Harvest for Arafura Sea Species List Created 22 Dec 18:20

Harvesting Log

# Logfile created on 2019-12-22 18:20:04 -0500 by logger.rb/56815
[START] [2019-12-22 18:20:04] logged process
[START] [2019-12-22 18:20:04] create_harvest_instance
[STOP] [2019-12-22 18:20:04] create_harvest_instance
[START] [2019-12-22 18:20:04] fetch_files
[STOP] [2019-12-22 18:20:04] fetch_files
[START] [2019-12-22 18:20:04] validate_each_file
[STOP] [2019-12-22 18:20:06] validate_each_file
[START] [2019-12-22 18:20:06] convert_to_csv
[CMD] [2019-12-22 18:20:06] /usr/bin/sort /app/public/converted_csv/arafura_sea_sp_l_refs_19012.csv > /app/public/converted_csv/arafura_sea_sp_l_refs_19012.csv_sorted
[CMD] [2019-12-22 18:20:06] /usr/bin/sort /app/public/converted_csv/arafura_sea_sp_l_nodes_19013.csv > /app/public/converted_csv/arafura_sea_sp_l_nodes_19013.csv_sorted
[CMD] [2019-12-22 18:20:06] /usr/bin/sort /app/public/converted_csv/arafura_sea_sp_l_occurrences_19015.csv > /app/public/converted_csv/arafura_sea_sp_l_occurrences_19015.csv_sorted
[CMD] [2019-12-22 18:20:06] /usr/bin/sort /app/public/converted_csv/arafura_sea_sp_l_measurements_19016.csv > /app/public/converted_csv/arafura_sea_sp_l_measurements_19016.csv_sorted
[STOP] [2019-12-22 18:20:06] convert_to_csv
[START] [2019-12-22 18:20:06] calculate_delta
[CMD] [2019-12-22 18:20:06] echo "0a" > /app/public/diff/arafura_sea_sp_l_refs_19012.diff
[CMD] [2019-12-22 18:20:06] tail -n +1 /app/public/converted_csv/arafura_sea_sp_l_refs_19012.csv >> /app/public/diff/arafura_sea_sp_l_refs_19012.diff
[CMD] [2019-12-22 18:20:06] echo "." >> /app/public/diff/arafura_sea_sp_l_refs_19012.diff
[CMD] [2019-12-22 18:20:06] echo "0a" > /app/public/diff/arafura_sea_sp_l_nodes_19013.diff
[CMD] [2019-12-22 18:20:06] tail -n +1 /app/public/converted_csv/arafura_sea_sp_l_nodes_19013.csv >> /app/public/diff/arafura_sea_sp_l_nodes_19013.diff
[CMD] [2019-12-22 18:20:06] echo "." >> /app/public/diff/arafura_sea_sp_l_nodes_19013.diff
[CMD] [2019-12-22 18:20:06] echo "0a" > /app/public/diff/arafura_sea_sp_l_occurrences_19015.diff
[CMD] [2019-12-22 18:20:06] tail -n +1 /app/public/converted_csv/arafura_sea_sp_l_occurrences_19015.csv >> /app/public/diff/arafura_sea_sp_l_occurrences_19015.diff
[CMD] [2019-12-22 18:20:06] echo "." >> /app/public/diff/arafura_sea_sp_l_occurrences_19015.diff
[CMD] [2019-12-22 18:20:06] echo "0a" > /app/public/diff/arafura_sea_sp_l_measurements_19016.diff
[CMD] [2019-12-22 18:20:06] tail -n +1 /app/public/converted_csv/arafura_sea_sp_l_measurements_19016.csv >> /app/public/diff/arafura_sea_sp_l_measurements_19016.diff
[CMD] [2019-12-22 18:20:06] echo "." >> /app/public/diff/arafura_sea_sp_l_measurements_19016.diff
[STOP] [2019-12-22 18:20:06] calculate_delta
[START] [2019-12-22 18:20:06] parse_diff_and_store
[INFO] [2019-12-22 18:20:06] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 18:20:06] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 18:20:11] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 18:20:12] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 18:20:54] Storing 2 References
[INFO] [2019-12-22 18:20:54] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 18:20:54] Average Time: 0.0
[INFO] [2019-12-22 18:20:54] Total Time: 1s
[INFO] [2019-12-22 18:20:54] Storing 12498 ScientificNames
[INFO] [2019-12-22 18:20:54] Processing group of 12498 in 13 groups of 1000
[INFO] [2019-12-22 18:20:59] Average Time: 0.379
[INFO] [2019-12-22 18:20:59] Total Time: 5s
[INFO] [2019-12-22 18:20:59] last 3 / first 3: 0.53
[INFO] [2019-12-22 18:20:59] Std.Dev: 0.12649110640673517; Max: 0.71
[INFO] [2019-12-22 18:20:59] Storing 12498 Nodes
[INFO] [2019-12-22 18:20:59] Processing group of 12498 in 13 groups of 1000
[INFO] [2019-12-22 18:21:03] Average Time: 0.291
[INFO] [2019-12-22 18:21:03] Total Time: 4s
[INFO] [2019-12-22 18:21:03] last 3 / first 3: 0.85
[INFO] [2019-12-22 18:21:03] Std.Dev: 0.044721359549995794; Max: 0.36
[INFO] [2019-12-22 18:21:03] Storing 7583 Occurrences
[INFO] [2019-12-22 18:21:03] Processing group of 7583 in 8 groups of 1000
[INFO] [2019-12-22 18:21:04] Average Time: 0.101
[INFO] [2019-12-22 18:21:04] Total Time: 1s
[INFO] [2019-12-22 18:21:04] last 3 / first 3: 0.84
[INFO] [2019-12-22 18:21:04] Std.Dev: 0.0; Max: 0.12
[INFO] [2019-12-22 18:21:04] Storing 15166 TraitsReferences
[INFO] [2019-12-22 18:21:04] Processing group of 15166 in 16 groups of 1000
[INFO] [2019-12-22 18:21:05] Average Time: 0.083
[INFO] [2019-12-22 18:21:05] Total Time: 2s
[INFO] [2019-12-22 18:21:05] last 3 / first 3: 1.15
[INFO] [2019-12-22 18:21:05] Std.Dev: 0.03162277660168379; Max: 0.17
[INFO] [2019-12-22 18:21:05] Storing 15166 Traits
[INFO] [2019-12-22 18:21:05] Processing group of 15166 in 16 groups of 1000
[INFO] [2019-12-22 18:21:11] Average Time: 0.326
[INFO] [2019-12-22 18:21:11] Total Time: 6s
[INFO] [2019-12-22 18:21:11] last 3 / first 3: 0.45
[INFO] [2019-12-22 18:21:11] Std.Dev: 0.11832159566199232; Max: 0.64
[INFO] [2019-12-22 18:21:11] Storing 15165 MetaTraits
[INFO] [2019-12-22 18:21:11] Processing group of 15165 in 16 groups of 1000
[INFO] [2019-12-22 18:21:14] Average Time: 0.175
[INFO] [2019-12-22 18:21:14] Total Time: 3s
[INFO] [2019-12-22 18:21:14] last 3 / first 3: 0.65
[INFO] [2019-12-22 18:21:14] Std.Dev: 0.13784048752090222; Max: 0.66
[STOP] [2019-12-22 18:21:14] parse_diff_and_store
[START] [2019-12-22 18:21:14] resolve_keys
[INFO] [2019-12-22 18:22:10] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 18:22:15] traits to occurrences...
[INFO] [2019-12-22 18:22:22] traits to nodes (through occurrences)...
[INFO] [2019-12-22 18:22:22] Traits to sex term...
[INFO] [2019-12-22 18:22:27] Traits to lifestage term...
[INFO] [2019-12-22 18:22:32] MetaTraits to traits...
[INFO] [2019-12-22 18:22:33] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 18:22:36] Assocs to occurrences...
[INFO] [2019-12-22 18:22:36] Assocs to nodes...
[INFO] [2019-12-22 18:22:36] Assoc to sex term...
[INFO] [2019-12-22 18:22:36] Assoc to lifestage term...
[STOP] [2019-12-22 18:22:36] resolve_keys
[START] [2019-12-22 18:22:36] hold_for_later_1
[STOP] [2019-12-22 18:22:36] hold_for_later_1
[START] [2019-12-22 18:22:36] hold_for_later_2
[STOP] [2019-12-22 18:22:36] hold_for_later_2
[START] [2019-12-22 18:22:36] resolve_missing_parents
[STOP] [2019-12-22 18:23:06] resolve_missing_parents
[START] [2019-12-22 18:23:06] rebuild_nodes
[START] [2019-12-22 18:23:06] Flattener#flatten
[START] [2019-12-22 18:23:06] Flattener#study_resource
[START] [2019-12-22 18:23:06] Flattener#build_ancestry
[STOP] [2019-12-22 18:23:07] Flattener#build_ancestry
[INFO] [2019-12-22 18:23:07] 12498 ancestry keys
[START] [2019-12-22 18:23:07] build_node_ancestors
[INFO] [2019-12-22 18:23:07] old ancestors deleted.
[STOP] [2019-12-22 18:23:12] build_node_ancestors
[START] [2019-12-22 18:23:17] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 18:23:19] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 18:23:19] Flattener#flatten
[STOP] [2019-12-22 18:23:20] rebuild_nodes
[START] [2019-12-22 18:23:20] resolve_missing_media_owners
[STOP] [2019-12-22 18:23:20] resolve_missing_media_owners
[START] [2019-12-22 18:23:20] sanitize_media_verbatims
[STOP] [2019-12-22 18:23:20] sanitize_media_verbatims
[START] [2019-12-22 18:23:20] queue_downloads
[STOP] [2019-12-22 18:23:20] queue_downloads
[START] [2019-12-22 18:23:20] parse_names
[WARN] [2019-12-22 18:23:20] I see 12498 names which still need to be parsed.
[STOP] [2019-12-22 18:23:33] parse_names
[START] [2019-12-22 18:23:33] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 18:23:33] denormalize_canonical_names_to_nodes
[START] [2019-12-22 18:23:33] match_nodes
[START] [2019-12-22 18:23:34] map_all_nodes_to_pages
[STOP] [2019-12-22 19:19:30] map_all_nodes_to_pages
[INFO] [2019-12-22 19:19:30] 573 Unmatched nodes (of 12498)! That's too many to output. First 10: Parupeneus auriflamma (#61679506); Apogon striatus (#61679391); Fowleria auritus (#61673081); Euchoristopus (#61675456); Giuris aporos (#61673125); Ptereleotridae (#61674352); Trachinocephalus (#61669550); Scorpaeniformes (#61668007); Gasterosteiformes (#61668637); Strophidon macrura (#61677223)
[START] [2019-12-22 19:19:30] update_nodes
[STOP] [2019-12-22 19:19:35] update_nodes
[STOP] [2019-12-22 19:19:35] match_nodes
[START] [2019-12-22 19:19:35] reindex_search
[STOP] [2019-12-22 19:20:18] reindex_search
[START] [2019-12-22 19:20:18] normalize_units
[STOP] [2019-12-22 19:20:18] normalize_units
[START] [2019-12-22 19:20:18] calculate_statistics
[STOP] [2019-12-22 19:20:18] calculate_statistics
[START] [2019-12-22 19:20:18] complete_harvest_instance
[START] [2019-12-22 19:20:18] overall_tsv_creation
[INFO] [2019-12-22 19:20:18] Processing group of 12498 in 2 batches of 10000
[INFO] [2019-12-22 19:22:01] 5835 Traits (unfiltered)...
[INFO] [2019-12-22 19:22:12] 5835 Traits (filtered)...
[INFO] [2019-12-22 19:22:12] 0 Associations (filtered)...
[INFO] [2019-12-22 19:23:06] 29174 metadata added.
[INFO] [2019-12-22 19:23:06] 0 metadata added.
[INFO] [2019-12-22 19:24:04] 1748 Traits (unfiltered)...
[INFO] [2019-12-22 19:24:18] 1748 Traits (filtered)...
[INFO] [2019-12-22 19:24:18] 0 Associations (filtered)...
[INFO] [2019-12-22 19:25:02] 8740 metadata added.
[INFO] [2019-12-22 19:25:02] 0 metadata added.
[INFO] [2019-12-22 19:25:03] Average Time: 113.645
[INFO] [2019-12-22 19:25:03] Total Time: 4m45s
[STOP] [2019-12-22 19:25:03] overall_tsv_creation
[INFO] [2019-12-22 19:25:03] Done. Check your files:
[INFO] [2019-12-22 19:25:03] (12498 lines) /app/public/data/arafura_sea_sp_l/publish_nodes.tsv
[INFO] [2019-12-22 19:25:03] (66793 lines) /app/public/data/arafura_sea_sp_l/publish_node_ancestors.tsv
[INFO] [2019-12-22 19:25:03] (12498 lines) /app/public/data/arafura_sea_sp_l/publish_scientific_names.tsv
[INFO] [2019-12-22 19:25:03] (7584 lines) /app/public/data/arafura_sea_sp_l/publish_traits.tsv
[INFO] [2019-12-22 19:25:03] (37915 lines) /app/public/data/arafura_sea_sp_l/publish_metadata.tsv
[STOP] [2019-12-22 19:25:03] complete_harvest_instance
[START] [2019-12-22 19:25:03] completed
[STOP] [2019-12-22 19:25:03] completed
[STOP] [2019-12-22 19:25:03] logged process, took 3899.31

Latest Process

22 Dec 18:20 EXITED currently processing 0