Harvest for Saudi Arabia Species List Created 15 Oct 16:45

Stage: completed
Fetched: 15 Oct 16:45
Validated: 15 Oct 16:46
Deltas Created 15 Oct 16:46
Units Normalized: 15 Oct 16:53
Ancestry Built: 15 Oct 16:47
Nodes Matched: 15 Oct 16:53
Names Parsed: 15 Oct 16:47
New Models Stored: 15 Oct 16:46
Indexed: 15 Oct 16:53
Completed: 15 Oct 16:55
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-15 16:45:59 -0400 by logger.rb/56815
[START] [2019-10-15 16:45:59] logged process
[START] [2019-10-15 16:45:59] create_harvest_instance
[STOP] [2019-10-15 16:45:59] create_harvest_instance
[START] [2019-10-15 16:45:59] fetch_files
[STOP] [2019-10-15 16:45:59] fetch_files
[START] [2019-10-15 16:45:59] validate_each_file
[STOP] [2019-10-15 16:46:00] validate_each_file
[START] [2019-10-15 16:46:00] convert_to_csv
[CMD] [2019-10-15 16:46:00] /usr/bin/sort /app/public/converted_csv/saudi_arabia_sp__refs_17101.csv > /app/public/converted_csv/saudi_arabia_sp__refs_17101.csv_sorted
[CMD] [2019-10-15 16:46:00] /usr/bin/sort /app/public/converted_csv/saudi_arabia_sp__nodes_17102.csv > /app/public/converted_csv/saudi_arabia_sp__nodes_17102.csv_sorted
[CMD] [2019-10-15 16:46:00] /usr/bin/sort /app/public/converted_csv/saudi_arabia_sp__occurrences_17103.csv > /app/public/converted_csv/saudi_arabia_sp__occurrences_17103.csv_sorted
[CMD] [2019-10-15 16:46:01] /usr/bin/sort /app/public/converted_csv/saudi_arabia_sp__measurements_17104.csv > /app/public/converted_csv/saudi_arabia_sp__measurements_17104.csv_sorted
[STOP] [2019-10-15 16:46:01] convert_to_csv
[START] [2019-10-15 16:46:01] calculate_delta
[CMD] [2019-10-15 16:46:01] echo "0a" > /app/public/diff/saudi_arabia_sp__refs_17101.diff
[CMD] [2019-10-15 16:46:01] tail -n +1 /app/public/converted_csv/saudi_arabia_sp__refs_17101.csv >> /app/public/diff/saudi_arabia_sp__refs_17101.diff
[CMD] [2019-10-15 16:46:01] echo "." >> /app/public/diff/saudi_arabia_sp__refs_17101.diff
[CMD] [2019-10-15 16:46:02] echo "0a" > /app/public/diff/saudi_arabia_sp__nodes_17102.diff
[CMD] [2019-10-15 16:46:02] tail -n +1 /app/public/converted_csv/saudi_arabia_sp__nodes_17102.csv >> /app/public/diff/saudi_arabia_sp__nodes_17102.diff
[CMD] [2019-10-15 16:46:02] echo "." >> /app/public/diff/saudi_arabia_sp__nodes_17102.diff
[CMD] [2019-10-15 16:46:03] echo "0a" > /app/public/diff/saudi_arabia_sp__occurrences_17103.diff
[CMD] [2019-10-15 16:46:03] tail -n +1 /app/public/converted_csv/saudi_arabia_sp__occurrences_17103.csv >> /app/public/diff/saudi_arabia_sp__occurrences_17103.diff
[CMD] [2019-10-15 16:46:03] echo "." >> /app/public/diff/saudi_arabia_sp__occurrences_17103.diff
[CMD] [2019-10-15 16:46:03] echo "0a" > /app/public/diff/saudi_arabia_sp__measurements_17104.diff
[CMD] [2019-10-15 16:46:04] tail -n +1 /app/public/converted_csv/saudi_arabia_sp__measurements_17104.csv >> /app/public/diff/saudi_arabia_sp__measurements_17104.diff
[CMD] [2019-10-15 16:46:04] echo "." >> /app/public/diff/saudi_arabia_sp__measurements_17104.diff
[STOP] [2019-10-15 16:46:04] calculate_delta
[START] [2019-10-15 16:46:04] parse_diff_and_store
[INFO] [2019-10-15 16:46:05] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 16:46:05] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 16:46:07] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 16:46:08] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 16:46:24] Storing 2 References
[INFO] [2019-10-15 16:46:24] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 16:46:24] Average Time: 0.0
[INFO] [2019-10-15 16:46:24] Total Time: 1s
[INFO] [2019-10-15 16:46:24] Storing 5421 ScientificNames
[INFO] [2019-10-15 16:46:24] Processing group of 5421 in 6 groups of 1000
[INFO] [2019-10-15 16:46:26] Average Time: 0.353
[INFO] [2019-10-15 16:46:26] Total Time: 3s
[INFO] [2019-10-15 16:46:26] Storing 5421 Nodes
[INFO] [2019-10-15 16:46:26] Processing group of 5421 in 6 groups of 1000
[INFO] [2019-10-15 16:46:28] Average Time: 0.308
[INFO] [2019-10-15 16:46:28] Total Time: 2s
[INFO] [2019-10-15 16:46:28] Storing 2892 Occurrences
[INFO] [2019-10-15 16:46:28] Processing group of 2892 in 3 groups of 1000
[INFO] [2019-10-15 16:46:29] Average Time: 0.103
[INFO] [2019-10-15 16:46:29] Total Time: 1s
[INFO] [2019-10-15 16:46:29] Storing 5850 TraitsReferences
[INFO] [2019-10-15 16:46:29] Processing group of 5850 in 6 groups of 1000
[INFO] [2019-10-15 16:46:29] Average Time: 0.08
[INFO] [2019-10-15 16:46:29] Total Time: 1s
[INFO] [2019-10-15 16:46:29] Storing 5849 Traits
[INFO] [2019-10-15 16:46:29] Processing group of 5849 in 6 groups of 1000
[INFO] [2019-10-15 16:46:31] Average Time: 0.312
[INFO] [2019-10-15 16:46:31] Total Time: 2s
[INFO] [2019-10-15 16:46:31] Storing 5850 MetaTraits
[INFO] [2019-10-15 16:46:31] Processing group of 5850 in 6 groups of 1000
[INFO] [2019-10-15 16:46:32] Average Time: 0.118
[INFO] [2019-10-15 16:46:32] Total Time: 1s
[STOP] [2019-10-15 16:46:32] parse_diff_and_store
[START] [2019-10-15 16:46:32] resolve_keys
[INFO] [2019-10-15 16:46:55] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 16:46:58] traits to occurrences...
[INFO] [2019-10-15 16:46:59] traits to nodes (through occurrences)...
[INFO] [2019-10-15 16:46:59] Traits to sex term...
[INFO] [2019-10-15 16:47:00] Traits to lifestage term...
[INFO] [2019-10-15 16:47:01] MetaTraits to traits...
[INFO] [2019-10-15 16:47:02] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 16:47:03] Assocs to occurrences...
[INFO] [2019-10-15 16:47:03] Assocs to nodes...
[INFO] [2019-10-15 16:47:03] Assoc to sex term...
[INFO] [2019-10-15 16:47:03] Assoc to lifestage term...
[STOP] [2019-10-15 16:47:03] resolve_keys
[START] [2019-10-15 16:47:03] hold_for_later_1
[STOP] [2019-10-15 16:47:03] hold_for_later_1
[START] [2019-10-15 16:47:03] hold_for_later_2
[STOP] [2019-10-15 16:47:03] hold_for_later_2
[START] [2019-10-15 16:47:03] resolve_missing_parents
[STOP] [2019-10-15 16:47:13] resolve_missing_parents
[START] [2019-10-15 16:47:13] rebuild_nodes
[START] [2019-10-15 16:47:13] Flattener#flatten
[START] [2019-10-15 16:47:13] Flattener#study_resource
[START] [2019-10-15 16:47:13] Flattener#build_ancestry
[STOP] [2019-10-15 16:47:13] Flattener#build_ancestry
[INFO] [2019-10-15 16:47:13] 5421 ancestry keys
[START] [2019-10-15 16:47:13] build_node_ancestors
[INFO] [2019-10-15 16:47:13] old ancestors deleted.
[STOP] [2019-10-15 16:47:14] build_node_ancestors
[START] [2019-10-15 16:47:15] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:47:15] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:47:15] Flattener#flatten
[STOP] [2019-10-15 16:47:15] rebuild_nodes
[START] [2019-10-15 16:47:15] resolve_missing_media_owners
[STOP] [2019-10-15 16:47:15] resolve_missing_media_owners
[START] [2019-10-15 16:47:15] sanitize_media_verbatims
[STOP] [2019-10-15 16:47:15] sanitize_media_verbatims
[START] [2019-10-15 16:47:15] queue_downloads
[STOP] [2019-10-15 16:47:15] queue_downloads
[START] [2019-10-15 16:47:15] parse_names
[WARN] [2019-10-15 16:47:15] I see 5421 names which still need to be parsed.
[STOP] [2019-10-15 16:47:20] parse_names
[START] [2019-10-15 16:47:20] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 16:47:20] denormalize_canonical_names_to_nodes
[START] [2019-10-15 16:47:20] match_nodes
[START] [2019-10-15 16:47:20] map_all_nodes_to_pages
[STOP] [2019-10-15 16:52:58] map_all_nodes_to_pages
[INFO] [2019-10-15 16:52:58] 440 Unmatched nodes (of 5421)! That's too many to output. First 10: Calandrella rufescens (#51762181); Erythropygia (#51761944); Erythropygia galactotes (#51761943); Cercomela (#51762036); Cercomela melanura (#51762035); Phylloscopus sibillatrix (#51764233); Sylvia rueppelli (#51765207); Turdoides squamiceps (#51762028); Hedydipna platurus (#51764933); Hedydipna metallicus (#51766294)
[START] [2019-10-15 16:52:58] update_nodes
[STOP] [2019-10-15 16:53:00] update_nodes
[STOP] [2019-10-15 16:53:00] match_nodes
[START] [2019-10-15 16:53:00] reindex_search
[STOP] [2019-10-15 16:53:13] reindex_search
[START] [2019-10-15 16:53:13] normalize_units
[STOP] [2019-10-15 16:53:13] normalize_units
[START] [2019-10-15 16:53:13] calculate_statistics
[STOP] [2019-10-15 16:53:13] calculate_statistics
[START] [2019-10-15 16:53:13] complete_harvest_instance
[START] [2019-10-15 16:53:13] overall_tsv_creation
[INFO] [2019-10-15 16:53:13] Processing group of 5421 in 1 batches of 10000
[INFO] [2019-10-15 16:54:21] 2892 Traits (unfiltered)...
[INFO] [2019-10-15 16:54:35] 2892 Traits (filtered)...
[INFO] [2019-10-15 16:54:35] 0 Associations (filtered)...
[INFO] [2019-10-15 16:55:19] 14460 metadata added.
[INFO] [2019-10-15 16:55:19] 0 metadata added.
[INFO] [2019-10-15 16:55:19] Average Time: 101.4
[INFO] [2019-10-15 16:55:19] Total Time: 2m6s
[STOP] [2019-10-15 16:55:19] overall_tsv_creation
[INFO] [2019-10-15 16:55:19] Done. Check your files:
[INFO] [2019-10-15 16:55:19] (5421 lines) /app/public/data/saudi_arabia_sp_/publish_nodes.tsv
[INFO] [2019-10-15 16:55:19] (12354 lines) /app/public/data/saudi_arabia_sp_/publish_node_ancestors.tsv
[INFO] [2019-10-15 16:55:19] (5421 lines) /app/public/data/saudi_arabia_sp_/publish_scientific_names.tsv
[INFO] [2019-10-15 16:55:20] (2893 lines) /app/public/data/saudi_arabia_sp_/publish_traits.tsv
[INFO] [2019-10-15 16:55:20] (14461 lines) /app/public/data/saudi_arabia_sp_/publish_metadata.tsv
[STOP] [2019-10-15 16:55:20] complete_harvest_instance
[START] [2019-10-15 16:55:20] completed
[STOP] [2019-10-15 16:55:20] completed
[STOP] [2019-10-15 16:55:20] logged process, took 561.57
Latest Process

15 Oct 16:45 EXITED currently processing 0