Harvest for Keller et al 1989 Created 16 Jun 09:35

Stage: completed
Fetched: 16 Jun 09:35
Validated: 16 Jun 09:35
Deltas Created 16 Jun 09:35
Units Normalized: 16 Jun 09:35
Ancestry Built: 16 Jun 09:35
Nodes Matched: 16 Jun 09:35
Names Parsed: 16 Jun 09:35
New Models Stored: 16 Jun 09:35
Indexed: 16 Jun 09:35
Completed: 16 Jun 09:37
Time to Harvest: less than a minute
Harvesting Log

(132 lines)
# Logfile created on 2020-06-16 09:35:16 -0400 by logger.rb/v1.4.2
[INFO] [2020-06-16 09:35:16] ## HARVEST: type = -harvest
[START] [2020-06-16 09:35:19] logged process
[START] [2020-06-16 09:35:19] create_harvest_instance
[STOP] [2020-06-16 09:35:20] create_harvest_instance
[START] [2020-06-16 09:35:20] fetch_files
[STOP] [2020-06-16 09:35:20] fetch_files
[START] [2020-06-16 09:35:20] validate_each_file
[STOP] [2020-06-16 09:35:20] validate_each_file
[START] [2020-06-16 09:35:20] convert_to_csv
[CMD] [2020-06-16 09:35:20] /usr/bin/sort /app/public/converted_csv/keller_et_al_kel_nodes_21286.csv > /app/public/converted_csv/keller_et_al_kel_nodes_21286.csv_sorted
[CMD] [2020-06-16 09:35:20] /usr/bin/sort /app/public/converted_csv/keller_et_al_kel_occurrences_21287.csv > /app/public/converted_csv/keller_et_al_kel_occurrences_21287.csv_sorted
[CMD] [2020-06-16 09:35:20] /usr/bin/sort /app/public/converted_csv/keller_et_al_kel_measurements_21288.csv > /app/public/converted_csv/keller_et_al_kel_measurements_21288.csv_sorted
[STOP] [2020-06-16 09:35:20] convert_to_csv
[START] [2020-06-16 09:35:20] calculate_delta
[CMD] [2020-06-16 09:35:20] echo "0a" > /app/public/diff/keller_et_al_kel_nodes_21286.diff
[CMD] [2020-06-16 09:35:20] tail -n +1 /app/public/converted_csv/keller_et_al_kel_nodes_21286.csv >> /app/public/diff/keller_et_al_kel_nodes_21286.diff
[CMD] [2020-06-16 09:35:20] echo "." >> /app/public/diff/keller_et_al_kel_nodes_21286.diff
[CMD] [2020-06-16 09:35:20] echo "0a" > /app/public/diff/keller_et_al_kel_occurrences_21287.diff
[CMD] [2020-06-16 09:35:20] tail -n +1 /app/public/converted_csv/keller_et_al_kel_occurrences_21287.csv >> /app/public/diff/keller_et_al_kel_occurrences_21287.diff
[CMD] [2020-06-16 09:35:20] echo "." >> /app/public/diff/keller_et_al_kel_occurrences_21287.diff
[CMD] [2020-06-16 09:35:20] echo "0a" > /app/public/diff/keller_et_al_kel_measurements_21288.diff
[CMD] [2020-06-16 09:35:20] tail -n +1 /app/public/converted_csv/keller_et_al_kel_measurements_21288.csv >> /app/public/diff/keller_et_al_kel_measurements_21288.diff
[CMD] [2020-06-16 09:35:20] echo "." >> /app/public/diff/keller_et_al_kel_measurements_21288.diff
[STOP] [2020-06-16 09:35:21] calculate_delta
[START] [2020-06-16 09:35:21] parse_diff_and_store
[INFO] [2020-06-16 09:35:21] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-16 09:35:21] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-16 09:35:21] Loading measurements diff file into memory (true lines)...
[INFO] [2020-06-16 09:35:21] Storing 87 ScientificNames
[INFO] [2020-06-16 09:35:21] Processing group of 87 in 1 groups of 1000
[INFO] [2020-06-16 09:35:22] Average Time: 0.06
[INFO] [2020-06-16 09:35:22] Total Time: 1s
[INFO] [2020-06-16 09:35:22] Storing 87 Nodes
[INFO] [2020-06-16 09:35:22] Processing group of 87 in 1 groups of 1000
[INFO] [2020-06-16 09:35:22] Average Time: 0.02
[INFO] [2020-06-16 09:35:22] Total Time: 1s
[INFO] [2020-06-16 09:35:22] Storing 74 Occurrences
[INFO] [2020-06-16 09:35:22] Processing group of 74 in 1 groups of 1000
[INFO] [2020-06-16 09:35:22] Average Time: 0.01
[INFO] [2020-06-16 09:35:22] Total Time: 1s
[INFO] [2020-06-16 09:35:22] Storing 222 Traits
[INFO] [2020-06-16 09:35:22] Processing group of 222 in 1 groups of 1000
[INFO] [2020-06-16 09:35:22] Average Time: 0.07
[INFO] [2020-06-16 09:35:22] Total Time: 1s
[INFO] [2020-06-16 09:35:22] Storing 222 MetaTraits
[INFO] [2020-06-16 09:35:22] Processing group of 222 in 1 groups of 1000
[INFO] [2020-06-16 09:35:22] Average Time: 0.02
[INFO] [2020-06-16 09:35:22] Total Time: 1s
[STOP] [2020-06-16 09:35:22] parse_diff_and_store
[START] [2020-06-16 09:35:22] resolve_keys
[INFO] [2020-06-16 09:35:29] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-16 09:35:29] traits to occurrences...
[INFO] [2020-06-16 09:35:29] traits to nodes (through occurrences)...
[INFO] [2020-06-16 09:35:29] Traits to sex term...
[INFO] [2020-06-16 09:35:29] Traits to lifestage term...
[INFO] [2020-06-16 09:35:29] MetaTraits to traits...
[INFO] [2020-06-16 09:35:29] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-16 09:35:29] Assocs to occurrences...
[INFO] [2020-06-16 09:35:29] Assocs to nodes...
[INFO] [2020-06-16 09:35:29] Assoc to sex term...
[INFO] [2020-06-16 09:35:29] Assoc to lifestage term...
[STOP] [2020-06-16 09:35:29] resolve_keys
[START] [2020-06-16 09:35:29] hold_for_later_1
[STOP] [2020-06-16 09:35:29] hold_for_later_1
[START] [2020-06-16 09:35:29] hold_for_later_2
[STOP] [2020-06-16 09:35:29] hold_for_later_2
[START] [2020-06-16 09:35:29] resolve_missing_parents
[STOP] [2020-06-16 09:35:29] resolve_missing_parents
[START] [2020-06-16 09:35:29] rebuild_nodes
[START] [2020-06-16 09:35:29] Flattener#flatten
[START] [2020-06-16 09:35:29] Flattener#study_resource
[START] [2020-06-16 09:35:29] Flattener#build_ancestry
[STOP] [2020-06-16 09:35:29] Flattener#build_ancestry
[INFO] [2020-06-16 09:35:29] 87 ancestry keys
[START] [2020-06-16 09:35:29] build_node_ancestors
[INFO] [2020-06-16 09:35:29] old ancestors deleted.
[STOP] [2020-06-16 09:35:29] build_node_ancestors
[START] [2020-06-16 09:35:29] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 09:35:29] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 09:35:29] Flattener#flatten
[STOP] [2020-06-16 09:35:29] rebuild_nodes
[START] [2020-06-16 09:35:29] resolve_missing_media_owners
[STOP] [2020-06-16 09:35:29] resolve_missing_media_owners
[START] [2020-06-16 09:35:29] sanitize_media_verbatims
[STOP] [2020-06-16 09:35:29] sanitize_media_verbatims
[START] [2020-06-16 09:35:29] queue_downloads
[STOP] [2020-06-16 09:35:29] queue_downloads
[START] [2020-06-16 09:35:29] parse_names
[WARN] [2020-06-16 09:35:29] I see 87 names which still need to be parsed.
[WARN] [2020-06-16 09:35:30] I see 11 names which still need to be parsed.
[WARN] [2020-06-16 09:35:31] I see 4 names which still need to be parsed.
[WARN] [2020-06-16 09:35:33] I see 3 names which still need to be parsed.
[WARN] [2020-06-16 09:35:34] I see 2 names which still need to be parsed.
[WARN] [2020-06-16 09:35:35] I see 1 names which still need to be parsed.
[STOP] [2020-06-16 09:35:36] parse_names
[START] [2020-06-16 09:35:36] denormalize_canonical_names_to_nodes
[STOP] [2020-06-16 09:35:36] denormalize_canonical_names_to_nodes
[START] [2020-06-16 09:35:36] match_nodes
[START] [2020-06-16 09:35:36] map_all_nodes_to_pages
[STOP] [2020-06-16 09:35:42] map_all_nodes_to_pages
[INFO] [2020-06-16 09:35:42] 13 Unmatched nodes (of 87)! That's too many to output. First 10: Pseudoscourfielda marina (#80097849); Pyraminonas (#80097850); Chlorella capsulata (#80097786); Dissodinium lunula (#80097803); Gymnodinium nelsoni (#80097810); Prorocentrum (#80097845); Prorocentrum (#80097846); Chrysochromulina herdlansis (#80097792); Coccolithus neohelis (#80097794); Pavlova pingus (#80097832)
[START] [2020-06-16 09:35:42] update_nodes
[STOP] [2020-06-16 09:35:42] update_nodes
[STOP] [2020-06-16 09:35:42] match_nodes
[START] [2020-06-16 09:35:42] reindex_search
[STOP] [2020-06-16 09:35:42] reindex_search
[START] [2020-06-16 09:35:42] normalize_units
[STOP] [2020-06-16 09:35:42] normalize_units
[START] [2020-06-16 09:35:42] calculate_statistics
[STOP] [2020-06-16 09:35:42] calculate_statistics
[START] [2020-06-16 09:35:42] complete_harvest_instance
[START] [2020-06-16 09:35:42] overall_tsv_creation
[INFO] [2020-06-16 09:35:42] Processing group of 87 in 1 batches of 10000
[INFO] [2020-06-16 09:36:34] 74 Traits (unfiltered)...
[INFO] [2020-06-16 09:36:47] 74 Traits (filtered)...
[INFO] [2020-06-16 09:36:47] 0 Associations (filtered)...
[INFO] [2020-06-16 09:37:25] 296 metadata added.
[INFO] [2020-06-16 09:37:25] 0 metadata added.
[INFO] [2020-06-16 09:37:25] Average Time: 73.89
[INFO] [2020-06-16 09:37:25] Total Time: 1m43s
[STOP] [2020-06-16 09:37:25] overall_tsv_creation
[INFO] [2020-06-16 09:37:25] Done. Check your files:
[INFO] [2020-06-16 09:37:25] (76 lines) /app/public/data/keller_et_al_kel/publish_nodes.tsv
[INFO] [2020-06-16 09:37:25] (118 lines) /app/public/data/keller_et_al_kel/publish_node_ancestors.tsv
[INFO] [2020-06-16 09:37:25] (87 lines) /app/public/data/keller_et_al_kel/publish_scientific_names.tsv
[INFO] [2020-06-16 09:37:25] (75 lines) /app/public/data/keller_et_al_kel/publish_traits.tsv
[INFO] [2020-06-16 09:37:25] (297 lines) /app/public/data/keller_et_al_kel/publish_metadata.tsv
[STOP] [2020-06-16 09:37:25] complete_harvest_instance
[START] [2020-06-16 09:37:25] completed
[STOP] [2020-06-16 09:37:25] completed
[STOP] [2020-06-16 09:37:25] logged process, took 125.61
Latest Process

16 Jun 09:35 EXITED currently processing 0