Harvest for Yellow Sea Species List Created 25 Dec 18:02

Stage: completed
Fetched: 25 Dec 18:02
Validated: 25 Dec 18:02
Deltas Created 25 Dec 18:02
Units Normalized: 25 Dec 18:09
Ancestry Built: 25 Dec 18:02
Nodes Matched: 25 Dec 18:09
Names Parsed: 25 Dec 18:02
New Models Stored: 25 Dec 18:02
Indexed: 25 Dec 18:09
Completed: 25 Dec 18:11
Time to Harvest: less than a minute

Harvesting Log (most recent first)

# Logfile created on 2019-12-25 18:02:04 -0500 by logger.rb/56815
[START] [2019-12-25 18:02:04] logged process
[START] [2019-12-25 18:02:04] create_harvest_instance
[STOP] [2019-12-25 18:02:05] create_harvest_instance
[START] [2019-12-25 18:02:05] fetch_files
[STOP] [2019-12-25 18:02:05] fetch_files
[START] [2019-12-25 18:02:05] validate_each_file
[STOP] [2019-12-25 18:02:05] validate_each_file
[START] [2019-12-25 18:02:05] convert_to_csv
[CMD] [2019-12-25 18:02:05] /usr/bin/sort /app/public/converted_csv/yellow_sea_sp_li_refs_19746.csv > /app/public/converted_csv/yellow_sea_sp_li_refs_19746.csv_sorted
[CMD] [2019-12-25 18:02:05] /usr/bin/sort /app/public/converted_csv/yellow_sea_sp_li_nodes_19747.csv > /app/public/converted_csv/yellow_sea_sp_li_nodes_19747.csv_sorted
[CMD] [2019-12-25 18:02:05] /usr/bin/sort /app/public/converted_csv/yellow_sea_sp_li_occurrences_19748.csv > /app/public/converted_csv/yellow_sea_sp_li_occurrences_19748.csv_sorted
[CMD] [2019-12-25 18:02:05] /usr/bin/sort /app/public/converted_csv/yellow_sea_sp_li_measurements_19749.csv > /app/public/converted_csv/yellow_sea_sp_li_measurements_19749.csv_sorted
[STOP] [2019-12-25 18:02:06] convert_to_csv
[START] [2019-12-25 18:02:06] calculate_delta
[CMD] [2019-12-25 18:02:06] echo "0a" > /app/public/diff/yellow_sea_sp_li_refs_19746.diff
[CMD] [2019-12-25 18:02:06] tail -n +1 /app/public/converted_csv/yellow_sea_sp_li_refs_19746.csv >> /app/public/diff/yellow_sea_sp_li_refs_19746.diff
[CMD] [2019-12-25 18:02:06] echo "." >> /app/public/diff/yellow_sea_sp_li_refs_19746.diff
[CMD] [2019-12-25 18:02:06] echo "0a" > /app/public/diff/yellow_sea_sp_li_nodes_19747.diff
[CMD] [2019-12-25 18:02:06] tail -n +1 /app/public/converted_csv/yellow_sea_sp_li_nodes_19747.csv >> /app/public/diff/yellow_sea_sp_li_nodes_19747.diff
[CMD] [2019-12-25 18:02:06] echo "." >> /app/public/diff/yellow_sea_sp_li_nodes_19747.diff
[CMD] [2019-12-25 18:02:07] echo "0a" > /app/public/diff/yellow_sea_sp_li_occurrences_19748.diff
[CMD] [2019-12-25 18:02:07] tail -n +1 /app/public/converted_csv/yellow_sea_sp_li_occurrences_19748.csv >> /app/public/diff/yellow_sea_sp_li_occurrences_19748.diff
[CMD] [2019-12-25 18:02:07] echo "." >> /app/public/diff/yellow_sea_sp_li_occurrences_19748.diff
[CMD] [2019-12-25 18:02:07] echo "0a" > /app/public/diff/yellow_sea_sp_li_measurements_19749.diff
[CMD] [2019-12-25 18:02:07] tail -n +1 /app/public/converted_csv/yellow_sea_sp_li_measurements_19749.csv >> /app/public/diff/yellow_sea_sp_li_measurements_19749.diff
[CMD] [2019-12-25 18:02:07] echo "." >> /app/public/diff/yellow_sea_sp_li_measurements_19749.diff
[STOP] [2019-12-25 18:02:07] calculate_delta
[START] [2019-12-25 18:02:07] parse_diff_and_store
[INFO] [2019-12-25 18:02:08] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 18:02:08] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 18:02:09] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 18:02:09] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 18:02:14] Storing 2 References
[INFO] [2019-12-25 18:02:14] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 18:02:14] Average Time: 0.0
[INFO] [2019-12-25 18:02:14] Total Time: 1s
[INFO] [2019-12-25 18:02:14] Storing 2315 ScientificNames
[INFO] [2019-12-25 18:02:14] Processing group of 2315 in 3 groups of 1000
[INFO] [2019-12-25 18:02:15] Average Time: 0.333
[INFO] [2019-12-25 18:02:15] Total Time: 2s
[INFO] [2019-12-25 18:02:15] Storing 2315 Nodes
[INFO] [2019-12-25 18:02:15] Processing group of 2315 in 3 groups of 1000
[INFO] [2019-12-25 18:02:16] Average Time: 0.253
[INFO] [2019-12-25 18:02:16] Total Time: 1s
[INFO] [2019-12-25 18:02:16] Storing 971 Occurrences
[INFO] [2019-12-25 18:02:16] Processing group of 971 in 1 groups of 1000
[INFO] [2019-12-25 18:02:16] Average Time: 0.13
[INFO] [2019-12-25 18:02:16] Total Time: 1s
[INFO] [2019-12-25 18:02:16] Storing 1942 TraitsReferences
[INFO] [2019-12-25 18:02:16] Processing group of 1942 in 2 groups of 1000
[INFO] [2019-12-25 18:02:16] Average Time: 0.115
[INFO] [2019-12-25 18:02:16] Total Time: 1s
[INFO] [2019-12-25 18:02:16] Storing 1942 Traits
[INFO] [2019-12-25 18:02:16] Processing group of 1942 in 2 groups of 1000
[INFO] [2019-12-25 18:02:17] Average Time: 0.39
[INFO] [2019-12-25 18:02:17] Total Time: 1s
[INFO] [2019-12-25 18:02:17] Storing 1942 MetaTraits
[INFO] [2019-12-25 18:02:17] Processing group of 1942 in 2 groups of 1000
[INFO] [2019-12-25 18:02:17] Average Time: 0.13
[INFO] [2019-12-25 18:02:17] Total Time: 1s
[STOP] [2019-12-25 18:02:17] parse_diff_and_store
[START] [2019-12-25 18:02:17] resolve_keys
[INFO] [2019-12-25 18:02:31] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 18:02:32] traits to occurrences...
[INFO] [2019-12-25 18:02:33] traits to nodes (through occurrences)...
[INFO] [2019-12-25 18:02:33] Traits to sex term...
[INFO] [2019-12-25 18:02:34] Traits to lifestage term...
[INFO] [2019-12-25 18:02:35] MetaTraits to traits...
[INFO] [2019-12-25 18:02:35] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 18:02:35] Assocs to occurrences...
[INFO] [2019-12-25 18:02:35] Assocs to nodes...
[INFO] [2019-12-25 18:02:35] Assoc to sex term...
[INFO] [2019-12-25 18:02:35] Assoc to lifestage term...
[STOP] [2019-12-25 18:02:35] resolve_keys
[START] [2019-12-25 18:02:35] hold_for_later_1
[STOP] [2019-12-25 18:02:35] hold_for_later_1
[START] [2019-12-25 18:02:35] hold_for_later_2
[STOP] [2019-12-25 18:02:35] hold_for_later_2
[START] [2019-12-25 18:02:35] resolve_missing_parents
[STOP] [2019-12-25 18:02:39] resolve_missing_parents
[START] [2019-12-25 18:02:39] rebuild_nodes
[START] [2019-12-25 18:02:39] Flattener#flatten
[START] [2019-12-25 18:02:39] Flattener#study_resource
[START] [2019-12-25 18:02:39] Flattener#build_ancestry
[STOP] [2019-12-25 18:02:39] Flattener#build_ancestry
[INFO] [2019-12-25 18:02:39] 2315 ancestry keys
[START] [2019-12-25 18:02:39] build_node_ancestors
[INFO] [2019-12-25 18:02:39] old ancestors deleted.
[STOP] [2019-12-25 18:02:40] build_node_ancestors
[START] [2019-12-25 18:02:41] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 18:02:41] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 18:02:41] Flattener#flatten
[STOP] [2019-12-25 18:02:41] rebuild_nodes
[START] [2019-12-25 18:02:41] resolve_missing_media_owners
[STOP] [2019-12-25 18:02:41] resolve_missing_media_owners
[START] [2019-12-25 18:02:41] sanitize_media_verbatims
[STOP] [2019-12-25 18:02:41] sanitize_media_verbatims
[START] [2019-12-25 18:02:41] queue_downloads
[STOP] [2019-12-25 18:02:41] queue_downloads
[START] [2019-12-25 18:02:41] parse_names
[WARN] [2019-12-25 18:02:41] I see 2315 names which still need to be parsed.
[STOP] [2019-12-25 18:02:44] parse_names
[START] [2019-12-25 18:02:44] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 18:02:44] denormalize_canonical_names_to_nodes
[START] [2019-12-25 18:02:44] match_nodes
[START] [2019-12-25 18:02:44] map_all_nodes_to_pages
[STOP] [2019-12-25 18:09:22] map_all_nodes_to_pages
[INFO] [2019-12-25 18:09:22] 102 Unmatched nodes (of 2315)! That's too many to output. First 10: Anas formosa (#62553145); Anas strepera (#62553197); Anas penelope (#62553202); Anas clypeata (#62553208); Anas falcata (#62553226); Anas querquedula (#62553270); Anas americana (#62555358); Chen (#62553854); Chen caerulescens (#62553853); Egretta intermedia (#62553307)
[START] [2019-12-25 18:09:22] update_nodes
[STOP] [2019-12-25 18:09:22] update_nodes
[STOP] [2019-12-25 18:09:22] match_nodes
[START] [2019-12-25 18:09:22] reindex_search
[STOP] [2019-12-25 18:09:28] reindex_search
[START] [2019-12-25 18:09:29] normalize_units
[STOP] [2019-12-25 18:09:29] normalize_units
[START] [2019-12-25 18:09:29] calculate_statistics
[STOP] [2019-12-25 18:09:29] calculate_statistics
[START] [2019-12-25 18:09:29] complete_harvest_instance
[START] [2019-12-25 18:09:29] overall_tsv_creation
[INFO] [2019-12-25 18:09:29] Processing group of 2315 in 1 batches of 10000
[INFO] [2019-12-25 18:10:24] 971 Traits (unfiltered)...
[INFO] [2019-12-25 18:10:37] 971 Traits (filtered)...
[INFO] [2019-12-25 18:10:37] 0 Associations (filtered)...
[INFO] [2019-12-25 18:11:16] 4855 metadata added.
[INFO] [2019-12-25 18:11:16] 0 metadata added.
[INFO] [2019-12-25 18:11:16] Average Time: 83.84
[INFO] [2019-12-25 18:11:16] Total Time: 1m48s
[STOP] [2019-12-25 18:11:16] overall_tsv_creation
[INFO] [2019-12-25 18:11:16] Done. Check your files:
[INFO] [2019-12-25 18:11:16] (2315 lines) /app/public/data/yellow_sea_sp_li/publish_nodes.tsv
[INFO] [2019-12-25 18:11:17] (11150 lines) /app/public/data/yellow_sea_sp_li/publish_node_ancestors.tsv
[INFO] [2019-12-25 18:11:17] (2315 lines) /app/public/data/yellow_sea_sp_li/publish_scientific_names.tsv
[INFO] [2019-12-25 18:11:17] (972 lines) /app/public/data/yellow_sea_sp_li/publish_traits.tsv
[INFO] [2019-12-25 18:11:17] (4856 lines) /app/public/data/yellow_sea_sp_li/publish_metadata.tsv
[STOP] [2019-12-25 18:11:17] complete_harvest_instance
[START] [2019-12-25 18:11:17] completed
[STOP] [2019-12-25 18:11:17] completed
[STOP] [2019-12-25 18:11:17] logged process, took 553.22

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