Harvest for Jardine et al 2015 Created 16 Jun 13:07

Harvesting Log

# Logfile created on 2020-06-16 09:09:20 -0400 by logger.rb/v1.4.2
[INFO] [2020-06-16 09:09:20] ## HARVEST: type = -harvest
[START] [2020-06-16 09:09:21] logged process
[START] [2020-06-16 09:09:21] create_harvest_instance
[STOP] [2020-06-16 09:09:22] create_harvest_instance
[START] [2020-06-16 09:09:22] fetch_files
[STOP] [2020-06-16 09:09:22] fetch_files
[START] [2020-06-16 09:09:22] validate_each_file
[STOP] [2020-06-16 09:09:22] validate_each_file
[ERR] [2020-06-16 09:09:22] Exceptions::ColumnEmpty
[ERR] [2020-06-16 09:09:22] Illegal empty value for measurements/measurementType on line 2
[ERR] [2020-06-16 09:09:22] ../models/resource_harvester.rb:194:in `check_header'
[ERR] [2020-06-16 09:09:22] ../models/resource_harvester.rb:182:in `block (2 levels) in validate_csv'
[ERR] [2020-06-16 09:09:22] ../models/resource_harvester.rb:181:in `each'
[ERR] [2020-06-16 09:09:22] ../models/resource_harvester.rb:181:in `block in validate_csv'
[ERR] [2020-06-16 09:09:22] ../models/csv_parser.rb:81:in `block in rows_as_hashes'
[ERR] [2020-06-16 09:09:22] ../models/csv_parser.rb:26:in `block in line_at_a_time'
[ERR] [2020-06-16 09:09:22] ../models/csv_parser.rb:24:in `line_at_a_time'
[ERR] [2020-06-16 09:09:22] ../models/csv_parser.rb:77:in `rows_as_hashes'
[ERR] [2020-06-16 09:09:22] ../models/resource_harvester.rb:178:in `validate_csv'
[ERR] [2020-06-16 09:09:22] ../models/resource_harvester.rb:146:in `block (2 levels) in validate_each_file'
[ERR] [2020-06-16 09:09:22] ../models/resource_harvester.rb:145:in `block in validate_each_file'
[ERR] [2020-06-16 09:09:22] ../models/resource_harvester.rb:666:in `block in each_format'
[ERR] [2020-06-16 09:09:22] ../models/resource_harvester.rb:651:in `each_format'
[ERR] [2020-06-16 09:09:22] ../models/resource_harvester.rb:132:in `validate_each_file'
[ERR] [2020-06-16 09:09:22] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2020-06-16 09:09:22] ../models/logged_process.rb:19:in `run_step'
[ERR] [2020-06-16 09:09:22] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2020-06-16 09:09:22] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2020-06-16 09:09:22] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2020-06-16 09:09:22] ../models/resource.rb:151:in `lock'
[ERR] [2020-06-16 09:09:22] ../models/resource_harvester.rb:72:in `start'
[ERR] [2020-06-16 09:09:22] ../models/resource.rb:232:in `harvest'
[ERR] [2020-06-16 09:09:22] bin/rails:4:in `require'
[ERR] [2020-06-16 09:09:22] bin/rails:4:in `<main>'
[STOP] [2020-06-16 09:09:22] logged process, took 1.2
[INFO] [2020-06-16 09:11:31] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-06-16 09:11:34] ## remove_type: ScientificName
[INFO] [2020-06-16 09:11:34] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:11:34] [09:11:34.597] Removed 0 Scientificnames
[INFO] [2020-06-16 09:11:34] ## remove_type: Vernacular
[INFO] [2020-06-16 09:11:34] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:11:34] [09:11:34.600] Removed 0 Vernaculars
[INFO] [2020-06-16 09:11:34] ## remove_type: Article
[INFO] [2020-06-16 09:11:34] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:11:34] [09:11:34.603] Removed 0 Articles
[INFO] [2020-06-16 09:11:34] ## remove_type: Medium
[INFO] [2020-06-16 09:11:34] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:11:34] [09:11:34.607] Removed 0 Media
[INFO] [2020-06-16 09:11:34] ## remove_type: Trait
[INFO] [2020-06-16 09:11:34] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:11:34] [09:11:34.610] Removed 0 Traits
[INFO] [2020-06-16 09:11:34] ## remove_type: MetaTrait
[INFO] [2020-06-16 09:11:34] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:11:34] [09:11:34.613] Removed 0 Metatraits
[INFO] [2020-06-16 09:11:34] ## remove_type: OccurrenceMetadatum
[INFO] [2020-06-16 09:11:34] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:11:34] [09:11:34.616] Removed 0 Occurrencemetadata
[INFO] [2020-06-16 09:11:34] ## remove_type: Assoc
[INFO] [2020-06-16 09:11:34] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:11:34] [09:11:34.619] Removed 0 Assocs
[INFO] [2020-06-16 09:11:34] ## remove_type: MetaAssoc
[INFO] [2020-06-16 09:11:34] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:11:34] [09:11:34.622] Removed 0 Metaassocs
[INFO] [2020-06-16 09:11:34] ## remove_type: Identifier
[INFO] [2020-06-16 09:11:34] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:11:34] [09:11:34.625] Removed 0 Identifiers
[INFO] [2020-06-16 09:11:34] ## remove_type: Reference
[INFO] [2020-06-16 09:11:34] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:11:34] [09:11:34.628] Removed 0 References
[INFO] [2020-06-16 09:11:34] ## remove_type: Node
[INFO] [2020-06-16 09:11:34] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:11:34] [09:11:34.650] Removed 0 Nodes
[START] [2020-06-16 09:11:34] logged process
[START] [2020-06-16 09:11:34] Creating resource from OpenData
[START] [2020-06-16 09:11:35] logged process
[START] [2020-06-16 09:11:35] Parse meta.xml file and create formats with fields
[STOP] [2020-06-16 09:11:35] Parse meta.xml file and create formats with fields
[STOP] [2020-06-16 09:11:35] Creating resource from OpenData
[START] [2020-06-16 09:11:35] logged process
[START] [2020-06-16 09:11:35] create_harvest_instance
[STOP] [2020-06-16 09:11:36] create_harvest_instance
[START] [2020-06-16 09:11:36] fetch_files
[STOP] [2020-06-16 09:11:36] fetch_files
[START] [2020-06-16 09:11:36] validate_each_file
[STOP] [2020-06-16 09:11:36] validate_each_file
[ERR] [2020-06-16 09:11:36] Exceptions::ColumnEmpty
[ERR] [2020-06-16 09:11:36] Illegal empty value for measurements/measurementType on line 2
[ERR] [2020-06-16 09:11:36] ../models/resource_harvester.rb:194:in `check_header'
[ERR] [2020-06-16 09:11:36] ../models/resource_harvester.rb:182:in `block (2 levels) in validate_csv'
[ERR] [2020-06-16 09:11:36] ../models/resource_harvester.rb:181:in `each'
[ERR] [2020-06-16 09:11:36] ../models/resource_harvester.rb:181:in `block in validate_csv'
[ERR] [2020-06-16 09:11:36] ../models/csv_parser.rb:81:in `block in rows_as_hashes'
[ERR] [2020-06-16 09:11:36] ../models/csv_parser.rb:26:in `block in line_at_a_time'
[ERR] [2020-06-16 09:11:36] ../models/csv_parser.rb:24:in `line_at_a_time'
[ERR] [2020-06-16 09:11:36] ../models/csv_parser.rb:77:in `rows_as_hashes'
[ERR] [2020-06-16 09:11:36] ../models/resource_harvester.rb:178:in `validate_csv'
[ERR] [2020-06-16 09:11:36] ../models/resource_harvester.rb:146:in `block (2 levels) in validate_each_file'
[ERR] [2020-06-16 09:11:36] ../models/resource_harvester.rb:145:in `block in validate_each_file'
[ERR] [2020-06-16 09:11:36] ../models/resource_harvester.rb:666:in `block in each_format'
[ERR] [2020-06-16 09:11:36] ../models/resource_harvester.rb:651:in `each_format'
[ERR] [2020-06-16 09:11:36] ../models/resource_harvester.rb:132:in `validate_each_file'
[ERR] [2020-06-16 09:11:36] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2020-06-16 09:11:36] ../models/logged_process.rb:19:in `run_step'
[ERR] [2020-06-16 09:11:36] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2020-06-16 09:11:36] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2020-06-16 09:11:36] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2020-06-16 09:11:36] ../models/resource.rb:151:in `lock'
[ERR] [2020-06-16 09:11:36] ../models/resource_harvester.rb:72:in `start'
[ERR] [2020-06-16 09:11:36] ../models/resource.rb:232:in `harvest'
[ERR] [2020-06-16 09:11:36] ../models/resource.rb:208:in `re_download_opendata_and_harvest'
[ERR] [2020-06-16 09:11:36] bin/rails:4:in `require'
[ERR] [2020-06-16 09:11:36] bin/rails:4:in `<main>'
[STOP] [2020-06-16 09:11:36] logged process, took 1.2
[START] [2020-06-16 09:12:18] logged process
[START] [2020-06-16 09:12:18] overall_tsv_creation
[INFO] [2020-06-16 09:12:18] Processing group of 0 in 0 batches of 10000
[INFO] [2020-06-16 09:12:18] Average Time: NaN
[INFO] [2020-06-16 09:12:18] Total Time: 1s
[STOP] [2020-06-16 09:12:18] overall_tsv_creation
[INFO] [2020-06-16 09:12:18] Done. Check your files:
[INFO] [2020-06-16 09:12:29] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-06-16 09:12:33] ## remove_type: ScientificName
[INFO] [2020-06-16 09:12:33] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:12:33] [09:12:33.132] Removed 0 Scientificnames
[INFO] [2020-06-16 09:12:33] ## remove_type: Vernacular
[INFO] [2020-06-16 09:12:33] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:12:33] [09:12:33.136] Removed 0 Vernaculars
[INFO] [2020-06-16 09:12:33] ## remove_type: Article
[INFO] [2020-06-16 09:12:33] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:12:33] [09:12:33.139] Removed 0 Articles
[INFO] [2020-06-16 09:12:33] ## remove_type: Medium
[INFO] [2020-06-16 09:12:33] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:12:33] [09:12:33.142] Removed 0 Media
[INFO] [2020-06-16 09:12:33] ## remove_type: Trait
[INFO] [2020-06-16 09:12:33] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:12:33] [09:12:33.145] Removed 0 Traits
[INFO] [2020-06-16 09:12:33] ## remove_type: MetaTrait
[INFO] [2020-06-16 09:12:33] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:12:33] [09:12:33.148] Removed 0 Metatraits
[INFO] [2020-06-16 09:12:33] ## remove_type: OccurrenceMetadatum
[INFO] [2020-06-16 09:12:33] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:12:33] [09:12:33.151] Removed 0 Occurrencemetadata
[INFO] [2020-06-16 09:12:33] ## remove_type: Assoc
[INFO] [2020-06-16 09:12:33] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:12:33] [09:12:33.154] Removed 0 Assocs
[INFO] [2020-06-16 09:12:33] ## remove_type: MetaAssoc
[INFO] [2020-06-16 09:12:33] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:12:33] [09:12:33.156] Removed 0 Metaassocs
[INFO] [2020-06-16 09:12:33] ## remove_type: Identifier
[INFO] [2020-06-16 09:12:33] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:12:33] [09:12:33.159] Removed 0 Identifiers
[INFO] [2020-06-16 09:12:33] ## remove_type: Reference
[INFO] [2020-06-16 09:12:33] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:12:33] [09:12:33.162] Removed 0 References
[INFO] [2020-06-16 09:12:33] ## remove_type: Node
[INFO] [2020-06-16 09:12:33] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 09:12:33] [09:12:33.192] Removed 0 Nodes
[START] [2020-06-16 09:12:33] logged process
[START] [2020-06-16 09:12:33] Creating resource from OpenData
[START] [2020-06-16 09:12:33] logged process
[START] [2020-06-16 09:12:33] Parse meta.xml file and create formats with fields
[STOP] [2020-06-16 09:12:33] Parse meta.xml file and create formats with fields
[STOP] [2020-06-16 09:12:33] Creating resource from OpenData
[START] [2020-06-16 09:12:33] logged process
[START] [2020-06-16 09:12:33] create_harvest_instance
[STOP] [2020-06-16 09:12:34] create_harvest_instance
[START] [2020-06-16 09:12:34] fetch_files
[STOP] [2020-06-16 09:12:34] fetch_files
[START] [2020-06-16 09:12:34] validate_each_file
[STOP] [2020-06-16 09:12:34] validate_each_file
[ERR] [2020-06-16 09:12:34] Exceptions::ColumnEmpty
[ERR] [2020-06-16 09:12:34] Illegal empty value for measurements/measurementType on line 2
[ERR] [2020-06-16 09:12:34] ../models/resource_harvester.rb:194:in `check_header'
[ERR] [2020-06-16 09:12:34] ../models/resource_harvester.rb:182:in `block (2 levels) in validate_csv'
[ERR] [2020-06-16 09:12:34] ../models/resource_harvester.rb:181:in `each'
[ERR] [2020-06-16 09:12:34] ../models/resource_harvester.rb:181:in `block in validate_csv'
[ERR] [2020-06-16 09:12:34] ../models/csv_parser.rb:81:in `block in rows_as_hashes'
[ERR] [2020-06-16 09:12:34] ../models/csv_parser.rb:26:in `block in line_at_a_time'
[ERR] [2020-06-16 09:12:34] ../models/csv_parser.rb:24:in `line_at_a_time'
[ERR] [2020-06-16 09:12:34] ../models/csv_parser.rb:77:in `rows_as_hashes'
[ERR] [2020-06-16 09:12:34] ../models/resource_harvester.rb:178:in `validate_csv'
[ERR] [2020-06-16 09:12:34] ../models/resource_harvester.rb:146:in `block (2 levels) in validate_each_file'
[ERR] [2020-06-16 09:12:34] ../models/resource_harvester.rb:145:in `block in validate_each_file'
[ERR] [2020-06-16 09:12:34] ../models/resource_harvester.rb:666:in `block in each_format'
[ERR] [2020-06-16 09:12:34] ../models/resource_harvester.rb:651:in `each_format'
[ERR] [2020-06-16 09:12:34] ../models/resource_harvester.rb:132:in `validate_each_file'
[ERR] [2020-06-16 09:12:34] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2020-06-16 09:12:34] ../models/logged_process.rb:19:in `run_step'
[ERR] [2020-06-16 09:12:34] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2020-06-16 09:12:34] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2020-06-16 09:12:34] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2020-06-16 09:12:34] ../models/resource.rb:151:in `lock'
[ERR] [2020-06-16 09:12:34] ../models/resource_harvester.rb:72:in `start'
[ERR] [2020-06-16 09:12:34] ../models/resource.rb:232:in `harvest'
[ERR] [2020-06-16 09:12:34] ../models/resource.rb:208:in `re_download_opendata_and_harvest'
[ERR] [2020-06-16 09:12:34] bin/rails:4:in `require'
[ERR] [2020-06-16 09:12:34] bin/rails:4:in `<main>'
[STOP] [2020-06-16 09:12:34] logged process, took 1.16
[INFO] [2020-06-16 09:12:55] ## HARVEST: type = resume_-harvest
[START] [2020-06-16 09:12:56] logged process
[ERR] [2020-06-16 09:12:56][hdls] *****
[ERR] [2020-06-16 09:12:56][hdls] ***** HARVEST ATTEMPT FAILED: This resource is locked; assuming it is already running. Remove lock if not.
[ERR] [2020-06-16 09:12:56][hdls] *****
[INFO] [2020-06-16 10:48:01] ## HARVEST: type = resume_-harvest
[START] [2020-06-16 10:48:04] logged process
[ERR] [2020-06-16 10:48:04][hdls] *****
[ERR] [2020-06-16 10:48:04][hdls] ***** HARVEST ATTEMPT FAILED: This resource is locked; assuming it is already running. Remove lock if not.
[ERR] [2020-06-16 10:48:04][hdls] *****
[INFO] [2020-06-16 11:32:20] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-06-16 11:32:23] ## remove_type: ScientificName
[INFO] [2020-06-16 11:32:23] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 11:32:23] [11:32:23.216] Removed 0 Scientificnames
[INFO] [2020-06-16 11:32:23] ## remove_type: Vernacular
[INFO] [2020-06-16 11:32:23] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 11:32:23] [11:32:23.219] Removed 0 Vernaculars
[INFO] [2020-06-16 11:32:23] ## remove_type: Article
[INFO] [2020-06-16 11:32:23] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 11:32:23] [11:32:23.222] Removed 0 Articles
[INFO] [2020-06-16 11:32:23] ## remove_type: Medium
[INFO] [2020-06-16 11:32:23] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 11:32:23] [11:32:23.225] Removed 0 Media
[INFO] [2020-06-16 11:32:23] ## remove_type: Trait
[INFO] [2020-06-16 11:32:23] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 11:32:23] [11:32:23.229] Removed 0 Traits
[INFO] [2020-06-16 11:32:23] ## remove_type: MetaTrait
[INFO] [2020-06-16 11:32:23] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 11:32:23] [11:32:23.232] Removed 0 Metatraits
[INFO] [2020-06-16 11:32:23] ## remove_type: OccurrenceMetadatum
[INFO] [2020-06-16 11:32:23] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 11:32:23] [11:32:23.235] Removed 0 Occurrencemetadata
[INFO] [2020-06-16 11:32:23] ## remove_type: Assoc
[INFO] [2020-06-16 11:32:23] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 11:32:23] [11:32:23.238] Removed 0 Assocs
[INFO] [2020-06-16 11:32:23] ## remove_type: MetaAssoc
[INFO] [2020-06-16 11:32:23] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 11:32:23] [11:32:23.241] Removed 0 Metaassocs
[INFO] [2020-06-16 11:32:23] ## remove_type: Identifier
[INFO] [2020-06-16 11:32:23] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 11:32:23] [11:32:23.243] Removed 0 Identifiers
[INFO] [2020-06-16 11:32:23] ## remove_type: Reference
[INFO] [2020-06-16 11:32:23] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 11:32:23] [11:32:23.246] Removed 0 References
[INFO] [2020-06-16 11:32:23] ## remove_type: Node
[INFO] [2020-06-16 11:32:23] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 11:32:23] [11:32:23.266] Removed 0 Nodes
[START] [2020-06-16 11:32:23] logged process
[START] [2020-06-16 11:32:23] Creating resource from OpenData
[START] [2020-06-16 11:32:23] logged process
[START] [2020-06-16 11:32:23] Parse meta.xml file and create formats with fields
[STOP] [2020-06-16 11:32:23] Parse meta.xml file and create formats with fields
[STOP] [2020-06-16 11:32:23] Creating resource from OpenData
[START] [2020-06-16 11:32:23] logged process
[START] [2020-06-16 11:32:23] create_harvest_instance
[STOP] [2020-06-16 11:32:24] create_harvest_instance
[START] [2020-06-16 11:32:24] fetch_files
[STOP] [2020-06-16 11:32:24] fetch_files
[START] [2020-06-16 11:32:24] validate_each_file
[STOP] [2020-06-16 11:32:24] validate_each_file
[ERR] [2020-06-16 11:32:24] Exceptions::ColumnEmpty
[ERR] [2020-06-16 11:32:24] Illegal empty value for measurements/measurementType on line 2
[ERR] [2020-06-16 11:32:24] ../models/resource_harvester.rb:194:in `check_header'
[ERR] [2020-06-16 11:32:24] ../models/resource_harvester.rb:182:in `block (2 levels) in validate_csv'
[ERR] [2020-06-16 11:32:24] ../models/resource_harvester.rb:181:in `each'
[ERR] [2020-06-16 11:32:24] ../models/resource_harvester.rb:181:in `block in validate_csv'
[ERR] [2020-06-16 11:32:24] ../models/csv_parser.rb:81:in `block in rows_as_hashes'
[ERR] [2020-06-16 11:32:24] ../models/csv_parser.rb:26:in `block in line_at_a_time'
[ERR] [2020-06-16 11:32:24] ../models/csv_parser.rb:24:in `line_at_a_time'
[ERR] [2020-06-16 11:32:24] ../models/csv_parser.rb:77:in `rows_as_hashes'
[ERR] [2020-06-16 11:32:24] ../models/resource_harvester.rb:178:in `validate_csv'
[ERR] [2020-06-16 11:32:24] ../models/resource_harvester.rb:146:in `block (2 levels) in validate_each_file'
[ERR] [2020-06-16 11:32:24] ../models/resource_harvester.rb:145:in `block in validate_each_file'
[ERR] [2020-06-16 11:32:24] ../models/resource_harvester.rb:666:in `block in each_format'
[ERR] [2020-06-16 11:32:24] ../models/resource_harvester.rb:651:in `each_format'
[ERR] [2020-06-16 11:32:24] ../models/resource_harvester.rb:132:in `validate_each_file'
[ERR] [2020-06-16 11:32:24] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2020-06-16 11:32:24] ../models/logged_process.rb:19:in `run_step'
[ERR] [2020-06-16 11:32:24] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2020-06-16 11:32:24] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2020-06-16 11:32:24] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2020-06-16 11:32:24] ../models/resource.rb:151:in `lock'
[ERR] [2020-06-16 11:32:24] ../models/resource_harvester.rb:72:in `start'
[ERR] [2020-06-16 11:32:24] ../models/resource.rb:232:in `harvest'
[ERR] [2020-06-16 11:32:24] ../models/resource.rb:208:in `re_download_opendata_and_harvest'
[ERR] [2020-06-16 11:32:24] bin/rails:4:in `require'
[ERR] [2020-06-16 11:32:24] bin/rails:4:in `<main>'
[STOP] [2020-06-16 11:32:24] logged process, took 1.21
[INFO] [2020-06-16 13:07:33] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-06-16 13:07:38] ## remove_type: ScientificName
[INFO] [2020-06-16 13:07:38] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 13:07:38] [13:07:38.997] Removed 0 Scientificnames
[INFO] [2020-06-16 13:07:38] ## remove_type: Vernacular
[INFO] [2020-06-16 13:07:38] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 13:07:39] [13:07:39.000] Removed 0 Vernaculars
[INFO] [2020-06-16 13:07:39] ## remove_type: Article
[INFO] [2020-06-16 13:07:39] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 13:07:39] [13:07:39.005] Removed 0 Articles
[INFO] [2020-06-16 13:07:39] ## remove_type: Medium
[INFO] [2020-06-16 13:07:39] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 13:07:39] [13:07:39.009] Removed 0 Media
[INFO] [2020-06-16 13:07:39] ## remove_type: Trait
[INFO] [2020-06-16 13:07:39] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 13:07:39] [13:07:39.012] Removed 0 Traits
[INFO] [2020-06-16 13:07:39] ## remove_type: MetaTrait
[INFO] [2020-06-16 13:07:39] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 13:07:39] [13:07:39.015] Removed 0 Metatraits
[INFO] [2020-06-16 13:07:39] ## remove_type: OccurrenceMetadatum
[INFO] [2020-06-16 13:07:39] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 13:07:39] [13:07:39.018] Removed 0 Occurrencemetadata
[INFO] [2020-06-16 13:07:39] ## remove_type: Assoc
[INFO] [2020-06-16 13:07:39] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 13:07:39] [13:07:39.021] Removed 0 Assocs
[INFO] [2020-06-16 13:07:39] ## remove_type: MetaAssoc
[INFO] [2020-06-16 13:07:39] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 13:07:39] [13:07:39.024] Removed 0 Metaassocs
[INFO] [2020-06-16 13:07:39] ## remove_type: Identifier
[INFO] [2020-06-16 13:07:39] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 13:07:39] [13:07:39.026] Removed 0 Identifiers
[INFO] [2020-06-16 13:07:39] ## remove_type: Reference
[INFO] [2020-06-16 13:07:39] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 13:07:39] [13:07:39.029] Removed 0 References
[INFO] [2020-06-16 13:07:39] ## remove_type: Node
[INFO] [2020-06-16 13:07:39] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-16 13:07:39] [13:07:39.061] Removed 0 Nodes
[START] [2020-06-16 13:07:39] logged process
[START] [2020-06-16 13:07:39] Creating resource from OpenData
[START] [2020-06-16 13:07:39] logged process
[START] [2020-06-16 13:07:39] Parse meta.xml file and create formats with fields
[STOP] [2020-06-16 13:07:39] Parse meta.xml file and create formats with fields
[STOP] [2020-06-16 13:07:39] Creating resource from OpenData
[START] [2020-06-16 13:07:39] logged process
[START] [2020-06-16 13:07:39] create_harvest_instance
[STOP] [2020-06-16 13:07:40] create_harvest_instance
[START] [2020-06-16 13:07:40] fetch_files
[STOP] [2020-06-16 13:07:40] fetch_files
[START] [2020-06-16 13:07:40] validate_each_file
[STOP] [2020-06-16 13:07:40] validate_each_file
[START] [2020-06-16 13:07:40] convert_to_csv
[CMD] [2020-06-16 13:07:40] /usr/bin/sort /app/public/converted_csv/jardine_et_al_ja_nodes_21350.csv > /app/public/converted_csv/jardine_et_al_ja_nodes_21350.csv_sorted
[CMD] [2020-06-16 13:07:40] /usr/bin/sort /app/public/converted_csv/jardine_et_al_ja_occurrences_21351.csv > /app/public/converted_csv/jardine_et_al_ja_occurrences_21351.csv_sorted
[CMD] [2020-06-16 13:07:40] /usr/bin/sort /app/public/converted_csv/jardine_et_al_ja_measurements_21352.csv > /app/public/converted_csv/jardine_et_al_ja_measurements_21352.csv_sorted
[STOP] [2020-06-16 13:07:40] convert_to_csv
[START] [2020-06-16 13:07:40] calculate_delta
[CMD] [2020-06-16 13:07:40] echo "0a" > /app/public/diff/jardine_et_al_ja_nodes_21350.diff
[CMD] [2020-06-16 13:07:40] tail -n +1 /app/public/converted_csv/jardine_et_al_ja_nodes_21350.csv >> /app/public/diff/jardine_et_al_ja_nodes_21350.diff
[CMD] [2020-06-16 13:07:40] echo "." >> /app/public/diff/jardine_et_al_ja_nodes_21350.diff
[CMD] [2020-06-16 13:07:40] echo "0a" > /app/public/diff/jardine_et_al_ja_occurrences_21351.diff
[CMD] [2020-06-16 13:07:40] tail -n +1 /app/public/converted_csv/jardine_et_al_ja_occurrences_21351.csv >> /app/public/diff/jardine_et_al_ja_occurrences_21351.diff
[CMD] [2020-06-16 13:07:40] echo "." >> /app/public/diff/jardine_et_al_ja_occurrences_21351.diff
[CMD] [2020-06-16 13:07:40] echo "0a" > /app/public/diff/jardine_et_al_ja_measurements_21352.diff
[CMD] [2020-06-16 13:07:40] tail -n +1 /app/public/converted_csv/jardine_et_al_ja_measurements_21352.csv >> /app/public/diff/jardine_et_al_ja_measurements_21352.diff
[CMD] [2020-06-16 13:07:40] echo "." >> /app/public/diff/jardine_et_al_ja_measurements_21352.diff
[STOP] [2020-06-16 13:07:40] calculate_delta
[START] [2020-06-16 13:07:40] parse_diff_and_store
[INFO] [2020-06-16 13:07:40] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-16 13:07:40] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-16 13:07:40] Loading measurements diff file into memory (true lines)...
[INFO] [2020-06-16 13:07:41] Storing 15 ScientificNames
[INFO] [2020-06-16 13:07:41] Processing group of 15 in 1 groups of 1000
[INFO] [2020-06-16 13:07:41] Average Time: 0.01
[INFO] [2020-06-16 13:07:41] Total Time: 1s
[INFO] [2020-06-16 13:07:41] Storing 15 Nodes
[INFO] [2020-06-16 13:07:41] Processing group of 15 in 1 groups of 1000
[INFO] [2020-06-16 13:07:41] Average Time: 0.01
[INFO] [2020-06-16 13:07:41] Total Time: 1s
[INFO] [2020-06-16 13:07:41] Storing 7 Occurrences
[INFO] [2020-06-16 13:07:41] Processing group of 7 in 1 groups of 1000
[INFO] [2020-06-16 13:07:41] Average Time: 0.0
[INFO] [2020-06-16 13:07:41] Total Time: 1s
[INFO] [2020-06-16 13:07:41] Storing 14 Traits
[INFO] [2020-06-16 13:07:41] Processing group of 14 in 1 groups of 1000
[INFO] [2020-06-16 13:07:41] Average Time: 0.01
[INFO] [2020-06-16 13:07:41] Total Time: 1s
[INFO] [2020-06-16 13:07:41] Storing 28 MetaTraits
[INFO] [2020-06-16 13:07:41] Processing group of 28 in 1 groups of 1000
[INFO] [2020-06-16 13:07:41] Average Time: 0.0
[INFO] [2020-06-16 13:07:41] Total Time: 1s
[STOP] [2020-06-16 13:07:41] parse_diff_and_store
[START] [2020-06-16 13:07:41] resolve_keys
[INFO] [2020-06-16 13:07:48] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-16 13:07:48] traits to occurrences...
[INFO] [2020-06-16 13:07:48] traits to nodes (through occurrences)...
[INFO] [2020-06-16 13:07:48] Traits to sex term...
[INFO] [2020-06-16 13:07:48] Traits to lifestage term...
[INFO] [2020-06-16 13:07:48] MetaTraits to traits...
[INFO] [2020-06-16 13:07:48] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-16 13:07:48] Assocs to occurrences...
[INFO] [2020-06-16 13:07:48] Assocs to nodes...
[INFO] [2020-06-16 13:07:48] Assoc to sex term...
[INFO] [2020-06-16 13:07:48] Assoc to lifestage term...
[STOP] [2020-06-16 13:07:48] resolve_keys
[START] [2020-06-16 13:07:48] hold_for_later_1
[STOP] [2020-06-16 13:07:48] hold_for_later_1
[START] [2020-06-16 13:07:48] hold_for_later_2
[STOP] [2020-06-16 13:07:48] hold_for_later_2
[START] [2020-06-16 13:07:48] resolve_missing_parents
[STOP] [2020-06-16 13:07:48] resolve_missing_parents
[START] [2020-06-16 13:07:48] rebuild_nodes
[START] [2020-06-16 13:07:48] Flattener#flatten
[START] [2020-06-16 13:07:48] Flattener#study_resource
[START] [2020-06-16 13:07:48] Flattener#build_ancestry
[STOP] [2020-06-16 13:07:48] Flattener#build_ancestry
[INFO] [2020-06-16 13:07:48] 15 ancestry keys
[START] [2020-06-16 13:07:48] build_node_ancestors
[INFO] [2020-06-16 13:07:48] old ancestors deleted.
[STOP] [2020-06-16 13:07:48] build_node_ancestors
[START] [2020-06-16 13:07:48] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 13:07:48] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 13:07:48] Flattener#flatten
[STOP] [2020-06-16 13:07:48] rebuild_nodes
[START] [2020-06-16 13:07:48] resolve_missing_media_owners
[STOP] [2020-06-16 13:07:48] resolve_missing_media_owners
[START] [2020-06-16 13:07:48] sanitize_media_verbatims
[STOP] [2020-06-16 13:07:48] sanitize_media_verbatims
[START] [2020-06-16 13:07:48] queue_downloads
[STOP] [2020-06-16 13:07:48] queue_downloads
[START] [2020-06-16 13:07:48] parse_names
[WARN] [2020-06-16 13:07:48] I see 15 names which still need to be parsed.
[WARN] [2020-06-16 13:07:49] I see 1 names which still need to be parsed.
[STOP] [2020-06-16 13:07:50] parse_names
[START] [2020-06-16 13:07:50] denormalize_canonical_names_to_nodes
[STOP] [2020-06-16 13:07:50] denormalize_canonical_names_to_nodes
[START] [2020-06-16 13:07:50] match_nodes
[START] [2020-06-16 13:07:50] map_all_nodes_to_pages
[STOP] [2020-06-16 13:07:52] map_all_nodes_to_pages
[INFO] [2020-06-16 13:07:52] Unmatched nodes (1 of 15): Cissus sicyodes (#80104426)
[START] [2020-06-16 13:07:52] update_nodes
[STOP] [2020-06-16 13:07:52] update_nodes
[STOP] [2020-06-16 13:07:52] match_nodes
[START] [2020-06-16 13:07:52] reindex_search
[STOP] [2020-06-16 13:07:53] reindex_search
[START] [2020-06-16 13:07:53] normalize_units
[STOP] [2020-06-16 13:07:53] normalize_units
[START] [2020-06-16 13:07:53] calculate_statistics
[STOP] [2020-06-16 13:07:53] calculate_statistics
[START] [2020-06-16 13:07:53] complete_harvest_instance
[START] [2020-06-16 13:07:53] overall_tsv_creation
[INFO] [2020-06-16 13:07:53] Processing group of 15 in 1 batches of 10000
[INFO] [2020-06-16 13:08:43] 7 Traits (unfiltered)...
[INFO] [2020-06-16 13:08:56] 7 Traits (filtered)...
[INFO] [2020-06-16 13:08:56] 0 Associations (filtered)...
[INFO] [2020-06-16 13:09:33] 28 metadata added.
[INFO] [2020-06-16 13:09:33] 0 metadata added.
[INFO] [2020-06-16 13:09:33] Average Time: 71.94
[INFO] [2020-06-16 13:09:33] Total Time: 1m41s
[STOP] [2020-06-16 13:09:33] overall_tsv_creation
[INFO] [2020-06-16 13:09:33] Done. Check your files:
[INFO] [2020-06-16 13:09:33] (14 lines) /app/public/data/jardine_et_al_ja/publish_nodes.tsv
[INFO] [2020-06-16 13:09:33] (20 lines) /app/public/data/jardine_et_al_ja/publish_node_ancestors.tsv
[INFO] [2020-06-16 13:09:33] (15 lines) /app/public/data/jardine_et_al_ja/publish_scientific_names.tsv
[INFO] [2020-06-16 13:09:33] (8 lines) /app/public/data/jardine_et_al_ja/publish_traits.tsv
[INFO] [2020-06-16 13:09:33] (29 lines) /app/public/data/jardine_et_al_ja/publish_metadata.tsv
[STOP] [2020-06-16 13:09:33] complete_harvest_instance
[START] [2020-06-16 13:09:33] completed
[STOP] [2020-06-16 13:09:33] completed
[STOP] [2020-06-16 13:09:33] logged process, took 113.85

Latest Process

16 Jun 13:07 EXITED currently processing 0