Harvest for New Caledonia Species List Created 14 Oct 11:51

Stage: completed
Fetched: 14 Oct 11:51
Validated: 14 Oct 11:51
Deltas Created 14 Oct 11:51
Units Normalized: 14 Oct 12:06
Ancestry Built: 14 Oct 11:53
Nodes Matched: 14 Oct 12:05
Names Parsed: 14 Oct 11:53
New Models Stored: 14 Oct 11:52
Indexed: 14 Oct 12:06
Completed: 14 Oct 12:10
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-14 11:51:00 -0400 by logger.rb/56815
[START] [2019-10-14 11:51:00] logged process
[START] [2019-10-14 11:51:00] create_harvest_instance
[STOP] [2019-10-14 11:51:01] create_harvest_instance
[START] [2019-10-14 11:51:01] fetch_files
[STOP] [2019-10-14 11:51:01] fetch_files
[START] [2019-10-14 11:51:01] validate_each_file
[STOP] [2019-10-14 11:51:02] validate_each_file
[START] [2019-10-14 11:51:02] convert_to_csv
[CMD] [2019-10-14 11:51:02] /usr/bin/sort /app/public/converted_csv/new_caledonia_sp_refs_16691.csv > /app/public/converted_csv/new_caledonia_sp_refs_16691.csv_sorted
[CMD] [2019-10-14 11:51:02] /usr/bin/sort /app/public/converted_csv/new_caledonia_sp_nodes_16692.csv > /app/public/converted_csv/new_caledonia_sp_nodes_16692.csv_sorted
[CMD] [2019-10-14 11:51:02] /usr/bin/sort /app/public/converted_csv/new_caledonia_sp_occurrences_16693.csv > /app/public/converted_csv/new_caledonia_sp_occurrences_16693.csv_sorted
[CMD] [2019-10-14 11:51:03] /usr/bin/sort /app/public/converted_csv/new_caledonia_sp_measurements_16694.csv > /app/public/converted_csv/new_caledonia_sp_measurements_16694.csv_sorted
[STOP] [2019-10-14 11:51:03] convert_to_csv
[START] [2019-10-14 11:51:03] calculate_delta
[CMD] [2019-10-14 11:51:03] echo "0a" > /app/public/diff/new_caledonia_sp_refs_16691.diff
[CMD] [2019-10-14 11:51:03] tail -n +1 /app/public/converted_csv/new_caledonia_sp_refs_16691.csv >> /app/public/diff/new_caledonia_sp_refs_16691.diff
[CMD] [2019-10-14 11:51:03] echo "." >> /app/public/diff/new_caledonia_sp_refs_16691.diff
[CMD] [2019-10-14 11:51:03] echo "0a" > /app/public/diff/new_caledonia_sp_nodes_16692.diff
[CMD] [2019-10-14 11:51:03] tail -n +1 /app/public/converted_csv/new_caledonia_sp_nodes_16692.csv >> /app/public/diff/new_caledonia_sp_nodes_16692.diff
[CMD] [2019-10-14 11:51:03] echo "." >> /app/public/diff/new_caledonia_sp_nodes_16692.diff
[CMD] [2019-10-14 11:51:03] echo "0a" > /app/public/diff/new_caledonia_sp_occurrences_16693.diff
[CMD] [2019-10-14 11:51:03] tail -n +1 /app/public/converted_csv/new_caledonia_sp_occurrences_16693.csv >> /app/public/diff/new_caledonia_sp_occurrences_16693.diff
[CMD] [2019-10-14 11:51:03] echo "." >> /app/public/diff/new_caledonia_sp_occurrences_16693.diff
[CMD] [2019-10-14 11:51:03] echo "0a" > /app/public/diff/new_caledonia_sp_measurements_16694.diff
[CMD] [2019-10-14 11:51:04] tail -n +1 /app/public/converted_csv/new_caledonia_sp_measurements_16694.csv >> /app/public/diff/new_caledonia_sp_measurements_16694.diff
[CMD] [2019-10-14 11:51:04] echo "." >> /app/public/diff/new_caledonia_sp_measurements_16694.diff
[STOP] [2019-10-14 11:51:04] calculate_delta
[START] [2019-10-14 11:51:04] parse_diff_and_store
[INFO] [2019-10-14 11:51:04] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 11:51:04] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 11:51:08] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 11:51:09] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 11:51:53] Storing 2 References
[INFO] [2019-10-14 11:51:53] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 11:51:53] Average Time: 0.0
[INFO] [2019-10-14 11:51:53] Total Time: 1s
[INFO] [2019-10-14 11:51:53] Storing 11217 ScientificNames
[INFO] [2019-10-14 11:51:53] Processing group of 11217 in 12 groups of 1000
[INFO] [2019-10-14 11:51:58] Average Time: 0.342
[INFO] [2019-10-14 11:51:58] Total Time: 5s
[INFO] [2019-10-14 11:51:58] last 3 / first 3: 0.65
[INFO] [2019-10-14 11:51:58] Std.Dev: 0.09486832980505137; Max: 0.46
[INFO] [2019-10-14 11:51:58] Storing 11217 Nodes
[INFO] [2019-10-14 11:51:58] Processing group of 11217 in 12 groups of 1000
[INFO] [2019-10-14 11:52:01] Average Time: 0.278
[INFO] [2019-10-14 11:52:01] Total Time: 4s
[INFO] [2019-10-14 11:52:01] last 3 / first 3: 0.74
[INFO] [2019-10-14 11:52:01] Std.Dev: 0.07071067811865475; Max: 0.37
[INFO] [2019-10-14 11:52:01] Storing 7230 Occurrences
[INFO] [2019-10-14 11:52:01] Processing group of 7230 in 8 groups of 1000
[INFO] [2019-10-14 11:52:02] Average Time: 0.089
[INFO] [2019-10-14 11:52:02] Total Time: 1s
[INFO] [2019-10-14 11:52:02] last 3 / first 3: 0.73
[INFO] [2019-10-14 11:52:02] Std.Dev: 0.03162277660168379; Max: 0.12
[INFO] [2019-10-14 11:52:02] Storing 14920 TraitsReferences
[INFO] [2019-10-14 11:52:02] Processing group of 14920 in 15 groups of 1000
[INFO] [2019-10-14 11:52:03] Average Time: 0.078
[INFO] [2019-10-14 11:52:03] Total Time: 2s
[INFO] [2019-10-14 11:52:03] last 3 / first 3: 1.03
[INFO] [2019-10-14 11:52:03] Std.Dev: 0.03162277660168379; Max: 0.18
[INFO] [2019-10-14 11:52:03] Storing 14919 Traits
[INFO] [2019-10-14 11:52:03] Processing group of 14919 in 15 groups of 1000
[INFO] [2019-10-14 11:52:08] Average Time: 0.3
[INFO] [2019-10-14 11:52:08] Total Time: 5s
[INFO] [2019-10-14 11:52:08] last 3 / first 3: 0.81
[INFO] [2019-10-14 11:52:08] Std.Dev: 0.03162277660168379; Max: 0.42
[INFO] [2019-10-14 11:52:08] Storing 14900 MetaTraits
[INFO] [2019-10-14 11:52:08] Processing group of 14900 in 15 groups of 1000
[INFO] [2019-10-14 11:52:11] Average Time: 0.204
[INFO] [2019-10-14 11:52:11] Total Time: 4s
[INFO] [2019-10-14 11:52:11] last 3 / first 3: 0.29
[INFO] [2019-10-14 11:52:11] Std.Dev: 0.260768096208106; Max: 0.89
[STOP] [2019-10-14 11:52:11] parse_diff_and_store
[START] [2019-10-14 11:52:11] resolve_keys
[INFO] [2019-10-14 11:52:52] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 11:52:56] traits to occurrences...
[INFO] [2019-10-14 11:53:02] traits to nodes (through occurrences)...
[INFO] [2019-10-14 11:53:02] Traits to sex term...
[INFO] [2019-10-14 11:53:06] Traits to lifestage term...
[INFO] [2019-10-14 11:53:11] MetaTraits to traits...
[INFO] [2019-10-14 11:53:12] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 11:53:14] Assocs to occurrences...
[INFO] [2019-10-14 11:53:14] Assocs to nodes...
[INFO] [2019-10-14 11:53:14] Assoc to sex term...
[INFO] [2019-10-14 11:53:14] Assoc to lifestage term...
[STOP] [2019-10-14 11:53:14] resolve_keys
[START] [2019-10-14 11:53:14] hold_for_later_1
[STOP] [2019-10-14 11:53:14] hold_for_later_1
[START] [2019-10-14 11:53:14] hold_for_later_2
[STOP] [2019-10-14 11:53:14] hold_for_later_2
[START] [2019-10-14 11:53:14] resolve_missing_parents
[STOP] [2019-10-14 11:53:35] resolve_missing_parents
[START] [2019-10-14 11:53:35] rebuild_nodes
[START] [2019-10-14 11:53:35] Flattener#flatten
[START] [2019-10-14 11:53:35] Flattener#study_resource
[START] [2019-10-14 11:53:35] Flattener#build_ancestry
[STOP] [2019-10-14 11:53:35] Flattener#build_ancestry
[INFO] [2019-10-14 11:53:35] 11217 ancestry keys
[START] [2019-10-14 11:53:35] build_node_ancestors
[INFO] [2019-10-14 11:53:35] old ancestors deleted.
[STOP] [2019-10-14 11:53:38] build_node_ancestors
[START] [2019-10-14 11:53:42] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 11:53:43] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 11:53:43] Flattener#flatten
[STOP] [2019-10-14 11:53:43] rebuild_nodes
[START] [2019-10-14 11:53:43] resolve_missing_media_owners
[STOP] [2019-10-14 11:53:43] resolve_missing_media_owners
[START] [2019-10-14 11:53:43] sanitize_media_verbatims
[STOP] [2019-10-14 11:53:43] sanitize_media_verbatims
[START] [2019-10-14 11:53:43] queue_downloads
[STOP] [2019-10-14 11:53:43] queue_downloads
[START] [2019-10-14 11:53:43] parse_names
[WARN] [2019-10-14 11:53:43] I see 11217 names which still need to be parsed.
[STOP] [2019-10-14 11:53:52] parse_names
[START] [2019-10-14 11:53:52] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 11:53:52] denormalize_canonical_names_to_nodes
[START] [2019-10-14 11:53:52] match_nodes
[START] [2019-10-14 11:53:52] map_all_nodes_to_pages
[STOP] [2019-10-14 12:05:25] map_all_nodes_to_pages
[INFO] [2019-10-14 12:05:25] 831 Unmatched nodes (of 11217)! That's too many to output. First 10: Caledoniscincus austro-caledonica (#50879889); Caledoniscincus austrocaledonica (#50881780); Hydrophiidae (#50877531); Phylidonyris undulatus (#50872064); Artamus leucoryn (#50879534); Coracina analis (#50878461); Analisoma (#50872285); Analisoma analis (#50872284); Todiramphus sancta (#50876965); Streptopelia chinensis (#50871719)
[START] [2019-10-14 12:05:25] update_nodes
[STOP] [2019-10-14 12:05:29] update_nodes
[STOP] [2019-10-14 12:05:29] match_nodes
[START] [2019-10-14 12:05:29] reindex_search
[STOP] [2019-10-14 12:06:05] reindex_search
[START] [2019-10-14 12:06:05] normalize_units
[STOP] [2019-10-14 12:06:05] normalize_units
[START] [2019-10-14 12:06:05] calculate_statistics
[STOP] [2019-10-14 12:06:05] calculate_statistics
[START] [2019-10-14 12:06:05] complete_harvest_instance
[START] [2019-10-14 12:06:05] overall_tsv_creation
[INFO] [2019-10-14 12:06:05] Processing group of 11217 in 2 batches of 10000
[INFO] [2019-10-14 12:07:33] 6556 Traits (unfiltered)...
[INFO] [2019-10-14 12:07:46] 6556 Traits (filtered)...
[INFO] [2019-10-14 12:07:46] 0 Associations (filtered)...
[INFO] [2019-10-14 12:08:37] 32763 metadata added.
[INFO] [2019-10-14 12:08:37] 0 metadata added.
[INFO] [2019-10-14 12:09:27] 674 Traits (unfiltered)...
[INFO] [2019-10-14 12:09:40] 674 Traits (filtered)...
[INFO] [2019-10-14 12:09:40] 0 Associations (filtered)...
[INFO] [2019-10-14 12:10:18] 3369 metadata added.
[INFO] [2019-10-14 12:10:18] 0 metadata added.
[INFO] [2019-10-14 12:10:18] Average Time: 102.245
[INFO] [2019-10-14 12:10:18] Total Time: 4m13s
[STOP] [2019-10-14 12:10:18] overall_tsv_creation
[INFO] [2019-10-14 12:10:18] Done. Check your files:
[INFO] [2019-10-14 12:10:18] (11217 lines) /app/public/data/new_caledonia_sp/publish_nodes.tsv
[INFO] [2019-10-14 12:10:18] (39962 lines) /app/public/data/new_caledonia_sp/publish_node_ancestors.tsv
[INFO] [2019-10-14 12:10:18] (11217 lines) /app/public/data/new_caledonia_sp/publish_scientific_names.tsv
[INFO] [2019-10-14 12:10:19] (7231 lines) /app/public/data/new_caledonia_sp/publish_traits.tsv
[INFO] [2019-10-14 12:10:19] (36133 lines) /app/public/data/new_caledonia_sp/publish_metadata.tsv
[STOP] [2019-10-14 12:10:19] complete_harvest_instance
[START] [2019-10-14 12:10:19] completed
[STOP] [2019-10-14 12:10:19] completed
[STOP] [2019-10-14 12:10:19] logged process, took 1158.95
Latest Process

14 Oct 11:51 EXITED currently processing 0