Harvest for Malaysia Species List Created 14 Oct 04:11

Stage: completed
Fetched: 14 Oct 04:11
Validated: 14 Oct 04:11
Deltas Created 14 Oct 04:11
Units Normalized: 14 Oct 04:35
Ancestry Built: 14 Oct 04:16
Nodes Matched: 14 Oct 04:34
Names Parsed: 14 Oct 04:16
New Models Stored: 14 Oct 04:13
Indexed: 14 Oct 04:35
Completed: 14 Oct 04:42
Time to Harvest: 1 minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-14 04:11:29 -0400 by logger.rb/56815
[START] [2019-10-14 04:11:29] logged process
[START] [2019-10-14 04:11:29] create_harvest_instance
[STOP] [2019-10-14 04:11:30] create_harvest_instance
[START] [2019-10-14 04:11:30] fetch_files
[STOP] [2019-10-14 04:11:30] fetch_files
[START] [2019-10-14 04:11:30] validate_each_file
[STOP] [2019-10-14 04:11:33] validate_each_file
[START] [2019-10-14 04:11:33] convert_to_csv
[CMD] [2019-10-14 04:11:33] /usr/bin/sort /app/public/converted_csv/malaysia_sp_list_refs_16499.csv > /app/public/converted_csv/malaysia_sp_list_refs_16499.csv_sorted
[CMD] [2019-10-14 04:11:33] /usr/bin/sort /app/public/converted_csv/malaysia_sp_list_nodes_16500.csv > /app/public/converted_csv/malaysia_sp_list_nodes_16500.csv_sorted
[CMD] [2019-10-14 04:11:33] /usr/bin/sort /app/public/converted_csv/malaysia_sp_list_occurrences_16501.csv > /app/public/converted_csv/malaysia_sp_list_occurrences_16501.csv_sorted
[CMD] [2019-10-14 04:11:34] /usr/bin/sort /app/public/converted_csv/malaysia_sp_list_measurements_16502.csv > /app/public/converted_csv/malaysia_sp_list_measurements_16502.csv_sorted
[STOP] [2019-10-14 04:11:34] convert_to_csv
[START] [2019-10-14 04:11:34] calculate_delta
[CMD] [2019-10-14 04:11:34] echo "0a" > /app/public/diff/malaysia_sp_list_refs_16499.diff
[CMD] [2019-10-14 04:11:34] tail -n +1 /app/public/converted_csv/malaysia_sp_list_refs_16499.csv >> /app/public/diff/malaysia_sp_list_refs_16499.diff
[CMD] [2019-10-14 04:11:34] echo "." >> /app/public/diff/malaysia_sp_list_refs_16499.diff
[CMD] [2019-10-14 04:11:34] echo "0a" > /app/public/diff/malaysia_sp_list_nodes_16500.diff
[CMD] [2019-10-14 04:11:34] tail -n +1 /app/public/converted_csv/malaysia_sp_list_nodes_16500.csv >> /app/public/diff/malaysia_sp_list_nodes_16500.diff
[CMD] [2019-10-14 04:11:34] echo "." >> /app/public/diff/malaysia_sp_list_nodes_16500.diff
[CMD] [2019-10-14 04:11:34] echo "0a" > /app/public/diff/malaysia_sp_list_occurrences_16501.diff
[CMD] [2019-10-14 04:11:34] tail -n +1 /app/public/converted_csv/malaysia_sp_list_occurrences_16501.csv >> /app/public/diff/malaysia_sp_list_occurrences_16501.diff
[CMD] [2019-10-14 04:11:34] echo "." >> /app/public/diff/malaysia_sp_list_occurrences_16501.diff
[CMD] [2019-10-14 04:11:35] echo "0a" > /app/public/diff/malaysia_sp_list_measurements_16502.diff
[CMD] [2019-10-14 04:11:35] tail -n +1 /app/public/converted_csv/malaysia_sp_list_measurements_16502.csv >> /app/public/diff/malaysia_sp_list_measurements_16502.diff
[CMD] [2019-10-14 04:11:35] echo "." >> /app/public/diff/malaysia_sp_list_measurements_16502.diff
[STOP] [2019-10-14 04:11:35] calculate_delta
[START] [2019-10-14 04:11:35] parse_diff_and_store
[INFO] [2019-10-14 04:11:35] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 04:11:35] Loading nodes diff file into memory (true lines)...
[WARN] [2019-10-14 04:11:40] Filtered Scientific Name `Dyakia  regalis` to `Dyakia regalis`
[INFO] [2019-10-14 04:11:44] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 04:11:47] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 04:13:19] Storing 2 References
[INFO] [2019-10-14 04:13:19] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 04:13:19] Average Time: 0.0
[INFO] [2019-10-14 04:13:19] Total Time: 1s
[INFO] [2019-10-14 04:13:19] Storing 22050 ScientificNames
[INFO] [2019-10-14 04:13:19] Processing group of 22050 in 23 groups of 1000
[INFO] [2019-10-14 04:13:27] Average Time: 0.35
[INFO] [2019-10-14 04:13:27] Total Time: 9s
[INFO] [2019-10-14 04:13:27] last 3 / first 3: 0.62
[INFO] [2019-10-14 04:13:27] Std.Dev: 0.07745966692414834; Max: 0.47
[INFO] [2019-10-14 04:13:27] Storing 22050 Nodes
[INFO] [2019-10-14 04:13:27] Processing group of 22050 in 23 groups of 1000
[INFO] [2019-10-14 04:13:35] Average Time: 0.333
[INFO] [2019-10-14 04:13:35] Total Time: 8s
[INFO] [2019-10-14 04:13:35] last 3 / first 3: 0.76
[INFO] [2019-10-14 04:13:35] Std.Dev: 0.12649110640673517; Max: 0.65
[INFO] [2019-10-14 04:13:35] Storing 15424 Occurrences
[INFO] [2019-10-14 04:13:35] Processing group of 15424 in 16 groups of 1000
[INFO] [2019-10-14 04:13:37] Average Time: 0.099
[INFO] [2019-10-14 04:13:37] Total Time: 2s
[INFO] [2019-10-14 04:13:37] last 3 / first 3: 0.81
[INFO] [2019-10-14 04:13:37] Std.Dev: 0.0; Max: 0.12
[INFO] [2019-10-14 04:13:37] Storing 31700 TraitsReferences
[INFO] [2019-10-14 04:13:37] Processing group of 31700 in 32 groups of 1000
[INFO] [2019-10-14 04:13:39] Average Time: 0.073
[INFO] [2019-10-14 04:13:39] Total Time: 3s
[INFO] [2019-10-14 04:13:39] last 3 / first 3: 0.62
[INFO] [2019-10-14 04:13:39] Std.Dev: 0.0; Max: 0.15
[INFO] [2019-10-14 04:13:39] Storing 31699 Traits
[INFO] [2019-10-14 04:13:39] Processing group of 31699 in 32 groups of 1000
[INFO] [2019-10-14 04:13:49] Average Time: 0.295
[INFO] [2019-10-14 04:13:49] Total Time: 10s
[INFO] [2019-10-14 04:13:49] last 3 / first 3: 0.8
[INFO] [2019-10-14 04:13:49] Std.Dev: 0.03162277660168379; Max: 0.4
[INFO] [2019-10-14 04:13:49] Storing 31654 MetaTraits
[INFO] [2019-10-14 04:13:49] Processing group of 31654 in 32 groups of 1000
[INFO] [2019-10-14 04:13:53] Average Time: 0.112
[INFO] [2019-10-14 04:13:53] Total Time: 4s
[INFO] [2019-10-14 04:13:53] last 3 / first 3: 0.77
[INFO] [2019-10-14 04:13:53] Std.Dev: 0.0; Max: 0.18
[STOP] [2019-10-14 04:13:53] parse_diff_and_store
[START] [2019-10-14 04:13:53] resolve_keys
[INFO] [2019-10-14 04:15:04] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 04:15:10] traits to occurrences...
[INFO] [2019-10-14 04:15:15] traits to nodes (through occurrences)...
[INFO] [2019-10-14 04:15:15] Traits to sex term...
[INFO] [2019-10-14 04:15:19] Traits to lifestage term...
[INFO] [2019-10-14 04:15:25] MetaTraits to traits...
[INFO] [2019-10-14 04:15:27] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 04:15:31] Assocs to occurrences...
[INFO] [2019-10-14 04:15:31] Assocs to nodes...
[INFO] [2019-10-14 04:15:31] Assoc to sex term...
[INFO] [2019-10-14 04:15:31] Assoc to lifestage term...
[STOP] [2019-10-14 04:15:31] resolve_keys
[START] [2019-10-14 04:15:31] hold_for_later_1
[STOP] [2019-10-14 04:15:31] hold_for_later_1
[START] [2019-10-14 04:15:31] hold_for_later_2
[STOP] [2019-10-14 04:15:31] hold_for_later_2
[START] [2019-10-14 04:15:31] resolve_missing_parents
[STOP] [2019-10-14 04:16:18] resolve_missing_parents
[START] [2019-10-14 04:16:18] rebuild_nodes
[START] [2019-10-14 04:16:18] Flattener#flatten
[START] [2019-10-14 04:16:18] Flattener#study_resource
[START] [2019-10-14 04:16:18] Flattener#build_ancestry
[STOP] [2019-10-14 04:16:21] Flattener#build_ancestry
[INFO] [2019-10-14 04:16:21] 22050 ancestry keys
[START] [2019-10-14 04:16:21] build_node_ancestors
[INFO] [2019-10-14 04:16:21] old ancestors deleted.
[STOP] [2019-10-14 04:16:25] build_node_ancestors
[START] [2019-10-14 04:16:29] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 04:16:31] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 04:16:31] Flattener#flatten
[STOP] [2019-10-14 04:16:31] rebuild_nodes
[START] [2019-10-14 04:16:31] resolve_missing_media_owners
[STOP] [2019-10-14 04:16:31] resolve_missing_media_owners
[START] [2019-10-14 04:16:31] sanitize_media_verbatims
[STOP] [2019-10-14 04:16:31] sanitize_media_verbatims
[START] [2019-10-14 04:16:31] queue_downloads
[STOP] [2019-10-14 04:16:31] queue_downloads
[START] [2019-10-14 04:16:31] parse_names
[WARN] [2019-10-14 04:16:31] I see 22050 names which still need to be parsed.
[WARN] [2019-10-14 04:16:50] I see 1 names which still need to be parsed.
[STOP] [2019-10-14 04:16:51] parse_names
[START] [2019-10-14 04:16:51] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 04:16:51] denormalize_canonical_names_to_nodes
[START] [2019-10-14 04:16:51] match_nodes
[START] [2019-10-14 04:16:51] map_all_nodes_to_pages
[STOP] [2019-10-14 04:34:42] map_all_nodes_to_pages
[INFO] [2019-10-14 04:34:42] 1555 Unmatched nodes (of 22050)! That's too many to output. First 10: Ficedula solitaris (#50630567); Muscicapa latirostris (#50622303); Brachypteryx leucophrys (#50624053); Myiomela leucurum (#50623472); Cinclidium leucurum (#50624664); Luscinia cyane (#50625823); Pycnonotus melanoleucus (#50624084); Hypsipetes mcclellandii (#50633756); Hypsipetes virescens (#50642814); Hirundo striolata (#50638186)
[START] [2019-10-14 04:34:42] update_nodes
[STOP] [2019-10-14 04:34:49] update_nodes
[STOP] [2019-10-14 04:34:49] match_nodes
[START] [2019-10-14 04:34:49] reindex_search
[STOP] [2019-10-14 04:35:43] reindex_search
[START] [2019-10-14 04:35:43] normalize_units
[STOP] [2019-10-14 04:35:44] normalize_units
[START] [2019-10-14 04:35:44] calculate_statistics
[STOP] [2019-10-14 04:35:44] calculate_statistics
[START] [2019-10-14 04:35:44] complete_harvest_instance
[START] [2019-10-14 04:35:44] overall_tsv_creation
[INFO] [2019-10-14 04:35:44] Processing group of 22050 in 3 batches of 10000
[INFO] [2019-10-14 04:37:12] 6569 Traits (unfiltered)...
[INFO] [2019-10-14 04:37:26] 6569 Traits (filtered)...
[INFO] [2019-10-14 04:37:26] 0 Associations (filtered)...
[INFO] [2019-10-14 04:38:17] 32836 metadata added.
[INFO] [2019-10-14 04:38:17] 0 metadata added.
[INFO] [2019-10-14 04:39:49] 7611 Traits (unfiltered)...
[INFO] [2019-10-14 04:40:04] 7611 Traits (filtered)...
[INFO] [2019-10-14 04:40:04] 0 Associations (filtered)...
[INFO] [2019-10-14 04:41:01] 38025 metadata added.
[INFO] [2019-10-14 04:41:01] 0 metadata added.
[INFO] [2019-10-14 04:41:55] 1244 Traits (unfiltered)...
[INFO] [2019-10-14 04:42:09] 1244 Traits (filtered)...
[INFO] [2019-10-14 04:42:09] 0 Associations (filtered)...
[INFO] [2019-10-14 04:42:49] 6215 metadata added.
[INFO] [2019-10-14 04:42:49] 0 metadata added.
[INFO] [2019-10-14 04:42:49] Average Time: 116.887
[INFO] [2019-10-14 04:42:49] Total Time: 7m5s
[STOP] [2019-10-14 04:42:49] overall_tsv_creation
[INFO] [2019-10-14 04:42:49] Done. Check your files:
[INFO] [2019-10-14 04:42:49] (22050 lines) /app/public/data/malaysia_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 04:42:49] (57448 lines) /app/public/data/malaysia_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 04:42:49] (22050 lines) /app/public/data/malaysia_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 04:42:49] (15425 lines) /app/public/data/malaysia_sp_list/publish_traits.tsv
[INFO] [2019-10-14 04:42:49] (77077 lines) /app/public/data/malaysia_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 04:42:49] complete_harvest_instance
[START] [2019-10-14 04:42:49] completed
[STOP] [2019-10-14 04:42:49] completed
[STOP] [2019-10-14 04:42:49] logged process, took 1880.18

Latest Process