Harvest for English Vernaculars for Landmark Taxa Created 04 Nov 10:46

Stage: completed
Fetched: 04 Nov 10:46
Validated: 04 Nov 10:46
Deltas Created 04 Nov 10:46
Units Normalized: 04 Nov 10:46
Ancestry Built: 04 Nov 10:46
Nodes Matched: 04 Nov 10:46
Names Parsed: 04 Nov 10:46
New Models Stored: 04 Nov 10:46
Indexed: 04 Nov 10:46
Completed: 04 Nov 10:47
Time to Harvest: less than a minute

Harvesting Log

(107 lines)
# Logfile created on 2019-11-04 10:46:26 -0500 by logger.rb/56815
[START] [2019-11-04 10:46:26] logged process
[START] [2019-11-04 10:46:26] create_harvest_instance
[STOP] [2019-11-04 10:46:26] create_harvest_instance
[START] [2019-11-04 10:46:26] fetch_files
[STOP] [2019-11-04 10:46:26] fetch_files
[START] [2019-11-04 10:46:26] validate_each_file
[STOP] [2019-11-04 10:46:27] validate_each_file
[START] [2019-11-04 10:46:27] convert_to_csv
[CMD] [2019-11-04 10:46:27] /usr/bin/sort /app/public/converted_csv/English_Vernacul_nodes_18006.csv > /app/public/converted_csv/English_Vernacul_nodes_18006.csv_sorted
[CMD] [2019-11-04 10:46:27] /usr/bin/sort /app/public/converted_csv/English_Vernacul_vernaculars_18007.csv > /app/public/converted_csv/English_Vernacul_vernaculars_18007.csv_sorted
[STOP] [2019-11-04 10:46:27] convert_to_csv
[START] [2019-11-04 10:46:27] calculate_delta
[CMD] [2019-11-04 10:46:27] echo "0a" > /app/public/diff/English_Vernacul_nodes_18006.diff
[CMD] [2019-11-04 10:46:28] tail -n +1 /app/public/converted_csv/English_Vernacul_nodes_18006.csv >> /app/public/diff/English_Vernacul_nodes_18006.diff
[CMD] [2019-11-04 10:46:28] echo "." >> /app/public/diff/English_Vernacul_nodes_18006.diff
[CMD] [2019-11-04 10:46:29] echo "0a" > /app/public/diff/English_Vernacul_vernaculars_18007.diff
[CMD] [2019-11-04 10:46:29] tail -n +1 /app/public/converted_csv/English_Vernacul_vernaculars_18007.csv >> /app/public/diff/English_Vernacul_vernaculars_18007.diff
[CMD] [2019-11-04 10:46:29] echo "." >> /app/public/diff/English_Vernacul_vernaculars_18007.diff
[STOP] [2019-11-04 10:46:30] calculate_delta
[START] [2019-11-04 10:46:30] parse_diff_and_store
[INFO] [2019-11-04 10:46:30] Loading nodes diff file into memory (true lines)...
[INFO] [2019-11-04 10:46:31] Loading vernaculars diff file into memory (true lines)...
[INFO] [2019-11-04 10:46:32] Storing 2507 ScientificNames
[INFO] [2019-11-04 10:46:32] Processing group of 2507 in 3 groups of 1000
[INFO] [2019-11-04 10:46:33] Average Time: 0.343
[INFO] [2019-11-04 10:46:33] Total Time: 2s
[INFO] [2019-11-04 10:46:33] Storing 2507 Nodes
[INFO] [2019-11-04 10:46:33] Processing group of 2507 in 3 groups of 1000
[INFO] [2019-11-04 10:46:34] Average Time: 0.397
[INFO] [2019-11-04 10:46:34] Total Time: 2s
[INFO] [2019-11-04 10:46:34] Storing 2507 Vernaculars
[INFO] [2019-11-04 10:46:34] Processing group of 2507 in 3 groups of 1000
[INFO] [2019-11-04 10:46:35] Average Time: 0.157
[INFO] [2019-11-04 10:46:35] Total Time: 1s
[STOP] [2019-11-04 10:46:35] parse_diff_and_store
[START] [2019-11-04 10:46:35] resolve_keys
[INFO] [2019-11-04 10:46:40] Occurrences to nodes (through scientific_names)...
[INFO] [2019-11-04 10:46:40] traits to occurrences...
[INFO] [2019-11-04 10:46:40] traits to nodes (through occurrences)...
[INFO] [2019-11-04 10:46:40] Traits to sex term...
[INFO] [2019-11-04 10:46:40] Traits to lifestage term...
[INFO] [2019-11-04 10:46:40] MetaTraits to traits...
[INFO] [2019-11-04 10:46:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-11-04 10:46:40] Assocs to occurrences...
[INFO] [2019-11-04 10:46:40] Assocs to nodes...
[INFO] [2019-11-04 10:46:40] Assoc to sex term...
[INFO] [2019-11-04 10:46:40] Assoc to lifestage term...
[STOP] [2019-11-04 10:46:40] resolve_keys
[START] [2019-11-04 10:46:40] hold_for_later_1
[STOP] [2019-11-04 10:46:40] hold_for_later_1
[START] [2019-11-04 10:46:40] hold_for_later_2
[STOP] [2019-11-04 10:46:40] hold_for_later_2
[START] [2019-11-04 10:46:40] resolve_missing_parents
[STOP] [2019-11-04 10:46:40] resolve_missing_parents
[START] [2019-11-04 10:46:40] rebuild_nodes
[START] [2019-11-04 10:46:40] Flattener#flatten
[START] [2019-11-04 10:46:40] Flattener#study_resource
[START] [2019-11-04 10:46:40] Flattener#build_ancestry
[STOP] [2019-11-04 10:46:40] Flattener#build_ancestry
[INFO] [2019-11-04 10:46:40] 2507 ancestry keys
[START] [2019-11-04 10:46:40] build_node_ancestors
[INFO] [2019-11-04 10:46:40] old ancestors deleted.
[STOP] [2019-11-04 10:46:40] build_node_ancestors
[WARN] [2019-11-04 10:46:40] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2019-11-04 10:46:40] Flattener#flatten
[STOP] [2019-11-04 10:46:40] rebuild_nodes
[START] [2019-11-04 10:46:40] resolve_missing_media_owners
[STOP] [2019-11-04 10:46:40] resolve_missing_media_owners
[START] [2019-11-04 10:46:40] sanitize_media_verbatims
[STOP] [2019-11-04 10:46:40] sanitize_media_verbatims
[START] [2019-11-04 10:46:40] queue_downloads
[STOP] [2019-11-04 10:46:40] queue_downloads
[START] [2019-11-04 10:46:40] parse_names
[WARN] [2019-11-04 10:46:40] I see 2507 names which still need to be parsed.
[WARN] [2019-11-04 10:46:43] I see 1 names which still need to be parsed.
[STOP] [2019-11-04 10:46:44] parse_names
[START] [2019-11-04 10:46:44] denormalize_canonical_names_to_nodes
[STOP] [2019-11-04 10:46:44] denormalize_canonical_names_to_nodes
[START] [2019-11-04 10:46:44] match_nodes
[START] [2019-11-04 10:46:44] map_all_nodes_to_pages
[STOP] [2019-11-04 10:46:46] map_all_nodes_to_pages
[INFO] [2019-11-04 10:46:46] ZERO unmatched nodes (of 2507)! Nicely done.
[START] [2019-11-04 10:46:46] update_nodes
[STOP] [2019-11-04 10:46:46] update_nodes
[STOP] [2019-11-04 10:46:46] match_nodes
[START] [2019-11-04 10:46:46] reindex_search
[STOP] [2019-11-04 10:46:50] reindex_search
[START] [2019-11-04 10:46:50] normalize_units
[STOP] [2019-11-04 10:46:50] normalize_units
[START] [2019-11-04 10:46:50] calculate_statistics
[2019-11-04 10:46:50] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2019-11-04 10:46:50] calculate_statistics
[START] [2019-11-04 10:46:50] complete_harvest_instance
[START] [2019-11-04 10:46:50] overall_tsv_creation
[INFO] [2019-11-04 10:46:50] Processing group of 2507 in 1 batches of 10000
[INFO] [2019-11-04 10:47:50] Average Time: 20.9
[INFO] [2019-11-04 10:47:50] Total Time: 1m1s
[STOP] [2019-11-04 10:47:50] overall_tsv_creation
[INFO] [2019-11-04 10:47:50] Done. Check your files:
[INFO] [2019-11-04 10:47:50] (2506 lines) /app/public/data/English_Vernacul/publish_nodes.tsv
[INFO] [2019-11-04 10:47:51] (2507 lines) /app/public/data/English_Vernacul/publish_scientific_names.tsv
[INFO] [2019-11-04 10:47:51] (2506 lines) /app/public/data/English_Vernacul/publish_vernaculars.tsv
[STOP] [2019-11-04 10:47:51] complete_harvest_instance
[START] [2019-11-04 10:47:51] completed
[STOP] [2019-11-04 10:47:51] completed
[STOP] [2019-11-04 10:47:51] logged process, took 85.21

Latest Process