Harvest for Hudson Strait Species List Created 23 Dec 18:55

Stage: completed
Fetched: 23 Dec 18:55
Validated: 23 Dec 18:55
Deltas Created 23 Dec 18:55
Units Normalized: 23 Dec 18:58
Ancestry Built: 23 Dec 18:56
Nodes Matched: 23 Dec 18:58
Names Parsed: 23 Dec 18:56
New Models Stored: 23 Dec 18:55
Indexed: 23 Dec 18:58
Completed: 23 Dec 19:00
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 18:55:22 -0500 by logger.rb/56815
[START] [2019-12-23 18:55:22] logged process
[START] [2019-12-23 18:55:22] create_harvest_instance
[STOP] [2019-12-23 18:55:23] create_harvest_instance
[START] [2019-12-23 18:55:23] fetch_files
[STOP] [2019-12-23 18:55:23] fetch_files
[START] [2019-12-23 18:55:23] validate_each_file
[STOP] [2019-12-23 18:55:23] validate_each_file
[START] [2019-12-23 18:55:23] convert_to_csv
[CMD] [2019-12-23 18:55:23] /usr/bin/sort /app/public/converted_csv/hudson_strait_sp_refs_19506.csv > /app/public/converted_csv/hudson_strait_sp_refs_19506.csv_sorted
[CMD] [2019-12-23 18:55:23] /usr/bin/sort /app/public/converted_csv/hudson_strait_sp_nodes_19507.csv > /app/public/converted_csv/hudson_strait_sp_nodes_19507.csv_sorted
[CMD] [2019-12-23 18:55:23] /usr/bin/sort /app/public/converted_csv/hudson_strait_sp_occurrences_19508.csv > /app/public/converted_csv/hudson_strait_sp_occurrences_19508.csv_sorted
[CMD] [2019-12-23 18:55:24] /usr/bin/sort /app/public/converted_csv/hudson_strait_sp_measurements_19509.csv > /app/public/converted_csv/hudson_strait_sp_measurements_19509.csv_sorted
[STOP] [2019-12-23 18:55:24] convert_to_csv
[START] [2019-12-23 18:55:24] calculate_delta
[CMD] [2019-12-23 18:55:24] echo "0a" > /app/public/diff/hudson_strait_sp_refs_19506.diff
[CMD] [2019-12-23 18:55:24] tail -n +1 /app/public/converted_csv/hudson_strait_sp_refs_19506.csv >> /app/public/diff/hudson_strait_sp_refs_19506.diff
[CMD] [2019-12-23 18:55:24] echo "." >> /app/public/diff/hudson_strait_sp_refs_19506.diff
[CMD] [2019-12-23 18:55:24] echo "0a" > /app/public/diff/hudson_strait_sp_nodes_19507.diff
[CMD] [2019-12-23 18:55:24] tail -n +1 /app/public/converted_csv/hudson_strait_sp_nodes_19507.csv >> /app/public/diff/hudson_strait_sp_nodes_19507.diff
[CMD] [2019-12-23 18:55:24] echo "." >> /app/public/diff/hudson_strait_sp_nodes_19507.diff
[CMD] [2019-12-23 18:55:24] echo "0a" > /app/public/diff/hudson_strait_sp_occurrences_19508.diff
[CMD] [2019-12-23 18:55:25] tail -n +1 /app/public/converted_csv/hudson_strait_sp_occurrences_19508.csv >> /app/public/diff/hudson_strait_sp_occurrences_19508.diff
[CMD] [2019-12-23 18:55:25] echo "." >> /app/public/diff/hudson_strait_sp_occurrences_19508.diff
[CMD] [2019-12-23 18:55:25] echo "0a" > /app/public/diff/hudson_strait_sp_measurements_19509.diff
[CMD] [2019-12-23 18:55:25] tail -n +1 /app/public/converted_csv/hudson_strait_sp_measurements_19509.csv >> /app/public/diff/hudson_strait_sp_measurements_19509.diff
[CMD] [2019-12-23 18:55:25] echo "." >> /app/public/diff/hudson_strait_sp_measurements_19509.diff
[STOP] [2019-12-23 18:55:25] calculate_delta
[START] [2019-12-23 18:55:25] parse_diff_and_store
[INFO] [2019-12-23 18:55:25] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 18:55:25] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 18:55:26] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 18:55:26] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 18:55:27] Storing 2 References
[INFO] [2019-12-23 18:55:27] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 18:55:27] Average Time: 0.0
[INFO] [2019-12-23 18:55:27] Total Time: 1s
[INFO] [2019-12-23 18:55:27] Storing 574 ScientificNames
[INFO] [2019-12-23 18:55:27] Processing group of 574 in 1 groups of 1000
[INFO] [2019-12-23 18:55:28] Average Time: 0.37
[INFO] [2019-12-23 18:55:28] Total Time: 1s
[INFO] [2019-12-23 18:55:28] Storing 574 Nodes
[INFO] [2019-12-23 18:55:28] Processing group of 574 in 1 groups of 1000
[INFO] [2019-12-23 18:55:28] Average Time: 0.24
[INFO] [2019-12-23 18:55:28] Total Time: 1s
[INFO] [2019-12-23 18:55:28] Storing 237 Occurrences
[INFO] [2019-12-23 18:55:28] Processing group of 237 in 1 groups of 1000
[INFO] [2019-12-23 18:55:28] Average Time: 0.05
[INFO] [2019-12-23 18:55:28] Total Time: 1s
[INFO] [2019-12-23 18:55:28] Storing 474 TraitsReferences
[INFO] [2019-12-23 18:55:28] Processing group of 474 in 1 groups of 1000
[INFO] [2019-12-23 18:55:28] Average Time: 0.21
[INFO] [2019-12-23 18:55:28] Total Time: 1s
[INFO] [2019-12-23 18:55:28] Storing 474 Traits
[INFO] [2019-12-23 18:55:28] Processing group of 474 in 1 groups of 1000
[INFO] [2019-12-23 18:55:34] Average Time: 5.67
[INFO] [2019-12-23 18:55:34] Total Time: 6s
[INFO] [2019-12-23 18:55:34] Storing 474 MetaTraits
[INFO] [2019-12-23 18:55:34] Processing group of 474 in 1 groups of 1000
[INFO] [2019-12-23 18:55:34] Average Time: 0.1
[INFO] [2019-12-23 18:55:34] Total Time: 1s
[STOP] [2019-12-23 18:55:34] parse_diff_and_store
[START] [2019-12-23 18:55:34] resolve_keys
[INFO] [2019-12-23 18:55:40] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 18:55:41] traits to occurrences...
[INFO] [2019-12-23 18:55:41] traits to nodes (through occurrences)...
[INFO] [2019-12-23 18:55:41] Traits to sex term...
[INFO] [2019-12-23 18:55:41] Traits to lifestage term...
[INFO] [2019-12-23 18:55:41] MetaTraits to traits...
[INFO] [2019-12-23 18:55:41] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 18:55:41] Assocs to occurrences...
[INFO] [2019-12-23 18:55:41] Assocs to nodes...
[INFO] [2019-12-23 18:55:41] Assoc to sex term...
[INFO] [2019-12-23 18:55:41] Assoc to lifestage term...
[STOP] [2019-12-23 18:55:41] resolve_keys
[START] [2019-12-23 18:55:41] hold_for_later_1
[STOP] [2019-12-23 18:55:41] hold_for_later_1
[START] [2019-12-23 18:55:41] hold_for_later_2
[STOP] [2019-12-23 18:55:41] hold_for_later_2
[START] [2019-12-23 18:55:41] resolve_missing_parents
[STOP] [2019-12-23 18:56:10] resolve_missing_parents
[START] [2019-12-23 18:56:10] rebuild_nodes
[START] [2019-12-23 18:56:10] Flattener#flatten
[START] [2019-12-23 18:56:10] Flattener#study_resource
[START] [2019-12-23 18:56:10] Flattener#build_ancestry
[STOP] [2019-12-23 18:56:10] Flattener#build_ancestry
[INFO] [2019-12-23 18:56:10] 574 ancestry keys
[START] [2019-12-23 18:56:10] build_node_ancestors
[INFO] [2019-12-23 18:56:10] old ancestors deleted.
[STOP] [2019-12-23 18:56:10] build_node_ancestors
[START] [2019-12-23 18:56:10] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 18:56:10] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 18:56:10] Flattener#flatten
[STOP] [2019-12-23 18:56:10] rebuild_nodes
[START] [2019-12-23 18:56:10] resolve_missing_media_owners
[STOP] [2019-12-23 18:56:10] resolve_missing_media_owners
[START] [2019-12-23 18:56:10] sanitize_media_verbatims
[STOP] [2019-12-23 18:56:10] sanitize_media_verbatims
[START] [2019-12-23 18:56:10] queue_downloads
[STOP] [2019-12-23 18:56:10] queue_downloads
[START] [2019-12-23 18:56:10] parse_names
[WARN] [2019-12-23 18:56:10] I see 574 names which still need to be parsed.
[STOP] [2019-12-23 18:56:12] parse_names
[START] [2019-12-23 18:56:12] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 18:56:12] denormalize_canonical_names_to_nodes
[START] [2019-12-23 18:56:12] match_nodes
[START] [2019-12-23 18:56:12] map_all_nodes_to_pages
[STOP] [2019-12-23 18:58:27] map_all_nodes_to_pages
[INFO] [2019-12-23 18:58:27] 66 Unmatched nodes (of 574)! That's too many to output. First 10: Larus thayeri (#62133453); Chen (#62133353); Chen caerulescens (#62133352); Anas clypeata (#62133714); Scorpaeniformes (#62133301); Ulcina (#62133355); Gasterosteiformes (#62133321); Neotaenioglossa (#62133543); Veneroida (#62133573); Plagiorchiida (#62133476)
[START] [2019-12-23 18:58:27] update_nodes
[STOP] [2019-12-23 18:58:27] update_nodes
[STOP] [2019-12-23 18:58:27] match_nodes
[START] [2019-12-23 18:58:27] reindex_search
[STOP] [2019-12-23 18:58:29] reindex_search
[START] [2019-12-23 18:58:29] normalize_units
[STOP] [2019-12-23 18:58:29] normalize_units
[START] [2019-12-23 18:58:29] calculate_statistics
[STOP] [2019-12-23 18:58:29] calculate_statistics
[START] [2019-12-23 18:58:29] complete_harvest_instance
[START] [2019-12-23 18:58:29] overall_tsv_creation
[INFO] [2019-12-23 18:58:29] Processing group of 574 in 1 batches of 10000
[INFO] [2019-12-23 18:59:17] 237 Traits (unfiltered)...
[INFO] [2019-12-23 18:59:30] 237 Traits (filtered)...
[INFO] [2019-12-23 18:59:30] 0 Associations (filtered)...
[INFO] [2019-12-23 19:00:08] 1185 metadata added.
[INFO] [2019-12-23 19:00:08] 0 metadata added.
[INFO] [2019-12-23 19:00:08] Average Time: 76.0
[INFO] [2019-12-23 19:00:08] Total Time: 1m39s
[STOP] [2019-12-23 19:00:08] overall_tsv_creation
[INFO] [2019-12-23 19:00:08] Done. Check your files:
[INFO] [2019-12-23 19:00:08] (574 lines) /app/public/data/hudson_strait_sp/publish_nodes.tsv
[INFO] [2019-12-23 19:00:08] (2566 lines) /app/public/data/hudson_strait_sp/publish_node_ancestors.tsv
[INFO] [2019-12-23 19:00:08] (574 lines) /app/public/data/hudson_strait_sp/publish_scientific_names.tsv
[INFO] [2019-12-23 19:00:08] (238 lines) /app/public/data/hudson_strait_sp/publish_traits.tsv
[INFO] [2019-12-23 19:00:08] (1186 lines) /app/public/data/hudson_strait_sp/publish_metadata.tsv
[STOP] [2019-12-23 19:00:08] complete_harvest_instance
[START] [2019-12-23 19:00:08] completed
[STOP] [2019-12-23 19:00:08] completed
[STOP] [2019-12-23 19:00:08] logged process, took 285.94
Latest Process

23 Dec 18:55 EXITED currently processing 0