Harvest for Celebes Sea Species List Created 22 Dec 23:16

Stage: completed
Fetched: 22 Dec 23:16
Validated: 22 Dec 23:16
Deltas Created 22 Dec 23:16
Units Normalized: 22 Dec 23:37
Ancestry Built: 22 Dec 23:18
Nodes Matched: 22 Dec 23:37
Names Parsed: 22 Dec 23:18
New Models Stored: 22 Dec 23:17
Indexed: 22 Dec 23:37
Completed: 22 Dec 23:39
Time to Harvest: less than a minute
Harvesting Log

(145 lines)
# Logfile created on 2019-12-22 23:16:53 -0500 by logger.rb/56815
[START] [2019-12-22 23:16:53] logged process
[START] [2019-12-22 23:16:53] create_harvest_instance
[STOP] [2019-12-22 23:16:53] create_harvest_instance
[START] [2019-12-22 23:16:53] fetch_files
[STOP] [2019-12-22 23:16:53] fetch_files
[START] [2019-12-22 23:16:53] validate_each_file
[STOP] [2019-12-22 23:16:54] validate_each_file
[START] [2019-12-22 23:16:54] convert_to_csv
[CMD] [2019-12-22 23:16:54] /usr/bin/sort /app/public/converted_csv/celebes_sea_sp_l_refs_19154.csv > /app/public/converted_csv/celebes_sea_sp_l_refs_19154.csv_sorted
[CMD] [2019-12-22 23:16:54] /usr/bin/sort /app/public/converted_csv/celebes_sea_sp_l_nodes_19155.csv > /app/public/converted_csv/celebes_sea_sp_l_nodes_19155.csv_sorted
[CMD] [2019-12-22 23:16:54] /usr/bin/sort /app/public/converted_csv/celebes_sea_sp_l_occurrences_19156.csv > /app/public/converted_csv/celebes_sea_sp_l_occurrences_19156.csv_sorted
[CMD] [2019-12-22 23:16:54] /usr/bin/sort /app/public/converted_csv/celebes_sea_sp_l_measurements_19157.csv > /app/public/converted_csv/celebes_sea_sp_l_measurements_19157.csv_sorted
[STOP] [2019-12-22 23:16:54] convert_to_csv
[START] [2019-12-22 23:16:54] calculate_delta
[CMD] [2019-12-22 23:16:54] echo "0a" > /app/public/diff/celebes_sea_sp_l_refs_19154.diff
[CMD] [2019-12-22 23:16:54] tail -n +1 /app/public/converted_csv/celebes_sea_sp_l_refs_19154.csv >> /app/public/diff/celebes_sea_sp_l_refs_19154.diff
[CMD] [2019-12-22 23:16:54] echo "." >> /app/public/diff/celebes_sea_sp_l_refs_19154.diff
[CMD] [2019-12-22 23:16:54] echo "0a" > /app/public/diff/celebes_sea_sp_l_nodes_19155.diff
[CMD] [2019-12-22 23:16:54] tail -n +1 /app/public/converted_csv/celebes_sea_sp_l_nodes_19155.csv >> /app/public/diff/celebes_sea_sp_l_nodes_19155.diff
[CMD] [2019-12-22 23:16:54] echo "." >> /app/public/diff/celebes_sea_sp_l_nodes_19155.diff
[CMD] [2019-12-22 23:16:54] echo "0a" > /app/public/diff/celebes_sea_sp_l_occurrences_19156.diff
[CMD] [2019-12-22 23:16:54] tail -n +1 /app/public/converted_csv/celebes_sea_sp_l_occurrences_19156.csv >> /app/public/diff/celebes_sea_sp_l_occurrences_19156.diff
[CMD] [2019-12-22 23:16:54] echo "." >> /app/public/diff/celebes_sea_sp_l_occurrences_19156.diff
[CMD] [2019-12-22 23:16:54] echo "0a" > /app/public/diff/celebes_sea_sp_l_measurements_19157.diff
[CMD] [2019-12-22 23:16:54] tail -n +1 /app/public/converted_csv/celebes_sea_sp_l_measurements_19157.csv >> /app/public/diff/celebes_sea_sp_l_measurements_19157.diff
[CMD] [2019-12-22 23:16:54] echo "." >> /app/public/diff/celebes_sea_sp_l_measurements_19157.diff
[STOP] [2019-12-22 23:16:55] calculate_delta
[START] [2019-12-22 23:16:55] parse_diff_and_store
[INFO] [2019-12-22 23:16:55] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 23:16:55] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 23:16:57] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 23:16:57] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 23:17:15] Storing 2 References
[INFO] [2019-12-22 23:17:15] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 23:17:15] Average Time: 0.0
[INFO] [2019-12-22 23:17:15] Total Time: 1s
[INFO] [2019-12-22 23:17:15] Storing 5791 ScientificNames
[INFO] [2019-12-22 23:17:15] Processing group of 5791 in 6 groups of 1000
[INFO] [2019-12-22 23:17:18] Average Time: 0.397
[INFO] [2019-12-22 23:17:18] Total Time: 3s
[INFO] [2019-12-22 23:17:18] Storing 5791 Nodes
[INFO] [2019-12-22 23:17:18] Processing group of 5791 in 6 groups of 1000
[INFO] [2019-12-22 23:17:20] Average Time: 0.323
[INFO] [2019-12-22 23:17:20] Total Time: 2s
[INFO] [2019-12-22 23:17:20] Storing 3229 Occurrences
[INFO] [2019-12-22 23:17:20] Processing group of 3229 in 4 groups of 1000
[INFO] [2019-12-22 23:17:20] Average Time: 0.09
[INFO] [2019-12-22 23:17:20] Total Time: 1s
[INFO] [2019-12-22 23:17:20] Storing 6458 TraitsReferences
[INFO] [2019-12-22 23:17:20] Processing group of 6458 in 7 groups of 1000
[INFO] [2019-12-22 23:17:21] Average Time: 0.079
[INFO] [2019-12-22 23:17:21] Total Time: 1s
[INFO] [2019-12-22 23:17:21] last 3 / first 3: 0.66
[INFO] [2019-12-22 23:17:21] Std.Dev: 0.03162277660168379; Max: 0.14
[INFO] [2019-12-22 23:17:21] Storing 6458 Traits
[INFO] [2019-12-22 23:17:21] Processing group of 6458 in 7 groups of 1000
[INFO] [2019-12-22 23:17:23] Average Time: 0.336
[INFO] [2019-12-22 23:17:23] Total Time: 3s
[INFO] [2019-12-22 23:17:23] last 3 / first 3: 0.74
[INFO] [2019-12-22 23:17:23] Std.Dev: 0.08366600265340755; Max: 0.42
[INFO] [2019-12-22 23:17:23] Storing 6458 MetaTraits
[INFO] [2019-12-22 23:17:23] Processing group of 6458 in 7 groups of 1000
[INFO] [2019-12-22 23:17:24] Average Time: 0.179
[INFO] [2019-12-22 23:17:24] Total Time: 2s
[INFO] [2019-12-22 23:17:24] last 3 / first 3: 1.52
[INFO] [2019-12-22 23:17:24] Std.Dev: 0.14491376746189438; Max: 0.5
[STOP] [2019-12-22 23:17:24] parse_diff_and_store
[START] [2019-12-22 23:17:24] resolve_keys
[INFO] [2019-12-22 23:17:48] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 23:17:50] traits to occurrences...
[INFO] [2019-12-22 23:17:52] traits to nodes (through occurrences)...
[INFO] [2019-12-22 23:17:52] Traits to sex term...
[INFO] [2019-12-22 23:17:53] Traits to lifestage term...
[INFO] [2019-12-22 23:17:55] MetaTraits to traits...
[INFO] [2019-12-22 23:17:55] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 23:17:56] Assocs to occurrences...
[INFO] [2019-12-22 23:17:56] Assocs to nodes...
[INFO] [2019-12-22 23:17:56] Assoc to sex term...
[INFO] [2019-12-22 23:17:56] Assoc to lifestage term...
[STOP] [2019-12-22 23:17:56] resolve_keys
[START] [2019-12-22 23:17:56] hold_for_later_1
[STOP] [2019-12-22 23:17:56] hold_for_later_1
[START] [2019-12-22 23:17:56] hold_for_later_2
[STOP] [2019-12-22 23:17:56] hold_for_later_2
[START] [2019-12-22 23:17:56] resolve_missing_parents
[STOP] [2019-12-22 23:18:09] resolve_missing_parents
[START] [2019-12-22 23:18:09] rebuild_nodes
[START] [2019-12-22 23:18:09] Flattener#flatten
[START] [2019-12-22 23:18:09] Flattener#study_resource
[START] [2019-12-22 23:18:09] Flattener#build_ancestry
[STOP] [2019-12-22 23:18:09] Flattener#build_ancestry
[INFO] [2019-12-22 23:18:09] 5791 ancestry keys
[START] [2019-12-22 23:18:09] build_node_ancestors
[INFO] [2019-12-22 23:18:09] old ancestors deleted.
[STOP] [2019-12-22 23:18:11] build_node_ancestors
[START] [2019-12-22 23:18:13] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 23:18:14] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 23:18:14] Flattener#flatten
[STOP] [2019-12-22 23:18:14] rebuild_nodes
[START] [2019-12-22 23:18:14] resolve_missing_media_owners
[STOP] [2019-12-22 23:18:14] resolve_missing_media_owners
[START] [2019-12-22 23:18:14] sanitize_media_verbatims
[STOP] [2019-12-22 23:18:14] sanitize_media_verbatims
[START] [2019-12-22 23:18:14] queue_downloads
[STOP] [2019-12-22 23:18:14] queue_downloads
[START] [2019-12-22 23:18:14] parse_names
[WARN] [2019-12-22 23:18:14] I see 5791 names which still need to be parsed.
[STOP] [2019-12-22 23:18:20] parse_names
[START] [2019-12-22 23:18:20] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 23:18:20] denormalize_canonical_names_to_nodes
[START] [2019-12-22 23:18:20] match_nodes
[START] [2019-12-22 23:18:20] map_all_nodes_to_pages
[STOP] [2019-12-22 23:37:20] map_all_nodes_to_pages
[INFO] [2019-12-22 23:37:20] 240 Unmatched nodes (of 5791)! That's too many to output. First 10: Adercotryma glomerata (#61782895); Reophax nodulosus (#61782904); Usbekistania charoides (#61782902); Turbinaria condensata (#61787842); Sagenista (#61786286); Bicosoecophyceae (#61786285); Boodleaceae (#61786283); Lampanyctus basili (#61788369); Chromis caeruleus (#61786658); Chrysiptera glaucus (#61787240)
[START] [2019-12-22 23:37:20] update_nodes
[STOP] [2019-12-22 23:37:22] update_nodes
[STOP] [2019-12-22 23:37:22] match_nodes
[START] [2019-12-22 23:37:22] reindex_search
[STOP] [2019-12-22 23:37:37] reindex_search
[START] [2019-12-22 23:37:37] normalize_units
[STOP] [2019-12-22 23:37:37] normalize_units
[START] [2019-12-22 23:37:38] calculate_statistics
[STOP] [2019-12-22 23:37:38] calculate_statistics
[START] [2019-12-22 23:37:38] complete_harvest_instance
[START] [2019-12-22 23:37:38] overall_tsv_creation
[INFO] [2019-12-22 23:37:38] Processing group of 5791 in 1 batches of 10000
[INFO] [2019-12-22 23:38:51] 3229 Traits (unfiltered)...
[INFO] [2019-12-22 23:39:04] 3229 Traits (filtered)...
[INFO] [2019-12-22 23:39:04] 0 Associations (filtered)...
[INFO] [2019-12-22 23:39:49] 16145 metadata added.
[INFO] [2019-12-22 23:39:49] 0 metadata added.
[INFO] [2019-12-22 23:39:49] Average Time: 104.41
[INFO] [2019-12-22 23:39:49] Total Time: 2m11s
[STOP] [2019-12-22 23:39:49] overall_tsv_creation
[INFO] [2019-12-22 23:39:49] Done. Check your files:
[INFO] [2019-12-22 23:39:49] (5791 lines) /app/public/data/celebes_sea_sp_l/publish_nodes.tsv
[INFO] [2019-12-22 23:39:49] (30370 lines) /app/public/data/celebes_sea_sp_l/publish_node_ancestors.tsv
[INFO] [2019-12-22 23:39:49] (5791 lines) /app/public/data/celebes_sea_sp_l/publish_scientific_names.tsv
[INFO] [2019-12-22 23:39:49] (3230 lines) /app/public/data/celebes_sea_sp_l/publish_traits.tsv
[INFO] [2019-12-22 23:39:49] (16146 lines) /app/public/data/celebes_sea_sp_l/publish_metadata.tsv
[STOP] [2019-12-22 23:39:49] complete_harvest_instance
[START] [2019-12-22 23:39:49] completed
[STOP] [2019-12-22 23:39:49] completed
[STOP] [2019-12-22 23:39:49] logged process, took 1376.4
Latest Process

22 Dec 23:16 EXITED currently processing 0