refs_17261.csv > /app/public/converted_csv/s_africa_sp_list_refs_17261.csv_sorted
[CMD] [2019-10-15 20:40:16] /usr/bin/sort /app/public/converted_csv/s_africa_sp_list_nodes_17262.csv > /app/public/converted_csv/s_africa_sp_list_nodes_17262.csv_sorted
[CMD] [2019-10-15 20:40:17] /usr/bin/sort /app/public/converted_csv/s_africa_sp_list_occurrences_17263.csv > /app/public/converted_csv/s_africa_sp_list_occurrences_17263.csv_sorted
[CMD] [2019-10-15 20:40:17] /usr/bin/sort /app/public/converted_csv/s_africa_sp_list_measurements_17264.csv > /app/public/converted_csv/s_africa_sp_list_measurements_17264.csv_sorted
[STOP] [2019-10-15 20:40:17] convert_to_csv
[START] [2019-10-15 20:40:17] calculate_delta
[CMD] [2019-10-15 20:40:17] echo "0a" > /app/public/diff/s_africa_sp_list_refs_17261.diff
[CMD] [2019-10-15 20:40:18] tail -n +1 /app/public/converted_csv/s_africa_sp_list_refs_17261.csv >> /app/public/diff/s_africa_sp_list_refs_17261.diff
[CMD] [2019-10-15 20:40:18] echo "." >> /app/public/diff/s_africa_sp_list_refs_17261.diff
[CMD] [2019-10-15 20:40:18] echo "0a" > /app/public/diff/s_africa_sp_list_nodes_17262.diff
[CMD] [2019-10-15 20:40:18] tail -n +1 /app/public/converted_csv/s_africa_sp_list_nodes_17262.csv >> /app/public/diff/s_africa_sp_list_nodes_17262.diff
[CMD] [2019-10-15 20:40:19] echo "." >> /app/public/diff/s_africa_sp_list_nodes_17262.diff
[CMD] [2019-10-15 20:40:19] echo "0a" > /app/public/diff/s_africa_sp_list_occurrences_17263.diff
[CMD] [2019-10-15 20:40:19] tail -n +1 /app/public/converted_csv/s_africa_sp_list_occurrences_17263.csv >> /app/public/diff/s_africa_sp_list_occurrences_17263.diff
[CMD] [2019-10-15 20:40:20] echo "." >> /app/public/diff/s_africa_sp_list_occurrences_17263.diff
[CMD] [2019-10-15 20:40:20] echo "0a" > /app/public/diff/s_africa_sp_list_measurements_17264.diff
[CMD] [2019-10-15 20:40:20] tail -n +1 /app/public/converted_csv/s_africa_sp_list_measurements_17264.csv >> /app/public/diff/s_africa_sp_list_measurements_17264.diff
[CMD] [2019-10-15 20:40:20] echo "." >> /app/public/diff/s_africa_sp_list_measurements_17264.diff
[STOP] [2019-10-15 20:40:21] calculate_delta
[START] [2019-10-15 20:40:21] parse_diff_and_store
[INFO] [2019-10-15 20:40:21] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 20:40:21] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 20:40:46] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 20:40:54] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 20:45:57] Storing 2 References
[INFO] [2019-10-15 20:45:57] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 20:45:57] Average Time: 0.0
[INFO] [2019-10-15 20:45:57] Total Time: 1s
[INFO] [2019-10-15 20:45:57] Storing 65746 ScientificNames
[INFO] [2019-10-15 20:45:57] Processing group of 65746 in 66 groups of 1000
[INFO] [2019-10-15 20:46:28] Average Time: 0.477
[INFO] [2019-10-15 20:46:28] Total Time: 32s
[INFO] [2019-10-15 20:46:28] last 3 / first 3: 0.94
[INFO] [2019-10-15 20:46:28] Std.Dev: 0.3492849839314596; Max: 2.74
[INFO] [2019-10-15 20:46:28] Storing 65746 Nodes
[INFO] [2019-10-15 20:46:28] Processing group of 65746 in 66 groups of 1000
[INFO] [2019-10-15 20:46:56] Average Time: 0.406
[INFO] [2019-10-15 20:46:56] Total Time: 28s
[INFO] [2019-10-15 20:46:56] last 3 / first 3: 1.08
[INFO] [2019-10-15 20:46:56] Std.Dev: 0.403732584763727; Max: 3.02
[INFO] [2019-10-15 20:46:56] Storing 50128 Occurrences
[INFO] [2019-10-15 20:46:56] Processing group of 50128 in 51 groups of 1000
[INFO] [2019-10-15 20:47:01] Average Time: 0.108
[INFO] [2019-10-15 20:47:01] Total Time: 6s
[INFO] [2019-10-15 20:47:01] last 3 / first 3: 0.78
[INFO] [2019-10-15 20:47:01] Std.Dev: 0.03162277660168379; Max: 0.23
[INFO] [2019-10-15 20:47:01] Storing 101080 TraitsReferences
[INFO] [2019-10-15 20:47:01] Processing group of 101080 in 102 groups of 1000
[INFO] [2019-10-15 20:47:15] Average Time: 0.13
[INFO] [2019-10-15 20:47:15] Total Time: 14s
[INFO] [2019-10-15 20:47:15] last 3 / first 3: 0.54
[INFO] [2019-10-15 20:47:15] Std.Dev: 0.3535533905932738; Max: 3.01
[INFO] [2019-10-15 20:47:15] Storing 101079 Traits
[INFO] [2019-10-15 20:47:15] Processing group of 101079 in 102 groups of 1000
[INFO] [2019-10-15 20:47:53] Average Time: 0.374
[INFO] [2019-10-15 20:47:53] Total Time: 39s
[INFO] [2019-10-15 20:47:53] last 3 / first 3: 1.57
[INFO] [2019-10-15 20:47:53] Std.Dev: 0.382099463490856; Max: 3.46
[INFO] [2019-10-15 20:47:53] Storing 100974 MetaTraits
[INFO] [2019-10-15 20:47:53] Processing group of 100974 in 101 groups of 1000
[INFO] [2019-10-15 20:48:08] Average Time: 0.135
[INFO] [2019-10-15 20:48:08] Total Time: 15s
[INFO] [2019-10-15 20:48:08] last 3 / first 3: 0.43
[INFO] [2019-10-15 20:48:08] Std.Dev: 0.17029386365926402; Max: 1.78
[STOP] [2019-10-15 20:48:08] parse_diff_and_store
[START] [2019-10-15 20:48:08] resolve_keys
[INFO] [2019-10-15 20:50:37] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 20:50:46] traits to occurrences...
[INFO] [2019-10-15 20:50:54] traits to nodes (through occurrences)...
[INFO] [2019-10-15 20:50:55] Traits to sex term...
[INFO] [2019-10-15 20:51:02] Traits to lifestage term...
[INFO] [2019-10-15 20:51:10] MetaTraits to traits...
[INFO] [2019-10-15 20:51:16] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 20:51:30] Assocs to occurrences...
[INFO] [2019-10-15 20:51:30] Assocs to nodes...
[INFO] [2019-10-15 20:51:30] Assoc to sex term...
[INFO] [2019-10-15 20:51:30] Assoc to lifestage term...
[STOP] [2019-10-15 20:51:30] resolve_keys
[START] [2019-10-15 20:51:30] hold_for_later_1
[STOP] [2019-10-15 20:51:30] hold_for_later_1
[START] [2019-10-15 20:51:30] hold_for_later_2
[STOP] [2019-10-15 20:51:30] hold_for_later_2
[START] [2019-10-15 20:51:30] resolve_missing_parents
[STOP] [2019-10-15 20:52:52] resolve_missing_parents
[START] [2019-10-15 20:52:52] rebuild_nodes
[START] [2019-10-15 20:52:52] Flattener#flatten
[START] [2019-10-15 20:52:52] Flattener#study_resource
[START] [2019-10-15 20:52:52] Flattener#build_ancestry
[STOP] [2019-10-15 20:53:07] Flattener#build_ancestry
[INFO] [2019-10-15 20:53:07] 65746 ancestry keys
[START] [2019-10-15 20:53:07] build_node_ancestors
[INFO] [2019-10-15 20:53:07] old ancestors deleted.
[STOP] [2019-10-15 20:53:38] build_node_ancestors
[START] [2019-10-15 20:53:41] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 20:53:47] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 20:53:47] Flattener#flatten
[STOP] [2019-10-15 20:53:47] rebuild_nodes
[START] [2019-10-15 20:53:47] resolve_missing_media_owners
[STOP] [2019-10-15 20:53:47] resolve_missing_media_owners
[START] [2019-10-15 20:53:47] sanitize_media_verbatims
[STOP] [2019-10-15 20:53:47] sanitize_media_verbatims
[START] [2019-10-15 20:53:47] queue_downloads
[STOP] [2019-10-15 20:53:47] queue_downloads
[START] [2019-10-15 20:53:47] parse_names
[WARN] [2019-10-15 20:53:47] I see 65746 names which still need to be parsed.
[STOP] [2019-10-15 20:54:38] parse_names
[START] [2019-10-15 20:54:38] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 20:54:39] denormalize_canonical_names_to_nodes
[START] [2019-10-15 20:54:39] match_nodes
[START] [2019-10-15 20:54:39] map_all_nodes_to_pages
[STOP] [2019-10-15 21:59:20] map_all_nodes_to_pages
[INFO] [2019-10-15 21:59:20] 4227 Unmatched nodes (of 65746)! That's too many to output. First 10: Euplectes macrourus (#51904574); Hirundo cucullata (#51866325); Hirundo fuligula (#51866385); Hirundo abyssinica (#51866475); Hirundo semirufa (#51866723); Hirundo senegalensis (#51868370); Hirundo striolata (#51930435); Delichon urbica (#51889463); Urolestes melanoleuca (#51866666); Hemimacronyx (#51871128)
[START] [2019-10-15 21:59:20] update_nodes
[STOP] [2019-10-15 21:59:47] update_nodes
[STOP] [2019-10-15 21:59:47] match_nodes
[START] [2019-10-15 21:59:47] reindex_search
[STOP] [2019-10-15 22:02:44] reindex_search
[START] [2019-10-15 22:02:44] normalize_units
[STOP] [2019-10-15 22:02:44] normalize_units
[START] [2019-10-15 22:02:44] calculate_statistics
[STOP] [2019-10-15 22:02:44] calculate_statistics
[START] [2019-10-15 22:02:44] complete_harvest_instance
[START] [2019-10-15 22:02:44] overall_tsv_creation
[INFO] [2019-10-15 22:02:44] Processing group of 65746 in 7 batches of 10000
[INFO] [2019-10-15 22:04:11] 6639 Traits (unfiltered)...
[INFO] [2019-10-15 22:04:25] 6639 Traits (filtered)...
[INFO] [2019-10-15 22:04:25] 0 Associations (filtered)...
[INFO] [2019-10-15 22:05:16] 33188 metadata added.
[INFO] [2019-10-15 22:05:16] 0 metadata added.
[INFO] [2019-10-15 22:06:48] 7971 Traits (unfiltered)...
[INFO] [2019-10-15 22:07:01] 7971 Traits (filtered)...
[INFO] [2019-10-15 22:07:01] 0 Associations (filtered)...
[INFO] [2019-10-15 22:07:55] 39851 metadata added.
[INFO] [2019-10-15 22:07:55] 0 metadata added.
[INFO] [2019-10-15 22:09:31] 7934 Traits (unfiltered)...
[INFO] [2019-10-15 22:09:46] 7934 Traits (filtered)...
[INFO] [2019-10-15 22:09:46] 0 Associations (filtered)...
[INFO] [2019-10-15 22:10:41] 39665 metadata added.
[INFO] [2019-10-15 22:10:41] 0 metadata added.
[INFO] [2019-10-15 22:12:15] 7805 Traits (unfiltered)...
[INFO] [2019-10-15 22:12:28] 7805 Traits (filtered)...
[INFO] [2019-10-15 22:12:29] 0 Associations (filtered)...
[INFO] [2019-10-15 22:13:25] 39011 metadata added.
[INFO] [2019-10-15 22:13:25] 0 metadata added.
[INFO] [2019-10-15 22:14:58] 7740 Traits (unfiltered)...
[INFO] [2019-10-15 22:15:12] 7740 Traits (filtered)...
[INFO] [2019-10-15 22:15:12] 0 Associations (filtered)...
[INFO] [2019-10-15 22:16:07] 38681 metadata added.
[INFO] [2019-10-15 22:16:07] 0 metadata added.
[INFO] [2019-10-15 22:17:40] 7797 Traits (unfiltered)...
[INFO] [2019-10-15 22:17:53] 7797 Traits (filtered)...
[INFO] [2019-10-15 22:17:54] 0 Associations (filtered)...
[INFO] [2019-10-15 22:18:49] 38956 metadata added.
[INFO] [2019-10-15 22:18:49] 0 metadata added.
[INFO] [2019-10-15 22:20:02] 4242 Traits (unfiltered)...
[INFO] [2019-10-15 22:20:16] 4242 Traits (filtered)...
[INFO] [2019-10-15 22:20:16] 0 Associations (filtered)...
[INFO] [2019-10-15 22:21:01] 21185 metadata added.
[INFO] [2019-10-15 22:21:01] 0 metadata added.
[INFO] [2019-10-15 22:21:01] Average Time: 130.493
[INFO] [2019-10-15 22:21:01] Total Time: 18m18s
[INFO] [2019-10-15 22:21:01] last 3 / first 3: 0.96
[INFO] [2019-10-15 22:21:01] Std.Dev: 10.627981934497255; Max: 137.64
[STOP] [2019-10-15 22:21:01] overall_tsv_creation
[INFO] [2019-10-15 22:21:01] Done. Check your files:
[INFO] [2019-10-15 22:21:01] (65746 lines) /app/public/data/s_africa_sp_list/publish_nodes.tsv
[INFO] [2019-10-15 22:21:02] (232493 lines) /app/public/data/s_africa_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-15 22:21:02] (65746 lines) /app/public/data/s_africa_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-15 22:21:02] (50129 lines) /app/public/data/s_africa_sp_list/publish_traits.tsv
[INFO] [2019-10-15 22:21:02] (250538 lines) /app/public/data/s_africa_sp_list/publish_metadata.tsv
[STOP] [2019-10-15 22:21:03] complete_harvest_instance
[START] [2019-10-15 22:21:03] completed
[STOP] [2019-10-15 22:21:03] completed
[STOP] [2019-10-15 22:21:03] logged process, took 6055.48

Latest Process

15 Oct 20:40 EXITED currently processing 0