Harvest for Gulf of Oman Species List Created 23 Dec 09:18

Stage: completed
Fetched: 23 Dec 09:18
Validated: 23 Dec 09:18
Deltas Created 23 Dec 09:18
Units Normalized: 23 Dec 09:31
Ancestry Built: 23 Dec 09:19
Nodes Matched: 23 Dec 09:31
Names Parsed: 23 Dec 09:19
New Models Stored: 23 Dec 09:18
Indexed: 23 Dec 09:31
Completed: 23 Dec 09:33
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 09:18:31 -0500 by logger.rb/56815
[START] [2019-12-23 09:18:31] logged process
[START] [2019-12-23 09:18:31] create_harvest_instance
[STOP] [2019-12-23 09:18:31] create_harvest_instance
[START] [2019-12-23 09:18:31] fetch_files
[STOP] [2019-12-23 09:18:31] fetch_files
[START] [2019-12-23 09:18:31] validate_each_file
[STOP] [2019-12-23 09:18:32] validate_each_file
[START] [2019-12-23 09:18:32] convert_to_csv
[CMD] [2019-12-23 09:18:32] /usr/bin/sort /app/public/converted_csv/gulf_oman_sp_lis_refs_19330.csv > /app/public/converted_csv/gulf_oman_sp_lis_refs_19330.csv_sorted
[CMD] [2019-12-23 09:18:32] /usr/bin/sort /app/public/converted_csv/gulf_oman_sp_lis_nodes_19331.csv > /app/public/converted_csv/gulf_oman_sp_lis_nodes_19331.csv_sorted
[CMD] [2019-12-23 09:18:33] /usr/bin/sort /app/public/converted_csv/gulf_oman_sp_lis_occurrences_19332.csv > /app/public/converted_csv/gulf_oman_sp_lis_occurrences_19332.csv_sorted
[CMD] [2019-12-23 09:18:34] /usr/bin/sort /app/public/converted_csv/gulf_oman_sp_lis_measurements_19333.csv > /app/public/converted_csv/gulf_oman_sp_lis_measurements_19333.csv_sorted
[STOP] [2019-12-23 09:18:34] convert_to_csv
[START] [2019-12-23 09:18:34] calculate_delta
[CMD] [2019-12-23 09:18:35] echo "0a" > /app/public/diff/gulf_oman_sp_lis_refs_19330.diff
[CMD] [2019-12-23 09:18:35] tail -n +1 /app/public/converted_csv/gulf_oman_sp_lis_refs_19330.csv >> /app/public/diff/gulf_oman_sp_lis_refs_19330.diff
[CMD] [2019-12-23 09:18:36] echo "." >> /app/public/diff/gulf_oman_sp_lis_refs_19330.diff
[CMD] [2019-12-23 09:18:37] echo "0a" > /app/public/diff/gulf_oman_sp_lis_nodes_19331.diff
[CMD] [2019-12-23 09:18:37] tail -n +1 /app/public/converted_csv/gulf_oman_sp_lis_nodes_19331.csv >> /app/public/diff/gulf_oman_sp_lis_nodes_19331.diff
[CMD] [2019-12-23 09:18:38] echo "." >> /app/public/diff/gulf_oman_sp_lis_nodes_19331.diff
[CMD] [2019-12-23 09:18:39] echo "0a" > /app/public/diff/gulf_oman_sp_lis_occurrences_19332.diff
[CMD] [2019-12-23 09:18:39] tail -n +1 /app/public/converted_csv/gulf_oman_sp_lis_occurrences_19332.csv >> /app/public/diff/gulf_oman_sp_lis_occurrences_19332.diff
[CMD] [2019-12-23 09:18:40] echo "." >> /app/public/diff/gulf_oman_sp_lis_occurrences_19332.diff
[CMD] [2019-12-23 09:18:41] echo "0a" > /app/public/diff/gulf_oman_sp_lis_measurements_19333.diff
[CMD] [2019-12-23 09:18:41] tail -n +1 /app/public/converted_csv/gulf_oman_sp_lis_measurements_19333.csv >> /app/public/diff/gulf_oman_sp_lis_measurements_19333.diff
[CMD] [2019-12-23 09:18:42] echo "." >> /app/public/diff/gulf_oman_sp_lis_measurements_19333.diff
[STOP] [2019-12-23 09:18:43] calculate_delta
[START] [2019-12-23 09:18:43] parse_diff_and_store
[INFO] [2019-12-23 09:18:43] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 09:18:44] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 09:18:46] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 09:18:47] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 09:18:55] Storing 2 References
[INFO] [2019-12-23 09:18:55] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 09:18:55] Average Time: 0.0
[INFO] [2019-12-23 09:18:55] Total Time: 1s
[INFO] [2019-12-23 09:18:55] Storing 2537 ScientificNames
[INFO] [2019-12-23 09:18:55] Processing group of 2537 in 3 groups of 1000
[INFO] [2019-12-23 09:18:56] Average Time: 0.35
[INFO] [2019-12-23 09:18:56] Total Time: 2s
[INFO] [2019-12-23 09:18:56] Storing 2537 Nodes
[INFO] [2019-12-23 09:18:56] Processing group of 2537 in 3 groups of 1000
[INFO] [2019-12-23 09:18:57] Average Time: 0.263
[INFO] [2019-12-23 09:18:57] Total Time: 1s
[INFO] [2019-12-23 09:18:57] Storing 1166 Occurrences
[INFO] [2019-12-23 09:18:57] Processing group of 1166 in 2 groups of 1000
[INFO] [2019-12-23 09:18:57] Average Time: 0.07
[INFO] [2019-12-23 09:18:57] Total Time: 1s
[INFO] [2019-12-23 09:18:57] Storing 2332 TraitsReferences
[INFO] [2019-12-23 09:18:57] Processing group of 2332 in 3 groups of 1000
[INFO] [2019-12-23 09:18:58] Average Time: 0.103
[INFO] [2019-12-23 09:18:58] Total Time: 1s
[INFO] [2019-12-23 09:18:58] Storing 2332 Traits
[INFO] [2019-12-23 09:18:58] Processing group of 2332 in 3 groups of 1000
[INFO] [2019-12-23 09:18:58] Average Time: 0.283
[INFO] [2019-12-23 09:18:58] Total Time: 1s
[INFO] [2019-12-23 09:18:58] Storing 2332 MetaTraits
[INFO] [2019-12-23 09:18:58] Processing group of 2332 in 3 groups of 1000
[INFO] [2019-12-23 09:18:59] Average Time: 0.11
[INFO] [2019-12-23 09:18:59] Total Time: 1s
[STOP] [2019-12-23 09:18:59] parse_diff_and_store
[START] [2019-12-23 09:18:59] resolve_keys
[INFO] [2019-12-23 09:19:12] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 09:19:13] traits to occurrences...
[INFO] [2019-12-23 09:19:14] traits to nodes (through occurrences)...
[INFO] [2019-12-23 09:19:14] Traits to sex term...
[INFO] [2019-12-23 09:19:14] Traits to lifestage term...
[INFO] [2019-12-23 09:19:15] MetaTraits to traits...
[INFO] [2019-12-23 09:19:15] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 09:19:15] Assocs to occurrences...
[INFO] [2019-12-23 09:19:15] Assocs to nodes...
[INFO] [2019-12-23 09:19:15] Assoc to sex term...
[INFO] [2019-12-23 09:19:15] Assoc to lifestage term...
[STOP] [2019-12-23 09:19:15] resolve_keys
[START] [2019-12-23 09:19:15] hold_for_later_1
[STOP] [2019-12-23 09:19:15] hold_for_later_1
[START] [2019-12-23 09:19:15] hold_for_later_2
[STOP] [2019-12-23 09:19:15] hold_for_later_2
[START] [2019-12-23 09:19:15] resolve_missing_parents
[STOP] [2019-12-23 09:19:19] resolve_missing_parents
[START] [2019-12-23 09:19:19] rebuild_nodes
[START] [2019-12-23 09:19:19] Flattener#flatten
[START] [2019-12-23 09:19:19] Flattener#study_resource
[START] [2019-12-23 09:19:19] Flattener#build_ancestry
[STOP] [2019-12-23 09:19:19] Flattener#build_ancestry
[INFO] [2019-12-23 09:19:19] 2537 ancestry keys
[START] [2019-12-23 09:19:19] build_node_ancestors
[INFO] [2019-12-23 09:19:19] old ancestors deleted.
[STOP] [2019-12-23 09:19:20] build_node_ancestors
[START] [2019-12-23 09:19:21] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 09:19:21] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 09:19:21] Flattener#flatten
[STOP] [2019-12-23 09:19:21] rebuild_nodes
[START] [2019-12-23 09:19:21] resolve_missing_media_owners
[STOP] [2019-12-23 09:19:21] resolve_missing_media_owners
[START] [2019-12-23 09:19:21] sanitize_media_verbatims
[STOP] [2019-12-23 09:19:21] sanitize_media_verbatims
[START] [2019-12-23 09:19:21] queue_downloads
[STOP] [2019-12-23 09:19:21] queue_downloads
[START] [2019-12-23 09:19:21] parse_names
[WARN] [2019-12-23 09:19:21] I see 2537 names which still need to be parsed.
[STOP] [2019-12-23 09:19:24] parse_names
[START] [2019-12-23 09:19:24] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 09:19:24] denormalize_canonical_names_to_nodes
[START] [2019-12-23 09:19:24] match_nodes
[START] [2019-12-23 09:19:24] map_all_nodes_to_pages
[STOP] [2019-12-23 09:31:16] map_all_nodes_to_pages
[INFO] [2019-12-23 09:31:16] 124 Unmatched nodes (of 2537)! That's too many to output. First 10: Larus hemprichii (#61955892); Philomachus (#61956420); Philomachus pugnax (#61956419); Puffinus carneipes (#61954994); Puffinus griseus (#61955012); Puffinus pacificus (#61955029); Anas clypeata (#61955996); Anas querquedula (#61956021); Apogon striatus (#61956668); Scorpaeniformes (#61955143)
[START] [2019-12-23 09:31:16] update_nodes
[STOP] [2019-12-23 09:31:17] update_nodes
[STOP] [2019-12-23 09:31:17] match_nodes
[START] [2019-12-23 09:31:17] reindex_search
[STOP] [2019-12-23 09:31:25] reindex_search
[START] [2019-12-23 09:31:25] normalize_units
[STOP] [2019-12-23 09:31:25] normalize_units
[START] [2019-12-23 09:31:25] calculate_statistics
[STOP] [2019-12-23 09:31:25] calculate_statistics
[START] [2019-12-23 09:31:25] complete_harvest_instance
[START] [2019-12-23 09:31:25] overall_tsv_creation
[INFO] [2019-12-23 09:31:25] Processing group of 2537 in 1 batches of 10000
[INFO] [2019-12-23 09:32:21] 1166 Traits (unfiltered)...
[INFO] [2019-12-23 09:32:34] 1166 Traits (filtered)...
[INFO] [2019-12-23 09:32:34] 0 Associations (filtered)...
[INFO] [2019-12-23 09:33:14] 5830 metadata added.
[INFO] [2019-12-23 09:33:14] 0 metadata added.
[INFO] [2019-12-23 09:33:14] Average Time: 85.23
[INFO] [2019-12-23 09:33:14] Total Time: 1m49s
[STOP] [2019-12-23 09:33:14] overall_tsv_creation
[INFO] [2019-12-23 09:33:14] Done. Check your files:
[INFO] [2019-12-23 09:33:14] (2537 lines) /app/public/data/gulf_oman_sp_lis/publish_nodes.tsv
[INFO] [2019-12-23 09:33:15] (12554 lines) /app/public/data/gulf_oman_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-12-23 09:33:16] (2537 lines) /app/public/data/gulf_oman_sp_lis/publish_scientific_names.tsv
[INFO] [2019-12-23 09:33:16] (1167 lines) /app/public/data/gulf_oman_sp_lis/publish_traits.tsv
[INFO] [2019-12-23 09:33:17] (5831 lines) /app/public/data/gulf_oman_sp_lis/publish_metadata.tsv
[STOP] [2019-12-23 09:33:17] complete_harvest_instance
[START] [2019-12-23 09:33:17] completed
[STOP] [2019-12-23 09:33:17] completed
[STOP] [2019-12-23 09:33:17] logged process, took 886.52
Latest Process

23 Dec 09:18 EXITED currently processing 0