Harvest for Niue Species List Created 14 Oct 14:10

Stage: completed
Fetched: 14 Oct 14:10
Validated: 14 Oct 14:10
Deltas Created 14 Oct 14:10
Units Normalized: 14 Oct 14:12
Ancestry Built: 14 Oct 14:11
Nodes Matched: 14 Oct 14:12
Names Parsed: 14 Oct 14:11
New Models Stored: 14 Oct 14:11
Indexed: 14 Oct 14:12
Completed: 14 Oct 14:14
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 14:10:57 -0400 by logger.rb/56815
[START] [2019-10-14 14:10:57] logged process
[START] [2019-10-14 14:10:57] create_harvest_instance
[STOP] [2019-10-14 14:10:58] create_harvest_instance
[START] [2019-10-14 14:10:58] fetch_files
[STOP] [2019-10-14 14:10:58] fetch_files
[START] [2019-10-14 14:10:58] validate_each_file
[STOP] [2019-10-14 14:10:58] validate_each_file
[START] [2019-10-14 14:10:58] convert_to_csv
[CMD] [2019-10-14 14:10:58] /usr/bin/sort /app/public/converted_csv/Niue_refs_16731.csv > /app/public/converted_csv/Niue_refs_16731.csv_sorted
[CMD] [2019-10-14 14:10:58] /usr/bin/sort /app/public/converted_csv/Niue_nodes_16732.csv > /app/public/converted_csv/Niue_nodes_16732.csv_sorted
[CMD] [2019-10-14 14:10:58] /usr/bin/sort /app/public/converted_csv/Niue_occurrences_16733.csv > /app/public/converted_csv/Niue_occurrences_16733.csv_sorted
[CMD] [2019-10-14 14:10:58] /usr/bin/sort /app/public/converted_csv/Niue_measurements_16734.csv > /app/public/converted_csv/Niue_measurements_16734.csv_sorted
[STOP] [2019-10-14 14:10:58] convert_to_csv
[START] [2019-10-14 14:10:58] calculate_delta
[CMD] [2019-10-14 14:10:58] echo "0a" > /app/public/diff/Niue_refs_16731.diff
[CMD] [2019-10-14 14:10:58] tail -n +1 /app/public/converted_csv/Niue_refs_16731.csv >> /app/public/diff/Niue_refs_16731.diff
[CMD] [2019-10-14 14:10:59] echo "." >> /app/public/diff/Niue_refs_16731.diff
[CMD] [2019-10-14 14:10:59] echo "0a" > /app/public/diff/Niue_nodes_16732.diff
[CMD] [2019-10-14 14:10:59] tail -n +1 /app/public/converted_csv/Niue_nodes_16732.csv >> /app/public/diff/Niue_nodes_16732.diff
[CMD] [2019-10-14 14:10:59] echo "." >> /app/public/diff/Niue_nodes_16732.diff
[CMD] [2019-10-14 14:10:59] echo "0a" > /app/public/diff/Niue_occurrences_16733.diff
[CMD] [2019-10-14 14:10:59] tail -n +1 /app/public/converted_csv/Niue_occurrences_16733.csv >> /app/public/diff/Niue_occurrences_16733.diff
[CMD] [2019-10-14 14:10:59] echo "." >> /app/public/diff/Niue_occurrences_16733.diff
[CMD] [2019-10-14 14:10:59] echo "0a" > /app/public/diff/Niue_measurements_16734.diff
[CMD] [2019-10-14 14:10:59] tail -n +1 /app/public/converted_csv/Niue_measurements_16734.csv >> /app/public/diff/Niue_measurements_16734.diff
[CMD] [2019-10-14 14:10:59] echo "." >> /app/public/diff/Niue_measurements_16734.diff
[STOP] [2019-10-14 14:10:59] calculate_delta
[START] [2019-10-14 14:10:59] parse_diff_and_store
[INFO] [2019-10-14 14:11:00] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 14:11:00] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 14:11:00] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 14:11:00] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 14:11:05] Storing 2 References
[INFO] [2019-10-14 14:11:05] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 14:11:05] Average Time: 0.0
[INFO] [2019-10-14 14:11:05] Total Time: 1s
[INFO] [2019-10-14 14:11:05] Storing 1538 ScientificNames
[INFO] [2019-10-14 14:11:05] Processing group of 1538 in 2 groups of 1000
[INFO] [2019-10-14 14:11:06] Average Time: 0.27
[INFO] [2019-10-14 14:11:06] Total Time: 1s
[INFO] [2019-10-14 14:11:06] Storing 1538 Nodes
[INFO] [2019-10-14 14:11:06] Processing group of 1538 in 2 groups of 1000
[INFO] [2019-10-14 14:11:06] Average Time: 0.23
[INFO] [2019-10-14 14:11:06] Total Time: 1s
[INFO] [2019-10-14 14:11:06] Storing 482 Occurrences
[INFO] [2019-10-14 14:11:06] Processing group of 482 in 1 groups of 1000
[INFO] [2019-10-14 14:11:06] Average Time: 0.06
[INFO] [2019-10-14 14:11:06] Total Time: 1s
[INFO] [2019-10-14 14:11:06] Storing 1590 TraitsReferences
[INFO] [2019-10-14 14:11:06] Processing group of 1590 in 2 groups of 1000
[INFO] [2019-10-14 14:11:06] Average Time: 0.095
[INFO] [2019-10-14 14:11:06] Total Time: 1s
[INFO] [2019-10-14 14:11:06] Storing 1589 Traits
[INFO] [2019-10-14 14:11:06] Processing group of 1589 in 2 groups of 1000
[INFO] [2019-10-14 14:11:07] Average Time: 0.295
[INFO] [2019-10-14 14:11:07] Total Time: 1s
[INFO] [2019-10-14 14:11:07] Storing 1586 MetaTraits
[INFO] [2019-10-14 14:11:07] Processing group of 1586 in 2 groups of 1000
[INFO] [2019-10-14 14:11:07] Average Time: 0.1
[INFO] [2019-10-14 14:11:07] Total Time: 1s
[STOP] [2019-10-14 14:11:07] parse_diff_and_store
[START] [2019-10-14 14:11:07] resolve_keys
[INFO] [2019-10-14 14:11:16] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 14:11:16] traits to occurrences...
[INFO] [2019-10-14 14:11:17] traits to nodes (through occurrences)...
[INFO] [2019-10-14 14:11:17] Traits to sex term...
[INFO] [2019-10-14 14:11:17] Traits to lifestage term...
[INFO] [2019-10-14 14:11:17] MetaTraits to traits...
[INFO] [2019-10-14 14:11:17] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 14:11:18] Assocs to occurrences...
[INFO] [2019-10-14 14:11:18] Assocs to nodes...
[INFO] [2019-10-14 14:11:18] Assoc to sex term...
[INFO] [2019-10-14 14:11:18] Assoc to lifestage term...
[STOP] [2019-10-14 14:11:18] resolve_keys
[START] [2019-10-14 14:11:18] hold_for_later_1
[STOP] [2019-10-14 14:11:18] hold_for_later_1
[START] [2019-10-14 14:11:18] hold_for_later_2
[STOP] [2019-10-14 14:11:18] hold_for_later_2
[START] [2019-10-14 14:11:18] resolve_missing_parents
[STOP] [2019-10-14 14:11:20] resolve_missing_parents
[START] [2019-10-14 14:11:20] rebuild_nodes
[START] [2019-10-14 14:11:20] Flattener#flatten
[START] [2019-10-14 14:11:20] Flattener#study_resource
[START] [2019-10-14 14:11:20] Flattener#build_ancestry
[STOP] [2019-10-14 14:11:20] Flattener#build_ancestry
[INFO] [2019-10-14 14:11:20] 1538 ancestry keys
[START] [2019-10-14 14:11:20] build_node_ancestors
[INFO] [2019-10-14 14:11:20] old ancestors deleted.
[STOP] [2019-10-14 14:11:20] build_node_ancestors
[START] [2019-10-14 14:11:20] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 14:11:20] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 14:11:20] Flattener#flatten
[STOP] [2019-10-14 14:11:20] rebuild_nodes
[START] [2019-10-14 14:11:20] resolve_missing_media_owners
[STOP] [2019-10-14 14:11:20] resolve_missing_media_owners
[START] [2019-10-14 14:11:20] sanitize_media_verbatims
[STOP] [2019-10-14 14:11:20] sanitize_media_verbatims
[START] [2019-10-14 14:11:20] queue_downloads
[STOP] [2019-10-14 14:11:20] queue_downloads
[START] [2019-10-14 14:11:20] parse_names
[WARN] [2019-10-14 14:11:20] I see 1538 names which still need to be parsed.
[STOP] [2019-10-14 14:11:23] parse_names
[START] [2019-10-14 14:11:23] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 14:11:23] denormalize_canonical_names_to_nodes
[START] [2019-10-14 14:11:23] match_nodes
[START] [2019-10-14 14:11:23] map_all_nodes_to_pages
[STOP] [2019-10-14 14:12:36] map_all_nodes_to_pages
[INFO] [2019-10-14 14:12:36] 107 Unmatched nodes (of 1538)! That's too many to output. First 10: Hydrophiidae (#50954040); Emoia lawesii (#50954633); Ostreoida (#50954046); Parahyotissa (#50954044); Arcoida (#50954050); Limoida (#50954054); Collonista inepta (#50954058); Vetigastropoda (#50954061); Archaeogastropoda (#50954068); Stomatellidae (#50954067)
[START] [2019-10-14 14:12:36] update_nodes
[STOP] [2019-10-14 14:12:37] update_nodes
[STOP] [2019-10-14 14:12:37] match_nodes
[START] [2019-10-14 14:12:37] reindex_search
[STOP] [2019-10-14 14:12:40] reindex_search
[START] [2019-10-14 14:12:40] normalize_units
[STOP] [2019-10-14 14:12:40] normalize_units
[START] [2019-10-14 14:12:40] calculate_statistics
[STOP] [2019-10-14 14:12:40] calculate_statistics
[START] [2019-10-14 14:12:40] complete_harvest_instance
[START] [2019-10-14 14:12:40] overall_tsv_creation
[INFO] [2019-10-14 14:12:40] Processing group of 1538 in 1 batches of 10000
[INFO] [2019-10-14 14:13:30] 482 Traits (unfiltered)...
[INFO] [2019-10-14 14:13:44] 482 Traits (filtered)...
[INFO] [2019-10-14 14:13:44] 0 Associations (filtered)...
[INFO] [2019-10-14 14:14:21] 2407 metadata added.
[INFO] [2019-10-14 14:14:21] 0 metadata added.
[INFO] [2019-10-14 14:14:21] Average Time: 79.83
[INFO] [2019-10-14 14:14:21] Total Time: 1m42s
[STOP] [2019-10-14 14:14:21] overall_tsv_creation
[INFO] [2019-10-14 14:14:21] Done. Check your files:
[INFO] [2019-10-14 14:14:21] (1538 lines) /app/public/data/Niue/publish_nodes.tsv
[INFO] [2019-10-14 14:14:21] (3124 lines) /app/public/data/Niue/publish_node_ancestors.tsv
[INFO] [2019-10-14 14:14:22] (1538 lines) /app/public/data/Niue/publish_scientific_names.tsv
[INFO] [2019-10-14 14:14:22] (483 lines) /app/public/data/Niue/publish_traits.tsv
[INFO] [2019-10-14 14:14:22] (2408 lines) /app/public/data/Niue/publish_metadata.tsv
[STOP] [2019-10-14 14:14:22] complete_harvest_instance
[START] [2019-10-14 14:14:22] completed
[STOP] [2019-10-14 14:14:22] completed
[STOP] [2019-10-14 14:14:22] logged process, took 204.56
Latest Process

14 Oct 14:10 EXITED currently processing 0