Harvest for Palm Traits 1.0 Created 10 Jun 12:33

Harvesting Log

# Logfile created on 2020-06-10 12:28:40 -0400 by logger.rb/v1.4.2
[INFO] [2020-06-10 12:28:40] ## HARVEST: type = -harvest
[START] [2020-06-10 12:28:43] logged process
[INFO] [2020-06-10 12:29:18] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-06-10 12:29:18] ## remove_type: ScientificName
[INFO] [2020-06-10 12:29:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:29:18] [12:29:18.809] Removed 0 Scientificnames
[INFO] [2020-06-10 12:29:18] ## remove_type: Vernacular
[INFO] [2020-06-10 12:29:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:29:18] [12:29:18.812] Removed 0 Vernaculars
[INFO] [2020-06-10 12:29:18] ## remove_type: Article
[INFO] [2020-06-10 12:29:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:29:18] [12:29:18.815] Removed 0 Articles
[INFO] [2020-06-10 12:29:18] ## remove_type: Medium
[INFO] [2020-06-10 12:29:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:29:18] [12:29:18.819] Removed 0 Media
[INFO] [2020-06-10 12:29:18] ## remove_type: Trait
[INFO] [2020-06-10 12:29:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:29:18] [12:29:18.822] Removed 0 Traits
[INFO] [2020-06-10 12:29:18] ## remove_type: MetaTrait
[INFO] [2020-06-10 12:29:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:29:18] [12:29:18.825] Removed 0 Metatraits
[INFO] [2020-06-10 12:29:18] ## remove_type: OccurrenceMetadatum
[INFO] [2020-06-10 12:29:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:29:18] [12:29:18.828] Removed 0 Occurrencemetadata
[INFO] [2020-06-10 12:29:18] ## remove_type: Assoc
[INFO] [2020-06-10 12:29:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:29:18] [12:29:18.831] Removed 0 Assocs
[INFO] [2020-06-10 12:29:18] ## remove_type: MetaAssoc
[INFO] [2020-06-10 12:29:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:29:18] [12:29:18.833] Removed 0 Metaassocs
[INFO] [2020-06-10 12:29:18] ## remove_type: Identifier
[INFO] [2020-06-10 12:29:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:29:18] [12:29:18.836] Removed 0 Identifiers
[INFO] [2020-06-10 12:29:18] ## remove_type: Reference
[INFO] [2020-06-10 12:29:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:29:18] [12:29:18.839] Removed 0 References
[INFO] [2020-06-10 12:29:19] ## remove_type: Node
[INFO] [2020-06-10 12:29:19] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:29:19] [12:29:19.016] Removed 0 Nodes
[START] [2020-06-10 12:29:19] logged process
[START] [2020-06-10 12:29:19] Creating resource from OpenData
[START] [2020-06-10 12:29:22] logged process
[START] [2020-06-10 12:29:22] Parse meta.xml file and create formats with fields
[WARN] [2020-06-10 12:29:22] SKIPPING missing file: /app/public/data/palm_traits_palm/measurementsorfacts.tsv
[STOP] [2020-06-10 12:29:22] Parse meta.xml file and create formats with fields
[STOP] [2020-06-10 12:29:22] Creating resource from OpenData
[START] [2020-06-10 12:29:22] logged process
[START] [2020-06-10 12:29:22] create_harvest_instance
[STOP] [2020-06-10 12:29:23] create_harvest_instance
[START] [2020-06-10 12:29:23] fetch_files
[STOP] [2020-06-10 12:29:23] fetch_files
[START] [2020-06-10 12:29:23] validate_each_file
[STOP] [2020-06-10 12:29:23] validate_each_file
[START] [2020-06-10 12:29:23] convert_to_csv
[CMD] [2020-06-10 12:29:23] /usr/bin/sort /app/public/converted_csv/palm_traits_palm_refs_21103.csv > /app/public/converted_csv/palm_traits_palm_refs_21103.csv_sorted
[CMD] [2020-06-10 12:29:23] /usr/bin/sort /app/public/converted_csv/palm_traits_palm_nodes_21104.csv > /app/public/converted_csv/palm_traits_palm_nodes_21104.csv_sorted
[CMD] [2020-06-10 12:29:23] /usr/bin/sort /app/public/converted_csv/palm_traits_palm_occurrences_21105.csv > /app/public/converted_csv/palm_traits_palm_occurrences_21105.csv_sorted
[STOP] [2020-06-10 12:29:23] convert_to_csv
[START] [2020-06-10 12:29:23] calculate_delta
[CMD] [2020-06-10 12:29:23] echo "0a" > /app/public/diff/palm_traits_palm_refs_21103.diff
[CMD] [2020-06-10 12:29:23] tail -n +1 /app/public/converted_csv/palm_traits_palm_refs_21103.csv >> /app/public/diff/palm_traits_palm_refs_21103.diff
[CMD] [2020-06-10 12:29:23] echo "." >> /app/public/diff/palm_traits_palm_refs_21103.diff
[CMD] [2020-06-10 12:29:23] echo "0a" > /app/public/diff/palm_traits_palm_nodes_21104.diff
[CMD] [2020-06-10 12:29:23] tail -n +1 /app/public/converted_csv/palm_traits_palm_nodes_21104.csv >> /app/public/diff/palm_traits_palm_nodes_21104.diff
[CMD] [2020-06-10 12:29:23] echo "." >> /app/public/diff/palm_traits_palm_nodes_21104.diff
[CMD] [2020-06-10 12:29:23] echo "0a" > /app/public/diff/palm_traits_palm_occurrences_21105.diff
[CMD] [2020-06-10 12:29:23] tail -n +1 /app/public/converted_csv/palm_traits_palm_occurrences_21105.csv >> /app/public/diff/palm_traits_palm_occurrences_21105.diff
[CMD] [2020-06-10 12:29:23] echo "." >> /app/public/diff/palm_traits_palm_occurrences_21105.diff
[STOP] [2020-06-10 12:29:23] calculate_delta
[START] [2020-06-10 12:29:23] parse_diff_and_store
[INFO] [2020-06-10 12:29:23] Loading refs diff file into memory (true lines)...
[INFO] [2020-06-10 12:29:23] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-10 12:29:24] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-10 12:29:24] Storing 3 References
[INFO] [2020-06-10 12:29:24] Processing group of 3 in 1 groups of 1000
[INFO] [2020-06-10 12:29:24] Average Time: 0.0
[INFO] [2020-06-10 12:29:24] Total Time: 1s
[INFO] [2020-06-10 12:29:24] Storing 2777 ScientificNames
[INFO] [2020-06-10 12:29:24] Processing group of 2777 in 3 groups of 1000
[INFO] [2020-06-10 12:29:25] Average Time: 0.363
[INFO] [2020-06-10 12:29:25] Total Time: 2s
[INFO] [2020-06-10 12:29:25] Storing 2777 Nodes
[INFO] [2020-06-10 12:29:25] Processing group of 2777 in 3 groups of 1000
[INFO] [2020-06-10 12:29:26] Average Time: 0.327
[INFO] [2020-06-10 12:29:26] Total Time: 2s
[INFO] [2020-06-10 12:29:26] Storing 2557 Occurrences
[INFO] [2020-06-10 12:29:26] Processing group of 2557 in 3 groups of 1000
[INFO] [2020-06-10 12:29:27] Average Time: 0.14
[INFO] [2020-06-10 12:29:27] Total Time: 1s
[STOP] [2020-06-10 12:29:27] parse_diff_and_store
[START] [2020-06-10 12:29:27] resolve_keys
[INFO] [2020-06-10 12:29:35] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-10 12:29:35] traits to occurrences...
[INFO] [2020-06-10 12:29:35] traits to nodes (through occurrences)...
[INFO] [2020-06-10 12:29:35] Traits to sex term...
[INFO] [2020-06-10 12:29:35] Traits to lifestage term...
[INFO] [2020-06-10 12:29:35] MetaTraits to traits...
[INFO] [2020-06-10 12:29:35] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-10 12:29:35] Assocs to occurrences...
[INFO] [2020-06-10 12:29:35] Assocs to nodes...
[INFO] [2020-06-10 12:29:35] Assoc to sex term...
[INFO] [2020-06-10 12:29:35] Assoc to lifestage term...
[STOP] [2020-06-10 12:29:35] resolve_keys
[START] [2020-06-10 12:29:35] hold_for_later_1
[STOP] [2020-06-10 12:29:35] hold_for_later_1
[START] [2020-06-10 12:29:35] hold_for_later_2
[STOP] [2020-06-10 12:29:35] hold_for_later_2
[START] [2020-06-10 12:29:35] resolve_missing_parents
[STOP] [2020-06-10 12:29:35] resolve_missing_parents
[START] [2020-06-10 12:29:35] rebuild_nodes
[START] [2020-06-10 12:29:35] Flattener#flatten
[START] [2020-06-10 12:29:35] Flattener#study_resource
[START] [2020-06-10 12:29:35] Flattener#build_ancestry
[STOP] [2020-06-10 12:29:35] Flattener#build_ancestry
[INFO] [2020-06-10 12:29:35] 2777 ancestry keys
[START] [2020-06-10 12:29:35] build_node_ancestors
[INFO] [2020-06-10 12:29:35] old ancestors deleted.
[STOP] [2020-06-10 12:29:35] build_node_ancestors
[START] [2020-06-10 12:29:36] Flattener#propagate_ancestor_ids
[STOP] [2020-06-10 12:29:36] Flattener#propagate_ancestor_ids
[STOP] [2020-06-10 12:29:36] Flattener#flatten
[STOP] [2020-06-10 12:29:36] rebuild_nodes
[START] [2020-06-10 12:29:36] resolve_missing_media_owners
[STOP] [2020-06-10 12:29:36] resolve_missing_media_owners
[START] [2020-06-10 12:29:36] sanitize_media_verbatims
[STOP] [2020-06-10 12:29:36] sanitize_media_verbatims
[START] [2020-06-10 12:29:36] queue_downloads
[STOP] [2020-06-10 12:29:36] queue_downloads
[START] [2020-06-10 12:29:36] parse_names
[WARN] [2020-06-10 12:29:36] I see 2777 names which still need to be parsed.
[WARN] [2020-06-10 12:29:39] I see 1 names which still need to be parsed.
[STOP] [2020-06-10 12:29:40] parse_names
[START] [2020-06-10 12:29:40] denormalize_canonical_names_to_nodes
[STOP] [2020-06-10 12:29:40] denormalize_canonical_names_to_nodes
[START] [2020-06-10 12:29:40] match_nodes
[START] [2020-06-10 12:29:40] map_all_nodes_to_pages
[STOP] [2020-06-10 12:31:11] map_all_nodes_to_pages
[INFO] [2020-06-10 12:31:11] 39 Unmatched nodes (of 2777)! That's too many to output. First 10: Areceae (#80054251); Cocoseae (#80055228); Butia stolonifera (#80054557); Prestoea longipetiolata (#80056530); Irarteeae (#80055883); Cyclosphatheae (#80055282); Trachycarpeae (#80056837); Licuala nauroannii (#80056074); Calameae (#80054562); Calamus (#80054943)
[START] [2020-06-10 12:31:11] update_nodes
[STOP] [2020-06-10 12:31:12] update_nodes
[STOP] [2020-06-10 12:31:12] match_nodes
[START] [2020-06-10 12:31:12] reindex_search
[STOP] [2020-06-10 12:31:15] reindex_search
[START] [2020-06-10 12:31:15] normalize_units
[STOP] [2020-06-10 12:31:15] normalize_units
[START] [2020-06-10 12:31:15] calculate_statistics
[STOP] [2020-06-10 12:31:15] calculate_statistics
[START] [2020-06-10 12:31:15] complete_harvest_instance
[START] [2020-06-10 12:31:15] overall_tsv_creation
[INFO] [2020-06-10 12:31:15] Processing group of 2777 in 1 batches of 10000
[INFO] [2020-06-10 12:31:28] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-06-10 12:33:11] Average Time: 18.29
[INFO] [2020-06-10 12:33:11] Total Time: 1m56s
[STOP] [2020-06-10 12:33:11] overall_tsv_creation
[INFO] [2020-06-10 12:33:11] Done. Check your files:
[INFO] [2020-06-10 12:33:11] (2776 lines) /app/public/data/palm_traits_palm/publish_nodes.tsv
[INFO] [2020-06-10 12:33:11] (10183 lines) /app/public/data/palm_traits_palm/publish_node_ancestors.tsv
[INFO] [2020-06-10 12:33:11] (2777 lines) /app/public/data/palm_traits_palm/publish_scientific_names.tsv
[STOP] [2020-06-10 12:33:11] complete_harvest_instance
[START] [2020-06-10 12:33:11] completed
[STOP] [2020-06-10 12:33:11] completed
[STOP] [2020-06-10 12:33:11] logged process, took 228.84
[INFO] [2020-06-10 12:33:11] ## remove_type: ScientificName
[INFO] [2020-06-10 12:33:11] ++ Calling delete_all on 2777 instances...
[INFO] [2020-06-10 12:33:11] [12:33:11.722] Removed 2777 Scientificnames
[INFO] [2020-06-10 12:33:11] ## remove_type: Vernacular
[INFO] [2020-06-10 12:33:11] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:11] [12:33:11.723] Removed 0 Vernaculars
[INFO] [2020-06-10 12:33:11] ## remove_type: Article
[INFO] [2020-06-10 12:33:11] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:11] [12:33:11.724] Removed 0 Articles
[INFO] [2020-06-10 12:33:11] ## remove_type: Medium
[INFO] [2020-06-10 12:33:11] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:11] [12:33:11.726] Removed 0 Media
[INFO] [2020-06-10 12:33:11] ## remove_type: Trait
[INFO] [2020-06-10 12:33:11] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:11] [12:33:11.727] Removed 0 Traits
[INFO] [2020-06-10 12:33:11] ## remove_type: MetaTrait
[INFO] [2020-06-10 12:33:11] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:11] [12:33:11.729] Removed 0 Metatraits
[INFO] [2020-06-10 12:33:11] ## remove_type: OccurrenceMetadatum
[INFO] [2020-06-10 12:33:11] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:11] [12:33:11.730] Removed 0 Occurrencemetadata
[INFO] [2020-06-10 12:33:11] ## remove_type: Assoc
[INFO] [2020-06-10 12:33:11] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:11] [12:33:11.732] Removed 0 Assocs
[INFO] [2020-06-10 12:33:11] ## remove_type: MetaAssoc
[INFO] [2020-06-10 12:33:11] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:11] [12:33:11.734] Removed 0 Metaassocs
[INFO] [2020-06-10 12:33:11] ## remove_type: Identifier
[INFO] [2020-06-10 12:33:11] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:11] [12:33:11.735] Removed 0 Identifiers
[INFO] [2020-06-10 12:33:11] ## remove_type: Reference
[INFO] [2020-06-10 12:33:11] ++ Calling delete_all on 3 instances...
[INFO] [2020-06-10 12:33:11] [12:33:11.737] Removed 3 References
[INFO] [2020-06-10 12:33:11] Starting batch with ID 80054719...
[INFO] [2020-06-10 12:33:12] Starting batch with ID 80054719...
[INFO] [2020-06-10 12:33:13] Starting batch with ID 80055141...
[INFO] [2020-06-10 12:33:13] ## remove_type: Node
[INFO] [2020-06-10 12:33:13] ++ Calling delete_all on 2777 instances...
[INFO] [2020-06-10 12:33:13] [12:33:13.274] Removed 2777 Nodes
[START] [2020-06-10 12:33:13] logged process
[START] [2020-06-10 12:33:13] Creating resource from OpenData
[START] [2020-06-10 12:33:14] logged process
[START] [2020-06-10 12:33:14] Parse meta.xml file and create formats with fields
[STOP] [2020-06-10 12:33:14] Parse meta.xml file and create formats with fields
[STOP] [2020-06-10 12:33:14] Creating resource from OpenData
[START] [2020-06-10 12:33:14] logged process
[START] [2020-06-10 12:33:14] create_harvest_instance
[STOP] [2020-06-10 12:33:14] create_harvest_instance
[ERR] [2020-06-10 12:33:14] ActiveRecord::StatementInvalid
[ERR] [2020-06-10 12:33:14] Mysql2::Error::ConnectionError: MySQL server has gone away: ROLLBACK
[ERR] [2020-06-10 12:33:14] ../models/format.rb:72:in `block in copy_to_harvest'
[ERR] [2020-06-10 12:33:14] ../models/format.rb:69:in `copy_to_harvest'
[ERR] [2020-06-10 12:33:14] ../models/resource.rb:280:in `block in create_harvest_instance'
[ERR] [2020-06-10 12:33:14] ../models/resource.rb:278:in `create_harvest_instance'
[ERR] [2020-06-10 12:33:14] ../models/resource_harvester.rb:108:in `create_harvest_instance'
[ERR] [2020-06-10 12:33:14] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2020-06-10 12:33:14] ../models/logged_process.rb:19:in `run_step'
[ERR] [2020-06-10 12:33:14] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2020-06-10 12:33:14] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2020-06-10 12:33:14] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2020-06-10 12:33:14] ../models/resource.rb:151:in `lock'
[ERR] [2020-06-10 12:33:14] ../models/resource_harvester.rb:72:in `start'
[ERR] [2020-06-10 12:33:14] ../models/resource.rb:232:in `harvest'
[ERR] [2020-06-10 12:33:14] ../models/resource.rb:208:in `re_download_opendata_and_harvest'
[ERR] [2020-06-10 12:33:14] bin/rails:4:in `require'
[ERR] [2020-06-10 12:33:14] bin/rails:4:in `<main>'
[STOP] [2020-06-10 12:33:14] logged process, took 0.72
[INFO] [2020-06-10 12:33:41] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-06-10 12:33:42] ## remove_type: ScientificName
[INFO] [2020-06-10 12:33:42] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:42] [12:33:42.069] Removed 0 Scientificnames
[INFO] [2020-06-10 12:33:42] ## remove_type: Vernacular
[INFO] [2020-06-10 12:33:42] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:42] [12:33:42.072] Removed 0 Vernaculars
[INFO] [2020-06-10 12:33:42] ## remove_type: Article
[INFO] [2020-06-10 12:33:42] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:42] [12:33:42.075] Removed 0 Articles
[INFO] [2020-06-10 12:33:42] ## remove_type: Medium
[INFO] [2020-06-10 12:33:42] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:42] [12:33:42.078] Removed 0 Media
[INFO] [2020-06-10 12:33:42] ## remove_type: Trait
[INFO] [2020-06-10 12:33:42] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:42] [12:33:42.081] Removed 0 Traits
[INFO] [2020-06-10 12:33:42] ## remove_type: MetaTrait
[INFO] [2020-06-10 12:33:42] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:42] [12:33:42.084] Removed 0 Metatraits
[INFO] [2020-06-10 12:33:42] ## remove_type: OccurrenceMetadatum
[INFO] [2020-06-10 12:33:42] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:42] [12:33:42.087] Removed 0 Occurrencemetadata
[INFO] [2020-06-10 12:33:42] ## remove_type: Assoc
[INFO] [2020-06-10 12:33:42] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:42] [12:33:42.090] Removed 0 Assocs
[INFO] [2020-06-10 12:33:42] ## remove_type: MetaAssoc
[INFO] [2020-06-10 12:33:42] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:42] [12:33:42.093] Removed 0 Metaassocs
[INFO] [2020-06-10 12:33:42] ## remove_type: Identifier
[INFO] [2020-06-10 12:33:42] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:42] [12:33:42.095] Removed 0 Identifiers
[INFO] [2020-06-10 12:33:42] ## remove_type: Reference
[INFO] [2020-06-10 12:33:42] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:42] [12:33:42.098] Removed 0 References
[INFO] [2020-06-10 12:33:42] ## remove_type: Node
[INFO] [2020-06-10 12:33:42] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-10 12:33:42] [12:33:42.118] Removed 0 Nodes
[START] [2020-06-10 12:33:42] logged process
[START] [2020-06-10 12:33:42] Creating resource from OpenData
[START] [2020-06-10 12:33:42] logged process
[START] [2020-06-10 12:33:42] Parse meta.xml file and create formats with fields
[STOP] [2020-06-10 12:33:42] Parse meta.xml file and create formats with fields
[STOP] [2020-06-10 12:33:42] Creating resource from OpenData
[START] [2020-06-10 12:33:42] logged process
[START] [2020-06-10 12:33:42] create_harvest_instance
[STOP] [2020-06-10 12:33:44] create_harvest_instance
[START] [2020-06-10 12:33:44] fetch_files
[STOP] [2020-06-10 12:33:44] fetch_files
[START] [2020-06-10 12:33:44] validate_each_file
[STOP] [2020-06-10 12:33:45] validate_each_file
[START] [2020-06-10 12:33:45] convert_to_csv
[CMD] [2020-06-10 12:33:45] /usr/bin/sort /app/public/converted_csv/palm_traits_palm_refs_21122.csv > /app/public/converted_csv/palm_traits_palm_refs_21122.csv_sorted
[CMD] [2020-06-10 12:33:45] /usr/bin/sort /app/public/converted_csv/palm_traits_palm_nodes_21123.csv > /app/public/converted_csv/palm_traits_palm_nodes_21123.csv_sorted
[CMD] [2020-06-10 12:33:45] /usr/bin/sort /app/public/converted_csv/palm_traits_palm_occurrences_21124.csv > /app/public/converted_csv/palm_traits_palm_occurrences_21124.csv_sorted
[CMD] [2020-06-10 12:33:45] /usr/bin/sort /app/public/converted_csv/palm_traits_palm_measurements_21125.csv > /app/public/converted_csv/palm_traits_palm_measurements_21125.csv_sorted
[STOP] [2020-06-10 12:33:45] convert_to_csv
[START] [2020-06-10 12:33:45] calculate_delta
[CMD] [2020-06-10 12:33:45] echo "0a" > /app/public/diff/palm_traits_palm_refs_21122.diff
[CMD] [2020-06-10 12:33:45] tail -n +1 /app/public/converted_csv/palm_traits_palm_refs_21122.csv >> /app/public/diff/palm_traits_palm_refs_21122.diff
[CMD] [2020-06-10 12:33:45] echo "." >> /app/public/diff/palm_traits_palm_refs_21122.diff
[CMD] [2020-06-10 12:33:45] echo "0a" > /app/public/diff/palm_traits_palm_nodes_21123.diff
[CMD] [2020-06-10 12:33:45] tail -n +1 /app/public/converted_csv/palm_traits_palm_nodes_21123.csv >> /app/public/diff/palm_traits_palm_nodes_21123.diff
[CMD] [2020-06-10 12:33:45] echo "." >> /app/public/diff/palm_traits_palm_nodes_21123.diff
[CMD] [2020-06-10 12:33:45] echo "0a" > /app/public/diff/palm_traits_palm_occurrences_21124.diff
[CMD] [2020-06-10 12:33:45] tail -n +1 /app/public/converted_csv/palm_traits_palm_occurrences_21124.csv >> /app/public/diff/palm_traits_palm_occurrences_21124.diff
[CMD] [2020-06-10 12:33:45] echo "." >> /app/public/diff/palm_traits_palm_occurrences_21124.diff
[CMD] [2020-06-10 12:33:45] echo "0a" > /app/public/diff/palm_traits_palm_measurements_21125.diff
[CMD] [2020-06-10 12:33:45] tail -n +1 /app/public/converted_csv/palm_traits_palm_measurements_21125.csv >> /app/public/diff/palm_traits_palm_measurements_21125.diff
[CMD] [2020-06-10 12:33:45] echo "." >> /app/public/diff/palm_traits_palm_measurements_21125.diff
[STOP] [2020-06-10 12:33:45] calculate_delta
[START] [2020-06-10 12:33:45] parse_diff_and_store
[INFO] [2020-06-10 12:33:45] Loading refs diff file into memory (true lines)...
[INFO] [2020-06-10 12:33:45] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-10 12:33:46] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-10 12:33:46] Loading measurements diff file into memory (true lines)...
[INFO] [2020-06-10 12:36:33] Storing 3 References
[INFO] [2020-06-10 12:36:33] Processing group of 3 in 1 groups of 1000
[INFO] [2020-06-10 12:36:33] Average Time: 0.0
[INFO] [2020-06-10 12:36:33] Total Time: 1s
[INFO] [2020-06-10 12:36:33] Storing 2777 ScientificNames
[INFO] [2020-06-10 12:36:33] Processing group of 2777 in 3 groups of 1000
[INFO] [2020-06-10 12:36:34] Average Time: 0.267
[INFO] [2020-06-10 12:36:34] Total Time: 1s
[INFO] [2020-06-10 12:36:34] Storing 2777 Nodes
[INFO] [2020-06-10 12:36:34] Processing group of 2777 in 3 groups of 1000
[INFO] [2020-06-10 12:36:35] Average Time: 0.23
[INFO] [2020-06-10 12:36:35] Total Time: 1s
[INFO] [2020-06-10 12:36:35] Storing 2557 Occurrences
[INFO] [2020-06-10 12:36:35] Processing group of 2557 in 3 groups of 1000
[INFO] [2020-06-10 12:36:35] Average Time: 0.077
[INFO] [2020-06-10 12:36:35] Total Time: 1s
[INFO] [2020-06-10 12:36:35] Storing 65490 TraitsReferences
[INFO] [2020-06-10 12:36:35] Processing group of 65490 in 66 groups of 1000
[INFO] [2020-06-10 12:36:40] Average Time: 0.065
[INFO] [2020-06-10 12:36:40] Total Time: 5s
[INFO] [2020-06-10 12:36:40] last 3 / first 3: 0.38
[INFO] [2020-06-10 12:36:40] Std.Dev: 0.03162277660168379; Max: 0.26
[INFO] [2020-06-10 12:36:40] Storing 23050 Traits
[INFO] [2020-06-10 12:36:40] Processing group of 23050 in 24 groups of 1000
[INFO] [2020-06-10 12:36:47] Average Time: 0.289
[INFO] [2020-06-10 12:36:47] Total Time: 8s
[INFO] [2020-06-10 12:36:47] last 3 / first 3: 0.45
[INFO] [2020-06-10 12:36:47] Std.Dev: 0.09486832980505137; Max: 0.49
[INFO] [2020-06-10 12:36:47] Storing 73798 MetaTraits
[INFO] [2020-06-10 12:36:47] Processing group of 73798 in 74 groups of 1000
[INFO] [2020-06-10 12:36:55] Average Time: 0.108
[INFO] [2020-06-10 12:36:55] Total Time: 9s
[INFO] [2020-06-10 12:36:55] last 3 / first 3: 0.68
[INFO] [2020-06-10 12:36:55] Std.Dev: 0.06324555320336758; Max: 0.59
[STOP] [2020-06-10 12:36:55] parse_diff_and_store
[START] [2020-06-10 12:36:55] resolve_keys
[INFO] [2020-06-10 12:37:02] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-10 12:37:02] traits to occurrences...
[INFO] [2020-06-10 12:37:03] traits to nodes (through occurrences)...
[INFO] [2020-06-10 12:37:04] Traits to sex term...
[INFO] [2020-06-10 12:37:04] Traits to lifestage term...
[INFO] [2020-06-10 12:37:04] MetaTraits to traits...
[INFO] [2020-06-10 12:37:05] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-10 12:37:12] Assocs to occurrences...
[INFO] [2020-06-10 12:37:12] Assocs to nodes...
[INFO] [2020-06-10 12:37:12] Assoc to sex term...
[INFO] [2020-06-10 12:37:12] Assoc to lifestage term...
[STOP] [2020-06-10 12:37:12] resolve_keys
[START] [2020-06-10 12:37:12] hold_for_later_1
[STOP] [2020-06-10 12:37:12] hold_for_later_1
[START] [2020-06-10 12:37:12] hold_for_later_2
[STOP] [2020-06-10 12:37:12] hold_for_later_2
[START] [2020-06-10 12:37:12] resolve_missing_parents
[STOP] [2020-06-10 12:37:12] resolve_missing_parents
[START] [2020-06-10 12:37:12] rebuild_nodes
[START] [2020-06-10 12:37:12] Flattener#flatten
[START] [2020-06-10 12:37:12] Flattener#study_resource
[START] [2020-06-10 12:37:12] Flattener#build_ancestry
[STOP] [2020-06-10 12:37:12] Flattener#build_ancestry
[INFO] [2020-06-10 12:37:12] 2777 ancestry keys
[START] [2020-06-10 12:37:12] build_node_ancestors
[INFO] [2020-06-10 12:37:12] old ancestors deleted.
[STOP] [2020-06-10 12:37:13] build_node_ancestors
[START] [2020-06-10 12:37:14] Flattener#propagate_ancestor_ids
[STOP] [2020-06-10 12:37:14] Flattener#propagate_ancestor_ids
[STOP] [2020-06-10 12:37:14] Flattener#flatten
[STOP] [2020-06-10 12:37:14] rebuild_nodes
[START] [2020-06-10 12:37:14] resolve_missing_media_owners
[STOP] [2020-06-10 12:37:14] resolve_missing_media_owners
[START] [2020-06-10 12:37:14] sanitize_media_verbatims
[STOP] [2020-06-10 12:37:14] sanitize_media_verbatims
[START] [2020-06-10 12:37:14] queue_downloads
[STOP] [2020-06-10 12:37:14] queue_downloads
[START] [2020-06-10 12:37:14] parse_names
[WARN] [2020-06-10 12:37:14] I see 2777 names which still need to be parsed.
[WARN] [2020-06-10 12:37:17] I see 1 names which still need to be parsed.
[STOP] [2020-06-10 12:37:18] parse_names
[START] [2020-06-10 12:37:18] denormalize_canonical_names_to_nodes
[STOP] [2020-06-10 12:37:18] denormalize_canonical_names_to_nodes
[START] [2020-06-10 12:37:18] match_nodes
[START] [2020-06-10 12:37:18] map_all_nodes_to_pages
[STOP] [2020-06-10 12:38:59] map_all_nodes_to_pages
[INFO] [2020-06-10 12:38:59] 39 Unmatched nodes (of 2777)! That's too many to output. First 10: Areceae (#80057028); Cocoseae (#80058005); Butia stolonifera (#80057334); Prestoea longipetiolata (#80059307); Irarteeae (#80058660); Cyclosphatheae (#80058059); Trachycarpeae (#80059614); Licuala nauroannii (#80058851); Calameae (#80057339); Calamus (#80057720)
[START] [2020-06-10 12:38:59] update_nodes
[STOP] [2020-06-10 12:39:00] update_nodes
[STOP] [2020-06-10 12:39:00] match_nodes
[START] [2020-06-10 12:39:00] reindex_search
[STOP] [2020-06-10 12:39:03] reindex_search
[START] [2020-06-10 12:39:03] normalize_units
[STOP] [2020-06-10 12:40:01] normalize_units
[START] [2020-06-10 12:40:01] calculate_statistics
[STOP] [2020-06-10 12:40:01] calculate_statistics
[START] [2020-06-10 12:40:01] complete_harvest_instance
[START] [2020-06-10 12:40:01] overall_tsv_creation
[INFO] [2020-06-10 12:40:01] Processing group of 2777 in 1 batches of 10000
[INFO] [2020-06-10 12:41:04] 21830 Traits (unfiltered)...
[INFO] [2020-06-10 12:41:17] 21830 Traits (filtered)...
[INFO] [2020-06-10 12:41:17] 0 Associations (filtered)...
[INFO] [2020-06-10 12:42:19] 140508 metadata added.
[INFO] [2020-06-10 12:42:19] 0 metadata added.
[INFO] [2020-06-10 12:42:20] Average Time: 106.03
[INFO] [2020-06-10 12:42:20] Total Time: 2m19s
[STOP] [2020-06-10 12:42:20] overall_tsv_creation
[INFO] [2020-06-10 12:42:20] Done. Check your files:
[INFO] [2020-06-10 12:42:20] (2776 lines) /app/public/data/palm_traits_palm/publish_nodes.tsv
[INFO] [2020-06-10 12:42:20] (10183 lines) /app/public/data/palm_traits_palm/publish_node_ancestors.tsv
[INFO] [2020-06-10 12:42:20] (2777 lines) /app/public/data/palm_traits_palm/publish_scientific_names.tsv
[INFO] [2020-06-10 12:42:20] (21831 lines) /app/public/data/palm_traits_palm/publish_traits.tsv
[INFO] [2020-06-10 12:42:20] (140509 lines) /app/public/data/palm_traits_palm/publish_metadata.tsv
[STOP] [2020-06-10 12:42:20] complete_harvest_instance
[START] [2020-06-10 12:42:20] completed
[STOP] [2020-06-10 12:42:20] completed
[STOP] [2020-06-10 12:42:20] logged process, took 517.69

Latest Process

10 Jun 12:33 EXITED currently processing 0