Harvest for Bering Sea Species List Created 22 Dec 22:07

Stage: completed
Fetched: 22 Dec 22:07
Validated: 22 Dec 22:07
Deltas Created 22 Dec 22:07
Units Normalized: 22 Dec 22:29
Ancestry Built: 22 Dec 22:09
Nodes Matched: 22 Dec 22:29
Names Parsed: 22 Dec 22:09
New Models Stored: 22 Dec 22:08
Indexed: 22 Dec 22:29
Completed: 22 Dec 22:32
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-12-22 22:07:19 -0500 by logger.rb/56815
[START] [2019-12-22 22:07:19] logged process
[START] [2019-12-22 22:07:19] create_harvest_instance
[STOP] [2019-12-22 22:07:19] create_harvest_instance
[START] [2019-12-22 22:07:19] fetch_files
[STOP] [2019-12-22 22:07:20] fetch_files
[START] [2019-12-22 22:07:20] validate_each_file
[STOP] [2019-12-22 22:07:21] validate_each_file
[START] [2019-12-22 22:07:21] convert_to_csv
[CMD] [2019-12-22 22:07:21] /usr/bin/sort /app/public/converted_csv/bering_sea_sp_li_refs_19114.csv > /app/public/converted_csv/bering_sea_sp_li_refs_19114.csv_sorted
[CMD] [2019-12-22 22:07:21] /usr/bin/sort /app/public/converted_csv/bering_sea_sp_li_nodes_19115.csv > /app/public/converted_csv/bering_sea_sp_li_nodes_19115.csv_sorted
[CMD] [2019-12-22 22:07:22] /usr/bin/sort /app/public/converted_csv/bering_sea_sp_li_occurrences_19116.csv > /app/public/converted_csv/bering_sea_sp_li_occurrences_19116.csv_sorted
[CMD] [2019-12-22 22:07:23] /usr/bin/sort /app/public/converted_csv/bering_sea_sp_li_measurements_19117.csv > /app/public/converted_csv/bering_sea_sp_li_measurements_19117.csv_sorted
[STOP] [2019-12-22 22:07:23] convert_to_csv
[START] [2019-12-22 22:07:23] calculate_delta
[CMD] [2019-12-22 22:07:23] echo "0a" > /app/public/diff/bering_sea_sp_li_refs_19114.diff
[CMD] [2019-12-22 22:07:24] tail -n +1 /app/public/converted_csv/bering_sea_sp_li_refs_19114.csv >> /app/public/diff/bering_sea_sp_li_refs_19114.diff
[CMD] [2019-12-22 22:07:25] echo "." >> /app/public/diff/bering_sea_sp_li_refs_19114.diff
[CMD] [2019-12-22 22:07:25] echo "0a" > /app/public/diff/bering_sea_sp_li_nodes_19115.diff
[CMD] [2019-12-22 22:07:26] tail -n +1 /app/public/converted_csv/bering_sea_sp_li_nodes_19115.csv >> /app/public/diff/bering_sea_sp_li_nodes_19115.diff
[CMD] [2019-12-22 22:07:26] echo "." >> /app/public/diff/bering_sea_sp_li_nodes_19115.diff
[CMD] [2019-12-22 22:07:27] echo "0a" > /app/public/diff/bering_sea_sp_li_occurrences_19116.diff
[CMD] [2019-12-22 22:07:28] tail -n +1 /app/public/converted_csv/bering_sea_sp_li_occurrences_19116.csv >> /app/public/diff/bering_sea_sp_li_occurrences_19116.diff
[CMD] [2019-12-22 22:07:28] echo "." >> /app/public/diff/bering_sea_sp_li_occurrences_19116.diff
[CMD] [2019-12-22 22:07:29] echo "0a" > /app/public/diff/bering_sea_sp_li_measurements_19117.diff
[CMD] [2019-12-22 22:07:29] tail -n +1 /app/public/converted_csv/bering_sea_sp_li_measurements_19117.csv >> /app/public/diff/bering_sea_sp_li_measurements_19117.diff
[CMD] [2019-12-22 22:07:30] echo "." >> /app/public/diff/bering_sea_sp_li_measurements_19117.diff
[STOP] [2019-12-22 22:07:31] calculate_delta
[START] [2019-12-22 22:07:31] parse_diff_and_store
[INFO] [2019-12-22 22:07:31] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 22:07:32] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 22:07:35] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 22:07:36] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 22:07:54] Storing 2 References
[INFO] [2019-12-22 22:07:54] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 22:07:54] Average Time: 0.0
[INFO] [2019-12-22 22:07:54] Total Time: 1s
[INFO] [2019-12-22 22:07:54] Storing 6723 ScientificNames
[INFO] [2019-12-22 22:07:54] Processing group of 6723 in 7 groups of 1000
[INFO] [2019-12-22 22:07:57] Average Time: 0.37
[INFO] [2019-12-22 22:07:57] Total Time: 3s
[INFO] [2019-12-22 22:07:57] last 3 / first 3: 0.87
[INFO] [2019-12-22 22:07:57] Std.Dev: 0.05477225575051661; Max: 0.45
[INFO] [2019-12-22 22:07:57] Storing 6723 Nodes
[INFO] [2019-12-22 22:07:57] Processing group of 6723 in 7 groups of 1000
[INFO] [2019-12-22 22:07:59] Average Time: 0.29
[INFO] [2019-12-22 22:07:59] Total Time: 3s
[INFO] [2019-12-22 22:07:59] last 3 / first 3: 0.87
[INFO] [2019-12-22 22:07:59] Std.Dev: 0.044721359549995794; Max: 0.33
[INFO] [2019-12-22 22:07:59] Storing 3590 Occurrences
[INFO] [2019-12-22 22:07:59] Processing group of 3590 in 4 groups of 1000
[INFO] [2019-12-22 22:07:59] Average Time: 0.103
[INFO] [2019-12-22 22:07:59] Total Time: 1s
[INFO] [2019-12-22 22:07:59] Storing 7180 TraitsReferences
[INFO] [2019-12-22 22:07:59] Processing group of 7180 in 8 groups of 1000
[INFO] [2019-12-22 22:08:00] Average Time: 0.076
[INFO] [2019-12-22 22:08:00] Total Time: 1s
[INFO] [2019-12-22 22:08:00] last 3 / first 3: 0.47
[INFO] [2019-12-22 22:08:00] Std.Dev: 0.044721359549995794; Max: 0.17
[INFO] [2019-12-22 22:08:00] Storing 7180 Traits
[INFO] [2019-12-22 22:08:00] Processing group of 7180 in 8 groups of 1000
[INFO] [2019-12-22 22:08:03] Average Time: 0.31
[INFO] [2019-12-22 22:08:03] Total Time: 3s
[INFO] [2019-12-22 22:08:03] last 3 / first 3: 0.62
[INFO] [2019-12-22 22:08:03] Std.Dev: 0.1224744871391589; Max: 0.49
[INFO] [2019-12-22 22:08:03] Storing 7165 MetaTraits
[INFO] [2019-12-22 22:08:03] Processing group of 7165 in 8 groups of 1000
[INFO] [2019-12-22 22:08:04] Average Time: 0.124
[INFO] [2019-12-22 22:08:04] Total Time: 2s
[INFO] [2019-12-22 22:08:04] last 3 / first 3: 0.72
[INFO] [2019-12-22 22:08:04] Std.Dev: 0.044721359549995794; Max: 0.16
[STOP] [2019-12-22 22:08:04] parse_diff_and_store
[START] [2019-12-22 22:08:04] resolve_keys
[INFO] [2019-12-22 22:08:37] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 22:08:40] traits to occurrences...
[INFO] [2019-12-22 22:08:41] traits to nodes (through occurrences)...
[INFO] [2019-12-22 22:08:41] Traits to sex term...
[INFO] [2019-12-22 22:08:43] Traits to lifestage term...
[INFO] [2019-12-22 22:08:44] MetaTraits to traits...
[INFO] [2019-12-22 22:08:45] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 22:08:46] Assocs to occurrences...
[INFO] [2019-12-22 22:08:46] Assocs to nodes...
[INFO] [2019-12-22 22:08:46] Assoc to sex term...
[INFO] [2019-12-22 22:08:46] Assoc to lifestage term...
[STOP] [2019-12-22 22:08:46] resolve_keys
[START] [2019-12-22 22:08:46] hold_for_later_1
[STOP] [2019-12-22 22:08:46] hold_for_later_1
[START] [2019-12-22 22:08:46] hold_for_later_2
[STOP] [2019-12-22 22:08:46] hold_for_later_2
[START] [2019-12-22 22:08:46] resolve_missing_parents
[STOP] [2019-12-22 22:09:05] resolve_missing_parents
[START] [2019-12-22 22:09:05] rebuild_nodes
[START] [2019-12-22 22:09:05] Flattener#flatten
[START] [2019-12-22 22:09:05] Flattener#study_resource
[START] [2019-12-22 22:09:05] Flattener#build_ancestry
[STOP] [2019-12-22 22:09:05] Flattener#build_ancestry
[INFO] [2019-12-22 22:09:05] 6723 ancestry keys
[START] [2019-12-22 22:09:05] build_node_ancestors
[INFO] [2019-12-22 22:09:05] old ancestors deleted.
[STOP] [2019-12-22 22:09:08] build_node_ancestors
[START] [2019-12-22 22:09:11] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 22:09:13] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 22:09:13] Flattener#flatten
[STOP] [2019-12-22 22:09:13] rebuild_nodes
[START] [2019-12-22 22:09:13] resolve_missing_media_owners
[STOP] [2019-12-22 22:09:13] resolve_missing_media_owners
[START] [2019-12-22 22:09:13] sanitize_media_verbatims
[STOP] [2019-12-22 22:09:13] sanitize_media_verbatims
[START] [2019-12-22 22:09:13] queue_downloads
[STOP] [2019-12-22 22:09:13] queue_downloads
[START] [2019-12-22 22:09:13] parse_names
[WARN] [2019-12-22 22:09:13] I see 6723 names which still need to be parsed.
[STOP] [2019-12-22 22:09:19] parse_names
[START] [2019-12-22 22:09:19] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 22:09:19] denormalize_canonical_names_to_nodes
[START] [2019-12-22 22:09:19] match_nodes
[START] [2019-12-22 22:09:19] map_all_nodes_to_pages
[STOP] [2019-12-22 22:29:38] map_all_nodes_to_pages
[INFO] [2019-12-22 22:29:38] 377 Unmatched nodes (of 6723)! That's too many to output. First 10: Scorpaeniformes (#61749634); Ulcina (#61750871); Stenobrachius leucopsarum (#61754869); Anotopteridae (#61751668); Gasterosteiformes (#61750767); Stephanoberyciformes (#61751283); Cetomimiformes (#61752693); Larus thayeri (#61750167); Limnodromus (#61749692); Philomachus (#61749998)
[START] [2019-12-22 22:29:38] update_nodes
[STOP] [2019-12-22 22:29:41] update_nodes
[STOP] [2019-12-22 22:29:41] match_nodes
[START] [2019-12-22 22:29:41] reindex_search
[STOP] [2019-12-22 22:29:58] reindex_search
[START] [2019-12-22 22:29:58] normalize_units
[STOP] [2019-12-22 22:29:58] normalize_units
[START] [2019-12-22 22:29:58] calculate_statistics
[STOP] [2019-12-22 22:29:58] calculate_statistics
[START] [2019-12-22 22:29:58] complete_harvest_instance
[START] [2019-12-22 22:29:58] overall_tsv_creation
[INFO] [2019-12-22 22:29:58] Processing group of 6723 in 1 batches of 10000
[INFO] [2019-12-22 22:31:15] 3590 Traits (unfiltered)...
[INFO] [2019-12-22 22:31:28] 3590 Traits (filtered)...
[INFO] [2019-12-22 22:31:28] 0 Associations (filtered)...
[INFO] [2019-12-22 22:32:13] 17935 metadata added.
[INFO] [2019-12-22 22:32:13] 0 metadata added.
[INFO] [2019-12-22 22:32:13] Average Time: 107.74
[INFO] [2019-12-22 22:32:13] Total Time: 2m15s
[STOP] [2019-12-22 22:32:13] overall_tsv_creation
[INFO] [2019-12-22 22:32:13] Done. Check your files:
[INFO] [2019-12-22 22:32:14] (6723 lines) /app/public/data/bering_sea_sp_li/publish_nodes.tsv
[INFO] [2019-12-22 22:32:15] (34369 lines) /app/public/data/bering_sea_sp_li/publish_node_ancestors.tsv
[INFO] [2019-12-22 22:32:15] (6723 lines) /app/public/data/bering_sea_sp_li/publish_scientific_names.tsv
[INFO] [2019-12-22 22:32:16] (3591 lines) /app/public/data/bering_sea_sp_li/publish_traits.tsv
[INFO] [2019-12-22 22:32:17] (17936 lines) /app/public/data/bering_sea_sp_li/publish_metadata.tsv
[STOP] [2019-12-22 22:32:17] complete_harvest_instance
[START] [2019-12-22 22:32:17] completed
[STOP] [2019-12-22 22:32:17] completed
[STOP] [2019-12-22 22:32:17] logged process, took 1498.0
Latest Process

22 Dec 22:07 EXITED currently processing 0