Harvest for Barbados Species List Created 02 Oct 10:23

Stage: completed
Fetched: 02 Oct 10:23
Validated: 02 Oct 10:23
Deltas Created 02 Oct 10:23
Units Normalized: 02 Oct 10:27
Ancestry Built: 02 Oct 10:24
Nodes Matched: 02 Oct 10:26
Names Parsed: 02 Oct 10:24
New Models Stored: 02 Oct 10:24
Indexed: 02 Oct 10:27
Completed: 02 Oct 10:28
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-02 10:23:25 -0400 by logger.rb/56815
[START] [2019-10-02 10:23:25] logged process
[START] [2019-10-02 10:23:25] create_harvest_instance
[STOP] [2019-10-02 10:23:25] create_harvest_instance
[START] [2019-10-02 10:23:25] fetch_files
[STOP] [2019-10-02 10:23:25] fetch_files
[START] [2019-10-02 10:23:25] validate_each_file
[STOP] [2019-10-02 10:23:25] validate_each_file
[START] [2019-10-02 10:23:25] convert_to_csv
[CMD] [2019-10-02 10:23:25] /usr/bin/sort /app/public/converted_csv/barbados_sp_list_refs_14928.csv > /app/public/converted_csv/barbados_sp_list_refs_14928.csv_sorted
[CMD] [2019-10-02 10:23:27] /usr/bin/sort /app/public/converted_csv/barbados_sp_list_nodes_14929.csv > /app/public/converted_csv/barbados_sp_list_nodes_14929.csv_sorted
[CMD] [2019-10-02 10:23:28] /usr/bin/sort /app/public/converted_csv/barbados_sp_list_occurrences_14930.csv > /app/public/converted_csv/barbados_sp_list_occurrences_14930.csv_sorted
[CMD] [2019-10-02 10:23:30] /usr/bin/sort /app/public/converted_csv/barbados_sp_list_measurements_14931.csv > /app/public/converted_csv/barbados_sp_list_measurements_14931.csv_sorted
[STOP] [2019-10-02 10:23:31] convert_to_csv
[START] [2019-10-02 10:23:31] calculate_delta
[CMD] [2019-10-02 10:23:31] echo "0a" > /app/public/diff/barbados_sp_list_refs_14928.diff
[CMD] [2019-10-02 10:23:33] tail -n +1 /app/public/converted_csv/barbados_sp_list_refs_14928.csv >> /app/public/diff/barbados_sp_list_refs_14928.diff
[CMD] [2019-10-02 10:23:34] echo "." >> /app/public/diff/barbados_sp_list_refs_14928.diff
[CMD] [2019-10-02 10:23:36] echo "0a" > /app/public/diff/barbados_sp_list_nodes_14929.diff
[CMD] [2019-10-02 10:23:37] tail -n +1 /app/public/converted_csv/barbados_sp_list_nodes_14929.csv >> /app/public/diff/barbados_sp_list_nodes_14929.diff
[CMD] [2019-10-02 10:23:39] echo "." >> /app/public/diff/barbados_sp_list_nodes_14929.diff
[CMD] [2019-10-02 10:23:40] echo "0a" > /app/public/diff/barbados_sp_list_occurrences_14930.diff
[CMD] [2019-10-02 10:23:42] tail -n +1 /app/public/converted_csv/barbados_sp_list_occurrences_14930.csv >> /app/public/diff/barbados_sp_list_occurrences_14930.diff
[CMD] [2019-10-02 10:23:43] echo "." >> /app/public/diff/barbados_sp_list_occurrences_14930.diff
[CMD] [2019-10-02 10:23:45] echo "0a" > /app/public/diff/barbados_sp_list_measurements_14931.diff
[CMD] [2019-10-02 10:23:46] tail -n +1 /app/public/converted_csv/barbados_sp_list_measurements_14931.csv >> /app/public/diff/barbados_sp_list_measurements_14931.diff
[CMD] [2019-10-02 10:23:48] echo "." >> /app/public/diff/barbados_sp_list_measurements_14931.diff
[STOP] [2019-10-02 10:23:49] calculate_delta
[START] [2019-10-02 10:23:49] parse_diff_and_store
[INFO] [2019-10-02 10:23:51] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-02 10:23:52] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-02 10:23:55] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-02 10:23:56] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-02 10:24:04] Storing 2 References
[INFO] [2019-10-02 10:24:04] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-02 10:24:04] Average Time: 0.0
[INFO] [2019-10-02 10:24:04] Total Time: 1s
[INFO] [2019-10-02 10:24:04] Storing 2844 ScientificNames
[INFO] [2019-10-02 10:24:04] Processing group of 2844 in 3 groups of 1000
[INFO] [2019-10-02 10:24:05] Average Time: 0.347
[INFO] [2019-10-02 10:24:05] Total Time: 2s
[INFO] [2019-10-02 10:24:05] Storing 2844 Nodes
[INFO] [2019-10-02 10:24:05] Processing group of 2844 in 3 groups of 1000
[INFO] [2019-10-02 10:24:06] Average Time: 0.327
[INFO] [2019-10-02 10:24:06] Total Time: 2s
[INFO] [2019-10-02 10:24:06] Storing 964 Occurrences
[INFO] [2019-10-02 10:24:06] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-02 10:24:06] Average Time: 0.11
[INFO] [2019-10-02 10:24:06] Total Time: 1s
[INFO] [2019-10-02 10:24:06] Storing 2760 TraitsReferences
[INFO] [2019-10-02 10:24:06] Processing group of 2760 in 3 groups of 1000
[INFO] [2019-10-02 10:24:06] Average Time: 0.093
[INFO] [2019-10-02 10:24:06] Total Time: 1s
[INFO] [2019-10-02 10:24:06] Storing 2759 Traits
[INFO] [2019-10-02 10:24:06] Processing group of 2759 in 3 groups of 1000
[INFO] [2019-10-02 10:24:08] Average Time: 0.417
[INFO] [2019-10-02 10:24:08] Total Time: 2s
[INFO] [2019-10-02 10:24:08] Storing 2758 MetaTraits
[INFO] [2019-10-02 10:24:08] Processing group of 2758 in 3 groups of 1000
[INFO] [2019-10-02 10:24:08] Average Time: 0.157
[INFO] [2019-10-02 10:24:08] Total Time: 1s
[STOP] [2019-10-02 10:24:08] parse_diff_and_store
[START] [2019-10-02 10:24:08] resolve_keys
[INFO] [2019-10-02 10:24:22] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-02 10:24:23] traits to occurrences...
[INFO] [2019-10-02 10:24:25] traits to nodes (through occurrences)...
[INFO] [2019-10-02 10:24:25] Traits to sex term...
[INFO] [2019-10-02 10:24:25] Traits to lifestage term...
[INFO] [2019-10-02 10:24:26] MetaTraits to traits...
[INFO] [2019-10-02 10:24:26] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-02 10:24:27] Assocs to occurrences...
[INFO] [2019-10-02 10:24:27] Assocs to nodes...
[INFO] [2019-10-02 10:24:27] Assoc to sex term...
[INFO] [2019-10-02 10:24:27] Assoc to lifestage term...
[STOP] [2019-10-02 10:24:27] resolve_keys
[START] [2019-10-02 10:24:27] hold_for_later_1
[STOP] [2019-10-02 10:24:27] hold_for_later_1
[START] [2019-10-02 10:24:27] hold_for_later_2
[STOP] [2019-10-02 10:24:27] hold_for_later_2
[START] [2019-10-02 10:24:27] resolve_missing_parents
[STOP] [2019-10-02 10:24:32] resolve_missing_parents
[START] [2019-10-02 10:24:32] rebuild_nodes
[START] [2019-10-02 10:24:32] Flattener#flatten
[START] [2019-10-02 10:24:32] Flattener#study_resource
[START] [2019-10-02 10:24:32] Flattener#build_ancestry
[STOP] [2019-10-02 10:24:32] Flattener#build_ancestry
[INFO] [2019-10-02 10:24:32] 2844 ancestry keys
[START] [2019-10-02 10:24:32] build_node_ancestors
[INFO] [2019-10-02 10:24:32] old ancestors deleted.
[STOP] [2019-10-02 10:24:32] build_node_ancestors
[START] [2019-10-02 10:24:33] Flattener#propagate_ancestor_ids
[STOP] [2019-10-02 10:24:33] Flattener#propagate_ancestor_ids
[STOP] [2019-10-02 10:24:33] Flattener#flatten
[STOP] [2019-10-02 10:24:33] rebuild_nodes
[START] [2019-10-02 10:24:33] resolve_missing_media_owners
[STOP] [2019-10-02 10:24:33] resolve_missing_media_owners
[START] [2019-10-02 10:24:33] sanitize_media_verbatims
[STOP] [2019-10-02 10:24:33] sanitize_media_verbatims
[START] [2019-10-02 10:24:33] queue_downloads
[STOP] [2019-10-02 10:24:33] queue_downloads
[START] [2019-10-02 10:24:33] parse_names
[WARN] [2019-10-02 10:24:33] I see 2844 names which still need to be parsed.
[STOP] [2019-10-02 10:24:36] parse_names
[START] [2019-10-02 10:24:36] denormalize_canonical_names_to_nodes
[STOP] [2019-10-02 10:24:36] denormalize_canonical_names_to_nodes
[START] [2019-10-02 10:24:36] match_nodes
[START] [2019-10-02 10:24:36] map_all_nodes_to_pages
[STOP] [2019-10-02 10:26:57] map_all_nodes_to_pages
[INFO] [2019-10-02 10:26:57] 224 Unmatched nodes (of 2844)! That's too many to output. First 10: Coerebidae (#47691550); Butorides striatus (#47694182); Strumigenys eggersi (#47692481); Strumigenys emmae (#47694331); Cardiocondyla minutior (#47693321); Limnodromus (#47691721); Thalaseus (#47691954); Thalaseus maximus (#47691953); Anas discors (#47691609); Anas americana (#47691827)
[START] [2019-10-02 10:26:57] update_nodes
[STOP] [2019-10-02 10:26:58] update_nodes
[STOP] [2019-10-02 10:26:58] match_nodes
[START] [2019-10-02 10:26:58] reindex_search
[STOP] [2019-10-02 10:27:04] reindex_search
[START] [2019-10-02 10:27:04] normalize_units
[STOP] [2019-10-02 10:27:04] normalize_units
[START] [2019-10-02 10:27:04] calculate_statistics
[STOP] [2019-10-02 10:27:04] calculate_statistics
[START] [2019-10-02 10:27:04] complete_harvest_instance
[START] [2019-10-02 10:27:04] overall_tsv_creation
[INFO] [2019-10-02 10:27:04] Processing group of 2844 in 1 batches of 10000
[INFO] [2019-10-02 10:28:00] 964 Traits (unfiltered)...
[INFO] [2019-10-02 10:28:13] 964 Traits (filtered)...
[INFO] [2019-10-02 10:28:13] 0 Associations (filtered)...
[INFO] [2019-10-02 10:28:50] 4820 metadata added.
[INFO] [2019-10-02 10:28:50] 0 metadata added.
[INFO] [2019-10-02 10:28:50] Average Time: 82.39
[INFO] [2019-10-02 10:28:50] Total Time: 1m46s
[STOP] [2019-10-02 10:28:50] overall_tsv_creation
[INFO] [2019-10-02 10:28:50] Done. Check your files:
[INFO] [2019-10-02 10:28:51] (2844 lines) /app/public/data/barbados_sp_list/publish_nodes.tsv
[INFO] [2019-10-02 10:28:53] (5909 lines) /app/public/data/barbados_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-02 10:28:54] (2844 lines) /app/public/data/barbados_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-02 10:28:56] (965 lines) /app/public/data/barbados_sp_list/publish_traits.tsv
[INFO] [2019-10-02 10:28:57] (4821 lines) /app/public/data/barbados_sp_list/publish_metadata.tsv
[STOP] [2019-10-02 10:28:57] complete_harvest_instance
[START] [2019-10-02 10:28:57] completed
[STOP] [2019-10-02 10:28:57] completed
[STOP] [2019-10-02 10:28:57] logged process, took 332.82
Latest Process

02 Oct 10:23 EXITED currently processing 0