Harvest for Seychelles Species List Created 15 Oct 18:04

Stage: completed
Fetched: 15 Oct 18:04
Validated: 15 Oct 18:04
Deltas Created 15 Oct 18:05
Units Normalized: 15 Oct 18:15
Ancestry Built: 15 Oct 18:06
Nodes Matched: 15 Oct 18:14
Names Parsed: 15 Oct 18:06
New Models Stored: 15 Oct 18:05
Indexed: 15 Oct 18:15
Completed: 15 Oct 18:17
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-10-15 18:04:56 -0400 by logger.rb/56815
[START] [2019-10-15 18:04:56] logged process
[START] [2019-10-15 18:04:56] create_harvest_instance
[STOP] [2019-10-15 18:04:57] create_harvest_instance
[START] [2019-10-15 18:04:57] fetch_files
[STOP] [2019-10-15 18:04:57] fetch_files
[START] [2019-10-15 18:04:57] validate_each_file
[STOP] [2019-10-15 18:04:58] validate_each_file
[START] [2019-10-15 18:04:58] convert_to_csv
[CMD] [2019-10-15 18:04:58] /usr/bin/sort /app/public/converted_csv/seychelles_sp_li_refs_17173.csv > /app/public/converted_csv/seychelles_sp_li_refs_17173.csv_sorted
[CMD] [2019-10-15 18:04:58] /usr/bin/sort /app/public/converted_csv/seychelles_sp_li_nodes_17174.csv > /app/public/converted_csv/seychelles_sp_li_nodes_17174.csv_sorted
[CMD] [2019-10-15 18:04:58] /usr/bin/sort /app/public/converted_csv/seychelles_sp_li_occurrences_17175.csv > /app/public/converted_csv/seychelles_sp_li_occurrences_17175.csv_sorted
[CMD] [2019-10-15 18:04:58] /usr/bin/sort /app/public/converted_csv/seychelles_sp_li_measurements_17176.csv > /app/public/converted_csv/seychelles_sp_li_measurements_17176.csv_sorted
[STOP] [2019-10-15 18:04:59] convert_to_csv
[START] [2019-10-15 18:04:59] calculate_delta
[CMD] [2019-10-15 18:04:59] echo "0a" > /app/public/diff/seychelles_sp_li_refs_17173.diff
[CMD] [2019-10-15 18:04:59] tail -n +1 /app/public/converted_csv/seychelles_sp_li_refs_17173.csv >> /app/public/diff/seychelles_sp_li_refs_17173.diff
[CMD] [2019-10-15 18:04:59] echo "." >> /app/public/diff/seychelles_sp_li_refs_17173.diff
[CMD] [2019-10-15 18:05:00] echo "0a" > /app/public/diff/seychelles_sp_li_nodes_17174.diff
[CMD] [2019-10-15 18:05:00] tail -n +1 /app/public/converted_csv/seychelles_sp_li_nodes_17174.csv >> /app/public/diff/seychelles_sp_li_nodes_17174.diff
[CMD] [2019-10-15 18:05:00] echo "." >> /app/public/diff/seychelles_sp_li_nodes_17174.diff
[CMD] [2019-10-15 18:05:01] echo "0a" > /app/public/diff/seychelles_sp_li_occurrences_17175.diff
[CMD] [2019-10-15 18:05:01] tail -n +1 /app/public/converted_csv/seychelles_sp_li_occurrences_17175.csv >> /app/public/diff/seychelles_sp_li_occurrences_17175.diff
[CMD] [2019-10-15 18:05:01] echo "." >> /app/public/diff/seychelles_sp_li_occurrences_17175.diff
[CMD] [2019-10-15 18:05:01] echo "0a" > /app/public/diff/seychelles_sp_li_measurements_17176.diff
[CMD] [2019-10-15 18:05:02] tail -n +1 /app/public/converted_csv/seychelles_sp_li_measurements_17176.csv >> /app/public/diff/seychelles_sp_li_measurements_17176.diff
[CMD] [2019-10-15 18:05:02] echo "." >> /app/public/diff/seychelles_sp_li_measurements_17176.diff
[STOP] [2019-10-15 18:05:02] calculate_delta
[START] [2019-10-15 18:05:02] parse_diff_and_store
[INFO] [2019-10-15 18:05:03] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 18:05:03] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 18:05:06] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 18:05:07] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 18:05:30] Storing 2 References
[INFO] [2019-10-15 18:05:30] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 18:05:30] Average Time: 0.0
[INFO] [2019-10-15 18:05:30] Total Time: 1s
[INFO] [2019-10-15 18:05:30] Storing 7233 ScientificNames
[INFO] [2019-10-15 18:05:30] Processing group of 7233 in 8 groups of 1000
[INFO] [2019-10-15 18:05:34] Average Time: 0.436
[INFO] [2019-10-15 18:05:34] Total Time: 4s
[INFO] [2019-10-15 18:05:34] last 3 / first 3: 0.46
[INFO] [2019-10-15 18:05:34] Std.Dev: 0.2588435821108957; Max: 1.02
[INFO] [2019-10-15 18:05:34] Storing 7233 Nodes
[INFO] [2019-10-15 18:05:34] Processing group of 7233 in 8 groups of 1000
[INFO] [2019-10-15 18:05:36] Average Time: 0.29
[INFO] [2019-10-15 18:05:36] Total Time: 3s
[INFO] [2019-10-15 18:05:36] last 3 / first 3: 0.61
[INFO] [2019-10-15 18:05:36] Std.Dev: 0.09486832980505137; Max: 0.39
[INFO] [2019-10-15 18:05:36] Storing 3856 Occurrences
[INFO] [2019-10-15 18:05:36] Processing group of 3856 in 4 groups of 1000
[INFO] [2019-10-15 18:05:37] Average Time: 0.098
[INFO] [2019-10-15 18:05:37] Total Time: 1s
[INFO] [2019-10-15 18:05:37] Storing 7940 TraitsReferences
[INFO] [2019-10-15 18:05:37] Processing group of 7940 in 8 groups of 1000
[INFO] [2019-10-15 18:05:37] Average Time: 0.079
[INFO] [2019-10-15 18:05:37] Total Time: 1s
[INFO] [2019-10-15 18:05:37] last 3 / first 3: 0.69
[INFO] [2019-10-15 18:05:37] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-15 18:05:37] Storing 7939 Traits
[INFO] [2019-10-15 18:05:37] Processing group of 7939 in 8 groups of 1000
[INFO] [2019-10-15 18:05:40] Average Time: 0.311
[INFO] [2019-10-15 18:05:40] Total Time: 3s
[INFO] [2019-10-15 18:05:40] last 3 / first 3: 0.78
[INFO] [2019-10-15 18:05:40] Std.Dev: 0.044721359549995794; Max: 0.4
[INFO] [2019-10-15 18:05:40] Storing 7939 MetaTraits
[INFO] [2019-10-15 18:05:40] Processing group of 7939 in 8 groups of 1000
[INFO] [2019-10-15 18:05:41] Average Time: 0.123
[INFO] [2019-10-15 18:05:41] Total Time: 2s
[INFO] [2019-10-15 18:05:41] last 3 / first 3: 1.06
[INFO] [2019-10-15 18:05:41] Std.Dev: 0.03162277660168379; Max: 0.17
[STOP] [2019-10-15 18:05:41] parse_diff_and_store
[START] [2019-10-15 18:05:41] resolve_keys
[INFO] [2019-10-15 18:06:09] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 18:06:12] traits to occurrences...
[INFO] [2019-10-15 18:06:13] traits to nodes (through occurrences)...
[INFO] [2019-10-15 18:06:14] Traits to sex term...
[INFO] [2019-10-15 18:06:15] Traits to lifestage term...
[INFO] [2019-10-15 18:06:17] MetaTraits to traits...
[INFO] [2019-10-15 18:06:17] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 18:06:18] Assocs to occurrences...
[INFO] [2019-10-15 18:06:18] Assocs to nodes...
[INFO] [2019-10-15 18:06:18] Assoc to sex term...
[INFO] [2019-10-15 18:06:18] Assoc to lifestage term...
[STOP] [2019-10-15 18:06:18] resolve_keys
[START] [2019-10-15 18:06:18] hold_for_later_1
[STOP] [2019-10-15 18:06:18] hold_for_later_1
[START] [2019-10-15 18:06:18] hold_for_later_2
[STOP] [2019-10-15 18:06:18] hold_for_later_2
[START] [2019-10-15 18:06:18] resolve_missing_parents
[STOP] [2019-10-15 18:06:32] resolve_missing_parents
[START] [2019-10-15 18:06:33] rebuild_nodes
[START] [2019-10-15 18:06:33] Flattener#flatten
[START] [2019-10-15 18:06:33] Flattener#study_resource
[START] [2019-10-15 18:06:33] Flattener#build_ancestry
[STOP] [2019-10-15 18:06:33] Flattener#build_ancestry
[INFO] [2019-10-15 18:06:33] 7233 ancestry keys
[START] [2019-10-15 18:06:33] build_node_ancestors
[INFO] [2019-10-15 18:06:33] old ancestors deleted.
[STOP] [2019-10-15 18:06:35] build_node_ancestors
[START] [2019-10-15 18:06:37] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 18:06:38] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 18:06:38] Flattener#flatten
[STOP] [2019-10-15 18:06:38] rebuild_nodes
[START] [2019-10-15 18:06:38] resolve_missing_media_owners
[STOP] [2019-10-15 18:06:38] resolve_missing_media_owners
[START] [2019-10-15 18:06:38] sanitize_media_verbatims
[STOP] [2019-10-15 18:06:38] sanitize_media_verbatims
[START] [2019-10-15 18:06:38] queue_downloads
[STOP] [2019-10-15 18:06:38] queue_downloads
[START] [2019-10-15 18:06:38] parse_names
[WARN] [2019-10-15 18:06:38] I see 7233 names which still need to be parsed.
[STOP] [2019-10-15 18:06:45] parse_names
[START] [2019-10-15 18:06:45] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 18:06:45] denormalize_canonical_names_to_nodes
[START] [2019-10-15 18:06:45] match_nodes
[START] [2019-10-15 18:06:45] map_all_nodes_to_pages
[STOP] [2019-10-15 18:14:39] map_all_nodes_to_pages
[INFO] [2019-10-15 18:14:39] 311 Unmatched nodes (of 7233)! That's too many to output. First 10: Kajikia albidus (#51797580); Scarus forsteri (#51801333); Chlorurus rhoduropterus (#51799469); Blenniella paulus (#51801532); Chromis caeruleus (#51801304); Fowleria auritus (#51801408); Cheilodipterus lineatus (#51795612); Ostorhinchus cyanosomus (#51798755); Vincentia punctatus (#51799248); Priolepis nocturnus (#51797095)
[START] [2019-10-15 18:14:39] update_nodes
[STOP] [2019-10-15 18:14:42] update_nodes
[STOP] [2019-10-15 18:14:42] match_nodes
[START] [2019-10-15 18:14:42] reindex_search
[STOP] [2019-10-15 18:15:03] reindex_search
[START] [2019-10-15 18:15:03] normalize_units
[STOP] [2019-10-15 18:15:03] normalize_units
[START] [2019-10-15 18:15:03] calculate_statistics
[STOP] [2019-10-15 18:15:03] calculate_statistics
[START] [2019-10-15 18:15:03] complete_harvest_instance
[START] [2019-10-15 18:15:03] overall_tsv_creation
[INFO] [2019-10-15 18:15:03] Processing group of 7233 in 1 batches of 10000
[INFO] [2019-10-15 18:16:19] 3856 Traits (unfiltered)...
[INFO] [2019-10-15 18:16:33] 3856 Traits (filtered)...
[INFO] [2019-10-15 18:16:33] 0 Associations (filtered)...
[INFO] [2019-10-15 18:17:19] 19279 metadata added.
[INFO] [2019-10-15 18:17:19] 0 metadata added.
[INFO] [2019-10-15 18:17:19] Average Time: 111.15
[INFO] [2019-10-15 18:17:19] Total Time: 2m16s
[STOP] [2019-10-15 18:17:19] overall_tsv_creation
[INFO] [2019-10-15 18:17:19] Done. Check your files:
[INFO] [2019-10-15 18:17:19] (7233 lines) /app/public/data/seychelles_sp_li/publish_nodes.tsv
[INFO] [2019-10-15 18:17:19] (30675 lines) /app/public/data/seychelles_sp_li/publish_node_ancestors.tsv
[INFO] [2019-10-15 18:17:20] (7233 lines) /app/public/data/seychelles_sp_li/publish_scientific_names.tsv
[INFO] [2019-10-15 18:17:20] (3857 lines) /app/public/data/seychelles_sp_li/publish_traits.tsv
[INFO] [2019-10-15 18:17:20] (19280 lines) /app/public/data/seychelles_sp_li/publish_metadata.tsv
[STOP] [2019-10-15 18:17:20] complete_harvest_instance
[START] [2019-10-15 18:17:20] completed
[STOP] [2019-10-15 18:17:20] completed
[STOP] [2019-10-15 18:17:20] logged process, took 744.14
Latest Process

15 Oct 18:04 EXITED currently processing 0