Harvest for Woodward et al 2016 Created 03 Apr 15:20

Stage: completed
Fetched: 03 Apr 15:20
Validated: 03 Apr 15:20
Deltas Created 03 Apr 15:20
Units Normalized: 03 Apr 15:21
Ancestry Built: 03 Apr 15:21
Nodes Matched: 03 Apr 15:21
Names Parsed: 03 Apr 15:21
New Models Stored: 03 Apr 15:20
Indexed: 03 Apr 15:21
Completed: 03 Apr 15:22
Time to Harvest: less than a minute
Harvesting Log

(138 lines)
# Logfile created on 2020-04-03 15:20:57 -0400 by logger.rb/56815
[START] [2020-04-03 15:20:57] logged process
[START] [2020-04-03 15:20:57] create_harvest_instance
[STOP] [2020-04-03 15:20:58] create_harvest_instance
[START] [2020-04-03 15:20:58] fetch_files
[STOP] [2020-04-03 15:20:58] fetch_files
[START] [2020-04-03 15:20:58] validate_each_file
[STOP] [2020-04-03 15:20:58] validate_each_file
[START] [2020-04-03 15:20:58] convert_to_csv
[CMD] [2020-04-03 15:20:58] /usr/bin/sort /app/public/converted_csv/woodward_et_al_w_refs_20634.csv > /app/public/converted_csv/woodward_et_al_w_refs_20634.csv_sorted
[CMD] [2020-04-03 15:20:58] /usr/bin/sort /app/public/converted_csv/woodward_et_al_w_nodes_20635.csv > /app/public/converted_csv/woodward_et_al_w_nodes_20635.csv_sorted
[CMD] [2020-04-03 15:20:58] /usr/bin/sort /app/public/converted_csv/woodward_et_al_w_occurrences_20636.csv > /app/public/converted_csv/woodward_et_al_w_occurrences_20636.csv_sorted
[CMD] [2020-04-03 15:20:58] /usr/bin/sort /app/public/converted_csv/woodward_et_al_w_measurements_20637.csv > /app/public/converted_csv/woodward_et_al_w_measurements_20637.csv_sorted
[STOP] [2020-04-03 15:20:58] convert_to_csv
[START] [2020-04-03 15:20:58] calculate_delta
[CMD] [2020-04-03 15:20:58] echo "0a" > /app/public/diff/woodward_et_al_w_refs_20634.diff
[CMD] [2020-04-03 15:20:58] tail -n +1 /app/public/converted_csv/woodward_et_al_w_refs_20634.csv >> /app/public/diff/woodward_et_al_w_refs_20634.diff
[CMD] [2020-04-03 15:20:58] echo "." >> /app/public/diff/woodward_et_al_w_refs_20634.diff
[CMD] [2020-04-03 15:20:58] echo "0a" > /app/public/diff/woodward_et_al_w_nodes_20635.diff
[CMD] [2020-04-03 15:20:58] tail -n +1 /app/public/converted_csv/woodward_et_al_w_nodes_20635.csv >> /app/public/diff/woodward_et_al_w_nodes_20635.diff
[CMD] [2020-04-03 15:20:58] echo "." >> /app/public/diff/woodward_et_al_w_nodes_20635.diff
[CMD] [2020-04-03 15:20:58] echo "0a" > /app/public/diff/woodward_et_al_w_occurrences_20636.diff
[CMD] [2020-04-03 15:20:58] tail -n +1 /app/public/converted_csv/woodward_et_al_w_occurrences_20636.csv >> /app/public/diff/woodward_et_al_w_occurrences_20636.diff
[CMD] [2020-04-03 15:20:58] echo "." >> /app/public/diff/woodward_et_al_w_occurrences_20636.diff
[CMD] [2020-04-03 15:20:58] echo "0a" > /app/public/diff/woodward_et_al_w_measurements_20637.diff
[CMD] [2020-04-03 15:20:58] tail -n +1 /app/public/converted_csv/woodward_et_al_w_measurements_20637.csv >> /app/public/diff/woodward_et_al_w_measurements_20637.diff
[CMD] [2020-04-03 15:20:58] echo "." >> /app/public/diff/woodward_et_al_w_measurements_20637.diff
[STOP] [2020-04-03 15:20:58] calculate_delta
[START] [2020-04-03 15:20:58] parse_diff_and_store
[INFO] [2020-04-03 15:20:58] Loading refs diff file into memory (true lines)...
[INFO] [2020-04-03 15:20:58] Loading nodes diff file into memory (true lines)...
[INFO] [2020-04-03 15:20:58] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-04-03 15:20:58] Loading measurements diff file into memory (true lines)...
[INFO] [2020-04-03 15:20:58] Storing 11 References
[INFO] [2020-04-03 15:20:58] Processing group of 11 in 1 groups of 1000
[INFO] [2020-04-03 15:20:58] Average Time: 0.0
[INFO] [2020-04-03 15:20:58] Total Time: 1s
[INFO] [2020-04-03 15:20:58] Storing 6 ScientificNames
[INFO] [2020-04-03 15:20:58] Processing group of 6 in 1 groups of 1000
[INFO] [2020-04-03 15:20:58] Average Time: 0.0
[INFO] [2020-04-03 15:20:58] Total Time: 1s
[INFO] [2020-04-03 15:20:58] Storing 6 Nodes
[INFO] [2020-04-03 15:20:58] Processing group of 6 in 1 groups of 1000
[INFO] [2020-04-03 15:20:58] Average Time: 0.0
[INFO] [2020-04-03 15:20:58] Total Time: 1s
[INFO] [2020-04-03 15:20:58] Storing 6 Occurrences
[INFO] [2020-04-03 15:20:58] Processing group of 6 in 1 groups of 1000
[INFO] [2020-04-03 15:20:58] Average Time: 0.0
[INFO] [2020-04-03 15:20:58] Total Time: 1s
[INFO] [2020-04-03 15:20:58] Storing 11 TraitsReferences
[INFO] [2020-04-03 15:20:58] Processing group of 11 in 1 groups of 1000
[INFO] [2020-04-03 15:20:58] Average Time: 0.0
[INFO] [2020-04-03 15:20:58] Total Time: 1s
[INFO] [2020-04-03 15:20:58] Storing 11 Traits
[INFO] [2020-04-03 15:20:58] Processing group of 11 in 1 groups of 1000
[INFO] [2020-04-03 15:20:58] Average Time: 0.0
[INFO] [2020-04-03 15:20:58] Total Time: 1s
[INFO] [2020-04-03 15:20:58] Storing 15 MetaTraits
[INFO] [2020-04-03 15:20:58] Processing group of 15 in 1 groups of 1000
[INFO] [2020-04-03 15:20:58] Average Time: 0.0
[INFO] [2020-04-03 15:20:58] Total Time: 1s
[STOP] [2020-04-03 15:20:58] parse_diff_and_store
[START] [2020-04-03 15:20:58] resolve_keys
[INFO] [2020-04-03 15:21:03] Occurrences to nodes (through scientific_names)...
[INFO] [2020-04-03 15:21:03] traits to occurrences...
[INFO] [2020-04-03 15:21:03] traits to nodes (through occurrences)...
[INFO] [2020-04-03 15:21:03] Traits to sex term...
[INFO] [2020-04-03 15:21:03] Traits to lifestage term...
[INFO] [2020-04-03 15:21:03] MetaTraits to traits...
[INFO] [2020-04-03 15:21:03] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-04-03 15:21:03] Assocs to occurrences...
[INFO] [2020-04-03 15:21:03] Assocs to nodes...
[INFO] [2020-04-03 15:21:03] Assoc to sex term...
[INFO] [2020-04-03 15:21:03] Assoc to lifestage term...
[STOP] [2020-04-03 15:21:03] resolve_keys
[START] [2020-04-03 15:21:03] hold_for_later_1
[STOP] [2020-04-03 15:21:03] hold_for_later_1
[START] [2020-04-03 15:21:03] hold_for_later_2
[STOP] [2020-04-03 15:21:03] hold_for_later_2
[START] [2020-04-03 15:21:03] resolve_missing_parents
[STOP] [2020-04-03 15:21:03] resolve_missing_parents
[START] [2020-04-03 15:21:03] rebuild_nodes
[START] [2020-04-03 15:21:03] Flattener#flatten
[START] [2020-04-03 15:21:03] Flattener#study_resource
[START] [2020-04-03 15:21:03] Flattener#build_ancestry
[STOP] [2020-04-03 15:21:03] Flattener#build_ancestry
[INFO] [2020-04-03 15:21:03] 6 ancestry keys
[START] [2020-04-03 15:21:03] build_node_ancestors
[INFO] [2020-04-03 15:21:03] old ancestors deleted.
[STOP] [2020-04-03 15:21:03] build_node_ancestors
[WARN] [2020-04-03 15:21:03] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-04-03 15:21:03] Flattener#flatten
[STOP] [2020-04-03 15:21:03] rebuild_nodes
[START] [2020-04-03 15:21:03] resolve_missing_media_owners
[STOP] [2020-04-03 15:21:03] resolve_missing_media_owners
[START] [2020-04-03 15:21:03] sanitize_media_verbatims
[STOP] [2020-04-03 15:21:03] sanitize_media_verbatims
[START] [2020-04-03 15:21:03] queue_downloads
[STOP] [2020-04-03 15:21:03] queue_downloads
[START] [2020-04-03 15:21:03] parse_names
[WARN] [2020-04-03 15:21:03] I see 6 names which still need to be parsed.
[STOP] [2020-04-03 15:21:05] parse_names
[START] [2020-04-03 15:21:05] denormalize_canonical_names_to_nodes
[STOP] [2020-04-03 15:21:05] denormalize_canonical_names_to_nodes
[START] [2020-04-03 15:21:05] match_nodes
[START] [2020-04-03 15:21:05] map_all_nodes_to_pages
[STOP] [2020-04-03 15:21:05] map_all_nodes_to_pages
[INFO] [2020-04-03 15:21:05] ZERO unmatched nodes (of 6)! Nicely done.
[START] [2020-04-03 15:21:05] update_nodes
[STOP] [2020-04-03 15:21:05] update_nodes
[STOP] [2020-04-03 15:21:05] match_nodes
[START] [2020-04-03 15:21:05] reindex_search
[STOP] [2020-04-03 15:21:05] reindex_search
[START] [2020-04-03 15:21:05] normalize_units
[STOP] [2020-04-03 15:21:05] normalize_units
[START] [2020-04-03 15:21:05] calculate_statistics
[2020-04-03 15:21:05] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-04-03 15:21:05] calculate_statistics
[START] [2020-04-03 15:21:05] complete_harvest_instance
[START] [2020-04-03 15:21:05] overall_tsv_creation
[INFO] [2020-04-03 15:21:05] Processing group of 6 in 1 batches of 10000
[INFO] [2020-04-03 15:21:54] 6 Traits (unfiltered)...
[INFO] [2020-04-03 15:22:07] 6 Traits (filtered)...
[INFO] [2020-04-03 15:22:07] 0 Associations (filtered)...
[INFO] [2020-04-03 15:22:42] 31 metadata added.
[INFO] [2020-04-03 15:22:42] 0 metadata added.
[INFO] [2020-04-03 15:22:42] Average Time: 69.39
[INFO] [2020-04-03 15:22:42] Total Time: 1m38s
[STOP] [2020-04-03 15:22:42] overall_tsv_creation
[INFO] [2020-04-03 15:22:42] Done. Check your files:
[INFO] [2020-04-03 15:22:42] (6 lines) /app/public/data/woodward_et_al_w/publish_nodes.tsv
[INFO] [2020-04-03 15:22:42] (6 lines) /app/public/data/woodward_et_al_w/publish_scientific_names.tsv
[INFO] [2020-04-03 15:22:42] (7 lines) /app/public/data/woodward_et_al_w/publish_traits.tsv
[INFO] [2020-04-03 15:22:42] (32 lines) /app/public/data/woodward_et_al_w/publish_metadata.tsv
[STOP] [2020-04-03 15:22:42] complete_harvest_instance
[START] [2020-04-03 15:22:42] completed
[STOP] [2020-04-03 15:22:42] completed
[STOP] [2020-04-03 15:22:42] logged process, took 105.13
Latest Process

03 Apr 15:20 EXITED currently processing 0