Harvest for Insect Wings Created 03 May 13:39

Stage: completed
Fetched: 03 May 13:39
Validated: 03 May 13:39
Deltas Created 03 May 13:39
Units Normalized: 03 May 13:39
Ancestry Built: 03 May 13:39
Nodes Matched: 03 May 13:39
Names Parsed: 03 May 13:39
New Models Stored: 03 May 13:39
Indexed: 03 May 13:39
Completed: 03 May 13:42
Time to Harvest: less than a minute

Harvesting Log (most recent first)

# Logfile created on 2021-04-29 14:04:06 -0400 by logger.rb/66358
[START] [2021-04-29 14:04:07] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-29 14:04:07] Creating resource from OpenData
[START] [2021-04-29 14:04:07] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-29 14:04:07] Parse meta.xml file and create formats with fields
[STOP] [2021-04-29 14:04:07] Parse meta.xml file and create formats with fields
[STOP] [2021-04-29 14:04:07] Creating resource from OpenData
[INFO] [2021-04-29 14:20:53] ## HARVEST: type = -harvest
[START] [2021-04-29 14:20:54] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-29 14:20:54] create_harvest_instance
[INFO] [2021-04-29 14:20:54] Created harvest instance #3837
[STOP] [2021-04-29 14:20:54] create_harvest_instance
[START] [2021-04-29 14:20:54] fetch_files
[STOP] [2021-04-29 14:20:54] fetch_files
[START] [2021-04-29 14:20:54] validate_each_file
[INFO] [2021-04-29 14:20:55] Looping over 3 formats...
[INFO] [2021-04-29 14:20:55] ...nodes (/app/public/data/insect_wings/taxa.txt)
[INFO] [2021-04-29 14:20:55] Valid: /app/public/converted_csv/insect_wings_nodes_3837.csv (311 lines)
[INFO] [2021-04-29 14:20:55] ...occurrences (/app/public/data/insect_wings/occurrences.txt)
[INFO] [2021-04-29 14:20:55] Valid: /app/public/converted_csv/insect_wings_occurrences_3837.csv (325 lines)
[INFO] [2021-04-29 14:20:55] ...measurements (/app/public/data/insect_wings/measurementsorfacts.txt)
[INFO] [2021-04-29 14:20:55] Valid: /app/public/converted_csv/insect_wings_measurements_3837.csv (528 lines)
[STOP] [2021-04-29 14:20:55] validate_each_file
[START] [2021-04-29 14:20:55] convert_to_csv
[INFO] [2021-04-29 14:20:55] Looping over 3 formats...
[INFO] [2021-04-29 14:20:55] ...nodes (/app/public/data/insect_wings/taxa.txt)
[CMD] [2021-04-29 14:20:55] /usr/bin/sort /app/public/converted_csv/insect_wings_nodes_3837.csv > /app/public/converted_csv/insect_wings_nodes_3837.csv_sorted
[INFO] [2021-04-29 14:20:55] Converted: /app/public/converted_csv/insect_wings_nodes_3837.csv (311 lines)
[INFO] [2021-04-29 14:20:55] ...occurrences (/app/public/data/insect_wings/occurrences.txt)
[CMD] [2021-04-29 14:20:55] /usr/bin/sort /app/public/converted_csv/insect_wings_occurrences_3837.csv > /app/public/converted_csv/insect_wings_occurrences_3837.csv_sorted
[INFO] [2021-04-29 14:20:55] Converted: /app/public/converted_csv/insect_wings_occurrences_3837.csv (325 lines)
[INFO] [2021-04-29 14:20:55] ...measurements (/app/public/data/insect_wings/measurementsorfacts.txt)
[CMD] [2021-04-29 14:20:55] /usr/bin/sort /app/public/converted_csv/insect_wings_measurements_3837.csv > /app/public/converted_csv/insect_wings_measurements_3837.csv_sorted
[INFO] [2021-04-29 14:20:55] Converted: /app/public/converted_csv/insect_wings_measurements_3837.csv (528 lines)
[STOP] [2021-04-29 14:20:55] convert_to_csv
[START] [2021-04-29 14:20:55] calculate_delta
[INFO] [2021-04-29 14:20:55] Looping over 3 formats...
[INFO] [2021-04-29 14:20:55] ...nodes (/app/public/data/insect_wings/taxa.txt)
[CMD] [2021-04-29 14:20:55] echo "0a" > /app/public/diff/insect_wings_nodes_3837.diff
[CMD] [2021-04-29 14:20:55] tail -n +1 /app/public/converted_csv/insect_wings_nodes_3837.csv >> /app/public/diff/insect_wings_nodes_3837.diff
[CMD] [2021-04-29 14:20:55] echo "." >> /app/public/diff/insect_wings_nodes_3837.diff
[INFO] [2021-04-29 14:20:55] Created diff: /app/public/diff/insect_wings_nodes_3837.diff (313 lines)
[INFO] [2021-04-29 14:20:55] ...occurrences (/app/public/data/insect_wings/occurrences.txt)
[CMD] [2021-04-29 14:20:55] echo "0a" > /app/public/diff/insect_wings_occurrences_3837.diff
[CMD] [2021-04-29 14:20:55] tail -n +1 /app/public/converted_csv/insect_wings_occurrences_3837.csv >> /app/public/diff/insect_wings_occurrences_3837.diff
[CMD] [2021-04-29 14:20:55] echo "." >> /app/public/diff/insect_wings_occurrences_3837.diff
[INFO] [2021-04-29 14:20:55] Created diff: /app/public/diff/insect_wings_occurrences_3837.diff (327 lines)
[INFO] [2021-04-29 14:20:55] ...measurements (/app/public/data/insect_wings/measurementsorfacts.txt)
[CMD] [2021-04-29 14:20:55] echo "0a" > /app/public/diff/insect_wings_measurements_3837.diff
[CMD] [2021-04-29 14:20:55] tail -n +1 /app/public/converted_csv/insect_wings_measurements_3837.csv >> /app/public/diff/insect_wings_measurements_3837.diff
[CMD] [2021-04-29 14:20:55] echo "." >> /app/public/diff/insect_wings_measurements_3837.diff
[INFO] [2021-04-29 14:20:55] Created diff: /app/public/diff/insect_wings_measurements_3837.diff (530 lines)
[STOP] [2021-04-29 14:20:55] calculate_delta
[START] [2021-04-29 14:20:55] parse_diff_and_store
[INFO] [2021-04-29 14:20:55] Handling diff: /app/public/diff/insect_wings_nodes_3837.diff (313 lines)
[INFO] [2021-04-29 14:20:55] Loading nodes diff file into memory (313 /app/public/diff/insect_wings_nodes_3837.diff lines)...
[INFO] [2021-04-29 14:20:55] Handling diff: /app/public/diff/insect_wings_occurrences_3837.diff (327 lines)
[INFO] [2021-04-29 14:20:55] Loading occurrences diff file into memory (327 /app/public/diff/insect_wings_occurrences_3837.diff lines)...
[INFO] [2021-04-29 14:20:55] Handling diff: /app/public/diff/insect_wings_measurements_3837.diff (530 lines)
[INFO] [2021-04-29 14:20:55] Loading measurements diff file into memory (530 /app/public/diff/insect_wings_measurements_3837.diff lines)...
[STOP] [2021-04-29 14:20:55] parse_diff_and_store
[ERR] [2021-04-29 14:20:55] RuntimeError
[ERR] [2021-04-29 14:20:55] Missing Term for URI `http://eol.org/schema/terms/stenopterous`, must be added!
[ERR] [2021-04-29 14:20:55] ../models/store/model_builder.rb:640:in `fail_on_bad_uri'
[ERR] [2021-04-29 14:20:55] ../models/store/model_builder.rb:594:in `convert_trait_value'
[ERR] [2021-04-29 14:20:55] ../models/store/model_builder.rb:415:in `build_trait'
[ERR] [2021-04-29 14:20:55] ../models/store/model_builder.rb:28:in `build_models'
[ERR] [2021-04-29 14:20:55] ../models/resource_harvester.rb:352:in `block (3 levels) in parse_diff_and_store'
[ERR] [2021-04-29 14:20:55] ../models/csv_parser.rb:111:in `block in diff_as_hashes'
[ERR] [2021-04-29 14:20:55] ../models/csv_parser.rb:28:in `block in line_at_a_time'
[ERR] [2021-04-29 14:20:55] ../models/csv_parser.rb:25:in `line_at_a_time'
[ERR] [2021-04-29 14:20:55] ../models/csv_parser.rb:96:in `diff_as_hashes'
[ERR] [2021-04-29 14:20:55] ../models/resource_harvester.rb:306:in `block (2 levels) in parse_diff_and_store'
[ERR] [2021-04-29 14:20:55] ../models/logged_process.rb:77:in `enter_group'
[ERR] [2021-04-29 14:20:55] ../models/resource_harvester.rb:305:in `block in parse_diff_and_store'
[ERR] [2021-04-29 14:20:55] ../models/resource_harvester.rb:702:in `block in each_diff'
[ERR] [2021-04-29 14:20:55] ../models/resource_harvester.rb:689:in `each_diff'
[ERR] [2021-04-29 14:20:55] ../models/resource_harvester.rb:300:in `parse_diff_and_store'
[ERR] [2021-04-29 14:20:55] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2021-04-29 14:20:55] ../models/logged_process.rb:34:in `run_step'
[ERR] [2021-04-29 14:20:55] ../models/resource_harvester.rb:86:in `block in start'
[ERR] [2021-04-29 14:20:55] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2021-04-29 14:20:55] ../models/resource_harvester.rb:75:in `start'
[ERR] [2021-04-29 14:20:55] ../models/resource.rb:261:in `harvest'
[ERR] [2021-04-29 14:20:55] bin/rails:4:in `require'
[ERR] [2021-04-29 14:20:55] bin/rails:4:in `<main>'
[STOP] [2021-04-29 14:20:55] logged process, took 0.56
[INFO] [2021-04-29 16:29:09] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-29 16:29:11] ## remove_type: ScientificName
[INFO] [2021-04-29 16:29:11] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 16:29:11] [16:29:11.870] Removed 0 Scientificnames
[INFO] [2021-04-29 16:29:11] ## remove_type: Vernacular
[INFO] [2021-04-29 16:29:11] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 16:29:11] [16:29:11.873] Removed 0 Vernaculars
[INFO] [2021-04-29 16:29:11] ## remove_type: Article
[INFO] [2021-04-29 16:29:11] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 16:29:11] [16:29:11.876] Removed 0 Articles
[INFO] [2021-04-29 16:29:11] ## remove_type: Medium
[INFO] [2021-04-29 16:29:11] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 16:29:11] [16:29:11.880] Removed 0 Media
[INFO] [2021-04-29 16:29:11] ## remove_type: Trait
[INFO] [2021-04-29 16:29:11] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 16:29:11] [16:29:11.883] Removed 0 Traits
[INFO] [2021-04-29 16:29:11] ## remove_type: MetaTrait
[INFO] [2021-04-29 16:29:11] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 16:29:11] [16:29:11.886] Removed 0 Metatraits
[INFO] [2021-04-29 16:29:11] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-29 16:29:11] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 16:29:11] [16:29:11.889] Removed 0 Occurrencemetadata
[INFO] [2021-04-29 16:29:11] ## remove_type: Assoc
[INFO] [2021-04-29 16:29:11] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 16:29:11] [16:29:11.893] Removed 0 Assocs
[INFO] [2021-04-29 16:29:11] ## remove_type: MetaAssoc
[INFO] [2021-04-29 16:29:11] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 16:29:11] [16:29:11.895] Removed 0 Metaassocs
[INFO] [2021-04-29 16:29:11] ## remove_type: Identifier
[INFO] [2021-04-29 16:29:11] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 16:29:11] [16:29:11.898] Removed 0 Identifiers
[INFO] [2021-04-29 16:29:11] ## remove_type: Reference
[INFO] [2021-04-29 16:29:11] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 16:29:11] [16:29:11.900] Removed 0 References
[INFO] [2021-04-29 16:29:11] ## remove_type: Node
[INFO] [2021-04-29 16:29:11] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 16:29:11] [16:29:11.917] Removed 0 Nodes
[START] [2021-04-29 16:29:12] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-29 16:29:12] Creating resource from OpenData
[START] [2021-04-29 16:29:12] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-29 16:29:12] Parse meta.xml file and create formats with fields
[STOP] [2021-04-29 16:29:12] Parse meta.xml file and create formats with fields
[STOP] [2021-04-29 16:29:12] Creating resource from OpenData
[START] [2021-04-29 16:29:12] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-29 16:29:12] create_harvest_instance
[INFO] [2021-04-29 16:29:12] Created harvest instance #3839
[STOP] [2021-04-29 16:29:12] create_harvest_instance
[START] [2021-04-29 16:29:12] fetch_files
[STOP] [2021-04-29 16:29:12] fetch_files
[START] [2021-04-29 16:29:12] validate_each_file
[INFO] [2021-04-29 16:29:12] Looping over 3 formats...
[INFO] [2021-04-29 16:29:12] ...nodes (/app/public/data/insect_wings/taxa.txt)
[INFO] [2021-04-29 16:29:12] Valid: /app/public/converted_csv/insect_wings_nodes_3839.csv (311 lines)
[INFO] [2021-04-29 16:29:12] ...occurrences (/app/public/data/insect_wings/occurrences.txt)
[INFO] [2021-04-29 16:29:12] Valid: /app/public/converted_csv/insect_wings_occurrences_3839.csv (325 lines)
[INFO] [2021-04-29 16:29:12] ...measurements (/app/public/data/insect_wings/measurementsorfacts.txt)
[INFO] [2021-04-29 16:29:12] Valid: /app/public/converted_csv/insect_wings_measurements_3839.csv (528 lines)
[STOP] [2021-04-29 16:29:12] validate_each_file
[START] [2021-04-29 16:29:12] convert_to_csv
[INFO] [2021-04-29 16:29:12] Looping over 3 formats...
[INFO] [2021-04-29 16:29:12] ...nodes (/app/public/data/insect_wings/taxa.txt)
[CMD] [2021-04-29 16:29:12] /usr/bin/sort /app/public/converted_csv/insect_wings_nodes_3839.csv > /app/public/converted_csv/insect_wings_nodes_3839.csv_sorted
[INFO] [2021-04-29 16:29:12] Converted: /app/public/converted_csv/insect_wings_nodes_3839.csv (311 lines)
[INFO] [2021-04-29 16:29:12] ...occurrences (/app/public/data/insect_wings/occurrences.txt)
[CMD] [2021-04-29 16:29:12] /usr/bin/sort /app/public/converted_csv/insect_wings_occurrences_3839.csv > /app/public/converted_csv/insect_wings_occurrences_3839.csv_sorted
[INFO] [2021-04-29 16:29:12] Converted: /app/public/converted_csv/insect_wings_occurrences_3839.csv (325 lines)
[INFO] [2021-04-29 16:29:12] ...measurements (/app/public/data/insect_wings/measurementsorfacts.txt)
[CMD] [2021-04-29 16:29:12] /usr/bin/sort /app/public/converted_csv/insect_wings_measurements_3839.csv > /app/public/converted_csv/insect_wings_measurements_3839.csv_sorted
[INFO] [2021-04-29 16:29:12] Converted: /app/public/converted_csv/insect_wings_measurements_3839.csv (528 lines)
[STOP] [2021-04-29 16:29:12] convert_to_csv
[START] [2021-04-29 16:29:12] calculate_delta
[INFO] [2021-04-29 16:29:12] Looping over 3 formats...
[INFO] [2021-04-29 16:29:12] ...nodes (/app/public/data/insect_wings/taxa.txt)
[CMD] [2021-04-29 16:29:12] echo "0a" > /app/public/diff/insect_wings_nodes_3839.diff
[CMD] [2021-04-29 16:29:12] tail -n +1 /app/public/converted_csv/insect_wings_nodes_3839.csv >> /app/public/diff/insect_wings_nodes_3839.diff
[CMD] [2021-04-29 16:29:12] echo "." >> /app/public/diff/insect_wings_nodes_3839.diff
[INFO] [2021-04-29 16:29:12] Created diff: /app/public/diff/insect_wings_nodes_3839.diff (313 lines)
[INFO] [2021-04-29 16:29:12] ...occurrences (/app/public/data/insect_wings/occurrences.txt)
[CMD] [2021-04-29 16:29:12] echo "0a" > /app/public/diff/insect_wings_occurrences_3839.diff
[CMD] [2021-04-29 16:29:12] tail -n +1 /app/public/converted_csv/insect_wings_occurrences_3839.csv >> /app/public/diff/insect_wings_occurrences_3839.diff
[CMD] [2021-04-29 16:29:12] echo "." >> /app/public/diff/insect_wings_occurrences_3839.diff
[INFO] [2021-04-29 16:29:12] Created diff: /app/public/diff/insect_wings_occurrences_3839.diff (327 lines)
[INFO] [2021-04-29 16:29:12] ...measurements (/app/public/data/insect_wings/measurementsorfacts.txt)
[CMD] [2021-04-29 16:29:12] echo "0a" > /app/public/diff/insect_wings_measurements_3839.diff
[CMD] [2021-04-29 16:29:12] tail -n +1 /app/public/converted_csv/insect_wings_measurements_3839.csv >> /app/public/diff/insect_wings_measurements_3839.diff
[CMD] [2021-04-29 16:29:12] echo "." >> /app/public/diff/insect_wings_measurements_3839.diff
[INFO] [2021-04-29 16:29:12] Created diff: /app/public/diff/insect_wings_measurements_3839.diff (530 lines)
[STOP] [2021-04-29 16:29:12] calculate_delta
[START] [2021-04-29 16:29:12] parse_diff_and_store
[INFO] [2021-04-29 16:29:12] Handling diff: /app/public/diff/insect_wings_nodes_3839.diff (313 lines)
[INFO] [2021-04-29 16:29:12] Loading nodes diff file into memory (313 /app/public/diff/insect_wings_nodes_3839.diff lines)...
[INFO] [2021-04-29 16:29:12] Handling diff: /app/public/diff/insect_wings_occurrences_3839.diff (327 lines)
[INFO] [2021-04-29 16:29:12] Loading occurrences diff file into memory (327 /app/public/diff/insect_wings_occurrences_3839.diff lines)...
[INFO] [2021-04-29 16:29:14] Handling diff: /app/public/diff/insect_wings_measurements_3839.diff (530 lines)
[INFO] [2021-04-29 16:29:14] Loading measurements diff file into memory (530 /app/public/diff/insect_wings_measurements_3839.diff lines)...
[INFO] [2021-04-29 16:29:14] Storing 311 ScientificNames
[INFO] [2021-04-29 16:29:14] Processing group of 311 in 1 groups of 1000
[INFO] [2021-04-29 16:29:14] Average Time: 0.23
[INFO] [2021-04-29 16:29:14] Total Time: 1s
[INFO] [2021-04-29 16:29:14] Storing 311 Nodes
[INFO] [2021-04-29 16:29:14] Processing group of 311 in 1 groups of 1000
[INFO] [2021-04-29 16:29:15] Average Time: 0.33
[INFO] [2021-04-29 16:29:15] Total Time: 1s
[INFO] [2021-04-29 16:29:15] Storing 325 Occurrences
[INFO] [2021-04-29 16:29:15] Processing group of 325 in 1 groups of 1000
[INFO] [2021-04-29 16:29:15] Average Time: 0.14
[INFO] [2021-04-29 16:29:15] Total Time: 1s
[INFO] [2021-04-29 16:29:15] Storing 528 OccurrenceMetadata
[INFO] [2021-04-29 16:29:15] Processing group of 528 in 1 groups of 1000
[INFO] [2021-04-29 16:29:15] Average Time: 0.07
[INFO] [2021-04-29 16:29:15] Total Time: 1s
[INFO] [2021-04-29 16:29:15] Storing 528 Traits
[INFO] [2021-04-29 16:29:15] Processing group of 528 in 1 groups of 1000
[INFO] [2021-04-29 16:29:15] Average Time: 0.39
[INFO] [2021-04-29 16:29:15] Total Time: 1s
[INFO] [2021-04-29 16:29:15] Storing 329 MetaTraits
[INFO] [2021-04-29 16:29:15] Processing group of 329 in 1 groups of 1000
[INFO] [2021-04-29 16:29:15] Average Time: 0.04
[INFO] [2021-04-29 16:29:15] Total Time: 1s
[STOP] [2021-04-29 16:29:15] parse_diff_and_store
[START] [2021-04-29 16:29:15] resolve_keys
[INFO] [2021-04-29 16:29:23] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-29 16:29:23] traits to occurrences...
[INFO] [2021-04-29 16:29:23] traits to nodes (through occurrences)...
[INFO] [2021-04-29 16:29:23] Traits to sex term...
[INFO] [2021-04-29 16:29:23] Traits to lifestage term...
[INFO] [2021-04-29 16:29:23] MetaTraits to traits...
[INFO] [2021-04-29 16:29:23] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-29 16:29:23] Assocs to occurrences...
[INFO] [2021-04-29 16:29:23] Assocs to nodes...
[INFO] [2021-04-29 16:29:23] Assoc to sex term...
[INFO] [2021-04-29 16:29:23] Assoc to lifestage term...
[INFO] [2021-04-29 16:29:23] MetaAssoc to assocs...
[STOP] [2021-04-29 16:29:23] resolve_keys
[START] [2021-04-29 16:29:23] hold_for_later_1
[STOP] [2021-04-29 16:29:23] hold_for_later_1
[START] [2021-04-29 16:29:23] hold_for_later_2
[STOP] [2021-04-29 16:29:23] hold_for_later_2
[START] [2021-04-29 16:29:23] resolve_missing_parents
[STOP] [2021-04-29 16:29:23] resolve_missing_parents
[START] [2021-04-29 16:29:23] rebuild_nodes
[START] [2021-04-29 16:29:23] Flattener#flatten
[START] [2021-04-29 16:29:23] Flattener#study_resource
[START] [2021-04-29 16:29:23] Flattener#build_ancestry
[STOP] [2021-04-29 16:29:23] Flattener#build_ancestry
[INFO] [2021-04-29 16:29:23] 311 ancestry keys
[START] [2021-04-29 16:29:23] build_node_ancestors
[INFO] [2021-04-29 16:29:23] old ancestors deleted.
[STOP] [2021-04-29 16:29:23] build_node_ancestors
[WARN] [2021-04-29 16:29:23] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-29 16:29:23] Flattener#flatten
[STOP] [2021-04-29 16:29:23] rebuild_nodes
[START] [2021-04-29 16:29:23] resolve_missing_media_owners
[STOP] [2021-04-29 16:29:23] resolve_missing_media_owners
[START] [2021-04-29 16:29:23] sanitize_media_verbatims
[STOP] [2021-04-29 16:29:23] sanitize_media_verbatims
[START] [2021-04-29 16:29:23] queue_downloads
[STOP] [2021-04-29 16:29:23] queue_downloads
[START] [2021-04-29 16:29:23] parse_names
[WARN] [2021-04-29 16:29:23] I see 311 names which still need to be parsed.
[STOP] [2021-04-29 16:29:25] parse_names
[START] [2021-04-29 16:29:25] denormalize_canonical_names_to_nodes
[STOP] [2021-04-29 16:29:25] denormalize_canonical_names_to_nodes
[START] [2021-04-29 16:29:25] match_nodes
[START] [2021-04-29 16:29:25] map_all_nodes_to_pages
[STOP] [2021-04-29 16:29:25] map_all_nodes_to_pages
[INFO] [2021-04-29 16:29:25] ZERO unmatched nodes (of 311)! Nicely done.
[START] [2021-04-29 16:29:25] update_nodes
[STOP] [2021-04-29 16:29:25] update_nodes
[STOP] [2021-04-29 16:29:25] match_nodes
[START] [2021-04-29 16:29:25] reindex_search
[STOP] [2021-04-29 16:29:25] reindex_search
[START] [2021-04-29 16:29:25] normalize_units
[STOP] [2021-04-29 16:29:25] normalize_units
[START] [2021-04-29 16:29:25] calculate_statistics
[2021-04-29 16:29:25] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-29 16:29:25] calculate_statistics
[START] [2021-04-29 16:29:25] complete_harvest_instance
[START] [2021-04-29 16:29:25] overall_tsv_creation
[INFO] [2021-04-29 16:29:25] Processing group of 311 in 1 batches of 10000
[INFO] [2021-04-29 16:30:06] 328 Traits (unfiltered)...
[INFO] [2021-04-29 16:30:41] 328 Traits (filtered)...
[INFO] [2021-04-29 16:30:41] 0 Associations (filtered)...
[INFO] [2021-04-29 16:30:41] 216 metadata added.
[INFO] [2021-04-29 16:30:41] 0 metadata added.
[INFO] [2021-04-29 16:31:08] Average Time: 79.22
[INFO] [2021-04-29 16:31:08] Total Time: 1m43s
[STOP] [2021-04-29 16:31:08] overall_tsv_creation
[INFO] [2021-04-29 16:31:08] Done. Check your files:
[INFO] [2021-04-29 16:31:08] (311 lines) /app/public/data/insect_wings/publish_nodes.tsv
[INFO] [2021-04-29 16:31:08] (311 lines) /app/public/data/insect_wings/publish_scientific_names.tsv
[INFO] [2021-04-29 16:31:08] (329 lines) /app/public/data/insect_wings/publish_traits.tsv
[INFO] [2021-04-29 16:31:08] (217 lines) /app/public/data/insect_wings/publish_metadata.tsv
[STOP] [2021-04-29 16:31:08] complete_harvest_instance
[START] [2021-04-29 16:31:08] completed
[STOP] [2021-04-29 16:31:08] completed
[STOP] [2021-04-29 16:31:08] logged process, took 115.76
[INFO] [2021-04-29 17:21:13] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-29 17:21:17] ## remove_type: ScientificName
[INFO] [2021-04-29 17:21:17] ++ Calling delete_all on 311 instances...
[INFO] [2021-04-29 17:21:17] [17:21:17.270] Removed 311 Scientificnames
[INFO] [2021-04-29 17:21:17] ## remove_type: Vernacular
[INFO] [2021-04-29 17:21:17] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 17:21:17] [17:21:17.271] Removed 0 Vernaculars
[INFO] [2021-04-29 17:21:17] ## remove_type: Article
[INFO] [2021-04-29 17:21:17] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 17:21:17] [17:21:17.272] Removed 0 Articles
[INFO] [2021-04-29 17:21:17] ## remove_type: Medium
[INFO] [2021-04-29 17:21:17] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 17:21:17] [17:21:17.274] Removed 0 Media
[INFO] [2021-04-29 17:21:17] ## remove_type: Trait
[INFO] [2021-04-29 17:21:17] ++ Calling delete_all on 528 instances...
[INFO] [2021-04-29 17:21:17] [17:21:17.317] Removed 528 Traits
[INFO] [2021-04-29 17:21:17] ## remove_type: MetaTrait
[INFO] [2021-04-29 17:21:17] ++ Calling delete_all on 329 instances...
[INFO] [2021-04-29 17:21:17] [17:21:17.321] Removed 329 Metatraits
[INFO] [2021-04-29 17:21:17] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-29 17:21:17] ++ Calling delete_all on 528 instances...
[INFO] [2021-04-29 17:21:17] [17:21:17.329] Removed 528 Occurrencemetadata
[INFO] [2021-04-29 17:21:17] ## remove_type: Assoc
[INFO] [2021-04-29 17:21:17] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 17:21:17] [17:21:17.330] Removed 0 Assocs
[INFO] [2021-04-29 17:21:17] ## remove_type: MetaAssoc
[INFO] [2021-04-29 17:21:17] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 17:21:17] [17:21:17.332] Removed 0 Metaassocs
[INFO] [2021-04-29 17:21:17] ## remove_type: Identifier
[INFO] [2021-04-29 17:21:17] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 17:21:17] [17:21:17.333] Removed 0 Identifiers
[INFO] [2021-04-29 17:21:17] ## remove_type: Reference
[INFO] [2021-04-29 17:21:17] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 17:21:17] [17:21:17.334] Removed 0 References
[INFO] [2021-04-29 17:21:17] Starting batch with ID 93345482...
[INFO] [2021-04-29 17:21:17] Starting batch with ID 93345482...
[INFO] [2021-04-29 17:21:17] Starting batch with ID 93345482...
[INFO] [2021-04-29 17:21:17] ## remove_type: Node
[INFO] [2021-04-29 17:21:17] ++ Calling delete_all on 311 instances...
[INFO] [2021-04-29 17:21:17] [17:21:17.505] Removed 311 Nodes
[START] [2021-04-29 17:21:17] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-29 17:21:17] Creating resource from OpenData
[START] [2021-04-29 17:21:17] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-29 17:21:17] Parse meta.xml file and create formats with fields
[STOP] [2021-04-29 17:21:17] Parse meta.xml file and create formats with fields
[STOP] [2021-04-29 17:21:17] Creating resource from OpenData
[START] [2021-04-29 17:21:17] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-29 17:21:17] create_harvest_instance
[INFO] [2021-04-29 17:21:17] Created harvest instance #3840
[STOP] [2021-04-29 17:21:17] create_harvest_instance
[START] [2021-04-29 17:21:17] fetch_files
[STOP] [2021-04-29 17:21:17] fetch_files
[START] [2021-04-29 17:21:17] validate_each_file
[INFO] [2021-04-29 17:21:17] Looping over 3 formats...
[INFO] [2021-04-29 17:21:17] ...nodes (/app/public/data/insect_wings/taxa.txt)
[INFO] [2021-04-29 17:21:17] Valid: /app/public/converted_csv/insect_wings_nodes_3840.csv (311 lines)
[INFO] [2021-04-29 17:21:17] ...occurrences (/app/public/data/insect_wings/occurrences.txt)
[INFO] [2021-04-29 17:21:17] Valid: /app/public/converted_csv/insect_wings_occurrences_3840.csv (326 lines)
[INFO] [2021-04-29 17:21:17] ...measurements (/app/public/data/insect_wings/measurementsorfacts.txt)
[INFO] [2021-04-29 17:21:17] Valid: /app/public/converted_csv/insect_wings_measurements_3840.csv (530 lines)
[STOP] [2021-04-29 17:21:17] validate_each_file
[START] [2021-04-29 17:21:17] convert_to_csv
[INFO] [2021-04-29 17:21:17] Looping over 3 formats...
[INFO] [2021-04-29 17:21:17] ...nodes (/app/public/data/insect_wings/taxa.txt)
[CMD] [2021-04-29 17:21:17] /usr/bin/sort /app/public/converted_csv/insect_wings_nodes_3840.csv > /app/public/converted_csv/insect_wings_nodes_3840.csv_sorted
[INFO] [2021-04-29 17:21:17] Converted: /app/public/converted_csv/insect_wings_nodes_3840.csv (311 lines)
[INFO] [2021-04-29 17:21:17] ...occurrences (/app/public/data/insect_wings/occurrences.txt)
[CMD] [2021-04-29 17:21:17] /usr/bin/sort /app/public/converted_csv/insect_wings_occurrences_3840.csv > /app/public/converted_csv/insect_wings_occurrences_3840.csv_sorted
[INFO] [2021-04-29 17:21:17] Converted: /app/public/converted_csv/insect_wings_occurrences_3840.csv (326 lines)
[INFO] [2021-04-29 17:21:17] ...measurements (/app/public/data/insect_wings/measurementsorfacts.txt)
[CMD] [2021-04-29 17:21:17] /usr/bin/sort /app/public/converted_csv/insect_wings_measurements_3840.csv > /app/public/converted_csv/insect_wings_measurements_3840.csv_sorted
[INFO] [2021-04-29 17:21:18] Converted: /app/public/converted_csv/insect_wings_measurements_3840.csv (530 lines)
[STOP] [2021-04-29 17:21:18] convert_to_csv
[START] [2021-04-29 17:21:18] calculate_delta
[INFO] [2021-04-29 17:21:18] Looping over 3 formats...
[INFO] [2021-04-29 17:21:18] ...nodes (/app/public/data/insect_wings/taxa.txt)
[CMD] [2021-04-29 17:21:18] echo "0a" > /app/public/diff/insect_wings_nodes_3840.diff
[CMD] [2021-04-29 17:21:18] tail -n +1 /app/public/converted_csv/insect_wings_nodes_3840.csv >> /app/public/diff/insect_wings_nodes_3840.diff
[CMD] [2021-04-29 17:21:18] echo "." >> /app/public/diff/insect_wings_nodes_3840.diff
[INFO] [2021-04-29 17:21:18] Created diff: /app/public/diff/insect_wings_nodes_3840.diff (313 lines)
[INFO] [2021-04-29 17:21:18] ...occurrences (/app/public/data/insect_wings/occurrences.txt)
[CMD] [2021-04-29 17:21:18] echo "0a" > /app/public/diff/insect_wings_occurrences_3840.diff
[CMD] [2021-04-29 17:21:18] tail -n +1 /app/public/converted_csv/insect_wings_occurrences_3840.csv >> /app/public/diff/insect_wings_occurrences_3840.diff
[CMD] [2021-04-29 17:21:18] echo "." >> /app/public/diff/insect_wings_occurrences_3840.diff
[INFO] [2021-04-29 17:21:18] Created diff: /app/public/diff/insect_wings_occurrences_3840.diff (328 lines)
[INFO] [2021-04-29 17:21:18] ...measurements (/app/public/data/insect_wings/measurementsorfacts.txt)
[CMD] [2021-04-29 17:21:18] echo "0a" > /app/public/diff/insect_wings_measurements_3840.diff
[CMD] [2021-04-29 17:21:18] tail -n +1 /app/public/converted_csv/insect_wings_measurements_3840.csv >> /app/public/diff/insect_wings_measurements_3840.diff
[CMD] [2021-04-29 17:21:18] echo "." >> /app/public/diff/insect_wings_measurements_3840.diff
[INFO] [2021-04-29 17:21:18] Created diff: /app/public/diff/insect_wings_measurements_3840.diff (532 lines)
[STOP] [2021-04-29 17:21:18] calculate_delta
[START] [2021-04-29 17:21:18] parse_diff_and_store
[INFO] [2021-04-29 17:21:18] Handling diff: /app/public/diff/insect_wings_nodes_3840.diff (313 lines)
[INFO] [2021-04-29 17:21:18] Loading nodes diff file into memory (313 /app/public/diff/insect_wings_nodes_3840.diff lines)...
[INFO] [2021-04-29 17:21:18] Handling diff: /app/public/diff/insect_wings_occurrences_3840.diff (328 lines)
[INFO] [2021-04-29 17:21:18] Loading occurrences diff file into memory (328 /app/public/diff/insect_wings_occurrences_3840.diff lines)...
[INFO] [2021-04-29 17:21:18] Handling diff: /app/public/diff/insect_wings_measurements_3840.diff (532 lines)
[INFO] [2021-04-29 17:21:18] Loading measurements diff file into memory (532 /app/public/diff/insect_wings_measurements_3840.diff lines)...
[INFO] [2021-04-29 17:21:18] Storing 311 ScientificNames
[INFO] [2021-04-29 17:21:18] Processing group of 311 in 1 groups of 1000
[INFO] [2021-04-29 17:21:18] Average Time: 0.1
[INFO] [2021-04-29 17:21:18] Total Time: 1s
[INFO] [2021-04-29 17:21:18] Storing 311 Nodes
[INFO] [2021-04-29 17:21:18] Processing group of 311 in 1 groups of 1000
[INFO] [2021-04-29 17:21:18] Average Time: 0.12
[INFO] [2021-04-29 17:21:18] Total Time: 1s
[INFO] [2021-04-29 17:21:18] Storing 326 Occurrences
[INFO] [2021-04-29 17:21:18] Processing group of 326 in 1 groups of 1000
[INFO] [2021-04-29 17:21:18] Average Time: 0.05
[INFO] [2021-04-29 17:21:18] Total Time: 1s
[INFO] [2021-04-29 17:21:18] Storing 531 OccurrenceMetadata
[INFO] [2021-04-29 17:21:18] Processing group of 531 in 1 groups of 1000
[INFO] [2021-04-29 17:21:18] Average Time: 0.07
[INFO] [2021-04-29 17:21:18] Total Time: 1s
[INFO] [2021-04-29 17:21:18] Storing 530 Traits
[INFO] [2021-04-29 17:21:18] Processing group of 530 in 1 groups of 1000
[INFO] [2021-04-29 17:21:19] Average Time: 0.19
[INFO] [2021-04-29 17:21:19] Total Time: 1s
[INFO] [2021-04-29 17:21:19] Storing 330 MetaTraits
[INFO] [2021-04-29 17:21:19] Processing group of 330 in 1 groups of 1000
[INFO] [2021-04-29 17:21:19] Average Time: 0.04
[INFO] [2021-04-29 17:21:19] Total Time: 1s
[STOP] [2021-04-29 17:21:19] parse_diff_and_store
[START] [2021-04-29 17:21:19] resolve_keys
[INFO] [2021-04-29 17:21:24] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-29 17:21:24] traits to occurrences...
[INFO] [2021-04-29 17:21:24] traits to nodes (through occurrences)...
[INFO] [2021-04-29 17:21:24] Traits to sex term...
[INFO] [2021-04-29 17:21:25] Traits to lifestage term...
[INFO] [2021-04-29 17:21:25] MetaTraits to traits...
[INFO] [2021-04-29 17:21:25] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-29 17:21:25] Assocs to occurrences...
[INFO] [2021-04-29 17:21:25] Assocs to nodes...
[INFO] [2021-04-29 17:21:25] Assoc to sex term...
[INFO] [2021-04-29 17:21:25] Assoc to lifestage term...
[INFO] [2021-04-29 17:21:25] MetaAssoc to assocs...
[STOP] [2021-04-29 17:21:25] resolve_keys
[START] [2021-04-29 17:21:25] hold_for_later_1
[STOP] [2021-04-29 17:21:25] hold_for_later_1
[START] [2021-04-29 17:21:25] hold_for_later_2
[STOP] [2021-04-29 17:21:25] hold_for_later_2
[START] [2021-04-29 17:21:25] resolve_missing_parents
[STOP] [2021-04-29 17:21:25] resolve_missing_parents
[START] [2021-04-29 17:21:25] rebuild_nodes
[START] [2021-04-29 17:21:25] Flattener#flatten
[START] [2021-04-29 17:21:25] Flattener#study_resource
[START] [2021-04-29 17:21:25] Flattener#build_ancestry
[STOP] [2021-04-29 17:21:25] Flattener#build_ancestry
[INFO] [2021-04-29 17:21:25] 311 ancestry keys
[START] [2021-04-29 17:21:25] build_node_ancestors
[INFO] [2021-04-29 17:21:25] old ancestors deleted.
[STOP] [2021-04-29 17:21:25] build_node_ancestors
[WARN] [2021-04-29 17:21:25] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-29 17:21:25] Flattener#flatten
[STOP] [2021-04-29 17:21:25] rebuild_nodes
[START] [2021-04-29 17:21:25] resolve_missing_media_owners
[STOP] [2021-04-29 17:21:25] resolve_missing_media_owners
[START] [2021-04-29 17:21:25] sanitize_media_verbatims
[STOP] [2021-04-29 17:21:25] sanitize_media_verbatims
[START] [2021-04-29 17:21:25] queue_downloads
[STOP] [2021-04-29 17:21:25] queue_downloads
[START] [2021-04-29 17:21:25] parse_names
[WARN] [2021-04-29 17:21:25] I see 311 names which still need to be parsed.
[STOP] [2021-04-29 17:21:26] parse_names
[START] [2021-04-29 17:21:26] denormalize_canonical_names_to_nodes
[STOP] [2021-04-29 17:21:26] denormalize_canonical_names_to_nodes
[START] [2021-04-29 17:21:26] match_nodes
[START] [2021-04-29 17:21:26] map_all_nodes_to_pages
[STOP] [2021-04-29 17:21:26] map_all_nodes_to_pages
[INFO] [2021-04-29 17:21:26] ZERO unmatched nodes (of 311)! Nicely done.
[START] [2021-04-29 17:21:26] update_nodes
[STOP] [2021-04-29 17:21:26] update_nodes
[STOP] [2021-04-29 17:21:26] match_nodes
[START] [2021-04-29 17:21:26] reindex_search
[STOP] [2021-04-29 17:21:27] reindex_search
[START] [2021-04-29 17:21:27] normalize_units
[STOP] [2021-04-29 17:21:27] normalize_units
[START] [2021-04-29 17:21:27] calculate_statistics
[2021-04-29 17:21:27] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-29 17:21:27] calculate_statistics
[START] [2021-04-29 17:21:27] complete_harvest_instance
[START] [2021-04-29 17:21:27] overall_tsv_creation
[INFO] [2021-04-29 17:21:27] Processing group of 311 in 1 batches of 10000
[INFO] [2021-04-29 17:22:04] 329 Traits (unfiltered)...
[INFO] [2021-04-29 17:22:39] 329 Traits (filtered)...
[INFO] [2021-04-29 17:22:39] 0 Associations (filtered)...
[INFO] [2021-04-29 17:22:39] 217 metadata added.
[INFO] [2021-04-29 17:22:39] 0 metadata added.
[INFO] [2021-04-29 17:23:05] Average Time: 75.66
[INFO] [2021-04-29 17:23:05] Total Time: 1m39s
[STOP] [2021-04-29 17:23:05] overall_tsv_creation
[INFO] [2021-04-29 17:23:05] Done. Check your files:
[INFO] [2021-04-29 17:23:05] (311 lines) /app/public/data/insect_wings/publish_nodes.tsv
[INFO] [2021-04-29 17:23:05] (311 lines) /app/public/data/insect_wings/publish_scientific_names.tsv
[INFO] [2021-04-29 17:23:05] (330 lines) /app/public/data/insect_wings/publish_traits.tsv
[INFO] [2021-04-29 17:23:05] (218 lines) /app/public/data/insect_wings/publish_metadata.tsv
[STOP] [2021-04-29 17:23:05] complete_harvest_instance
[START] [2021-04-29 17:23:05] completed
[STOP] [2021-04-29 17:23:05] completed
[STOP] [2021-04-29 17:23:05] logged process, took 107.83
[INFO] [2021-05-03 13:39:16] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-05-03 13:39:20] ## remove_type: ScientificName
[INFO] [2021-05-03 13:39:20] ++ Calling delete_all on 311 instances...
[INFO] [2021-05-03 13:39:20] [13:39:20.203] Removed 311 Scientificnames
[INFO] [2021-05-03 13:39:20] ## remove_type: Vernacular
[INFO] [2021-05-03 13:39:20] ++ Calling delete_all on 0 instances...
[INFO] [2021-05-03 13:39:20] [13:39:20.205] Removed 0 Vernaculars
[INFO] [2021-05-03 13:39:20] ## remove_type: Article
[INFO] [2021-05-03 13:39:20] ++ Calling delete_all on 0 instances...
[INFO] [2021-05-03 13:39:20] [13:39:20.206] Removed 0 Articles
[INFO] [2021-05-03 13:39:20] ## remove_type: Medium
[INFO] [2021-05-03 13:39:20] ++ Calling delete_all on 0 instances...
[INFO] [2021-05-03 13:39:20] [13:39:20.208] Removed 0 Media
[INFO] [2021-05-03 13:39:20] ## remove_type: Trait
[INFO] [2021-05-03 13:39:20] ++ Calling delete_all on 530 instances...
[INFO] [2021-05-03 13:39:20] [13:39:20.224] Removed 530 Traits
[INFO] [2021-05-03 13:39:20] ## remove_type: MetaTrait
[INFO] [2021-05-03 13:39:20] ++ Calling delete_all on 330 instances...
[INFO] [2021-05-03 13:39:20] [13:39:20.229] Removed 330 Metatraits
[INFO] [2021-05-03 13:39:20] ## remove_type: OccurrenceMetadatum
[INFO] [2021-05-03 13:39:20] ++ Calling delete_all on 531 instances...
[INFO] [2021-05-03 13:39:20] [13:39:20.238] Removed 531 Occurrencemetadata
[INFO] [2021-05-03 13:39:20] ## remove_type: Assoc
[INFO] [2021-05-03 13:39:20] ++ Calling delete_all on 0 instances...
[INFO] [2021-05-03 13:39:20] [13:39:20.240] Removed 0 Assocs
[INFO] [2021-05-03 13:39:20] ## remove_type: MetaAssoc
[INFO] [2021-05-03 13:39:20] ++ Calling delete_all on 0 instances...
[INFO] [2021-05-03 13:39:20] [13:39:20.241] Removed 0 Metaassocs
[INFO] [2021-05-03 13:39:20] ## remove_type: Identifier
[INFO] [2021-05-03 13:39:20] ++ Calling delete_all on 0 instances...
[INFO] [2021-05-03 13:39:20] [13:39:20.243] Removed 0 Identifiers
[INFO] [2021-05-03 13:39:20] ## remove_type: Reference
[INFO] [2021-05-03 13:39:20] ++ Calling delete_all on 0 instances...
[INFO] [2021-05-03 13:39:20] [13:39:20.244] Removed 0 References
[INFO] [2021-05-03 13:39:20] Starting batch with ID 93345789...
[INFO] [2021-05-03 13:39:20] Starting batch with ID 93345789...
[INFO] [2021-05-03 13:39:20] ## remove_type: Node
[INFO] [2021-05-03 13:39:20] ++ Calling delete_all on 311 instances...
[INFO] [2021-05-03 13:39:20] [13:39:20.502] Removed 311 Nodes
[START] [2021-05-03 13:39:20] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-05-03 13:39:20] Creating resource from OpenData
[START] [2021-05-03 13:39:21] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-05-03 13:39:21] Parse meta.xml file and create formats with fields
[STOP] [2021-05-03 13:39:21] Parse meta.xml file and create formats with fields
[STOP] [2021-05-03 13:39:21] Creating resource from OpenData
[START] [2021-05-03 13:39:21] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-05-03 13:39:21] create_harvest_instance
[INFO] [2021-05-03 13:39:21] Created harvest instance #3841
[STOP] [2021-05-03 13:39:21] create_harvest_instance
[START] [2021-05-03 13:39:21] fetch_files
[STOP] [2021-05-03 13:39:21] fetch_files
[START] [2021-05-03 13:39:21] validate_each_file
[INFO] [2021-05-03 13:39:21] Looping over 3 formats...
[INFO] [2021-05-03 13:39:21] ...nodes (/app/public/data/insect_wings/taxa.txt)
[INFO] [2021-05-03 13:39:21] Valid: /app/public/converted_csv/insect_wings_nodes_3841.csv (312 lines)
[INFO] [2021-05-03 13:39:21] ...occurrences (/app/public/data/insect_wings/occurrences.txt)
[INFO] [2021-05-03 13:39:21] Valid: /app/public/converted_csv/insect_wings_occurrences_3841.csv (327 lines)
[INFO] [2021-05-03 13:39:21] ...measurements (/app/public/data/insect_wings/measurementsorfacts.txt)
[INFO] [2021-05-03 13:39:21] Valid: /app/public/converted_csv/insect_wings_measurements_3841.csv (532 lines)
[STOP] [2021-05-03 13:39:21] validate_each_file
[START] [2021-05-03 13:39:21] convert_to_csv
[INFO] [2021-05-03 13:39:21] Looping over 3 formats...
[INFO] [2021-05-03 13:39:21] ...nodes (/app/public/data/insect_wings/taxa.txt)
[CMD] [2021-05-03 13:39:21] /usr/bin/sort /app/public/converted_csv/insect_wings_nodes_3841.csv > /app/public/converted_csv/insect_wings_nodes_3841.csv_sorted
[INFO] [2021-05-03 13:39:21] Converted: /app/public/converted_csv/insect_wings_nodes_3841.csv (312 lines)
[INFO] [2021-05-03 13:39:21] ...occurrences (/app/public/data/insect_wings/occurrences.txt)
[CMD] [2021-05-03 13:39:21] /usr/bin/sort /app/public/converted_csv/insect_wings_occurrences_3841.csv > /app/public/converted_csv/insect_wings_occurrences_3841.csv_sorted
[INFO] [2021-05-03 13:39:21] Converted: /app/public/converted_csv/insect_wings_occurrences_3841.csv (327 lines)
[INFO] [2021-05-03 13:39:21] ...measurements (/app/public/data/insect_wings/measurementsorfacts.txt)
[CMD] [2021-05-03 13:39:21] /usr/bin/sort /app/public/converted_csv/insect_wings_measurements_3841.csv > /app/public/converted_csv/insect_wings_measurements_3841.csv_sorted
[INFO] [2021-05-03 13:39:21] Converted: /app/public/converted_csv/insect_wings_measurements_3841.csv (532 lines)
[STOP] [2021-05-03 13:39:21] convert_to_csv
[START] [2021-05-03 13:39:21] calculate_delta
[INFO] [2021-05-03 13:39:21] Looping over 3 formats...
[INFO] [2021-05-03 13:39:21] ...nodes (/app/public/data/insect_wings/taxa.txt)
[CMD] [2021-05-03 13:39:21] echo "0a" > /app/public/diff/insect_wings_nodes_3841.diff
[CMD] [2021-05-03 13:39:21] tail -n +1 /app/public/converted_csv/insect_wings_nodes_3841.csv >> /app/public/diff/insect_wings_nodes_3841.diff
[CMD] [2021-05-03 13:39:21] echo "." >> /app/public/diff/insect_wings_nodes_3841.diff
[INFO] [2021-05-03 13:39:21] Created diff: /app/public/diff/insect_wings_nodes_3841.diff (314 lines)
[INFO] [2021-05-03 13:39:21] ...occurrences (/app/public/data/insect_wings/occurrences.txt)
[CMD] [2021-05-03 13:39:21] echo "0a" > /app/public/diff/insect_wings_occurrences_3841.diff
[CMD] [2021-05-03 13:39:21] tail -n +1 /app/public/converted_csv/insect_wings_occurrences_3841.csv >> /app/public/diff/insect_wings_occurrences_3841.diff
[CMD] [2021-05-03 13:39:21] echo "." >> /app/public/diff/insect_wings_occurrences_3841.diff
[INFO] [2021-05-03 13:39:21] Created diff: /app/public/diff/insect_wings_occurrences_3841.diff (329 lines)
[INFO] [2021-05-03 13:39:21] ...measurements (/app/public/data/insect_wings/measurementsorfacts.txt)
[CMD] [2021-05-03 13:39:21] echo "0a" > /app/public/diff/insect_wings_measurements_3841.diff
[CMD] [2021-05-03 13:39:21] tail -n +1 /app/public/converted_csv/insect_wings_measurements_3841.csv >> /app/public/diff/insect_wings_measurements_3841.diff
[CMD] [2021-05-03 13:39:21] echo "." >> /app/public/diff/insect_wings_measurements_3841.diff
[INFO] [2021-05-03 13:39:21] Created diff: /app/public/diff/insect_wings_measurements_3841.diff (534 lines)
[STOP] [2021-05-03 13:39:21] calculate_delta
[START] [2021-05-03 13:39:21] parse_diff_and_store
[INFO] [2021-05-03 13:39:21] Handling diff: /app/public/diff/insect_wings_nodes_3841.diff (314 lines)
[INFO] [2021-05-03 13:39:21] Loading nodes diff file into memory (314 /app/public/diff/insect_wings_nodes_3841.diff lines)...
[INFO] [2021-05-03 13:39:21] Handling diff: /app/public/diff/insect_wings_occurrences_3841.diff (329 lines)
[INFO] [2021-05-03 13:39:21] Loading occurrences diff file into memory (329 /app/public/diff/insect_wings_occurrences_3841.diff lines)...
[INFO] [2021-05-03 13:39:21] Handling diff: /app/public/diff/insect_wings_measurements_3841.diff (534 lines)
[INFO] [2021-05-03 13:39:21] Loading measurements diff file into memory (534 /app/public/diff/insect_wings_measurements_3841.diff lines)...
[INFO] [2021-05-03 13:39:22] Storing 312 ScientificNames
[INFO] [2021-05-03 13:39:22] Processing group of 312 in 1 groups of 1000
[INFO] [2021-05-03 13:39:22] Average Time: 0.12
[INFO] [2021-05-03 13:39:22] Total Time: 1s
[INFO] [2021-05-03 13:39:22] Storing 312 Nodes
[INFO] [2021-05-03 13:39:22] Processing group of 312 in 1 groups of 1000
[INFO] [2021-05-03 13:39:22] Average Time: 0.09
[INFO] [2021-05-03 13:39:22] Total Time: 1s
[INFO] [2021-05-03 13:39:22] Storing 327 Occurrences
[INFO] [2021-05-03 13:39:22] Processing group of 327 in 1 groups of 1000
[INFO] [2021-05-03 13:39:22] Average Time: 0.04
[INFO] [2021-05-03 13:39:22] Total Time: 1s
[INFO] [2021-05-03 13:39:22] Storing 532 OccurrenceMetadata
[INFO] [2021-05-03 13:39:22] Processing group of 532 in 1 groups of 1000
[INFO] [2021-05-03 13:39:22] Average Time: 0.06
[INFO] [2021-05-03 13:39:22] Total Time: 1s
[INFO] [2021-05-03 13:39:22] Storing 532 Traits
[INFO] [2021-05-03 13:39:22] Processing group of 532 in 1 groups of 1000
[INFO] [2021-05-03 13:39:22] Average Time: 0.14
[INFO] [2021-05-03 13:39:22] Total Time: 1s
[INFO] [2021-05-03 13:39:22] Storing 331 MetaTraits
[INFO] [2021-05-03 13:39:22] Processing group of 331 in 1 groups of 1000
[INFO] [2021-05-03 13:39:22] Average Time: 0.04
[INFO] [2021-05-03 13:39:22] Total Time: 1s
[STOP] [2021-05-03 13:39:22] parse_diff_and_store
[START] [2021-05-03 13:39:22] resolve_keys
[INFO] [2021-05-03 13:39:29] Occurrences to nodes (through scientific_names)...
[INFO] [2021-05-03 13:39:29] traits to occurrences...
[INFO] [2021-05-03 13:39:29] traits to nodes (through occurrences)...
[INFO] [2021-05-03 13:39:29] Traits to sex term...
[INFO] [2021-05-03 13:39:29] Traits to lifestage term...
[INFO] [2021-05-03 13:39:29] MetaTraits to traits...
[INFO] [2021-05-03 13:39:29] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-05-03 13:39:29] Assocs to occurrences...
[INFO] [2021-05-03 13:39:29] Assocs to nodes...
[INFO] [2021-05-03 13:39:29] Assoc to sex term...
[INFO] [2021-05-03 13:39:29] Assoc to lifestage term...
[INFO] [2021-05-03 13:39:29] MetaAssoc to assocs...
[STOP] [2021-05-03 13:39:29] resolve_keys
[START] [2021-05-03 13:39:29] hold_for_later_1
[STOP] [2021-05-03 13:39:29] hold_for_later_1
[START] [2021-05-03 13:39:29] hold_for_later_2
[STOP] [2021-05-03 13:39:29] hold_for_later_2
[START] [2021-05-03 13:39:29] resolve_missing_parents
[STOP] [2021-05-03 13:39:29] resolve_missing_parents
[START] [2021-05-03 13:39:29] rebuild_nodes
[START] [2021-05-03 13:39:29] Flattener#flatten
[START] [2021-05-03 13:39:29] Flattener#study_resource
[START] [2021-05-03 13:39:29] Flattener#build_ancestry
[STOP] [2021-05-03 13:39:29] Flattener#build_ancestry
[INFO] [2021-05-03 13:39:29] 312 ancestry keys
[START] [2021-05-03 13:39:29] build_node_ancestors
[INFO] [2021-05-03 13:39:29] old ancestors deleted.
[STOP] [2021-05-03 13:39:29] build_node_ancestors
[WARN] [2021-05-03 13:39:29] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-05-03 13:39:29] Flattener#flatten
[STOP] [2021-05-03 13:39:29] rebuild_nodes
[START] [2021-05-03 13:39:29] resolve_missing_media_owners
[STOP] [2021-05-03 13:39:29] resolve_missing_media_owners
[START] [2021-05-03 13:39:29] sanitize_media_verbatims
[STOP] [2021-05-03 13:39:29] sanitize_media_verbatims
[START] [2021-05-03 13:39:29] queue_downloads
[STOP] [2021-05-03 13:39:29] queue_downloads
[START] [2021-05-03 13:39:29] parse_names
[WARN] [2021-05-03 13:39:29] I see 312 names which still need to be parsed.
[STOP] [2021-05-03 13:39:30] parse_names
[START] [2021-05-03 13:39:30] denormalize_canonical_names_to_nodes
[STOP] [2021-05-03 13:39:30] denormalize_canonical_names_to_nodes
[START] [2021-05-03 13:39:30] match_nodes
[START] [2021-05-03 13:39:30] map_all_nodes_to_pages
[STOP] [2021-05-03 13:39:31] map_all_nodes_to_pages
[INFO] [2021-05-03 13:39:31] ZERO unmatched nodes (of 312)! Nicely done.
[START] [2021-05-03 13:39:31] update_nodes
[STOP] [2021-05-03 13:39:31] update_nodes
[STOP] [2021-05-03 13:39:31] match_nodes
[START] [2021-05-03 13:39:31] reindex_search
[STOP] [2021-05-03 13:39:31] reindex_search
[START] [2021-05-03 13:39:31] normalize_units
[STOP] [2021-05-03 13:39:31] normalize_units
[START] [2021-05-03 13:39:31] calculate_statistics
[2021-05-03 13:39:31] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-05-03 13:39:31] calculate_statistics
[START] [2021-05-03 13:39:31] complete_harvest_instance
[START] [2021-05-03 13:39:31] overall_tsv_creation
[INFO] [2021-05-03 13:39:31] Processing group of 312 in 1 batches of 10000
[INFO] [2021-05-03 13:41:34] 330 Traits (unfiltered)...
[INFO] [2021-05-03 13:42:12] 330 Traits (filtered)...
[INFO] [2021-05-03 13:42:12] 0 Associations (filtered)...
[INFO] [2021-05-03 13:42:12] 218 metadata added.
[INFO] [2021-05-03 13:42:12] 0 metadata added.
[INFO] [2021-05-03 13:42:39] Average Time: 89.32
[INFO] [2021-05-03 13:42:39] Total Time: 3m8s
[STOP] [2021-05-03 13:42:39] overall_tsv_creation
[INFO] [2021-05-03 13:42:39] Done. Check your files:
[INFO] [2021-05-03 13:42:39] (312 lines) /app/public/data/insect_wings/publish_nodes.tsv
[INFO] [2021-05-03 13:42:39] (312 lines) /app/public/data/insect_wings/publish_scientific_names.tsv
[INFO] [2021-05-03 13:42:39] (331 lines) /app/public/data/insect_wings/publish_traits.tsv
[INFO] [2021-05-03 13:42:39] (219 lines) /app/public/data/insect_wings/publish_metadata.tsv
[STOP] [2021-05-03 13:42:39] complete_harvest_instance
[START] [2021-05-03 13:42:39] completed
[STOP] [2021-05-03 13:42:39] completed
[STOP] [2021-05-03 13:42:39] logged process, took 197.88

Latest Process