Harvest for Lesotho Species List Created 14 Oct 01:41

Stage: completed
Fetched: 14 Oct 01:41
Validated: 14 Oct 01:41
Deltas Created 14 Oct 01:41
Units Normalized: 14 Oct 01:46
Ancestry Built: 14 Oct 01:42
Nodes Matched: 14 Oct 01:46
Names Parsed: 14 Oct 01:42
New Models Stored: 14 Oct 01:41
Indexed: 14 Oct 01:46
Completed: 14 Oct 01:48
Time to Harvest: less than a minute
Harvesting Log

(145 lines)
# Logfile created on 2019-10-14 01:41:06 -0400 by logger.rb/56815
[START] [2019-10-14 01:41:06] logged process
[START] [2019-10-14 01:41:06] create_harvest_instance
[STOP] [2019-10-14 01:41:07] create_harvest_instance
[START] [2019-10-14 01:41:07] fetch_files
[STOP] [2019-10-14 01:41:07] fetch_files
[START] [2019-10-14 01:41:07] validate_each_file
[STOP] [2019-10-14 01:41:07] validate_each_file
[START] [2019-10-14 01:41:07] convert_to_csv
[CMD] [2019-10-14 01:41:07] /usr/bin/sort /app/public/converted_csv/lesotho_sp_list_refs_16387.csv > /app/public/converted_csv/lesotho_sp_list_refs_16387.csv_sorted
[CMD] [2019-10-14 01:41:07] /usr/bin/sort /app/public/converted_csv/lesotho_sp_list_nodes_16388.csv > /app/public/converted_csv/lesotho_sp_list_nodes_16388.csv_sorted
[CMD] [2019-10-14 01:41:07] /usr/bin/sort /app/public/converted_csv/lesotho_sp_list_occurrences_16389.csv > /app/public/converted_csv/lesotho_sp_list_occurrences_16389.csv_sorted
[CMD] [2019-10-14 01:41:08] /usr/bin/sort /app/public/converted_csv/lesotho_sp_list_measurements_16390.csv > /app/public/converted_csv/lesotho_sp_list_measurements_16390.csv_sorted
[STOP] [2019-10-14 01:41:08] convert_to_csv
[START] [2019-10-14 01:41:08] calculate_delta
[CMD] [2019-10-14 01:41:08] echo "0a" > /app/public/diff/lesotho_sp_list_refs_16387.diff
[CMD] [2019-10-14 01:41:08] tail -n +1 /app/public/converted_csv/lesotho_sp_list_refs_16387.csv >> /app/public/diff/lesotho_sp_list_refs_16387.diff
[CMD] [2019-10-14 01:41:08] echo "." >> /app/public/diff/lesotho_sp_list_refs_16387.diff
[CMD] [2019-10-14 01:41:08] echo "0a" > /app/public/diff/lesotho_sp_list_nodes_16388.diff
[CMD] [2019-10-14 01:41:08] tail -n +1 /app/public/converted_csv/lesotho_sp_list_nodes_16388.csv >> /app/public/diff/lesotho_sp_list_nodes_16388.diff
[CMD] [2019-10-14 01:41:08] echo "." >> /app/public/diff/lesotho_sp_list_nodes_16388.diff
[CMD] [2019-10-14 01:41:08] echo "0a" > /app/public/diff/lesotho_sp_list_occurrences_16389.diff
[CMD] [2019-10-14 01:41:08] tail -n +1 /app/public/converted_csv/lesotho_sp_list_occurrences_16389.csv >> /app/public/diff/lesotho_sp_list_occurrences_16389.diff
[CMD] [2019-10-14 01:41:08] echo "." >> /app/public/diff/lesotho_sp_list_occurrences_16389.diff
[CMD] [2019-10-14 01:41:09] echo "0a" > /app/public/diff/lesotho_sp_list_measurements_16390.diff
[CMD] [2019-10-14 01:41:09] tail -n +1 /app/public/converted_csv/lesotho_sp_list_measurements_16390.csv >> /app/public/diff/lesotho_sp_list_measurements_16390.diff
[CMD] [2019-10-14 01:41:09] echo "." >> /app/public/diff/lesotho_sp_list_measurements_16390.diff
[STOP] [2019-10-14 01:41:09] calculate_delta
[START] [2019-10-14 01:41:09] parse_diff_and_store
[INFO] [2019-10-14 01:41:09] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 01:41:09] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 01:41:11] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 01:41:11] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 01:41:29] Storing 2 References
[INFO] [2019-10-14 01:41:29] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 01:41:29] Average Time: 0.0
[INFO] [2019-10-14 01:41:29] Total Time: 1s
[INFO] [2019-10-14 01:41:29] Storing 4766 ScientificNames
[INFO] [2019-10-14 01:41:29] Processing group of 4766 in 5 groups of 1000
[INFO] [2019-10-14 01:41:31] Average Time: 0.366
[INFO] [2019-10-14 01:41:31] Total Time: 2s
[INFO] [2019-10-14 01:41:31] Storing 4766 Nodes
[INFO] [2019-10-14 01:41:31] Processing group of 4766 in 5 groups of 1000
[INFO] [2019-10-14 01:41:33] Average Time: 0.29
[INFO] [2019-10-14 01:41:33] Total Time: 2s
[INFO] [2019-10-14 01:41:33] Storing 2892 Occurrences
[INFO] [2019-10-14 01:41:33] Processing group of 2892 in 3 groups of 1000
[INFO] [2019-10-14 01:41:33] Average Time: 0.093
[INFO] [2019-10-14 01:41:33] Total Time: 1s
[INFO] [2019-10-14 01:41:33] Storing 6230 TraitsReferences
[INFO] [2019-10-14 01:41:33] Processing group of 6230 in 7 groups of 1000
[INFO] [2019-10-14 01:41:33] Average Time: 0.084
[INFO] [2019-10-14 01:41:33] Total Time: 1s
[INFO] [2019-10-14 01:41:33] last 3 / first 3: 0.58
[INFO] [2019-10-14 01:41:33] Std.Dev: 0.044721359549995794; Max: 0.16
[INFO] [2019-10-14 01:41:33] Storing 6229 Traits
[INFO] [2019-10-14 01:41:33] Processing group of 6229 in 7 groups of 1000
[INFO] [2019-10-14 01:41:36] Average Time: 0.33
[INFO] [2019-10-14 01:41:36] Total Time: 3s
[INFO] [2019-10-14 01:41:36] last 3 / first 3: 0.52
[INFO] [2019-10-14 01:41:36] Std.Dev: 0.15165750888103102; Max: 0.54
[INFO] [2019-10-14 01:41:36] Storing 6228 MetaTraits
[INFO] [2019-10-14 01:41:36] Processing group of 6228 in 7 groups of 1000
[INFO] [2019-10-14 01:41:37] Average Time: 0.116
[INFO] [2019-10-14 01:41:37] Total Time: 1s
[INFO] [2019-10-14 01:41:37] last 3 / first 3: 0.77
[INFO] [2019-10-14 01:41:37] Std.Dev: 0.03162277660168379; Max: 0.15
[STOP] [2019-10-14 01:41:37] parse_diff_and_store
[START] [2019-10-14 01:41:37] resolve_keys
[INFO] [2019-10-14 01:41:58] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 01:42:00] traits to occurrences...
[INFO] [2019-10-14 01:42:01] traits to nodes (through occurrences)...
[INFO] [2019-10-14 01:42:01] Traits to sex term...
[INFO] [2019-10-14 01:42:02] Traits to lifestage term...
[INFO] [2019-10-14 01:42:04] MetaTraits to traits...
[INFO] [2019-10-14 01:42:04] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 01:42:05] Assocs to occurrences...
[INFO] [2019-10-14 01:42:05] Assocs to nodes...
[INFO] [2019-10-14 01:42:05] Assoc to sex term...
[INFO] [2019-10-14 01:42:05] Assoc to lifestage term...
[STOP] [2019-10-14 01:42:05] resolve_keys
[START] [2019-10-14 01:42:05] hold_for_later_1
[STOP] [2019-10-14 01:42:05] hold_for_later_1
[START] [2019-10-14 01:42:05] hold_for_later_2
[STOP] [2019-10-14 01:42:05] hold_for_later_2
[START] [2019-10-14 01:42:05] resolve_missing_parents
[STOP] [2019-10-14 01:42:14] resolve_missing_parents
[START] [2019-10-14 01:42:14] rebuild_nodes
[START] [2019-10-14 01:42:14] Flattener#flatten
[START] [2019-10-14 01:42:14] Flattener#study_resource
[START] [2019-10-14 01:42:14] Flattener#build_ancestry
[STOP] [2019-10-14 01:42:14] Flattener#build_ancestry
[INFO] [2019-10-14 01:42:14] 4766 ancestry keys
[START] [2019-10-14 01:42:14] build_node_ancestors
[INFO] [2019-10-14 01:42:14] old ancestors deleted.
[STOP] [2019-10-14 01:42:15] build_node_ancestors
[START] [2019-10-14 01:42:15] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 01:42:16] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 01:42:16] Flattener#flatten
[STOP] [2019-10-14 01:42:16] rebuild_nodes
[START] [2019-10-14 01:42:16] resolve_missing_media_owners
[STOP] [2019-10-14 01:42:16] resolve_missing_media_owners
[START] [2019-10-14 01:42:16] sanitize_media_verbatims
[STOP] [2019-10-14 01:42:16] sanitize_media_verbatims
[START] [2019-10-14 01:42:16] queue_downloads
[STOP] [2019-10-14 01:42:16] queue_downloads
[START] [2019-10-14 01:42:16] parse_names
[WARN] [2019-10-14 01:42:16] I see 4766 names which still need to be parsed.
[STOP] [2019-10-14 01:42:20] parse_names
[START] [2019-10-14 01:42:20] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 01:42:20] denormalize_canonical_names_to_nodes
[START] [2019-10-14 01:42:20] match_nodes
[START] [2019-10-14 01:42:20] map_all_nodes_to_pages
[STOP] [2019-10-14 01:46:39] map_all_nodes_to_pages
[INFO] [2019-10-14 01:46:39] 216 Unmatched nodes (of 4766)! That's too many to output. First 10: Streptopelia senegalensis (#50535096); Spreo (#50535161); Spreo bicolor (#50535160); Saxicola bifasciatus (#50537498); Oenanthe monticola (#50535173); Oenanthe bifasciata (#50535792); Cercomela (#50535225); Cercomela familiaris (#50535224); Cercomela sinuata (#50535290); Sigelus (#50535765)
[START] [2019-10-14 01:46:39] update_nodes
[STOP] [2019-10-14 01:46:41] update_nodes
[STOP] [2019-10-14 01:46:41] match_nodes
[START] [2019-10-14 01:46:41] reindex_search
[STOP] [2019-10-14 01:46:53] reindex_search
[START] [2019-10-14 01:46:53] normalize_units
[STOP] [2019-10-14 01:46:53] normalize_units
[START] [2019-10-14 01:46:53] calculate_statistics
[STOP] [2019-10-14 01:46:53] calculate_statistics
[START] [2019-10-14 01:46:53] complete_harvest_instance
[START] [2019-10-14 01:46:53] overall_tsv_creation
[INFO] [2019-10-14 01:46:53] Processing group of 4766 in 1 batches of 10000
[INFO] [2019-10-14 01:48:00] 2892 Traits (unfiltered)...
[INFO] [2019-10-14 01:48:14] 2892 Traits (filtered)...
[INFO] [2019-10-14 01:48:14] 0 Associations (filtered)...
[INFO] [2019-10-14 01:48:57] 14459 metadata added.
[INFO] [2019-10-14 01:48:57] 0 metadata added.
[INFO] [2019-10-14 01:48:57] Average Time: 99.99
[INFO] [2019-10-14 01:48:57] Total Time: 2m5s
[STOP] [2019-10-14 01:48:57] overall_tsv_creation
[INFO] [2019-10-14 01:48:57] Done. Check your files:
[INFO] [2019-10-14 01:48:57] (4766 lines) /app/public/data/lesotho_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 01:48:57] (7386 lines) /app/public/data/lesotho_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 01:48:57] (4766 lines) /app/public/data/lesotho_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 01:48:57] (2893 lines) /app/public/data/lesotho_sp_list/publish_traits.tsv
[INFO] [2019-10-14 01:48:57] (14460 lines) /app/public/data/lesotho_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 01:48:58] complete_harvest_instance
[START] [2019-10-14 01:48:58] completed
[STOP] [2019-10-14 01:48:58] completed
[STOP] [2019-10-14 01:48:58] logged process, took 471.62
Latest Process

14 Oct 01:41 EXITED currently processing 0