Harvest for Skagerrak Species List Created 25 Dec 13:54

Stage: completed
Fetched: 25 Dec 13:54
Validated: 25 Dec 13:54
Deltas Created 25 Dec 13:54
Units Normalized: 25 Dec 14:17
Ancestry Built: 25 Dec 13:56
Nodes Matched: 25 Dec 14:17
Names Parsed: 25 Dec 13:56
New Models Stored: 25 Dec 13:55
Indexed: 25 Dec 14:17
Completed: 25 Dec 14:19
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-12-25 13:54:51 -0500 by logger.rb/56815
[START] [2019-12-25 13:54:51] logged process
[START] [2019-12-25 13:54:51] create_harvest_instance
[STOP] [2019-12-25 13:54:52] create_harvest_instance
[START] [2019-12-25 13:54:52] fetch_files
[STOP] [2019-12-25 13:54:52] fetch_files
[START] [2019-12-25 13:54:52] validate_each_file
[STOP] [2019-12-25 13:54:53] validate_each_file
[START] [2019-12-25 13:54:53] convert_to_csv
[CMD] [2019-12-25 13:54:53] /usr/bin/sort /app/public/converted_csv/skagerrak_sp_lis_refs_19666.csv > /app/public/converted_csv/skagerrak_sp_lis_refs_19666.csv_sorted
[CMD] [2019-12-25 13:54:53] /usr/bin/sort /app/public/converted_csv/skagerrak_sp_lis_nodes_19667.csv > /app/public/converted_csv/skagerrak_sp_lis_nodes_19667.csv_sorted
[CMD] [2019-12-25 13:54:53] /usr/bin/sort /app/public/converted_csv/skagerrak_sp_lis_occurrences_19668.csv > /app/public/converted_csv/skagerrak_sp_lis_occurrences_19668.csv_sorted
[CMD] [2019-12-25 13:54:54] /usr/bin/sort /app/public/converted_csv/skagerrak_sp_lis_measurements_19669.csv > /app/public/converted_csv/skagerrak_sp_lis_measurements_19669.csv_sorted
[STOP] [2019-12-25 13:54:54] convert_to_csv
[START] [2019-12-25 13:54:54] calculate_delta
[CMD] [2019-12-25 13:54:54] echo "0a" > /app/public/diff/skagerrak_sp_lis_refs_19666.diff
[CMD] [2019-12-25 13:54:54] tail -n +1 /app/public/converted_csv/skagerrak_sp_lis_refs_19666.csv >> /app/public/diff/skagerrak_sp_lis_refs_19666.diff
[CMD] [2019-12-25 13:54:54] echo "." >> /app/public/diff/skagerrak_sp_lis_refs_19666.diff
[CMD] [2019-12-25 13:54:54] echo "0a" > /app/public/diff/skagerrak_sp_lis_nodes_19667.diff
[CMD] [2019-12-25 13:54:54] tail -n +1 /app/public/converted_csv/skagerrak_sp_lis_nodes_19667.csv >> /app/public/diff/skagerrak_sp_lis_nodes_19667.diff
[CMD] [2019-12-25 13:54:55] echo "." >> /app/public/diff/skagerrak_sp_lis_nodes_19667.diff
[CMD] [2019-12-25 13:54:55] echo "0a" > /app/public/diff/skagerrak_sp_lis_occurrences_19668.diff
[CMD] [2019-12-25 13:54:55] tail -n +1 /app/public/converted_csv/skagerrak_sp_lis_occurrences_19668.csv >> /app/public/diff/skagerrak_sp_lis_occurrences_19668.diff
[CMD] [2019-12-25 13:54:55] echo "." >> /app/public/diff/skagerrak_sp_lis_occurrences_19668.diff
[CMD] [2019-12-25 13:54:55] echo "0a" > /app/public/diff/skagerrak_sp_lis_measurements_19669.diff
[CMD] [2019-12-25 13:54:55] tail -n +1 /app/public/converted_csv/skagerrak_sp_lis_measurements_19669.csv >> /app/public/diff/skagerrak_sp_lis_measurements_19669.diff
[CMD] [2019-12-25 13:54:56] echo "." >> /app/public/diff/skagerrak_sp_lis_measurements_19669.diff
[STOP] [2019-12-25 13:54:56] calculate_delta
[START] [2019-12-25 13:54:56] parse_diff_and_store
[INFO] [2019-12-25 13:54:56] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 13:54:56] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 13:54:59] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 13:55:00] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 13:55:22] Storing 2 References
[INFO] [2019-12-25 13:55:22] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 13:55:22] Average Time: 0.0
[INFO] [2019-12-25 13:55:22] Total Time: 1s
[INFO] [2019-12-25 13:55:22] Storing 7631 ScientificNames
[INFO] [2019-12-25 13:55:22] Processing group of 7631 in 8 groups of 1000
[INFO] [2019-12-25 13:55:25] Average Time: 0.409
[INFO] [2019-12-25 13:55:25] Total Time: 4s
[INFO] [2019-12-25 13:55:25] last 3 / first 3: 0.91
[INFO] [2019-12-25 13:55:25] Std.Dev: 0.07071067811865475; Max: 0.49
[INFO] [2019-12-25 13:55:25] Storing 7631 Nodes
[INFO] [2019-12-25 13:55:25] Processing group of 7631 in 8 groups of 1000
[INFO] [2019-12-25 13:55:28] Average Time: 0.313
[INFO] [2019-12-25 13:55:28] Total Time: 3s
[INFO] [2019-12-25 13:55:28] last 3 / first 3: 0.9
[INFO] [2019-12-25 13:55:28] Std.Dev: 0.044721359549995794; Max: 0.36
[INFO] [2019-12-25 13:55:28] Storing 3830 Occurrences
[INFO] [2019-12-25 13:55:28] Processing group of 3830 in 4 groups of 1000
[INFO] [2019-12-25 13:55:28] Average Time: 0.11
[INFO] [2019-12-25 13:55:28] Total Time: 1s
[INFO] [2019-12-25 13:55:28] Storing 7660 TraitsReferences
[INFO] [2019-12-25 13:55:28] Processing group of 7660 in 8 groups of 1000
[INFO] [2019-12-25 13:55:29] Average Time: 0.088
[INFO] [2019-12-25 13:55:29] Total Time: 1s
[INFO] [2019-12-25 13:55:29] last 3 / first 3: 0.64
[INFO] [2019-12-25 13:55:29] Std.Dev: 0.03162277660168379; Max: 0.17
[INFO] [2019-12-25 13:55:29] Storing 7660 Traits
[INFO] [2019-12-25 13:55:29] Processing group of 7660 in 8 groups of 1000
[INFO] [2019-12-25 13:55:32] Average Time: 0.353
[INFO] [2019-12-25 13:55:32] Total Time: 3s
[INFO] [2019-12-25 13:55:32] last 3 / first 3: 0.82
[INFO] [2019-12-25 13:55:32] Std.Dev: 0.06324555320336758; Max: 0.44
[INFO] [2019-12-25 13:55:32] Storing 7659 MetaTraits
[INFO] [2019-12-25 13:55:32] Processing group of 7659 in 8 groups of 1000
[INFO] [2019-12-25 13:55:33] Average Time: 0.141
[INFO] [2019-12-25 13:55:33] Total Time: 2s
[INFO] [2019-12-25 13:55:33] last 3 / first 3: 0.83
[INFO] [2019-12-25 13:55:33] Std.Dev: 0.0; Max: 0.18
[STOP] [2019-12-25 13:55:33] parse_diff_and_store
[START] [2019-12-25 13:55:33] resolve_keys
[INFO] [2019-12-25 13:56:03] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 13:56:06] traits to occurrences...
[INFO] [2019-12-25 13:56:10] traits to nodes (through occurrences)...
[INFO] [2019-12-25 13:56:10] Traits to sex term...
[INFO] [2019-12-25 13:56:13] Traits to lifestage term...
[INFO] [2019-12-25 13:56:16] MetaTraits to traits...
[INFO] [2019-12-25 13:56:17] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 13:56:18] Assocs to occurrences...
[INFO] [2019-12-25 13:56:18] Assocs to nodes...
[INFO] [2019-12-25 13:56:18] Assoc to sex term...
[INFO] [2019-12-25 13:56:18] Assoc to lifestage term...
[STOP] [2019-12-25 13:56:18] resolve_keys
[START] [2019-12-25 13:56:18] hold_for_later_1
[STOP] [2019-12-25 13:56:18] hold_for_later_1
[START] [2019-12-25 13:56:18] hold_for_later_2
[STOP] [2019-12-25 13:56:18] hold_for_later_2
[START] [2019-12-25 13:56:18] resolve_missing_parents
[STOP] [2019-12-25 13:56:33] resolve_missing_parents
[START] [2019-12-25 13:56:33] rebuild_nodes
[START] [2019-12-25 13:56:33] Flattener#flatten
[START] [2019-12-25 13:56:33] Flattener#study_resource
[START] [2019-12-25 13:56:33] Flattener#build_ancestry
[STOP] [2019-12-25 13:56:34] Flattener#build_ancestry
[INFO] [2019-12-25 13:56:34] 7631 ancestry keys
[START] [2019-12-25 13:56:34] build_node_ancestors
[INFO] [2019-12-25 13:56:34] old ancestors deleted.
[STOP] [2019-12-25 13:56:37] build_node_ancestors
[START] [2019-12-25 13:56:40] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 13:56:41] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 13:56:41] Flattener#flatten
[STOP] [2019-12-25 13:56:41] rebuild_nodes
[START] [2019-12-25 13:56:41] resolve_missing_media_owners
[STOP] [2019-12-25 13:56:41] resolve_missing_media_owners
[START] [2019-12-25 13:56:41] sanitize_media_verbatims
[STOP] [2019-12-25 13:56:41] sanitize_media_verbatims
[START] [2019-12-25 13:56:41] queue_downloads
[STOP] [2019-12-25 13:56:41] queue_downloads
[START] [2019-12-25 13:56:41] parse_names
[WARN] [2019-12-25 13:56:41] I see 7631 names which still need to be parsed.
[STOP] [2019-12-25 13:56:49] parse_names
[START] [2019-12-25 13:56:49] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 13:56:49] denormalize_canonical_names_to_nodes
[START] [2019-12-25 13:56:49] match_nodes
[START] [2019-12-25 13:56:49] map_all_nodes_to_pages
[STOP] [2019-12-25 14:17:00] map_all_nodes_to_pages
[INFO] [2019-12-25 14:17:00] 376 Unmatched nodes (of 7631)! That's too many to output. First 10: Larus melanocephalus (#62452069); Larus ichthyaetus (#62456688); Tringa semipalmatus (#62452064); Philomachus (#62450505); Philomachus pugnax (#62450504); Limicola (#62450943); Limicola falcinellus (#62450942); Anas penelope (#62450485); Anas clypeata (#62450551); Anas strepera (#62450581)
[START] [2019-12-25 14:17:00] update_nodes
[STOP] [2019-12-25 14:17:03] update_nodes
[STOP] [2019-12-25 14:17:03] match_nodes
[START] [2019-12-25 14:17:03] reindex_search
[STOP] [2019-12-25 14:17:19] reindex_search
[START] [2019-12-25 14:17:19] normalize_units
[STOP] [2019-12-25 14:17:19] normalize_units
[START] [2019-12-25 14:17:19] calculate_statistics
[STOP] [2019-12-25 14:17:19] calculate_statistics
[START] [2019-12-25 14:17:19] complete_harvest_instance
[START] [2019-12-25 14:17:19] overall_tsv_creation
[INFO] [2019-12-25 14:17:19] Processing group of 7631 in 1 batches of 10000
[INFO] [2019-12-25 14:18:42] 3830 Traits (unfiltered)...
[INFO] [2019-12-25 14:18:55] 3830 Traits (filtered)...
[INFO] [2019-12-25 14:18:55] 0 Associations (filtered)...
[INFO] [2019-12-25 14:19:41] 19149 metadata added.
[INFO] [2019-12-25 14:19:41] 0 metadata added.
[INFO] [2019-12-25 14:19:41] Average Time: 113.0
[INFO] [2019-12-25 14:19:41] Total Time: 2m22s
[STOP] [2019-12-25 14:19:41] overall_tsv_creation
[INFO] [2019-12-25 14:19:41] Done. Check your files:
[INFO] [2019-12-25 14:19:41] (7631 lines) /app/public/data/skagerrak_sp_lis/publish_nodes.tsv
[INFO] [2019-12-25 14:19:41] (38126 lines) /app/public/data/skagerrak_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-12-25 14:19:41] (7631 lines) /app/public/data/skagerrak_sp_lis/publish_scientific_names.tsv
[INFO] [2019-12-25 14:19:42] (3831 lines) /app/public/data/skagerrak_sp_lis/publish_traits.tsv
[INFO] [2019-12-25 14:19:42] (19150 lines) /app/public/data/skagerrak_sp_lis/publish_metadata.tsv
[STOP] [2019-12-25 14:19:42] complete_harvest_instance
[START] [2019-12-25 14:19:42] completed
[STOP] [2019-12-25 14:19:42] completed
[STOP] [2019-12-25 14:19:42] logged process, took 1490.54
Latest Process

25 Dec 13:54 EXITED currently processing 0