Harvest for Mauritius Species List Created 14 Oct 05:26

Stage: completed
Fetched: 14 Oct 05:26
Validated: 14 Oct 05:26
Deltas Created 14 Oct 05:26
Units Normalized: 14 Oct 05:33
Ancestry Built: 14 Oct 05:28
Nodes Matched: 14 Oct 05:33
Names Parsed: 14 Oct 05:28
New Models Stored: 14 Oct 05:27
Indexed: 14 Oct 05:33
Completed: 14 Oct 05:35
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 05:26:48 -0400 by logger.rb/56815
[START] [2019-10-14 05:26:48] logged process
[START] [2019-10-14 05:26:48] create_harvest_instance
[STOP] [2019-10-14 05:26:49] create_harvest_instance
[START] [2019-10-14 05:26:49] fetch_files
[STOP] [2019-10-14 05:26:49] fetch_files
[START] [2019-10-14 05:26:49] validate_each_file
[STOP] [2019-10-14 05:26:49] validate_each_file
[START] [2019-10-14 05:26:49] convert_to_csv
[CMD] [2019-10-14 05:26:49] /usr/bin/sort /app/public/converted_csv/mauritius_sp_lis_refs_16563.csv > /app/public/converted_csv/mauritius_sp_lis_refs_16563.csv_sorted
[CMD] [2019-10-14 05:26:50] /usr/bin/sort /app/public/converted_csv/mauritius_sp_lis_nodes_16564.csv > /app/public/converted_csv/mauritius_sp_lis_nodes_16564.csv_sorted
[CMD] [2019-10-14 05:26:50] /usr/bin/sort /app/public/converted_csv/mauritius_sp_lis_occurrences_16565.csv > /app/public/converted_csv/mauritius_sp_lis_occurrences_16565.csv_sorted
[CMD] [2019-10-14 05:26:50] /usr/bin/sort /app/public/converted_csv/mauritius_sp_lis_measurements_16566.csv > /app/public/converted_csv/mauritius_sp_lis_measurements_16566.csv_sorted
[STOP] [2019-10-14 05:26:50] convert_to_csv
[START] [2019-10-14 05:26:50] calculate_delta
[CMD] [2019-10-14 05:26:50] echo "0a" > /app/public/diff/mauritius_sp_lis_refs_16563.diff
[CMD] [2019-10-14 05:26:50] tail -n +1 /app/public/converted_csv/mauritius_sp_lis_refs_16563.csv >> /app/public/diff/mauritius_sp_lis_refs_16563.diff
[CMD] [2019-10-14 05:26:50] echo "." >> /app/public/diff/mauritius_sp_lis_refs_16563.diff
[CMD] [2019-10-14 05:26:50] echo "0a" > /app/public/diff/mauritius_sp_lis_nodes_16564.diff
[CMD] [2019-10-14 05:26:50] tail -n +1 /app/public/converted_csv/mauritius_sp_lis_nodes_16564.csv >> /app/public/diff/mauritius_sp_lis_nodes_16564.diff
[CMD] [2019-10-14 05:26:50] echo "." >> /app/public/diff/mauritius_sp_lis_nodes_16564.diff
[CMD] [2019-10-14 05:26:50] echo "0a" > /app/public/diff/mauritius_sp_lis_occurrences_16565.diff
[CMD] [2019-10-14 05:26:51] tail -n +1 /app/public/converted_csv/mauritius_sp_lis_occurrences_16565.csv >> /app/public/diff/mauritius_sp_lis_occurrences_16565.diff
[CMD] [2019-10-14 05:26:51] echo "." >> /app/public/diff/mauritius_sp_lis_occurrences_16565.diff
[CMD] [2019-10-14 05:26:51] echo "0a" > /app/public/diff/mauritius_sp_lis_measurements_16566.diff
[CMD] [2019-10-14 05:26:51] tail -n +1 /app/public/converted_csv/mauritius_sp_lis_measurements_16566.csv >> /app/public/diff/mauritius_sp_lis_measurements_16566.diff
[CMD] [2019-10-14 05:26:51] echo "." >> /app/public/diff/mauritius_sp_lis_measurements_16566.diff
[STOP] [2019-10-14 05:26:51] calculate_delta
[START] [2019-10-14 05:26:51] parse_diff_and_store
[INFO] [2019-10-14 05:26:51] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 05:26:51] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 05:26:53] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 05:26:54] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 05:27:11] Storing 2 References
[INFO] [2019-10-14 05:27:11] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 05:27:11] Average Time: 0.0
[INFO] [2019-10-14 05:27:11] Total Time: 1s
[INFO] [2019-10-14 05:27:11] Storing 5327 ScientificNames
[INFO] [2019-10-14 05:27:11] Processing group of 5327 in 6 groups of 1000
[INFO] [2019-10-14 05:27:13] Average Time: 0.36
[INFO] [2019-10-14 05:27:13] Total Time: 3s
[INFO] [2019-10-14 05:27:13] Storing 5327 Nodes
[INFO] [2019-10-14 05:27:13] Processing group of 5327 in 6 groups of 1000
[INFO] [2019-10-14 05:27:15] Average Time: 0.267
[INFO] [2019-10-14 05:27:15] Total Time: 2s
[INFO] [2019-10-14 05:27:15] Storing 2892 Occurrences
[INFO] [2019-10-14 05:27:15] Processing group of 2892 in 3 groups of 1000
[INFO] [2019-10-14 05:27:15] Average Time: 0.107
[INFO] [2019-10-14 05:27:15] Total Time: 1s
[INFO] [2019-10-14 05:27:15] Storing 5870 TraitsReferences
[INFO] [2019-10-14 05:27:15] Processing group of 5870 in 6 groups of 1000
[INFO] [2019-10-14 05:27:16] Average Time: 0.087
[INFO] [2019-10-14 05:27:16] Total Time: 1s
[INFO] [2019-10-14 05:27:16] Storing 5869 Traits
[INFO] [2019-10-14 05:27:16] Processing group of 5869 in 6 groups of 1000
[INFO] [2019-10-14 05:27:18] Average Time: 0.312
[INFO] [2019-10-14 05:27:18] Total Time: 2s
[INFO] [2019-10-14 05:27:18] Storing 5867 MetaTraits
[INFO] [2019-10-14 05:27:18] Processing group of 5867 in 6 groups of 1000
[INFO] [2019-10-14 05:27:18] Average Time: 0.115
[INFO] [2019-10-14 05:27:18] Total Time: 1s
[STOP] [2019-10-14 05:27:18] parse_diff_and_store
[START] [2019-10-14 05:27:18] resolve_keys
[INFO] [2019-10-14 05:27:41] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 05:27:43] traits to occurrences...
[INFO] [2019-10-14 05:27:45] traits to nodes (through occurrences)...
[INFO] [2019-10-14 05:27:45] Traits to sex term...
[INFO] [2019-10-14 05:27:46] Traits to lifestage term...
[INFO] [2019-10-14 05:27:47] MetaTraits to traits...
[INFO] [2019-10-14 05:27:47] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 05:27:48] Assocs to occurrences...
[INFO] [2019-10-14 05:27:48] Assocs to nodes...
[INFO] [2019-10-14 05:27:48] Assoc to sex term...
[INFO] [2019-10-14 05:27:48] Assoc to lifestage term...
[STOP] [2019-10-14 05:27:48] resolve_keys
[START] [2019-10-14 05:27:48] hold_for_later_1
[STOP] [2019-10-14 05:27:48] hold_for_later_1
[START] [2019-10-14 05:27:48] hold_for_later_2
[STOP] [2019-10-14 05:27:48] hold_for_later_2
[START] [2019-10-14 05:27:48] resolve_missing_parents
[STOP] [2019-10-14 05:27:59] resolve_missing_parents
[START] [2019-10-14 05:27:59] rebuild_nodes
[START] [2019-10-14 05:27:59] Flattener#flatten
[START] [2019-10-14 05:27:59] Flattener#study_resource
[START] [2019-10-14 05:27:59] Flattener#build_ancestry
[STOP] [2019-10-14 05:27:59] Flattener#build_ancestry
[INFO] [2019-10-14 05:27:59] 5327 ancestry keys
[START] [2019-10-14 05:27:59] build_node_ancestors
[INFO] [2019-10-14 05:27:59] old ancestors deleted.
[STOP] [2019-10-14 05:28:00] build_node_ancestors
[START] [2019-10-14 05:28:01] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 05:28:01] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 05:28:01] Flattener#flatten
[STOP] [2019-10-14 05:28:01] rebuild_nodes
[START] [2019-10-14 05:28:01] resolve_missing_media_owners
[STOP] [2019-10-14 05:28:01] resolve_missing_media_owners
[START] [2019-10-14 05:28:01] sanitize_media_verbatims
[STOP] [2019-10-14 05:28:01] sanitize_media_verbatims
[START] [2019-10-14 05:28:01] queue_downloads
[STOP] [2019-10-14 05:28:01] queue_downloads
[START] [2019-10-14 05:28:01] parse_names
[WARN] [2019-10-14 05:28:01] I see 5327 names which still need to be parsed.
[STOP] [2019-10-14 05:28:07] parse_names
[START] [2019-10-14 05:28:07] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 05:28:07] denormalize_canonical_names_to_nodes
[START] [2019-10-14 05:28:07] match_nodes
[START] [2019-10-14 05:28:07] map_all_nodes_to_pages
[STOP] [2019-10-14 05:33:24] map_all_nodes_to_pages
[INFO] [2019-10-14 05:33:24] 328 Unmatched nodes (of 5327)! That's too many to output. First 10: Onychoprion fuscata (#50667524); Thalaseus (#50670769); Thalaseus bergii (#50670768); Technomyrmex pallipes (#50668191); Strumigenys ludovici (#50667513); Strumigenys simoni (#50667534); Strumigenys emmae (#50667588); Strumigenys agetos (#50667916); Syllophopsis (#50667676); Syllophopsis cryptobia (#50667675)
[START] [2019-10-14 05:33:24] update_nodes
[STOP] [2019-10-14 05:33:26] update_nodes
[STOP] [2019-10-14 05:33:26] match_nodes
[START] [2019-10-14 05:33:26] reindex_search
[STOP] [2019-10-14 05:33:39] reindex_search
[START] [2019-10-14 05:33:39] normalize_units
[STOP] [2019-10-14 05:33:39] normalize_units
[START] [2019-10-14 05:33:39] calculate_statistics
[STOP] [2019-10-14 05:33:39] calculate_statistics
[START] [2019-10-14 05:33:39] complete_harvest_instance
[START] [2019-10-14 05:33:39] overall_tsv_creation
[INFO] [2019-10-14 05:33:39] Processing group of 5327 in 1 batches of 10000
[INFO] [2019-10-14 05:34:50] 2892 Traits (unfiltered)...
[INFO] [2019-10-14 05:35:07] 2892 Traits (filtered)...
[INFO] [2019-10-14 05:35:07] 0 Associations (filtered)...
[INFO] [2019-10-14 05:35:57] 14457 metadata added.
[INFO] [2019-10-14 05:35:57] 0 metadata added.
[INFO] [2019-10-14 05:35:57] Average Time: 113.23
[INFO] [2019-10-14 05:35:57] Total Time: 2m18s
[STOP] [2019-10-14 05:35:57] overall_tsv_creation
[INFO] [2019-10-14 05:35:57] Done. Check your files:
[INFO] [2019-10-14 05:35:57] (5327 lines) /app/public/data/mauritius_sp_lis/publish_nodes.tsv
[INFO] [2019-10-14 05:35:57] (11939 lines) /app/public/data/mauritius_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-10-14 05:35:57] (5327 lines) /app/public/data/mauritius_sp_lis/publish_scientific_names.tsv
[INFO] [2019-10-14 05:35:57] (2893 lines) /app/public/data/mauritius_sp_lis/publish_traits.tsv
[INFO] [2019-10-14 05:35:57] (14458 lines) /app/public/data/mauritius_sp_lis/publish_metadata.tsv
[STOP] [2019-10-14 05:35:57] complete_harvest_instance
[START] [2019-10-14 05:35:57] completed
[STOP] [2019-10-14 05:35:58] completed
[STOP] [2019-10-14 05:35:58] logged process, took 549.25
Latest Process

14 Oct 05:26 EXITED currently processing 0