Harvest for Hunt et al 2009 Created 19 Apr 17:08

Harvesting Log

# Logfile created on 2021-02-03 10:26:46 -0500 by logger.rb/v1.4.2
[START] [2021-02-03 10:26:46] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 10:26:46] Creating resource from OpenData
[START] [2021-02-03 10:26:46] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 10:26:46] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 10:26:46] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 10:26:46] Creating resource from OpenData
[INFO] [2021-02-03 10:27:42] ## HARVEST: type = -harvest
[START] [2021-02-03 10:27:44] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 10:27:44] create_harvest_instance
[STOP] [2021-02-03 10:27:45] create_harvest_instance
[START] [2021-02-03 10:27:45] fetch_files
[STOP] [2021-02-03 10:27:45] fetch_files
[START] [2021-02-03 10:27:45] validate_each_file
[STOP] [2021-02-03 10:27:45] validate_each_file
[START] [2021-02-03 10:27:45] convert_to_csv
[CMD] [2021-02-03 10:27:45] /usr/bin/sort /app/public/converted_csv/hunt_et_al_hunt__nodes_26569.csv > /app/public/converted_csv/hunt_et_al_hunt__nodes_26569.csv_sorted
[CMD] [2021-02-03 10:27:45] /usr/bin/sort /app/public/converted_csv/hunt_et_al_hunt__occurrences_26570.csv > /app/public/converted_csv/hunt_et_al_hunt__occurrences_26570.csv_sorted
[CMD] [2021-02-03 10:27:45] /usr/bin/sort /app/public/converted_csv/hunt_et_al_hunt__measurements_26571.csv > /app/public/converted_csv/hunt_et_al_hunt__measurements_26571.csv_sorted
[STOP] [2021-02-03 10:27:45] convert_to_csv
[START] [2021-02-03 10:27:45] calculate_delta
[CMD] [2021-02-03 10:27:45] echo "0a" > /app/public/diff/hunt_et_al_hunt__nodes_26569.diff
[CMD] [2021-02-03 10:27:45] tail -n +1 /app/public/converted_csv/hunt_et_al_hunt__nodes_26569.csv >> /app/public/diff/hunt_et_al_hunt__nodes_26569.diff
[CMD] [2021-02-03 10:27:45] echo "." >> /app/public/diff/hunt_et_al_hunt__nodes_26569.diff
[CMD] [2021-02-03 10:27:45] echo "0a" > /app/public/diff/hunt_et_al_hunt__occurrences_26570.diff
[CMD] [2021-02-03 10:27:45] tail -n +1 /app/public/converted_csv/hunt_et_al_hunt__occurrences_26570.csv >> /app/public/diff/hunt_et_al_hunt__occurrences_26570.diff
[CMD] [2021-02-03 10:27:45] echo "." >> /app/public/diff/hunt_et_al_hunt__occurrences_26570.diff
[CMD] [2021-02-03 10:27:45] echo "0a" > /app/public/diff/hunt_et_al_hunt__measurements_26571.diff
[CMD] [2021-02-03 10:27:45] tail -n +1 /app/public/converted_csv/hunt_et_al_hunt__measurements_26571.csv >> /app/public/diff/hunt_et_al_hunt__measurements_26571.diff
[CMD] [2021-02-03 10:27:45] echo "." >> /app/public/diff/hunt_et_al_hunt__measurements_26571.diff
[STOP] [2021-02-03 10:27:45] calculate_delta
[START] [2021-02-03 10:27:45] parse_diff_and_store
[INFO] [2021-02-03 10:27:45] Loading nodes diff file into memory (true lines)...
[INFO] [2021-02-03 10:27:45] Loading occurrences diff file into memory (true lines)...
[INFO] [2021-02-03 10:27:45] Loading measurements diff file into memory (true lines)...
[INFO] [2021-02-03 10:27:46] Storing 9 ScientificNames
[INFO] [2021-02-03 10:27:46] Processing group of 9 in 1 groups of 1000
[INFO] [2021-02-03 10:27:46] Average Time: 0.01
[INFO] [2021-02-03 10:27:46] Total Time: 1s
[INFO] [2021-02-03 10:27:46] Storing 9 Nodes
[INFO] [2021-02-03 10:27:46] Processing group of 9 in 1 groups of 1000
[INFO] [2021-02-03 10:27:46] Average Time: 0.0
[INFO] [2021-02-03 10:27:46] Total Time: 1s
[INFO] [2021-02-03 10:27:46] Storing 9 Occurrences
[INFO] [2021-02-03 10:27:46] Processing group of 9 in 1 groups of 1000
[INFO] [2021-02-03 10:27:46] Average Time: 0.0
[INFO] [2021-02-03 10:27:46] Total Time: 1s
[INFO] [2021-02-03 10:27:46] Storing 17 Traits
[INFO] [2021-02-03 10:27:46] Processing group of 17 in 1 groups of 1000
[INFO] [2021-02-03 10:27:46] Average Time: 0.01
[INFO] [2021-02-03 10:27:46] Total Time: 1s
[INFO] [2021-02-03 10:27:46] Storing 12 MetaTraits
[INFO] [2021-02-03 10:27:46] Processing group of 12 in 1 groups of 1000
[INFO] [2021-02-03 10:27:46] Average Time: 0.0
[INFO] [2021-02-03 10:27:46] Total Time: 1s
[STOP] [2021-02-03 10:27:46] parse_diff_and_store
[START] [2021-02-03 10:27:46] resolve_keys
[INFO] [2021-02-03 10:27:52] Occurrences to nodes (through scientific_names)...
[INFO] [2021-02-03 10:27:52] traits to occurrences...
[INFO] [2021-02-03 10:27:52] traits to nodes (through occurrences)...
[INFO] [2021-02-03 10:27:52] Traits to sex term...
[INFO] [2021-02-03 10:27:52] Traits to lifestage term...
[INFO] [2021-02-03 10:27:52] MetaTraits to traits...
[INFO] [2021-02-03 10:27:52] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-02-03 10:27:52] Assocs to occurrences...
[INFO] [2021-02-03 10:27:52] Assocs to nodes...
[INFO] [2021-02-03 10:27:52] Assoc to sex term...
[INFO] [2021-02-03 10:27:52] Assoc to lifestage term...
[INFO] [2021-02-03 10:27:52] MetaAssoc to assocs...
[STOP] [2021-02-03 10:27:52] resolve_keys
[START] [2021-02-03 10:27:52] hold_for_later_1
[STOP] [2021-02-03 10:27:52] hold_for_later_1
[START] [2021-02-03 10:27:52] hold_for_later_2
[STOP] [2021-02-03 10:27:52] hold_for_later_2
[START] [2021-02-03 10:27:52] resolve_missing_parents
[STOP] [2021-02-03 10:27:52] resolve_missing_parents
[START] [2021-02-03 10:27:52] rebuild_nodes
[START] [2021-02-03 10:27:52] Flattener#flatten
[START] [2021-02-03 10:27:52] Flattener#study_resource
[START] [2021-02-03 10:27:52] Flattener#build_ancestry
[STOP] [2021-02-03 10:27:52] Flattener#build_ancestry
[INFO] [2021-02-03 10:27:52] 9 ancestry keys
[START] [2021-02-03 10:27:52] build_node_ancestors
[INFO] [2021-02-03 10:27:52] old ancestors deleted.
[STOP] [2021-02-03 10:27:52] build_node_ancestors
[WARN] [2021-02-03 10:27:52] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-02-03 10:27:52] Flattener#flatten
[STOP] [2021-02-03 10:27:52] rebuild_nodes
[START] [2021-02-03 10:27:52] resolve_missing_media_owners
[STOP] [2021-02-03 10:27:52] resolve_missing_media_owners
[START] [2021-02-03 10:27:52] sanitize_media_verbatims
[STOP] [2021-02-03 10:27:52] sanitize_media_verbatims
[START] [2021-02-03 10:27:52] queue_downloads
[STOP] [2021-02-03 10:27:52] queue_downloads
[START] [2021-02-03 10:27:52] parse_names
[WARN] [2021-02-03 10:27:52] I see 9 names which still need to be parsed.
[STOP] [2021-02-03 10:27:53] parse_names
[START] [2021-02-03 10:27:53] denormalize_canonical_names_to_nodes
[STOP] [2021-02-03 10:27:53] denormalize_canonical_names_to_nodes
[START] [2021-02-03 10:27:53] match_nodes
[START] [2021-02-03 10:27:53] map_all_nodes_to_pages
[STOP] [2021-02-03 10:27:53] map_all_nodes_to_pages
[INFO] [2021-02-03 10:27:53] ZERO unmatched nodes (of 9)! Nicely done.
[START] [2021-02-03 10:27:53] update_nodes
[STOP] [2021-02-03 10:27:53] update_nodes
[STOP] [2021-02-03 10:27:53] match_nodes
[START] [2021-02-03 10:27:53] reindex_search
[STOP] [2021-02-03 10:27:53] reindex_search
[START] [2021-02-03 10:27:53] normalize_units
[STOP] [2021-02-03 10:27:53] normalize_units
[START] [2021-02-03 10:27:53] calculate_statistics
[2021-02-03 10:27:53] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-02-03 10:27:53] calculate_statistics
[START] [2021-02-03 10:27:53] complete_harvest_instance
[START] [2021-02-03 10:27:53] overall_tsv_creation
[INFO] [2021-02-03 10:27:54] Processing group of 9 in 1 batches of 10000
[INFO] [2021-02-03 10:28:33] 9 Traits (unfiltered)...
[INFO] [2021-02-03 10:29:10] 9 Traits (filtered)...
[INFO] [2021-02-03 10:29:10] 0 Associations (filtered)...
[INFO] [2021-02-03 10:29:10] 20 metadata added.
[INFO] [2021-02-03 10:29:10] 0 metadata added.
[INFO] [2021-02-03 10:29:42] Average Time: 82.19
[INFO] [2021-02-03 10:29:42] Total Time: 1m49s
[STOP] [2021-02-03 10:29:42] overall_tsv_creation
[INFO] [2021-02-03 10:29:42] Done. Check your files:
[INFO] [2021-02-03 10:29:42] (9 lines) /app/public/data/hunt_et_al_hunt_/publish_nodes.tsv
[INFO] [2021-02-03 10:29:42] (9 lines) /app/public/data/hunt_et_al_hunt_/publish_scientific_names.tsv
[INFO] [2021-02-03 10:29:42] (10 lines) /app/public/data/hunt_et_al_hunt_/publish_traits.tsv
[INFO] [2021-02-03 10:29:42] (21 lines) /app/public/data/hunt_et_al_hunt_/publish_metadata.tsv
[STOP] [2021-02-03 10:29:42] complete_harvest_instance
[START] [2021-02-03 10:29:42] completed
[STOP] [2021-02-03 10:29:42] completed
[STOP] [2021-02-03 10:29:42] logged process, took 117.91
[INFO] [2021-04-19 16:54:25] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 17:08:28] ## remove_type: ScientificName
[INFO] [2021-04-19 17:08:28] ++ Calling delete_all on 9 instances...
[INFO] [2021-04-19 17:08:29] [17:08:29.000] Removed 9 Scientificnames
[INFO] [2021-04-19 17:08:29] ## remove_type: Vernacular
[INFO] [2021-04-19 17:08:29] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:08:29] [17:08:29.002] Removed 0 Vernaculars
[INFO] [2021-04-19 17:08:29] ## remove_type: Article
[INFO] [2021-04-19 17:08:29] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:08:29] [17:08:29.003] Removed 0 Articles
[INFO] [2021-04-19 17:08:29] ## remove_type: Medium
[INFO] [2021-04-19 17:08:29] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:08:29] [17:08:29.005] Removed 0 Media
[INFO] [2021-04-19 17:08:29] ## remove_type: Trait
[INFO] [2021-04-19 17:08:29] ++ Calling delete_all on 17 instances...
[INFO] [2021-04-19 17:08:29] [17:08:29.008] Removed 17 Traits
[INFO] [2021-04-19 17:08:29] ## remove_type: MetaTrait
[INFO] [2021-04-19 17:08:29] ++ Calling delete_all on 12 instances...
[INFO] [2021-04-19 17:08:29] [17:08:29.010] Removed 12 Metatraits
[INFO] [2021-04-19 17:08:29] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 17:08:29] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:08:29] [17:08:29.012] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 17:08:29] ## remove_type: Assoc
[INFO] [2021-04-19 17:08:29] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:08:29] [17:08:29.013] Removed 0 Assocs
[INFO] [2021-04-19 17:08:29] ## remove_type: MetaAssoc
[INFO] [2021-04-19 17:08:29] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:08:29] [17:08:29.015] Removed 0 Metaassocs
[INFO] [2021-04-19 17:08:29] ## remove_type: Identifier
[INFO] [2021-04-19 17:08:29] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:08:29] [17:08:29.016] Removed 0 Identifiers
[INFO] [2021-04-19 17:08:29] ## remove_type: Reference
[INFO] [2021-04-19 17:08:29] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:08:29] [17:08:29.017] Removed 0 References
[INFO] [2021-04-19 17:08:29] Starting batch with ID 87728754...
[INFO] [2021-04-19 17:08:29] Starting batch with ID 87728754...
[INFO] [2021-04-19 17:08:29] Starting batch with ID 87728754...
[INFO] [2021-04-19 17:08:29] Starting batch with ID 87728754...
[INFO] [2021-04-19 17:08:29] Starting batch with ID 87728754...
[INFO] [2021-04-19 17:08:29] Starting batch with ID 87728754...
[INFO] [2021-04-19 17:08:29] Starting batch with ID 87728754...
[INFO] [2021-04-19 17:08:29] Starting batch with ID 87728754...
[INFO] [2021-04-19 17:08:29] Starting batch with ID 87728754...
[INFO] [2021-04-19 17:08:29] Starting batch with ID 87728754...
[INFO] [2021-04-19 17:08:29] Starting batch with ID 87728754...
[INFO] [2021-04-19 17:08:29] ## remove_type: Node
[INFO] [2021-04-19 17:08:29] ++ Calling delete_all on 9 instances...
[INFO] [2021-04-19 17:08:29] [17:08:29.219] Removed 9 Nodes
[START] [2021-04-19 17:08:29] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:08:29] Creating resource from OpenData
[START] [2021-04-19 17:08:29] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:08:29] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 17:08:29] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 17:08:29] Creating resource from OpenData
[START] [2021-04-19 17:08:29] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:08:29] create_harvest_instance
[INFO] [2021-04-19 17:08:29] Created harvest instance #3817
[STOP] [2021-04-19 17:08:29] create_harvest_instance
[START] [2021-04-19 17:08:29] fetch_files
[STOP] [2021-04-19 17:08:29] fetch_files
[START] [2021-04-19 17:08:29] validate_each_file
[INFO] [2021-04-19 17:08:29] Looping over 3 formats...
[INFO] [2021-04-19 17:08:29] ...nodes (/app/public/data/hunt_et_al_hunt_/taxa.txt)
[INFO] [2021-04-19 17:08:29] Valid: /app/public/converted_csv/hunt_et_al_hunt__nodes_3817.csv (9 lines)
[INFO] [2021-04-19 17:08:29] ...occurrences (/app/public/data/hunt_et_al_hunt_/occurrences.txt)
[INFO] [2021-04-19 17:08:29] Valid: /app/public/converted_csv/hunt_et_al_hunt__occurrences_3817.csv (9 lines)
[INFO] [2021-04-19 17:08:29] ...measurements (/app/public/data/hunt_et_al_hunt_/measurementsorfacts.txt)
[INFO] [2021-04-19 17:08:29] Valid: /app/public/converted_csv/hunt_et_al_hunt__measurements_3817.csv (17 lines)
[STOP] [2021-04-19 17:08:29] validate_each_file
[START] [2021-04-19 17:08:29] convert_to_csv
[INFO] [2021-04-19 17:08:29] Looping over 3 formats...
[INFO] [2021-04-19 17:08:29] ...nodes (/app/public/data/hunt_et_al_hunt_/taxa.txt)
[CMD] [2021-04-19 17:08:29] /usr/bin/sort /app/public/converted_csv/hunt_et_al_hunt__nodes_3817.csv > /app/public/converted_csv/hunt_et_al_hunt__nodes_3817.csv_sorted
[INFO] [2021-04-19 17:08:29] Converted: /app/public/converted_csv/hunt_et_al_hunt__nodes_3817.csv (9 lines)
[INFO] [2021-04-19 17:08:29] ...occurrences (/app/public/data/hunt_et_al_hunt_/occurrences.txt)
[CMD] [2021-04-19 17:08:29] /usr/bin/sort /app/public/converted_csv/hunt_et_al_hunt__occurrences_3817.csv > /app/public/converted_csv/hunt_et_al_hunt__occurrences_3817.csv_sorted
[INFO] [2021-04-19 17:08:29] Converted: /app/public/converted_csv/hunt_et_al_hunt__occurrences_3817.csv (9 lines)
[INFO] [2021-04-19 17:08:29] ...measurements (/app/public/data/hunt_et_al_hunt_/measurementsorfacts.txt)
[CMD] [2021-04-19 17:08:29] /usr/bin/sort /app/public/converted_csv/hunt_et_al_hunt__measurements_3817.csv > /app/public/converted_csv/hunt_et_al_hunt__measurements_3817.csv_sorted
[INFO] [2021-04-19 17:08:29] Converted: /app/public/converted_csv/hunt_et_al_hunt__measurements_3817.csv (17 lines)
[STOP] [2021-04-19 17:08:29] convert_to_csv
[START] [2021-04-19 17:08:29] calculate_delta
[INFO] [2021-04-19 17:08:29] Looping over 3 formats...
[INFO] [2021-04-19 17:08:29] ...nodes (/app/public/data/hunt_et_al_hunt_/taxa.txt)
[CMD] [2021-04-19 17:08:29] echo "0a" > /app/public/diff/hunt_et_al_hunt__nodes_3817.diff
[CMD] [2021-04-19 17:08:29] tail -n +1 /app/public/converted_csv/hunt_et_al_hunt__nodes_3817.csv >> /app/public/diff/hunt_et_al_hunt__nodes_3817.diff
[CMD] [2021-04-19 17:08:29] echo "." >> /app/public/diff/hunt_et_al_hunt__nodes_3817.diff
[INFO] [2021-04-19 17:08:29] Created diff: /app/public/diff/hunt_et_al_hunt__nodes_3817.diff (11 lines)
[INFO] [2021-04-19 17:08:29] ...occurrences (/app/public/data/hunt_et_al_hunt_/occurrences.txt)
[CMD] [2021-04-19 17:08:29] echo "0a" > /app/public/diff/hunt_et_al_hunt__occurrences_3817.diff
[CMD] [2021-04-19 17:08:29] tail -n +1 /app/public/converted_csv/hunt_et_al_hunt__occurrences_3817.csv >> /app/public/diff/hunt_et_al_hunt__occurrences_3817.diff
[CMD] [2021-04-19 17:08:29] echo "." >> /app/public/diff/hunt_et_al_hunt__occurrences_3817.diff
[INFO] [2021-04-19 17:08:29] Created diff: /app/public/diff/hunt_et_al_hunt__occurrences_3817.diff (11 lines)
[INFO] [2021-04-19 17:08:29] ...measurements (/app/public/data/hunt_et_al_hunt_/measurementsorfacts.txt)
[CMD] [2021-04-19 17:08:29] echo "0a" > /app/public/diff/hunt_et_al_hunt__measurements_3817.diff
[CMD] [2021-04-19 17:08:29] tail -n +1 /app/public/converted_csv/hunt_et_al_hunt__measurements_3817.csv >> /app/public/diff/hunt_et_al_hunt__measurements_3817.diff
[CMD] [2021-04-19 17:08:29] echo "." >> /app/public/diff/hunt_et_al_hunt__measurements_3817.diff
[INFO] [2021-04-19 17:08:29] Created diff: /app/public/diff/hunt_et_al_hunt__measurements_3817.diff (19 lines)
[STOP] [2021-04-19 17:08:29] calculate_delta
[START] [2021-04-19 17:08:29] parse_diff_and_store
[INFO] [2021-04-19 17:08:29] Handling diff: /app/public/diff/hunt_et_al_hunt__nodes_3817.diff (11 lines)
[INFO] [2021-04-19 17:08:29] Loading nodes diff file into memory (11 /app/public/diff/hunt_et_al_hunt__nodes_3817.diff lines)...
[INFO] [2021-04-19 17:08:29] Handling diff: /app/public/diff/hunt_et_al_hunt__occurrences_3817.diff (11 lines)
[INFO] [2021-04-19 17:08:29] Loading occurrences diff file into memory (11 /app/public/diff/hunt_et_al_hunt__occurrences_3817.diff lines)...
[INFO] [2021-04-19 17:08:29] Handling diff: /app/public/diff/hunt_et_al_hunt__measurements_3817.diff (19 lines)
[INFO] [2021-04-19 17:08:29] Loading measurements diff file into memory (19 /app/public/diff/hunt_et_al_hunt__measurements_3817.diff lines)...
[INFO] [2021-04-19 17:08:29] Storing 9 ScientificNames
[INFO] [2021-04-19 17:08:29] Processing group of 9 in 1 groups of 1000
[INFO] [2021-04-19 17:08:29] Average Time: 0.0
[INFO] [2021-04-19 17:08:29] Total Time: 1s
[INFO] [2021-04-19 17:08:29] Storing 9 Nodes
[INFO] [2021-04-19 17:08:29] Processing group of 9 in 1 groups of 1000
[INFO] [2021-04-19 17:08:29] Average Time: 0.0
[INFO] [2021-04-19 17:08:29] Total Time: 1s
[INFO] [2021-04-19 17:08:29] Storing 9 Occurrences
[INFO] [2021-04-19 17:08:29] Processing group of 9 in 1 groups of 1000
[INFO] [2021-04-19 17:08:29] Average Time: 0.0
[INFO] [2021-04-19 17:08:29] Total Time: 1s
[INFO] [2021-04-19 17:08:29] Storing 17 Traits
[INFO] [2021-04-19 17:08:29] Processing group of 17 in 1 groups of 1000
[INFO] [2021-04-19 17:08:29] Average Time: 0.01
[INFO] [2021-04-19 17:08:29] Total Time: 1s
[INFO] [2021-04-19 17:08:29] Storing 12 MetaTraits
[INFO] [2021-04-19 17:08:29] Processing group of 12 in 1 groups of 1000
[INFO] [2021-04-19 17:08:30] Average Time: 0.0
[INFO] [2021-04-19 17:08:30] Total Time: 1s
[STOP] [2021-04-19 17:08:30] parse_diff_and_store
[START] [2021-04-19 17:08:30] resolve_keys
[INFO] [2021-04-19 17:08:35] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 17:08:35] traits to occurrences...
[INFO] [2021-04-19 17:08:35] traits to nodes (through occurrences)...
[INFO] [2021-04-19 17:08:35] Traits to sex term...
[INFO] [2021-04-19 17:08:35] Traits to lifestage term...
[INFO] [2021-04-19 17:08:35] MetaTraits to traits...
[INFO] [2021-04-19 17:08:35] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 17:08:35] Assocs to occurrences...
[INFO] [2021-04-19 17:08:35] Assocs to nodes...
[INFO] [2021-04-19 17:08:35] Assoc to sex term...
[INFO] [2021-04-19 17:08:35] Assoc to lifestage term...
[INFO] [2021-04-19 17:08:35] MetaAssoc to assocs...
[STOP] [2021-04-19 17:08:35] resolve_keys
[START] [2021-04-19 17:08:35] hold_for_later_1
[STOP] [2021-04-19 17:08:35] hold_for_later_1
[START] [2021-04-19 17:08:35] hold_for_later_2
[STOP] [2021-04-19 17:08:35] hold_for_later_2
[START] [2021-04-19 17:08:35] resolve_missing_parents
[STOP] [2021-04-19 17:08:35] resolve_missing_parents
[START] [2021-04-19 17:08:35] rebuild_nodes
[START] [2021-04-19 17:08:35] Flattener#flatten
[START] [2021-04-19 17:08:35] Flattener#study_resource
[START] [2021-04-19 17:08:35] Flattener#build_ancestry
[STOP] [2021-04-19 17:08:35] Flattener#build_ancestry
[INFO] [2021-04-19 17:08:35] 9 ancestry keys
[START] [2021-04-19 17:08:35] build_node_ancestors
[INFO] [2021-04-19 17:08:35] old ancestors deleted.
[STOP] [2021-04-19 17:08:35] build_node_ancestors
[WARN] [2021-04-19 17:08:35] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 17:08:35] Flattener#flatten
[STOP] [2021-04-19 17:08:35] rebuild_nodes
[START] [2021-04-19 17:08:35] resolve_missing_media_owners
[STOP] [2021-04-19 17:08:35] resolve_missing_media_owners
[START] [2021-04-19 17:08:35] sanitize_media_verbatims
[STOP] [2021-04-19 17:08:35] sanitize_media_verbatims
[START] [2021-04-19 17:08:35] queue_downloads
[STOP] [2021-04-19 17:08:35] queue_downloads
[START] [2021-04-19 17:08:35] parse_names
[WARN] [2021-04-19 17:08:35] I see 9 names which still need to be parsed.
[STOP] [2021-04-19 17:08:37] parse_names
[START] [2021-04-19 17:08:37] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 17:08:37] denormalize_canonical_names_to_nodes
[START] [2021-04-19 17:08:37] match_nodes
[START] [2021-04-19 17:08:37] map_all_nodes_to_pages
[STOP] [2021-04-19 17:08:37] map_all_nodes_to_pages
[INFO] [2021-04-19 17:08:37] ZERO unmatched nodes (of 9)! Nicely done.
[START] [2021-04-19 17:08:37] update_nodes
[STOP] [2021-04-19 17:08:37] update_nodes
[STOP] [2021-04-19 17:08:37] match_nodes
[START] [2021-04-19 17:08:37] reindex_search
[STOP] [2021-04-19 17:08:37] reindex_search
[START] [2021-04-19 17:08:37] normalize_units
[STOP] [2021-04-19 17:08:37] normalize_units
[START] [2021-04-19 17:08:37] calculate_statistics
[2021-04-19 17:08:37] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 17:08:37] calculate_statistics
[START] [2021-04-19 17:08:37] complete_harvest_instance
[START] [2021-04-19 17:08:37] overall_tsv_creation
[INFO] [2021-04-19 17:08:37] Processing group of 9 in 1 batches of 10000
[INFO] [2021-04-19 17:09:13] 9 Traits (unfiltered)...
[INFO] [2021-04-19 17:09:46] 9 Traits (filtered)...
[INFO] [2021-04-19 17:09:46] 0 Associations (filtered)...
[INFO] [2021-04-19 17:09:46] 8 metadata added.
[INFO] [2021-04-19 17:09:46] 0 metadata added.
[INFO] [2021-04-19 17:10:12] Average Time: 71.66
[INFO] [2021-04-19 17:10:12] Total Time: 1m36s
[STOP] [2021-04-19 17:10:12] overall_tsv_creation
[INFO] [2021-04-19 17:10:12] Done. Check your files:
[INFO] [2021-04-19 17:10:12] (9 lines) /app/public/data/hunt_et_al_hunt_/publish_nodes.tsv
[INFO] [2021-04-19 17:10:12] (9 lines) /app/public/data/hunt_et_al_hunt_/publish_scientific_names.tsv
[INFO] [2021-04-19 17:10:12] (10 lines) /app/public/data/hunt_et_al_hunt_/publish_traits.tsv
[INFO] [2021-04-19 17:10:12] (9 lines) /app/public/data/hunt_et_al_hunt_/publish_metadata.tsv
[STOP] [2021-04-19 17:10:12] complete_harvest_instance
[START] [2021-04-19 17:10:12] completed
[STOP] [2021-04-19 17:10:12] completed
[STOP] [2021-04-19 17:10:12] logged process, took 103.16

Latest Process

19 Apr 17:08 EXITED currently processing 0