Harvest for Balearic Sea Species List Created 22 Dec 19:34

Stage: completed
Fetched: 22 Dec 19:34
Validated: 22 Dec 19:34
Deltas Created 22 Dec 19:34
Units Normalized: 22 Dec 20:03
Ancestry Built: 22 Dec 19:35
Nodes Matched: 22 Dec 20:03
Names Parsed: 22 Dec 19:36
New Models Stored: 22 Dec 19:35
Indexed: 22 Dec 20:03
Completed: 22 Dec 20:06
Time to Harvest: 1 minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-22 19:34:29 -0500 by logger.rb/56815
[START] [2019-12-22 19:34:29] logged process
[START] [2019-12-22 19:34:29] create_harvest_instance
[STOP] [2019-12-22 19:34:29] create_harvest_instance
[START] [2019-12-22 19:34:29] fetch_files
[STOP] [2019-12-22 19:34:29] fetch_files
[START] [2019-12-22 19:34:29] validate_each_file
[STOP] [2019-12-22 19:34:30] validate_each_file
[START] [2019-12-22 19:34:30] convert_to_csv
[CMD] [2019-12-22 19:34:30] /usr/bin/sort /app/public/converted_csv/balearic_sea_sp__refs_19042.csv > /app/public/converted_csv/balearic_sea_sp__refs_19042.csv_sorted
[CMD] [2019-12-22 19:34:31] /usr/bin/sort /app/public/converted_csv/balearic_sea_sp__nodes_19043.csv > /app/public/converted_csv/balearic_sea_sp__nodes_19043.csv_sorted
[CMD] [2019-12-22 19:34:31] /usr/bin/sort /app/public/converted_csv/balearic_sea_sp__occurrences_19044.csv > /app/public/converted_csv/balearic_sea_sp__occurrences_19044.csv_sorted
[CMD] [2019-12-22 19:34:32] /usr/bin/sort /app/public/converted_csv/balearic_sea_sp__measurements_19045.csv > /app/public/converted_csv/balearic_sea_sp__measurements_19045.csv_sorted
[STOP] [2019-12-22 19:34:33] convert_to_csv
[START] [2019-12-22 19:34:33] calculate_delta
[CMD] [2019-12-22 19:34:33] echo "0a" > /app/public/diff/balearic_sea_sp__refs_19042.diff
[CMD] [2019-12-22 19:34:33] tail -n +1 /app/public/converted_csv/balearic_sea_sp__refs_19042.csv >> /app/public/diff/balearic_sea_sp__refs_19042.diff
[CMD] [2019-12-22 19:34:34] echo "." >> /app/public/diff/balearic_sea_sp__refs_19042.diff
[CMD] [2019-12-22 19:34:35] echo "0a" > /app/public/diff/balearic_sea_sp__nodes_19043.diff
[CMD] [2019-12-22 19:34:35] tail -n +1 /app/public/converted_csv/balearic_sea_sp__nodes_19043.csv >> /app/public/diff/balearic_sea_sp__nodes_19043.diff
[CMD] [2019-12-22 19:34:36] echo "." >> /app/public/diff/balearic_sea_sp__nodes_19043.diff
[CMD] [2019-12-22 19:34:37] echo "0a" > /app/public/diff/balearic_sea_sp__occurrences_19044.diff
[CMD] [2019-12-22 19:34:37] tail -n +1 /app/public/converted_csv/balearic_sea_sp__occurrences_19044.csv >> /app/public/diff/balearic_sea_sp__occurrences_19044.diff
[CMD] [2019-12-22 19:34:38] echo "." >> /app/public/diff/balearic_sea_sp__occurrences_19044.diff
[CMD] [2019-12-22 19:34:39] echo "0a" > /app/public/diff/balearic_sea_sp__measurements_19045.diff
[CMD] [2019-12-22 19:34:39] tail -n +1 /app/public/converted_csv/balearic_sea_sp__measurements_19045.csv >> /app/public/diff/balearic_sea_sp__measurements_19045.diff
[CMD] [2019-12-22 19:34:40] echo "." >> /app/public/diff/balearic_sea_sp__measurements_19045.diff
[STOP] [2019-12-22 19:34:41] calculate_delta
[START] [2019-12-22 19:34:41] parse_diff_and_store
[INFO] [2019-12-22 19:34:41] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 19:34:42] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 19:34:45] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 19:34:46] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 19:35:02] Storing 2 References
[INFO] [2019-12-22 19:35:02] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 19:35:02] Average Time: 0.0
[INFO] [2019-12-22 19:35:02] Total Time: 1s
[INFO] [2019-12-22 19:35:02] Storing 5348 ScientificNames
[INFO] [2019-12-22 19:35:02] Processing group of 5348 in 6 groups of 1000
[INFO] [2019-12-22 19:35:04] Average Time: 0.37
[INFO] [2019-12-22 19:35:04] Total Time: 3s
[INFO] [2019-12-22 19:35:04] Storing 5348 Nodes
[INFO] [2019-12-22 19:35:04] Processing group of 5348 in 6 groups of 1000
[INFO] [2019-12-22 19:35:06] Average Time: 0.293
[INFO] [2019-12-22 19:35:06] Total Time: 2s
[INFO] [2019-12-22 19:35:06] Storing 2642 Occurrences
[INFO] [2019-12-22 19:35:06] Processing group of 2642 in 3 groups of 1000
[INFO] [2019-12-22 19:35:06] Average Time: 0.107
[INFO] [2019-12-22 19:35:06] Total Time: 1s
[INFO] [2019-12-22 19:35:06] Storing 5284 TraitsReferences
[INFO] [2019-12-22 19:35:06] Processing group of 5284 in 6 groups of 1000
[INFO] [2019-12-22 19:35:06] Average Time: 0.085
[INFO] [2019-12-22 19:35:06] Total Time: 1s
[INFO] [2019-12-22 19:35:06] Storing 5284 Traits
[INFO] [2019-12-22 19:35:06] Processing group of 5284 in 6 groups of 1000
[INFO] [2019-12-22 19:35:09] Average Time: 0.352
[INFO] [2019-12-22 19:35:09] Total Time: 3s
[INFO] [2019-12-22 19:35:09] Storing 5284 MetaTraits
[INFO] [2019-12-22 19:35:09] Processing group of 5284 in 6 groups of 1000
[INFO] [2019-12-22 19:35:09] Average Time: 0.125
[INFO] [2019-12-22 19:35:09] Total Time: 1s
[STOP] [2019-12-22 19:35:09] parse_diff_and_store
[START] [2019-12-22 19:35:09] resolve_keys
[INFO] [2019-12-22 19:35:32] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 19:35:34] traits to occurrences...
[INFO] [2019-12-22 19:35:36] traits to nodes (through occurrences)...
[INFO] [2019-12-22 19:35:36] Traits to sex term...
[INFO] [2019-12-22 19:35:37] Traits to lifestage term...
[INFO] [2019-12-22 19:35:38] MetaTraits to traits...
[INFO] [2019-12-22 19:35:38] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 19:35:39] Assocs to occurrences...
[INFO] [2019-12-22 19:35:39] Assocs to nodes...
[INFO] [2019-12-22 19:35:39] Assoc to sex term...
[INFO] [2019-12-22 19:35:39] Assoc to lifestage term...
[STOP] [2019-12-22 19:35:39] resolve_keys
[START] [2019-12-22 19:35:39] hold_for_later_1
[STOP] [2019-12-22 19:35:39] hold_for_later_1
[START] [2019-12-22 19:35:39] hold_for_later_2
[STOP] [2019-12-22 19:35:39] hold_for_later_2
[START] [2019-12-22 19:35:39] resolve_missing_parents
[STOP] [2019-12-22 19:35:49] resolve_missing_parents
[START] [2019-12-22 19:35:49] rebuild_nodes
[START] [2019-12-22 19:35:49] Flattener#flatten
[START] [2019-12-22 19:35:49] Flattener#study_resource
[START] [2019-12-22 19:35:49] Flattener#build_ancestry
[STOP] [2019-12-22 19:35:49] Flattener#build_ancestry
[INFO] [2019-12-22 19:35:49] 5348 ancestry keys
[START] [2019-12-22 19:35:49] build_node_ancestors
[INFO] [2019-12-22 19:35:49] old ancestors deleted.
[STOP] [2019-12-22 19:35:51] build_node_ancestors
[START] [2019-12-22 19:35:54] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 19:35:54] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 19:35:54] Flattener#flatten
[STOP] [2019-12-22 19:35:54] rebuild_nodes
[START] [2019-12-22 19:35:54] resolve_missing_media_owners
[STOP] [2019-12-22 19:35:54] resolve_missing_media_owners
[START] [2019-12-22 19:35:54] sanitize_media_verbatims
[STOP] [2019-12-22 19:35:54] sanitize_media_verbatims
[START] [2019-12-22 19:35:54] queue_downloads
[STOP] [2019-12-22 19:35:54] queue_downloads
[START] [2019-12-22 19:35:54] parse_names
[WARN] [2019-12-22 19:35:54] I see 5348 names which still need to be parsed.
[STOP] [2019-12-22 19:36:00] parse_names
[START] [2019-12-22 19:36:00] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 19:36:00] denormalize_canonical_names_to_nodes
[START] [2019-12-22 19:36:00] match_nodes
[START] [2019-12-22 19:36:00] map_all_nodes_to_pages
[STOP] [2019-12-22 20:03:21] map_all_nodes_to_pages
[INFO] [2019-12-22 20:03:21] 252 Unmatched nodes (of 5348)! That's too many to output. First 10: Puffinus griseus (#61701773); Anas strepera (#61699769); Anas clypeata (#61699782); Anas penelope (#61699876); Anas querquedula (#61700001); Anas discors (#61701283); Anas cyanoptera (#61704198); Anas falcata (#61704733); Chen (#61703324); Chen caerulescens (#61703323)
[START] [2019-12-22 20:03:21] update_nodes
[STOP] [2019-12-22 20:03:23] update_nodes
[STOP] [2019-12-22 20:03:23] match_nodes
[START] [2019-12-22 20:03:23] reindex_search
[STOP] [2019-12-22 20:03:46] reindex_search
[START] [2019-12-22 20:03:46] normalize_units
[STOP] [2019-12-22 20:03:46] normalize_units
[START] [2019-12-22 20:03:46] calculate_statistics
[STOP] [2019-12-22 20:03:47] calculate_statistics
[START] [2019-12-22 20:03:47] complete_harvest_instance
[START] [2019-12-22 20:03:47] overall_tsv_creation
[INFO] [2019-12-22 20:03:47] Processing group of 5348 in 1 batches of 10000
[INFO] [2019-12-22 20:04:57] 2642 Traits (unfiltered)...
[INFO] [2019-12-22 20:05:11] 2642 Traits (filtered)...
[INFO] [2019-12-22 20:05:11] 0 Associations (filtered)...
[INFO] [2019-12-22 20:06:05] 13210 metadata added.
[INFO] [2019-12-22 20:06:05] 0 metadata added.
[INFO] [2019-12-22 20:06:05] Average Time: 111.72
[INFO] [2019-12-22 20:06:05] Total Time: 2m19s
[STOP] [2019-12-22 20:06:05] overall_tsv_creation
[INFO] [2019-12-22 20:06:05] Done. Check your files:
[INFO] [2019-12-22 20:06:06] (5348 lines) /app/public/data/balearic_sea_sp_/publish_nodes.tsv
[INFO] [2019-12-22 20:06:07] (26396 lines) /app/public/data/balearic_sea_sp_/publish_node_ancestors.tsv
[INFO] [2019-12-22 20:06:07] (5348 lines) /app/public/data/balearic_sea_sp_/publish_scientific_names.tsv
[INFO] [2019-12-22 20:06:08] (2643 lines) /app/public/data/balearic_sea_sp_/publish_traits.tsv
[INFO] [2019-12-22 20:06:09] (13211 lines) /app/public/data/balearic_sea_sp_/publish_metadata.tsv
[STOP] [2019-12-22 20:06:09] complete_harvest_instance
[START] [2019-12-22 20:06:09] completed
[STOP] [2019-12-22 20:06:09] completed
[STOP] [2019-12-22 20:06:09] logged process, took 1900.36
Latest Process

22 Dec 19:34 EXITED currently processing 0