Harvest for Eswatini Species List Created 12 Oct 20:08

Stage: completed
Fetched: 12 Oct 20:08
Validated: 12 Oct 20:08
Deltas Created 12 Oct 20:08
Units Normalized: 12 Oct 20:16
Ancestry Built: 12 Oct 20:10
Nodes Matched: 12 Oct 20:16
Names Parsed: 12 Oct 20:10
New Models Stored: 12 Oct 20:09
Indexed: 12 Oct 20:16
Completed: 12 Oct 20:18
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-10-12 20:08:51 -0400 by logger.rb/56815
[START] [2019-10-12 20:08:51] logged process
[START] [2019-10-12 20:08:51] create_harvest_instance
[STOP] [2019-10-12 20:08:51] create_harvest_instance
[START] [2019-10-12 20:08:51] fetch_files
[STOP] [2019-10-12 20:08:51] fetch_files
[START] [2019-10-12 20:08:51] validate_each_file
[STOP] [2019-10-12 20:08:52] validate_each_file
[START] [2019-10-12 20:08:52] convert_to_csv
[CMD] [2019-10-12 20:08:52] /usr/bin/sort /app/public/converted_csv/swaziland_sp_lis_refs_15715.csv > /app/public/converted_csv/swaziland_sp_lis_refs_15715.csv_sorted
[CMD] [2019-10-12 20:08:52] /usr/bin/sort /app/public/converted_csv/swaziland_sp_lis_nodes_15716.csv > /app/public/converted_csv/swaziland_sp_lis_nodes_15716.csv_sorted
[CMD] [2019-10-12 20:08:52] /usr/bin/sort /app/public/converted_csv/swaziland_sp_lis_occurrences_15717.csv > /app/public/converted_csv/swaziland_sp_lis_occurrences_15717.csv_sorted
[CMD] [2019-10-12 20:08:53] /usr/bin/sort /app/public/converted_csv/swaziland_sp_lis_measurements_15718.csv > /app/public/converted_csv/swaziland_sp_lis_measurements_15718.csv_sorted
[STOP] [2019-10-12 20:08:53] convert_to_csv
[START] [2019-10-12 20:08:53] calculate_delta
[CMD] [2019-10-12 20:08:53] echo "0a" > /app/public/diff/swaziland_sp_lis_refs_15715.diff
[CMD] [2019-10-12 20:08:53] tail -n +1 /app/public/converted_csv/swaziland_sp_lis_refs_15715.csv >> /app/public/diff/swaziland_sp_lis_refs_15715.diff
[CMD] [2019-10-12 20:08:53] echo "." >> /app/public/diff/swaziland_sp_lis_refs_15715.diff
[CMD] [2019-10-12 20:08:53] echo "0a" > /app/public/diff/swaziland_sp_lis_nodes_15716.diff
[CMD] [2019-10-12 20:08:53] tail -n +1 /app/public/converted_csv/swaziland_sp_lis_nodes_15716.csv >> /app/public/diff/swaziland_sp_lis_nodes_15716.diff
[CMD] [2019-10-12 20:08:53] echo "." >> /app/public/diff/swaziland_sp_lis_nodes_15716.diff
[CMD] [2019-10-12 20:08:53] echo "0a" > /app/public/diff/swaziland_sp_lis_occurrences_15717.diff
[CMD] [2019-10-12 20:08:53] tail -n +1 /app/public/converted_csv/swaziland_sp_lis_occurrences_15717.csv >> /app/public/diff/swaziland_sp_lis_occurrences_15717.diff
[CMD] [2019-10-12 20:08:53] echo "." >> /app/public/diff/swaziland_sp_lis_occurrences_15717.diff
[CMD] [2019-10-12 20:08:53] echo "0a" > /app/public/diff/swaziland_sp_lis_measurements_15718.diff
[CMD] [2019-10-12 20:08:54] tail -n +1 /app/public/converted_csv/swaziland_sp_lis_measurements_15718.csv >> /app/public/diff/swaziland_sp_lis_measurements_15718.diff
[CMD] [2019-10-12 20:08:54] echo "." >> /app/public/diff/swaziland_sp_lis_measurements_15718.diff
[STOP] [2019-10-12 20:08:54] calculate_delta
[START] [2019-10-12 20:08:54] parse_diff_and_store
[INFO] [2019-10-12 20:08:54] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 20:08:54] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 20:08:57] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 20:08:57] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 20:09:24] Storing 2 References
[INFO] [2019-10-12 20:09:24] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 20:09:24] Average Time: 0.0
[INFO] [2019-10-12 20:09:24] Total Time: 1s
[INFO] [2019-10-12 20:09:24] Storing 6691 ScientificNames
[INFO] [2019-10-12 20:09:24] Processing group of 6691 in 7 groups of 1000
[INFO] [2019-10-12 20:09:26] Average Time: 0.387
[INFO] [2019-10-12 20:09:26] Total Time: 3s
[INFO] [2019-10-12 20:09:26] last 3 / first 3: 0.63
[INFO] [2019-10-12 20:09:26] Std.Dev: 0.14491376746189438; Max: 0.69
[INFO] [2019-10-12 20:09:26] Storing 6691 Nodes
[INFO] [2019-10-12 20:09:26] Processing group of 6691 in 7 groups of 1000
[INFO] [2019-10-12 20:09:28] Average Time: 0.296
[INFO] [2019-10-12 20:09:28] Total Time: 3s
[INFO] [2019-10-12 20:09:28] last 3 / first 3: 0.88
[INFO] [2019-10-12 20:09:28] Std.Dev: 0.044721359549995794; Max: 0.4
[INFO] [2019-10-12 20:09:28] Storing 3856 Occurrences
[INFO] [2019-10-12 20:09:28] Processing group of 3856 in 4 groups of 1000
[INFO] [2019-10-12 20:09:29] Average Time: 0.098
[INFO] [2019-10-12 20:09:29] Total Time: 1s
[INFO] [2019-10-12 20:09:29] Storing 8470 TraitsReferences
[INFO] [2019-10-12 20:09:29] Processing group of 8470 in 9 groups of 1000
[INFO] [2019-10-12 20:09:30] Average Time: 0.074
[INFO] [2019-10-12 20:09:30] Total Time: 1s
[INFO] [2019-10-12 20:09:30] last 3 / first 3: 0.57
[INFO] [2019-10-12 20:09:30] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-12 20:09:30] Storing 8469 Traits
[INFO] [2019-10-12 20:09:30] Processing group of 8469 in 9 groups of 1000
[INFO] [2019-10-12 20:09:32] Average Time: 0.283
[INFO] [2019-10-12 20:09:32] Total Time: 3s
[INFO] [2019-10-12 20:09:32] last 3 / first 3: 0.87
[INFO] [2019-10-12 20:09:32] Std.Dev: 0.07071067811865475; Max: 0.4
[INFO] [2019-10-12 20:09:32] Storing 8469 MetaTraits
[INFO] [2019-10-12 20:09:32] Processing group of 8469 in 9 groups of 1000
[INFO] [2019-10-12 20:09:33] Average Time: 0.106
[INFO] [2019-10-12 20:09:33] Total Time: 1s
[INFO] [2019-10-12 20:09:33] last 3 / first 3: 0.7
[INFO] [2019-10-12 20:09:33] Std.Dev: 0.03162277660168379; Max: 0.14
[STOP] [2019-10-12 20:09:33] parse_diff_and_store
[START] [2019-10-12 20:09:33] resolve_keys
[INFO] [2019-10-12 20:10:02] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 20:10:05] traits to occurrences...
[INFO] [2019-10-12 20:10:07] traits to nodes (through occurrences)...
[INFO] [2019-10-12 20:10:07] Traits to sex term...
[INFO] [2019-10-12 20:10:08] Traits to lifestage term...
[INFO] [2019-10-12 20:10:10] MetaTraits to traits...
[INFO] [2019-10-12 20:10:10] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 20:10:12] Assocs to occurrences...
[INFO] [2019-10-12 20:10:12] Assocs to nodes...
[INFO] [2019-10-12 20:10:12] Assoc to sex term...
[INFO] [2019-10-12 20:10:12] Assoc to lifestage term...
[STOP] [2019-10-12 20:10:12] resolve_keys
[START] [2019-10-12 20:10:12] hold_for_later_1
[STOP] [2019-10-12 20:10:12] hold_for_later_1
[START] [2019-10-12 20:10:12] hold_for_later_2
[STOP] [2019-10-12 20:10:12] hold_for_later_2
[START] [2019-10-12 20:10:12] resolve_missing_parents
[STOP] [2019-10-12 20:10:27] resolve_missing_parents
[START] [2019-10-12 20:10:27] rebuild_nodes
[START] [2019-10-12 20:10:27] Flattener#flatten
[START] [2019-10-12 20:10:27] Flattener#study_resource
[START] [2019-10-12 20:10:27] Flattener#build_ancestry
[STOP] [2019-10-12 20:10:27] Flattener#build_ancestry
[INFO] [2019-10-12 20:10:27] 6691 ancestry keys
[START] [2019-10-12 20:10:27] build_node_ancestors
[INFO] [2019-10-12 20:10:27] old ancestors deleted.
[STOP] [2019-10-12 20:10:29] build_node_ancestors
[START] [2019-10-12 20:10:31] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 20:10:32] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 20:10:32] Flattener#flatten
[STOP] [2019-10-12 20:10:32] rebuild_nodes
[START] [2019-10-12 20:10:32] resolve_missing_media_owners
[STOP] [2019-10-12 20:10:32] resolve_missing_media_owners
[START] [2019-10-12 20:10:32] sanitize_media_verbatims
[STOP] [2019-10-12 20:10:32] sanitize_media_verbatims
[START] [2019-10-12 20:10:32] queue_downloads
[STOP] [2019-10-12 20:10:32] queue_downloads
[START] [2019-10-12 20:10:32] parse_names
[WARN] [2019-10-12 20:10:32] I see 6691 names which still need to be parsed.
[STOP] [2019-10-12 20:10:39] parse_names
[START] [2019-10-12 20:10:39] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 20:10:39] denormalize_canonical_names_to_nodes
[START] [2019-10-12 20:10:39] match_nodes
[START] [2019-10-12 20:10:39] map_all_nodes_to_pages
[STOP] [2019-10-12 20:15:57] map_all_nodes_to_pages
[INFO] [2019-10-12 20:15:57] 273 Unmatched nodes (of 6691)! That's too many to output. First 10: Ortygospiza fuscocrissa (#49622816); Parus niger (#49617566); Tchagra senegala (#49620415); Telophorus sulfureopectus (#49617782); Telophorus olivaceus (#49618089); Lamprotornis corruscus (#49618292); Buphagus erythrorhynchus (#49618119); Spreo (#49618250); Spreo bicolor (#49618249); Notopholia corruscus (#49618271)
[START] [2019-10-12 20:15:57] update_nodes
[STOP] [2019-10-12 20:16:00] update_nodes
[STOP] [2019-10-12 20:16:00] match_nodes
[START] [2019-10-12 20:16:00] reindex_search
[STOP] [2019-10-12 20:16:15] reindex_search
[START] [2019-10-12 20:16:15] normalize_units
[STOP] [2019-10-12 20:16:15] normalize_units
[START] [2019-10-12 20:16:15] calculate_statistics
[STOP] [2019-10-12 20:16:15] calculate_statistics
[START] [2019-10-12 20:16:15] complete_harvest_instance
[START] [2019-10-12 20:16:15] overall_tsv_creation
[INFO] [2019-10-12 20:16:15] Processing group of 6691 in 1 batches of 10000
[INFO] [2019-10-12 20:17:31] 3856 Traits (unfiltered)...
[INFO] [2019-10-12 20:17:45] 3856 Traits (filtered)...
[INFO] [2019-10-12 20:17:45] 0 Associations (filtered)...
[INFO] [2019-10-12 20:18:30] 19279 metadata added.
[INFO] [2019-10-12 20:18:30] 0 metadata added.
[INFO] [2019-10-12 20:18:30] Average Time: 108.25
[INFO] [2019-10-12 20:18:30] Total Time: 2m15s
[STOP] [2019-10-12 20:18:30] overall_tsv_creation
[INFO] [2019-10-12 20:18:30] Done. Check your files:
[INFO] [2019-10-12 20:18:30] (6691 lines) /app/public/data/swaziland_sp_lis/publish_nodes.tsv
[INFO] [2019-10-12 20:18:30] (29916 lines) /app/public/data/swaziland_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-10-12 20:18:30] (6691 lines) /app/public/data/swaziland_sp_lis/publish_scientific_names.tsv
[INFO] [2019-10-12 20:18:30] (3857 lines) /app/public/data/swaziland_sp_lis/publish_traits.tsv
[INFO] [2019-10-12 20:18:30] (19280 lines) /app/public/data/swaziland_sp_lis/publish_metadata.tsv
[STOP] [2019-10-12 20:18:30] complete_harvest_instance
[START] [2019-10-12 20:18:30] completed
[STOP] [2019-10-12 20:18:30] completed
[STOP] [2019-10-12 20:18:30] logged process, took 579.4
Latest Process

12 Oct 20:08 EXITED currently processing 0