Harvest for Bond 1983 Created 15 Apr 10:39

Stage: completed
Fetched: 15 Apr 10:39
Validated: 15 Apr 10:39
Deltas Created 15 Apr 10:40
Units Normalized: 15 Apr 10:40
Ancestry Built: 15 Apr 10:40
Nodes Matched: 15 Apr 10:40
Names Parsed: 15 Apr 10:40
New Models Stored: 15 Apr 10:40
Indexed: 15 Apr 10:40
Completed: 15 Apr 10:42
Time to Harvest: less than a minute
Harvesting Log

(131 lines)
# Logfile created on 2020-04-15 10:39:51 -0400 by logger.rb/v1.4.2
[INFO] [2020-04-15 10:39:51] ## HARVEST: type = -harvest
[START] [2020-04-15 10:39:55] logged process
[START] [2020-04-15 10:39:55] create_harvest_instance
[STOP] [2020-04-15 10:39:56] create_harvest_instance
[START] [2020-04-15 10:39:56] fetch_files
[STOP] [2020-04-15 10:39:56] fetch_files
[START] [2020-04-15 10:39:56] validate_each_file
[STOP] [2020-04-15 10:39:56] validate_each_file
[START] [2020-04-15 10:39:56] convert_to_csv
[CMD] [2020-04-15 10:39:56] /usr/bin/sort /app/public/converted_csv/bond_bond_1983_refs_20799.csv > /app/public/converted_csv/bond_bond_1983_refs_20799.csv_sorted
[CMD] [2020-04-15 10:39:57] /usr/bin/sort /app/public/converted_csv/bond_bond_1983_nodes_20800.csv > /app/public/converted_csv/bond_bond_1983_nodes_20800.csv_sorted
[CMD] [2020-04-15 10:39:59] /usr/bin/sort /app/public/converted_csv/bond_bond_1983_occurrences_20801.csv > /app/public/converted_csv/bond_bond_1983_occurrences_20801.csv_sorted
[CMD] [2020-04-15 10:40:00] /usr/bin/sort /app/public/converted_csv/bond_bond_1983_measurements_20802.csv > /app/public/converted_csv/bond_bond_1983_measurements_20802.csv_sorted
[STOP] [2020-04-15 10:40:01] convert_to_csv
[START] [2020-04-15 10:40:01] calculate_delta
[CMD] [2020-04-15 10:40:01] echo "0a" > /app/public/diff/bond_bond_1983_refs_20799.diff
[CMD] [2020-04-15 10:40:02] tail -n +1 /app/public/converted_csv/bond_bond_1983_refs_20799.csv >> /app/public/diff/bond_bond_1983_refs_20799.diff
[CMD] [2020-04-15 10:40:04] echo "." >> /app/public/diff/bond_bond_1983_refs_20799.diff
[CMD] [2020-04-15 10:40:05] echo "0a" > /app/public/diff/bond_bond_1983_nodes_20800.diff
[CMD] [2020-04-15 10:40:06] tail -n +1 /app/public/converted_csv/bond_bond_1983_nodes_20800.csv >> /app/public/diff/bond_bond_1983_nodes_20800.diff
[CMD] [2020-04-15 10:40:08] echo "." >> /app/public/diff/bond_bond_1983_nodes_20800.diff
[CMD] [2020-04-15 10:40:09] echo "0a" > /app/public/diff/bond_bond_1983_occurrences_20801.diff
[CMD] [2020-04-15 10:40:10] tail -n +1 /app/public/converted_csv/bond_bond_1983_occurrences_20801.csv >> /app/public/diff/bond_bond_1983_occurrences_20801.diff
[CMD] [2020-04-15 10:40:11] echo "." >> /app/public/diff/bond_bond_1983_occurrences_20801.diff
[CMD] [2020-04-15 10:40:13] echo "0a" > /app/public/diff/bond_bond_1983_measurements_20802.diff
[CMD] [2020-04-15 10:40:14] tail -n +1 /app/public/converted_csv/bond_bond_1983_measurements_20802.csv >> /app/public/diff/bond_bond_1983_measurements_20802.diff
[CMD] [2020-04-15 10:40:15] echo "." >> /app/public/diff/bond_bond_1983_measurements_20802.diff
[STOP] [2020-04-15 10:40:17] calculate_delta
[START] [2020-04-15 10:40:17] parse_diff_and_store
[INFO] [2020-04-15 10:40:18] Loading refs diff file into memory (true lines)...
[INFO] [2020-04-15 10:40:19] Loading nodes diff file into memory (true lines)...
[INFO] [2020-04-15 10:40:20] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-04-15 10:40:22] Loading measurements diff file into memory (true lines)...
[INFO] [2020-04-15 10:40:22] Storing 13 ScientificNames
[INFO] [2020-04-15 10:40:22] Processing group of 13 in 1 groups of 1000
[INFO] [2020-04-15 10:40:22] Average Time: 0.05
[INFO] [2020-04-15 10:40:22] Total Time: 1s
[INFO] [2020-04-15 10:40:22] Storing 13 Nodes
[INFO] [2020-04-15 10:40:22] Processing group of 13 in 1 groups of 1000
[INFO] [2020-04-15 10:40:22] Average Time: 0.02
[INFO] [2020-04-15 10:40:22] Total Time: 1s
[INFO] [2020-04-15 10:40:22] Storing 13 Occurrences
[INFO] [2020-04-15 10:40:22] Processing group of 13 in 1 groups of 1000
[INFO] [2020-04-15 10:40:22] Average Time: 0.02
[INFO] [2020-04-15 10:40:22] Total Time: 1s
[INFO] [2020-04-15 10:40:22] Storing 26 Traits
[INFO] [2020-04-15 10:40:22] Processing group of 26 in 1 groups of 1000
[INFO] [2020-04-15 10:40:22] Average Time: 0.01
[INFO] [2020-04-15 10:40:22] Total Time: 1s
[INFO] [2020-04-15 10:40:22] Storing 52 MetaTraits
[INFO] [2020-04-15 10:40:22] Processing group of 52 in 1 groups of 1000
[INFO] [2020-04-15 10:40:22] Average Time: 0.01
[INFO] [2020-04-15 10:40:22] Total Time: 1s
[STOP] [2020-04-15 10:40:22] parse_diff_and_store
[START] [2020-04-15 10:40:22] resolve_keys
[INFO] [2020-04-15 10:40:27] Occurrences to nodes (through scientific_names)...
[INFO] [2020-04-15 10:40:27] traits to occurrences...
[INFO] [2020-04-15 10:40:27] traits to nodes (through occurrences)...
[INFO] [2020-04-15 10:40:27] Traits to sex term...
[INFO] [2020-04-15 10:40:27] Traits to lifestage term...
[INFO] [2020-04-15 10:40:27] MetaTraits to traits...
[INFO] [2020-04-15 10:40:27] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-04-15 10:40:27] Assocs to occurrences...
[INFO] [2020-04-15 10:40:27] Assocs to nodes...
[INFO] [2020-04-15 10:40:27] Assoc to sex term...
[INFO] [2020-04-15 10:40:27] Assoc to lifestage term...
[STOP] [2020-04-15 10:40:27] resolve_keys
[START] [2020-04-15 10:40:27] hold_for_later_1
[STOP] [2020-04-15 10:40:27] hold_for_later_1
[START] [2020-04-15 10:40:27] hold_for_later_2
[STOP] [2020-04-15 10:40:27] hold_for_later_2
[START] [2020-04-15 10:40:27] resolve_missing_parents
[STOP] [2020-04-15 10:40:27] resolve_missing_parents
[START] [2020-04-15 10:40:27] rebuild_nodes
[START] [2020-04-15 10:40:27] Flattener#flatten
[START] [2020-04-15 10:40:27] Flattener#study_resource
[START] [2020-04-15 10:40:27] Flattener#build_ancestry
[STOP] [2020-04-15 10:40:27] Flattener#build_ancestry
[INFO] [2020-04-15 10:40:27] 13 ancestry keys
[START] [2020-04-15 10:40:27] build_node_ancestors
[INFO] [2020-04-15 10:40:27] old ancestors deleted.
[STOP] [2020-04-15 10:40:27] build_node_ancestors
[WARN] [2020-04-15 10:40:27] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-04-15 10:40:27] Flattener#flatten
[STOP] [2020-04-15 10:40:27] rebuild_nodes
[START] [2020-04-15 10:40:27] resolve_missing_media_owners
[STOP] [2020-04-15 10:40:27] resolve_missing_media_owners
[START] [2020-04-15 10:40:27] sanitize_media_verbatims
[STOP] [2020-04-15 10:40:27] sanitize_media_verbatims
[START] [2020-04-15 10:40:27] queue_downloads
[STOP] [2020-04-15 10:40:27] queue_downloads
[START] [2020-04-15 10:40:27] parse_names
[WARN] [2020-04-15 10:40:27] I see 13 names which still need to be parsed.
[STOP] [2020-04-15 10:40:29] parse_names
[START] [2020-04-15 10:40:29] denormalize_canonical_names_to_nodes
[STOP] [2020-04-15 10:40:29] denormalize_canonical_names_to_nodes
[START] [2020-04-15 10:40:29] match_nodes
[START] [2020-04-15 10:40:29] map_all_nodes_to_pages
[STOP] [2020-04-15 10:40:29] map_all_nodes_to_pages
[INFO] [2020-04-15 10:40:29] ZERO unmatched nodes (of 13)! Nicely done.
[START] [2020-04-15 10:40:29] update_nodes
[STOP] [2020-04-15 10:40:29] update_nodes
[STOP] [2020-04-15 10:40:29] match_nodes
[START] [2020-04-15 10:40:29] reindex_search
[STOP] [2020-04-15 10:40:29] reindex_search
[START] [2020-04-15 10:40:29] normalize_units
[STOP] [2020-04-15 10:40:29] normalize_units
[START] [2020-04-15 10:40:29] calculate_statistics
[2020-04-15 10:40:29] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-04-15 10:40:29] calculate_statistics
[START] [2020-04-15 10:40:29] complete_harvest_instance
[START] [2020-04-15 10:40:29] overall_tsv_creation
[INFO] [2020-04-15 10:40:29] Processing group of 13 in 1 batches of 10000
[INFO] [2020-04-15 10:41:20] 13 Traits (unfiltered)...
[INFO] [2020-04-15 10:41:33] 13 Traits (filtered)...
[INFO] [2020-04-15 10:41:33] 0 Associations (filtered)...
[INFO] [2020-04-15 10:42:09] 65 metadata added.
[INFO] [2020-04-15 10:42:09] 0 metadata added.
[INFO] [2020-04-15 10:42:09] Average Time: 71.43
[INFO] [2020-04-15 10:42:09] Total Time: 1m41s
[STOP] [2020-04-15 10:42:09] overall_tsv_creation
[INFO] [2020-04-15 10:42:09] Done. Check your files:
[INFO] [2020-04-15 10:42:10] (13 lines) /app/public/data/bond_bond_1983/publish_nodes.tsv
[INFO] [2020-04-15 10:42:11] (13 lines) /app/public/data/bond_bond_1983/publish_scientific_names.tsv
[INFO] [2020-04-15 10:42:13] (14 lines) /app/public/data/bond_bond_1983/publish_traits.tsv
[INFO] [2020-04-15 10:42:14] (66 lines) /app/public/data/bond_bond_1983/publish_metadata.tsv
[STOP] [2020-04-15 10:42:14] complete_harvest_instance
[START] [2020-04-15 10:42:14] completed
[STOP] [2020-04-15 10:42:14] completed
[STOP] [2020-04-15 10:42:14] logged process, took 139.37
Latest Process

15 Apr 10:39 EXITED currently processing 0