Harvest for North Sea Species List Created 25 Dec 08:41

Stage: completed
Fetched: 25 Dec 08:41
Validated: 25 Dec 08:41
Deltas Created 25 Dec 08:41
Units Normalized: 25 Dec 09:48
Ancestry Built: 25 Dec 08:44
Nodes Matched: 25 Dec 09:47
Names Parsed: 25 Dec 08:45
New Models Stored: 25 Dec 08:42
Indexed: 25 Dec 09:48
Completed: 25 Dec 09:53
Time to Harvest: 1 minute
Harvesting Log

(156 lines)
# Logfile created on 2019-12-25 08:41:33 -0500 by logger.rb/56815
[START] [2019-12-25 08:41:33] logged process
[START] [2019-12-25 08:41:33] create_harvest_instance
[STOP] [2019-12-25 08:41:33] create_harvest_instance
[START] [2019-12-25 08:41:33] fetch_files
[STOP] [2019-12-25 08:41:33] fetch_files
[START] [2019-12-25 08:41:33] validate_each_file
[STOP] [2019-12-25 08:41:36] validate_each_file
[START] [2019-12-25 08:41:36] convert_to_csv
[CMD] [2019-12-25 08:41:36] /usr/bin/sort /app/public/converted_csv/n_sea_sp_list_refs_19562.csv > /app/public/converted_csv/n_sea_sp_list_refs_19562.csv_sorted
[CMD] [2019-12-25 08:41:36] /usr/bin/sort /app/public/converted_csv/n_sea_sp_list_nodes_19563.csv > /app/public/converted_csv/n_sea_sp_list_nodes_19563.csv_sorted
[CMD] [2019-12-25 08:41:36] /usr/bin/sort /app/public/converted_csv/n_sea_sp_list_occurrences_19564.csv > /app/public/converted_csv/n_sea_sp_list_occurrences_19564.csv_sorted
[CMD] [2019-12-25 08:41:36] /usr/bin/sort /app/public/converted_csv/n_sea_sp_list_measurements_19565.csv > /app/public/converted_csv/n_sea_sp_list_measurements_19565.csv_sorted
[STOP] [2019-12-25 08:41:36] convert_to_csv
[START] [2019-12-25 08:41:36] calculate_delta
[CMD] [2019-12-25 08:41:36] echo "0a" > /app/public/diff/n_sea_sp_list_refs_19562.diff
[CMD] [2019-12-25 08:41:36] tail -n +1 /app/public/converted_csv/n_sea_sp_list_refs_19562.csv >> /app/public/diff/n_sea_sp_list_refs_19562.diff
[CMD] [2019-12-25 08:41:37] echo "." >> /app/public/diff/n_sea_sp_list_refs_19562.diff
[CMD] [2019-12-25 08:41:37] echo "0a" > /app/public/diff/n_sea_sp_list_nodes_19563.diff
[CMD] [2019-12-25 08:41:37] tail -n +1 /app/public/converted_csv/n_sea_sp_list_nodes_19563.csv >> /app/public/diff/n_sea_sp_list_nodes_19563.diff
[CMD] [2019-12-25 08:41:37] echo "." >> /app/public/diff/n_sea_sp_list_nodes_19563.diff
[CMD] [2019-12-25 08:41:37] echo "0a" > /app/public/diff/n_sea_sp_list_occurrences_19564.diff
[CMD] [2019-12-25 08:41:37] tail -n +1 /app/public/converted_csv/n_sea_sp_list_occurrences_19564.csv >> /app/public/diff/n_sea_sp_list_occurrences_19564.diff
[CMD] [2019-12-25 08:41:37] echo "." >> /app/public/diff/n_sea_sp_list_occurrences_19564.diff
[CMD] [2019-12-25 08:41:38] echo "0a" > /app/public/diff/n_sea_sp_list_measurements_19565.diff
[CMD] [2019-12-25 08:41:38] tail -n +1 /app/public/converted_csv/n_sea_sp_list_measurements_19565.csv >> /app/public/diff/n_sea_sp_list_measurements_19565.diff
[CMD] [2019-12-25 08:41:38] echo "." >> /app/public/diff/n_sea_sp_list_measurements_19565.diff
[STOP] [2019-12-25 08:41:38] calculate_delta
[START] [2019-12-25 08:41:38] parse_diff_and_store
[INFO] [2019-12-25 08:41:38] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 08:41:38] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 08:41:46] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 08:41:47] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 08:42:29] Storing 2 References
[INFO] [2019-12-25 08:42:29] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 08:42:29] Average Time: 0.0
[INFO] [2019-12-25 08:42:29] Total Time: 1s
[INFO] [2019-12-25 08:42:29] Storing 13691 ScientificNames
[INFO] [2019-12-25 08:42:29] Processing group of 13691 in 14 groups of 1000
[INFO] [2019-12-25 08:42:35] Average Time: 0.384
[INFO] [2019-12-25 08:42:35] Total Time: 6s
[INFO] [2019-12-25 08:42:35] last 3 / first 3: 0.84
[INFO] [2019-12-25 08:42:35] Std.Dev: 0.03162277660168379; Max: 0.44
[INFO] [2019-12-25 08:42:35] Storing 13691 Nodes
[INFO] [2019-12-25 08:42:35] Processing group of 13691 in 14 groups of 1000
[INFO] [2019-12-25 08:42:39] Average Time: 0.325
[INFO] [2019-12-25 08:42:39] Total Time: 5s
[INFO] [2019-12-25 08:42:39] last 3 / first 3: 0.89
[INFO] [2019-12-25 08:42:39] Std.Dev: 0.03162277660168379; Max: 0.37
[INFO] [2019-12-25 08:42:39] Storing 7688 Occurrences
[INFO] [2019-12-25 08:42:39] Processing group of 7688 in 8 groups of 1000
[INFO] [2019-12-25 08:42:40] Average Time: 0.116
[INFO] [2019-12-25 08:42:40] Total Time: 1s
[INFO] [2019-12-25 08:42:40] last 3 / first 3: 0.81
[INFO] [2019-12-25 08:42:40] Std.Dev: 0.0; Max: 0.15
[INFO] [2019-12-25 08:42:40] Storing 15376 TraitsReferences
[INFO] [2019-12-25 08:42:40] Processing group of 15376 in 16 groups of 1000
[INFO] [2019-12-25 08:42:42] Average Time: 0.084
[INFO] [2019-12-25 08:42:42] Total Time: 2s
[INFO] [2019-12-25 08:42:42] last 3 / first 3: 0.83
[INFO] [2019-12-25 08:42:42] Std.Dev: 0.03162277660168379; Max: 0.14
[INFO] [2019-12-25 08:42:42] Storing 15376 Traits
[INFO] [2019-12-25 08:42:42] Processing group of 15376 in 16 groups of 1000
[INFO] [2019-12-25 08:42:47] Average Time: 0.331
[INFO] [2019-12-25 08:42:47] Total Time: 6s
[INFO] [2019-12-25 08:42:47] last 3 / first 3: 0.74
[INFO] [2019-12-25 08:42:47] Std.Dev: 0.07071067811865475; Max: 0.48
[INFO] [2019-12-25 08:42:47] Storing 15374 MetaTraits
[INFO] [2019-12-25 08:42:47] Processing group of 15374 in 16 groups of 1000
[INFO] [2019-12-25 08:42:50] Average Time: 0.169
[INFO] [2019-12-25 08:42:50] Total Time: 3s
[INFO] [2019-12-25 08:42:50] last 3 / first 3: 0.53
[INFO] [2019-12-25 08:42:50] Std.Dev: 0.07071067811865475; Max: 0.31
[STOP] [2019-12-25 08:42:50] parse_diff_and_store
[START] [2019-12-25 08:42:50] resolve_keys
[INFO] [2019-12-25 08:43:42] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 08:43:46] traits to occurrences...
[INFO] [2019-12-25 08:43:52] traits to nodes (through occurrences)...
[INFO] [2019-12-25 08:43:52] Traits to sex term...
[INFO] [2019-12-25 08:43:57] Traits to lifestage term...
[INFO] [2019-12-25 08:44:02] MetaTraits to traits...
[INFO] [2019-12-25 08:44:03] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 08:44:05] Assocs to occurrences...
[INFO] [2019-12-25 08:44:05] Assocs to nodes...
[INFO] [2019-12-25 08:44:05] Assoc to sex term...
[INFO] [2019-12-25 08:44:05] Assoc to lifestage term...
[STOP] [2019-12-25 08:44:05] resolve_keys
[START] [2019-12-25 08:44:05] hold_for_later_1
[STOP] [2019-12-25 08:44:05] hold_for_later_1
[START] [2019-12-25 08:44:05] hold_for_later_2
[STOP] [2019-12-25 08:44:05] hold_for_later_2
[START] [2019-12-25 08:44:05] resolve_missing_parents
[STOP] [2019-12-25 08:44:33] resolve_missing_parents
[START] [2019-12-25 08:44:33] rebuild_nodes
[START] [2019-12-25 08:44:33] Flattener#flatten
[START] [2019-12-25 08:44:33] Flattener#study_resource
[START] [2019-12-25 08:44:33] Flattener#build_ancestry
[STOP] [2019-12-25 08:44:34] Flattener#build_ancestry
[INFO] [2019-12-25 08:44:34] 13691 ancestry keys
[START] [2019-12-25 08:44:34] build_node_ancestors
[INFO] [2019-12-25 08:44:34] old ancestors deleted.
[STOP] [2019-12-25 08:44:40] build_node_ancestors
[START] [2019-12-25 08:44:48] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 08:44:50] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 08:44:50] Flattener#flatten
[STOP] [2019-12-25 08:44:50] rebuild_nodes
[START] [2019-12-25 08:44:50] resolve_missing_media_owners
[STOP] [2019-12-25 08:44:50] resolve_missing_media_owners
[START] [2019-12-25 08:44:50] sanitize_media_verbatims
[STOP] [2019-12-25 08:44:50] sanitize_media_verbatims
[START] [2019-12-25 08:44:50] queue_downloads
[STOP] [2019-12-25 08:44:50] queue_downloads
[START] [2019-12-25 08:44:50] parse_names
[WARN] [2019-12-25 08:44:50] I see 13691 names which still need to be parsed.
[STOP] [2019-12-25 08:45:02] parse_names
[START] [2019-12-25 08:45:02] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 08:45:02] denormalize_canonical_names_to_nodes
[START] [2019-12-25 08:45:02] match_nodes
[START] [2019-12-25 08:45:02] map_all_nodes_to_pages
[STOP] [2019-12-25 09:47:44] map_all_nodes_to_pages
[INFO] [2019-12-25 09:47:44] 960 Unmatched nodes (of 13691)! That's too many to output. First 10: Anas penelope (#62381580); Anas clypeata (#62381697); Anas strepera (#62381720); Anas querquedula (#62381883); Anas americana (#62382454); Anas discors (#62385160); Anas sibilatrix (#62387094); Anas formosa (#62388909); Anas falcata (#62391033); Anas versicolor (#62391884)
[START] [2019-12-25 09:47:44] update_nodes
[STOP] [2019-12-25 09:47:49] update_nodes
[STOP] [2019-12-25 09:47:49] match_nodes
[START] [2019-12-25 09:47:49] reindex_search
[STOP] [2019-12-25 09:48:46] reindex_search
[START] [2019-12-25 09:48:46] normalize_units
[STOP] [2019-12-25 09:48:46] normalize_units
[START] [2019-12-25 09:48:46] calculate_statistics
[STOP] [2019-12-25 09:48:46] calculate_statistics
[START] [2019-12-25 09:48:46] complete_harvest_instance
[START] [2019-12-25 09:48:46] overall_tsv_creation
[INFO] [2019-12-25 09:48:46] Processing group of 13691 in 2 batches of 10000
[INFO] [2019-12-25 09:50:20] 5267 Traits (unfiltered)...
[INFO] [2019-12-25 09:50:33] 5267 Traits (filtered)...
[INFO] [2019-12-25 09:50:33] 0 Associations (filtered)...
[INFO] [2019-12-25 09:51:23] 26333 metadata added.
[INFO] [2019-12-25 09:51:23] 0 metadata added.
[INFO] [2019-12-25 09:52:26] 2421 Traits (unfiltered)...
[INFO] [2019-12-25 09:52:39] 2421 Traits (filtered)...
[INFO] [2019-12-25 09:52:39] 0 Associations (filtered)...
[INFO] [2019-12-25 09:53:21] 12105 metadata added.
[INFO] [2019-12-25 09:53:21] 0 metadata added.
[INFO] [2019-12-25 09:53:21] Average Time: 110.365
[INFO] [2019-12-25 09:53:21] Total Time: 4m36s
[STOP] [2019-12-25 09:53:21] overall_tsv_creation
[INFO] [2019-12-25 09:53:21] Done. Check your files:
[INFO] [2019-12-25 09:53:22] (13691 lines) /app/public/data/n_sea_sp_list/publish_nodes.tsv
[INFO] [2019-12-25 09:53:22] (70376 lines) /app/public/data/n_sea_sp_list/publish_node_ancestors.tsv
[INFO] [2019-12-25 09:53:22] (13691 lines) /app/public/data/n_sea_sp_list/publish_scientific_names.tsv
[INFO] [2019-12-25 09:53:22] (7689 lines) /app/public/data/n_sea_sp_list/publish_traits.tsv
[INFO] [2019-12-25 09:53:22] (38439 lines) /app/public/data/n_sea_sp_list/publish_metadata.tsv
[STOP] [2019-12-25 09:53:22] complete_harvest_instance
[START] [2019-12-25 09:53:22] completed
[STOP] [2019-12-25 09:53:22] completed
[STOP] [2019-12-25 09:53:22] logged process, took 4309.63
Latest Process

25 Dec 08:41 EXITED currently processing 0