Harvest for Laptev Sea Species List Created 23 Dec 17:22

Stage: completed
Fetched: 23 Dec 17:22
Validated: 23 Dec 17:22
Deltas Created 23 Dec 17:22
Units Normalized: 23 Dec 17:29
Ancestry Built: 23 Dec 17:22
Nodes Matched: 23 Dec 17:29
Names Parsed: 23 Dec 17:22
New Models Stored: 23 Dec 17:22
Indexed: 23 Dec 17:29
Completed: 23 Dec 17:31
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 17:22:19 -0500 by logger.rb/56815
[START] [2019-12-23 17:22:19] logged process
[START] [2019-12-23 17:22:19] create_harvest_instance
[STOP] [2019-12-23 17:22:19] create_harvest_instance
[START] [2019-12-23 17:22:19] fetch_files
[STOP] [2019-12-23 17:22:19] fetch_files
[START] [2019-12-23 17:22:19] validate_each_file
[STOP] [2019-12-23 17:22:19] validate_each_file
[START] [2019-12-23 17:22:19] convert_to_csv
[CMD] [2019-12-23 17:22:19] /usr/bin/sort /app/public/converted_csv/laptev_sea_sp_li_refs_19442.csv > /app/public/converted_csv/laptev_sea_sp_li_refs_19442.csv_sorted
[CMD] [2019-12-23 17:22:20] /usr/bin/sort /app/public/converted_csv/laptev_sea_sp_li_nodes_19443.csv > /app/public/converted_csv/laptev_sea_sp_li_nodes_19443.csv_sorted
[CMD] [2019-12-23 17:22:21] /usr/bin/sort /app/public/converted_csv/laptev_sea_sp_li_occurrences_19444.csv > /app/public/converted_csv/laptev_sea_sp_li_occurrences_19444.csv_sorted
[CMD] [2019-12-23 17:22:21] /usr/bin/sort /app/public/converted_csv/laptev_sea_sp_li_measurements_19445.csv > /app/public/converted_csv/laptev_sea_sp_li_measurements_19445.csv_sorted
[STOP] [2019-12-23 17:22:22] convert_to_csv
[START] [2019-12-23 17:22:22] calculate_delta
[CMD] [2019-12-23 17:22:22] echo "0a" > /app/public/diff/laptev_sea_sp_li_refs_19442.diff
[CMD] [2019-12-23 17:22:23] tail -n +1 /app/public/converted_csv/laptev_sea_sp_li_refs_19442.csv >> /app/public/diff/laptev_sea_sp_li_refs_19442.diff
[CMD] [2019-12-23 17:22:24] echo "." >> /app/public/diff/laptev_sea_sp_li_refs_19442.diff
[CMD] [2019-12-23 17:22:24] echo "0a" > /app/public/diff/laptev_sea_sp_li_nodes_19443.diff
[CMD] [2019-12-23 17:22:25] tail -n +1 /app/public/converted_csv/laptev_sea_sp_li_nodes_19443.csv >> /app/public/diff/laptev_sea_sp_li_nodes_19443.diff
[CMD] [2019-12-23 17:22:26] echo "." >> /app/public/diff/laptev_sea_sp_li_nodes_19443.diff
[CMD] [2019-12-23 17:22:26] echo "0a" > /app/public/diff/laptev_sea_sp_li_occurrences_19444.diff
[CMD] [2019-12-23 17:22:27] tail -n +1 /app/public/converted_csv/laptev_sea_sp_li_occurrences_19444.csv >> /app/public/diff/laptev_sea_sp_li_occurrences_19444.diff
[CMD] [2019-12-23 17:22:28] echo "." >> /app/public/diff/laptev_sea_sp_li_occurrences_19444.diff
[CMD] [2019-12-23 17:22:28] echo "0a" > /app/public/diff/laptev_sea_sp_li_measurements_19445.diff
[CMD] [2019-12-23 17:22:29] tail -n +1 /app/public/converted_csv/laptev_sea_sp_li_measurements_19445.csv >> /app/public/diff/laptev_sea_sp_li_measurements_19445.diff
[CMD] [2019-12-23 17:22:30] echo "." >> /app/public/diff/laptev_sea_sp_li_measurements_19445.diff
[STOP] [2019-12-23 17:22:30] calculate_delta
[START] [2019-12-23 17:22:30] parse_diff_and_store
[INFO] [2019-12-23 17:22:31] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 17:22:32] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 17:22:33] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 17:22:34] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 17:22:36] Storing 2 References
[INFO] [2019-12-23 17:22:36] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 17:22:36] Average Time: 0.0
[INFO] [2019-12-23 17:22:36] Total Time: 1s
[INFO] [2019-12-23 17:22:36] Storing 1057 ScientificNames
[INFO] [2019-12-23 17:22:36] Processing group of 1057 in 2 groups of 1000
[INFO] [2019-12-23 17:22:37] Average Time: 0.275
[INFO] [2019-12-23 17:22:37] Total Time: 1s
[INFO] [2019-12-23 17:22:37] Storing 1057 Nodes
[INFO] [2019-12-23 17:22:37] Processing group of 1057 in 2 groups of 1000
[INFO] [2019-12-23 17:22:37] Average Time: 0.185
[INFO] [2019-12-23 17:22:37] Total Time: 1s
[INFO] [2019-12-23 17:22:37] Storing 438 Occurrences
[INFO] [2019-12-23 17:22:37] Processing group of 438 in 1 groups of 1000
[INFO] [2019-12-23 17:22:37] Average Time: 0.08
[INFO] [2019-12-23 17:22:37] Total Time: 1s
[INFO] [2019-12-23 17:22:37] Storing 876 TraitsReferences
[INFO] [2019-12-23 17:22:37] Processing group of 876 in 1 groups of 1000
[INFO] [2019-12-23 17:22:37] Average Time: 0.16
[INFO] [2019-12-23 17:22:37] Total Time: 1s
[INFO] [2019-12-23 17:22:37] Storing 876 Traits
[INFO] [2019-12-23 17:22:37] Processing group of 876 in 1 groups of 1000
[INFO] [2019-12-23 17:22:38] Average Time: 0.35
[INFO] [2019-12-23 17:22:38] Total Time: 1s
[INFO] [2019-12-23 17:22:38] Storing 876 MetaTraits
[INFO] [2019-12-23 17:22:38] Processing group of 876 in 1 groups of 1000
[INFO] [2019-12-23 17:22:38] Average Time: 0.17
[INFO] [2019-12-23 17:22:38] Total Time: 1s
[STOP] [2019-12-23 17:22:38] parse_diff_and_store
[START] [2019-12-23 17:22:38] resolve_keys
[INFO] [2019-12-23 17:22:44] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 17:22:45] traits to occurrences...
[INFO] [2019-12-23 17:22:45] traits to nodes (through occurrences)...
[INFO] [2019-12-23 17:22:45] Traits to sex term...
[INFO] [2019-12-23 17:22:45] Traits to lifestage term...
[INFO] [2019-12-23 17:22:45] MetaTraits to traits...
[INFO] [2019-12-23 17:22:45] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 17:22:45] Assocs to occurrences...
[INFO] [2019-12-23 17:22:45] Assocs to nodes...
[INFO] [2019-12-23 17:22:45] Assoc to sex term...
[INFO] [2019-12-23 17:22:45] Assoc to lifestage term...
[STOP] [2019-12-23 17:22:45] resolve_keys
[START] [2019-12-23 17:22:45] hold_for_later_1
[STOP] [2019-12-23 17:22:45] hold_for_later_1
[START] [2019-12-23 17:22:45] hold_for_later_2
[STOP] [2019-12-23 17:22:45] hold_for_later_2
[START] [2019-12-23 17:22:45] resolve_missing_parents
[STOP] [2019-12-23 17:22:46] resolve_missing_parents
[START] [2019-12-23 17:22:46] rebuild_nodes
[START] [2019-12-23 17:22:46] Flattener#flatten
[START] [2019-12-23 17:22:46] Flattener#study_resource
[START] [2019-12-23 17:22:46] Flattener#build_ancestry
[STOP] [2019-12-23 17:22:46] Flattener#build_ancestry
[INFO] [2019-12-23 17:22:46] 1057 ancestry keys
[START] [2019-12-23 17:22:46] build_node_ancestors
[INFO] [2019-12-23 17:22:46] old ancestors deleted.
[STOP] [2019-12-23 17:22:47] build_node_ancestors
[START] [2019-12-23 17:22:47] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 17:22:47] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 17:22:47] Flattener#flatten
[STOP] [2019-12-23 17:22:47] rebuild_nodes
[START] [2019-12-23 17:22:47] resolve_missing_media_owners
[STOP] [2019-12-23 17:22:47] resolve_missing_media_owners
[START] [2019-12-23 17:22:47] sanitize_media_verbatims
[STOP] [2019-12-23 17:22:47] sanitize_media_verbatims
[START] [2019-12-23 17:22:47] queue_downloads
[STOP] [2019-12-23 17:22:47] queue_downloads
[START] [2019-12-23 17:22:47] parse_names
[WARN] [2019-12-23 17:22:47] I see 1057 names which still need to be parsed.
[STOP] [2019-12-23 17:22:50] parse_names
[START] [2019-12-23 17:22:50] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 17:22:50] denormalize_canonical_names_to_nodes
[START] [2019-12-23 17:22:50] match_nodes
[START] [2019-12-23 17:22:50] map_all_nodes_to_pages
[STOP] [2019-12-23 17:29:47] map_all_nodes_to_pages
[INFO] [2019-12-23 17:29:47] 84 Unmatched nodes (of 1057)! That's too many to output. First 10: Krithe glacialis (#62094613); Paracyprideis pseudopunctillata (#62094620); Cytheropteron tumefactum (#62094633); Cytheropteron suzdalskyi (#62094645); Cytheropteron arcuatum (#62094649); Cytheropteron sulense (#62094653); Cytheropteron biconvexa (#62094673); Cytheropteron paralatissimum (#62094674); Cytheropteron champlainum (#62094762); Semicytherura complanata (#62094640)
[START] [2019-12-23 17:29:47] update_nodes
[STOP] [2019-12-23 17:29:48] update_nodes
[STOP] [2019-12-23 17:29:48] match_nodes
[START] [2019-12-23 17:29:48] reindex_search
[STOP] [2019-12-23 17:29:53] reindex_search
[START] [2019-12-23 17:29:53] normalize_units
[STOP] [2019-12-23 17:29:53] normalize_units
[START] [2019-12-23 17:29:53] calculate_statistics
[STOP] [2019-12-23 17:29:53] calculate_statistics
[START] [2019-12-23 17:29:53] complete_harvest_instance
[START] [2019-12-23 17:29:53] overall_tsv_creation
[INFO] [2019-12-23 17:29:53] Processing group of 1057 in 1 batches of 10000
[INFO] [2019-12-23 17:30:42] 438 Traits (unfiltered)...
[INFO] [2019-12-23 17:30:55] 438 Traits (filtered)...
[INFO] [2019-12-23 17:30:55] 0 Associations (filtered)...
[INFO] [2019-12-23 17:31:33] 2190 metadata added.
[INFO] [2019-12-23 17:31:33] 0 metadata added.
[INFO] [2019-12-23 17:31:33] Average Time: 77.51
[INFO] [2019-12-23 17:31:33] Total Time: 1m41s
[STOP] [2019-12-23 17:31:33] overall_tsv_creation
[INFO] [2019-12-23 17:31:33] Done. Check your files:
[INFO] [2019-12-23 17:31:34] (1057 lines) /app/public/data/laptev_sea_sp_li/publish_nodes.tsv
[INFO] [2019-12-23 17:31:34] (4826 lines) /app/public/data/laptev_sea_sp_li/publish_node_ancestors.tsv
[INFO] [2019-12-23 17:31:35] (1057 lines) /app/public/data/laptev_sea_sp_li/publish_scientific_names.tsv
[INFO] [2019-12-23 17:31:36] (439 lines) /app/public/data/laptev_sea_sp_li/publish_traits.tsv
[INFO] [2019-12-23 17:31:36] (2191 lines) /app/public/data/laptev_sea_sp_li/publish_metadata.tsv
[STOP] [2019-12-23 17:31:36] complete_harvest_instance
[START] [2019-12-23 17:31:36] completed
[STOP] [2019-12-23 17:31:36] completed
[STOP] [2019-12-23 17:31:36] logged process, took 557.64
Latest Process

23 Dec 17:22 EXITED currently processing 0