Harvest for Lesser et al 2004 Created 15 Apr 10:13

Stage: completed
Fetched: 15 Apr 10:13
Validated: 15 Apr 10:13
Deltas Created 15 Apr 10:14
Units Normalized: 15 Apr 10:14
Ancestry Built: 15 Apr 10:14
Nodes Matched: 15 Apr 10:14
Names Parsed: 15 Apr 10:14
New Models Stored: 15 Apr 10:14
Indexed: 15 Apr 10:14
Completed: 15 Apr 10:15
Time to Harvest: less than a minute
Harvesting Log

(131 lines)
# Logfile created on 2020-04-15 10:13:36 -0400 by logger.rb/v1.4.2
[INFO] [2020-04-15 10:13:36] ## HARVEST: type = -harvest
[START] [2020-04-15 10:13:41] logged process
[START] [2020-04-15 10:13:41] create_harvest_instance
[STOP] [2020-04-15 10:13:42] create_harvest_instance
[START] [2020-04-15 10:13:42] fetch_files
[STOP] [2020-04-15 10:13:42] fetch_files
[START] [2020-04-15 10:13:42] validate_each_file
[STOP] [2020-04-15 10:13:42] validate_each_file
[START] [2020-04-15 10:13:42] convert_to_csv
[CMD] [2020-04-15 10:13:42] /usr/bin/sort /app/public/converted_csv/lesser_et_al_les_refs_20775.csv > /app/public/converted_csv/lesser_et_al_les_refs_20775.csv_sorted
[CMD] [2020-04-15 10:13:43] /usr/bin/sort /app/public/converted_csv/lesser_et_al_les_nodes_20776.csv > /app/public/converted_csv/lesser_et_al_les_nodes_20776.csv_sorted
[CMD] [2020-04-15 10:13:44] /usr/bin/sort /app/public/converted_csv/lesser_et_al_les_occurrences_20777.csv > /app/public/converted_csv/lesser_et_al_les_occurrences_20777.csv_sorted
[CMD] [2020-04-15 10:13:46] /usr/bin/sort /app/public/converted_csv/lesser_et_al_les_measurements_20778.csv > /app/public/converted_csv/lesser_et_al_les_measurements_20778.csv_sorted
[STOP] [2020-04-15 10:13:47] convert_to_csv
[START] [2020-04-15 10:13:47] calculate_delta
[CMD] [2020-04-15 10:13:47] echo "0a" > /app/public/diff/lesser_et_al_les_refs_20775.diff
[CMD] [2020-04-15 10:13:48] tail -n +1 /app/public/converted_csv/lesser_et_al_les_refs_20775.csv >> /app/public/diff/lesser_et_al_les_refs_20775.diff
[CMD] [2020-04-15 10:13:50] echo "." >> /app/public/diff/lesser_et_al_les_refs_20775.diff
[CMD] [2020-04-15 10:13:51] echo "0a" > /app/public/diff/lesser_et_al_les_nodes_20776.diff
[CMD] [2020-04-15 10:13:52] tail -n +1 /app/public/converted_csv/lesser_et_al_les_nodes_20776.csv >> /app/public/diff/lesser_et_al_les_nodes_20776.diff
[CMD] [2020-04-15 10:13:53] echo "." >> /app/public/diff/lesser_et_al_les_nodes_20776.diff
[CMD] [2020-04-15 10:13:55] echo "0a" > /app/public/diff/lesser_et_al_les_occurrences_20777.diff
[CMD] [2020-04-15 10:13:56] tail -n +1 /app/public/converted_csv/lesser_et_al_les_occurrences_20777.csv >> /app/public/diff/lesser_et_al_les_occurrences_20777.diff
[CMD] [2020-04-15 10:13:57] echo "." >> /app/public/diff/lesser_et_al_les_occurrences_20777.diff
[CMD] [2020-04-15 10:13:59] echo "0a" > /app/public/diff/lesser_et_al_les_measurements_20778.diff
[CMD] [2020-04-15 10:14:00] tail -n +1 /app/public/converted_csv/lesser_et_al_les_measurements_20778.csv >> /app/public/diff/lesser_et_al_les_measurements_20778.diff
[CMD] [2020-04-15 10:14:01] echo "." >> /app/public/diff/lesser_et_al_les_measurements_20778.diff
[STOP] [2020-04-15 10:14:02] calculate_delta
[START] [2020-04-15 10:14:02] parse_diff_and_store
[INFO] [2020-04-15 10:14:04] Loading refs diff file into memory (true lines)...
[INFO] [2020-04-15 10:14:05] Loading nodes diff file into memory (true lines)...
[INFO] [2020-04-15 10:14:06] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-04-15 10:14:07] Loading measurements diff file into memory (true lines)...
[INFO] [2020-04-15 10:14:07] Storing 1 ScientificNames
[INFO] [2020-04-15 10:14:07] Processing group of 1 in 1 groups of 1000
[INFO] [2020-04-15 10:14:07] Average Time: 0.01
[INFO] [2020-04-15 10:14:07] Total Time: 1s
[INFO] [2020-04-15 10:14:07] Storing 1 Nodes
[INFO] [2020-04-15 10:14:07] Processing group of 1 in 1 groups of 1000
[INFO] [2020-04-15 10:14:07] Average Time: 0.0
[INFO] [2020-04-15 10:14:07] Total Time: 1s
[INFO] [2020-04-15 10:14:07] Storing 1 Occurrences
[INFO] [2020-04-15 10:14:07] Processing group of 1 in 1 groups of 1000
[INFO] [2020-04-15 10:14:08] Average Time: 0.0
[INFO] [2020-04-15 10:14:08] Total Time: 1s
[INFO] [2020-04-15 10:14:08] Storing 3 Traits
[INFO] [2020-04-15 10:14:08] Processing group of 3 in 1 groups of 1000
[INFO] [2020-04-15 10:14:08] Average Time: 0.0
[INFO] [2020-04-15 10:14:08] Total Time: 1s
[INFO] [2020-04-15 10:14:08] Storing 8 MetaTraits
[INFO] [2020-04-15 10:14:08] Processing group of 8 in 1 groups of 1000
[INFO] [2020-04-15 10:14:08] Average Time: 0.0
[INFO] [2020-04-15 10:14:08] Total Time: 1s
[STOP] [2020-04-15 10:14:08] parse_diff_and_store
[START] [2020-04-15 10:14:08] resolve_keys
[INFO] [2020-04-15 10:14:13] Occurrences to nodes (through scientific_names)...
[INFO] [2020-04-15 10:14:13] traits to occurrences...
[INFO] [2020-04-15 10:14:13] traits to nodes (through occurrences)...
[INFO] [2020-04-15 10:14:13] Traits to sex term...
[INFO] [2020-04-15 10:14:13] Traits to lifestage term...
[INFO] [2020-04-15 10:14:13] MetaTraits to traits...
[INFO] [2020-04-15 10:14:13] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-04-15 10:14:13] Assocs to occurrences...
[INFO] [2020-04-15 10:14:13] Assocs to nodes...
[INFO] [2020-04-15 10:14:13] Assoc to sex term...
[INFO] [2020-04-15 10:14:13] Assoc to lifestage term...
[STOP] [2020-04-15 10:14:13] resolve_keys
[START] [2020-04-15 10:14:13] hold_for_later_1
[STOP] [2020-04-15 10:14:13] hold_for_later_1
[START] [2020-04-15 10:14:13] hold_for_later_2
[STOP] [2020-04-15 10:14:13] hold_for_later_2
[START] [2020-04-15 10:14:13] resolve_missing_parents
[STOP] [2020-04-15 10:14:13] resolve_missing_parents
[START] [2020-04-15 10:14:13] rebuild_nodes
[START] [2020-04-15 10:14:13] Flattener#flatten
[START] [2020-04-15 10:14:13] Flattener#study_resource
[START] [2020-04-15 10:14:13] Flattener#build_ancestry
[STOP] [2020-04-15 10:14:13] Flattener#build_ancestry
[INFO] [2020-04-15 10:14:13] 1 ancestry keys
[START] [2020-04-15 10:14:13] build_node_ancestors
[INFO] [2020-04-15 10:14:13] old ancestors deleted.
[STOP] [2020-04-15 10:14:13] build_node_ancestors
[WARN] [2020-04-15 10:14:13] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-04-15 10:14:13] Flattener#flatten
[STOP] [2020-04-15 10:14:13] rebuild_nodes
[START] [2020-04-15 10:14:13] resolve_missing_media_owners
[STOP] [2020-04-15 10:14:13] resolve_missing_media_owners
[START] [2020-04-15 10:14:13] sanitize_media_verbatims
[STOP] [2020-04-15 10:14:13] sanitize_media_verbatims
[START] [2020-04-15 10:14:13] queue_downloads
[STOP] [2020-04-15 10:14:13] queue_downloads
[START] [2020-04-15 10:14:13] parse_names
[WARN] [2020-04-15 10:14:13] I see 1 names which still need to be parsed.
[STOP] [2020-04-15 10:14:14] parse_names
[START] [2020-04-15 10:14:14] denormalize_canonical_names_to_nodes
[STOP] [2020-04-15 10:14:14] denormalize_canonical_names_to_nodes
[START] [2020-04-15 10:14:14] match_nodes
[START] [2020-04-15 10:14:14] map_all_nodes_to_pages
[STOP] [2020-04-15 10:14:14] map_all_nodes_to_pages
[INFO] [2020-04-15 10:14:14] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-04-15 10:14:14] update_nodes
[STOP] [2020-04-15 10:14:14] update_nodes
[STOP] [2020-04-15 10:14:14] match_nodes
[START] [2020-04-15 10:14:14] reindex_search
[STOP] [2020-04-15 10:14:14] reindex_search
[START] [2020-04-15 10:14:14] normalize_units
[STOP] [2020-04-15 10:14:14] normalize_units
[START] [2020-04-15 10:14:14] calculate_statistics
[2020-04-15 10:14:14] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-04-15 10:14:14] calculate_statistics
[START] [2020-04-15 10:14:14] complete_harvest_instance
[START] [2020-04-15 10:14:14] overall_tsv_creation
[INFO] [2020-04-15 10:14:14] Processing group of 1 in 1 batches of 10000
[INFO] [2020-04-15 10:15:04] 3 Traits (unfiltered)...
[INFO] [2020-04-15 10:15:16] 3 Traits (filtered)...
[INFO] [2020-04-15 10:15:16] 0 Associations (filtered)...
[INFO] [2020-04-15 10:15:51] 8 metadata added.
[INFO] [2020-04-15 10:15:51] 0 metadata added.
[INFO] [2020-04-15 10:15:51] Average Time: 67.85
[INFO] [2020-04-15 10:15:51] Total Time: 1m37s
[STOP] [2020-04-15 10:15:51] overall_tsv_creation
[INFO] [2020-04-15 10:15:51] Done. Check your files:
[INFO] [2020-04-15 10:15:52] (1 lines) /app/public/data/lesser_et_al_les/publish_nodes.tsv
[INFO] [2020-04-15 10:15:53] (1 lines) /app/public/data/lesser_et_al_les/publish_scientific_names.tsv
[INFO] [2020-04-15 10:15:54] (4 lines) /app/public/data/lesser_et_al_les/publish_traits.tsv
[INFO] [2020-04-15 10:15:56] (9 lines) /app/public/data/lesser_et_al_les/publish_metadata.tsv
[STOP] [2020-04-15 10:15:56] complete_harvest_instance
[START] [2020-04-15 10:15:56] completed
[STOP] [2020-04-15 10:15:56] completed
[STOP] [2020-04-15 10:15:56] logged process, took 135.03
Latest Process

15 Apr 10:13 EXITED currently processing 0