Harvest for Martin 2000 Created 09 Jul 14:41

Stage: completed
Fetched: 09 Jul 14:41
Validated: 09 Jul 14:41
Deltas Created 09 Jul 14:41
Units Normalized: 09 Jul 14:41
Ancestry Built: 09 Jul 14:41
Nodes Matched: 09 Jul 14:41
Names Parsed: 09 Jul 14:41
New Models Stored: 09 Jul 14:41
Indexed: 09 Jul 14:41
Completed: 09 Jul 14:43
Time to Harvest: less than a minute
Harvesting Log

(126 lines)
# Logfile created on 2020-07-09 14:41:18 -0400 by logger.rb/v1.4.2
[INFO] [2020-07-09 14:41:18] ## HARVEST: type = -harvest
[START] [2020-07-09 14:41:19] logged process
[START] [2020-07-09 14:41:19] create_harvest_instance
[STOP] [2020-07-09 14:41:20] create_harvest_instance
[START] [2020-07-09 14:41:20] fetch_files
[STOP] [2020-07-09 14:41:20] fetch_files
[START] [2020-07-09 14:41:20] validate_each_file
[STOP] [2020-07-09 14:41:20] validate_each_file
[START] [2020-07-09 14:41:20] convert_to_csv
[CMD] [2020-07-09 14:41:20] /usr/bin/sort /app/public/converted_csv/martin_martin_20_nodes_21542.csv > /app/public/converted_csv/martin_martin_20_nodes_21542.csv_sorted
[CMD] [2020-07-09 14:41:20] /usr/bin/sort /app/public/converted_csv/martin_martin_20_occurrences_21543.csv > /app/public/converted_csv/martin_martin_20_occurrences_21543.csv_sorted
[CMD] [2020-07-09 14:41:20] /usr/bin/sort /app/public/converted_csv/martin_martin_20_measurements_21544.csv > /app/public/converted_csv/martin_martin_20_measurements_21544.csv_sorted
[STOP] [2020-07-09 14:41:20] convert_to_csv
[START] [2020-07-09 14:41:20] calculate_delta
[CMD] [2020-07-09 14:41:20] echo "0a" > /app/public/diff/martin_martin_20_nodes_21542.diff
[CMD] [2020-07-09 14:41:20] tail -n +1 /app/public/converted_csv/martin_martin_20_nodes_21542.csv >> /app/public/diff/martin_martin_20_nodes_21542.diff
[CMD] [2020-07-09 14:41:20] echo "." >> /app/public/diff/martin_martin_20_nodes_21542.diff
[CMD] [2020-07-09 14:41:21] echo "0a" > /app/public/diff/martin_martin_20_occurrences_21543.diff
[CMD] [2020-07-09 14:41:21] tail -n +1 /app/public/converted_csv/martin_martin_20_occurrences_21543.csv >> /app/public/diff/martin_martin_20_occurrences_21543.diff
[CMD] [2020-07-09 14:41:21] echo "." >> /app/public/diff/martin_martin_20_occurrences_21543.diff
[CMD] [2020-07-09 14:41:21] echo "0a" > /app/public/diff/martin_martin_20_measurements_21544.diff
[CMD] [2020-07-09 14:41:21] tail -n +1 /app/public/converted_csv/martin_martin_20_measurements_21544.csv >> /app/public/diff/martin_martin_20_measurements_21544.diff
[CMD] [2020-07-09 14:41:21] echo "." >> /app/public/diff/martin_martin_20_measurements_21544.diff
[STOP] [2020-07-09 14:41:21] calculate_delta
[START] [2020-07-09 14:41:21] parse_diff_and_store
[INFO] [2020-07-09 14:41:21] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-09 14:41:21] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-09 14:41:21] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-09 14:41:21] Storing 4 ScientificNames
[INFO] [2020-07-09 14:41:21] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-09 14:41:21] Average Time: 0.0
[INFO] [2020-07-09 14:41:21] Total Time: 1s
[INFO] [2020-07-09 14:41:21] Storing 4 Nodes
[INFO] [2020-07-09 14:41:21] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-09 14:41:21] Average Time: 0.01
[INFO] [2020-07-09 14:41:21] Total Time: 1s
[INFO] [2020-07-09 14:41:21] Storing 4 Occurrences
[INFO] [2020-07-09 14:41:21] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-09 14:41:21] Average Time: 0.0
[INFO] [2020-07-09 14:41:21] Total Time: 1s
[INFO] [2020-07-09 14:41:21] Storing 4 Traits
[INFO] [2020-07-09 14:41:21] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-09 14:41:21] Average Time: 0.0
[INFO] [2020-07-09 14:41:21] Total Time: 1s
[INFO] [2020-07-09 14:41:21] Storing 8 MetaTraits
[INFO] [2020-07-09 14:41:21] Processing group of 8 in 1 groups of 1000
[INFO] [2020-07-09 14:41:21] Average Time: 0.0
[INFO] [2020-07-09 14:41:21] Total Time: 1s
[STOP] [2020-07-09 14:41:21] parse_diff_and_store
[START] [2020-07-09 14:41:21] resolve_keys
[INFO] [2020-07-09 14:41:27] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-09 14:41:27] traits to occurrences...
[INFO] [2020-07-09 14:41:27] traits to nodes (through occurrences)...
[INFO] [2020-07-09 14:41:27] Traits to sex term...
[INFO] [2020-07-09 14:41:27] Traits to lifestage term...
[INFO] [2020-07-09 14:41:27] MetaTraits to traits...
[INFO] [2020-07-09 14:41:27] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-09 14:41:27] Assocs to occurrences...
[INFO] [2020-07-09 14:41:27] Assocs to nodes...
[INFO] [2020-07-09 14:41:27] Assoc to sex term...
[INFO] [2020-07-09 14:41:27] Assoc to lifestage term...
[STOP] [2020-07-09 14:41:27] resolve_keys
[START] [2020-07-09 14:41:27] hold_for_later_1
[STOP] [2020-07-09 14:41:27] hold_for_later_1
[START] [2020-07-09 14:41:27] hold_for_later_2
[STOP] [2020-07-09 14:41:27] hold_for_later_2
[START] [2020-07-09 14:41:27] resolve_missing_parents
[STOP] [2020-07-09 14:41:27] resolve_missing_parents
[START] [2020-07-09 14:41:27] rebuild_nodes
[START] [2020-07-09 14:41:27] Flattener#flatten
[START] [2020-07-09 14:41:27] Flattener#study_resource
[START] [2020-07-09 14:41:27] Flattener#build_ancestry
[STOP] [2020-07-09 14:41:27] Flattener#build_ancestry
[INFO] [2020-07-09 14:41:27] 4 ancestry keys
[START] [2020-07-09 14:41:27] build_node_ancestors
[INFO] [2020-07-09 14:41:27] old ancestors deleted.
[STOP] [2020-07-09 14:41:27] build_node_ancestors
[WARN] [2020-07-09 14:41:27] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-09 14:41:27] Flattener#flatten
[STOP] [2020-07-09 14:41:27] rebuild_nodes
[START] [2020-07-09 14:41:27] resolve_missing_media_owners
[STOP] [2020-07-09 14:41:27] resolve_missing_media_owners
[START] [2020-07-09 14:41:27] sanitize_media_verbatims
[STOP] [2020-07-09 14:41:27] sanitize_media_verbatims
[START] [2020-07-09 14:41:27] queue_downloads
[STOP] [2020-07-09 14:41:27] queue_downloads
[START] [2020-07-09 14:41:27] parse_names
[WARN] [2020-07-09 14:41:27] I see 4 names which still need to be parsed.
[STOP] [2020-07-09 14:41:29] parse_names
[START] [2020-07-09 14:41:29] denormalize_canonical_names_to_nodes
[STOP] [2020-07-09 14:41:29] denormalize_canonical_names_to_nodes
[START] [2020-07-09 14:41:29] match_nodes
[START] [2020-07-09 14:41:29] map_all_nodes_to_pages
[STOP] [2020-07-09 14:41:29] map_all_nodes_to_pages
[INFO] [2020-07-09 14:41:29] ZERO unmatched nodes (of 4)! Nicely done.
[START] [2020-07-09 14:41:29] update_nodes
[STOP] [2020-07-09 14:41:29] update_nodes
[STOP] [2020-07-09 14:41:29] match_nodes
[START] [2020-07-09 14:41:29] reindex_search
[STOP] [2020-07-09 14:41:29] reindex_search
[START] [2020-07-09 14:41:29] normalize_units
[STOP] [2020-07-09 14:41:29] normalize_units
[START] [2020-07-09 14:41:29] calculate_statistics
[2020-07-09 14:41:29] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-09 14:41:29] calculate_statistics
[START] [2020-07-09 14:41:29] complete_harvest_instance
[START] [2020-07-09 14:41:29] overall_tsv_creation
[INFO] [2020-07-09 14:41:29] Processing group of 4 in 1 batches of 10000
[INFO] [2020-07-09 14:42:17] 4 Traits (unfiltered)...
[INFO] [2020-07-09 14:42:30] 4 Traits (filtered)...
[INFO] [2020-07-09 14:42:30] 0 Associations (filtered)...
[INFO] [2020-07-09 14:43:06] 8 metadata added.
[INFO] [2020-07-09 14:43:06] 0 metadata added.
[INFO] [2020-07-09 14:43:06] Average Time: 70.35
[INFO] [2020-07-09 14:43:06] Total Time: 1m38s
[STOP] [2020-07-09 14:43:06] overall_tsv_creation
[INFO] [2020-07-09 14:43:06] Done. Check your files:
[INFO] [2020-07-09 14:43:06] (4 lines) /app/public/data/martin_martin_20/publish_nodes.tsv
[INFO] [2020-07-09 14:43:06] (4 lines) /app/public/data/martin_martin_20/publish_scientific_names.tsv
[INFO] [2020-07-09 14:43:06] (5 lines) /app/public/data/martin_martin_20/publish_traits.tsv
[INFO] [2020-07-09 14:43:06] (9 lines) /app/public/data/martin_martin_20/publish_metadata.tsv
[STOP] [2020-07-09 14:43:06] complete_harvest_instance
[START] [2020-07-09 14:43:06] completed
[STOP] [2020-07-09 14:43:06] completed
[STOP] [2020-07-09 14:43:06] logged process, took 106.68
Latest Process

09 Jul 14:41 EXITED currently processing 0