Harvest for Savu Sea Species List Created 25 Dec 10:33

Stage: completed
Fetched: 25 Dec 10:33
Validated: 25 Dec 10:33
Deltas Created 25 Dec 10:33
Units Normalized: 25 Dec 10:52
Ancestry Built: 25 Dec 10:33
Nodes Matched: 25 Dec 10:52
Names Parsed: 25 Dec 10:33
New Models Stored: 25 Dec 10:33
Indexed: 25 Dec 10:52
Completed: 25 Dec 10:54
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-25 10:33:04 -0500 by logger.rb/56815
[START] [2019-12-25 10:33:04] logged process
[START] [2019-12-25 10:33:04] create_harvest_instance
[STOP] [2019-12-25 10:33:05] create_harvest_instance
[START] [2019-12-25 10:33:05] fetch_files
[STOP] [2019-12-25 10:33:05] fetch_files
[START] [2019-12-25 10:33:05] validate_each_file
[STOP] [2019-12-25 10:33:05] validate_each_file
[START] [2019-12-25 10:33:05] convert_to_csv
[CMD] [2019-12-25 10:33:05] /usr/bin/sort /app/public/converted_csv/savu_sea_sp_list_refs_19610.csv > /app/public/converted_csv/savu_sea_sp_list_refs_19610.csv_sorted
[CMD] [2019-12-25 10:33:05] /usr/bin/sort /app/public/converted_csv/savu_sea_sp_list_nodes_19611.csv > /app/public/converted_csv/savu_sea_sp_list_nodes_19611.csv_sorted
[CMD] [2019-12-25 10:33:06] /usr/bin/sort /app/public/converted_csv/savu_sea_sp_list_occurrences_19612.csv > /app/public/converted_csv/savu_sea_sp_list_occurrences_19612.csv_sorted
[CMD] [2019-12-25 10:33:06] /usr/bin/sort /app/public/converted_csv/savu_sea_sp_list_measurements_19613.csv > /app/public/converted_csv/savu_sea_sp_list_measurements_19613.csv_sorted
[STOP] [2019-12-25 10:33:06] convert_to_csv
[START] [2019-12-25 10:33:06] calculate_delta
[CMD] [2019-12-25 10:33:06] echo "0a" > /app/public/diff/savu_sea_sp_list_refs_19610.diff
[CMD] [2019-12-25 10:33:06] tail -n +1 /app/public/converted_csv/savu_sea_sp_list_refs_19610.csv >> /app/public/diff/savu_sea_sp_list_refs_19610.diff
[CMD] [2019-12-25 10:33:06] echo "." >> /app/public/diff/savu_sea_sp_list_refs_19610.diff
[CMD] [2019-12-25 10:33:06] echo "0a" > /app/public/diff/savu_sea_sp_list_nodes_19611.diff
[CMD] [2019-12-25 10:33:06] tail -n +1 /app/public/converted_csv/savu_sea_sp_list_nodes_19611.csv >> /app/public/diff/savu_sea_sp_list_nodes_19611.diff
[CMD] [2019-12-25 10:33:07] echo "." >> /app/public/diff/savu_sea_sp_list_nodes_19611.diff
[CMD] [2019-12-25 10:33:07] echo "0a" > /app/public/diff/savu_sea_sp_list_occurrences_19612.diff
[CMD] [2019-12-25 10:33:07] tail -n +1 /app/public/converted_csv/savu_sea_sp_list_occurrences_19612.csv >> /app/public/diff/savu_sea_sp_list_occurrences_19612.diff
[CMD] [2019-12-25 10:33:07] echo "." >> /app/public/diff/savu_sea_sp_list_occurrences_19612.diff
[CMD] [2019-12-25 10:33:07] echo "0a" > /app/public/diff/savu_sea_sp_list_measurements_19613.diff
[CMD] [2019-12-25 10:33:07] tail -n +1 /app/public/converted_csv/savu_sea_sp_list_measurements_19613.csv >> /app/public/diff/savu_sea_sp_list_measurements_19613.diff
[CMD] [2019-12-25 10:33:08] echo "." >> /app/public/diff/savu_sea_sp_list_measurements_19613.diff
[STOP] [2019-12-25 10:33:08] calculate_delta
[START] [2019-12-25 10:33:08] parse_diff_and_store
[INFO] [2019-12-25 10:33:08] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 10:33:08] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 10:33:09] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 10:33:10] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 10:33:18] Storing 2 References
[INFO] [2019-12-25 10:33:18] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 10:33:18] Average Time: 0.0
[INFO] [2019-12-25 10:33:18] Total Time: 1s
[INFO] [2019-12-25 10:33:18] Storing 2940 ScientificNames
[INFO] [2019-12-25 10:33:18] Processing group of 2940 in 3 groups of 1000
[INFO] [2019-12-25 10:33:20] Average Time: 0.46
[INFO] [2019-12-25 10:33:20] Total Time: 2s
[INFO] [2019-12-25 10:33:20] Storing 2940 Nodes
[INFO] [2019-12-25 10:33:20] Processing group of 2940 in 3 groups of 1000
[INFO] [2019-12-25 10:33:21] Average Time: 0.35
[INFO] [2019-12-25 10:33:21] Total Time: 2s
[INFO] [2019-12-25 10:33:21] Storing 1477 Occurrences
[INFO] [2019-12-25 10:33:21] Processing group of 1477 in 2 groups of 1000
[INFO] [2019-12-25 10:33:21] Average Time: 0.09
[INFO] [2019-12-25 10:33:21] Total Time: 1s
[INFO] [2019-12-25 10:33:21] Storing 2954 TraitsReferences
[INFO] [2019-12-25 10:33:21] Processing group of 2954 in 3 groups of 1000
[INFO] [2019-12-25 10:33:21] Average Time: 0.103
[INFO] [2019-12-25 10:33:21] Total Time: 1s
[INFO] [2019-12-25 10:33:21] Storing 2954 Traits
[INFO] [2019-12-25 10:33:21] Processing group of 2954 in 3 groups of 1000
[INFO] [2019-12-25 10:33:22] Average Time: 0.413
[INFO] [2019-12-25 10:33:22] Total Time: 2s
[INFO] [2019-12-25 10:33:22] Storing 2954 MetaTraits
[INFO] [2019-12-25 10:33:22] Processing group of 2954 in 3 groups of 1000
[INFO] [2019-12-25 10:33:23] Average Time: 0.147
[INFO] [2019-12-25 10:33:23] Total Time: 1s
[STOP] [2019-12-25 10:33:23] parse_diff_and_store
[START] [2019-12-25 10:33:23] resolve_keys
[INFO] [2019-12-25 10:33:37] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 10:33:38] traits to occurrences...
[INFO] [2019-12-25 10:33:39] traits to nodes (through occurrences)...
[INFO] [2019-12-25 10:33:40] Traits to sex term...
[INFO] [2019-12-25 10:33:41] Traits to lifestage term...
[INFO] [2019-12-25 10:33:42] MetaTraits to traits...
[INFO] [2019-12-25 10:33:42] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 10:33:43] Assocs to occurrences...
[INFO] [2019-12-25 10:33:43] Assocs to nodes...
[INFO] [2019-12-25 10:33:43] Assoc to sex term...
[INFO] [2019-12-25 10:33:43] Assoc to lifestage term...
[STOP] [2019-12-25 10:33:43] resolve_keys
[START] [2019-12-25 10:33:43] hold_for_later_1
[STOP] [2019-12-25 10:33:43] hold_for_later_1
[START] [2019-12-25 10:33:43] hold_for_later_2
[STOP] [2019-12-25 10:33:43] hold_for_later_2
[START] [2019-12-25 10:33:43] resolve_missing_parents
[STOP] [2019-12-25 10:33:47] resolve_missing_parents
[START] [2019-12-25 10:33:47] rebuild_nodes
[START] [2019-12-25 10:33:47] Flattener#flatten
[START] [2019-12-25 10:33:47] Flattener#study_resource
[START] [2019-12-25 10:33:47] Flattener#build_ancestry
[STOP] [2019-12-25 10:33:48] Flattener#build_ancestry
[INFO] [2019-12-25 10:33:48] 2940 ancestry keys
[START] [2019-12-25 10:33:48] build_node_ancestors
[INFO] [2019-12-25 10:33:48] old ancestors deleted.
[STOP] [2019-12-25 10:33:49] build_node_ancestors
[START] [2019-12-25 10:33:50] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 10:33:51] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 10:33:51] Flattener#flatten
[STOP] [2019-12-25 10:33:51] rebuild_nodes
[START] [2019-12-25 10:33:51] resolve_missing_media_owners
[STOP] [2019-12-25 10:33:51] resolve_missing_media_owners
[START] [2019-12-25 10:33:51] sanitize_media_verbatims
[STOP] [2019-12-25 10:33:51] sanitize_media_verbatims
[START] [2019-12-25 10:33:51] queue_downloads
[STOP] [2019-12-25 10:33:51] queue_downloads
[START] [2019-12-25 10:33:51] parse_names
[WARN] [2019-12-25 10:33:51] I see 2940 names which still need to be parsed.
[STOP] [2019-12-25 10:33:55] parse_names
[START] [2019-12-25 10:33:55] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 10:33:55] denormalize_canonical_names_to_nodes
[START] [2019-12-25 10:33:55] match_nodes
[START] [2019-12-25 10:33:55] map_all_nodes_to_pages
[STOP] [2019-12-25 10:52:22] map_all_nodes_to_pages
[INFO] [2019-12-25 10:52:22] 97 Unmatched nodes (of 2940)! That's too many to output. First 10: Ceyx erithacus (#62430082); Egretta intermedia (#62429795); Ptereleotridae (#62431906); Scorpaeniformes (#62429501); Hydrophiidae (#62429827); Manta (#62429566); Pleurogona (#62429687); Enterogona (#62430630); Pectiniidae (#62430013); Euphyllidae (#62430527)
[START] [2019-12-25 10:52:22] update_nodes
[STOP] [2019-12-25 10:52:24] update_nodes
[STOP] [2019-12-25 10:52:24] match_nodes
[START] [2019-12-25 10:52:24] reindex_search
[STOP] [2019-12-25 10:52:35] reindex_search
[START] [2019-12-25 10:52:35] normalize_units
[STOP] [2019-12-25 10:52:35] normalize_units
[START] [2019-12-25 10:52:35] calculate_statistics
[STOP] [2019-12-25 10:52:35] calculate_statistics
[START] [2019-12-25 10:52:35] complete_harvest_instance
[START] [2019-12-25 10:52:35] overall_tsv_creation
[INFO] [2019-12-25 10:52:35] Processing group of 2940 in 1 batches of 10000
[INFO] [2019-12-25 10:53:34] 1477 Traits (unfiltered)...
[INFO] [2019-12-25 10:53:47] 1477 Traits (filtered)...
[INFO] [2019-12-25 10:53:47] 0 Associations (filtered)...
[INFO] [2019-12-25 10:54:28] 7385 metadata added.
[INFO] [2019-12-25 10:54:28] 0 metadata added.
[INFO] [2019-12-25 10:54:28] Average Time: 88.99
[INFO] [2019-12-25 10:54:28] Total Time: 1m54s
[STOP] [2019-12-25 10:54:28] overall_tsv_creation
[INFO] [2019-12-25 10:54:28] Done. Check your files:
[INFO] [2019-12-25 10:54:29] (2940 lines) /app/public/data/savu_sea_sp_list/publish_nodes.tsv
[INFO] [2019-12-25 10:54:29] (14920 lines) /app/public/data/savu_sea_sp_list/publish_node_ancestors.tsv
[INFO] [2019-12-25 10:54:29] (2940 lines) /app/public/data/savu_sea_sp_list/publish_scientific_names.tsv
[INFO] [2019-12-25 10:54:29] (1478 lines) /app/public/data/savu_sea_sp_list/publish_traits.tsv
[INFO] [2019-12-25 10:54:29] (7386 lines) /app/public/data/savu_sea_sp_list/publish_metadata.tsv
[STOP] [2019-12-25 10:54:29] complete_harvest_instance
[START] [2019-12-25 10:54:29] completed
[STOP] [2019-12-25 10:54:29] completed
[STOP] [2019-12-25 10:54:29] logged process, took 1285.29
Latest Process

25 Dec 10:33 EXITED currently processing 0