Harvest for Madigan et al Created 15 Apr 09:59

Stage: completed
Fetched: 15 Apr 09:59
Validated: 15 Apr 09:59
Deltas Created 15 Apr 10:00
Units Normalized: 15 Apr 10:00
Ancestry Built: 15 Apr 10:00
Nodes Matched: 15 Apr 10:00
Names Parsed: 15 Apr 10:00
New Models Stored: 15 Apr 10:00
Indexed: 15 Apr 10:00
Completed: 15 Apr 10:02
Time to Harvest: less than a minute
Harvesting Log

(131 lines)
# Logfile created on 2020-04-15 09:59:55 -0400 by logger.rb/v1.4.2
[INFO] [2020-04-15 09:59:55] ## HARVEST: type = -harvest
[START] [2020-04-15 09:59:56] logged process
[START] [2020-04-15 09:59:56] create_harvest_instance
[STOP] [2020-04-15 09:59:58] create_harvest_instance
[START] [2020-04-15 09:59:58] fetch_files
[STOP] [2020-04-15 09:59:58] fetch_files
[START] [2020-04-15 09:59:58] validate_each_file
[STOP] [2020-04-15 09:59:58] validate_each_file
[START] [2020-04-15 09:59:58] convert_to_csv
[CMD] [2020-04-15 09:59:58] /usr/bin/sort /app/public/converted_csv/madigan_et_al_refs_20755.csv > /app/public/converted_csv/madigan_et_al_refs_20755.csv_sorted
[CMD] [2020-04-15 09:59:59] /usr/bin/sort /app/public/converted_csv/madigan_et_al_nodes_20756.csv > /app/public/converted_csv/madigan_et_al_nodes_20756.csv_sorted
[CMD] [2020-04-15 10:00:00] /usr/bin/sort /app/public/converted_csv/madigan_et_al_occurrences_20757.csv > /app/public/converted_csv/madigan_et_al_occurrences_20757.csv_sorted
[CMD] [2020-04-15 10:00:02] /usr/bin/sort /app/public/converted_csv/madigan_et_al_measurements_20758.csv > /app/public/converted_csv/madigan_et_al_measurements_20758.csv_sorted
[STOP] [2020-04-15 10:00:03] convert_to_csv
[START] [2020-04-15 10:00:03] calculate_delta
[CMD] [2020-04-15 10:00:03] echo "0a" > /app/public/diff/madigan_et_al_refs_20755.diff
[CMD] [2020-04-15 10:00:04] tail -n +1 /app/public/converted_csv/madigan_et_al_refs_20755.csv >> /app/public/diff/madigan_et_al_refs_20755.diff
[CMD] [2020-04-15 10:00:05] echo "." >> /app/public/diff/madigan_et_al_refs_20755.diff
[CMD] [2020-04-15 10:00:07] echo "0a" > /app/public/diff/madigan_et_al_nodes_20756.diff
[CMD] [2020-04-15 10:00:08] tail -n +1 /app/public/converted_csv/madigan_et_al_nodes_20756.csv >> /app/public/diff/madigan_et_al_nodes_20756.diff
[CMD] [2020-04-15 10:00:09] echo "." >> /app/public/diff/madigan_et_al_nodes_20756.diff
[CMD] [2020-04-15 10:00:10] echo "0a" > /app/public/diff/madigan_et_al_occurrences_20757.diff
[CMD] [2020-04-15 10:00:12] tail -n +1 /app/public/converted_csv/madigan_et_al_occurrences_20757.csv >> /app/public/diff/madigan_et_al_occurrences_20757.diff
[CMD] [2020-04-15 10:00:13] echo "." >> /app/public/diff/madigan_et_al_occurrences_20757.diff
[CMD] [2020-04-15 10:00:14] echo "0a" > /app/public/diff/madigan_et_al_measurements_20758.diff
[CMD] [2020-04-15 10:00:16] tail -n +1 /app/public/converted_csv/madigan_et_al_measurements_20758.csv >> /app/public/diff/madigan_et_al_measurements_20758.diff
[CMD] [2020-04-15 10:00:17] echo "." >> /app/public/diff/madigan_et_al_measurements_20758.diff
[STOP] [2020-04-15 10:00:18] calculate_delta
[START] [2020-04-15 10:00:18] parse_diff_and_store
[INFO] [2020-04-15 10:00:19] Loading refs diff file into memory (true lines)...
[INFO] [2020-04-15 10:00:21] Loading nodes diff file into memory (true lines)...
[INFO] [2020-04-15 10:00:22] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-04-15 10:00:23] Loading measurements diff file into memory (true lines)...
[INFO] [2020-04-15 10:00:23] Storing 17 ScientificNames
[INFO] [2020-04-15 10:00:23] Processing group of 17 in 1 groups of 1000
[INFO] [2020-04-15 10:00:23] Average Time: 0.04
[INFO] [2020-04-15 10:00:23] Total Time: 1s
[INFO] [2020-04-15 10:00:23] Storing 17 Nodes
[INFO] [2020-04-15 10:00:23] Processing group of 17 in 1 groups of 1000
[INFO] [2020-04-15 10:00:23] Average Time: 0.03
[INFO] [2020-04-15 10:00:23] Total Time: 1s
[INFO] [2020-04-15 10:00:23] Storing 16 Occurrences
[INFO] [2020-04-15 10:00:23] Processing group of 16 in 1 groups of 1000
[INFO] [2020-04-15 10:00:23] Average Time: 0.01
[INFO] [2020-04-15 10:00:23] Total Time: 1s
[INFO] [2020-04-15 10:00:23] Storing 17 Traits
[INFO] [2020-04-15 10:00:23] Processing group of 17 in 1 groups of 1000
[INFO] [2020-04-15 10:00:23] Average Time: 0.01
[INFO] [2020-04-15 10:00:23] Total Time: 1s
[INFO] [2020-04-15 10:00:23] Storing 51 MetaTraits
[INFO] [2020-04-15 10:00:23] Processing group of 51 in 1 groups of 1000
[INFO] [2020-04-15 10:00:23] Average Time: 0.02
[INFO] [2020-04-15 10:00:23] Total Time: 1s
[STOP] [2020-04-15 10:00:23] parse_diff_and_store
[START] [2020-04-15 10:00:23] resolve_keys
[INFO] [2020-04-15 10:00:29] Occurrences to nodes (through scientific_names)...
[INFO] [2020-04-15 10:00:29] traits to occurrences...
[INFO] [2020-04-15 10:00:29] traits to nodes (through occurrences)...
[INFO] [2020-04-15 10:00:29] Traits to sex term...
[INFO] [2020-04-15 10:00:29] Traits to lifestage term...
[INFO] [2020-04-15 10:00:29] MetaTraits to traits...
[INFO] [2020-04-15 10:00:29] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-04-15 10:00:29] Assocs to occurrences...
[INFO] [2020-04-15 10:00:29] Assocs to nodes...
[INFO] [2020-04-15 10:00:29] Assoc to sex term...
[INFO] [2020-04-15 10:00:29] Assoc to lifestage term...
[STOP] [2020-04-15 10:00:29] resolve_keys
[START] [2020-04-15 10:00:29] hold_for_later_1
[STOP] [2020-04-15 10:00:29] hold_for_later_1
[START] [2020-04-15 10:00:29] hold_for_later_2
[STOP] [2020-04-15 10:00:29] hold_for_later_2
[START] [2020-04-15 10:00:29] resolve_missing_parents
[STOP] [2020-04-15 10:00:29] resolve_missing_parents
[START] [2020-04-15 10:00:29] rebuild_nodes
[START] [2020-04-15 10:00:29] Flattener#flatten
[START] [2020-04-15 10:00:29] Flattener#study_resource
[START] [2020-04-15 10:00:29] Flattener#build_ancestry
[STOP] [2020-04-15 10:00:29] Flattener#build_ancestry
[INFO] [2020-04-15 10:00:30] 17 ancestry keys
[START] [2020-04-15 10:00:30] build_node_ancestors
[INFO] [2020-04-15 10:00:30] old ancestors deleted.
[STOP] [2020-04-15 10:00:30] build_node_ancestors
[WARN] [2020-04-15 10:00:30] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-04-15 10:00:30] Flattener#flatten
[STOP] [2020-04-15 10:00:30] rebuild_nodes
[START] [2020-04-15 10:00:30] resolve_missing_media_owners
[STOP] [2020-04-15 10:00:30] resolve_missing_media_owners
[START] [2020-04-15 10:00:30] sanitize_media_verbatims
[STOP] [2020-04-15 10:00:30] sanitize_media_verbatims
[START] [2020-04-15 10:00:30] queue_downloads
[STOP] [2020-04-15 10:00:30] queue_downloads
[START] [2020-04-15 10:00:30] parse_names
[WARN] [2020-04-15 10:00:30] I see 17 names which still need to be parsed.
[STOP] [2020-04-15 10:00:31] parse_names
[START] [2020-04-15 10:00:31] denormalize_canonical_names_to_nodes
[STOP] [2020-04-15 10:00:31] denormalize_canonical_names_to_nodes
[START] [2020-04-15 10:00:31] match_nodes
[START] [2020-04-15 10:00:31] map_all_nodes_to_pages
[STOP] [2020-04-15 10:00:31] map_all_nodes_to_pages
[INFO] [2020-04-15 10:00:31] ZERO unmatched nodes (of 17)! Nicely done.
[START] [2020-04-15 10:00:31] update_nodes
[STOP] [2020-04-15 10:00:31] update_nodes
[STOP] [2020-04-15 10:00:31] match_nodes
[START] [2020-04-15 10:00:31] reindex_search
[STOP] [2020-04-15 10:00:31] reindex_search
[START] [2020-04-15 10:00:31] normalize_units
[STOP] [2020-04-15 10:00:31] normalize_units
[START] [2020-04-15 10:00:31] calculate_statistics
[2020-04-15 10:00:31] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-04-15 10:00:31] calculate_statistics
[START] [2020-04-15 10:00:31] complete_harvest_instance
[START] [2020-04-15 10:00:31] overall_tsv_creation
[INFO] [2020-04-15 10:00:31] Processing group of 17 in 1 batches of 10000
[INFO] [2020-04-15 10:01:23] 16 Traits (unfiltered)...
[INFO] [2020-04-15 10:01:36] 16 Traits (filtered)...
[INFO] [2020-04-15 10:01:36] 0 Associations (filtered)...
[INFO] [2020-04-15 10:02:13] 48 metadata added.
[INFO] [2020-04-15 10:02:13] 0 metadata added.
[INFO] [2020-04-15 10:02:13] Average Time: 72.37
[INFO] [2020-04-15 10:02:13] Total Time: 1m42s
[STOP] [2020-04-15 10:02:13] overall_tsv_creation
[INFO] [2020-04-15 10:02:13] Done. Check your files:
[INFO] [2020-04-15 10:02:14] (17 lines) /app/public/data/madigan_et_al/publish_nodes.tsv
[INFO] [2020-04-15 10:02:16] (17 lines) /app/public/data/madigan_et_al/publish_scientific_names.tsv
[INFO] [2020-04-15 10:02:17] (17 lines) /app/public/data/madigan_et_al/publish_traits.tsv
[INFO] [2020-04-15 10:02:18] (49 lines) /app/public/data/madigan_et_al/publish_metadata.tsv
[STOP] [2020-04-15 10:02:18] complete_harvest_instance
[START] [2020-04-15 10:02:18] completed
[STOP] [2020-04-15 10:02:18] completed
[STOP] [2020-04-15 10:02:18] logged process, took 141.85
Latest Process

15 Apr 09:59 EXITED currently processing 0