Harvest for Gatesy and Middleton 1997 Created 22 Jul 15:34

Stage: completed
Fetched: 22 Jul 15:34
Validated: 22 Jul 15:34
Deltas Created 22 Jul 15:34
Units Normalized: 22 Jul 15:34
Ancestry Built: 22 Jul 15:34
Nodes Matched: 22 Jul 15:34
Names Parsed: 22 Jul 15:34
New Models Stored: 22 Jul 15:34
Indexed: 22 Jul 15:34
Completed: 22 Jul 15:35
Time to Harvest: less than a minute
Harvesting Log

(447 lines)
# Logfile created on 2020-07-22 15:15:36 -0400 by logger.rb/v1.4.2
[START] [2020-07-22 15:15:36] logged process
[START] [2020-07-22 15:15:36] Creating resource from OpenData
[START] [2020-07-22 15:15:36] logged process
[START] [2020-07-22 15:15:36] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:15:37] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:15:37] Creating resource from OpenData
[INFO] [2020-07-22 15:20:15] ## HARVEST: type = -harvest
[START] [2020-07-22 15:20:16] logged process
[START] [2020-07-22 15:20:16] create_harvest_instance
[STOP] [2020-07-22 15:20:17] create_harvest_instance
[START] [2020-07-22 15:20:17] fetch_files
[STOP] [2020-07-22 15:20:17] fetch_files
[START] [2020-07-22 15:20:17] validate_each_file
[STOP] [2020-07-22 15:20:17] validate_each_file
[ERR] [2020-07-22 15:20:17] Exceptions::ColumnMissing
[ERR] [2020-07-22 15:20:17] MISSING COLUMN: occurrences: 
[ERR] [2020-07-22 15:20:17] ../models/resource_harvester.rb:157:in `block in check_each_column'
[ERR] [2020-07-22 15:20:17] ../models/resource_harvester.rb:156:in `each_with_index'
[ERR] [2020-07-22 15:20:17] ../models/resource_harvester.rb:156:in `check_each_column'
[ERR] [2020-07-22 15:20:17] ../models/resource_harvester.rb:135:in `block in validate_each_file'
[ERR] [2020-07-22 15:20:17] ../models/resource_harvester.rb:665:in `block in each_format'
[ERR] [2020-07-22 15:20:17] ../models/resource_harvester.rb:650:in `each_format'
[ERR] [2020-07-22 15:20:17] ../models/resource_harvester.rb:132:in `validate_each_file'
[ERR] [2020-07-22 15:20:17] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2020-07-22 15:20:17] ../models/logged_process.rb:19:in `run_step'
[ERR] [2020-07-22 15:20:17] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2020-07-22 15:20:17] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2020-07-22 15:20:17] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2020-07-22 15:20:17] ../models/resource.rb:151:in `lock'
[ERR] [2020-07-22 15:20:17] ../models/resource_harvester.rb:72:in `start'
[ERR] [2020-07-22 15:20:17] ../models/resource.rb:232:in `harvest'
[ERR] [2020-07-22 15:20:17] bin/rails:4:in `require'
[ERR] [2020-07-22 15:20:17] bin/rails:4:in `<main>'
[STOP] [2020-07-22 15:20:17] logged process, took 1.22
[INFO] [2020-07-22 15:23:42] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-07-22 15:23:45] ## remove_type: ScientificName
[INFO] [2020-07-22 15:23:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:23:45] [15:23:45.411] Removed 0 Scientificnames
[INFO] [2020-07-22 15:23:45] ## remove_type: Vernacular
[INFO] [2020-07-22 15:23:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:23:45] [15:23:45.414] Removed 0 Vernaculars
[INFO] [2020-07-22 15:23:45] ## remove_type: Article
[INFO] [2020-07-22 15:23:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:23:45] [15:23:45.417] Removed 0 Articles
[INFO] [2020-07-22 15:23:45] ## remove_type: Medium
[INFO] [2020-07-22 15:23:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:23:45] [15:23:45.421] Removed 0 Media
[INFO] [2020-07-22 15:23:45] ## remove_type: Trait
[INFO] [2020-07-22 15:23:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:23:45] [15:23:45.425] Removed 0 Traits
[INFO] [2020-07-22 15:23:45] ## remove_type: MetaTrait
[INFO] [2020-07-22 15:23:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:23:45] [15:23:45.427] Removed 0 Metatraits
[INFO] [2020-07-22 15:23:45] ## remove_type: OccurrenceMetadatum
[INFO] [2020-07-22 15:23:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:23:45] [15:23:45.430] Removed 0 Occurrencemetadata
[INFO] [2020-07-22 15:23:45] ## remove_type: Assoc
[INFO] [2020-07-22 15:23:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:23:45] [15:23:45.433] Removed 0 Assocs
[INFO] [2020-07-22 15:23:45] ## remove_type: MetaAssoc
[INFO] [2020-07-22 15:23:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:23:45] [15:23:45.436] Removed 0 Metaassocs
[INFO] [2020-07-22 15:23:45] ## remove_type: Identifier
[INFO] [2020-07-22 15:23:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:23:45] [15:23:45.438] Removed 0 Identifiers
[INFO] [2020-07-22 15:23:45] ## remove_type: Reference
[INFO] [2020-07-22 15:23:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:23:45] [15:23:45.441] Removed 0 References
[INFO] [2020-07-22 15:23:45] ## remove_type: Node
[INFO] [2020-07-22 15:23:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:23:45] [15:23:45.463] Removed 0 Nodes
[START] [2020-07-22 15:23:45] logged process
[START] [2020-07-22 15:23:45] Creating resource from OpenData
[START] [2020-07-22 15:23:45] logged process
[START] [2020-07-22 15:23:45] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:23:45] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:23:45] Creating resource from OpenData
[START] [2020-07-22 15:23:45] logged process
[START] [2020-07-22 15:23:45] create_harvest_instance
[STOP] [2020-07-22 15:23:47] create_harvest_instance
[START] [2020-07-22 15:23:47] fetch_files
[STOP] [2020-07-22 15:23:47] fetch_files
[START] [2020-07-22 15:23:47] validate_each_file
[STOP] [2020-07-22 15:23:47] validate_each_file
[ERR] [2020-07-22 15:23:47] Exceptions::ColumnMissing
[ERR] [2020-07-22 15:23:47] MISSING COLUMN: measurements: 
[ERR] [2020-07-22 15:23:47] ../models/resource_harvester.rb:157:in `block in check_each_column'
[ERR] [2020-07-22 15:23:47] ../models/resource_harvester.rb:156:in `each_with_index'
[ERR] [2020-07-22 15:23:47] ../models/resource_harvester.rb:156:in `check_each_column'
[ERR] [2020-07-22 15:23:47] ../models/resource_harvester.rb:135:in `block in validate_each_file'
[ERR] [2020-07-22 15:23:47] ../models/resource_harvester.rb:665:in `block in each_format'
[ERR] [2020-07-22 15:23:47] ../models/resource_harvester.rb:650:in `each_format'
[ERR] [2020-07-22 15:23:47] ../models/resource_harvester.rb:132:in `validate_each_file'
[ERR] [2020-07-22 15:23:47] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2020-07-22 15:23:47] ../models/logged_process.rb:19:in `run_step'
[ERR] [2020-07-22 15:23:47] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2020-07-22 15:23:47] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2020-07-22 15:23:47] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2020-07-22 15:23:47] ../models/resource.rb:151:in `lock'
[ERR] [2020-07-22 15:23:47] ../models/resource_harvester.rb:72:in `start'
[ERR] [2020-07-22 15:23:47] ../models/resource.rb:232:in `harvest'
[ERR] [2020-07-22 15:23:47] ../models/resource.rb:208:in `re_download_opendata_and_harvest'
[ERR] [2020-07-22 15:23:47] bin/rails:4:in `require'
[ERR] [2020-07-22 15:23:47] bin/rails:4:in `<main>'
[STOP] [2020-07-22 15:23:47] logged process, took 1.14
[INFO] [2020-07-22 15:29:27] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-07-22 15:29:29] ## remove_type: ScientificName
[INFO] [2020-07-22 15:29:29] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:29:29] [15:29:29.862] Removed 0 Scientificnames
[INFO] [2020-07-22 15:29:29] ## remove_type: Vernacular
[INFO] [2020-07-22 15:29:29] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:29:29] [15:29:29.866] Removed 0 Vernaculars
[INFO] [2020-07-22 15:29:29] ## remove_type: Article
[INFO] [2020-07-22 15:29:29] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:29:29] [15:29:29.869] Removed 0 Articles
[INFO] [2020-07-22 15:29:29] ## remove_type: Medium
[INFO] [2020-07-22 15:29:29] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:29:29] [15:29:29.873] Removed 0 Media
[INFO] [2020-07-22 15:29:29] ## remove_type: Trait
[INFO] [2020-07-22 15:29:29] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:29:29] [15:29:29.877] Removed 0 Traits
[INFO] [2020-07-22 15:29:29] ## remove_type: MetaTrait
[INFO] [2020-07-22 15:29:29] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:29:29] [15:29:29.880] Removed 0 Metatraits
[INFO] [2020-07-22 15:29:29] ## remove_type: OccurrenceMetadatum
[INFO] [2020-07-22 15:29:29] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:29:29] [15:29:29.883] Removed 0 Occurrencemetadata
[INFO] [2020-07-22 15:29:29] ## remove_type: Assoc
[INFO] [2020-07-22 15:29:29] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:29:29] [15:29:29.885] Removed 0 Assocs
[INFO] [2020-07-22 15:29:29] ## remove_type: MetaAssoc
[INFO] [2020-07-22 15:29:29] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:29:29] [15:29:29.888] Removed 0 Metaassocs
[INFO] [2020-07-22 15:29:29] ## remove_type: Identifier
[INFO] [2020-07-22 15:29:29] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:29:29] [15:29:29.890] Removed 0 Identifiers
[INFO] [2020-07-22 15:29:29] ## remove_type: Reference
[INFO] [2020-07-22 15:29:29] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:29:29] [15:29:29.893] Removed 0 References
[INFO] [2020-07-22 15:29:29] ## remove_type: Node
[INFO] [2020-07-22 15:29:29] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:29:29] [15:29:29.912] Removed 0 Nodes
[START] [2020-07-22 15:29:30] logged process
[START] [2020-07-22 15:29:30] Creating resource from OpenData
[START] [2020-07-22 15:29:30] logged process
[START] [2020-07-22 15:29:30] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:29:30] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:29:30] Creating resource from OpenData
[START] [2020-07-22 15:29:30] logged process
[START] [2020-07-22 15:29:30] create_harvest_instance
[STOP] [2020-07-22 15:29:31] create_harvest_instance
[START] [2020-07-22 15:29:31] fetch_files
[STOP] [2020-07-22 15:29:31] fetch_files
[START] [2020-07-22 15:29:31] validate_each_file
[STOP] [2020-07-22 15:29:31] validate_each_file
[START] [2020-07-22 15:29:31] convert_to_csv
[CMD] [2020-07-22 15:29:31] /usr/bin/sort /app/public/converted_csv/gatesy_middleton_nodes_22099.csv > /app/public/converted_csv/gatesy_middleton_nodes_22099.csv_sorted
[CMD] [2020-07-22 15:29:31] /usr/bin/sort /app/public/converted_csv/gatesy_middleton_occurrences_22100.csv > /app/public/converted_csv/gatesy_middleton_occurrences_22100.csv_sorted
[CMD] [2020-07-22 15:29:31] /usr/bin/sort /app/public/converted_csv/gatesy_middleton_measurements_22101.csv > /app/public/converted_csv/gatesy_middleton_measurements_22101.csv_sorted
[STOP] [2020-07-22 15:29:31] convert_to_csv
[START] [2020-07-22 15:29:31] calculate_delta
[CMD] [2020-07-22 15:29:31] echo "0a" > /app/public/diff/gatesy_middleton_nodes_22099.diff
[CMD] [2020-07-22 15:29:31] tail -n +1 /app/public/converted_csv/gatesy_middleton_nodes_22099.csv >> /app/public/diff/gatesy_middleton_nodes_22099.diff
[CMD] [2020-07-22 15:29:31] echo "." >> /app/public/diff/gatesy_middleton_nodes_22099.diff
[CMD] [2020-07-22 15:29:31] echo "0a" > /app/public/diff/gatesy_middleton_occurrences_22100.diff
[CMD] [2020-07-22 15:29:31] tail -n +1 /app/public/converted_csv/gatesy_middleton_occurrences_22100.csv >> /app/public/diff/gatesy_middleton_occurrences_22100.diff
[CMD] [2020-07-22 15:29:31] echo "." >> /app/public/diff/gatesy_middleton_occurrences_22100.diff
[CMD] [2020-07-22 15:29:31] echo "0a" > /app/public/diff/gatesy_middleton_measurements_22101.diff
[CMD] [2020-07-22 15:29:31] tail -n +1 /app/public/converted_csv/gatesy_middleton_measurements_22101.csv >> /app/public/diff/gatesy_middleton_measurements_22101.diff
[CMD] [2020-07-22 15:29:31] echo "." >> /app/public/diff/gatesy_middleton_measurements_22101.diff
[STOP] [2020-07-22 15:29:31] calculate_delta
[START] [2020-07-22 15:29:31] parse_diff_and_store
[INFO] [2020-07-22 15:29:31] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-22 15:29:31] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-22 15:29:31] Loading measurements diff file into memory (true lines)...
[WARN] [2020-07-22 15:29:31] IGNORING a measurement NOT of a taxon (2) with NO parent and NO occurrence ID.
[INFO] [2020-07-22 15:29:31] Storing 1 ScientificNames
[INFO] [2020-07-22 15:29:31] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 15:29:31] Average Time: 0.0
[INFO] [2020-07-22 15:29:31] Total Time: 1s
[INFO] [2020-07-22 15:29:31] Storing 1 Nodes
[INFO] [2020-07-22 15:29:31] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 15:29:31] Average Time: 0.0
[INFO] [2020-07-22 15:29:31] Total Time: 1s
[INFO] [2020-07-22 15:29:31] Storing 1 Occurrences
[INFO] [2020-07-22 15:29:31] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 15:29:31] Average Time: 0.0
[INFO] [2020-07-22 15:29:31] Total Time: 1s
[STOP] [2020-07-22 15:29:31] parse_diff_and_store
[START] [2020-07-22 15:29:31] resolve_keys
[INFO] [2020-07-22 15:29:38] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-22 15:29:38] traits to occurrences...
[INFO] [2020-07-22 15:29:38] traits to nodes (through occurrences)...
[INFO] [2020-07-22 15:29:38] Traits to sex term...
[INFO] [2020-07-22 15:29:38] Traits to lifestage term...
[INFO] [2020-07-22 15:29:38] MetaTraits to traits...
[INFO] [2020-07-22 15:29:38] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-22 15:29:38] Assocs to occurrences...
[INFO] [2020-07-22 15:29:38] Assocs to nodes...
[INFO] [2020-07-22 15:29:38] Assoc to sex term...
[INFO] [2020-07-22 15:29:38] Assoc to lifestage term...
[STOP] [2020-07-22 15:29:38] resolve_keys
[START] [2020-07-22 15:29:38] hold_for_later_1
[STOP] [2020-07-22 15:29:38] hold_for_later_1
[START] [2020-07-22 15:29:38] hold_for_later_2
[STOP] [2020-07-22 15:29:38] hold_for_later_2
[START] [2020-07-22 15:29:38] resolve_missing_parents
[STOP] [2020-07-22 15:29:38] resolve_missing_parents
[START] [2020-07-22 15:29:38] rebuild_nodes
[START] [2020-07-22 15:29:38] Flattener#flatten
[START] [2020-07-22 15:29:38] Flattener#study_resource
[START] [2020-07-22 15:29:38] Flattener#build_ancestry
[STOP] [2020-07-22 15:29:38] Flattener#build_ancestry
[INFO] [2020-07-22 15:29:38] 1 ancestry keys
[START] [2020-07-22 15:29:38] build_node_ancestors
[INFO] [2020-07-22 15:29:38] old ancestors deleted.
[STOP] [2020-07-22 15:29:38] build_node_ancestors
[WARN] [2020-07-22 15:29:38] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-22 15:29:38] Flattener#flatten
[STOP] [2020-07-22 15:29:38] rebuild_nodes
[START] [2020-07-22 15:29:38] resolve_missing_media_owners
[STOP] [2020-07-22 15:29:38] resolve_missing_media_owners
[START] [2020-07-22 15:29:38] sanitize_media_verbatims
[STOP] [2020-07-22 15:29:38] sanitize_media_verbatims
[START] [2020-07-22 15:29:38] queue_downloads
[STOP] [2020-07-22 15:29:38] queue_downloads
[START] [2020-07-22 15:29:38] parse_names
[WARN] [2020-07-22 15:29:38] I see 1 names which still need to be parsed.
[STOP] [2020-07-22 15:29:39] parse_names
[START] [2020-07-22 15:29:39] denormalize_canonical_names_to_nodes
[STOP] [2020-07-22 15:29:39] denormalize_canonical_names_to_nodes
[START] [2020-07-22 15:29:39] match_nodes
[START] [2020-07-22 15:29:39] map_all_nodes_to_pages
[STOP] [2020-07-22 15:29:39] map_all_nodes_to_pages
[INFO] [2020-07-22 15:29:39] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-07-22 15:29:39] update_nodes
[STOP] [2020-07-22 15:29:39] update_nodes
[STOP] [2020-07-22 15:29:39] match_nodes
[START] [2020-07-22 15:29:39] reindex_search
[STOP] [2020-07-22 15:29:39] reindex_search
[START] [2020-07-22 15:29:39] normalize_units
[STOP] [2020-07-22 15:29:39] normalize_units
[START] [2020-07-22 15:29:39] calculate_statistics
[2020-07-22 15:29:39] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-22 15:29:39] calculate_statistics
[START] [2020-07-22 15:29:39] complete_harvest_instance
[START] [2020-07-22 15:29:39] overall_tsv_creation
[INFO] [2020-07-22 15:29:39] Processing group of 1 in 1 batches of 10000
[INFO] [2020-07-22 15:30:17] Average Time: 10.76
[INFO] [2020-07-22 15:30:17] Total Time: 38s
[STOP] [2020-07-22 15:30:17] overall_tsv_creation
[INFO] [2020-07-22 15:30:17] Done. Check your files:
[INFO] [2020-07-22 15:30:17] (1 lines) /app/public/data/gatesy_middleton/publish_nodes.tsv
[INFO] [2020-07-22 15:30:17] (1 lines) /app/public/data/gatesy_middleton/publish_scientific_names.tsv
[STOP] [2020-07-22 15:30:17] complete_harvest_instance
[START] [2020-07-22 15:30:17] completed
[STOP] [2020-07-22 15:30:17] completed
[STOP] [2020-07-22 15:30:17] logged process, took 47.14
[INFO] [2020-07-22 15:34:11] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-07-22 15:34:14] ## remove_type: ScientificName
[INFO] [2020-07-22 15:34:14] ++ Calling delete_all on 1 instances...
[INFO] [2020-07-22 15:34:14] [15:34:14.179] Removed 1 Scientificnames
[INFO] [2020-07-22 15:34:14] ## remove_type: Vernacular
[INFO] [2020-07-22 15:34:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:34:14] [15:34:14.182] Removed 0 Vernaculars
[INFO] [2020-07-22 15:34:14] ## remove_type: Article
[INFO] [2020-07-22 15:34:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:34:14] [15:34:14.185] Removed 0 Articles
[INFO] [2020-07-22 15:34:14] ## remove_type: Medium
[INFO] [2020-07-22 15:34:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:34:14] [15:34:14.188] Removed 0 Media
[INFO] [2020-07-22 15:34:14] ## remove_type: Trait
[INFO] [2020-07-22 15:34:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:34:14] [15:34:14.192] Removed 0 Traits
[INFO] [2020-07-22 15:34:14] ## remove_type: MetaTrait
[INFO] [2020-07-22 15:34:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:34:14] [15:34:14.194] Removed 0 Metatraits
[INFO] [2020-07-22 15:34:14] ## remove_type: OccurrenceMetadatum
[INFO] [2020-07-22 15:34:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:34:14] [15:34:14.198] Removed 0 Occurrencemetadata
[INFO] [2020-07-22 15:34:14] ## remove_type: Assoc
[INFO] [2020-07-22 15:34:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:34:14] [15:34:14.200] Removed 0 Assocs
[INFO] [2020-07-22 15:34:14] ## remove_type: MetaAssoc
[INFO] [2020-07-22 15:34:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:34:14] [15:34:14.203] Removed 0 Metaassocs
[INFO] [2020-07-22 15:34:14] ## remove_type: Identifier
[INFO] [2020-07-22 15:34:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:34:14] [15:34:14.205] Removed 0 Identifiers
[INFO] [2020-07-22 15:34:14] ## remove_type: Reference
[INFO] [2020-07-22 15:34:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:34:14] [15:34:14.208] Removed 0 References
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:14] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:15] Starting batch with ID 80633665...
[INFO] [2020-07-22 15:34:15] ## remove_type: Node
[INFO] [2020-07-22 15:34:15] ++ Calling delete_all on 1 instances...
[INFO] [2020-07-22 15:34:15] [15:34:15.202] Removed 1 Nodes
[START] [2020-07-22 15:34:15] logged process
[START] [2020-07-22 15:34:15] Creating resource from OpenData
[START] [2020-07-22 15:34:15] logged process
[START] [2020-07-22 15:34:15] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:34:15] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:34:15] Creating resource from OpenData
[START] [2020-07-22 15:34:15] logged process
[START] [2020-07-22 15:34:15] create_harvest_instance
[STOP] [2020-07-22 15:34:16] create_harvest_instance
[START] [2020-07-22 15:34:16] fetch_files
[STOP] [2020-07-22 15:34:16] fetch_files
[START] [2020-07-22 15:34:16] validate_each_file
[STOP] [2020-07-22 15:34:16] validate_each_file
[START] [2020-07-22 15:34:16] convert_to_csv
[CMD] [2020-07-22 15:34:16] /usr/bin/sort /app/public/converted_csv/gatesy_middleton_nodes_22111.csv > /app/public/converted_csv/gatesy_middleton_nodes_22111.csv_sorted
[CMD] [2020-07-22 15:34:16] /usr/bin/sort /app/public/converted_csv/gatesy_middleton_occurrences_22112.csv > /app/public/converted_csv/gatesy_middleton_occurrences_22112.csv_sorted
[CMD] [2020-07-22 15:34:16] /usr/bin/sort /app/public/converted_csv/gatesy_middleton_measurements_22113.csv > /app/public/converted_csv/gatesy_middleton_measurements_22113.csv_sorted
[STOP] [2020-07-22 15:34:16] convert_to_csv
[START] [2020-07-22 15:34:16] calculate_delta
[CMD] [2020-07-22 15:34:16] echo "0a" > /app/public/diff/gatesy_middleton_nodes_22111.diff
[CMD] [2020-07-22 15:34:16] tail -n +1 /app/public/converted_csv/gatesy_middleton_nodes_22111.csv >> /app/public/diff/gatesy_middleton_nodes_22111.diff
[CMD] [2020-07-22 15:34:16] echo "." >> /app/public/diff/gatesy_middleton_nodes_22111.diff
[CMD] [2020-07-22 15:34:16] echo "0a" > /app/public/diff/gatesy_middleton_occurrences_22112.diff
[CMD] [2020-07-22 15:34:16] tail -n +1 /app/public/converted_csv/gatesy_middleton_occurrences_22112.csv >> /app/public/diff/gatesy_middleton_occurrences_22112.diff
[CMD] [2020-07-22 15:34:16] echo "." >> /app/public/diff/gatesy_middleton_occurrences_22112.diff
[CMD] [2020-07-22 15:34:16] echo "0a" > /app/public/diff/gatesy_middleton_measurements_22113.diff
[CMD] [2020-07-22 15:34:16] tail -n +1 /app/public/converted_csv/gatesy_middleton_measurements_22113.csv >> /app/public/diff/gatesy_middleton_measurements_22113.diff
[CMD] [2020-07-22 15:34:16] echo "." >> /app/public/diff/gatesy_middleton_measurements_22113.diff
[STOP] [2020-07-22 15:34:16] calculate_delta
[START] [2020-07-22 15:34:16] parse_diff_and_store
[INFO] [2020-07-22 15:34:16] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-22 15:34:16] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-22 15:34:16] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-22 15:34:17] Storing 1 ScientificNames
[INFO] [2020-07-22 15:34:17] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 15:34:17] Average Time: 0.0
[INFO] [2020-07-22 15:34:17] Total Time: 1s
[INFO] [2020-07-22 15:34:17] Storing 1 Nodes
[INFO] [2020-07-22 15:34:17] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 15:34:17] Average Time: 0.0
[INFO] [2020-07-22 15:34:17] Total Time: 1s
[INFO] [2020-07-22 15:34:17] Storing 1 Occurrences
[INFO] [2020-07-22 15:34:17] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 15:34:17] Average Time: 0.0
[INFO] [2020-07-22 15:34:17] Total Time: 1s
[INFO] [2020-07-22 15:34:17] Storing 2 Traits
[INFO] [2020-07-22 15:34:17] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 15:34:17] Average Time: 0.0
[INFO] [2020-07-22 15:34:17] Total Time: 1s
[INFO] [2020-07-22 15:34:17] Storing 2 MetaTraits
[INFO] [2020-07-22 15:34:17] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 15:34:17] Average Time: 0.0
[INFO] [2020-07-22 15:34:17] Total Time: 1s
[STOP] [2020-07-22 15:34:17] parse_diff_and_store
[START] [2020-07-22 15:34:17] resolve_keys
[INFO] [2020-07-22 15:34:23] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-22 15:34:23] traits to occurrences...
[INFO] [2020-07-22 15:34:23] traits to nodes (through occurrences)...
[INFO] [2020-07-22 15:34:23] Traits to sex term...
[INFO] [2020-07-22 15:34:23] Traits to lifestage term...
[INFO] [2020-07-22 15:34:23] MetaTraits to traits...
[INFO] [2020-07-22 15:34:23] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-22 15:34:23] Assocs to occurrences...
[INFO] [2020-07-22 15:34:23] Assocs to nodes...
[INFO] [2020-07-22 15:34:23] Assoc to sex term...
[INFO] [2020-07-22 15:34:23] Assoc to lifestage term...
[STOP] [2020-07-22 15:34:23] resolve_keys
[START] [2020-07-22 15:34:23] hold_for_later_1
[STOP] [2020-07-22 15:34:23] hold_for_later_1
[START] [2020-07-22 15:34:23] hold_for_later_2
[STOP] [2020-07-22 15:34:23] hold_for_later_2
[START] [2020-07-22 15:34:23] resolve_missing_parents
[STOP] [2020-07-22 15:34:23] resolve_missing_parents
[START] [2020-07-22 15:34:23] rebuild_nodes
[START] [2020-07-22 15:34:23] Flattener#flatten
[START] [2020-07-22 15:34:23] Flattener#study_resource
[START] [2020-07-22 15:34:23] Flattener#build_ancestry
[STOP] [2020-07-22 15:34:23] Flattener#build_ancestry
[INFO] [2020-07-22 15:34:23] 1 ancestry keys
[START] [2020-07-22 15:34:23] build_node_ancestors
[INFO] [2020-07-22 15:34:23] old ancestors deleted.
[STOP] [2020-07-22 15:34:23] build_node_ancestors
[WARN] [2020-07-22 15:34:23] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-22 15:34:23] Flattener#flatten
[STOP] [2020-07-22 15:34:23] rebuild_nodes
[START] [2020-07-22 15:34:23] resolve_missing_media_owners
[STOP] [2020-07-22 15:34:23] resolve_missing_media_owners
[START] [2020-07-22 15:34:23] sanitize_media_verbatims
[STOP] [2020-07-22 15:34:23] sanitize_media_verbatims
[START] [2020-07-22 15:34:23] queue_downloads
[STOP] [2020-07-22 15:34:23] queue_downloads
[START] [2020-07-22 15:34:23] parse_names
[WARN] [2020-07-22 15:34:23] I see 1 names which still need to be parsed.
[STOP] [2020-07-22 15:34:25] parse_names
[START] [2020-07-22 15:34:25] denormalize_canonical_names_to_nodes
[STOP] [2020-07-22 15:34:25] denormalize_canonical_names_to_nodes
[START] [2020-07-22 15:34:25] match_nodes
[START] [2020-07-22 15:34:25] map_all_nodes_to_pages
[STOP] [2020-07-22 15:34:25] map_all_nodes_to_pages
[INFO] [2020-07-22 15:34:25] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-07-22 15:34:25] update_nodes
[STOP] [2020-07-22 15:34:25] update_nodes
[STOP] [2020-07-22 15:34:25] match_nodes
[START] [2020-07-22 15:34:25] reindex_search
[STOP] [2020-07-22 15:34:25] reindex_search
[START] [2020-07-22 15:34:25] normalize_units
[STOP] [2020-07-22 15:34:25] normalize_units
[START] [2020-07-22 15:34:25] calculate_statistics
[2020-07-22 15:34:25] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-22 15:34:25] calculate_statistics
[START] [2020-07-22 15:34:25] complete_harvest_instance
[START] [2020-07-22 15:34:25] overall_tsv_creation
[INFO] [2020-07-22 15:34:25] Processing group of 1 in 1 batches of 10000
[INFO] [2020-07-22 15:35:13] 1 Traits (unfiltered)...
[INFO] [2020-07-22 15:35:47] 1 Traits (filtered)...
[INFO] [2020-07-22 15:35:47] 0 Associations (filtered)...
[INFO] [2020-07-22 15:35:47] 3 metadata added.
[INFO] [2020-07-22 15:35:47] 0 metadata added.
[INFO] [2020-07-22 15:35:47] Average Time: 55.58
[INFO] [2020-07-22 15:35:47] Total Time: 1m23s
[STOP] [2020-07-22 15:35:47] overall_tsv_creation
[INFO] [2020-07-22 15:35:47] Done. Check your files:
[INFO] [2020-07-22 15:35:47] (1 lines) /app/public/data/gatesy_middleton/publish_nodes.tsv
[INFO] [2020-07-22 15:35:47] (1 lines) /app/public/data/gatesy_middleton/publish_scientific_names.tsv
[INFO] [2020-07-22 15:35:47] (2 lines) /app/public/data/gatesy_middleton/publish_traits.tsv
[INFO] [2020-07-22 15:35:47] (2 lines) /app/public/data/gatesy_middleton/publish_metadata.tsv
[STOP] [2020-07-22 15:35:47] complete_harvest_instance
[START] [2020-07-22 15:35:47] completed
[STOP] [2020-07-22 15:35:47] completed
[STOP] [2020-07-22 15:35:47] logged process, took 92.04
Latest Process

22 Jul 15:34 EXITED currently processing 0