Harvest for Gulf of Aden Species List Created 23 Dec 03:21

Stage: completed
Fetched: 23 Dec 03:21
Validated: 23 Dec 03:21
Deltas Created 23 Dec 03:22
Units Normalized: 23 Dec 03:34
Ancestry Built: 23 Dec 03:22
Nodes Matched: 23 Dec 03:34
Names Parsed: 23 Dec 03:22
New Models Stored: 23 Dec 03:22
Indexed: 23 Dec 03:34
Completed: 23 Dec 03:37
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 03:21:52 -0500 by logger.rb/56815
[START] [2019-12-23 03:21:52] logged process
[START] [2019-12-23 03:21:52] create_harvest_instance
[STOP] [2019-12-23 03:21:53] create_harvest_instance
[START] [2019-12-23 03:21:53] fetch_files
[STOP] [2019-12-23 03:21:53] fetch_files
[START] [2019-12-23 03:21:53] validate_each_file
[STOP] [2019-12-23 03:21:54] validate_each_file
[START] [2019-12-23 03:21:54] convert_to_csv
[CMD] [2019-12-23 03:21:54] /usr/bin/sort /app/public/converted_csv/gulf_aden_sp_lis_refs_19258.csv > /app/public/converted_csv/gulf_aden_sp_lis_refs_19258.csv_sorted
[CMD] [2019-12-23 03:21:54] /usr/bin/sort /app/public/converted_csv/gulf_aden_sp_lis_nodes_19259.csv > /app/public/converted_csv/gulf_aden_sp_lis_nodes_19259.csv_sorted
[CMD] [2019-12-23 03:21:55] /usr/bin/sort /app/public/converted_csv/gulf_aden_sp_lis_occurrences_19260.csv > /app/public/converted_csv/gulf_aden_sp_lis_occurrences_19260.csv_sorted
[CMD] [2019-12-23 03:21:56] /usr/bin/sort /app/public/converted_csv/gulf_aden_sp_lis_measurements_19261.csv > /app/public/converted_csv/gulf_aden_sp_lis_measurements_19261.csv_sorted
[STOP] [2019-12-23 03:21:56] convert_to_csv
[START] [2019-12-23 03:21:56] calculate_delta
[CMD] [2019-12-23 03:21:56] echo "0a" > /app/public/diff/gulf_aden_sp_lis_refs_19258.diff
[CMD] [2019-12-23 03:21:57] tail -n +1 /app/public/converted_csv/gulf_aden_sp_lis_refs_19258.csv >> /app/public/diff/gulf_aden_sp_lis_refs_19258.diff
[CMD] [2019-12-23 03:21:58] echo "." >> /app/public/diff/gulf_aden_sp_lis_refs_19258.diff
[CMD] [2019-12-23 03:21:58] echo "0a" > /app/public/diff/gulf_aden_sp_lis_nodes_19259.diff
[CMD] [2019-12-23 03:21:59] tail -n +1 /app/public/converted_csv/gulf_aden_sp_lis_nodes_19259.csv >> /app/public/diff/gulf_aden_sp_lis_nodes_19259.diff
[CMD] [2019-12-23 03:22:00] echo "." >> /app/public/diff/gulf_aden_sp_lis_nodes_19259.diff
[CMD] [2019-12-23 03:22:00] echo "0a" > /app/public/diff/gulf_aden_sp_lis_occurrences_19260.diff
[CMD] [2019-12-23 03:22:01] tail -n +1 /app/public/converted_csv/gulf_aden_sp_lis_occurrences_19260.csv >> /app/public/diff/gulf_aden_sp_lis_occurrences_19260.diff
[CMD] [2019-12-23 03:22:02] echo "." >> /app/public/diff/gulf_aden_sp_lis_occurrences_19260.diff
[CMD] [2019-12-23 03:22:02] echo "0a" > /app/public/diff/gulf_aden_sp_lis_measurements_19261.diff
[CMD] [2019-12-23 03:22:03] tail -n +1 /app/public/converted_csv/gulf_aden_sp_lis_measurements_19261.csv >> /app/public/diff/gulf_aden_sp_lis_measurements_19261.diff
[CMD] [2019-12-23 03:22:04] echo "." >> /app/public/diff/gulf_aden_sp_lis_measurements_19261.diff
[STOP] [2019-12-23 03:22:04] calculate_delta
[START] [2019-12-23 03:22:04] parse_diff_and_store
[INFO] [2019-12-23 03:22:05] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 03:22:06] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 03:22:08] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 03:22:08] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 03:22:17] Storing 2 References
[INFO] [2019-12-23 03:22:17] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 03:22:17] Average Time: 0.0
[INFO] [2019-12-23 03:22:17] Total Time: 1s
[INFO] [2019-12-23 03:22:17] Storing 3150 ScientificNames
[INFO] [2019-12-23 03:22:17] Processing group of 3150 in 4 groups of 1000
[INFO] [2019-12-23 03:22:19] Average Time: 0.345
[INFO] [2019-12-23 03:22:19] Total Time: 2s
[INFO] [2019-12-23 03:22:19] Storing 3150 Nodes
[INFO] [2019-12-23 03:22:19] Processing group of 3150 in 4 groups of 1000
[INFO] [2019-12-23 03:22:20] Average Time: 0.243
[INFO] [2019-12-23 03:22:20] Total Time: 1s
[INFO] [2019-12-23 03:22:20] Storing 1499 Occurrences
[INFO] [2019-12-23 03:22:20] Processing group of 1499 in 2 groups of 1000
[INFO] [2019-12-23 03:22:20] Average Time: 0.08
[INFO] [2019-12-23 03:22:20] Total Time: 1s
[INFO] [2019-12-23 03:22:20] Storing 2998 TraitsReferences
[INFO] [2019-12-23 03:22:20] Processing group of 2998 in 3 groups of 1000
[INFO] [2019-12-23 03:22:20] Average Time: 0.097
[INFO] [2019-12-23 03:22:20] Total Time: 1s
[INFO] [2019-12-23 03:22:20] Storing 2998 Traits
[INFO] [2019-12-23 03:22:20] Processing group of 2998 in 3 groups of 1000
[INFO] [2019-12-23 03:22:22] Average Time: 0.443
[INFO] [2019-12-23 03:22:22] Total Time: 2s
[INFO] [2019-12-23 03:22:22] Storing 2998 MetaTraits
[INFO] [2019-12-23 03:22:22] Processing group of 2998 in 3 groups of 1000
[INFO] [2019-12-23 03:22:22] Average Time: 0.15
[INFO] [2019-12-23 03:22:22] Total Time: 1s
[STOP] [2019-12-23 03:22:22] parse_diff_and_store
[START] [2019-12-23 03:22:22] resolve_keys
[INFO] [2019-12-23 03:22:36] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 03:22:38] traits to occurrences...
[INFO] [2019-12-23 03:22:39] traits to nodes (through occurrences)...
[INFO] [2019-12-23 03:22:39] Traits to sex term...
[INFO] [2019-12-23 03:22:39] Traits to lifestage term...
[INFO] [2019-12-23 03:22:40] MetaTraits to traits...
[INFO] [2019-12-23 03:22:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 03:22:41] Assocs to occurrences...
[INFO] [2019-12-23 03:22:41] Assocs to nodes...
[INFO] [2019-12-23 03:22:41] Assoc to sex term...
[INFO] [2019-12-23 03:22:41] Assoc to lifestage term...
[STOP] [2019-12-23 03:22:41] resolve_keys
[START] [2019-12-23 03:22:41] hold_for_later_1
[STOP] [2019-12-23 03:22:41] hold_for_later_1
[START] [2019-12-23 03:22:41] hold_for_later_2
[STOP] [2019-12-23 03:22:41] hold_for_later_2
[START] [2019-12-23 03:22:41] resolve_missing_parents
[STOP] [2019-12-23 03:22:46] resolve_missing_parents
[START] [2019-12-23 03:22:46] rebuild_nodes
[START] [2019-12-23 03:22:46] Flattener#flatten
[START] [2019-12-23 03:22:46] Flattener#study_resource
[START] [2019-12-23 03:22:46] Flattener#build_ancestry
[STOP] [2019-12-23 03:22:46] Flattener#build_ancestry
[INFO] [2019-12-23 03:22:46] 3150 ancestry keys
[START] [2019-12-23 03:22:46] build_node_ancestors
[INFO] [2019-12-23 03:22:46] old ancestors deleted.
[STOP] [2019-12-23 03:22:47] build_node_ancestors
[START] [2019-12-23 03:22:48] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 03:22:49] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 03:22:49] Flattener#flatten
[STOP] [2019-12-23 03:22:49] rebuild_nodes
[START] [2019-12-23 03:22:49] resolve_missing_media_owners
[STOP] [2019-12-23 03:22:49] resolve_missing_media_owners
[START] [2019-12-23 03:22:49] sanitize_media_verbatims
[STOP] [2019-12-23 03:22:49] sanitize_media_verbatims
[START] [2019-12-23 03:22:49] queue_downloads
[STOP] [2019-12-23 03:22:49] queue_downloads
[START] [2019-12-23 03:22:49] parse_names
[WARN] [2019-12-23 03:22:49] I see 3150 names which still need to be parsed.
[STOP] [2019-12-23 03:22:55] parse_names
[START] [2019-12-23 03:22:55] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 03:22:55] denormalize_canonical_names_to_nodes
[START] [2019-12-23 03:22:55] match_nodes
[START] [2019-12-23 03:22:55] map_all_nodes_to_pages
[STOP] [2019-12-23 03:34:46] map_all_nodes_to_pages
[INFO] [2019-12-23 03:34:46] 200 Unmatched nodes (of 3150)! That's too many to output. First 10: Manta (#61898421); Ptereleotridae (#61898361); Trachinocephalus (#61896225); Scorpaeniformes (#61895997); Stephanoberyciformes (#61896097); Philomachus (#61896921); Philomachus pugnax (#61896920); Larus hemprichii (#61898594); Enterogona (#61897527); Branchiostomidae (#61898552)
[START] [2019-12-23 03:34:46] update_nodes
[STOP] [2019-12-23 03:34:46] update_nodes
[STOP] [2019-12-23 03:34:46] match_nodes
[START] [2019-12-23 03:34:46] reindex_search
[STOP] [2019-12-23 03:34:53] reindex_search
[START] [2019-12-23 03:34:53] normalize_units
[STOP] [2019-12-23 03:34:53] normalize_units
[START] [2019-12-23 03:34:53] calculate_statistics
[STOP] [2019-12-23 03:34:53] calculate_statistics
[START] [2019-12-23 03:34:53] complete_harvest_instance
[START] [2019-12-23 03:34:53] overall_tsv_creation
[INFO] [2019-12-23 03:34:53] Processing group of 3150 in 1 batches of 10000
[INFO] [2019-12-23 03:36:02] 1499 Traits (unfiltered)...
[INFO] [2019-12-23 03:36:20] 1499 Traits (filtered)...
[INFO] [2019-12-23 03:36:20] 0 Associations (filtered)...
[INFO] [2019-12-23 03:37:09] 7495 metadata added.
[INFO] [2019-12-23 03:37:09] 0 metadata added.
[INFO] [2019-12-23 03:37:09] Average Time: 110.43
[INFO] [2019-12-23 03:37:09] Total Time: 2m17s
[STOP] [2019-12-23 03:37:09] overall_tsv_creation
[INFO] [2019-12-23 03:37:09] Done. Check your files:
[INFO] [2019-12-23 03:37:10] (3150 lines) /app/public/data/gulf_aden_sp_lis/publish_nodes.tsv
[INFO] [2019-12-23 03:37:11] (15737 lines) /app/public/data/gulf_aden_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-12-23 03:37:11] (3150 lines) /app/public/data/gulf_aden_sp_lis/publish_scientific_names.tsv
[INFO] [2019-12-23 03:37:12] (1500 lines) /app/public/data/gulf_aden_sp_lis/publish_traits.tsv
[INFO] [2019-12-23 03:37:13] (7496 lines) /app/public/data/gulf_aden_sp_lis/publish_metadata.tsv
[STOP] [2019-12-23 03:37:13] complete_harvest_instance
[START] [2019-12-23 03:37:13] completed
[STOP] [2019-12-23 03:37:13] completed
[STOP] [2019-12-23 03:37:13] logged process, took 920.53
Latest Process

23 Dec 03:21 EXITED currently processing 0