Harvest for Lithuania Species List Created 14 Oct 02:13

Stage: completed
Fetched: 14 Oct 02:13
Validated: 14 Oct 02:13
Deltas Created 14 Oct 02:13
Units Normalized: 14 Oct 02:18
Ancestry Built: 14 Oct 02:14
Nodes Matched: 14 Oct 02:18
Names Parsed: 14 Oct 02:14
New Models Stored: 14 Oct 02:14
Indexed: 14 Oct 02:18
Completed: 14 Oct 02:20
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 02:13:40 -0400 by logger.rb/56815
[START] [2019-10-14 02:13:40] logged process
[START] [2019-10-14 02:13:40] create_harvest_instance
[STOP] [2019-10-14 02:13:41] create_harvest_instance
[START] [2019-10-14 02:13:41] fetch_files
[STOP] [2019-10-14 02:13:41] fetch_files
[START] [2019-10-14 02:13:41] validate_each_file
[STOP] [2019-10-14 02:13:41] validate_each_file
[START] [2019-10-14 02:13:41] convert_to_csv
[CMD] [2019-10-14 02:13:41] /usr/bin/sort /app/public/converted_csv/lithuania_sp_lis_refs_16435.csv > /app/public/converted_csv/lithuania_sp_lis_refs_16435.csv_sorted
[CMD] [2019-10-14 02:13:41] /usr/bin/sort /app/public/converted_csv/lithuania_sp_lis_nodes_16436.csv > /app/public/converted_csv/lithuania_sp_lis_nodes_16436.csv_sorted
[CMD] [2019-10-14 02:13:42] /usr/bin/sort /app/public/converted_csv/lithuania_sp_lis_occurrences_16437.csv > /app/public/converted_csv/lithuania_sp_lis_occurrences_16437.csv_sorted
[CMD] [2019-10-14 02:13:42] /usr/bin/sort /app/public/converted_csv/lithuania_sp_lis_measurements_16438.csv > /app/public/converted_csv/lithuania_sp_lis_measurements_16438.csv_sorted
[STOP] [2019-10-14 02:13:42] convert_to_csv
[START] [2019-10-14 02:13:42] calculate_delta
[CMD] [2019-10-14 02:13:42] echo "0a" > /app/public/diff/lithuania_sp_lis_refs_16435.diff
[CMD] [2019-10-14 02:13:42] tail -n +1 /app/public/converted_csv/lithuania_sp_lis_refs_16435.csv >> /app/public/diff/lithuania_sp_lis_refs_16435.diff
[CMD] [2019-10-14 02:13:42] echo "." >> /app/public/diff/lithuania_sp_lis_refs_16435.diff
[CMD] [2019-10-14 02:13:42] echo "0a" > /app/public/diff/lithuania_sp_lis_nodes_16436.diff
[CMD] [2019-10-14 02:13:42] tail -n +1 /app/public/converted_csv/lithuania_sp_lis_nodes_16436.csv >> /app/public/diff/lithuania_sp_lis_nodes_16436.diff
[CMD] [2019-10-14 02:13:42] echo "." >> /app/public/diff/lithuania_sp_lis_nodes_16436.diff
[CMD] [2019-10-14 02:13:42] echo "0a" > /app/public/diff/lithuania_sp_lis_occurrences_16437.diff
[CMD] [2019-10-14 02:13:42] tail -n +1 /app/public/converted_csv/lithuania_sp_lis_occurrences_16437.csv >> /app/public/diff/lithuania_sp_lis_occurrences_16437.diff
[CMD] [2019-10-14 02:13:42] echo "." >> /app/public/diff/lithuania_sp_lis_occurrences_16437.diff
[CMD] [2019-10-14 02:13:43] echo "0a" > /app/public/diff/lithuania_sp_lis_measurements_16438.diff
[CMD] [2019-10-14 02:13:43] tail -n +1 /app/public/converted_csv/lithuania_sp_lis_measurements_16438.csv >> /app/public/diff/lithuania_sp_lis_measurements_16438.diff
[CMD] [2019-10-14 02:13:43] echo "." >> /app/public/diff/lithuania_sp_lis_measurements_16438.diff
[STOP] [2019-10-14 02:13:43] calculate_delta
[START] [2019-10-14 02:13:43] parse_diff_and_store
[INFO] [2019-10-14 02:13:43] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 02:13:43] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 02:13:44] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 02:13:45] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 02:13:55] Storing 2 References
[INFO] [2019-10-14 02:13:55] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 02:13:55] Average Time: 0.0
[INFO] [2019-10-14 02:13:55] Total Time: 1s
[INFO] [2019-10-14 02:13:55] Storing 3791 ScientificNames
[INFO] [2019-10-14 02:13:55] Processing group of 3791 in 4 groups of 1000
[INFO] [2019-10-14 02:13:57] Average Time: 0.368
[INFO] [2019-10-14 02:13:57] Total Time: 2s
[INFO] [2019-10-14 02:13:57] Storing 3791 Nodes
[INFO] [2019-10-14 02:13:57] Processing group of 3791 in 4 groups of 1000
[INFO] [2019-10-14 02:13:58] Average Time: 0.288
[INFO] [2019-10-14 02:13:58] Total Time: 2s
[INFO] [2019-10-14 02:13:58] Storing 1446 Occurrences
[INFO] [2019-10-14 02:13:58] Processing group of 1446 in 2 groups of 1000
[INFO] [2019-10-14 02:13:58] Average Time: 0.09
[INFO] [2019-10-14 02:13:58] Total Time: 1s
[INFO] [2019-10-14 02:13:58] Storing 3660 TraitsReferences
[INFO] [2019-10-14 02:13:58] Processing group of 3660 in 4 groups of 1000
[INFO] [2019-10-14 02:13:59] Average Time: 0.083
[INFO] [2019-10-14 02:13:59] Total Time: 1s
[INFO] [2019-10-14 02:13:59] Storing 3659 Traits
[INFO] [2019-10-14 02:13:59] Processing group of 3659 in 4 groups of 1000
[INFO] [2019-10-14 02:14:00] Average Time: 0.31
[INFO] [2019-10-14 02:14:00] Total Time: 2s
[INFO] [2019-10-14 02:14:00] Storing 3659 MetaTraits
[INFO] [2019-10-14 02:14:00] Processing group of 3659 in 4 groups of 1000
[INFO] [2019-10-14 02:14:00] Average Time: 0.118
[INFO] [2019-10-14 02:14:00] Total Time: 1s
[STOP] [2019-10-14 02:14:00] parse_diff_and_store
[START] [2019-10-14 02:14:00] resolve_keys
[INFO] [2019-10-14 02:14:17] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 02:14:19] traits to occurrences...
[INFO] [2019-10-14 02:14:20] traits to nodes (through occurrences)...
[INFO] [2019-10-14 02:14:20] Traits to sex term...
[INFO] [2019-10-14 02:14:20] Traits to lifestage term...
[INFO] [2019-10-14 02:14:21] MetaTraits to traits...
[INFO] [2019-10-14 02:14:22] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 02:14:22] Assocs to occurrences...
[INFO] [2019-10-14 02:14:22] Assocs to nodes...
[INFO] [2019-10-14 02:14:22] Assoc to sex term...
[INFO] [2019-10-14 02:14:22] Assoc to lifestage term...
[STOP] [2019-10-14 02:14:22] resolve_keys
[START] [2019-10-14 02:14:22] hold_for_later_1
[STOP] [2019-10-14 02:14:22] hold_for_later_1
[START] [2019-10-14 02:14:22] hold_for_later_2
[STOP] [2019-10-14 02:14:22] hold_for_later_2
[START] [2019-10-14 02:14:22] resolve_missing_parents
[STOP] [2019-10-14 02:14:29] resolve_missing_parents
[START] [2019-10-14 02:14:29] rebuild_nodes
[START] [2019-10-14 02:14:29] Flattener#flatten
[START] [2019-10-14 02:14:29] Flattener#study_resource
[START] [2019-10-14 02:14:29] Flattener#build_ancestry
[STOP] [2019-10-14 02:14:29] Flattener#build_ancestry
[INFO] [2019-10-14 02:14:29] 3791 ancestry keys
[START] [2019-10-14 02:14:29] build_node_ancestors
[INFO] [2019-10-14 02:14:29] old ancestors deleted.
[STOP] [2019-10-14 02:14:29] build_node_ancestors
[START] [2019-10-14 02:14:30] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 02:14:31] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 02:14:31] Flattener#flatten
[STOP] [2019-10-14 02:14:31] rebuild_nodes
[START] [2019-10-14 02:14:31] resolve_missing_media_owners
[STOP] [2019-10-14 02:14:31] resolve_missing_media_owners
[START] [2019-10-14 02:14:31] sanitize_media_verbatims
[STOP] [2019-10-14 02:14:31] sanitize_media_verbatims
[START] [2019-10-14 02:14:31] queue_downloads
[STOP] [2019-10-14 02:14:31] queue_downloads
[START] [2019-10-14 02:14:31] parse_names
[WARN] [2019-10-14 02:14:31] I see 3791 names which still need to be parsed.
[STOP] [2019-10-14 02:14:34] parse_names
[START] [2019-10-14 02:14:34] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 02:14:34] denormalize_canonical_names_to_nodes
[START] [2019-10-14 02:14:34] match_nodes
[START] [2019-10-14 02:14:34] map_all_nodes_to_pages
[STOP] [2019-10-14 02:18:00] map_all_nodes_to_pages
[INFO] [2019-10-14 02:18:00] 353 Unmatched nodes (of 3791)! That's too many to output. First 10: Thalaseus (#50552466); Thalaseus sandvicensis (#50552465); Philomachus pugnax (#50551732); Pelophylax esculentus (#50554060); Parus montanus (#50552751); Parus caeruleus (#50554640); Corvus monedula (#50551709); Carduelis spinus (#50552467); Carduelis cannabina (#50554324); Delichon urbica (#50554394)
[START] [2019-10-14 02:18:00] update_nodes
[STOP] [2019-10-14 02:18:01] update_nodes
[STOP] [2019-10-14 02:18:01] match_nodes
[START] [2019-10-14 02:18:01] reindex_search
[STOP] [2019-10-14 02:18:08] reindex_search
[START] [2019-10-14 02:18:08] normalize_units
[STOP] [2019-10-14 02:18:08] normalize_units
[START] [2019-10-14 02:18:08] calculate_statistics
[STOP] [2019-10-14 02:18:08] calculate_statistics
[START] [2019-10-14 02:18:08] complete_harvest_instance
[START] [2019-10-14 02:18:08] overall_tsv_creation
[INFO] [2019-10-14 02:18:08] Processing group of 3791 in 1 batches of 10000
[INFO] [2019-10-14 02:19:10] 1446 Traits (unfiltered)...
[INFO] [2019-10-14 02:19:25] 1446 Traits (filtered)...
[INFO] [2019-10-14 02:19:25] 0 Associations (filtered)...
[INFO] [2019-10-14 02:20:06] 7230 metadata added.
[INFO] [2019-10-14 02:20:06] 0 metadata added.
[INFO] [2019-10-14 02:20:06] Average Time: 94.56
[INFO] [2019-10-14 02:20:06] Total Time: 1m58s
[STOP] [2019-10-14 02:20:06] overall_tsv_creation
[INFO] [2019-10-14 02:20:06] Done. Check your files:
[INFO] [2019-10-14 02:20:06] (3791 lines) /app/public/data/lithuania_sp_lis/publish_nodes.tsv
[INFO] [2019-10-14 02:20:07] (8044 lines) /app/public/data/lithuania_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-10-14 02:20:07] (3791 lines) /app/public/data/lithuania_sp_lis/publish_scientific_names.tsv
[INFO] [2019-10-14 02:20:07] (1447 lines) /app/public/data/lithuania_sp_lis/publish_traits.tsv
[INFO] [2019-10-14 02:20:07] (7231 lines) /app/public/data/lithuania_sp_lis/publish_metadata.tsv
[STOP] [2019-10-14 02:20:07] complete_harvest_instance
[START] [2019-10-14 02:20:07] completed
[STOP] [2019-10-14 02:20:07] completed
[STOP] [2019-10-14 02:20:07] logged process, took 386.82
Latest Process

14 Oct 02:13 EXITED currently processing 0