Harvest for Vidal et al 2010 Created 19 Apr 16:00

Harvesting Log

# Logfile created on 2020-08-27 15:49:34 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:49:34] logged process
[START] [2020-08-27 15:49:34] Creating resource from OpenData
[START] [2020-08-27 15:49:34] logged process
[START] [2020-08-27 15:49:34] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:49:35] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:49:35] Creating resource from OpenData
[INFO] [2020-12-03 12:11:31] ## HARVEST: type = -harvest
[START] [2020-12-03 12:11:36] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-03 12:11:36] create_harvest_instance
[STOP] [2020-12-03 12:11:38] create_harvest_instance
[START] [2020-12-03 12:11:38] fetch_files
[STOP] [2020-12-03 12:11:38] fetch_files
[START] [2020-12-03 12:11:38] validate_each_file
[STOP] [2020-12-03 12:11:38] validate_each_file
[START] [2020-12-03 12:11:38] convert_to_csv
[CMD] [2020-12-03 12:11:38] /usr/bin/sort /app/public/converted_csv/vidal_et_al_vida_refs_24884.csv > /app/public/converted_csv/vidal_et_al_vida_refs_24884.csv_sorted
[CMD] [2020-12-03 12:11:38] /usr/bin/sort /app/public/converted_csv/vidal_et_al_vida_nodes_24885.csv > /app/public/converted_csv/vidal_et_al_vida_nodes_24885.csv_sorted
[CMD] [2020-12-03 12:11:38] /usr/bin/sort /app/public/converted_csv/vidal_et_al_vida_occurrences_24886.csv > /app/public/converted_csv/vidal_et_al_vida_occurrences_24886.csv_sorted
[CMD] [2020-12-03 12:11:38] /usr/bin/sort /app/public/converted_csv/vidal_et_al_vida_measurements_24887.csv > /app/public/converted_csv/vidal_et_al_vida_measurements_24887.csv_sorted
[STOP] [2020-12-03 12:11:38] convert_to_csv
[START] [2020-12-03 12:11:38] calculate_delta
[CMD] [2020-12-03 12:11:38] echo "0a" > /app/public/diff/vidal_et_al_vida_refs_24884.diff
[CMD] [2020-12-03 12:11:38] tail -n +1 /app/public/converted_csv/vidal_et_al_vida_refs_24884.csv >> /app/public/diff/vidal_et_al_vida_refs_24884.diff
[CMD] [2020-12-03 12:11:38] echo "." >> /app/public/diff/vidal_et_al_vida_refs_24884.diff
[CMD] [2020-12-03 12:11:38] echo "0a" > /app/public/diff/vidal_et_al_vida_nodes_24885.diff
[CMD] [2020-12-03 12:11:38] tail -n +1 /app/public/converted_csv/vidal_et_al_vida_nodes_24885.csv >> /app/public/diff/vidal_et_al_vida_nodes_24885.diff
[CMD] [2020-12-03 12:11:38] echo "." >> /app/public/diff/vidal_et_al_vida_nodes_24885.diff
[CMD] [2020-12-03 12:11:38] echo "0a" > /app/public/diff/vidal_et_al_vida_occurrences_24886.diff
[CMD] [2020-12-03 12:11:38] tail -n +1 /app/public/converted_csv/vidal_et_al_vida_occurrences_24886.csv >> /app/public/diff/vidal_et_al_vida_occurrences_24886.diff
[CMD] [2020-12-03 12:11:38] echo "." >> /app/public/diff/vidal_et_al_vida_occurrences_24886.diff
[CMD] [2020-12-03 12:11:38] echo "0a" > /app/public/diff/vidal_et_al_vida_measurements_24887.diff
[CMD] [2020-12-03 12:11:38] tail -n +1 /app/public/converted_csv/vidal_et_al_vida_measurements_24887.csv >> /app/public/diff/vidal_et_al_vida_measurements_24887.diff
[CMD] [2020-12-03 12:11:38] echo "." >> /app/public/diff/vidal_et_al_vida_measurements_24887.diff
[STOP] [2020-12-03 12:11:38] calculate_delta
[START] [2020-12-03 12:11:38] parse_diff_and_store
[INFO] [2020-12-03 12:11:38] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 12:11:38] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 12:11:38] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 12:11:38] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 12:11:39] Storing 6 ScientificNames
[INFO] [2020-12-03 12:11:39] Processing group of 6 in 1 groups of 1000
[INFO] [2020-12-03 12:11:39] Average Time: 0.01
[INFO] [2020-12-03 12:11:39] Total Time: 1s
[INFO] [2020-12-03 12:11:39] Storing 6 Nodes
[INFO] [2020-12-03 12:11:39] Processing group of 6 in 1 groups of 1000
[INFO] [2020-12-03 12:11:39] Average Time: 0.02
[INFO] [2020-12-03 12:11:39] Total Time: 1s
[INFO] [2020-12-03 12:11:39] Storing 6 Occurrences
[INFO] [2020-12-03 12:11:39] Processing group of 6 in 1 groups of 1000
[INFO] [2020-12-03 12:11:39] Average Time: 0.0
[INFO] [2020-12-03 12:11:39] Total Time: 1s
[INFO] [2020-12-03 12:11:39] Storing 12 Traits
[INFO] [2020-12-03 12:11:39] Processing group of 12 in 1 groups of 1000
[INFO] [2020-12-03 12:11:39] Average Time: 0.01
[INFO] [2020-12-03 12:11:39] Total Time: 1s
[INFO] [2020-12-03 12:11:39] Storing 11 MetaTraits
[INFO] [2020-12-03 12:11:39] Processing group of 11 in 1 groups of 1000
[INFO] [2020-12-03 12:11:39] Average Time: 0.0
[INFO] [2020-12-03 12:11:39] Total Time: 1s
[STOP] [2020-12-03 12:11:39] parse_diff_and_store
[START] [2020-12-03 12:11:39] resolve_keys
[INFO] [2020-12-03 12:11:45] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 12:11:45] traits to occurrences...
[INFO] [2020-12-03 12:11:45] traits to nodes (through occurrences)...
[INFO] [2020-12-03 12:11:45] Traits to sex term...
[INFO] [2020-12-03 12:11:45] Traits to lifestage term...
[INFO] [2020-12-03 12:11:45] MetaTraits to traits...
[INFO] [2020-12-03 12:11:45] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 12:11:45] Assocs to occurrences...
[INFO] [2020-12-03 12:11:45] Assocs to nodes...
[INFO] [2020-12-03 12:11:45] Assoc to sex term...
[INFO] [2020-12-03 12:11:45] Assoc to lifestage term...
[INFO] [2020-12-03 12:11:45] MetaAssoc to assocs...
[STOP] [2020-12-03 12:11:45] resolve_keys
[START] [2020-12-03 12:11:45] hold_for_later_1
[STOP] [2020-12-03 12:11:45] hold_for_later_1
[START] [2020-12-03 12:11:45] hold_for_later_2
[STOP] [2020-12-03 12:11:45] hold_for_later_2
[START] [2020-12-03 12:11:45] resolve_missing_parents
[STOP] [2020-12-03 12:11:45] resolve_missing_parents
[START] [2020-12-03 12:11:45] rebuild_nodes
[START] [2020-12-03 12:11:45] Flattener#flatten
[START] [2020-12-03 12:11:45] Flattener#study_resource
[START] [2020-12-03 12:11:45] Flattener#build_ancestry
[STOP] [2020-12-03 12:11:45] Flattener#build_ancestry
[INFO] [2020-12-03 12:11:45] 6 ancestry keys
[START] [2020-12-03 12:11:45] build_node_ancestors
[INFO] [2020-12-03 12:11:45] old ancestors deleted.
[STOP] [2020-12-03 12:11:45] build_node_ancestors
[WARN] [2020-12-03 12:11:45] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 12:11:45] Flattener#flatten
[STOP] [2020-12-03 12:11:45] rebuild_nodes
[START] [2020-12-03 12:11:45] resolve_missing_media_owners
[STOP] [2020-12-03 12:11:45] resolve_missing_media_owners
[START] [2020-12-03 12:11:45] sanitize_media_verbatims
[STOP] [2020-12-03 12:11:45] sanitize_media_verbatims
[START] [2020-12-03 12:11:45] queue_downloads
[STOP] [2020-12-03 12:11:45] queue_downloads
[START] [2020-12-03 12:11:45] parse_names
[WARN] [2020-12-03 12:11:45] I see 6 names which still need to be parsed.
[STOP] [2020-12-03 12:11:46] parse_names
[START] [2020-12-03 12:11:46] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 12:11:46] denormalize_canonical_names_to_nodes
[START] [2020-12-03 12:11:46] match_nodes
[START] [2020-12-03 12:11:46] map_all_nodes_to_pages
[STOP] [2020-12-03 12:11:46] map_all_nodes_to_pages
[INFO] [2020-12-03 12:11:46] ZERO unmatched nodes (of 6)! Nicely done.
[START] [2020-12-03 12:11:46] update_nodes
[STOP] [2020-12-03 12:11:46] update_nodes
[STOP] [2020-12-03 12:11:46] match_nodes
[START] [2020-12-03 12:11:46] reindex_search
[STOP] [2020-12-03 12:11:46] reindex_search
[START] [2020-12-03 12:11:46] normalize_units
[STOP] [2020-12-03 12:11:46] normalize_units
[START] [2020-12-03 12:11:46] calculate_statistics
[2020-12-03 12:11:46] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 12:11:46] calculate_statistics
[START] [2020-12-03 12:11:46] complete_harvest_instance
[START] [2020-12-03 12:11:46] overall_tsv_creation
[INFO] [2020-12-03 12:11:46] Processing group of 6 in 1 batches of 10000
[INFO] [2020-12-03 12:12:25] 6 Traits (unfiltered)...
[INFO] [2020-12-03 12:13:02] 6 Traits (filtered)...
[INFO] [2020-12-03 12:13:02] 0 Associations (filtered)...
[INFO] [2020-12-03 12:13:02] 17 metadata added.
[INFO] [2020-12-03 12:13:02] 0 metadata added.
[INFO] [2020-12-03 12:13:02] Average Time: 53.4
[INFO] [2020-12-03 12:13:02] Total Time: 1m17s
[STOP] [2020-12-03 12:13:02] overall_tsv_creation
[INFO] [2020-12-03 12:13:02] Done. Check your files:
[INFO] [2020-12-03 12:13:02] (6 lines) /app/public/data/vidal_et_al_vida/publish_nodes.tsv
[INFO] [2020-12-03 12:13:02] (6 lines) /app/public/data/vidal_et_al_vida/publish_scientific_names.tsv
[INFO] [2020-12-03 12:13:02] (7 lines) /app/public/data/vidal_et_al_vida/publish_traits.tsv
[INFO] [2020-12-03 12:13:02] (18 lines) /app/public/data/vidal_et_al_vida/publish_metadata.tsv
[STOP] [2020-12-03 12:13:02] complete_harvest_instance
[START] [2020-12-03 12:13:02] completed
[STOP] [2020-12-03 12:13:02] completed
[STOP] [2020-12-03 12:13:02] logged process, took 86.12
[INFO] [2021-04-19 15:57:59] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 16:00:51] ## remove_type: ScientificName
[INFO] [2021-04-19 16:00:51] ++ Calling delete_all on 6 instances...
[INFO] [2021-04-19 16:00:51] [16:00:51.764] Removed 6 Scientificnames
[INFO] [2021-04-19 16:00:51] ## remove_type: Vernacular
[INFO] [2021-04-19 16:00:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:00:51] [16:00:51.766] Removed 0 Vernaculars
[INFO] [2021-04-19 16:00:51] ## remove_type: Article
[INFO] [2021-04-19 16:00:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:00:51] [16:00:51.768] Removed 0 Articles
[INFO] [2021-04-19 16:00:51] ## remove_type: Medium
[INFO] [2021-04-19 16:00:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:00:51] [16:00:51.769] Removed 0 Media
[INFO] [2021-04-19 16:00:51] ## remove_type: Trait
[INFO] [2021-04-19 16:00:51] ++ Calling delete_all on 12 instances...
[INFO] [2021-04-19 16:00:51] [16:00:51.772] Removed 12 Traits
[INFO] [2021-04-19 16:00:51] ## remove_type: MetaTrait
[INFO] [2021-04-19 16:00:51] ++ Calling delete_all on 11 instances...
[INFO] [2021-04-19 16:00:51] [16:00:51.774] Removed 11 Metatraits
[INFO] [2021-04-19 16:00:51] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 16:00:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:00:51] [16:00:51.776] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 16:00:51] ## remove_type: Assoc
[INFO] [2021-04-19 16:00:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:00:51] [16:00:51.777] Removed 0 Assocs
[INFO] [2021-04-19 16:00:51] ## remove_type: MetaAssoc
[INFO] [2021-04-19 16:00:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:00:51] [16:00:51.779] Removed 0 Metaassocs
[INFO] [2021-04-19 16:00:51] ## remove_type: Identifier
[INFO] [2021-04-19 16:00:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:00:51] [16:00:51.781] Removed 0 Identifiers
[INFO] [2021-04-19 16:00:51] ## remove_type: Reference
[INFO] [2021-04-19 16:00:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:00:51] [16:00:51.782] Removed 0 References
[INFO] [2021-04-19 16:00:51] Starting batch with ID 86116218...
[INFO] [2021-04-19 16:00:51] Starting batch with ID 86116218...
[INFO] [2021-04-19 16:00:51] Starting batch with ID 86116218...
[INFO] [2021-04-19 16:00:51] Starting batch with ID 86116218...
[INFO] [2021-04-19 16:00:51] Starting batch with ID 86116218...
[INFO] [2021-04-19 16:00:51] Starting batch with ID 86116218...
[INFO] [2021-04-19 16:00:51] ## remove_type: Node
[INFO] [2021-04-19 16:00:51] ++ Calling delete_all on 6 instances...
[INFO] [2021-04-19 16:00:51] [16:00:51.846] Removed 6 Nodes
[START] [2021-04-19 16:00:52] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:00:52] Creating resource from OpenData
[START] [2021-04-19 16:00:52] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:00:52] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:00:52] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:00:52] Creating resource from OpenData
[START] [2021-04-19 16:00:52] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:00:52] create_harvest_instance
[INFO] [2021-04-19 16:00:52] Created harvest instance #3784
[STOP] [2021-04-19 16:00:52] create_harvest_instance
[START] [2021-04-19 16:00:52] fetch_files
[STOP] [2021-04-19 16:00:52] fetch_files
[START] [2021-04-19 16:00:52] validate_each_file
[INFO] [2021-04-19 16:00:52] Looping over 4 formats...
[INFO] [2021-04-19 16:00:52] ...refs (/app/public/data/vidal_et_al_vida/references.tsv)
[INFO] [2021-04-19 16:00:52] Valid: /app/public/converted_csv/vidal_et_al_vida_refs_3784.csv (0 lines)
[INFO] [2021-04-19 16:00:52] ...nodes (/app/public/data/vidal_et_al_vida/taxa.txt)
[INFO] [2021-04-19 16:00:52] Valid: /app/public/converted_csv/vidal_et_al_vida_nodes_3784.csv (6 lines)
[INFO] [2021-04-19 16:00:52] ...occurrences (/app/public/data/vidal_et_al_vida/occurrences.txt)
[INFO] [2021-04-19 16:00:52] Valid: /app/public/converted_csv/vidal_et_al_vida_occurrences_3784.csv (6 lines)
[INFO] [2021-04-19 16:00:52] ...measurements (/app/public/data/vidal_et_al_vida/measurementsorfacts.txt)
[INFO] [2021-04-19 16:00:52] Valid: /app/public/converted_csv/vidal_et_al_vida_measurements_3784.csv (12 lines)
[STOP] [2021-04-19 16:00:52] validate_each_file
[START] [2021-04-19 16:00:52] convert_to_csv
[INFO] [2021-04-19 16:00:52] Looping over 4 formats...
[INFO] [2021-04-19 16:00:52] ...refs (/app/public/data/vidal_et_al_vida/references.tsv)
[CMD] [2021-04-19 16:00:52] /usr/bin/sort /app/public/converted_csv/vidal_et_al_vida_refs_3784.csv > /app/public/converted_csv/vidal_et_al_vida_refs_3784.csv_sorted
[INFO] [2021-04-19 16:00:52] Converted: /app/public/converted_csv/vidal_et_al_vida_refs_3784.csv (0 lines)
[INFO] [2021-04-19 16:00:52] ...nodes (/app/public/data/vidal_et_al_vida/taxa.txt)
[CMD] [2021-04-19 16:00:52] /usr/bin/sort /app/public/converted_csv/vidal_et_al_vida_nodes_3784.csv > /app/public/converted_csv/vidal_et_al_vida_nodes_3784.csv_sorted
[INFO] [2021-04-19 16:00:52] Converted: /app/public/converted_csv/vidal_et_al_vida_nodes_3784.csv (6 lines)
[INFO] [2021-04-19 16:00:52] ...occurrences (/app/public/data/vidal_et_al_vida/occurrences.txt)
[CMD] [2021-04-19 16:00:52] /usr/bin/sort /app/public/converted_csv/vidal_et_al_vida_occurrences_3784.csv > /app/public/converted_csv/vidal_et_al_vida_occurrences_3784.csv_sorted
[INFO] [2021-04-19 16:00:52] Converted: /app/public/converted_csv/vidal_et_al_vida_occurrences_3784.csv (6 lines)
[INFO] [2021-04-19 16:00:52] ...measurements (/app/public/data/vidal_et_al_vida/measurementsorfacts.txt)
[CMD] [2021-04-19 16:00:52] /usr/bin/sort /app/public/converted_csv/vidal_et_al_vida_measurements_3784.csv > /app/public/converted_csv/vidal_et_al_vida_measurements_3784.csv_sorted
[INFO] [2021-04-19 16:00:52] Converted: /app/public/converted_csv/vidal_et_al_vida_measurements_3784.csv (12 lines)
[STOP] [2021-04-19 16:00:52] convert_to_csv
[START] [2021-04-19 16:00:52] calculate_delta
[INFO] [2021-04-19 16:00:52] Looping over 4 formats...
[INFO] [2021-04-19 16:00:52] ...refs (/app/public/data/vidal_et_al_vida/references.tsv)
[CMD] [2021-04-19 16:00:52] echo "0a" > /app/public/diff/vidal_et_al_vida_refs_3784.diff
[CMD] [2021-04-19 16:00:52] tail -n +1 /app/public/converted_csv/vidal_et_al_vida_refs_3784.csv >> /app/public/diff/vidal_et_al_vida_refs_3784.diff
[CMD] [2021-04-19 16:00:52] echo "." >> /app/public/diff/vidal_et_al_vida_refs_3784.diff
[INFO] [2021-04-19 16:00:52] Created diff: /app/public/diff/vidal_et_al_vida_refs_3784.diff (2 lines)
[INFO] [2021-04-19 16:00:52] ...nodes (/app/public/data/vidal_et_al_vida/taxa.txt)
[CMD] [2021-04-19 16:00:52] echo "0a" > /app/public/diff/vidal_et_al_vida_nodes_3784.diff
[CMD] [2021-04-19 16:00:52] tail -n +1 /app/public/converted_csv/vidal_et_al_vida_nodes_3784.csv >> /app/public/diff/vidal_et_al_vida_nodes_3784.diff
[CMD] [2021-04-19 16:00:52] echo "." >> /app/public/diff/vidal_et_al_vida_nodes_3784.diff
[INFO] [2021-04-19 16:00:52] Created diff: /app/public/diff/vidal_et_al_vida_nodes_3784.diff (8 lines)
[INFO] [2021-04-19 16:00:52] ...occurrences (/app/public/data/vidal_et_al_vida/occurrences.txt)
[CMD] [2021-04-19 16:00:52] echo "0a" > /app/public/diff/vidal_et_al_vida_occurrences_3784.diff
[CMD] [2021-04-19 16:00:52] tail -n +1 /app/public/converted_csv/vidal_et_al_vida_occurrences_3784.csv >> /app/public/diff/vidal_et_al_vida_occurrences_3784.diff
[CMD] [2021-04-19 16:00:52] echo "." >> /app/public/diff/vidal_et_al_vida_occurrences_3784.diff
[INFO] [2021-04-19 16:00:52] Created diff: /app/public/diff/vidal_et_al_vida_occurrences_3784.diff (8 lines)
[INFO] [2021-04-19 16:00:52] ...measurements (/app/public/data/vidal_et_al_vida/measurementsorfacts.txt)
[CMD] [2021-04-19 16:00:52] echo "0a" > /app/public/diff/vidal_et_al_vida_measurements_3784.diff
[CMD] [2021-04-19 16:00:52] tail -n +1 /app/public/converted_csv/vidal_et_al_vida_measurements_3784.csv >> /app/public/diff/vidal_et_al_vida_measurements_3784.diff
[CMD] [2021-04-19 16:00:52] echo "." >> /app/public/diff/vidal_et_al_vida_measurements_3784.diff
[INFO] [2021-04-19 16:00:52] Created diff: /app/public/diff/vidal_et_al_vida_measurements_3784.diff (14 lines)
[STOP] [2021-04-19 16:00:52] calculate_delta
[START] [2021-04-19 16:00:52] parse_diff_and_store
[INFO] [2021-04-19 16:00:52] Handling diff: /app/public/diff/vidal_et_al_vida_refs_3784.diff (2 lines)
[INFO] [2021-04-19 16:00:52] Loading refs diff file into memory (2 /app/public/diff/vidal_et_al_vida_refs_3784.diff lines)...
[INFO] [2021-04-19 16:00:52] Handling diff: /app/public/diff/vidal_et_al_vida_nodes_3784.diff (8 lines)
[INFO] [2021-04-19 16:00:52] Loading nodes diff file into memory (8 /app/public/diff/vidal_et_al_vida_nodes_3784.diff lines)...
[INFO] [2021-04-19 16:00:52] Handling diff: /app/public/diff/vidal_et_al_vida_occurrences_3784.diff (8 lines)
[INFO] [2021-04-19 16:00:52] Loading occurrences diff file into memory (8 /app/public/diff/vidal_et_al_vida_occurrences_3784.diff lines)...
[INFO] [2021-04-19 16:00:52] Handling diff: /app/public/diff/vidal_et_al_vida_measurements_3784.diff (14 lines)
[INFO] [2021-04-19 16:00:52] Loading measurements diff file into memory (14 /app/public/diff/vidal_et_al_vida_measurements_3784.diff lines)...
[INFO] [2021-04-19 16:00:52] Storing 6 ScientificNames
[INFO] [2021-04-19 16:00:52] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 16:00:52] Average Time: 0.0
[INFO] [2021-04-19 16:00:52] Total Time: 1s
[INFO] [2021-04-19 16:00:52] Storing 6 Nodes
[INFO] [2021-04-19 16:00:52] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 16:00:52] Average Time: 0.0
[INFO] [2021-04-19 16:00:52] Total Time: 1s
[INFO] [2021-04-19 16:00:52] Storing 6 Occurrences
[INFO] [2021-04-19 16:00:52] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 16:00:52] Average Time: 0.0
[INFO] [2021-04-19 16:00:52] Total Time: 1s
[INFO] [2021-04-19 16:00:52] Storing 12 Traits
[INFO] [2021-04-19 16:00:52] Processing group of 12 in 1 groups of 1000
[INFO] [2021-04-19 16:00:52] Average Time: 0.0
[INFO] [2021-04-19 16:00:52] Total Time: 1s
[INFO] [2021-04-19 16:00:52] Storing 11 MetaTraits
[INFO] [2021-04-19 16:00:52] Processing group of 11 in 1 groups of 1000
[INFO] [2021-04-19 16:00:52] Average Time: 0.0
[INFO] [2021-04-19 16:00:52] Total Time: 1s
[STOP] [2021-04-19 16:00:52] parse_diff_and_store
[START] [2021-04-19 16:00:52] resolve_keys
[INFO] [2021-04-19 16:00:58] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 16:00:58] traits to occurrences...
[INFO] [2021-04-19 16:00:58] traits to nodes (through occurrences)...
[INFO] [2021-04-19 16:00:58] Traits to sex term...
[INFO] [2021-04-19 16:00:58] Traits to lifestage term...
[INFO] [2021-04-19 16:00:58] MetaTraits to traits...
[INFO] [2021-04-19 16:00:58] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 16:00:58] Assocs to occurrences...
[INFO] [2021-04-19 16:00:58] Assocs to nodes...
[INFO] [2021-04-19 16:00:58] Assoc to sex term...
[INFO] [2021-04-19 16:00:58] Assoc to lifestage term...
[INFO] [2021-04-19 16:00:58] MetaAssoc to assocs...
[STOP] [2021-04-19 16:00:58] resolve_keys
[START] [2021-04-19 16:00:58] hold_for_later_1
[STOP] [2021-04-19 16:00:58] hold_for_later_1
[START] [2021-04-19 16:00:58] hold_for_later_2
[STOP] [2021-04-19 16:00:58] hold_for_later_2
[START] [2021-04-19 16:00:58] resolve_missing_parents
[STOP] [2021-04-19 16:00:58] resolve_missing_parents
[START] [2021-04-19 16:00:58] rebuild_nodes
[START] [2021-04-19 16:00:58] Flattener#flatten
[START] [2021-04-19 16:00:58] Flattener#study_resource
[START] [2021-04-19 16:00:58] Flattener#build_ancestry
[STOP] [2021-04-19 16:00:58] Flattener#build_ancestry
[INFO] [2021-04-19 16:00:58] 6 ancestry keys
[START] [2021-04-19 16:00:58] build_node_ancestors
[INFO] [2021-04-19 16:00:58] old ancestors deleted.
[STOP] [2021-04-19 16:00:58] build_node_ancestors
[WARN] [2021-04-19 16:00:58] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 16:00:58] Flattener#flatten
[STOP] [2021-04-19 16:00:58] rebuild_nodes
[START] [2021-04-19 16:00:58] resolve_missing_media_owners
[STOP] [2021-04-19 16:00:58] resolve_missing_media_owners
[START] [2021-04-19 16:00:58] sanitize_media_verbatims
[STOP] [2021-04-19 16:00:58] sanitize_media_verbatims
[START] [2021-04-19 16:00:58] queue_downloads
[STOP] [2021-04-19 16:00:58] queue_downloads
[START] [2021-04-19 16:00:58] parse_names
[WARN] [2021-04-19 16:00:58] I see 6 names which still need to be parsed.
[STOP] [2021-04-19 16:00:59] parse_names
[START] [2021-04-19 16:00:59] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 16:00:59] denormalize_canonical_names_to_nodes
[START] [2021-04-19 16:00:59] match_nodes
[START] [2021-04-19 16:00:59] map_all_nodes_to_pages
[STOP] [2021-04-19 16:00:59] map_all_nodes_to_pages
[INFO] [2021-04-19 16:00:59] ZERO unmatched nodes (of 6)! Nicely done.
[START] [2021-04-19 16:00:59] update_nodes
[STOP] [2021-04-19 16:00:59] update_nodes
[STOP] [2021-04-19 16:00:59] match_nodes
[START] [2021-04-19 16:00:59] reindex_search
[STOP] [2021-04-19 16:01:00] reindex_search
[START] [2021-04-19 16:01:00] normalize_units
[STOP] [2021-04-19 16:01:00] normalize_units
[START] [2021-04-19 16:01:00] calculate_statistics
[2021-04-19 16:01:00] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 16:01:00] calculate_statistics
[START] [2021-04-19 16:01:00] complete_harvest_instance
[START] [2021-04-19 16:01:00] overall_tsv_creation
[INFO] [2021-04-19 16:01:00] Processing group of 6 in 1 batches of 10000
[INFO] [2021-04-19 16:01:36] 6 Traits (unfiltered)...
[INFO] [2021-04-19 16:02:08] 6 Traits (filtered)...
[INFO] [2021-04-19 16:02:08] 0 Associations (filtered)...
[INFO] [2021-04-19 16:02:08] 6 metadata added.
[INFO] [2021-04-19 16:02:08] 0 metadata added.
[INFO] [2021-04-19 16:02:34] Average Time: 70.61
[INFO] [2021-04-19 16:02:34] Total Time: 1m35s
[STOP] [2021-04-19 16:02:34] overall_tsv_creation
[INFO] [2021-04-19 16:02:34] Done. Check your files:
[INFO] [2021-04-19 16:02:34] (6 lines) /app/public/data/vidal_et_al_vida/publish_nodes.tsv
[INFO] [2021-04-19 16:02:34] (6 lines) /app/public/data/vidal_et_al_vida/publish_scientific_names.tsv
[INFO] [2021-04-19 16:02:34] (7 lines) /app/public/data/vidal_et_al_vida/publish_traits.tsv
[INFO] [2021-04-19 16:02:34] (7 lines) /app/public/data/vidal_et_al_vida/publish_metadata.tsv
[STOP] [2021-04-19 16:02:34] complete_harvest_instance
[START] [2021-04-19 16:02:34] completed
[STOP] [2021-04-19 16:02:34] completed
[STOP] [2021-04-19 16:02:34] logged process, took 102.33

Latest Process

19 Apr 16:00 EXITED currently processing 0