Harvest for Namibia Species List Created 14 Oct 11:09

Stage: completed
Fetched: 14 Oct 11:09
Validated: 14 Oct 11:09
Deltas Created 14 Oct 11:09
Units Normalized: 14 Oct 11:26
Ancestry Built: 14 Oct 11:12
Nodes Matched: 14 Oct 11:25
Names Parsed: 14 Oct 11:12
New Models Stored: 14 Oct 11:10
Indexed: 14 Oct 11:26
Completed: 14 Oct 11:30
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-14 11:09:19 -0400 by logger.rb/56815
[START] [2019-10-14 11:09:19] logged process
[START] [2019-10-14 11:09:19] create_harvest_instance
[STOP] [2019-10-14 11:09:20] create_harvest_instance
[START] [2019-10-14 11:09:20] fetch_files
[STOP] [2019-10-14 11:09:20] fetch_files
[START] [2019-10-14 11:09:20] validate_each_file
[STOP] [2019-10-14 11:09:21] validate_each_file
[START] [2019-10-14 11:09:21] convert_to_csv
[CMD] [2019-10-14 11:09:21] /usr/bin/sort /app/public/converted_csv/namibia_sp_list_refs_16667.csv > /app/public/converted_csv/namibia_sp_list_refs_16667.csv_sorted
[CMD] [2019-10-14 11:09:22] /usr/bin/sort /app/public/converted_csv/namibia_sp_list_nodes_16668.csv > /app/public/converted_csv/namibia_sp_list_nodes_16668.csv_sorted
[CMD] [2019-10-14 11:09:22] /usr/bin/sort /app/public/converted_csv/namibia_sp_list_occurrences_16669.csv > /app/public/converted_csv/namibia_sp_list_occurrences_16669.csv_sorted
[CMD] [2019-10-14 11:09:22] /usr/bin/sort /app/public/converted_csv/namibia_sp_list_measurements_16670.csv > /app/public/converted_csv/namibia_sp_list_measurements_16670.csv_sorted
[STOP] [2019-10-14 11:09:22] convert_to_csv
[START] [2019-10-14 11:09:22] calculate_delta
[CMD] [2019-10-14 11:09:22] echo "0a" > /app/public/diff/namibia_sp_list_refs_16667.diff
[CMD] [2019-10-14 11:09:22] tail -n +1 /app/public/converted_csv/namibia_sp_list_refs_16667.csv >> /app/public/diff/namibia_sp_list_refs_16667.diff
[CMD] [2019-10-14 11:09:22] echo "." >> /app/public/diff/namibia_sp_list_refs_16667.diff
[CMD] [2019-10-14 11:09:22] echo "0a" > /app/public/diff/namibia_sp_list_nodes_16668.diff
[CMD] [2019-10-14 11:09:22] tail -n +1 /app/public/converted_csv/namibia_sp_list_nodes_16668.csv >> /app/public/diff/namibia_sp_list_nodes_16668.diff
[CMD] [2019-10-14 11:09:22] echo "." >> /app/public/diff/namibia_sp_list_nodes_16668.diff
[CMD] [2019-10-14 11:09:22] echo "0a" > /app/public/diff/namibia_sp_list_occurrences_16669.diff
[CMD] [2019-10-14 11:09:22] tail -n +1 /app/public/converted_csv/namibia_sp_list_occurrences_16669.csv >> /app/public/diff/namibia_sp_list_occurrences_16669.diff
[CMD] [2019-10-14 11:09:23] echo "." >> /app/public/diff/namibia_sp_list_occurrences_16669.diff
[CMD] [2019-10-14 11:09:23] echo "0a" > /app/public/diff/namibia_sp_list_measurements_16670.diff
[CMD] [2019-10-14 11:09:23] tail -n +1 /app/public/converted_csv/namibia_sp_list_measurements_16670.csv >> /app/public/diff/namibia_sp_list_measurements_16670.diff
[CMD] [2019-10-14 11:09:23] echo "." >> /app/public/diff/namibia_sp_list_measurements_16670.diff
[STOP] [2019-10-14 11:09:23] calculate_delta
[START] [2019-10-14 11:09:23] parse_diff_and_store
[INFO] [2019-10-14 11:09:23] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 11:09:23] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 11:09:28] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 11:09:29] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 11:10:19] Storing 2 References
[INFO] [2019-10-14 11:10:19] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 11:10:19] Average Time: 0.0
[INFO] [2019-10-14 11:10:19] Total Time: 1s
[INFO] [2019-10-14 11:10:19] Storing 13084 ScientificNames
[INFO] [2019-10-14 11:10:19] Processing group of 13084 in 14 groups of 1000
[INFO] [2019-10-14 11:10:24] Average Time: 0.336
[INFO] [2019-10-14 11:10:24] Total Time: 5s
[INFO] [2019-10-14 11:10:24] last 3 / first 3: 0.61
[INFO] [2019-10-14 11:10:24] Std.Dev: 0.09486832980505137; Max: 0.45
[INFO] [2019-10-14 11:10:24] Storing 13084 Nodes
[INFO] [2019-10-14 11:10:24] Processing group of 13084 in 14 groups of 1000
[INFO] [2019-10-14 11:10:29] Average Time: 0.323
[INFO] [2019-10-14 11:10:29] Total Time: 5s
[INFO] [2019-10-14 11:10:29] last 3 / first 3: 0.71
[INFO] [2019-10-14 11:10:29] Std.Dev: 0.11401754250991379; Max: 0.54
[INFO] [2019-10-14 11:10:29] Storing 8676 Occurrences
[INFO] [2019-10-14 11:10:29] Processing group of 8676 in 9 groups of 1000
[INFO] [2019-10-14 11:10:30] Average Time: 0.104
[INFO] [2019-10-14 11:10:30] Total Time: 1s
[INFO] [2019-10-14 11:10:30] last 3 / first 3: 1.0
[INFO] [2019-10-14 11:10:30] Std.Dev: 0.0; Max: 0.14
[INFO] [2019-10-14 11:10:30] Storing 17530 TraitsReferences
[INFO] [2019-10-14 11:10:30] Processing group of 17530 in 18 groups of 1000
[INFO] [2019-10-14 11:10:31] Average Time: 0.073
[INFO] [2019-10-14 11:10:31] Total Time: 2s
[INFO] [2019-10-14 11:10:31] last 3 / first 3: 0.67
[INFO] [2019-10-14 11:10:31] Std.Dev: 0.0; Max: 0.13
[INFO] [2019-10-14 11:10:31] Storing 17529 Traits
[INFO] [2019-10-14 11:10:31] Processing group of 17529 in 18 groups of 1000
[INFO] [2019-10-14 11:10:37] Average Time: 0.324
[INFO] [2019-10-14 11:10:37] Total Time: 6s
[INFO] [2019-10-14 11:10:37] last 3 / first 3: 0.71
[INFO] [2019-10-14 11:10:37] Std.Dev: 0.1; Max: 0.62
[INFO] [2019-10-14 11:10:37] Storing 17521 MetaTraits
[INFO] [2019-10-14 11:10:37] Processing group of 17521 in 18 groups of 1000
[INFO] [2019-10-14 11:10:39] Average Time: 0.108
[INFO] [2019-10-14 11:10:39] Total Time: 3s
[INFO] [2019-10-14 11:10:39] last 3 / first 3: 0.78
[INFO] [2019-10-14 11:10:39] Std.Dev: 0.0; Max: 0.17
[STOP] [2019-10-14 11:10:39] parse_diff_and_store
[START] [2019-10-14 11:10:39] resolve_keys
[INFO] [2019-10-14 11:11:27] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 11:11:31] traits to occurrences...
[INFO] [2019-10-14 11:11:37] traits to nodes (through occurrences)...
[INFO] [2019-10-14 11:11:38] Traits to sex term...
[INFO] [2019-10-14 11:11:43] Traits to lifestage term...
[INFO] [2019-10-14 11:11:48] MetaTraits to traits...
[INFO] [2019-10-14 11:11:49] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 11:11:51] Assocs to occurrences...
[INFO] [2019-10-14 11:11:51] Assocs to nodes...
[INFO] [2019-10-14 11:11:51] Assoc to sex term...
[INFO] [2019-10-14 11:11:51] Assoc to lifestage term...
[STOP] [2019-10-14 11:11:51] resolve_keys
[START] [2019-10-14 11:11:51] hold_for_later_1
[STOP] [2019-10-14 11:11:51] hold_for_later_1
[START] [2019-10-14 11:11:51] hold_for_later_2
[STOP] [2019-10-14 11:11:51] hold_for_later_2
[START] [2019-10-14 11:11:51] resolve_missing_parents
[STOP] [2019-10-14 11:12:16] resolve_missing_parents
[START] [2019-10-14 11:12:16] rebuild_nodes
[START] [2019-10-14 11:12:16] Flattener#flatten
[START] [2019-10-14 11:12:16] Flattener#study_resource
[START] [2019-10-14 11:12:16] Flattener#build_ancestry
[STOP] [2019-10-14 11:12:17] Flattener#build_ancestry
[INFO] [2019-10-14 11:12:17] 13084 ancestry keys
[START] [2019-10-14 11:12:17] build_node_ancestors
[INFO] [2019-10-14 11:12:17] old ancestors deleted.
[STOP] [2019-10-14 11:12:19] build_node_ancestors
[START] [2019-10-14 11:12:21] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 11:12:22] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 11:12:22] Flattener#flatten
[STOP] [2019-10-14 11:12:22] rebuild_nodes
[START] [2019-10-14 11:12:22] resolve_missing_media_owners
[STOP] [2019-10-14 11:12:22] resolve_missing_media_owners
[START] [2019-10-14 11:12:22] sanitize_media_verbatims
[STOP] [2019-10-14 11:12:22] sanitize_media_verbatims
[START] [2019-10-14 11:12:22] queue_downloads
[STOP] [2019-10-14 11:12:22] queue_downloads
[START] [2019-10-14 11:12:22] parse_names
[WARN] [2019-10-14 11:12:22] I see 13084 names which still need to be parsed.
[STOP] [2019-10-14 11:12:33] parse_names
[START] [2019-10-14 11:12:33] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 11:12:33] denormalize_canonical_names_to_nodes
[START] [2019-10-14 11:12:33] match_nodes
[START] [2019-10-14 11:12:33] map_all_nodes_to_pages
[STOP] [2019-10-14 11:25:30] map_all_nodes_to_pages
[INFO] [2019-10-14 11:25:30] 728 Unmatched nodes (of 13084)! That's too many to output. First 10: Ortygospiza fuscocrissa (#50851442); Arizelocichla tephrolaemus (#50851590); Andropadus tephrolaemus (#50851742); Andropadus masukuensis (#50860184); Hirundo fuligula (#50848370); Hirundo cucullata (#50849441); Hirundo abyssinica (#50851694); Hirundo semirufa (#50852147); Hirundo rupestris (#50856765); Delichon urbica (#50854946)
[START] [2019-10-14 11:25:30] update_nodes
[STOP] [2019-10-14 11:25:35] update_nodes
[STOP] [2019-10-14 11:25:35] match_nodes
[START] [2019-10-14 11:25:35] reindex_search
[STOP] [2019-10-14 11:26:13] reindex_search
[START] [2019-10-14 11:26:13] normalize_units
[STOP] [2019-10-14 11:26:13] normalize_units
[START] [2019-10-14 11:26:13] calculate_statistics
[STOP] [2019-10-14 11:26:13] calculate_statistics
[START] [2019-10-14 11:26:13] complete_harvest_instance
[START] [2019-10-14 11:26:13] overall_tsv_creation
[INFO] [2019-10-14 11:26:13] Processing group of 13084 in 2 batches of 10000
[INFO] [2019-10-14 11:27:40] 6568 Traits (unfiltered)...
[INFO] [2019-10-14 11:27:54] 6568 Traits (filtered)...
[INFO] [2019-10-14 11:27:54] 0 Associations (filtered)...
[INFO] [2019-10-14 11:28:44] 32836 metadata added.
[INFO] [2019-10-14 11:28:44] 0 metadata added.
[INFO] [2019-10-14 11:29:42] 2108 Traits (unfiltered)...
[INFO] [2019-10-14 11:29:56] 2108 Traits (filtered)...
[INFO] [2019-10-14 11:29:56] 0 Associations (filtered)...
[INFO] [2019-10-14 11:30:38] 10535 metadata added.
[INFO] [2019-10-14 11:30:38] 0 metadata added.
[INFO] [2019-10-14 11:30:38] Average Time: 108.225
[INFO] [2019-10-14 11:30:38] Total Time: 4m25s
[STOP] [2019-10-14 11:30:38] overall_tsv_creation
[INFO] [2019-10-14 11:30:38] Done. Check your files:
[INFO] [2019-10-14 11:30:38] (13084 lines) /app/public/data/namibia_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 11:30:38] (32451 lines) /app/public/data/namibia_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 11:30:38] (13084 lines) /app/public/data/namibia_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 11:30:39] (8677 lines) /app/public/data/namibia_sp_list/publish_traits.tsv
[INFO] [2019-10-14 11:30:39] (43372 lines) /app/public/data/namibia_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 11:30:39] complete_harvest_instance
[START] [2019-10-14 11:30:39] completed
[STOP] [2019-10-14 11:30:39] completed
[STOP] [2019-10-14 11:30:39] logged process, took 1279.62
Latest Process

14 Oct 11:09 EXITED currently processing 0