Harvest for Iceland Species List Created 13 Oct 11:40

Stage: completed
Fetched: 13 Oct 11:40
Validated: 13 Oct 11:40
Deltas Created 13 Oct 11:40
Units Normalized: 13 Oct 11:49
Ancestry Built: 13 Oct 11:42
Nodes Matched: 13 Oct 11:49
Names Parsed: 13 Oct 11:42
New Models Stored: 13 Oct 11:41
Indexed: 13 Oct 11:49
Completed: 13 Oct 11:51
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-10-13 11:40:39 -0400 by logger.rb/56815
[START] [2019-10-13 11:40:39] logged process
[START] [2019-10-13 11:40:39] create_harvest_instance
[STOP] [2019-10-13 11:40:40] create_harvest_instance
[START] [2019-10-13 11:40:40] fetch_files
[STOP] [2019-10-13 11:40:40] fetch_files
[START] [2019-10-13 11:40:40] validate_each_file
[STOP] [2019-10-13 11:40:41] validate_each_file
[START] [2019-10-13 11:40:41] convert_to_csv
[CMD] [2019-10-13 11:40:41] /usr/bin/sort /app/public/converted_csv/iceland_sp_list_refs_16131.csv > /app/public/converted_csv/iceland_sp_list_refs_16131.csv_sorted
[CMD] [2019-10-13 11:40:41] /usr/bin/sort /app/public/converted_csv/iceland_sp_list_nodes_16132.csv > /app/public/converted_csv/iceland_sp_list_nodes_16132.csv_sorted
[CMD] [2019-10-13 11:40:41] /usr/bin/sort /app/public/converted_csv/iceland_sp_list_occurrences_16133.csv > /app/public/converted_csv/iceland_sp_list_occurrences_16133.csv_sorted
[CMD] [2019-10-13 11:40:41] /usr/bin/sort /app/public/converted_csv/iceland_sp_list_measurements_16134.csv > /app/public/converted_csv/iceland_sp_list_measurements_16134.csv_sorted
[STOP] [2019-10-13 11:40:41] convert_to_csv
[START] [2019-10-13 11:40:41] calculate_delta
[CMD] [2019-10-13 11:40:41] echo "0a" > /app/public/diff/iceland_sp_list_refs_16131.diff
[CMD] [2019-10-13 11:40:41] tail -n +1 /app/public/converted_csv/iceland_sp_list_refs_16131.csv >> /app/public/diff/iceland_sp_list_refs_16131.diff
[CMD] [2019-10-13 11:40:42] echo "." >> /app/public/diff/iceland_sp_list_refs_16131.diff
[CMD] [2019-10-13 11:40:42] echo "0a" > /app/public/diff/iceland_sp_list_nodes_16132.diff
[CMD] [2019-10-13 11:40:42] tail -n +1 /app/public/converted_csv/iceland_sp_list_nodes_16132.csv >> /app/public/diff/iceland_sp_list_nodes_16132.diff
[CMD] [2019-10-13 11:40:42] echo "." >> /app/public/diff/iceland_sp_list_nodes_16132.diff
[CMD] [2019-10-13 11:40:42] echo "0a" > /app/public/diff/iceland_sp_list_occurrences_16133.diff
[CMD] [2019-10-13 11:40:42] tail -n +1 /app/public/converted_csv/iceland_sp_list_occurrences_16133.csv >> /app/public/diff/iceland_sp_list_occurrences_16133.diff
[CMD] [2019-10-13 11:40:42] echo "." >> /app/public/diff/iceland_sp_list_occurrences_16133.diff
[CMD] [2019-10-13 11:40:42] echo "0a" > /app/public/diff/iceland_sp_list_measurements_16134.diff
[CMD] [2019-10-13 11:40:42] tail -n +1 /app/public/converted_csv/iceland_sp_list_measurements_16134.csv >> /app/public/diff/iceland_sp_list_measurements_16134.diff
[CMD] [2019-10-13 11:40:42] echo "." >> /app/public/diff/iceland_sp_list_measurements_16134.diff
[STOP] [2019-10-13 11:40:42] calculate_delta
[START] [2019-10-13 11:40:42] parse_diff_and_store
[INFO] [2019-10-13 11:40:43] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 11:40:43] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 11:40:45] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 11:40:46] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 11:41:11] Storing 2 References
[INFO] [2019-10-13 11:41:11] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 11:41:11] Average Time: 0.0
[INFO] [2019-10-13 11:41:11] Total Time: 1s
[INFO] [2019-10-13 11:41:11] Storing 6697 ScientificNames
[INFO] [2019-10-13 11:41:11] Processing group of 6697 in 7 groups of 1000
[INFO] [2019-10-13 11:41:14] Average Time: 0.37
[INFO] [2019-10-13 11:41:14] Total Time: 3s
[INFO] [2019-10-13 11:41:14] last 3 / first 3: 0.76
[INFO] [2019-10-13 11:41:14] Std.Dev: 0.07071067811865475; Max: 0.45
[INFO] [2019-10-13 11:41:14] Storing 6697 Nodes
[INFO] [2019-10-13 11:41:14] Processing group of 6697 in 7 groups of 1000
[INFO] [2019-10-13 11:41:16] Average Time: 0.283
[INFO] [2019-10-13 11:41:16] Total Time: 3s
[INFO] [2019-10-13 11:41:16] last 3 / first 3: 0.93
[INFO] [2019-10-13 11:41:16] Std.Dev: 0.03162277660168379; Max: 0.32
[INFO] [2019-10-13 11:41:16] Storing 3856 Occurrences
[INFO] [2019-10-13 11:41:16] Processing group of 3856 in 4 groups of 1000
[INFO] [2019-10-13 11:41:17] Average Time: 0.225
[INFO] [2019-10-13 11:41:17] Total Time: 1s
[INFO] [2019-10-13 11:41:17] Storing 8176 TraitsReferences
[INFO] [2019-10-13 11:41:17] Processing group of 8176 in 9 groups of 1000
[INFO] [2019-10-13 11:41:17] Average Time: 0.072
[INFO] [2019-10-13 11:41:17] Total Time: 1s
[INFO] [2019-10-13 11:41:17] last 3 / first 3: 0.52
[INFO] [2019-10-13 11:41:17] Std.Dev: 0.03162277660168379; Max: 0.14
[INFO] [2019-10-13 11:41:17] Storing 8175 Traits
[INFO] [2019-10-13 11:41:17] Processing group of 8175 in 9 groups of 1000
[INFO] [2019-10-13 11:41:20] Average Time: 0.324
[INFO] [2019-10-13 11:41:20] Total Time: 3s
[INFO] [2019-10-13 11:41:20] last 3 / first 3: 0.65
[INFO] [2019-10-13 11:41:20] Std.Dev: 0.11401754250991379; Max: 0.49
[INFO] [2019-10-13 11:41:20] Storing 8175 MetaTraits
[INFO] [2019-10-13 11:41:20] Processing group of 8175 in 9 groups of 1000
[INFO] [2019-10-13 11:41:22] Average Time: 0.144
[INFO] [2019-10-13 11:41:22] Total Time: 2s
[INFO] [2019-10-13 11:41:22] last 3 / first 3: 0.7
[INFO] [2019-10-13 11:41:22] Std.Dev: 0.05477225575051661; Max: 0.21
[STOP] [2019-10-13 11:41:22] parse_diff_and_store
[START] [2019-10-13 11:41:22] resolve_keys
[INFO] [2019-10-13 11:41:50] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 11:41:53] traits to occurrences...
[INFO] [2019-10-13 11:41:55] traits to nodes (through occurrences)...
[INFO] [2019-10-13 11:41:55] Traits to sex term...
[INFO] [2019-10-13 11:41:56] Traits to lifestage term...
[INFO] [2019-10-13 11:41:58] MetaTraits to traits...
[INFO] [2019-10-13 11:41:58] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 11:42:00] Assocs to occurrences...
[INFO] [2019-10-13 11:42:00] Assocs to nodes...
[INFO] [2019-10-13 11:42:00] Assoc to sex term...
[INFO] [2019-10-13 11:42:00] Assoc to lifestage term...
[STOP] [2019-10-13 11:42:00] resolve_keys
[START] [2019-10-13 11:42:00] hold_for_later_1
[STOP] [2019-10-13 11:42:00] hold_for_later_1
[START] [2019-10-13 11:42:00] hold_for_later_2
[STOP] [2019-10-13 11:42:00] hold_for_later_2
[START] [2019-10-13 11:42:00] resolve_missing_parents
[STOP] [2019-10-13 11:42:14] resolve_missing_parents
[START] [2019-10-13 11:42:14] rebuild_nodes
[START] [2019-10-13 11:42:14] Flattener#flatten
[START] [2019-10-13 11:42:14] Flattener#study_resource
[START] [2019-10-13 11:42:14] Flattener#build_ancestry
[STOP] [2019-10-13 11:42:14] Flattener#build_ancestry
[INFO] [2019-10-13 11:42:14] 6697 ancestry keys
[START] [2019-10-13 11:42:14] build_node_ancestors
[INFO] [2019-10-13 11:42:14] old ancestors deleted.
[STOP] [2019-10-13 11:42:15] build_node_ancestors
[START] [2019-10-13 11:42:17] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 11:42:18] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 11:42:18] Flattener#flatten
[STOP] [2019-10-13 11:42:18] rebuild_nodes
[START] [2019-10-13 11:42:18] resolve_missing_media_owners
[STOP] [2019-10-13 11:42:18] resolve_missing_media_owners
[START] [2019-10-13 11:42:18] sanitize_media_verbatims
[STOP] [2019-10-13 11:42:18] sanitize_media_verbatims
[START] [2019-10-13 11:42:18] queue_downloads
[STOP] [2019-10-13 11:42:18] queue_downloads
[START] [2019-10-13 11:42:18] parse_names
[WARN] [2019-10-13 11:42:18] I see 6697 names which still need to be parsed.
[STOP] [2019-10-13 11:42:23] parse_names
[START] [2019-10-13 11:42:23] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 11:42:23] denormalize_canonical_names_to_nodes
[START] [2019-10-13 11:42:23] match_nodes
[START] [2019-10-13 11:42:23] map_all_nodes_to_pages
[STOP] [2019-10-13 11:49:11] map_all_nodes_to_pages
[INFO] [2019-10-13 11:49:11] 573 Unmatched nodes (of 6697)! That's too many to output. First 10: Anas penelope (#50093247); Anas strepera (#50093299); Anas clypeata (#50093773); Anas americana (#50094328); Anas querquedula (#50094953); Anas discors (#50098600); Chen (#50096781); Chen rossii (#50096780); Chen caerulescens (#50097859); Thalaseus (#50097213)
[START] [2019-10-13 11:49:11] update_nodes
[STOP] [2019-10-13 11:49:14] update_nodes
[STOP] [2019-10-13 11:49:14] match_nodes
[START] [2019-10-13 11:49:14] reindex_search
[STOP] [2019-10-13 11:49:33] reindex_search
[START] [2019-10-13 11:49:33] normalize_units
[STOP] [2019-10-13 11:49:33] normalize_units
[START] [2019-10-13 11:49:33] calculate_statistics
[STOP] [2019-10-13 11:49:33] calculate_statistics
[START] [2019-10-13 11:49:33] complete_harvest_instance
[START] [2019-10-13 11:49:33] overall_tsv_creation
[INFO] [2019-10-13 11:49:33] Processing group of 6697 in 1 batches of 10000
[INFO] [2019-10-13 11:50:47] 3856 Traits (unfiltered)...
[INFO] [2019-10-13 11:51:01] 3856 Traits (filtered)...
[INFO] [2019-10-13 11:51:01] 0 Associations (filtered)...
[INFO] [2019-10-13 11:51:46] 19280 metadata added.
[INFO] [2019-10-13 11:51:46] 0 metadata added.
[INFO] [2019-10-13 11:51:46] Average Time: 108.24
[INFO] [2019-10-13 11:51:46] Total Time: 2m14s
[STOP] [2019-10-13 11:51:46] overall_tsv_creation
[INFO] [2019-10-13 11:51:46] Done. Check your files:
[INFO] [2019-10-13 11:51:46] (6697 lines) /app/public/data/iceland_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 11:51:46] (22184 lines) /app/public/data/iceland_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 11:51:46] (6697 lines) /app/public/data/iceland_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 11:51:46] (3857 lines) /app/public/data/iceland_sp_list/publish_traits.tsv
[INFO] [2019-10-13 11:51:46] (19281 lines) /app/public/data/iceland_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 11:51:47] complete_harvest_instance
[START] [2019-10-13 11:51:47] completed
[STOP] [2019-10-13 11:51:47] completed
[STOP] [2019-10-13 11:51:47] logged process, took 667.41
Latest Process

13 Oct 11:40 EXITED currently processing 0