Harvest for Liberia Species List Created 14 Oct 01:49

Stage: completed
Fetched: 14 Oct 01:49
Validated: 14 Oct 01:49
Deltas Created 14 Oct 01:49
Units Normalized: 14 Oct 01:56
Ancestry Built: 14 Oct 01:50
Nodes Matched: 14 Oct 01:56
Names Parsed: 14 Oct 01:50
New Models Stored: 14 Oct 01:49
Indexed: 14 Oct 01:56
Completed: 14 Oct 01:58
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-10-14 01:49:06 -0400 by logger.rb/56815
[START] [2019-10-14 01:49:06] logged process
[START] [2019-10-14 01:49:06] create_harvest_instance
[STOP] [2019-10-14 01:49:06] create_harvest_instance
[START] [2019-10-14 01:49:06] fetch_files
[STOP] [2019-10-14 01:49:06] fetch_files
[START] [2019-10-14 01:49:06] validate_each_file
[STOP] [2019-10-14 01:49:07] validate_each_file
[START] [2019-10-14 01:49:07] convert_to_csv
[CMD] [2019-10-14 01:49:07] /usr/bin/sort /app/public/converted_csv/liberia_sp_list_refs_16395.csv > /app/public/converted_csv/liberia_sp_list_refs_16395.csv_sorted
[CMD] [2019-10-14 01:49:07] /usr/bin/sort /app/public/converted_csv/liberia_sp_list_nodes_16396.csv > /app/public/converted_csv/liberia_sp_list_nodes_16396.csv_sorted
[CMD] [2019-10-14 01:49:07] /usr/bin/sort /app/public/converted_csv/liberia_sp_list_occurrences_16397.csv > /app/public/converted_csv/liberia_sp_list_occurrences_16397.csv_sorted
[CMD] [2019-10-14 01:49:07] /usr/bin/sort /app/public/converted_csv/liberia_sp_list_measurements_16398.csv > /app/public/converted_csv/liberia_sp_list_measurements_16398.csv_sorted
[STOP] [2019-10-14 01:49:07] convert_to_csv
[START] [2019-10-14 01:49:07] calculate_delta
[CMD] [2019-10-14 01:49:07] echo "0a" > /app/public/diff/liberia_sp_list_refs_16395.diff
[CMD] [2019-10-14 01:49:08] tail -n +1 /app/public/converted_csv/liberia_sp_list_refs_16395.csv >> /app/public/diff/liberia_sp_list_refs_16395.diff
[CMD] [2019-10-14 01:49:08] echo "." >> /app/public/diff/liberia_sp_list_refs_16395.diff
[CMD] [2019-10-14 01:49:08] echo "0a" > /app/public/diff/liberia_sp_list_nodes_16396.diff
[CMD] [2019-10-14 01:49:08] tail -n +1 /app/public/converted_csv/liberia_sp_list_nodes_16396.csv >> /app/public/diff/liberia_sp_list_nodes_16396.diff
[CMD] [2019-10-14 01:49:08] echo "." >> /app/public/diff/liberia_sp_list_nodes_16396.diff
[CMD] [2019-10-14 01:49:08] echo "0a" > /app/public/diff/liberia_sp_list_occurrences_16397.diff
[CMD] [2019-10-14 01:49:08] tail -n +1 /app/public/converted_csv/liberia_sp_list_occurrences_16397.csv >> /app/public/diff/liberia_sp_list_occurrences_16397.diff
[CMD] [2019-10-14 01:49:08] echo "." >> /app/public/diff/liberia_sp_list_occurrences_16397.diff
[CMD] [2019-10-14 01:49:08] echo "0a" > /app/public/diff/liberia_sp_list_measurements_16398.diff
[CMD] [2019-10-14 01:49:08] tail -n +1 /app/public/converted_csv/liberia_sp_list_measurements_16398.csv >> /app/public/diff/liberia_sp_list_measurements_16398.diff
[CMD] [2019-10-14 01:49:08] echo "." >> /app/public/diff/liberia_sp_list_measurements_16398.diff
[STOP] [2019-10-14 01:49:09] calculate_delta
[START] [2019-10-14 01:49:09] parse_diff_and_store
[INFO] [2019-10-14 01:49:09] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 01:49:09] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 01:49:11] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 01:49:12] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 01:49:34] Storing 2 References
[INFO] [2019-10-14 01:49:34] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 01:49:34] Average Time: 0.0
[INFO] [2019-10-14 01:49:34] Total Time: 1s
[INFO] [2019-10-14 01:49:34] Storing 6202 ScientificNames
[INFO] [2019-10-14 01:49:34] Processing group of 6202 in 7 groups of 1000
[INFO] [2019-10-14 01:49:37] Average Time: 0.334
[INFO] [2019-10-14 01:49:37] Total Time: 3s
[INFO] [2019-10-14 01:49:37] last 3 / first 3: 0.64
[INFO] [2019-10-14 01:49:37] Std.Dev: 0.1224744871391589; Max: 0.43
[INFO] [2019-10-14 01:49:37] Storing 6202 Nodes
[INFO] [2019-10-14 01:49:37] Processing group of 6202 in 7 groups of 1000
[INFO] [2019-10-14 01:49:39] Average Time: 0.316
[INFO] [2019-10-14 01:49:39] Total Time: 3s
[INFO] [2019-10-14 01:49:39] last 3 / first 3: 1.02
[INFO] [2019-10-14 01:49:39] Std.Dev: 0.08366600265340755; Max: 0.42
[INFO] [2019-10-14 01:49:39] Storing 3856 Occurrences
[INFO] [2019-10-14 01:49:39] Processing group of 3856 in 4 groups of 1000
[INFO] [2019-10-14 01:49:39] Average Time: 0.118
[INFO] [2019-10-14 01:49:39] Total Time: 1s
[INFO] [2019-10-14 01:49:39] Storing 7880 TraitsReferences
[INFO] [2019-10-14 01:49:39] Processing group of 7880 in 8 groups of 1000
[INFO] [2019-10-14 01:49:40] Average Time: 0.076
[INFO] [2019-10-14 01:49:40] Total Time: 1s
[INFO] [2019-10-14 01:49:40] last 3 / first 3: 0.71
[INFO] [2019-10-14 01:49:40] Std.Dev: 0.03162277660168379; Max: 0.14
[INFO] [2019-10-14 01:49:40] Storing 7879 Traits
[INFO] [2019-10-14 01:49:40] Processing group of 7879 in 8 groups of 1000
[INFO] [2019-10-14 01:49:43] Average Time: 0.313
[INFO] [2019-10-14 01:49:43] Total Time: 3s
[INFO] [2019-10-14 01:49:43] last 3 / first 3: 0.85
[INFO] [2019-10-14 01:49:43] Std.Dev: 0.05477225575051661; Max: 0.44
[INFO] [2019-10-14 01:49:43] Storing 7878 MetaTraits
[INFO] [2019-10-14 01:49:43] Processing group of 7878 in 8 groups of 1000
[INFO] [2019-10-14 01:49:44] Average Time: 0.124
[INFO] [2019-10-14 01:49:44] Total Time: 2s
[INFO] [2019-10-14 01:49:44] last 3 / first 3: 0.92
[INFO] [2019-10-14 01:49:44] Std.Dev: 0.0; Max: 0.15
[STOP] [2019-10-14 01:49:44] parse_diff_and_store
[START] [2019-10-14 01:49:44] resolve_keys
[INFO] [2019-10-14 01:50:10] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 01:50:12] traits to occurrences...
[INFO] [2019-10-14 01:50:14] traits to nodes (through occurrences)...
[INFO] [2019-10-14 01:50:14] Traits to sex term...
[INFO] [2019-10-14 01:50:15] Traits to lifestage term...
[INFO] [2019-10-14 01:50:17] MetaTraits to traits...
[INFO] [2019-10-14 01:50:17] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 01:50:19] Assocs to occurrences...
[INFO] [2019-10-14 01:50:19] Assocs to nodes...
[INFO] [2019-10-14 01:50:19] Assoc to sex term...
[INFO] [2019-10-14 01:50:19] Assoc to lifestage term...
[STOP] [2019-10-14 01:50:19] resolve_keys
[START] [2019-10-14 01:50:19] hold_for_later_1
[STOP] [2019-10-14 01:50:19] hold_for_later_1
[START] [2019-10-14 01:50:19] hold_for_later_2
[STOP] [2019-10-14 01:50:19] hold_for_later_2
[START] [2019-10-14 01:50:19] resolve_missing_parents
[STOP] [2019-10-14 01:50:32] resolve_missing_parents
[START] [2019-10-14 01:50:32] rebuild_nodes
[START] [2019-10-14 01:50:32] Flattener#flatten
[START] [2019-10-14 01:50:32] Flattener#study_resource
[START] [2019-10-14 01:50:32] Flattener#build_ancestry
[STOP] [2019-10-14 01:50:33] Flattener#build_ancestry
[INFO] [2019-10-14 01:50:33] 6202 ancestry keys
[START] [2019-10-14 01:50:33] build_node_ancestors
[INFO] [2019-10-14 01:50:33] old ancestors deleted.
[STOP] [2019-10-14 01:50:34] build_node_ancestors
[START] [2019-10-14 01:50:35] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 01:50:35] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 01:50:35] Flattener#flatten
[STOP] [2019-10-14 01:50:35] rebuild_nodes
[START] [2019-10-14 01:50:35] resolve_missing_media_owners
[STOP] [2019-10-14 01:50:35] resolve_missing_media_owners
[START] [2019-10-14 01:50:35] sanitize_media_verbatims
[STOP] [2019-10-14 01:50:35] sanitize_media_verbatims
[START] [2019-10-14 01:50:35] queue_downloads
[STOP] [2019-10-14 01:50:35] queue_downloads
[START] [2019-10-14 01:50:35] parse_names
[WARN] [2019-10-14 01:50:35] I see 6202 names which still need to be parsed.
[STOP] [2019-10-14 01:50:40] parse_names
[START] [2019-10-14 01:50:40] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 01:50:40] denormalize_canonical_names_to_nodes
[START] [2019-10-14 01:50:40] match_nodes
[START] [2019-10-14 01:50:40] map_all_nodes_to_pages
[STOP] [2019-10-14 01:56:27] map_all_nodes_to_pages
[INFO] [2019-10-14 01:56:27] 292 Unmatched nodes (of 6202)! That's too many to output. First 10: Oplismenus burmannii (#50545461); Paspalum polystachyon (#50543643); Pennisetum uniseta (#50545505); Pennisetum purpureus (#50545974); Polytrias indicum (#50543579); Fimbristylis obtusifolia (#50544909); Hypolytrum heteromorpha (#50545310); Hypolytrum costatum (#50545746); Cyperus halpan (#50541055); Cyperus cylindristachyus (#50542905)
[START] [2019-10-14 01:56:27] update_nodes
[STOP] [2019-10-14 01:56:29] update_nodes
[STOP] [2019-10-14 01:56:29] match_nodes
[START] [2019-10-14 01:56:29] reindex_search
[STOP] [2019-10-14 01:56:45] reindex_search
[START] [2019-10-14 01:56:45] normalize_units
[STOP] [2019-10-14 01:56:45] normalize_units
[START] [2019-10-14 01:56:45] calculate_statistics
[STOP] [2019-10-14 01:56:45] calculate_statistics
[START] [2019-10-14 01:56:45] complete_harvest_instance
[START] [2019-10-14 01:56:45] overall_tsv_creation
[INFO] [2019-10-14 01:56:45] Processing group of 6202 in 1 batches of 10000
[INFO] [2019-10-14 01:57:57] 3856 Traits (unfiltered)...
[INFO] [2019-10-14 01:58:11] 3856 Traits (filtered)...
[INFO] [2019-10-14 01:58:11] 0 Associations (filtered)...
[INFO] [2019-10-14 01:58:56] 19278 metadata added.
[INFO] [2019-10-14 01:58:56] 0 metadata added.
[INFO] [2019-10-14 01:58:56] Average Time: 106.01
[INFO] [2019-10-14 01:58:56] Total Time: 2m11s
[STOP] [2019-10-14 01:58:56] overall_tsv_creation
[INFO] [2019-10-14 01:58:56] Done. Check your files:
[INFO] [2019-10-14 01:58:56] (6202 lines) /app/public/data/liberia_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 01:58:56] (15456 lines) /app/public/data/liberia_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 01:58:56] (6202 lines) /app/public/data/liberia_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 01:58:56] (3857 lines) /app/public/data/liberia_sp_list/publish_traits.tsv
[INFO] [2019-10-14 01:58:56] (19279 lines) /app/public/data/liberia_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 01:58:57] complete_harvest_instance
[START] [2019-10-14 01:58:57] completed
[STOP] [2019-10-14 01:58:57] completed
[STOP] [2019-10-14 01:58:57] logged process, took 590.9
Latest Process

14 Oct 01:49 EXITED currently processing 0