Harvest for Hudson Bay Species List Created 23 Dec 19:00

Stage: completed
Fetched: 23 Dec 19:00
Validated: 23 Dec 19:00
Deltas Created 23 Dec 19:00
Units Normalized: 23 Dec 19:07
Ancestry Built: 23 Dec 19:00
Nodes Matched: 23 Dec 19:07
Names Parsed: 23 Dec 19:00
New Models Stored: 23 Dec 19:00
Indexed: 23 Dec 19:07
Completed: 23 Dec 19:09
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 19:00:12 -0500 by logger.rb/56815
[START] [2019-12-23 19:00:12] logged process
[START] [2019-12-23 19:00:12] create_harvest_instance
[STOP] [2019-12-23 19:00:12] create_harvest_instance
[START] [2019-12-23 19:00:12] fetch_files
[STOP] [2019-12-23 19:00:12] fetch_files
[START] [2019-12-23 19:00:12] validate_each_file
[STOP] [2019-12-23 19:00:12] validate_each_file
[START] [2019-12-23 19:00:12] convert_to_csv
[CMD] [2019-12-23 19:00:12] /usr/bin/sort /app/public/converted_csv/hudson_bay_sp_li_refs_19514.csv > /app/public/converted_csv/hudson_bay_sp_li_refs_19514.csv_sorted
[CMD] [2019-12-23 19:00:13] /usr/bin/sort /app/public/converted_csv/hudson_bay_sp_li_nodes_19515.csv > /app/public/converted_csv/hudson_bay_sp_li_nodes_19515.csv_sorted
[CMD] [2019-12-23 19:00:13] /usr/bin/sort /app/public/converted_csv/hudson_bay_sp_li_occurrences_19516.csv > /app/public/converted_csv/hudson_bay_sp_li_occurrences_19516.csv_sorted
[CMD] [2019-12-23 19:00:13] /usr/bin/sort /app/public/converted_csv/hudson_bay_sp_li_measurements_19517.csv > /app/public/converted_csv/hudson_bay_sp_li_measurements_19517.csv_sorted
[STOP] [2019-12-23 19:00:13] convert_to_csv
[START] [2019-12-23 19:00:13] calculate_delta
[CMD] [2019-12-23 19:00:13] echo "0a" > /app/public/diff/hudson_bay_sp_li_refs_19514.diff
[CMD] [2019-12-23 19:00:13] tail -n +1 /app/public/converted_csv/hudson_bay_sp_li_refs_19514.csv >> /app/public/diff/hudson_bay_sp_li_refs_19514.diff
[CMD] [2019-12-23 19:00:13] echo "." >> /app/public/diff/hudson_bay_sp_li_refs_19514.diff
[CMD] [2019-12-23 19:00:13] echo "0a" > /app/public/diff/hudson_bay_sp_li_nodes_19515.diff
[CMD] [2019-12-23 19:00:14] tail -n +1 /app/public/converted_csv/hudson_bay_sp_li_nodes_19515.csv >> /app/public/diff/hudson_bay_sp_li_nodes_19515.diff
[CMD] [2019-12-23 19:00:14] echo "." >> /app/public/diff/hudson_bay_sp_li_nodes_19515.diff
[CMD] [2019-12-23 19:00:14] echo "0a" > /app/public/diff/hudson_bay_sp_li_occurrences_19516.diff
[CMD] [2019-12-23 19:00:14] tail -n +1 /app/public/converted_csv/hudson_bay_sp_li_occurrences_19516.csv >> /app/public/diff/hudson_bay_sp_li_occurrences_19516.diff
[CMD] [2019-12-23 19:00:14] echo "." >> /app/public/diff/hudson_bay_sp_li_occurrences_19516.diff
[CMD] [2019-12-23 19:00:14] echo "0a" > /app/public/diff/hudson_bay_sp_li_measurements_19517.diff
[CMD] [2019-12-23 19:00:14] tail -n +1 /app/public/converted_csv/hudson_bay_sp_li_measurements_19517.csv >> /app/public/diff/hudson_bay_sp_li_measurements_19517.diff
[CMD] [2019-12-23 19:00:14] echo "." >> /app/public/diff/hudson_bay_sp_li_measurements_19517.diff
[STOP] [2019-12-23 19:00:15] calculate_delta
[START] [2019-12-23 19:00:15] parse_diff_and_store
[INFO] [2019-12-23 19:00:15] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 19:00:15] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 19:00:16] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 19:00:16] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 19:00:19] Storing 2 References
[INFO] [2019-12-23 19:00:19] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 19:00:19] Average Time: 0.0
[INFO] [2019-12-23 19:00:19] Total Time: 1s
[INFO] [2019-12-23 19:00:19] Storing 1427 ScientificNames
[INFO] [2019-12-23 19:00:19] Processing group of 1427 in 2 groups of 1000
[INFO] [2019-12-23 19:00:20] Average Time: 0.32
[INFO] [2019-12-23 19:00:20] Total Time: 1s
[INFO] [2019-12-23 19:00:20] Storing 1427 Nodes
[INFO] [2019-12-23 19:00:20] Processing group of 1427 in 2 groups of 1000
[INFO] [2019-12-23 19:00:20] Average Time: 0.295
[INFO] [2019-12-23 19:00:20] Total Time: 1s
[INFO] [2019-12-23 19:00:20] Storing 570 Occurrences
[INFO] [2019-12-23 19:00:20] Processing group of 570 in 1 groups of 1000
[INFO] [2019-12-23 19:00:21] Average Time: 0.1
[INFO] [2019-12-23 19:00:21] Total Time: 1s
[INFO] [2019-12-23 19:00:21] Storing 1140 TraitsReferences
[INFO] [2019-12-23 19:00:21] Processing group of 1140 in 2 groups of 1000
[INFO] [2019-12-23 19:00:21] Average Time: 0.09
[INFO] [2019-12-23 19:00:21] Total Time: 1s
[INFO] [2019-12-23 19:00:21] Storing 1140 Traits
[INFO] [2019-12-23 19:00:21] Processing group of 1140 in 2 groups of 1000
[INFO] [2019-12-23 19:00:21] Average Time: 0.275
[INFO] [2019-12-23 19:00:21] Total Time: 1s
[INFO] [2019-12-23 19:00:21] Storing 1138 MetaTraits
[INFO] [2019-12-23 19:00:21] Processing group of 1138 in 2 groups of 1000
[INFO] [2019-12-23 19:00:22] Average Time: 0.105
[INFO] [2019-12-23 19:00:22] Total Time: 1s
[STOP] [2019-12-23 19:00:22] parse_diff_and_store
[START] [2019-12-23 19:00:22] resolve_keys
[INFO] [2019-12-23 19:00:29] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 19:00:30] traits to occurrences...
[INFO] [2019-12-23 19:00:30] traits to nodes (through occurrences)...
[INFO] [2019-12-23 19:00:30] Traits to sex term...
[INFO] [2019-12-23 19:00:30] Traits to lifestage term...
[INFO] [2019-12-23 19:00:30] MetaTraits to traits...
[INFO] [2019-12-23 19:00:30] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 19:00:30] Assocs to occurrences...
[INFO] [2019-12-23 19:00:30] Assocs to nodes...
[INFO] [2019-12-23 19:00:30] Assoc to sex term...
[INFO] [2019-12-23 19:00:30] Assoc to lifestage term...
[STOP] [2019-12-23 19:00:30] resolve_keys
[START] [2019-12-23 19:00:30] hold_for_later_1
[STOP] [2019-12-23 19:00:30] hold_for_later_1
[START] [2019-12-23 19:00:30] hold_for_later_2
[STOP] [2019-12-23 19:00:30] hold_for_later_2
[START] [2019-12-23 19:00:30] resolve_missing_parents
[STOP] [2019-12-23 19:00:32] resolve_missing_parents
[START] [2019-12-23 19:00:32] rebuild_nodes
[START] [2019-12-23 19:00:32] Flattener#flatten
[START] [2019-12-23 19:00:32] Flattener#study_resource
[START] [2019-12-23 19:00:32] Flattener#build_ancestry
[STOP] [2019-12-23 19:00:32] Flattener#build_ancestry
[INFO] [2019-12-23 19:00:32] 1427 ancestry keys
[START] [2019-12-23 19:00:32] build_node_ancestors
[INFO] [2019-12-23 19:00:32] old ancestors deleted.
[STOP] [2019-12-23 19:00:32] build_node_ancestors
[START] [2019-12-23 19:00:33] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 19:00:33] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 19:00:33] Flattener#flatten
[STOP] [2019-12-23 19:00:33] rebuild_nodes
[START] [2019-12-23 19:00:33] resolve_missing_media_owners
[STOP] [2019-12-23 19:00:33] resolve_missing_media_owners
[START] [2019-12-23 19:00:33] sanitize_media_verbatims
[STOP] [2019-12-23 19:00:33] sanitize_media_verbatims
[START] [2019-12-23 19:00:33] queue_downloads
[STOP] [2019-12-23 19:00:33] queue_downloads
[START] [2019-12-23 19:00:33] parse_names
[WARN] [2019-12-23 19:00:33] I see 1427 names which still need to be parsed.
[STOP] [2019-12-23 19:00:35] parse_names
[START] [2019-12-23 19:00:35] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 19:00:35] denormalize_canonical_names_to_nodes
[START] [2019-12-23 19:00:35] match_nodes
[START] [2019-12-23 19:00:35] map_all_nodes_to_pages
[STOP] [2019-12-23 19:07:15] map_all_nodes_to_pages
[INFO] [2019-12-23 19:07:15] 104 Unmatched nodes (of 1427)! That's too many to output. First 10: Larus thayeri (#62133917); Tringa semipalmatus (#62134589); Limnodromus (#62133867); Philomachus (#62134636); Philomachus pugnax (#62134635); Anas americana (#62133886); Anas clypeata (#62133888); Anas strepera (#62133940); Anas discors (#62133974); Anas penelope (#62134318)
[START] [2019-12-23 19:07:15] update_nodes
[STOP] [2019-12-23 19:07:15] update_nodes
[STOP] [2019-12-23 19:07:15] match_nodes
[START] [2019-12-23 19:07:15] reindex_search
[STOP] [2019-12-23 19:07:19] reindex_search
[START] [2019-12-23 19:07:19] normalize_units
[STOP] [2019-12-23 19:07:19] normalize_units
[START] [2019-12-23 19:07:19] calculate_statistics
[STOP] [2019-12-23 19:07:19] calculate_statistics
[START] [2019-12-23 19:07:19] complete_harvest_instance
[START] [2019-12-23 19:07:19] overall_tsv_creation
[INFO] [2019-12-23 19:07:19] Processing group of 1427 in 1 batches of 10000
[INFO] [2019-12-23 19:08:11] 570 Traits (unfiltered)...
[INFO] [2019-12-23 19:08:24] 570 Traits (filtered)...
[INFO] [2019-12-23 19:08:24] 0 Associations (filtered)...
[INFO] [2019-12-23 19:09:02] 2848 metadata added.
[INFO] [2019-12-23 19:09:02] 0 metadata added.
[INFO] [2019-12-23 19:09:02] Average Time: 79.64
[INFO] [2019-12-23 19:09:02] Total Time: 1m43s
[STOP] [2019-12-23 19:09:02] overall_tsv_creation
[INFO] [2019-12-23 19:09:02] Done. Check your files:
[INFO] [2019-12-23 19:09:02] (1427 lines) /app/public/data/hudson_bay_sp_li/publish_nodes.tsv
[INFO] [2019-12-23 19:09:02] (6766 lines) /app/public/data/hudson_bay_sp_li/publish_node_ancestors.tsv
[INFO] [2019-12-23 19:09:02] (1427 lines) /app/public/data/hudson_bay_sp_li/publish_scientific_names.tsv
[INFO] [2019-12-23 19:09:03] (571 lines) /app/public/data/hudson_bay_sp_li/publish_traits.tsv
[INFO] [2019-12-23 19:09:03] (2849 lines) /app/public/data/hudson_bay_sp_li/publish_metadata.tsv
[STOP] [2019-12-23 19:09:03] complete_harvest_instance
[START] [2019-12-23 19:09:03] completed
[STOP] [2019-12-23 19:09:03] completed
[STOP] [2019-12-23 19:09:03] logged process, took 531.14
Latest Process

23 Dec 19:00 EXITED currently processing 0