Stage:
completed
Fetched:
19 Apr 16:25
Validated:
19 Apr 16:25
Deltas Created
19 Apr 16:25
Units Normalized:
19 Apr 16:25
Ancestry Built:
19 Apr 16:25
Nodes Matched:
19 Apr 16:25
Names Parsed:
19 Apr 16:25
New Models Stored:
19 Apr 16:25
Indexed:
19 Apr 16:25
Completed:
19 Apr 16:27
Time to Harvest:
less than a minute
Harvesting Log
(355 lines)
# Logfile created on 2020-09-24 09:04:12 -0400 by logger.rb/v1.4.2
[START] [2020-09-24 09:04:12] logged process
[START] [2020-09-24 09:04:12] Creating resource from OpenData
[START] [2020-09-24 09:04:12] logged process
[START] [2020-09-24 09:04:12] Parse meta.xml file and create formats with fields
[STOP] [2020-09-24 09:04:13] Parse meta.xml file and create formats with fields
[STOP] [2020-09-24 09:04:13] Creating resource from OpenData
[INFO] [2020-12-03 14:26:57] ## HARVEST: type = -harvest
[START] [2020-12-03 14:27:01] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-12-03 14:27:01] create_harvest_instance
[STOP] [2020-12-03 14:27:02] create_harvest_instance
[START] [2020-12-03 14:27:02] fetch_files
[STOP] [2020-12-03 14:27:02] fetch_files
[START] [2020-12-03 14:27:02] validate_each_file
[STOP] [2020-12-03 14:27:02] validate_each_file
[START] [2020-12-03 14:27:02] convert_to_csv
[CMD] [2020-12-03 14:27:02] /usr/bin/sort /app/public/converted_csv/wilkinson_et_al__nodes_24955.csv > /app/public/converted_csv/wilkinson_et_al__nodes_24955.csv_sorted
[CMD] [2020-12-03 14:27:02] /usr/bin/sort /app/public/converted_csv/wilkinson_et_al__occurrences_24956.csv > /app/public/converted_csv/wilkinson_et_al__occurrences_24956.csv_sorted
[CMD] [2020-12-03 14:27:02] /usr/bin/sort /app/public/converted_csv/wilkinson_et_al__measurements_24957.csv > /app/public/converted_csv/wilkinson_et_al__measurements_24957.csv_sorted
[STOP] [2020-12-03 14:27:02] convert_to_csv
[START] [2020-12-03 14:27:02] calculate_delta
[CMD] [2020-12-03 14:27:02] echo "0a" > /app/public/diff/wilkinson_et_al__nodes_24955.diff
[CMD] [2020-12-03 14:27:02] tail -n +1 /app/public/converted_csv/wilkinson_et_al__nodes_24955.csv >> /app/public/diff/wilkinson_et_al__nodes_24955.diff
[CMD] [2020-12-03 14:27:02] echo "." >> /app/public/diff/wilkinson_et_al__nodes_24955.diff
[CMD] [2020-12-03 14:27:02] echo "0a" > /app/public/diff/wilkinson_et_al__occurrences_24956.diff
[CMD] [2020-12-03 14:27:02] tail -n +1 /app/public/converted_csv/wilkinson_et_al__occurrences_24956.csv >> /app/public/diff/wilkinson_et_al__occurrences_24956.diff
[CMD] [2020-12-03 14:27:02] echo "." >> /app/public/diff/wilkinson_et_al__occurrences_24956.diff
[CMD] [2020-12-03 14:27:02] echo "0a" > /app/public/diff/wilkinson_et_al__measurements_24957.diff
[CMD] [2020-12-03 14:27:02] tail -n +1 /app/public/converted_csv/wilkinson_et_al__measurements_24957.csv >> /app/public/diff/wilkinson_et_al__measurements_24957.diff
[CMD] [2020-12-03 14:27:02] echo "." >> /app/public/diff/wilkinson_et_al__measurements_24957.diff
[STOP] [2020-12-03 14:27:02] calculate_delta
[START] [2020-12-03 14:27:02] parse_diff_and_store
[INFO] [2020-12-03 14:27:02] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 14:27:03] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 14:27:03] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 14:27:03] Storing 1 ScientificNames
[INFO] [2020-12-03 14:27:03] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 14:27:03] Average Time: 0.0
[INFO] [2020-12-03 14:27:03] Total Time: 1s
[INFO] [2020-12-03 14:27:03] Storing 1 Nodes
[INFO] [2020-12-03 14:27:03] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 14:27:03] Average Time: 0.0
[INFO] [2020-12-03 14:27:03] Total Time: 1s
[INFO] [2020-12-03 14:27:03] Storing 1 Occurrences
[INFO] [2020-12-03 14:27:03] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 14:27:03] Average Time: 0.0
[INFO] [2020-12-03 14:27:03] Total Time: 1s
[INFO] [2020-12-03 14:27:03] Storing 2 Traits
[INFO] [2020-12-03 14:27:03] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 14:27:03] Average Time: 0.0
[INFO] [2020-12-03 14:27:03] Total Time: 1s
[INFO] [2020-12-03 14:27:03] Storing 2 MetaTraits
[INFO] [2020-12-03 14:27:03] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 14:27:03] Average Time: 0.0
[INFO] [2020-12-03 14:27:03] Total Time: 1s
[STOP] [2020-12-03 14:27:03] parse_diff_and_store
[START] [2020-12-03 14:27:03] resolve_keys
[INFO] [2020-12-03 14:27:09] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 14:27:09] traits to occurrences...
[INFO] [2020-12-03 14:27:09] traits to nodes (through occurrences)...
[INFO] [2020-12-03 14:27:09] Traits to sex term...
[INFO] [2020-12-03 14:27:09] Traits to lifestage term...
[INFO] [2020-12-03 14:27:09] MetaTraits to traits...
[INFO] [2020-12-03 14:27:09] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 14:27:09] Assocs to occurrences...
[INFO] [2020-12-03 14:27:09] Assocs to nodes...
[INFO] [2020-12-03 14:27:09] Assoc to sex term...
[INFO] [2020-12-03 14:27:09] Assoc to lifestage term...
[INFO] [2020-12-03 14:27:09] MetaAssoc to assocs...
[STOP] [2020-12-03 14:27:09] resolve_keys
[START] [2020-12-03 14:27:09] hold_for_later_1
[STOP] [2020-12-03 14:27:09] hold_for_later_1
[START] [2020-12-03 14:27:09] hold_for_later_2
[STOP] [2020-12-03 14:27:09] hold_for_later_2
[START] [2020-12-03 14:27:09] resolve_missing_parents
[STOP] [2020-12-03 14:27:09] resolve_missing_parents
[START] [2020-12-03 14:27:09] rebuild_nodes
[START] [2020-12-03 14:27:09] Flattener#flatten
[START] [2020-12-03 14:27:09] Flattener#study_resource
[START] [2020-12-03 14:27:09] Flattener#build_ancestry
[STOP] [2020-12-03 14:27:09] Flattener#build_ancestry
[INFO] [2020-12-03 14:27:09] 1 ancestry keys
[START] [2020-12-03 14:27:09] build_node_ancestors
[INFO] [2020-12-03 14:27:09] old ancestors deleted.
[STOP] [2020-12-03 14:27:09] build_node_ancestors
[WARN] [2020-12-03 14:27:09] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 14:27:09] Flattener#flatten
[STOP] [2020-12-03 14:27:09] rebuild_nodes
[START] [2020-12-03 14:27:09] resolve_missing_media_owners
[STOP] [2020-12-03 14:27:09] resolve_missing_media_owners
[START] [2020-12-03 14:27:09] sanitize_media_verbatims
[STOP] [2020-12-03 14:27:09] sanitize_media_verbatims
[START] [2020-12-03 14:27:09] queue_downloads
[STOP] [2020-12-03 14:27:09] queue_downloads
[START] [2020-12-03 14:27:09] parse_names
[WARN] [2020-12-03 14:27:09] I see 1 names which still need to be parsed.
[STOP] [2020-12-03 14:27:10] parse_names
[START] [2020-12-03 14:27:10] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 14:27:10] denormalize_canonical_names_to_nodes
[START] [2020-12-03 14:27:10] match_nodes
[START] [2020-12-03 14:27:10] map_all_nodes_to_pages
[STOP] [2020-12-03 14:27:10] map_all_nodes_to_pages
[INFO] [2020-12-03 14:27:10] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-12-03 14:27:10] update_nodes
[STOP] [2020-12-03 14:27:10] update_nodes
[STOP] [2020-12-03 14:27:10] match_nodes
[START] [2020-12-03 14:27:10] reindex_search
[STOP] [2020-12-03 14:27:10] reindex_search
[START] [2020-12-03 14:27:10] normalize_units
[STOP] [2020-12-03 14:27:10] normalize_units
[START] [2020-12-03 14:27:10] calculate_statistics
[2020-12-03 14:27:10] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 14:27:10] calculate_statistics
[START] [2020-12-03 14:27:10] complete_harvest_instance
[START] [2020-12-03 14:27:10] overall_tsv_creation
[INFO] [2020-12-03 14:27:10] Processing group of 1 in 1 batches of 10000
[INFO] [2020-12-03 14:27:48] 1 Traits (unfiltered)...
[INFO] [2020-12-03 14:28:24] 1 Traits (filtered)...
[INFO] [2020-12-03 14:28:24] 0 Associations (filtered)...
[INFO] [2020-12-03 14:28:24] 3 metadata added.
[INFO] [2020-12-03 14:28:24] 0 metadata added.
[INFO] [2020-12-03 14:28:24] Average Time: 51.51
[INFO] [2020-12-03 14:28:24] Total Time: 1m14s
[STOP] [2020-12-03 14:28:24] overall_tsv_creation
[INFO] [2020-12-03 14:28:24] Done. Check your files:
[INFO] [2020-12-03 14:28:24] (1 lines) /app/public/data/wilkinson_et_al_/publish_nodes.tsv
[INFO] [2020-12-03 14:28:24] (1 lines) /app/public/data/wilkinson_et_al_/publish_scientific_names.tsv
[INFO] [2020-12-03 14:28:24] (2 lines) /app/public/data/wilkinson_et_al_/publish_traits.tsv
[INFO] [2020-12-03 14:28:24] (4 lines) /app/public/data/wilkinson_et_al_/publish_metadata.tsv
[STOP] [2020-12-03 14:28:24] complete_harvest_instance
[START] [2020-12-03 14:28:24] completed
[STOP] [2020-12-03 14:28:24] completed
[STOP] [2020-12-03 14:28:24] logged process, took 83.22
[INFO] [2021-04-19 16:20:35] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 16:25:33] ## remove_type: ScientificName
[INFO] [2021-04-19 16:25:33] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 16:25:33] [16:25:33.780] Removed 1 Scientificnames
[INFO] [2021-04-19 16:25:33] ## remove_type: Vernacular
[INFO] [2021-04-19 16:25:33] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:25:33] [16:25:33.781] Removed 0 Vernaculars
[INFO] [2021-04-19 16:25:33] ## remove_type: Article
[INFO] [2021-04-19 16:25:33] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:25:33] [16:25:33.782] Removed 0 Articles
[INFO] [2021-04-19 16:25:33] ## remove_type: Medium
[INFO] [2021-04-19 16:25:33] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:25:33] [16:25:33.784] Removed 0 Media
[INFO] [2021-04-19 16:25:33] ## remove_type: Trait
[INFO] [2021-04-19 16:25:33] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 16:25:33] [16:25:33.786] Removed 2 Traits
[INFO] [2021-04-19 16:25:33] ## remove_type: MetaTrait
[INFO] [2021-04-19 16:25:33] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 16:25:33] [16:25:33.788] Removed 2 Metatraits
[INFO] [2021-04-19 16:25:33] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 16:25:33] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:25:33] [16:25:33.790] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 16:25:33] ## remove_type: Assoc
[INFO] [2021-04-19 16:25:33] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:25:33] [16:25:33.791] Removed 0 Assocs
[INFO] [2021-04-19 16:25:33] ## remove_type: MetaAssoc
[INFO] [2021-04-19 16:25:33] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:25:33] [16:25:33.792] Removed 0 Metaassocs
[INFO] [2021-04-19 16:25:33] ## remove_type: Identifier
[INFO] [2021-04-19 16:25:33] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:25:33] [16:25:33.794] Removed 0 Identifiers
[INFO] [2021-04-19 16:25:33] ## remove_type: Reference
[INFO] [2021-04-19 16:25:33] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:25:33] [16:25:33.795] Removed 0 References
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] Starting batch with ID 86116299...
[INFO] [2021-04-19 16:25:33] ## remove_type: Node
[INFO] [2021-04-19 16:25:33] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 16:25:33] [16:25:33.993] Removed 1 Nodes
[START] [2021-04-19 16:25:34] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:25:34] Creating resource from OpenData
[START] [2021-04-19 16:25:34] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:25:34] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:25:34] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:25:34] Creating resource from OpenData
[START] [2021-04-19 16:25:34] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:25:34] create_harvest_instance
[INFO] [2021-04-19 16:25:34] Created harvest instance #3793
[STOP] [2021-04-19 16:25:34] create_harvest_instance
[START] [2021-04-19 16:25:34] fetch_files
[STOP] [2021-04-19 16:25:34] fetch_files
[START] [2021-04-19 16:25:34] validate_each_file
[INFO] [2021-04-19 16:25:34] Looping over 3 formats...
[INFO] [2021-04-19 16:25:34] ...nodes (/app/public/data/wilkinson_et_al_/taxa.txt)
[INFO] [2021-04-19 16:25:34] Valid: /app/public/converted_csv/wilkinson_et_al__nodes_3793.csv (1 lines)
[INFO] [2021-04-19 16:25:34] ...occurrences (/app/public/data/wilkinson_et_al_/occurrences.txt)
[INFO] [2021-04-19 16:25:34] Valid: /app/public/converted_csv/wilkinson_et_al__occurrences_3793.csv (1 lines)
[INFO] [2021-04-19 16:25:34] ...measurements (/app/public/data/wilkinson_et_al_/measurementsorfacts.txt)
[INFO] [2021-04-19 16:25:34] Valid: /app/public/converted_csv/wilkinson_et_al__measurements_3793.csv (2 lines)
[STOP] [2021-04-19 16:25:34] validate_each_file
[START] [2021-04-19 16:25:34] convert_to_csv
[INFO] [2021-04-19 16:25:34] Looping over 3 formats...
[INFO] [2021-04-19 16:25:34] ...nodes (/app/public/data/wilkinson_et_al_/taxa.txt)
[CMD] [2021-04-19 16:25:34] /usr/bin/sort /app/public/converted_csv/wilkinson_et_al__nodes_3793.csv > /app/public/converted_csv/wilkinson_et_al__nodes_3793.csv_sorted
[INFO] [2021-04-19 16:25:34] Converted: /app/public/converted_csv/wilkinson_et_al__nodes_3793.csv (1 lines)
[INFO] [2021-04-19 16:25:34] ...occurrences (/app/public/data/wilkinson_et_al_/occurrences.txt)
[CMD] [2021-04-19 16:25:34] /usr/bin/sort /app/public/converted_csv/wilkinson_et_al__occurrences_3793.csv > /app/public/converted_csv/wilkinson_et_al__occurrences_3793.csv_sorted
[INFO] [2021-04-19 16:25:34] Converted: /app/public/converted_csv/wilkinson_et_al__occurrences_3793.csv (1 lines)
[INFO] [2021-04-19 16:25:34] ...measurements (/app/public/data/wilkinson_et_al_/measurementsorfacts.txt)
[CMD] [2021-04-19 16:25:34] /usr/bin/sort /app/public/converted_csv/wilkinson_et_al__measurements_3793.csv > /app/public/converted_csv/wilkinson_et_al__measurements_3793.csv_sorted
[INFO] [2021-04-19 16:25:34] Converted: /app/public/converted_csv/wilkinson_et_al__measurements_3793.csv (2 lines)
[STOP] [2021-04-19 16:25:34] convert_to_csv
[START] [2021-04-19 16:25:34] calculate_delta
[INFO] [2021-04-19 16:25:34] Looping over 3 formats...
[INFO] [2021-04-19 16:25:34] ...nodes (/app/public/data/wilkinson_et_al_/taxa.txt)
[CMD] [2021-04-19 16:25:34] echo "0a" > /app/public/diff/wilkinson_et_al__nodes_3793.diff
[CMD] [2021-04-19 16:25:34] tail -n +1 /app/public/converted_csv/wilkinson_et_al__nodes_3793.csv >> /app/public/diff/wilkinson_et_al__nodes_3793.diff
[CMD] [2021-04-19 16:25:34] echo "." >> /app/public/diff/wilkinson_et_al__nodes_3793.diff
[INFO] [2021-04-19 16:25:34] Created diff: /app/public/diff/wilkinson_et_al__nodes_3793.diff (3 lines)
[INFO] [2021-04-19 16:25:34] ...occurrences (/app/public/data/wilkinson_et_al_/occurrences.txt)
[CMD] [2021-04-19 16:25:34] echo "0a" > /app/public/diff/wilkinson_et_al__occurrences_3793.diff
[CMD] [2021-04-19 16:25:34] tail -n +1 /app/public/converted_csv/wilkinson_et_al__occurrences_3793.csv >> /app/public/diff/wilkinson_et_al__occurrences_3793.diff
[CMD] [2021-04-19 16:25:34] echo "." >> /app/public/diff/wilkinson_et_al__occurrences_3793.diff
[INFO] [2021-04-19 16:25:34] Created diff: /app/public/diff/wilkinson_et_al__occurrences_3793.diff (3 lines)
[INFO] [2021-04-19 16:25:34] ...measurements (/app/public/data/wilkinson_et_al_/measurementsorfacts.txt)
[CMD] [2021-04-19 16:25:34] echo "0a" > /app/public/diff/wilkinson_et_al__measurements_3793.diff
[CMD] [2021-04-19 16:25:34] tail -n +1 /app/public/converted_csv/wilkinson_et_al__measurements_3793.csv >> /app/public/diff/wilkinson_et_al__measurements_3793.diff
[CMD] [2021-04-19 16:25:34] echo "." >> /app/public/diff/wilkinson_et_al__measurements_3793.diff
[INFO] [2021-04-19 16:25:34] Created diff: /app/public/diff/wilkinson_et_al__measurements_3793.diff (4 lines)
[STOP] [2021-04-19 16:25:34] calculate_delta
[START] [2021-04-19 16:25:34] parse_diff_and_store
[INFO] [2021-04-19 16:25:34] Handling diff: /app/public/diff/wilkinson_et_al__nodes_3793.diff (3 lines)
[INFO] [2021-04-19 16:25:34] Loading nodes diff file into memory (3 /app/public/diff/wilkinson_et_al__nodes_3793.diff lines)...
[INFO] [2021-04-19 16:25:34] Handling diff: /app/public/diff/wilkinson_et_al__occurrences_3793.diff (3 lines)
[INFO] [2021-04-19 16:25:34] Loading occurrences diff file into memory (3 /app/public/diff/wilkinson_et_al__occurrences_3793.diff lines)...
[INFO] [2021-04-19 16:25:34] Handling diff: /app/public/diff/wilkinson_et_al__measurements_3793.diff (4 lines)
[INFO] [2021-04-19 16:25:34] Loading measurements diff file into memory (4 /app/public/diff/wilkinson_et_al__measurements_3793.diff lines)...
[INFO] [2021-04-19 16:25:34] Storing 1 ScientificNames
[INFO] [2021-04-19 16:25:34] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:25:34] Average Time: 0.0
[INFO] [2021-04-19 16:25:34] Total Time: 1s
[INFO] [2021-04-19 16:25:34] Storing 1 Nodes
[INFO] [2021-04-19 16:25:34] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:25:34] Average Time: 0.0
[INFO] [2021-04-19 16:25:34] Total Time: 1s
[INFO] [2021-04-19 16:25:34] Storing 1 Occurrences
[INFO] [2021-04-19 16:25:34] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:25:34] Average Time: 0.0
[INFO] [2021-04-19 16:25:34] Total Time: 1s
[INFO] [2021-04-19 16:25:34] Storing 2 Traits
[INFO] [2021-04-19 16:25:34] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 16:25:34] Average Time: 0.0
[INFO] [2021-04-19 16:25:34] Total Time: 1s
[INFO] [2021-04-19 16:25:34] Storing 2 MetaTraits
[INFO] [2021-04-19 16:25:34] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 16:25:34] Average Time: 0.0
[INFO] [2021-04-19 16:25:34] Total Time: 1s
[STOP] [2021-04-19 16:25:34] parse_diff_and_store
[START] [2021-04-19 16:25:34] resolve_keys
[INFO] [2021-04-19 16:25:40] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 16:25:40] traits to occurrences...
[INFO] [2021-04-19 16:25:40] traits to nodes (through occurrences)...
[INFO] [2021-04-19 16:25:40] Traits to sex term...
[INFO] [2021-04-19 16:25:40] Traits to lifestage term...
[INFO] [2021-04-19 16:25:40] MetaTraits to traits...
[INFO] [2021-04-19 16:25:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 16:25:40] Assocs to occurrences...
[INFO] [2021-04-19 16:25:40] Assocs to nodes...
[INFO] [2021-04-19 16:25:40] Assoc to sex term...
[INFO] [2021-04-19 16:25:40] Assoc to lifestage term...
[INFO] [2021-04-19 16:25:40] MetaAssoc to assocs...
[STOP] [2021-04-19 16:25:40] resolve_keys
[START] [2021-04-19 16:25:40] hold_for_later_1
[STOP] [2021-04-19 16:25:40] hold_for_later_1
[START] [2021-04-19 16:25:40] hold_for_later_2
[STOP] [2021-04-19 16:25:40] hold_for_later_2
[START] [2021-04-19 16:25:40] resolve_missing_parents
[STOP] [2021-04-19 16:25:40] resolve_missing_parents
[START] [2021-04-19 16:25:40] rebuild_nodes
[START] [2021-04-19 16:25:40] Flattener#flatten
[START] [2021-04-19 16:25:40] Flattener#study_resource
[START] [2021-04-19 16:25:40] Flattener#build_ancestry
[STOP] [2021-04-19 16:25:40] Flattener#build_ancestry
[INFO] [2021-04-19 16:25:40] 1 ancestry keys
[START] [2021-04-19 16:25:40] build_node_ancestors
[INFO] [2021-04-19 16:25:40] old ancestors deleted.
[STOP] [2021-04-19 16:25:40] build_node_ancestors
[WARN] [2021-04-19 16:25:40] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 16:25:40] Flattener#flatten
[STOP] [2021-04-19 16:25:40] rebuild_nodes
[START] [2021-04-19 16:25:40] resolve_missing_media_owners
[STOP] [2021-04-19 16:25:40] resolve_missing_media_owners
[START] [2021-04-19 16:25:40] sanitize_media_verbatims
[STOP] [2021-04-19 16:25:40] sanitize_media_verbatims
[START] [2021-04-19 16:25:40] queue_downloads
[STOP] [2021-04-19 16:25:40] queue_downloads
[START] [2021-04-19 16:25:40] parse_names
[WARN] [2021-04-19 16:25:40] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 16:25:41] parse_names
[START] [2021-04-19 16:25:41] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 16:25:41] denormalize_canonical_names_to_nodes
[START] [2021-04-19 16:25:41] match_nodes
[START] [2021-04-19 16:25:41] map_all_nodes_to_pages
[STOP] [2021-04-19 16:25:41] map_all_nodes_to_pages
[INFO] [2021-04-19 16:25:41] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 16:25:41] update_nodes
[STOP] [2021-04-19 16:25:41] update_nodes
[STOP] [2021-04-19 16:25:41] match_nodes
[START] [2021-04-19 16:25:41] reindex_search
[STOP] [2021-04-19 16:25:41] reindex_search
[START] [2021-04-19 16:25:41] normalize_units
[STOP] [2021-04-19 16:25:41] normalize_units
[START] [2021-04-19 16:25:41] calculate_statistics
[2021-04-19 16:25:41] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 16:25:41] calculate_statistics
[START] [2021-04-19 16:25:41] complete_harvest_instance
[START] [2021-04-19 16:25:41] overall_tsv_creation
[INFO] [2021-04-19 16:25:41] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 16:26:17] 1 Traits (unfiltered)...
[INFO] [2021-04-19 16:26:49] 1 Traits (filtered)...
[INFO] [2021-04-19 16:26:49] 0 Associations (filtered)...
[INFO] [2021-04-19 16:26:49] 1 metadata added.
[INFO] [2021-04-19 16:26:49] 0 metadata added.
[INFO] [2021-04-19 16:27:16] Average Time: 70.43
[INFO] [2021-04-19 16:27:16] Total Time: 1m35s
[STOP] [2021-04-19 16:27:16] overall_tsv_creation
[INFO] [2021-04-19 16:27:16] Done. Check your files:
[INFO] [2021-04-19 16:27:16] (1 lines) /app/public/data/wilkinson_et_al_/publish_nodes.tsv
[INFO] [2021-04-19 16:27:16] (1 lines) /app/public/data/wilkinson_et_al_/publish_scientific_names.tsv
[INFO] [2021-04-19 16:27:16] (2 lines) /app/public/data/wilkinson_et_al_/publish_traits.tsv
[INFO] [2021-04-19 16:27:16] (2 lines) /app/public/data/wilkinson_et_al_/publish_metadata.tsv
[STOP] [2021-04-19 16:27:16] complete_harvest_instance
[START] [2021-04-19 16:27:16] completed
[STOP] [2021-04-19 16:27:16] completed
[STOP] [2021-04-19 16:27:16] logged process, took 101.95
Latest Process