Harvest for Ashihara et al 2008 Created 11 Jun 12:50

Stage: completed
Fetched: 11 Jun 12:50
Validated: 11 Jun 12:50
Deltas Created 11 Jun 12:50
Units Normalized: 11 Jun 12:50
Ancestry Built: 11 Jun 12:50
Nodes Matched: 11 Jun 12:50
Names Parsed: 11 Jun 12:50
New Models Stored: 11 Jun 12:50
Indexed: 11 Jun 12:50
Completed: 11 Jun 12:53
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2020-06-11 12:50:08 -0400 by logger.rb/v1.4.2
[INFO] [2020-06-11 12:50:08] ## HARVEST: type = -harvest
[START] [2020-06-11 12:50:12] logged process
[START] [2020-06-11 12:50:12] create_harvest_instance
[STOP] [2020-06-11 12:50:13] create_harvest_instance
[START] [2020-06-11 12:50:13] fetch_files
[STOP] [2020-06-11 12:50:13] fetch_files
[START] [2020-06-11 12:50:13] validate_each_file
[STOP] [2020-06-11 12:50:13] validate_each_file
[START] [2020-06-11 12:50:14] convert_to_csv
[CMD] [2020-06-11 12:50:14] /usr/bin/sort /app/public/converted_csv/ashihara_et_al_a_refs_21134.csv > /app/public/converted_csv/ashihara_et_al_a_refs_21134.csv_sorted
[CMD] [2020-06-11 12:50:14] /usr/bin/sort /app/public/converted_csv/ashihara_et_al_a_nodes_21135.csv > /app/public/converted_csv/ashihara_et_al_a_nodes_21135.csv_sorted
[CMD] [2020-06-11 12:50:14] /usr/bin/sort /app/public/converted_csv/ashihara_et_al_a_occurrences_21136.csv > /app/public/converted_csv/ashihara_et_al_a_occurrences_21136.csv_sorted
[CMD] [2020-06-11 12:50:14] /usr/bin/sort /app/public/converted_csv/ashihara_et_al_a_measurements_21137.csv > /app/public/converted_csv/ashihara_et_al_a_measurements_21137.csv_sorted
[STOP] [2020-06-11 12:50:14] convert_to_csv
[START] [2020-06-11 12:50:14] calculate_delta
[CMD] [2020-06-11 12:50:14] echo "0a" > /app/public/diff/ashihara_et_al_a_refs_21134.diff
[CMD] [2020-06-11 12:50:14] tail -n +1 /app/public/converted_csv/ashihara_et_al_a_refs_21134.csv >> /app/public/diff/ashihara_et_al_a_refs_21134.diff
[CMD] [2020-06-11 12:50:14] echo "." >> /app/public/diff/ashihara_et_al_a_refs_21134.diff
[CMD] [2020-06-11 12:50:14] echo "0a" > /app/public/diff/ashihara_et_al_a_nodes_21135.diff
[CMD] [2020-06-11 12:50:14] tail -n +1 /app/public/converted_csv/ashihara_et_al_a_nodes_21135.csv >> /app/public/diff/ashihara_et_al_a_nodes_21135.diff
[CMD] [2020-06-11 12:50:14] echo "." >> /app/public/diff/ashihara_et_al_a_nodes_21135.diff
[CMD] [2020-06-11 12:50:14] echo "0a" > /app/public/diff/ashihara_et_al_a_occurrences_21136.diff
[CMD] [2020-06-11 12:50:14] tail -n +1 /app/public/converted_csv/ashihara_et_al_a_occurrences_21136.csv >> /app/public/diff/ashihara_et_al_a_occurrences_21136.diff
[CMD] [2020-06-11 12:50:14] echo "." >> /app/public/diff/ashihara_et_al_a_occurrences_21136.diff
[CMD] [2020-06-11 12:50:14] echo "0a" > /app/public/diff/ashihara_et_al_a_measurements_21137.diff
[CMD] [2020-06-11 12:50:14] tail -n +1 /app/public/converted_csv/ashihara_et_al_a_measurements_21137.csv >> /app/public/diff/ashihara_et_al_a_measurements_21137.diff
[CMD] [2020-06-11 12:50:14] echo "." >> /app/public/diff/ashihara_et_al_a_measurements_21137.diff
[STOP] [2020-06-11 12:50:14] calculate_delta
[START] [2020-06-11 12:50:14] parse_diff_and_store
[INFO] [2020-06-11 12:50:14] Loading refs diff file into memory (true lines)...
[INFO] [2020-06-11 12:50:14] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-11 12:50:14] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-11 12:50:14] Loading measurements diff file into memory (true lines)...
[INFO] [2020-06-11 12:50:14] Storing 8 References
[INFO] [2020-06-11 12:50:14] Processing group of 8 in 1 groups of 1000
[INFO] [2020-06-11 12:50:14] Average Time: 0.01
[INFO] [2020-06-11 12:50:14] Total Time: 1s
[INFO] [2020-06-11 12:50:14] Storing 29 ScientificNames
[INFO] [2020-06-11 12:50:14] Processing group of 29 in 1 groups of 1000
[INFO] [2020-06-11 12:50:14] Average Time: 0.01
[INFO] [2020-06-11 12:50:14] Total Time: 1s
[INFO] [2020-06-11 12:50:14] Storing 29 Nodes
[INFO] [2020-06-11 12:50:14] Processing group of 29 in 1 groups of 1000
[INFO] [2020-06-11 12:50:14] Average Time: 0.02
[INFO] [2020-06-11 12:50:14] Total Time: 1s
[INFO] [2020-06-11 12:50:14] Storing 16 Occurrences
[INFO] [2020-06-11 12:50:14] Processing group of 16 in 1 groups of 1000
[INFO] [2020-06-11 12:50:14] Average Time: 0.0
[INFO] [2020-06-11 12:50:14] Total Time: 1s
[INFO] [2020-06-11 12:50:14] Storing 16 TraitsReferences
[INFO] [2020-06-11 12:50:14] Processing group of 16 in 1 groups of 1000
[INFO] [2020-06-11 12:50:14] Average Time: 0.0
[INFO] [2020-06-11 12:50:14] Total Time: 1s
[INFO] [2020-06-11 12:50:14] Storing 48 Traits
[INFO] [2020-06-11 12:50:14] Processing group of 48 in 1 groups of 1000
[INFO] [2020-06-11 12:50:14] Average Time: 0.02
[INFO] [2020-06-11 12:50:14] Total Time: 1s
[INFO] [2020-06-11 12:50:14] Storing 48 MetaTraits
[INFO] [2020-06-11 12:50:14] Processing group of 48 in 1 groups of 1000
[INFO] [2020-06-11 12:50:14] Average Time: 0.04
[INFO] [2020-06-11 12:50:14] Total Time: 1s
[STOP] [2020-06-11 12:50:14] parse_diff_and_store
[START] [2020-06-11 12:50:14] resolve_keys
[INFO] [2020-06-11 12:50:22] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-11 12:50:22] traits to occurrences...
[INFO] [2020-06-11 12:50:22] traits to nodes (through occurrences)...
[INFO] [2020-06-11 12:50:22] Traits to sex term...
[INFO] [2020-06-11 12:50:22] Traits to lifestage term...
[INFO] [2020-06-11 12:50:22] MetaTraits to traits...
[INFO] [2020-06-11 12:50:22] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-11 12:50:22] Assocs to occurrences...
[INFO] [2020-06-11 12:50:22] Assocs to nodes...
[INFO] [2020-06-11 12:50:22] Assoc to sex term...
[INFO] [2020-06-11 12:50:22] Assoc to lifestage term...
[STOP] [2020-06-11 12:50:22] resolve_keys
[START] [2020-06-11 12:50:22] hold_for_later_1
[STOP] [2020-06-11 12:50:22] hold_for_later_1
[START] [2020-06-11 12:50:22] hold_for_later_2
[STOP] [2020-06-11 12:50:22] hold_for_later_2
[START] [2020-06-11 12:50:22] resolve_missing_parents
[STOP] [2020-06-11 12:50:22] resolve_missing_parents
[START] [2020-06-11 12:50:22] rebuild_nodes
[START] [2020-06-11 12:50:22] Flattener#flatten
[START] [2020-06-11 12:50:22] Flattener#study_resource
[START] [2020-06-11 12:50:22] Flattener#build_ancestry
[STOP] [2020-06-11 12:50:22] Flattener#build_ancestry
[INFO] [2020-06-11 12:50:22] 29 ancestry keys
[START] [2020-06-11 12:50:22] build_node_ancestors
[INFO] [2020-06-11 12:50:22] old ancestors deleted.
[STOP] [2020-06-11 12:50:22] build_node_ancestors
[START] [2020-06-11 12:50:22] Flattener#propagate_ancestor_ids
[STOP] [2020-06-11 12:50:22] Flattener#propagate_ancestor_ids
[STOP] [2020-06-11 12:50:22] Flattener#flatten
[STOP] [2020-06-11 12:50:22] rebuild_nodes
[START] [2020-06-11 12:50:22] resolve_missing_media_owners
[STOP] [2020-06-11 12:50:22] resolve_missing_media_owners
[START] [2020-06-11 12:50:22] sanitize_media_verbatims
[STOP] [2020-06-11 12:50:22] sanitize_media_verbatims
[START] [2020-06-11 12:50:22] queue_downloads
[STOP] [2020-06-11 12:50:22] queue_downloads
[START] [2020-06-11 12:50:22] parse_names
[WARN] [2020-06-11 12:50:22] I see 29 names which still need to be parsed.
[STOP] [2020-06-11 12:50:24] parse_names
[START] [2020-06-11 12:50:24] denormalize_canonical_names_to_nodes
[STOP] [2020-06-11 12:50:24] denormalize_canonical_names_to_nodes
[START] [2020-06-11 12:50:24] match_nodes
[START] [2020-06-11 12:50:24] map_all_nodes_to_pages
[STOP] [2020-06-11 12:50:31] map_all_nodes_to_pages
[INFO] [2020-06-11 12:50:31] Unmatched nodes (1 of 29): Coffea eugeniodes (#80059700)
[START] [2020-06-11 12:50:31] update_nodes
[STOP] [2020-06-11 12:50:31] update_nodes
[STOP] [2020-06-11 12:50:31] match_nodes
[START] [2020-06-11 12:50:31] reindex_search
[STOP] [2020-06-11 12:50:31] reindex_search
[START] [2020-06-11 12:50:31] normalize_units
[STOP] [2020-06-11 12:50:31] normalize_units
[START] [2020-06-11 12:50:31] calculate_statistics
[STOP] [2020-06-11 12:50:31] calculate_statistics
[START] [2020-06-11 12:50:31] complete_harvest_instance
[START] [2020-06-11 12:50:31] overall_tsv_creation
[INFO] [2020-06-11 12:50:31] Processing group of 29 in 1 batches of 10000
[INFO] [2020-06-11 12:52:41] 16 Traits (unfiltered)...
[INFO] [2020-06-11 12:52:54] 16 Traits (filtered)...
[INFO] [2020-06-11 12:52:54] 0 Associations (filtered)...
[INFO] [2020-06-11 12:53:33] 80 metadata added.
[INFO] [2020-06-11 12:53:33] 0 metadata added.
[INFO] [2020-06-11 12:53:33] Average Time: 74.64
[INFO] [2020-06-11 12:53:33] Total Time: 3m2s
[STOP] [2020-06-11 12:53:33] overall_tsv_creation
[INFO] [2020-06-11 12:53:33] Done. Check your files:
[INFO] [2020-06-11 12:53:33] (29 lines) /app/public/data/ashihara_et_al_a/publish_nodes.tsv
[INFO] [2020-06-11 12:53:33] (66 lines) /app/public/data/ashihara_et_al_a/publish_node_ancestors.tsv
[INFO] [2020-06-11 12:53:33] (29 lines) /app/public/data/ashihara_et_al_a/publish_scientific_names.tsv
[INFO] [2020-06-11 12:53:33] (17 lines) /app/public/data/ashihara_et_al_a/publish_traits.tsv
[INFO] [2020-06-11 12:53:33] (81 lines) /app/public/data/ashihara_et_al_a/publish_metadata.tsv
[STOP] [2020-06-11 12:53:33] complete_harvest_instance
[START] [2020-06-11 12:53:33] completed
[STOP] [2020-06-11 12:53:33] completed
[STOP] [2020-06-11 12:53:33] logged process, took 200.44

Latest Process