Harvest for Sprent 2008 Created 15 Apr 10:48

Stage: completed
Fetched: 15 Apr 10:48
Validated: 15 Apr 10:48
Deltas Created 15 Apr 10:48
Units Normalized: 15 Apr 10:48
Ancestry Built: 15 Apr 10:48
Nodes Matched: 15 Apr 10:48
Names Parsed: 15 Apr 10:48
New Models Stored: 15 Apr 10:48
Indexed: 15 Apr 10:48
Completed: 15 Apr 10:50
Time to Harvest: less than a minute
Harvesting Log

(131 lines)
# Logfile created on 2020-04-15 10:48:06 -0400 by logger.rb/v1.4.2
[INFO] [2020-04-15 10:48:06] ## HARVEST: type = -harvest
[START] [2020-04-15 10:48:11] logged process
[START] [2020-04-15 10:48:11] create_harvest_instance
[STOP] [2020-04-15 10:48:12] create_harvest_instance
[START] [2020-04-15 10:48:12] fetch_files
[STOP] [2020-04-15 10:48:12] fetch_files
[START] [2020-04-15 10:48:12] validate_each_file
[STOP] [2020-04-15 10:48:13] validate_each_file
[START] [2020-04-15 10:48:13] convert_to_csv
[CMD] [2020-04-15 10:48:13] /usr/bin/sort /app/public/converted_csv/sprent_sprent_20_refs_20815.csv > /app/public/converted_csv/sprent_sprent_20_refs_20815.csv_sorted
[CMD] [2020-04-15 10:48:14] /usr/bin/sort /app/public/converted_csv/sprent_sprent_20_nodes_20816.csv > /app/public/converted_csv/sprent_sprent_20_nodes_20816.csv_sorted
[CMD] [2020-04-15 10:48:15] /usr/bin/sort /app/public/converted_csv/sprent_sprent_20_occurrences_20817.csv > /app/public/converted_csv/sprent_sprent_20_occurrences_20817.csv_sorted
[CMD] [2020-04-15 10:48:16] /usr/bin/sort /app/public/converted_csv/sprent_sprent_20_measurements_20818.csv > /app/public/converted_csv/sprent_sprent_20_measurements_20818.csv_sorted
[STOP] [2020-04-15 10:48:18] convert_to_csv
[START] [2020-04-15 10:48:18] calculate_delta
[CMD] [2020-04-15 10:48:18] echo "0a" > /app/public/diff/sprent_sprent_20_refs_20815.diff
[CMD] [2020-04-15 10:48:19] tail -n +1 /app/public/converted_csv/sprent_sprent_20_refs_20815.csv >> /app/public/diff/sprent_sprent_20_refs_20815.diff
[CMD] [2020-04-15 10:48:20] echo "." >> /app/public/diff/sprent_sprent_20_refs_20815.diff
[CMD] [2020-04-15 10:48:22] echo "0a" > /app/public/diff/sprent_sprent_20_nodes_20816.diff
[CMD] [2020-04-15 10:48:23] tail -n +1 /app/public/converted_csv/sprent_sprent_20_nodes_20816.csv >> /app/public/diff/sprent_sprent_20_nodes_20816.diff
[CMD] [2020-04-15 10:48:24] echo "." >> /app/public/diff/sprent_sprent_20_nodes_20816.diff
[CMD] [2020-04-15 10:48:25] echo "0a" > /app/public/diff/sprent_sprent_20_occurrences_20817.diff
[CMD] [2020-04-15 10:48:27] tail -n +1 /app/public/converted_csv/sprent_sprent_20_occurrences_20817.csv >> /app/public/diff/sprent_sprent_20_occurrences_20817.diff
[CMD] [2020-04-15 10:48:28] echo "." >> /app/public/diff/sprent_sprent_20_occurrences_20817.diff
[CMD] [2020-04-15 10:48:29] echo "0a" > /app/public/diff/sprent_sprent_20_measurements_20818.diff
[CMD] [2020-04-15 10:48:30] tail -n +1 /app/public/converted_csv/sprent_sprent_20_measurements_20818.csv >> /app/public/diff/sprent_sprent_20_measurements_20818.diff
[CMD] [2020-04-15 10:48:32] echo "." >> /app/public/diff/sprent_sprent_20_measurements_20818.diff
[STOP] [2020-04-15 10:48:33] calculate_delta
[START] [2020-04-15 10:48:33] parse_diff_and_store
[INFO] [2020-04-15 10:48:34] Loading refs diff file into memory (true lines)...
[INFO] [2020-04-15 10:48:36] Loading nodes diff file into memory (true lines)...
[INFO] [2020-04-15 10:48:37] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-04-15 10:48:38] Loading measurements diff file into memory (true lines)...
[INFO] [2020-04-15 10:48:38] Storing 12 ScientificNames
[INFO] [2020-04-15 10:48:38] Processing group of 12 in 1 groups of 1000
[INFO] [2020-04-15 10:48:38] Average Time: 0.04
[INFO] [2020-04-15 10:48:38] Total Time: 1s
[INFO] [2020-04-15 10:48:38] Storing 12 Nodes
[INFO] [2020-04-15 10:48:38] Processing group of 12 in 1 groups of 1000
[INFO] [2020-04-15 10:48:38] Average Time: 0.02
[INFO] [2020-04-15 10:48:38] Total Time: 1s
[INFO] [2020-04-15 10:48:38] Storing 12 Occurrences
[INFO] [2020-04-15 10:48:38] Processing group of 12 in 1 groups of 1000
[INFO] [2020-04-15 10:48:38] Average Time: 0.02
[INFO] [2020-04-15 10:48:38] Total Time: 1s
[INFO] [2020-04-15 10:48:38] Storing 102 Traits
[INFO] [2020-04-15 10:48:38] Processing group of 102 in 1 groups of 1000
[INFO] [2020-04-15 10:48:38] Average Time: 0.07
[INFO] [2020-04-15 10:48:38] Total Time: 1s
[INFO] [2020-04-15 10:48:38] Storing 24 MetaTraits
[INFO] [2020-04-15 10:48:38] Processing group of 24 in 1 groups of 1000
[INFO] [2020-04-15 10:48:38] Average Time: 0.01
[INFO] [2020-04-15 10:48:38] Total Time: 1s
[STOP] [2020-04-15 10:48:38] parse_diff_and_store
[START] [2020-04-15 10:48:38] resolve_keys
[INFO] [2020-04-15 10:48:44] Occurrences to nodes (through scientific_names)...
[INFO] [2020-04-15 10:48:44] traits to occurrences...
[INFO] [2020-04-15 10:48:44] traits to nodes (through occurrences)...
[INFO] [2020-04-15 10:48:44] Traits to sex term...
[INFO] [2020-04-15 10:48:44] Traits to lifestage term...
[INFO] [2020-04-15 10:48:44] MetaTraits to traits...
[INFO] [2020-04-15 10:48:44] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-04-15 10:48:44] Assocs to occurrences...
[INFO] [2020-04-15 10:48:44] Assocs to nodes...
[INFO] [2020-04-15 10:48:44] Assoc to sex term...
[INFO] [2020-04-15 10:48:44] Assoc to lifestage term...
[STOP] [2020-04-15 10:48:44] resolve_keys
[START] [2020-04-15 10:48:44] hold_for_later_1
[STOP] [2020-04-15 10:48:44] hold_for_later_1
[START] [2020-04-15 10:48:44] hold_for_later_2
[STOP] [2020-04-15 10:48:44] hold_for_later_2
[START] [2020-04-15 10:48:44] resolve_missing_parents
[STOP] [2020-04-15 10:48:44] resolve_missing_parents
[START] [2020-04-15 10:48:44] rebuild_nodes
[START] [2020-04-15 10:48:44] Flattener#flatten
[START] [2020-04-15 10:48:44] Flattener#study_resource
[START] [2020-04-15 10:48:44] Flattener#build_ancestry
[STOP] [2020-04-15 10:48:44] Flattener#build_ancestry
[INFO] [2020-04-15 10:48:44] 12 ancestry keys
[START] [2020-04-15 10:48:44] build_node_ancestors
[INFO] [2020-04-15 10:48:44] old ancestors deleted.
[STOP] [2020-04-15 10:48:44] build_node_ancestors
[WARN] [2020-04-15 10:48:44] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-04-15 10:48:44] Flattener#flatten
[STOP] [2020-04-15 10:48:44] rebuild_nodes
[START] [2020-04-15 10:48:44] resolve_missing_media_owners
[STOP] [2020-04-15 10:48:44] resolve_missing_media_owners
[START] [2020-04-15 10:48:44] sanitize_media_verbatims
[STOP] [2020-04-15 10:48:44] sanitize_media_verbatims
[START] [2020-04-15 10:48:44] queue_downloads
[STOP] [2020-04-15 10:48:44] queue_downloads
[START] [2020-04-15 10:48:44] parse_names
[WARN] [2020-04-15 10:48:44] I see 12 names which still need to be parsed.
[STOP] [2020-04-15 10:48:45] parse_names
[START] [2020-04-15 10:48:45] denormalize_canonical_names_to_nodes
[STOP] [2020-04-15 10:48:45] denormalize_canonical_names_to_nodes
[START] [2020-04-15 10:48:45] match_nodes
[START] [2020-04-15 10:48:45] map_all_nodes_to_pages
[STOP] [2020-04-15 10:48:45] map_all_nodes_to_pages
[INFO] [2020-04-15 10:48:45] ZERO unmatched nodes (of 12)! Nicely done.
[START] [2020-04-15 10:48:45] update_nodes
[STOP] [2020-04-15 10:48:45] update_nodes
[STOP] [2020-04-15 10:48:45] match_nodes
[START] [2020-04-15 10:48:45] reindex_search
[STOP] [2020-04-15 10:48:45] reindex_search
[START] [2020-04-15 10:48:45] normalize_units
[STOP] [2020-04-15 10:48:45] normalize_units
[START] [2020-04-15 10:48:45] calculate_statistics
[2020-04-15 10:48:45] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-04-15 10:48:45] calculate_statistics
[START] [2020-04-15 10:48:45] complete_harvest_instance
[START] [2020-04-15 10:48:45] overall_tsv_creation
[INFO] [2020-04-15 10:48:45] Processing group of 12 in 1 batches of 10000
[INFO] [2020-04-15 10:49:36] 12 Traits (unfiltered)...
[INFO] [2020-04-15 10:49:49] 12 Traits (filtered)...
[INFO] [2020-04-15 10:49:49] 0 Associations (filtered)...
[INFO] [2020-04-15 10:50:25] 114 metadata added.
[INFO] [2020-04-15 10:50:25] 0 metadata added.
[INFO] [2020-04-15 10:50:25] Average Time: 71.34
[INFO] [2020-04-15 10:50:25] Total Time: 1m41s
[STOP] [2020-04-15 10:50:25] overall_tsv_creation
[INFO] [2020-04-15 10:50:25] Done. Check your files:
[INFO] [2020-04-15 10:50:27] (12 lines) /app/public/data/sprent_sprent_20/publish_nodes.tsv
[INFO] [2020-04-15 10:50:28] (12 lines) /app/public/data/sprent_sprent_20/publish_scientific_names.tsv
[INFO] [2020-04-15 10:50:29] (13 lines) /app/public/data/sprent_sprent_20/publish_traits.tsv
[INFO] [2020-04-15 10:50:31] (115 lines) /app/public/data/sprent_sprent_20/publish_metadata.tsv
[STOP] [2020-04-15 10:50:31] complete_harvest_instance
[START] [2020-04-15 10:50:31] completed
[STOP] [2020-04-15 10:50:31] completed
[STOP] [2020-04-15 10:50:31] logged process, took 139.54
Latest Process

15 Apr 10:48 EXITED currently processing 0