Harvest for Chukchi Sea Species List Created 23 Dec 00:26

Stage: completed
Fetched: 23 Dec 00:26
Validated: 23 Dec 00:26
Deltas Created 23 Dec 00:26
Units Normalized: 23 Dec 00:32
Ancestry Built: 23 Dec 00:27
Nodes Matched: 23 Dec 00:32
Names Parsed: 23 Dec 00:27
New Models Stored: 23 Dec 00:26
Indexed: 23 Dec 00:32
Completed: 23 Dec 00:34
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 00:26:48 -0500 by logger.rb/56815
[START] [2019-12-23 00:26:48] logged process
[START] [2019-12-23 00:26:48] create_harvest_instance
[STOP] [2019-12-23 00:26:48] create_harvest_instance
[START] [2019-12-23 00:26:48] fetch_files
[STOP] [2019-12-23 00:26:49] fetch_files
[START] [2019-12-23 00:26:49] validate_each_file
[STOP] [2019-12-23 00:26:49] validate_each_file
[START] [2019-12-23 00:26:49] convert_to_csv
[CMD] [2019-12-23 00:26:49] /usr/bin/sort /app/public/converted_csv/chukchi_sea_sp_l_refs_19186.csv > /app/public/converted_csv/chukchi_sea_sp_l_refs_19186.csv_sorted
[CMD] [2019-12-23 00:26:49] /usr/bin/sort /app/public/converted_csv/chukchi_sea_sp_l_nodes_19187.csv > /app/public/converted_csv/chukchi_sea_sp_l_nodes_19187.csv_sorted
[CMD] [2019-12-23 00:26:49] /usr/bin/sort /app/public/converted_csv/chukchi_sea_sp_l_occurrences_19188.csv > /app/public/converted_csv/chukchi_sea_sp_l_occurrences_19188.csv_sorted
[CMD] [2019-12-23 00:26:49] /usr/bin/sort /app/public/converted_csv/chukchi_sea_sp_l_measurements_19189.csv > /app/public/converted_csv/chukchi_sea_sp_l_measurements_19189.csv_sorted
[STOP] [2019-12-23 00:26:49] convert_to_csv
[START] [2019-12-23 00:26:49] calculate_delta
[CMD] [2019-12-23 00:26:49] echo "0a" > /app/public/diff/chukchi_sea_sp_l_refs_19186.diff
[CMD] [2019-12-23 00:26:49] tail -n +1 /app/public/converted_csv/chukchi_sea_sp_l_refs_19186.csv >> /app/public/diff/chukchi_sea_sp_l_refs_19186.diff
[CMD] [2019-12-23 00:26:49] echo "." >> /app/public/diff/chukchi_sea_sp_l_refs_19186.diff
[CMD] [2019-12-23 00:26:49] echo "0a" > /app/public/diff/chukchi_sea_sp_l_nodes_19187.diff
[CMD] [2019-12-23 00:26:49] tail -n +1 /app/public/converted_csv/chukchi_sea_sp_l_nodes_19187.csv >> /app/public/diff/chukchi_sea_sp_l_nodes_19187.diff
[CMD] [2019-12-23 00:26:49] echo "." >> /app/public/diff/chukchi_sea_sp_l_nodes_19187.diff
[CMD] [2019-12-23 00:26:49] echo "0a" > /app/public/diff/chukchi_sea_sp_l_occurrences_19188.diff
[CMD] [2019-12-23 00:26:49] tail -n +1 /app/public/converted_csv/chukchi_sea_sp_l_occurrences_19188.csv >> /app/public/diff/chukchi_sea_sp_l_occurrences_19188.diff
[CMD] [2019-12-23 00:26:49] echo "." >> /app/public/diff/chukchi_sea_sp_l_occurrences_19188.diff
[CMD] [2019-12-23 00:26:49] echo "0a" > /app/public/diff/chukchi_sea_sp_l_measurements_19189.diff
[CMD] [2019-12-23 00:26:49] tail -n +1 /app/public/converted_csv/chukchi_sea_sp_l_measurements_19189.csv >> /app/public/diff/chukchi_sea_sp_l_measurements_19189.diff
[CMD] [2019-12-23 00:26:49] echo "." >> /app/public/diff/chukchi_sea_sp_l_measurements_19189.diff
[STOP] [2019-12-23 00:26:49] calculate_delta
[START] [2019-12-23 00:26:49] parse_diff_and_store
[INFO] [2019-12-23 00:26:49] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 00:26:49] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 00:26:50] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 00:26:50] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 00:26:55] Storing 2 References
[INFO] [2019-12-23 00:26:55] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 00:26:55] Average Time: 0.0
[INFO] [2019-12-23 00:26:55] Total Time: 1s
[INFO] [2019-12-23 00:26:55] Storing 2029 ScientificNames
[INFO] [2019-12-23 00:26:55] Processing group of 2029 in 3 groups of 1000
[INFO] [2019-12-23 00:26:56] Average Time: 0.3
[INFO] [2019-12-23 00:26:56] Total Time: 1s
[INFO] [2019-12-23 00:26:56] Storing 2029 Nodes
[INFO] [2019-12-23 00:26:56] Processing group of 2029 in 3 groups of 1000
[INFO] [2019-12-23 00:26:57] Average Time: 0.223
[INFO] [2019-12-23 00:26:57] Total Time: 1s
[INFO] [2019-12-23 00:26:57] Storing 920 Occurrences
[INFO] [2019-12-23 00:26:57] Processing group of 920 in 1 groups of 1000
[INFO] [2019-12-23 00:26:57] Average Time: 0.12
[INFO] [2019-12-23 00:26:57] Total Time: 1s
[INFO] [2019-12-23 00:26:57] Storing 1840 TraitsReferences
[INFO] [2019-12-23 00:26:57] Processing group of 1840 in 2 groups of 1000
[INFO] [2019-12-23 00:26:57] Average Time: 0.135
[INFO] [2019-12-23 00:26:57] Total Time: 1s
[INFO] [2019-12-23 00:26:57] Storing 1840 Traits
[INFO] [2019-12-23 00:26:57] Processing group of 1840 in 2 groups of 1000
[INFO] [2019-12-23 00:26:58] Average Time: 0.355
[INFO] [2019-12-23 00:26:58] Total Time: 1s
[INFO] [2019-12-23 00:26:58] Storing 1840 MetaTraits
[INFO] [2019-12-23 00:26:58] Processing group of 1840 in 2 groups of 1000
[INFO] [2019-12-23 00:26:58] Average Time: 0.125
[INFO] [2019-12-23 00:26:58] Total Time: 1s
[STOP] [2019-12-23 00:26:58] parse_diff_and_store
[START] [2019-12-23 00:26:58] resolve_keys
[INFO] [2019-12-23 00:27:11] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 00:27:12] traits to occurrences...
[INFO] [2019-12-23 00:27:12] traits to nodes (through occurrences)...
[INFO] [2019-12-23 00:27:12] Traits to sex term...
[INFO] [2019-12-23 00:27:12] Traits to lifestage term...
[INFO] [2019-12-23 00:27:12] MetaTraits to traits...
[INFO] [2019-12-23 00:27:13] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 00:27:13] Assocs to occurrences...
[INFO] [2019-12-23 00:27:13] Assocs to nodes...
[INFO] [2019-12-23 00:27:13] Assoc to sex term...
[INFO] [2019-12-23 00:27:13] Assoc to lifestage term...
[STOP] [2019-12-23 00:27:13] resolve_keys
[START] [2019-12-23 00:27:13] hold_for_later_1
[STOP] [2019-12-23 00:27:13] hold_for_later_1
[START] [2019-12-23 00:27:13] hold_for_later_2
[STOP] [2019-12-23 00:27:13] hold_for_later_2
[START] [2019-12-23 00:27:13] resolve_missing_parents
[STOP] [2019-12-23 00:27:16] resolve_missing_parents
[START] [2019-12-23 00:27:16] rebuild_nodes
[START] [2019-12-23 00:27:16] Flattener#flatten
[START] [2019-12-23 00:27:16] Flattener#study_resource
[START] [2019-12-23 00:27:16] Flattener#build_ancestry
[STOP] [2019-12-23 00:27:16] Flattener#build_ancestry
[INFO] [2019-12-23 00:27:16] 2029 ancestry keys
[START] [2019-12-23 00:27:16] build_node_ancestors
[INFO] [2019-12-23 00:27:16] old ancestors deleted.
[STOP] [2019-12-23 00:27:17] build_node_ancestors
[START] [2019-12-23 00:27:17] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 00:27:18] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 00:27:18] Flattener#flatten
[STOP] [2019-12-23 00:27:18] rebuild_nodes
[START] [2019-12-23 00:27:18] resolve_missing_media_owners
[STOP] [2019-12-23 00:27:18] resolve_missing_media_owners
[START] [2019-12-23 00:27:18] sanitize_media_verbatims
[STOP] [2019-12-23 00:27:18] sanitize_media_verbatims
[START] [2019-12-23 00:27:18] queue_downloads
[STOP] [2019-12-23 00:27:18] queue_downloads
[START] [2019-12-23 00:27:18] parse_names
[WARN] [2019-12-23 00:27:18] I see 2029 names which still need to be parsed.
[STOP] [2019-12-23 00:27:20] parse_names
[START] [2019-12-23 00:27:20] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 00:27:20] denormalize_canonical_names_to_nodes
[START] [2019-12-23 00:27:20] match_nodes
[START] [2019-12-23 00:27:20] map_all_nodes_to_pages
[STOP] [2019-12-23 00:32:12] map_all_nodes_to_pages
[INFO] [2019-12-23 00:32:12] 103 Unmatched nodes (of 2029)! That's too many to output. First 10: Larus thayeri (#61819805); Limnodromus (#61818464); Eurynorhynchus (#61819066); Eurynorhynchus pygmeus (#61819065); Philomachus (#61819280); Philomachus pugnax (#61819279); Anas americana (#61818467); Anas clypeata (#61818549); Anas strepera (#61818807); Anas penelope (#61819695)
[START] [2019-12-23 00:32:12] update_nodes
[STOP] [2019-12-23 00:32:13] update_nodes
[STOP] [2019-12-23 00:32:13] match_nodes
[START] [2019-12-23 00:32:13] reindex_search
[STOP] [2019-12-23 00:32:17] reindex_search
[START] [2019-12-23 00:32:17] normalize_units
[STOP] [2019-12-23 00:32:17] normalize_units
[START] [2019-12-23 00:32:17] calculate_statistics
[STOP] [2019-12-23 00:32:17] calculate_statistics
[START] [2019-12-23 00:32:17] complete_harvest_instance
[START] [2019-12-23 00:32:17] overall_tsv_creation
[INFO] [2019-12-23 00:32:17] Processing group of 2029 in 1 batches of 10000
[INFO] [2019-12-23 00:33:13] 920 Traits (unfiltered)...
[INFO] [2019-12-23 00:33:27] 920 Traits (filtered)...
[INFO] [2019-12-23 00:33:27] 0 Associations (filtered)...
[INFO] [2019-12-23 00:34:08] 4600 metadata added.
[INFO] [2019-12-23 00:34:08] 0 metadata added.
[INFO] [2019-12-23 00:34:08] Average Time: 87.33
[INFO] [2019-12-23 00:34:08] Total Time: 1m52s
[STOP] [2019-12-23 00:34:08] overall_tsv_creation
[INFO] [2019-12-23 00:34:08] Done. Check your files:
[INFO] [2019-12-23 00:34:09] (2029 lines) /app/public/data/chukchi_sea_sp_l/publish_nodes.tsv
[INFO] [2019-12-23 00:34:09] (9852 lines) /app/public/data/chukchi_sea_sp_l/publish_node_ancestors.tsv
[INFO] [2019-12-23 00:34:09] (2029 lines) /app/public/data/chukchi_sea_sp_l/publish_scientific_names.tsv
[INFO] [2019-12-23 00:34:09] (921 lines) /app/public/data/chukchi_sea_sp_l/publish_traits.tsv
[INFO] [2019-12-23 00:34:09] (4601 lines) /app/public/data/chukchi_sea_sp_l/publish_metadata.tsv
[STOP] [2019-12-23 00:34:09] complete_harvest_instance
[START] [2019-12-23 00:34:09] completed
[STOP] [2019-12-23 00:34:09] completed
[STOP] [2019-12-23 00:34:09] logged process, took 440.98
Latest Process

23 Dec 00:26 EXITED currently processing 0