Harvest for Parker 1995 Created 19 Apr 14:55

Harvesting Log

# Logfile created on 2020-08-27 15:22:54 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:22:54] logged process
[START] [2020-08-27 15:22:54] Creating resource from OpenData
[START] [2020-08-27 15:22:54] logged process
[START] [2020-08-27 15:22:54] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:22:54] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:22:54] Creating resource from OpenData
[INFO] [2020-11-19 13:29:24] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-11-19 13:29:28] ## remove_type: ScientificName
[INFO] [2020-11-19 13:29:28] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:29:28] [13:29:28.868] Removed 0 Scientificnames
[INFO] [2020-11-19 13:29:28] ## remove_type: Vernacular
[INFO] [2020-11-19 13:29:28] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:29:28] [13:29:28.871] Removed 0 Vernaculars
[INFO] [2020-11-19 13:29:28] ## remove_type: Article
[INFO] [2020-11-19 13:29:28] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:29:28] [13:29:28.874] Removed 0 Articles
[INFO] [2020-11-19 13:29:28] ## remove_type: Medium
[INFO] [2020-11-19 13:29:28] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:29:28] [13:29:28.877] Removed 0 Media
[INFO] [2020-11-19 13:29:28] ## remove_type: Trait
[INFO] [2020-11-19 13:29:28] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:29:28] [13:29:28.880] Removed 0 Traits
[INFO] [2020-11-19 13:29:28] ## remove_type: MetaTrait
[INFO] [2020-11-19 13:29:28] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:29:28] [13:29:28.883] Removed 0 Metatraits
[INFO] [2020-11-19 13:29:28] ## remove_type: OccurrenceMetadatum
[INFO] [2020-11-19 13:29:28] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:29:28] [13:29:28.885] Removed 0 Occurrencemetadata
[INFO] [2020-11-19 13:29:28] ## remove_type: Assoc
[INFO] [2020-11-19 13:29:28] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:29:28] [13:29:28.888] Removed 0 Assocs
[INFO] [2020-11-19 13:29:28] ## remove_type: MetaAssoc
[INFO] [2020-11-19 13:29:28] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:29:28] [13:29:28.891] Removed 0 Metaassocs
[INFO] [2020-11-19 13:29:28] ## remove_type: Identifier
[INFO] [2020-11-19 13:29:28] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:29:28] [13:29:28.894] Removed 0 Identifiers
[INFO] [2020-11-19 13:29:28] ## remove_type: Reference
[INFO] [2020-11-19 13:29:28] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:29:28] [13:29:28.896] Removed 0 References
[INFO] [2020-11-19 13:29:29] ## remove_type: Node
[INFO] [2020-11-19 13:29:29] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:29:29] [13:29:29.186] Removed 0 Nodes
[START] [2020-11-19 13:29:29] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 13:29:29] Creating resource from OpenData
[START] [2020-11-19 13:29:29] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 13:29:29] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 13:29:29] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 13:29:29] Creating resource from OpenData
[START] [2020-11-19 13:29:29] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 13:29:29] create_harvest_instance
[STOP] [2020-11-19 13:29:31] create_harvest_instance
[START] [2020-11-19 13:29:31] fetch_files
[STOP] [2020-11-19 13:29:31] fetch_files
[START] [2020-11-19 13:29:31] validate_each_file
[STOP] [2020-11-19 13:29:31] validate_each_file
[START] [2020-11-19 13:29:31] convert_to_csv
[CMD] [2020-11-19 13:29:31] /usr/bin/sort /app/public/converted_csv/parker_parker_19_refs_24422.csv > /app/public/converted_csv/parker_parker_19_refs_24422.csv_sorted
[CMD] [2020-11-19 13:29:31] /usr/bin/sort /app/public/converted_csv/parker_parker_19_nodes_24423.csv > /app/public/converted_csv/parker_parker_19_nodes_24423.csv_sorted
[CMD] [2020-11-19 13:29:31] /usr/bin/sort /app/public/converted_csv/parker_parker_19_occurrences_24424.csv > /app/public/converted_csv/parker_parker_19_occurrences_24424.csv_sorted
[CMD] [2020-11-19 13:29:31] /usr/bin/sort /app/public/converted_csv/parker_parker_19_measurements_24425.csv > /app/public/converted_csv/parker_parker_19_measurements_24425.csv_sorted
[STOP] [2020-11-19 13:29:31] convert_to_csv
[START] [2020-11-19 13:29:31] calculate_delta
[CMD] [2020-11-19 13:29:31] echo "0a" > /app/public/diff/parker_parker_19_refs_24422.diff
[CMD] [2020-11-19 13:29:31] tail -n +1 /app/public/converted_csv/parker_parker_19_refs_24422.csv >> /app/public/diff/parker_parker_19_refs_24422.diff
[CMD] [2020-11-19 13:29:31] echo "." >> /app/public/diff/parker_parker_19_refs_24422.diff
[CMD] [2020-11-19 13:29:31] echo "0a" > /app/public/diff/parker_parker_19_nodes_24423.diff
[CMD] [2020-11-19 13:29:31] tail -n +1 /app/public/converted_csv/parker_parker_19_nodes_24423.csv >> /app/public/diff/parker_parker_19_nodes_24423.diff
[CMD] [2020-11-19 13:29:31] echo "." >> /app/public/diff/parker_parker_19_nodes_24423.diff
[CMD] [2020-11-19 13:29:31] echo "0a" > /app/public/diff/parker_parker_19_occurrences_24424.diff
[CMD] [2020-11-19 13:29:31] tail -n +1 /app/public/converted_csv/parker_parker_19_occurrences_24424.csv >> /app/public/diff/parker_parker_19_occurrences_24424.diff
[CMD] [2020-11-19 13:29:31] echo "." >> /app/public/diff/parker_parker_19_occurrences_24424.diff
[CMD] [2020-11-19 13:29:31] echo "0a" > /app/public/diff/parker_parker_19_measurements_24425.diff
[CMD] [2020-11-19 13:29:31] tail -n +1 /app/public/converted_csv/parker_parker_19_measurements_24425.csv >> /app/public/diff/parker_parker_19_measurements_24425.diff
[CMD] [2020-11-19 13:29:31] echo "." >> /app/public/diff/parker_parker_19_measurements_24425.diff
[STOP] [2020-11-19 13:29:31] calculate_delta
[START] [2020-11-19 13:29:31] parse_diff_and_store
[INFO] [2020-11-19 13:29:31] Loading refs diff file into memory (true lines)...
[INFO] [2020-11-19 13:29:31] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-19 13:29:31] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-19 13:29:31] Loading measurements diff file into memory (true lines)...
[INFO] [2020-11-19 13:29:32] Storing 1 ScientificNames
[INFO] [2020-11-19 13:29:32] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 13:29:32] Average Time: 0.0
[INFO] [2020-11-19 13:29:32] Total Time: 1s
[INFO] [2020-11-19 13:29:32] Storing 1 Nodes
[INFO] [2020-11-19 13:29:32] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 13:29:32] Average Time: 0.0
[INFO] [2020-11-19 13:29:32] Total Time: 1s
[INFO] [2020-11-19 13:29:32] Storing 1 Occurrences
[INFO] [2020-11-19 13:29:32] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 13:29:32] Average Time: 0.01
[INFO] [2020-11-19 13:29:32] Total Time: 1s
[INFO] [2020-11-19 13:29:32] Storing 8 Traits
[INFO] [2020-11-19 13:29:32] Processing group of 8 in 1 groups of 1000
[INFO] [2020-11-19 13:29:32] Average Time: 0.02
[INFO] [2020-11-19 13:29:32] Total Time: 1s
[INFO] [2020-11-19 13:29:32] Storing 1 MetaTraits
[INFO] [2020-11-19 13:29:32] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 13:29:32] Average Time: 0.0
[INFO] [2020-11-19 13:29:32] Total Time: 1s
[STOP] [2020-11-19 13:29:32] parse_diff_and_store
[START] [2020-11-19 13:29:32] resolve_keys
[INFO] [2020-11-19 13:29:38] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-19 13:29:38] traits to occurrences...
[INFO] [2020-11-19 13:29:38] traits to nodes (through occurrences)...
[INFO] [2020-11-19 13:29:38] Traits to sex term...
[INFO] [2020-11-19 13:29:38] Traits to lifestage term...
[INFO] [2020-11-19 13:29:38] MetaTraits to traits...
[INFO] [2020-11-19 13:29:38] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-19 13:29:38] Assocs to occurrences...
[INFO] [2020-11-19 13:29:38] Assocs to nodes...
[INFO] [2020-11-19 13:29:38] Assoc to sex term...
[INFO] [2020-11-19 13:29:38] Assoc to lifestage term...
[INFO] [2020-11-19 13:29:38] MetaAssoc to assocs...
[STOP] [2020-11-19 13:29:38] resolve_keys
[START] [2020-11-19 13:29:38] hold_for_later_1
[STOP] [2020-11-19 13:29:38] hold_for_later_1
[START] [2020-11-19 13:29:38] hold_for_later_2
[STOP] [2020-11-19 13:29:38] hold_for_later_2
[START] [2020-11-19 13:29:38] resolve_missing_parents
[STOP] [2020-11-19 13:29:38] resolve_missing_parents
[START] [2020-11-19 13:29:38] rebuild_nodes
[START] [2020-11-19 13:29:38] Flattener#flatten
[START] [2020-11-19 13:29:38] Flattener#study_resource
[START] [2020-11-19 13:29:38] Flattener#build_ancestry
[STOP] [2020-11-19 13:29:38] Flattener#build_ancestry
[INFO] [2020-11-19 13:29:38] 1 ancestry keys
[START] [2020-11-19 13:29:38] build_node_ancestors
[INFO] [2020-11-19 13:29:38] old ancestors deleted.
[STOP] [2020-11-19 13:29:38] build_node_ancestors
[WARN] [2020-11-19 13:29:38] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-11-19 13:29:38] Flattener#flatten
[STOP] [2020-11-19 13:29:38] rebuild_nodes
[START] [2020-11-19 13:29:38] resolve_missing_media_owners
[STOP] [2020-11-19 13:29:38] resolve_missing_media_owners
[START] [2020-11-19 13:29:38] sanitize_media_verbatims
[STOP] [2020-11-19 13:29:38] sanitize_media_verbatims
[START] [2020-11-19 13:29:38] queue_downloads
[STOP] [2020-11-19 13:29:38] queue_downloads
[START] [2020-11-19 13:29:38] parse_names
[WARN] [2020-11-19 13:29:38] I see 1 names which still need to be parsed.
[STOP] [2020-11-19 13:29:39] parse_names
[START] [2020-11-19 13:29:39] denormalize_canonical_names_to_nodes
[STOP] [2020-11-19 13:29:39] denormalize_canonical_names_to_nodes
[START] [2020-11-19 13:29:39] match_nodes
[START] [2020-11-19 13:29:39] map_all_nodes_to_pages
[STOP] [2020-11-19 13:29:39] map_all_nodes_to_pages
[INFO] [2020-11-19 13:29:39] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-11-19 13:29:39] update_nodes
[STOP] [2020-11-19 13:29:39] update_nodes
[STOP] [2020-11-19 13:29:39] match_nodes
[START] [2020-11-19 13:29:39] reindex_search
[STOP] [2020-11-19 13:29:39] reindex_search
[START] [2020-11-19 13:29:39] normalize_units
[STOP] [2020-11-19 13:29:39] normalize_units
[START] [2020-11-19 13:29:39] calculate_statistics
[2020-11-19 13:29:39] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-11-19 13:29:39] calculate_statistics
[START] [2020-11-19 13:29:39] complete_harvest_instance
[START] [2020-11-19 13:29:39] overall_tsv_creation
[INFO] [2020-11-19 13:29:39] Processing group of 1 in 1 batches of 10000
[INFO] [2020-11-19 13:30:22] 1 Traits (unfiltered)...
[INFO] [2020-11-19 13:31:04] 1 Traits (filtered)...
[INFO] [2020-11-19 13:31:04] 0 Associations (filtered)...
[INFO] [2020-11-19 13:31:04] 8 metadata added.
[INFO] [2020-11-19 13:31:04] 0 metadata added.
[INFO] [2020-11-19 13:31:04] Average Time: 65.15
[INFO] [2020-11-19 13:31:04] Total Time: 1m25s
[STOP] [2020-11-19 13:31:04] overall_tsv_creation
[INFO] [2020-11-19 13:31:04] Done. Check your files:
[INFO] [2020-11-19 13:31:04] (1 lines) /app/public/data/parker_parker_19/publish_nodes.tsv
[INFO] [2020-11-19 13:31:04] (1 lines) /app/public/data/parker_parker_19/publish_scientific_names.tsv
[INFO] [2020-11-19 13:31:04] (2 lines) /app/public/data/parker_parker_19/publish_traits.tsv
[INFO] [2020-11-19 13:31:04] (9 lines) /app/public/data/parker_parker_19/publish_metadata.tsv
[STOP] [2020-11-19 13:31:04] complete_harvest_instance
[START] [2020-11-19 13:31:04] completed
[STOP] [2020-11-19 13:31:04] completed
[STOP] [2020-11-19 13:31:04] logged process, took 95.23
[INFO] [2021-04-19 14:52:04] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 14:55:19] ## remove_type: ScientificName
[INFO] [2021-04-19 14:55:19] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 14:55:19] [14:55:19.259] Removed 1 Scientificnames
[INFO] [2021-04-19 14:55:19] ## remove_type: Vernacular
[INFO] [2021-04-19 14:55:19] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:55:19] [14:55:19.261] Removed 0 Vernaculars
[INFO] [2021-04-19 14:55:19] ## remove_type: Article
[INFO] [2021-04-19 14:55:19] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:55:19] [14:55:19.262] Removed 0 Articles
[INFO] [2021-04-19 14:55:19] ## remove_type: Medium
[INFO] [2021-04-19 14:55:19] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:55:19] [14:55:19.264] Removed 0 Media
[INFO] [2021-04-19 14:55:19] ## remove_type: Trait
[INFO] [2021-04-19 14:55:19] ++ Calling delete_all on 8 instances...
[INFO] [2021-04-19 14:55:19] [14:55:19.266] Removed 8 Traits
[INFO] [2021-04-19 14:55:19] ## remove_type: MetaTrait
[INFO] [2021-04-19 14:55:19] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 14:55:19] [14:55:19.268] Removed 1 Metatraits
[INFO] [2021-04-19 14:55:19] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 14:55:19] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:55:19] [14:55:19.269] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 14:55:19] ## remove_type: Assoc
[INFO] [2021-04-19 14:55:19] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:55:19] [14:55:19.271] Removed 0 Assocs
[INFO] [2021-04-19 14:55:19] ## remove_type: MetaAssoc
[INFO] [2021-04-19 14:55:19] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:55:19] [14:55:19.272] Removed 0 Metaassocs
[INFO] [2021-04-19 14:55:19] ## remove_type: Identifier
[INFO] [2021-04-19 14:55:19] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:55:19] [14:55:19.274] Removed 0 Identifiers
[INFO] [2021-04-19 14:55:19] ## remove_type: Reference
[INFO] [2021-04-19 14:55:19] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:55:19] [14:55:19.275] Removed 0 References
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] Starting batch with ID 84620780...
[INFO] [2021-04-19 14:55:19] ## remove_type: Node
[INFO] [2021-04-19 14:55:19] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 14:55:19] [14:55:19.609] Removed 1 Nodes
[START] [2021-04-19 14:55:19] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:55:19] Creating resource from OpenData
[START] [2021-04-19 14:55:19] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:55:19] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 14:55:20] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 14:55:20] Creating resource from OpenData
[START] [2021-04-19 14:55:20] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:55:20] create_harvest_instance
[INFO] [2021-04-19 14:55:20] Created harvest instance #3754
[STOP] [2021-04-19 14:55:20] create_harvest_instance
[START] [2021-04-19 14:55:20] fetch_files
[STOP] [2021-04-19 14:55:20] fetch_files
[START] [2021-04-19 14:55:20] validate_each_file
[INFO] [2021-04-19 14:55:20] Looping over 4 formats...
[INFO] [2021-04-19 14:55:20] ...refs (/app/public/data/parker_parker_19/references.tsv)
[INFO] [2021-04-19 14:55:20] Valid: /app/public/converted_csv/parker_parker_19_refs_3754.csv (0 lines)
[INFO] [2021-04-19 14:55:20] ...nodes (/app/public/data/parker_parker_19/taxa.txt)
[INFO] [2021-04-19 14:55:20] Valid: /app/public/converted_csv/parker_parker_19_nodes_3754.csv (1 lines)
[INFO] [2021-04-19 14:55:20] ...occurrences (/app/public/data/parker_parker_19/occurrences.txt)
[INFO] [2021-04-19 14:55:20] Valid: /app/public/converted_csv/parker_parker_19_occurrences_3754.csv (1 lines)
[INFO] [2021-04-19 14:55:20] ...measurements (/app/public/data/parker_parker_19/measurementsorfacts.txt)
[INFO] [2021-04-19 14:55:20] Valid: /app/public/converted_csv/parker_parker_19_measurements_3754.csv (8 lines)
[STOP] [2021-04-19 14:55:20] validate_each_file
[START] [2021-04-19 14:55:20] convert_to_csv
[INFO] [2021-04-19 14:55:20] Looping over 4 formats...
[INFO] [2021-04-19 14:55:20] ...refs (/app/public/data/parker_parker_19/references.tsv)
[CMD] [2021-04-19 14:55:20] /usr/bin/sort /app/public/converted_csv/parker_parker_19_refs_3754.csv > /app/public/converted_csv/parker_parker_19_refs_3754.csv_sorted
[INFO] [2021-04-19 14:55:20] Converted: /app/public/converted_csv/parker_parker_19_refs_3754.csv (0 lines)
[INFO] [2021-04-19 14:55:20] ...nodes (/app/public/data/parker_parker_19/taxa.txt)
[CMD] [2021-04-19 14:55:20] /usr/bin/sort /app/public/converted_csv/parker_parker_19_nodes_3754.csv > /app/public/converted_csv/parker_parker_19_nodes_3754.csv_sorted
[INFO] [2021-04-19 14:55:20] Converted: /app/public/converted_csv/parker_parker_19_nodes_3754.csv (1 lines)
[INFO] [2021-04-19 14:55:20] ...occurrences (/app/public/data/parker_parker_19/occurrences.txt)
[CMD] [2021-04-19 14:55:20] /usr/bin/sort /app/public/converted_csv/parker_parker_19_occurrences_3754.csv > /app/public/converted_csv/parker_parker_19_occurrences_3754.csv_sorted
[INFO] [2021-04-19 14:55:20] Converted: /app/public/converted_csv/parker_parker_19_occurrences_3754.csv (1 lines)
[INFO] [2021-04-19 14:55:20] ...measurements (/app/public/data/parker_parker_19/measurementsorfacts.txt)
[CMD] [2021-04-19 14:55:20] /usr/bin/sort /app/public/converted_csv/parker_parker_19_measurements_3754.csv > /app/public/converted_csv/parker_parker_19_measurements_3754.csv_sorted
[INFO] [2021-04-19 14:55:20] Converted: /app/public/converted_csv/parker_parker_19_measurements_3754.csv (8 lines)
[STOP] [2021-04-19 14:55:20] convert_to_csv
[START] [2021-04-19 14:55:20] calculate_delta
[INFO] [2021-04-19 14:55:20] Looping over 4 formats...
[INFO] [2021-04-19 14:55:20] ...refs (/app/public/data/parker_parker_19/references.tsv)
[CMD] [2021-04-19 14:55:20] echo "0a" > /app/public/diff/parker_parker_19_refs_3754.diff
[CMD] [2021-04-19 14:55:20] tail -n +1 /app/public/converted_csv/parker_parker_19_refs_3754.csv >> /app/public/diff/parker_parker_19_refs_3754.diff
[CMD] [2021-04-19 14:55:20] echo "." >> /app/public/diff/parker_parker_19_refs_3754.diff
[INFO] [2021-04-19 14:55:20] Created diff: /app/public/diff/parker_parker_19_refs_3754.diff (2 lines)
[INFO] [2021-04-19 14:55:20] ...nodes (/app/public/data/parker_parker_19/taxa.txt)
[CMD] [2021-04-19 14:55:20] echo "0a" > /app/public/diff/parker_parker_19_nodes_3754.diff
[CMD] [2021-04-19 14:55:20] tail -n +1 /app/public/converted_csv/parker_parker_19_nodes_3754.csv >> /app/public/diff/parker_parker_19_nodes_3754.diff
[CMD] [2021-04-19 14:55:20] echo "." >> /app/public/diff/parker_parker_19_nodes_3754.diff
[INFO] [2021-04-19 14:55:20] Created diff: /app/public/diff/parker_parker_19_nodes_3754.diff (3 lines)
[INFO] [2021-04-19 14:55:20] ...occurrences (/app/public/data/parker_parker_19/occurrences.txt)
[CMD] [2021-04-19 14:55:20] echo "0a" > /app/public/diff/parker_parker_19_occurrences_3754.diff
[CMD] [2021-04-19 14:55:20] tail -n +1 /app/public/converted_csv/parker_parker_19_occurrences_3754.csv >> /app/public/diff/parker_parker_19_occurrences_3754.diff
[CMD] [2021-04-19 14:55:20] echo "." >> /app/public/diff/parker_parker_19_occurrences_3754.diff
[INFO] [2021-04-19 14:55:20] Created diff: /app/public/diff/parker_parker_19_occurrences_3754.diff (3 lines)
[INFO] [2021-04-19 14:55:20] ...measurements (/app/public/data/parker_parker_19/measurementsorfacts.txt)
[CMD] [2021-04-19 14:55:20] echo "0a" > /app/public/diff/parker_parker_19_measurements_3754.diff
[CMD] [2021-04-19 14:55:20] tail -n +1 /app/public/converted_csv/parker_parker_19_measurements_3754.csv >> /app/public/diff/parker_parker_19_measurements_3754.diff
[CMD] [2021-04-19 14:55:20] echo "." >> /app/public/diff/parker_parker_19_measurements_3754.diff
[INFO] [2021-04-19 14:55:20] Created diff: /app/public/diff/parker_parker_19_measurements_3754.diff (10 lines)
[STOP] [2021-04-19 14:55:20] calculate_delta
[START] [2021-04-19 14:55:20] parse_diff_and_store
[INFO] [2021-04-19 14:55:20] Handling diff: /app/public/diff/parker_parker_19_refs_3754.diff (2 lines)
[INFO] [2021-04-19 14:55:20] Loading refs diff file into memory (2 /app/public/diff/parker_parker_19_refs_3754.diff lines)...
[INFO] [2021-04-19 14:55:20] Handling diff: /app/public/diff/parker_parker_19_nodes_3754.diff (3 lines)
[INFO] [2021-04-19 14:55:20] Loading nodes diff file into memory (3 /app/public/diff/parker_parker_19_nodes_3754.diff lines)...
[INFO] [2021-04-19 14:55:20] Handling diff: /app/public/diff/parker_parker_19_occurrences_3754.diff (3 lines)
[INFO] [2021-04-19 14:55:20] Loading occurrences diff file into memory (3 /app/public/diff/parker_parker_19_occurrences_3754.diff lines)...
[INFO] [2021-04-19 14:55:20] Handling diff: /app/public/diff/parker_parker_19_measurements_3754.diff (10 lines)
[INFO] [2021-04-19 14:55:20] Loading measurements diff file into memory (10 /app/public/diff/parker_parker_19_measurements_3754.diff lines)...
[INFO] [2021-04-19 14:55:20] Storing 1 ScientificNames
[INFO] [2021-04-19 14:55:20] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:55:20] Average Time: 0.0
[INFO] [2021-04-19 14:55:20] Total Time: 1s
[INFO] [2021-04-19 14:55:20] Storing 1 Nodes
[INFO] [2021-04-19 14:55:20] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:55:20] Average Time: 0.0
[INFO] [2021-04-19 14:55:20] Total Time: 1s
[INFO] [2021-04-19 14:55:20] Storing 1 Occurrences
[INFO] [2021-04-19 14:55:20] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:55:20] Average Time: 0.0
[INFO] [2021-04-19 14:55:20] Total Time: 1s
[INFO] [2021-04-19 14:55:20] Storing 8 Traits
[INFO] [2021-04-19 14:55:20] Processing group of 8 in 1 groups of 1000
[INFO] [2021-04-19 14:55:20] Average Time: 0.0
[INFO] [2021-04-19 14:55:20] Total Time: 1s
[INFO] [2021-04-19 14:55:20] Storing 1 MetaTraits
[INFO] [2021-04-19 14:55:20] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:55:20] Average Time: 0.01
[INFO] [2021-04-19 14:55:20] Total Time: 1s
[STOP] [2021-04-19 14:55:20] parse_diff_and_store
[START] [2021-04-19 14:55:20] resolve_keys
[INFO] [2021-04-19 14:55:26] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 14:55:26] traits to occurrences...
[INFO] [2021-04-19 14:55:26] traits to nodes (through occurrences)...
[INFO] [2021-04-19 14:55:26] Traits to sex term...
[INFO] [2021-04-19 14:55:26] Traits to lifestage term...
[INFO] [2021-04-19 14:55:26] MetaTraits to traits...
[INFO] [2021-04-19 14:55:26] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 14:55:26] Assocs to occurrences...
[INFO] [2021-04-19 14:55:26] Assocs to nodes...
[INFO] [2021-04-19 14:55:26] Assoc to sex term...
[INFO] [2021-04-19 14:55:26] Assoc to lifestage term...
[INFO] [2021-04-19 14:55:26] MetaAssoc to assocs...
[STOP] [2021-04-19 14:55:26] resolve_keys
[START] [2021-04-19 14:55:26] hold_for_later_1
[STOP] [2021-04-19 14:55:26] hold_for_later_1
[START] [2021-04-19 14:55:26] hold_for_later_2
[STOP] [2021-04-19 14:55:26] hold_for_later_2
[START] [2021-04-19 14:55:26] resolve_missing_parents
[STOP] [2021-04-19 14:55:26] resolve_missing_parents
[START] [2021-04-19 14:55:26] rebuild_nodes
[START] [2021-04-19 14:55:26] Flattener#flatten
[START] [2021-04-19 14:55:26] Flattener#study_resource
[START] [2021-04-19 14:55:26] Flattener#build_ancestry
[STOP] [2021-04-19 14:55:26] Flattener#build_ancestry
[INFO] [2021-04-19 14:55:26] 1 ancestry keys
[START] [2021-04-19 14:55:26] build_node_ancestors
[INFO] [2021-04-19 14:55:26] old ancestors deleted.
[STOP] [2021-04-19 14:55:26] build_node_ancestors
[WARN] [2021-04-19 14:55:26] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 14:55:26] Flattener#flatten
[STOP] [2021-04-19 14:55:26] rebuild_nodes
[START] [2021-04-19 14:55:26] resolve_missing_media_owners
[STOP] [2021-04-19 14:55:26] resolve_missing_media_owners
[START] [2021-04-19 14:55:26] sanitize_media_verbatims
[STOP] [2021-04-19 14:55:26] sanitize_media_verbatims
[START] [2021-04-19 14:55:26] queue_downloads
[STOP] [2021-04-19 14:55:26] queue_downloads
[START] [2021-04-19 14:55:26] parse_names
[WARN] [2021-04-19 14:55:26] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 14:55:27] parse_names
[START] [2021-04-19 14:55:27] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 14:55:27] denormalize_canonical_names_to_nodes
[START] [2021-04-19 14:55:27] match_nodes
[START] [2021-04-19 14:55:27] map_all_nodes_to_pages
[STOP] [2021-04-19 14:55:27] map_all_nodes_to_pages
[INFO] [2021-04-19 14:55:27] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 14:55:27] update_nodes
[STOP] [2021-04-19 14:55:27] update_nodes
[STOP] [2021-04-19 14:55:27] match_nodes
[START] [2021-04-19 14:55:27] reindex_search
[STOP] [2021-04-19 14:55:27] reindex_search
[START] [2021-04-19 14:55:27] normalize_units
[STOP] [2021-04-19 14:55:27] normalize_units
[START] [2021-04-19 14:55:27] calculate_statistics
[2021-04-19 14:55:27] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 14:55:27] calculate_statistics
[START] [2021-04-19 14:55:27] complete_harvest_instance
[START] [2021-04-19 14:55:27] overall_tsv_creation
[INFO] [2021-04-19 14:55:27] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 14:56:02] 1 Traits (unfiltered)...
[INFO] [2021-04-19 14:56:33] 1 Traits (filtered)...
[INFO] [2021-04-19 14:56:33] 0 Associations (filtered)...
[INFO] [2021-04-19 14:56:33] 7 metadata added.
[INFO] [2021-04-19 14:56:33] 0 metadata added.
[INFO] [2021-04-19 14:56:58] Average Time: 67.73
[INFO] [2021-04-19 14:56:58] Total Time: 1m32s
[STOP] [2021-04-19 14:56:58] overall_tsv_creation
[INFO] [2021-04-19 14:56:58] Done. Check your files:
[INFO] [2021-04-19 14:56:58] (1 lines) /app/public/data/parker_parker_19/publish_nodes.tsv
[INFO] [2021-04-19 14:56:58] (1 lines) /app/public/data/parker_parker_19/publish_scientific_names.tsv
[INFO] [2021-04-19 14:56:59] (2 lines) /app/public/data/parker_parker_19/publish_traits.tsv
[INFO] [2021-04-19 14:56:59] (8 lines) /app/public/data/parker_parker_19/publish_metadata.tsv
[STOP] [2021-04-19 14:56:59] complete_harvest_instance
[START] [2021-04-19 14:56:59] completed
[STOP] [2021-04-19 14:56:59] completed
[STOP] [2021-04-19 14:56:59] logged process, took 98.98

Latest Process

19 Apr 14:55 EXITED currently processing 0