Harvest for Rogers et al 1980 Created 19 Apr 16:59

Stage: completed
Fetched: 19 Apr 16:59
Validated: 19 Apr 16:59
Deltas Created 19 Apr 16:59
Units Normalized: 19 Apr 16:59
Ancestry Built: 19 Apr 16:59
Nodes Matched: 19 Apr 16:59
Names Parsed: 19 Apr 16:59
New Models Stored: 19 Apr 16:59
Indexed: 19 Apr 16:59
Completed: 19 Apr 17:01
Time to Harvest: less than a minute
Harvesting Log

(401 lines)
# Logfile created on 2020-12-08 15:30:04 -0500 by logger.rb/v1.4.2
[START] [2020-12-08 15:30:04] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-08 15:30:04] Creating resource from OpenData
[START] [2020-12-08 15:30:04] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-08 15:30:04] Parse meta.xml file and create formats with fields
[STOP] [2020-12-08 15:30:04] Parse meta.xml file and create formats with fields
[STOP] [2020-12-08 15:30:04] Creating resource from OpenData
[INFO] [2020-12-08 15:30:07] ## HARVEST: type = -harvest
[START] [2020-12-08 15:30:10] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-08 15:30:10] create_harvest_instance
[STOP] [2020-12-08 15:30:11] create_harvest_instance
[START] [2020-12-08 15:30:11] fetch_files
[STOP] [2020-12-08 15:30:11] fetch_files
[START] [2020-12-08 15:30:11] validate_each_file
[STOP] [2020-12-08 15:30:11] validate_each_file
[START] [2020-12-08 15:30:11] convert_to_csv
[CMD] [2020-12-08 15:30:11] /usr/bin/sort /app/public/converted_csv/rogers_et_al_rog_nodes_25309.csv > /app/public/converted_csv/rogers_et_al_rog_nodes_25309.csv_sorted
[CMD] [2020-12-08 15:30:11] /usr/bin/sort /app/public/converted_csv/rogers_et_al_rog_occurrences_25310.csv > /app/public/converted_csv/rogers_et_al_rog_occurrences_25310.csv_sorted
[CMD] [2020-12-08 15:30:11] /usr/bin/sort /app/public/converted_csv/rogers_et_al_rog_measurements_25311.csv > /app/public/converted_csv/rogers_et_al_rog_measurements_25311.csv_sorted
[STOP] [2020-12-08 15:30:11] convert_to_csv
[START] [2020-12-08 15:30:11] calculate_delta
[CMD] [2020-12-08 15:30:11] echo "0a" > /app/public/diff/rogers_et_al_rog_nodes_25309.diff
[CMD] [2020-12-08 15:30:11] tail -n +1 /app/public/converted_csv/rogers_et_al_rog_nodes_25309.csv >> /app/public/diff/rogers_et_al_rog_nodes_25309.diff
[CMD] [2020-12-08 15:30:11] echo "." >> /app/public/diff/rogers_et_al_rog_nodes_25309.diff
[CMD] [2020-12-08 15:30:11] echo "0a" > /app/public/diff/rogers_et_al_rog_occurrences_25310.diff
[CMD] [2020-12-08 15:30:11] tail -n +1 /app/public/converted_csv/rogers_et_al_rog_occurrences_25310.csv >> /app/public/diff/rogers_et_al_rog_occurrences_25310.diff
[CMD] [2020-12-08 15:30:11] echo "." >> /app/public/diff/rogers_et_al_rog_occurrences_25310.diff
[CMD] [2020-12-08 15:30:11] echo "0a" > /app/public/diff/rogers_et_al_rog_measurements_25311.diff
[CMD] [2020-12-08 15:30:11] tail -n +1 /app/public/converted_csv/rogers_et_al_rog_measurements_25311.csv >> /app/public/diff/rogers_et_al_rog_measurements_25311.diff
[CMD] [2020-12-08 15:30:11] echo "." >> /app/public/diff/rogers_et_al_rog_measurements_25311.diff
[STOP] [2020-12-08 15:30:11] calculate_delta
[START] [2020-12-08 15:30:11] parse_diff_and_store
[INFO] [2020-12-08 15:30:11] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-08 15:30:11] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-08 15:30:11] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-08 15:30:12] Storing 1 ScientificNames
[INFO] [2020-12-08 15:30:12] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-08 15:30:12] Average Time: 0.0
[INFO] [2020-12-08 15:30:12] Total Time: 1s
[INFO] [2020-12-08 15:30:12] Storing 1 Nodes
[INFO] [2020-12-08 15:30:12] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-08 15:30:12] Average Time: 0.0
[INFO] [2020-12-08 15:30:12] Total Time: 1s
[INFO] [2020-12-08 15:30:12] Storing 1 Occurrences
[INFO] [2020-12-08 15:30:12] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-08 15:30:12] Average Time: 0.0
[INFO] [2020-12-08 15:30:12] Total Time: 1s
[INFO] [2020-12-08 15:30:12] Storing 2 Traits
[INFO] [2020-12-08 15:30:12] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-08 15:30:12] Average Time: 0.0
[INFO] [2020-12-08 15:30:12] Total Time: 1s
[INFO] [2020-12-08 15:30:12] Storing 1 MetaTraits
[INFO] [2020-12-08 15:30:12] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-08 15:30:12] Average Time: 0.0
[INFO] [2020-12-08 15:30:12] Total Time: 1s
[STOP] [2020-12-08 15:30:12] parse_diff_and_store
[START] [2020-12-08 15:30:12] resolve_keys
[INFO] [2020-12-08 15:30:17] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-08 15:30:17] traits to occurrences...
[INFO] [2020-12-08 15:30:17] traits to nodes (through occurrences)...
[INFO] [2020-12-08 15:30:17] Traits to sex term...
[INFO] [2020-12-08 15:30:17] Traits to lifestage term...
[INFO] [2020-12-08 15:30:17] MetaTraits to traits...
[INFO] [2020-12-08 15:30:17] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-08 15:30:17] Assocs to occurrences...
[INFO] [2020-12-08 15:30:17] Assocs to nodes...
[INFO] [2020-12-08 15:30:17] Assoc to sex term...
[INFO] [2020-12-08 15:30:17] Assoc to lifestage term...
[INFO] [2020-12-08 15:30:17] MetaAssoc to assocs...
[STOP] [2020-12-08 15:30:17] resolve_keys
[START] [2020-12-08 15:30:17] hold_for_later_1
[STOP] [2020-12-08 15:30:17] hold_for_later_1
[START] [2020-12-08 15:30:17] hold_for_later_2
[STOP] [2020-12-08 15:30:17] hold_for_later_2
[START] [2020-12-08 15:30:17] resolve_missing_parents
[STOP] [2020-12-08 15:30:17] resolve_missing_parents
[START] [2020-12-08 15:30:17] rebuild_nodes
[START] [2020-12-08 15:30:17] Flattener#flatten
[START] [2020-12-08 15:30:17] Flattener#study_resource
[START] [2020-12-08 15:30:17] Flattener#build_ancestry
[STOP] [2020-12-08 15:30:17] Flattener#build_ancestry
[INFO] [2020-12-08 15:30:17] 1 ancestry keys
[START] [2020-12-08 15:30:17] build_node_ancestors
[INFO] [2020-12-08 15:30:17] old ancestors deleted.
[STOP] [2020-12-08 15:30:17] build_node_ancestors
[WARN] [2020-12-08 15:30:17] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-08 15:30:17] Flattener#flatten
[STOP] [2020-12-08 15:30:17] rebuild_nodes
[START] [2020-12-08 15:30:17] resolve_missing_media_owners
[STOP] [2020-12-08 15:30:17] resolve_missing_media_owners
[START] [2020-12-08 15:30:17] sanitize_media_verbatims
[STOP] [2020-12-08 15:30:17] sanitize_media_verbatims
[START] [2020-12-08 15:30:17] queue_downloads
[STOP] [2020-12-08 15:30:17] queue_downloads
[START] [2020-12-08 15:30:17] parse_names
[WARN] [2020-12-08 15:30:17] I see 1 names which still need to be parsed.
[STOP] [2020-12-08 15:30:19] parse_names
[START] [2020-12-08 15:30:19] denormalize_canonical_names_to_nodes
[STOP] [2020-12-08 15:30:19] denormalize_canonical_names_to_nodes
[START] [2020-12-08 15:30:19] match_nodes
[START] [2020-12-08 15:30:19] map_all_nodes_to_pages
[STOP] [2020-12-08 15:30:19] map_all_nodes_to_pages
[INFO] [2020-12-08 15:30:19] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-12-08 15:30:19] update_nodes
[STOP] [2020-12-08 15:30:19] update_nodes
[STOP] [2020-12-08 15:30:19] match_nodes
[START] [2020-12-08 15:30:19] reindex_search
[STOP] [2020-12-08 15:30:19] reindex_search
[START] [2020-12-08 15:30:19] normalize_units
[STOP] [2020-12-08 15:30:19] normalize_units
[START] [2020-12-08 15:30:19] calculate_statistics
[2020-12-08 15:30:19] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-08 15:30:19] calculate_statistics
[START] [2020-12-08 15:30:19] complete_harvest_instance
[START] [2020-12-08 15:30:19] overall_tsv_creation
[INFO] [2020-12-08 15:30:19] Processing group of 1 in 1 batches of 10000
[INFO] [2020-12-08 15:30:57] 1 Traits (unfiltered)...
[INFO] [2020-12-08 15:31:33] 1 Traits (filtered)...
[INFO] [2020-12-08 15:31:33] 0 Associations (filtered)...
[INFO] [2020-12-08 15:31:33] 2 metadata added.
[INFO] [2020-12-08 15:31:33] 0 metadata added.
[INFO] [2020-12-08 15:31:33] Average Time: 51.17
[INFO] [2020-12-08 15:31:33] Total Time: 1m14s
[STOP] [2020-12-08 15:31:33] overall_tsv_creation
[INFO] [2020-12-08 15:31:33] Done. Check your files:
[INFO] [2020-12-08 15:31:33] (1 lines) /app/public/data/rogers_et_al_rog/publish_nodes.tsv
[INFO] [2020-12-08 15:31:33] (1 lines) /app/public/data/rogers_et_al_rog/publish_scientific_names.tsv
[INFO] [2020-12-08 15:31:33] (2 lines) /app/public/data/rogers_et_al_rog/publish_traits.tsv
[INFO] [2020-12-08 15:31:33] (3 lines) /app/public/data/rogers_et_al_rog/publish_metadata.tsv
[STOP] [2020-12-08 15:31:33] complete_harvest_instance
[START] [2020-12-08 15:31:33] completed
[STOP] [2020-12-08 15:31:33] completed
[STOP] [2020-12-08 15:31:33] logged process, took 83.11
[INFO] [2021-04-19 16:47:52] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 16:59:51] ## remove_type: ScientificName
[INFO] [2021-04-19 16:59:51] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 16:59:51] [16:59:51.289] Removed 1 Scientificnames
[INFO] [2021-04-19 16:59:51] ## remove_type: Vernacular
[INFO] [2021-04-19 16:59:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:59:51] [16:59:51.290] Removed 0 Vernaculars
[INFO] [2021-04-19 16:59:51] ## remove_type: Article
[INFO] [2021-04-19 16:59:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:59:51] [16:59:51.292] Removed 0 Articles
[INFO] [2021-04-19 16:59:51] ## remove_type: Medium
[INFO] [2021-04-19 16:59:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:59:51] [16:59:51.293] Removed 0 Media
[INFO] [2021-04-19 16:59:51] ## remove_type: Trait
[INFO] [2021-04-19 16:59:51] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 16:59:51] [16:59:51.295] Removed 2 Traits
[INFO] [2021-04-19 16:59:51] ## remove_type: MetaTrait
[INFO] [2021-04-19 16:59:51] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 16:59:51] [16:59:51.296] Removed 1 Metatraits
[INFO] [2021-04-19 16:59:51] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 16:59:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:59:51] [16:59:51.298] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 16:59:51] ## remove_type: Assoc
[INFO] [2021-04-19 16:59:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:59:51] [16:59:51.299] Removed 0 Assocs
[INFO] [2021-04-19 16:59:51] ## remove_type: MetaAssoc
[INFO] [2021-04-19 16:59:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:59:51] [16:59:51.301] Removed 0 Metaassocs
[INFO] [2021-04-19 16:59:51] ## remove_type: Identifier
[INFO] [2021-04-19 16:59:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:59:51] [16:59:51.302] Removed 0 Identifiers
[INFO] [2021-04-19 16:59:51] ## remove_type: Reference
[INFO] [2021-04-19 16:59:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:59:51] [16:59:51.304] Removed 0 References
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] Starting batch with ID 86121273...
[INFO] [2021-04-19 16:59:51] ## remove_type: Node
[INFO] [2021-04-19 16:59:51] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 16:59:51] [16:59:51.796] Removed 1 Nodes
[START] [2021-04-19 16:59:51] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:59:51] Creating resource from OpenData
[START] [2021-04-19 16:59:52] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:59:52] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:59:52] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:59:52] Creating resource from OpenData
[START] [2021-04-19 16:59:52] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:59:52] create_harvest_instance
[INFO] [2021-04-19 16:59:52] Created harvest instance #3812
[STOP] [2021-04-19 16:59:52] create_harvest_instance
[START] [2021-04-19 16:59:52] fetch_files
[STOP] [2021-04-19 16:59:52] fetch_files
[START] [2021-04-19 16:59:52] validate_each_file
[INFO] [2021-04-19 16:59:52] Looping over 3 formats...
[INFO] [2021-04-19 16:59:52] ...nodes (/app/public/data/rogers_et_al_rog/taxa.txt)
[INFO] [2021-04-19 16:59:52] Valid: /app/public/converted_csv/rogers_et_al_rog_nodes_3812.csv (1 lines)
[INFO] [2021-04-19 16:59:52] ...occurrences (/app/public/data/rogers_et_al_rog/occurrences.txt)
[INFO] [2021-04-19 16:59:52] Valid: /app/public/converted_csv/rogers_et_al_rog_occurrences_3812.csv (1 lines)
[INFO] [2021-04-19 16:59:52] ...measurements (/app/public/data/rogers_et_al_rog/measurementsorfacts.txt)
[INFO] [2021-04-19 16:59:52] Valid: /app/public/converted_csv/rogers_et_al_rog_measurements_3812.csv (2 lines)
[STOP] [2021-04-19 16:59:52] validate_each_file
[START] [2021-04-19 16:59:52] convert_to_csv
[INFO] [2021-04-19 16:59:52] Looping over 3 formats...
[INFO] [2021-04-19 16:59:52] ...nodes (/app/public/data/rogers_et_al_rog/taxa.txt)
[CMD] [2021-04-19 16:59:52] /usr/bin/sort /app/public/converted_csv/rogers_et_al_rog_nodes_3812.csv > /app/public/converted_csv/rogers_et_al_rog_nodes_3812.csv_sorted
[INFO] [2021-04-19 16:59:52] Converted: /app/public/converted_csv/rogers_et_al_rog_nodes_3812.csv (1 lines)
[INFO] [2021-04-19 16:59:52] ...occurrences (/app/public/data/rogers_et_al_rog/occurrences.txt)
[CMD] [2021-04-19 16:59:52] /usr/bin/sort /app/public/converted_csv/rogers_et_al_rog_occurrences_3812.csv > /app/public/converted_csv/rogers_et_al_rog_occurrences_3812.csv_sorted
[INFO] [2021-04-19 16:59:52] Converted: /app/public/converted_csv/rogers_et_al_rog_occurrences_3812.csv (1 lines)
[INFO] [2021-04-19 16:59:52] ...measurements (/app/public/data/rogers_et_al_rog/measurementsorfacts.txt)
[CMD] [2021-04-19 16:59:52] /usr/bin/sort /app/public/converted_csv/rogers_et_al_rog_measurements_3812.csv > /app/public/converted_csv/rogers_et_al_rog_measurements_3812.csv_sorted
[INFO] [2021-04-19 16:59:52] Converted: /app/public/converted_csv/rogers_et_al_rog_measurements_3812.csv (2 lines)
[STOP] [2021-04-19 16:59:52] convert_to_csv
[START] [2021-04-19 16:59:52] calculate_delta
[INFO] [2021-04-19 16:59:52] Looping over 3 formats...
[INFO] [2021-04-19 16:59:52] ...nodes (/app/public/data/rogers_et_al_rog/taxa.txt)
[CMD] [2021-04-19 16:59:52] echo "0a" > /app/public/diff/rogers_et_al_rog_nodes_3812.diff
[CMD] [2021-04-19 16:59:52] tail -n +1 /app/public/converted_csv/rogers_et_al_rog_nodes_3812.csv >> /app/public/diff/rogers_et_al_rog_nodes_3812.diff
[CMD] [2021-04-19 16:59:52] echo "." >> /app/public/diff/rogers_et_al_rog_nodes_3812.diff
[INFO] [2021-04-19 16:59:52] Created diff: /app/public/diff/rogers_et_al_rog_nodes_3812.diff (3 lines)
[INFO] [2021-04-19 16:59:52] ...occurrences (/app/public/data/rogers_et_al_rog/occurrences.txt)
[CMD] [2021-04-19 16:59:52] echo "0a" > /app/public/diff/rogers_et_al_rog_occurrences_3812.diff
[CMD] [2021-04-19 16:59:52] tail -n +1 /app/public/converted_csv/rogers_et_al_rog_occurrences_3812.csv >> /app/public/diff/rogers_et_al_rog_occurrences_3812.diff
[CMD] [2021-04-19 16:59:52] echo "." >> /app/public/diff/rogers_et_al_rog_occurrences_3812.diff
[INFO] [2021-04-19 16:59:52] Created diff: /app/public/diff/rogers_et_al_rog_occurrences_3812.diff (3 lines)
[INFO] [2021-04-19 16:59:52] ...measurements (/app/public/data/rogers_et_al_rog/measurementsorfacts.txt)
[CMD] [2021-04-19 16:59:52] echo "0a" > /app/public/diff/rogers_et_al_rog_measurements_3812.diff
[CMD] [2021-04-19 16:59:52] tail -n +1 /app/public/converted_csv/rogers_et_al_rog_measurements_3812.csv >> /app/public/diff/rogers_et_al_rog_measurements_3812.diff
[CMD] [2021-04-19 16:59:52] echo "." >> /app/public/diff/rogers_et_al_rog_measurements_3812.diff
[INFO] [2021-04-19 16:59:52] Created diff: /app/public/diff/rogers_et_al_rog_measurements_3812.diff (4 lines)
[STOP] [2021-04-19 16:59:52] calculate_delta
[START] [2021-04-19 16:59:52] parse_diff_and_store
[INFO] [2021-04-19 16:59:52] Handling diff: /app/public/diff/rogers_et_al_rog_nodes_3812.diff (3 lines)
[INFO] [2021-04-19 16:59:52] Loading nodes diff file into memory (3 /app/public/diff/rogers_et_al_rog_nodes_3812.diff lines)...
[INFO] [2021-04-19 16:59:52] Handling diff: /app/public/diff/rogers_et_al_rog_occurrences_3812.diff (3 lines)
[INFO] [2021-04-19 16:59:52] Loading occurrences diff file into memory (3 /app/public/diff/rogers_et_al_rog_occurrences_3812.diff lines)...
[INFO] [2021-04-19 16:59:52] Handling diff: /app/public/diff/rogers_et_al_rog_measurements_3812.diff (4 lines)
[INFO] [2021-04-19 16:59:52] Loading measurements diff file into memory (4 /app/public/diff/rogers_et_al_rog_measurements_3812.diff lines)...
[INFO] [2021-04-19 16:59:52] Storing 1 ScientificNames
[INFO] [2021-04-19 16:59:52] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:59:52] Average Time: 0.0
[INFO] [2021-04-19 16:59:52] Total Time: 1s
[INFO] [2021-04-19 16:59:52] Storing 1 Nodes
[INFO] [2021-04-19 16:59:52] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:59:52] Average Time: 0.0
[INFO] [2021-04-19 16:59:52] Total Time: 1s
[INFO] [2021-04-19 16:59:52] Storing 1 Occurrences
[INFO] [2021-04-19 16:59:52] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:59:52] Average Time: 0.0
[INFO] [2021-04-19 16:59:52] Total Time: 1s
[INFO] [2021-04-19 16:59:52] Storing 2 Traits
[INFO] [2021-04-19 16:59:52] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 16:59:52] Average Time: 0.0
[INFO] [2021-04-19 16:59:52] Total Time: 1s
[INFO] [2021-04-19 16:59:52] Storing 1 MetaTraits
[INFO] [2021-04-19 16:59:52] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:59:52] Average Time: 0.0
[INFO] [2021-04-19 16:59:52] Total Time: 1s
[STOP] [2021-04-19 16:59:52] parse_diff_and_store
[START] [2021-04-19 16:59:52] resolve_keys
[INFO] [2021-04-19 16:59:58] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 16:59:58] traits to occurrences...
[INFO] [2021-04-19 16:59:58] traits to nodes (through occurrences)...
[INFO] [2021-04-19 16:59:58] Traits to sex term...
[INFO] [2021-04-19 16:59:58] Traits to lifestage term...
[INFO] [2021-04-19 16:59:58] MetaTraits to traits...
[INFO] [2021-04-19 16:59:58] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 16:59:58] Assocs to occurrences...
[INFO] [2021-04-19 16:59:58] Assocs to nodes...
[INFO] [2021-04-19 16:59:58] Assoc to sex term...
[INFO] [2021-04-19 16:59:58] Assoc to lifestage term...
[INFO] [2021-04-19 16:59:58] MetaAssoc to assocs...
[STOP] [2021-04-19 16:59:58] resolve_keys
[START] [2021-04-19 16:59:58] hold_for_later_1
[STOP] [2021-04-19 16:59:58] hold_for_later_1
[START] [2021-04-19 16:59:58] hold_for_later_2
[STOP] [2021-04-19 16:59:58] hold_for_later_2
[START] [2021-04-19 16:59:58] resolve_missing_parents
[STOP] [2021-04-19 16:59:58] resolve_missing_parents
[START] [2021-04-19 16:59:58] rebuild_nodes
[START] [2021-04-19 16:59:58] Flattener#flatten
[START] [2021-04-19 16:59:58] Flattener#study_resource
[START] [2021-04-19 16:59:58] Flattener#build_ancestry
[STOP] [2021-04-19 16:59:58] Flattener#build_ancestry
[INFO] [2021-04-19 16:59:58] 1 ancestry keys
[START] [2021-04-19 16:59:58] build_node_ancestors
[INFO] [2021-04-19 16:59:58] old ancestors deleted.
[STOP] [2021-04-19 16:59:58] build_node_ancestors
[WARN] [2021-04-19 16:59:58] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 16:59:58] Flattener#flatten
[STOP] [2021-04-19 16:59:58] rebuild_nodes
[START] [2021-04-19 16:59:58] resolve_missing_media_owners
[STOP] [2021-04-19 16:59:58] resolve_missing_media_owners
[START] [2021-04-19 16:59:58] sanitize_media_verbatims
[STOP] [2021-04-19 16:59:58] sanitize_media_verbatims
[START] [2021-04-19 16:59:58] queue_downloads
[STOP] [2021-04-19 16:59:58] queue_downloads
[START] [2021-04-19 16:59:58] parse_names
[WARN] [2021-04-19 16:59:58] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 16:59:59] parse_names
[START] [2021-04-19 16:59:59] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 16:59:59] denormalize_canonical_names_to_nodes
[START] [2021-04-19 16:59:59] match_nodes
[START] [2021-04-19 16:59:59] map_all_nodes_to_pages
[STOP] [2021-04-19 16:59:59] map_all_nodes_to_pages
[INFO] [2021-04-19 16:59:59] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 16:59:59] update_nodes
[STOP] [2021-04-19 16:59:59] update_nodes
[STOP] [2021-04-19 16:59:59] match_nodes
[START] [2021-04-19 16:59:59] reindex_search
[STOP] [2021-04-19 16:59:59] reindex_search
[START] [2021-04-19 16:59:59] normalize_units
[STOP] [2021-04-19 16:59:59] normalize_units
[START] [2021-04-19 16:59:59] calculate_statistics
[2021-04-19 16:59:59] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 16:59:59] calculate_statistics
[START] [2021-04-19 16:59:59] complete_harvest_instance
[START] [2021-04-19 16:59:59] overall_tsv_creation
[INFO] [2021-04-19 16:59:59] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 17:00:35] 1 Traits (unfiltered)...
[INFO] [2021-04-19 17:01:06] 1 Traits (filtered)...
[INFO] [2021-04-19 17:01:06] 0 Associations (filtered)...
[INFO] [2021-04-19 17:01:06] 1 metadata added.
[INFO] [2021-04-19 17:01:06] 0 metadata added.
[INFO] [2021-04-19 17:01:32] Average Time: 69.15
[INFO] [2021-04-19 17:01:32] Total Time: 1m34s
[STOP] [2021-04-19 17:01:32] overall_tsv_creation
[INFO] [2021-04-19 17:01:32] Done. Check your files:
[INFO] [2021-04-19 17:01:32] (1 lines) /app/public/data/rogers_et_al_rog/publish_nodes.tsv
[INFO] [2021-04-19 17:01:32] (1 lines) /app/public/data/rogers_et_al_rog/publish_scientific_names.tsv
[INFO] [2021-04-19 17:01:32] (2 lines) /app/public/data/rogers_et_al_rog/publish_traits.tsv
[INFO] [2021-04-19 17:01:32] (2 lines) /app/public/data/rogers_et_al_rog/publish_metadata.tsv
[STOP] [2021-04-19 17:01:32] complete_harvest_instance
[START] [2021-04-19 17:01:32] completed
[STOP] [2021-04-19 17:01:32] completed
[STOP] [2021-04-19 17:01:32] logged process, took 100.67
Latest Process

19 Apr 16:59 EXITED currently processing 0