Harvest for Greenland Sea Species List Created 23 Dec 03:17

Stage: completed
Fetched: 23 Dec 03:17
Validated: 23 Dec 03:17
Deltas Created 23 Dec 03:17
Units Normalized: 23 Dec 03:33
Ancestry Built: 23 Dec 03:18
Nodes Matched: 23 Dec 03:32
Names Parsed: 23 Dec 03:18
New Models Stored: 23 Dec 03:17
Indexed: 23 Dec 03:33
Completed: 23 Dec 03:35
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 03:17:34 -0500 by logger.rb/56815
[START] [2019-12-23 03:17:34] logged process
[START] [2019-12-23 03:17:34] create_harvest_instance
[STOP] [2019-12-23 03:17:35] create_harvest_instance
[START] [2019-12-23 03:17:35] fetch_files
[STOP] [2019-12-23 03:17:35] fetch_files
[START] [2019-12-23 03:17:35] validate_each_file
[STOP] [2019-12-23 03:17:36] validate_each_file
[START] [2019-12-23 03:17:36] convert_to_csv
[CMD] [2019-12-23 03:17:36] /usr/bin/sort /app/public/converted_csv/greenland_sea_sp_refs_19250.csv > /app/public/converted_csv/greenland_sea_sp_refs_19250.csv_sorted
[CMD] [2019-12-23 03:17:36] /usr/bin/sort /app/public/converted_csv/greenland_sea_sp_nodes_19251.csv > /app/public/converted_csv/greenland_sea_sp_nodes_19251.csv_sorted
[CMD] [2019-12-23 03:17:36] /usr/bin/sort /app/public/converted_csv/greenland_sea_sp_occurrences_19252.csv > /app/public/converted_csv/greenland_sea_sp_occurrences_19252.csv_sorted
[CMD] [2019-12-23 03:17:36] /usr/bin/sort /app/public/converted_csv/greenland_sea_sp_measurements_19253.csv > /app/public/converted_csv/greenland_sea_sp_measurements_19253.csv_sorted
[STOP] [2019-12-23 03:17:36] convert_to_csv
[START] [2019-12-23 03:17:36] calculate_delta
[CMD] [2019-12-23 03:17:36] echo "0a" > /app/public/diff/greenland_sea_sp_refs_19250.diff
[CMD] [2019-12-23 03:17:36] tail -n +1 /app/public/converted_csv/greenland_sea_sp_refs_19250.csv >> /app/public/diff/greenland_sea_sp_refs_19250.diff
[CMD] [2019-12-23 03:17:36] echo "." >> /app/public/diff/greenland_sea_sp_refs_19250.diff
[CMD] [2019-12-23 03:17:36] echo "0a" > /app/public/diff/greenland_sea_sp_nodes_19251.diff
[CMD] [2019-12-23 03:17:36] tail -n +1 /app/public/converted_csv/greenland_sea_sp_nodes_19251.csv >> /app/public/diff/greenland_sea_sp_nodes_19251.diff
[CMD] [2019-12-23 03:17:36] echo "." >> /app/public/diff/greenland_sea_sp_nodes_19251.diff
[CMD] [2019-12-23 03:17:36] echo "0a" > /app/public/diff/greenland_sea_sp_occurrences_19252.diff
[CMD] [2019-12-23 03:17:36] tail -n +1 /app/public/converted_csv/greenland_sea_sp_occurrences_19252.csv >> /app/public/diff/greenland_sea_sp_occurrences_19252.diff
[CMD] [2019-12-23 03:17:36] echo "." >> /app/public/diff/greenland_sea_sp_occurrences_19252.diff
[CMD] [2019-12-23 03:17:36] echo "0a" > /app/public/diff/greenland_sea_sp_measurements_19253.diff
[CMD] [2019-12-23 03:17:36] tail -n +1 /app/public/converted_csv/greenland_sea_sp_measurements_19253.csv >> /app/public/diff/greenland_sea_sp_measurements_19253.diff
[CMD] [2019-12-23 03:17:36] echo "." >> /app/public/diff/greenland_sea_sp_measurements_19253.diff
[STOP] [2019-12-23 03:17:36] calculate_delta
[START] [2019-12-23 03:17:36] parse_diff_and_store
[INFO] [2019-12-23 03:17:36] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 03:17:36] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 03:17:38] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 03:17:38] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 03:17:51] Storing 2 References
[INFO] [2019-12-23 03:17:51] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 03:17:51] Average Time: 0.0
[INFO] [2019-12-23 03:17:51] Total Time: 1s
[INFO] [2019-12-23 03:17:51] Storing 4568 ScientificNames
[INFO] [2019-12-23 03:17:51] Processing group of 4568 in 5 groups of 1000
[INFO] [2019-12-23 03:17:54] Average Time: 0.426
[INFO] [2019-12-23 03:17:54] Total Time: 3s
[INFO] [2019-12-23 03:17:54] Storing 4568 Nodes
[INFO] [2019-12-23 03:17:54] Processing group of 4568 in 5 groups of 1000
[INFO] [2019-12-23 03:17:55] Average Time: 0.326
[INFO] [2019-12-23 03:17:55] Total Time: 2s
[INFO] [2019-12-23 03:17:55] Storing 2226 Occurrences
[INFO] [2019-12-23 03:17:55] Processing group of 2226 in 3 groups of 1000
[INFO] [2019-12-23 03:17:55] Average Time: 0.073
[INFO] [2019-12-23 03:17:55] Total Time: 1s
[INFO] [2019-12-23 03:17:55] Storing 4452 TraitsReferences
[INFO] [2019-12-23 03:17:55] Processing group of 4452 in 5 groups of 1000
[INFO] [2019-12-23 03:17:56] Average Time: 0.08
[INFO] [2019-12-23 03:17:56] Total Time: 1s
[INFO] [2019-12-23 03:17:56] Storing 4452 Traits
[INFO] [2019-12-23 03:17:56] Processing group of 4452 in 5 groups of 1000
[INFO] [2019-12-23 03:17:57] Average Time: 0.304
[INFO] [2019-12-23 03:17:57] Total Time: 2s
[INFO] [2019-12-23 03:17:57] Storing 4450 MetaTraits
[INFO] [2019-12-23 03:17:57] Processing group of 4450 in 5 groups of 1000
[INFO] [2019-12-23 03:17:58] Average Time: 0.128
[INFO] [2019-12-23 03:17:58] Total Time: 1s
[STOP] [2019-12-23 03:17:58] parse_diff_and_store
[START] [2019-12-23 03:17:58] resolve_keys
[INFO] [2019-12-23 03:18:23] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 03:18:25] traits to occurrences...
[INFO] [2019-12-23 03:18:26] traits to nodes (through occurrences)...
[INFO] [2019-12-23 03:18:26] Traits to sex term...
[INFO] [2019-12-23 03:18:27] Traits to lifestage term...
[INFO] [2019-12-23 03:18:28] MetaTraits to traits...
[INFO] [2019-12-23 03:18:28] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 03:18:29] Assocs to occurrences...
[INFO] [2019-12-23 03:18:29] Assocs to nodes...
[INFO] [2019-12-23 03:18:29] Assoc to sex term...
[INFO] [2019-12-23 03:18:29] Assoc to lifestage term...
[STOP] [2019-12-23 03:18:29] resolve_keys
[START] [2019-12-23 03:18:29] hold_for_later_1
[STOP] [2019-12-23 03:18:29] hold_for_later_1
[START] [2019-12-23 03:18:29] hold_for_later_2
[STOP] [2019-12-23 03:18:29] hold_for_later_2
[START] [2019-12-23 03:18:29] resolve_missing_parents
[STOP] [2019-12-23 03:18:40] resolve_missing_parents
[START] [2019-12-23 03:18:40] rebuild_nodes
[START] [2019-12-23 03:18:40] Flattener#flatten
[START] [2019-12-23 03:18:40] Flattener#study_resource
[START] [2019-12-23 03:18:40] Flattener#build_ancestry
[STOP] [2019-12-23 03:18:41] Flattener#build_ancestry
[INFO] [2019-12-23 03:18:41] 4568 ancestry keys
[START] [2019-12-23 03:18:41] build_node_ancestors
[INFO] [2019-12-23 03:18:41] old ancestors deleted.
[STOP] [2019-12-23 03:18:42] build_node_ancestors
[START] [2019-12-23 03:18:43] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 03:18:44] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 03:18:44] Flattener#flatten
[STOP] [2019-12-23 03:18:44] rebuild_nodes
[START] [2019-12-23 03:18:44] resolve_missing_media_owners
[STOP] [2019-12-23 03:18:44] resolve_missing_media_owners
[START] [2019-12-23 03:18:44] sanitize_media_verbatims
[STOP] [2019-12-23 03:18:44] sanitize_media_verbatims
[START] [2019-12-23 03:18:44] queue_downloads
[STOP] [2019-12-23 03:18:44] queue_downloads
[START] [2019-12-23 03:18:44] parse_names
[WARN] [2019-12-23 03:18:44] I see 4568 names which still need to be parsed.
[STOP] [2019-12-23 03:18:48] parse_names
[START] [2019-12-23 03:18:48] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 03:18:48] denormalize_canonical_names_to_nodes
[START] [2019-12-23 03:18:48] match_nodes
[START] [2019-12-23 03:18:48] map_all_nodes_to_pages
[STOP] [2019-12-23 03:32:54] map_all_nodes_to_pages
[INFO] [2019-12-23 03:32:54] 350 Unmatched nodes (of 4568)! That's too many to output. First 10: Globigerina pachyderma (#61891174); Globigerina ciperoensis (#61893814); Globigerina praebulloides (#61894142); Globigerinita humilis (#61892859); Globigerinoides triloba (#61893203); Globigerinoides trilobus (#61893277); Globigerinoides conglobata (#61894472); Oridorsalis tener (#61891720); Cassidulina islandica (#61895359); Planulina wuellerstorfi (#61891028)
[START] [2019-12-23 03:32:54] update_nodes
[STOP] [2019-12-23 03:32:56] update_nodes
[STOP] [2019-12-23 03:32:56] match_nodes
[START] [2019-12-23 03:32:56] reindex_search
[STOP] [2019-12-23 03:33:08] reindex_search
[START] [2019-12-23 03:33:08] normalize_units
[STOP] [2019-12-23 03:33:08] normalize_units
[START] [2019-12-23 03:33:08] calculate_statistics
[STOP] [2019-12-23 03:33:08] calculate_statistics
[START] [2019-12-23 03:33:08] complete_harvest_instance
[START] [2019-12-23 03:33:08] overall_tsv_creation
[INFO] [2019-12-23 03:33:08] Processing group of 4568 in 1 batches of 10000
[INFO] [2019-12-23 03:34:15] 2226 Traits (unfiltered)...
[INFO] [2019-12-23 03:34:28] 2226 Traits (filtered)...
[INFO] [2019-12-23 03:34:28] 0 Associations (filtered)...
[INFO] [2019-12-23 03:35:12] 11128 metadata added.
[INFO] [2019-12-23 03:35:12] 0 metadata added.
[INFO] [2019-12-23 03:35:12] Average Time: 98.35
[INFO] [2019-12-23 03:35:12] Total Time: 2m4s
[STOP] [2019-12-23 03:35:12] overall_tsv_creation
[INFO] [2019-12-23 03:35:12] Done. Check your files:
[INFO] [2019-12-23 03:35:12] (4568 lines) /app/public/data/greenland_sea_sp/publish_nodes.tsv
[INFO] [2019-12-23 03:35:12] (22007 lines) /app/public/data/greenland_sea_sp/publish_node_ancestors.tsv
[INFO] [2019-12-23 03:35:12] (4568 lines) /app/public/data/greenland_sea_sp/publish_scientific_names.tsv
[INFO] [2019-12-23 03:35:12] (2227 lines) /app/public/data/greenland_sea_sp/publish_traits.tsv
[INFO] [2019-12-23 03:35:12] (11129 lines) /app/public/data/greenland_sea_sp/publish_metadata.tsv
[STOP] [2019-12-23 03:35:12] complete_harvest_instance
[START] [2019-12-23 03:35:12] completed
[STOP] [2019-12-23 03:35:12] completed
[STOP] [2019-12-23 03:35:12] logged process, took 1058.07
Latest Process

23 Dec 03:17 EXITED currently processing 0