Harvest for Sulu Sea Species List Created 25 Dec 15:56

Stage: completed
Fetched: 25 Dec 15:56
Validated: 25 Dec 15:56
Deltas Created 25 Dec 15:56
Units Normalized: 25 Dec 16:33
Ancestry Built: 25 Dec 15:59
Nodes Matched: 25 Dec 16:33
Names Parsed: 25 Dec 15:59
New Models Stored: 25 Dec 15:57
Indexed: 25 Dec 16:33
Completed: 25 Dec 16:36
Time to Harvest: 1 minute
Harvesting Log

(149 lines)
# Logfile created on 2019-12-25 15:56:39 -0500 by logger.rb/56815
[START] [2019-12-25 15:56:39] logged process
[START] [2019-12-25 15:56:39] create_harvest_instance
[STOP] [2019-12-25 15:56:40] create_harvest_instance
[START] [2019-12-25 15:56:40] fetch_files
[STOP] [2019-12-25 15:56:40] fetch_files
[START] [2019-12-25 15:56:40] validate_each_file
[STOP] [2019-12-25 15:56:41] validate_each_file
[START] [2019-12-25 15:56:41] convert_to_csv
[CMD] [2019-12-25 15:56:41] /usr/bin/sort /app/public/converted_csv/sulu_sea_sp_list_refs_19706.csv > /app/public/converted_csv/sulu_sea_sp_list_refs_19706.csv_sorted
[CMD] [2019-12-25 15:56:41] /usr/bin/sort /app/public/converted_csv/sulu_sea_sp_list_nodes_19707.csv > /app/public/converted_csv/sulu_sea_sp_list_nodes_19707.csv_sorted
[CMD] [2019-12-25 15:56:42] /usr/bin/sort /app/public/converted_csv/sulu_sea_sp_list_occurrences_19708.csv > /app/public/converted_csv/sulu_sea_sp_list_occurrences_19708.csv_sorted
[CMD] [2019-12-25 15:56:43] /usr/bin/sort /app/public/converted_csv/sulu_sea_sp_list_measurements_19709.csv > /app/public/converted_csv/sulu_sea_sp_list_measurements_19709.csv_sorted
[STOP] [2019-12-25 15:56:43] convert_to_csv
[START] [2019-12-25 15:56:43] calculate_delta
[CMD] [2019-12-25 15:56:43] echo "0a" > /app/public/diff/sulu_sea_sp_list_refs_19706.diff
[CMD] [2019-12-25 15:56:44] tail -n +1 /app/public/converted_csv/sulu_sea_sp_list_refs_19706.csv >> /app/public/diff/sulu_sea_sp_list_refs_19706.diff
[CMD] [2019-12-25 15:56:45] echo "." >> /app/public/diff/sulu_sea_sp_list_refs_19706.diff
[CMD] [2019-12-25 15:56:45] echo "0a" > /app/public/diff/sulu_sea_sp_list_nodes_19707.diff
[CMD] [2019-12-25 15:56:46] tail -n +1 /app/public/converted_csv/sulu_sea_sp_list_nodes_19707.csv >> /app/public/diff/sulu_sea_sp_list_nodes_19707.diff
[CMD] [2019-12-25 15:56:47] echo "." >> /app/public/diff/sulu_sea_sp_list_nodes_19707.diff
[CMD] [2019-12-25 15:56:47] echo "0a" > /app/public/diff/sulu_sea_sp_list_occurrences_19708.diff
[CMD] [2019-12-25 15:56:48] tail -n +1 /app/public/converted_csv/sulu_sea_sp_list_occurrences_19708.csv >> /app/public/diff/sulu_sea_sp_list_occurrences_19708.diff
[CMD] [2019-12-25 15:56:49] echo "." >> /app/public/diff/sulu_sea_sp_list_occurrences_19708.diff
[CMD] [2019-12-25 15:56:49] echo "0a" > /app/public/diff/sulu_sea_sp_list_measurements_19709.diff
[CMD] [2019-12-25 15:56:50] tail -n +1 /app/public/converted_csv/sulu_sea_sp_list_measurements_19709.csv >> /app/public/diff/sulu_sea_sp_list_measurements_19709.diff
[CMD] [2019-12-25 15:56:51] echo "." >> /app/public/diff/sulu_sea_sp_list_measurements_19709.diff
[STOP] [2019-12-25 15:56:51] calculate_delta
[START] [2019-12-25 15:56:51] parse_diff_and_store
[INFO] [2019-12-25 15:56:52] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 15:56:53] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 15:56:56] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 15:56:58] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 15:57:26] Storing 2 References
[INFO] [2019-12-25 15:57:26] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 15:57:26] Average Time: 0.0
[INFO] [2019-12-25 15:57:26] Total Time: 1s
[INFO] [2019-12-25 15:57:26] Storing 8661 ScientificNames
[INFO] [2019-12-25 15:57:26] Processing group of 8661 in 9 groups of 1000
[INFO] [2019-12-25 15:57:29] Average Time: 0.363
[INFO] [2019-12-25 15:57:29] Total Time: 4s
[INFO] [2019-12-25 15:57:29] last 3 / first 3: 0.89
[INFO] [2019-12-25 15:57:29] Std.Dev: 0.05477225575051661; Max: 0.43
[INFO] [2019-12-25 15:57:29] Storing 8661 Nodes
[INFO] [2019-12-25 15:57:29] Processing group of 8661 in 9 groups of 1000
[INFO] [2019-12-25 15:57:32] Average Time: 0.278
[INFO] [2019-12-25 15:57:32] Total Time: 3s
[INFO] [2019-12-25 15:57:32] last 3 / first 3: 0.83
[INFO] [2019-12-25 15:57:32] Std.Dev: 0.044721359549995794; Max: 0.33
[INFO] [2019-12-25 15:57:32] Storing 5133 Occurrences
[INFO] [2019-12-25 15:57:32] Processing group of 5133 in 6 groups of 1000
[INFO] [2019-12-25 15:57:32] Average Time: 0.1
[INFO] [2019-12-25 15:57:32] Total Time: 1s
[INFO] [2019-12-25 15:57:32] Storing 10266 TraitsReferences
[INFO] [2019-12-25 15:57:32] Processing group of 10266 in 11 groups of 1000
[INFO] [2019-12-25 15:57:33] Average Time: 0.069
[INFO] [2019-12-25 15:57:33] Total Time: 1s
[INFO] [2019-12-25 15:57:33] last 3 / first 3: 0.54
[INFO] [2019-12-25 15:57:33] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-12-25 15:57:33] Storing 10266 Traits
[INFO] [2019-12-25 15:57:33] Processing group of 10266 in 11 groups of 1000
[INFO] [2019-12-25 15:57:37] Average Time: 0.347
[INFO] [2019-12-25 15:57:37] Total Time: 4s
[INFO] [2019-12-25 15:57:37] last 3 / first 3: 0.62
[INFO] [2019-12-25 15:57:37] Std.Dev: 0.14832396974191325; Max: 0.7
[INFO] [2019-12-25 15:57:37] Storing 10266 MetaTraits
[INFO] [2019-12-25 15:57:37] Processing group of 10266 in 11 groups of 1000
[INFO] [2019-12-25 15:57:38] Average Time: 0.125
[INFO] [2019-12-25 15:57:38] Total Time: 2s
[INFO] [2019-12-25 15:57:38] last 3 / first 3: 0.71
[INFO] [2019-12-25 15:57:38] Std.Dev: 0.03162277660168379; Max: 0.16
[STOP] [2019-12-25 15:57:38] parse_diff_and_store
[START] [2019-12-25 15:57:38] resolve_keys
[INFO] [2019-12-25 15:58:15] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 15:58:18] traits to occurrences...
[INFO] [2019-12-25 15:58:23] traits to nodes (through occurrences)...
[INFO] [2019-12-25 15:58:23] Traits to sex term...
[INFO] [2019-12-25 15:58:26] Traits to lifestage term...
[INFO] [2019-12-25 15:58:30] MetaTraits to traits...
[INFO] [2019-12-25 15:58:31] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 15:58:32] Assocs to occurrences...
[INFO] [2019-12-25 15:58:32] Assocs to nodes...
[INFO] [2019-12-25 15:58:32] Assoc to sex term...
[INFO] [2019-12-25 15:58:32] Assoc to lifestage term...
[STOP] [2019-12-25 15:58:32] resolve_keys
[START] [2019-12-25 15:58:32] hold_for_later_1
[STOP] [2019-12-25 15:58:32] hold_for_later_1
[START] [2019-12-25 15:58:32] hold_for_later_2
[STOP] [2019-12-25 15:58:32] hold_for_later_2
[START] [2019-12-25 15:58:32] resolve_missing_parents
[STOP] [2019-12-25 15:58:51] resolve_missing_parents
[START] [2019-12-25 15:58:51] rebuild_nodes
[START] [2019-12-25 15:58:51] Flattener#flatten
[START] [2019-12-25 15:58:51] Flattener#study_resource
[START] [2019-12-25 15:58:51] Flattener#build_ancestry
[STOP] [2019-12-25 15:58:52] Flattener#build_ancestry
[INFO] [2019-12-25 15:58:52] 8661 ancestry keys
[START] [2019-12-25 15:58:52] build_node_ancestors
[INFO] [2019-12-25 15:58:52] old ancestors deleted.
[STOP] [2019-12-25 15:58:55] build_node_ancestors
[START] [2019-12-25 15:58:59] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 15:59:00] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 15:59:00] Flattener#flatten
[STOP] [2019-12-25 15:59:00] rebuild_nodes
[START] [2019-12-25 15:59:00] resolve_missing_media_owners
[STOP] [2019-12-25 15:59:00] resolve_missing_media_owners
[START] [2019-12-25 15:59:00] sanitize_media_verbatims
[STOP] [2019-12-25 15:59:00] sanitize_media_verbatims
[START] [2019-12-25 15:59:00] queue_downloads
[STOP] [2019-12-25 15:59:00] queue_downloads
[START] [2019-12-25 15:59:00] parse_names
[WARN] [2019-12-25 15:59:00] I see 8661 names which still need to be parsed.
[STOP] [2019-12-25 15:59:08] parse_names
[START] [2019-12-25 15:59:08] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 15:59:08] denormalize_canonical_names_to_nodes
[START] [2019-12-25 15:59:08] match_nodes
[START] [2019-12-25 15:59:08] map_all_nodes_to_pages
[STOP] [2019-12-25 16:33:25] map_all_nodes_to_pages
[INFO] [2019-12-25 16:33:25] 357 Unmatched nodes (of 8661)! That's too many to output. First 10: Limicola (#62501059); Limicola falcinellus (#62501058); Limnodromus (#62501074); Philomachus (#62507177); Philomachus pugnax (#62507176); Ceyx erithacus (#62503663); Egretta intermedia (#62500102); Megalaima (#62501589); Megalaima haemacephala (#62501588); Anas querquedula (#62501728)
[START] [2019-12-25 16:33:25] update_nodes
[STOP] [2019-12-25 16:33:28] update_nodes
[STOP] [2019-12-25 16:33:28] match_nodes
[START] [2019-12-25 16:33:28] reindex_search
[STOP] [2019-12-25 16:33:51] reindex_search
[START] [2019-12-25 16:33:51] normalize_units
[STOP] [2019-12-25 16:33:51] normalize_units
[START] [2019-12-25 16:33:51] calculate_statistics
[STOP] [2019-12-25 16:33:52] calculate_statistics
[START] [2019-12-25 16:33:52] complete_harvest_instance
[START] [2019-12-25 16:33:52] overall_tsv_creation
[INFO] [2019-12-25 16:33:52] Processing group of 8661 in 1 batches of 10000
[INFO] [2019-12-25 16:35:18] 5133 Traits (unfiltered)...
[INFO] [2019-12-25 16:35:32] 5133 Traits (filtered)...
[INFO] [2019-12-25 16:35:32] 0 Associations (filtered)...
[INFO] [2019-12-25 16:36:21] 25665 metadata added.
[INFO] [2019-12-25 16:36:21] 0 metadata added.
[INFO] [2019-12-25 16:36:22] Average Time: 121.22
[INFO] [2019-12-25 16:36:22] Total Time: 2m30s
[STOP] [2019-12-25 16:36:22] overall_tsv_creation
[INFO] [2019-12-25 16:36:22] Done. Check your files:
[INFO] [2019-12-25 16:36:22] (8661 lines) /app/public/data/sulu_sea_sp_list/publish_nodes.tsv
[INFO] [2019-12-25 16:36:23] (46275 lines) /app/public/data/sulu_sea_sp_list/publish_node_ancestors.tsv
[INFO] [2019-12-25 16:36:24] (8661 lines) /app/public/data/sulu_sea_sp_list/publish_scientific_names.tsv
[INFO] [2019-12-25 16:36:24] (5134 lines) /app/public/data/sulu_sea_sp_list/publish_traits.tsv
[INFO] [2019-12-25 16:36:25] (25666 lines) /app/public/data/sulu_sea_sp_list/publish_metadata.tsv
[STOP] [2019-12-25 16:36:25] complete_harvest_instance
[START] [2019-12-25 16:36:25] completed
[STOP] [2019-12-25 16:36:25] completed
[STOP] [2019-12-25 16:36:25] logged process, took 2385.87
Latest Process

25 Dec 15:56 EXITED currently processing 0