Harvest for Ojasti 1996 Created 09 Jul 14:48

Stage: completed
Fetched: 09 Jul 14:48
Validated: 09 Jul 14:48
Deltas Created 09 Jul 14:48
Units Normalized: 09 Jul 14:48
Ancestry Built: 09 Jul 14:48
Nodes Matched: 09 Jul 14:48
Names Parsed: 09 Jul 14:48
New Models Stored: 09 Jul 14:48
Indexed: 09 Jul 14:48
Completed: 09 Jul 14:50
Time to Harvest: less than a minute
Harvesting Log

(126 lines)
# Logfile created on 2020-07-09 14:48:14 -0400 by logger.rb/v1.4.2
[INFO] [2020-07-09 14:48:14] ## HARVEST: type = -harvest
[START] [2020-07-09 14:48:18] logged process
[START] [2020-07-09 14:48:18] create_harvest_instance
[STOP] [2020-07-09 14:48:19] create_harvest_instance
[START] [2020-07-09 14:48:19] fetch_files
[STOP] [2020-07-09 14:48:19] fetch_files
[START] [2020-07-09 14:48:19] validate_each_file
[STOP] [2020-07-09 14:48:19] validate_each_file
[START] [2020-07-09 14:48:19] convert_to_csv
[CMD] [2020-07-09 14:48:19] /usr/bin/sort /app/public/converted_csv/ojasti_ojasti_19_nodes_21548.csv > /app/public/converted_csv/ojasti_ojasti_19_nodes_21548.csv_sorted
[CMD] [2020-07-09 14:48:19] /usr/bin/sort /app/public/converted_csv/ojasti_ojasti_19_occurrences_21549.csv > /app/public/converted_csv/ojasti_ojasti_19_occurrences_21549.csv_sorted
[CMD] [2020-07-09 14:48:19] /usr/bin/sort /app/public/converted_csv/ojasti_ojasti_19_measurements_21550.csv > /app/public/converted_csv/ojasti_ojasti_19_measurements_21550.csv_sorted
[STOP] [2020-07-09 14:48:19] convert_to_csv
[START] [2020-07-09 14:48:19] calculate_delta
[CMD] [2020-07-09 14:48:19] echo "0a" > /app/public/diff/ojasti_ojasti_19_nodes_21548.diff
[CMD] [2020-07-09 14:48:19] tail -n +1 /app/public/converted_csv/ojasti_ojasti_19_nodes_21548.csv >> /app/public/diff/ojasti_ojasti_19_nodes_21548.diff
[CMD] [2020-07-09 14:48:19] echo "." >> /app/public/diff/ojasti_ojasti_19_nodes_21548.diff
[CMD] [2020-07-09 14:48:19] echo "0a" > /app/public/diff/ojasti_ojasti_19_occurrences_21549.diff
[CMD] [2020-07-09 14:48:19] tail -n +1 /app/public/converted_csv/ojasti_ojasti_19_occurrences_21549.csv >> /app/public/diff/ojasti_ojasti_19_occurrences_21549.diff
[CMD] [2020-07-09 14:48:20] echo "." >> /app/public/diff/ojasti_ojasti_19_occurrences_21549.diff
[CMD] [2020-07-09 14:48:20] echo "0a" > /app/public/diff/ojasti_ojasti_19_measurements_21550.diff
[CMD] [2020-07-09 14:48:20] tail -n +1 /app/public/converted_csv/ojasti_ojasti_19_measurements_21550.csv >> /app/public/diff/ojasti_ojasti_19_measurements_21550.diff
[CMD] [2020-07-09 14:48:20] echo "." >> /app/public/diff/ojasti_ojasti_19_measurements_21550.diff
[STOP] [2020-07-09 14:48:20] calculate_delta
[START] [2020-07-09 14:48:20] parse_diff_and_store
[INFO] [2020-07-09 14:48:20] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-09 14:48:20] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-09 14:48:20] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-09 14:48:21] Storing 37 ScientificNames
[INFO] [2020-07-09 14:48:21] Processing group of 37 in 1 groups of 1000
[INFO] [2020-07-09 14:48:21] Average Time: 0.02
[INFO] [2020-07-09 14:48:21] Total Time: 1s
[INFO] [2020-07-09 14:48:21] Storing 37 Nodes
[INFO] [2020-07-09 14:48:21] Processing group of 37 in 1 groups of 1000
[INFO] [2020-07-09 14:48:22] Average Time: 0.06
[INFO] [2020-07-09 14:48:22] Total Time: 1s
[INFO] [2020-07-09 14:48:22] Storing 37 Occurrences
[INFO] [2020-07-09 14:48:22] Processing group of 37 in 1 groups of 1000
[INFO] [2020-07-09 14:48:22] Average Time: 0.03
[INFO] [2020-07-09 14:48:22] Total Time: 1s
[INFO] [2020-07-09 14:48:22] Storing 424 Traits
[INFO] [2020-07-09 14:48:22] Processing group of 424 in 1 groups of 1000
[INFO] [2020-07-09 14:48:22] Average Time: 0.21
[INFO] [2020-07-09 14:48:22] Total Time: 1s
[INFO] [2020-07-09 14:48:22] Storing 848 MetaTraits
[INFO] [2020-07-09 14:48:22] Processing group of 848 in 1 groups of 1000
[INFO] [2020-07-09 14:48:22] Average Time: 0.13
[INFO] [2020-07-09 14:48:22] Total Time: 1s
[STOP] [2020-07-09 14:48:22] parse_diff_and_store
[START] [2020-07-09 14:48:22] resolve_keys
[INFO] [2020-07-09 14:48:29] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-09 14:48:29] traits to occurrences...
[INFO] [2020-07-09 14:48:29] traits to nodes (through occurrences)...
[INFO] [2020-07-09 14:48:29] Traits to sex term...
[INFO] [2020-07-09 14:48:29] Traits to lifestage term...
[INFO] [2020-07-09 14:48:29] MetaTraits to traits...
[INFO] [2020-07-09 14:48:29] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-09 14:48:29] Assocs to occurrences...
[INFO] [2020-07-09 14:48:29] Assocs to nodes...
[INFO] [2020-07-09 14:48:29] Assoc to sex term...
[INFO] [2020-07-09 14:48:29] Assoc to lifestage term...
[STOP] [2020-07-09 14:48:29] resolve_keys
[START] [2020-07-09 14:48:29] hold_for_later_1
[STOP] [2020-07-09 14:48:29] hold_for_later_1
[START] [2020-07-09 14:48:29] hold_for_later_2
[STOP] [2020-07-09 14:48:29] hold_for_later_2
[START] [2020-07-09 14:48:29] resolve_missing_parents
[STOP] [2020-07-09 14:48:29] resolve_missing_parents
[START] [2020-07-09 14:48:29] rebuild_nodes
[START] [2020-07-09 14:48:29] Flattener#flatten
[START] [2020-07-09 14:48:29] Flattener#study_resource
[START] [2020-07-09 14:48:29] Flattener#build_ancestry
[STOP] [2020-07-09 14:48:29] Flattener#build_ancestry
[INFO] [2020-07-09 14:48:29] 37 ancestry keys
[START] [2020-07-09 14:48:29] build_node_ancestors
[INFO] [2020-07-09 14:48:29] old ancestors deleted.
[STOP] [2020-07-09 14:48:29] build_node_ancestors
[WARN] [2020-07-09 14:48:29] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-09 14:48:29] Flattener#flatten
[STOP] [2020-07-09 14:48:29] rebuild_nodes
[START] [2020-07-09 14:48:29] resolve_missing_media_owners
[STOP] [2020-07-09 14:48:29] resolve_missing_media_owners
[START] [2020-07-09 14:48:29] sanitize_media_verbatims
[STOP] [2020-07-09 14:48:29] sanitize_media_verbatims
[START] [2020-07-09 14:48:29] queue_downloads
[STOP] [2020-07-09 14:48:29] queue_downloads
[START] [2020-07-09 14:48:29] parse_names
[WARN] [2020-07-09 14:48:29] I see 37 names which still need to be parsed.
[STOP] [2020-07-09 14:48:30] parse_names
[START] [2020-07-09 14:48:30] denormalize_canonical_names_to_nodes
[STOP] [2020-07-09 14:48:30] denormalize_canonical_names_to_nodes
[START] [2020-07-09 14:48:30] match_nodes
[START] [2020-07-09 14:48:30] map_all_nodes_to_pages
[STOP] [2020-07-09 14:48:30] map_all_nodes_to_pages
[INFO] [2020-07-09 14:48:30] ZERO unmatched nodes (of 37)! Nicely done.
[START] [2020-07-09 14:48:30] update_nodes
[STOP] [2020-07-09 14:48:30] update_nodes
[STOP] [2020-07-09 14:48:30] match_nodes
[START] [2020-07-09 14:48:30] reindex_search
[STOP] [2020-07-09 14:48:30] reindex_search
[START] [2020-07-09 14:48:30] normalize_units
[STOP] [2020-07-09 14:48:30] normalize_units
[START] [2020-07-09 14:48:30] calculate_statistics
[2020-07-09 14:48:30] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-09 14:48:30] calculate_statistics
[START] [2020-07-09 14:48:30] complete_harvest_instance
[START] [2020-07-09 14:48:30] overall_tsv_creation
[INFO] [2020-07-09 14:48:30] Processing group of 37 in 1 batches of 10000
[INFO] [2020-07-09 14:49:19] 424 Traits (unfiltered)...
[INFO] [2020-07-09 14:49:32] 424 Traits (filtered)...
[INFO] [2020-07-09 14:49:32] 0 Associations (filtered)...
[INFO] [2020-07-09 14:50:09] 848 metadata added.
[INFO] [2020-07-09 14:50:09] 0 metadata added.
[INFO] [2020-07-09 14:50:09] Average Time: 71.38
[INFO] [2020-07-09 14:50:09] Total Time: 1m39s
[STOP] [2020-07-09 14:50:09] overall_tsv_creation
[INFO] [2020-07-09 14:50:09] Done. Check your files:
[INFO] [2020-07-09 14:50:09] (37 lines) /app/public/data/ojasti_ojasti_19/publish_nodes.tsv
[INFO] [2020-07-09 14:50:09] (37 lines) /app/public/data/ojasti_ojasti_19/publish_scientific_names.tsv
[INFO] [2020-07-09 14:50:09] (425 lines) /app/public/data/ojasti_ojasti_19/publish_traits.tsv
[INFO] [2020-07-09 14:50:09] (849 lines) /app/public/data/ojasti_ojasti_19/publish_metadata.tsv
[STOP] [2020-07-09 14:50:09] complete_harvest_instance
[START] [2020-07-09 14:50:09] completed
[STOP] [2020-07-09 14:50:09] completed
[STOP] [2020-07-09 14:50:09] logged process, took 110.61
Latest Process

09 Jul 14:48 EXITED currently processing 0