Harvest for Turkey Species List Created 16 Oct 18:38

Stage: completed
Fetched: 16 Oct 18:38
Validated: 16 Oct 18:38
Deltas Created 16 Oct 18:38
Units Normalized: 16 Oct 19:00
Ancestry Built: 16 Oct 18:42
Nodes Matched: 16 Oct 18:59
Names Parsed: 16 Oct 18:42
New Models Stored: 16 Oct 18:40
Indexed: 16 Oct 19:00
Completed: 16 Oct 19:04
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-16 18:38:55 -0400 by logger.rb/56815
[START] [2019-10-16 18:38:55] logged process
[START] [2019-10-16 18:38:55] create_harvest_instance
[STOP] [2019-10-16 18:38:55] create_harvest_instance
[START] [2019-10-16 18:38:55] fetch_files
[STOP] [2019-10-16 18:38:55] fetch_files
[START] [2019-10-16 18:38:55] validate_each_file
[STOP] [2019-10-16 18:38:57] validate_each_file
[START] [2019-10-16 18:38:57] convert_to_csv
[CMD] [2019-10-16 18:38:57] /usr/bin/sort /app/public/converted_csv/turkey_sp_list_refs_17545.csv > /app/public/converted_csv/turkey_sp_list_refs_17545.csv_sorted
[CMD] [2019-10-16 18:38:57] /usr/bin/sort /app/public/converted_csv/turkey_sp_list_nodes_17546.csv > /app/public/converted_csv/turkey_sp_list_nodes_17546.csv_sorted
[CMD] [2019-10-16 18:38:58] /usr/bin/sort /app/public/converted_csv/turkey_sp_list_occurrences_17547.csv > /app/public/converted_csv/turkey_sp_list_occurrences_17547.csv_sorted
[CMD] [2019-10-16 18:38:58] /usr/bin/sort /app/public/converted_csv/turkey_sp_list_measurements_17548.csv > /app/public/converted_csv/turkey_sp_list_measurements_17548.csv_sorted
[STOP] [2019-10-16 18:38:58] convert_to_csv
[START] [2019-10-16 18:38:58] calculate_delta
[CMD] [2019-10-16 18:38:58] echo "0a" > /app/public/diff/turkey_sp_list_refs_17545.diff
[CMD] [2019-10-16 18:38:58] tail -n +1 /app/public/converted_csv/turkey_sp_list_refs_17545.csv >> /app/public/diff/turkey_sp_list_refs_17545.diff
[CMD] [2019-10-16 18:38:58] echo "." >> /app/public/diff/turkey_sp_list_refs_17545.diff
[CMD] [2019-10-16 18:38:58] echo "0a" > /app/public/diff/turkey_sp_list_nodes_17546.diff
[CMD] [2019-10-16 18:38:58] tail -n +1 /app/public/converted_csv/turkey_sp_list_nodes_17546.csv >> /app/public/diff/turkey_sp_list_nodes_17546.diff
[CMD] [2019-10-16 18:38:58] echo "." >> /app/public/diff/turkey_sp_list_nodes_17546.diff
[CMD] [2019-10-16 18:38:58] echo "0a" > /app/public/diff/turkey_sp_list_occurrences_17547.diff
[CMD] [2019-10-16 18:38:58] tail -n +1 /app/public/converted_csv/turkey_sp_list_occurrences_17547.csv >> /app/public/diff/turkey_sp_list_occurrences_17547.diff
[CMD] [2019-10-16 18:38:58] echo "." >> /app/public/diff/turkey_sp_list_occurrences_17547.diff
[CMD] [2019-10-16 18:38:58] echo "0a" > /app/public/diff/turkey_sp_list_measurements_17548.diff
[CMD] [2019-10-16 18:38:58] tail -n +1 /app/public/converted_csv/turkey_sp_list_measurements_17548.csv >> /app/public/diff/turkey_sp_list_measurements_17548.diff
[CMD] [2019-10-16 18:38:58] echo "." >> /app/public/diff/turkey_sp_list_measurements_17548.diff
[STOP] [2019-10-16 18:38:58] calculate_delta
[START] [2019-10-16 18:38:58] parse_diff_and_store
[INFO] [2019-10-16 18:38:58] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 18:38:58] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 18:39:04] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 18:39:05] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 18:40:01] Storing 2 References
[INFO] [2019-10-16 18:40:01] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 18:40:01] Average Time: 0.0
[INFO] [2019-10-16 18:40:01] Total Time: 1s
[INFO] [2019-10-16 18:40:01] Storing 14847 ScientificNames
[INFO] [2019-10-16 18:40:01] Processing group of 14847 in 15 groups of 1000
[INFO] [2019-10-16 18:40:06] Average Time: 0.33
[INFO] [2019-10-16 18:40:06] Total Time: 6s
[INFO] [2019-10-16 18:40:06] last 3 / first 3: 0.91
[INFO] [2019-10-16 18:40:06] Std.Dev: 0.03162277660168379; Max: 0.4
[INFO] [2019-10-16 18:40:06] Storing 14847 Nodes
[INFO] [2019-10-16 18:40:06] Processing group of 14847 in 15 groups of 1000
[INFO] [2019-10-16 18:40:11] Average Time: 0.315
[INFO] [2019-10-16 18:40:11] Total Time: 5s
[INFO] [2019-10-16 18:40:11] last 3 / first 3: 0.91
[INFO] [2019-10-16 18:40:11] Std.Dev: 0.1; Max: 0.63
[INFO] [2019-10-16 18:40:11] Storing 10122 Occurrences
[INFO] [2019-10-16 18:40:11] Processing group of 10122 in 11 groups of 1000
[INFO] [2019-10-16 18:40:12] Average Time: 0.093
[INFO] [2019-10-16 18:40:12] Total Time: 2s
[INFO] [2019-10-16 18:40:12] last 3 / first 3: 0.75
[INFO] [2019-10-16 18:40:12] Std.Dev: 0.03162277660168379; Max: 0.14
[INFO] [2019-10-16 18:40:12] Storing 20530 TraitsReferences
[INFO] [2019-10-16 18:40:12] Processing group of 20530 in 21 groups of 1000
[INFO] [2019-10-16 18:40:14] Average Time: 0.065
[INFO] [2019-10-16 18:40:14] Total Time: 2s
[INFO] [2019-10-16 18:40:14] last 3 / first 3: 0.64
[INFO] [2019-10-16 18:40:14] Std.Dev: 0.0; Max: 0.13
[INFO] [2019-10-16 18:40:14] Storing 20529 Traits
[INFO] [2019-10-16 18:40:14] Processing group of 20529 in 21 groups of 1000
[INFO] [2019-10-16 18:40:20] Average Time: 0.276
[INFO] [2019-10-16 18:40:20] Total Time: 6s
[INFO] [2019-10-16 18:40:20] last 3 / first 3: 0.68
[INFO] [2019-10-16 18:40:20] Std.Dev: 0.044721359549995794; Max: 0.4
[INFO] [2019-10-16 18:40:20] Storing 20519 MetaTraits
[INFO] [2019-10-16 18:40:20] Processing group of 20519 in 21 groups of 1000
[INFO] [2019-10-16 18:40:22] Average Time: 0.105
[INFO] [2019-10-16 18:40:22] Total Time: 3s
[INFO] [2019-10-16 18:40:22] last 3 / first 3: 0.76
[INFO] [2019-10-16 18:40:22] Std.Dev: 0.0; Max: 0.14
[STOP] [2019-10-16 18:40:22] parse_diff_and_store
[START] [2019-10-16 18:40:22] resolve_keys
[INFO] [2019-10-16 18:41:18] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 18:41:23] traits to occurrences...
[INFO] [2019-10-16 18:41:29] traits to nodes (through occurrences)...
[INFO] [2019-10-16 18:41:29] Traits to sex term...
[INFO] [2019-10-16 18:41:35] Traits to lifestage term...
[INFO] [2019-10-16 18:41:40] MetaTraits to traits...
[INFO] [2019-10-16 18:41:42] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 18:41:45] Assocs to occurrences...
[INFO] [2019-10-16 18:41:45] Assocs to nodes...
[INFO] [2019-10-16 18:41:45] Assoc to sex term...
[INFO] [2019-10-16 18:41:45] Assoc to lifestage term...
[STOP] [2019-10-16 18:41:45] resolve_keys
[START] [2019-10-16 18:41:45] hold_for_later_1
[STOP] [2019-10-16 18:41:45] hold_for_later_1
[START] [2019-10-16 18:41:45] hold_for_later_2
[STOP] [2019-10-16 18:41:45] hold_for_later_2
[START] [2019-10-16 18:41:45] resolve_missing_parents
[STOP] [2019-10-16 18:42:14] resolve_missing_parents
[START] [2019-10-16 18:42:14] rebuild_nodes
[START] [2019-10-16 18:42:14] Flattener#flatten
[START] [2019-10-16 18:42:14] Flattener#study_resource
[START] [2019-10-16 18:42:14] Flattener#build_ancestry
[STOP] [2019-10-16 18:42:15] Flattener#build_ancestry
[INFO] [2019-10-16 18:42:15] 14847 ancestry keys
[START] [2019-10-16 18:42:15] build_node_ancestors
[INFO] [2019-10-16 18:42:15] old ancestors deleted.
[STOP] [2019-10-16 18:42:18] build_node_ancestors
[START] [2019-10-16 18:42:20] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 18:42:21] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 18:42:21] Flattener#flatten
[STOP] [2019-10-16 18:42:21] rebuild_nodes
[START] [2019-10-16 18:42:21] resolve_missing_media_owners
[STOP] [2019-10-16 18:42:21] resolve_missing_media_owners
[START] [2019-10-16 18:42:21] sanitize_media_verbatims
[STOP] [2019-10-16 18:42:21] sanitize_media_verbatims
[START] [2019-10-16 18:42:21] queue_downloads
[STOP] [2019-10-16 18:42:21] queue_downloads
[START] [2019-10-16 18:42:21] parse_names
[WARN] [2019-10-16 18:42:21] I see 14847 names which still need to be parsed.
[STOP] [2019-10-16 18:42:33] parse_names
[START] [2019-10-16 18:42:33] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 18:42:33] denormalize_canonical_names_to_nodes
[START] [2019-10-16 18:42:33] match_nodes
[START] [2019-10-16 18:42:33] map_all_nodes_to_pages
[STOP] [2019-10-16 18:59:08] map_all_nodes_to_pages
[INFO] [2019-10-16 18:59:08] 1353 Unmatched nodes (of 14847)! That's too many to output. First 10: Petronia xanthocollis (#52511477); Petronia brachydactyla (#52514442); Hirundo rupestris (#52510708); Delichon urbica (#52510672); Corvus monedula (#52510250); Calandrella rufescens (#52510621); Carduelis cannabina (#52510389); Carduelis chloris (#52510661); Carduelis flavirostris (#52510998); Carduelis spinus (#52511365)
[START] [2019-10-16 18:59:08] update_nodes
[STOP] [2019-10-16 18:59:13] update_nodes
[STOP] [2019-10-16 18:59:13] match_nodes
[START] [2019-10-16 18:59:13] reindex_search
[STOP] [2019-10-16 19:00:07] reindex_search
[START] [2019-10-16 19:00:07] normalize_units
[STOP] [2019-10-16 19:00:07] normalize_units
[START] [2019-10-16 19:00:07] calculate_statistics
[STOP] [2019-10-16 19:00:07] calculate_statistics
[START] [2019-10-16 19:00:07] complete_harvest_instance
[START] [2019-10-16 19:00:07] overall_tsv_creation
[INFO] [2019-10-16 19:00:07] Processing group of 14847 in 2 batches of 10000
[INFO] [2019-10-16 19:01:31] 6565 Traits (unfiltered)...
[INFO] [2019-10-16 19:01:44] 6565 Traits (filtered)...
[INFO] [2019-10-16 19:01:44] 0 Associations (filtered)...
[INFO] [2019-10-16 19:02:34] 32822 metadata added.
[INFO] [2019-10-16 19:02:34] 0 metadata added.
[INFO] [2019-10-16 19:03:38] 3557 Traits (unfiltered)...
[INFO] [2019-10-16 19:03:51] 3557 Traits (filtered)...
[INFO] [2019-10-16 19:03:51] 0 Associations (filtered)...
[INFO] [2019-10-16 19:04:35] 17778 metadata added.
[INFO] [2019-10-16 19:04:35] 0 metadata added.
[INFO] [2019-10-16 19:04:35] Average Time: 109.735
[INFO] [2019-10-16 19:04:35] Total Time: 4m29s
[STOP] [2019-10-16 19:04:35] overall_tsv_creation
[INFO] [2019-10-16 19:04:35] Done. Check your files:
[INFO] [2019-10-16 19:04:35] (14847 lines) /app/public/data/turkey_sp_list/publish_nodes.tsv
[INFO] [2019-10-16 19:04:35] (37906 lines) /app/public/data/turkey_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-16 19:04:35] (14847 lines) /app/public/data/turkey_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-16 19:04:35] (10123 lines) /app/public/data/turkey_sp_list/publish_traits.tsv
[INFO] [2019-10-16 19:04:35] (50601 lines) /app/public/data/turkey_sp_list/publish_metadata.tsv
[STOP] [2019-10-16 19:04:36] complete_harvest_instance
[START] [2019-10-16 19:04:36] completed
[STOP] [2019-10-16 19:04:36] completed
[STOP] [2019-10-16 19:04:36] logged process, took 1540.75
Latest Process

16 Oct 18:38 EXITED currently processing 0