Harvest for Nev 1979 Created 19 Apr 16:02

Harvesting Log

# Logfile created on 2020-08-27 15:49:59 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:49:59] logged process
[START] [2020-08-27 15:49:59] Creating resource from OpenData
[START] [2020-08-27 15:50:00] logged process
[START] [2020-08-27 15:50:00] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:50:00] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:50:00] Creating resource from OpenData
[INFO] [2020-12-03 12:13:06] ## HARVEST: type = -harvest
[START] [2020-12-03 12:13:09] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-03 12:13:09] create_harvest_instance
[STOP] [2020-12-03 12:13:10] create_harvest_instance
[START] [2020-12-03 12:13:10] fetch_files
[STOP] [2020-12-03 12:13:10] fetch_files
[START] [2020-12-03 12:13:10] validate_each_file
[STOP] [2020-12-03 12:13:11] validate_each_file
[START] [2020-12-03 12:13:11] convert_to_csv
[CMD] [2020-12-03 12:13:11] /usr/bin/sort /app/public/converted_csv/nev_nev_1979_refs_24888.csv > /app/public/converted_csv/nev_nev_1979_refs_24888.csv_sorted
[CMD] [2020-12-03 12:13:11] /usr/bin/sort /app/public/converted_csv/nev_nev_1979_nodes_24889.csv > /app/public/converted_csv/nev_nev_1979_nodes_24889.csv_sorted
[CMD] [2020-12-03 12:13:11] /usr/bin/sort /app/public/converted_csv/nev_nev_1979_occurrences_24890.csv > /app/public/converted_csv/nev_nev_1979_occurrences_24890.csv_sorted
[CMD] [2020-12-03 12:13:11] /usr/bin/sort /app/public/converted_csv/nev_nev_1979_measurements_24891.csv > /app/public/converted_csv/nev_nev_1979_measurements_24891.csv_sorted
[STOP] [2020-12-03 12:13:11] convert_to_csv
[START] [2020-12-03 12:13:11] calculate_delta
[CMD] [2020-12-03 12:13:11] echo "0a" > /app/public/diff/nev_nev_1979_refs_24888.diff
[CMD] [2020-12-03 12:13:11] tail -n +1 /app/public/converted_csv/nev_nev_1979_refs_24888.csv >> /app/public/diff/nev_nev_1979_refs_24888.diff
[CMD] [2020-12-03 12:13:11] echo "." >> /app/public/diff/nev_nev_1979_refs_24888.diff
[CMD] [2020-12-03 12:13:11] echo "0a" > /app/public/diff/nev_nev_1979_nodes_24889.diff
[CMD] [2020-12-03 12:13:11] tail -n +1 /app/public/converted_csv/nev_nev_1979_nodes_24889.csv >> /app/public/diff/nev_nev_1979_nodes_24889.diff
[CMD] [2020-12-03 12:13:11] echo "." >> /app/public/diff/nev_nev_1979_nodes_24889.diff
[CMD] [2020-12-03 12:13:11] echo "0a" > /app/public/diff/nev_nev_1979_occurrences_24890.diff
[CMD] [2020-12-03 12:13:11] tail -n +1 /app/public/converted_csv/nev_nev_1979_occurrences_24890.csv >> /app/public/diff/nev_nev_1979_occurrences_24890.diff
[CMD] [2020-12-03 12:13:11] echo "." >> /app/public/diff/nev_nev_1979_occurrences_24890.diff
[CMD] [2020-12-03 12:13:11] echo "0a" > /app/public/diff/nev_nev_1979_measurements_24891.diff
[CMD] [2020-12-03 12:13:11] tail -n +1 /app/public/converted_csv/nev_nev_1979_measurements_24891.csv >> /app/public/diff/nev_nev_1979_measurements_24891.diff
[CMD] [2020-12-03 12:13:11] echo "." >> /app/public/diff/nev_nev_1979_measurements_24891.diff
[STOP] [2020-12-03 12:13:11] calculate_delta
[START] [2020-12-03 12:13:11] parse_diff_and_store
[INFO] [2020-12-03 12:13:11] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 12:13:11] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 12:13:11] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 12:13:11] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 12:13:12] Storing 7 ScientificNames
[INFO] [2020-12-03 12:13:12] Processing group of 7 in 1 groups of 1000
[INFO] [2020-12-03 12:13:12] Average Time: 0.01
[INFO] [2020-12-03 12:13:12] Total Time: 1s
[INFO] [2020-12-03 12:13:12] Storing 7 Nodes
[INFO] [2020-12-03 12:13:12] Processing group of 7 in 1 groups of 1000
[INFO] [2020-12-03 12:13:12] Average Time: 0.02
[INFO] [2020-12-03 12:13:12] Total Time: 1s
[INFO] [2020-12-03 12:13:12] Storing 7 Occurrences
[INFO] [2020-12-03 12:13:12] Processing group of 7 in 1 groups of 1000
[INFO] [2020-12-03 12:13:12] Average Time: 0.0
[INFO] [2020-12-03 12:13:12] Total Time: 1s
[INFO] [2020-12-03 12:13:12] Storing 13 Traits
[INFO] [2020-12-03 12:13:12] Processing group of 13 in 1 groups of 1000
[INFO] [2020-12-03 12:13:12] Average Time: 0.01
[INFO] [2020-12-03 12:13:12] Total Time: 1s
[INFO] [2020-12-03 12:13:12] Storing 14 MetaTraits
[INFO] [2020-12-03 12:13:12] Processing group of 14 in 1 groups of 1000
[INFO] [2020-12-03 12:13:12] Average Time: 0.0
[INFO] [2020-12-03 12:13:12] Total Time: 1s
[STOP] [2020-12-03 12:13:12] parse_diff_and_store
[START] [2020-12-03 12:13:12] resolve_keys
[INFO] [2020-12-03 12:13:17] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 12:13:17] traits to occurrences...
[INFO] [2020-12-03 12:13:17] traits to nodes (through occurrences)...
[INFO] [2020-12-03 12:13:17] Traits to sex term...
[INFO] [2020-12-03 12:13:17] Traits to lifestage term...
[INFO] [2020-12-03 12:13:17] MetaTraits to traits...
[INFO] [2020-12-03 12:13:17] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 12:13:17] Assocs to occurrences...
[INFO] [2020-12-03 12:13:17] Assocs to nodes...
[INFO] [2020-12-03 12:13:17] Assoc to sex term...
[INFO] [2020-12-03 12:13:17] Assoc to lifestage term...
[INFO] [2020-12-03 12:13:17] MetaAssoc to assocs...
[STOP] [2020-12-03 12:13:17] resolve_keys
[START] [2020-12-03 12:13:17] hold_for_later_1
[STOP] [2020-12-03 12:13:17] hold_for_later_1
[START] [2020-12-03 12:13:17] hold_for_later_2
[STOP] [2020-12-03 12:13:17] hold_for_later_2
[START] [2020-12-03 12:13:17] resolve_missing_parents
[STOP] [2020-12-03 12:13:17] resolve_missing_parents
[START] [2020-12-03 12:13:17] rebuild_nodes
[START] [2020-12-03 12:13:17] Flattener#flatten
[START] [2020-12-03 12:13:17] Flattener#study_resource
[START] [2020-12-03 12:13:17] Flattener#build_ancestry
[STOP] [2020-12-03 12:13:17] Flattener#build_ancestry
[INFO] [2020-12-03 12:13:17] 7 ancestry keys
[START] [2020-12-03 12:13:17] build_node_ancestors
[INFO] [2020-12-03 12:13:17] old ancestors deleted.
[STOP] [2020-12-03 12:13:18] build_node_ancestors
[WARN] [2020-12-03 12:13:18] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 12:13:18] Flattener#flatten
[STOP] [2020-12-03 12:13:18] rebuild_nodes
[START] [2020-12-03 12:13:18] resolve_missing_media_owners
[STOP] [2020-12-03 12:13:18] resolve_missing_media_owners
[START] [2020-12-03 12:13:18] sanitize_media_verbatims
[STOP] [2020-12-03 12:13:18] sanitize_media_verbatims
[START] [2020-12-03 12:13:18] queue_downloads
[STOP] [2020-12-03 12:13:18] queue_downloads
[START] [2020-12-03 12:13:18] parse_names
[WARN] [2020-12-03 12:13:18] I see 7 names which still need to be parsed.
[STOP] [2020-12-03 12:13:19] parse_names
[START] [2020-12-03 12:13:19] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 12:13:19] denormalize_canonical_names_to_nodes
[START] [2020-12-03 12:13:19] match_nodes
[START] [2020-12-03 12:13:19] map_all_nodes_to_pages
[STOP] [2020-12-03 12:13:19] map_all_nodes_to_pages
[INFO] [2020-12-03 12:13:19] ZERO unmatched nodes (of 7)! Nicely done.
[START] [2020-12-03 12:13:19] update_nodes
[STOP] [2020-12-03 12:13:19] update_nodes
[STOP] [2020-12-03 12:13:19] match_nodes
[START] [2020-12-03 12:13:19] reindex_search
[STOP] [2020-12-03 12:13:19] reindex_search
[START] [2020-12-03 12:13:19] normalize_units
[STOP] [2020-12-03 12:13:19] normalize_units
[START] [2020-12-03 12:13:19] calculate_statistics
[2020-12-03 12:13:19] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 12:13:19] calculate_statistics
[START] [2020-12-03 12:13:19] complete_harvest_instance
[START] [2020-12-03 12:13:19] overall_tsv_creation
[INFO] [2020-12-03 12:13:19] Processing group of 7 in 1 batches of 10000
[INFO] [2020-12-03 12:13:58] 7 Traits (unfiltered)...
[INFO] [2020-12-03 12:14:37] 7 Traits (filtered)...
[INFO] [2020-12-03 12:14:37] 0 Associations (filtered)...
[INFO] [2020-12-03 12:14:37] 20 metadata added.
[INFO] [2020-12-03 12:14:37] 0 metadata added.
[INFO] [2020-12-03 12:14:37] Average Time: 55.46
[INFO] [2020-12-03 12:14:37] Total Time: 1m19s
[STOP] [2020-12-03 12:14:37] overall_tsv_creation
[INFO] [2020-12-03 12:14:37] Done. Check your files:
[INFO] [2020-12-03 12:14:37] (7 lines) /app/public/data/nev_nev_1979/publish_nodes.tsv
[INFO] [2020-12-03 12:14:37] (7 lines) /app/public/data/nev_nev_1979/publish_scientific_names.tsv
[INFO] [2020-12-03 12:14:37] (8 lines) /app/public/data/nev_nev_1979/publish_traits.tsv
[INFO] [2020-12-03 12:14:37] (21 lines) /app/public/data/nev_nev_1979/publish_metadata.tsv
[STOP] [2020-12-03 12:14:37] complete_harvest_instance
[START] [2020-12-03 12:14:37] completed
[STOP] [2020-12-03 12:14:37] completed
[STOP] [2020-12-03 12:14:37] logged process, took 88.43
[INFO] [2021-04-19 15:58:04] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 16:02:34] ## remove_type: ScientificName
[INFO] [2021-04-19 16:02:34] ++ Calling delete_all on 7 instances...
[INFO] [2021-04-19 16:02:34] [16:02:34.671] Removed 7 Scientificnames
[INFO] [2021-04-19 16:02:34] ## remove_type: Vernacular
[INFO] [2021-04-19 16:02:34] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:02:34] [16:02:34.673] Removed 0 Vernaculars
[INFO] [2021-04-19 16:02:34] ## remove_type: Article
[INFO] [2021-04-19 16:02:34] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:02:34] [16:02:34.674] Removed 0 Articles
[INFO] [2021-04-19 16:02:34] ## remove_type: Medium
[INFO] [2021-04-19 16:02:34] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:02:34] [16:02:34.676] Removed 0 Media
[INFO] [2021-04-19 16:02:34] ## remove_type: Trait
[INFO] [2021-04-19 16:02:34] ++ Calling delete_all on 13 instances...
[INFO] [2021-04-19 16:02:34] [16:02:34.679] Removed 13 Traits
[INFO] [2021-04-19 16:02:34] ## remove_type: MetaTrait
[INFO] [2021-04-19 16:02:34] ++ Calling delete_all on 14 instances...
[INFO] [2021-04-19 16:02:34] [16:02:34.681] Removed 14 Metatraits
[INFO] [2021-04-19 16:02:34] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 16:02:34] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:02:34] [16:02:34.682] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 16:02:34] ## remove_type: Assoc
[INFO] [2021-04-19 16:02:34] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:02:34] [16:02:34.683] Removed 0 Assocs
[INFO] [2021-04-19 16:02:34] ## remove_type: MetaAssoc
[INFO] [2021-04-19 16:02:34] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:02:34] [16:02:34.685] Removed 0 Metaassocs
[INFO] [2021-04-19 16:02:34] ## remove_type: Identifier
[INFO] [2021-04-19 16:02:34] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:02:34] [16:02:34.686] Removed 0 Identifiers
[INFO] [2021-04-19 16:02:34] ## remove_type: Reference
[INFO] [2021-04-19 16:02:34] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:02:34] [16:02:34.687] Removed 0 References
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:34] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:35] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:35] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:35] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:35] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:35] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:35] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:35] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:35] Starting batch with ID 86116221...
[INFO] [2021-04-19 16:02:35] ## remove_type: Node
[INFO] [2021-04-19 16:02:35] ++ Calling delete_all on 7 instances...
[INFO] [2021-04-19 16:02:35] [16:02:35.064] Removed 7 Nodes
[START] [2021-04-19 16:02:35] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:02:35] Creating resource from OpenData
[START] [2021-04-19 16:02:35] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:02:35] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:02:35] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:02:35] Creating resource from OpenData
[START] [2021-04-19 16:02:35] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:02:35] create_harvest_instance
[INFO] [2021-04-19 16:02:35] Created harvest instance #3785
[STOP] [2021-04-19 16:02:35] create_harvest_instance
[START] [2021-04-19 16:02:35] fetch_files
[STOP] [2021-04-19 16:02:35] fetch_files
[START] [2021-04-19 16:02:35] validate_each_file
[INFO] [2021-04-19 16:02:35] Looping over 4 formats...
[INFO] [2021-04-19 16:02:35] ...refs (/app/public/data/nev_nev_1979/references.tsv)
[INFO] [2021-04-19 16:02:35] Valid: /app/public/converted_csv/nev_nev_1979_refs_3785.csv (0 lines)
[INFO] [2021-04-19 16:02:35] ...nodes (/app/public/data/nev_nev_1979/taxa.txt)
[INFO] [2021-04-19 16:02:35] Valid: /app/public/converted_csv/nev_nev_1979_nodes_3785.csv (7 lines)
[INFO] [2021-04-19 16:02:35] ...occurrences (/app/public/data/nev_nev_1979/occurrences.txt)
[INFO] [2021-04-19 16:02:35] Valid: /app/public/converted_csv/nev_nev_1979_occurrences_3785.csv (7 lines)
[INFO] [2021-04-19 16:02:35] ...measurements (/app/public/data/nev_nev_1979/measurementsorfacts.txt)
[INFO] [2021-04-19 16:02:35] Valid: /app/public/converted_csv/nev_nev_1979_measurements_3785.csv (13 lines)
[STOP] [2021-04-19 16:02:35] validate_each_file
[START] [2021-04-19 16:02:35] convert_to_csv
[INFO] [2021-04-19 16:02:35] Looping over 4 formats...
[INFO] [2021-04-19 16:02:35] ...refs (/app/public/data/nev_nev_1979/references.tsv)
[CMD] [2021-04-19 16:02:35] /usr/bin/sort /app/public/converted_csv/nev_nev_1979_refs_3785.csv > /app/public/converted_csv/nev_nev_1979_refs_3785.csv_sorted
[INFO] [2021-04-19 16:02:35] Converted: /app/public/converted_csv/nev_nev_1979_refs_3785.csv (0 lines)
[INFO] [2021-04-19 16:02:35] ...nodes (/app/public/data/nev_nev_1979/taxa.txt)
[CMD] [2021-04-19 16:02:35] /usr/bin/sort /app/public/converted_csv/nev_nev_1979_nodes_3785.csv > /app/public/converted_csv/nev_nev_1979_nodes_3785.csv_sorted
[INFO] [2021-04-19 16:02:35] Converted: /app/public/converted_csv/nev_nev_1979_nodes_3785.csv (7 lines)
[INFO] [2021-04-19 16:02:35] ...occurrences (/app/public/data/nev_nev_1979/occurrences.txt)
[CMD] [2021-04-19 16:02:35] /usr/bin/sort /app/public/converted_csv/nev_nev_1979_occurrences_3785.csv > /app/public/converted_csv/nev_nev_1979_occurrences_3785.csv_sorted
[INFO] [2021-04-19 16:02:35] Converted: /app/public/converted_csv/nev_nev_1979_occurrences_3785.csv (7 lines)
[INFO] [2021-04-19 16:02:35] ...measurements (/app/public/data/nev_nev_1979/measurementsorfacts.txt)
[CMD] [2021-04-19 16:02:35] /usr/bin/sort /app/public/converted_csv/nev_nev_1979_measurements_3785.csv > /app/public/converted_csv/nev_nev_1979_measurements_3785.csv_sorted
[INFO] [2021-04-19 16:02:35] Converted: /app/public/converted_csv/nev_nev_1979_measurements_3785.csv (13 lines)
[STOP] [2021-04-19 16:02:35] convert_to_csv
[START] [2021-04-19 16:02:35] calculate_delta
[INFO] [2021-04-19 16:02:35] Looping over 4 formats...
[INFO] [2021-04-19 16:02:35] ...refs (/app/public/data/nev_nev_1979/references.tsv)
[CMD] [2021-04-19 16:02:35] echo "0a" > /app/public/diff/nev_nev_1979_refs_3785.diff
[CMD] [2021-04-19 16:02:35] tail -n +1 /app/public/converted_csv/nev_nev_1979_refs_3785.csv >> /app/public/diff/nev_nev_1979_refs_3785.diff
[CMD] [2021-04-19 16:02:35] echo "." >> /app/public/diff/nev_nev_1979_refs_3785.diff
[INFO] [2021-04-19 16:02:35] Created diff: /app/public/diff/nev_nev_1979_refs_3785.diff (2 lines)
[INFO] [2021-04-19 16:02:35] ...nodes (/app/public/data/nev_nev_1979/taxa.txt)
[CMD] [2021-04-19 16:02:35] echo "0a" > /app/public/diff/nev_nev_1979_nodes_3785.diff
[CMD] [2021-04-19 16:02:35] tail -n +1 /app/public/converted_csv/nev_nev_1979_nodes_3785.csv >> /app/public/diff/nev_nev_1979_nodes_3785.diff
[CMD] [2021-04-19 16:02:35] echo "." >> /app/public/diff/nev_nev_1979_nodes_3785.diff
[INFO] [2021-04-19 16:02:35] Created diff: /app/public/diff/nev_nev_1979_nodes_3785.diff (9 lines)
[INFO] [2021-04-19 16:02:35] ...occurrences (/app/public/data/nev_nev_1979/occurrences.txt)
[CMD] [2021-04-19 16:02:35] echo "0a" > /app/public/diff/nev_nev_1979_occurrences_3785.diff
[CMD] [2021-04-19 16:02:35] tail -n +1 /app/public/converted_csv/nev_nev_1979_occurrences_3785.csv >> /app/public/diff/nev_nev_1979_occurrences_3785.diff
[CMD] [2021-04-19 16:02:35] echo "." >> /app/public/diff/nev_nev_1979_occurrences_3785.diff
[INFO] [2021-04-19 16:02:35] Created diff: /app/public/diff/nev_nev_1979_occurrences_3785.diff (9 lines)
[INFO] [2021-04-19 16:02:35] ...measurements (/app/public/data/nev_nev_1979/measurementsorfacts.txt)
[CMD] [2021-04-19 16:02:35] echo "0a" > /app/public/diff/nev_nev_1979_measurements_3785.diff
[CMD] [2021-04-19 16:02:35] tail -n +1 /app/public/converted_csv/nev_nev_1979_measurements_3785.csv >> /app/public/diff/nev_nev_1979_measurements_3785.diff
[CMD] [2021-04-19 16:02:35] echo "." >> /app/public/diff/nev_nev_1979_measurements_3785.diff
[INFO] [2021-04-19 16:02:35] Created diff: /app/public/diff/nev_nev_1979_measurements_3785.diff (15 lines)
[STOP] [2021-04-19 16:02:35] calculate_delta
[START] [2021-04-19 16:02:35] parse_diff_and_store
[INFO] [2021-04-19 16:02:35] Handling diff: /app/public/diff/nev_nev_1979_refs_3785.diff (2 lines)
[INFO] [2021-04-19 16:02:35] Loading refs diff file into memory (2 /app/public/diff/nev_nev_1979_refs_3785.diff lines)...
[INFO] [2021-04-19 16:02:35] Handling diff: /app/public/diff/nev_nev_1979_nodes_3785.diff (9 lines)
[INFO] [2021-04-19 16:02:35] Loading nodes diff file into memory (9 /app/public/diff/nev_nev_1979_nodes_3785.diff lines)...
[INFO] [2021-04-19 16:02:35] Handling diff: /app/public/diff/nev_nev_1979_occurrences_3785.diff (9 lines)
[INFO] [2021-04-19 16:02:35] Loading occurrences diff file into memory (9 /app/public/diff/nev_nev_1979_occurrences_3785.diff lines)...
[INFO] [2021-04-19 16:02:35] Handling diff: /app/public/diff/nev_nev_1979_measurements_3785.diff (15 lines)
[INFO] [2021-04-19 16:02:35] Loading measurements diff file into memory (15 /app/public/diff/nev_nev_1979_measurements_3785.diff lines)...
[INFO] [2021-04-19 16:02:35] Storing 7 ScientificNames
[INFO] [2021-04-19 16:02:35] Processing group of 7 in 1 groups of 1000
[INFO] [2021-04-19 16:02:35] Average Time: 0.0
[INFO] [2021-04-19 16:02:35] Total Time: 1s
[INFO] [2021-04-19 16:02:35] Storing 7 Nodes
[INFO] [2021-04-19 16:02:35] Processing group of 7 in 1 groups of 1000
[INFO] [2021-04-19 16:02:35] Average Time: 0.0
[INFO] [2021-04-19 16:02:35] Total Time: 1s
[INFO] [2021-04-19 16:02:35] Storing 7 Occurrences
[INFO] [2021-04-19 16:02:35] Processing group of 7 in 1 groups of 1000
[INFO] [2021-04-19 16:02:35] Average Time: 0.0
[INFO] [2021-04-19 16:02:35] Total Time: 1s
[INFO] [2021-04-19 16:02:35] Storing 13 Traits
[INFO] [2021-04-19 16:02:35] Processing group of 13 in 1 groups of 1000
[INFO] [2021-04-19 16:02:35] Average Time: 0.0
[INFO] [2021-04-19 16:02:35] Total Time: 1s
[INFO] [2021-04-19 16:02:35] Storing 14 MetaTraits
[INFO] [2021-04-19 16:02:35] Processing group of 14 in 1 groups of 1000
[INFO] [2021-04-19 16:02:35] Average Time: 0.0
[INFO] [2021-04-19 16:02:35] Total Time: 1s
[STOP] [2021-04-19 16:02:35] parse_diff_and_store
[START] [2021-04-19 16:02:35] resolve_keys
[INFO] [2021-04-19 16:02:41] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 16:02:41] traits to occurrences...
[INFO] [2021-04-19 16:02:41] traits to nodes (through occurrences)...
[INFO] [2021-04-19 16:02:41] Traits to sex term...
[INFO] [2021-04-19 16:02:41] Traits to lifestage term...
[INFO] [2021-04-19 16:02:41] MetaTraits to traits...
[INFO] [2021-04-19 16:02:41] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 16:02:41] Assocs to occurrences...
[INFO] [2021-04-19 16:02:41] Assocs to nodes...
[INFO] [2021-04-19 16:02:41] Assoc to sex term...
[INFO] [2021-04-19 16:02:41] Assoc to lifestage term...
[INFO] [2021-04-19 16:02:41] MetaAssoc to assocs...
[STOP] [2021-04-19 16:02:41] resolve_keys
[START] [2021-04-19 16:02:41] hold_for_later_1
[STOP] [2021-04-19 16:02:41] hold_for_later_1
[START] [2021-04-19 16:02:41] hold_for_later_2
[STOP] [2021-04-19 16:02:41] hold_for_later_2
[START] [2021-04-19 16:02:41] resolve_missing_parents
[STOP] [2021-04-19 16:02:41] resolve_missing_parents
[START] [2021-04-19 16:02:41] rebuild_nodes
[START] [2021-04-19 16:02:41] Flattener#flatten
[START] [2021-04-19 16:02:41] Flattener#study_resource
[START] [2021-04-19 16:02:41] Flattener#build_ancestry
[STOP] [2021-04-19 16:02:41] Flattener#build_ancestry
[INFO] [2021-04-19 16:02:41] 7 ancestry keys
[START] [2021-04-19 16:02:41] build_node_ancestors
[INFO] [2021-04-19 16:02:41] old ancestors deleted.
[STOP] [2021-04-19 16:02:41] build_node_ancestors
[WARN] [2021-04-19 16:02:41] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 16:02:41] Flattener#flatten
[STOP] [2021-04-19 16:02:41] rebuild_nodes
[START] [2021-04-19 16:02:41] resolve_missing_media_owners
[STOP] [2021-04-19 16:02:41] resolve_missing_media_owners
[START] [2021-04-19 16:02:41] sanitize_media_verbatims
[STOP] [2021-04-19 16:02:41] sanitize_media_verbatims
[START] [2021-04-19 16:02:41] queue_downloads
[STOP] [2021-04-19 16:02:41] queue_downloads
[START] [2021-04-19 16:02:41] parse_names
[WARN] [2021-04-19 16:02:41] I see 7 names which still need to be parsed.
[STOP] [2021-04-19 16:02:43] parse_names
[START] [2021-04-19 16:02:43] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 16:02:43] denormalize_canonical_names_to_nodes
[START] [2021-04-19 16:02:43] match_nodes
[START] [2021-04-19 16:02:43] map_all_nodes_to_pages
[STOP] [2021-04-19 16:02:43] map_all_nodes_to_pages
[INFO] [2021-04-19 16:02:43] ZERO unmatched nodes (of 7)! Nicely done.
[START] [2021-04-19 16:02:43] update_nodes
[STOP] [2021-04-19 16:02:43] update_nodes
[STOP] [2021-04-19 16:02:43] match_nodes
[START] [2021-04-19 16:02:43] reindex_search
[STOP] [2021-04-19 16:02:43] reindex_search
[START] [2021-04-19 16:02:43] normalize_units
[STOP] [2021-04-19 16:02:43] normalize_units
[START] [2021-04-19 16:02:43] calculate_statistics
[2021-04-19 16:02:43] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 16:02:43] calculate_statistics
[START] [2021-04-19 16:02:43] complete_harvest_instance
[START] [2021-04-19 16:02:43] overall_tsv_creation
[INFO] [2021-04-19 16:02:43] Processing group of 7 in 1 batches of 10000
[INFO] [2021-04-19 16:03:19] 7 Traits (unfiltered)...
[INFO] [2021-04-19 16:03:52] 7 Traits (filtered)...
[INFO] [2021-04-19 16:03:52] 0 Associations (filtered)...
[INFO] [2021-04-19 16:03:52] 6 metadata added.
[INFO] [2021-04-19 16:03:52] 0 metadata added.
[INFO] [2021-04-19 16:04:18] Average Time: 71.52
[INFO] [2021-04-19 16:04:18] Total Time: 1m36s
[STOP] [2021-04-19 16:04:18] overall_tsv_creation
[INFO] [2021-04-19 16:04:18] Done. Check your files:
[INFO] [2021-04-19 16:04:18] (7 lines) /app/public/data/nev_nev_1979/publish_nodes.tsv
[INFO] [2021-04-19 16:04:18] (7 lines) /app/public/data/nev_nev_1979/publish_scientific_names.tsv
[INFO] [2021-04-19 16:04:18] (8 lines) /app/public/data/nev_nev_1979/publish_traits.tsv
[INFO] [2021-04-19 16:04:18] (7 lines) /app/public/data/nev_nev_1979/publish_metadata.tsv
[STOP] [2021-04-19 16:04:18] complete_harvest_instance
[START] [2021-04-19 16:04:18] completed
[STOP] [2021-04-19 16:04:18] completed
[STOP] [2021-04-19 16:04:18] logged process, took 103.45

Latest Process

19 Apr 16:02 EXITED currently processing 0