Harvest for Cameroon Species List Created 11 Oct 23:45

Stage: completed
Fetched: 11 Oct 23:45
Validated: 11 Oct 23:45
Deltas Created 11 Oct 23:45
Units Normalized: 12 Oct 00:02
Ancestry Built: 11 Oct 23:50
Nodes Matched: 12 Oct 00:01
Names Parsed: 11 Oct 23:50
New Models Stored: 11 Oct 23:47
Indexed: 12 Oct 00:02
Completed: 12 Oct 00:07
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-11 23:45:44 -0400 by logger.rb/56815
[START] [2019-10-11 23:45:44] logged process
[START] [2019-10-11 23:45:44] create_harvest_instance
[STOP] [2019-10-11 23:45:44] create_harvest_instance
[START] [2019-10-11 23:45:44] fetch_files
[STOP] [2019-10-11 23:45:44] fetch_files
[START] [2019-10-11 23:45:44] validate_each_file
[STOP] [2019-10-11 23:45:47] validate_each_file
[START] [2019-10-11 23:45:47] convert_to_csv
[CMD] [2019-10-11 23:45:47] /usr/bin/sort /app/public/converted_csv/cameroon_sp_list_refs_15363.csv > /app/public/converted_csv/cameroon_sp_list_refs_15363.csv_sorted
[CMD] [2019-10-11 23:45:47] /usr/bin/sort /app/public/converted_csv/cameroon_sp_list_nodes_15364.csv > /app/public/converted_csv/cameroon_sp_list_nodes_15364.csv_sorted
[CMD] [2019-10-11 23:45:47] /usr/bin/sort /app/public/converted_csv/cameroon_sp_list_occurrences_15365.csv > /app/public/converted_csv/cameroon_sp_list_occurrences_15365.csv_sorted
[CMD] [2019-10-11 23:45:47] /usr/bin/sort /app/public/converted_csv/cameroon_sp_list_measurements_15366.csv > /app/public/converted_csv/cameroon_sp_list_measurements_15366.csv_sorted
[STOP] [2019-10-11 23:45:48] convert_to_csv
[START] [2019-10-11 23:45:48] calculate_delta
[CMD] [2019-10-11 23:45:48] echo "0a" > /app/public/diff/cameroon_sp_list_refs_15363.diff
[CMD] [2019-10-11 23:45:48] tail -n +1 /app/public/converted_csv/cameroon_sp_list_refs_15363.csv >> /app/public/diff/cameroon_sp_list_refs_15363.diff
[CMD] [2019-10-11 23:45:48] echo "." >> /app/public/diff/cameroon_sp_list_refs_15363.diff
[CMD] [2019-10-11 23:45:48] echo "0a" > /app/public/diff/cameroon_sp_list_nodes_15364.diff
[CMD] [2019-10-11 23:45:48] tail -n +1 /app/public/converted_csv/cameroon_sp_list_nodes_15364.csv >> /app/public/diff/cameroon_sp_list_nodes_15364.diff
[CMD] [2019-10-11 23:45:48] echo "." >> /app/public/diff/cameroon_sp_list_nodes_15364.diff
[CMD] [2019-10-11 23:45:48] echo "0a" > /app/public/diff/cameroon_sp_list_occurrences_15365.diff
[CMD] [2019-10-11 23:45:48] tail -n +1 /app/public/converted_csv/cameroon_sp_list_occurrences_15365.csv >> /app/public/diff/cameroon_sp_list_occurrences_15365.diff
[CMD] [2019-10-11 23:45:48] echo "." >> /app/public/diff/cameroon_sp_list_occurrences_15365.diff
[CMD] [2019-10-11 23:45:48] echo "0a" > /app/public/diff/cameroon_sp_list_measurements_15366.diff
[CMD] [2019-10-11 23:45:49] tail -n +1 /app/public/converted_csv/cameroon_sp_list_measurements_15366.csv >> /app/public/diff/cameroon_sp_list_measurements_15366.diff
[CMD] [2019-10-11 23:45:49] echo "." >> /app/public/diff/cameroon_sp_list_measurements_15366.diff
[STOP] [2019-10-11 23:45:49] calculate_delta
[START] [2019-10-11 23:45:49] parse_diff_and_store
[INFO] [2019-10-11 23:45:49] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-11 23:45:49] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-11 23:45:56] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-11 23:45:58] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-11 23:47:14] Storing 2 References
[INFO] [2019-10-11 23:47:14] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-11 23:47:14] Average Time: 0.0
[INFO] [2019-10-11 23:47:14] Total Time: 1s
[INFO] [2019-10-11 23:47:14] Storing 17737 ScientificNames
[INFO] [2019-10-11 23:47:14] Processing group of 17737 in 18 groups of 1000
[INFO] [2019-10-11 23:47:21] Average Time: 0.391
[INFO] [2019-10-11 23:47:21] Total Time: 8s
[INFO] [2019-10-11 23:47:21] last 3 / first 3: 0.84
[INFO] [2019-10-11 23:47:21] Std.Dev: 0.11401754250991379; Max: 0.79
[INFO] [2019-10-11 23:47:21] Storing 17737 Nodes
[INFO] [2019-10-11 23:47:21] Processing group of 17737 in 18 groups of 1000
[INFO] [2019-10-11 23:47:27] Average Time: 0.288
[INFO] [2019-10-11 23:47:27] Total Time: 6s
[INFO] [2019-10-11 23:47:27] last 3 / first 3: 0.9
[INFO] [2019-10-11 23:47:27] Std.Dev: 0.03162277660168379; Max: 0.35
[INFO] [2019-10-11 23:47:27] Storing 13014 Occurrences
[INFO] [2019-10-11 23:47:27] Processing group of 13014 in 14 groups of 1000
[INFO] [2019-10-11 23:47:28] Average Time: 0.098
[INFO] [2019-10-11 23:47:28] Total Time: 2s
[INFO] [2019-10-11 23:47:28] last 3 / first 3: 0.65
[INFO] [2019-10-11 23:47:28] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-11 23:47:28] Storing 26250 TraitsReferences
[INFO] [2019-10-11 23:47:28] Processing group of 26250 in 27 groups of 1000
[INFO] [2019-10-11 23:47:30] Average Time: 0.073
[INFO] [2019-10-11 23:47:30] Total Time: 3s
[INFO] [2019-10-11 23:47:30] last 3 / first 3: 0.57
[INFO] [2019-10-11 23:47:30] Std.Dev: 0.0; Max: 0.15
[INFO] [2019-10-11 23:47:30] Storing 26249 Traits
[INFO] [2019-10-11 23:47:30] Processing group of 26249 in 27 groups of 1000
[INFO] [2019-10-11 23:47:40] Average Time: 0.353
[INFO] [2019-10-11 23:47:40] Total Time: 10s
[INFO] [2019-10-11 23:47:40] last 3 / first 3: 0.63
[INFO] [2019-10-11 23:47:40] Std.Dev: 0.12649110640673517; Max: 0.87
[INFO] [2019-10-11 23:47:40] Storing 26230 MetaTraits
[INFO] [2019-10-11 23:47:40] Processing group of 26230 in 27 groups of 1000
[INFO] [2019-10-11 23:47:45] Average Time: 0.176
[INFO] [2019-10-11 23:47:45] Total Time: 5s
[INFO] [2019-10-11 23:47:45] last 3 / first 3: 0.72
[INFO] [2019-10-11 23:47:45] Std.Dev: 0.1414213562373095; Max: 0.84
[STOP] [2019-10-11 23:47:45] parse_diff_and_store
[START] [2019-10-11 23:47:45] resolve_keys
[INFO] [2019-10-11 23:48:47] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-11 23:48:53] traits to occurrences...
[INFO] [2019-10-11 23:49:00] traits to nodes (through occurrences)...
[INFO] [2019-10-11 23:49:00] Traits to sex term...
[INFO] [2019-10-11 23:49:06] Traits to lifestage term...
[INFO] [2019-10-11 23:49:12] MetaTraits to traits...
[INFO] [2019-10-11 23:49:14] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-11 23:49:17] Assocs to occurrences...
[INFO] [2019-10-11 23:49:17] Assocs to nodes...
[INFO] [2019-10-11 23:49:17] Assoc to sex term...
[INFO] [2019-10-11 23:49:17] Assoc to lifestage term...
[STOP] [2019-10-11 23:49:17] resolve_keys
[START] [2019-10-11 23:49:17] hold_for_later_1
[STOP] [2019-10-11 23:49:17] hold_for_later_1
[START] [2019-10-11 23:49:17] hold_for_later_2
[STOP] [2019-10-11 23:49:17] hold_for_later_2
[START] [2019-10-11 23:49:17] resolve_missing_parents
[STOP] [2019-10-11 23:49:51] resolve_missing_parents
[START] [2019-10-11 23:49:51] rebuild_nodes
[START] [2019-10-11 23:49:51] Flattener#flatten
[START] [2019-10-11 23:49:51] Flattener#study_resource
[START] [2019-10-11 23:49:51] Flattener#build_ancestry
[STOP] [2019-10-11 23:49:51] Flattener#build_ancestry
[INFO] [2019-10-11 23:49:51] 17737 ancestry keys
[START] [2019-10-11 23:49:51] build_node_ancestors
[INFO] [2019-10-11 23:49:51] old ancestors deleted.
[STOP] [2019-10-11 23:49:56] build_node_ancestors
[START] [2019-10-11 23:50:00] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 23:50:02] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 23:50:02] Flattener#flatten
[STOP] [2019-10-11 23:50:02] rebuild_nodes
[START] [2019-10-11 23:50:02] resolve_missing_media_owners
[STOP] [2019-10-11 23:50:02] resolve_missing_media_owners
[START] [2019-10-11 23:50:02] sanitize_media_verbatims
[STOP] [2019-10-11 23:50:02] sanitize_media_verbatims
[START] [2019-10-11 23:50:02] queue_downloads
[STOP] [2019-10-11 23:50:02] queue_downloads
[START] [2019-10-11 23:50:02] parse_names
[WARN] [2019-10-11 23:50:02] I see 17737 names which still need to be parsed.
[STOP] [2019-10-11 23:50:16] parse_names
[START] [2019-10-11 23:50:16] denormalize_canonical_names_to_nodes
[STOP] [2019-10-11 23:50:16] denormalize_canonical_names_to_nodes
[START] [2019-10-11 23:50:16] match_nodes
[START] [2019-10-11 23:50:17] map_all_nodes_to_pages
[STOP] [2019-10-12 00:01:34] map_all_nodes_to_pages
[INFO] [2019-10-12 00:01:34] 1089 Unmatched nodes (of 17737)! That's too many to output. First 10: Culex taeniarostris (#49010079); Bactrocera curcubitae (#49009419); Ceratitoides nigromaculatus (#49013386); Richardidae (#49009420); Diachlorus rondanii (#49014648); Heteronychia ovazzai (#49012200); Taurrhina longiceps (#49013768); Elaphidion nebulosus (#49014618); Garreta azureus (#49011019); Pseudomacronychus (#49007500)
[START] [2019-10-12 00:01:34] update_nodes
[STOP] [2019-10-12 00:01:40] update_nodes
[STOP] [2019-10-12 00:01:40] match_nodes
[START] [2019-10-12 00:01:40] reindex_search
[STOP] [2019-10-12 00:02:17] reindex_search
[START] [2019-10-12 00:02:17] normalize_units
[STOP] [2019-10-12 00:02:17] normalize_units
[START] [2019-10-12 00:02:17] calculate_statistics
[STOP] [2019-10-12 00:02:17] calculate_statistics
[START] [2019-10-12 00:02:17] complete_harvest_instance
[START] [2019-10-12 00:02:17] overall_tsv_creation
[INFO] [2019-10-12 00:02:17] Processing group of 17737 in 2 batches of 10000
[INFO] [2019-10-12 00:03:48] 7015 Traits (unfiltered)...
[INFO] [2019-10-12 00:04:02] 7015 Traits (filtered)...
[INFO] [2019-10-12 00:04:02] 0 Associations (filtered)...
[INFO] [2019-10-12 00:04:54] 35060 metadata added.
[INFO] [2019-10-12 00:04:54] 0 metadata added.
[INFO] [2019-10-12 00:06:16] 5999 Traits (unfiltered)...
[INFO] [2019-10-12 00:06:30] 5999 Traits (filtered)...
[INFO] [2019-10-12 00:06:30] 0 Associations (filtered)...
[INFO] [2019-10-12 00:07:21] 29990 metadata added.
[INFO] [2019-10-12 00:07:21] 0 metadata added.
[INFO] [2019-10-12 00:07:21] Average Time: 125.595
[INFO] [2019-10-12 00:07:21] Total Time: 5m5s
[STOP] [2019-10-12 00:07:21] overall_tsv_creation
[INFO] [2019-10-12 00:07:21] Done. Check your files:
[INFO] [2019-10-12 00:07:22] (17737 lines) /app/public/data/cameroon_sp_list/publish_nodes.tsv
[INFO] [2019-10-12 00:07:22] (64664 lines) /app/public/data/cameroon_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-12 00:07:22] (17737 lines) /app/public/data/cameroon_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-12 00:07:22] (13015 lines) /app/public/data/cameroon_sp_list/publish_traits.tsv
[INFO] [2019-10-12 00:07:22] (65051 lines) /app/public/data/cameroon_sp_list/publish_metadata.tsv
[STOP] [2019-10-12 00:07:22] complete_harvest_instance
[START] [2019-10-12 00:07:22] completed
[STOP] [2019-10-12 00:07:22] completed
[STOP] [2019-10-12 00:07:22] logged process, took 1298.66
Latest Process

11 Oct 23:45 EXITED currently processing 0