Harvest for Ivory Coast Species List Created 13 Oct 20:57

Stage: completed
Fetched: 13 Oct 20:57
Validated: 13 Oct 20:57
Deltas Created 13 Oct 20:57
Units Normalized: 13 Oct 21:13
Ancestry Built: 13 Oct 21:00
Nodes Matched: 13 Oct 21:13
Names Parsed: 13 Oct 21:00
New Models Stored: 13 Oct 20:58
Indexed: 13 Oct 21:13
Completed: 13 Oct 21:17
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-13 20:57:54 -0400 by logger.rb/56815
[START] [2019-10-13 20:57:54] logged process
[START] [2019-10-13 20:57:54] create_harvest_instance
[STOP] [2019-10-13 20:57:54] create_harvest_instance
[START] [2019-10-13 20:57:54] fetch_files
[STOP] [2019-10-13 20:57:54] fetch_files
[START] [2019-10-13 20:57:54] validate_each_file
[STOP] [2019-10-13 20:57:56] validate_each_file
[START] [2019-10-13 20:57:56] convert_to_csv
[CMD] [2019-10-13 20:57:56] /usr/bin/sort /app/public/converted_csv/ivory_coast_sp_l_refs_16235.csv > /app/public/converted_csv/ivory_coast_sp_l_refs_16235.csv_sorted
[CMD] [2019-10-13 20:57:56] /usr/bin/sort /app/public/converted_csv/ivory_coast_sp_l_nodes_16236.csv > /app/public/converted_csv/ivory_coast_sp_l_nodes_16236.csv_sorted
[CMD] [2019-10-13 20:57:56] /usr/bin/sort /app/public/converted_csv/ivory_coast_sp_l_occurrences_16237.csv > /app/public/converted_csv/ivory_coast_sp_l_occurrences_16237.csv_sorted
[CMD] [2019-10-13 20:57:56] /usr/bin/sort /app/public/converted_csv/ivory_coast_sp_l_measurements_16238.csv > /app/public/converted_csv/ivory_coast_sp_l_measurements_16238.csv_sorted
[STOP] [2019-10-13 20:57:56] convert_to_csv
[START] [2019-10-13 20:57:56] calculate_delta
[CMD] [2019-10-13 20:57:56] echo "0a" > /app/public/diff/ivory_coast_sp_l_refs_16235.diff
[CMD] [2019-10-13 20:57:56] tail -n +1 /app/public/converted_csv/ivory_coast_sp_l_refs_16235.csv >> /app/public/diff/ivory_coast_sp_l_refs_16235.diff
[CMD] [2019-10-13 20:57:57] echo "." >> /app/public/diff/ivory_coast_sp_l_refs_16235.diff
[CMD] [2019-10-13 20:57:57] echo "0a" > /app/public/diff/ivory_coast_sp_l_nodes_16236.diff
[CMD] [2019-10-13 20:57:57] tail -n +1 /app/public/converted_csv/ivory_coast_sp_l_nodes_16236.csv >> /app/public/diff/ivory_coast_sp_l_nodes_16236.diff
[CMD] [2019-10-13 20:57:57] echo "." >> /app/public/diff/ivory_coast_sp_l_nodes_16236.diff
[CMD] [2019-10-13 20:57:57] echo "0a" > /app/public/diff/ivory_coast_sp_l_occurrences_16237.diff
[CMD] [2019-10-13 20:57:57] tail -n +1 /app/public/converted_csv/ivory_coast_sp_l_occurrences_16237.csv >> /app/public/diff/ivory_coast_sp_l_occurrences_16237.diff
[CMD] [2019-10-13 20:57:57] echo "." >> /app/public/diff/ivory_coast_sp_l_occurrences_16237.diff
[CMD] [2019-10-13 20:57:57] echo "0a" > /app/public/diff/ivory_coast_sp_l_measurements_16238.diff
[CMD] [2019-10-13 20:57:57] tail -n +1 /app/public/converted_csv/ivory_coast_sp_l_measurements_16238.csv >> /app/public/diff/ivory_coast_sp_l_measurements_16238.diff
[CMD] [2019-10-13 20:57:57] echo "." >> /app/public/diff/ivory_coast_sp_l_measurements_16238.diff
[STOP] [2019-10-13 20:57:58] calculate_delta
[START] [2019-10-13 20:57:58] parse_diff_and_store
[INFO] [2019-10-13 20:57:58] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 20:57:58] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 20:58:02] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 20:58:02] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 20:58:41] Storing 2 References
[INFO] [2019-10-13 20:58:41] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 20:58:41] Average Time: 0.0
[INFO] [2019-10-13 20:58:41] Total Time: 1s
[INFO] [2019-10-13 20:58:41] Storing 10136 ScientificNames
[INFO] [2019-10-13 20:58:41] Processing group of 10136 in 11 groups of 1000
[INFO] [2019-10-13 20:58:45] Average Time: 0.341
[INFO] [2019-10-13 20:58:45] Total Time: 4s
[INFO] [2019-10-13 20:58:45] last 3 / first 3: 0.64
[INFO] [2019-10-13 20:58:45] Std.Dev: 0.10488088481701516; Max: 0.48
[INFO] [2019-10-13 20:58:45] Storing 10136 Nodes
[INFO] [2019-10-13 20:58:45] Processing group of 10136 in 11 groups of 1000
[INFO] [2019-10-13 20:58:48] Average Time: 0.279
[INFO] [2019-10-13 20:58:48] Total Time: 4s
[INFO] [2019-10-13 20:58:48] last 3 / first 3: 0.71
[INFO] [2019-10-13 20:58:48] Std.Dev: 0.07745966692414834; Max: 0.32
[INFO] [2019-10-13 20:58:48] Storing 6725 Occurrences
[INFO] [2019-10-13 20:58:48] Processing group of 6725 in 7 groups of 1000
[INFO] [2019-10-13 20:58:49] Average Time: 0.101
[INFO] [2019-10-13 20:58:49] Total Time: 1s
[INFO] [2019-10-13 20:58:49] last 3 / first 3: 0.85
[INFO] [2019-10-13 20:58:49] Std.Dev: 0.0; Max: 0.12
[INFO] [2019-10-13 20:58:49] Storing 13348 TraitsReferences
[INFO] [2019-10-13 20:58:49] Processing group of 13348 in 14 groups of 1000
[INFO] [2019-10-13 20:58:50] Average Time: 0.076
[INFO] [2019-10-13 20:58:50] Total Time: 2s
[INFO] [2019-10-13 20:58:50] last 3 / first 3: 0.52
[INFO] [2019-10-13 20:58:50] Std.Dev: 0.03162277660168379; Max: 0.16
[INFO] [2019-10-13 20:58:50] Storing 13348 Traits
[INFO] [2019-10-13 20:58:50] Processing group of 13348 in 14 groups of 1000
[INFO] [2019-10-13 20:58:55] Average Time: 0.327
[INFO] [2019-10-13 20:58:55] Total Time: 5s
[INFO] [2019-10-13 20:58:55] last 3 / first 3: 0.58
[INFO] [2019-10-13 20:58:55] Std.Dev: 0.1; Max: 0.52
[INFO] [2019-10-13 20:58:55] Storing 13329 MetaTraits
[INFO] [2019-10-13 20:58:55] Processing group of 13329 in 14 groups of 1000
[INFO] [2019-10-13 20:58:57] Average Time: 0.148
[INFO] [2019-10-13 20:58:57] Total Time: 3s
[INFO] [2019-10-13 20:58:57] last 3 / first 3: 1.16
[INFO] [2019-10-13 20:58:57] Std.Dev: 0.07071067811865475; Max: 0.29
[STOP] [2019-10-13 20:58:57] parse_diff_and_store
[START] [2019-10-13 20:58:57] resolve_keys
[INFO] [2019-10-13 20:59:36] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 20:59:40] traits to occurrences...
[INFO] [2019-10-13 20:59:45] traits to nodes (through occurrences)...
[INFO] [2019-10-13 20:59:45] Traits to sex term...
[INFO] [2019-10-13 20:59:49] Traits to lifestage term...
[INFO] [2019-10-13 20:59:53] MetaTraits to traits...
[INFO] [2019-10-13 20:59:54] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 20:59:56] Assocs to occurrences...
[INFO] [2019-10-13 20:59:56] Assocs to nodes...
[INFO] [2019-10-13 20:59:56] Assoc to sex term...
[INFO] [2019-10-13 20:59:56] Assoc to lifestage term...
[STOP] [2019-10-13 20:59:56] resolve_keys
[START] [2019-10-13 20:59:56] hold_for_later_1
[STOP] [2019-10-13 20:59:56] hold_for_later_1
[START] [2019-10-13 20:59:56] hold_for_later_2
[STOP] [2019-10-13 20:59:56] hold_for_later_2
[START] [2019-10-13 20:59:56] resolve_missing_parents
[STOP] [2019-10-13 21:00:16] resolve_missing_parents
[START] [2019-10-13 21:00:16] rebuild_nodes
[START] [2019-10-13 21:00:16] Flattener#flatten
[START] [2019-10-13 21:00:16] Flattener#study_resource
[START] [2019-10-13 21:00:16] Flattener#build_ancestry
[STOP] [2019-10-13 21:00:16] Flattener#build_ancestry
[INFO] [2019-10-13 21:00:16] 10136 ancestry keys
[START] [2019-10-13 21:00:16] build_node_ancestors
[INFO] [2019-10-13 21:00:16] old ancestors deleted.
[STOP] [2019-10-13 21:00:20] build_node_ancestors
[START] [2019-10-13 21:00:24] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 21:00:26] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 21:00:26] Flattener#flatten
[STOP] [2019-10-13 21:00:26] rebuild_nodes
[START] [2019-10-13 21:00:26] resolve_missing_media_owners
[STOP] [2019-10-13 21:00:26] resolve_missing_media_owners
[START] [2019-10-13 21:00:26] sanitize_media_verbatims
[STOP] [2019-10-13 21:00:26] sanitize_media_verbatims
[START] [2019-10-13 21:00:26] queue_downloads
[STOP] [2019-10-13 21:00:26] queue_downloads
[START] [2019-10-13 21:00:26] parse_names
[WARN] [2019-10-13 21:00:26] I see 10136 names which still need to be parsed.
[STOP] [2019-10-13 21:00:34] parse_names
[START] [2019-10-13 21:00:34] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 21:00:34] denormalize_canonical_names_to_nodes
[START] [2019-10-13 21:00:34] match_nodes
[START] [2019-10-13 21:00:34] map_all_nodes_to_pages
[STOP] [2019-10-13 21:13:00] map_all_nodes_to_pages
[INFO] [2019-10-13 21:13:00] 466 Unmatched nodes (of 10136)! That's too many to output. First 10: Gerbilliscus valida (#50400234); Mylomys lowei (#50401847); Myonycteris leptodon (#50400051); Myonycteris angolensis (#50401069); Tadarida leucogaster (#50397675); Tadarida brachyptera (#50401368); Marattiopsida (#50403373); Pipistrellus tenuipinnis (#50400905); Pipistrellus brunneus (#50400980); Pipistrellus somalicus (#50401235)
[START] [2019-10-13 21:13:00] update_nodes
[STOP] [2019-10-13 21:13:04] update_nodes
[STOP] [2019-10-13 21:13:04] match_nodes
[START] [2019-10-13 21:13:04] reindex_search
[STOP] [2019-10-13 21:13:29] reindex_search
[START] [2019-10-13 21:13:29] normalize_units
[STOP] [2019-10-13 21:13:29] normalize_units
[START] [2019-10-13 21:13:29] calculate_statistics
[STOP] [2019-10-13 21:13:29] calculate_statistics
[START] [2019-10-13 21:13:29] complete_harvest_instance
[START] [2019-10-13 21:13:29] overall_tsv_creation
[INFO] [2019-10-13 21:13:29] Processing group of 10136 in 2 batches of 10000
[INFO] [2019-10-13 21:14:58] 6616 Traits (unfiltered)...
[INFO] [2019-10-13 21:15:12] 6616 Traits (filtered)...
[INFO] [2019-10-13 21:15:12] 0 Associations (filtered)...
[INFO] [2019-10-13 21:16:04] 33061 metadata added.
[INFO] [2019-10-13 21:16:04] 0 metadata added.
[INFO] [2019-10-13 21:16:48] 57 Traits (unfiltered)...
[INFO] [2019-10-13 21:17:02] 57 Traits (filtered)...
[INFO] [2019-10-13 21:17:02] 0 Associations (filtered)...
[INFO] [2019-10-13 21:17:38] 285 metadata added.
[INFO] [2019-10-13 21:17:38] 0 metadata added.
[INFO] [2019-10-13 21:17:39] Average Time: 100.98
[INFO] [2019-10-13 21:17:39] Total Time: 4m10s
[STOP] [2019-10-13 21:17:39] overall_tsv_creation
[INFO] [2019-10-13 21:17:39] Done. Check your files:
[INFO] [2019-10-13 21:17:39] (10136 lines) /app/public/data/ivory_coast_sp_l/publish_nodes.tsv
[INFO] [2019-10-13 21:17:39] (55732 lines) /app/public/data/ivory_coast_sp_l/publish_node_ancestors.tsv
[INFO] [2019-10-13 21:17:39] (10136 lines) /app/public/data/ivory_coast_sp_l/publish_scientific_names.tsv
[INFO] [2019-10-13 21:17:39] (6674 lines) /app/public/data/ivory_coast_sp_l/publish_traits.tsv
[INFO] [2019-10-13 21:17:39] (33347 lines) /app/public/data/ivory_coast_sp_l/publish_metadata.tsv
[STOP] [2019-10-13 21:17:39] complete_harvest_instance
[START] [2019-10-13 21:17:39] completed
[STOP] [2019-10-13 21:17:39] completed
[STOP] [2019-10-13 21:17:39] logged process, took 1185.32
Latest Process

13 Oct 20:57 EXITED currently processing 0