Harvest for Park et al 2017 Created 09 Jul 14:22

Stage: completed
Fetched: 09 Jul 14:22
Validated: 09 Jul 14:22
Deltas Created 09 Jul 14:22
Units Normalized: 09 Jul 14:22
Ancestry Built: 09 Jul 14:22
Nodes Matched: 09 Jul 14:22
Names Parsed: 09 Jul 14:22
New Models Stored: 09 Jul 14:22
Indexed: 09 Jul 14:22
Completed: 09 Jul 14:25
Time to Harvest: less than a minute
Harvesting Log

(128 lines)
# Logfile created on 2020-07-09 14:21:35 -0400 by logger.rb/v1.4.2
[INFO] [2020-07-09 14:21:35] ## HARVEST: type = -harvest
[START] [2020-07-09 14:21:39] logged process
[INFO] [2020-07-09 14:22:24] ## HARVEST: type = -harvest
[START] [2020-07-09 14:22:24] logged process
[START] [2020-07-09 14:22:24] create_harvest_instance
[STOP] [2020-07-09 14:22:25] create_harvest_instance
[START] [2020-07-09 14:22:25] fetch_files
[STOP] [2020-07-09 14:22:25] fetch_files
[START] [2020-07-09 14:22:25] validate_each_file
[STOP] [2020-07-09 14:22:25] validate_each_file
[START] [2020-07-09 14:22:25] convert_to_csv
[CMD] [2020-07-09 14:22:25] /usr/bin/sort /app/public/converted_csv/park_et_al_park__nodes_21524.csv > /app/public/converted_csv/park_et_al_park__nodes_21524.csv_sorted
[CMD] [2020-07-09 14:22:25] /usr/bin/sort /app/public/converted_csv/park_et_al_park__occurrences_21525.csv > /app/public/converted_csv/park_et_al_park__occurrences_21525.csv_sorted
[CMD] [2020-07-09 14:22:25] /usr/bin/sort /app/public/converted_csv/park_et_al_park__measurements_21526.csv > /app/public/converted_csv/park_et_al_park__measurements_21526.csv_sorted
[STOP] [2020-07-09 14:22:25] convert_to_csv
[START] [2020-07-09 14:22:25] calculate_delta
[CMD] [2020-07-09 14:22:25] echo "0a" > /app/public/diff/park_et_al_park__nodes_21524.diff
[CMD] [2020-07-09 14:22:25] tail -n +1 /app/public/converted_csv/park_et_al_park__nodes_21524.csv >> /app/public/diff/park_et_al_park__nodes_21524.diff
[CMD] [2020-07-09 14:22:25] echo "." >> /app/public/diff/park_et_al_park__nodes_21524.diff
[CMD] [2020-07-09 14:22:26] echo "0a" > /app/public/diff/park_et_al_park__occurrences_21525.diff
[CMD] [2020-07-09 14:22:26] tail -n +1 /app/public/converted_csv/park_et_al_park__occurrences_21525.csv >> /app/public/diff/park_et_al_park__occurrences_21525.diff
[CMD] [2020-07-09 14:22:26] echo "." >> /app/public/diff/park_et_al_park__occurrences_21525.diff
[CMD] [2020-07-09 14:22:26] echo "0a" > /app/public/diff/park_et_al_park__measurements_21526.diff
[CMD] [2020-07-09 14:22:26] tail -n +1 /app/public/converted_csv/park_et_al_park__measurements_21526.csv >> /app/public/diff/park_et_al_park__measurements_21526.diff
[CMD] [2020-07-09 14:22:26] echo "." >> /app/public/diff/park_et_al_park__measurements_21526.diff
[STOP] [2020-07-09 14:22:26] calculate_delta
[START] [2020-07-09 14:22:26] parse_diff_and_store
[INFO] [2020-07-09 14:22:26] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-09 14:22:26] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-09 14:22:26] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-09 14:22:26] Storing 11 ScientificNames
[INFO] [2020-07-09 14:22:26] Processing group of 11 in 1 groups of 1000
[INFO] [2020-07-09 14:22:26] Average Time: 0.01
[INFO] [2020-07-09 14:22:26] Total Time: 1s
[INFO] [2020-07-09 14:22:26] Storing 11 Nodes
[INFO] [2020-07-09 14:22:26] Processing group of 11 in 1 groups of 1000
[INFO] [2020-07-09 14:22:26] Average Time: 0.01
[INFO] [2020-07-09 14:22:26] Total Time: 1s
[INFO] [2020-07-09 14:22:26] Storing 11 Occurrences
[INFO] [2020-07-09 14:22:26] Processing group of 11 in 1 groups of 1000
[INFO] [2020-07-09 14:22:26] Average Time: 0.0
[INFO] [2020-07-09 14:22:26] Total Time: 1s
[INFO] [2020-07-09 14:22:26] Storing 11 Traits
[INFO] [2020-07-09 14:22:26] Processing group of 11 in 1 groups of 1000
[INFO] [2020-07-09 14:22:26] Average Time: 0.01
[INFO] [2020-07-09 14:22:26] Total Time: 1s
[INFO] [2020-07-09 14:22:26] Storing 22 MetaTraits
[INFO] [2020-07-09 14:22:26] Processing group of 22 in 1 groups of 1000
[INFO] [2020-07-09 14:22:26] Average Time: 0.0
[INFO] [2020-07-09 14:22:26] Total Time: 1s
[STOP] [2020-07-09 14:22:26] parse_diff_and_store
[START] [2020-07-09 14:22:26] resolve_keys
[INFO] [2020-07-09 14:22:33] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-09 14:22:33] traits to occurrences...
[INFO] [2020-07-09 14:22:33] traits to nodes (through occurrences)...
[INFO] [2020-07-09 14:22:33] Traits to sex term...
[INFO] [2020-07-09 14:22:33] Traits to lifestage term...
[INFO] [2020-07-09 14:22:33] MetaTraits to traits...
[INFO] [2020-07-09 14:22:33] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-09 14:22:33] Assocs to occurrences...
[INFO] [2020-07-09 14:22:33] Assocs to nodes...
[INFO] [2020-07-09 14:22:33] Assoc to sex term...
[INFO] [2020-07-09 14:22:33] Assoc to lifestage term...
[STOP] [2020-07-09 14:22:33] resolve_keys
[START] [2020-07-09 14:22:33] hold_for_later_1
[STOP] [2020-07-09 14:22:33] hold_for_later_1
[START] [2020-07-09 14:22:33] hold_for_later_2
[STOP] [2020-07-09 14:22:33] hold_for_later_2
[START] [2020-07-09 14:22:33] resolve_missing_parents
[STOP] [2020-07-09 14:22:33] resolve_missing_parents
[START] [2020-07-09 14:22:33] rebuild_nodes
[START] [2020-07-09 14:22:33] Flattener#flatten
[START] [2020-07-09 14:22:33] Flattener#study_resource
[START] [2020-07-09 14:22:33] Flattener#build_ancestry
[STOP] [2020-07-09 14:22:33] Flattener#build_ancestry
[INFO] [2020-07-09 14:22:33] 11 ancestry keys
[START] [2020-07-09 14:22:33] build_node_ancestors
[INFO] [2020-07-09 14:22:33] old ancestors deleted.
[STOP] [2020-07-09 14:22:33] build_node_ancestors
[WARN] [2020-07-09 14:22:33] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-09 14:22:33] Flattener#flatten
[STOP] [2020-07-09 14:22:33] rebuild_nodes
[START] [2020-07-09 14:22:33] resolve_missing_media_owners
[STOP] [2020-07-09 14:22:33] resolve_missing_media_owners
[START] [2020-07-09 14:22:33] sanitize_media_verbatims
[STOP] [2020-07-09 14:22:33] sanitize_media_verbatims
[START] [2020-07-09 14:22:33] queue_downloads
[STOP] [2020-07-09 14:22:33] queue_downloads
[START] [2020-07-09 14:22:33] parse_names
[WARN] [2020-07-09 14:22:33] I see 11 names which still need to be parsed.
[STOP] [2020-07-09 14:22:34] parse_names
[START] [2020-07-09 14:22:34] denormalize_canonical_names_to_nodes
[STOP] [2020-07-09 14:22:34] denormalize_canonical_names_to_nodes
[START] [2020-07-09 14:22:34] match_nodes
[START] [2020-07-09 14:22:34] map_all_nodes_to_pages
[STOP] [2020-07-09 14:22:34] map_all_nodes_to_pages
[INFO] [2020-07-09 14:22:34] ZERO unmatched nodes (of 11)! Nicely done.
[START] [2020-07-09 14:22:34] update_nodes
[STOP] [2020-07-09 14:22:34] update_nodes
[STOP] [2020-07-09 14:22:34] match_nodes
[START] [2020-07-09 14:22:34] reindex_search
[STOP] [2020-07-09 14:22:35] reindex_search
[START] [2020-07-09 14:22:35] normalize_units
[STOP] [2020-07-09 14:22:35] normalize_units
[START] [2020-07-09 14:22:35] calculate_statistics
[2020-07-09 14:22:35] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-09 14:22:35] calculate_statistics
[START] [2020-07-09 14:22:35] complete_harvest_instance
[START] [2020-07-09 14:22:35] overall_tsv_creation
[INFO] [2020-07-09 14:22:35] Processing group of 11 in 1 batches of 10000
[INFO] [2020-07-09 14:24:30] 11 Traits (unfiltered)...
[INFO] [2020-07-09 14:24:43] 11 Traits (filtered)...
[INFO] [2020-07-09 14:24:43] 0 Associations (filtered)...
[INFO] [2020-07-09 14:25:19] 22 metadata added.
[INFO] [2020-07-09 14:25:19] 0 metadata added.
[INFO] [2020-07-09 14:25:19] Average Time: 70.36
[INFO] [2020-07-09 14:25:19] Total Time: 2m44s
[STOP] [2020-07-09 14:25:19] overall_tsv_creation
[INFO] [2020-07-09 14:25:19] Done. Check your files:
[INFO] [2020-07-09 14:25:19] (11 lines) /app/public/data/park_et_al_park_/publish_nodes.tsv
[INFO] [2020-07-09 14:25:19] (11 lines) /app/public/data/park_et_al_park_/publish_scientific_names.tsv
[INFO] [2020-07-09 14:25:19] (12 lines) /app/public/data/park_et_al_park_/publish_traits.tsv
[INFO] [2020-07-09 14:25:19] (23 lines) /app/public/data/park_et_al_park_/publish_metadata.tsv
[STOP] [2020-07-09 14:25:19] complete_harvest_instance
[START] [2020-07-09 14:25:19] completed
[STOP] [2020-07-09 14:25:19] completed
[STOP] [2020-07-09 14:25:19] logged process, took 174.9
Latest Process

09 Jul 14:22 EXITED currently processing 0