Harvest for Yoch 2002 Created 16 Jun 09:46

Harvesting Log

# Logfile created on 2020-06-16 09:39:33 -0400 by logger.rb/v1.4.2
[INFO] [2020-06-16 09:39:33] ## HARVEST: type = -harvest
[START] [2020-06-16 09:39:37] logged process
[START] [2020-06-16 09:39:37] create_harvest_instance
[STOP] [2020-06-16 09:39:39] create_harvest_instance
[START] [2020-06-16 09:39:39] fetch_files
[STOP] [2020-06-16 09:39:39] fetch_files
[START] [2020-06-16 09:39:39] validate_each_file
[STOP] [2020-06-16 09:39:39] validate_each_file
[START] [2020-06-16 09:39:39] convert_to_csv
[CMD] [2020-06-16 09:39:39] /usr/bin/sort /app/public/converted_csv/yoch_yoch_2002_refs_21293.csv > /app/public/converted_csv/yoch_yoch_2002_refs_21293.csv_sorted
[CMD] [2020-06-16 09:39:39] /usr/bin/sort /app/public/converted_csv/yoch_yoch_2002_nodes_21294.csv > /app/public/converted_csv/yoch_yoch_2002_nodes_21294.csv_sorted
[CMD] [2020-06-16 09:39:39] /usr/bin/sort /app/public/converted_csv/yoch_yoch_2002_occurrences_21295.csv > /app/public/converted_csv/yoch_yoch_2002_occurrences_21295.csv_sorted
[CMD] [2020-06-16 09:39:39] /usr/bin/sort /app/public/converted_csv/yoch_yoch_2002_measurements_21296.csv > /app/public/converted_csv/yoch_yoch_2002_measurements_21296.csv_sorted
[STOP] [2020-06-16 09:39:39] convert_to_csv
[START] [2020-06-16 09:39:39] calculate_delta
[CMD] [2020-06-16 09:39:39] echo "0a" > /app/public/diff/yoch_yoch_2002_refs_21293.diff
[CMD] [2020-06-16 09:39:39] tail -n +1 /app/public/converted_csv/yoch_yoch_2002_refs_21293.csv >> /app/public/diff/yoch_yoch_2002_refs_21293.diff
[CMD] [2020-06-16 09:39:39] echo "." >> /app/public/diff/yoch_yoch_2002_refs_21293.diff
[CMD] [2020-06-16 09:39:39] echo "0a" > /app/public/diff/yoch_yoch_2002_nodes_21294.diff
[CMD] [2020-06-16 09:39:39] tail -n +1 /app/public/converted_csv/yoch_yoch_2002_nodes_21294.csv >> /app/public/diff/yoch_yoch_2002_nodes_21294.diff
[CMD] [2020-06-16 09:39:39] echo "." >> /app/public/diff/yoch_yoch_2002_nodes_21294.diff
[CMD] [2020-06-16 09:39:39] echo "0a" > /app/public/diff/yoch_yoch_2002_occurrences_21295.diff
[CMD] [2020-06-16 09:39:39] tail -n +1 /app/public/converted_csv/yoch_yoch_2002_occurrences_21295.csv >> /app/public/diff/yoch_yoch_2002_occurrences_21295.diff
[CMD] [2020-06-16 09:39:39] echo "." >> /app/public/diff/yoch_yoch_2002_occurrences_21295.diff
[CMD] [2020-06-16 09:39:39] echo "0a" > /app/public/diff/yoch_yoch_2002_measurements_21296.diff
[CMD] [2020-06-16 09:39:39] tail -n +1 /app/public/converted_csv/yoch_yoch_2002_measurements_21296.csv >> /app/public/diff/yoch_yoch_2002_measurements_21296.diff
[CMD] [2020-06-16 09:39:39] echo "." >> /app/public/diff/yoch_yoch_2002_measurements_21296.diff
[STOP] [2020-06-16 09:39:39] calculate_delta
[START] [2020-06-16 09:39:39] parse_diff_and_store
[INFO] [2020-06-16 09:39:39] Loading refs diff file into memory (true lines)...
[INFO] [2020-06-16 09:39:39] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-16 09:39:39] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-16 09:39:39] Loading measurements diff file into memory (true lines)...
[INFO] [2020-06-16 09:39:39] Storing 6 References
[INFO] [2020-06-16 09:39:39] Processing group of 6 in 1 groups of 1000
[INFO] [2020-06-16 09:39:39] Average Time: 0.03
[INFO] [2020-06-16 09:39:39] Total Time: 1s
[INFO] [2020-06-16 09:39:39] Storing 29 ScientificNames
[INFO] [2020-06-16 09:39:39] Processing group of 29 in 1 groups of 1000
[INFO] [2020-06-16 09:39:39] Average Time: 0.01
[INFO] [2020-06-16 09:39:39] Total Time: 1s
[INFO] [2020-06-16 09:39:39] Storing 29 Nodes
[INFO] [2020-06-16 09:39:39] Processing group of 29 in 1 groups of 1000
[INFO] [2020-06-16 09:39:39] Average Time: 0.01
[INFO] [2020-06-16 09:39:39] Total Time: 1s
[INFO] [2020-06-16 09:39:39] Storing 9 Occurrences
[INFO] [2020-06-16 09:39:39] Processing group of 9 in 1 groups of 1000
[INFO] [2020-06-16 09:39:39] Average Time: 0.0
[INFO] [2020-06-16 09:39:39] Total Time: 1s
[INFO] [2020-06-16 09:39:39] Storing 6 TraitsReferences
[INFO] [2020-06-16 09:39:39] Processing group of 6 in 1 groups of 1000
[INFO] [2020-06-16 09:39:39] Average Time: 0.0
[INFO] [2020-06-16 09:39:39] Total Time: 1s
[INFO] [2020-06-16 09:39:39] Storing 27 Traits
[INFO] [2020-06-16 09:39:39] Processing group of 27 in 1 groups of 1000
[INFO] [2020-06-16 09:39:39] Average Time: 0.01
[INFO] [2020-06-16 09:39:39] Total Time: 1s
[INFO] [2020-06-16 09:39:39] Storing 10 MetaTraits
[INFO] [2020-06-16 09:39:39] Processing group of 10 in 1 groups of 1000
[INFO] [2020-06-16 09:39:39] Average Time: 0.0
[INFO] [2020-06-16 09:39:39] Total Time: 1s
[STOP] [2020-06-16 09:39:39] parse_diff_and_store
[START] [2020-06-16 09:39:39] resolve_keys
[INFO] [2020-06-16 09:39:46] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-16 09:39:46] traits to occurrences...
[INFO] [2020-06-16 09:39:46] traits to nodes (through occurrences)...
[INFO] [2020-06-16 09:39:46] Traits to sex term...
[INFO] [2020-06-16 09:39:46] Traits to lifestage term...
[INFO] [2020-06-16 09:39:46] MetaTraits to traits...
[INFO] [2020-06-16 09:39:46] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-16 09:39:46] Assocs to occurrences...
[INFO] [2020-06-16 09:39:46] Assocs to nodes...
[INFO] [2020-06-16 09:39:46] Assoc to sex term...
[INFO] [2020-06-16 09:39:46] Assoc to lifestage term...
[STOP] [2020-06-16 09:39:46] resolve_keys
[START] [2020-06-16 09:39:46] hold_for_later_1
[STOP] [2020-06-16 09:39:46] hold_for_later_1
[START] [2020-06-16 09:39:46] hold_for_later_2
[STOP] [2020-06-16 09:39:46] hold_for_later_2
[START] [2020-06-16 09:39:46] resolve_missing_parents
[STOP] [2020-06-16 09:39:46] resolve_missing_parents
[START] [2020-06-16 09:39:46] rebuild_nodes
[START] [2020-06-16 09:39:46] Flattener#flatten
[START] [2020-06-16 09:39:46] Flattener#study_resource
[START] [2020-06-16 09:39:46] Flattener#build_ancestry
[STOP] [2020-06-16 09:39:46] Flattener#build_ancestry
[INFO] [2020-06-16 09:39:46] 29 ancestry keys
[START] [2020-06-16 09:39:46] build_node_ancestors
[INFO] [2020-06-16 09:39:46] old ancestors deleted.
[STOP] [2020-06-16 09:39:47] build_node_ancestors
[START] [2020-06-16 09:39:47] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 09:39:47] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 09:39:47] Flattener#flatten
[STOP] [2020-06-16 09:39:47] rebuild_nodes
[START] [2020-06-16 09:39:47] resolve_missing_media_owners
[STOP] [2020-06-16 09:39:47] resolve_missing_media_owners
[START] [2020-06-16 09:39:47] sanitize_media_verbatims
[STOP] [2020-06-16 09:39:47] sanitize_media_verbatims
[START] [2020-06-16 09:39:47] queue_downloads
[STOP] [2020-06-16 09:39:47] queue_downloads
[START] [2020-06-16 09:39:47] parse_names
[WARN] [2020-06-16 09:39:47] I see 29 names which still need to be parsed.
[STOP] [2020-06-16 09:39:48] parse_names
[START] [2020-06-16 09:39:48] denormalize_canonical_names_to_nodes
[STOP] [2020-06-16 09:39:48] denormalize_canonical_names_to_nodes
[START] [2020-06-16 09:39:48] match_nodes
[START] [2020-06-16 09:39:48] map_all_nodes_to_pages
[STOP] [2020-06-16 09:39:50] map_all_nodes_to_pages
[INFO] [2020-06-16 09:39:50] Unmatched nodes (2 of 29): Chrysameoba (#80097871); Melosira numuloides (#80097883)
[START] [2020-06-16 09:39:50] update_nodes
[STOP] [2020-06-16 09:39:50] update_nodes
[STOP] [2020-06-16 09:39:50] match_nodes
[START] [2020-06-16 09:39:50] reindex_search
[STOP] [2020-06-16 09:39:50] reindex_search
[START] [2020-06-16 09:39:50] normalize_units
[STOP] [2020-06-16 09:39:50] normalize_units
[START] [2020-06-16 09:39:50] calculate_statistics
[STOP] [2020-06-16 09:39:50] calculate_statistics
[START] [2020-06-16 09:39:50] complete_harvest_instance
[START] [2020-06-16 09:39:50] overall_tsv_creation
[INFO] [2020-06-16 09:39:50] Processing group of 29 in 1 batches of 10000
[INFO] [2020-06-16 09:40:42] 9 Traits (unfiltered)...
[INFO] [2020-06-16 09:40:55] 9 Traits (filtered)...
[INFO] [2020-06-16 09:40:55] 0 Associations (filtered)...
[INFO] [2020-06-16 09:41:32] 25 metadata added.
[INFO] [2020-06-16 09:41:32] 0 metadata added.
[INFO] [2020-06-16 09:41:32] Average Time: 73.27
[INFO] [2020-06-16 09:41:32] Total Time: 1m43s
[STOP] [2020-06-16 09:41:32] overall_tsv_creation
[INFO] [2020-06-16 09:41:32] Done. Check your files:
[INFO] [2020-06-16 09:41:32] (29 lines) /app/public/data/yoch_yoch_2002/publish_nodes.tsv
[INFO] [2020-06-16 09:41:32] (36 lines) /app/public/data/yoch_yoch_2002/publish_node_ancestors.tsv
[INFO] [2020-06-16 09:41:32] (29 lines) /app/public/data/yoch_yoch_2002/publish_scientific_names.tsv
[INFO] [2020-06-16 09:41:32] (10 lines) /app/public/data/yoch_yoch_2002/publish_traits.tsv
[INFO] [2020-06-16 09:41:32] (26 lines) /app/public/data/yoch_yoch_2002/publish_metadata.tsv
[STOP] [2020-06-16 09:41:32] complete_harvest_instance
[START] [2020-06-16 09:41:32] completed
[STOP] [2020-06-16 09:41:32] completed
[STOP] [2020-06-16 09:41:32] logged process, took 114.67
[INFO] [2020-06-16 09:46:14] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-06-16 09:46:14] ## remove_type: ScientificName
[INFO] [2020-06-16 09:46:14] ++ Calling delete_all on 29 instances...
[INFO] [2020-06-16 09:46:14] [09:46:14.663] Removed 29 Scientificnames
[INFO] [2020-06-16 09:46:14] ## remove_type: Vernacular
[INFO] [2020-06-16 09:46:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:46:14] [09:46:14.665] Removed 0 Vernaculars
[INFO] [2020-06-16 09:46:14] ## remove_type: Article
[INFO] [2020-06-16 09:46:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:46:14] [09:46:14.668] Removed 0 Articles
[INFO] [2020-06-16 09:46:14] ## remove_type: Medium
[INFO] [2020-06-16 09:46:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:46:14] [09:46:14.672] Removed 0 Media
[INFO] [2020-06-16 09:46:14] ## remove_type: Trait
[INFO] [2020-06-16 09:46:14] ++ Calling delete_all on 27 instances...
[INFO] [2020-06-16 09:46:14] [09:46:14.676] Removed 27 Traits
[INFO] [2020-06-16 09:46:14] ## remove_type: MetaTrait
[INFO] [2020-06-16 09:46:14] ++ Calling delete_all on 10 instances...
[INFO] [2020-06-16 09:46:14] [09:46:14.680] Removed 10 Metatraits
[INFO] [2020-06-16 09:46:14] ## remove_type: OccurrenceMetadatum
[INFO] [2020-06-16 09:46:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:46:14] [09:46:14.682] Removed 0 Occurrencemetadata
[INFO] [2020-06-16 09:46:14] ## remove_type: Assoc
[INFO] [2020-06-16 09:46:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:46:14] [09:46:14.685] Removed 0 Assocs
[INFO] [2020-06-16 09:46:14] ## remove_type: MetaAssoc
[INFO] [2020-06-16 09:46:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:46:14] [09:46:14.687] Removed 0 Metaassocs
[INFO] [2020-06-16 09:46:14] ## remove_type: Identifier
[INFO] [2020-06-16 09:46:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:46:14] [09:46:14.690] Removed 0 Identifiers
[INFO] [2020-06-16 09:46:14] ## remove_type: Reference
[INFO] [2020-06-16 09:46:14] ++ Calling delete_all on 6 instances...
[INFO] [2020-06-16 09:46:14] [09:46:14.693] Removed 6 References
[INFO] [2020-06-16 09:46:14] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:14] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:14] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:14] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:14] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:14] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:14] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:14] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:14] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] Starting batch with ID 80097867...
[INFO] [2020-06-16 09:46:15] ## remove_type: Node
[INFO] [2020-06-16 09:46:15] ++ Calling delete_all on 29 instances...
[INFO] [2020-06-16 09:46:15] [09:46:15.847] Removed 29 Nodes
[START] [2020-06-16 09:46:16] logged process
[START] [2020-06-16 09:46:16] Creating resource from OpenData
[START] [2020-06-16 09:46:16] logged process
[START] [2020-06-16 09:46:16] Parse meta.xml file and create formats with fields
[STOP] [2020-06-16 09:46:16] Parse meta.xml file and create formats with fields
[STOP] [2020-06-16 09:46:16] Creating resource from OpenData
[START] [2020-06-16 09:46:16] logged process
[START] [2020-06-16 09:46:16] create_harvest_instance
[STOP] [2020-06-16 09:46:17] create_harvest_instance
[START] [2020-06-16 09:46:17] fetch_files
[STOP] [2020-06-16 09:46:17] fetch_files
[START] [2020-06-16 09:46:17] validate_each_file
[STOP] [2020-06-16 09:46:17] validate_each_file
[START] [2020-06-16 09:46:17] convert_to_csv
[CMD] [2020-06-16 09:46:17] /usr/bin/sort /app/public/converted_csv/yoch_yoch_2002_refs_21307.csv > /app/public/converted_csv/yoch_yoch_2002_refs_21307.csv_sorted
[CMD] [2020-06-16 09:46:17] /usr/bin/sort /app/public/converted_csv/yoch_yoch_2002_nodes_21308.csv > /app/public/converted_csv/yoch_yoch_2002_nodes_21308.csv_sorted
[CMD] [2020-06-16 09:46:17] /usr/bin/sort /app/public/converted_csv/yoch_yoch_2002_occurrences_21309.csv > /app/public/converted_csv/yoch_yoch_2002_occurrences_21309.csv_sorted
[CMD] [2020-06-16 09:46:17] /usr/bin/sort /app/public/converted_csv/yoch_yoch_2002_measurements_21310.csv > /app/public/converted_csv/yoch_yoch_2002_measurements_21310.csv_sorted
[STOP] [2020-06-16 09:46:17] convert_to_csv
[START] [2020-06-16 09:46:17] calculate_delta
[CMD] [2020-06-16 09:46:17] echo "0a" > /app/public/diff/yoch_yoch_2002_refs_21307.diff
[CMD] [2020-06-16 09:46:17] tail -n +1 /app/public/converted_csv/yoch_yoch_2002_refs_21307.csv >> /app/public/diff/yoch_yoch_2002_refs_21307.diff
[CMD] [2020-06-16 09:46:17] echo "." >> /app/public/diff/yoch_yoch_2002_refs_21307.diff
[CMD] [2020-06-16 09:46:17] echo "0a" > /app/public/diff/yoch_yoch_2002_nodes_21308.diff
[CMD] [2020-06-16 09:46:17] tail -n +1 /app/public/converted_csv/yoch_yoch_2002_nodes_21308.csv >> /app/public/diff/yoch_yoch_2002_nodes_21308.diff
[CMD] [2020-06-16 09:46:17] echo "." >> /app/public/diff/yoch_yoch_2002_nodes_21308.diff
[CMD] [2020-06-16 09:46:18] echo "0a" > /app/public/diff/yoch_yoch_2002_occurrences_21309.diff
[CMD] [2020-06-16 09:46:18] tail -n +1 /app/public/converted_csv/yoch_yoch_2002_occurrences_21309.csv >> /app/public/diff/yoch_yoch_2002_occurrences_21309.diff
[CMD] [2020-06-16 09:46:18] echo "." >> /app/public/diff/yoch_yoch_2002_occurrences_21309.diff
[CMD] [2020-06-16 09:46:18] echo "0a" > /app/public/diff/yoch_yoch_2002_measurements_21310.diff
[CMD] [2020-06-16 09:46:18] tail -n +1 /app/public/converted_csv/yoch_yoch_2002_measurements_21310.csv >> /app/public/diff/yoch_yoch_2002_measurements_21310.diff
[CMD] [2020-06-16 09:46:18] echo "." >> /app/public/diff/yoch_yoch_2002_measurements_21310.diff
[STOP] [2020-06-16 09:46:18] calculate_delta
[START] [2020-06-16 09:46:18] parse_diff_and_store
[INFO] [2020-06-16 09:46:18] Loading refs diff file into memory (true lines)...
[INFO] [2020-06-16 09:46:18] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-16 09:46:18] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-16 09:46:18] Loading measurements diff file into memory (true lines)...
[INFO] [2020-06-16 09:46:18] Storing 6 References
[INFO] [2020-06-16 09:46:18] Processing group of 6 in 1 groups of 1000
[INFO] [2020-06-16 09:46:18] Average Time: 0.0
[INFO] [2020-06-16 09:46:18] Total Time: 1s
[INFO] [2020-06-16 09:46:18] Storing 29 ScientificNames
[INFO] [2020-06-16 09:46:18] Processing group of 29 in 1 groups of 1000
[INFO] [2020-06-16 09:46:18] Average Time: 0.01
[INFO] [2020-06-16 09:46:18] Total Time: 1s
[INFO] [2020-06-16 09:46:18] Storing 29 Nodes
[INFO] [2020-06-16 09:46:18] Processing group of 29 in 1 groups of 1000
[INFO] [2020-06-16 09:46:18] Average Time: 0.01
[INFO] [2020-06-16 09:46:18] Total Time: 1s
[INFO] [2020-06-16 09:46:18] Storing 9 Occurrences
[INFO] [2020-06-16 09:46:18] Processing group of 9 in 1 groups of 1000
[INFO] [2020-06-16 09:46:18] Average Time: 0.0
[INFO] [2020-06-16 09:46:18] Total Time: 1s
[INFO] [2020-06-16 09:46:18] Storing 6 TraitsReferences
[INFO] [2020-06-16 09:46:18] Processing group of 6 in 1 groups of 1000
[INFO] [2020-06-16 09:46:18] Average Time: 0.0
[INFO] [2020-06-16 09:46:18] Total Time: 1s
[INFO] [2020-06-16 09:46:18] Storing 27 Traits
[INFO] [2020-06-16 09:46:18] Processing group of 27 in 1 groups of 1000
[INFO] [2020-06-16 09:46:18] Average Time: 0.01
[INFO] [2020-06-16 09:46:18] Total Time: 1s
[INFO] [2020-06-16 09:46:18] Storing 28 MetaTraits
[INFO] [2020-06-16 09:46:18] Processing group of 28 in 1 groups of 1000
[INFO] [2020-06-16 09:46:18] Average Time: 0.0
[INFO] [2020-06-16 09:46:18] Total Time: 1s
[STOP] [2020-06-16 09:46:18] parse_diff_and_store
[START] [2020-06-16 09:46:18] resolve_keys
[INFO] [2020-06-16 09:46:25] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-16 09:46:25] traits to occurrences...
[INFO] [2020-06-16 09:46:25] traits to nodes (through occurrences)...
[INFO] [2020-06-16 09:46:25] Traits to sex term...
[INFO] [2020-06-16 09:46:25] Traits to lifestage term...
[INFO] [2020-06-16 09:46:25] MetaTraits to traits...
[INFO] [2020-06-16 09:46:25] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-16 09:46:25] Assocs to occurrences...
[INFO] [2020-06-16 09:46:25] Assocs to nodes...
[INFO] [2020-06-16 09:46:25] Assoc to sex term...
[INFO] [2020-06-16 09:46:25] Assoc to lifestage term...
[STOP] [2020-06-16 09:46:25] resolve_keys
[START] [2020-06-16 09:46:25] hold_for_later_1
[STOP] [2020-06-16 09:46:25] hold_for_later_1
[START] [2020-06-16 09:46:25] hold_for_later_2
[STOP] [2020-06-16 09:46:25] hold_for_later_2
[START] [2020-06-16 09:46:25] resolve_missing_parents
[STOP] [2020-06-16 09:46:25] resolve_missing_parents
[START] [2020-06-16 09:46:25] rebuild_nodes
[START] [2020-06-16 09:46:25] Flattener#flatten
[START] [2020-06-16 09:46:25] Flattener#study_resource
[START] [2020-06-16 09:46:25] Flattener#build_ancestry
[STOP] [2020-06-16 09:46:25] Flattener#build_ancestry
[INFO] [2020-06-16 09:46:25] 29 ancestry keys
[START] [2020-06-16 09:46:25] build_node_ancestors
[INFO] [2020-06-16 09:46:25] old ancestors deleted.
[STOP] [2020-06-16 09:46:25] build_node_ancestors
[START] [2020-06-16 09:46:25] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 09:46:25] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 09:46:25] Flattener#flatten
[STOP] [2020-06-16 09:46:25] rebuild_nodes
[START] [2020-06-16 09:46:25] resolve_missing_media_owners
[STOP] [2020-06-16 09:46:25] resolve_missing_media_owners
[START] [2020-06-16 09:46:25] sanitize_media_verbatims
[STOP] [2020-06-16 09:46:25] sanitize_media_verbatims
[START] [2020-06-16 09:46:25] queue_downloads
[STOP] [2020-06-16 09:46:25] queue_downloads
[START] [2020-06-16 09:46:25] parse_names
[WARN] [2020-06-16 09:46:25] I see 29 names which still need to be parsed.
[STOP] [2020-06-16 09:46:26] parse_names
[START] [2020-06-16 09:46:26] denormalize_canonical_names_to_nodes
[STOP] [2020-06-16 09:46:26] denormalize_canonical_names_to_nodes
[START] [2020-06-16 09:46:26] match_nodes
[START] [2020-06-16 09:46:26] map_all_nodes_to_pages
[STOP] [2020-06-16 09:46:28] map_all_nodes_to_pages
[INFO] [2020-06-16 09:46:28] Unmatched nodes (2 of 29): Chrysameoba (#80097904); Melosira numuloides (#80097916)
[START] [2020-06-16 09:46:28] update_nodes
[STOP] [2020-06-16 09:46:28] update_nodes
[STOP] [2020-06-16 09:46:28] match_nodes
[START] [2020-06-16 09:46:28] reindex_search
[STOP] [2020-06-16 09:46:28] reindex_search
[START] [2020-06-16 09:46:28] normalize_units
[STOP] [2020-06-16 09:46:28] normalize_units
[START] [2020-06-16 09:46:28] calculate_statistics
[STOP] [2020-06-16 09:46:28] calculate_statistics
[START] [2020-06-16 09:46:28] complete_harvest_instance
[START] [2020-06-16 09:46:28] overall_tsv_creation
[INFO] [2020-06-16 09:46:28] Processing group of 29 in 1 batches of 10000
[INFO] [2020-06-16 09:47:19] 9 Traits (unfiltered)...
[INFO] [2020-06-16 09:47:33] 9 Traits (filtered)...
[INFO] [2020-06-16 09:47:33] 0 Associations (filtered)...
[INFO] [2020-06-16 09:48:11] 43 metadata added.
[INFO] [2020-06-16 09:48:11] 0 metadata added.
[INFO] [2020-06-16 09:48:11] Average Time: 74.4
[INFO] [2020-06-16 09:48:11] Total Time: 1m44s
[STOP] [2020-06-16 09:48:11] overall_tsv_creation
[INFO] [2020-06-16 09:48:11] Done. Check your files:
[INFO] [2020-06-16 09:48:11] (29 lines) /app/public/data/yoch_yoch_2002/publish_nodes.tsv
[INFO] [2020-06-16 09:48:11] (36 lines) /app/public/data/yoch_yoch_2002/publish_node_ancestors.tsv
[INFO] [2020-06-16 09:48:11] (29 lines) /app/public/data/yoch_yoch_2002/publish_scientific_names.tsv
[INFO] [2020-06-16 09:48:11] (10 lines) /app/public/data/yoch_yoch_2002/publish_traits.tsv
[INFO] [2020-06-16 09:48:11] (44 lines) /app/public/data/yoch_yoch_2002/publish_metadata.tsv
[STOP] [2020-06-16 09:48:11] complete_harvest_instance
[START] [2020-06-16 09:48:11] completed
[STOP] [2020-06-16 09:48:11] completed
[STOP] [2020-06-16 09:48:11] logged process, took 115.04

Latest Process

16 Jun 09:46 EXITED currently processing 0