Harvest for Garm and Nilsson 2014 Created 19 Apr 15:26

Stage: completed
Fetched: 19 Apr 15:26
Validated: 19 Apr 15:26
Deltas Created 19 Apr 15:26
Units Normalized: 19 Apr 15:26
Ancestry Built: 19 Apr 15:26
Nodes Matched: 19 Apr 15:26
Names Parsed: 19 Apr 15:26
New Models Stored: 19 Apr 15:26
Indexed: 19 Apr 15:26
Completed: 19 Apr 15:28
Time to Harvest: less than a minute

Harvesting Log

(421 lines)
# Logfile created on 2020-08-27 15:40:28 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:40:28] logged process
[START] [2020-08-27 15:40:28] Creating resource from OpenData
[START] [2020-08-27 15:40:28] logged process
[START] [2020-08-27 15:40:28] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:40:29] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:40:29] Creating resource from OpenData
[INFO] [2020-12-03 11:00:25] ## HARVEST: type = -harvest
[START] [2020-12-03 11:00:27] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-03 11:00:27] create_harvest_instance
[STOP] [2020-12-03 11:00:28] create_harvest_instance
[START] [2020-12-03 11:00:28] fetch_files
[STOP] [2020-12-03 11:00:28] fetch_files
[START] [2020-12-03 11:00:28] validate_each_file
[STOP] [2020-12-03 11:00:29] validate_each_file
[START] [2020-12-03 11:00:29] convert_to_csv
[CMD] [2020-12-03 11:00:29] /usr/bin/sort /app/public/converted_csv/garm_nilsson_gar_refs_24788.csv > /app/public/converted_csv/garm_nilsson_gar_refs_24788.csv_sorted
[CMD] [2020-12-03 11:00:29] /usr/bin/sort /app/public/converted_csv/garm_nilsson_gar_nodes_24789.csv > /app/public/converted_csv/garm_nilsson_gar_nodes_24789.csv_sorted
[CMD] [2020-12-03 11:00:29] /usr/bin/sort /app/public/converted_csv/garm_nilsson_gar_occurrences_24790.csv > /app/public/converted_csv/garm_nilsson_gar_occurrences_24790.csv_sorted
[CMD] [2020-12-03 11:00:29] /usr/bin/sort /app/public/converted_csv/garm_nilsson_gar_measurements_24791.csv > /app/public/converted_csv/garm_nilsson_gar_measurements_24791.csv_sorted
[STOP] [2020-12-03 11:00:29] convert_to_csv
[START] [2020-12-03 11:00:29] calculate_delta
[CMD] [2020-12-03 11:00:29] echo "0a" > /app/public/diff/garm_nilsson_gar_refs_24788.diff
[CMD] [2020-12-03 11:00:29] tail -n +1 /app/public/converted_csv/garm_nilsson_gar_refs_24788.csv >> /app/public/diff/garm_nilsson_gar_refs_24788.diff
[CMD] [2020-12-03 11:00:29] echo "." >> /app/public/diff/garm_nilsson_gar_refs_24788.diff
[CMD] [2020-12-03 11:00:29] echo "0a" > /app/public/diff/garm_nilsson_gar_nodes_24789.diff
[CMD] [2020-12-03 11:00:29] tail -n +1 /app/public/converted_csv/garm_nilsson_gar_nodes_24789.csv >> /app/public/diff/garm_nilsson_gar_nodes_24789.diff
[CMD] [2020-12-03 11:00:29] echo "." >> /app/public/diff/garm_nilsson_gar_nodes_24789.diff
[CMD] [2020-12-03 11:00:29] echo "0a" > /app/public/diff/garm_nilsson_gar_occurrences_24790.diff
[CMD] [2020-12-03 11:00:29] tail -n +1 /app/public/converted_csv/garm_nilsson_gar_occurrences_24790.csv >> /app/public/diff/garm_nilsson_gar_occurrences_24790.diff
[CMD] [2020-12-03 11:00:29] echo "." >> /app/public/diff/garm_nilsson_gar_occurrences_24790.diff
[CMD] [2020-12-03 11:00:29] echo "0a" > /app/public/diff/garm_nilsson_gar_measurements_24791.diff
[CMD] [2020-12-03 11:00:29] tail -n +1 /app/public/converted_csv/garm_nilsson_gar_measurements_24791.csv >> /app/public/diff/garm_nilsson_gar_measurements_24791.diff
[CMD] [2020-12-03 11:00:29] echo "." >> /app/public/diff/garm_nilsson_gar_measurements_24791.diff
[STOP] [2020-12-03 11:00:29] calculate_delta
[START] [2020-12-03 11:00:29] parse_diff_and_store
[INFO] [2020-12-03 11:00:29] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 11:00:29] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 11:00:29] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 11:00:29] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 11:00:30] Storing 1 References
[INFO] [2020-12-03 11:00:30] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:00:30] Average Time: 0.0
[INFO] [2020-12-03 11:00:30] Total Time: 1s
[INFO] [2020-12-03 11:00:30] Storing 2 ScientificNames
[INFO] [2020-12-03 11:00:30] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 11:00:30] Average Time: 0.01
[INFO] [2020-12-03 11:00:30] Total Time: 1s
[INFO] [2020-12-03 11:00:30] Storing 2 Nodes
[INFO] [2020-12-03 11:00:30] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 11:00:30] Average Time: 0.0
[INFO] [2020-12-03 11:00:30] Total Time: 1s
[INFO] [2020-12-03 11:00:30] Storing 2 Occurrences
[INFO] [2020-12-03 11:00:30] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 11:00:30] Average Time: 0.0
[INFO] [2020-12-03 11:00:30] Total Time: 1s
[INFO] [2020-12-03 11:00:30] Storing 4 Traits
[INFO] [2020-12-03 11:00:30] Processing group of 4 in 1 groups of 1000
[INFO] [2020-12-03 11:00:30] Average Time: 0.03
[INFO] [2020-12-03 11:00:30] Total Time: 1s
[INFO] [2020-12-03 11:00:30] Storing 3 MetaTraits
[INFO] [2020-12-03 11:00:30] Processing group of 3 in 1 groups of 1000
[INFO] [2020-12-03 11:00:30] Average Time: 0.0
[INFO] [2020-12-03 11:00:30] Total Time: 1s
[INFO] [2020-12-03 11:00:30] Storing 1 TraitsReferences
[INFO] [2020-12-03 11:00:30] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:00:30] Average Time: 0.0
[INFO] [2020-12-03 11:00:30] Total Time: 1s
[STOP] [2020-12-03 11:00:30] parse_diff_and_store
[START] [2020-12-03 11:00:30] resolve_keys
[INFO] [2020-12-03 11:00:35] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 11:00:35] traits to occurrences...
[INFO] [2020-12-03 11:00:36] traits to nodes (through occurrences)...
[INFO] [2020-12-03 11:00:36] Traits to sex term...
[INFO] [2020-12-03 11:00:36] Traits to lifestage term...
[INFO] [2020-12-03 11:00:36] MetaTraits to traits...
[INFO] [2020-12-03 11:00:36] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 11:00:36] Assocs to occurrences...
[INFO] [2020-12-03 11:00:36] Assocs to nodes...
[INFO] [2020-12-03 11:00:36] Assoc to sex term...
[INFO] [2020-12-03 11:00:36] Assoc to lifestage term...
[INFO] [2020-12-03 11:00:36] MetaAssoc to assocs...
[STOP] [2020-12-03 11:00:36] resolve_keys
[START] [2020-12-03 11:00:36] hold_for_later_1
[STOP] [2020-12-03 11:00:36] hold_for_later_1
[START] [2020-12-03 11:00:36] hold_for_later_2
[STOP] [2020-12-03 11:00:36] hold_for_later_2
[START] [2020-12-03 11:00:36] resolve_missing_parents
[STOP] [2020-12-03 11:00:36] resolve_missing_parents
[START] [2020-12-03 11:00:36] rebuild_nodes
[START] [2020-12-03 11:00:36] Flattener#flatten
[START] [2020-12-03 11:00:36] Flattener#study_resource
[START] [2020-12-03 11:00:36] Flattener#build_ancestry
[STOP] [2020-12-03 11:00:36] Flattener#build_ancestry
[INFO] [2020-12-03 11:00:36] 2 ancestry keys
[START] [2020-12-03 11:00:36] build_node_ancestors
[INFO] [2020-12-03 11:00:36] old ancestors deleted.
[STOP] [2020-12-03 11:00:36] build_node_ancestors
[WARN] [2020-12-03 11:00:36] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 11:00:36] Flattener#flatten
[STOP] [2020-12-03 11:00:36] rebuild_nodes
[START] [2020-12-03 11:00:36] resolve_missing_media_owners
[STOP] [2020-12-03 11:00:36] resolve_missing_media_owners
[START] [2020-12-03 11:00:36] sanitize_media_verbatims
[STOP] [2020-12-03 11:00:36] sanitize_media_verbatims
[START] [2020-12-03 11:00:36] queue_downloads
[STOP] [2020-12-03 11:00:36] queue_downloads
[START] [2020-12-03 11:00:36] parse_names
[WARN] [2020-12-03 11:00:36] I see 2 names which still need to be parsed.
[STOP] [2020-12-03 11:00:37] parse_names
[START] [2020-12-03 11:00:37] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 11:00:37] denormalize_canonical_names_to_nodes
[START] [2020-12-03 11:00:37] match_nodes
[START] [2020-12-03 11:00:37] map_all_nodes_to_pages
[STOP] [2020-12-03 11:00:37] map_all_nodes_to_pages
[INFO] [2020-12-03 11:00:37] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2020-12-03 11:00:37] update_nodes
[STOP] [2020-12-03 11:00:37] update_nodes
[STOP] [2020-12-03 11:00:37] match_nodes
[START] [2020-12-03 11:00:37] reindex_search
[STOP] [2020-12-03 11:00:37] reindex_search
[START] [2020-12-03 11:00:37] normalize_units
[STOP] [2020-12-03 11:00:37] normalize_units
[START] [2020-12-03 11:00:37] calculate_statistics
[2020-12-03 11:00:37] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 11:00:37] calculate_statistics
[START] [2020-12-03 11:00:37] complete_harvest_instance
[START] [2020-12-03 11:00:37] overall_tsv_creation
[INFO] [2020-12-03 11:00:37] Processing group of 2 in 1 batches of 10000
[INFO] [2020-12-03 11:01:17] 2 Traits (unfiltered)...
[INFO] [2020-12-03 11:01:56] 2 Traits (filtered)...
[INFO] [2020-12-03 11:01:56] 0 Associations (filtered)...
[INFO] [2020-12-03 11:01:56] 6 metadata added.
[INFO] [2020-12-03 11:01:56] 0 metadata added.
[INFO] [2020-12-03 11:01:56] Average Time: 55.58
[INFO] [2020-12-03 11:01:56] Total Time: 1m19s
[STOP] [2020-12-03 11:01:56] overall_tsv_creation
[INFO] [2020-12-03 11:01:56] Done. Check your files:
[INFO] [2020-12-03 11:01:56] (2 lines) /app/public/data/garm_nilsson_gar/publish_nodes.tsv
[INFO] [2020-12-03 11:01:56] (2 lines) /app/public/data/garm_nilsson_gar/publish_scientific_names.tsv
[INFO] [2020-12-03 11:01:56] (3 lines) /app/public/data/garm_nilsson_gar/publish_traits.tsv
[INFO] [2020-12-03 11:01:56] (7 lines) /app/public/data/garm_nilsson_gar/publish_metadata.tsv
[STOP] [2020-12-03 11:01:56] complete_harvest_instance
[START] [2020-12-03 11:01:56] completed
[STOP] [2020-12-03 11:01:56] completed
[STOP] [2020-12-03 11:01:56] logged process, took 88.94
[INFO] [2021-04-19 15:16:16] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:26:41] ## remove_type: ScientificName
[INFO] [2021-04-19 15:26:41] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:26:41] [15:26:41.377] Removed 2 Scientificnames
[INFO] [2021-04-19 15:26:41] ## remove_type: Vernacular
[INFO] [2021-04-19 15:26:41] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:26:41] [15:26:41.379] Removed 0 Vernaculars
[INFO] [2021-04-19 15:26:41] ## remove_type: Article
[INFO] [2021-04-19 15:26:41] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:26:41] [15:26:41.380] Removed 0 Articles
[INFO] [2021-04-19 15:26:41] ## remove_type: Medium
[INFO] [2021-04-19 15:26:41] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:26:41] [15:26:41.382] Removed 0 Media
[INFO] [2021-04-19 15:26:41] ## remove_type: Trait
[INFO] [2021-04-19 15:26:41] ++ Calling delete_all on 4 instances...
[INFO] [2021-04-19 15:26:41] [15:26:41.384] Removed 4 Traits
[INFO] [2021-04-19 15:26:41] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:26:41] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 15:26:41] [15:26:41.386] Removed 3 Metatraits
[INFO] [2021-04-19 15:26:41] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:26:41] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:26:41] [15:26:41.387] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 15:26:41] ## remove_type: Assoc
[INFO] [2021-04-19 15:26:41] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:26:41] [15:26:41.388] Removed 0 Assocs
[INFO] [2021-04-19 15:26:41] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:26:41] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:26:41] [15:26:41.390] Removed 0 Metaassocs
[INFO] [2021-04-19 15:26:41] ## remove_type: Identifier
[INFO] [2021-04-19 15:26:41] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:26:41] [15:26:41.391] Removed 0 Identifiers
[INFO] [2021-04-19 15:26:41] ## remove_type: Reference
[INFO] [2021-04-19 15:26:41] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:26:41] [15:26:41.393] Removed 1 References
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] Starting batch with ID 86115901...
[INFO] [2021-04-19 15:26:41] ## remove_type: Node
[INFO] [2021-04-19 15:26:41] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:26:41] [15:26:41.808] Removed 2 Nodes
[START] [2021-04-19 15:26:41] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:26:41] Creating resource from OpenData
[START] [2021-04-19 15:26:42] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:26:42] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:26:42] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:26:42] Creating resource from OpenData
[START] [2021-04-19 15:26:42] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:26:42] create_harvest_instance
[INFO] [2021-04-19 15:26:42] Created harvest instance #3766
[STOP] [2021-04-19 15:26:42] create_harvest_instance
[START] [2021-04-19 15:26:42] fetch_files
[STOP] [2021-04-19 15:26:42] fetch_files
[START] [2021-04-19 15:26:42] validate_each_file
[INFO] [2021-04-19 15:26:42] Looping over 4 formats...
[INFO] [2021-04-19 15:26:42] ...refs (/app/public/data/garm_nilsson_gar/references.tsv)
[INFO] [2021-04-19 15:26:42] Valid: /app/public/converted_csv/garm_nilsson_gar_refs_3766.csv (1 lines)
[INFO] [2021-04-19 15:26:42] ...nodes (/app/public/data/garm_nilsson_gar/taxa.txt)
[INFO] [2021-04-19 15:26:42] Valid: /app/public/converted_csv/garm_nilsson_gar_nodes_3766.csv (2 lines)
[INFO] [2021-04-19 15:26:42] ...occurrences (/app/public/data/garm_nilsson_gar/occurrences.txt)
[INFO] [2021-04-19 15:26:42] Valid: /app/public/converted_csv/garm_nilsson_gar_occurrences_3766.csv (2 lines)
[INFO] [2021-04-19 15:26:42] ...measurements (/app/public/data/garm_nilsson_gar/measurementsorfacts.txt)
[INFO] [2021-04-19 15:26:42] Valid: /app/public/converted_csv/garm_nilsson_gar_measurements_3766.csv (4 lines)
[STOP] [2021-04-19 15:26:42] validate_each_file
[START] [2021-04-19 15:26:42] convert_to_csv
[INFO] [2021-04-19 15:26:42] Looping over 4 formats...
[INFO] [2021-04-19 15:26:42] ...refs (/app/public/data/garm_nilsson_gar/references.tsv)
[CMD] [2021-04-19 15:26:42] /usr/bin/sort /app/public/converted_csv/garm_nilsson_gar_refs_3766.csv > /app/public/converted_csv/garm_nilsson_gar_refs_3766.csv_sorted
[INFO] [2021-04-19 15:26:42] Converted: /app/public/converted_csv/garm_nilsson_gar_refs_3766.csv (1 lines)
[INFO] [2021-04-19 15:26:42] ...nodes (/app/public/data/garm_nilsson_gar/taxa.txt)
[CMD] [2021-04-19 15:26:42] /usr/bin/sort /app/public/converted_csv/garm_nilsson_gar_nodes_3766.csv > /app/public/converted_csv/garm_nilsson_gar_nodes_3766.csv_sorted
[INFO] [2021-04-19 15:26:42] Converted: /app/public/converted_csv/garm_nilsson_gar_nodes_3766.csv (2 lines)
[INFO] [2021-04-19 15:26:42] ...occurrences (/app/public/data/garm_nilsson_gar/occurrences.txt)
[CMD] [2021-04-19 15:26:42] /usr/bin/sort /app/public/converted_csv/garm_nilsson_gar_occurrences_3766.csv > /app/public/converted_csv/garm_nilsson_gar_occurrences_3766.csv_sorted
[INFO] [2021-04-19 15:26:42] Converted: /app/public/converted_csv/garm_nilsson_gar_occurrences_3766.csv (2 lines)
[INFO] [2021-04-19 15:26:42] ...measurements (/app/public/data/garm_nilsson_gar/measurementsorfacts.txt)
[CMD] [2021-04-19 15:26:42] /usr/bin/sort /app/public/converted_csv/garm_nilsson_gar_measurements_3766.csv > /app/public/converted_csv/garm_nilsson_gar_measurements_3766.csv_sorted
[INFO] [2021-04-19 15:26:42] Converted: /app/public/converted_csv/garm_nilsson_gar_measurements_3766.csv (4 lines)
[STOP] [2021-04-19 15:26:42] convert_to_csv
[START] [2021-04-19 15:26:42] calculate_delta
[INFO] [2021-04-19 15:26:42] Looping over 4 formats...
[INFO] [2021-04-19 15:26:42] ...refs (/app/public/data/garm_nilsson_gar/references.tsv)
[CMD] [2021-04-19 15:26:42] echo "0a" > /app/public/diff/garm_nilsson_gar_refs_3766.diff
[CMD] [2021-04-19 15:26:42] tail -n +1 /app/public/converted_csv/garm_nilsson_gar_refs_3766.csv >> /app/public/diff/garm_nilsson_gar_refs_3766.diff
[CMD] [2021-04-19 15:26:42] echo "." >> /app/public/diff/garm_nilsson_gar_refs_3766.diff
[INFO] [2021-04-19 15:26:42] Created diff: /app/public/diff/garm_nilsson_gar_refs_3766.diff (3 lines)
[INFO] [2021-04-19 15:26:42] ...nodes (/app/public/data/garm_nilsson_gar/taxa.txt)
[CMD] [2021-04-19 15:26:42] echo "0a" > /app/public/diff/garm_nilsson_gar_nodes_3766.diff
[CMD] [2021-04-19 15:26:42] tail -n +1 /app/public/converted_csv/garm_nilsson_gar_nodes_3766.csv >> /app/public/diff/garm_nilsson_gar_nodes_3766.diff
[CMD] [2021-04-19 15:26:42] echo "." >> /app/public/diff/garm_nilsson_gar_nodes_3766.diff
[INFO] [2021-04-19 15:26:42] Created diff: /app/public/diff/garm_nilsson_gar_nodes_3766.diff (4 lines)
[INFO] [2021-04-19 15:26:42] ...occurrences (/app/public/data/garm_nilsson_gar/occurrences.txt)
[CMD] [2021-04-19 15:26:42] echo "0a" > /app/public/diff/garm_nilsson_gar_occurrences_3766.diff
[CMD] [2021-04-19 15:26:42] tail -n +1 /app/public/converted_csv/garm_nilsson_gar_occurrences_3766.csv >> /app/public/diff/garm_nilsson_gar_occurrences_3766.diff
[CMD] [2021-04-19 15:26:42] echo "." >> /app/public/diff/garm_nilsson_gar_occurrences_3766.diff
[INFO] [2021-04-19 15:26:42] Created diff: /app/public/diff/garm_nilsson_gar_occurrences_3766.diff (4 lines)
[INFO] [2021-04-19 15:26:42] ...measurements (/app/public/data/garm_nilsson_gar/measurementsorfacts.txt)
[CMD] [2021-04-19 15:26:42] echo "0a" > /app/public/diff/garm_nilsson_gar_measurements_3766.diff
[CMD] [2021-04-19 15:26:42] tail -n +1 /app/public/converted_csv/garm_nilsson_gar_measurements_3766.csv >> /app/public/diff/garm_nilsson_gar_measurements_3766.diff
[CMD] [2021-04-19 15:26:42] echo "." >> /app/public/diff/garm_nilsson_gar_measurements_3766.diff
[INFO] [2021-04-19 15:26:42] Created diff: /app/public/diff/garm_nilsson_gar_measurements_3766.diff (6 lines)
[STOP] [2021-04-19 15:26:42] calculate_delta
[START] [2021-04-19 15:26:42] parse_diff_and_store
[INFO] [2021-04-19 15:26:42] Handling diff: /app/public/diff/garm_nilsson_gar_refs_3766.diff (3 lines)
[INFO] [2021-04-19 15:26:42] Loading refs diff file into memory (3 /app/public/diff/garm_nilsson_gar_refs_3766.diff lines)...
[INFO] [2021-04-19 15:26:42] Handling diff: /app/public/diff/garm_nilsson_gar_nodes_3766.diff (4 lines)
[INFO] [2021-04-19 15:26:42] Loading nodes diff file into memory (4 /app/public/diff/garm_nilsson_gar_nodes_3766.diff lines)...
[INFO] [2021-04-19 15:26:42] Handling diff: /app/public/diff/garm_nilsson_gar_occurrences_3766.diff (4 lines)
[INFO] [2021-04-19 15:26:42] Loading occurrences diff file into memory (4 /app/public/diff/garm_nilsson_gar_occurrences_3766.diff lines)...
[INFO] [2021-04-19 15:26:42] Handling diff: /app/public/diff/garm_nilsson_gar_measurements_3766.diff (6 lines)
[INFO] [2021-04-19 15:26:42] Loading measurements diff file into memory (6 /app/public/diff/garm_nilsson_gar_measurements_3766.diff lines)...
[INFO] [2021-04-19 15:26:42] Storing 1 References
[INFO] [2021-04-19 15:26:42] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:26:42] Average Time: 0.0
[INFO] [2021-04-19 15:26:42] Total Time: 1s
[INFO] [2021-04-19 15:26:42] Storing 2 ScientificNames
[INFO] [2021-04-19 15:26:42] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:26:42] Average Time: 0.0
[INFO] [2021-04-19 15:26:42] Total Time: 1s
[INFO] [2021-04-19 15:26:42] Storing 2 Nodes
[INFO] [2021-04-19 15:26:42] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:26:42] Average Time: 0.0
[INFO] [2021-04-19 15:26:42] Total Time: 1s
[INFO] [2021-04-19 15:26:42] Storing 2 Occurrences
[INFO] [2021-04-19 15:26:42] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:26:42] Average Time: 0.0
[INFO] [2021-04-19 15:26:42] Total Time: 1s
[INFO] [2021-04-19 15:26:42] Storing 4 Traits
[INFO] [2021-04-19 15:26:42] Processing group of 4 in 1 groups of 1000
[INFO] [2021-04-19 15:26:42] Average Time: 0.0
[INFO] [2021-04-19 15:26:42] Total Time: 1s
[INFO] [2021-04-19 15:26:42] Storing 3 MetaTraits
[INFO] [2021-04-19 15:26:42] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 15:26:42] Average Time: 0.0
[INFO] [2021-04-19 15:26:42] Total Time: 1s
[INFO] [2021-04-19 15:26:42] Storing 1 TraitsReferences
[INFO] [2021-04-19 15:26:42] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:26:42] Average Time: 0.0
[INFO] [2021-04-19 15:26:42] Total Time: 1s
[STOP] [2021-04-19 15:26:42] parse_diff_and_store
[START] [2021-04-19 15:26:42] resolve_keys
[INFO] [2021-04-19 15:26:48] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:26:48] traits to occurrences...
[INFO] [2021-04-19 15:26:48] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:26:48] Traits to sex term...
[INFO] [2021-04-19 15:26:48] Traits to lifestage term...
[INFO] [2021-04-19 15:26:48] MetaTraits to traits...
[INFO] [2021-04-19 15:26:48] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:26:48] Assocs to occurrences...
[INFO] [2021-04-19 15:26:48] Assocs to nodes...
[INFO] [2021-04-19 15:26:48] Assoc to sex term...
[INFO] [2021-04-19 15:26:48] Assoc to lifestage term...
[INFO] [2021-04-19 15:26:48] MetaAssoc to assocs...
[STOP] [2021-04-19 15:26:48] resolve_keys
[START] [2021-04-19 15:26:48] hold_for_later_1
[STOP] [2021-04-19 15:26:48] hold_for_later_1
[START] [2021-04-19 15:26:48] hold_for_later_2
[STOP] [2021-04-19 15:26:48] hold_for_later_2
[START] [2021-04-19 15:26:48] resolve_missing_parents
[STOP] [2021-04-19 15:26:48] resolve_missing_parents
[START] [2021-04-19 15:26:48] rebuild_nodes
[START] [2021-04-19 15:26:48] Flattener#flatten
[START] [2021-04-19 15:26:48] Flattener#study_resource
[START] [2021-04-19 15:26:48] Flattener#build_ancestry
[STOP] [2021-04-19 15:26:48] Flattener#build_ancestry
[INFO] [2021-04-19 15:26:48] 2 ancestry keys
[START] [2021-04-19 15:26:48] build_node_ancestors
[INFO] [2021-04-19 15:26:48] old ancestors deleted.
[STOP] [2021-04-19 15:26:48] build_node_ancestors
[WARN] [2021-04-19 15:26:48] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:26:48] Flattener#flatten
[STOP] [2021-04-19 15:26:48] rebuild_nodes
[START] [2021-04-19 15:26:48] resolve_missing_media_owners
[STOP] [2021-04-19 15:26:48] resolve_missing_media_owners
[START] [2021-04-19 15:26:48] sanitize_media_verbatims
[STOP] [2021-04-19 15:26:48] sanitize_media_verbatims
[START] [2021-04-19 15:26:48] queue_downloads
[STOP] [2021-04-19 15:26:48] queue_downloads
[START] [2021-04-19 15:26:48] parse_names
[WARN] [2021-04-19 15:26:48] I see 2 names which still need to be parsed.
[STOP] [2021-04-19 15:26:49] parse_names
[START] [2021-04-19 15:26:49] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:26:49] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:26:49] match_nodes
[START] [2021-04-19 15:26:49] map_all_nodes_to_pages
[STOP] [2021-04-19 15:26:49] map_all_nodes_to_pages
[INFO] [2021-04-19 15:26:49] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2021-04-19 15:26:49] update_nodes
[STOP] [2021-04-19 15:26:49] update_nodes
[STOP] [2021-04-19 15:26:49] match_nodes
[START] [2021-04-19 15:26:49] reindex_search
[STOP] [2021-04-19 15:26:49] reindex_search
[START] [2021-04-19 15:26:49] normalize_units
[STOP] [2021-04-19 15:26:49] normalize_units
[START] [2021-04-19 15:26:49] calculate_statistics
[2021-04-19 15:26:49] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:26:49] calculate_statistics
[START] [2021-04-19 15:26:49] complete_harvest_instance
[START] [2021-04-19 15:26:49] overall_tsv_creation
[INFO] [2021-04-19 15:26:49] Processing group of 2 in 1 batches of 10000
[INFO] [2021-04-19 15:27:25] 2 Traits (unfiltered)...
[INFO] [2021-04-19 15:27:58] 2 Traits (filtered)...
[INFO] [2021-04-19 15:27:58] 0 Associations (filtered)...
[INFO] [2021-04-19 15:27:58] 3 metadata added.
[INFO] [2021-04-19 15:27:58] 0 metadata added.
[INFO] [2021-04-19 15:28:24] Average Time: 70.9
[INFO] [2021-04-19 15:28:24] Total Time: 1m35s
[STOP] [2021-04-19 15:28:24] overall_tsv_creation
[INFO] [2021-04-19 15:28:24] Done. Check your files:
[INFO] [2021-04-19 15:28:24] (2 lines) /app/public/data/garm_nilsson_gar/publish_nodes.tsv
[INFO] [2021-04-19 15:28:24] (2 lines) /app/public/data/garm_nilsson_gar/publish_scientific_names.tsv
[INFO] [2021-04-19 15:28:24] (3 lines) /app/public/data/garm_nilsson_gar/publish_traits.tsv
[INFO] [2021-04-19 15:28:24] (4 lines) /app/public/data/garm_nilsson_gar/publish_metadata.tsv
[STOP] [2021-04-19 15:28:24] complete_harvest_instance
[START] [2021-04-19 15:28:24] completed
[STOP] [2021-04-19 15:28:24] completed
[STOP] [2021-04-19 15:28:24] logged process, took 102.32

Latest Process