Harvest for Beaufort Sea Species List Created 22 Dec 21:58

Stage: completed
Fetched: 22 Dec 21:58
Validated: 22 Dec 21:58
Deltas Created 22 Dec 21:58
Units Normalized: 22 Dec 22:06
Ancestry Built: 22 Dec 21:59
Nodes Matched: 22 Dec 22:06
Names Parsed: 22 Dec 21:59
New Models Stored: 22 Dec 21:59
Indexed: 22 Dec 22:06
Completed: 22 Dec 22:08
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-22 21:58:52 -0500 by logger.rb/56815
[START] [2019-12-22 21:58:52] logged process
[START] [2019-12-22 21:58:52] create_harvest_instance
[STOP] [2019-12-22 21:58:52] create_harvest_instance
[START] [2019-12-22 21:58:52] fetch_files
[STOP] [2019-12-22 21:58:52] fetch_files
[START] [2019-12-22 21:58:52] validate_each_file
[STOP] [2019-12-22 21:58:53] validate_each_file
[START] [2019-12-22 21:58:53] convert_to_csv
[CMD] [2019-12-22 21:58:53] /usr/bin/sort /app/public/converted_csv/beaufort_sea_sp__refs_19106.csv > /app/public/converted_csv/beaufort_sea_sp__refs_19106.csv_sorted
[CMD] [2019-12-22 21:58:53] /usr/bin/sort /app/public/converted_csv/beaufort_sea_sp__nodes_19107.csv > /app/public/converted_csv/beaufort_sea_sp__nodes_19107.csv_sorted
[CMD] [2019-12-22 21:58:53] /usr/bin/sort /app/public/converted_csv/beaufort_sea_sp__occurrences_19108.csv > /app/public/converted_csv/beaufort_sea_sp__occurrences_19108.csv_sorted
[CMD] [2019-12-22 21:58:53] /usr/bin/sort /app/public/converted_csv/beaufort_sea_sp__measurements_19109.csv > /app/public/converted_csv/beaufort_sea_sp__measurements_19109.csv_sorted
[STOP] [2019-12-22 21:58:53] convert_to_csv
[START] [2019-12-22 21:58:53] calculate_delta
[CMD] [2019-12-22 21:58:53] echo "0a" > /app/public/diff/beaufort_sea_sp__refs_19106.diff
[CMD] [2019-12-22 21:58:53] tail -n +1 /app/public/converted_csv/beaufort_sea_sp__refs_19106.csv >> /app/public/diff/beaufort_sea_sp__refs_19106.diff
[CMD] [2019-12-22 21:58:53] echo "." >> /app/public/diff/beaufort_sea_sp__refs_19106.diff
[CMD] [2019-12-22 21:58:53] echo "0a" > /app/public/diff/beaufort_sea_sp__nodes_19107.diff
[CMD] [2019-12-22 21:58:53] tail -n +1 /app/public/converted_csv/beaufort_sea_sp__nodes_19107.csv >> /app/public/diff/beaufort_sea_sp__nodes_19107.diff
[CMD] [2019-12-22 21:58:53] echo "." >> /app/public/diff/beaufort_sea_sp__nodes_19107.diff
[CMD] [2019-12-22 21:58:53] echo "0a" > /app/public/diff/beaufort_sea_sp__occurrences_19108.diff
[CMD] [2019-12-22 21:58:53] tail -n +1 /app/public/converted_csv/beaufort_sea_sp__occurrences_19108.csv >> /app/public/diff/beaufort_sea_sp__occurrences_19108.diff
[CMD] [2019-12-22 21:58:53] echo "." >> /app/public/diff/beaufort_sea_sp__occurrences_19108.diff
[CMD] [2019-12-22 21:58:53] echo "0a" > /app/public/diff/beaufort_sea_sp__measurements_19109.diff
[CMD] [2019-12-22 21:58:53] tail -n +1 /app/public/converted_csv/beaufort_sea_sp__measurements_19109.csv >> /app/public/diff/beaufort_sea_sp__measurements_19109.diff
[CMD] [2019-12-22 21:58:53] echo "." >> /app/public/diff/beaufort_sea_sp__measurements_19109.diff
[STOP] [2019-12-22 21:58:53] calculate_delta
[START] [2019-12-22 21:58:53] parse_diff_and_store
[INFO] [2019-12-22 21:58:53] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 21:58:53] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 21:58:55] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 21:58:55] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 21:59:02] Storing 2 References
[INFO] [2019-12-22 21:59:02] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 21:59:02] Average Time: 0.0
[INFO] [2019-12-22 21:59:02] Total Time: 1s
[INFO] [2019-12-22 21:59:02] Storing 2701 ScientificNames
[INFO] [2019-12-22 21:59:02] Processing group of 2701 in 3 groups of 1000
[INFO] [2019-12-22 21:59:03] Average Time: 0.393
[INFO] [2019-12-22 21:59:03] Total Time: 2s
[INFO] [2019-12-22 21:59:03] Storing 2701 Nodes
[INFO] [2019-12-22 21:59:03] Processing group of 2701 in 3 groups of 1000
[INFO] [2019-12-22 21:59:04] Average Time: 0.317
[INFO] [2019-12-22 21:59:04] Total Time: 1s
[INFO] [2019-12-22 21:59:04] Storing 1234 Occurrences
[INFO] [2019-12-22 21:59:04] Processing group of 1234 in 2 groups of 1000
[INFO] [2019-12-22 21:59:04] Average Time: 0.07
[INFO] [2019-12-22 21:59:04] Total Time: 1s
[INFO] [2019-12-22 21:59:04] Storing 2468 TraitsReferences
[INFO] [2019-12-22 21:59:04] Processing group of 2468 in 3 groups of 1000
[INFO] [2019-12-22 21:59:05] Average Time: 0.093
[INFO] [2019-12-22 21:59:05] Total Time: 1s
[INFO] [2019-12-22 21:59:05] Storing 2468 Traits
[INFO] [2019-12-22 21:59:05] Processing group of 2468 in 3 groups of 1000
[INFO] [2019-12-22 21:59:06] Average Time: 0.33
[INFO] [2019-12-22 21:59:06] Total Time: 2s
[INFO] [2019-12-22 21:59:06] Storing 2468 MetaTraits
[INFO] [2019-12-22 21:59:06] Processing group of 2468 in 3 groups of 1000
[INFO] [2019-12-22 21:59:06] Average Time: 0.173
[INFO] [2019-12-22 21:59:06] Total Time: 1s
[STOP] [2019-12-22 21:59:06] parse_diff_and_store
[START] [2019-12-22 21:59:06] resolve_keys
[INFO] [2019-12-22 21:59:19] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 21:59:20] traits to occurrences...
[INFO] [2019-12-22 21:59:20] traits to nodes (through occurrences)...
[INFO] [2019-12-22 21:59:20] Traits to sex term...
[INFO] [2019-12-22 21:59:21] Traits to lifestage term...
[INFO] [2019-12-22 21:59:21] MetaTraits to traits...
[INFO] [2019-12-22 21:59:22] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 21:59:22] Assocs to occurrences...
[INFO] [2019-12-22 21:59:22] Assocs to nodes...
[INFO] [2019-12-22 21:59:22] Assoc to sex term...
[INFO] [2019-12-22 21:59:22] Assoc to lifestage term...
[STOP] [2019-12-22 21:59:22] resolve_keys
[START] [2019-12-22 21:59:22] hold_for_later_1
[STOP] [2019-12-22 21:59:22] hold_for_later_1
[START] [2019-12-22 21:59:22] hold_for_later_2
[STOP] [2019-12-22 21:59:22] hold_for_later_2
[START] [2019-12-22 21:59:22] resolve_missing_parents
[STOP] [2019-12-22 21:59:26] resolve_missing_parents
[START] [2019-12-22 21:59:26] rebuild_nodes
[START] [2019-12-22 21:59:26] Flattener#flatten
[START] [2019-12-22 21:59:26] Flattener#study_resource
[START] [2019-12-22 21:59:26] Flattener#build_ancestry
[STOP] [2019-12-22 21:59:26] Flattener#build_ancestry
[INFO] [2019-12-22 21:59:26] 2701 ancestry keys
[START] [2019-12-22 21:59:26] build_node_ancestors
[INFO] [2019-12-22 21:59:26] old ancestors deleted.
[STOP] [2019-12-22 21:59:27] build_node_ancestors
[START] [2019-12-22 21:59:28] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 21:59:29] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 21:59:29] Flattener#flatten
[STOP] [2019-12-22 21:59:29] rebuild_nodes
[START] [2019-12-22 21:59:29] resolve_missing_media_owners
[STOP] [2019-12-22 21:59:29] resolve_missing_media_owners
[START] [2019-12-22 21:59:29] sanitize_media_verbatims
[STOP] [2019-12-22 21:59:29] sanitize_media_verbatims
[START] [2019-12-22 21:59:29] queue_downloads
[STOP] [2019-12-22 21:59:29] queue_downloads
[START] [2019-12-22 21:59:29] parse_names
[WARN] [2019-12-22 21:59:29] I see 2701 names which still need to be parsed.
[STOP] [2019-12-22 21:59:32] parse_names
[START] [2019-12-22 21:59:32] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 21:59:32] denormalize_canonical_names_to_nodes
[START] [2019-12-22 21:59:32] match_nodes
[START] [2019-12-22 21:59:32] map_all_nodes_to_pages
[STOP] [2019-12-22 22:06:40] map_all_nodes_to_pages
[INFO] [2019-12-22 22:06:40] 145 Unmatched nodes (of 2701)! That's too many to output. First 10: Anas clypeata (#61746922); Anas americana (#61746924); Anas strepera (#61747243); Anas penelope (#61748287); Anas discors (#61748567); Anas formosa (#61748979); Chen (#61746844); Chen caerulescens (#61746843); Chen rossii (#61748600); Larus thayeri (#61747107)
[START] [2019-12-22 22:06:40] update_nodes
[STOP] [2019-12-22 22:06:40] update_nodes
[STOP] [2019-12-22 22:06:40] match_nodes
[START] [2019-12-22 22:06:40] reindex_search
[STOP] [2019-12-22 22:06:45] reindex_search
[START] [2019-12-22 22:06:45] normalize_units
[STOP] [2019-12-22 22:06:45] normalize_units
[START] [2019-12-22 22:06:45] calculate_statistics
[STOP] [2019-12-22 22:06:45] calculate_statistics
[START] [2019-12-22 22:06:45] complete_harvest_instance
[START] [2019-12-22 22:06:45] overall_tsv_creation
[INFO] [2019-12-22 22:06:45] Processing group of 2701 in 1 batches of 10000
[INFO] [2019-12-22 22:07:46] 1234 Traits (unfiltered)...
[INFO] [2019-12-22 22:08:00] 1234 Traits (filtered)...
[INFO] [2019-12-22 22:08:00] 0 Associations (filtered)...
[INFO] [2019-12-22 22:08:52] 6170 metadata added.
[INFO] [2019-12-22 22:08:52] 0 metadata added.
[INFO] [2019-12-22 22:08:52] Average Time: 101.64
[INFO] [2019-12-22 22:08:52] Total Time: 2m8s
[STOP] [2019-12-22 22:08:52] overall_tsv_creation
[INFO] [2019-12-22 22:08:52] Done. Check your files:
[INFO] [2019-12-22 22:08:53] (2701 lines) /app/public/data/beaufort_sea_sp_/publish_nodes.tsv
[INFO] [2019-12-22 22:08:53] (13054 lines) /app/public/data/beaufort_sea_sp_/publish_node_ancestors.tsv
[INFO] [2019-12-22 22:08:53] (2701 lines) /app/public/data/beaufort_sea_sp_/publish_scientific_names.tsv
[INFO] [2019-12-22 22:08:53] (1235 lines) /app/public/data/beaufort_sea_sp_/publish_traits.tsv
[INFO] [2019-12-22 22:08:53] (6171 lines) /app/public/data/beaufort_sea_sp_/publish_metadata.tsv
[STOP] [2019-12-22 22:08:53] complete_harvest_instance
[START] [2019-12-22 22:08:53] completed
[STOP] [2019-12-22 22:08:53] completed
[STOP] [2019-12-22 22:08:53] logged process, took 601.29
Latest Process

22 Dec 21:58 EXITED currently processing 0