Harvest for Solomon Sea Species List Created 25 Dec 14:01

Harvesting Log

# Logfile created on 2019-12-25 14:01:05 -0500 by logger.rb/56815
[START] [2019-12-25 14:01:05] logged process
[START] [2019-12-25 14:01:05] create_harvest_instance
[STOP] [2019-12-25 14:01:06] create_harvest_instance
[START] [2019-12-25 14:01:06] fetch_files
[STOP] [2019-12-25 14:01:06] fetch_files
[START] [2019-12-25 14:01:06] validate_each_file
[STOP] [2019-12-25 14:01:07] validate_each_file
[START] [2019-12-25 14:01:07] convert_to_csv
[CMD] [2019-12-25 14:01:07] /usr/bin/sort /app/public/converted_csv/solomon_sea_sp_l_refs_19674.csv > /app/public/converted_csv/solomon_sea_sp_l_refs_19674.csv_sorted
[CMD] [2019-12-25 14:01:08] /usr/bin/sort /app/public/converted_csv/solomon_sea_sp_l_nodes_19675.csv > /app/public/converted_csv/solomon_sea_sp_l_nodes_19675.csv_sorted
[CMD] [2019-12-25 14:01:08] /usr/bin/sort /app/public/converted_csv/solomon_sea_sp_l_occurrences_19676.csv > /app/public/converted_csv/solomon_sea_sp_l_occurrences_19676.csv_sorted
[CMD] [2019-12-25 14:01:09] /usr/bin/sort /app/public/converted_csv/solomon_sea_sp_l_measurements_19677.csv > /app/public/converted_csv/solomon_sea_sp_l_measurements_19677.csv_sorted
[STOP] [2019-12-25 14:01:10] convert_to_csv
[START] [2019-12-25 14:01:10] calculate_delta
[CMD] [2019-12-25 14:01:10] echo "0a" > /app/public/diff/solomon_sea_sp_l_refs_19674.diff
[CMD] [2019-12-25 14:01:10] tail -n +1 /app/public/converted_csv/solomon_sea_sp_l_refs_19674.csv >> /app/public/diff/solomon_sea_sp_l_refs_19674.diff
[CMD] [2019-12-25 14:01:11] echo "." >> /app/public/diff/solomon_sea_sp_l_refs_19674.diff
[CMD] [2019-12-25 14:01:12] echo "0a" > /app/public/diff/solomon_sea_sp_l_nodes_19675.diff
[CMD] [2019-12-25 14:01:12] tail -n +1 /app/public/converted_csv/solomon_sea_sp_l_nodes_19675.csv >> /app/public/diff/solomon_sea_sp_l_nodes_19675.diff
[CMD] [2019-12-25 14:01:13] echo "." >> /app/public/diff/solomon_sea_sp_l_nodes_19675.diff
[CMD] [2019-12-25 14:01:14] echo "0a" > /app/public/diff/solomon_sea_sp_l_occurrences_19676.diff
[CMD] [2019-12-25 14:01:14] tail -n +1 /app/public/converted_csv/solomon_sea_sp_l_occurrences_19676.csv >> /app/public/diff/solomon_sea_sp_l_occurrences_19676.diff
[CMD] [2019-12-25 14:01:15] echo "." >> /app/public/diff/solomon_sea_sp_l_occurrences_19676.diff
[CMD] [2019-12-25 14:01:16] echo "0a" > /app/public/diff/solomon_sea_sp_l_measurements_19677.diff
[CMD] [2019-12-25 14:01:17] tail -n +1 /app/public/converted_csv/solomon_sea_sp_l_measurements_19677.csv >> /app/public/diff/solomon_sea_sp_l_measurements_19677.diff
[CMD] [2019-12-25 14:01:17] echo "." >> /app/public/diff/solomon_sea_sp_l_measurements_19677.diff
[STOP] [2019-12-25 14:01:18] calculate_delta
[START] [2019-12-25 14:01:18] parse_diff_and_store
[INFO] [2019-12-25 14:01:19] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 14:01:19] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 14:01:23] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 14:01:24] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 14:01:52] Storing 2 References
[INFO] [2019-12-25 14:01:52] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 14:01:52] Average Time: 0.0
[INFO] [2019-12-25 14:01:52] Total Time: 1s
[INFO] [2019-12-25 14:01:52] Storing 7764 ScientificNames
[INFO] [2019-12-25 14:01:52] Processing group of 7764 in 8 groups of 1000
[INFO] [2019-12-25 14:01:55] Average Time: 0.418
[INFO] [2019-12-25 14:01:55] Total Time: 4s
[INFO] [2019-12-25 14:01:55] last 3 / first 3: 0.81
[INFO] [2019-12-25 14:01:55] Std.Dev: 0.05477225575051661; Max: 0.52
[INFO] [2019-12-25 14:01:55] Storing 7764 Nodes
[INFO] [2019-12-25 14:01:55] Processing group of 7764 in 8 groups of 1000
[INFO] [2019-12-25 14:01:58] Average Time: 0.323
[INFO] [2019-12-25 14:01:58] Total Time: 3s
[INFO] [2019-12-25 14:01:58] last 3 / first 3: 0.78
[INFO] [2019-12-25 14:01:58] Std.Dev: 0.044721359549995794; Max: 0.38
[INFO] [2019-12-25 14:01:58] Storing 4689 Occurrences
[INFO] [2019-12-25 14:01:58] Processing group of 4689 in 5 groups of 1000
[INFO] [2019-12-25 14:01:58] Average Time: 0.108
[INFO] [2019-12-25 14:01:58] Total Time: 1s
[INFO] [2019-12-25 14:01:58] Storing 9378 TraitsReferences
[INFO] [2019-12-25 14:01:58] Processing group of 9378 in 10 groups of 1000
[INFO] [2019-12-25 14:01:59] Average Time: 0.082
[INFO] [2019-12-25 14:01:59] Total Time: 1s
[INFO] [2019-12-25 14:01:59] last 3 / first 3: 0.56
[INFO] [2019-12-25 14:01:59] Std.Dev: 0.03162277660168379; Max: 0.16
[INFO] [2019-12-25 14:01:59] Storing 9378 Traits
[INFO] [2019-12-25 14:01:59] Processing group of 9378 in 10 groups of 1000
[INFO] [2019-12-25 14:02:03] Average Time: 0.314
[INFO] [2019-12-25 14:02:03] Total Time: 4s
[INFO] [2019-12-25 14:02:03] last 3 / first 3: 0.66
[INFO] [2019-12-25 14:02:03] Std.Dev: 0.09486832980505137; Max: 0.51
[INFO] [2019-12-25 14:02:03] Storing 9376 MetaTraits
[INFO] [2019-12-25 14:02:03] Processing group of 9376 in 10 groups of 1000
[INFO] [2019-12-25 14:02:04] Average Time: 0.129
[INFO] [2019-12-25 14:02:04] Total Time: 2s
[INFO] [2019-12-25 14:02:04] last 3 / first 3: 0.61
[INFO] [2019-12-25 14:02:04] Std.Dev: 0.044721359549995794; Max: 0.19
[STOP] [2019-12-25 14:02:04] parse_diff_and_store
[START] [2019-12-25 14:02:04] resolve_keys
[INFO] [2019-12-25 14:02:36] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 14:02:39] traits to occurrences...
[INFO] [2019-12-25 14:02:43] traits to nodes (through occurrences)...
[INFO] [2019-12-25 14:02:43] Traits to sex term...
[INFO] [2019-12-25 14:02:47] Traits to lifestage term...
[INFO] [2019-12-25 14:02:50] MetaTraits to traits...
[INFO] [2019-12-25 14:02:51] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 14:02:52] Assocs to occurrences...
[INFO] [2019-12-25 14:02:52] Assocs to nodes...
[INFO] [2019-12-25 14:02:52] Assoc to sex term...
[INFO] [2019-12-25 14:02:52] Assoc to lifestage term...
[STOP] [2019-12-25 14:02:52] resolve_keys
[START] [2019-12-25 14:02:52] hold_for_later_1
[STOP] [2019-12-25 14:02:52] hold_for_later_1
[START] [2019-12-25 14:02:52] hold_for_later_2
[STOP] [2019-12-25 14:02:52] hold_for_later_2
[START] [2019-12-25 14:02:52] resolve_missing_parents
[STOP] [2019-12-25 14:03:07] resolve_missing_parents
[START] [2019-12-25 14:03:07] rebuild_nodes
[START] [2019-12-25 14:03:07] Flattener#flatten
[START] [2019-12-25 14:03:07] Flattener#study_resource
[START] [2019-12-25 14:03:07] Flattener#build_ancestry
[STOP] [2019-12-25 14:03:08] Flattener#build_ancestry
[INFO] [2019-12-25 14:03:08] 7764 ancestry keys
[START] [2019-12-25 14:03:08] build_node_ancestors
[INFO] [2019-12-25 14:03:08] old ancestors deleted.
[STOP] [2019-12-25 14:03:11] build_node_ancestors
[START] [2019-12-25 14:03:15] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 14:03:16] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 14:03:16] Flattener#flatten
[STOP] [2019-12-25 14:03:16] rebuild_nodes
[START] [2019-12-25 14:03:16] resolve_missing_media_owners
[STOP] [2019-12-25 14:03:16] resolve_missing_media_owners
[START] [2019-12-25 14:03:16] sanitize_media_verbatims
[STOP] [2019-12-25 14:03:16] sanitize_media_verbatims
[START] [2019-12-25 14:03:16] queue_downloads
[STOP] [2019-12-25 14:03:16] queue_downloads
[START] [2019-12-25 14:03:16] parse_names
[WARN] [2019-12-25 14:03:16] I see 7764 names which still need to be parsed.
[STOP] [2019-12-25 14:03:23] parse_names
[START] [2019-12-25 14:03:23] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 14:03:23] denormalize_canonical_names_to_nodes
[START] [2019-12-25 14:03:23] match_nodes
[START] [2019-12-25 14:03:23] map_all_nodes_to_pages
[STOP] [2019-12-25 14:25:01] map_all_nodes_to_pages
[INFO] [2019-12-25 14:25:01] 371 Unmatched nodes (of 7764)! That's too many to output. First 10: Granuloreticulosea (#62458046); Foraminiferida (#62458045); Fohsella (#62461671); Fohsella peripheroronda (#62461670); Globigerinoides triloba (#62458069); Globigerinoides quadrilobata (#62458070); Globigerinoides quadrilobatus (#62458071); Globigerinoides trilobus (#62458073); Globigerinoides conglobata (#62458076); Globigerinoides obliqua (#62458659)
[START] [2019-12-25 14:25:01] update_nodes
[STOP] [2019-12-25 14:25:03] update_nodes
[STOP] [2019-12-25 14:25:03] match_nodes
[START] [2019-12-25 14:25:03] reindex_search
[STOP] [2019-12-25 14:25:17] reindex_search
[START] [2019-12-25 14:25:17] normalize_units
[STOP] [2019-12-25 14:25:17] normalize_units
[START] [2019-12-25 14:25:17] calculate_statistics
[STOP] [2019-12-25 14:25:18] calculate_statistics
[START] [2019-12-25 14:25:18] complete_harvest_instance
[START] [2019-12-25 14:25:18] overall_tsv_creation
[INFO] [2019-12-25 14:25:18] Processing group of 7764 in 1 batches of 10000
[INFO] [2019-12-25 14:26:36] 4689 Traits (unfiltered)...
[INFO] [2019-12-25 14:26:49] 4689 Traits (filtered)...
[INFO] [2019-12-25 14:26:50] 0 Associations (filtered)...
[INFO] [2019-12-25 14:27:34] 23443 metadata added.
[INFO] [2019-12-25 14:27:34] 0 metadata added.
[INFO] [2019-12-25 14:27:35] Average Time: 109.08
[INFO] [2019-12-25 14:27:35] Total Time: 2m17s
[STOP] [2019-12-25 14:27:35] overall_tsv_creation
[INFO] [2019-12-25 14:27:35] Done. Check your files:
[INFO] [2019-12-25 14:27:35] (7764 lines) /app/public/data/solomon_sea_sp_l/publish_nodes.tsv
[INFO] [2019-12-25 14:27:36] (40999 lines) /app/public/data/solomon_sea_sp_l/publish_node_ancestors.tsv
[INFO] [2019-12-25 14:27:36] (7764 lines) /app/public/data/solomon_sea_sp_l/publish_scientific_names.tsv
[INFO] [2019-12-25 14:27:37] (4690 lines) /app/public/data/solomon_sea_sp_l/publish_traits.tsv
[INFO] [2019-12-25 14:27:38] (23444 lines) /app/public/data/solomon_sea_sp_l/publish_metadata.tsv
[STOP] [2019-12-25 14:27:38] complete_harvest_instance
[START] [2019-12-25 14:27:38] completed
[STOP] [2019-12-25 14:27:38] completed
[STOP] [2019-12-25 14:27:38] logged process, took 1592.37

Latest Process

25 Dec 14:01 EXITED currently processing 0