Harvest for Papua New Guinea Species List Created 15 Oct 07:18

Harvesting Log

# Logfile created on 2019-10-15 07:18:37 -0400 by logger.rb/56815
[START] [2019-10-15 07:18:37] logged process
[START] [2019-10-15 07:18:37] create_harvest_instance
[STOP] [2019-10-15 07:18:37] create_harvest_instance
[START] [2019-10-15 07:18:37] fetch_files
[STOP] [2019-10-15 07:18:37] fetch_files
[START] [2019-10-15 07:18:37] validate_each_file
[STOP] [2019-10-15 07:18:42] validate_each_file
[START] [2019-10-15 07:18:42] convert_to_csv
[CMD] [2019-10-15 07:18:42] /usr/bin/sort /app/public/converted_csv/pngsl_refs_16877.csv > /app/public/converted_csv/pngsl_refs_16877.csv_sorted
[CMD] [2019-10-15 07:18:42] /usr/bin/sort /app/public/converted_csv/pngsl_nodes_16878.csv > /app/public/converted_csv/pngsl_nodes_16878.csv_sorted
[CMD] [2019-10-15 07:18:43] /usr/bin/sort /app/public/converted_csv/pngsl_occurrences_16879.csv > /app/public/converted_csv/pngsl_occurrences_16879.csv_sorted
[CMD] [2019-10-15 07:18:43] /usr/bin/sort /app/public/converted_csv/pngsl_measurements_16880.csv > /app/public/converted_csv/pngsl_measurements_16880.csv_sorted
[STOP] [2019-10-15 07:18:43] convert_to_csv
[START] [2019-10-15 07:18:43] calculate_delta
[CMD] [2019-10-15 07:18:43] echo "0a" > /app/public/diff/pngsl_refs_16877.diff
[CMD] [2019-10-15 07:18:44] tail -n +1 /app/public/converted_csv/pngsl_refs_16877.csv >> /app/public/diff/pngsl_refs_16877.diff
[CMD] [2019-10-15 07:18:44] echo "." >> /app/public/diff/pngsl_refs_16877.diff
[CMD] [2019-10-15 07:18:44] echo "0a" > /app/public/diff/pngsl_nodes_16878.diff
[CMD] [2019-10-15 07:18:45] tail -n +1 /app/public/converted_csv/pngsl_nodes_16878.csv >> /app/public/diff/pngsl_nodes_16878.diff
[CMD] [2019-10-15 07:18:45] echo "." >> /app/public/diff/pngsl_nodes_16878.diff
[CMD] [2019-10-15 07:18:45] echo "0a" > /app/public/diff/pngsl_occurrences_16879.diff
[CMD] [2019-10-15 07:18:45] tail -n +1 /app/public/converted_csv/pngsl_occurrences_16879.csv >> /app/public/diff/pngsl_occurrences_16879.diff
[CMD] [2019-10-15 07:18:46] echo "." >> /app/public/diff/pngsl_occurrences_16879.diff
[CMD] [2019-10-15 07:18:46] echo "0a" > /app/public/diff/pngsl_measurements_16880.diff
[CMD] [2019-10-15 07:18:46] tail -n +1 /app/public/converted_csv/pngsl_measurements_16880.csv >> /app/public/diff/pngsl_measurements_16880.diff
[CMD] [2019-10-15 07:18:47] echo "." >> /app/public/diff/pngsl_measurements_16880.diff
[STOP] [2019-10-15 07:18:47] calculate_delta
[START] [2019-10-15 07:18:47] parse_diff_and_store
[INFO] [2019-10-15 07:18:47] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 07:18:47] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 07:19:03] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 07:19:08] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 07:22:04] Storing 2 References
[INFO] [2019-10-15 07:22:04] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 07:22:04] Average Time: 0.0
[INFO] [2019-10-15 07:22:04] Total Time: 1s
[INFO] [2019-10-15 07:22:04] Storing 40349 ScientificNames
[INFO] [2019-10-15 07:22:04] Processing group of 40349 in 41 groups of 1000
[INFO] [2019-10-15 07:22:20] Average Time: 0.39
[INFO] [2019-10-15 07:22:20] Total Time: 17s
[INFO] [2019-10-15 07:22:20] last 3 / first 3: 0.84
[INFO] [2019-10-15 07:22:20] Std.Dev: 0.12649110640673517; Max: 0.94
[INFO] [2019-10-15 07:22:20] Storing 40349 Nodes
[INFO] [2019-10-15 07:22:20] Processing group of 40349 in 41 groups of 1000
[INFO] [2019-10-15 07:22:34] Average Time: 0.336
[INFO] [2019-10-15 07:22:34] Total Time: 14s
[INFO] [2019-10-15 07:22:34] last 3 / first 3: 0.85
[INFO] [2019-10-15 07:22:34] Std.Dev: 0.15491933384829668; Max: 1.19
[INFO] [2019-10-15 07:22:34] Storing 29884 Occurrences
[INFO] [2019-10-15 07:22:34] Processing group of 29884 in 30 groups of 1000
[INFO] [2019-10-15 07:22:38] Average Time: 0.106
[INFO] [2019-10-15 07:22:38] Total Time: 4s
[INFO] [2019-10-15 07:22:38] last 3 / first 3: 1.03
[INFO] [2019-10-15 07:22:38] Std.Dev: 0.0; Max: 0.2
[INFO] [2019-10-15 07:22:38] Storing 60370 TraitsReferences
[INFO] [2019-10-15 07:22:38] Processing group of 60370 in 61 groups of 1000
[INFO] [2019-10-15 07:22:42] Average Time: 0.072
[INFO] [2019-10-15 07:22:42] Total Time: 5s
[INFO] [2019-10-15 07:22:42] last 3 / first 3: 0.55
[INFO] [2019-10-15 07:22:42] Std.Dev: 0.0; Max: 0.17
[INFO] [2019-10-15 07:22:42] Storing 60369 Traits
[INFO] [2019-10-15 07:22:42] Processing group of 60369 in 61 groups of 1000
[INFO] [2019-10-15 07:23:03] Average Time: 0.329
[INFO] [2019-10-15 07:23:03] Total Time: 21s
[INFO] [2019-10-15 07:23:03] last 3 / first 3: 0.68
[INFO] [2019-10-15 07:23:03] Std.Dev: 0.1224744871391589; Max: 0.94
[INFO] [2019-10-15 07:23:03] Storing 60321 MetaTraits
[INFO] [2019-10-15 07:23:03] Processing group of 60321 in 61 groups of 1000
[INFO] [2019-10-15 07:23:12] Average Time: 0.147
[INFO] [2019-10-15 07:23:12] Total Time: 10s
[INFO] [2019-10-15 07:23:12] last 3 / first 3: 0.69
[INFO] [2019-10-15 07:23:12] Std.Dev: 0.18708286933869708; Max: 1.56
[STOP] [2019-10-15 07:23:12] parse_diff_and_store
[START] [2019-10-15 07:23:12] resolve_keys
[INFO] [2019-10-15 07:25:09] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 07:25:17] traits to occurrences...
[INFO] [2019-10-15 07:25:27] traits to nodes (through occurrences)...
[INFO] [2019-10-15 07:25:28] Traits to sex term...
[INFO] [2019-10-15 07:25:37] Traits to lifestage term...
[INFO] [2019-10-15 07:25:46] MetaTraits to traits...
[INFO] [2019-10-15 07:25:50] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 07:25:58] Assocs to occurrences...
[INFO] [2019-10-15 07:25:58] Assocs to nodes...
[INFO] [2019-10-15 07:25:58] Assoc to sex term...
[INFO] [2019-10-15 07:25:58] Assoc to lifestage term...
[STOP] [2019-10-15 07:25:58] resolve_keys
[START] [2019-10-15 07:25:58] hold_for_later_1
[STOP] [2019-10-15 07:25:58] hold_for_later_1
[START] [2019-10-15 07:25:58] hold_for_later_2
[STOP] [2019-10-15 07:25:58] hold_for_later_2
[START] [2019-10-15 07:25:58] resolve_missing_parents
[STOP] [2019-10-15 07:27:02] resolve_missing_parents
[START] [2019-10-15 07:27:02] rebuild_nodes
[START] [2019-10-15 07:27:02] Flattener#flatten
[START] [2019-10-15 07:27:02] Flattener#study_resource
[START] [2019-10-15 07:27:02] Flattener#build_ancestry
[STOP] [2019-10-15 07:27:08] Flattener#build_ancestry
[INFO] [2019-10-15 07:27:08] 40349 ancestry keys
[START] [2019-10-15 07:27:08] build_node_ancestors
[INFO] [2019-10-15 07:27:08] old ancestors deleted.
[STOP] [2019-10-15 07:27:24] build_node_ancestors
[START] [2019-10-15 07:27:24] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 07:27:27] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 07:27:27] Flattener#flatten
[STOP] [2019-10-15 07:27:27] rebuild_nodes
[START] [2019-10-15 07:27:27] resolve_missing_media_owners
[STOP] [2019-10-15 07:27:27] resolve_missing_media_owners
[START] [2019-10-15 07:27:27] sanitize_media_verbatims
[STOP] [2019-10-15 07:27:27] sanitize_media_verbatims
[START] [2019-10-15 07:27:27] queue_downloads
[STOP] [2019-10-15 07:27:27] queue_downloads
[START] [2019-10-15 07:27:27] parse_names
[WARN] [2019-10-15 07:27:27] I see 40349 names which still need to be parsed.
[STOP] [2019-10-15 07:27:58] parse_names
[START] [2019-10-15 07:27:58] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 07:27:59] denormalize_canonical_names_to_nodes
[START] [2019-10-15 07:27:59] match_nodes
[START] [2019-10-15 07:27:59] map_all_nodes_to_pages
[STOP] [2019-10-15 08:03:03] map_all_nodes_to_pages
[INFO] [2019-10-15 08:03:03] 3152 Unmatched nodes (of 40349)! That's too many to output. First 10: Xenorhina rostratus (#51459935); Xenorhina obesus (#51462045); Xenorhina subcroceus (#51484834); Litoria infrafrenata (#51455704); Litoria disruptus (#51456921); Litoria intercastellus (#51459527); Litoria glandulosa (#51460225); Litoria semipalmatus (#51461596); Litoria obsoletus (#51462225); Hyla bicolor (#51488719)
[START] [2019-10-15 08:03:03] update_nodes
[STOP] [2019-10-15 08:03:17] update_nodes
[STOP] [2019-10-15 08:03:17] match_nodes
[START] [2019-10-15 08:03:17] reindex_search
[STOP] [2019-10-15 08:04:54] reindex_search
[START] [2019-10-15 08:04:54] normalize_units
[STOP] [2019-10-15 08:04:54] normalize_units
[START] [2019-10-15 08:04:54] calculate_statistics
[STOP] [2019-10-15 08:04:54] calculate_statistics
[START] [2019-10-15 08:04:54] complete_harvest_instance
[START] [2019-10-15 08:04:54] overall_tsv_creation
[INFO] [2019-10-15 08:04:54] Processing group of 40349 in 5 batches of 10000
[INFO] [2019-10-15 08:06:21] 6524 Traits (unfiltered)...
[INFO] [2019-10-15 08:06:35] 6524 Traits (filtered)...
[INFO] [2019-10-15 08:06:35] 0 Associations (filtered)...
[INFO] [2019-10-15 08:07:29] 32615 metadata added.
[INFO] [2019-10-15 08:07:29] 0 metadata added.
[INFO] [2019-10-15 08:09:00] 7537 Traits (unfiltered)...
[INFO] [2019-10-15 08:09:14] 7537 Traits (filtered)...
[INFO] [2019-10-15 08:09:14] 0 Associations (filtered)...
[INFO] [2019-10-15 08:10:10] 37675 metadata added.
[INFO] [2019-10-15 08:10:10] 0 metadata added.
[INFO] [2019-10-15 08:11:45] 7760 Traits (unfiltered)...
[INFO] [2019-10-15 08:11:59] 7760 Traits (filtered)...
[INFO] [2019-10-15 08:11:59] 0 Associations (filtered)...
[INFO] [2019-10-15 08:12:56] 38792 metadata added.
[INFO] [2019-10-15 08:12:56] 0 metadata added.
[INFO] [2019-10-15 08:14:29] 8063 Traits (unfiltered)...
[INFO] [2019-10-15 08:14:43] 8063 Traits (filtered)...
[INFO] [2019-10-15 08:14:43] 0 Associations (filtered)...
[INFO] [2019-10-15 08:15:40] 40290 metadata added.
[INFO] [2019-10-15 08:15:40] 0 metadata added.
[INFO] [2019-10-15 08:16:15] Average Time: 110.98
[INFO] [2019-10-15 08:16:15] Total Time: 11m21s
[STOP] [2019-10-15 08:16:15] overall_tsv_creation
[INFO] [2019-10-15 08:16:15] Done. Check your files:
[INFO] [2019-10-15 08:16:15] (40349 lines) /app/public/data/pngsl/publish_nodes.tsv
[INFO] [2019-10-15 08:16:15] (106668 lines) /app/public/data/pngsl/publish_node_ancestors.tsv
[INFO] [2019-10-15 08:16:16] (40349 lines) /app/public/data/pngsl/publish_scientific_names.tsv
[INFO] [2019-10-15 08:16:16] (29885 lines) /app/public/data/pngsl/publish_traits.tsv
[INFO] [2019-10-15 08:16:16] (149373 lines) /app/public/data/pngsl/publish_metadata.tsv
[STOP] [2019-10-15 08:16:16] complete_harvest_instance
[START] [2019-10-15 08:16:16] completed
[STOP] [2019-10-15 08:16:16] completed
[STOP] [2019-10-15 08:16:16] logged process, took 3459.84

Latest Process

15 Oct 07:18 EXITED currently processing 0