Harvest for Halmahera Sea Species List Created 23 Dec 19:09

Stage: completed
Fetched: 23 Dec 19:09
Validated: 23 Dec 19:09
Deltas Created 23 Dec 19:09
Units Normalized: 23 Dec 19:24
Ancestry Built: 23 Dec 19:09
Nodes Matched: 23 Dec 19:23
Names Parsed: 23 Dec 19:09
New Models Stored: 23 Dec 19:09
Indexed: 23 Dec 19:24
Completed: 23 Dec 19:25
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 19:09:07 -0500 by logger.rb/56815
[START] [2019-12-23 19:09:07] logged process
[START] [2019-12-23 19:09:07] create_harvest_instance
[STOP] [2019-12-23 19:09:08] create_harvest_instance
[START] [2019-12-23 19:09:08] fetch_files
[STOP] [2019-12-23 19:09:08] fetch_files
[START] [2019-12-23 19:09:08] validate_each_file
[STOP] [2019-12-23 19:09:08] validate_each_file
[START] [2019-12-23 19:09:08] convert_to_csv
[CMD] [2019-12-23 19:09:08] /usr/bin/sort /app/public/converted_csv/halmahera_sea_sp_refs_19522.csv > /app/public/converted_csv/halmahera_sea_sp_refs_19522.csv_sorted
[CMD] [2019-12-23 19:09:08] /usr/bin/sort /app/public/converted_csv/halmahera_sea_sp_nodes_19523.csv > /app/public/converted_csv/halmahera_sea_sp_nodes_19523.csv_sorted
[CMD] [2019-12-23 19:09:08] /usr/bin/sort /app/public/converted_csv/halmahera_sea_sp_occurrences_19524.csv > /app/public/converted_csv/halmahera_sea_sp_occurrences_19524.csv_sorted
[CMD] [2019-12-23 19:09:09] /usr/bin/sort /app/public/converted_csv/halmahera_sea_sp_measurements_19525.csv > /app/public/converted_csv/halmahera_sea_sp_measurements_19525.csv_sorted
[STOP] [2019-12-23 19:09:09] convert_to_csv
[START] [2019-12-23 19:09:09] calculate_delta
[CMD] [2019-12-23 19:09:09] echo "0a" > /app/public/diff/halmahera_sea_sp_refs_19522.diff
[CMD] [2019-12-23 19:09:09] tail -n +1 /app/public/converted_csv/halmahera_sea_sp_refs_19522.csv >> /app/public/diff/halmahera_sea_sp_refs_19522.diff
[CMD] [2019-12-23 19:09:09] echo "." >> /app/public/diff/halmahera_sea_sp_refs_19522.diff
[CMD] [2019-12-23 19:09:09] echo "0a" > /app/public/diff/halmahera_sea_sp_nodes_19523.diff
[CMD] [2019-12-23 19:09:09] tail -n +1 /app/public/converted_csv/halmahera_sea_sp_nodes_19523.csv >> /app/public/diff/halmahera_sea_sp_nodes_19523.diff
[CMD] [2019-12-23 19:09:09] echo "." >> /app/public/diff/halmahera_sea_sp_nodes_19523.diff
[CMD] [2019-12-23 19:09:10] echo "0a" > /app/public/diff/halmahera_sea_sp_occurrences_19524.diff
[CMD] [2019-12-23 19:09:10] tail -n +1 /app/public/converted_csv/halmahera_sea_sp_occurrences_19524.csv >> /app/public/diff/halmahera_sea_sp_occurrences_19524.diff
[CMD] [2019-12-23 19:09:10] echo "." >> /app/public/diff/halmahera_sea_sp_occurrences_19524.diff
[CMD] [2019-12-23 19:09:10] echo "0a" > /app/public/diff/halmahera_sea_sp_measurements_19525.diff
[CMD] [2019-12-23 19:09:10] tail -n +1 /app/public/converted_csv/halmahera_sea_sp_measurements_19525.csv >> /app/public/diff/halmahera_sea_sp_measurements_19525.diff
[CMD] [2019-12-23 19:09:10] echo "." >> /app/public/diff/halmahera_sea_sp_measurements_19525.diff
[STOP] [2019-12-23 19:09:10] calculate_delta
[START] [2019-12-23 19:09:10] parse_diff_and_store
[INFO] [2019-12-23 19:09:11] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 19:09:11] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 19:09:12] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 19:09:12] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 19:09:21] Storing 2 References
[INFO] [2019-12-23 19:09:21] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 19:09:21] Average Time: 0.0
[INFO] [2019-12-23 19:09:21] Total Time: 1s
[INFO] [2019-12-23 19:09:21] Storing 2807 ScientificNames
[INFO] [2019-12-23 19:09:21] Processing group of 2807 in 3 groups of 1000
[INFO] [2019-12-23 19:09:22] Average Time: 0.457
[INFO] [2019-12-23 19:09:22] Total Time: 2s
[INFO] [2019-12-23 19:09:22] Storing 2807 Nodes
[INFO] [2019-12-23 19:09:22] Processing group of 2807 in 3 groups of 1000
[INFO] [2019-12-23 19:09:23] Average Time: 0.31
[INFO] [2019-12-23 19:09:23] Total Time: 1s
[INFO] [2019-12-23 19:09:23] Storing 1421 Occurrences
[INFO] [2019-12-23 19:09:23] Processing group of 1421 in 2 groups of 1000
[INFO] [2019-12-23 19:09:23] Average Time: 0.09
[INFO] [2019-12-23 19:09:23] Total Time: 1s
[INFO] [2019-12-23 19:09:23] Storing 2842 TraitsReferences
[INFO] [2019-12-23 19:09:23] Processing group of 2842 in 3 groups of 1000
[INFO] [2019-12-23 19:09:24] Average Time: 0.103
[INFO] [2019-12-23 19:09:24] Total Time: 1s
[INFO] [2019-12-23 19:09:24] Storing 2842 Traits
[INFO] [2019-12-23 19:09:24] Processing group of 2842 in 3 groups of 1000
[INFO] [2019-12-23 19:09:25] Average Time: 0.37
[INFO] [2019-12-23 19:09:25] Total Time: 2s
[INFO] [2019-12-23 19:09:25] Storing 2841 MetaTraits
[INFO] [2019-12-23 19:09:25] Processing group of 2841 in 3 groups of 1000
[INFO] [2019-12-23 19:09:25] Average Time: 0.16
[INFO] [2019-12-23 19:09:25] Total Time: 1s
[STOP] [2019-12-23 19:09:25] parse_diff_and_store
[START] [2019-12-23 19:09:25] resolve_keys
[INFO] [2019-12-23 19:09:39] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 19:09:40] traits to occurrences...
[INFO] [2019-12-23 19:09:41] traits to nodes (through occurrences)...
[INFO] [2019-12-23 19:09:41] Traits to sex term...
[INFO] [2019-12-23 19:09:41] Traits to lifestage term...
[INFO] [2019-12-23 19:09:42] MetaTraits to traits...
[INFO] [2019-12-23 19:09:42] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 19:09:42] Assocs to occurrences...
[INFO] [2019-12-23 19:09:42] Assocs to nodes...
[INFO] [2019-12-23 19:09:42] Assoc to sex term...
[INFO] [2019-12-23 19:09:42] Assoc to lifestage term...
[STOP] [2019-12-23 19:09:42] resolve_keys
[START] [2019-12-23 19:09:42] hold_for_later_1
[STOP] [2019-12-23 19:09:42] hold_for_later_1
[START] [2019-12-23 19:09:42] hold_for_later_2
[STOP] [2019-12-23 19:09:42] hold_for_later_2
[START] [2019-12-23 19:09:42] resolve_missing_parents
[STOP] [2019-12-23 19:09:47] resolve_missing_parents
[START] [2019-12-23 19:09:47] rebuild_nodes
[START] [2019-12-23 19:09:47] Flattener#flatten
[START] [2019-12-23 19:09:47] Flattener#study_resource
[START] [2019-12-23 19:09:47] Flattener#build_ancestry
[STOP] [2019-12-23 19:09:47] Flattener#build_ancestry
[INFO] [2019-12-23 19:09:47] 2807 ancestry keys
[START] [2019-12-23 19:09:47] build_node_ancestors
[INFO] [2019-12-23 19:09:47] old ancestors deleted.
[STOP] [2019-12-23 19:09:48] build_node_ancestors
[START] [2019-12-23 19:09:50] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 19:09:50] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 19:09:50] Flattener#flatten
[STOP] [2019-12-23 19:09:50] rebuild_nodes
[START] [2019-12-23 19:09:50] resolve_missing_media_owners
[STOP] [2019-12-23 19:09:50] resolve_missing_media_owners
[START] [2019-12-23 19:09:50] sanitize_media_verbatims
[STOP] [2019-12-23 19:09:50] sanitize_media_verbatims
[START] [2019-12-23 19:09:50] queue_downloads
[STOP] [2019-12-23 19:09:50] queue_downloads
[START] [2019-12-23 19:09:50] parse_names
[WARN] [2019-12-23 19:09:50] I see 2807 names which still need to be parsed.
[STOP] [2019-12-23 19:09:54] parse_names
[START] [2019-12-23 19:09:54] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 19:09:54] denormalize_canonical_names_to_nodes
[START] [2019-12-23 19:09:54] match_nodes
[START] [2019-12-23 19:09:54] map_all_nodes_to_pages
[STOP] [2019-12-23 19:23:49] map_all_nodes_to_pages
[INFO] [2019-12-23 19:23:49] 79 Unmatched nodes (of 2807)! That's too many to output. First 10: Giuris aporos (#62135482); Ptereleotridae (#62136604); Stephanoberyciformes (#62135551); Trachinocephalus (#62137828); Benthalbella lowei (#62136506); Scorpaeniformes (#62135636); Cetomimiformes (#62136972); Philomachus (#62137485); Philomachus pugnax (#62137484); Egretta intermedia (#62137956)
[START] [2019-12-23 19:23:49] update_nodes
[STOP] [2019-12-23 19:23:50] update_nodes
[STOP] [2019-12-23 19:23:50] match_nodes
[START] [2019-12-23 19:23:50] reindex_search
[STOP] [2019-12-23 19:24:01] reindex_search
[START] [2019-12-23 19:24:01] normalize_units
[STOP] [2019-12-23 19:24:01] normalize_units
[START] [2019-12-23 19:24:01] calculate_statistics
[STOP] [2019-12-23 19:24:01] calculate_statistics
[START] [2019-12-23 19:24:01] complete_harvest_instance
[START] [2019-12-23 19:24:01] overall_tsv_creation
[INFO] [2019-12-23 19:24:01] Processing group of 2807 in 1 batches of 10000
[INFO] [2019-12-23 19:25:00] 1421 Traits (unfiltered)...
[INFO] [2019-12-23 19:25:13] 1421 Traits (filtered)...
[INFO] [2019-12-23 19:25:13] 0 Associations (filtered)...
[INFO] [2019-12-23 19:25:54] 7104 metadata added.
[INFO] [2019-12-23 19:25:54] 0 metadata added.
[INFO] [2019-12-23 19:25:54] Average Time: 88.8
[INFO] [2019-12-23 19:25:54] Total Time: 1m54s
[STOP] [2019-12-23 19:25:54] overall_tsv_creation
[INFO] [2019-12-23 19:25:54] Done. Check your files:
[INFO] [2019-12-23 19:25:54] (2807 lines) /app/public/data/halmahera_sea_sp/publish_nodes.tsv
[INFO] [2019-12-23 19:25:54] (14450 lines) /app/public/data/halmahera_sea_sp/publish_node_ancestors.tsv
[INFO] [2019-12-23 19:25:54] (2807 lines) /app/public/data/halmahera_sea_sp/publish_scientific_names.tsv
[INFO] [2019-12-23 19:25:54] (1422 lines) /app/public/data/halmahera_sea_sp/publish_traits.tsv
[INFO] [2019-12-23 19:25:55] (7105 lines) /app/public/data/halmahera_sea_sp/publish_metadata.tsv
[STOP] [2019-12-23 19:25:55] complete_harvest_instance
[START] [2019-12-23 19:25:55] completed
[STOP] [2019-12-23 19:25:55] completed
[STOP] [2019-12-23 19:25:55] logged process, took 1007.63
Latest Process

23 Dec 19:09 EXITED currently processing 0