Harvest for Madigan and Jung 2008 Created 03 Apr 15:22

Stage: completed
Fetched: 03 Apr 15:22
Validated: 03 Apr 15:22
Deltas Created 03 Apr 15:22
Units Normalized: 03 Apr 15:22
Ancestry Built: 03 Apr 15:22
Nodes Matched: 03 Apr 15:22
Names Parsed: 03 Apr 15:22
New Models Stored: 03 Apr 15:22
Indexed: 03 Apr 15:22
Completed: 03 Apr 15:24
Time to Harvest: less than a minute
Harvesting Log

(125 lines)
# Logfile created on 2020-04-03 15:22:42 -0400 by logger.rb/56815
[START] [2020-04-03 15:22:42] logged process
[START] [2020-04-03 15:22:42] create_harvest_instance
[STOP] [2020-04-03 15:22:43] create_harvest_instance
[START] [2020-04-03 15:22:43] fetch_files
[STOP] [2020-04-03 15:22:43] fetch_files
[START] [2020-04-03 15:22:43] validate_each_file
[STOP] [2020-04-03 15:22:43] validate_each_file
[START] [2020-04-03 15:22:43] convert_to_csv
[CMD] [2020-04-03 15:22:43] /usr/bin/sort /app/public/converted_csv/madigan_jung_mad_nodes_20638.csv > /app/public/converted_csv/madigan_jung_mad_nodes_20638.csv_sorted
[CMD] [2020-04-03 15:22:43] /usr/bin/sort /app/public/converted_csv/madigan_jung_mad_occurrences_20639.csv > /app/public/converted_csv/madigan_jung_mad_occurrences_20639.csv_sorted
[CMD] [2020-04-03 15:22:43] /usr/bin/sort /app/public/converted_csv/madigan_jung_mad_measurements_20640.csv > /app/public/converted_csv/madigan_jung_mad_measurements_20640.csv_sorted
[STOP] [2020-04-03 15:22:43] convert_to_csv
[START] [2020-04-03 15:22:43] calculate_delta
[CMD] [2020-04-03 15:22:43] echo "0a" > /app/public/diff/madigan_jung_mad_nodes_20638.diff
[CMD] [2020-04-03 15:22:43] tail -n +1 /app/public/converted_csv/madigan_jung_mad_nodes_20638.csv >> /app/public/diff/madigan_jung_mad_nodes_20638.diff
[CMD] [2020-04-03 15:22:43] echo "." >> /app/public/diff/madigan_jung_mad_nodes_20638.diff
[CMD] [2020-04-03 15:22:43] echo "0a" > /app/public/diff/madigan_jung_mad_occurrences_20639.diff
[CMD] [2020-04-03 15:22:43] tail -n +1 /app/public/converted_csv/madigan_jung_mad_occurrences_20639.csv >> /app/public/diff/madigan_jung_mad_occurrences_20639.diff
[CMD] [2020-04-03 15:22:43] echo "." >> /app/public/diff/madigan_jung_mad_occurrences_20639.diff
[CMD] [2020-04-03 15:22:43] echo "0a" > /app/public/diff/madigan_jung_mad_measurements_20640.diff
[CMD] [2020-04-03 15:22:43] tail -n +1 /app/public/converted_csv/madigan_jung_mad_measurements_20640.csv >> /app/public/diff/madigan_jung_mad_measurements_20640.diff
[CMD] [2020-04-03 15:22:43] echo "." >> /app/public/diff/madigan_jung_mad_measurements_20640.diff
[STOP] [2020-04-03 15:22:43] calculate_delta
[START] [2020-04-03 15:22:43] parse_diff_and_store
[INFO] [2020-04-03 15:22:43] Loading nodes diff file into memory (true lines)...
[INFO] [2020-04-03 15:22:43] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-04-03 15:22:43] Loading measurements diff file into memory (true lines)...
[INFO] [2020-04-03 15:22:43] Storing 48 ScientificNames
[INFO] [2020-04-03 15:22:43] Processing group of 48 in 1 groups of 1000
[INFO] [2020-04-03 15:22:43] Average Time: 0.02
[INFO] [2020-04-03 15:22:43] Total Time: 1s
[INFO] [2020-04-03 15:22:43] Storing 48 Nodes
[INFO] [2020-04-03 15:22:43] Processing group of 48 in 1 groups of 1000
[INFO] [2020-04-03 15:22:43] Average Time: 0.02
[INFO] [2020-04-03 15:22:43] Total Time: 1s
[INFO] [2020-04-03 15:22:43] Storing 48 Occurrences
[INFO] [2020-04-03 15:22:43] Processing group of 48 in 1 groups of 1000
[INFO] [2020-04-03 15:22:44] Average Time: 0.01
[INFO] [2020-04-03 15:22:44] Total Time: 1s
[INFO] [2020-04-03 15:22:44] Storing 95 Traits
[INFO] [2020-04-03 15:22:44] Processing group of 95 in 1 groups of 1000
[INFO] [2020-04-03 15:22:44] Average Time: 0.05
[INFO] [2020-04-03 15:22:44] Total Time: 1s
[INFO] [2020-04-03 15:22:44] Storing 96 MetaTraits
[INFO] [2020-04-03 15:22:44] Processing group of 96 in 1 groups of 1000
[INFO] [2020-04-03 15:22:44] Average Time: 0.02
[INFO] [2020-04-03 15:22:44] Total Time: 1s
[STOP] [2020-04-03 15:22:44] parse_diff_and_store
[START] [2020-04-03 15:22:44] resolve_keys
[INFO] [2020-04-03 15:22:49] Occurrences to nodes (through scientific_names)...
[INFO] [2020-04-03 15:22:49] traits to occurrences...
[INFO] [2020-04-03 15:22:49] traits to nodes (through occurrences)...
[INFO] [2020-04-03 15:22:49] Traits to sex term...
[INFO] [2020-04-03 15:22:49] Traits to lifestage term...
[INFO] [2020-04-03 15:22:49] MetaTraits to traits...
[INFO] [2020-04-03 15:22:49] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-04-03 15:22:49] Assocs to occurrences...
[INFO] [2020-04-03 15:22:49] Assocs to nodes...
[INFO] [2020-04-03 15:22:49] Assoc to sex term...
[INFO] [2020-04-03 15:22:49] Assoc to lifestage term...
[STOP] [2020-04-03 15:22:49] resolve_keys
[START] [2020-04-03 15:22:49] hold_for_later_1
[STOP] [2020-04-03 15:22:49] hold_for_later_1
[START] [2020-04-03 15:22:49] hold_for_later_2
[STOP] [2020-04-03 15:22:49] hold_for_later_2
[START] [2020-04-03 15:22:49] resolve_missing_parents
[STOP] [2020-04-03 15:22:49] resolve_missing_parents
[START] [2020-04-03 15:22:49] rebuild_nodes
[START] [2020-04-03 15:22:49] Flattener#flatten
[START] [2020-04-03 15:22:49] Flattener#study_resource
[START] [2020-04-03 15:22:49] Flattener#build_ancestry
[STOP] [2020-04-03 15:22:49] Flattener#build_ancestry
[INFO] [2020-04-03 15:22:49] 48 ancestry keys
[START] [2020-04-03 15:22:49] build_node_ancestors
[INFO] [2020-04-03 15:22:49] old ancestors deleted.
[STOP] [2020-04-03 15:22:49] build_node_ancestors
[WARN] [2020-04-03 15:22:49] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-04-03 15:22:49] Flattener#flatten
[STOP] [2020-04-03 15:22:49] rebuild_nodes
[START] [2020-04-03 15:22:49] resolve_missing_media_owners
[STOP] [2020-04-03 15:22:49] resolve_missing_media_owners
[START] [2020-04-03 15:22:49] sanitize_media_verbatims
[STOP] [2020-04-03 15:22:49] sanitize_media_verbatims
[START] [2020-04-03 15:22:49] queue_downloads
[STOP] [2020-04-03 15:22:49] queue_downloads
[START] [2020-04-03 15:22:49] parse_names
[WARN] [2020-04-03 15:22:49] I see 48 names which still need to be parsed.
[STOP] [2020-04-03 15:22:50] parse_names
[START] [2020-04-03 15:22:50] denormalize_canonical_names_to_nodes
[STOP] [2020-04-03 15:22:50] denormalize_canonical_names_to_nodes
[START] [2020-04-03 15:22:50] match_nodes
[START] [2020-04-03 15:22:50] map_all_nodes_to_pages
[STOP] [2020-04-03 15:22:50] map_all_nodes_to_pages
[INFO] [2020-04-03 15:22:50] Unmatched nodes (1 of 48): Rhodothallasium (#68185431)
[START] [2020-04-03 15:22:50] update_nodes
[STOP] [2020-04-03 15:22:50] update_nodes
[STOP] [2020-04-03 15:22:50] match_nodes
[START] [2020-04-03 15:22:50] reindex_search
[STOP] [2020-04-03 15:22:50] reindex_search
[START] [2020-04-03 15:22:50] normalize_units
[STOP] [2020-04-03 15:22:50] normalize_units
[START] [2020-04-03 15:22:50] calculate_statistics
[2020-04-03 15:22:50] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-04-03 15:22:50] calculate_statistics
[START] [2020-04-03 15:22:50] complete_harvest_instance
[START] [2020-04-03 15:22:50] overall_tsv_creation
[INFO] [2020-04-03 15:22:50] Processing group of 48 in 1 batches of 10000
[INFO] [2020-04-03 15:23:41] 48 Traits (unfiltered)...
[INFO] [2020-04-03 15:23:53] 48 Traits (filtered)...
[INFO] [2020-04-03 15:23:53] 0 Associations (filtered)...
[INFO] [2020-04-03 15:24:29] 143 metadata added.
[INFO] [2020-04-03 15:24:29] 0 metadata added.
[INFO] [2020-04-03 15:24:29] Average Time: 70.48
[INFO] [2020-04-03 15:24:29] Total Time: 1m40s
[STOP] [2020-04-03 15:24:29] overall_tsv_creation
[INFO] [2020-04-03 15:24:29] Done. Check your files:
[INFO] [2020-04-03 15:24:29] (48 lines) /app/public/data/madigan_jung_mad/publish_nodes.tsv
[INFO] [2020-04-03 15:24:29] (48 lines) /app/public/data/madigan_jung_mad/publish_scientific_names.tsv
[INFO] [2020-04-03 15:24:29] (49 lines) /app/public/data/madigan_jung_mad/publish_traits.tsv
[INFO] [2020-04-03 15:24:29] (144 lines) /app/public/data/madigan_jung_mad/publish_metadata.tsv
[STOP] [2020-04-03 15:24:29] complete_harvest_instance
[START] [2020-04-03 15:24:29] completed
[STOP] [2020-04-03 15:24:29] completed
[STOP] [2020-04-03 15:24:29] logged process, took 106.91
Latest Process

03 Apr 15:22 EXITED currently processing 0