Harvest for Gulf of Thailand Species List Created 23 Dec 10:04

Stage: completed
Fetched: 23 Dec 10:04
Validated: 23 Dec 10:04
Deltas Created 23 Dec 10:04
Units Normalized: 23 Dec 10:25
Ancestry Built: 23 Dec 10:05
Nodes Matched: 23 Dec 10:24
Names Parsed: 23 Dec 10:05
New Models Stored: 23 Dec 10:05
Indexed: 23 Dec 10:25
Completed: 23 Dec 10:27
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 10:04:29 -0500 by logger.rb/56815
[START] [2019-12-23 10:04:29] logged process
[START] [2019-12-23 10:04:29] create_harvest_instance
[STOP] [2019-12-23 10:04:29] create_harvest_instance
[START] [2019-12-23 10:04:29] fetch_files
[STOP] [2019-12-23 10:04:29] fetch_files
[START] [2019-12-23 10:04:29] validate_each_file
[STOP] [2019-12-23 10:04:30] validate_each_file
[START] [2019-12-23 10:04:30] convert_to_csv
[CMD] [2019-12-23 10:04:30] /usr/bin/sort /app/public/converted_csv/gulf_thailand_sp_refs_19362.csv > /app/public/converted_csv/gulf_thailand_sp_refs_19362.csv_sorted
[CMD] [2019-12-23 10:04:31] /usr/bin/sort /app/public/converted_csv/gulf_thailand_sp_nodes_19363.csv > /app/public/converted_csv/gulf_thailand_sp_nodes_19363.csv_sorted
[CMD] [2019-12-23 10:04:31] /usr/bin/sort /app/public/converted_csv/gulf_thailand_sp_occurrences_19364.csv > /app/public/converted_csv/gulf_thailand_sp_occurrences_19364.csv_sorted
[CMD] [2019-12-23 10:04:32] /usr/bin/sort /app/public/converted_csv/gulf_thailand_sp_measurements_19365.csv > /app/public/converted_csv/gulf_thailand_sp_measurements_19365.csv_sorted
[STOP] [2019-12-23 10:04:33] convert_to_csv
[START] [2019-12-23 10:04:33] calculate_delta
[CMD] [2019-12-23 10:04:33] echo "0a" > /app/public/diff/gulf_thailand_sp_refs_19362.diff
[CMD] [2019-12-23 10:04:33] tail -n +1 /app/public/converted_csv/gulf_thailand_sp_refs_19362.csv >> /app/public/diff/gulf_thailand_sp_refs_19362.diff
[CMD] [2019-12-23 10:04:34] echo "." >> /app/public/diff/gulf_thailand_sp_refs_19362.diff
[CMD] [2019-12-23 10:04:35] echo "0a" > /app/public/diff/gulf_thailand_sp_nodes_19363.diff
[CMD] [2019-12-23 10:04:35] tail -n +1 /app/public/converted_csv/gulf_thailand_sp_nodes_19363.csv >> /app/public/diff/gulf_thailand_sp_nodes_19363.diff
[CMD] [2019-12-23 10:04:36] echo "." >> /app/public/diff/gulf_thailand_sp_nodes_19363.diff
[CMD] [2019-12-23 10:04:37] echo "0a" > /app/public/diff/gulf_thailand_sp_occurrences_19364.diff
[CMD] [2019-12-23 10:04:37] tail -n +1 /app/public/converted_csv/gulf_thailand_sp_occurrences_19364.csv >> /app/public/diff/gulf_thailand_sp_occurrences_19364.diff
[CMD] [2019-12-23 10:04:38] echo "." >> /app/public/diff/gulf_thailand_sp_occurrences_19364.diff
[CMD] [2019-12-23 10:04:39] echo "0a" > /app/public/diff/gulf_thailand_sp_measurements_19365.diff
[CMD] [2019-12-23 10:04:39] tail -n +1 /app/public/converted_csv/gulf_thailand_sp_measurements_19365.csv >> /app/public/diff/gulf_thailand_sp_measurements_19365.diff
[CMD] [2019-12-23 10:04:40] echo "." >> /app/public/diff/gulf_thailand_sp_measurements_19365.diff
[STOP] [2019-12-23 10:04:41] calculate_delta
[START] [2019-12-23 10:04:41] parse_diff_and_store
[INFO] [2019-12-23 10:04:42] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 10:04:42] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 10:04:44] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 10:04:45] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 10:04:57] Storing 2 References
[INFO] [2019-12-23 10:04:57] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 10:04:57] Average Time: 0.0
[INFO] [2019-12-23 10:04:57] Total Time: 1s
[INFO] [2019-12-23 10:04:57] Storing 3543 ScientificNames
[INFO] [2019-12-23 10:04:57] Processing group of 3543 in 4 groups of 1000
[INFO] [2019-12-23 10:04:58] Average Time: 0.413
[INFO] [2019-12-23 10:04:58] Total Time: 2s
[INFO] [2019-12-23 10:04:58] Storing 3543 Nodes
[INFO] [2019-12-23 10:04:58] Processing group of 3543 in 4 groups of 1000
[INFO] [2019-12-23 10:05:00] Average Time: 0.32
[INFO] [2019-12-23 10:05:00] Total Time: 2s
[INFO] [2019-12-23 10:05:00] Storing 1862 Occurrences
[INFO] [2019-12-23 10:05:00] Processing group of 1862 in 2 groups of 1000
[INFO] [2019-12-23 10:05:00] Average Time: 0.11
[INFO] [2019-12-23 10:05:00] Total Time: 1s
[INFO] [2019-12-23 10:05:00] Storing 3724 TraitsReferences
[INFO] [2019-12-23 10:05:00] Processing group of 3724 in 4 groups of 1000
[INFO] [2019-12-23 10:05:00] Average Time: 0.1
[INFO] [2019-12-23 10:05:00] Total Time: 1s
[INFO] [2019-12-23 10:05:00] Storing 3724 Traits
[INFO] [2019-12-23 10:05:00] Processing group of 3724 in 4 groups of 1000
[INFO] [2019-12-23 10:05:02] Average Time: 0.363
[INFO] [2019-12-23 10:05:02] Total Time: 2s
[INFO] [2019-12-23 10:05:02] Storing 3724 MetaTraits
[INFO] [2019-12-23 10:05:02] Processing group of 3724 in 4 groups of 1000
[INFO] [2019-12-23 10:05:02] Average Time: 0.145
[INFO] [2019-12-23 10:05:02] Total Time: 1s
[STOP] [2019-12-23 10:05:02] parse_diff_and_store
[START] [2019-12-23 10:05:02] resolve_keys
[INFO] [2019-12-23 10:05:19] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 10:05:20] traits to occurrences...
[INFO] [2019-12-23 10:05:21] traits to nodes (through occurrences)...
[INFO] [2019-12-23 10:05:21] Traits to sex term...
[INFO] [2019-12-23 10:05:22] Traits to lifestage term...
[INFO] [2019-12-23 10:05:22] MetaTraits to traits...
[INFO] [2019-12-23 10:05:23] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 10:05:23] Assocs to occurrences...
[INFO] [2019-12-23 10:05:23] Assocs to nodes...
[INFO] [2019-12-23 10:05:23] Assoc to sex term...
[INFO] [2019-12-23 10:05:23] Assoc to lifestage term...
[STOP] [2019-12-23 10:05:23] resolve_keys
[START] [2019-12-23 10:05:23] hold_for_later_1
[STOP] [2019-12-23 10:05:23] hold_for_later_1
[START] [2019-12-23 10:05:23] hold_for_later_2
[STOP] [2019-12-23 10:05:23] hold_for_later_2
[START] [2019-12-23 10:05:23] resolve_missing_parents
[STOP] [2019-12-23 10:05:30] resolve_missing_parents
[START] [2019-12-23 10:05:30] rebuild_nodes
[START] [2019-12-23 10:05:30] Flattener#flatten
[START] [2019-12-23 10:05:30] Flattener#study_resource
[START] [2019-12-23 10:05:30] Flattener#build_ancestry
[STOP] [2019-12-23 10:05:30] Flattener#build_ancestry
[INFO] [2019-12-23 10:05:30] 3543 ancestry keys
[START] [2019-12-23 10:05:30] build_node_ancestors
[INFO] [2019-12-23 10:05:30] old ancestors deleted.
[STOP] [2019-12-23 10:05:32] build_node_ancestors
[START] [2019-12-23 10:05:33] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 10:05:34] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 10:05:34] Flattener#flatten
[STOP] [2019-12-23 10:05:34] rebuild_nodes
[START] [2019-12-23 10:05:34] resolve_missing_media_owners
[STOP] [2019-12-23 10:05:34] resolve_missing_media_owners
[START] [2019-12-23 10:05:34] sanitize_media_verbatims
[STOP] [2019-12-23 10:05:34] sanitize_media_verbatims
[START] [2019-12-23 10:05:34] queue_downloads
[STOP] [2019-12-23 10:05:34] queue_downloads
[START] [2019-12-23 10:05:34] parse_names
[WARN] [2019-12-23 10:05:34] I see 3543 names which still need to be parsed.
[STOP] [2019-12-23 10:05:38] parse_names
[START] [2019-12-23 10:05:38] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 10:05:38] denormalize_canonical_names_to_nodes
[START] [2019-12-23 10:05:38] match_nodes
[START] [2019-12-23 10:05:38] map_all_nodes_to_pages
[STOP] [2019-12-23 10:24:57] map_all_nodes_to_pages
[INFO] [2019-12-23 10:24:57] 114 Unmatched nodes (of 3543)! That's too many to output. First 10: Limicola (#61961865); Limicola falcinellus (#61961864); Philomachus (#61961882); Philomachus pugnax (#61961881); Limnodromus (#61961900); Egretta intermedia (#61961827); Megalaima (#61962616); Megalaima haemacephala (#61962615); Anas querquedula (#61962470); Anas clypeata (#61962562)
[START] [2019-12-23 10:24:57] update_nodes
[STOP] [2019-12-23 10:24:58] update_nodes
[STOP] [2019-12-23 10:24:58] match_nodes
[START] [2019-12-23 10:24:58] reindex_search
[STOP] [2019-12-23 10:25:11] reindex_search
[START] [2019-12-23 10:25:11] normalize_units
[STOP] [2019-12-23 10:25:11] normalize_units
[START] [2019-12-23 10:25:11] calculate_statistics
[STOP] [2019-12-23 10:25:11] calculate_statistics
[START] [2019-12-23 10:25:11] complete_harvest_instance
[START] [2019-12-23 10:25:11] overall_tsv_creation
[INFO] [2019-12-23 10:25:11] Processing group of 3543 in 1 batches of 10000
[INFO] [2019-12-23 10:26:13] 1862 Traits (unfiltered)...
[INFO] [2019-12-23 10:26:26] 1862 Traits (filtered)...
[INFO] [2019-12-23 10:26:26] 0 Associations (filtered)...
[INFO] [2019-12-23 10:27:06] 9310 metadata added.
[INFO] [2019-12-23 10:27:06] 0 metadata added.
[INFO] [2019-12-23 10:27:06] Average Time: 90.74
[INFO] [2019-12-23 10:27:06] Total Time: 1m56s
[STOP] [2019-12-23 10:27:06] overall_tsv_creation
[INFO] [2019-12-23 10:27:06] Done. Check your files:
[INFO] [2019-12-23 10:27:07] (3543 lines) /app/public/data/gulf_thailand_sp/publish_nodes.tsv
[INFO] [2019-12-23 10:27:08] (18288 lines) /app/public/data/gulf_thailand_sp/publish_node_ancestors.tsv
[INFO] [2019-12-23 10:27:08] (3543 lines) /app/public/data/gulf_thailand_sp/publish_scientific_names.tsv
[INFO] [2019-12-23 10:27:09] (1863 lines) /app/public/data/gulf_thailand_sp/publish_traits.tsv
[INFO] [2019-12-23 10:27:10] (9311 lines) /app/public/data/gulf_thailand_sp/publish_metadata.tsv
[STOP] [2019-12-23 10:27:10] complete_harvest_instance
[START] [2019-12-23 10:27:10] completed
[STOP] [2019-12-23 10:27:10] completed
[STOP] [2019-12-23 10:27:10] logged process, took 1361.21
Latest Process

23 Dec 10:04 EXITED currently processing 0