Harvest for Solomon Islands Species List Created 15 Oct 20:04

Stage: completed
Fetched: 15 Oct 20:04
Validated: 15 Oct 20:04
Deltas Created 15 Oct 20:04
Units Normalized: 15 Oct 20:07
Ancestry Built: 15 Oct 20:05
Nodes Matched: 15 Oct 20:07
Names Parsed: 15 Oct 20:05
New Models Stored: 15 Oct 20:04
Indexed: 15 Oct 20:07
Completed: 15 Oct 20:09
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-15 20:04:27 -0400 by logger.rb/56815
[START] [2019-10-15 20:04:27] logged process
[START] [2019-10-15 20:04:27] create_harvest_instance
[STOP] [2019-10-15 20:04:27] create_harvest_instance
[START] [2019-10-15 20:04:27] fetch_files
[STOP] [2019-10-15 20:04:27] fetch_files
[START] [2019-10-15 20:04:27] validate_each_file
[STOP] [2019-10-15 20:04:28] validate_each_file
[START] [2019-10-15 20:04:28] convert_to_csv
[CMD] [2019-10-15 20:04:28] /usr/bin/sort /app/public/converted_csv/solomon_islands__refs_17237.csv > /app/public/converted_csv/solomon_islands__refs_17237.csv_sorted
[CMD] [2019-10-15 20:04:28] /usr/bin/sort /app/public/converted_csv/solomon_islands__nodes_17238.csv > /app/public/converted_csv/solomon_islands__nodes_17238.csv_sorted
[CMD] [2019-10-15 20:04:28] /usr/bin/sort /app/public/converted_csv/solomon_islands__occurrences_17239.csv > /app/public/converted_csv/solomon_islands__occurrences_17239.csv_sorted
[CMD] [2019-10-15 20:04:28] /usr/bin/sort /app/public/converted_csv/solomon_islands__measurements_17240.csv > /app/public/converted_csv/solomon_islands__measurements_17240.csv_sorted
[STOP] [2019-10-15 20:04:29] convert_to_csv
[START] [2019-10-15 20:04:29] calculate_delta
[CMD] [2019-10-15 20:04:29] echo "0a" > /app/public/diff/solomon_islands__refs_17237.diff
[CMD] [2019-10-15 20:04:29] tail -n +1 /app/public/converted_csv/solomon_islands__refs_17237.csv >> /app/public/diff/solomon_islands__refs_17237.diff
[CMD] [2019-10-15 20:04:29] echo "." >> /app/public/diff/solomon_islands__refs_17237.diff
[CMD] [2019-10-15 20:04:30] echo "0a" > /app/public/diff/solomon_islands__nodes_17238.diff
[CMD] [2019-10-15 20:04:30] tail -n +1 /app/public/converted_csv/solomon_islands__nodes_17238.csv >> /app/public/diff/solomon_islands__nodes_17238.diff
[CMD] [2019-10-15 20:04:30] echo "." >> /app/public/diff/solomon_islands__nodes_17238.diff
[CMD] [2019-10-15 20:04:31] echo "0a" > /app/public/diff/solomon_islands__occurrences_17239.diff
[CMD] [2019-10-15 20:04:31] tail -n +1 /app/public/converted_csv/solomon_islands__occurrences_17239.csv >> /app/public/diff/solomon_islands__occurrences_17239.diff
[CMD] [2019-10-15 20:04:31] echo "." >> /app/public/diff/solomon_islands__occurrences_17239.diff
[CMD] [2019-10-15 20:04:31] echo "0a" > /app/public/diff/solomon_islands__measurements_17240.diff
[CMD] [2019-10-15 20:04:32] tail -n +1 /app/public/converted_csv/solomon_islands__measurements_17240.csv >> /app/public/diff/solomon_islands__measurements_17240.diff
[CMD] [2019-10-15 20:04:32] echo "." >> /app/public/diff/solomon_islands__measurements_17240.diff
[STOP] [2019-10-15 20:04:32] calculate_delta
[START] [2019-10-15 20:04:32] parse_diff_and_store
[INFO] [2019-10-15 20:04:33] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 20:04:33] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 20:04:34] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 20:04:34] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 20:04:42] Storing 2 References
[INFO] [2019-10-15 20:04:42] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 20:04:42] Average Time: 0.0
[INFO] [2019-10-15 20:04:42] Total Time: 1s
[INFO] [2019-10-15 20:04:42] Storing 2603 ScientificNames
[INFO] [2019-10-15 20:04:42] Processing group of 2603 in 3 groups of 1000
[INFO] [2019-10-15 20:04:43] Average Time: 0.407
[INFO] [2019-10-15 20:04:43] Total Time: 2s
[INFO] [2019-10-15 20:04:43] Storing 2603 Nodes
[INFO] [2019-10-15 20:04:43] Processing group of 2603 in 3 groups of 1000
[INFO] [2019-10-15 20:04:44] Average Time: 0.253
[INFO] [2019-10-15 20:04:44] Total Time: 1s
[INFO] [2019-10-15 20:04:44] Storing 964 Occurrences
[INFO] [2019-10-15 20:04:44] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-15 20:04:44] Average Time: 0.12
[INFO] [2019-10-15 20:04:44] Total Time: 1s
[INFO] [2019-10-15 20:04:44] Storing 2660 TraitsReferences
[INFO] [2019-10-15 20:04:44] Processing group of 2660 in 3 groups of 1000
[INFO] [2019-10-15 20:04:46] Average Time: 0.48
[INFO] [2019-10-15 20:04:46] Total Time: 2s
[INFO] [2019-10-15 20:04:46] Storing 2659 Traits
[INFO] [2019-10-15 20:04:46] Processing group of 2659 in 3 groups of 1000
[INFO] [2019-10-15 20:04:46] Average Time: 0.297
[INFO] [2019-10-15 20:04:46] Total Time: 1s
[INFO] [2019-10-15 20:04:46] Storing 2659 MetaTraits
[INFO] [2019-10-15 20:04:46] Processing group of 2659 in 3 groups of 1000
[INFO] [2019-10-15 20:04:47] Average Time: 0.107
[INFO] [2019-10-15 20:04:47] Total Time: 1s
[STOP] [2019-10-15 20:04:47] parse_diff_and_store
[START] [2019-10-15 20:04:47] resolve_keys
[INFO] [2019-10-15 20:05:01] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 20:05:02] traits to occurrences...
[INFO] [2019-10-15 20:05:03] traits to nodes (through occurrences)...
[INFO] [2019-10-15 20:05:03] Traits to sex term...
[INFO] [2019-10-15 20:05:04] Traits to lifestage term...
[INFO] [2019-10-15 20:05:05] MetaTraits to traits...
[INFO] [2019-10-15 20:05:05] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 20:05:06] Assocs to occurrences...
[INFO] [2019-10-15 20:05:06] Assocs to nodes...
[INFO] [2019-10-15 20:05:06] Assoc to sex term...
[INFO] [2019-10-15 20:05:06] Assoc to lifestage term...
[STOP] [2019-10-15 20:05:06] resolve_keys
[START] [2019-10-15 20:05:06] hold_for_later_1
[STOP] [2019-10-15 20:05:06] hold_for_later_1
[START] [2019-10-15 20:05:06] hold_for_later_2
[STOP] [2019-10-15 20:05:06] hold_for_later_2
[START] [2019-10-15 20:05:06] resolve_missing_parents
[STOP] [2019-10-15 20:05:10] resolve_missing_parents
[START] [2019-10-15 20:05:10] rebuild_nodes
[START] [2019-10-15 20:05:10] Flattener#flatten
[START] [2019-10-15 20:05:10] Flattener#study_resource
[START] [2019-10-15 20:05:10] Flattener#build_ancestry
[STOP] [2019-10-15 20:05:10] Flattener#build_ancestry
[INFO] [2019-10-15 20:05:10] 2603 ancestry keys
[START] [2019-10-15 20:05:10] build_node_ancestors
[INFO] [2019-10-15 20:05:10] old ancestors deleted.
[STOP] [2019-10-15 20:05:11] build_node_ancestors
[START] [2019-10-15 20:05:12] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 20:05:12] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 20:05:12] Flattener#flatten
[STOP] [2019-10-15 20:05:12] rebuild_nodes
[START] [2019-10-15 20:05:12] resolve_missing_media_owners
[STOP] [2019-10-15 20:05:12] resolve_missing_media_owners
[START] [2019-10-15 20:05:12] sanitize_media_verbatims
[STOP] [2019-10-15 20:05:12] sanitize_media_verbatims
[START] [2019-10-15 20:05:12] queue_downloads
[STOP] [2019-10-15 20:05:12] queue_downloads
[START] [2019-10-15 20:05:12] parse_names
[WARN] [2019-10-15 20:05:12] I see 2603 names which still need to be parsed.
[STOP] [2019-10-15 20:05:15] parse_names
[START] [2019-10-15 20:05:15] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 20:05:15] denormalize_canonical_names_to_nodes
[START] [2019-10-15 20:05:15] match_nodes
[START] [2019-10-15 20:05:15] map_all_nodes_to_pages
[STOP] [2019-10-15 20:07:50] map_all_nodes_to_pages
[INFO] [2019-10-15 20:07:50] 149 Unmatched nodes (of 2603)! That's too many to output. First 10: Hydrophiidae (#51851320); Rana guppyii (#51851406); Monarcha barbatus (#51850971); Monarcha viduus (#51851176); Monarcha cinerescens (#51852376); Nectarinia jugularis (#51851030); Coracina tenuirostris (#51850990); Coracina holopolia (#51851286); Coracina salomonis (#51852683); Phylloscopus poliocephalus (#51853281)
[START] [2019-10-15 20:07:50] update_nodes
[STOP] [2019-10-15 20:07:51] update_nodes
[STOP] [2019-10-15 20:07:51] match_nodes
[START] [2019-10-15 20:07:51] reindex_search
[STOP] [2019-10-15 20:07:57] reindex_search
[START] [2019-10-15 20:07:57] normalize_units
[STOP] [2019-10-15 20:07:57] normalize_units
[START] [2019-10-15 20:07:57] calculate_statistics
[STOP] [2019-10-15 20:07:57] calculate_statistics
[START] [2019-10-15 20:07:57] complete_harvest_instance
[START] [2019-10-15 20:07:57] overall_tsv_creation
[INFO] [2019-10-15 20:07:57] Processing group of 2603 in 1 batches of 10000
[INFO] [2019-10-15 20:09:04] 964 Traits (unfiltered)...
[INFO] [2019-10-15 20:09:18] 964 Traits (filtered)...
[INFO] [2019-10-15 20:09:18] 0 Associations (filtered)...
[INFO] [2019-10-15 20:09:57] 4819 metadata added.
[INFO] [2019-10-15 20:09:57] 0 metadata added.
[INFO] [2019-10-15 20:09:57] Average Time: 87.75
[INFO] [2019-10-15 20:09:57] Total Time: 1m60s
[STOP] [2019-10-15 20:09:57] overall_tsv_creation
[INFO] [2019-10-15 20:09:57] Done. Check your files:
[INFO] [2019-10-15 20:09:57] (2603 lines) /app/public/data/solomon_islands_/publish_nodes.tsv
[INFO] [2019-10-15 20:09:58] (8279 lines) /app/public/data/solomon_islands_/publish_node_ancestors.tsv
[INFO] [2019-10-15 20:09:58] (2603 lines) /app/public/data/solomon_islands_/publish_scientific_names.tsv
[INFO] [2019-10-15 20:09:58] (965 lines) /app/public/data/solomon_islands_/publish_traits.tsv
[INFO] [2019-10-15 20:09:58] (4820 lines) /app/public/data/solomon_islands_/publish_metadata.tsv
[STOP] [2019-10-15 20:09:59] complete_harvest_instance
[START] [2019-10-15 20:09:59] completed
[STOP] [2019-10-15 20:09:59] completed
[STOP] [2019-10-15 20:09:59] logged process, took 332.13
Latest Process

15 Oct 20:04 EXITED currently processing 0