Harvest for Iwaniuk et al 2020 Created 19 Apr 17:10

Harvesting Log

# Logfile created on 2021-02-03 10:40:22 -0500 by logger.rb/v1.4.2
[START] [2021-02-03 10:40:22] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 10:40:22] Creating resource from OpenData
[START] [2021-02-03 10:40:23] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 10:40:23] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 10:40:23] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 10:40:23] Creating resource from OpenData
[INFO] [2021-02-03 10:40:39] ## HARVEST: type = -harvest
[START] [2021-02-03 10:40:40] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 10:40:40] create_harvest_instance
[STOP] [2021-02-03 10:40:41] create_harvest_instance
[START] [2021-02-03 10:40:41] fetch_files
[STOP] [2021-02-03 10:40:41] fetch_files
[START] [2021-02-03 10:40:41] validate_each_file
[STOP] [2021-02-03 10:40:41] validate_each_file
[START] [2021-02-03 10:40:41] convert_to_csv
[CMD] [2021-02-03 10:40:41] /usr/bin/sort /app/public/converted_csv/iwaniuk_et_al_iw_nodes_26575.csv > /app/public/converted_csv/iwaniuk_et_al_iw_nodes_26575.csv_sorted
[CMD] [2021-02-03 10:40:41] /usr/bin/sort /app/public/converted_csv/iwaniuk_et_al_iw_occurrences_26576.csv > /app/public/converted_csv/iwaniuk_et_al_iw_occurrences_26576.csv_sorted
[CMD] [2021-02-03 10:40:41] /usr/bin/sort /app/public/converted_csv/iwaniuk_et_al_iw_measurements_26577.csv > /app/public/converted_csv/iwaniuk_et_al_iw_measurements_26577.csv_sorted
[STOP] [2021-02-03 10:40:41] convert_to_csv
[START] [2021-02-03 10:40:41] calculate_delta
[CMD] [2021-02-03 10:40:41] echo "0a" > /app/public/diff/iwaniuk_et_al_iw_nodes_26575.diff
[CMD] [2021-02-03 10:40:41] tail -n +1 /app/public/converted_csv/iwaniuk_et_al_iw_nodes_26575.csv >> /app/public/diff/iwaniuk_et_al_iw_nodes_26575.diff
[CMD] [2021-02-03 10:40:41] echo "." >> /app/public/diff/iwaniuk_et_al_iw_nodes_26575.diff
[CMD] [2021-02-03 10:40:41] echo "0a" > /app/public/diff/iwaniuk_et_al_iw_occurrences_26576.diff
[CMD] [2021-02-03 10:40:41] tail -n +1 /app/public/converted_csv/iwaniuk_et_al_iw_occurrences_26576.csv >> /app/public/diff/iwaniuk_et_al_iw_occurrences_26576.diff
[CMD] [2021-02-03 10:40:41] echo "." >> /app/public/diff/iwaniuk_et_al_iw_occurrences_26576.diff
[CMD] [2021-02-03 10:40:41] echo "0a" > /app/public/diff/iwaniuk_et_al_iw_measurements_26577.diff
[CMD] [2021-02-03 10:40:41] tail -n +1 /app/public/converted_csv/iwaniuk_et_al_iw_measurements_26577.csv >> /app/public/diff/iwaniuk_et_al_iw_measurements_26577.diff
[CMD] [2021-02-03 10:40:41] echo "." >> /app/public/diff/iwaniuk_et_al_iw_measurements_26577.diff
[STOP] [2021-02-03 10:40:41] calculate_delta
[START] [2021-02-03 10:40:41] parse_diff_and_store
[INFO] [2021-02-03 10:40:41] Loading nodes diff file into memory (true lines)...
[INFO] [2021-02-03 10:40:41] Loading occurrences diff file into memory (true lines)...
[INFO] [2021-02-03 10:40:41] Loading measurements diff file into memory (true lines)...
[INFO] [2021-02-03 10:40:42] Storing 3 ScientificNames
[INFO] [2021-02-03 10:40:42] Processing group of 3 in 1 groups of 1000
[INFO] [2021-02-03 10:40:42] Average Time: 0.0
[INFO] [2021-02-03 10:40:42] Total Time: 1s
[INFO] [2021-02-03 10:40:42] Storing 3 Nodes
[INFO] [2021-02-03 10:40:42] Processing group of 3 in 1 groups of 1000
[INFO] [2021-02-03 10:40:42] Average Time: 0.0
[INFO] [2021-02-03 10:40:42] Total Time: 1s
[INFO] [2021-02-03 10:40:42] Storing 4 Occurrences
[INFO] [2021-02-03 10:40:42] Processing group of 4 in 1 groups of 1000
[INFO] [2021-02-03 10:40:42] Average Time: 0.0
[INFO] [2021-02-03 10:40:42] Total Time: 1s
[INFO] [2021-02-03 10:40:42] Storing 6 Traits
[INFO] [2021-02-03 10:40:42] Processing group of 6 in 1 groups of 1000
[INFO] [2021-02-03 10:40:42] Average Time: 0.0
[INFO] [2021-02-03 10:40:42] Total Time: 1s
[INFO] [2021-02-03 10:40:42] Storing 3 MetaTraits
[INFO] [2021-02-03 10:40:42] Processing group of 3 in 1 groups of 1000
[INFO] [2021-02-03 10:40:42] Average Time: 0.0
[INFO] [2021-02-03 10:40:42] Total Time: 1s
[STOP] [2021-02-03 10:40:42] parse_diff_and_store
[START] [2021-02-03 10:40:42] resolve_keys
[INFO] [2021-02-03 10:40:48] Occurrences to nodes (through scientific_names)...
[INFO] [2021-02-03 10:40:48] traits to occurrences...
[INFO] [2021-02-03 10:40:48] traits to nodes (through occurrences)...
[INFO] [2021-02-03 10:40:48] Traits to sex term...
[INFO] [2021-02-03 10:40:48] Traits to lifestage term...
[INFO] [2021-02-03 10:40:48] MetaTraits to traits...
[INFO] [2021-02-03 10:40:48] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-02-03 10:40:48] Assocs to occurrences...
[INFO] [2021-02-03 10:40:48] Assocs to nodes...
[INFO] [2021-02-03 10:40:48] Assoc to sex term...
[INFO] [2021-02-03 10:40:48] Assoc to lifestage term...
[INFO] [2021-02-03 10:40:48] MetaAssoc to assocs...
[STOP] [2021-02-03 10:40:48] resolve_keys
[START] [2021-02-03 10:40:48] hold_for_later_1
[STOP] [2021-02-03 10:40:48] hold_for_later_1
[START] [2021-02-03 10:40:48] hold_for_later_2
[STOP] [2021-02-03 10:40:48] hold_for_later_2
[START] [2021-02-03 10:40:48] resolve_missing_parents
[STOP] [2021-02-03 10:40:48] resolve_missing_parents
[START] [2021-02-03 10:40:48] rebuild_nodes
[START] [2021-02-03 10:40:48] Flattener#flatten
[START] [2021-02-03 10:40:48] Flattener#study_resource
[START] [2021-02-03 10:40:48] Flattener#build_ancestry
[STOP] [2021-02-03 10:40:48] Flattener#build_ancestry
[INFO] [2021-02-03 10:40:48] 3 ancestry keys
[START] [2021-02-03 10:40:48] build_node_ancestors
[INFO] [2021-02-03 10:40:48] old ancestors deleted.
[STOP] [2021-02-03 10:40:48] build_node_ancestors
[WARN] [2021-02-03 10:40:48] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-02-03 10:40:48] Flattener#flatten
[STOP] [2021-02-03 10:40:48] rebuild_nodes
[START] [2021-02-03 10:40:48] resolve_missing_media_owners
[STOP] [2021-02-03 10:40:48] resolve_missing_media_owners
[START] [2021-02-03 10:40:48] sanitize_media_verbatims
[STOP] [2021-02-03 10:40:48] sanitize_media_verbatims
[START] [2021-02-03 10:40:48] queue_downloads
[STOP] [2021-02-03 10:40:48] queue_downloads
[START] [2021-02-03 10:40:48] parse_names
[WARN] [2021-02-03 10:40:48] I see 3 names which still need to be parsed.
[STOP] [2021-02-03 10:40:49] parse_names
[START] [2021-02-03 10:40:49] denormalize_canonical_names_to_nodes
[STOP] [2021-02-03 10:40:49] denormalize_canonical_names_to_nodes
[START] [2021-02-03 10:40:49] match_nodes
[START] [2021-02-03 10:40:49] map_all_nodes_to_pages
[STOP] [2021-02-03 10:40:49] map_all_nodes_to_pages
[INFO] [2021-02-03 10:40:49] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2021-02-03 10:40:49] update_nodes
[STOP] [2021-02-03 10:40:49] update_nodes
[STOP] [2021-02-03 10:40:49] match_nodes
[START] [2021-02-03 10:40:49] reindex_search
[STOP] [2021-02-03 10:40:49] reindex_search
[START] [2021-02-03 10:40:49] normalize_units
[STOP] [2021-02-03 10:40:49] normalize_units
[START] [2021-02-03 10:40:49] calculate_statistics
[2021-02-03 10:40:49] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-02-03 10:40:49] calculate_statistics
[START] [2021-02-03 10:40:49] complete_harvest_instance
[START] [2021-02-03 10:40:49] overall_tsv_creation
[INFO] [2021-02-03 10:40:49] Processing group of 3 in 1 batches of 10000
[INFO] [2021-02-03 10:41:29] 3 Traits (unfiltered)...
[INFO] [2021-02-03 10:42:05] 3 Traits (filtered)...
[INFO] [2021-02-03 10:42:05] 0 Associations (filtered)...
[INFO] [2021-02-03 10:42:05] 6 metadata added.
[INFO] [2021-02-03 10:42:05] 0 metadata added.
[INFO] [2021-02-03 10:42:36] Average Time: 80.89
[INFO] [2021-02-03 10:42:36] Total Time: 1m47s
[STOP] [2021-02-03 10:42:36] overall_tsv_creation
[INFO] [2021-02-03 10:42:36] Done. Check your files:
[INFO] [2021-02-03 10:42:36] (3 lines) /app/public/data/iwaniuk_et_al_iw/publish_nodes.tsv
[INFO] [2021-02-03 10:42:36] (3 lines) /app/public/data/iwaniuk_et_al_iw/publish_scientific_names.tsv
[INFO] [2021-02-03 10:42:36] (4 lines) /app/public/data/iwaniuk_et_al_iw/publish_traits.tsv
[INFO] [2021-02-03 10:42:36] (7 lines) /app/public/data/iwaniuk_et_al_iw/publish_metadata.tsv
[STOP] [2021-02-03 10:42:36] complete_harvest_instance
[START] [2021-02-03 10:42:36] completed
[STOP] [2021-02-03 10:42:36] completed
[STOP] [2021-02-03 10:42:36] logged process, took 116.54
[INFO] [2021-04-19 16:54:28] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 17:10:12] ## remove_type: ScientificName
[INFO] [2021-04-19 17:10:12] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 17:10:12] [17:10:12.815] Removed 3 Scientificnames
[INFO] [2021-04-19 17:10:12] ## remove_type: Vernacular
[INFO] [2021-04-19 17:10:12] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:10:12] [17:10:12.816] Removed 0 Vernaculars
[INFO] [2021-04-19 17:10:12] ## remove_type: Article
[INFO] [2021-04-19 17:10:12] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:10:12] [17:10:12.818] Removed 0 Articles
[INFO] [2021-04-19 17:10:12] ## remove_type: Medium
[INFO] [2021-04-19 17:10:12] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:10:12] [17:10:12.819] Removed 0 Media
[INFO] [2021-04-19 17:10:12] ## remove_type: Trait
[INFO] [2021-04-19 17:10:12] ++ Calling delete_all on 6 instances...
[INFO] [2021-04-19 17:10:12] [17:10:12.821] Removed 6 Traits
[INFO] [2021-04-19 17:10:12] ## remove_type: MetaTrait
[INFO] [2021-04-19 17:10:12] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 17:10:12] [17:10:12.823] Removed 3 Metatraits
[INFO] [2021-04-19 17:10:12] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 17:10:12] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:10:12] [17:10:12.824] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 17:10:12] ## remove_type: Assoc
[INFO] [2021-04-19 17:10:12] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:10:12] [17:10:12.826] Removed 0 Assocs
[INFO] [2021-04-19 17:10:12] ## remove_type: MetaAssoc
[INFO] [2021-04-19 17:10:12] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:10:12] [17:10:12.827] Removed 0 Metaassocs
[INFO] [2021-04-19 17:10:12] ## remove_type: Identifier
[INFO] [2021-04-19 17:10:12] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:10:12] [17:10:12.828] Removed 0 Identifiers
[INFO] [2021-04-19 17:10:12] ## remove_type: Reference
[INFO] [2021-04-19 17:10:12] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:10:12] [17:10:12.830] Removed 0 References
[INFO] [2021-04-19 17:10:12] Starting batch with ID 87728756...
[INFO] [2021-04-19 17:10:12] Starting batch with ID 87728756...
[INFO] [2021-04-19 17:10:12] Starting batch with ID 87728756...
[INFO] [2021-04-19 17:10:12] Starting batch with ID 87728756...
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[INFO] [2021-04-19 17:10:13] Starting batch with ID 87728756...
[INFO] [2021-04-19 17:10:13] Starting batch with ID 87728756...
[INFO] [2021-04-19 17:10:13] Starting batch with ID 87728756...
[INFO] [2021-04-19 17:10:13] Starting batch with ID 87728756...
[INFO] [2021-04-19 17:10:13] Starting batch with ID 87728756...
[INFO] [2021-04-19 17:10:13] Starting batch with ID 87728756...
[INFO] [2021-04-19 17:10:13] Starting batch with ID 87728756...
[INFO] [2021-04-19 17:10:13] Starting batch with ID 87728756...
[INFO] [2021-04-19 17:10:13] Starting batch with ID 87728756...
[INFO] [2021-04-19 17:10:13] Starting batch with ID 87728756...
[INFO] [2021-04-19 17:10:13] Starting batch with ID 87728756...
[INFO] [2021-04-19 17:10:13] Starting batch with ID 87728756...
[INFO] [2021-04-19 17:10:13] ## remove_type: Node
[INFO] [2021-04-19 17:10:13] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 17:10:13] [17:10:13.447] Removed 3 Nodes
[START] [2021-04-19 17:10:13] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:10:13] Creating resource from OpenData
[START] [2021-04-19 17:10:13] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:10:13] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 17:10:13] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 17:10:13] Creating resource from OpenData
[START] [2021-04-19 17:10:13] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:10:13] create_harvest_instance
[INFO] [2021-04-19 17:10:13] Created harvest instance #3818
[STOP] [2021-04-19 17:10:13] create_harvest_instance
[START] [2021-04-19 17:10:13] fetch_files
[STOP] [2021-04-19 17:10:13] fetch_files
[START] [2021-04-19 17:10:13] validate_each_file
[INFO] [2021-04-19 17:10:13] Looping over 3 formats...
[INFO] [2021-04-19 17:10:13] ...nodes (/app/public/data/iwaniuk_et_al_iw/taxa.txt)
[INFO] [2021-04-19 17:10:13] Valid: /app/public/converted_csv/iwaniuk_et_al_iw_nodes_3818.csv (3 lines)
[INFO] [2021-04-19 17:10:13] ...occurrences (/app/public/data/iwaniuk_et_al_iw/occurrences.txt)
[INFO] [2021-04-19 17:10:13] Valid: /app/public/converted_csv/iwaniuk_et_al_iw_occurrences_3818.csv (4 lines)
[INFO] [2021-04-19 17:10:13] ...measurements (/app/public/data/iwaniuk_et_al_iw/measurementsorfacts.txt)
[INFO] [2021-04-19 17:10:13] Valid: /app/public/converted_csv/iwaniuk_et_al_iw_measurements_3818.csv (6 lines)
[STOP] [2021-04-19 17:10:13] validate_each_file
[START] [2021-04-19 17:10:13] convert_to_csv
[INFO] [2021-04-19 17:10:13] Looping over 3 formats...
[INFO] [2021-04-19 17:10:13] ...nodes (/app/public/data/iwaniuk_et_al_iw/taxa.txt)
[CMD] [2021-04-19 17:10:13] /usr/bin/sort /app/public/converted_csv/iwaniuk_et_al_iw_nodes_3818.csv > /app/public/converted_csv/iwaniuk_et_al_iw_nodes_3818.csv_sorted
[INFO] [2021-04-19 17:10:13] Converted: /app/public/converted_csv/iwaniuk_et_al_iw_nodes_3818.csv (3 lines)
[INFO] [2021-04-19 17:10:13] ...occurrences (/app/public/data/iwaniuk_et_al_iw/occurrences.txt)
[CMD] [2021-04-19 17:10:13] /usr/bin/sort /app/public/converted_csv/iwaniuk_et_al_iw_occurrences_3818.csv > /app/public/converted_csv/iwaniuk_et_al_iw_occurrences_3818.csv_sorted
[INFO] [2021-04-19 17:10:13] Converted: /app/public/converted_csv/iwaniuk_et_al_iw_occurrences_3818.csv (4 lines)
[INFO] [2021-04-19 17:10:13] ...measurements (/app/public/data/iwaniuk_et_al_iw/measurementsorfacts.txt)
[CMD] [2021-04-19 17:10:13] /usr/bin/sort /app/public/converted_csv/iwaniuk_et_al_iw_measurements_3818.csv > /app/public/converted_csv/iwaniuk_et_al_iw_measurements_3818.csv_sorted
[INFO] [2021-04-19 17:10:13] Converted: /app/public/converted_csv/iwaniuk_et_al_iw_measurements_3818.csv (6 lines)
[STOP] [2021-04-19 17:10:13] convert_to_csv
[START] [2021-04-19 17:10:13] calculate_delta
[INFO] [2021-04-19 17:10:13] Looping over 3 formats...
[INFO] [2021-04-19 17:10:13] ...nodes (/app/public/data/iwaniuk_et_al_iw/taxa.txt)
[CMD] [2021-04-19 17:10:13] echo "0a" > /app/public/diff/iwaniuk_et_al_iw_nodes_3818.diff
[CMD] [2021-04-19 17:10:13] tail -n +1 /app/public/converted_csv/iwaniuk_et_al_iw_nodes_3818.csv >> /app/public/diff/iwaniuk_et_al_iw_nodes_3818.diff
[CMD] [2021-04-19 17:10:13] echo "." >> /app/public/diff/iwaniuk_et_al_iw_nodes_3818.diff
[INFO] [2021-04-19 17:10:13] Created diff: /app/public/diff/iwaniuk_et_al_iw_nodes_3818.diff (5 lines)
[INFO] [2021-04-19 17:10:13] ...occurrences (/app/public/data/iwaniuk_et_al_iw/occurrences.txt)
[CMD] [2021-04-19 17:10:13] echo "0a" > /app/public/diff/iwaniuk_et_al_iw_occurrences_3818.diff
[CMD] [2021-04-19 17:10:13] tail -n +1 /app/public/converted_csv/iwaniuk_et_al_iw_occurrences_3818.csv >> /app/public/diff/iwaniuk_et_al_iw_occurrences_3818.diff
[CMD] [2021-04-19 17:10:13] echo "." >> /app/public/diff/iwaniuk_et_al_iw_occurrences_3818.diff
[INFO] [2021-04-19 17:10:13] Created diff: /app/public/diff/iwaniuk_et_al_iw_occurrences_3818.diff (6 lines)
[INFO] [2021-04-19 17:10:13] ...measurements (/app/public/data/iwaniuk_et_al_iw/measurementsorfacts.txt)
[CMD] [2021-04-19 17:10:13] echo "0a" > /app/public/diff/iwaniuk_et_al_iw_measurements_3818.diff
[CMD] [2021-04-19 17:10:14] tail -n +1 /app/public/converted_csv/iwaniuk_et_al_iw_measurements_3818.csv >> /app/public/diff/iwaniuk_et_al_iw_measurements_3818.diff
[CMD] [2021-04-19 17:10:14] echo "." >> /app/public/diff/iwaniuk_et_al_iw_measurements_3818.diff
[INFO] [2021-04-19 17:10:14] Created diff: /app/public/diff/iwaniuk_et_al_iw_measurements_3818.diff (8 lines)
[STOP] [2021-04-19 17:10:14] calculate_delta
[START] [2021-04-19 17:10:14] parse_diff_and_store
[INFO] [2021-04-19 17:10:14] Handling diff: /app/public/diff/iwaniuk_et_al_iw_nodes_3818.diff (5 lines)
[INFO] [2021-04-19 17:10:14] Loading nodes diff file into memory (5 /app/public/diff/iwaniuk_et_al_iw_nodes_3818.diff lines)...
[INFO] [2021-04-19 17:10:14] Handling diff: /app/public/diff/iwaniuk_et_al_iw_occurrences_3818.diff (6 lines)
[INFO] [2021-04-19 17:10:14] Loading occurrences diff file into memory (6 /app/public/diff/iwaniuk_et_al_iw_occurrences_3818.diff lines)...
[INFO] [2021-04-19 17:10:14] Handling diff: /app/public/diff/iwaniuk_et_al_iw_measurements_3818.diff (8 lines)
[INFO] [2021-04-19 17:10:14] Loading measurements diff file into memory (8 /app/public/diff/iwaniuk_et_al_iw_measurements_3818.diff lines)...
[INFO] [2021-04-19 17:10:14] Storing 3 ScientificNames
[INFO] [2021-04-19 17:10:14] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 17:10:14] Average Time: 0.0
[INFO] [2021-04-19 17:10:14] Total Time: 1s
[INFO] [2021-04-19 17:10:14] Storing 3 Nodes
[INFO] [2021-04-19 17:10:14] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 17:10:14] Average Time: 0.0
[INFO] [2021-04-19 17:10:14] Total Time: 1s
[INFO] [2021-04-19 17:10:14] Storing 4 Occurrences
[INFO] [2021-04-19 17:10:14] Processing group of 4 in 1 groups of 1000
[INFO] [2021-04-19 17:10:14] Average Time: 0.0
[INFO] [2021-04-19 17:10:14] Total Time: 1s
[INFO] [2021-04-19 17:10:14] Storing 6 Traits
[INFO] [2021-04-19 17:10:14] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 17:10:14] Average Time: 0.0
[INFO] [2021-04-19 17:10:14] Total Time: 1s
[INFO] [2021-04-19 17:10:14] Storing 3 MetaTraits
[INFO] [2021-04-19 17:10:14] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 17:10:14] Average Time: 0.0
[INFO] [2021-04-19 17:10:14] Total Time: 1s
[STOP] [2021-04-19 17:10:14] parse_diff_and_store
[START] [2021-04-19 17:10:14] resolve_keys
[INFO] [2021-04-19 17:10:20] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 17:10:20] traits to occurrences...
[INFO] [2021-04-19 17:10:20] traits to nodes (through occurrences)...
[INFO] [2021-04-19 17:10:20] Traits to sex term...
[INFO] [2021-04-19 17:10:20] Traits to lifestage term...
[INFO] [2021-04-19 17:10:20] MetaTraits to traits...
[INFO] [2021-04-19 17:10:20] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 17:10:20] Assocs to occurrences...
[INFO] [2021-04-19 17:10:20] Assocs to nodes...
[INFO] [2021-04-19 17:10:20] Assoc to sex term...
[INFO] [2021-04-19 17:10:20] Assoc to lifestage term...
[INFO] [2021-04-19 17:10:20] MetaAssoc to assocs...
[STOP] [2021-04-19 17:10:20] resolve_keys
[START] [2021-04-19 17:10:20] hold_for_later_1
[STOP] [2021-04-19 17:10:20] hold_for_later_1
[START] [2021-04-19 17:10:20] hold_for_later_2
[STOP] [2021-04-19 17:10:20] hold_for_later_2
[START] [2021-04-19 17:10:20] resolve_missing_parents
[STOP] [2021-04-19 17:10:20] resolve_missing_parents
[START] [2021-04-19 17:10:20] rebuild_nodes
[START] [2021-04-19 17:10:20] Flattener#flatten
[START] [2021-04-19 17:10:20] Flattener#study_resource
[START] [2021-04-19 17:10:20] Flattener#build_ancestry
[STOP] [2021-04-19 17:10:20] Flattener#build_ancestry
[INFO] [2021-04-19 17:10:20] 3 ancestry keys
[START] [2021-04-19 17:10:20] build_node_ancestors
[INFO] [2021-04-19 17:10:20] old ancestors deleted.
[STOP] [2021-04-19 17:10:20] build_node_ancestors
[WARN] [2021-04-19 17:10:20] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 17:10:20] Flattener#flatten
[STOP] [2021-04-19 17:10:20] rebuild_nodes
[START] [2021-04-19 17:10:20] resolve_missing_media_owners
[STOP] [2021-04-19 17:10:20] resolve_missing_media_owners
[START] [2021-04-19 17:10:20] sanitize_media_verbatims
[STOP] [2021-04-19 17:10:20] sanitize_media_verbatims
[START] [2021-04-19 17:10:20] queue_downloads
[STOP] [2021-04-19 17:10:20] queue_downloads
[START] [2021-04-19 17:10:20] parse_names
[WARN] [2021-04-19 17:10:20] I see 3 names which still need to be parsed.
[STOP] [2021-04-19 17:10:21] parse_names
[START] [2021-04-19 17:10:21] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 17:10:21] denormalize_canonical_names_to_nodes
[START] [2021-04-19 17:10:21] match_nodes
[START] [2021-04-19 17:10:21] map_all_nodes_to_pages
[STOP] [2021-04-19 17:10:21] map_all_nodes_to_pages
[INFO] [2021-04-19 17:10:21] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2021-04-19 17:10:21] update_nodes
[STOP] [2021-04-19 17:10:21] update_nodes
[STOP] [2021-04-19 17:10:21] match_nodes
[START] [2021-04-19 17:10:21] reindex_search
[STOP] [2021-04-19 17:10:21] reindex_search
[START] [2021-04-19 17:10:21] normalize_units
[STOP] [2021-04-19 17:10:21] normalize_units
[START] [2021-04-19 17:10:21] calculate_statistics
[2021-04-19 17:10:21] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 17:10:21] calculate_statistics
[START] [2021-04-19 17:10:21] complete_harvest_instance
[START] [2021-04-19 17:10:21] overall_tsv_creation
[INFO] [2021-04-19 17:10:21] Processing group of 3 in 1 batches of 10000
[INFO] [2021-04-19 17:10:57] 3 Traits (unfiltered)...
[INFO] [2021-04-19 17:11:31] 3 Traits (filtered)...
[INFO] [2021-04-19 17:11:31] 0 Associations (filtered)...
[INFO] [2021-04-19 17:11:31] 3 metadata added.
[INFO] [2021-04-19 17:11:31] 0 metadata added.
[INFO] [2021-04-19 17:11:58] Average Time: 73.27
[INFO] [2021-04-19 17:11:58] Total Time: 1m38s
[STOP] [2021-04-19 17:11:58] overall_tsv_creation
[INFO] [2021-04-19 17:11:58] Done. Check your files:
[INFO] [2021-04-19 17:11:58] (3 lines) /app/public/data/iwaniuk_et_al_iw/publish_nodes.tsv
[INFO] [2021-04-19 17:11:58] (3 lines) /app/public/data/iwaniuk_et_al_iw/publish_scientific_names.tsv
[INFO] [2021-04-19 17:11:58] (4 lines) /app/public/data/iwaniuk_et_al_iw/publish_traits.tsv
[INFO] [2021-04-19 17:11:58] (4 lines) /app/public/data/iwaniuk_et_al_iw/publish_metadata.tsv
[STOP] [2021-04-19 17:11:58] complete_harvest_instance
[START] [2021-04-19 17:11:58] completed
[STOP] [2021-04-19 17:11:58] completed
[STOP] [2021-04-19 17:11:58] logged process, took 104.86

Latest Process

19 Apr 17:10 EXITED currently processing 0