Harvest for The Netherlands Species List Created 16 Oct 16:09

Stage: completed
Fetched: 16 Oct 16:09
Validated: 16 Oct 16:09
Deltas Created 16 Oct 16:09
Units Normalized: 16 Oct 17:08
Ancestry Built: 16 Oct 16:16
Nodes Matched: 16 Oct 17:06
Names Parsed: 16 Oct 16:16
New Models Stored: 16 Oct 16:12
Indexed: 16 Oct 17:08
Completed: 16 Oct 17:18
Time to Harvest: 1 minute

Harvesting Log

(166 lines)
# Logfile created on 2019-10-16 16:09:24 -0400 by logger.rb/56815
[START] [2019-10-16 16:09:24] logged process
[START] [2019-10-16 16:09:24] create_harvest_instance
[STOP] [2019-10-16 16:09:24] create_harvest_instance
[START] [2019-10-16 16:09:24] fetch_files
[STOP] [2019-10-16 16:09:24] fetch_files
[START] [2019-10-16 16:09:24] validate_each_file
[STOP] [2019-10-16 16:09:28] validate_each_file
[START] [2019-10-16 16:09:28] convert_to_csv
[CMD] [2019-10-16 16:09:28] /usr/bin/sort /app/public/converted_csv/netherlands_sp_l_refs_17481.csv > /app/public/converted_csv/netherlands_sp_l_refs_17481.csv_sorted
[CMD] [2019-10-16 16:09:28] /usr/bin/sort /app/public/converted_csv/netherlands_sp_l_nodes_17482.csv > /app/public/converted_csv/netherlands_sp_l_nodes_17482.csv_sorted
[CMD] [2019-10-16 16:09:28] /usr/bin/sort /app/public/converted_csv/netherlands_sp_l_occurrences_17483.csv > /app/public/converted_csv/netherlands_sp_l_occurrences_17483.csv_sorted
[CMD] [2019-10-16 16:09:28] /usr/bin/sort /app/public/converted_csv/netherlands_sp_l_measurements_17484.csv > /app/public/converted_csv/netherlands_sp_l_measurements_17484.csv_sorted
[STOP] [2019-10-16 16:09:28] convert_to_csv
[START] [2019-10-16 16:09:28] calculate_delta
[CMD] [2019-10-16 16:09:28] echo "0a" > /app/public/diff/netherlands_sp_l_refs_17481.diff
[CMD] [2019-10-16 16:09:29] tail -n +1 /app/public/converted_csv/netherlands_sp_l_refs_17481.csv >> /app/public/diff/netherlands_sp_l_refs_17481.diff
[CMD] [2019-10-16 16:09:29] echo "." >> /app/public/diff/netherlands_sp_l_refs_17481.diff
[CMD] [2019-10-16 16:09:29] echo "0a" > /app/public/diff/netherlands_sp_l_nodes_17482.diff
[CMD] [2019-10-16 16:09:29] tail -n +1 /app/public/converted_csv/netherlands_sp_l_nodes_17482.csv >> /app/public/diff/netherlands_sp_l_nodes_17482.diff
[CMD] [2019-10-16 16:09:29] echo "." >> /app/public/diff/netherlands_sp_l_nodes_17482.diff
[CMD] [2019-10-16 16:09:29] echo "0a" > /app/public/diff/netherlands_sp_l_occurrences_17483.diff
[CMD] [2019-10-16 16:09:29] tail -n +1 /app/public/converted_csv/netherlands_sp_l_occurrences_17483.csv >> /app/public/diff/netherlands_sp_l_occurrences_17483.diff
[CMD] [2019-10-16 16:09:29] echo "." >> /app/public/diff/netherlands_sp_l_occurrences_17483.diff
[CMD] [2019-10-16 16:09:29] echo "0a" > /app/public/diff/netherlands_sp_l_measurements_17484.diff
[CMD] [2019-10-16 16:09:29] tail -n +1 /app/public/converted_csv/netherlands_sp_l_measurements_17484.csv >> /app/public/diff/netherlands_sp_l_measurements_17484.diff
[CMD] [2019-10-16 16:09:29] echo "." >> /app/public/diff/netherlands_sp_l_measurements_17484.diff
[STOP] [2019-10-16 16:09:29] calculate_delta
[START] [2019-10-16 16:09:29] parse_diff_and_store
[INFO] [2019-10-16 16:09:29] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 16:09:29] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 16:09:42] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 16:09:45] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 16:11:57] Storing 2 References
[INFO] [2019-10-16 16:11:57] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 16:11:57] Average Time: 0.0
[INFO] [2019-10-16 16:11:57] Total Time: 1s
[INFO] [2019-10-16 16:11:57] Storing 36184 ScientificNames
[INFO] [2019-10-16 16:11:57] Processing group of 36184 in 37 groups of 1000
[INFO] [2019-10-16 16:12:10] Average Time: 0.362
[INFO] [2019-10-16 16:12:10] Total Time: 14s
[INFO] [2019-10-16 16:12:10] last 3 / first 3: 0.61
[INFO] [2019-10-16 16:12:10] Std.Dev: 0.10954451150103323; Max: 0.72
[INFO] [2019-10-16 16:12:10] Storing 36184 Nodes
[INFO] [2019-10-16 16:12:10] Processing group of 36184 in 37 groups of 1000
[INFO] [2019-10-16 16:12:22] Average Time: 0.313
[INFO] [2019-10-16 16:12:22] Total Time: 12s
[INFO] [2019-10-16 16:12:22] last 3 / first 3: 0.83
[INFO] [2019-10-16 16:12:22] Std.Dev: 0.15165750888103102; Max: 1.13
[INFO] [2019-10-16 16:12:22] Storing 24100 Occurrences
[INFO] [2019-10-16 16:12:22] Processing group of 24100 in 25 groups of 1000
[INFO] [2019-10-16 16:12:24] Average Time: 0.097
[INFO] [2019-10-16 16:12:24] Total Time: 3s
[INFO] [2019-10-16 16:12:24] last 3 / first 3: 0.94
[INFO] [2019-10-16 16:12:24] Std.Dev: 0.03162277660168379; Max: 0.2
[INFO] [2019-10-16 16:12:24] Storing 48610 TraitsReferences
[INFO] [2019-10-16 16:12:24] Processing group of 48610 in 49 groups of 1000
[INFO] [2019-10-16 16:12:28] Average Time: 0.066
[INFO] [2019-10-16 16:12:28] Total Time: 4s
[INFO] [2019-10-16 16:12:28] last 3 / first 3: 0.69
[INFO] [2019-10-16 16:12:28] Std.Dev: 0.0; Max: 0.15
[INFO] [2019-10-16 16:12:28] Storing 48609 Traits
[INFO] [2019-10-16 16:12:28] Processing group of 48609 in 49 groups of 1000
[INFO] [2019-10-16 16:12:43] Average Time: 0.308
[INFO] [2019-10-16 16:12:43] Total Time: 16s
[INFO] [2019-10-16 16:12:43] last 3 / first 3: 0.92
[INFO] [2019-10-16 16:12:43] Std.Dev: 0.1; Max: 0.7
[INFO] [2019-10-16 16:12:43] Storing 48567 MetaTraits
[INFO] [2019-10-16 16:12:43] Processing group of 48567 in 49 groups of 1000
[INFO] [2019-10-16 16:12:48] Average Time: 0.104
[INFO] [2019-10-16 16:12:48] Total Time: 6s
[INFO] [2019-10-16 16:12:48] last 3 / first 3: 0.79
[INFO] [2019-10-16 16:12:48] Std.Dev: 0.0; Max: 0.2
[STOP] [2019-10-16 16:12:48] parse_diff_and_store
[START] [2019-10-16 16:12:48] resolve_keys
[INFO] [2019-10-16 16:14:20] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 16:14:28] traits to occurrences...
[INFO] [2019-10-16 16:14:39] traits to nodes (through occurrences)...
[INFO] [2019-10-16 16:14:40] Traits to sex term...
[INFO] [2019-10-16 16:14:49] Traits to lifestage term...
[INFO] [2019-10-16 16:14:58] MetaTraits to traits...
[INFO] [2019-10-16 16:15:01] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 16:15:08] Assocs to occurrences...
[INFO] [2019-10-16 16:15:08] Assocs to nodes...
[INFO] [2019-10-16 16:15:08] Assoc to sex term...
[INFO] [2019-10-16 16:15:08] Assoc to lifestage term...
[STOP] [2019-10-16 16:15:08] resolve_keys
[START] [2019-10-16 16:15:08] hold_for_later_1
[STOP] [2019-10-16 16:15:08] hold_for_later_1
[START] [2019-10-16 16:15:08] hold_for_later_2
[STOP] [2019-10-16 16:15:08] hold_for_later_2
[START] [2019-10-16 16:15:08] resolve_missing_parents
[STOP] [2019-10-16 16:16:00] resolve_missing_parents
[START] [2019-10-16 16:16:00] rebuild_nodes
[START] [2019-10-16 16:16:00] Flattener#flatten
[START] [2019-10-16 16:16:00] Flattener#study_resource
[START] [2019-10-16 16:16:00] Flattener#build_ancestry
[STOP] [2019-10-16 16:16:06] Flattener#build_ancestry
[INFO] [2019-10-16 16:16:06] 36184 ancestry keys
[START] [2019-10-16 16:16:06] build_node_ancestors
[INFO] [2019-10-16 16:16:06] old ancestors deleted.
[STOP] [2019-10-16 16:16:24] build_node_ancestors
[START] [2019-10-16 16:16:26] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 16:16:29] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 16:16:29] Flattener#flatten
[STOP] [2019-10-16 16:16:29] rebuild_nodes
[START] [2019-10-16 16:16:29] resolve_missing_media_owners
[STOP] [2019-10-16 16:16:29] resolve_missing_media_owners
[START] [2019-10-16 16:16:29] sanitize_media_verbatims
[STOP] [2019-10-16 16:16:29] sanitize_media_verbatims
[START] [2019-10-16 16:16:29] queue_downloads
[STOP] [2019-10-16 16:16:29] queue_downloads
[START] [2019-10-16 16:16:29] parse_names
[WARN] [2019-10-16 16:16:29] I see 36184 names which still need to be parsed.
[STOP] [2019-10-16 16:16:56] parse_names
[START] [2019-10-16 16:16:56] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 16:16:56] denormalize_canonical_names_to_nodes
[START] [2019-10-16 16:16:56] match_nodes
[START] [2019-10-16 16:16:56] map_all_nodes_to_pages
[STOP] [2019-10-16 17:06:16] map_all_nodes_to_pages
[INFO] [2019-10-16 17:06:16] 4650 Unmatched nodes (of 36184)! That's too many to output. First 10: Poa arenaria (#52438814); Poa caespitosa (#52469891); Festuca pratensis (#52437368); Festuca arenaria (#52449762); Elytrigia (#52437035); Elymus atherica (#52437513); Elymus juncea (#52439315); Elymus maritima (#52442404); Elymus littorea (#52448101); Elymus junceiforme (#52464032)
[START] [2019-10-16 17:06:16] update_nodes
[STOP] [2019-10-16 17:06:28] update_nodes
[STOP] [2019-10-16 17:06:28] match_nodes
[START] [2019-10-16 17:06:28] reindex_search
[STOP] [2019-10-16 17:08:44] reindex_search
[START] [2019-10-16 17:08:44] normalize_units
[STOP] [2019-10-16 17:08:44] normalize_units
[START] [2019-10-16 17:08:44] calculate_statistics
[STOP] [2019-10-16 17:08:44] calculate_statistics
[START] [2019-10-16 17:08:44] complete_harvest_instance
[START] [2019-10-16 17:08:44] overall_tsv_creation
[INFO] [2019-10-16 17:08:45] Processing group of 36184 in 4 batches of 10000
[INFO] [2019-10-16 17:10:09] 5849 Traits (unfiltered)...
[INFO] [2019-10-16 17:10:22] 5849 Traits (filtered)...
[INFO] [2019-10-16 17:10:23] 0 Associations (filtered)...
[INFO] [2019-10-16 17:11:11] 29240 metadata added.
[INFO] [2019-10-16 17:11:11] 0 metadata added.
[INFO] [2019-10-16 17:12:41] 6734 Traits (unfiltered)...
[INFO] [2019-10-16 17:12:54] 6734 Traits (filtered)...
[INFO] [2019-10-16 17:12:54] 0 Associations (filtered)...
[INFO] [2019-10-16 17:13:46] 33655 metadata added.
[INFO] [2019-10-16 17:13:46] 0 metadata added.
[INFO] [2019-10-16 17:15:17] 7172 Traits (unfiltered)...
[INFO] [2019-10-16 17:15:30] 7172 Traits (filtered)...
[INFO] [2019-10-16 17:15:30] 0 Associations (filtered)...
[INFO] [2019-10-16 17:16:24] 35848 metadata added.
[INFO] [2019-10-16 17:16:24] 0 metadata added.
[INFO] [2019-10-16 17:17:37] 4345 Traits (unfiltered)...
[INFO] [2019-10-16 17:17:50] 4345 Traits (filtered)...
[INFO] [2019-10-16 17:17:50] 0 Associations (filtered)...
[INFO] [2019-10-16 17:18:38] 21714 metadata added.
[INFO] [2019-10-16 17:18:38] 0 metadata added.
[INFO] [2019-10-16 17:18:38] Average Time: 122.785
[INFO] [2019-10-16 17:18:38] Total Time: 9m54s
[STOP] [2019-10-16 17:18:38] overall_tsv_creation
[INFO] [2019-10-16 17:18:38] Done. Check your files:
[INFO] [2019-10-16 17:18:38] (36184 lines) /app/public/data/netherlands_sp_l/publish_nodes.tsv
[INFO] [2019-10-16 17:18:38] (127145 lines) /app/public/data/netherlands_sp_l/publish_node_ancestors.tsv
[INFO] [2019-10-16 17:18:38] (36184 lines) /app/public/data/netherlands_sp_l/publish_scientific_names.tsv
[INFO] [2019-10-16 17:18:38] (24101 lines) /app/public/data/netherlands_sp_l/publish_traits.tsv
[INFO] [2019-10-16 17:18:39] (120458 lines) /app/public/data/netherlands_sp_l/publish_metadata.tsv
[STOP] [2019-10-16 17:18:39] complete_harvest_instance
[START] [2019-10-16 17:18:39] completed
[STOP] [2019-10-16 17:18:39] completed
[STOP] [2019-10-16 17:18:39] logged process, took 4155.31

Latest Process