Harvest for Norfolk Island Species List Created 14 Oct 19:42

Stage: completed
Fetched: 14 Oct 19:42
Validated: 14 Oct 19:42
Deltas Created 14 Oct 19:42
Units Normalized: 14 Oct 19:45
Ancestry Built: 14 Oct 19:43
Nodes Matched: 14 Oct 19:45
Names Parsed: 14 Oct 19:43
New Models Stored: 14 Oct 19:42
Indexed: 14 Oct 19:45
Completed: 14 Oct 19:47
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 19:42:24 -0400 by logger.rb/56815
[START] [2019-10-14 19:42:24] logged process
[START] [2019-10-14 19:42:24] create_harvest_instance
[STOP] [2019-10-14 19:42:25] create_harvest_instance
[START] [2019-10-14 19:42:25] fetch_files
[STOP] [2019-10-14 19:42:25] fetch_files
[START] [2019-10-14 19:42:25] validate_each_file
[STOP] [2019-10-14 19:42:25] validate_each_file
[START] [2019-10-14 19:42:25] convert_to_csv
[CMD] [2019-10-14 19:42:25] /usr/bin/sort /app/public/converted_csv/norfolk_island_s_refs_16773.csv > /app/public/converted_csv/norfolk_island_s_refs_16773.csv_sorted
[CMD] [2019-10-14 19:42:26] /usr/bin/sort /app/public/converted_csv/norfolk_island_s_nodes_16774.csv > /app/public/converted_csv/norfolk_island_s_nodes_16774.csv_sorted
[CMD] [2019-10-14 19:42:26] /usr/bin/sort /app/public/converted_csv/norfolk_island_s_occurrences_16775.csv > /app/public/converted_csv/norfolk_island_s_occurrences_16775.csv_sorted
[CMD] [2019-10-14 19:42:26] /usr/bin/sort /app/public/converted_csv/norfolk_island_s_measurements_16776.csv > /app/public/converted_csv/norfolk_island_s_measurements_16776.csv_sorted
[STOP] [2019-10-14 19:42:26] convert_to_csv
[START] [2019-10-14 19:42:26] calculate_delta
[CMD] [2019-10-14 19:42:26] echo "0a" > /app/public/diff/norfolk_island_s_refs_16773.diff
[CMD] [2019-10-14 19:42:27] tail -n +1 /app/public/converted_csv/norfolk_island_s_refs_16773.csv >> /app/public/diff/norfolk_island_s_refs_16773.diff
[CMD] [2019-10-14 19:42:27] echo "." >> /app/public/diff/norfolk_island_s_refs_16773.diff
[CMD] [2019-10-14 19:42:27] echo "0a" > /app/public/diff/norfolk_island_s_nodes_16774.diff
[CMD] [2019-10-14 19:42:28] tail -n +1 /app/public/converted_csv/norfolk_island_s_nodes_16774.csv >> /app/public/diff/norfolk_island_s_nodes_16774.diff
[CMD] [2019-10-14 19:42:28] echo "." >> /app/public/diff/norfolk_island_s_nodes_16774.diff
[CMD] [2019-10-14 19:42:28] echo "0a" > /app/public/diff/norfolk_island_s_occurrences_16775.diff
[CMD] [2019-10-14 19:42:28] tail -n +1 /app/public/converted_csv/norfolk_island_s_occurrences_16775.csv >> /app/public/diff/norfolk_island_s_occurrences_16775.diff
[CMD] [2019-10-14 19:42:29] echo "." >> /app/public/diff/norfolk_island_s_occurrences_16775.diff
[CMD] [2019-10-14 19:42:29] echo "0a" > /app/public/diff/norfolk_island_s_measurements_16776.diff
[CMD] [2019-10-14 19:42:29] tail -n +1 /app/public/converted_csv/norfolk_island_s_measurements_16776.csv >> /app/public/diff/norfolk_island_s_measurements_16776.diff
[CMD] [2019-10-14 19:42:30] echo "." >> /app/public/diff/norfolk_island_s_measurements_16776.diff
[STOP] [2019-10-14 19:42:30] calculate_delta
[START] [2019-10-14 19:42:30] parse_diff_and_store
[INFO] [2019-10-14 19:42:30] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 19:42:30] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 19:42:37] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 19:42:38] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 19:42:47] Storing 2 References
[INFO] [2019-10-14 19:42:47] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 19:42:47] Average Time: 0.0
[INFO] [2019-10-14 19:42:47] Total Time: 1s
[INFO] [2019-10-14 19:42:47] Storing 3275 ScientificNames
[INFO] [2019-10-14 19:42:47] Processing group of 3275 in 4 groups of 1000
[INFO] [2019-10-14 19:42:49] Average Time: 0.298
[INFO] [2019-10-14 19:42:49] Total Time: 2s
[INFO] [2019-10-14 19:42:49] Storing 3275 Nodes
[INFO] [2019-10-14 19:42:49] Processing group of 3275 in 4 groups of 1000
[INFO] [2019-10-14 19:42:50] Average Time: 0.275
[INFO] [2019-10-14 19:42:50] Total Time: 2s
[INFO] [2019-10-14 19:42:50] Storing 1446 Occurrences
[INFO] [2019-10-14 19:42:50] Processing group of 1446 in 2 groups of 1000
[INFO] [2019-10-14 19:42:50] Average Time: 0.08
[INFO] [2019-10-14 19:42:50] Total Time: 1s
[INFO] [2019-10-14 19:42:50] Storing 3250 TraitsReferences
[INFO] [2019-10-14 19:42:50] Processing group of 3250 in 4 groups of 1000
[INFO] [2019-10-14 19:42:50] Average Time: 0.08
[INFO] [2019-10-14 19:42:50] Total Time: 1s
[INFO] [2019-10-14 19:42:50] Storing 3249 Traits
[INFO] [2019-10-14 19:42:50] Processing group of 3249 in 4 groups of 1000
[INFO] [2019-10-14 19:42:51] Average Time: 0.253
[INFO] [2019-10-14 19:42:51] Total Time: 2s
[INFO] [2019-10-14 19:42:51] Storing 3249 MetaTraits
[INFO] [2019-10-14 19:42:51] Processing group of 3249 in 4 groups of 1000
[INFO] [2019-10-14 19:42:52] Average Time: 0.098
[INFO] [2019-10-14 19:42:52] Total Time: 1s
[STOP] [2019-10-14 19:42:52] parse_diff_and_store
[START] [2019-10-14 19:42:52] resolve_keys
[INFO] [2019-10-14 19:43:07] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 19:43:08] traits to occurrences...
[INFO] [2019-10-14 19:43:10] traits to nodes (through occurrences)...
[INFO] [2019-10-14 19:43:10] Traits to sex term...
[INFO] [2019-10-14 19:43:11] Traits to lifestage term...
[INFO] [2019-10-14 19:43:12] MetaTraits to traits...
[INFO] [2019-10-14 19:43:12] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 19:43:13] Assocs to occurrences...
[INFO] [2019-10-14 19:43:13] Assocs to nodes...
[INFO] [2019-10-14 19:43:13] Assoc to sex term...
[INFO] [2019-10-14 19:43:13] Assoc to lifestage term...
[STOP] [2019-10-14 19:43:13] resolve_keys
[START] [2019-10-14 19:43:13] hold_for_later_1
[STOP] [2019-10-14 19:43:13] hold_for_later_1
[START] [2019-10-14 19:43:13] hold_for_later_2
[STOP] [2019-10-14 19:43:13] hold_for_later_2
[START] [2019-10-14 19:43:13] resolve_missing_parents
[STOP] [2019-10-14 19:43:19] resolve_missing_parents
[START] [2019-10-14 19:43:19] rebuild_nodes
[START] [2019-10-14 19:43:19] Flattener#flatten
[START] [2019-10-14 19:43:19] Flattener#study_resource
[START] [2019-10-14 19:43:19] Flattener#build_ancestry
[STOP] [2019-10-14 19:43:19] Flattener#build_ancestry
[INFO] [2019-10-14 19:43:19] 3275 ancestry keys
[START] [2019-10-14 19:43:19] build_node_ancestors
[INFO] [2019-10-14 19:43:19] old ancestors deleted.
[STOP] [2019-10-14 19:43:19] build_node_ancestors
[START] [2019-10-14 19:43:20] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 19:43:20] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 19:43:20] Flattener#flatten
[STOP] [2019-10-14 19:43:20] rebuild_nodes
[START] [2019-10-14 19:43:20] resolve_missing_media_owners
[STOP] [2019-10-14 19:43:20] resolve_missing_media_owners
[START] [2019-10-14 19:43:20] sanitize_media_verbatims
[STOP] [2019-10-14 19:43:20] sanitize_media_verbatims
[START] [2019-10-14 19:43:20] queue_downloads
[STOP] [2019-10-14 19:43:20] queue_downloads
[START] [2019-10-14 19:43:20] parse_names
[WARN] [2019-10-14 19:43:20] I see 3275 names which still need to be parsed.
[STOP] [2019-10-14 19:43:23] parse_names
[START] [2019-10-14 19:43:23] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 19:43:23] denormalize_canonical_names_to_nodes
[START] [2019-10-14 19:43:23] match_nodes
[START] [2019-10-14 19:43:23] map_all_nodes_to_pages
[STOP] [2019-10-14 19:45:41] map_all_nodes_to_pages
[INFO] [2019-10-14 19:45:41] 206 Unmatched nodes (of 3275)! That's too many to output. First 10: Onychoprion fuscata (#51086960); Procelsterna cerulea (#51086625); Todiramphus sancta (#51089700); Greenwoodoconcha castaneocincta (#51089564); Roybellia depressa (#51087020); Mathewsoconcha belli (#51086958); Mathewsoconcha compacta (#51088309); Tornatellinops norfolkensis (#51086677); Tornatellinops nepeanensis (#51087698); Tornatellinops moohuensis (#51088427)
[START] [2019-10-14 19:45:41] update_nodes
[STOP] [2019-10-14 19:45:42] update_nodes
[STOP] [2019-10-14 19:45:42] match_nodes
[START] [2019-10-14 19:45:42] reindex_search
[STOP] [2019-10-14 19:45:49] reindex_search
[START] [2019-10-14 19:45:49] normalize_units
[STOP] [2019-10-14 19:45:49] normalize_units
[START] [2019-10-14 19:45:49] calculate_statistics
[STOP] [2019-10-14 19:45:49] calculate_statistics
[START] [2019-10-14 19:45:49] complete_harvest_instance
[START] [2019-10-14 19:45:49] overall_tsv_creation
[INFO] [2019-10-14 19:45:49] Processing group of 3275 in 1 batches of 10000
[INFO] [2019-10-14 19:46:48] 1446 Traits (unfiltered)...
[INFO] [2019-10-14 19:47:02] 1446 Traits (filtered)...
[INFO] [2019-10-14 19:47:02] 0 Associations (filtered)...
[INFO] [2019-10-14 19:47:42] 7229 metadata added.
[INFO] [2019-10-14 19:47:42] 0 metadata added.
[INFO] [2019-10-14 19:47:42] Average Time: 90.13
[INFO] [2019-10-14 19:47:42] Total Time: 1m54s
[STOP] [2019-10-14 19:47:42] overall_tsv_creation
[INFO] [2019-10-14 19:47:42] Done. Check your files:
[INFO] [2019-10-14 19:47:43] (3275 lines) /app/public/data/norfolk_island_s/publish_nodes.tsv
[INFO] [2019-10-14 19:47:43] (6072 lines) /app/public/data/norfolk_island_s/publish_node_ancestors.tsv
[INFO] [2019-10-14 19:47:43] (3275 lines) /app/public/data/norfolk_island_s/publish_scientific_names.tsv
[INFO] [2019-10-14 19:47:44] (1447 lines) /app/public/data/norfolk_island_s/publish_traits.tsv
[INFO] [2019-10-14 19:47:44] (7230 lines) /app/public/data/norfolk_island_s/publish_metadata.tsv
[STOP] [2019-10-14 19:47:44] complete_harvest_instance
[START] [2019-10-14 19:47:44] completed
[STOP] [2019-10-14 19:47:44] completed
[STOP] [2019-10-14 19:47:44] logged process, took 319.98
Latest Process

14 Oct 19:42 EXITED currently processing 0