Harvest for McLay 2007 Created 19 Apr 15:35

Harvesting Log

# Logfile created on 2020-08-27 15:42:49 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:42:49] logged process
[START] [2020-08-27 15:42:49] Creating resource from OpenData
[START] [2020-08-27 15:42:50] logged process
[START] [2020-08-27 15:42:50] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:42:50] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:42:50] Creating resource from OpenData
[INFO] [2020-12-03 11:29:15] ## HARVEST: type = -harvest
[START] [2020-12-03 11:29:19] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-03 11:29:19] create_harvest_instance
[STOP] [2020-12-03 11:29:21] create_harvest_instance
[START] [2020-12-03 11:29:21] fetch_files
[STOP] [2020-12-03 11:29:21] fetch_files
[START] [2020-12-03 11:29:21] validate_each_file
[STOP] [2020-12-03 11:29:21] validate_each_file
[START] [2020-12-03 11:29:21] convert_to_csv
[CMD] [2020-12-03 11:29:21] /usr/bin/sort /app/public/converted_csv/mc_lay_mclay_200_refs_24816.csv > /app/public/converted_csv/mc_lay_mclay_200_refs_24816.csv_sorted
[CMD] [2020-12-03 11:29:21] /usr/bin/sort /app/public/converted_csv/mc_lay_mclay_200_nodes_24817.csv > /app/public/converted_csv/mc_lay_mclay_200_nodes_24817.csv_sorted
[CMD] [2020-12-03 11:29:21] /usr/bin/sort /app/public/converted_csv/mc_lay_mclay_200_occurrences_24818.csv > /app/public/converted_csv/mc_lay_mclay_200_occurrences_24818.csv_sorted
[CMD] [2020-12-03 11:29:21] /usr/bin/sort /app/public/converted_csv/mc_lay_mclay_200_measurements_24819.csv > /app/public/converted_csv/mc_lay_mclay_200_measurements_24819.csv_sorted
[STOP] [2020-12-03 11:29:21] convert_to_csv
[START] [2020-12-03 11:29:21] calculate_delta
[CMD] [2020-12-03 11:29:21] echo "0a" > /app/public/diff/mc_lay_mclay_200_refs_24816.diff
[CMD] [2020-12-03 11:29:21] tail -n +1 /app/public/converted_csv/mc_lay_mclay_200_refs_24816.csv >> /app/public/diff/mc_lay_mclay_200_refs_24816.diff
[CMD] [2020-12-03 11:29:21] echo "." >> /app/public/diff/mc_lay_mclay_200_refs_24816.diff
[CMD] [2020-12-03 11:29:21] echo "0a" > /app/public/diff/mc_lay_mclay_200_nodes_24817.diff
[CMD] [2020-12-03 11:29:21] tail -n +1 /app/public/converted_csv/mc_lay_mclay_200_nodes_24817.csv >> /app/public/diff/mc_lay_mclay_200_nodes_24817.diff
[CMD] [2020-12-03 11:29:21] echo "." >> /app/public/diff/mc_lay_mclay_200_nodes_24817.diff
[CMD] [2020-12-03 11:29:21] echo "0a" > /app/public/diff/mc_lay_mclay_200_occurrences_24818.diff
[CMD] [2020-12-03 11:29:21] tail -n +1 /app/public/converted_csv/mc_lay_mclay_200_occurrences_24818.csv >> /app/public/diff/mc_lay_mclay_200_occurrences_24818.diff
[CMD] [2020-12-03 11:29:21] echo "." >> /app/public/diff/mc_lay_mclay_200_occurrences_24818.diff
[CMD] [2020-12-03 11:29:21] echo "0a" > /app/public/diff/mc_lay_mclay_200_measurements_24819.diff
[CMD] [2020-12-03 11:29:21] tail -n +1 /app/public/converted_csv/mc_lay_mclay_200_measurements_24819.csv >> /app/public/diff/mc_lay_mclay_200_measurements_24819.diff
[CMD] [2020-12-03 11:29:21] echo "." >> /app/public/diff/mc_lay_mclay_200_measurements_24819.diff
[STOP] [2020-12-03 11:29:21] calculate_delta
[START] [2020-12-03 11:29:21] parse_diff_and_store
[INFO] [2020-12-03 11:29:21] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 11:29:21] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 11:29:21] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 11:29:21] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 11:29:22] Storing 2 ScientificNames
[INFO] [2020-12-03 11:29:22] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 11:29:22] Average Time: 0.01
[INFO] [2020-12-03 11:29:22] Total Time: 1s
[INFO] [2020-12-03 11:29:22] Storing 2 Nodes
[INFO] [2020-12-03 11:29:22] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 11:29:22] Average Time: 0.0
[INFO] [2020-12-03 11:29:22] Total Time: 1s
[INFO] [2020-12-03 11:29:22] Storing 2 Occurrences
[INFO] [2020-12-03 11:29:22] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 11:29:22] Average Time: 0.0
[INFO] [2020-12-03 11:29:22] Total Time: 1s
[INFO] [2020-12-03 11:29:22] Storing 4 Traits
[INFO] [2020-12-03 11:29:22] Processing group of 4 in 1 groups of 1000
[INFO] [2020-12-03 11:29:22] Average Time: 0.0
[INFO] [2020-12-03 11:29:22] Total Time: 1s
[INFO] [2020-12-03 11:29:22] Storing 2 MetaTraits
[INFO] [2020-12-03 11:29:22] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 11:29:22] Average Time: 0.0
[INFO] [2020-12-03 11:29:22] Total Time: 1s
[STOP] [2020-12-03 11:29:22] parse_diff_and_store
[START] [2020-12-03 11:29:22] resolve_keys
[INFO] [2020-12-03 11:29:28] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 11:29:28] traits to occurrences...
[INFO] [2020-12-03 11:29:28] traits to nodes (through occurrences)...
[INFO] [2020-12-03 11:29:28] Traits to sex term...
[INFO] [2020-12-03 11:29:28] Traits to lifestage term...
[INFO] [2020-12-03 11:29:28] MetaTraits to traits...
[INFO] [2020-12-03 11:29:28] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 11:29:28] Assocs to occurrences...
[INFO] [2020-12-03 11:29:28] Assocs to nodes...
[INFO] [2020-12-03 11:29:28] Assoc to sex term...
[INFO] [2020-12-03 11:29:28] Assoc to lifestage term...
[INFO] [2020-12-03 11:29:28] MetaAssoc to assocs...
[STOP] [2020-12-03 11:29:28] resolve_keys
[START] [2020-12-03 11:29:28] hold_for_later_1
[STOP] [2020-12-03 11:29:28] hold_for_later_1
[START] [2020-12-03 11:29:28] hold_for_later_2
[STOP] [2020-12-03 11:29:28] hold_for_later_2
[START] [2020-12-03 11:29:28] resolve_missing_parents
[STOP] [2020-12-03 11:29:28] resolve_missing_parents
[START] [2020-12-03 11:29:28] rebuild_nodes
[START] [2020-12-03 11:29:28] Flattener#flatten
[START] [2020-12-03 11:29:28] Flattener#study_resource
[START] [2020-12-03 11:29:28] Flattener#build_ancestry
[STOP] [2020-12-03 11:29:28] Flattener#build_ancestry
[INFO] [2020-12-03 11:29:28] 2 ancestry keys
[START] [2020-12-03 11:29:28] build_node_ancestors
[INFO] [2020-12-03 11:29:28] old ancestors deleted.
[STOP] [2020-12-03 11:29:28] build_node_ancestors
[WARN] [2020-12-03 11:29:28] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 11:29:28] Flattener#flatten
[STOP] [2020-12-03 11:29:28] rebuild_nodes
[START] [2020-12-03 11:29:28] resolve_missing_media_owners
[STOP] [2020-12-03 11:29:28] resolve_missing_media_owners
[START] [2020-12-03 11:29:28] sanitize_media_verbatims
[STOP] [2020-12-03 11:29:28] sanitize_media_verbatims
[START] [2020-12-03 11:29:28] queue_downloads
[STOP] [2020-12-03 11:29:28] queue_downloads
[START] [2020-12-03 11:29:28] parse_names
[WARN] [2020-12-03 11:29:28] I see 2 names which still need to be parsed.
[STOP] [2020-12-03 11:29:29] parse_names
[START] [2020-12-03 11:29:29] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 11:29:29] denormalize_canonical_names_to_nodes
[START] [2020-12-03 11:29:29] match_nodes
[START] [2020-12-03 11:29:29] map_all_nodes_to_pages
[STOP] [2020-12-03 11:29:29] map_all_nodes_to_pages
[INFO] [2020-12-03 11:29:29] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2020-12-03 11:29:29] update_nodes
[STOP] [2020-12-03 11:29:29] update_nodes
[STOP] [2020-12-03 11:29:29] match_nodes
[START] [2020-12-03 11:29:29] reindex_search
[STOP] [2020-12-03 11:29:29] reindex_search
[START] [2020-12-03 11:29:29] normalize_units
[STOP] [2020-12-03 11:29:29] normalize_units
[START] [2020-12-03 11:29:29] calculate_statistics
[2020-12-03 11:29:29] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 11:29:29] calculate_statistics
[START] [2020-12-03 11:29:29] complete_harvest_instance
[START] [2020-12-03 11:29:29] overall_tsv_creation
[INFO] [2020-12-03 11:29:29] Processing group of 2 in 1 batches of 10000
[INFO] [2020-12-03 11:30:08] 2 Traits (unfiltered)...
[INFO] [2020-12-03 11:30:45] 2 Traits (filtered)...
[INFO] [2020-12-03 11:30:45] 0 Associations (filtered)...
[INFO] [2020-12-03 11:30:45] 4 metadata added.
[INFO] [2020-12-03 11:30:45] 0 metadata added.
[INFO] [2020-12-03 11:30:45] Average Time: 53.37
[INFO] [2020-12-03 11:30:45] Total Time: 1m16s
[STOP] [2020-12-03 11:30:45] overall_tsv_creation
[INFO] [2020-12-03 11:30:45] Done. Check your files:
[INFO] [2020-12-03 11:30:45] (2 lines) /app/public/data/mc_lay_mclay_200/publish_nodes.tsv
[INFO] [2020-12-03 11:30:45] (2 lines) /app/public/data/mc_lay_mclay_200/publish_scientific_names.tsv
[INFO] [2020-12-03 11:30:45] (3 lines) /app/public/data/mc_lay_mclay_200/publish_traits.tsv
[INFO] [2020-12-03 11:30:45] (5 lines) /app/public/data/mc_lay_mclay_200/publish_metadata.tsv
[STOP] [2020-12-03 11:30:45] complete_harvest_instance
[START] [2020-12-03 11:30:45] completed
[STOP] [2020-12-03 11:30:45] completed
[STOP] [2020-12-03 11:30:45] logged process, took 85.79
[INFO] [2021-04-19 15:17:24] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:35:22] ## remove_type: ScientificName
[INFO] [2021-04-19 15:35:22] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:35:22] [15:35:22.242] Removed 2 Scientificnames
[INFO] [2021-04-19 15:35:22] ## remove_type: Vernacular
[INFO] [2021-04-19 15:35:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:35:22] [15:35:22.244] Removed 0 Vernaculars
[INFO] [2021-04-19 15:35:22] ## remove_type: Article
[INFO] [2021-04-19 15:35:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:35:22] [15:35:22.245] Removed 0 Articles
[INFO] [2021-04-19 15:35:22] ## remove_type: Medium
[INFO] [2021-04-19 15:35:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:35:22] [15:35:22.246] Removed 0 Media
[INFO] [2021-04-19 15:35:22] ## remove_type: Trait
[INFO] [2021-04-19 15:35:22] ++ Calling delete_all on 4 instances...
[INFO] [2021-04-19 15:35:22] [15:35:22.249] Removed 4 Traits
[INFO] [2021-04-19 15:35:22] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:35:22] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:35:22] [15:35:22.250] Removed 2 Metatraits
[INFO] [2021-04-19 15:35:22] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:35:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:35:22] [15:35:22.252] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 15:35:22] ## remove_type: Assoc
[INFO] [2021-04-19 15:35:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:35:22] [15:35:22.253] Removed 0 Assocs
[INFO] [2021-04-19 15:35:22] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:35:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:35:22] [15:35:22.255] Removed 0 Metaassocs
[INFO] [2021-04-19 15:35:22] ## remove_type: Identifier
[INFO] [2021-04-19 15:35:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:35:22] [15:35:22.257] Removed 0 Identifiers
[INFO] [2021-04-19 15:35:22] ## remove_type: Reference
[INFO] [2021-04-19 15:35:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:35:22] [15:35:22.258] Removed 0 References
[INFO] [2021-04-19 15:35:22] Starting batch with ID 86115919...
[INFO] [2021-04-19 15:35:22] Starting batch with ID 86115919...
[INFO] [2021-04-19 15:35:22] Starting batch with ID 86115919...
[INFO] [2021-04-19 15:35:22] Starting batch with ID 86115919...
[INFO] [2021-04-19 15:35:22] ## remove_type: Node
[INFO] [2021-04-19 15:35:22] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:35:22] [15:35:22.299] Removed 2 Nodes
[START] [2021-04-19 15:35:22] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:35:22] Creating resource from OpenData
[START] [2021-04-19 15:35:22] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:35:22] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:35:22] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:35:22] Creating resource from OpenData
[START] [2021-04-19 15:35:22] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:35:22] create_harvest_instance
[INFO] [2021-04-19 15:35:22] Created harvest instance #3771
[STOP] [2021-04-19 15:35:22] create_harvest_instance
[START] [2021-04-19 15:35:22] fetch_files
[STOP] [2021-04-19 15:35:22] fetch_files
[START] [2021-04-19 15:35:22] validate_each_file
[INFO] [2021-04-19 15:35:22] Looping over 4 formats...
[INFO] [2021-04-19 15:35:22] ...refs (/app/public/data/mc_lay_mclay_200/references.tsv)
[INFO] [2021-04-19 15:35:22] Valid: /app/public/converted_csv/mc_lay_mclay_200_refs_3771.csv (0 lines)
[INFO] [2021-04-19 15:35:22] ...nodes (/app/public/data/mc_lay_mclay_200/taxa.txt)
[INFO] [2021-04-19 15:35:22] Valid: /app/public/converted_csv/mc_lay_mclay_200_nodes_3771.csv (2 lines)
[INFO] [2021-04-19 15:35:22] ...occurrences (/app/public/data/mc_lay_mclay_200/occurrences.txt)
[INFO] [2021-04-19 15:35:22] Valid: /app/public/converted_csv/mc_lay_mclay_200_occurrences_3771.csv (2 lines)
[INFO] [2021-04-19 15:35:22] ...measurements (/app/public/data/mc_lay_mclay_200/measurementsorfacts.txt)
[INFO] [2021-04-19 15:35:22] Valid: /app/public/converted_csv/mc_lay_mclay_200_measurements_3771.csv (4 lines)
[STOP] [2021-04-19 15:35:22] validate_each_file
[START] [2021-04-19 15:35:22] convert_to_csv
[INFO] [2021-04-19 15:35:22] Looping over 4 formats...
[INFO] [2021-04-19 15:35:22] ...refs (/app/public/data/mc_lay_mclay_200/references.tsv)
[CMD] [2021-04-19 15:35:22] /usr/bin/sort /app/public/converted_csv/mc_lay_mclay_200_refs_3771.csv > /app/public/converted_csv/mc_lay_mclay_200_refs_3771.csv_sorted
[INFO] [2021-04-19 15:35:22] Converted: /app/public/converted_csv/mc_lay_mclay_200_refs_3771.csv (0 lines)
[INFO] [2021-04-19 15:35:22] ...nodes (/app/public/data/mc_lay_mclay_200/taxa.txt)
[CMD] [2021-04-19 15:35:22] /usr/bin/sort /app/public/converted_csv/mc_lay_mclay_200_nodes_3771.csv > /app/public/converted_csv/mc_lay_mclay_200_nodes_3771.csv_sorted
[INFO] [2021-04-19 15:35:22] Converted: /app/public/converted_csv/mc_lay_mclay_200_nodes_3771.csv (2 lines)
[INFO] [2021-04-19 15:35:22] ...occurrences (/app/public/data/mc_lay_mclay_200/occurrences.txt)
[CMD] [2021-04-19 15:35:22] /usr/bin/sort /app/public/converted_csv/mc_lay_mclay_200_occurrences_3771.csv > /app/public/converted_csv/mc_lay_mclay_200_occurrences_3771.csv_sorted
[INFO] [2021-04-19 15:35:22] Converted: /app/public/converted_csv/mc_lay_mclay_200_occurrences_3771.csv (2 lines)
[INFO] [2021-04-19 15:35:22] ...measurements (/app/public/data/mc_lay_mclay_200/measurementsorfacts.txt)
[CMD] [2021-04-19 15:35:22] /usr/bin/sort /app/public/converted_csv/mc_lay_mclay_200_measurements_3771.csv > /app/public/converted_csv/mc_lay_mclay_200_measurements_3771.csv_sorted
[INFO] [2021-04-19 15:35:22] Converted: /app/public/converted_csv/mc_lay_mclay_200_measurements_3771.csv (4 lines)
[STOP] [2021-04-19 15:35:22] convert_to_csv
[START] [2021-04-19 15:35:22] calculate_delta
[INFO] [2021-04-19 15:35:22] Looping over 4 formats...
[INFO] [2021-04-19 15:35:22] ...refs (/app/public/data/mc_lay_mclay_200/references.tsv)
[CMD] [2021-04-19 15:35:22] echo "0a" > /app/public/diff/mc_lay_mclay_200_refs_3771.diff
[CMD] [2021-04-19 15:35:22] tail -n +1 /app/public/converted_csv/mc_lay_mclay_200_refs_3771.csv >> /app/public/diff/mc_lay_mclay_200_refs_3771.diff
[CMD] [2021-04-19 15:35:22] echo "." >> /app/public/diff/mc_lay_mclay_200_refs_3771.diff
[INFO] [2021-04-19 15:35:22] Created diff: /app/public/diff/mc_lay_mclay_200_refs_3771.diff (2 lines)
[INFO] [2021-04-19 15:35:22] ...nodes (/app/public/data/mc_lay_mclay_200/taxa.txt)
[CMD] [2021-04-19 15:35:22] echo "0a" > /app/public/diff/mc_lay_mclay_200_nodes_3771.diff
[CMD] [2021-04-19 15:35:22] tail -n +1 /app/public/converted_csv/mc_lay_mclay_200_nodes_3771.csv >> /app/public/diff/mc_lay_mclay_200_nodes_3771.diff
[CMD] [2021-04-19 15:35:22] echo "." >> /app/public/diff/mc_lay_mclay_200_nodes_3771.diff
[INFO] [2021-04-19 15:35:22] Created diff: /app/public/diff/mc_lay_mclay_200_nodes_3771.diff (4 lines)
[INFO] [2021-04-19 15:35:22] ...occurrences (/app/public/data/mc_lay_mclay_200/occurrences.txt)
[CMD] [2021-04-19 15:35:22] echo "0a" > /app/public/diff/mc_lay_mclay_200_occurrences_3771.diff
[CMD] [2021-04-19 15:35:22] tail -n +1 /app/public/converted_csv/mc_lay_mclay_200_occurrences_3771.csv >> /app/public/diff/mc_lay_mclay_200_occurrences_3771.diff
[CMD] [2021-04-19 15:35:22] echo "." >> /app/public/diff/mc_lay_mclay_200_occurrences_3771.diff
[INFO] [2021-04-19 15:35:22] Created diff: /app/public/diff/mc_lay_mclay_200_occurrences_3771.diff (4 lines)
[INFO] [2021-04-19 15:35:22] ...measurements (/app/public/data/mc_lay_mclay_200/measurementsorfacts.txt)
[CMD] [2021-04-19 15:35:22] echo "0a" > /app/public/diff/mc_lay_mclay_200_measurements_3771.diff
[CMD] [2021-04-19 15:35:22] tail -n +1 /app/public/converted_csv/mc_lay_mclay_200_measurements_3771.csv >> /app/public/diff/mc_lay_mclay_200_measurements_3771.diff
[CMD] [2021-04-19 15:35:22] echo "." >> /app/public/diff/mc_lay_mclay_200_measurements_3771.diff
[INFO] [2021-04-19 15:35:22] Created diff: /app/public/diff/mc_lay_mclay_200_measurements_3771.diff (6 lines)
[STOP] [2021-04-19 15:35:22] calculate_delta
[START] [2021-04-19 15:35:22] parse_diff_and_store
[INFO] [2021-04-19 15:35:22] Handling diff: /app/public/diff/mc_lay_mclay_200_refs_3771.diff (2 lines)
[INFO] [2021-04-19 15:35:22] Loading refs diff file into memory (2 /app/public/diff/mc_lay_mclay_200_refs_3771.diff lines)...
[INFO] [2021-04-19 15:35:22] Handling diff: /app/public/diff/mc_lay_mclay_200_nodes_3771.diff (4 lines)
[INFO] [2021-04-19 15:35:22] Loading nodes diff file into memory (4 /app/public/diff/mc_lay_mclay_200_nodes_3771.diff lines)...
[INFO] [2021-04-19 15:35:22] Handling diff: /app/public/diff/mc_lay_mclay_200_occurrences_3771.diff (4 lines)
[INFO] [2021-04-19 15:35:22] Loading occurrences diff file into memory (4 /app/public/diff/mc_lay_mclay_200_occurrences_3771.diff lines)...
[INFO] [2021-04-19 15:35:22] Handling diff: /app/public/diff/mc_lay_mclay_200_measurements_3771.diff (6 lines)
[INFO] [2021-04-19 15:35:22] Loading measurements diff file into memory (6 /app/public/diff/mc_lay_mclay_200_measurements_3771.diff lines)...
[INFO] [2021-04-19 15:35:22] Storing 2 ScientificNames
[INFO] [2021-04-19 15:35:22] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:35:23] Average Time: 0.0
[INFO] [2021-04-19 15:35:23] Total Time: 1s
[INFO] [2021-04-19 15:35:23] Storing 2 Nodes
[INFO] [2021-04-19 15:35:23] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:35:23] Average Time: 0.0
[INFO] [2021-04-19 15:35:23] Total Time: 1s
[INFO] [2021-04-19 15:35:23] Storing 2 Occurrences
[INFO] [2021-04-19 15:35:23] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:35:23] Average Time: 0.0
[INFO] [2021-04-19 15:35:23] Total Time: 1s
[INFO] [2021-04-19 15:35:23] Storing 4 Traits
[INFO] [2021-04-19 15:35:23] Processing group of 4 in 1 groups of 1000
[INFO] [2021-04-19 15:35:23] Average Time: 0.0
[INFO] [2021-04-19 15:35:23] Total Time: 1s
[INFO] [2021-04-19 15:35:23] Storing 2 MetaTraits
[INFO] [2021-04-19 15:35:23] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:35:23] Average Time: 0.0
[INFO] [2021-04-19 15:35:23] Total Time: 1s
[STOP] [2021-04-19 15:35:23] parse_diff_and_store
[START] [2021-04-19 15:35:23] resolve_keys
[INFO] [2021-04-19 15:35:28] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:35:28] traits to occurrences...
[INFO] [2021-04-19 15:35:28] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:35:28] Traits to sex term...
[INFO] [2021-04-19 15:35:28] Traits to lifestage term...
[INFO] [2021-04-19 15:35:28] MetaTraits to traits...
[INFO] [2021-04-19 15:35:28] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:35:28] Assocs to occurrences...
[INFO] [2021-04-19 15:35:28] Assocs to nodes...
[INFO] [2021-04-19 15:35:28] Assoc to sex term...
[INFO] [2021-04-19 15:35:28] Assoc to lifestage term...
[INFO] [2021-04-19 15:35:28] MetaAssoc to assocs...
[STOP] [2021-04-19 15:35:28] resolve_keys
[START] [2021-04-19 15:35:28] hold_for_later_1
[STOP] [2021-04-19 15:35:28] hold_for_later_1
[START] [2021-04-19 15:35:28] hold_for_later_2
[STOP] [2021-04-19 15:35:28] hold_for_later_2
[START] [2021-04-19 15:35:28] resolve_missing_parents
[STOP] [2021-04-19 15:35:28] resolve_missing_parents
[START] [2021-04-19 15:35:28] rebuild_nodes
[START] [2021-04-19 15:35:29] Flattener#flatten
[START] [2021-04-19 15:35:29] Flattener#study_resource
[START] [2021-04-19 15:35:29] Flattener#build_ancestry
[STOP] [2021-04-19 15:35:29] Flattener#build_ancestry
[INFO] [2021-04-19 15:35:29] 2 ancestry keys
[START] [2021-04-19 15:35:29] build_node_ancestors
[INFO] [2021-04-19 15:35:29] old ancestors deleted.
[STOP] [2021-04-19 15:35:29] build_node_ancestors
[WARN] [2021-04-19 15:35:29] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:35:29] Flattener#flatten
[STOP] [2021-04-19 15:35:29] rebuild_nodes
[START] [2021-04-19 15:35:29] resolve_missing_media_owners
[STOP] [2021-04-19 15:35:29] resolve_missing_media_owners
[START] [2021-04-19 15:35:29] sanitize_media_verbatims
[STOP] [2021-04-19 15:35:29] sanitize_media_verbatims
[START] [2021-04-19 15:35:29] queue_downloads
[STOP] [2021-04-19 15:35:29] queue_downloads
[START] [2021-04-19 15:35:29] parse_names
[WARN] [2021-04-19 15:35:29] I see 2 names which still need to be parsed.
[STOP] [2021-04-19 15:35:30] parse_names
[START] [2021-04-19 15:35:30] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:35:30] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:35:30] match_nodes
[START] [2021-04-19 15:35:30] map_all_nodes_to_pages
[STOP] [2021-04-19 15:35:30] map_all_nodes_to_pages
[INFO] [2021-04-19 15:35:30] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2021-04-19 15:35:30] update_nodes
[STOP] [2021-04-19 15:35:30] update_nodes
[STOP] [2021-04-19 15:35:30] match_nodes
[START] [2021-04-19 15:35:30] reindex_search
[STOP] [2021-04-19 15:35:30] reindex_search
[START] [2021-04-19 15:35:30] normalize_units
[STOP] [2021-04-19 15:35:30] normalize_units
[START] [2021-04-19 15:35:30] calculate_statistics
[2021-04-19 15:35:30] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:35:30] calculate_statistics
[START] [2021-04-19 15:35:30] complete_harvest_instance
[START] [2021-04-19 15:35:30] overall_tsv_creation
[INFO] [2021-04-19 15:35:30] Processing group of 2 in 1 batches of 10000
[INFO] [2021-04-19 15:36:06] 2 Traits (unfiltered)...
[INFO] [2021-04-19 15:36:39] 2 Traits (filtered)...
[INFO] [2021-04-19 15:36:39] 0 Associations (filtered)...
[INFO] [2021-04-19 15:36:39] 2 metadata added.
[INFO] [2021-04-19 15:36:39] 0 metadata added.
[INFO] [2021-04-19 15:37:06] Average Time: 72.37
[INFO] [2021-04-19 15:37:06] Total Time: 1m37s
[STOP] [2021-04-19 15:37:06] overall_tsv_creation
[INFO] [2021-04-19 15:37:06] Done. Check your files:
[INFO] [2021-04-19 15:37:06] (2 lines) /app/public/data/mc_lay_mclay_200/publish_nodes.tsv
[INFO] [2021-04-19 15:37:06] (2 lines) /app/public/data/mc_lay_mclay_200/publish_scientific_names.tsv
[INFO] [2021-04-19 15:37:06] (3 lines) /app/public/data/mc_lay_mclay_200/publish_traits.tsv
[INFO] [2021-04-19 15:37:06] (3 lines) /app/public/data/mc_lay_mclay_200/publish_metadata.tsv
[STOP] [2021-04-19 15:37:06] complete_harvest_instance
[START] [2021-04-19 15:37:06] completed
[STOP] [2021-04-19 15:37:06] completed
[STOP] [2021-04-19 15:37:06] logged process, took 104.13

Latest Process

19 Apr 15:35 EXITED currently processing 0