Harvest for Lambio 2012 Created 09 Jul 14:54

Stage: completed
Fetched: 09 Jul 14:54
Validated: 09 Jul 14:54
Deltas Created 09 Jul 14:54
Units Normalized: 09 Jul 14:54
Ancestry Built: 09 Jul 14:54
Nodes Matched: 09 Jul 14:54
Names Parsed: 09 Jul 14:54
New Models Stored: 09 Jul 14:54
Indexed: 09 Jul 14:54
Completed: 09 Jul 14:55
Time to Harvest: less than a minute
Harvesting Log

(126 lines)
# Logfile created on 2020-07-09 14:54:01 -0400 by logger.rb/v1.4.2
[INFO] [2020-07-09 14:54:01] ## HARVEST: type = -harvest
[START] [2020-07-09 14:54:02] logged process
[START] [2020-07-09 14:54:02] create_harvest_instance
[STOP] [2020-07-09 14:54:03] create_harvest_instance
[START] [2020-07-09 14:54:03] fetch_files
[STOP] [2020-07-09 14:54:03] fetch_files
[START] [2020-07-09 14:54:03] validate_each_file
[STOP] [2020-07-09 14:54:03] validate_each_file
[START] [2020-07-09 14:54:03] convert_to_csv
[CMD] [2020-07-09 14:54:03] /usr/bin/sort /app/public/converted_csv/lambio_lambio_20_nodes_21560.csv > /app/public/converted_csv/lambio_lambio_20_nodes_21560.csv_sorted
[CMD] [2020-07-09 14:54:03] /usr/bin/sort /app/public/converted_csv/lambio_lambio_20_occurrences_21561.csv > /app/public/converted_csv/lambio_lambio_20_occurrences_21561.csv_sorted
[CMD] [2020-07-09 14:54:03] /usr/bin/sort /app/public/converted_csv/lambio_lambio_20_measurements_21562.csv > /app/public/converted_csv/lambio_lambio_20_measurements_21562.csv_sorted
[STOP] [2020-07-09 14:54:03] convert_to_csv
[START] [2020-07-09 14:54:03] calculate_delta
[CMD] [2020-07-09 14:54:03] echo "0a" > /app/public/diff/lambio_lambio_20_nodes_21560.diff
[CMD] [2020-07-09 14:54:03] tail -n +1 /app/public/converted_csv/lambio_lambio_20_nodes_21560.csv >> /app/public/diff/lambio_lambio_20_nodes_21560.diff
[CMD] [2020-07-09 14:54:03] echo "." >> /app/public/diff/lambio_lambio_20_nodes_21560.diff
[CMD] [2020-07-09 14:54:03] echo "0a" > /app/public/diff/lambio_lambio_20_occurrences_21561.diff
[CMD] [2020-07-09 14:54:03] tail -n +1 /app/public/converted_csv/lambio_lambio_20_occurrences_21561.csv >> /app/public/diff/lambio_lambio_20_occurrences_21561.diff
[CMD] [2020-07-09 14:54:03] echo "." >> /app/public/diff/lambio_lambio_20_occurrences_21561.diff
[CMD] [2020-07-09 14:54:03] echo "0a" > /app/public/diff/lambio_lambio_20_measurements_21562.diff
[CMD] [2020-07-09 14:54:03] tail -n +1 /app/public/converted_csv/lambio_lambio_20_measurements_21562.csv >> /app/public/diff/lambio_lambio_20_measurements_21562.diff
[CMD] [2020-07-09 14:54:03] echo "." >> /app/public/diff/lambio_lambio_20_measurements_21562.diff
[STOP] [2020-07-09 14:54:03] calculate_delta
[START] [2020-07-09 14:54:03] parse_diff_and_store
[INFO] [2020-07-09 14:54:03] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-09 14:54:03] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-09 14:54:03] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-09 14:54:04] Storing 11 ScientificNames
[INFO] [2020-07-09 14:54:04] Processing group of 11 in 1 groups of 1000
[INFO] [2020-07-09 14:54:04] Average Time: 0.01
[INFO] [2020-07-09 14:54:04] Total Time: 1s
[INFO] [2020-07-09 14:54:04] Storing 11 Nodes
[INFO] [2020-07-09 14:54:04] Processing group of 11 in 1 groups of 1000
[INFO] [2020-07-09 14:54:04] Average Time: 0.01
[INFO] [2020-07-09 14:54:04] Total Time: 1s
[INFO] [2020-07-09 14:54:04] Storing 11 Occurrences
[INFO] [2020-07-09 14:54:04] Processing group of 11 in 1 groups of 1000
[INFO] [2020-07-09 14:54:04] Average Time: 0.0
[INFO] [2020-07-09 14:54:04] Total Time: 1s
[INFO] [2020-07-09 14:54:04] Storing 47 Traits
[INFO] [2020-07-09 14:54:04] Processing group of 47 in 1 groups of 1000
[INFO] [2020-07-09 14:54:04] Average Time: 0.02
[INFO] [2020-07-09 14:54:04] Total Time: 1s
[INFO] [2020-07-09 14:54:04] Storing 78 MetaTraits
[INFO] [2020-07-09 14:54:04] Processing group of 78 in 1 groups of 1000
[INFO] [2020-07-09 14:54:04] Average Time: 0.01
[INFO] [2020-07-09 14:54:04] Total Time: 1s
[STOP] [2020-07-09 14:54:04] parse_diff_and_store
[START] [2020-07-09 14:54:04] resolve_keys
[INFO] [2020-07-09 14:54:10] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-09 14:54:11] traits to occurrences...
[INFO] [2020-07-09 14:54:11] traits to nodes (through occurrences)...
[INFO] [2020-07-09 14:54:11] Traits to sex term...
[INFO] [2020-07-09 14:54:11] Traits to lifestage term...
[INFO] [2020-07-09 14:54:11] MetaTraits to traits...
[INFO] [2020-07-09 14:54:11] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-09 14:54:11] Assocs to occurrences...
[INFO] [2020-07-09 14:54:11] Assocs to nodes...
[INFO] [2020-07-09 14:54:11] Assoc to sex term...
[INFO] [2020-07-09 14:54:11] Assoc to lifestage term...
[STOP] [2020-07-09 14:54:11] resolve_keys
[START] [2020-07-09 14:54:11] hold_for_later_1
[STOP] [2020-07-09 14:54:11] hold_for_later_1
[START] [2020-07-09 14:54:11] hold_for_later_2
[STOP] [2020-07-09 14:54:11] hold_for_later_2
[START] [2020-07-09 14:54:11] resolve_missing_parents
[STOP] [2020-07-09 14:54:11] resolve_missing_parents
[START] [2020-07-09 14:54:11] rebuild_nodes
[START] [2020-07-09 14:54:11] Flattener#flatten
[START] [2020-07-09 14:54:11] Flattener#study_resource
[START] [2020-07-09 14:54:11] Flattener#build_ancestry
[STOP] [2020-07-09 14:54:11] Flattener#build_ancestry
[INFO] [2020-07-09 14:54:11] 11 ancestry keys
[START] [2020-07-09 14:54:11] build_node_ancestors
[INFO] [2020-07-09 14:54:11] old ancestors deleted.
[STOP] [2020-07-09 14:54:11] build_node_ancestors
[WARN] [2020-07-09 14:54:11] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-09 14:54:11] Flattener#flatten
[STOP] [2020-07-09 14:54:11] rebuild_nodes
[START] [2020-07-09 14:54:11] resolve_missing_media_owners
[STOP] [2020-07-09 14:54:11] resolve_missing_media_owners
[START] [2020-07-09 14:54:11] sanitize_media_verbatims
[STOP] [2020-07-09 14:54:11] sanitize_media_verbatims
[START] [2020-07-09 14:54:11] queue_downloads
[STOP] [2020-07-09 14:54:11] queue_downloads
[START] [2020-07-09 14:54:11] parse_names
[WARN] [2020-07-09 14:54:11] I see 11 names which still need to be parsed.
[STOP] [2020-07-09 14:54:12] parse_names
[START] [2020-07-09 14:54:12] denormalize_canonical_names_to_nodes
[STOP] [2020-07-09 14:54:12] denormalize_canonical_names_to_nodes
[START] [2020-07-09 14:54:12] match_nodes
[START] [2020-07-09 14:54:12] map_all_nodes_to_pages
[STOP] [2020-07-09 14:54:12] map_all_nodes_to_pages
[INFO] [2020-07-09 14:54:12] ZERO unmatched nodes (of 11)! Nicely done.
[START] [2020-07-09 14:54:12] update_nodes
[STOP] [2020-07-09 14:54:12] update_nodes
[STOP] [2020-07-09 14:54:12] match_nodes
[START] [2020-07-09 14:54:12] reindex_search
[STOP] [2020-07-09 14:54:12] reindex_search
[START] [2020-07-09 14:54:12] normalize_units
[STOP] [2020-07-09 14:54:12] normalize_units
[START] [2020-07-09 14:54:12] calculate_statistics
[2020-07-09 14:54:12] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-09 14:54:12] calculate_statistics
[START] [2020-07-09 14:54:12] complete_harvest_instance
[START] [2020-07-09 14:54:12] overall_tsv_creation
[INFO] [2020-07-09 14:54:12] Processing group of 11 in 1 batches of 10000
[INFO] [2020-07-09 14:55:01] 37 Traits (unfiltered)...
[INFO] [2020-07-09 14:55:13] 37 Traits (filtered)...
[INFO] [2020-07-09 14:55:13] 0 Associations (filtered)...
[INFO] [2020-07-09 14:55:50] 84 metadata added.
[INFO] [2020-07-09 14:55:50] 0 metadata added.
[INFO] [2020-07-09 14:55:50] Average Time: 70.68
[INFO] [2020-07-09 14:55:50] Total Time: 1m38s
[STOP] [2020-07-09 14:55:50] overall_tsv_creation
[INFO] [2020-07-09 14:55:50] Done. Check your files:
[INFO] [2020-07-09 14:55:50] (11 lines) /app/public/data/lambio_lambio_20/publish_nodes.tsv
[INFO] [2020-07-09 14:55:50] (11 lines) /app/public/data/lambio_lambio_20/publish_scientific_names.tsv
[INFO] [2020-07-09 14:55:50] (38 lines) /app/public/data/lambio_lambio_20/publish_traits.tsv
[INFO] [2020-07-09 14:55:50] (85 lines) /app/public/data/lambio_lambio_20/publish_metadata.tsv
[STOP] [2020-07-09 14:55:50] complete_harvest_instance
[START] [2020-07-09 14:55:50] completed
[STOP] [2020-07-09 14:55:50] completed
[STOP] [2020-07-09 14:55:50] logged process, took 107.54
Latest Process

09 Jul 14:54 EXITED currently processing 0