Harvest for Bullock et al 1983 Created 19 Apr 09:33

Stage: completed
Fetched: 19 Apr 09:33
Validated: 19 Apr 09:33
Deltas Created 19 Apr 09:33
Units Normalized: 19 Apr 09:34
Ancestry Built: 19 Apr 09:34
Nodes Matched: 19 Apr 09:34
Names Parsed: 19 Apr 09:34
New Models Stored: 19 Apr 09:33
Indexed: 19 Apr 09:34
Completed: 19 Apr 09:35
Time to Harvest: less than a minute

Harvesting Log

(355 lines)
# Logfile created on 2020-08-27 15:18:31 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:18:31] logged process
[START] [2020-08-27 15:18:31] Creating resource from OpenData
[START] [2020-08-27 15:18:31] logged process
[START] [2020-08-27 15:18:31] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:18:32] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:18:32] Creating resource from OpenData
[INFO] [2020-11-16 09:07:37] ## HARVEST: type = -harvest
[START] [2020-11-16 09:07:38] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-16 09:07:38] create_harvest_instance
[STOP] [2020-11-16 09:07:40] create_harvest_instance
[START] [2020-11-16 09:07:40] fetch_files
[STOP] [2020-11-16 09:07:40] fetch_files
[START] [2020-11-16 09:07:40] validate_each_file
[STOP] [2020-11-16 09:07:40] validate_each_file
[START] [2020-11-16 09:07:40] convert_to_csv
[CMD] [2020-11-16 09:07:40] /usr/bin/sort /app/public/converted_csv/bullock_et_al_bu_refs_24264.csv > /app/public/converted_csv/bullock_et_al_bu_refs_24264.csv_sorted
[CMD] [2020-11-16 09:07:40] /usr/bin/sort /app/public/converted_csv/bullock_et_al_bu_nodes_24265.csv > /app/public/converted_csv/bullock_et_al_bu_nodes_24265.csv_sorted
[CMD] [2020-11-16 09:07:40] /usr/bin/sort /app/public/converted_csv/bullock_et_al_bu_occurrences_24266.csv > /app/public/converted_csv/bullock_et_al_bu_occurrences_24266.csv_sorted
[CMD] [2020-11-16 09:07:40] /usr/bin/sort /app/public/converted_csv/bullock_et_al_bu_measurements_24267.csv > /app/public/converted_csv/bullock_et_al_bu_measurements_24267.csv_sorted
[STOP] [2020-11-16 09:07:40] convert_to_csv
[START] [2020-11-16 09:07:40] calculate_delta
[CMD] [2020-11-16 09:07:40] echo "0a" > /app/public/diff/bullock_et_al_bu_refs_24264.diff
[CMD] [2020-11-16 09:07:40] tail -n +1 /app/public/converted_csv/bullock_et_al_bu_refs_24264.csv >> /app/public/diff/bullock_et_al_bu_refs_24264.diff
[CMD] [2020-11-16 09:07:40] echo "." >> /app/public/diff/bullock_et_al_bu_refs_24264.diff
[CMD] [2020-11-16 09:07:40] echo "0a" > /app/public/diff/bullock_et_al_bu_nodes_24265.diff
[CMD] [2020-11-16 09:07:40] tail -n +1 /app/public/converted_csv/bullock_et_al_bu_nodes_24265.csv >> /app/public/diff/bullock_et_al_bu_nodes_24265.diff
[CMD] [2020-11-16 09:07:40] echo "." >> /app/public/diff/bullock_et_al_bu_nodes_24265.diff
[CMD] [2020-11-16 09:07:40] echo "0a" > /app/public/diff/bullock_et_al_bu_occurrences_24266.diff
[CMD] [2020-11-16 09:07:40] tail -n +1 /app/public/converted_csv/bullock_et_al_bu_occurrences_24266.csv >> /app/public/diff/bullock_et_al_bu_occurrences_24266.diff
[CMD] [2020-11-16 09:07:40] echo "." >> /app/public/diff/bullock_et_al_bu_occurrences_24266.diff
[CMD] [2020-11-16 09:07:40] echo "0a" > /app/public/diff/bullock_et_al_bu_measurements_24267.diff
[CMD] [2020-11-16 09:07:40] tail -n +1 /app/public/converted_csv/bullock_et_al_bu_measurements_24267.csv >> /app/public/diff/bullock_et_al_bu_measurements_24267.diff
[CMD] [2020-11-16 09:07:40] echo "." >> /app/public/diff/bullock_et_al_bu_measurements_24267.diff
[STOP] [2020-11-16 09:07:40] calculate_delta
[START] [2020-11-16 09:07:40] parse_diff_and_store
[INFO] [2020-11-16 09:07:40] Loading refs diff file into memory (true lines)...
[INFO] [2020-11-16 09:07:40] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-16 09:07:40] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-16 09:07:40] Loading measurements diff file into memory (true lines)...
[INFO] [2020-11-16 09:07:41] Storing 14 ScientificNames
[INFO] [2020-11-16 09:07:41] Processing group of 14 in 1 groups of 1000
[INFO] [2020-11-16 09:07:41] Average Time: 0.01
[INFO] [2020-11-16 09:07:41] Total Time: 1s
[INFO] [2020-11-16 09:07:41] Storing 14 Nodes
[INFO] [2020-11-16 09:07:41] Processing group of 14 in 1 groups of 1000
[INFO] [2020-11-16 09:07:41] Average Time: 0.02
[INFO] [2020-11-16 09:07:41] Total Time: 1s
[INFO] [2020-11-16 09:07:41] Storing 14 Occurrences
[INFO] [2020-11-16 09:07:41] Processing group of 14 in 1 groups of 1000
[INFO] [2020-11-16 09:07:41] Average Time: 0.01
[INFO] [2020-11-16 09:07:41] Total Time: 1s
[INFO] [2020-11-16 09:07:41] Storing 27 Traits
[INFO] [2020-11-16 09:07:41] Processing group of 27 in 1 groups of 1000
[INFO] [2020-11-16 09:07:41] Average Time: 0.01
[INFO] [2020-11-16 09:07:41] Total Time: 1s
[INFO] [2020-11-16 09:07:41] Storing 14 MetaTraits
[INFO] [2020-11-16 09:07:41] Processing group of 14 in 1 groups of 1000
[INFO] [2020-11-16 09:07:41] Average Time: 0.01
[INFO] [2020-11-16 09:07:41] Total Time: 1s
[STOP] [2020-11-16 09:07:41] parse_diff_and_store
[START] [2020-11-16 09:07:41] resolve_keys
[INFO] [2020-11-16 09:07:47] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-16 09:07:47] traits to occurrences...
[INFO] [2020-11-16 09:07:47] traits to nodes (through occurrences)...
[INFO] [2020-11-16 09:07:47] Traits to sex term...
[INFO] [2020-11-16 09:07:47] Traits to lifestage term...
[INFO] [2020-11-16 09:07:47] MetaTraits to traits...
[INFO] [2020-11-16 09:07:47] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-16 09:07:47] Assocs to occurrences...
[INFO] [2020-11-16 09:07:47] Assocs to nodes...
[INFO] [2020-11-16 09:07:47] Assoc to sex term...
[INFO] [2020-11-16 09:07:47] Assoc to lifestage term...
[INFO] [2020-11-16 09:07:47] MetaAssoc to assocs...
[STOP] [2020-11-16 09:07:47] resolve_keys
[START] [2020-11-16 09:07:47] hold_for_later_1
[STOP] [2020-11-16 09:07:47] hold_for_later_1
[START] [2020-11-16 09:07:47] hold_for_later_2
[STOP] [2020-11-16 09:07:47] hold_for_later_2
[START] [2020-11-16 09:07:47] resolve_missing_parents
[STOP] [2020-11-16 09:07:47] resolve_missing_parents
[START] [2020-11-16 09:07:47] rebuild_nodes
[START] [2020-11-16 09:07:47] Flattener#flatten
[START] [2020-11-16 09:07:47] Flattener#study_resource
[START] [2020-11-16 09:07:47] Flattener#build_ancestry
[STOP] [2020-11-16 09:07:47] Flattener#build_ancestry
[INFO] [2020-11-16 09:07:47] 14 ancestry keys
[START] [2020-11-16 09:07:47] build_node_ancestors
[INFO] [2020-11-16 09:07:47] old ancestors deleted.
[STOP] [2020-11-16 09:07:47] build_node_ancestors
[WARN] [2020-11-16 09:07:47] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-11-16 09:07:47] Flattener#flatten
[STOP] [2020-11-16 09:07:47] rebuild_nodes
[START] [2020-11-16 09:07:47] resolve_missing_media_owners
[STOP] [2020-11-16 09:07:47] resolve_missing_media_owners
[START] [2020-11-16 09:07:47] sanitize_media_verbatims
[STOP] [2020-11-16 09:07:47] sanitize_media_verbatims
[START] [2020-11-16 09:07:47] queue_downloads
[STOP] [2020-11-16 09:07:47] queue_downloads
[START] [2020-11-16 09:07:47] parse_names
[WARN] [2020-11-16 09:07:47] I see 14 names which still need to be parsed.
[STOP] [2020-11-16 09:07:48] parse_names
[START] [2020-11-16 09:07:48] denormalize_canonical_names_to_nodes
[STOP] [2020-11-16 09:07:48] denormalize_canonical_names_to_nodes
[START] [2020-11-16 09:07:48] match_nodes
[START] [2020-11-16 09:07:48] map_all_nodes_to_pages
[STOP] [2020-11-16 09:07:48] map_all_nodes_to_pages
[INFO] [2020-11-16 09:07:48] ZERO unmatched nodes (of 14)! Nicely done.
[START] [2020-11-16 09:07:48] update_nodes
[STOP] [2020-11-16 09:07:48] update_nodes
[STOP] [2020-11-16 09:07:48] match_nodes
[START] [2020-11-16 09:07:48] reindex_search
[STOP] [2020-11-16 09:07:49] reindex_search
[START] [2020-11-16 09:07:49] normalize_units
[STOP] [2020-11-16 09:07:49] normalize_units
[START] [2020-11-16 09:07:49] calculate_statistics
[2020-11-16 09:07:49] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-11-16 09:07:49] calculate_statistics
[START] [2020-11-16 09:07:49] complete_harvest_instance
[START] [2020-11-16 09:07:49] overall_tsv_creation
[INFO] [2020-11-16 09:07:49] Processing group of 14 in 1 batches of 10000
[INFO] [2020-11-16 09:08:43] 14 Traits (unfiltered)...
[INFO] [2020-11-16 09:09:20] 14 Traits (filtered)...
[INFO] [2020-11-16 09:09:20] 0 Associations (filtered)...
[INFO] [2020-11-16 09:09:20] 27 metadata added.
[INFO] [2020-11-16 09:09:20] 0 metadata added.
[INFO] [2020-11-16 09:09:20] Average Time: 53.11
[INFO] [2020-11-16 09:09:20] Total Time: 1m32s
[STOP] [2020-11-16 09:09:20] overall_tsv_creation
[INFO] [2020-11-16 09:09:20] Done. Check your files:
[INFO] [2020-11-16 09:09:20] (14 lines) /app/public/data/bullock_et_al_bu/publish_nodes.tsv
[INFO] [2020-11-16 09:09:20] (14 lines) /app/public/data/bullock_et_al_bu/publish_scientific_names.tsv
[INFO] [2020-11-16 09:09:20] (15 lines) /app/public/data/bullock_et_al_bu/publish_traits.tsv
[INFO] [2020-11-16 09:09:20] (28 lines) /app/public/data/bullock_et_al_bu/publish_metadata.tsv
[STOP] [2020-11-16 09:09:20] complete_harvest_instance
[START] [2020-11-16 09:09:20] completed
[STOP] [2020-11-16 09:09:20] completed
[STOP] [2020-11-16 09:09:20] logged process, took 102.22
[INFO] [2021-04-19 09:33:35] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 09:33:37] ## remove_type: ScientificName
[INFO] [2021-04-19 09:33:37] ++ Calling delete_all on 14 instances...
[INFO] [2021-04-19 09:33:37] [09:33:37.128] Removed 14 Scientificnames
[INFO] [2021-04-19 09:33:37] ## remove_type: Vernacular
[INFO] [2021-04-19 09:33:37] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:33:37] [09:33:37.130] Removed 0 Vernaculars
[INFO] [2021-04-19 09:33:37] ## remove_type: Article
[INFO] [2021-04-19 09:33:37] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:33:37] [09:33:37.131] Removed 0 Articles
[INFO] [2021-04-19 09:33:37] ## remove_type: Medium
[INFO] [2021-04-19 09:33:37] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:33:37] [09:33:37.133] Removed 0 Media
[INFO] [2021-04-19 09:33:37] ## remove_type: Trait
[INFO] [2021-04-19 09:33:37] ++ Calling delete_all on 27 instances...
[INFO] [2021-04-19 09:33:37] [09:33:37.142] Removed 27 Traits
[INFO] [2021-04-19 09:33:37] ## remove_type: MetaTrait
[INFO] [2021-04-19 09:33:37] ++ Calling delete_all on 14 instances...
[INFO] [2021-04-19 09:33:37] [09:33:37.144] Removed 14 Metatraits
[INFO] [2021-04-19 09:33:37] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 09:33:37] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:33:37] [09:33:37.146] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 09:33:37] ## remove_type: Assoc
[INFO] [2021-04-19 09:33:37] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:33:37] [09:33:37.147] Removed 0 Assocs
[INFO] [2021-04-19 09:33:37] ## remove_type: MetaAssoc
[INFO] [2021-04-19 09:33:37] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:33:37] [09:33:37.149] Removed 0 Metaassocs
[INFO] [2021-04-19 09:33:37] ## remove_type: Identifier
[INFO] [2021-04-19 09:33:37] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:33:37] [09:33:37.151] Removed 0 Identifiers
[INFO] [2021-04-19 09:33:37] ## remove_type: Reference
[INFO] [2021-04-19 09:33:37] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:33:37] [09:33:37.152] Removed 0 References
[INFO] [2021-04-19 09:33:37] Starting batch with ID 81660456...
[INFO] [2021-04-19 09:33:37] Starting batch with ID 81660456...
[INFO] [2021-04-19 09:33:37] Starting batch with ID 81660456...
[INFO] [2021-04-19 09:33:37] Starting batch with ID 81660456...
[INFO] [2021-04-19 09:33:37] Starting batch with ID 81660456...
[INFO] [2021-04-19 09:33:37] Starting batch with ID 81660456...
[INFO] [2021-04-19 09:33:37] Starting batch with ID 81660456...
[INFO] [2021-04-19 09:33:37] Starting batch with ID 81660456...
[INFO] [2021-04-19 09:33:37] Starting batch with ID 81660456...
[INFO] [2021-04-19 09:33:37] Starting batch with ID 81660456...
[INFO] [2021-04-19 09:33:37] Starting batch with ID 81660456...
[INFO] [2021-04-19 09:33:37] ## remove_type: Node
[INFO] [2021-04-19 09:33:37] ++ Calling delete_all on 14 instances...
[INFO] [2021-04-19 09:33:37] [09:33:37.285] Removed 14 Nodes
[START] [2021-04-19 09:33:37] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 09:33:37] Creating resource from OpenData
[START] [2021-04-19 09:33:38] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 09:33:38] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 09:33:43] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 09:33:43] Creating resource from OpenData
[START] [2021-04-19 09:33:44] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 09:33:44] create_harvest_instance
[INFO] [2021-04-19 09:33:44] Created harvest instance #3716
[STOP] [2021-04-19 09:33:44] create_harvest_instance
[START] [2021-04-19 09:33:44] fetch_files
[STOP] [2021-04-19 09:33:44] fetch_files
[START] [2021-04-19 09:33:44] validate_each_file
[INFO] [2021-04-19 09:33:44] Looping over 4 formats...
[INFO] [2021-04-19 09:33:44] ...refs (/app/public/data/bullock_et_al_bu/references.tsv)
[INFO] [2021-04-19 09:33:44] Valid: /app/public/converted_csv/bullock_et_al_bu_refs_3716.csv (0 lines)
[INFO] [2021-04-19 09:33:44] ...nodes (/app/public/data/bullock_et_al_bu/taxa.txt)
[INFO] [2021-04-19 09:33:44] Valid: /app/public/converted_csv/bullock_et_al_bu_nodes_3716.csv (14 lines)
[INFO] [2021-04-19 09:33:44] ...occurrences (/app/public/data/bullock_et_al_bu/occurrences.txt)
[INFO] [2021-04-19 09:33:44] Valid: /app/public/converted_csv/bullock_et_al_bu_occurrences_3716.csv (14 lines)
[INFO] [2021-04-19 09:33:44] ...measurements (/app/public/data/bullock_et_al_bu/measurementsorfacts.txt)
[INFO] [2021-04-19 09:33:44] Valid: /app/public/converted_csv/bullock_et_al_bu_measurements_3716.csv (27 lines)
[STOP] [2021-04-19 09:33:44] validate_each_file
[START] [2021-04-19 09:33:44] convert_to_csv
[INFO] [2021-04-19 09:33:44] Looping over 4 formats...
[INFO] [2021-04-19 09:33:44] ...refs (/app/public/data/bullock_et_al_bu/references.tsv)
[CMD] [2021-04-19 09:33:44] /usr/bin/sort /app/public/converted_csv/bullock_et_al_bu_refs_3716.csv > /app/public/converted_csv/bullock_et_al_bu_refs_3716.csv_sorted
[INFO] [2021-04-19 09:33:44] Converted: /app/public/converted_csv/bullock_et_al_bu_refs_3716.csv (0 lines)
[INFO] [2021-04-19 09:33:44] ...nodes (/app/public/data/bullock_et_al_bu/taxa.txt)
[CMD] [2021-04-19 09:33:44] /usr/bin/sort /app/public/converted_csv/bullock_et_al_bu_nodes_3716.csv > /app/public/converted_csv/bullock_et_al_bu_nodes_3716.csv_sorted
[INFO] [2021-04-19 09:33:44] Converted: /app/public/converted_csv/bullock_et_al_bu_nodes_3716.csv (14 lines)
[INFO] [2021-04-19 09:33:44] ...occurrences (/app/public/data/bullock_et_al_bu/occurrences.txt)
[CMD] [2021-04-19 09:33:44] /usr/bin/sort /app/public/converted_csv/bullock_et_al_bu_occurrences_3716.csv > /app/public/converted_csv/bullock_et_al_bu_occurrences_3716.csv_sorted
[INFO] [2021-04-19 09:33:45] Converted: /app/public/converted_csv/bullock_et_al_bu_occurrences_3716.csv (14 lines)
[INFO] [2021-04-19 09:33:45] ...measurements (/app/public/data/bullock_et_al_bu/measurementsorfacts.txt)
[CMD] [2021-04-19 09:33:45] /usr/bin/sort /app/public/converted_csv/bullock_et_al_bu_measurements_3716.csv > /app/public/converted_csv/bullock_et_al_bu_measurements_3716.csv_sorted
[INFO] [2021-04-19 09:33:45] Converted: /app/public/converted_csv/bullock_et_al_bu_measurements_3716.csv (27 lines)
[STOP] [2021-04-19 09:33:45] convert_to_csv
[START] [2021-04-19 09:33:45] calculate_delta
[INFO] [2021-04-19 09:33:45] Looping over 4 formats...
[INFO] [2021-04-19 09:33:45] ...refs (/app/public/data/bullock_et_al_bu/references.tsv)
[CMD] [2021-04-19 09:33:45] echo "0a" > /app/public/diff/bullock_et_al_bu_refs_3716.diff
[CMD] [2021-04-19 09:33:46] tail -n +1 /app/public/converted_csv/bullock_et_al_bu_refs_3716.csv >> /app/public/diff/bullock_et_al_bu_refs_3716.diff
[CMD] [2021-04-19 09:33:46] echo "." >> /app/public/diff/bullock_et_al_bu_refs_3716.diff
[INFO] [2021-04-19 09:33:46] Created diff: /app/public/diff/bullock_et_al_bu_refs_3716.diff (2 lines)
[INFO] [2021-04-19 09:33:46] ...nodes (/app/public/data/bullock_et_al_bu/taxa.txt)
[CMD] [2021-04-19 09:33:46] echo "0a" > /app/public/diff/bullock_et_al_bu_nodes_3716.diff
[CMD] [2021-04-19 09:33:47] tail -n +1 /app/public/converted_csv/bullock_et_al_bu_nodes_3716.csv >> /app/public/diff/bullock_et_al_bu_nodes_3716.diff
[CMD] [2021-04-19 09:33:47] echo "." >> /app/public/diff/bullock_et_al_bu_nodes_3716.diff
[INFO] [2021-04-19 09:33:48] Created diff: /app/public/diff/bullock_et_al_bu_nodes_3716.diff (16 lines)
[INFO] [2021-04-19 09:33:48] ...occurrences (/app/public/data/bullock_et_al_bu/occurrences.txt)
[CMD] [2021-04-19 09:33:48] echo "0a" > /app/public/diff/bullock_et_al_bu_occurrences_3716.diff
[CMD] [2021-04-19 09:33:48] tail -n +1 /app/public/converted_csv/bullock_et_al_bu_occurrences_3716.csv >> /app/public/diff/bullock_et_al_bu_occurrences_3716.diff
[CMD] [2021-04-19 09:33:48] echo "." >> /app/public/diff/bullock_et_al_bu_occurrences_3716.diff
[INFO] [2021-04-19 09:33:49] Created diff: /app/public/diff/bullock_et_al_bu_occurrences_3716.diff (16 lines)
[INFO] [2021-04-19 09:33:49] ...measurements (/app/public/data/bullock_et_al_bu/measurementsorfacts.txt)
[CMD] [2021-04-19 09:33:49] echo "0a" > /app/public/diff/bullock_et_al_bu_measurements_3716.diff
[CMD] [2021-04-19 09:33:49] tail -n +1 /app/public/converted_csv/bullock_et_al_bu_measurements_3716.csv >> /app/public/diff/bullock_et_al_bu_measurements_3716.diff
[CMD] [2021-04-19 09:33:50] echo "." >> /app/public/diff/bullock_et_al_bu_measurements_3716.diff
[INFO] [2021-04-19 09:33:50] Created diff: /app/public/diff/bullock_et_al_bu_measurements_3716.diff (29 lines)
[STOP] [2021-04-19 09:33:50] calculate_delta
[START] [2021-04-19 09:33:50] parse_diff_and_store
[INFO] [2021-04-19 09:33:50] Handling diff: /app/public/diff/bullock_et_al_bu_refs_3716.diff (2 lines)
[INFO] [2021-04-19 09:33:50] Loading refs diff file into memory (2 /app/public/diff/bullock_et_al_bu_refs_3716.diff lines)...
[INFO] [2021-04-19 09:33:51] Handling diff: /app/public/diff/bullock_et_al_bu_nodes_3716.diff (16 lines)
[INFO] [2021-04-19 09:33:51] Loading nodes diff file into memory (16 /app/public/diff/bullock_et_al_bu_nodes_3716.diff lines)...
[INFO] [2021-04-19 09:33:52] Handling diff: /app/public/diff/bullock_et_al_bu_occurrences_3716.diff (16 lines)
[INFO] [2021-04-19 09:33:52] Loading occurrences diff file into memory (16 /app/public/diff/bullock_et_al_bu_occurrences_3716.diff lines)...
[INFO] [2021-04-19 09:33:52] Handling diff: /app/public/diff/bullock_et_al_bu_measurements_3716.diff (29 lines)
[INFO] [2021-04-19 09:33:53] Loading measurements diff file into memory (29 /app/public/diff/bullock_et_al_bu_measurements_3716.diff lines)...
[INFO] [2021-04-19 09:33:53] Storing 14 ScientificNames
[INFO] [2021-04-19 09:33:53] Processing group of 14 in 1 groups of 1000
[INFO] [2021-04-19 09:33:53] Average Time: 0.01
[INFO] [2021-04-19 09:33:53] Total Time: 1s
[INFO] [2021-04-19 09:33:53] Storing 14 Nodes
[INFO] [2021-04-19 09:33:53] Processing group of 14 in 1 groups of 1000
[INFO] [2021-04-19 09:33:53] Average Time: 0.01
[INFO] [2021-04-19 09:33:53] Total Time: 1s
[INFO] [2021-04-19 09:33:53] Storing 14 Occurrences
[INFO] [2021-04-19 09:33:53] Processing group of 14 in 1 groups of 1000
[INFO] [2021-04-19 09:33:53] Average Time: 0.0
[INFO] [2021-04-19 09:33:53] Total Time: 1s
[INFO] [2021-04-19 09:33:53] Storing 27 Traits
[INFO] [2021-04-19 09:33:53] Processing group of 27 in 1 groups of 1000
[INFO] [2021-04-19 09:33:53] Average Time: 0.01
[INFO] [2021-04-19 09:33:53] Total Time: 1s
[INFO] [2021-04-19 09:33:53] Storing 14 MetaTraits
[INFO] [2021-04-19 09:33:53] Processing group of 14 in 1 groups of 1000
[INFO] [2021-04-19 09:33:53] Average Time: 0.0
[INFO] [2021-04-19 09:33:53] Total Time: 1s
[STOP] [2021-04-19 09:33:53] parse_diff_and_store
[START] [2021-04-19 09:33:53] resolve_keys
[INFO] [2021-04-19 09:33:59] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 09:33:59] traits to occurrences...
[INFO] [2021-04-19 09:33:59] traits to nodes (through occurrences)...
[INFO] [2021-04-19 09:33:59] Traits to sex term...
[INFO] [2021-04-19 09:33:59] Traits to lifestage term...
[INFO] [2021-04-19 09:33:59] MetaTraits to traits...
[INFO] [2021-04-19 09:33:59] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 09:33:59] Assocs to occurrences...
[INFO] [2021-04-19 09:33:59] Assocs to nodes...
[INFO] [2021-04-19 09:33:59] Assoc to sex term...
[INFO] [2021-04-19 09:33:59] Assoc to lifestage term...
[INFO] [2021-04-19 09:33:59] MetaAssoc to assocs...
[STOP] [2021-04-19 09:33:59] resolve_keys
[START] [2021-04-19 09:33:59] hold_for_later_1
[STOP] [2021-04-19 09:33:59] hold_for_later_1
[START] [2021-04-19 09:33:59] hold_for_later_2
[STOP] [2021-04-19 09:33:59] hold_for_later_2
[START] [2021-04-19 09:34:00] resolve_missing_parents
[STOP] [2021-04-19 09:34:00] resolve_missing_parents
[START] [2021-04-19 09:34:00] rebuild_nodes
[START] [2021-04-19 09:34:00] Flattener#flatten
[START] [2021-04-19 09:34:00] Flattener#study_resource
[START] [2021-04-19 09:34:00] Flattener#build_ancestry
[STOP] [2021-04-19 09:34:00] Flattener#build_ancestry
[INFO] [2021-04-19 09:34:00] 14 ancestry keys
[START] [2021-04-19 09:34:00] build_node_ancestors
[INFO] [2021-04-19 09:34:00] old ancestors deleted.
[STOP] [2021-04-19 09:34:00] build_node_ancestors
[WARN] [2021-04-19 09:34:00] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 09:34:00] Flattener#flatten
[STOP] [2021-04-19 09:34:00] rebuild_nodes
[START] [2021-04-19 09:34:00] resolve_missing_media_owners
[STOP] [2021-04-19 09:34:00] resolve_missing_media_owners
[START] [2021-04-19 09:34:00] sanitize_media_verbatims
[STOP] [2021-04-19 09:34:00] sanitize_media_verbatims
[START] [2021-04-19 09:34:00] queue_downloads
[STOP] [2021-04-19 09:34:00] queue_downloads
[START] [2021-04-19 09:34:00] parse_names
[WARN] [2021-04-19 09:34:00] I see 14 names which still need to be parsed.
[STOP] [2021-04-19 09:34:01] parse_names
[START] [2021-04-19 09:34:01] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 09:34:01] denormalize_canonical_names_to_nodes
[START] [2021-04-19 09:34:01] match_nodes
[START] [2021-04-19 09:34:01] map_all_nodes_to_pages
[STOP] [2021-04-19 09:34:01] map_all_nodes_to_pages
[INFO] [2021-04-19 09:34:01] ZERO unmatched nodes (of 14)! Nicely done.
[START] [2021-04-19 09:34:01] update_nodes
[STOP] [2021-04-19 09:34:01] update_nodes
[STOP] [2021-04-19 09:34:01] match_nodes
[START] [2021-04-19 09:34:01] reindex_search
[STOP] [2021-04-19 09:34:01] reindex_search
[START] [2021-04-19 09:34:01] normalize_units
[STOP] [2021-04-19 09:34:01] normalize_units
[START] [2021-04-19 09:34:01] calculate_statistics
[2021-04-19 09:34:01] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 09:34:01] calculate_statistics
[START] [2021-04-19 09:34:01] complete_harvest_instance
[START] [2021-04-19 09:34:01] overall_tsv_creation
[INFO] [2021-04-19 09:34:01] Processing group of 14 in 1 batches of 10000
[INFO] [2021-04-19 09:34:37] 14 Traits (unfiltered)...
[INFO] [2021-04-19 09:35:11] 14 Traits (filtered)...
[INFO] [2021-04-19 09:35:11] 0 Associations (filtered)...
[INFO] [2021-04-19 09:35:11] 13 metadata added.
[INFO] [2021-04-19 09:35:11] 0 metadata added.
[INFO] [2021-04-19 09:35:37] Average Time: 71.3
[INFO] [2021-04-19 09:35:37] Total Time: 1m36s
[STOP] [2021-04-19 09:35:37] overall_tsv_creation
[INFO] [2021-04-19 09:35:37] Done. Check your files:
[INFO] [2021-04-19 09:35:37] (14 lines) /app/public/data/bullock_et_al_bu/publish_nodes.tsv
[INFO] [2021-04-19 09:35:37] (14 lines) /app/public/data/bullock_et_al_bu/publish_scientific_names.tsv
[INFO] [2021-04-19 09:35:38] (15 lines) /app/public/data/bullock_et_al_bu/publish_traits.tsv
[INFO] [2021-04-19 09:35:38] (14 lines) /app/public/data/bullock_et_al_bu/publish_metadata.tsv
[STOP] [2021-04-19 09:35:38] complete_harvest_instance
[START] [2021-04-19 09:35:38] completed
[STOP] [2021-04-19 09:35:38] completed
[STOP] [2021-04-19 09:35:38] logged process, took 115.08

Latest Process