Harvest for Bhutan Species List Created 11 Oct 15:44

Stage: completed
Fetched: 11 Oct 15:44
Validated: 11 Oct 15:44
Deltas Created 11 Oct 15:44
Units Normalized: 11 Oct 15:47
Ancestry Built: 11 Oct 15:45
Nodes Matched: 11 Oct 15:47
Names Parsed: 11 Oct 15:45
New Models Stored: 11 Oct 15:45
Indexed: 11 Oct 15:47
Completed: 11 Oct 15:50
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-11 15:44:42 -0400 by logger.rb/56815
[START] [2019-10-11 15:44:42] logged process
[START] [2019-10-11 15:44:42] create_harvest_instance
[STOP] [2019-10-11 15:44:43] create_harvest_instance
[START] [2019-10-11 15:44:43] fetch_files
[STOP] [2019-10-11 15:44:43] fetch_files
[START] [2019-10-11 15:44:43] validate_each_file
[STOP] [2019-10-11 15:44:44] validate_each_file
[START] [2019-10-11 15:44:44] convert_to_csv
[CMD] [2019-10-11 15:44:44] /usr/bin/sort /app/public/converted_csv/bhutan_sp_list_refs_15204.csv > /app/public/converted_csv/bhutan_sp_list_refs_15204.csv_sorted
[CMD] [2019-10-11 15:44:44] /usr/bin/sort /app/public/converted_csv/bhutan_sp_list_nodes_15205.csv > /app/public/converted_csv/bhutan_sp_list_nodes_15205.csv_sorted
[CMD] [2019-10-11 15:44:44] /usr/bin/sort /app/public/converted_csv/bhutan_sp_list_occurrences_15206.csv > /app/public/converted_csv/bhutan_sp_list_occurrences_15206.csv_sorted
[CMD] [2019-10-11 15:44:44] /usr/bin/sort /app/public/converted_csv/bhutan_sp_list_measurements_15207.csv > /app/public/converted_csv/bhutan_sp_list_measurements_15207.csv_sorted
[STOP] [2019-10-11 15:44:44] convert_to_csv
[START] [2019-10-11 15:44:44] calculate_delta
[CMD] [2019-10-11 15:44:44] echo "0a" > /app/public/diff/bhutan_sp_list_refs_15204.diff
[CMD] [2019-10-11 15:44:44] tail -n +1 /app/public/converted_csv/bhutan_sp_list_refs_15204.csv >> /app/public/diff/bhutan_sp_list_refs_15204.diff
[CMD] [2019-10-11 15:44:44] echo "." >> /app/public/diff/bhutan_sp_list_refs_15204.diff
[CMD] [2019-10-11 15:44:44] echo "0a" > /app/public/diff/bhutan_sp_list_nodes_15205.diff
[CMD] [2019-10-11 15:44:44] tail -n +1 /app/public/converted_csv/bhutan_sp_list_nodes_15205.csv >> /app/public/diff/bhutan_sp_list_nodes_15205.diff
[CMD] [2019-10-11 15:44:44] echo "." >> /app/public/diff/bhutan_sp_list_nodes_15205.diff
[CMD] [2019-10-11 15:44:44] echo "0a" > /app/public/diff/bhutan_sp_list_occurrences_15206.diff
[CMD] [2019-10-11 15:44:44] tail -n +1 /app/public/converted_csv/bhutan_sp_list_occurrences_15206.csv >> /app/public/diff/bhutan_sp_list_occurrences_15206.diff
[CMD] [2019-10-11 15:44:44] echo "." >> /app/public/diff/bhutan_sp_list_occurrences_15206.diff
[CMD] [2019-10-11 15:44:44] echo "0a" > /app/public/diff/bhutan_sp_list_measurements_15207.diff
[CMD] [2019-10-11 15:44:44] tail -n +1 /app/public/converted_csv/bhutan_sp_list_measurements_15207.csv >> /app/public/diff/bhutan_sp_list_measurements_15207.diff
[CMD] [2019-10-11 15:44:44] echo "." >> /app/public/diff/bhutan_sp_list_measurements_15207.diff
[STOP] [2019-10-11 15:44:44] calculate_delta
[START] [2019-10-11 15:44:44] parse_diff_and_store
[INFO] [2019-10-11 15:44:44] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-11 15:44:44] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-11 15:44:46] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-11 15:44:46] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-11 15:45:02] Storing 2 References
[INFO] [2019-10-11 15:45:02] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-11 15:45:02] Average Time: 0.0
[INFO] [2019-10-11 15:45:02] Total Time: 1s
[INFO] [2019-10-11 15:45:02] Storing 4390 ScientificNames
[INFO] [2019-10-11 15:45:02] Processing group of 4390 in 5 groups of 1000
[INFO] [2019-10-11 15:45:04] Average Time: 0.38
[INFO] [2019-10-11 15:45:04] Total Time: 2s
[INFO] [2019-10-11 15:45:04] Storing 4390 Nodes
[INFO] [2019-10-11 15:45:04] Processing group of 4390 in 5 groups of 1000
[INFO] [2019-10-11 15:45:06] Average Time: 0.294
[INFO] [2019-10-11 15:45:06] Total Time: 2s
[INFO] [2019-10-11 15:45:06] Storing 2410 Occurrences
[INFO] [2019-10-11 15:45:06] Processing group of 2410 in 3 groups of 1000
[INFO] [2019-10-11 15:45:06] Average Time: 0.133
[INFO] [2019-10-11 15:45:06] Total Time: 1s
[INFO] [2019-10-11 15:45:06] Storing 5400 TraitsReferences
[INFO] [2019-10-11 15:45:06] Processing group of 5400 in 6 groups of 1000
[INFO] [2019-10-11 15:45:07] Average Time: 0.083
[INFO] [2019-10-11 15:45:07] Total Time: 1s
[INFO] [2019-10-11 15:45:07] Storing 5399 Traits
[INFO] [2019-10-11 15:45:07] Processing group of 5399 in 6 groups of 1000
[INFO] [2019-10-11 15:45:09] Average Time: 0.33
[INFO] [2019-10-11 15:45:09] Total Time: 3s
[INFO] [2019-10-11 15:45:09] Storing 5398 MetaTraits
[INFO] [2019-10-11 15:45:09] Processing group of 5398 in 6 groups of 1000
[INFO] [2019-10-11 15:45:10] Average Time: 0.13
[INFO] [2019-10-11 15:45:10] Total Time: 1s
[STOP] [2019-10-11 15:45:10] parse_diff_and_store
[START] [2019-10-11 15:45:10] resolve_keys
[INFO] [2019-10-11 15:45:29] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-11 15:45:31] traits to occurrences...
[INFO] [2019-10-11 15:45:33] traits to nodes (through occurrences)...
[INFO] [2019-10-11 15:45:33] Traits to sex term...
[INFO] [2019-10-11 15:45:35] Traits to lifestage term...
[INFO] [2019-10-11 15:45:37] MetaTraits to traits...
[INFO] [2019-10-11 15:45:38] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-11 15:45:38] Assocs to occurrences...
[INFO] [2019-10-11 15:45:38] Assocs to nodes...
[INFO] [2019-10-11 15:45:38] Assoc to sex term...
[INFO] [2019-10-11 15:45:38] Assoc to lifestage term...
[STOP] [2019-10-11 15:45:39] resolve_keys
[START] [2019-10-11 15:45:39] hold_for_later_1
[STOP] [2019-10-11 15:45:39] hold_for_later_1
[START] [2019-10-11 15:45:39] hold_for_later_2
[STOP] [2019-10-11 15:45:39] hold_for_later_2
[START] [2019-10-11 15:45:39] resolve_missing_parents
[STOP] [2019-10-11 15:45:47] resolve_missing_parents
[START] [2019-10-11 15:45:47] rebuild_nodes
[START] [2019-10-11 15:45:47] Flattener#flatten
[START] [2019-10-11 15:45:47] Flattener#study_resource
[START] [2019-10-11 15:45:47] Flattener#build_ancestry
[STOP] [2019-10-11 15:45:47] Flattener#build_ancestry
[INFO] [2019-10-11 15:45:47] 4390 ancestry keys
[START] [2019-10-11 15:45:47] build_node_ancestors
[INFO] [2019-10-11 15:45:47] old ancestors deleted.
[STOP] [2019-10-11 15:45:48] build_node_ancestors
[START] [2019-10-11 15:45:49] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 15:45:49] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 15:45:49] Flattener#flatten
[STOP] [2019-10-11 15:45:49] rebuild_nodes
[START] [2019-10-11 15:45:49] resolve_missing_media_owners
[STOP] [2019-10-11 15:45:49] resolve_missing_media_owners
[START] [2019-10-11 15:45:49] sanitize_media_verbatims
[STOP] [2019-10-11 15:45:49] sanitize_media_verbatims
[START] [2019-10-11 15:45:49] queue_downloads
[STOP] [2019-10-11 15:45:49] queue_downloads
[START] [2019-10-11 15:45:49] parse_names
[WARN] [2019-10-11 15:45:49] I see 4390 names which still need to be parsed.
[STOP] [2019-10-11 15:45:54] parse_names
[START] [2019-10-11 15:45:54] denormalize_canonical_names_to_nodes
[STOP] [2019-10-11 15:45:54] denormalize_canonical_names_to_nodes
[START] [2019-10-11 15:45:54] match_nodes
[START] [2019-10-11 15:45:54] map_all_nodes_to_pages
[STOP] [2019-10-11 15:47:39] map_all_nodes_to_pages
[INFO] [2019-10-11 15:47:39] 275 Unmatched nodes (of 4390)! That's too many to output. First 10: Parus spilonotus (#48790746); Parus dichrous (#48794336); Parus rubidiventris (#48794646); Hypsipetes mcclellandii (#48794048); Passer rutilans (#48790755); Phoenicurus caeruleocephalus (#48792074); Phoenicurus caeruleocephala (#48792171); Muscicapa latirostris (#48791421); Myiomela leucurum (#48791013); Cinclidium leucurum (#48791073)
[START] [2019-10-11 15:47:39] update_nodes
[STOP] [2019-10-11 15:47:41] update_nodes
[STOP] [2019-10-11 15:47:41] match_nodes
[START] [2019-10-11 15:47:41] reindex_search
[STOP] [2019-10-11 15:47:48] reindex_search
[START] [2019-10-11 15:47:48] normalize_units
[STOP] [2019-10-11 15:47:48] normalize_units
[START] [2019-10-11 15:47:48] calculate_statistics
[STOP] [2019-10-11 15:47:48] calculate_statistics
[START] [2019-10-11 15:47:48] complete_harvest_instance
[START] [2019-10-11 15:47:48] overall_tsv_creation
[INFO] [2019-10-11 15:47:48] Processing group of 4390 in 1 batches of 10000
[INFO] [2019-10-11 15:49:01] 2410 Traits (unfiltered)...
[INFO] [2019-10-11 15:49:19] 2410 Traits (filtered)...
[INFO] [2019-10-11 15:49:19] 0 Associations (filtered)...
[INFO] [2019-10-11 15:50:04] 12048 metadata added.
[INFO] [2019-10-11 15:50:04] 0 metadata added.
[INFO] [2019-10-11 15:50:04] Average Time: 109.78
[INFO] [2019-10-11 15:50:04] Total Time: 2m16s
[STOP] [2019-10-11 15:50:04] overall_tsv_creation
[INFO] [2019-10-11 15:50:04] Done. Check your files:
[INFO] [2019-10-11 15:50:04] (4390 lines) /app/public/data/bhutan_sp_list/publish_nodes.tsv
[INFO] [2019-10-11 15:50:04] (10808 lines) /app/public/data/bhutan_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-11 15:50:04] (4390 lines) /app/public/data/bhutan_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-11 15:50:04] (2411 lines) /app/public/data/bhutan_sp_list/publish_traits.tsv
[INFO] [2019-10-11 15:50:04] (12049 lines) /app/public/data/bhutan_sp_list/publish_metadata.tsv
[STOP] [2019-10-11 15:50:04] complete_harvest_instance
[START] [2019-10-11 15:50:04] completed
[STOP] [2019-10-11 15:50:04] completed
[STOP] [2019-10-11 15:50:04] logged process, took 321.84
Latest Process

11 Oct 15:44 EXITED currently processing 0