Harvest for Kenya Species List Created 14 Oct 00:08

Stage: completed
Fetched: 14 Oct 00:08
Validated: 14 Oct 00:08
Deltas Created 14 Oct 00:08
Units Normalized: 14 Oct 00:29
Ancestry Built: 14 Oct 00:12
Nodes Matched: 14 Oct 00:28
Names Parsed: 14 Oct 00:12
New Models Stored: 14 Oct 00:09
Indexed: 14 Oct 00:29
Completed: 14 Oct 00:34
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-14 00:08:13 -0400 by logger.rb/56815
[START] [2019-10-14 00:08:13] logged process
[START] [2019-10-14 00:08:13] create_harvest_instance
[STOP] [2019-10-14 00:08:13] create_harvest_instance
[START] [2019-10-14 00:08:13] fetch_files
[STOP] [2019-10-14 00:08:13] fetch_files
[START] [2019-10-14 00:08:13] validate_each_file
[STOP] [2019-10-14 00:08:15] validate_each_file
[START] [2019-10-14 00:08:15] convert_to_csv
[CMD] [2019-10-14 00:08:15] /usr/bin/sort /app/public/converted_csv/kenya_sp_list_refs_16299.csv > /app/public/converted_csv/kenya_sp_list_refs_16299.csv_sorted
[CMD] [2019-10-14 00:08:15] /usr/bin/sort /app/public/converted_csv/kenya_sp_list_nodes_16300.csv > /app/public/converted_csv/kenya_sp_list_nodes_16300.csv_sorted
[CMD] [2019-10-14 00:08:16] /usr/bin/sort /app/public/converted_csv/kenya_sp_list_occurrences_16301.csv > /app/public/converted_csv/kenya_sp_list_occurrences_16301.csv_sorted
[CMD] [2019-10-14 00:08:16] /usr/bin/sort /app/public/converted_csv/kenya_sp_list_measurements_16302.csv > /app/public/converted_csv/kenya_sp_list_measurements_16302.csv_sorted
[STOP] [2019-10-14 00:08:16] convert_to_csv
[START] [2019-10-14 00:08:16] calculate_delta
[CMD] [2019-10-14 00:08:16] echo "0a" > /app/public/diff/kenya_sp_list_refs_16299.diff
[CMD] [2019-10-14 00:08:16] tail -n +1 /app/public/converted_csv/kenya_sp_list_refs_16299.csv >> /app/public/diff/kenya_sp_list_refs_16299.diff
[CMD] [2019-10-14 00:08:16] echo "." >> /app/public/diff/kenya_sp_list_refs_16299.diff
[CMD] [2019-10-14 00:08:16] echo "0a" > /app/public/diff/kenya_sp_list_nodes_16300.diff
[CMD] [2019-10-14 00:08:16] tail -n +1 /app/public/converted_csv/kenya_sp_list_nodes_16300.csv >> /app/public/diff/kenya_sp_list_nodes_16300.diff
[CMD] [2019-10-14 00:08:16] echo "." >> /app/public/diff/kenya_sp_list_nodes_16300.diff
[CMD] [2019-10-14 00:08:16] echo "0a" > /app/public/diff/kenya_sp_list_occurrences_16301.diff
[CMD] [2019-10-14 00:08:16] tail -n +1 /app/public/converted_csv/kenya_sp_list_occurrences_16301.csv >> /app/public/diff/kenya_sp_list_occurrences_16301.diff
[CMD] [2019-10-14 00:08:16] echo "." >> /app/public/diff/kenya_sp_list_occurrences_16301.diff
[CMD] [2019-10-14 00:08:17] echo "0a" > /app/public/diff/kenya_sp_list_measurements_16302.diff
[CMD] [2019-10-14 00:08:17] tail -n +1 /app/public/converted_csv/kenya_sp_list_measurements_16302.csv >> /app/public/diff/kenya_sp_list_measurements_16302.diff
[CMD] [2019-10-14 00:08:17] echo "." >> /app/public/diff/kenya_sp_list_measurements_16302.diff
[STOP] [2019-10-14 00:08:17] calculate_delta
[START] [2019-10-14 00:08:17] parse_diff_and_store
[INFO] [2019-10-14 00:08:17] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 00:08:17] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 00:08:23] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 00:08:25] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 00:09:33] Storing 2 References
[INFO] [2019-10-14 00:09:33] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 00:09:33] Average Time: 0.0
[INFO] [2019-10-14 00:09:33] Total Time: 1s
[INFO] [2019-10-14 00:09:33] Storing 16906 ScientificNames
[INFO] [2019-10-14 00:09:33] Processing group of 16906 in 17 groups of 1000
[INFO] [2019-10-14 00:09:39] Average Time: 0.367
[INFO] [2019-10-14 00:09:39] Total Time: 7s
[INFO] [2019-10-14 00:09:39] last 3 / first 3: 0.87
[INFO] [2019-10-14 00:09:39] Std.Dev: 0.03162277660168379; Max: 0.46
[INFO] [2019-10-14 00:09:39] Storing 16906 Nodes
[INFO] [2019-10-14 00:09:39] Processing group of 16906 in 17 groups of 1000
[INFO] [2019-10-14 00:09:44] Average Time: 0.303
[INFO] [2019-10-14 00:09:44] Total Time: 6s
[INFO] [2019-10-14 00:09:44] last 3 / first 3: 0.9
[INFO] [2019-10-14 00:09:44] Std.Dev: 0.03162277660168379; Max: 0.38
[INFO] [2019-10-14 00:09:44] Storing 11568 Occurrences
[INFO] [2019-10-14 00:09:44] Processing group of 11568 in 12 groups of 1000
[INFO] [2019-10-14 00:09:46] Average Time: 0.106
[INFO] [2019-10-14 00:09:46] Total Time: 2s
[INFO] [2019-10-14 00:09:46] last 3 / first 3: 0.84
[INFO] [2019-10-14 00:09:46] Std.Dev: 0.03162277660168379; Max: 0.16
[INFO] [2019-10-14 00:09:46] Storing 23300 TraitsReferences
[INFO] [2019-10-14 00:09:46] Processing group of 23300 in 24 groups of 1000
[INFO] [2019-10-14 00:09:47] Average Time: 0.072
[INFO] [2019-10-14 00:09:47] Total Time: 2s
[INFO] [2019-10-14 00:09:47] last 3 / first 3: 0.52
[INFO] [2019-10-14 00:09:47] Std.Dev: 0.0; Max: 0.16
[INFO] [2019-10-14 00:09:47] Storing 23299 Traits
[INFO] [2019-10-14 00:09:47] Processing group of 23299 in 24 groups of 1000
[INFO] [2019-10-14 00:09:56] Average Time: 0.342
[INFO] [2019-10-14 00:09:56] Total Time: 9s
[INFO] [2019-10-14 00:09:56] last 3 / first 3: 0.59
[INFO] [2019-10-14 00:09:56] Std.Dev: 0.14491376746189438; Max: 0.94
[INFO] [2019-10-14 00:09:56] Storing 23288 MetaTraits
[INFO] [2019-10-14 00:09:56] Processing group of 23288 in 24 groups of 1000
[INFO] [2019-10-14 00:09:58] Average Time: 0.109
[INFO] [2019-10-14 00:09:58] Total Time: 3s
[INFO] [2019-10-14 00:09:58] last 3 / first 3: 0.71
[INFO] [2019-10-14 00:09:58] Std.Dev: 0.0; Max: 0.16
[STOP] [2019-10-14 00:09:58] parse_diff_and_store
[START] [2019-10-14 00:09:58] resolve_keys
[INFO] [2019-10-14 00:11:01] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 00:11:06] traits to occurrences...
[INFO] [2019-10-14 00:11:10] traits to nodes (through occurrences)...
[INFO] [2019-10-14 00:11:10] Traits to sex term...
[INFO] [2019-10-14 00:11:14] Traits to lifestage term...
[INFO] [2019-10-14 00:11:18] MetaTraits to traits...
[INFO] [2019-10-14 00:11:20] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 00:11:23] Assocs to occurrences...
[INFO] [2019-10-14 00:11:23] Assocs to nodes...
[INFO] [2019-10-14 00:11:23] Assoc to sex term...
[INFO] [2019-10-14 00:11:23] Assoc to lifestage term...
[STOP] [2019-10-14 00:11:23] resolve_keys
[START] [2019-10-14 00:11:23] hold_for_later_1
[STOP] [2019-10-14 00:11:23] hold_for_later_1
[START] [2019-10-14 00:11:23] hold_for_later_2
[STOP] [2019-10-14 00:11:23] hold_for_later_2
[START] [2019-10-14 00:11:23] resolve_missing_parents
[STOP] [2019-10-14 00:11:57] resolve_missing_parents
[START] [2019-10-14 00:11:57] rebuild_nodes
[START] [2019-10-14 00:11:57] Flattener#flatten
[START] [2019-10-14 00:11:57] Flattener#study_resource
[START] [2019-10-14 00:11:57] Flattener#build_ancestry
[STOP] [2019-10-14 00:11:59] Flattener#build_ancestry
[INFO] [2019-10-14 00:11:59] 16906 ancestry keys
[START] [2019-10-14 00:11:59] build_node_ancestors
[INFO] [2019-10-14 00:11:59] old ancestors deleted.
[STOP] [2019-10-14 00:12:02] build_node_ancestors
[START] [2019-10-14 00:12:06] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 00:12:07] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 00:12:07] Flattener#flatten
[STOP] [2019-10-14 00:12:07] rebuild_nodes
[START] [2019-10-14 00:12:07] resolve_missing_media_owners
[STOP] [2019-10-14 00:12:07] resolve_missing_media_owners
[START] [2019-10-14 00:12:07] sanitize_media_verbatims
[STOP] [2019-10-14 00:12:07] sanitize_media_verbatims
[START] [2019-10-14 00:12:07] queue_downloads
[STOP] [2019-10-14 00:12:07] queue_downloads
[START] [2019-10-14 00:12:07] parse_names
[WARN] [2019-10-14 00:12:07] I see 16906 names which still need to be parsed.
[STOP] [2019-10-14 00:12:20] parse_names
[START] [2019-10-14 00:12:20] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 00:12:20] denormalize_canonical_names_to_nodes
[START] [2019-10-14 00:12:20] match_nodes
[START] [2019-10-14 00:12:20] map_all_nodes_to_pages
[STOP] [2019-10-14 00:28:42] map_all_nodes_to_pages
[INFO] [2019-10-14 00:28:42] 1201 Unmatched nodes (of 16906)! That's too many to output. First 10: Andropadus latirostris (#50491891); Andropadus virens (#50491968); Andropadus curvirostris (#50493175); Andropadus gracilirostris (#50496192); Andropadus gracilis (#50497340); Andropadus ansorgei (#50497585); Andropadus masukuensis (#50498325); Lamprotornis corruscus (#50489890); Lamprotornis purpuropterus (#50491315); Cinnyricinclus sharpii (#50493353)
[START] [2019-10-14 00:28:42] update_nodes
[STOP] [2019-10-14 00:28:49] update_nodes
[STOP] [2019-10-14 00:28:49] match_nodes
[START] [2019-10-14 00:28:49] reindex_search
[STOP] [2019-10-14 00:29:35] reindex_search
[START] [2019-10-14 00:29:35] normalize_units
[STOP] [2019-10-14 00:29:35] normalize_units
[START] [2019-10-14 00:29:35] calculate_statistics
[STOP] [2019-10-14 00:29:35] calculate_statistics
[START] [2019-10-14 00:29:35] complete_harvest_instance
[START] [2019-10-14 00:29:35] overall_tsv_creation
[INFO] [2019-10-14 00:29:35] Processing group of 16906 in 2 batches of 10000
[INFO] [2019-10-14 00:31:03] 6589 Traits (unfiltered)...
[INFO] [2019-10-14 00:31:17] 6589 Traits (filtered)...
[INFO] [2019-10-14 00:31:17] 0 Associations (filtered)...
[INFO] [2019-10-14 00:32:08] 32942 metadata added.
[INFO] [2019-10-14 00:32:08] 0 metadata added.
[INFO] [2019-10-14 00:33:25] 4979 Traits (unfiltered)...
[INFO] [2019-10-14 00:33:39] 4979 Traits (filtered)...
[INFO] [2019-10-14 00:33:39] 0 Associations (filtered)...
[INFO] [2019-10-14 00:34:28] 24887 metadata added.
[INFO] [2019-10-14 00:34:28] 0 metadata added.
[INFO] [2019-10-14 00:34:28] Average Time: 121.11
[INFO] [2019-10-14 00:34:28] Total Time: 4m53s
[STOP] [2019-10-14 00:34:28] overall_tsv_creation
[INFO] [2019-10-14 00:34:28] Done. Check your files:
[INFO] [2019-10-14 00:34:28] (16906 lines) /app/public/data/kenya_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 00:34:28] (43181 lines) /app/public/data/kenya_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 00:34:28] (16906 lines) /app/public/data/kenya_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 00:34:28] (11569 lines) /app/public/data/kenya_sp_list/publish_traits.tsv
[INFO] [2019-10-14 00:34:28] (57830 lines) /app/public/data/kenya_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 00:34:29] complete_harvest_instance
[START] [2019-10-14 00:34:29] completed
[STOP] [2019-10-14 00:34:29] completed
[STOP] [2019-10-14 00:34:29] logged process, took 1575.85
Latest Process

14 Oct 00:08 EXITED currently processing 0