Stage:
completed
Fetched:
17 Oct 11:16
Validated:
17 Oct 11:16
Deltas Created
17 Oct 11:16
Units Normalized:
17 Oct 11:23
Ancestry Built:
17 Oct 11:17
Nodes Matched:
17 Oct 11:23
Names Parsed:
17 Oct 11:17
New Models Stored:
17 Oct 11:16
Indexed:
17 Oct 11:23
Completed:
17 Oct 11:25
Time to Harvest:
less than a minute
Harvesting Log
(139 lines)
# Logfile created on 2019-10-17 11:16:32 -0400 by logger.rb/56815
[START] [2019-10-17 11:16:32] logged process
[START] [2019-10-17 11:16:32] create_harvest_instance
[STOP] [2019-10-17 11:16:33] create_harvest_instance
[START] [2019-10-17 11:16:33] fetch_files
[STOP] [2019-10-17 11:16:33] fetch_files
[START] [2019-10-17 11:16:33] validate_each_file
[STOP] [2019-10-17 11:16:34] validate_each_file
[START] [2019-10-17 11:16:34] convert_to_csv
[CMD] [2019-10-17 11:16:34] /usr/bin/sort /app/public/converted_csv/vanuatu_sp_list_refs_17729.csv > /app/public/converted_csv/vanuatu_sp_list_refs_17729.csv_sorted
[CMD] [2019-10-17 11:16:34] /usr/bin/sort /app/public/converted_csv/vanuatu_sp_list_nodes_17730.csv > /app/public/converted_csv/vanuatu_sp_list_nodes_17730.csv_sorted
[CMD] [2019-10-17 11:16:34] /usr/bin/sort /app/public/converted_csv/vanuatu_sp_list_occurrences_17731.csv > /app/public/converted_csv/vanuatu_sp_list_occurrences_17731.csv_sorted
[CMD] [2019-10-17 11:16:34] /usr/bin/sort /app/public/converted_csv/vanuatu_sp_list_measurements_17732.csv > /app/public/converted_csv/vanuatu_sp_list_measurements_17732.csv_sorted
[STOP] [2019-10-17 11:16:34] convert_to_csv
[START] [2019-10-17 11:16:34] calculate_delta
[CMD] [2019-10-17 11:16:34] echo "0a" > /app/public/diff/vanuatu_sp_list_refs_17729.diff
[CMD] [2019-10-17 11:16:34] tail -n +1 /app/public/converted_csv/vanuatu_sp_list_refs_17729.csv >> /app/public/diff/vanuatu_sp_list_refs_17729.diff
[CMD] [2019-10-17 11:16:34] echo "." >> /app/public/diff/vanuatu_sp_list_refs_17729.diff
[CMD] [2019-10-17 11:16:34] echo "0a" > /app/public/diff/vanuatu_sp_list_nodes_17730.diff
[CMD] [2019-10-17 11:16:34] tail -n +1 /app/public/converted_csv/vanuatu_sp_list_nodes_17730.csv >> /app/public/diff/vanuatu_sp_list_nodes_17730.diff
[CMD] [2019-10-17 11:16:34] echo "." >> /app/public/diff/vanuatu_sp_list_nodes_17730.diff
[CMD] [2019-10-17 11:16:34] echo "0a" > /app/public/diff/vanuatu_sp_list_occurrences_17731.diff
[CMD] [2019-10-17 11:16:35] tail -n +1 /app/public/converted_csv/vanuatu_sp_list_occurrences_17731.csv >> /app/public/diff/vanuatu_sp_list_occurrences_17731.diff
[CMD] [2019-10-17 11:16:35] echo "." >> /app/public/diff/vanuatu_sp_list_occurrences_17731.diff
[CMD] [2019-10-17 11:16:35] echo "0a" > /app/public/diff/vanuatu_sp_list_measurements_17732.diff
[CMD] [2019-10-17 11:16:35] tail -n +1 /app/public/converted_csv/vanuatu_sp_list_measurements_17732.csv >> /app/public/diff/vanuatu_sp_list_measurements_17732.diff
[CMD] [2019-10-17 11:16:35] echo "." >> /app/public/diff/vanuatu_sp_list_measurements_17732.diff
[STOP] [2019-10-17 11:16:35] calculate_delta
[START] [2019-10-17 11:16:35] parse_diff_and_store
[INFO] [2019-10-17 11:16:35] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-17 11:16:35] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-17 11:16:37] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-17 11:16:37] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-17 11:16:53] Storing 2 References
[INFO] [2019-10-17 11:16:53] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-17 11:16:53] Average Time: 0.0
[INFO] [2019-10-17 11:16:53] Total Time: 1s
[INFO] [2019-10-17 11:16:53] Storing 4990 ScientificNames
[INFO] [2019-10-17 11:16:53] Processing group of 4990 in 5 groups of 1000
[INFO] [2019-10-17 11:16:55] Average Time: 0.376
[INFO] [2019-10-17 11:16:55] Total Time: 2s
[INFO] [2019-10-17 11:16:55] Storing 4990 Nodes
[INFO] [2019-10-17 11:16:55] Processing group of 4990 in 5 groups of 1000
[INFO] [2019-10-17 11:16:56] Average Time: 0.274
[INFO] [2019-10-17 11:16:56] Total Time: 2s
[INFO] [2019-10-17 11:16:56] Storing 2726 Occurrences
[INFO] [2019-10-17 11:16:56] Processing group of 2726 in 3 groups of 1000
[INFO] [2019-10-17 11:16:56] Average Time: 0.1
[INFO] [2019-10-17 11:16:56] Total Time: 1s
[INFO] [2019-10-17 11:16:56] Storing 5452 TraitsReferences
[INFO] [2019-10-17 11:16:56] Processing group of 5452 in 6 groups of 1000
[INFO] [2019-10-17 11:16:57] Average Time: 0.078
[INFO] [2019-10-17 11:16:57] Total Time: 1s
[INFO] [2019-10-17 11:16:57] Storing 5452 Traits
[INFO] [2019-10-17 11:16:57] Processing group of 5452 in 6 groups of 1000
[INFO] [2019-10-17 11:16:58] Average Time: 0.268
[INFO] [2019-10-17 11:16:58] Total Time: 2s
[INFO] [2019-10-17 11:16:58] Storing 5445 MetaTraits
[INFO] [2019-10-17 11:16:58] Processing group of 5445 in 6 groups of 1000
[INFO] [2019-10-17 11:16:59] Average Time: 0.105
[INFO] [2019-10-17 11:16:59] Total Time: 1s
[STOP] [2019-10-17 11:16:59] parse_diff_and_store
[START] [2019-10-17 11:16:59] resolve_keys
[INFO] [2019-10-17 11:17:20] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-17 11:17:22] traits to occurrences...
[INFO] [2019-10-17 11:17:25] traits to nodes (through occurrences)...
[INFO] [2019-10-17 11:17:25] Traits to sex term...
[INFO] [2019-10-17 11:17:27] Traits to lifestage term...
[INFO] [2019-10-17 11:17:29] MetaTraits to traits...
[INFO] [2019-10-17 11:17:30] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-17 11:17:31] Assocs to occurrences...
[INFO] [2019-10-17 11:17:31] Assocs to nodes...
[INFO] [2019-10-17 11:17:31] Assoc to sex term...
[INFO] [2019-10-17 11:17:31] Assoc to lifestage term...
[STOP] [2019-10-17 11:17:31] resolve_keys
[START] [2019-10-17 11:17:31] hold_for_later_1
[STOP] [2019-10-17 11:17:31] hold_for_later_1
[START] [2019-10-17 11:17:31] hold_for_later_2
[STOP] [2019-10-17 11:17:31] hold_for_later_2
[START] [2019-10-17 11:17:31] resolve_missing_parents
[STOP] [2019-10-17 11:17:40] resolve_missing_parents
[START] [2019-10-17 11:17:40] rebuild_nodes
[START] [2019-10-17 11:17:40] Flattener#flatten
[START] [2019-10-17 11:17:40] Flattener#study_resource
[START] [2019-10-17 11:17:40] Flattener#build_ancestry
[STOP] [2019-10-17 11:17:40] Flattener#build_ancestry
[INFO] [2019-10-17 11:17:40] 4990 ancestry keys
[START] [2019-10-17 11:17:40] build_node_ancestors
[INFO] [2019-10-17 11:17:40] old ancestors deleted.
[STOP] [2019-10-17 11:17:42] build_node_ancestors
[START] [2019-10-17 11:17:44] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 11:17:44] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 11:17:44] Flattener#flatten
[STOP] [2019-10-17 11:17:44] rebuild_nodes
[START] [2019-10-17 11:17:44] resolve_missing_media_owners
[STOP] [2019-10-17 11:17:44] resolve_missing_media_owners
[START] [2019-10-17 11:17:44] sanitize_media_verbatims
[STOP] [2019-10-17 11:17:44] sanitize_media_verbatims
[START] [2019-10-17 11:17:44] queue_downloads
[STOP] [2019-10-17 11:17:44] queue_downloads
[START] [2019-10-17 11:17:44] parse_names
[WARN] [2019-10-17 11:17:44] I see 4990 names which still need to be parsed.
[STOP] [2019-10-17 11:17:49] parse_names
[START] [2019-10-17 11:17:49] denormalize_canonical_names_to_nodes
[STOP] [2019-10-17 11:17:49] denormalize_canonical_names_to_nodes
[START] [2019-10-17 11:17:49] match_nodes
[START] [2019-10-17 11:17:49] map_all_nodes_to_pages
[STOP] [2019-10-17 11:23:19] map_all_nodes_to_pages
[INFO] [2019-10-17 11:23:19] 273 Unmatched nodes (of 4990)! That's too many to output. First 10: Thalaseus (#52717607); Thalaseus bergii (#52717606); Collocalia spodiopygia (#52720957); Puffinus pacificus (#52720894); Ostorhinchus cyanosomus (#52721959); Fowleria auritus (#52721881); Nectamia guamensis (#52722046); Abudefduf bicolor (#52721411); Kuhlia marginatus (#52720185); Giuris aporos (#52721947)
[START] [2019-10-17 11:23:19] update_nodes
[STOP] [2019-10-17 11:23:21] update_nodes
[STOP] [2019-10-17 11:23:21] match_nodes
[START] [2019-10-17 11:23:21] reindex_search
[STOP] [2019-10-17 11:23:30] reindex_search
[START] [2019-10-17 11:23:30] normalize_units
[STOP] [2019-10-17 11:23:30] normalize_units
[START] [2019-10-17 11:23:30] calculate_statistics
[STOP] [2019-10-17 11:23:30] calculate_statistics
[START] [2019-10-17 11:23:30] complete_harvest_instance
[START] [2019-10-17 11:23:30] overall_tsv_creation
[INFO] [2019-10-17 11:23:30] Processing group of 4990 in 1 batches of 10000
[INFO] [2019-10-17 11:24:34] 2726 Traits (unfiltered)...
[INFO] [2019-10-17 11:24:47] 2726 Traits (filtered)...
[INFO] [2019-10-17 11:24:47] 0 Associations (filtered)...
[INFO] [2019-10-17 11:25:28] 13623 metadata added.
[INFO] [2019-10-17 11:25:28] 0 metadata added.
[INFO] [2019-10-17 11:25:29] Average Time: 94.71
[INFO] [2019-10-17 11:25:29] Total Time: 1m59s
[STOP] [2019-10-17 11:25:29] overall_tsv_creation
[INFO] [2019-10-17 11:25:29] Done. Check your files:
[INFO] [2019-10-17 11:25:29] (4990 lines) /app/public/data/vanuatu_sp_list/publish_nodes.tsv
[INFO] [2019-10-17 11:25:29] (25812 lines) /app/public/data/vanuatu_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-17 11:25:29] (4990 lines) /app/public/data/vanuatu_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-17 11:25:29] (2727 lines) /app/public/data/vanuatu_sp_list/publish_traits.tsv
[INFO] [2019-10-17 11:25:29] (13624 lines) /app/public/data/vanuatu_sp_list/publish_metadata.tsv
[STOP] [2019-10-17 11:25:29] complete_harvest_instance
[START] [2019-10-17 11:25:29] completed
[STOP] [2019-10-17 11:25:29] completed
[STOP] [2019-10-17 11:25:29] logged process, took 536.83
Latest Process