Harvest for Bay of Fundy Species List Created 22 Dec 21:54

Stage: completed
Fetched: 22 Dec 21:54
Validated: 22 Dec 21:54
Deltas Created 22 Dec 21:55
Units Normalized: 22 Dec 22:04
Ancestry Built: 22 Dec 21:56
Nodes Matched: 22 Dec 22:04
Names Parsed: 22 Dec 21:56
New Models Stored: 22 Dec 21:55
Indexed: 22 Dec 22:04
Completed: 22 Dec 22:06
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-22 21:54:57 -0500 by logger.rb/56815
[START] [2019-12-22 21:54:57] logged process
[START] [2019-12-22 21:54:57] create_harvest_instance
[STOP] [2019-12-22 21:54:58] create_harvest_instance
[START] [2019-12-22 21:54:58] fetch_files
[STOP] [2019-12-22 21:54:58] fetch_files
[START] [2019-12-22 21:54:58] validate_each_file
[STOP] [2019-12-22 21:54:59] validate_each_file
[START] [2019-12-22 21:54:59] convert_to_csv
[CMD] [2019-12-22 21:54:59] /usr/bin/sort /app/public/converted_csv/bay_fundy_sp_lis_refs_19098.csv > /app/public/converted_csv/bay_fundy_sp_lis_refs_19098.csv_sorted
[CMD] [2019-12-22 21:54:59] /usr/bin/sort /app/public/converted_csv/bay_fundy_sp_lis_nodes_19099.csv > /app/public/converted_csv/bay_fundy_sp_lis_nodes_19099.csv_sorted
[CMD] [2019-12-22 21:55:00] /usr/bin/sort /app/public/converted_csv/bay_fundy_sp_lis_occurrences_19100.csv > /app/public/converted_csv/bay_fundy_sp_lis_occurrences_19100.csv_sorted
[CMD] [2019-12-22 21:55:01] /usr/bin/sort /app/public/converted_csv/bay_fundy_sp_lis_measurements_19101.csv > /app/public/converted_csv/bay_fundy_sp_lis_measurements_19101.csv_sorted
[STOP] [2019-12-22 21:55:01] convert_to_csv
[START] [2019-12-22 21:55:01] calculate_delta
[CMD] [2019-12-22 21:55:01] echo "0a" > /app/public/diff/bay_fundy_sp_lis_refs_19098.diff
[CMD] [2019-12-22 21:55:02] tail -n +1 /app/public/converted_csv/bay_fundy_sp_lis_refs_19098.csv >> /app/public/diff/bay_fundy_sp_lis_refs_19098.diff
[CMD] [2019-12-22 21:55:03] echo "." >> /app/public/diff/bay_fundy_sp_lis_refs_19098.diff
[CMD] [2019-12-22 21:55:03] echo "0a" > /app/public/diff/bay_fundy_sp_lis_nodes_19099.diff
[CMD] [2019-12-22 21:55:04] tail -n +1 /app/public/converted_csv/bay_fundy_sp_lis_nodes_19099.csv >> /app/public/diff/bay_fundy_sp_lis_nodes_19099.diff
[CMD] [2019-12-22 21:55:05] echo "." >> /app/public/diff/bay_fundy_sp_lis_nodes_19099.diff
[CMD] [2019-12-22 21:55:05] echo "0a" > /app/public/diff/bay_fundy_sp_lis_occurrences_19100.diff
[CMD] [2019-12-22 21:55:06] tail -n +1 /app/public/converted_csv/bay_fundy_sp_lis_occurrences_19100.csv >> /app/public/diff/bay_fundy_sp_lis_occurrences_19100.diff
[CMD] [2019-12-22 21:55:07] echo "." >> /app/public/diff/bay_fundy_sp_lis_occurrences_19100.diff
[CMD] [2019-12-22 21:55:07] echo "0a" > /app/public/diff/bay_fundy_sp_lis_measurements_19101.diff
[CMD] [2019-12-22 21:55:08] tail -n +1 /app/public/converted_csv/bay_fundy_sp_lis_measurements_19101.csv >> /app/public/diff/bay_fundy_sp_lis_measurements_19101.diff
[CMD] [2019-12-22 21:55:09] echo "." >> /app/public/diff/bay_fundy_sp_lis_measurements_19101.diff
[STOP] [2019-12-22 21:55:09] calculate_delta
[START] [2019-12-22 21:55:09] parse_diff_and_store
[INFO] [2019-12-22 21:55:10] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 21:55:11] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 21:55:13] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 21:55:15] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 21:55:25] Storing 2 References
[INFO] [2019-12-22 21:55:25] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 21:55:25] Average Time: 0.0
[INFO] [2019-12-22 21:55:25] Total Time: 1s
[INFO] [2019-12-22 21:55:25] Storing 3568 ScientificNames
[INFO] [2019-12-22 21:55:25] Processing group of 3568 in 4 groups of 1000
[INFO] [2019-12-22 21:55:26] Average Time: 0.385
[INFO] [2019-12-22 21:55:26] Total Time: 2s
[INFO] [2019-12-22 21:55:26] Storing 3568 Nodes
[INFO] [2019-12-22 21:55:26] Processing group of 3568 in 4 groups of 1000
[INFO] [2019-12-22 21:55:28] Average Time: 0.277
[INFO] [2019-12-22 21:55:28] Total Time: 2s
[INFO] [2019-12-22 21:55:28] Storing 1669 Occurrences
[INFO] [2019-12-22 21:55:28] Processing group of 1669 in 2 groups of 1000
[INFO] [2019-12-22 21:55:28] Average Time: 0.1
[INFO] [2019-12-22 21:55:28] Total Time: 1s
[INFO] [2019-12-22 21:55:28] Storing 3338 TraitsReferences
[INFO] [2019-12-22 21:55:28] Processing group of 3338 in 4 groups of 1000
[INFO] [2019-12-22 21:55:28] Average Time: 0.08
[INFO] [2019-12-22 21:55:28] Total Time: 1s
[INFO] [2019-12-22 21:55:28] Storing 3338 Traits
[INFO] [2019-12-22 21:55:28] Processing group of 3338 in 4 groups of 1000
[INFO] [2019-12-22 21:55:29] Average Time: 0.305
[INFO] [2019-12-22 21:55:29] Total Time: 2s
[INFO] [2019-12-22 21:55:29] Storing 3337 MetaTraits
[INFO] [2019-12-22 21:55:29] Processing group of 3337 in 4 groups of 1000
[INFO] [2019-12-22 21:55:30] Average Time: 0.12
[INFO] [2019-12-22 21:55:30] Total Time: 1s
[STOP] [2019-12-22 21:55:30] parse_diff_and_store
[START] [2019-12-22 21:55:30] resolve_keys
[INFO] [2019-12-22 21:55:50] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 21:55:52] traits to occurrences...
[INFO] [2019-12-22 21:55:53] traits to nodes (through occurrences)...
[INFO] [2019-12-22 21:55:53] Traits to sex term...
[INFO] [2019-12-22 21:55:53] Traits to lifestage term...
[INFO] [2019-12-22 21:55:54] MetaTraits to traits...
[INFO] [2019-12-22 21:55:54] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 21:55:55] Assocs to occurrences...
[INFO] [2019-12-22 21:55:55] Assocs to nodes...
[INFO] [2019-12-22 21:55:55] Assoc to sex term...
[INFO] [2019-12-22 21:55:55] Assoc to lifestage term...
[STOP] [2019-12-22 21:55:55] resolve_keys
[START] [2019-12-22 21:55:55] hold_for_later_1
[STOP] [2019-12-22 21:55:55] hold_for_later_1
[START] [2019-12-22 21:55:55] hold_for_later_2
[STOP] [2019-12-22 21:55:55] hold_for_later_2
[START] [2019-12-22 21:55:55] resolve_missing_parents
[STOP] [2019-12-22 21:56:03] resolve_missing_parents
[START] [2019-12-22 21:56:03] rebuild_nodes
[START] [2019-12-22 21:56:03] Flattener#flatten
[START] [2019-12-22 21:56:03] Flattener#study_resource
[START] [2019-12-22 21:56:03] Flattener#build_ancestry
[STOP] [2019-12-22 21:56:04] Flattener#build_ancestry
[INFO] [2019-12-22 21:56:04] 3568 ancestry keys
[START] [2019-12-22 21:56:04] build_node_ancestors
[INFO] [2019-12-22 21:56:04] old ancestors deleted.
[STOP] [2019-12-22 21:56:05] build_node_ancestors
[START] [2019-12-22 21:56:06] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 21:56:07] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 21:56:07] Flattener#flatten
[STOP] [2019-12-22 21:56:07] rebuild_nodes
[START] [2019-12-22 21:56:07] resolve_missing_media_owners
[STOP] [2019-12-22 21:56:07] resolve_missing_media_owners
[START] [2019-12-22 21:56:07] sanitize_media_verbatims
[STOP] [2019-12-22 21:56:07] sanitize_media_verbatims
[START] [2019-12-22 21:56:07] queue_downloads
[STOP] [2019-12-22 21:56:07] queue_downloads
[START] [2019-12-22 21:56:07] parse_names
[WARN] [2019-12-22 21:56:07] I see 3568 names which still need to be parsed.
[STOP] [2019-12-22 21:56:10] parse_names
[START] [2019-12-22 21:56:10] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 21:56:10] denormalize_canonical_names_to_nodes
[START] [2019-12-22 21:56:10] match_nodes
[START] [2019-12-22 21:56:10] map_all_nodes_to_pages
[STOP] [2019-12-22 22:04:24] map_all_nodes_to_pages
[INFO] [2019-12-22 22:04:24] 139 Unmatched nodes (of 3568)! That's too many to output. First 10: Tringa semipalmatus (#61745713); Limnodromus (#61743390); Philomachus (#61745637); Philomachus pugnax (#61745636); Anas americana (#61743385); Anas discors (#61743449); Anas strepera (#61743530); Anas clypeata (#61743704); Anas penelope (#61744351); Chen (#61744242)
[START] [2019-12-22 22:04:24] update_nodes
[STOP] [2019-12-22 22:04:25] update_nodes
[STOP] [2019-12-22 22:04:25] match_nodes
[START] [2019-12-22 22:04:25] reindex_search
[STOP] [2019-12-22 22:04:33] reindex_search
[START] [2019-12-22 22:04:33] normalize_units
[STOP] [2019-12-22 22:04:33] normalize_units
[START] [2019-12-22 22:04:33] calculate_statistics
[STOP] [2019-12-22 22:04:33] calculate_statistics
[START] [2019-12-22 22:04:33] complete_harvest_instance
[START] [2019-12-22 22:04:33] overall_tsv_creation
[INFO] [2019-12-22 22:04:33] Processing group of 3568 in 1 batches of 10000
[INFO] [2019-12-22 22:05:35] 1669 Traits (unfiltered)...
[INFO] [2019-12-22 22:05:48] 1669 Traits (filtered)...
[INFO] [2019-12-22 22:05:48] 0 Associations (filtered)...
[INFO] [2019-12-22 22:06:29] 8344 metadata added.
[INFO] [2019-12-22 22:06:29] 0 metadata added.
[INFO] [2019-12-22 22:06:29] Average Time: 91.25
[INFO] [2019-12-22 22:06:29] Total Time: 1m56s
[STOP] [2019-12-22 22:06:29] overall_tsv_creation
[INFO] [2019-12-22 22:06:29] Done. Check your files:
[INFO] [2019-12-22 22:06:30] (3568 lines) /app/public/data/bay_fundy_sp_lis/publish_nodes.tsv
[INFO] [2019-12-22 22:06:30] (17555 lines) /app/public/data/bay_fundy_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-12-22 22:06:31] (3568 lines) /app/public/data/bay_fundy_sp_lis/publish_scientific_names.tsv
[INFO] [2019-12-22 22:06:32] (1670 lines) /app/public/data/bay_fundy_sp_lis/publish_traits.tsv
[INFO] [2019-12-22 22:06:32] (8345 lines) /app/public/data/bay_fundy_sp_lis/publish_metadata.tsv
[STOP] [2019-12-22 22:06:33] complete_harvest_instance
[START] [2019-12-22 22:06:33] completed
[STOP] [2019-12-22 22:06:33] completed
[STOP] [2019-12-22 22:06:33] logged process, took 695.08
Latest Process

22 Dec 21:54 EXITED currently processing 0