Harvest for
Burr 1984
Created
19 Apr 15:19
Stage:
completed
Fetched:
19 Apr 15:19
Validated:
19 Apr 15:19
Deltas Created
19 Apr 15:19
Units Normalized:
19 Apr 15:19
Ancestry Built:
19 Apr 15:19
Nodes Matched:
19 Apr 15:19
Names Parsed:
19 Apr 15:19
New Models Stored:
19 Apr 15:19
Indexed:
19 Apr 15:19
Completed:
19 Apr 15:21
Time to Harvest:
less than a minute
Harvesting Log
(641 lines)
# Logfile created on 2020-08-27 15:37:44 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:37:44] logged process
[START] [2020-08-27 15:37:44] Creating resource from OpenData
[START] [2020-08-27 15:37:45] logged process
[START] [2020-08-27 15:37:45] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:37:45] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:37:45] Creating resource from OpenData
[INFO] [2020-11-19 14:00:53] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-11-19 14:01:27] ## remove_type: ScientificName
[INFO] [2020-11-19 14:01:27] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:01:27] [14:01:27.451] Removed 0 Scientificnames
[INFO] [2020-11-19 14:01:27] ## remove_type: Vernacular
[INFO] [2020-11-19 14:01:27] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:01:27] [14:01:27.452] Removed 0 Vernaculars
[INFO] [2020-11-19 14:01:27] ## remove_type: Article
[INFO] [2020-11-19 14:01:27] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:01:27] [14:01:27.453] Removed 0 Articles
[INFO] [2020-11-19 14:01:27] ## remove_type: Medium
[INFO] [2020-11-19 14:01:27] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:01:27] [14:01:27.454] Removed 0 Media
[INFO] [2020-11-19 14:01:27] ## remove_type: Trait
[INFO] [2020-11-19 14:01:27] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:01:27] [14:01:27.456] Removed 0 Traits
[INFO] [2020-11-19 14:01:27] ## remove_type: MetaTrait
[INFO] [2020-11-19 14:01:27] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:01:27] [14:01:27.457] Removed 0 Metatraits
[INFO] [2020-11-19 14:01:27] ## remove_type: OccurrenceMetadatum
[INFO] [2020-11-19 14:01:27] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:01:27] [14:01:27.458] Removed 0 Occurrencemetadata
[INFO] [2020-11-19 14:01:27] ## remove_type: Assoc
[INFO] [2020-11-19 14:01:27] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:01:27] [14:01:27.459] Removed 0 Assocs
[INFO] [2020-11-19 14:01:27] ## remove_type: MetaAssoc
[INFO] [2020-11-19 14:01:27] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:01:27] [14:01:27.460] Removed 0 Metaassocs
[INFO] [2020-11-19 14:01:27] ## remove_type: Identifier
[INFO] [2020-11-19 14:01:27] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:01:27] [14:01:27.461] Removed 0 Identifiers
[INFO] [2020-11-19 14:01:27] ## remove_type: Reference
[INFO] [2020-11-19 14:01:27] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:01:27] [14:01:27.463] Removed 0 References
[INFO] [2020-11-19 14:01:27] ## remove_type: Node
[INFO] [2020-11-19 14:01:27] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:01:27] [14:01:27.475] Removed 0 Nodes
[START] [2020-11-19 14:01:27] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 14:01:27] Creating resource from OpenData
[START] [2020-11-19 14:01:27] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 14:01:27] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 14:01:27] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 14:01:27] Creating resource from OpenData
[START] [2020-11-19 14:01:27] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 14:01:27] create_harvest_instance
[STOP] [2020-11-19 14:01:29] create_harvest_instance
[START] [2020-11-19 14:01:29] fetch_files
[STOP] [2020-11-19 14:01:29] fetch_files
[START] [2020-11-19 14:01:29] validate_each_file
[STOP] [2020-11-19 14:01:29] validate_each_file
[START] [2020-11-19 14:01:29] convert_to_csv
[CMD] [2020-11-19 14:01:29] /usr/bin/sort /app/public/converted_csv/burr_burr_1984_refs_24510.csv > /app/public/converted_csv/burr_burr_1984_refs_24510.csv_sorted
[CMD] [2020-11-19 14:01:29] /usr/bin/sort /app/public/converted_csv/burr_burr_1984_nodes_24511.csv > /app/public/converted_csv/burr_burr_1984_nodes_24511.csv_sorted
[CMD] [2020-11-19 14:01:29] /usr/bin/sort /app/public/converted_csv/burr_burr_1984_occurrences_24512.csv > /app/public/converted_csv/burr_burr_1984_occurrences_24512.csv_sorted
[CMD] [2020-11-19 14:01:29] /usr/bin/sort /app/public/converted_csv/burr_burr_1984_measurements_24513.csv > /app/public/converted_csv/burr_burr_1984_measurements_24513.csv_sorted
[STOP] [2020-11-19 14:01:29] convert_to_csv
[START] [2020-11-19 14:01:29] calculate_delta
[CMD] [2020-11-19 14:01:29] echo "0a" > /app/public/diff/burr_burr_1984_refs_24510.diff
[CMD] [2020-11-19 14:01:29] tail -n +1 /app/public/converted_csv/burr_burr_1984_refs_24510.csv >> /app/public/diff/burr_burr_1984_refs_24510.diff
[CMD] [2020-11-19 14:01:29] echo "." >> /app/public/diff/burr_burr_1984_refs_24510.diff
[CMD] [2020-11-19 14:01:29] echo "0a" > /app/public/diff/burr_burr_1984_nodes_24511.diff
[CMD] [2020-11-19 14:01:29] tail -n +1 /app/public/converted_csv/burr_burr_1984_nodes_24511.csv >> /app/public/diff/burr_burr_1984_nodes_24511.diff
[CMD] [2020-11-19 14:01:29] echo "." >> /app/public/diff/burr_burr_1984_nodes_24511.diff
[CMD] [2020-11-19 14:01:29] echo "0a" > /app/public/diff/burr_burr_1984_occurrences_24512.diff
[CMD] [2020-11-19 14:01:29] tail -n +1 /app/public/converted_csv/burr_burr_1984_occurrences_24512.csv >> /app/public/diff/burr_burr_1984_occurrences_24512.diff
[CMD] [2020-11-19 14:01:29] echo "." >> /app/public/diff/burr_burr_1984_occurrences_24512.diff
[CMD] [2020-11-19 14:01:29] echo "0a" > /app/public/diff/burr_burr_1984_measurements_24513.diff
[CMD] [2020-11-19 14:01:29] tail -n +1 /app/public/converted_csv/burr_burr_1984_measurements_24513.csv >> /app/public/diff/burr_burr_1984_measurements_24513.diff
[CMD] [2020-11-19 14:01:29] echo "." >> /app/public/diff/burr_burr_1984_measurements_24513.diff
[STOP] [2020-11-19 14:01:29] calculate_delta
[START] [2020-11-19 14:01:29] parse_diff_and_store
[INFO] [2020-11-19 14:01:29] Loading refs diff file into memory (true lines)...
[INFO] [2020-11-19 14:01:29] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-19 14:01:29] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-19 14:01:29] Loading measurements diff file into memory (true lines)...
[INFO] [2020-11-19 14:01:29] Storing 6 ScientificNames
[INFO] [2020-11-19 14:01:29] Processing group of 6 in 1 groups of 1000
[INFO] [2020-11-19 14:01:29] Average Time: 0.0
[INFO] [2020-11-19 14:01:29] Total Time: 1s
[INFO] [2020-11-19 14:01:29] Storing 6 Nodes
[INFO] [2020-11-19 14:01:29] Processing group of 6 in 1 groups of 1000
[INFO] [2020-11-19 14:01:29] Average Time: 0.0
[INFO] [2020-11-19 14:01:29] Total Time: 1s
[INFO] [2020-11-19 14:01:29] Storing 6 Occurrences
[INFO] [2020-11-19 14:01:29] Processing group of 6 in 1 groups of 1000
[INFO] [2020-11-19 14:01:29] Average Time: 0.01
[INFO] [2020-11-19 14:01:29] Total Time: 1s
[INFO] [2020-11-19 14:01:29] Storing 1 OccurrenceMetadata
[INFO] [2020-11-19 14:01:29] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 14:01:29] Average Time: 0.0
[INFO] [2020-11-19 14:01:29] Total Time: 1s
[INFO] [2020-11-19 14:01:29] Storing 7 Traits
[INFO] [2020-11-19 14:01:29] Processing group of 7 in 1 groups of 1000
[INFO] [2020-11-19 14:01:29] Average Time: 0.01
[INFO] [2020-11-19 14:01:29] Total Time: 1s
[INFO] [2020-11-19 14:01:29] Storing 12 MetaTraits
[INFO] [2020-11-19 14:01:29] Processing group of 12 in 1 groups of 1000
[INFO] [2020-11-19 14:01:29] Average Time: 0.0
[INFO] [2020-11-19 14:01:29] Total Time: 1s
[STOP] [2020-11-19 14:01:29] parse_diff_and_store
[START] [2020-11-19 14:01:29] resolve_keys
[STOP] [2020-11-19 14:01:31] resolve_keys
[ERR] [2020-11-19 14:01:31] ActiveRecord::StatementInvalid
[ERR] [2020-11-19 14:01:31] Lockfile::StolenLockError: Lockfile::StolenLockError: SELECT MIN(`articles_sections`.`id`) FROM `articles_sections` WHERE (1=1) AND `articles_sections`.`harvest_id` = 3223
[ERR] [2020-11-19 14:01:31] ./config/initializers/core_extensions.rb:14:in `propagate_id'
[ERR] [2020-11-19 14:01:31] ../models/resource_harvester.rb:593:in `propagate_id'
[ERR] [2020-11-19 14:01:31] ../models/resource_harvester.rb:488:in `resolve_article_keys'
[ERR] [2020-11-19 14:01:31] ../models/resource_harvester.rb:446:in `resolve_keys'
[ERR] [2020-11-19 14:01:31] ../models/resource_harvester.rb:85:in `block (3 levels) in start'
[ERR] [2020-11-19 14:01:31] ../models/logged_process.rb:19:in `run_step'
[ERR] [2020-11-19 14:01:31] ../models/resource_harvester.rb:85:in `block (2 levels) in start'
[ERR] [2020-11-19 14:01:31] ../models/resource_harvester.rb:74:in `each_key'
[ERR] [2020-11-19 14:01:31] ../models/resource_harvester.rb:74:in `block in start'
[ERR] [2020-11-19 14:01:31] ../models/resource.rb:151:in `lock'
[ERR] [2020-11-19 14:01:31] ../models/resource_harvester.rb:72:in `start'
[ERR] [2020-11-19 14:01:31] ../models/resource.rb:232:in `harvest'
[ERR] [2020-11-19 14:01:31] ../models/resource.rb:208:in `re_download_opendata_and_harvest'
[ERR] [2020-11-19 14:01:31] bin/rails:4:in `require'
[ERR] [2020-11-19 14:01:31] bin/rails:4:in `<main>'
[STOP] [2020-11-19 14:01:31] logged process, took 4.09
[INFO] [2020-11-19 14:02:32] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-11-19 14:02:35] ## remove_type: ScientificName
[INFO] [2020-11-19 14:02:35] ++ Calling delete_all on 6 instances...
[INFO] [2020-11-19 14:02:35] [14:02:35.783] Removed 6 Scientificnames
[INFO] [2020-11-19 14:02:35] ## remove_type: Vernacular
[INFO] [2020-11-19 14:02:35] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:02:35] [14:02:35.785] Removed 0 Vernaculars
[INFO] [2020-11-19 14:02:35] ## remove_type: Article
[INFO] [2020-11-19 14:02:35] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:02:35] [14:02:35.788] Removed 0 Articles
[INFO] [2020-11-19 14:02:35] ## remove_type: Medium
[INFO] [2020-11-19 14:02:35] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:02:35] [14:02:35.792] Removed 0 Media
[INFO] [2020-11-19 14:02:35] ## remove_type: Trait
[INFO] [2020-11-19 14:02:35] ++ Calling delete_all on 7 instances...
[INFO] [2020-11-19 14:02:35] [14:02:35.796] Removed 7 Traits
[INFO] [2020-11-19 14:02:35] ## remove_type: MetaTrait
[INFO] [2020-11-19 14:02:35] ++ Calling delete_all on 12 instances...
[INFO] [2020-11-19 14:02:35] [14:02:35.799] Removed 12 Metatraits
[INFO] [2020-11-19 14:02:35] ## remove_type: OccurrenceMetadatum
[INFO] [2020-11-19 14:02:35] ++ Calling delete_all on 1 instances...
[INFO] [2020-11-19 14:02:35] [14:02:35.802] Removed 1 Occurrencemetadata
[INFO] [2020-11-19 14:02:35] ## remove_type: Assoc
[INFO] [2020-11-19 14:02:35] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:02:35] [14:02:35.805] Removed 0 Assocs
[INFO] [2020-11-19 14:02:35] ## remove_type: MetaAssoc
[INFO] [2020-11-19 14:02:35] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:02:35] [14:02:35.809] Removed 0 Metaassocs
[INFO] [2020-11-19 14:02:35] ## remove_type: Identifier
[INFO] [2020-11-19 14:02:35] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:02:35] [14:02:35.811] Removed 0 Identifiers
[INFO] [2020-11-19 14:02:35] ## remove_type: Reference
[INFO] [2020-11-19 14:02:35] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:02:35] [14:02:35.814] Removed 0 References
[INFO] [2020-11-19 14:02:35] ## remove_type: Node
[INFO] [2020-11-19 14:02:35] ++ Calling delete_all on 6 instances...
[INFO] [2020-11-19 14:02:35] [14:02:35.833] Removed 6 Nodes
[START] [2020-11-19 14:02:36] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 14:02:36] Creating resource from OpenData
[START] [2020-11-19 14:02:36] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 14:02:36] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 14:02:36] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 14:02:36] Creating resource from OpenData
[START] [2020-11-19 14:02:36] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 14:02:36] create_harvest_instance
[STOP] [2020-11-19 14:02:37] create_harvest_instance
[START] [2020-11-19 14:02:37] fetch_files
[STOP] [2020-11-19 14:02:38] fetch_files
[START] [2020-11-19 14:02:38] validate_each_file
[STOP] [2020-11-19 14:02:38] validate_each_file
[START] [2020-11-19 14:02:38] convert_to_csv
[CMD] [2020-11-19 14:02:38] /usr/bin/sort /app/public/converted_csv/burr_burr_1984_refs_24518.csv > /app/public/converted_csv/burr_burr_1984_refs_24518.csv_sorted
[CMD] [2020-11-19 14:02:38] /usr/bin/sort /app/public/converted_csv/burr_burr_1984_nodes_24519.csv > /app/public/converted_csv/burr_burr_1984_nodes_24519.csv_sorted
[CMD] [2020-11-19 14:02:38] /usr/bin/sort /app/public/converted_csv/burr_burr_1984_occurrences_24520.csv > /app/public/converted_csv/burr_burr_1984_occurrences_24520.csv_sorted
[CMD] [2020-11-19 14:02:38] /usr/bin/sort /app/public/converted_csv/burr_burr_1984_measurements_24521.csv > /app/public/converted_csv/burr_burr_1984_measurements_24521.csv_sorted
[STOP] [2020-11-19 14:02:38] convert_to_csv
[START] [2020-11-19 14:02:38] calculate_delta
[CMD] [2020-11-19 14:02:38] echo "0a" > /app/public/diff/burr_burr_1984_refs_24518.diff
[CMD] [2020-11-19 14:02:38] tail -n +1 /app/public/converted_csv/burr_burr_1984_refs_24518.csv >> /app/public/diff/burr_burr_1984_refs_24518.diff
[CMD] [2020-11-19 14:02:38] echo "." >> /app/public/diff/burr_burr_1984_refs_24518.diff
[CMD] [2020-11-19 14:02:38] echo "0a" > /app/public/diff/burr_burr_1984_nodes_24519.diff
[CMD] [2020-11-19 14:02:38] tail -n +1 /app/public/converted_csv/burr_burr_1984_nodes_24519.csv >> /app/public/diff/burr_burr_1984_nodes_24519.diff
[CMD] [2020-11-19 14:02:38] echo "." >> /app/public/diff/burr_burr_1984_nodes_24519.diff
[CMD] [2020-11-19 14:02:38] echo "0a" > /app/public/diff/burr_burr_1984_occurrences_24520.diff
[CMD] [2020-11-19 14:02:38] tail -n +1 /app/public/converted_csv/burr_burr_1984_occurrences_24520.csv >> /app/public/diff/burr_burr_1984_occurrences_24520.diff
[CMD] [2020-11-19 14:02:38] echo "." >> /app/public/diff/burr_burr_1984_occurrences_24520.diff
[CMD] [2020-11-19 14:02:38] echo "0a" > /app/public/diff/burr_burr_1984_measurements_24521.diff
[CMD] [2020-11-19 14:02:38] tail -n +1 /app/public/converted_csv/burr_burr_1984_measurements_24521.csv >> /app/public/diff/burr_burr_1984_measurements_24521.diff
[CMD] [2020-11-19 14:02:38] echo "." >> /app/public/diff/burr_burr_1984_measurements_24521.diff
[STOP] [2020-11-19 14:02:38] calculate_delta
[START] [2020-11-19 14:02:38] parse_diff_and_store
[INFO] [2020-11-19 14:02:38] Loading refs diff file into memory (true lines)...
[INFO] [2020-11-19 14:02:38] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-19 14:02:38] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-19 14:02:39] Loading measurements diff file into memory (true lines)...
[INFO] [2020-11-19 14:02:39] Storing 6 ScientificNames
[INFO] [2020-11-19 14:02:39] Processing group of 6 in 1 groups of 1000
[INFO] [2020-11-19 14:02:39] Average Time: 0.0
[INFO] [2020-11-19 14:02:39] Total Time: 1s
[INFO] [2020-11-19 14:02:39] Storing 6 Nodes
[INFO] [2020-11-19 14:02:39] Processing group of 6 in 1 groups of 1000
[INFO] [2020-11-19 14:02:39] Average Time: 0.0
[INFO] [2020-11-19 14:02:39] Total Time: 1s
[INFO] [2020-11-19 14:02:39] Storing 6 Occurrences
[INFO] [2020-11-19 14:02:39] Processing group of 6 in 1 groups of 1000
[INFO] [2020-11-19 14:02:39] Average Time: 0.0
[INFO] [2020-11-19 14:02:39] Total Time: 1s
[INFO] [2020-11-19 14:02:39] Storing 1 OccurrenceMetadata
[INFO] [2020-11-19 14:02:39] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 14:02:39] Average Time: 0.0
[INFO] [2020-11-19 14:02:39] Total Time: 1s
[INFO] [2020-11-19 14:02:39] Storing 7 Traits
[INFO] [2020-11-19 14:02:39] Processing group of 7 in 1 groups of 1000
[INFO] [2020-11-19 14:02:39] Average Time: 0.0
[INFO] [2020-11-19 14:02:39] Total Time: 1s
[INFO] [2020-11-19 14:02:39] Storing 12 MetaTraits
[INFO] [2020-11-19 14:02:39] Processing group of 12 in 1 groups of 1000
[INFO] [2020-11-19 14:02:39] Average Time: 0.0
[INFO] [2020-11-19 14:02:39] Total Time: 1s
[STOP] [2020-11-19 14:02:39] parse_diff_and_store
[START] [2020-11-19 14:02:39] resolve_keys
[INFO] [2020-11-19 14:02:45] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-19 14:02:45] traits to occurrences...
[INFO] [2020-11-19 14:02:45] traits to nodes (through occurrences)...
[INFO] [2020-11-19 14:02:45] Traits to sex term...
[INFO] [2020-11-19 14:02:45] Traits to lifestage term...
[INFO] [2020-11-19 14:02:45] MetaTraits to traits...
[INFO] [2020-11-19 14:02:45] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-19 14:02:45] Assocs to occurrences...
[INFO] [2020-11-19 14:02:45] Assocs to nodes...
[INFO] [2020-11-19 14:02:45] Assoc to sex term...
[INFO] [2020-11-19 14:02:45] Assoc to lifestage term...
[INFO] [2020-11-19 14:02:45] MetaAssoc to assocs...
[STOP] [2020-11-19 14:02:45] resolve_keys
[START] [2020-11-19 14:02:45] hold_for_later_1
[STOP] [2020-11-19 14:02:45] hold_for_later_1
[START] [2020-11-19 14:02:45] hold_for_later_2
[STOP] [2020-11-19 14:02:45] hold_for_later_2
[START] [2020-11-19 14:02:45] resolve_missing_parents
[STOP] [2020-11-19 14:02:45] resolve_missing_parents
[START] [2020-11-19 14:02:45] rebuild_nodes
[START] [2020-11-19 14:02:45] Flattener#flatten
[START] [2020-11-19 14:02:45] Flattener#study_resource
[START] [2020-11-19 14:02:45] Flattener#build_ancestry
[STOP] [2020-11-19 14:02:45] Flattener#build_ancestry
[INFO] [2020-11-19 14:02:45] 6 ancestry keys
[START] [2020-11-19 14:02:45] build_node_ancestors
[INFO] [2020-11-19 14:02:45] old ancestors deleted.
[STOP] [2020-11-19 14:02:45] build_node_ancestors
[WARN] [2020-11-19 14:02:45] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-11-19 14:02:45] Flattener#flatten
[STOP] [2020-11-19 14:02:45] rebuild_nodes
[START] [2020-11-19 14:02:45] resolve_missing_media_owners
[STOP] [2020-11-19 14:02:45] resolve_missing_media_owners
[START] [2020-11-19 14:02:45] sanitize_media_verbatims
[STOP] [2020-11-19 14:02:45] sanitize_media_verbatims
[START] [2020-11-19 14:02:45] queue_downloads
[STOP] [2020-11-19 14:02:45] queue_downloads
[START] [2020-11-19 14:02:45] parse_names
[WARN] [2020-11-19 14:02:45] I see 6 names which still need to be parsed.
[STOP] [2020-11-19 14:02:46] parse_names
[START] [2020-11-19 14:02:46] denormalize_canonical_names_to_nodes
[STOP] [2020-11-19 14:02:46] denormalize_canonical_names_to_nodes
[START] [2020-11-19 14:02:46] match_nodes
[START] [2020-11-19 14:02:46] map_all_nodes_to_pages
[STOP] [2020-11-19 14:02:46] map_all_nodes_to_pages
[INFO] [2020-11-19 14:02:46] ZERO unmatched nodes (of 6)! Nicely done.
[START] [2020-11-19 14:02:46] update_nodes
[STOP] [2020-11-19 14:02:46] update_nodes
[STOP] [2020-11-19 14:02:46] match_nodes
[START] [2020-11-19 14:02:46] reindex_search
[STOP] [2020-11-19 14:02:46] reindex_search
[START] [2020-11-19 14:02:46] normalize_units
[STOP] [2020-11-19 14:02:46] normalize_units
[START] [2020-11-19 14:02:46] calculate_statistics
[2020-11-19 14:02:46] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-11-19 14:02:46] calculate_statistics
[START] [2020-11-19 14:02:46] complete_harvest_instance
[START] [2020-11-19 14:02:46] overall_tsv_creation
[INFO] [2020-11-19 14:02:46] Processing group of 6 in 1 batches of 10000
[INFO] [2020-11-19 14:03:29] 6 Traits (unfiltered)...
[INFO] [2020-11-19 14:04:14] 6 Traits (filtered)...
[INFO] [2020-11-19 14:04:14] 0 Associations (filtered)...
[INFO] [2020-11-19 14:04:14] 14 metadata added.
[INFO] [2020-11-19 14:04:14] 0 metadata added.
[INFO] [2020-11-19 14:04:14] Average Time: 68.18
[INFO] [2020-11-19 14:04:14] Total Time: 1m28s
[STOP] [2020-11-19 14:04:14] overall_tsv_creation
[INFO] [2020-11-19 14:04:14] Done. Check your files:
[INFO] [2020-11-19 14:04:14] (6 lines) /app/public/data/burr_burr_1984/publish_nodes.tsv
[INFO] [2020-11-19 14:04:14] (6 lines) /app/public/data/burr_burr_1984/publish_scientific_names.tsv
[INFO] [2020-11-19 14:04:14] (7 lines) /app/public/data/burr_burr_1984/publish_traits.tsv
[INFO] [2020-11-19 14:04:14] (14 lines) /app/public/data/burr_burr_1984/publish_metadata.tsv
[STOP] [2020-11-19 14:04:14] complete_harvest_instance
[START] [2020-11-19 14:04:14] completed
[STOP] [2020-11-19 14:04:14] completed
[STOP] [2020-11-19 14:04:14] logged process, took 97.85
[INFO] [2021-04-19 15:14:45] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:19:49] ## remove_type: ScientificName
[INFO] [2021-04-19 15:19:49] ++ Calling delete_all on 6 instances...
[INFO] [2021-04-19 15:19:49] [15:19:49.559] Removed 6 Scientificnames
[INFO] [2021-04-19 15:19:49] ## remove_type: Vernacular
[INFO] [2021-04-19 15:19:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:19:49] [15:19:49.561] Removed 0 Vernaculars
[INFO] [2021-04-19 15:19:49] ## remove_type: Article
[INFO] [2021-04-19 15:19:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:19:49] [15:19:49.562] Removed 0 Articles
[INFO] [2021-04-19 15:19:49] ## remove_type: Medium
[INFO] [2021-04-19 15:19:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:19:49] [15:19:49.564] Removed 0 Media
[INFO] [2021-04-19 15:19:49] ## remove_type: Trait
[INFO] [2021-04-19 15:19:49] ++ Calling delete_all on 7 instances...
[INFO] [2021-04-19 15:19:49] [15:19:49.566] Removed 7 Traits
[INFO] [2021-04-19 15:19:49] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:19:49] ++ Calling delete_all on 12 instances...
[INFO] [2021-04-19 15:19:49] [15:19:49.567] Removed 12 Metatraits
[INFO] [2021-04-19 15:19:49] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:19:49] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:19:49] [15:19:49.569] Removed 1 Occurrencemetadata
[INFO] [2021-04-19 15:19:49] ## remove_type: Assoc
[INFO] [2021-04-19 15:19:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:19:49] [15:19:49.570] Removed 0 Assocs
[INFO] [2021-04-19 15:19:49] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:19:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:19:49] [15:19:49.572] Removed 0 Metaassocs
[INFO] [2021-04-19 15:19:49] ## remove_type: Identifier
[INFO] [2021-04-19 15:19:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:19:49] [15:19:49.573] Removed 0 Identifiers
[INFO] [2021-04-19 15:19:49] ## remove_type: Reference
[INFO] [2021-04-19 15:19:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:19:49] [15:19:49.574] Removed 0 References
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:49] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] Starting batch with ID 84620930...
[INFO] [2021-04-19 15:19:50] ## remove_type: Node
[INFO] [2021-04-19 15:19:50] ++ Calling delete_all on 6 instances...
[INFO] [2021-04-19 15:19:50] [15:19:50.468] Removed 6 Nodes
[START] [2021-04-19 15:19:50] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:19:50] Creating resource from OpenData
[START] [2021-04-19 15:19:50] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:19:50] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:19:50] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:19:50] Creating resource from OpenData
[START] [2021-04-19 15:19:50] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:19:50] create_harvest_instance
[INFO] [2021-04-19 15:19:50] Created harvest instance #3762
[STOP] [2021-04-19 15:19:50] create_harvest_instance
[START] [2021-04-19 15:19:50] fetch_files
[STOP] [2021-04-19 15:19:50] fetch_files
[START] [2021-04-19 15:19:50] validate_each_file
[INFO] [2021-04-19 15:19:50] Looping over 4 formats...
[INFO] [2021-04-19 15:19:50] ...refs (/app/public/data/burr_burr_1984/references.tsv)
[INFO] [2021-04-19 15:19:50] Valid: /app/public/converted_csv/burr_burr_1984_refs_3762.csv (0 lines)
[INFO] [2021-04-19 15:19:50] ...nodes (/app/public/data/burr_burr_1984/taxa.txt)
[INFO] [2021-04-19 15:19:50] Valid: /app/public/converted_csv/burr_burr_1984_nodes_3762.csv (6 lines)
[INFO] [2021-04-19 15:19:50] ...occurrences (/app/public/data/burr_burr_1984/occurrences.txt)
[INFO] [2021-04-19 15:19:50] Valid: /app/public/converted_csv/burr_burr_1984_occurrences_3762.csv (6 lines)
[INFO] [2021-04-19 15:19:50] ...measurements (/app/public/data/burr_burr_1984/measurementsorfacts.txt)
[INFO] [2021-04-19 15:19:50] Valid: /app/public/converted_csv/burr_burr_1984_measurements_3762.csv (7 lines)
[STOP] [2021-04-19 15:19:50] validate_each_file
[START] [2021-04-19 15:19:50] convert_to_csv
[INFO] [2021-04-19 15:19:50] Looping over 4 formats...
[INFO] [2021-04-19 15:19:50] ...refs (/app/public/data/burr_burr_1984/references.tsv)
[CMD] [2021-04-19 15:19:50] /usr/bin/sort /app/public/converted_csv/burr_burr_1984_refs_3762.csv > /app/public/converted_csv/burr_burr_1984_refs_3762.csv_sorted
[INFO] [2021-04-19 15:19:50] Converted: /app/public/converted_csv/burr_burr_1984_refs_3762.csv (0 lines)
[INFO] [2021-04-19 15:19:50] ...nodes (/app/public/data/burr_burr_1984/taxa.txt)
[CMD] [2021-04-19 15:19:50] /usr/bin/sort /app/public/converted_csv/burr_burr_1984_nodes_3762.csv > /app/public/converted_csv/burr_burr_1984_nodes_3762.csv_sorted
[INFO] [2021-04-19 15:19:50] Converted: /app/public/converted_csv/burr_burr_1984_nodes_3762.csv (6 lines)
[INFO] [2021-04-19 15:19:50] ...occurrences (/app/public/data/burr_burr_1984/occurrences.txt)
[CMD] [2021-04-19 15:19:50] /usr/bin/sort /app/public/converted_csv/burr_burr_1984_occurrences_3762.csv > /app/public/converted_csv/burr_burr_1984_occurrences_3762.csv_sorted
[INFO] [2021-04-19 15:19:50] Converted: /app/public/converted_csv/burr_burr_1984_occurrences_3762.csv (6 lines)
[INFO] [2021-04-19 15:19:50] ...measurements (/app/public/data/burr_burr_1984/measurementsorfacts.txt)
[CMD] [2021-04-19 15:19:50] /usr/bin/sort /app/public/converted_csv/burr_burr_1984_measurements_3762.csv > /app/public/converted_csv/burr_burr_1984_measurements_3762.csv_sorted
[INFO] [2021-04-19 15:19:50] Converted: /app/public/converted_csv/burr_burr_1984_measurements_3762.csv (7 lines)
[STOP] [2021-04-19 15:19:50] convert_to_csv
[START] [2021-04-19 15:19:50] calculate_delta
[INFO] [2021-04-19 15:19:50] Looping over 4 formats...
[INFO] [2021-04-19 15:19:50] ...refs (/app/public/data/burr_burr_1984/references.tsv)
[CMD] [2021-04-19 15:19:50] echo "0a" > /app/public/diff/burr_burr_1984_refs_3762.diff
[CMD] [2021-04-19 15:19:50] tail -n +1 /app/public/converted_csv/burr_burr_1984_refs_3762.csv >> /app/public/diff/burr_burr_1984_refs_3762.diff
[CMD] [2021-04-19 15:19:50] echo "." >> /app/public/diff/burr_burr_1984_refs_3762.diff
[INFO] [2021-04-19 15:19:50] Created diff: /app/public/diff/burr_burr_1984_refs_3762.diff (2 lines)
[INFO] [2021-04-19 15:19:50] ...nodes (/app/public/data/burr_burr_1984/taxa.txt)
[CMD] [2021-04-19 15:19:50] echo "0a" > /app/public/diff/burr_burr_1984_nodes_3762.diff
[CMD] [2021-04-19 15:19:50] tail -n +1 /app/public/converted_csv/burr_burr_1984_nodes_3762.csv >> /app/public/diff/burr_burr_1984_nodes_3762.diff
[CMD] [2021-04-19 15:19:51] echo "." >> /app/public/diff/burr_burr_1984_nodes_3762.diff
[INFO] [2021-04-19 15:19:51] Created diff: /app/public/diff/burr_burr_1984_nodes_3762.diff (8 lines)
[INFO] [2021-04-19 15:19:51] ...occurrences (/app/public/data/burr_burr_1984/occurrences.txt)
[CMD] [2021-04-19 15:19:51] echo "0a" > /app/public/diff/burr_burr_1984_occurrences_3762.diff
[CMD] [2021-04-19 15:19:51] tail -n +1 /app/public/converted_csv/burr_burr_1984_occurrences_3762.csv >> /app/public/diff/burr_burr_1984_occurrences_3762.diff
[CMD] [2021-04-19 15:19:51] echo "." >> /app/public/diff/burr_burr_1984_occurrences_3762.diff
[INFO] [2021-04-19 15:19:51] Created diff: /app/public/diff/burr_burr_1984_occurrences_3762.diff (8 lines)
[INFO] [2021-04-19 15:19:51] ...measurements (/app/public/data/burr_burr_1984/measurementsorfacts.txt)
[CMD] [2021-04-19 15:19:51] echo "0a" > /app/public/diff/burr_burr_1984_measurements_3762.diff
[CMD] [2021-04-19 15:19:51] tail -n +1 /app/public/converted_csv/burr_burr_1984_measurements_3762.csv >> /app/public/diff/burr_burr_1984_measurements_3762.diff
[CMD] [2021-04-19 15:19:51] echo "." >> /app/public/diff/burr_burr_1984_measurements_3762.diff
[INFO] [2021-04-19 15:19:51] Created diff: /app/public/diff/burr_burr_1984_measurements_3762.diff (9 lines)
[STOP] [2021-04-19 15:19:51] calculate_delta
[START] [2021-04-19 15:19:51] parse_diff_and_store
[INFO] [2021-04-19 15:19:51] Handling diff: /app/public/diff/burr_burr_1984_refs_3762.diff (2 lines)
[INFO] [2021-04-19 15:19:51] Loading refs diff file into memory (2 /app/public/diff/burr_burr_1984_refs_3762.diff lines)...
[INFO] [2021-04-19 15:19:51] Handling diff: /app/public/diff/burr_burr_1984_nodes_3762.diff (8 lines)
[INFO] [2021-04-19 15:19:51] Loading nodes diff file into memory (8 /app/public/diff/burr_burr_1984_nodes_3762.diff lines)...
[INFO] [2021-04-19 15:19:51] Handling diff: /app/public/diff/burr_burr_1984_occurrences_3762.diff (8 lines)
[INFO] [2021-04-19 15:19:51] Loading occurrences diff file into memory (8 /app/public/diff/burr_burr_1984_occurrences_3762.diff lines)...
[INFO] [2021-04-19 15:19:51] Handling diff: /app/public/diff/burr_burr_1984_measurements_3762.diff (9 lines)
[INFO] [2021-04-19 15:19:51] Loading measurements diff file into memory (9 /app/public/diff/burr_burr_1984_measurements_3762.diff lines)...
[INFO] [2021-04-19 15:19:51] Storing 6 ScientificNames
[INFO] [2021-04-19 15:19:51] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 15:19:51] Average Time: 0.0
[INFO] [2021-04-19 15:19:51] Total Time: 1s
[INFO] [2021-04-19 15:19:51] Storing 6 Nodes
[INFO] [2021-04-19 15:19:51] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 15:19:51] Average Time: 0.0
[INFO] [2021-04-19 15:19:51] Total Time: 1s
[INFO] [2021-04-19 15:19:51] Storing 6 Occurrences
[INFO] [2021-04-19 15:19:51] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 15:19:51] Average Time: 0.0
[INFO] [2021-04-19 15:19:51] Total Time: 1s
[INFO] [2021-04-19 15:19:51] Storing 1 OccurrenceMetadata
[INFO] [2021-04-19 15:19:51] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:19:51] Average Time: 0.0
[INFO] [2021-04-19 15:19:51] Total Time: 1s
[INFO] [2021-04-19 15:19:51] Storing 7 Traits
[INFO] [2021-04-19 15:19:51] Processing group of 7 in 1 groups of 1000
[INFO] [2021-04-19 15:19:51] Average Time: 0.0
[INFO] [2021-04-19 15:19:51] Total Time: 1s
[INFO] [2021-04-19 15:19:51] Storing 12 MetaTraits
[INFO] [2021-04-19 15:19:51] Processing group of 12 in 1 groups of 1000
[INFO] [2021-04-19 15:19:51] Average Time: 0.0
[INFO] [2021-04-19 15:19:51] Total Time: 1s
[STOP] [2021-04-19 15:19:51] parse_diff_and_store
[START] [2021-04-19 15:19:51] resolve_keys
[INFO] [2021-04-19 15:19:57] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:19:57] traits to occurrences...
[INFO] [2021-04-19 15:19:57] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:19:57] Traits to sex term...
[INFO] [2021-04-19 15:19:57] Traits to lifestage term...
[INFO] [2021-04-19 15:19:57] MetaTraits to traits...
[INFO] [2021-04-19 15:19:57] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:19:57] Assocs to occurrences...
[INFO] [2021-04-19 15:19:57] Assocs to nodes...
[INFO] [2021-04-19 15:19:57] Assoc to sex term...
[INFO] [2021-04-19 15:19:57] Assoc to lifestage term...
[INFO] [2021-04-19 15:19:57] MetaAssoc to assocs...
[STOP] [2021-04-19 15:19:57] resolve_keys
[START] [2021-04-19 15:19:57] hold_for_later_1
[STOP] [2021-04-19 15:19:57] hold_for_later_1
[START] [2021-04-19 15:19:57] hold_for_later_2
[STOP] [2021-04-19 15:19:57] hold_for_later_2
[START] [2021-04-19 15:19:57] resolve_missing_parents
[STOP] [2021-04-19 15:19:57] resolve_missing_parents
[START] [2021-04-19 15:19:57] rebuild_nodes
[START] [2021-04-19 15:19:57] Flattener#flatten
[START] [2021-04-19 15:19:57] Flattener#study_resource
[START] [2021-04-19 15:19:57] Flattener#build_ancestry
[STOP] [2021-04-19 15:19:57] Flattener#build_ancestry
[INFO] [2021-04-19 15:19:57] 6 ancestry keys
[START] [2021-04-19 15:19:57] build_node_ancestors
[INFO] [2021-04-19 15:19:57] old ancestors deleted.
[STOP] [2021-04-19 15:19:57] build_node_ancestors
[WARN] [2021-04-19 15:19:57] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:19:57] Flattener#flatten
[STOP] [2021-04-19 15:19:57] rebuild_nodes
[START] [2021-04-19 15:19:57] resolve_missing_media_owners
[STOP] [2021-04-19 15:19:57] resolve_missing_media_owners
[START] [2021-04-19 15:19:57] sanitize_media_verbatims
[STOP] [2021-04-19 15:19:57] sanitize_media_verbatims
[START] [2021-04-19 15:19:57] queue_downloads
[STOP] [2021-04-19 15:19:57] queue_downloads
[START] [2021-04-19 15:19:57] parse_names
[WARN] [2021-04-19 15:19:57] I see 6 names which still need to be parsed.
[STOP] [2021-04-19 15:19:58] parse_names
[START] [2021-04-19 15:19:58] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:19:58] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:19:58] match_nodes
[START] [2021-04-19 15:19:58] map_all_nodes_to_pages
[STOP] [2021-04-19 15:19:58] map_all_nodes_to_pages
[INFO] [2021-04-19 15:19:58] ZERO unmatched nodes (of 6)! Nicely done.
[START] [2021-04-19 15:19:58] update_nodes
[STOP] [2021-04-19 15:19:58] update_nodes
[STOP] [2021-04-19 15:19:58] match_nodes
[START] [2021-04-19 15:19:58] reindex_search
[STOP] [2021-04-19 15:19:58] reindex_search
[START] [2021-04-19 15:19:58] normalize_units
[STOP] [2021-04-19 15:19:58] normalize_units
[START] [2021-04-19 15:19:58] calculate_statistics
[2021-04-19 15:19:58] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:19:58] calculate_statistics
[START] [2021-04-19 15:19:58] complete_harvest_instance
[START] [2021-04-19 15:19:58] overall_tsv_creation
[INFO] [2021-04-19 15:19:58] Processing group of 6 in 1 batches of 10000
[INFO] [2021-04-19 15:20:34] 6 Traits (unfiltered)...
[INFO] [2021-04-19 15:21:08] 6 Traits (filtered)...
[INFO] [2021-04-19 15:21:08] 0 Associations (filtered)...
[INFO] [2021-04-19 15:21:08] 1 metadata added.
[INFO] [2021-04-19 15:21:08] 0 metadata added.
[INFO] [2021-04-19 15:21:34] Average Time: 71.7
[INFO] [2021-04-19 15:21:34] Total Time: 1m36s
[STOP] [2021-04-19 15:21:34] overall_tsv_creation
[INFO] [2021-04-19 15:21:34] Done. Check your files:
[INFO] [2021-04-19 15:21:34] (6 lines) /app/public/data/burr_burr_1984/publish_nodes.tsv
[INFO] [2021-04-19 15:21:34] (6 lines) /app/public/data/burr_burr_1984/publish_scientific_names.tsv
[INFO] [2021-04-19 15:21:34] (7 lines) /app/public/data/burr_burr_1984/publish_traits.tsv
[INFO] [2021-04-19 15:21:34] (2 lines) /app/public/data/burr_burr_1984/publish_metadata.tsv
[STOP] [2021-04-19 15:21:34] complete_harvest_instance
[START] [2021-04-19 15:21:34] completed
[STOP] [2021-04-19 15:21:34] completed
[STOP] [2021-04-19 15:21:34] logged process, took 103.59
Latest Process