Harvest for Laccadive Sea Species List Created 23 Dec 16:36

Stage: completed
Fetched: 23 Dec 16:36
Validated: 23 Dec 16:36
Deltas Created 23 Dec 16:36
Units Normalized: 23 Dec 17:19
Ancestry Built: 23 Dec 16:37
Nodes Matched: 23 Dec 17:19
Names Parsed: 23 Dec 16:37
New Models Stored: 23 Dec 16:36
Indexed: 23 Dec 17:19
Completed: 23 Dec 17:22
Time to Harvest: 1 minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 16:36:06 -0500 by logger.rb/56815
[START] [2019-12-23 16:36:06] logged process
[START] [2019-12-23 16:36:06] create_harvest_instance
[STOP] [2019-12-23 16:36:06] create_harvest_instance
[START] [2019-12-23 16:36:06] fetch_files
[STOP] [2019-12-23 16:36:06] fetch_files
[START] [2019-12-23 16:36:06] validate_each_file
[STOP] [2019-12-23 16:36:07] validate_each_file
[START] [2019-12-23 16:36:07] convert_to_csv
[CMD] [2019-12-23 16:36:07] /usr/bin/sort /app/public/converted_csv/laccadive_sea_sp_refs_19434.csv > /app/public/converted_csv/laccadive_sea_sp_refs_19434.csv_sorted
[CMD] [2019-12-23 16:36:08] /usr/bin/sort /app/public/converted_csv/laccadive_sea_sp_nodes_19435.csv > /app/public/converted_csv/laccadive_sea_sp_nodes_19435.csv_sorted
[CMD] [2019-12-23 16:36:08] /usr/bin/sort /app/public/converted_csv/laccadive_sea_sp_occurrences_19436.csv > /app/public/converted_csv/laccadive_sea_sp_occurrences_19436.csv_sorted
[CMD] [2019-12-23 16:36:09] /usr/bin/sort /app/public/converted_csv/laccadive_sea_sp_measurements_19437.csv > /app/public/converted_csv/laccadive_sea_sp_measurements_19437.csv_sorted
[STOP] [2019-12-23 16:36:10] convert_to_csv
[START] [2019-12-23 16:36:10] calculate_delta
[CMD] [2019-12-23 16:36:10] echo "0a" > /app/public/diff/laccadive_sea_sp_refs_19434.diff
[CMD] [2019-12-23 16:36:10] tail -n +1 /app/public/converted_csv/laccadive_sea_sp_refs_19434.csv >> /app/public/diff/laccadive_sea_sp_refs_19434.diff
[CMD] [2019-12-23 16:36:11] echo "." >> /app/public/diff/laccadive_sea_sp_refs_19434.diff
[CMD] [2019-12-23 16:36:12] echo "0a" > /app/public/diff/laccadive_sea_sp_nodes_19435.diff
[CMD] [2019-12-23 16:36:12] tail -n +1 /app/public/converted_csv/laccadive_sea_sp_nodes_19435.csv >> /app/public/diff/laccadive_sea_sp_nodes_19435.diff
[CMD] [2019-12-23 16:36:13] echo "." >> /app/public/diff/laccadive_sea_sp_nodes_19435.diff
[CMD] [2019-12-23 16:36:14] echo "0a" > /app/public/diff/laccadive_sea_sp_occurrences_19436.diff
[CMD] [2019-12-23 16:36:14] tail -n +1 /app/public/converted_csv/laccadive_sea_sp_occurrences_19436.csv >> /app/public/diff/laccadive_sea_sp_occurrences_19436.diff
[CMD] [2019-12-23 16:36:15] echo "." >> /app/public/diff/laccadive_sea_sp_occurrences_19436.diff
[CMD] [2019-12-23 16:36:16] echo "0a" > /app/public/diff/laccadive_sea_sp_measurements_19437.diff
[CMD] [2019-12-23 16:36:16] tail -n +1 /app/public/converted_csv/laccadive_sea_sp_measurements_19437.csv >> /app/public/diff/laccadive_sea_sp_measurements_19437.diff
[CMD] [2019-12-23 16:36:17] echo "." >> /app/public/diff/laccadive_sea_sp_measurements_19437.diff
[STOP] [2019-12-23 16:36:18] calculate_delta
[START] [2019-12-23 16:36:18] parse_diff_and_store
[INFO] [2019-12-23 16:36:18] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 16:36:19] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 16:36:22] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 16:36:23] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 16:36:40] Storing 2 References
[INFO] [2019-12-23 16:36:40] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 16:36:40] Average Time: 0.0
[INFO] [2019-12-23 16:36:40] Total Time: 1s
[INFO] [2019-12-23 16:36:40] Storing 5668 ScientificNames
[INFO] [2019-12-23 16:36:40] Processing group of 5668 in 6 groups of 1000
[INFO] [2019-12-23 16:36:43] Average Time: 0.423
[INFO] [2019-12-23 16:36:43] Total Time: 3s
[INFO] [2019-12-23 16:36:43] Storing 5668 Nodes
[INFO] [2019-12-23 16:36:43] Processing group of 5668 in 6 groups of 1000
[INFO] [2019-12-23 16:36:45] Average Time: 0.333
[INFO] [2019-12-23 16:36:45] Total Time: 3s
[INFO] [2019-12-23 16:36:45] Storing 2871 Occurrences
[INFO] [2019-12-23 16:36:45] Processing group of 2871 in 3 groups of 1000
[INFO] [2019-12-23 16:36:45] Average Time: 0.113
[INFO] [2019-12-23 16:36:45] Total Time: 1s
[INFO] [2019-12-23 16:36:45] Storing 5742 TraitsReferences
[INFO] [2019-12-23 16:36:45] Processing group of 5742 in 6 groups of 1000
[INFO] [2019-12-23 16:36:46] Average Time: 0.085
[INFO] [2019-12-23 16:36:46] Total Time: 1s
[INFO] [2019-12-23 16:36:46] Storing 5742 Traits
[INFO] [2019-12-23 16:36:46] Processing group of 5742 in 6 groups of 1000
[INFO] [2019-12-23 16:36:48] Average Time: 0.333
[INFO] [2019-12-23 16:36:48] Total Time: 3s
[INFO] [2019-12-23 16:36:48] Storing 5740 MetaTraits
[INFO] [2019-12-23 16:36:48] Processing group of 5740 in 6 groups of 1000
[INFO] [2019-12-23 16:36:48] Average Time: 0.14
[INFO] [2019-12-23 16:36:48] Total Time: 1s
[STOP] [2019-12-23 16:36:48] parse_diff_and_store
[START] [2019-12-23 16:36:48] resolve_keys
[INFO] [2019-12-23 16:37:12] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 16:37:14] traits to occurrences...
[INFO] [2019-12-23 16:37:15] traits to nodes (through occurrences)...
[INFO] [2019-12-23 16:37:16] Traits to sex term...
[INFO] [2019-12-23 16:37:17] Traits to lifestage term...
[INFO] [2019-12-23 16:37:18] MetaTraits to traits...
[INFO] [2019-12-23 16:37:18] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 16:37:19] Assocs to occurrences...
[INFO] [2019-12-23 16:37:19] Assocs to nodes...
[INFO] [2019-12-23 16:37:19] Assoc to sex term...
[INFO] [2019-12-23 16:37:19] Assoc to lifestage term...
[STOP] [2019-12-23 16:37:19] resolve_keys
[START] [2019-12-23 16:37:19] hold_for_later_1
[STOP] [2019-12-23 16:37:19] hold_for_later_1
[START] [2019-12-23 16:37:19] hold_for_later_2
[STOP] [2019-12-23 16:37:19] hold_for_later_2
[START] [2019-12-23 16:37:19] resolve_missing_parents
[STOP] [2019-12-23 16:37:30] resolve_missing_parents
[START] [2019-12-23 16:37:30] rebuild_nodes
[START] [2019-12-23 16:37:30] Flattener#flatten
[START] [2019-12-23 16:37:30] Flattener#study_resource
[START] [2019-12-23 16:37:30] Flattener#build_ancestry
[STOP] [2019-12-23 16:37:30] Flattener#build_ancestry
[INFO] [2019-12-23 16:37:30] 5668 ancestry keys
[START] [2019-12-23 16:37:30] build_node_ancestors
[INFO] [2019-12-23 16:37:30] old ancestors deleted.
[STOP] [2019-12-23 16:37:32] build_node_ancestors
[START] [2019-12-23 16:37:34] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 16:37:35] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 16:37:35] Flattener#flatten
[STOP] [2019-12-23 16:37:35] rebuild_nodes
[START] [2019-12-23 16:37:35] resolve_missing_media_owners
[STOP] [2019-12-23 16:37:35] resolve_missing_media_owners
[START] [2019-12-23 16:37:35] sanitize_media_verbatims
[STOP] [2019-12-23 16:37:35] sanitize_media_verbatims
[START] [2019-12-23 16:37:35] queue_downloads
[STOP] [2019-12-23 16:37:35] queue_downloads
[START] [2019-12-23 16:37:35] parse_names
[WARN] [2019-12-23 16:37:35] I see 5668 names which still need to be parsed.
[STOP] [2019-12-23 16:37:41] parse_names
[START] [2019-12-23 16:37:41] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 16:37:41] denormalize_canonical_names_to_nodes
[START] [2019-12-23 16:37:41] match_nodes
[START] [2019-12-23 16:37:41] map_all_nodes_to_pages
[STOP] [2019-12-23 17:19:24] map_all_nodes_to_pages
[INFO] [2019-12-23 17:19:24] 350 Unmatched nodes (of 5668)! That's too many to output. First 10: Egretta intermedia (#62088954); Limicola (#62089442); Limicola falcinellus (#62089441); Philomachus (#62089466); Philomachus pugnax (#62089465); Larus leucophthalmus (#62094514); Anas querquedula (#62089152); Anas clypeata (#62089603); Anas penelope (#62090891); Coracina melanoptera (#62093580)
[START] [2019-12-23 17:19:24] update_nodes
[STOP] [2019-12-23 17:19:26] update_nodes
[STOP] [2019-12-23 17:19:26] match_nodes
[START] [2019-12-23 17:19:26] reindex_search
[STOP] [2019-12-23 17:19:57] reindex_search
[START] [2019-12-23 17:19:57] normalize_units
[STOP] [2019-12-23 17:19:57] normalize_units
[START] [2019-12-23 17:19:57] calculate_statistics
[STOP] [2019-12-23 17:19:57] calculate_statistics
[START] [2019-12-23 17:19:57] complete_harvest_instance
[START] [2019-12-23 17:19:57] overall_tsv_creation
[INFO] [2019-12-23 17:19:57] Processing group of 5668 in 1 batches of 10000
[INFO] [2019-12-23 17:21:09] 2871 Traits (unfiltered)...
[INFO] [2019-12-23 17:21:22] 2871 Traits (filtered)...
[INFO] [2019-12-23 17:21:22] 0 Associations (filtered)...
[INFO] [2019-12-23 17:22:04] 14353 metadata added.
[INFO] [2019-12-23 17:22:04] 0 metadata added.
[INFO] [2019-12-23 17:22:04] Average Time: 101.42
[INFO] [2019-12-23 17:22:04] Total Time: 2m8s
[STOP] [2019-12-23 17:22:04] overall_tsv_creation
[INFO] [2019-12-23 17:22:04] Done. Check your files:
[INFO] [2019-12-23 17:22:05] (5668 lines) /app/public/data/laccadive_sea_sp/publish_nodes.tsv
[INFO] [2019-12-23 17:22:06] (28774 lines) /app/public/data/laccadive_sea_sp/publish_node_ancestors.tsv
[INFO] [2019-12-23 17:22:06] (5668 lines) /app/public/data/laccadive_sea_sp/publish_scientific_names.tsv
[INFO] [2019-12-23 17:22:07] (2872 lines) /app/public/data/laccadive_sea_sp/publish_traits.tsv
[INFO] [2019-12-23 17:22:08] (14354 lines) /app/public/data/laccadive_sea_sp/publish_metadata.tsv
[STOP] [2019-12-23 17:22:08] complete_harvest_instance
[START] [2019-12-23 17:22:08] completed
[STOP] [2019-12-23 17:22:08] completed
[STOP] [2019-12-23 17:22:08] logged process, took 2762.44
Latest Process

23 Dec 16:36 EXITED currently processing 0