Harvest for North Korean Species List Created 14 Oct 23:19

Stage: completed
Fetched: 14 Oct 23:19
Validated: 14 Oct 23:19
Deltas Created 14 Oct 23:19
Units Normalized: 14 Oct 23:21
Ancestry Built: 14 Oct 23:20
Nodes Matched: 14 Oct 23:21
Names Parsed: 14 Oct 23:20
New Models Stored: 14 Oct 23:19
Indexed: 14 Oct 23:21
Completed: 14 Oct 23:23
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 23:19:35 -0400 by logger.rb/56815
[START] [2019-10-14 23:19:35] logged process
[START] [2019-10-14 23:19:35] create_harvest_instance
[STOP] [2019-10-14 23:19:36] create_harvest_instance
[START] [2019-10-14 23:19:36] fetch_files
[STOP] [2019-10-14 23:19:36] fetch_files
[START] [2019-10-14 23:19:36] validate_each_file
[STOP] [2019-10-14 23:19:36] validate_each_file
[START] [2019-10-14 23:19:36] convert_to_csv
[CMD] [2019-10-14 23:19:36] /usr/bin/sort /app/public/converted_csv/n_korean_sp_list_refs_16789.csv > /app/public/converted_csv/n_korean_sp_list_refs_16789.csv_sorted
[CMD] [2019-10-14 23:19:37] /usr/bin/sort /app/public/converted_csv/n_korean_sp_list_nodes_16790.csv > /app/public/converted_csv/n_korean_sp_list_nodes_16790.csv_sorted
[CMD] [2019-10-14 23:19:37] /usr/bin/sort /app/public/converted_csv/n_korean_sp_list_occurrences_16791.csv > /app/public/converted_csv/n_korean_sp_list_occurrences_16791.csv_sorted
[CMD] [2019-10-14 23:19:37] /usr/bin/sort /app/public/converted_csv/n_korean_sp_list_measurements_16792.csv > /app/public/converted_csv/n_korean_sp_list_measurements_16792.csv_sorted
[STOP] [2019-10-14 23:19:37] convert_to_csv
[START] [2019-10-14 23:19:37] calculate_delta
[CMD] [2019-10-14 23:19:37] echo "0a" > /app/public/diff/n_korean_sp_list_refs_16789.diff
[CMD] [2019-10-14 23:19:38] tail -n +1 /app/public/converted_csv/n_korean_sp_list_refs_16789.csv >> /app/public/diff/n_korean_sp_list_refs_16789.diff
[CMD] [2019-10-14 23:19:38] echo "." >> /app/public/diff/n_korean_sp_list_refs_16789.diff
[CMD] [2019-10-14 23:19:38] echo "0a" > /app/public/diff/n_korean_sp_list_nodes_16790.diff
[CMD] [2019-10-14 23:19:38] tail -n +1 /app/public/converted_csv/n_korean_sp_list_nodes_16790.csv >> /app/public/diff/n_korean_sp_list_nodes_16790.diff
[CMD] [2019-10-14 23:19:39] echo "." >> /app/public/diff/n_korean_sp_list_nodes_16790.diff
[CMD] [2019-10-14 23:19:39] echo "0a" > /app/public/diff/n_korean_sp_list_occurrences_16791.diff
[CMD] [2019-10-14 23:19:39] tail -n +1 /app/public/converted_csv/n_korean_sp_list_occurrences_16791.csv >> /app/public/diff/n_korean_sp_list_occurrences_16791.diff
[CMD] [2019-10-14 23:19:40] echo "." >> /app/public/diff/n_korean_sp_list_occurrences_16791.diff
[CMD] [2019-10-14 23:19:40] echo "0a" > /app/public/diff/n_korean_sp_list_measurements_16792.diff
[CMD] [2019-10-14 23:19:40] tail -n +1 /app/public/converted_csv/n_korean_sp_list_measurements_16792.csv >> /app/public/diff/n_korean_sp_list_measurements_16792.diff
[CMD] [2019-10-14 23:19:40] echo "." >> /app/public/diff/n_korean_sp_list_measurements_16792.diff
[STOP] [2019-10-14 23:19:41] calculate_delta
[START] [2019-10-14 23:19:41] parse_diff_and_store
[INFO] [2019-10-14 23:19:41] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 23:19:41] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 23:19:42] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 23:19:42] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 23:19:49] Storing 2 References
[INFO] [2019-10-14 23:19:49] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 23:19:49] Average Time: 0.0
[INFO] [2019-10-14 23:19:49] Total Time: 1s
[INFO] [2019-10-14 23:19:49] Storing 1576 ScientificNames
[INFO] [2019-10-14 23:19:49] Processing group of 1576 in 2 groups of 1000
[INFO] [2019-10-14 23:19:50] Average Time: 0.305
[INFO] [2019-10-14 23:19:50] Total Time: 1s
[INFO] [2019-10-14 23:19:50] Storing 1576 Nodes
[INFO] [2019-10-14 23:19:50] Processing group of 1576 in 2 groups of 1000
[INFO] [2019-10-14 23:19:50] Average Time: 0.275
[INFO] [2019-10-14 23:19:50] Total Time: 1s
[INFO] [2019-10-14 23:19:50] Storing 482 Occurrences
[INFO] [2019-10-14 23:19:50] Processing group of 482 in 1 groups of 1000
[INFO] [2019-10-14 23:19:50] Average Time: 0.06
[INFO] [2019-10-14 23:19:50] Total Time: 1s
[INFO] [2019-10-14 23:19:50] Storing 1490 TraitsReferences
[INFO] [2019-10-14 23:19:50] Processing group of 1490 in 2 groups of 1000
[INFO] [2019-10-14 23:19:50] Average Time: 0.08
[INFO] [2019-10-14 23:19:50] Total Time: 1s
[INFO] [2019-10-14 23:19:50] Storing 1489 Traits
[INFO] [2019-10-14 23:19:50] Processing group of 1489 in 2 groups of 1000
[INFO] [2019-10-14 23:19:51] Average Time: 0.26
[INFO] [2019-10-14 23:19:51] Total Time: 1s
[INFO] [2019-10-14 23:19:51] Storing 1486 MetaTraits
[INFO] [2019-10-14 23:19:51] Processing group of 1486 in 2 groups of 1000
[INFO] [2019-10-14 23:19:51] Average Time: 0.1
[INFO] [2019-10-14 23:19:51] Total Time: 1s
[STOP] [2019-10-14 23:19:51] parse_diff_and_store
[START] [2019-10-14 23:19:51] resolve_keys
[INFO] [2019-10-14 23:19:59] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 23:20:00] traits to occurrences...
[INFO] [2019-10-14 23:20:00] traits to nodes (through occurrences)...
[INFO] [2019-10-14 23:20:00] Traits to sex term...
[INFO] [2019-10-14 23:20:01] Traits to lifestage term...
[INFO] [2019-10-14 23:20:01] MetaTraits to traits...
[INFO] [2019-10-14 23:20:01] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 23:20:02] Assocs to occurrences...
[INFO] [2019-10-14 23:20:02] Assocs to nodes...
[INFO] [2019-10-14 23:20:02] Assoc to sex term...
[INFO] [2019-10-14 23:20:02] Assoc to lifestage term...
[STOP] [2019-10-14 23:20:02] resolve_keys
[START] [2019-10-14 23:20:02] hold_for_later_1
[STOP] [2019-10-14 23:20:02] hold_for_later_1
[START] [2019-10-14 23:20:02] hold_for_later_2
[STOP] [2019-10-14 23:20:02] hold_for_later_2
[START] [2019-10-14 23:20:02] resolve_missing_parents
[STOP] [2019-10-14 23:20:04] resolve_missing_parents
[START] [2019-10-14 23:20:04] rebuild_nodes
[START] [2019-10-14 23:20:04] Flattener#flatten
[START] [2019-10-14 23:20:04] Flattener#study_resource
[START] [2019-10-14 23:20:04] Flattener#build_ancestry
[STOP] [2019-10-14 23:20:04] Flattener#build_ancestry
[INFO] [2019-10-14 23:20:04] 1576 ancestry keys
[START] [2019-10-14 23:20:04] build_node_ancestors
[INFO] [2019-10-14 23:20:04] old ancestors deleted.
[STOP] [2019-10-14 23:20:04] build_node_ancestors
[START] [2019-10-14 23:20:05] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 23:20:05] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 23:20:05] Flattener#flatten
[STOP] [2019-10-14 23:20:05] rebuild_nodes
[START] [2019-10-14 23:20:05] resolve_missing_media_owners
[STOP] [2019-10-14 23:20:05] resolve_missing_media_owners
[START] [2019-10-14 23:20:05] sanitize_media_verbatims
[STOP] [2019-10-14 23:20:05] sanitize_media_verbatims
[START] [2019-10-14 23:20:05] queue_downloads
[STOP] [2019-10-14 23:20:05] queue_downloads
[START] [2019-10-14 23:20:05] parse_names
[WARN] [2019-10-14 23:20:05] I see 1576 names which still need to be parsed.
[STOP] [2019-10-14 23:20:07] parse_names
[START] [2019-10-14 23:20:07] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 23:20:07] denormalize_canonical_names_to_nodes
[START] [2019-10-14 23:20:07] match_nodes
[START] [2019-10-14 23:20:07] map_all_nodes_to_pages
[STOP] [2019-10-14 23:21:14] map_all_nodes_to_pages
[INFO] [2019-10-14 23:21:14] 111 Unmatched nodes (of 1576)! That's too many to output. First 10: Grus vipio (#51205312); Grus canadensis (#51205973); Grus leucogeranus (#51206319); Anthropoides (#51206248); Anthropoides virgo (#51206247); Corvus dauuricus (#51206821); Ixos amaurotis (#51206779); Parus palustris (#51205741); Parus ater (#51206633); Sinosuthora webbianus (#51206718)
[START] [2019-10-14 23:21:14] update_nodes
[STOP] [2019-10-14 23:21:15] update_nodes
[STOP] [2019-10-14 23:21:15] match_nodes
[START] [2019-10-14 23:21:15] reindex_search
[STOP] [2019-10-14 23:21:17] reindex_search
[START] [2019-10-14 23:21:17] normalize_units
[STOP] [2019-10-14 23:21:17] normalize_units
[START] [2019-10-14 23:21:17] calculate_statistics
[STOP] [2019-10-14 23:21:17] calculate_statistics
[START] [2019-10-14 23:21:17] complete_harvest_instance
[START] [2019-10-14 23:21:17] overall_tsv_creation
[INFO] [2019-10-14 23:21:17] Processing group of 1576 in 1 batches of 10000
[INFO] [2019-10-14 23:22:09] 482 Traits (unfiltered)...
[INFO] [2019-10-14 23:22:23] 482 Traits (filtered)...
[INFO] [2019-10-14 23:22:23] 0 Associations (filtered)...
[INFO] [2019-10-14 23:23:03] 2409 metadata added.
[INFO] [2019-10-14 23:23:03] 0 metadata added.
[INFO] [2019-10-14 23:23:03] Average Time: 83.85
[INFO] [2019-10-14 23:23:03] Total Time: 1m46s
[STOP] [2019-10-14 23:23:03] overall_tsv_creation
[INFO] [2019-10-14 23:23:03] Done. Check your files:
[INFO] [2019-10-14 23:23:03] (1576 lines) /app/public/data/n_korean_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 23:23:04] (4832 lines) /app/public/data/n_korean_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 23:23:04] (1576 lines) /app/public/data/n_korean_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 23:23:04] (483 lines) /app/public/data/n_korean_sp_list/publish_traits.tsv
[INFO] [2019-10-14 23:23:04] (2410 lines) /app/public/data/n_korean_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 23:23:04] complete_harvest_instance
[START] [2019-10-14 23:23:04] completed
[STOP] [2019-10-14 23:23:04] completed
[STOP] [2019-10-14 23:23:04] logged process, took 208.99
Latest Process

14 Oct 23:19 EXITED currently processing 0