Harvest for Finland Species List Created 12 Oct 21:15

Stage: completed
Fetched: 12 Oct 21:15
Validated: 12 Oct 21:15
Deltas Created 12 Oct 21:15
Units Normalized: 12 Oct 22:10
Ancestry Built: 12 Oct 21:22
Nodes Matched: 12 Oct 22:08
Names Parsed: 12 Oct 21:22
New Models Stored: 12 Oct 21:18
Indexed: 12 Oct 22:10
Completed: 12 Oct 22:18
Time to Harvest: 1 minute
Harvesting Log

(161 lines)
# Logfile created on 2019-10-12 21:15:35 -0400 by logger.rb/56815
[START] [2019-10-12 21:15:35] logged process
[START] [2019-10-12 21:15:35] create_harvest_instance
[STOP] [2019-10-12 21:15:35] create_harvest_instance
[START] [2019-10-12 21:15:35] fetch_files
[STOP] [2019-10-12 21:15:35] fetch_files
[START] [2019-10-12 21:15:35] validate_each_file
[STOP] [2019-10-12 21:15:39] validate_each_file
[START] [2019-10-12 21:15:39] convert_to_csv
[CMD] [2019-10-12 21:15:39] /usr/bin/sort /app/public/converted_csv/finland_sp_list_refs_15763.csv > /app/public/converted_csv/finland_sp_list_refs_15763.csv_sorted
[CMD] [2019-10-12 21:15:39] /usr/bin/sort /app/public/converted_csv/finland_sp_list_nodes_15764.csv > /app/public/converted_csv/finland_sp_list_nodes_15764.csv_sorted
[CMD] [2019-10-12 21:15:39] /usr/bin/sort /app/public/converted_csv/finland_sp_list_occurrences_15765.csv > /app/public/converted_csv/finland_sp_list_occurrences_15765.csv_sorted
[CMD] [2019-10-12 21:15:39] /usr/bin/sort /app/public/converted_csv/finland_sp_list_measurements_15766.csv > /app/public/converted_csv/finland_sp_list_measurements_15766.csv_sorted
[STOP] [2019-10-12 21:15:39] convert_to_csv
[START] [2019-10-12 21:15:39] calculate_delta
[CMD] [2019-10-12 21:15:39] echo "0a" > /app/public/diff/finland_sp_list_refs_15763.diff
[CMD] [2019-10-12 21:15:39] tail -n +1 /app/public/converted_csv/finland_sp_list_refs_15763.csv >> /app/public/diff/finland_sp_list_refs_15763.diff
[CMD] [2019-10-12 21:15:40] echo "." >> /app/public/diff/finland_sp_list_refs_15763.diff
[CMD] [2019-10-12 21:15:40] echo "0a" > /app/public/diff/finland_sp_list_nodes_15764.diff
[CMD] [2019-10-12 21:15:40] tail -n +1 /app/public/converted_csv/finland_sp_list_nodes_15764.csv >> /app/public/diff/finland_sp_list_nodes_15764.diff
[CMD] [2019-10-12 21:15:40] echo "." >> /app/public/diff/finland_sp_list_nodes_15764.diff
[CMD] [2019-10-12 21:15:40] echo "0a" > /app/public/diff/finland_sp_list_occurrences_15765.diff
[CMD] [2019-10-12 21:15:40] tail -n +1 /app/public/converted_csv/finland_sp_list_occurrences_15765.csv >> /app/public/diff/finland_sp_list_occurrences_15765.diff
[CMD] [2019-10-12 21:15:40] echo "." >> /app/public/diff/finland_sp_list_occurrences_15765.diff
[CMD] [2019-10-12 21:15:40] echo "0a" > /app/public/diff/finland_sp_list_measurements_15766.diff
[CMD] [2019-10-12 21:15:40] tail -n +1 /app/public/converted_csv/finland_sp_list_measurements_15766.csv >> /app/public/diff/finland_sp_list_measurements_15766.diff
[CMD] [2019-10-12 21:15:40] echo "." >> /app/public/diff/finland_sp_list_measurements_15766.diff
[STOP] [2019-10-12 21:15:40] calculate_delta
[START] [2019-10-12 21:15:40] parse_diff_and_store
[INFO] [2019-10-12 21:15:41] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 21:15:41] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 21:15:51] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 21:15:55] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 21:17:57] Storing 2 References
[INFO] [2019-10-12 21:17:57] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 21:17:57] Average Time: 0.0
[INFO] [2019-10-12 21:17:57] Total Time: 1s
[INFO] [2019-10-12 21:17:57] Storing 29411 ScientificNames
[INFO] [2019-10-12 21:17:57] Processing group of 29411 in 30 groups of 1000
[INFO] [2019-10-12 21:18:09] Average Time: 0.394
[INFO] [2019-10-12 21:18:09] Total Time: 12s
[INFO] [2019-10-12 21:18:09] last 3 / first 3: 0.9
[INFO] [2019-10-12 21:18:09] Std.Dev: 0.10488088481701516; Max: 0.66
[INFO] [2019-10-12 21:18:09] Storing 29411 Nodes
[INFO] [2019-10-12 21:18:09] Processing group of 29411 in 30 groups of 1000
[INFO] [2019-10-12 21:18:19] Average Time: 0.344
[INFO] [2019-10-12 21:18:19] Total Time: 11s
[INFO] [2019-10-12 21:18:19] last 3 / first 3: 1.2
[INFO] [2019-10-12 21:18:19] Std.Dev: 0.1341640786499874; Max: 0.77
[INFO] [2019-10-12 21:18:19] Storing 21278 Occurrences
[INFO] [2019-10-12 21:18:19] Processing group of 21278 in 22 groups of 1000
[INFO] [2019-10-12 21:18:22] Average Time: 0.105
[INFO] [2019-10-12 21:18:22] Total Time: 3s
[INFO] [2019-10-12 21:18:22] last 3 / first 3: 0.56
[INFO] [2019-10-12 21:18:22] Std.Dev: 0.03162277660168379; Max: 0.22
[INFO] [2019-10-12 21:18:22] Storing 42556 TraitsReferences
[INFO] [2019-10-12 21:18:22] Processing group of 42556 in 43 groups of 1000
[INFO] [2019-10-12 21:18:25] Average Time: 0.068
[INFO] [2019-10-12 21:18:25] Total Time: 4s
[INFO] [2019-10-12 21:18:25] last 3 / first 3: 0.47
[INFO] [2019-10-12 21:18:25] Std.Dev: 0.03162277660168379; Max: 0.24
[INFO] [2019-10-12 21:18:25] Storing 42556 Traits
[INFO] [2019-10-12 21:18:25] Processing group of 42556 in 43 groups of 1000
[INFO] [2019-10-12 21:18:40] Average Time: 0.342
[INFO] [2019-10-12 21:18:40] Total Time: 15s
[INFO] [2019-10-12 21:18:40] last 3 / first 3: 0.78
[INFO] [2019-10-12 21:18:40] Std.Dev: 0.161245154965971; Max: 1.31
[INFO] [2019-10-12 21:18:40] Storing 42545 MetaTraits
[INFO] [2019-10-12 21:18:40] Processing group of 42545 in 43 groups of 1000
[INFO] [2019-10-12 21:18:45] Average Time: 0.118
[INFO] [2019-10-12 21:18:45] Total Time: 6s
[INFO] [2019-10-12 21:18:45] last 3 / first 3: 0.64
[INFO] [2019-10-12 21:18:45] Std.Dev: 0.0; Max: 0.19
[STOP] [2019-10-12 21:18:45] parse_diff_and_store
[START] [2019-10-12 21:18:45] resolve_keys
[INFO] [2019-10-12 21:20:14] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 21:20:21] traits to occurrences...
[INFO] [2019-10-12 21:20:26] traits to nodes (through occurrences)...
[INFO] [2019-10-12 21:20:27] Traits to sex term...
[INFO] [2019-10-12 21:20:33] Traits to lifestage term...
[INFO] [2019-10-12 21:20:39] MetaTraits to traits...
[INFO] [2019-10-12 21:20:42] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 21:20:48] Assocs to occurrences...
[INFO] [2019-10-12 21:20:48] Assocs to nodes...
[INFO] [2019-10-12 21:20:48] Assoc to sex term...
[INFO] [2019-10-12 21:20:48] Assoc to lifestage term...
[STOP] [2019-10-12 21:20:48] resolve_keys
[START] [2019-10-12 21:20:48] hold_for_later_1
[STOP] [2019-10-12 21:20:48] hold_for_later_1
[START] [2019-10-12 21:20:48] hold_for_later_2
[STOP] [2019-10-12 21:20:48] hold_for_later_2
[START] [2019-10-12 21:20:48] resolve_missing_parents
[STOP] [2019-10-12 21:21:35] resolve_missing_parents
[START] [2019-10-12 21:21:35] rebuild_nodes
[START] [2019-10-12 21:21:35] Flattener#flatten
[START] [2019-10-12 21:21:35] Flattener#study_resource
[START] [2019-10-12 21:21:36] Flattener#build_ancestry
[STOP] [2019-10-12 21:21:39] Flattener#build_ancestry
[INFO] [2019-10-12 21:21:39] 29411 ancestry keys
[START] [2019-10-12 21:21:39] build_node_ancestors
[INFO] [2019-10-12 21:21:39] old ancestors deleted.
[STOP] [2019-10-12 21:21:58] build_node_ancestors
[START] [2019-10-12 21:22:03] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 21:22:07] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 21:22:07] Flattener#flatten
[STOP] [2019-10-12 21:22:07] rebuild_nodes
[START] [2019-10-12 21:22:07] resolve_missing_media_owners
[STOP] [2019-10-12 21:22:07] resolve_missing_media_owners
[START] [2019-10-12 21:22:07] sanitize_media_verbatims
[STOP] [2019-10-12 21:22:07] sanitize_media_verbatims
[START] [2019-10-12 21:22:07] queue_downloads
[STOP] [2019-10-12 21:22:07] queue_downloads
[START] [2019-10-12 21:22:07] parse_names
[WARN] [2019-10-12 21:22:07] I see 29411 names which still need to be parsed.
[STOP] [2019-10-12 21:22:30] parse_names
[START] [2019-10-12 21:22:30] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 21:22:30] denormalize_canonical_names_to_nodes
[START] [2019-10-12 21:22:30] match_nodes
[START] [2019-10-12 21:22:31] map_all_nodes_to_pages
[STOP] [2019-10-12 22:08:32] map_all_nodes_to_pages
[INFO] [2019-10-12 22:08:32] 2916 Unmatched nodes (of 29411)! That's too many to output. First 10: Anas penelope (#49653636); Anas clypeata (#49653759); Anas strepera (#49653900); Anas querquedula (#49653974); Anas americana (#49659184); Anas discors (#49659338); Anas formosa (#49663049); Anas cyanoptera (#49674302); Anas sibilatrix (#49676372); Anas falcata (#49682764)
[START] [2019-10-12 22:08:32] update_nodes
[STOP] [2019-10-12 22:08:41] update_nodes
[STOP] [2019-10-12 22:08:41] match_nodes
[START] [2019-10-12 22:08:41] reindex_search
[STOP] [2019-10-12 22:10:21] reindex_search
[START] [2019-10-12 22:10:21] normalize_units
[STOP] [2019-10-12 22:10:21] normalize_units
[START] [2019-10-12 22:10:21] calculate_statistics
[STOP] [2019-10-12 22:10:21] calculate_statistics
[START] [2019-10-12 22:10:21] complete_harvest_instance
[START] [2019-10-12 22:10:21] overall_tsv_creation
[INFO] [2019-10-12 22:10:21] Processing group of 29411 in 3 batches of 10000
[INFO] [2019-10-12 22:11:52] 6491 Traits (unfiltered)...
[INFO] [2019-10-12 22:12:06] 6491 Traits (filtered)...
[INFO] [2019-10-12 22:12:06] 0 Associations (filtered)...
[INFO] [2019-10-12 22:12:57] 32475 metadata added.
[INFO] [2019-10-12 22:12:57] 0 metadata added.
[INFO] [2019-10-12 22:14:31] 7418 Traits (unfiltered)...
[INFO] [2019-10-12 22:14:45] 7418 Traits (filtered)...
[INFO] [2019-10-12 22:14:45] 0 Associations (filtered)...
[INFO] [2019-10-12 22:15:42] 37088 metadata added.
[INFO] [2019-10-12 22:15:42] 0 metadata added.
[INFO] [2019-10-12 22:17:16] 7369 Traits (unfiltered)...
[INFO] [2019-10-12 22:17:30] 7369 Traits (filtered)...
[INFO] [2019-10-12 22:17:30] 0 Associations (filtered)...
[INFO] [2019-10-12 22:18:25] 36816 metadata added.
[INFO] [2019-10-12 22:18:25] 0 metadata added.
[INFO] [2019-10-12 22:18:25] Average Time: 133.967
[INFO] [2019-10-12 22:18:25] Total Time: 8m4s
[STOP] [2019-10-12 22:18:25] overall_tsv_creation
[INFO] [2019-10-12 22:18:25] Done. Check your files:
[INFO] [2019-10-12 22:18:25] (29411 lines) /app/public/data/finland_sp_list/publish_nodes.tsv
[INFO] [2019-10-12 22:18:25] (164743 lines) /app/public/data/finland_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-12 22:18:25] (29411 lines) /app/public/data/finland_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-12 22:18:25] (21279 lines) /app/public/data/finland_sp_list/publish_traits.tsv
[INFO] [2019-10-12 22:18:25] (106380 lines) /app/public/data/finland_sp_list/publish_metadata.tsv
[STOP] [2019-10-12 22:18:25] complete_harvest_instance
[START] [2019-10-12 22:18:25] completed
[STOP] [2019-10-12 22:18:25] completed
[STOP] [2019-10-12 22:18:25] logged process, took 3770.66
Latest Process

12 Oct 21:15 EXITED currently processing 0