Stage:
completed
Fetched:
19 Apr 16:27
Validated:
19 Apr 16:27
Deltas Created
19 Apr 16:27
Units Normalized:
19 Apr 16:27
Ancestry Built:
19 Apr 16:27
Nodes Matched:
19 Apr 16:27
Names Parsed:
19 Apr 16:27
New Models Stored:
19 Apr 16:27
Indexed:
19 Apr 16:27
Completed:
19 Apr 16:28
Time to Harvest:
less than a minute
Harvesting Log
(439 lines)
# Logfile created on 2020-09-24 09:04:43 -0400 by logger.rb/v1.4.2
[START] [2020-09-24 09:04:43] logged process
[START] [2020-09-24 09:04:43] Creating resource from OpenData
[START] [2020-09-24 09:04:43] logged process
[START] [2020-09-24 09:04:43] Parse meta.xml file and create formats with fields
[STOP] [2020-09-24 09:04:43] Parse meta.xml file and create formats with fields
[STOP] [2020-09-24 09:04:43] Creating resource from OpenData
[INFO] [2020-12-03 14:28:48] ## HARVEST: type = -harvest
[START] [2020-12-03 14:28:49] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-12-03 14:28:49] create_harvest_instance
[STOP] [2020-12-03 14:28:50] create_harvest_instance
[START] [2020-12-03 14:28:50] fetch_files
[STOP] [2020-12-03 14:28:50] fetch_files
[START] [2020-12-03 14:28:50] validate_each_file
[STOP] [2020-12-03 14:28:50] validate_each_file
[START] [2020-12-03 14:28:50] convert_to_csv
[CMD] [2020-12-03 14:28:50] /usr/bin/sort /app/public/converted_csv/wilkinson_et_al2_nodes_24958.csv > /app/public/converted_csv/wilkinson_et_al2_nodes_24958.csv_sorted
[CMD] [2020-12-03 14:28:50] /usr/bin/sort /app/public/converted_csv/wilkinson_et_al2_occurrences_24959.csv > /app/public/converted_csv/wilkinson_et_al2_occurrences_24959.csv_sorted
[CMD] [2020-12-03 14:28:50] /usr/bin/sort /app/public/converted_csv/wilkinson_et_al2_measurements_24960.csv > /app/public/converted_csv/wilkinson_et_al2_measurements_24960.csv_sorted
[STOP] [2020-12-03 14:28:50] convert_to_csv
[START] [2020-12-03 14:28:50] calculate_delta
[CMD] [2020-12-03 14:28:50] echo "0a" > /app/public/diff/wilkinson_et_al2_nodes_24958.diff
[CMD] [2020-12-03 14:28:50] tail -n +1 /app/public/converted_csv/wilkinson_et_al2_nodes_24958.csv >> /app/public/diff/wilkinson_et_al2_nodes_24958.diff
[CMD] [2020-12-03 14:28:50] echo "." >> /app/public/diff/wilkinson_et_al2_nodes_24958.diff
[CMD] [2020-12-03 14:28:50] echo "0a" > /app/public/diff/wilkinson_et_al2_occurrences_24959.diff
[CMD] [2020-12-03 14:28:50] tail -n +1 /app/public/converted_csv/wilkinson_et_al2_occurrences_24959.csv >> /app/public/diff/wilkinson_et_al2_occurrences_24959.diff
[CMD] [2020-12-03 14:28:50] echo "." >> /app/public/diff/wilkinson_et_al2_occurrences_24959.diff
[CMD] [2020-12-03 14:28:50] echo "0a" > /app/public/diff/wilkinson_et_al2_measurements_24960.diff
[CMD] [2020-12-03 14:28:50] tail -n +1 /app/public/converted_csv/wilkinson_et_al2_measurements_24960.csv >> /app/public/diff/wilkinson_et_al2_measurements_24960.diff
[CMD] [2020-12-03 14:28:50] echo "." >> /app/public/diff/wilkinson_et_al2_measurements_24960.diff
[STOP] [2020-12-03 14:28:50] calculate_delta
[START] [2020-12-03 14:28:50] parse_diff_and_store
[INFO] [2020-12-03 14:28:50] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 14:28:51] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 14:28:51] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 14:28:51] Storing 2 ScientificNames
[INFO] [2020-12-03 14:28:51] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 14:28:51] Average Time: 0.0
[INFO] [2020-12-03 14:28:51] Total Time: 1s
[INFO] [2020-12-03 14:28:51] Storing 2 Nodes
[INFO] [2020-12-03 14:28:51] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 14:28:51] Average Time: 0.01
[INFO] [2020-12-03 14:28:51] Total Time: 1s
[INFO] [2020-12-03 14:28:51] Storing 2 Occurrences
[INFO] [2020-12-03 14:28:51] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 14:28:51] Average Time: 0.0
[INFO] [2020-12-03 14:28:51] Total Time: 1s
[INFO] [2020-12-03 14:28:51] Storing 4 Traits
[INFO] [2020-12-03 14:28:51] Processing group of 4 in 1 groups of 1000
[INFO] [2020-12-03 14:28:51] Average Time: 0.0
[INFO] [2020-12-03 14:28:51] Total Time: 1s
[INFO] [2020-12-03 14:28:51] Storing 4 MetaTraits
[INFO] [2020-12-03 14:28:51] Processing group of 4 in 1 groups of 1000
[INFO] [2020-12-03 14:28:51] Average Time: 0.0
[INFO] [2020-12-03 14:28:51] Total Time: 1s
[STOP] [2020-12-03 14:28:51] parse_diff_and_store
[START] [2020-12-03 14:28:51] resolve_keys
[INFO] [2020-12-03 14:28:57] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 14:28:57] traits to occurrences...
[INFO] [2020-12-03 14:28:57] traits to nodes (through occurrences)...
[INFO] [2020-12-03 14:28:57] Traits to sex term...
[INFO] [2020-12-03 14:28:57] Traits to lifestage term...
[INFO] [2020-12-03 14:28:57] MetaTraits to traits...
[INFO] [2020-12-03 14:28:57] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 14:28:57] Assocs to occurrences...
[INFO] [2020-12-03 14:28:57] Assocs to nodes...
[INFO] [2020-12-03 14:28:57] Assoc to sex term...
[INFO] [2020-12-03 14:28:57] Assoc to lifestage term...
[INFO] [2020-12-03 14:28:57] MetaAssoc to assocs...
[STOP] [2020-12-03 14:28:57] resolve_keys
[START] [2020-12-03 14:28:57] hold_for_later_1
[STOP] [2020-12-03 14:28:57] hold_for_later_1
[START] [2020-12-03 14:28:57] hold_for_later_2
[STOP] [2020-12-03 14:28:57] hold_for_later_2
[START] [2020-12-03 14:28:57] resolve_missing_parents
[STOP] [2020-12-03 14:28:57] resolve_missing_parents
[START] [2020-12-03 14:28:57] rebuild_nodes
[START] [2020-12-03 14:28:57] Flattener#flatten
[START] [2020-12-03 14:28:57] Flattener#study_resource
[START] [2020-12-03 14:28:57] Flattener#build_ancestry
[STOP] [2020-12-03 14:28:57] Flattener#build_ancestry
[INFO] [2020-12-03 14:28:57] 2 ancestry keys
[START] [2020-12-03 14:28:57] build_node_ancestors
[INFO] [2020-12-03 14:28:57] old ancestors deleted.
[STOP] [2020-12-03 14:28:57] build_node_ancestors
[WARN] [2020-12-03 14:28:57] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 14:28:57] Flattener#flatten
[STOP] [2020-12-03 14:28:57] rebuild_nodes
[START] [2020-12-03 14:28:57] resolve_missing_media_owners
[STOP] [2020-12-03 14:28:57] resolve_missing_media_owners
[START] [2020-12-03 14:28:57] sanitize_media_verbatims
[STOP] [2020-12-03 14:28:57] sanitize_media_verbatims
[START] [2020-12-03 14:28:57] queue_downloads
[STOP] [2020-12-03 14:28:57] queue_downloads
[START] [2020-12-03 14:28:57] parse_names
[WARN] [2020-12-03 14:28:57] I see 2 names which still need to be parsed.
[STOP] [2020-12-03 14:28:58] parse_names
[START] [2020-12-03 14:28:58] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 14:28:58] denormalize_canonical_names_to_nodes
[START] [2020-12-03 14:28:58] match_nodes
[START] [2020-12-03 14:28:58] map_all_nodes_to_pages
[STOP] [2020-12-03 14:28:58] map_all_nodes_to_pages
[INFO] [2020-12-03 14:28:58] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2020-12-03 14:28:58] update_nodes
[STOP] [2020-12-03 14:28:58] update_nodes
[STOP] [2020-12-03 14:28:58] match_nodes
[START] [2020-12-03 14:28:58] reindex_search
[STOP] [2020-12-03 14:28:59] reindex_search
[START] [2020-12-03 14:28:59] normalize_units
[STOP] [2020-12-03 14:28:59] normalize_units
[START] [2020-12-03 14:28:59] calculate_statistics
[2020-12-03 14:28:59] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 14:28:59] calculate_statistics
[START] [2020-12-03 14:28:59] complete_harvest_instance
[START] [2020-12-03 14:28:59] overall_tsv_creation
[INFO] [2020-12-03 14:28:59] Processing group of 2 in 1 batches of 10000
[INFO] [2020-12-03 14:29:38] 2 Traits (unfiltered)...
[INFO] [2020-12-03 14:30:15] 2 Traits (filtered)...
[INFO] [2020-12-03 14:30:15] 0 Associations (filtered)...
[INFO] [2020-12-03 14:30:15] 6 metadata added.
[INFO] [2020-12-03 14:30:15] 0 metadata added.
[INFO] [2020-12-03 14:30:15] Average Time: 54.01
[INFO] [2020-12-03 14:30:15] Total Time: 1m17s
[STOP] [2020-12-03 14:30:15] overall_tsv_creation
[INFO] [2020-12-03 14:30:15] Done. Check your files:
[INFO] [2020-12-03 14:30:15] (2 lines) /app/public/data/wilkinson_et_al2/publish_nodes.tsv
[INFO] [2020-12-03 14:30:15] (2 lines) /app/public/data/wilkinson_et_al2/publish_scientific_names.tsv
[INFO] [2020-12-03 14:30:15] (3 lines) /app/public/data/wilkinson_et_al2/publish_traits.tsv
[INFO] [2020-12-03 14:30:15] (7 lines) /app/public/data/wilkinson_et_al2/publish_metadata.tsv
[STOP] [2020-12-03 14:30:16] complete_harvest_instance
[START] [2020-12-03 14:30:16] completed
[STOP] [2020-12-03 14:30:16] completed
[STOP] [2020-12-03 14:30:16] logged process, took 86.44
[INFO] [2021-04-19 16:20:39] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 16:27:16] ## remove_type: ScientificName
[INFO] [2021-04-19 16:27:16] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 16:27:16] [16:27:16.296] Removed 2 Scientificnames
[INFO] [2021-04-19 16:27:16] ## remove_type: Vernacular
[INFO] [2021-04-19 16:27:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:27:16] [16:27:16.297] Removed 0 Vernaculars
[INFO] [2021-04-19 16:27:16] ## remove_type: Article
[INFO] [2021-04-19 16:27:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:27:16] [16:27:16.299] Removed 0 Articles
[INFO] [2021-04-19 16:27:16] ## remove_type: Medium
[INFO] [2021-04-19 16:27:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:27:16] [16:27:16.301] Removed 0 Media
[INFO] [2021-04-19 16:27:16] ## remove_type: Trait
[INFO] [2021-04-19 16:27:16] ++ Calling delete_all on 4 instances...
[INFO] [2021-04-19 16:27:16] [16:27:16.303] Removed 4 Traits
[INFO] [2021-04-19 16:27:16] ## remove_type: MetaTrait
[INFO] [2021-04-19 16:27:16] ++ Calling delete_all on 4 instances...
[INFO] [2021-04-19 16:27:16] [16:27:16.305] Removed 4 Metatraits
[INFO] [2021-04-19 16:27:16] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 16:27:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:27:16] [16:27:16.307] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 16:27:16] ## remove_type: Assoc
[INFO] [2021-04-19 16:27:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:27:16] [16:27:16.308] Removed 0 Assocs
[INFO] [2021-04-19 16:27:16] ## remove_type: MetaAssoc
[INFO] [2021-04-19 16:27:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:27:16] [16:27:16.309] Removed 0 Metaassocs
[INFO] [2021-04-19 16:27:16] ## remove_type: Identifier
[INFO] [2021-04-19 16:27:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:27:16] [16:27:16.311] Removed 0 Identifiers
[INFO] [2021-04-19 16:27:16] ## remove_type: Reference
[INFO] [2021-04-19 16:27:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:27:16] [16:27:16.313] Removed 0 References
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:16] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:17] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:17] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:17] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:17] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:17] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:17] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:17] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:17] Starting batch with ID 86116300...
[INFO] [2021-04-19 16:27:17] ## remove_type: Node
[INFO] [2021-04-19 16:27:17] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 16:27:17] [16:27:17.055] Removed 2 Nodes
[START] [2021-04-19 16:27:17] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:27:17] Creating resource from OpenData
[START] [2021-04-19 16:27:17] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:27:17] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:27:17] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:27:17] Creating resource from OpenData
[START] [2021-04-19 16:27:17] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:27:17] create_harvest_instance
[INFO] [2021-04-19 16:27:17] Created harvest instance #3794
[STOP] [2021-04-19 16:27:17] create_harvest_instance
[START] [2021-04-19 16:27:17] fetch_files
[STOP] [2021-04-19 16:27:17] fetch_files
[START] [2021-04-19 16:27:17] validate_each_file
[INFO] [2021-04-19 16:27:17] Looping over 3 formats...
[INFO] [2021-04-19 16:27:17] ...nodes (/app/public/data/wilkinson_et_al2/taxa.txt)
[INFO] [2021-04-19 16:27:17] Valid: /app/public/converted_csv/wilkinson_et_al2_nodes_3794.csv (2 lines)
[INFO] [2021-04-19 16:27:17] ...occurrences (/app/public/data/wilkinson_et_al2/occurrences.txt)
[INFO] [2021-04-19 16:27:17] Valid: /app/public/converted_csv/wilkinson_et_al2_occurrences_3794.csv (2 lines)
[INFO] [2021-04-19 16:27:17] ...measurements (/app/public/data/wilkinson_et_al2/measurementsorfacts.txt)
[INFO] [2021-04-19 16:27:17] Valid: /app/public/converted_csv/wilkinson_et_al2_measurements_3794.csv (4 lines)
[STOP] [2021-04-19 16:27:17] validate_each_file
[START] [2021-04-19 16:27:17] convert_to_csv
[INFO] [2021-04-19 16:27:17] Looping over 3 formats...
[INFO] [2021-04-19 16:27:17] ...nodes (/app/public/data/wilkinson_et_al2/taxa.txt)
[CMD] [2021-04-19 16:27:17] /usr/bin/sort /app/public/converted_csv/wilkinson_et_al2_nodes_3794.csv > /app/public/converted_csv/wilkinson_et_al2_nodes_3794.csv_sorted
[INFO] [2021-04-19 16:27:17] Converted: /app/public/converted_csv/wilkinson_et_al2_nodes_3794.csv (2 lines)
[INFO] [2021-04-19 16:27:17] ...occurrences (/app/public/data/wilkinson_et_al2/occurrences.txt)
[CMD] [2021-04-19 16:27:17] /usr/bin/sort /app/public/converted_csv/wilkinson_et_al2_occurrences_3794.csv > /app/public/converted_csv/wilkinson_et_al2_occurrences_3794.csv_sorted
[INFO] [2021-04-19 16:27:17] Converted: /app/public/converted_csv/wilkinson_et_al2_occurrences_3794.csv (2 lines)
[INFO] [2021-04-19 16:27:17] ...measurements (/app/public/data/wilkinson_et_al2/measurementsorfacts.txt)
[CMD] [2021-04-19 16:27:17] /usr/bin/sort /app/public/converted_csv/wilkinson_et_al2_measurements_3794.csv > /app/public/converted_csv/wilkinson_et_al2_measurements_3794.csv_sorted
[INFO] [2021-04-19 16:27:17] Converted: /app/public/converted_csv/wilkinson_et_al2_measurements_3794.csv (4 lines)
[STOP] [2021-04-19 16:27:17] convert_to_csv
[START] [2021-04-19 16:27:17] calculate_delta
[INFO] [2021-04-19 16:27:17] Looping over 3 formats...
[INFO] [2021-04-19 16:27:17] ...nodes (/app/public/data/wilkinson_et_al2/taxa.txt)
[CMD] [2021-04-19 16:27:17] echo "0a" > /app/public/diff/wilkinson_et_al2_nodes_3794.diff
[CMD] [2021-04-19 16:27:17] tail -n +1 /app/public/converted_csv/wilkinson_et_al2_nodes_3794.csv >> /app/public/diff/wilkinson_et_al2_nodes_3794.diff
[CMD] [2021-04-19 16:27:17] echo "." >> /app/public/diff/wilkinson_et_al2_nodes_3794.diff
[INFO] [2021-04-19 16:27:17] Created diff: /app/public/diff/wilkinson_et_al2_nodes_3794.diff (4 lines)
[INFO] [2021-04-19 16:27:17] ...occurrences (/app/public/data/wilkinson_et_al2/occurrences.txt)
[CMD] [2021-04-19 16:27:17] echo "0a" > /app/public/diff/wilkinson_et_al2_occurrences_3794.diff
[CMD] [2021-04-19 16:27:17] tail -n +1 /app/public/converted_csv/wilkinson_et_al2_occurrences_3794.csv >> /app/public/diff/wilkinson_et_al2_occurrences_3794.diff
[CMD] [2021-04-19 16:27:17] echo "." >> /app/public/diff/wilkinson_et_al2_occurrences_3794.diff
[INFO] [2021-04-19 16:27:17] Created diff: /app/public/diff/wilkinson_et_al2_occurrences_3794.diff (4 lines)
[INFO] [2021-04-19 16:27:17] ...measurements (/app/public/data/wilkinson_et_al2/measurementsorfacts.txt)
[CMD] [2021-04-19 16:27:17] echo "0a" > /app/public/diff/wilkinson_et_al2_measurements_3794.diff
[CMD] [2021-04-19 16:27:17] tail -n +1 /app/public/converted_csv/wilkinson_et_al2_measurements_3794.csv >> /app/public/diff/wilkinson_et_al2_measurements_3794.diff
[CMD] [2021-04-19 16:27:17] echo "." >> /app/public/diff/wilkinson_et_al2_measurements_3794.diff
[INFO] [2021-04-19 16:27:17] Created diff: /app/public/diff/wilkinson_et_al2_measurements_3794.diff (6 lines)
[STOP] [2021-04-19 16:27:17] calculate_delta
[START] [2021-04-19 16:27:17] parse_diff_and_store
[INFO] [2021-04-19 16:27:17] Handling diff: /app/public/diff/wilkinson_et_al2_nodes_3794.diff (4 lines)
[INFO] [2021-04-19 16:27:17] Loading nodes diff file into memory (4 /app/public/diff/wilkinson_et_al2_nodes_3794.diff lines)...
[INFO] [2021-04-19 16:27:17] Handling diff: /app/public/diff/wilkinson_et_al2_occurrences_3794.diff (4 lines)
[INFO] [2021-04-19 16:27:17] Loading occurrences diff file into memory (4 /app/public/diff/wilkinson_et_al2_occurrences_3794.diff lines)...
[INFO] [2021-04-19 16:27:17] Handling diff: /app/public/diff/wilkinson_et_al2_measurements_3794.diff (6 lines)
[INFO] [2021-04-19 16:27:17] Loading measurements diff file into memory (6 /app/public/diff/wilkinson_et_al2_measurements_3794.diff lines)...
[INFO] [2021-04-19 16:27:17] Storing 2 ScientificNames
[INFO] [2021-04-19 16:27:17] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 16:27:17] Average Time: 0.0
[INFO] [2021-04-19 16:27:17] Total Time: 1s
[INFO] [2021-04-19 16:27:17] Storing 2 Nodes
[INFO] [2021-04-19 16:27:17] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 16:27:17] Average Time: 0.0
[INFO] [2021-04-19 16:27:17] Total Time: 1s
[INFO] [2021-04-19 16:27:17] Storing 2 Occurrences
[INFO] [2021-04-19 16:27:17] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 16:27:17] Average Time: 0.0
[INFO] [2021-04-19 16:27:17] Total Time: 1s
[INFO] [2021-04-19 16:27:17] Storing 4 Traits
[INFO] [2021-04-19 16:27:17] Processing group of 4 in 1 groups of 1000
[INFO] [2021-04-19 16:27:17] Average Time: 0.0
[INFO] [2021-04-19 16:27:17] Total Time: 1s
[INFO] [2021-04-19 16:27:17] Storing 4 MetaTraits
[INFO] [2021-04-19 16:27:17] Processing group of 4 in 1 groups of 1000
[INFO] [2021-04-19 16:27:17] Average Time: 0.0
[INFO] [2021-04-19 16:27:17] Total Time: 1s
[STOP] [2021-04-19 16:27:17] parse_diff_and_store
[START] [2021-04-19 16:27:17] resolve_keys
[INFO] [2021-04-19 16:27:23] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 16:27:23] traits to occurrences...
[INFO] [2021-04-19 16:27:23] traits to nodes (through occurrences)...
[INFO] [2021-04-19 16:27:23] Traits to sex term...
[INFO] [2021-04-19 16:27:23] Traits to lifestage term...
[INFO] [2021-04-19 16:27:23] MetaTraits to traits...
[INFO] [2021-04-19 16:27:23] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 16:27:23] Assocs to occurrences...
[INFO] [2021-04-19 16:27:23] Assocs to nodes...
[INFO] [2021-04-19 16:27:23] Assoc to sex term...
[INFO] [2021-04-19 16:27:23] Assoc to lifestage term...
[INFO] [2021-04-19 16:27:23] MetaAssoc to assocs...
[STOP] [2021-04-19 16:27:23] resolve_keys
[START] [2021-04-19 16:27:23] hold_for_later_1
[STOP] [2021-04-19 16:27:23] hold_for_later_1
[START] [2021-04-19 16:27:23] hold_for_later_2
[STOP] [2021-04-19 16:27:23] hold_for_later_2
[START] [2021-04-19 16:27:23] resolve_missing_parents
[STOP] [2021-04-19 16:27:23] resolve_missing_parents
[START] [2021-04-19 16:27:23] rebuild_nodes
[START] [2021-04-19 16:27:23] Flattener#flatten
[START] [2021-04-19 16:27:23] Flattener#study_resource
[START] [2021-04-19 16:27:23] Flattener#build_ancestry
[STOP] [2021-04-19 16:27:23] Flattener#build_ancestry
[INFO] [2021-04-19 16:27:23] 2 ancestry keys
[START] [2021-04-19 16:27:23] build_node_ancestors
[INFO] [2021-04-19 16:27:23] old ancestors deleted.
[STOP] [2021-04-19 16:27:23] build_node_ancestors
[WARN] [2021-04-19 16:27:23] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 16:27:23] Flattener#flatten
[STOP] [2021-04-19 16:27:23] rebuild_nodes
[START] [2021-04-19 16:27:23] resolve_missing_media_owners
[STOP] [2021-04-19 16:27:23] resolve_missing_media_owners
[START] [2021-04-19 16:27:23] sanitize_media_verbatims
[STOP] [2021-04-19 16:27:23] sanitize_media_verbatims
[START] [2021-04-19 16:27:23] queue_downloads
[STOP] [2021-04-19 16:27:23] queue_downloads
[START] [2021-04-19 16:27:23] parse_names
[WARN] [2021-04-19 16:27:23] I see 2 names which still need to be parsed.
[STOP] [2021-04-19 16:27:24] parse_names
[START] [2021-04-19 16:27:24] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 16:27:24] denormalize_canonical_names_to_nodes
[START] [2021-04-19 16:27:24] match_nodes
[START] [2021-04-19 16:27:24] map_all_nodes_to_pages
[STOP] [2021-04-19 16:27:24] map_all_nodes_to_pages
[INFO] [2021-04-19 16:27:24] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2021-04-19 16:27:24] update_nodes
[STOP] [2021-04-19 16:27:24] update_nodes
[STOP] [2021-04-19 16:27:24] match_nodes
[START] [2021-04-19 16:27:24] reindex_search
[STOP] [2021-04-19 16:27:25] reindex_search
[START] [2021-04-19 16:27:25] normalize_units
[STOP] [2021-04-19 16:27:25] normalize_units
[START] [2021-04-19 16:27:25] calculate_statistics
[2021-04-19 16:27:25] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 16:27:25] calculate_statistics
[START] [2021-04-19 16:27:25] complete_harvest_instance
[START] [2021-04-19 16:27:25] overall_tsv_creation
[INFO] [2021-04-19 16:27:25] Processing group of 2 in 1 batches of 10000
[INFO] [2021-04-19 16:28:00] 2 Traits (unfiltered)...
[INFO] [2021-04-19 16:28:33] 2 Traits (filtered)...
[INFO] [2021-04-19 16:28:33] 0 Associations (filtered)...
[INFO] [2021-04-19 16:28:33] 2 metadata added.
[INFO] [2021-04-19 16:28:33] 0 metadata added.
[INFO] [2021-04-19 16:28:59] Average Time: 70.89
[INFO] [2021-04-19 16:28:59] Total Time: 1m35s
[STOP] [2021-04-19 16:28:59] overall_tsv_creation
[INFO] [2021-04-19 16:28:59] Done. Check your files:
[INFO] [2021-04-19 16:28:59] (2 lines) /app/public/data/wilkinson_et_al2/publish_nodes.tsv
[INFO] [2021-04-19 16:28:59] (2 lines) /app/public/data/wilkinson_et_al2/publish_scientific_names.tsv
[INFO] [2021-04-19 16:28:59] (3 lines) /app/public/data/wilkinson_et_al2/publish_traits.tsv
[INFO] [2021-04-19 16:28:59] (3 lines) /app/public/data/wilkinson_et_al2/publish_metadata.tsv
[STOP] [2021-04-19 16:28:59] complete_harvest_instance
[START] [2021-04-19 16:28:59] completed
[STOP] [2021-04-19 16:28:59] completed
[STOP] [2021-04-19 16:28:59] logged process, took 102.18
Latest Process