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

Stage: completed
Fetched: 22 Dec 18:20
Validated: 22 Dec 18:20
Deltas Created 22 Dec 18:20
Units Normalized: 22 Dec 19:20
Ancestry Built: 22 Dec 18:24
Nodes Matched: 22 Dec 19:19
Names Parsed: 22 Dec 18:24
New Models Stored: 22 Dec 18:22
Indexed: 22 Dec 19:20
Completed: 22 Dec 19:25
Time to Harvest: 1 minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-12-22 18:20:06 -0500 by logger.rb/56815
[START] [2019-12-22 18:20:06] logged process
[START] [2019-12-22 18:20:06] create_harvest_instance
[STOP] [2019-12-22 18:20:07] create_harvest_instance
[START] [2019-12-22 18:20:07] fetch_files
[STOP] [2019-12-22 18:20:07] fetch_files
[START] [2019-12-22 18:20:07] validate_each_file
[STOP] [2019-12-22 18:20:08] validate_each_file
[START] [2019-12-22 18:20:08] convert_to_csv
[CMD] [2019-12-22 18:20:08] /usr/bin/sort /app/public/converted_csv/arabian_sea_sp_l_refs_19018.csv > /app/public/converted_csv/arabian_sea_sp_l_refs_19018.csv_sorted
[CMD] [2019-12-22 18:20:09] /usr/bin/sort /app/public/converted_csv/arabian_sea_sp_l_nodes_19019.csv > /app/public/converted_csv/arabian_sea_sp_l_nodes_19019.csv_sorted
[CMD] [2019-12-22 18:20:10] /usr/bin/sort /app/public/converted_csv/arabian_sea_sp_l_occurrences_19020.csv > /app/public/converted_csv/arabian_sea_sp_l_occurrences_19020.csv_sorted
[CMD] [2019-12-22 18:20:10] /usr/bin/sort /app/public/converted_csv/arabian_sea_sp_l_measurements_19021.csv > /app/public/converted_csv/arabian_sea_sp_l_measurements_19021.csv_sorted
[STOP] [2019-12-22 18:20:11] convert_to_csv
[START] [2019-12-22 18:20:11] calculate_delta
[CMD] [2019-12-22 18:20:11] echo "0a" > /app/public/diff/arabian_sea_sp_l_refs_19018.diff
[CMD] [2019-12-22 18:20:12] tail -n +1 /app/public/converted_csv/arabian_sea_sp_l_refs_19018.csv >> /app/public/diff/arabian_sea_sp_l_refs_19018.diff
[CMD] [2019-12-22 18:20:12] echo "." >> /app/public/diff/arabian_sea_sp_l_refs_19018.diff
[CMD] [2019-12-22 18:20:13] echo "0a" > /app/public/diff/arabian_sea_sp_l_nodes_19019.diff
[CMD] [2019-12-22 18:20:13] tail -n +1 /app/public/converted_csv/arabian_sea_sp_l_nodes_19019.csv >> /app/public/diff/arabian_sea_sp_l_nodes_19019.diff
[CMD] [2019-12-22 18:20:14] echo "." >> /app/public/diff/arabian_sea_sp_l_nodes_19019.diff
[CMD] [2019-12-22 18:20:15] echo "0a" > /app/public/diff/arabian_sea_sp_l_occurrences_19020.diff
[CMD] [2019-12-22 18:20:15] tail -n +1 /app/public/converted_csv/arabian_sea_sp_l_occurrences_19020.csv >> /app/public/diff/arabian_sea_sp_l_occurrences_19020.diff
[CMD] [2019-12-22 18:20:16] echo "." >> /app/public/diff/arabian_sea_sp_l_occurrences_19020.diff
[CMD] [2019-12-22 18:20:17] echo "0a" > /app/public/diff/arabian_sea_sp_l_measurements_19021.diff
[CMD] [2019-12-22 18:20:17] tail -n +1 /app/public/converted_csv/arabian_sea_sp_l_measurements_19021.csv >> /app/public/diff/arabian_sea_sp_l_measurements_19021.diff
[CMD] [2019-12-22 18:20:18] echo "." >> /app/public/diff/arabian_sea_sp_l_measurements_19021.diff
[STOP] [2019-12-22 18:20:19] calculate_delta
[START] [2019-12-22 18:20:19] parse_diff_and_store
[INFO] [2019-12-22 18:20:19] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 18:20:20] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 18:20:25] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 18:20:27] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 18:21:08] Storing 2 References
[INFO] [2019-12-22 18:21:08] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 18:21:08] Average Time: 0.0
[INFO] [2019-12-22 18:21:08] Total Time: 1s
[INFO] [2019-12-22 18:21:08] Storing 12816 ScientificNames
[INFO] [2019-12-22 18:21:08] Processing group of 12816 in 13 groups of 1000
[INFO] [2019-12-22 18:21:12] Average Time: 0.349
[INFO] [2019-12-22 18:21:12] Total Time: 5s
[INFO] [2019-12-22 18:21:12] last 3 / first 3: 0.96
[INFO] [2019-12-22 18:21:12] Std.Dev: 0.03162277660168379; Max: 0.4
[INFO] [2019-12-22 18:21:12] Storing 12816 Nodes
[INFO] [2019-12-22 18:21:12] Processing group of 12816 in 13 groups of 1000
[INFO] [2019-12-22 18:21:51] Average Time: 2.976
[INFO] [2019-12-22 18:21:51] Total Time: 39s
[INFO] [2019-12-22 18:21:51] last 3 / first 3: 1.19
[INFO] [2019-12-22 18:21:51] Std.Dev: 9.637063868212143; Max: 35.05
[INFO] [2019-12-22 18:21:51] Storing 7225 Occurrences
[INFO] [2019-12-22 18:21:51] Processing group of 7225 in 8 groups of 1000
[INFO] [2019-12-22 18:21:52] Average Time: 0.114
[INFO] [2019-12-22 18:21:52] Total Time: 1s
[INFO] [2019-12-22 18:21:52] last 3 / first 3: 0.76
[INFO] [2019-12-22 18:21:52] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-12-22 18:21:52] Storing 14450 TraitsReferences
[INFO] [2019-12-22 18:21:52] Processing group of 14450 in 15 groups of 1000
[INFO] [2019-12-22 18:21:53] Average Time: 0.081
[INFO] [2019-12-22 18:21:53] Total Time: 2s
[INFO] [2019-12-22 18:21:53] last 3 / first 3: 0.59
[INFO] [2019-12-22 18:21:53] Std.Dev: 0.03162277660168379; Max: 0.18
[INFO] [2019-12-22 18:21:53] Storing 14450 Traits
[INFO] [2019-12-22 18:21:53] Processing group of 14450 in 15 groups of 1000
[INFO] [2019-12-22 18:22:00] Average Time: 0.403
[INFO] [2019-12-22 18:22:00] Total Time: 7s
[INFO] [2019-12-22 18:22:00] last 3 / first 3: 0.8
[INFO] [2019-12-22 18:22:00] Std.Dev: 0.22803508501982758; Max: 0.98
[INFO] [2019-12-22 18:22:00] Storing 14443 MetaTraits
[INFO] [2019-12-22 18:22:00] Processing group of 14443 in 15 groups of 1000
[INFO] [2019-12-22 18:22:01] Average Time: 0.121
[INFO] [2019-12-22 18:22:01] Total Time: 2s
[INFO] [2019-12-22 18:22:01] last 3 / first 3: 0.77
[INFO] [2019-12-22 18:22:01] Std.Dev: 0.03162277660168379; Max: 0.15
[STOP] [2019-12-22 18:22:01] parse_diff_and_store
[START] [2019-12-22 18:22:01] resolve_keys
[INFO] [2019-12-22 18:23:25] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 18:23:29] traits to occurrences...
[INFO] [2019-12-22 18:23:34] traits to nodes (through occurrences)...
[INFO] [2019-12-22 18:23:35] Traits to sex term...
[INFO] [2019-12-22 18:23:40] Traits to lifestage term...
[INFO] [2019-12-22 18:23:45] MetaTraits to traits...
[INFO] [2019-12-22 18:23:46] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 18:23:48] Assocs to occurrences...
[INFO] [2019-12-22 18:23:48] Assocs to nodes...
[INFO] [2019-12-22 18:23:48] Assoc to sex term...
[INFO] [2019-12-22 18:23:48] Assoc to lifestage term...
[STOP] [2019-12-22 18:23:48] resolve_keys
[START] [2019-12-22 18:23:48] hold_for_later_1
[STOP] [2019-12-22 18:23:48] hold_for_later_1
[START] [2019-12-22 18:23:48] hold_for_later_2
[STOP] [2019-12-22 18:23:48] hold_for_later_2
[START] [2019-12-22 18:23:48] resolve_missing_parents
[STOP] [2019-12-22 18:24:16] resolve_missing_parents
[START] [2019-12-22 18:24:16] rebuild_nodes
[START] [2019-12-22 18:24:16] Flattener#flatten
[START] [2019-12-22 18:24:16] Flattener#study_resource
[START] [2019-12-22 18:24:16] Flattener#build_ancestry
[STOP] [2019-12-22 18:24:17] Flattener#build_ancestry
[INFO] [2019-12-22 18:24:17] 12816 ancestry keys
[START] [2019-12-22 18:24:17] build_node_ancestors
[INFO] [2019-12-22 18:24:17] old ancestors deleted.
[STOP] [2019-12-22 18:24:23] build_node_ancestors
[START] [2019-12-22 18:24:28] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 18:24:29] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 18:24:29] Flattener#flatten
[STOP] [2019-12-22 18:24:29] rebuild_nodes
[START] [2019-12-22 18:24:29] resolve_missing_media_owners
[STOP] [2019-12-22 18:24:29] resolve_missing_media_owners
[START] [2019-12-22 18:24:29] sanitize_media_verbatims
[STOP] [2019-12-22 18:24:29] sanitize_media_verbatims
[START] [2019-12-22 18:24:29] queue_downloads
[STOP] [2019-12-22 18:24:29] queue_downloads
[START] [2019-12-22 18:24:29] parse_names
[WARN] [2019-12-22 18:24:30] I see 12816 names which still need to be parsed.
[STOP] [2019-12-22 18:24:41] parse_names
[START] [2019-12-22 18:24:41] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 18:24:41] denormalize_canonical_names_to_nodes
[START] [2019-12-22 18:24:41] match_nodes
[START] [2019-12-22 18:24:41] map_all_nodes_to_pages
[STOP] [2019-12-22 19:19:50] map_all_nodes_to_pages
[INFO] [2019-12-22 19:19:50] 906 Unmatched nodes (of 12816)! That's too many to output. First 10: Granuloreticulosea (#61680416); Globigerinoides sacculifer (#61680418); Globigerinoides conglobata (#61680447); Globigerinoides triloba (#61680566); Globigerinoides trilobus (#61680567); Globigerinoides obliqua (#61680597); Globigerinoides quadrilobata (#61680723); Globigerinoides quadrilobatus (#61680938); Globigerinita boweni (#61682206); Globigerinita bradyi (#61685858)
[START] [2019-12-22 19:19:50] update_nodes
[STOP] [2019-12-22 19:19:55] update_nodes
[STOP] [2019-12-22 19:19:55] match_nodes
[START] [2019-12-22 19:19:55] reindex_search
[STOP] [2019-12-22 19:20:33] reindex_search
[START] [2019-12-22 19:20:33] normalize_units
[STOP] [2019-12-22 19:20:33] normalize_units
[START] [2019-12-22 19:20:33] calculate_statistics
[STOP] [2019-12-22 19:20:33] calculate_statistics
[START] [2019-12-22 19:20:33] complete_harvest_instance
[START] [2019-12-22 19:20:33] overall_tsv_creation
[INFO] [2019-12-22 19:20:33] Processing group of 12816 in 2 batches of 10000
[INFO] [2019-12-22 19:22:12] 5508 Traits (unfiltered)...
[INFO] [2019-12-22 19:22:26] 5508 Traits (filtered)...
[INFO] [2019-12-22 19:22:26] 0 Associations (filtered)...
[INFO] [2019-12-22 19:23:18] 27537 metadata added.
[INFO] [2019-12-22 19:23:18] 0 metadata added.
[INFO] [2019-12-22 19:24:19] 1717 Traits (unfiltered)...
[INFO] [2019-12-22 19:24:33] 1717 Traits (filtered)...
[INFO] [2019-12-22 19:24:33] 0 Associations (filtered)...
[INFO] [2019-12-22 19:25:18] 8581 metadata added.
[INFO] [2019-12-22 19:25:18] 0 metadata added.
[INFO] [2019-12-22 19:25:19] Average Time: 115.13
[INFO] [2019-12-22 19:25:19] Total Time: 4m46s
[STOP] [2019-12-22 19:25:19] overall_tsv_creation
[INFO] [2019-12-22 19:25:19] Done. Check your files:
[INFO] [2019-12-22 19:25:19] (12816 lines) /app/public/data/arabian_sea_sp_l/publish_nodes.tsv
[INFO] [2019-12-22 19:25:20] (66592 lines) /app/public/data/arabian_sea_sp_l/publish_node_ancestors.tsv
[INFO] [2019-12-22 19:25:21] (12816 lines) /app/public/data/arabian_sea_sp_l/publish_scientific_names.tsv
[INFO] [2019-12-22 19:25:21] (7226 lines) /app/public/data/arabian_sea_sp_l/publish_traits.tsv
[INFO] [2019-12-22 19:25:22] (36119 lines) /app/public/data/arabian_sea_sp_l/publish_metadata.tsv
[STOP] [2019-12-22 19:25:22] complete_harvest_instance
[START] [2019-12-22 19:25:22] completed
[STOP] [2019-12-22 19:25:22] completed
[STOP] [2019-12-22 19:25:22] logged process, took 3915.58

Latest Process