Harvest for Italy Species List Created 13 Oct 19:42

Stage: completed
Fetched: 13 Oct 19:42
Validated: 13 Oct 19:42
Deltas Created 13 Oct 19:42
Units Normalized: 13 Oct 20:45
Ancestry Built: 13 Oct 19:50
Nodes Matched: 13 Oct 20:43
Names Parsed: 13 Oct 19:51
New Models Stored: 13 Oct 19:46
Indexed: 13 Oct 20:45
Completed: 13 Oct 20:57
Time to Harvest: 1 minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-13 19:42:05 -0400 by logger.rb/56815
[START] [2019-10-13 19:42:05] logged process
[START] [2019-10-13 19:42:05] create_harvest_instance
[STOP] [2019-10-13 19:42:06] create_harvest_instance
[START] [2019-10-13 19:42:06] fetch_files
[STOP] [2019-10-13 19:42:06] fetch_files
[START] [2019-10-13 19:42:06] validate_each_file
[STOP] [2019-10-13 19:42:11] validate_each_file
[START] [2019-10-13 19:42:11] convert_to_csv
[CMD] [2019-10-13 19:42:11] /usr/bin/sort /app/public/converted_csv/italy_sp_list_refs_16227.csv > /app/public/converted_csv/italy_sp_list_refs_16227.csv_sorted
[CMD] [2019-10-13 19:42:11] /usr/bin/sort /app/public/converted_csv/italy_sp_list_nodes_16228.csv > /app/public/converted_csv/italy_sp_list_nodes_16228.csv_sorted
[CMD] [2019-10-13 19:42:11] /usr/bin/sort /app/public/converted_csv/italy_sp_list_occurrences_16229.csv > /app/public/converted_csv/italy_sp_list_occurrences_16229.csv_sorted
[CMD] [2019-10-13 19:42:11] /usr/bin/sort /app/public/converted_csv/italy_sp_list_measurements_16230.csv > /app/public/converted_csv/italy_sp_list_measurements_16230.csv_sorted
[STOP] [2019-10-13 19:42:11] convert_to_csv
[START] [2019-10-13 19:42:11] calculate_delta
[CMD] [2019-10-13 19:42:11] echo "0a" > /app/public/diff/italy_sp_list_refs_16227.diff
[CMD] [2019-10-13 19:42:11] tail -n +1 /app/public/converted_csv/italy_sp_list_refs_16227.csv >> /app/public/diff/italy_sp_list_refs_16227.diff
[CMD] [2019-10-13 19:42:11] echo "." >> /app/public/diff/italy_sp_list_refs_16227.diff
[CMD] [2019-10-13 19:42:11] echo "0a" > /app/public/diff/italy_sp_list_nodes_16228.diff
[CMD] [2019-10-13 19:42:11] tail -n +1 /app/public/converted_csv/italy_sp_list_nodes_16228.csv >> /app/public/diff/italy_sp_list_nodes_16228.diff
[CMD] [2019-10-13 19:42:11] echo "." >> /app/public/diff/italy_sp_list_nodes_16228.diff
[CMD] [2019-10-13 19:42:12] echo "0a" > /app/public/diff/italy_sp_list_occurrences_16229.diff
[CMD] [2019-10-13 19:42:12] tail -n +1 /app/public/converted_csv/italy_sp_list_occurrences_16229.csv >> /app/public/diff/italy_sp_list_occurrences_16229.diff
[CMD] [2019-10-13 19:42:12] echo "." >> /app/public/diff/italy_sp_list_occurrences_16229.diff
[CMD] [2019-10-13 19:42:12] echo "0a" > /app/public/diff/italy_sp_list_measurements_16230.diff
[CMD] [2019-10-13 19:42:12] tail -n +1 /app/public/converted_csv/italy_sp_list_measurements_16230.csv >> /app/public/diff/italy_sp_list_measurements_16230.diff
[CMD] [2019-10-13 19:42:12] echo "." >> /app/public/diff/italy_sp_list_measurements_16230.diff
[STOP] [2019-10-13 19:42:12] calculate_delta
[START] [2019-10-13 19:42:12] parse_diff_and_store
[INFO] [2019-10-13 19:42:12] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 19:42:12] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 19:42:29] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 19:42:33] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 19:45:21] Storing 2 References
[INFO] [2019-10-13 19:45:21] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 19:45:21] Average Time: 0.0
[INFO] [2019-10-13 19:45:21] Total Time: 1s
[INFO] [2019-10-13 19:45:21] Storing 41662 ScientificNames
[INFO] [2019-10-13 19:45:21] Processing group of 41662 in 42 groups of 1000
[INFO] [2019-10-13 19:45:39] Average Time: 0.433
[INFO] [2019-10-13 19:45:39] Total Time: 19s
[INFO] [2019-10-13 19:45:39] last 3 / first 3: 0.83
[INFO] [2019-10-13 19:45:39] Std.Dev: 0.1673320053068151; Max: 0.94
[INFO] [2019-10-13 19:45:39] Storing 41662 Nodes
[INFO] [2019-10-13 19:45:39] Processing group of 41662 in 42 groups of 1000
[INFO] [2019-10-13 19:45:53] Average Time: 0.316
[INFO] [2019-10-13 19:45:53] Total Time: 14s
[INFO] [2019-10-13 19:45:53] last 3 / first 3: 1.55
[INFO] [2019-10-13 19:45:53] Std.Dev: 0.06324555320336758; Max: 0.61
[INFO] [2019-10-13 19:45:53] Storing 28438 Occurrences
[INFO] [2019-10-13 19:45:53] Processing group of 28438 in 29 groups of 1000
[INFO] [2019-10-13 19:45:57] Average Time: 0.143
[INFO] [2019-10-13 19:45:57] Total Time: 5s
[INFO] [2019-10-13 19:45:57] last 3 / first 3: 0.59
[INFO] [2019-10-13 19:45:57] Std.Dev: 0.17888543819998318; Max: 1.07
[INFO] [2019-10-13 19:45:57] Storing 56980 TraitsReferences
[INFO] [2019-10-13 19:45:57] Processing group of 56980 in 57 groups of 1000
[INFO] [2019-10-13 19:46:01] Average Time: 0.069
[INFO] [2019-10-13 19:46:01] Total Time: 5s
[INFO] [2019-10-13 19:46:01] last 3 / first 3: 0.8
[INFO] [2019-10-13 19:46:01] Std.Dev: 0.0; Max: 0.16
[INFO] [2019-10-13 19:46:01] Storing 56979 Traits
[INFO] [2019-10-13 19:46:01] Processing group of 56979 in 57 groups of 1000
[INFO] [2019-10-13 19:46:20] Average Time: 0.333
[INFO] [2019-10-13 19:46:20] Total Time: 20s
[INFO] [2019-10-13 19:46:20] last 3 / first 3: 0.89
[INFO] [2019-10-13 19:46:20] Std.Dev: 0.1341640786499874; Max: 1.16
[INFO] [2019-10-13 19:46:20] Storing 56929 MetaTraits
[INFO] [2019-10-13 19:46:20] Processing group of 56929 in 57 groups of 1000
[INFO] [2019-10-13 19:46:27] Average Time: 0.11
[INFO] [2019-10-13 19:46:27] Total Time: 7s
[INFO] [2019-10-13 19:46:27] last 3 / first 3: 0.83
[INFO] [2019-10-13 19:46:27] Std.Dev: 0.03162277660168379; Max: 0.2
[STOP] [2019-10-13 19:46:27] parse_diff_and_store
[START] [2019-10-13 19:46:27] resolve_keys
[INFO] [2019-10-13 19:48:10] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 19:48:19] traits to occurrences...
[INFO] [2019-10-13 19:48:25] traits to nodes (through occurrences)...
[INFO] [2019-10-13 19:48:26] Traits to sex term...
[INFO] [2019-10-13 19:48:33] Traits to lifestage term...
[INFO] [2019-10-13 19:48:41] MetaTraits to traits...
[INFO] [2019-10-13 19:48:46] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 19:48:54] Assocs to occurrences...
[INFO] [2019-10-13 19:48:54] Assocs to nodes...
[INFO] [2019-10-13 19:48:54] Assoc to sex term...
[INFO] [2019-10-13 19:48:54] Assoc to lifestage term...
[STOP] [2019-10-13 19:48:54] resolve_keys
[START] [2019-10-13 19:48:54] hold_for_later_1
[STOP] [2019-10-13 19:48:54] hold_for_later_1
[START] [2019-10-13 19:48:54] hold_for_later_2
[STOP] [2019-10-13 19:48:54] hold_for_later_2
[START] [2019-10-13 19:48:54] resolve_missing_parents
[STOP] [2019-10-13 19:50:00] resolve_missing_parents
[START] [2019-10-13 19:50:00] rebuild_nodes
[START] [2019-10-13 19:50:00] Flattener#flatten
[START] [2019-10-13 19:50:00] Flattener#study_resource
[START] [2019-10-13 19:50:00] Flattener#build_ancestry
[STOP] [2019-10-13 19:50:06] Flattener#build_ancestry
[INFO] [2019-10-13 19:50:06] 41662 ancestry keys
[START] [2019-10-13 19:50:06] build_node_ancestors
[INFO] [2019-10-13 19:50:06] old ancestors deleted.
[STOP] [2019-10-13 19:50:25] build_node_ancestors
[START] [2019-10-13 19:50:29] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 19:50:33] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 19:50:33] Flattener#flatten
[STOP] [2019-10-13 19:50:33] rebuild_nodes
[START] [2019-10-13 19:50:33] resolve_missing_media_owners
[STOP] [2019-10-13 19:50:33] resolve_missing_media_owners
[START] [2019-10-13 19:50:33] sanitize_media_verbatims
[STOP] [2019-10-13 19:50:33] sanitize_media_verbatims
[START] [2019-10-13 19:50:33] queue_downloads
[STOP] [2019-10-13 19:50:33] queue_downloads
[START] [2019-10-13 19:50:33] parse_names
[WARN] [2019-10-13 19:50:33] I see 41662 names which still need to be parsed.
[STOP] [2019-10-13 19:51:05] parse_names
[START] [2019-10-13 19:51:05] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 19:51:05] denormalize_canonical_names_to_nodes
[START] [2019-10-13 19:51:05] match_nodes
[START] [2019-10-13 19:51:05] map_all_nodes_to_pages
[STOP] [2019-10-13 20:42:54] map_all_nodes_to_pages
[INFO] [2019-10-13 20:42:54] 5664 Unmatched nodes (of 41662)! That's too many to output. First 10: Squalius lapacinus (#50388155); Leucos erythrophthalmus (#50351724); Romanogobio gobio (#50374620); Knipowitschia punctatissimus (#50372545); Awaous niger (#50392646); Microlipophrys canevai (#50369911); Spondyliosoma lineatus (#50379555); Spicara vulgaris (#50388014); Lichia vadigo (#50392527); Trachinotus glauca (#50376147)
[START] [2019-10-13 20:42:54] update_nodes
[STOP] [2019-10-13 20:43:09] update_nodes
[STOP] [2019-10-13 20:43:09] match_nodes
[START] [2019-10-13 20:43:09] reindex_search
[STOP] [2019-10-13 20:45:00] reindex_search
[START] [2019-10-13 20:45:00] normalize_units
[STOP] [2019-10-13 20:45:00] normalize_units
[START] [2019-10-13 20:45:00] calculate_statistics
[STOP] [2019-10-13 20:45:00] calculate_statistics
[START] [2019-10-13 20:45:00] complete_harvest_instance
[START] [2019-10-13 20:45:00] overall_tsv_creation
[INFO] [2019-10-13 20:45:00] Processing group of 41662 in 5 batches of 10000
[INFO] [2019-10-13 20:46:29] 5926 Traits (unfiltered)...
[INFO] [2019-10-13 20:46:43] 5926 Traits (filtered)...
[INFO] [2019-10-13 20:46:43] 0 Associations (filtered)...
[INFO] [2019-10-13 20:47:32] 29625 metadata added.
[INFO] [2019-10-13 20:47:32] 0 metadata added.
[INFO] [2019-10-13 20:49:07] 6816 Traits (unfiltered)...
[INFO] [2019-10-13 20:49:22] 6816 Traits (filtered)...
[INFO] [2019-10-13 20:49:22] 0 Associations (filtered)...
[INFO] [2019-10-13 20:50:18] 34071 metadata added.
[INFO] [2019-10-13 20:50:18] 0 metadata added.
[INFO] [2019-10-13 20:51:54] 7081 Traits (unfiltered)...
[INFO] [2019-10-13 20:52:08] 7081 Traits (filtered)...
[INFO] [2019-10-13 20:52:08] 0 Associations (filtered)...
[INFO] [2019-10-13 20:53:02] 35395 metadata added.
[INFO] [2019-10-13 20:53:02] 0 metadata added.
[INFO] [2019-10-13 20:54:38] 7381 Traits (unfiltered)...
[INFO] [2019-10-13 20:54:54] 7381 Traits (filtered)...
[INFO] [2019-10-13 20:54:54] 0 Associations (filtered)...
[INFO] [2019-10-13 20:55:49] 36886 metadata added.
[INFO] [2019-10-13 20:55:49] 0 metadata added.
[INFO] [2019-10-13 20:56:41] 1234 Traits (unfiltered)...
[INFO] [2019-10-13 20:56:54] 1234 Traits (filtered)...
[INFO] [2019-10-13 20:56:54] 0 Associations (filtered)...
[INFO] [2019-10-13 20:57:33] 6162 metadata added.
[INFO] [2019-10-13 20:57:33] 0 metadata added.
[INFO] [2019-10-13 20:57:33] Average Time: 124.872
[INFO] [2019-10-13 20:57:33] Total Time: 12m34s
[STOP] [2019-10-13 20:57:33] overall_tsv_creation
[INFO] [2019-10-13 20:57:33] Done. Check your files:
[INFO] [2019-10-13 20:57:34] (41662 lines) /app/public/data/italy_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 20:57:34] (157001 lines) /app/public/data/italy_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 20:57:34] (41662 lines) /app/public/data/italy_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 20:57:34] (28439 lines) /app/public/data/italy_sp_list/publish_traits.tsv
[INFO] [2019-10-13 20:57:34] (142140 lines) /app/public/data/italy_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 20:57:34] complete_harvest_instance
[START] [2019-10-13 20:57:34] completed
[STOP] [2019-10-13 20:57:34] completed
[STOP] [2019-10-13 20:57:34] logged process, took 4528.89

Latest Process