Harvest for
Cubo 2000
Created
19 Apr 14:42
Stage:
completed
Fetched:
19 Apr 14:42
Validated:
19 Apr 14:42
Deltas Created
19 Apr 14:42
Units Normalized:
19 Apr 14:42
Ancestry Built:
19 Apr 14:42
Nodes Matched:
19 Apr 14:42
Names Parsed:
19 Apr 14:42
New Models Stored:
19 Apr 14:42
Indexed:
19 Apr 14:42
Completed:
19 Apr 14:44
Time to Harvest:
less than a minute
Harvesting Log
(613 lines)
# Logfile created on 2020-07-22 15:28:26 -0400 by logger.rb/v1.4.2
[START] [2020-07-22 15:28:26] logged process
[START] [2020-07-22 15:28:26] Creating resource from OpenData
[START] [2020-07-22 15:28:27] logged process
[START] [2020-07-22 15:28:27] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:28:27] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:28:27] Creating resource from OpenData
[INFO] [2020-07-22 15:31:06] ## HARVEST: type = -harvest
[START] [2020-07-22 15:31:08] logged process
[START] [2020-07-22 15:31:08] create_harvest_instance
[STOP] [2020-07-22 15:31:09] create_harvest_instance
[START] [2020-07-22 15:31:09] fetch_files
[STOP] [2020-07-22 15:31:09] fetch_files
[START] [2020-07-22 15:31:09] validate_each_file
[STOP] [2020-07-22 15:31:09] validate_each_file
[START] [2020-07-22 15:31:09] convert_to_csv
[CMD] [2020-07-22 15:31:09] /usr/bin/sort /app/public/converted_csv/cubo_cubo_2000_nodes_22105.csv > /app/public/converted_csv/cubo_cubo_2000_nodes_22105.csv_sorted
[CMD] [2020-07-22 15:31:09] /usr/bin/sort /app/public/converted_csv/cubo_cubo_2000_occurrences_22106.csv > /app/public/converted_csv/cubo_cubo_2000_occurrences_22106.csv_sorted
[CMD] [2020-07-22 15:31:09] /usr/bin/sort /app/public/converted_csv/cubo_cubo_2000_measurements_22107.csv > /app/public/converted_csv/cubo_cubo_2000_measurements_22107.csv_sorted
[STOP] [2020-07-22 15:31:09] convert_to_csv
[START] [2020-07-22 15:31:09] calculate_delta
[CMD] [2020-07-22 15:31:09] echo "0a" > /app/public/diff/cubo_cubo_2000_nodes_22105.diff
[CMD] [2020-07-22 15:31:09] tail -n +1 /app/public/converted_csv/cubo_cubo_2000_nodes_22105.csv >> /app/public/diff/cubo_cubo_2000_nodes_22105.diff
[CMD] [2020-07-22 15:31:09] echo "." >> /app/public/diff/cubo_cubo_2000_nodes_22105.diff
[CMD] [2020-07-22 15:31:09] echo "0a" > /app/public/diff/cubo_cubo_2000_occurrences_22106.diff
[CMD] [2020-07-22 15:31:09] tail -n +1 /app/public/converted_csv/cubo_cubo_2000_occurrences_22106.csv >> /app/public/diff/cubo_cubo_2000_occurrences_22106.diff
[CMD] [2020-07-22 15:31:09] echo "." >> /app/public/diff/cubo_cubo_2000_occurrences_22106.diff
[CMD] [2020-07-22 15:31:09] echo "0a" > /app/public/diff/cubo_cubo_2000_measurements_22107.diff
[CMD] [2020-07-22 15:31:09] tail -n +1 /app/public/converted_csv/cubo_cubo_2000_measurements_22107.csv >> /app/public/diff/cubo_cubo_2000_measurements_22107.diff
[CMD] [2020-07-22 15:31:09] echo "." >> /app/public/diff/cubo_cubo_2000_measurements_22107.diff
[STOP] [2020-07-22 15:31:09] calculate_delta
[START] [2020-07-22 15:31:09] parse_diff_and_store
[INFO] [2020-07-22 15:31:09] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-22 15:31:09] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-22 15:31:09] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-22 15:31:09] Storing 1 ScientificNames
[INFO] [2020-07-22 15:31:09] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 15:31:09] Average Time: 0.0
[INFO] [2020-07-22 15:31:09] Total Time: 1s
[INFO] [2020-07-22 15:31:09] Storing 1 Nodes
[INFO] [2020-07-22 15:31:09] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 15:31:09] Average Time: 0.0
[INFO] [2020-07-22 15:31:09] Total Time: 1s
[INFO] [2020-07-22 15:31:09] Storing 1 Occurrences
[INFO] [2020-07-22 15:31:09] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 15:31:09] Average Time: 0.0
[INFO] [2020-07-22 15:31:09] Total Time: 1s
[INFO] [2020-07-22 15:31:09] Storing 19 Traits
[INFO] [2020-07-22 15:31:09] Processing group of 19 in 1 groups of 1000
[INFO] [2020-07-22 15:31:09] Average Time: 0.01
[INFO] [2020-07-22 15:31:09] Total Time: 1s
[INFO] [2020-07-22 15:31:09] Storing 2 MetaTraits
[INFO] [2020-07-22 15:31:09] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 15:31:09] Average Time: 0.0
[INFO] [2020-07-22 15:31:09] Total Time: 1s
[STOP] [2020-07-22 15:31:09] parse_diff_and_store
[START] [2020-07-22 15:31:09] resolve_keys
[INFO] [2020-07-22 15:31:16] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-22 15:31:16] traits to occurrences...
[INFO] [2020-07-22 15:31:16] traits to nodes (through occurrences)...
[INFO] [2020-07-22 15:31:16] Traits to sex term...
[INFO] [2020-07-22 15:31:16] Traits to lifestage term...
[INFO] [2020-07-22 15:31:16] MetaTraits to traits...
[INFO] [2020-07-22 15:31:16] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-22 15:31:16] Assocs to occurrences...
[INFO] [2020-07-22 15:31:16] Assocs to nodes...
[INFO] [2020-07-22 15:31:16] Assoc to sex term...
[INFO] [2020-07-22 15:31:16] Assoc to lifestage term...
[STOP] [2020-07-22 15:31:16] resolve_keys
[START] [2020-07-22 15:31:16] hold_for_later_1
[STOP] [2020-07-22 15:31:16] hold_for_later_1
[START] [2020-07-22 15:31:16] hold_for_later_2
[STOP] [2020-07-22 15:31:16] hold_for_later_2
[START] [2020-07-22 15:31:16] resolve_missing_parents
[STOP] [2020-07-22 15:31:16] resolve_missing_parents
[START] [2020-07-22 15:31:16] rebuild_nodes
[START] [2020-07-22 15:31:16] Flattener#flatten
[START] [2020-07-22 15:31:16] Flattener#study_resource
[START] [2020-07-22 15:31:16] Flattener#build_ancestry
[STOP] [2020-07-22 15:31:16] Flattener#build_ancestry
[INFO] [2020-07-22 15:31:16] 1 ancestry keys
[START] [2020-07-22 15:31:16] build_node_ancestors
[INFO] [2020-07-22 15:31:16] old ancestors deleted.
[STOP] [2020-07-22 15:31:16] build_node_ancestors
[WARN] [2020-07-22 15:31:16] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-22 15:31:16] Flattener#flatten
[STOP] [2020-07-22 15:31:16] rebuild_nodes
[START] [2020-07-22 15:31:16] resolve_missing_media_owners
[STOP] [2020-07-22 15:31:16] resolve_missing_media_owners
[START] [2020-07-22 15:31:16] sanitize_media_verbatims
[STOP] [2020-07-22 15:31:16] sanitize_media_verbatims
[START] [2020-07-22 15:31:16] queue_downloads
[STOP] [2020-07-22 15:31:16] queue_downloads
[START] [2020-07-22 15:31:16] parse_names
[WARN] [2020-07-22 15:31:16] I see 1 names which still need to be parsed.
[STOP] [2020-07-22 15:31:17] parse_names
[START] [2020-07-22 15:31:17] denormalize_canonical_names_to_nodes
[STOP] [2020-07-22 15:31:17] denormalize_canonical_names_to_nodes
[START] [2020-07-22 15:31:17] match_nodes
[START] [2020-07-22 15:31:17] map_all_nodes_to_pages
[STOP] [2020-07-22 15:31:17] map_all_nodes_to_pages
[INFO] [2020-07-22 15:31:17] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-07-22 15:31:17] update_nodes
[STOP] [2020-07-22 15:31:17] update_nodes
[STOP] [2020-07-22 15:31:17] match_nodes
[START] [2020-07-22 15:31:17] reindex_search
[STOP] [2020-07-22 15:31:17] reindex_search
[START] [2020-07-22 15:31:17] normalize_units
[STOP] [2020-07-22 15:31:17] normalize_units
[START] [2020-07-22 15:31:17] calculate_statistics
[2020-07-22 15:31:17] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-22 15:31:17] calculate_statistics
[START] [2020-07-22 15:31:17] complete_harvest_instance
[START] [2020-07-22 15:31:17] overall_tsv_creation
[INFO] [2020-07-22 15:31:17] Processing group of 1 in 1 batches of 10000
[INFO] [2020-07-22 15:32:06] 1 Traits (unfiltered)...
[INFO] [2020-07-22 15:32:40] 1 Traits (filtered)...
[INFO] [2020-07-22 15:32:40] 0 Associations (filtered)...
[INFO] [2020-07-22 15:32:40] 20 metadata added.
[INFO] [2020-07-22 15:32:40] 0 metadata added.
[INFO] [2020-07-22 15:32:40] Average Time: 55.84
[INFO] [2020-07-22 15:32:40] Total Time: 1m23s
[STOP] [2020-07-22 15:32:40] overall_tsv_creation
[INFO] [2020-07-22 15:32:40] Done. Check your files:
[INFO] [2020-07-22 15:32:40] (1 lines) /app/public/data/cubo_cubo_2000/publish_nodes.tsv
[INFO] [2020-07-22 15:32:40] (1 lines) /app/public/data/cubo_cubo_2000/publish_scientific_names.tsv
[INFO] [2020-07-22 15:32:40] (2 lines) /app/public/data/cubo_cubo_2000/publish_traits.tsv
[INFO] [2020-07-22 15:32:40] (19 lines) /app/public/data/cubo_cubo_2000/publish_metadata.tsv
[STOP] [2020-07-22 15:32:40] complete_harvest_instance
[START] [2020-07-22 15:32:40] completed
[STOP] [2020-07-22 15:32:40] completed
[STOP] [2020-07-22 15:32:40] logged process, took 92.67
[INFO] [2020-11-13 10:43:09] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-11-13 10:43:10] ## remove_type: ScientificName
[INFO] [2020-11-13 10:43:10] ++ Calling delete_all on 1 instances...
[INFO] [2020-11-13 10:43:10] [10:43:10.213] Removed 1 Scientificnames
[INFO] [2020-11-13 10:43:10] ## remove_type: Vernacular
[INFO] [2020-11-13 10:43:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-13 10:43:10] [10:43:10.215] Removed 0 Vernaculars
[INFO] [2020-11-13 10:43:10] ## remove_type: Article
[INFO] [2020-11-13 10:43:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-13 10:43:10] [10:43:10.218] Removed 0 Articles
[INFO] [2020-11-13 10:43:10] ## remove_type: Medium
[INFO] [2020-11-13 10:43:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-13 10:43:10] [10:43:10.221] Removed 0 Media
[INFO] [2020-11-13 10:43:10] ## remove_type: Trait
[INFO] [2020-11-13 10:43:10] ++ Calling delete_all on 19 instances...
[INFO] [2020-11-13 10:43:10] [10:43:10.225] Removed 19 Traits
[INFO] [2020-11-13 10:43:10] ## remove_type: MetaTrait
[INFO] [2020-11-13 10:43:10] ++ Calling delete_all on 2 instances...
[INFO] [2020-11-13 10:43:10] [10:43:10.234] Removed 2 Metatraits
[INFO] [2020-11-13 10:43:10] ## remove_type: OccurrenceMetadatum
[INFO] [2020-11-13 10:43:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-13 10:43:10] [10:43:10.237] Removed 0 Occurrencemetadata
[INFO] [2020-11-13 10:43:10] ## remove_type: Assoc
[INFO] [2020-11-13 10:43:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-13 10:43:10] [10:43:10.240] Removed 0 Assocs
[INFO] [2020-11-13 10:43:10] ## remove_type: MetaAssoc
[INFO] [2020-11-13 10:43:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-13 10:43:10] [10:43:10.243] Removed 0 Metaassocs
[INFO] [2020-11-13 10:43:10] ## remove_type: Identifier
[INFO] [2020-11-13 10:43:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-13 10:43:10] [10:43:10.250] Removed 0 Identifiers
[INFO] [2020-11-13 10:43:10] ## remove_type: Reference
[INFO] [2020-11-13 10:43:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-13 10:43:10] [10:43:10.252] Removed 0 References
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:10] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:11] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:11] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:11] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:11] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:11] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:11] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:11] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:11] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:11] Starting batch with ID 80633666...
[INFO] [2020-11-13 10:43:11] ## remove_type: Node
[INFO] [2020-11-13 10:43:11] ++ Calling delete_all on 1 instances...
[INFO] [2020-11-13 10:43:11] [10:43:11.493] Removed 1 Nodes
[START] [2020-11-13 10:43:11] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-13 10:43:11] Creating resource from OpenData
[START] [2020-11-13 10:43:11] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-13 10:43:11] Parse meta.xml file and create formats with fields
[STOP] [2020-11-13 10:43:12] Parse meta.xml file and create formats with fields
[STOP] [2020-11-13 10:43:12] Creating resource from OpenData
[START] [2020-11-13 10:43:12] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-13 10:43:12] create_harvest_instance
[STOP] [2020-11-13 10:43:13] create_harvest_instance
[START] [2020-11-13 10:43:13] fetch_files
[STOP] [2020-11-13 10:43:13] fetch_files
[START] [2020-11-13 10:43:13] validate_each_file
[STOP] [2020-11-13 10:43:13] validate_each_file
[START] [2020-11-13 10:43:13] convert_to_csv
[CMD] [2020-11-13 10:43:13] /usr/bin/sort /app/public/converted_csv/cubo_cubo_2000_nodes_24139.csv > /app/public/converted_csv/cubo_cubo_2000_nodes_24139.csv_sorted
[CMD] [2020-11-13 10:43:13] /usr/bin/sort /app/public/converted_csv/cubo_cubo_2000_occurrences_24140.csv > /app/public/converted_csv/cubo_cubo_2000_occurrences_24140.csv_sorted
[CMD] [2020-11-13 10:43:13] /usr/bin/sort /app/public/converted_csv/cubo_cubo_2000_measurements_24141.csv > /app/public/converted_csv/cubo_cubo_2000_measurements_24141.csv_sorted
[STOP] [2020-11-13 10:43:13] convert_to_csv
[START] [2020-11-13 10:43:13] calculate_delta
[CMD] [2020-11-13 10:43:13] echo "0a" > /app/public/diff/cubo_cubo_2000_nodes_24139.diff
[CMD] [2020-11-13 10:43:13] tail -n +1 /app/public/converted_csv/cubo_cubo_2000_nodes_24139.csv >> /app/public/diff/cubo_cubo_2000_nodes_24139.diff
[CMD] [2020-11-13 10:43:13] echo "." >> /app/public/diff/cubo_cubo_2000_nodes_24139.diff
[CMD] [2020-11-13 10:43:13] echo "0a" > /app/public/diff/cubo_cubo_2000_occurrences_24140.diff
[CMD] [2020-11-13 10:43:13] tail -n +1 /app/public/converted_csv/cubo_cubo_2000_occurrences_24140.csv >> /app/public/diff/cubo_cubo_2000_occurrences_24140.diff
[CMD] [2020-11-13 10:43:13] echo "." >> /app/public/diff/cubo_cubo_2000_occurrences_24140.diff
[CMD] [2020-11-13 10:43:13] echo "0a" > /app/public/diff/cubo_cubo_2000_measurements_24141.diff
[CMD] [2020-11-13 10:43:13] tail -n +1 /app/public/converted_csv/cubo_cubo_2000_measurements_24141.csv >> /app/public/diff/cubo_cubo_2000_measurements_24141.diff
[CMD] [2020-11-13 10:43:13] echo "." >> /app/public/diff/cubo_cubo_2000_measurements_24141.diff
[STOP] [2020-11-13 10:43:13] calculate_delta
[START] [2020-11-13 10:43:13] parse_diff_and_store
[INFO] [2020-11-13 10:43:13] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-13 10:43:13] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-13 10:43:13] Loading measurements diff file into memory (true lines)...
[INFO] [2020-11-13 10:43:14] Storing 1 ScientificNames
[INFO] [2020-11-13 10:43:14] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-13 10:43:14] Average Time: 0.0
[INFO] [2020-11-13 10:43:14] Total Time: 1s
[INFO] [2020-11-13 10:43:14] Storing 1 Nodes
[INFO] [2020-11-13 10:43:14] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-13 10:43:14] Average Time: 0.0
[INFO] [2020-11-13 10:43:14] Total Time: 1s
[INFO] [2020-11-13 10:43:14] Storing 1 Occurrences
[INFO] [2020-11-13 10:43:14] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-13 10:43:14] Average Time: 0.0
[INFO] [2020-11-13 10:43:14] Total Time: 1s
[INFO] [2020-11-13 10:43:14] Storing 21 Traits
[INFO] [2020-11-13 10:43:14] Processing group of 21 in 1 groups of 1000
[INFO] [2020-11-13 10:43:14] Average Time: 0.01
[INFO] [2020-11-13 10:43:14] Total Time: 1s
[INFO] [2020-11-13 10:43:14] Storing 3 MetaTraits
[INFO] [2020-11-13 10:43:14] Processing group of 3 in 1 groups of 1000
[INFO] [2020-11-13 10:43:14] Average Time: 0.0
[INFO] [2020-11-13 10:43:14] Total Time: 1s
[STOP] [2020-11-13 10:43:14] parse_diff_and_store
[START] [2020-11-13 10:43:14] resolve_keys
[INFO] [2020-11-13 10:43:20] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-13 10:43:20] traits to occurrences...
[INFO] [2020-11-13 10:43:20] traits to nodes (through occurrences)...
[INFO] [2020-11-13 10:43:20] Traits to sex term...
[INFO] [2020-11-13 10:43:20] Traits to lifestage term...
[INFO] [2020-11-13 10:43:20] MetaTraits to traits...
[INFO] [2020-11-13 10:43:20] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-13 10:43:20] Assocs to occurrences...
[INFO] [2020-11-13 10:43:20] Assocs to nodes...
[INFO] [2020-11-13 10:43:20] Assoc to sex term...
[INFO] [2020-11-13 10:43:20] Assoc to lifestage term...
[INFO] [2020-11-13 10:43:20] MetaAssoc to assocs...
[STOP] [2020-11-13 10:43:20] resolve_keys
[START] [2020-11-13 10:43:20] hold_for_later_1
[STOP] [2020-11-13 10:43:20] hold_for_later_1
[START] [2020-11-13 10:43:20] hold_for_later_2
[STOP] [2020-11-13 10:43:20] hold_for_later_2
[START] [2020-11-13 10:43:20] resolve_missing_parents
[STOP] [2020-11-13 10:43:20] resolve_missing_parents
[START] [2020-11-13 10:43:20] rebuild_nodes
[START] [2020-11-13 10:43:20] Flattener#flatten
[START] [2020-11-13 10:43:20] Flattener#study_resource
[START] [2020-11-13 10:43:20] Flattener#build_ancestry
[STOP] [2020-11-13 10:43:20] Flattener#build_ancestry
[INFO] [2020-11-13 10:43:20] 1 ancestry keys
[START] [2020-11-13 10:43:20] build_node_ancestors
[INFO] [2020-11-13 10:43:20] old ancestors deleted.
[STOP] [2020-11-13 10:43:20] build_node_ancestors
[WARN] [2020-11-13 10:43:20] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-11-13 10:43:20] Flattener#flatten
[STOP] [2020-11-13 10:43:20] rebuild_nodes
[START] [2020-11-13 10:43:20] resolve_missing_media_owners
[STOP] [2020-11-13 10:43:20] resolve_missing_media_owners
[START] [2020-11-13 10:43:20] sanitize_media_verbatims
[STOP] [2020-11-13 10:43:20] sanitize_media_verbatims
[START] [2020-11-13 10:43:20] queue_downloads
[STOP] [2020-11-13 10:43:20] queue_downloads
[START] [2020-11-13 10:43:20] parse_names
[WARN] [2020-11-13 10:43:20] I see 1 names which still need to be parsed.
[STOP] [2020-11-13 10:43:21] parse_names
[START] [2020-11-13 10:43:21] denormalize_canonical_names_to_nodes
[STOP] [2020-11-13 10:43:21] denormalize_canonical_names_to_nodes
[START] [2020-11-13 10:43:21] match_nodes
[START] [2020-11-13 10:43:21] map_all_nodes_to_pages
[STOP] [2020-11-13 10:43:21] map_all_nodes_to_pages
[INFO] [2020-11-13 10:43:21] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-11-13 10:43:21] update_nodes
[STOP] [2020-11-13 10:43:21] update_nodes
[STOP] [2020-11-13 10:43:21] match_nodes
[START] [2020-11-13 10:43:21] reindex_search
[STOP] [2020-11-13 10:43:21] reindex_search
[START] [2020-11-13 10:43:21] normalize_units
[STOP] [2020-11-13 10:43:21] normalize_units
[START] [2020-11-13 10:43:21] calculate_statistics
[2020-11-13 10:43:21] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-11-13 10:43:21] calculate_statistics
[START] [2020-11-13 10:43:21] complete_harvest_instance
[START] [2020-11-13 10:43:21] overall_tsv_creation
[INFO] [2020-11-13 10:43:21] Processing group of 1 in 1 batches of 10000
[INFO] [2020-11-13 10:44:00] 1 Traits (unfiltered)...
[INFO] [2020-11-13 10:44:35] 1 Traits (filtered)...
[INFO] [2020-11-13 10:44:35] 0 Associations (filtered)...
[INFO] [2020-11-13 10:44:35] 20 metadata added.
[INFO] [2020-11-13 10:44:35] 0 metadata added.
[INFO] [2020-11-13 10:44:35] Average Time: 49.54
[INFO] [2020-11-13 10:44:35] Total Time: 1m14s
[STOP] [2020-11-13 10:44:35] overall_tsv_creation
[INFO] [2020-11-13 10:44:35] Done. Check your files:
[INFO] [2020-11-13 10:44:35] (1 lines) /app/public/data/cubo_cubo_2000/publish_nodes.tsv
[INFO] [2020-11-13 10:44:35] (1 lines) /app/public/data/cubo_cubo_2000/publish_scientific_names.tsv
[INFO] [2020-11-13 10:44:35] (2 lines) /app/public/data/cubo_cubo_2000/publish_traits.tsv
[INFO] [2020-11-13 10:44:35] (21 lines) /app/public/data/cubo_cubo_2000/publish_metadata.tsv
[STOP] [2020-11-13 10:44:35] complete_harvest_instance
[START] [2020-11-13 10:44:35] completed
[STOP] [2020-11-13 10:44:35] completed
[STOP] [2020-11-13 10:44:35] logged process, took 83.3
[INFO] [2021-04-19 14:39:30] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 14:42:49] ## remove_type: ScientificName
[INFO] [2021-04-19 14:42:49] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 14:42:49] [14:42:49.645] Removed 1 Scientificnames
[INFO] [2021-04-19 14:42:49] ## remove_type: Vernacular
[INFO] [2021-04-19 14:42:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:42:49] [14:42:49.646] Removed 0 Vernaculars
[INFO] [2021-04-19 14:42:49] ## remove_type: Article
[INFO] [2021-04-19 14:42:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:42:49] [14:42:49.648] Removed 0 Articles
[INFO] [2021-04-19 14:42:49] ## remove_type: Medium
[INFO] [2021-04-19 14:42:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:42:49] [14:42:49.650] Removed 0 Media
[INFO] [2021-04-19 14:42:49] ## remove_type: Trait
[INFO] [2021-04-19 14:42:49] ++ Calling delete_all on 21 instances...
[INFO] [2021-04-19 14:42:49] [14:42:49.652] Removed 21 Traits
[INFO] [2021-04-19 14:42:49] ## remove_type: MetaTrait
[INFO] [2021-04-19 14:42:49] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 14:42:49] [14:42:49.654] Removed 3 Metatraits
[INFO] [2021-04-19 14:42:49] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 14:42:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:42:49] [14:42:49.656] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 14:42:49] ## remove_type: Assoc
[INFO] [2021-04-19 14:42:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:42:49] [14:42:49.658] Removed 0 Assocs
[INFO] [2021-04-19 14:42:49] ## remove_type: MetaAssoc
[INFO] [2021-04-19 14:42:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:42:49] [14:42:49.659] Removed 0 Metaassocs
[INFO] [2021-04-19 14:42:49] ## remove_type: Identifier
[INFO] [2021-04-19 14:42:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:42:49] [14:42:49.661] Removed 0 Identifiers
[INFO] [2021-04-19 14:42:49] ## remove_type: Reference
[INFO] [2021-04-19 14:42:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:42:49] [14:42:49.662] Removed 0 References
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:49] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] Starting batch with ID 81658605...
[INFO] [2021-04-19 14:42:50] ## remove_type: Node
[INFO] [2021-04-19 14:42:50] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 14:42:50] [14:42:50.151] Removed 1 Nodes
[START] [2021-04-19 14:42:50] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:42:50] Creating resource from OpenData
[START] [2021-04-19 14:42:50] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:42:50] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 14:42:50] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 14:42:50] Creating resource from OpenData
[START] [2021-04-19 14:42:50] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:42:50] create_harvest_instance
[INFO] [2021-04-19 14:42:50] Created harvest instance #3748
[STOP] [2021-04-19 14:42:50] create_harvest_instance
[START] [2021-04-19 14:42:50] fetch_files
[STOP] [2021-04-19 14:42:50] fetch_files
[START] [2021-04-19 14:42:50] validate_each_file
[INFO] [2021-04-19 14:42:50] Looping over 3 formats...
[INFO] [2021-04-19 14:42:50] ...nodes (/app/public/data/cubo_cubo_2000/taxa.txt)
[INFO] [2021-04-19 14:42:50] Valid: /app/public/converted_csv/cubo_cubo_2000_nodes_3748.csv (1 lines)
[INFO] [2021-04-19 14:42:50] ...occurrences (/app/public/data/cubo_cubo_2000/occurrences.txt)
[INFO] [2021-04-19 14:42:50] Valid: /app/public/converted_csv/cubo_cubo_2000_occurrences_3748.csv (1 lines)
[INFO] [2021-04-19 14:42:50] ...measurements (/app/public/data/cubo_cubo_2000/measurementsorfacts.txt)
[INFO] [2021-04-19 14:42:50] Valid: /app/public/converted_csv/cubo_cubo_2000_measurements_3748.csv (21 lines)
[STOP] [2021-04-19 14:42:50] validate_each_file
[START] [2021-04-19 14:42:50] convert_to_csv
[INFO] [2021-04-19 14:42:50] Looping over 3 formats...
[INFO] [2021-04-19 14:42:50] ...nodes (/app/public/data/cubo_cubo_2000/taxa.txt)
[CMD] [2021-04-19 14:42:50] /usr/bin/sort /app/public/converted_csv/cubo_cubo_2000_nodes_3748.csv > /app/public/converted_csv/cubo_cubo_2000_nodes_3748.csv_sorted
[INFO] [2021-04-19 14:42:50] Converted: /app/public/converted_csv/cubo_cubo_2000_nodes_3748.csv (1 lines)
[INFO] [2021-04-19 14:42:50] ...occurrences (/app/public/data/cubo_cubo_2000/occurrences.txt)
[CMD] [2021-04-19 14:42:50] /usr/bin/sort /app/public/converted_csv/cubo_cubo_2000_occurrences_3748.csv > /app/public/converted_csv/cubo_cubo_2000_occurrences_3748.csv_sorted
[INFO] [2021-04-19 14:42:50] Converted: /app/public/converted_csv/cubo_cubo_2000_occurrences_3748.csv (1 lines)
[INFO] [2021-04-19 14:42:50] ...measurements (/app/public/data/cubo_cubo_2000/measurementsorfacts.txt)
[CMD] [2021-04-19 14:42:50] /usr/bin/sort /app/public/converted_csv/cubo_cubo_2000_measurements_3748.csv > /app/public/converted_csv/cubo_cubo_2000_measurements_3748.csv_sorted
[INFO] [2021-04-19 14:42:50] Converted: /app/public/converted_csv/cubo_cubo_2000_measurements_3748.csv (21 lines)
[STOP] [2021-04-19 14:42:50] convert_to_csv
[START] [2021-04-19 14:42:50] calculate_delta
[INFO] [2021-04-19 14:42:50] Looping over 3 formats...
[INFO] [2021-04-19 14:42:50] ...nodes (/app/public/data/cubo_cubo_2000/taxa.txt)
[CMD] [2021-04-19 14:42:50] echo "0a" > /app/public/diff/cubo_cubo_2000_nodes_3748.diff
[CMD] [2021-04-19 14:42:50] tail -n +1 /app/public/converted_csv/cubo_cubo_2000_nodes_3748.csv >> /app/public/diff/cubo_cubo_2000_nodes_3748.diff
[CMD] [2021-04-19 14:42:50] echo "." >> /app/public/diff/cubo_cubo_2000_nodes_3748.diff
[INFO] [2021-04-19 14:42:50] Created diff: /app/public/diff/cubo_cubo_2000_nodes_3748.diff (3 lines)
[INFO] [2021-04-19 14:42:50] ...occurrences (/app/public/data/cubo_cubo_2000/occurrences.txt)
[CMD] [2021-04-19 14:42:50] echo "0a" > /app/public/diff/cubo_cubo_2000_occurrences_3748.diff
[CMD] [2021-04-19 14:42:50] tail -n +1 /app/public/converted_csv/cubo_cubo_2000_occurrences_3748.csv >> /app/public/diff/cubo_cubo_2000_occurrences_3748.diff
[CMD] [2021-04-19 14:42:50] echo "." >> /app/public/diff/cubo_cubo_2000_occurrences_3748.diff
[INFO] [2021-04-19 14:42:50] Created diff: /app/public/diff/cubo_cubo_2000_occurrences_3748.diff (3 lines)
[INFO] [2021-04-19 14:42:50] ...measurements (/app/public/data/cubo_cubo_2000/measurementsorfacts.txt)
[CMD] [2021-04-19 14:42:50] echo "0a" > /app/public/diff/cubo_cubo_2000_measurements_3748.diff
[CMD] [2021-04-19 14:42:50] tail -n +1 /app/public/converted_csv/cubo_cubo_2000_measurements_3748.csv >> /app/public/diff/cubo_cubo_2000_measurements_3748.diff
[CMD] [2021-04-19 14:42:50] echo "." >> /app/public/diff/cubo_cubo_2000_measurements_3748.diff
[INFO] [2021-04-19 14:42:50] Created diff: /app/public/diff/cubo_cubo_2000_measurements_3748.diff (23 lines)
[STOP] [2021-04-19 14:42:50] calculate_delta
[START] [2021-04-19 14:42:50] parse_diff_and_store
[INFO] [2021-04-19 14:42:50] Handling diff: /app/public/diff/cubo_cubo_2000_nodes_3748.diff (3 lines)
[INFO] [2021-04-19 14:42:50] Loading nodes diff file into memory (3 /app/public/diff/cubo_cubo_2000_nodes_3748.diff lines)...
[INFO] [2021-04-19 14:42:50] Handling diff: /app/public/diff/cubo_cubo_2000_occurrences_3748.diff (3 lines)
[INFO] [2021-04-19 14:42:50] Loading occurrences diff file into memory (3 /app/public/diff/cubo_cubo_2000_occurrences_3748.diff lines)...
[INFO] [2021-04-19 14:42:50] Handling diff: /app/public/diff/cubo_cubo_2000_measurements_3748.diff (23 lines)
[INFO] [2021-04-19 14:42:50] Loading measurements diff file into memory (23 /app/public/diff/cubo_cubo_2000_measurements_3748.diff lines)...
[INFO] [2021-04-19 14:42:50] Storing 1 ScientificNames
[INFO] [2021-04-19 14:42:50] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:42:50] Average Time: 0.0
[INFO] [2021-04-19 14:42:50] Total Time: 1s
[INFO] [2021-04-19 14:42:50] Storing 1 Nodes
[INFO] [2021-04-19 14:42:50] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:42:50] Average Time: 0.0
[INFO] [2021-04-19 14:42:50] Total Time: 1s
[INFO] [2021-04-19 14:42:50] Storing 1 Occurrences
[INFO] [2021-04-19 14:42:50] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:42:50] Average Time: 0.0
[INFO] [2021-04-19 14:42:50] Total Time: 1s
[INFO] [2021-04-19 14:42:50] Storing 21 Traits
[INFO] [2021-04-19 14:42:50] Processing group of 21 in 1 groups of 1000
[INFO] [2021-04-19 14:42:50] Average Time: 0.01
[INFO] [2021-04-19 14:42:50] Total Time: 1s
[INFO] [2021-04-19 14:42:50] Storing 3 MetaTraits
[INFO] [2021-04-19 14:42:50] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 14:42:50] Average Time: 0.0
[INFO] [2021-04-19 14:42:50] Total Time: 1s
[STOP] [2021-04-19 14:42:50] parse_diff_and_store
[START] [2021-04-19 14:42:50] resolve_keys
[INFO] [2021-04-19 14:42:56] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 14:42:56] traits to occurrences...
[INFO] [2021-04-19 14:42:56] traits to nodes (through occurrences)...
[INFO] [2021-04-19 14:42:56] Traits to sex term...
[INFO] [2021-04-19 14:42:56] Traits to lifestage term...
[INFO] [2021-04-19 14:42:56] MetaTraits to traits...
[INFO] [2021-04-19 14:42:56] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 14:42:56] Assocs to occurrences...
[INFO] [2021-04-19 14:42:56] Assocs to nodes...
[INFO] [2021-04-19 14:42:56] Assoc to sex term...
[INFO] [2021-04-19 14:42:56] Assoc to lifestage term...
[INFO] [2021-04-19 14:42:56] MetaAssoc to assocs...
[STOP] [2021-04-19 14:42:56] resolve_keys
[START] [2021-04-19 14:42:56] hold_for_later_1
[STOP] [2021-04-19 14:42:56] hold_for_later_1
[START] [2021-04-19 14:42:56] hold_for_later_2
[STOP] [2021-04-19 14:42:56] hold_for_later_2
[START] [2021-04-19 14:42:56] resolve_missing_parents
[STOP] [2021-04-19 14:42:56] resolve_missing_parents
[START] [2021-04-19 14:42:56] rebuild_nodes
[START] [2021-04-19 14:42:56] Flattener#flatten
[START] [2021-04-19 14:42:56] Flattener#study_resource
[START] [2021-04-19 14:42:56] Flattener#build_ancestry
[STOP] [2021-04-19 14:42:56] Flattener#build_ancestry
[INFO] [2021-04-19 14:42:56] 1 ancestry keys
[START] [2021-04-19 14:42:56] build_node_ancestors
[INFO] [2021-04-19 14:42:56] old ancestors deleted.
[STOP] [2021-04-19 14:42:56] build_node_ancestors
[WARN] [2021-04-19 14:42:56] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 14:42:56] Flattener#flatten
[STOP] [2021-04-19 14:42:56] rebuild_nodes
[START] [2021-04-19 14:42:56] resolve_missing_media_owners
[STOP] [2021-04-19 14:42:56] resolve_missing_media_owners
[START] [2021-04-19 14:42:56] sanitize_media_verbatims
[STOP] [2021-04-19 14:42:56] sanitize_media_verbatims
[START] [2021-04-19 14:42:56] queue_downloads
[STOP] [2021-04-19 14:42:56] queue_downloads
[START] [2021-04-19 14:42:56] parse_names
[WARN] [2021-04-19 14:42:56] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 14:42:58] parse_names
[START] [2021-04-19 14:42:58] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 14:42:58] denormalize_canonical_names_to_nodes
[START] [2021-04-19 14:42:58] match_nodes
[START] [2021-04-19 14:42:58] map_all_nodes_to_pages
[STOP] [2021-04-19 14:42:58] map_all_nodes_to_pages
[INFO] [2021-04-19 14:42:58] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 14:42:58] update_nodes
[STOP] [2021-04-19 14:42:58] update_nodes
[STOP] [2021-04-19 14:42:58] match_nodes
[START] [2021-04-19 14:42:58] reindex_search
[STOP] [2021-04-19 14:42:58] reindex_search
[START] [2021-04-19 14:42:58] normalize_units
[STOP] [2021-04-19 14:42:58] normalize_units
[START] [2021-04-19 14:42:58] calculate_statistics
[2021-04-19 14:42:58] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 14:42:58] calculate_statistics
[START] [2021-04-19 14:42:58] complete_harvest_instance
[START] [2021-04-19 14:42:58] overall_tsv_creation
[INFO] [2021-04-19 14:42:58] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 14:43:33] 1 Traits (unfiltered)...
[INFO] [2021-04-19 14:44:06] 1 Traits (filtered)...
[INFO] [2021-04-19 14:44:06] 0 Associations (filtered)...
[INFO] [2021-04-19 14:44:06] 19 metadata added.
[INFO] [2021-04-19 14:44:06] 0 metadata added.
[INFO] [2021-04-19 14:44:33] Average Time: 71.33
[INFO] [2021-04-19 14:44:33] Total Time: 1m36s
[STOP] [2021-04-19 14:44:33] overall_tsv_creation
[INFO] [2021-04-19 14:44:33] Done. Check your files:
[INFO] [2021-04-19 14:44:33] (1 lines) /app/public/data/cubo_cubo_2000/publish_nodes.tsv
[INFO] [2021-04-19 14:44:33] (1 lines) /app/public/data/cubo_cubo_2000/publish_scientific_names.tsv
[INFO] [2021-04-19 14:44:33] (2 lines) /app/public/data/cubo_cubo_2000/publish_traits.tsv
[INFO] [2021-04-19 14:44:33] (20 lines) /app/public/data/cubo_cubo_2000/publish_metadata.tsv
[STOP] [2021-04-19 14:44:33] complete_harvest_instance
[START] [2021-04-19 14:44:33] completed
[STOP] [2021-04-19 14:44:33] completed
[STOP] [2021-04-19 14:44:33] logged process, took 103.14
Latest Process