Harvest for Labrador Sea Species List Created 23 Dec 16:13

Stage: completed
Fetched: 23 Dec 16:13
Validated: 23 Dec 16:13
Deltas Created 23 Dec 16:13
Units Normalized: 23 Dec 16:33
Ancestry Built: 23 Dec 16:14
Nodes Matched: 23 Dec 16:33
Names Parsed: 23 Dec 16:14
New Models Stored: 23 Dec 16:13
Indexed: 23 Dec 16:33
Completed: 23 Dec 16:35
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 16:13:21 -0500 by logger.rb/56815
[START] [2019-12-23 16:13:21] logged process
[START] [2019-12-23 16:13:21] create_harvest_instance
[STOP] [2019-12-23 16:13:22] create_harvest_instance
[START] [2019-12-23 16:13:22] fetch_files
[STOP] [2019-12-23 16:13:22] fetch_files
[START] [2019-12-23 16:13:22] validate_each_file
[STOP] [2019-12-23 16:13:22] validate_each_file
[START] [2019-12-23 16:13:22] convert_to_csv
[CMD] [2019-12-23 16:13:22] /usr/bin/sort /app/public/converted_csv/labrador_sea_sp__refs_19426.csv > /app/public/converted_csv/labrador_sea_sp__refs_19426.csv_sorted
[CMD] [2019-12-23 16:13:23] /usr/bin/sort /app/public/converted_csv/labrador_sea_sp__nodes_19427.csv > /app/public/converted_csv/labrador_sea_sp__nodes_19427.csv_sorted
[CMD] [2019-12-23 16:13:23] /usr/bin/sort /app/public/converted_csv/labrador_sea_sp__occurrences_19428.csv > /app/public/converted_csv/labrador_sea_sp__occurrences_19428.csv_sorted
[CMD] [2019-12-23 16:13:24] /usr/bin/sort /app/public/converted_csv/labrador_sea_sp__measurements_19429.csv > /app/public/converted_csv/labrador_sea_sp__measurements_19429.csv_sorted
[STOP] [2019-12-23 16:13:25] convert_to_csv
[START] [2019-12-23 16:13:25] calculate_delta
[CMD] [2019-12-23 16:13:25] echo "0a" > /app/public/diff/labrador_sea_sp__refs_19426.diff
[CMD] [2019-12-23 16:13:25] tail -n +1 /app/public/converted_csv/labrador_sea_sp__refs_19426.csv >> /app/public/diff/labrador_sea_sp__refs_19426.diff
[CMD] [2019-12-23 16:13:26] echo "." >> /app/public/diff/labrador_sea_sp__refs_19426.diff
[CMD] [2019-12-23 16:13:27] echo "0a" > /app/public/diff/labrador_sea_sp__nodes_19427.diff
[CMD] [2019-12-23 16:13:27] tail -n +1 /app/public/converted_csv/labrador_sea_sp__nodes_19427.csv >> /app/public/diff/labrador_sea_sp__nodes_19427.diff
[CMD] [2019-12-23 16:13:28] echo "." >> /app/public/diff/labrador_sea_sp__nodes_19427.diff
[CMD] [2019-12-23 16:13:29] echo "0a" > /app/public/diff/labrador_sea_sp__occurrences_19428.diff
[CMD] [2019-12-23 16:13:29] tail -n +1 /app/public/converted_csv/labrador_sea_sp__occurrences_19428.csv >> /app/public/diff/labrador_sea_sp__occurrences_19428.diff
[CMD] [2019-12-23 16:13:30] echo "." >> /app/public/diff/labrador_sea_sp__occurrences_19428.diff
[CMD] [2019-12-23 16:13:31] echo "0a" > /app/public/diff/labrador_sea_sp__measurements_19429.diff
[CMD] [2019-12-23 16:13:31] tail -n +1 /app/public/converted_csv/labrador_sea_sp__measurements_19429.csv >> /app/public/diff/labrador_sea_sp__measurements_19429.diff
[CMD] [2019-12-23 16:13:32] echo "." >> /app/public/diff/labrador_sea_sp__measurements_19429.diff
[STOP] [2019-12-23 16:13:33] calculate_delta
[START] [2019-12-23 16:13:33] parse_diff_and_store
[INFO] [2019-12-23 16:13:34] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 16:13:34] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 16:13:36] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 16:13:37] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 16:13:45] Storing 2 References
[INFO] [2019-12-23 16:13:45] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 16:13:45] Average Time: 0.0
[INFO] [2019-12-23 16:13:45] Total Time: 1s
[INFO] [2019-12-23 16:13:45] Storing 3086 ScientificNames
[INFO] [2019-12-23 16:13:45] Processing group of 3086 in 4 groups of 1000
[INFO] [2019-12-23 16:13:48] Average Time: 0.673
[INFO] [2019-12-23 16:13:48] Total Time: 3s
[INFO] [2019-12-23 16:13:48] Storing 3086 Nodes
[INFO] [2019-12-23 16:13:48] Processing group of 3086 in 4 groups of 1000
[INFO] [2019-12-23 16:13:49] Average Time: 0.263
[INFO] [2019-12-23 16:13:49] Total Time: 2s
[INFO] [2019-12-23 16:13:49] Storing 1365 Occurrences
[INFO] [2019-12-23 16:13:49] Processing group of 1365 in 2 groups of 1000
[INFO] [2019-12-23 16:13:49] Average Time: 0.09
[INFO] [2019-12-23 16:13:49] Total Time: 1s
[INFO] [2019-12-23 16:13:49] Storing 2730 TraitsReferences
[INFO] [2019-12-23 16:13:49] Processing group of 2730 in 3 groups of 1000
[INFO] [2019-12-23 16:13:49] Average Time: 0.093
[INFO] [2019-12-23 16:13:49] Total Time: 1s
[INFO] [2019-12-23 16:13:49] Storing 2730 Traits
[INFO] [2019-12-23 16:13:49] Processing group of 2730 in 3 groups of 1000
[INFO] [2019-12-23 16:13:50] Average Time: 0.377
[INFO] [2019-12-23 16:13:50] Total Time: 2s
[INFO] [2019-12-23 16:13:50] Storing 2729 MetaTraits
[INFO] [2019-12-23 16:13:50] Processing group of 2729 in 3 groups of 1000
[INFO] [2019-12-23 16:13:51] Average Time: 0.157
[INFO] [2019-12-23 16:13:51] Total Time: 1s
[STOP] [2019-12-23 16:13:51] parse_diff_and_store
[START] [2019-12-23 16:13:51] resolve_keys
[INFO] [2019-12-23 16:14:06] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 16:14:07] traits to occurrences...
[INFO] [2019-12-23 16:14:08] traits to nodes (through occurrences)...
[INFO] [2019-12-23 16:14:08] Traits to sex term...
[INFO] [2019-12-23 16:14:08] Traits to lifestage term...
[INFO] [2019-12-23 16:14:09] MetaTraits to traits...
[INFO] [2019-12-23 16:14:09] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 16:14:10] Assocs to occurrences...
[INFO] [2019-12-23 16:14:10] Assocs to nodes...
[INFO] [2019-12-23 16:14:10] Assoc to sex term...
[INFO] [2019-12-23 16:14:10] Assoc to lifestage term...
[STOP] [2019-12-23 16:14:10] resolve_keys
[START] [2019-12-23 16:14:10] hold_for_later_1
[STOP] [2019-12-23 16:14:10] hold_for_later_1
[START] [2019-12-23 16:14:10] hold_for_later_2
[STOP] [2019-12-23 16:14:10] hold_for_later_2
[START] [2019-12-23 16:14:10] resolve_missing_parents
[STOP] [2019-12-23 16:14:15] resolve_missing_parents
[START] [2019-12-23 16:14:15] rebuild_nodes
[START] [2019-12-23 16:14:15] Flattener#flatten
[START] [2019-12-23 16:14:15] Flattener#study_resource
[START] [2019-12-23 16:14:15] Flattener#build_ancestry
[STOP] [2019-12-23 16:14:15] Flattener#build_ancestry
[INFO] [2019-12-23 16:14:15] 3086 ancestry keys
[START] [2019-12-23 16:14:15] build_node_ancestors
[INFO] [2019-12-23 16:14:15] old ancestors deleted.
[STOP] [2019-12-23 16:14:16] build_node_ancestors
[START] [2019-12-23 16:14:17] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 16:14:18] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 16:14:18] Flattener#flatten
[STOP] [2019-12-23 16:14:18] rebuild_nodes
[START] [2019-12-23 16:14:18] resolve_missing_media_owners
[STOP] [2019-12-23 16:14:18] resolve_missing_media_owners
[START] [2019-12-23 16:14:18] sanitize_media_verbatims
[STOP] [2019-12-23 16:14:18] sanitize_media_verbatims
[START] [2019-12-23 16:14:18] queue_downloads
[STOP] [2019-12-23 16:14:18] queue_downloads
[START] [2019-12-23 16:14:18] parse_names
[WARN] [2019-12-23 16:14:18] I see 3086 names which still need to be parsed.
[STOP] [2019-12-23 16:14:21] parse_names
[START] [2019-12-23 16:14:21] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 16:14:21] denormalize_canonical_names_to_nodes
[START] [2019-12-23 16:14:21] match_nodes
[START] [2019-12-23 16:14:21] map_all_nodes_to_pages
[STOP] [2019-12-23 16:33:38] map_all_nodes_to_pages
[INFO] [2019-12-23 16:33:38] 205 Unmatched nodes (of 3086)! That's too many to output. First 10: Puffinus griseus (#62085918); Puffinus creatopus (#62088293); Larus thayeri (#62086688); Larus hemprichii (#62087992); Limnodromus (#62086733); Philomachus (#62087777); Philomachus pugnax (#62087776); Anas americana (#62086571); Anas penelope (#62086651); Anas strepera (#62086807)
[START] [2019-12-23 16:33:38] update_nodes
[STOP] [2019-12-23 16:33:39] update_nodes
[STOP] [2019-12-23 16:33:39] match_nodes
[START] [2019-12-23 16:33:39] reindex_search
[STOP] [2019-12-23 16:33:52] reindex_search
[START] [2019-12-23 16:33:52] normalize_units
[STOP] [2019-12-23 16:33:52] normalize_units
[START] [2019-12-23 16:33:52] calculate_statistics
[STOP] [2019-12-23 16:33:52] calculate_statistics
[START] [2019-12-23 16:33:52] complete_harvest_instance
[START] [2019-12-23 16:33:52] overall_tsv_creation
[INFO] [2019-12-23 16:33:52] Processing group of 3086 in 1 batches of 10000
[INFO] [2019-12-23 16:34:52] 1365 Traits (unfiltered)...
[INFO] [2019-12-23 16:35:05] 1365 Traits (filtered)...
[INFO] [2019-12-23 16:35:05] 0 Associations (filtered)...
[INFO] [2019-12-23 16:35:45] 6824 metadata added.
[INFO] [2019-12-23 16:35:45] 0 metadata added.
[INFO] [2019-12-23 16:35:45] Average Time: 88.48
[INFO] [2019-12-23 16:35:45] Total Time: 1m53s
[STOP] [2019-12-23 16:35:45] overall_tsv_creation
[INFO] [2019-12-23 16:35:45] Done. Check your files:
[INFO] [2019-12-23 16:35:45] (3086 lines) /app/public/data/labrador_sea_sp_/publish_nodes.tsv
[INFO] [2019-12-23 16:35:46] (14727 lines) /app/public/data/labrador_sea_sp_/publish_node_ancestors.tsv
[INFO] [2019-12-23 16:35:47] (3086 lines) /app/public/data/labrador_sea_sp_/publish_scientific_names.tsv
[INFO] [2019-12-23 16:35:47] (1366 lines) /app/public/data/labrador_sea_sp_/publish_traits.tsv
[INFO] [2019-12-23 16:35:48] (6825 lines) /app/public/data/labrador_sea_sp_/publish_metadata.tsv
[STOP] [2019-12-23 16:35:48] complete_harvest_instance
[START] [2019-12-23 16:35:48] completed
[STOP] [2019-12-23 16:35:48] completed
[STOP] [2019-12-23 16:35:48] logged process, took 1347.28
Latest Process

23 Dec 16:13 EXITED currently processing 0