Harvest for Hanotte and Mensah 2002 Created 09 Jul 14:50

Stage: completed
Fetched: 09 Jul 14:51
Validated: 09 Jul 14:51
Deltas Created 09 Jul 14:51
Units Normalized: 09 Jul 14:51
Ancestry Built: 09 Jul 14:51
Nodes Matched: 09 Jul 14:51
Names Parsed: 09 Jul 14:51
New Models Stored: 09 Jul 14:51
Indexed: 09 Jul 14:51
Completed: 09 Jul 14:52
Time to Harvest: less than a minute
Harvesting Log

(126 lines)
# Logfile created on 2020-07-09 14:50:56 -0400 by logger.rb/v1.4.2
[INFO] [2020-07-09 14:50:56] ## HARVEST: type = -harvest
[START] [2020-07-09 14:50:59] logged process
[START] [2020-07-09 14:50:59] create_harvest_instance
[STOP] [2020-07-09 14:51:00] create_harvest_instance
[START] [2020-07-09 14:51:00] fetch_files
[STOP] [2020-07-09 14:51:00] fetch_files
[START] [2020-07-09 14:51:00] validate_each_file
[STOP] [2020-07-09 14:51:00] validate_each_file
[START] [2020-07-09 14:51:00] convert_to_csv
[CMD] [2020-07-09 14:51:00] /usr/bin/sort /app/public/converted_csv/hanotte_mensah_h_nodes_21554.csv > /app/public/converted_csv/hanotte_mensah_h_nodes_21554.csv_sorted
[CMD] [2020-07-09 14:51:00] /usr/bin/sort /app/public/converted_csv/hanotte_mensah_h_occurrences_21555.csv > /app/public/converted_csv/hanotte_mensah_h_occurrences_21555.csv_sorted
[CMD] [2020-07-09 14:51:00] /usr/bin/sort /app/public/converted_csv/hanotte_mensah_h_measurements_21556.csv > /app/public/converted_csv/hanotte_mensah_h_measurements_21556.csv_sorted
[STOP] [2020-07-09 14:51:00] convert_to_csv
[START] [2020-07-09 14:51:00] calculate_delta
[CMD] [2020-07-09 14:51:00] echo "0a" > /app/public/diff/hanotte_mensah_h_nodes_21554.diff
[CMD] [2020-07-09 14:51:00] tail -n +1 /app/public/converted_csv/hanotte_mensah_h_nodes_21554.csv >> /app/public/diff/hanotte_mensah_h_nodes_21554.diff
[CMD] [2020-07-09 14:51:00] echo "." >> /app/public/diff/hanotte_mensah_h_nodes_21554.diff
[CMD] [2020-07-09 14:51:00] echo "0a" > /app/public/diff/hanotte_mensah_h_occurrences_21555.diff
[CMD] [2020-07-09 14:51:00] tail -n +1 /app/public/converted_csv/hanotte_mensah_h_occurrences_21555.csv >> /app/public/diff/hanotte_mensah_h_occurrences_21555.diff
[CMD] [2020-07-09 14:51:00] echo "." >> /app/public/diff/hanotte_mensah_h_occurrences_21555.diff
[CMD] [2020-07-09 14:51:00] echo "0a" > /app/public/diff/hanotte_mensah_h_measurements_21556.diff
[CMD] [2020-07-09 14:51:00] tail -n +1 /app/public/converted_csv/hanotte_mensah_h_measurements_21556.csv >> /app/public/diff/hanotte_mensah_h_measurements_21556.diff
[CMD] [2020-07-09 14:51:00] echo "." >> /app/public/diff/hanotte_mensah_h_measurements_21556.diff
[STOP] [2020-07-09 14:51:00] calculate_delta
[START] [2020-07-09 14:51:00] parse_diff_and_store
[INFO] [2020-07-09 14:51:00] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-09 14:51:00] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-09 14:51:00] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-09 14:51:01] Storing 26 ScientificNames
[INFO] [2020-07-09 14:51:01] Processing group of 26 in 1 groups of 1000
[INFO] [2020-07-09 14:51:01] Average Time: 0.01
[INFO] [2020-07-09 14:51:01] Total Time: 1s
[INFO] [2020-07-09 14:51:01] Storing 26 Nodes
[INFO] [2020-07-09 14:51:01] Processing group of 26 in 1 groups of 1000
[INFO] [2020-07-09 14:51:01] Average Time: 0.05
[INFO] [2020-07-09 14:51:01] Total Time: 1s
[INFO] [2020-07-09 14:51:01] Storing 26 Occurrences
[INFO] [2020-07-09 14:51:01] Processing group of 26 in 1 groups of 1000
[INFO] [2020-07-09 14:51:01] Average Time: 0.01
[INFO] [2020-07-09 14:51:01] Total Time: 1s
[INFO] [2020-07-09 14:51:01] Storing 65 Traits
[INFO] [2020-07-09 14:51:01] Processing group of 65 in 1 groups of 1000
[INFO] [2020-07-09 14:51:01] Average Time: 0.03
[INFO] [2020-07-09 14:51:01] Total Time: 1s
[INFO] [2020-07-09 14:51:01] Storing 127 MetaTraits
[INFO] [2020-07-09 14:51:01] Processing group of 127 in 1 groups of 1000
[INFO] [2020-07-09 14:51:01] Average Time: 0.03
[INFO] [2020-07-09 14:51:01] Total Time: 1s
[STOP] [2020-07-09 14:51:01] parse_diff_and_store
[START] [2020-07-09 14:51:01] resolve_keys
[INFO] [2020-07-09 14:51:08] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-09 14:51:08] traits to occurrences...
[INFO] [2020-07-09 14:51:08] traits to nodes (through occurrences)...
[INFO] [2020-07-09 14:51:08] Traits to sex term...
[INFO] [2020-07-09 14:51:08] Traits to lifestage term...
[INFO] [2020-07-09 14:51:08] MetaTraits to traits...
[INFO] [2020-07-09 14:51:08] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-09 14:51:08] Assocs to occurrences...
[INFO] [2020-07-09 14:51:08] Assocs to nodes...
[INFO] [2020-07-09 14:51:08] Assoc to sex term...
[INFO] [2020-07-09 14:51:08] Assoc to lifestage term...
[STOP] [2020-07-09 14:51:08] resolve_keys
[START] [2020-07-09 14:51:08] hold_for_later_1
[STOP] [2020-07-09 14:51:08] hold_for_later_1
[START] [2020-07-09 14:51:08] hold_for_later_2
[STOP] [2020-07-09 14:51:08] hold_for_later_2
[START] [2020-07-09 14:51:08] resolve_missing_parents
[STOP] [2020-07-09 14:51:08] resolve_missing_parents
[START] [2020-07-09 14:51:08] rebuild_nodes
[START] [2020-07-09 14:51:08] Flattener#flatten
[START] [2020-07-09 14:51:08] Flattener#study_resource
[START] [2020-07-09 14:51:08] Flattener#build_ancestry
[STOP] [2020-07-09 14:51:08] Flattener#build_ancestry
[INFO] [2020-07-09 14:51:08] 26 ancestry keys
[START] [2020-07-09 14:51:08] build_node_ancestors
[INFO] [2020-07-09 14:51:08] old ancestors deleted.
[STOP] [2020-07-09 14:51:08] build_node_ancestors
[WARN] [2020-07-09 14:51:08] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-09 14:51:08] Flattener#flatten
[STOP] [2020-07-09 14:51:08] rebuild_nodes
[START] [2020-07-09 14:51:08] resolve_missing_media_owners
[STOP] [2020-07-09 14:51:08] resolve_missing_media_owners
[START] [2020-07-09 14:51:08] sanitize_media_verbatims
[STOP] [2020-07-09 14:51:08] sanitize_media_verbatims
[START] [2020-07-09 14:51:08] queue_downloads
[STOP] [2020-07-09 14:51:08] queue_downloads
[START] [2020-07-09 14:51:08] parse_names
[WARN] [2020-07-09 14:51:08] I see 26 names which still need to be parsed.
[STOP] [2020-07-09 14:51:09] parse_names
[START] [2020-07-09 14:51:09] denormalize_canonical_names_to_nodes
[STOP] [2020-07-09 14:51:09] denormalize_canonical_names_to_nodes
[START] [2020-07-09 14:51:09] match_nodes
[START] [2020-07-09 14:51:09] map_all_nodes_to_pages
[STOP] [2020-07-09 14:51:09] map_all_nodes_to_pages
[INFO] [2020-07-09 14:51:09] ZERO unmatched nodes (of 26)! Nicely done.
[START] [2020-07-09 14:51:09] update_nodes
[STOP] [2020-07-09 14:51:09] update_nodes
[STOP] [2020-07-09 14:51:09] match_nodes
[START] [2020-07-09 14:51:09] reindex_search
[STOP] [2020-07-09 14:51:09] reindex_search
[START] [2020-07-09 14:51:09] normalize_units
[STOP] [2020-07-09 14:51:09] normalize_units
[START] [2020-07-09 14:51:09] calculate_statistics
[2020-07-09 14:51:09] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-09 14:51:09] calculate_statistics
[START] [2020-07-09 14:51:09] complete_harvest_instance
[START] [2020-07-09 14:51:09] overall_tsv_creation
[INFO] [2020-07-09 14:51:09] Processing group of 26 in 1 batches of 10000
[INFO] [2020-07-09 14:51:58] 63 Traits (unfiltered)...
[INFO] [2020-07-09 14:52:11] 63 Traits (filtered)...
[INFO] [2020-07-09 14:52:11] 0 Associations (filtered)...
[INFO] [2020-07-09 14:52:47] 128 metadata added.
[INFO] [2020-07-09 14:52:47] 0 metadata added.
[INFO] [2020-07-09 14:52:47] Average Time: 71.09
[INFO] [2020-07-09 14:52:47] Total Time: 1m38s
[STOP] [2020-07-09 14:52:47] overall_tsv_creation
[INFO] [2020-07-09 14:52:47] Done. Check your files:
[INFO] [2020-07-09 14:52:47] (26 lines) /app/public/data/hanotte_mensah_h/publish_nodes.tsv
[INFO] [2020-07-09 14:52:47] (26 lines) /app/public/data/hanotte_mensah_h/publish_scientific_names.tsv
[INFO] [2020-07-09 14:52:47] (64 lines) /app/public/data/hanotte_mensah_h/publish_traits.tsv
[INFO] [2020-07-09 14:52:47] (129 lines) /app/public/data/hanotte_mensah_h/publish_metadata.tsv
[STOP] [2020-07-09 14:52:47] complete_harvest_instance
[START] [2020-07-09 14:52:47] completed
[STOP] [2020-07-09 14:52:47] completed
[STOP] [2020-07-09 14:52:47] logged process, took 107.99
Latest Process

09 Jul 14:50 EXITED currently processing 0