Harvest for Sea of Okhostk Species List Created 25 Dec 13:41

Stage: completed
Fetched: 25 Dec 13:41
Validated: 25 Dec 13:41
Deltas Created 25 Dec 13:41
Units Normalized: 25 Dec 13:45
Ancestry Built: 25 Dec 13:42
Nodes Matched: 25 Dec 13:45
Names Parsed: 25 Dec 13:42
New Models Stored: 25 Dec 13:42
Indexed: 25 Dec 13:45
Completed: 25 Dec 13:47
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-25 13:41:38 -0500 by logger.rb/56815
[START] [2019-12-25 13:41:38] logged process
[START] [2019-12-25 13:41:38] create_harvest_instance
[STOP] [2019-12-25 13:41:38] create_harvest_instance
[START] [2019-12-25 13:41:38] fetch_files
[STOP] [2019-12-25 13:41:38] fetch_files
[START] [2019-12-25 13:41:38] validate_each_file
[STOP] [2019-12-25 13:41:38] validate_each_file
[START] [2019-12-25 13:41:38] convert_to_csv
[CMD] [2019-12-25 13:41:38] /usr/bin/sort /app/public/converted_csv/sea_okhostk_sp_l_refs_19642.csv > /app/public/converted_csv/sea_okhostk_sp_l_refs_19642.csv_sorted
[CMD] [2019-12-25 13:41:39] /usr/bin/sort /app/public/converted_csv/sea_okhostk_sp_l_nodes_19643.csv > /app/public/converted_csv/sea_okhostk_sp_l_nodes_19643.csv_sorted
[CMD] [2019-12-25 13:41:40] /usr/bin/sort /app/public/converted_csv/sea_okhostk_sp_l_occurrences_19644.csv > /app/public/converted_csv/sea_okhostk_sp_l_occurrences_19644.csv_sorted
[CMD] [2019-12-25 13:41:40] /usr/bin/sort /app/public/converted_csv/sea_okhostk_sp_l_measurements_19645.csv > /app/public/converted_csv/sea_okhostk_sp_l_measurements_19645.csv_sorted
[STOP] [2019-12-25 13:41:41] convert_to_csv
[START] [2019-12-25 13:41:41] calculate_delta
[CMD] [2019-12-25 13:41:41] echo "0a" > /app/public/diff/sea_okhostk_sp_l_refs_19642.diff
[CMD] [2019-12-25 13:41:42] tail -n +1 /app/public/converted_csv/sea_okhostk_sp_l_refs_19642.csv >> /app/public/diff/sea_okhostk_sp_l_refs_19642.diff
[CMD] [2019-12-25 13:41:42] echo "." >> /app/public/diff/sea_okhostk_sp_l_refs_19642.diff
[CMD] [2019-12-25 13:41:43] echo "0a" > /app/public/diff/sea_okhostk_sp_l_nodes_19643.diff
[CMD] [2019-12-25 13:41:43] tail -n +1 /app/public/converted_csv/sea_okhostk_sp_l_nodes_19643.csv >> /app/public/diff/sea_okhostk_sp_l_nodes_19643.diff
[CMD] [2019-12-25 13:41:44] echo "." >> /app/public/diff/sea_okhostk_sp_l_nodes_19643.diff
[CMD] [2019-12-25 13:41:45] echo "0a" > /app/public/diff/sea_okhostk_sp_l_occurrences_19644.diff
[CMD] [2019-12-25 13:41:45] tail -n +1 /app/public/converted_csv/sea_okhostk_sp_l_occurrences_19644.csv >> /app/public/diff/sea_okhostk_sp_l_occurrences_19644.diff
[CMD] [2019-12-25 13:41:46] echo "." >> /app/public/diff/sea_okhostk_sp_l_occurrences_19644.diff
[CMD] [2019-12-25 13:41:47] echo "0a" > /app/public/diff/sea_okhostk_sp_l_measurements_19645.diff
[CMD] [2019-12-25 13:41:47] tail -n +1 /app/public/converted_csv/sea_okhostk_sp_l_measurements_19645.csv >> /app/public/diff/sea_okhostk_sp_l_measurements_19645.diff
[CMD] [2019-12-25 13:41:48] echo "." >> /app/public/diff/sea_okhostk_sp_l_measurements_19645.diff
[STOP] [2019-12-25 13:41:49] calculate_delta
[START] [2019-12-25 13:41:49] parse_diff_and_store
[INFO] [2019-12-25 13:41:49] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 13:41:50] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 13:41:51] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 13:41:52] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 13:41:59] Storing 2 References
[INFO] [2019-12-25 13:41:59] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 13:41:59] Average Time: 0.0
[INFO] [2019-12-25 13:41:59] Total Time: 1s
[INFO] [2019-12-25 13:41:59] Storing 2056 ScientificNames
[INFO] [2019-12-25 13:41:59] Processing group of 2056 in 3 groups of 1000
[INFO] [2019-12-25 13:42:00] Average Time: 0.313
[INFO] [2019-12-25 13:42:00] Total Time: 1s
[INFO] [2019-12-25 13:42:00] Storing 2056 Nodes
[INFO] [2019-12-25 13:42:00] Processing group of 2056 in 3 groups of 1000
[INFO] [2019-12-25 13:42:01] Average Time: 0.22
[INFO] [2019-12-25 13:42:01] Total Time: 1s
[INFO] [2019-12-25 13:42:01] Storing 958 Occurrences
[INFO] [2019-12-25 13:42:01] Processing group of 958 in 1 groups of 1000
[INFO] [2019-12-25 13:42:01] Average Time: 0.12
[INFO] [2019-12-25 13:42:01] Total Time: 1s
[INFO] [2019-12-25 13:42:01] Storing 1916 TraitsReferences
[INFO] [2019-12-25 13:42:01] Processing group of 1916 in 2 groups of 1000
[INFO] [2019-12-25 13:42:01] Average Time: 0.1
[INFO] [2019-12-25 13:42:01] Total Time: 1s
[INFO] [2019-12-25 13:42:01] Storing 1916 Traits
[INFO] [2019-12-25 13:42:01] Processing group of 1916 in 2 groups of 1000
[INFO] [2019-12-25 13:42:02] Average Time: 0.325
[INFO] [2019-12-25 13:42:02] Total Time: 1s
[INFO] [2019-12-25 13:42:02] Storing 1916 MetaTraits
[INFO] [2019-12-25 13:42:02] Processing group of 1916 in 2 groups of 1000
[INFO] [2019-12-25 13:42:02] Average Time: 0.16
[INFO] [2019-12-25 13:42:02] Total Time: 1s
[STOP] [2019-12-25 13:42:02] parse_diff_and_store
[START] [2019-12-25 13:42:02] resolve_keys
[INFO] [2019-12-25 13:42:13] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 13:42:13] traits to occurrences...
[INFO] [2019-12-25 13:42:14] traits to nodes (through occurrences)...
[INFO] [2019-12-25 13:42:15] Traits to sex term...
[INFO] [2019-12-25 13:42:15] Traits to lifestage term...
[INFO] [2019-12-25 13:42:16] MetaTraits to traits...
[INFO] [2019-12-25 13:42:16] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 13:42:17] Assocs to occurrences...
[INFO] [2019-12-25 13:42:17] Assocs to nodes...
[INFO] [2019-12-25 13:42:17] Assoc to sex term...
[INFO] [2019-12-25 13:42:17] Assoc to lifestage term...
[STOP] [2019-12-25 13:42:17] resolve_keys
[START] [2019-12-25 13:42:17] hold_for_later_1
[STOP] [2019-12-25 13:42:17] hold_for_later_1
[START] [2019-12-25 13:42:17] hold_for_later_2
[STOP] [2019-12-25 13:42:17] hold_for_later_2
[START] [2019-12-25 13:42:17] resolve_missing_parents
[STOP] [2019-12-25 13:42:19] resolve_missing_parents
[START] [2019-12-25 13:42:19] rebuild_nodes
[START] [2019-12-25 13:42:19] Flattener#flatten
[START] [2019-12-25 13:42:19] Flattener#study_resource
[START] [2019-12-25 13:42:19] Flattener#build_ancestry
[STOP] [2019-12-25 13:42:19] Flattener#build_ancestry
[INFO] [2019-12-25 13:42:19] 2056 ancestry keys
[START] [2019-12-25 13:42:19] build_node_ancestors
[INFO] [2019-12-25 13:42:19] old ancestors deleted.
[STOP] [2019-12-25 13:42:20] build_node_ancestors
[START] [2019-12-25 13:42:21] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 13:42:21] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 13:42:21] Flattener#flatten
[STOP] [2019-12-25 13:42:21] rebuild_nodes
[START] [2019-12-25 13:42:21] resolve_missing_media_owners
[STOP] [2019-12-25 13:42:21] resolve_missing_media_owners
[START] [2019-12-25 13:42:21] sanitize_media_verbatims
[STOP] [2019-12-25 13:42:21] sanitize_media_verbatims
[START] [2019-12-25 13:42:21] queue_downloads
[STOP] [2019-12-25 13:42:21] queue_downloads
[START] [2019-12-25 13:42:21] parse_names
[WARN] [2019-12-25 13:42:21] I see 2056 names which still need to be parsed.
[STOP] [2019-12-25 13:42:23] parse_names
[START] [2019-12-25 13:42:23] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 13:42:23] denormalize_canonical_names_to_nodes
[START] [2019-12-25 13:42:23] match_nodes
[START] [2019-12-25 13:42:23] map_all_nodes_to_pages
[STOP] [2019-12-25 13:45:30] map_all_nodes_to_pages
[INFO] [2019-12-25 13:45:30] 97 Unmatched nodes (of 2056)! That's too many to output. First 10: Ophiophthalmus (#62442079); Ophiophthalmus normani (#62442078); Florometra laodice (#62442312); Limicola (#62441517); Limicola falcinellus (#62441516); Eurynorhynchus (#62441697); Eurynorhynchus pygmeus (#62441696); Anas penelope (#62441063); Anas falcata (#62441142); Anas clypeata (#62441184)
[START] [2019-12-25 13:45:30] update_nodes
[STOP] [2019-12-25 13:45:31] update_nodes
[STOP] [2019-12-25 13:45:31] match_nodes
[START] [2019-12-25 13:45:31] reindex_search
[STOP] [2019-12-25 13:45:34] reindex_search
[START] [2019-12-25 13:45:34] normalize_units
[STOP] [2019-12-25 13:45:34] normalize_units
[START] [2019-12-25 13:45:34] calculate_statistics
[STOP] [2019-12-25 13:45:35] calculate_statistics
[START] [2019-12-25 13:45:35] complete_harvest_instance
[START] [2019-12-25 13:45:35] overall_tsv_creation
[INFO] [2019-12-25 13:45:35] Processing group of 2056 in 1 batches of 10000
[INFO] [2019-12-25 13:46:29] 958 Traits (unfiltered)...
[INFO] [2019-12-25 13:46:43] 958 Traits (filtered)...
[INFO] [2019-12-25 13:46:43] 0 Associations (filtered)...
[INFO] [2019-12-25 13:47:21] 4790 metadata added.
[INFO] [2019-12-25 13:47:21] 0 metadata added.
[INFO] [2019-12-25 13:47:21] Average Time: 83.14
[INFO] [2019-12-25 13:47:21] Total Time: 1m47s
[STOP] [2019-12-25 13:47:21] overall_tsv_creation
[INFO] [2019-12-25 13:47:21] Done. Check your files:
[INFO] [2019-12-25 13:47:22] (2056 lines) /app/public/data/sea_okhostk_sp_l/publish_nodes.tsv
[INFO] [2019-12-25 13:47:23] (9983 lines) /app/public/data/sea_okhostk_sp_l/publish_node_ancestors.tsv
[INFO] [2019-12-25 13:47:24] (2056 lines) /app/public/data/sea_okhostk_sp_l/publish_scientific_names.tsv
[INFO] [2019-12-25 13:47:24] (959 lines) /app/public/data/sea_okhostk_sp_l/publish_traits.tsv
[INFO] [2019-12-25 13:47:25] (4791 lines) /app/public/data/sea_okhostk_sp_l/publish_metadata.tsv
[STOP] [2019-12-25 13:47:25] complete_harvest_instance
[START] [2019-12-25 13:47:25] completed
[STOP] [2019-12-25 13:47:25] completed
[STOP] [2019-12-25 13:47:25] logged process, took 347.57
Latest Process

25 Dec 13:41 EXITED currently processing 0