Harvest for Israel Species List Created 13 Oct 19:27

Stage: completed
Fetched: 13 Oct 19:27
Validated: 13 Oct 19:27
Deltas Created 13 Oct 19:27
Units Normalized: 13 Oct 19:38
Ancestry Built: 13 Oct 19:29
Nodes Matched: 13 Oct 19:38
Names Parsed: 13 Oct 19:29
New Models Stored: 13 Oct 19:28
Indexed: 13 Oct 19:38
Completed: 13 Oct 19:41
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-10-13 19:27:39 -0400 by logger.rb/56815
[START] [2019-10-13 19:27:39] logged process
[START] [2019-10-13 19:27:39] create_harvest_instance
[STOP] [2019-10-13 19:27:39] create_harvest_instance
[START] [2019-10-13 19:27:39] fetch_files
[STOP] [2019-10-13 19:27:39] fetch_files
[START] [2019-10-13 19:27:39] validate_each_file
[STOP] [2019-10-13 19:27:40] validate_each_file
[START] [2019-10-13 19:27:40] convert_to_csv
[CMD] [2019-10-13 19:27:40] /usr/bin/sort /app/public/converted_csv/israel_sp_list_refs_16219.csv > /app/public/converted_csv/israel_sp_list_refs_16219.csv_sorted
[CMD] [2019-10-13 19:27:40] /usr/bin/sort /app/public/converted_csv/israel_sp_list_nodes_16220.csv > /app/public/converted_csv/israel_sp_list_nodes_16220.csv_sorted
[CMD] [2019-10-13 19:27:41] /usr/bin/sort /app/public/converted_csv/israel_sp_list_occurrences_16221.csv > /app/public/converted_csv/israel_sp_list_occurrences_16221.csv_sorted
[CMD] [2019-10-13 19:27:41] /usr/bin/sort /app/public/converted_csv/israel_sp_list_measurements_16222.csv > /app/public/converted_csv/israel_sp_list_measurements_16222.csv_sorted
[STOP] [2019-10-13 19:27:41] convert_to_csv
[START] [2019-10-13 19:27:41] calculate_delta
[CMD] [2019-10-13 19:27:41] echo "0a" > /app/public/diff/israel_sp_list_refs_16219.diff
[CMD] [2019-10-13 19:27:41] tail -n +1 /app/public/converted_csv/israel_sp_list_refs_16219.csv >> /app/public/diff/israel_sp_list_refs_16219.diff
[CMD] [2019-10-13 19:27:41] echo "." >> /app/public/diff/israel_sp_list_refs_16219.diff
[CMD] [2019-10-13 19:27:41] echo "0a" > /app/public/diff/israel_sp_list_nodes_16220.diff
[CMD] [2019-10-13 19:27:41] tail -n +1 /app/public/converted_csv/israel_sp_list_nodes_16220.csv >> /app/public/diff/israel_sp_list_nodes_16220.diff
[CMD] [2019-10-13 19:27:41] echo "." >> /app/public/diff/israel_sp_list_nodes_16220.diff
[CMD] [2019-10-13 19:27:41] echo "0a" > /app/public/diff/israel_sp_list_occurrences_16221.diff
[CMD] [2019-10-13 19:27:41] tail -n +1 /app/public/converted_csv/israel_sp_list_occurrences_16221.csv >> /app/public/diff/israel_sp_list_occurrences_16221.diff
[CMD] [2019-10-13 19:27:42] echo "." >> /app/public/diff/israel_sp_list_occurrences_16221.diff
[CMD] [2019-10-13 19:27:42] echo "0a" > /app/public/diff/israel_sp_list_measurements_16222.diff
[CMD] [2019-10-13 19:27:42] tail -n +1 /app/public/converted_csv/israel_sp_list_measurements_16222.csv >> /app/public/diff/israel_sp_list_measurements_16222.diff
[CMD] [2019-10-13 19:27:42] echo "." >> /app/public/diff/israel_sp_list_measurements_16222.diff
[STOP] [2019-10-13 19:27:42] calculate_delta
[START] [2019-10-13 19:27:42] parse_diff_and_store
[INFO] [2019-10-13 19:27:42] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 19:27:42] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 19:27:45] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 19:27:46] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 19:28:19] Storing 2 References
[INFO] [2019-10-13 19:28:19] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 19:28:19] Average Time: 0.0
[INFO] [2019-10-13 19:28:19] Total Time: 1s
[INFO] [2019-10-13 19:28:19] Storing 8682 ScientificNames
[INFO] [2019-10-13 19:28:19] Processing group of 8682 in 9 groups of 1000
[INFO] [2019-10-13 19:28:22] Average Time: 0.348
[INFO] [2019-10-13 19:28:22] Total Time: 4s
[INFO] [2019-10-13 19:28:22] last 3 / first 3: 0.92
[INFO] [2019-10-13 19:28:22] Std.Dev: 0.05477225575051661; Max: 0.45
[INFO] [2019-10-13 19:28:22] Storing 8682 Nodes
[INFO] [2019-10-13 19:28:22] Processing group of 8682 in 9 groups of 1000
[INFO] [2019-10-13 19:28:25] Average Time: 0.288
[INFO] [2019-10-13 19:28:25] Total Time: 3s
[INFO] [2019-10-13 19:28:25] last 3 / first 3: 0.93
[INFO] [2019-10-13 19:28:25] Std.Dev: 0.0; Max: 0.31
[INFO] [2019-10-13 19:28:25] Storing 5302 Occurrences
[INFO] [2019-10-13 19:28:25] Processing group of 5302 in 6 groups of 1000
[INFO] [2019-10-13 19:28:25] Average Time: 0.093
[INFO] [2019-10-13 19:28:25] Total Time: 1s
[INFO] [2019-10-13 19:28:25] Storing 10890 TraitsReferences
[INFO] [2019-10-13 19:28:25] Processing group of 10890 in 11 groups of 1000
[INFO] [2019-10-13 19:28:26] Average Time: 0.075
[INFO] [2019-10-13 19:28:26] Total Time: 1s
[INFO] [2019-10-13 19:28:26] last 3 / first 3: 0.71
[INFO] [2019-10-13 19:28:26] Std.Dev: 0.0; Max: 0.14
[INFO] [2019-10-13 19:28:26] Storing 10889 Traits
[INFO] [2019-10-13 19:28:26] Processing group of 10889 in 11 groups of 1000
[INFO] [2019-10-13 19:28:30] Average Time: 0.31
[INFO] [2019-10-13 19:28:30] Total Time: 4s
[INFO] [2019-10-13 19:28:30] last 3 / first 3: 0.91
[INFO] [2019-10-13 19:28:30] Std.Dev: 0.044721359549995794; Max: 0.42
[INFO] [2019-10-13 19:28:30] Storing 10886 MetaTraits
[INFO] [2019-10-13 19:28:30] Processing group of 10886 in 11 groups of 1000
[INFO] [2019-10-13 19:28:31] Average Time: 0.114
[INFO] [2019-10-13 19:28:31] Total Time: 2s
[INFO] [2019-10-13 19:28:31] last 3 / first 3: 0.84
[INFO] [2019-10-13 19:28:31] Std.Dev: 0.0; Max: 0.15
[STOP] [2019-10-13 19:28:31] parse_diff_and_store
[START] [2019-10-13 19:28:31] resolve_keys
[INFO] [2019-10-13 19:29:06] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 19:29:09] traits to occurrences...
[INFO] [2019-10-13 19:29:11] traits to nodes (through occurrences)...
[INFO] [2019-10-13 19:29:12] Traits to sex term...
[INFO] [2019-10-13 19:29:14] Traits to lifestage term...
[INFO] [2019-10-13 19:29:16] MetaTraits to traits...
[INFO] [2019-10-13 19:29:16] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 19:29:18] Assocs to occurrences...
[INFO] [2019-10-13 19:29:18] Assocs to nodes...
[INFO] [2019-10-13 19:29:18] Assoc to sex term...
[INFO] [2019-10-13 19:29:18] Assoc to lifestage term...
[STOP] [2019-10-13 19:29:18] resolve_keys
[START] [2019-10-13 19:29:18] hold_for_later_1
[STOP] [2019-10-13 19:29:18] hold_for_later_1
[START] [2019-10-13 19:29:18] hold_for_later_2
[STOP] [2019-10-13 19:29:18] hold_for_later_2
[START] [2019-10-13 19:29:18] resolve_missing_parents
[STOP] [2019-10-13 19:29:36] resolve_missing_parents
[START] [2019-10-13 19:29:36] rebuild_nodes
[START] [2019-10-13 19:29:36] Flattener#flatten
[START] [2019-10-13 19:29:36] Flattener#study_resource
[START] [2019-10-13 19:29:36] Flattener#build_ancestry
[STOP] [2019-10-13 19:29:37] Flattener#build_ancestry
[INFO] [2019-10-13 19:29:37] 8682 ancestry keys
[START] [2019-10-13 19:29:37] build_node_ancestors
[INFO] [2019-10-13 19:29:37] old ancestors deleted.
[STOP] [2019-10-13 19:29:39] build_node_ancestors
[START] [2019-10-13 19:29:40] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 19:29:40] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 19:29:40] Flattener#flatten
[STOP] [2019-10-13 19:29:40] rebuild_nodes
[START] [2019-10-13 19:29:40] resolve_missing_media_owners
[STOP] [2019-10-13 19:29:40] resolve_missing_media_owners
[START] [2019-10-13 19:29:40] sanitize_media_verbatims
[STOP] [2019-10-13 19:29:40] sanitize_media_verbatims
[START] [2019-10-13 19:29:40] queue_downloads
[STOP] [2019-10-13 19:29:40] queue_downloads
[START] [2019-10-13 19:29:40] parse_names
[WARN] [2019-10-13 19:29:40] I see 8682 names which still need to be parsed.
[STOP] [2019-10-13 19:29:48] parse_names
[START] [2019-10-13 19:29:48] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 19:29:48] denormalize_canonical_names_to_nodes
[START] [2019-10-13 19:29:48] match_nodes
[START] [2019-10-13 19:29:48] map_all_nodes_to_pages
[STOP] [2019-10-13 19:38:06] map_all_nodes_to_pages
[INFO] [2019-10-13 19:38:06] 606 Unmatched nodes (of 8682)! That's too many to output. First 10: Sus goramensis (#50345561); Kolpochoerus evronensis (#50350930); Hippopotamus gorgops (#50350698); Vulpes rueppelli (#50346842); Megantereon (#50350750); Megantereon whitei (#50350749); Anas clypeata (#50342969); Anas strepera (#50343179); Anas querquedula (#50343385); Anas penelope (#50343442)
[START] [2019-10-13 19:38:06] update_nodes
[STOP] [2019-10-13 19:38:09] update_nodes
[STOP] [2019-10-13 19:38:09] match_nodes
[START] [2019-10-13 19:38:09] reindex_search
[STOP] [2019-10-13 19:38:30] reindex_search
[START] [2019-10-13 19:38:30] normalize_units
[STOP] [2019-10-13 19:38:30] normalize_units
[START] [2019-10-13 19:38:30] calculate_statistics
[STOP] [2019-10-13 19:38:30] calculate_statistics
[START] [2019-10-13 19:38:30] complete_harvest_instance
[START] [2019-10-13 19:38:30] overall_tsv_creation
[INFO] [2019-10-13 19:38:30] Processing group of 8682 in 1 batches of 10000
[INFO] [2019-10-13 19:39:53] 5302 Traits (unfiltered)...
[INFO] [2019-10-13 19:40:10] 5302 Traits (filtered)...
[INFO] [2019-10-13 19:40:10] 0 Associations (filtered)...
[INFO] [2019-10-13 19:41:04] 26506 metadata added.
[INFO] [2019-10-13 19:41:04] 0 metadata added.
[INFO] [2019-10-13 19:41:04] Average Time: 127.94
[INFO] [2019-10-13 19:41:04] Total Time: 2m35s
[STOP] [2019-10-13 19:41:04] overall_tsv_creation
[INFO] [2019-10-13 19:41:04] Done. Check your files:
[INFO] [2019-10-13 19:41:04] (8682 lines) /app/public/data/israel_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 19:41:05] (20255 lines) /app/public/data/israel_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 19:41:05] (8682 lines) /app/public/data/israel_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 19:41:05] (5303 lines) /app/public/data/israel_sp_list/publish_traits.tsv
[INFO] [2019-10-13 19:41:05] (26507 lines) /app/public/data/israel_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 19:41:05] complete_harvest_instance
[START] [2019-10-13 19:41:05] completed
[STOP] [2019-10-13 19:41:05] completed
[STOP] [2019-10-13 19:41:05] logged process, took 806.28
Latest Process

13 Oct 19:27 EXITED currently processing 0