Harvest for Nilsson 2013 Created 19 Apr 15:31

Harvesting Log

# Logfile created on 2020-08-27 15:41:56 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:41:56] logged process
[START] [2020-08-27 15:41:56] Creating resource from OpenData
[START] [2020-08-27 15:41:56] logged process
[START] [2020-08-27 15:41:56] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:41:56] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:41:56] Creating resource from OpenData
[INFO] [2020-12-03 11:21:15] ## HARVEST: type = -harvest
[START] [2020-12-03 11:21:18] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-03 11:21:18] create_harvest_instance
[STOP] [2020-12-03 11:21:20] create_harvest_instance
[START] [2020-12-03 11:21:20] fetch_files
[STOP] [2020-12-03 11:21:20] fetch_files
[START] [2020-12-03 11:21:20] validate_each_file
[STOP] [2020-12-03 11:21:20] validate_each_file
[START] [2020-12-03 11:21:20] convert_to_csv
[CMD] [2020-12-03 11:21:20] /usr/bin/sort /app/public/converted_csv/nilsson_nilsson__refs_24808.csv > /app/public/converted_csv/nilsson_nilsson__refs_24808.csv_sorted
[CMD] [2020-12-03 11:21:20] /usr/bin/sort /app/public/converted_csv/nilsson_nilsson__nodes_24809.csv > /app/public/converted_csv/nilsson_nilsson__nodes_24809.csv_sorted
[CMD] [2020-12-03 11:21:20] /usr/bin/sort /app/public/converted_csv/nilsson_nilsson__occurrences_24810.csv > /app/public/converted_csv/nilsson_nilsson__occurrences_24810.csv_sorted
[CMD] [2020-12-03 11:21:20] /usr/bin/sort /app/public/converted_csv/nilsson_nilsson__measurements_24811.csv > /app/public/converted_csv/nilsson_nilsson__measurements_24811.csv_sorted
[STOP] [2020-12-03 11:21:20] convert_to_csv
[START] [2020-12-03 11:21:20] calculate_delta
[CMD] [2020-12-03 11:21:20] echo "0a" > /app/public/diff/nilsson_nilsson__refs_24808.diff
[CMD] [2020-12-03 11:21:20] tail -n +1 /app/public/converted_csv/nilsson_nilsson__refs_24808.csv >> /app/public/diff/nilsson_nilsson__refs_24808.diff
[CMD] [2020-12-03 11:21:20] echo "." >> /app/public/diff/nilsson_nilsson__refs_24808.diff
[CMD] [2020-12-03 11:21:20] echo "0a" > /app/public/diff/nilsson_nilsson__nodes_24809.diff
[CMD] [2020-12-03 11:21:20] tail -n +1 /app/public/converted_csv/nilsson_nilsson__nodes_24809.csv >> /app/public/diff/nilsson_nilsson__nodes_24809.diff
[CMD] [2020-12-03 11:21:20] echo "." >> /app/public/diff/nilsson_nilsson__nodes_24809.diff
[CMD] [2020-12-03 11:21:20] echo "0a" > /app/public/diff/nilsson_nilsson__occurrences_24810.diff
[CMD] [2020-12-03 11:21:20] tail -n +1 /app/public/converted_csv/nilsson_nilsson__occurrences_24810.csv >> /app/public/diff/nilsson_nilsson__occurrences_24810.diff
[CMD] [2020-12-03 11:21:20] echo "." >> /app/public/diff/nilsson_nilsson__occurrences_24810.diff
[CMD] [2020-12-03 11:21:20] echo "0a" > /app/public/diff/nilsson_nilsson__measurements_24811.diff
[CMD] [2020-12-03 11:21:20] tail -n +1 /app/public/converted_csv/nilsson_nilsson__measurements_24811.csv >> /app/public/diff/nilsson_nilsson__measurements_24811.diff
[CMD] [2020-12-03 11:21:20] echo "." >> /app/public/diff/nilsson_nilsson__measurements_24811.diff
[STOP] [2020-12-03 11:21:20] calculate_delta
[START] [2020-12-03 11:21:20] parse_diff_and_store
[INFO] [2020-12-03 11:21:20] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 11:21:20] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 11:21:20] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 11:21:21] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 11:21:21] Storing 7 ScientificNames
[INFO] [2020-12-03 11:21:21] Processing group of 7 in 1 groups of 1000
[INFO] [2020-12-03 11:21:21] Average Time: 0.02
[INFO] [2020-12-03 11:21:21] Total Time: 1s
[INFO] [2020-12-03 11:21:21] Storing 7 Nodes
[INFO] [2020-12-03 11:21:21] Processing group of 7 in 1 groups of 1000
[INFO] [2020-12-03 11:21:21] Average Time: 0.01
[INFO] [2020-12-03 11:21:21] Total Time: 1s
[INFO] [2020-12-03 11:21:21] Storing 7 Occurrences
[INFO] [2020-12-03 11:21:21] Processing group of 7 in 1 groups of 1000
[INFO] [2020-12-03 11:21:21] Average Time: 0.01
[INFO] [2020-12-03 11:21:21] Total Time: 1s
[INFO] [2020-12-03 11:21:21] Storing 1 OccurrenceMetadata
[INFO] [2020-12-03 11:21:21] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:21:21] Average Time: 0.0
[INFO] [2020-12-03 11:21:21] Total Time: 1s
[INFO] [2020-12-03 11:21:21] Storing 16 Traits
[INFO] [2020-12-03 11:21:21] Processing group of 16 in 1 groups of 1000
[INFO] [2020-12-03 11:21:21] Average Time: 0.01
[INFO] [2020-12-03 11:21:21] Total Time: 1s
[INFO] [2020-12-03 11:21:21] Storing 10 MetaTraits
[INFO] [2020-12-03 11:21:21] Processing group of 10 in 1 groups of 1000
[INFO] [2020-12-03 11:21:21] Average Time: 0.0
[INFO] [2020-12-03 11:21:21] Total Time: 1s
[STOP] [2020-12-03 11:21:21] parse_diff_and_store
[START] [2020-12-03 11:21:21] resolve_keys
[INFO] [2020-12-03 11:21:27] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 11:21:27] traits to occurrences...
[INFO] [2020-12-03 11:21:27] traits to nodes (through occurrences)...
[INFO] [2020-12-03 11:21:27] Traits to sex term...
[INFO] [2020-12-03 11:21:27] Traits to lifestage term...
[INFO] [2020-12-03 11:21:27] MetaTraits to traits...
[INFO] [2020-12-03 11:21:27] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 11:21:27] Assocs to occurrences...
[INFO] [2020-12-03 11:21:27] Assocs to nodes...
[INFO] [2020-12-03 11:21:27] Assoc to sex term...
[INFO] [2020-12-03 11:21:27] Assoc to lifestage term...
[INFO] [2020-12-03 11:21:27] MetaAssoc to assocs...
[STOP] [2020-12-03 11:21:27] resolve_keys
[START] [2020-12-03 11:21:27] hold_for_later_1
[STOP] [2020-12-03 11:21:27] hold_for_later_1
[START] [2020-12-03 11:21:27] hold_for_later_2
[STOP] [2020-12-03 11:21:27] hold_for_later_2
[START] [2020-12-03 11:21:27] resolve_missing_parents
[STOP] [2020-12-03 11:21:27] resolve_missing_parents
[START] [2020-12-03 11:21:27] rebuild_nodes
[START] [2020-12-03 11:21:27] Flattener#flatten
[START] [2020-12-03 11:21:27] Flattener#study_resource
[START] [2020-12-03 11:21:27] Flattener#build_ancestry
[STOP] [2020-12-03 11:21:27] Flattener#build_ancestry
[INFO] [2020-12-03 11:21:27] 7 ancestry keys
[START] [2020-12-03 11:21:27] build_node_ancestors
[INFO] [2020-12-03 11:21:27] old ancestors deleted.
[STOP] [2020-12-03 11:21:27] build_node_ancestors
[WARN] [2020-12-03 11:21:27] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 11:21:27] Flattener#flatten
[STOP] [2020-12-03 11:21:27] rebuild_nodes
[START] [2020-12-03 11:21:27] resolve_missing_media_owners
[STOP] [2020-12-03 11:21:27] resolve_missing_media_owners
[START] [2020-12-03 11:21:27] sanitize_media_verbatims
[STOP] [2020-12-03 11:21:27] sanitize_media_verbatims
[START] [2020-12-03 11:21:27] queue_downloads
[STOP] [2020-12-03 11:21:27] queue_downloads
[START] [2020-12-03 11:21:27] parse_names
[WARN] [2020-12-03 11:21:27] I see 7 names which still need to be parsed.
[STOP] [2020-12-03 11:21:28] parse_names
[START] [2020-12-03 11:21:28] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 11:21:28] denormalize_canonical_names_to_nodes
[START] [2020-12-03 11:21:28] match_nodes
[START] [2020-12-03 11:21:28] map_all_nodes_to_pages
[STOP] [2020-12-03 11:21:28] map_all_nodes_to_pages
[INFO] [2020-12-03 11:21:28] ZERO unmatched nodes (of 7)! Nicely done.
[START] [2020-12-03 11:21:28] update_nodes
[STOP] [2020-12-03 11:21:28] update_nodes
[STOP] [2020-12-03 11:21:28] match_nodes
[START] [2020-12-03 11:21:28] reindex_search
[STOP] [2020-12-03 11:21:28] reindex_search
[START] [2020-12-03 11:21:28] normalize_units
[STOP] [2020-12-03 11:21:28] normalize_units
[START] [2020-12-03 11:21:28] calculate_statistics
[2020-12-03 11:21:28] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 11:21:28] calculate_statistics
[START] [2020-12-03 11:21:28] complete_harvest_instance
[START] [2020-12-03 11:21:28] overall_tsv_creation
[INFO] [2020-12-03 11:21:28] Processing group of 7 in 1 batches of 10000
[INFO] [2020-12-03 11:22:07] 7 Traits (unfiltered)...
[INFO] [2020-12-03 11:22:45] 7 Traits (filtered)...
[INFO] [2020-12-03 11:22:45] 0 Associations (filtered)...
[INFO] [2020-12-03 11:22:45] 20 metadata added.
[INFO] [2020-12-03 11:22:45] 0 metadata added.
[INFO] [2020-12-03 11:22:45] Average Time: 54.17
[INFO] [2020-12-03 11:22:45] Total Time: 1m17s
[STOP] [2020-12-03 11:22:45] overall_tsv_creation
[INFO] [2020-12-03 11:22:45] Done. Check your files:
[INFO] [2020-12-03 11:22:45] (7 lines) /app/public/data/nilsson_nilsson_/publish_nodes.tsv
[INFO] [2020-12-03 11:22:45] (7 lines) /app/public/data/nilsson_nilsson_/publish_scientific_names.tsv
[INFO] [2020-12-03 11:22:45] (8 lines) /app/public/data/nilsson_nilsson_/publish_traits.tsv
[INFO] [2020-12-03 11:22:45] (20 lines) /app/public/data/nilsson_nilsson_/publish_metadata.tsv
[STOP] [2020-12-03 11:22:45] complete_harvest_instance
[START] [2020-12-03 11:22:45] completed
[STOP] [2020-12-03 11:22:45] completed
[STOP] [2020-12-03 11:22:45] logged process, took 86.98
[INFO] [2021-04-19 15:17:14] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:31:53] ## remove_type: ScientificName
[INFO] [2021-04-19 15:31:53] ++ Calling delete_all on 7 instances...
[INFO] [2021-04-19 15:31:53] [15:31:53.756] Removed 7 Scientificnames
[INFO] [2021-04-19 15:31:53] ## remove_type: Vernacular
[INFO] [2021-04-19 15:31:53] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:31:53] [15:31:53.758] Removed 0 Vernaculars
[INFO] [2021-04-19 15:31:53] ## remove_type: Article
[INFO] [2021-04-19 15:31:53] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:31:53] [15:31:53.759] Removed 0 Articles
[INFO] [2021-04-19 15:31:53] ## remove_type: Medium
[INFO] [2021-04-19 15:31:53] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:31:53] [15:31:53.760] Removed 0 Media
[INFO] [2021-04-19 15:31:53] ## remove_type: Trait
[INFO] [2021-04-19 15:31:53] ++ Calling delete_all on 16 instances...
[INFO] [2021-04-19 15:31:53] [15:31:53.763] Removed 16 Traits
[INFO] [2021-04-19 15:31:53] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:31:53] ++ Calling delete_all on 10 instances...
[INFO] [2021-04-19 15:31:53] [15:31:53.765] Removed 10 Metatraits
[INFO] [2021-04-19 15:31:53] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:31:53] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:31:53] [15:31:53.767] Removed 1 Occurrencemetadata
[INFO] [2021-04-19 15:31:53] ## remove_type: Assoc
[INFO] [2021-04-19 15:31:53] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:31:53] [15:31:53.768] Removed 0 Assocs
[INFO] [2021-04-19 15:31:53] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:31:53] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:31:53] [15:31:53.770] Removed 0 Metaassocs
[INFO] [2021-04-19 15:31:53] ## remove_type: Identifier
[INFO] [2021-04-19 15:31:53] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:31:53] [15:31:53.771] Removed 0 Identifiers
[INFO] [2021-04-19 15:31:53] ## remove_type: Reference
[INFO] [2021-04-19 15:31:53] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:31:53] [15:31:53.772] Removed 0 References
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:53] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:54] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:54] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:54] Starting batch with ID 86115908...
[INFO] [2021-04-19 15:31:54] ## remove_type: Node
[INFO] [2021-04-19 15:31:54] ++ Calling delete_all on 7 instances...
[INFO] [2021-04-19 15:31:54] [15:31:54.025] Removed 7 Nodes
[START] [2021-04-19 15:31:54] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:31:54] Creating resource from OpenData
[START] [2021-04-19 15:31:54] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:31:54] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:31:54] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:31:54] Creating resource from OpenData
[START] [2021-04-19 15:31:54] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:31:54] create_harvest_instance
[INFO] [2021-04-19 15:31:54] Created harvest instance #3769
[STOP] [2021-04-19 15:31:54] create_harvest_instance
[START] [2021-04-19 15:31:54] fetch_files
[STOP] [2021-04-19 15:31:54] fetch_files
[START] [2021-04-19 15:31:54] validate_each_file
[INFO] [2021-04-19 15:31:54] Looping over 4 formats...
[INFO] [2021-04-19 15:31:54] ...refs (/app/public/data/nilsson_nilsson_/references.tsv)
[INFO] [2021-04-19 15:31:54] Valid: /app/public/converted_csv/nilsson_nilsson__refs_3769.csv (0 lines)
[INFO] [2021-04-19 15:31:54] ...nodes (/app/public/data/nilsson_nilsson_/taxa.txt)
[INFO] [2021-04-19 15:31:54] Valid: /app/public/converted_csv/nilsson_nilsson__nodes_3769.csv (7 lines)
[INFO] [2021-04-19 15:31:54] ...occurrences (/app/public/data/nilsson_nilsson_/occurrences.txt)
[INFO] [2021-04-19 15:31:54] Valid: /app/public/converted_csv/nilsson_nilsson__occurrences_3769.csv (7 lines)
[INFO] [2021-04-19 15:31:54] ...measurements (/app/public/data/nilsson_nilsson_/measurementsorfacts.txt)
[INFO] [2021-04-19 15:31:54] Valid: /app/public/converted_csv/nilsson_nilsson__measurements_3769.csv (16 lines)
[STOP] [2021-04-19 15:31:54] validate_each_file
[START] [2021-04-19 15:31:54] convert_to_csv
[INFO] [2021-04-19 15:31:54] Looping over 4 formats...
[INFO] [2021-04-19 15:31:54] ...refs (/app/public/data/nilsson_nilsson_/references.tsv)
[CMD] [2021-04-19 15:31:54] /usr/bin/sort /app/public/converted_csv/nilsson_nilsson__refs_3769.csv > /app/public/converted_csv/nilsson_nilsson__refs_3769.csv_sorted
[INFO] [2021-04-19 15:31:54] Converted: /app/public/converted_csv/nilsson_nilsson__refs_3769.csv (0 lines)
[INFO] [2021-04-19 15:31:54] ...nodes (/app/public/data/nilsson_nilsson_/taxa.txt)
[CMD] [2021-04-19 15:31:54] /usr/bin/sort /app/public/converted_csv/nilsson_nilsson__nodes_3769.csv > /app/public/converted_csv/nilsson_nilsson__nodes_3769.csv_sorted
[INFO] [2021-04-19 15:31:54] Converted: /app/public/converted_csv/nilsson_nilsson__nodes_3769.csv (7 lines)
[INFO] [2021-04-19 15:31:54] ...occurrences (/app/public/data/nilsson_nilsson_/occurrences.txt)
[CMD] [2021-04-19 15:31:54] /usr/bin/sort /app/public/converted_csv/nilsson_nilsson__occurrences_3769.csv > /app/public/converted_csv/nilsson_nilsson__occurrences_3769.csv_sorted
[INFO] [2021-04-19 15:31:54] Converted: /app/public/converted_csv/nilsson_nilsson__occurrences_3769.csv (7 lines)
[INFO] [2021-04-19 15:31:54] ...measurements (/app/public/data/nilsson_nilsson_/measurementsorfacts.txt)
[CMD] [2021-04-19 15:31:54] /usr/bin/sort /app/public/converted_csv/nilsson_nilsson__measurements_3769.csv > /app/public/converted_csv/nilsson_nilsson__measurements_3769.csv_sorted
[INFO] [2021-04-19 15:31:54] Converted: /app/public/converted_csv/nilsson_nilsson__measurements_3769.csv (16 lines)
[STOP] [2021-04-19 15:31:54] convert_to_csv
[START] [2021-04-19 15:31:54] calculate_delta
[INFO] [2021-04-19 15:31:54] Looping over 4 formats...
[INFO] [2021-04-19 15:31:54] ...refs (/app/public/data/nilsson_nilsson_/references.tsv)
[CMD] [2021-04-19 15:31:54] echo "0a" > /app/public/diff/nilsson_nilsson__refs_3769.diff
[CMD] [2021-04-19 15:31:54] tail -n +1 /app/public/converted_csv/nilsson_nilsson__refs_3769.csv >> /app/public/diff/nilsson_nilsson__refs_3769.diff
[CMD] [2021-04-19 15:31:54] echo "." >> /app/public/diff/nilsson_nilsson__refs_3769.diff
[INFO] [2021-04-19 15:31:54] Created diff: /app/public/diff/nilsson_nilsson__refs_3769.diff (2 lines)
[INFO] [2021-04-19 15:31:54] ...nodes (/app/public/data/nilsson_nilsson_/taxa.txt)
[CMD] [2021-04-19 15:31:54] echo "0a" > /app/public/diff/nilsson_nilsson__nodes_3769.diff
[CMD] [2021-04-19 15:31:54] tail -n +1 /app/public/converted_csv/nilsson_nilsson__nodes_3769.csv >> /app/public/diff/nilsson_nilsson__nodes_3769.diff
[CMD] [2021-04-19 15:31:54] echo "." >> /app/public/diff/nilsson_nilsson__nodes_3769.diff
[INFO] [2021-04-19 15:31:54] Created diff: /app/public/diff/nilsson_nilsson__nodes_3769.diff (9 lines)
[INFO] [2021-04-19 15:31:54] ...occurrences (/app/public/data/nilsson_nilsson_/occurrences.txt)
[CMD] [2021-04-19 15:31:54] echo "0a" > /app/public/diff/nilsson_nilsson__occurrences_3769.diff
[CMD] [2021-04-19 15:31:54] tail -n +1 /app/public/converted_csv/nilsson_nilsson__occurrences_3769.csv >> /app/public/diff/nilsson_nilsson__occurrences_3769.diff
[CMD] [2021-04-19 15:31:54] echo "." >> /app/public/diff/nilsson_nilsson__occurrences_3769.diff
[INFO] [2021-04-19 15:31:54] Created diff: /app/public/diff/nilsson_nilsson__occurrences_3769.diff (9 lines)
[INFO] [2021-04-19 15:31:54] ...measurements (/app/public/data/nilsson_nilsson_/measurementsorfacts.txt)
[CMD] [2021-04-19 15:31:54] echo "0a" > /app/public/diff/nilsson_nilsson__measurements_3769.diff
[CMD] [2021-04-19 15:31:54] tail -n +1 /app/public/converted_csv/nilsson_nilsson__measurements_3769.csv >> /app/public/diff/nilsson_nilsson__measurements_3769.diff
[CMD] [2021-04-19 15:31:54] echo "." >> /app/public/diff/nilsson_nilsson__measurements_3769.diff
[INFO] [2021-04-19 15:31:54] Created diff: /app/public/diff/nilsson_nilsson__measurements_3769.diff (18 lines)
[STOP] [2021-04-19 15:31:54] calculate_delta
[START] [2021-04-19 15:31:54] parse_diff_and_store
[INFO] [2021-04-19 15:31:54] Handling diff: /app/public/diff/nilsson_nilsson__refs_3769.diff (2 lines)
[INFO] [2021-04-19 15:31:54] Loading refs diff file into memory (2 /app/public/diff/nilsson_nilsson__refs_3769.diff lines)...
[INFO] [2021-04-19 15:31:54] Handling diff: /app/public/diff/nilsson_nilsson__nodes_3769.diff (9 lines)
[INFO] [2021-04-19 15:31:54] Loading nodes diff file into memory (9 /app/public/diff/nilsson_nilsson__nodes_3769.diff lines)...
[INFO] [2021-04-19 15:31:54] Handling diff: /app/public/diff/nilsson_nilsson__occurrences_3769.diff (9 lines)
[INFO] [2021-04-19 15:31:54] Loading occurrences diff file into memory (9 /app/public/diff/nilsson_nilsson__occurrences_3769.diff lines)...
[INFO] [2021-04-19 15:31:54] Handling diff: /app/public/diff/nilsson_nilsson__measurements_3769.diff (18 lines)
[INFO] [2021-04-19 15:31:54] Loading measurements diff file into memory (18 /app/public/diff/nilsson_nilsson__measurements_3769.diff lines)...
[INFO] [2021-04-19 15:31:54] Storing 7 ScientificNames
[INFO] [2021-04-19 15:31:54] Processing group of 7 in 1 groups of 1000
[INFO] [2021-04-19 15:31:54] Average Time: 0.0
[INFO] [2021-04-19 15:31:54] Total Time: 1s
[INFO] [2021-04-19 15:31:54] Storing 7 Nodes
[INFO] [2021-04-19 15:31:54] Processing group of 7 in 1 groups of 1000
[INFO] [2021-04-19 15:31:54] Average Time: 0.0
[INFO] [2021-04-19 15:31:54] Total Time: 1s
[INFO] [2021-04-19 15:31:54] Storing 7 Occurrences
[INFO] [2021-04-19 15:31:54] Processing group of 7 in 1 groups of 1000
[INFO] [2021-04-19 15:31:54] Average Time: 0.0
[INFO] [2021-04-19 15:31:54] Total Time: 1s
[INFO] [2021-04-19 15:31:54] Storing 1 OccurrenceMetadata
[INFO] [2021-04-19 15:31:54] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:31:54] Average Time: 0.0
[INFO] [2021-04-19 15:31:54] Total Time: 1s
[INFO] [2021-04-19 15:31:54] Storing 16 Traits
[INFO] [2021-04-19 15:31:54] Processing group of 16 in 1 groups of 1000
[INFO] [2021-04-19 15:31:54] Average Time: 0.01
[INFO] [2021-04-19 15:31:54] Total Time: 1s
[INFO] [2021-04-19 15:31:54] Storing 10 MetaTraits
[INFO] [2021-04-19 15:31:54] Processing group of 10 in 1 groups of 1000
[INFO] [2021-04-19 15:31:54] Average Time: 0.0
[INFO] [2021-04-19 15:31:54] Total Time: 1s
[STOP] [2021-04-19 15:31:54] parse_diff_and_store
[START] [2021-04-19 15:31:54] resolve_keys
[INFO] [2021-04-19 15:32:00] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:32:00] traits to occurrences...
[INFO] [2021-04-19 15:32:00] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:32:00] Traits to sex term...
[INFO] [2021-04-19 15:32:00] Traits to lifestage term...
[INFO] [2021-04-19 15:32:00] MetaTraits to traits...
[INFO] [2021-04-19 15:32:00] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:32:00] Assocs to occurrences...
[INFO] [2021-04-19 15:32:00] Assocs to nodes...
[INFO] [2021-04-19 15:32:00] Assoc to sex term...
[INFO] [2021-04-19 15:32:00] Assoc to lifestage term...
[INFO] [2021-04-19 15:32:00] MetaAssoc to assocs...
[STOP] [2021-04-19 15:32:00] resolve_keys
[START] [2021-04-19 15:32:00] hold_for_later_1
[STOP] [2021-04-19 15:32:00] hold_for_later_1
[START] [2021-04-19 15:32:00] hold_for_later_2
[STOP] [2021-04-19 15:32:00] hold_for_later_2
[START] [2021-04-19 15:32:00] resolve_missing_parents
[STOP] [2021-04-19 15:32:00] resolve_missing_parents
[START] [2021-04-19 15:32:00] rebuild_nodes
[START] [2021-04-19 15:32:00] Flattener#flatten
[START] [2021-04-19 15:32:00] Flattener#study_resource
[START] [2021-04-19 15:32:00] Flattener#build_ancestry
[STOP] [2021-04-19 15:32:00] Flattener#build_ancestry
[INFO] [2021-04-19 15:32:00] 7 ancestry keys
[START] [2021-04-19 15:32:00] build_node_ancestors
[INFO] [2021-04-19 15:32:00] old ancestors deleted.
[STOP] [2021-04-19 15:32:00] build_node_ancestors
[WARN] [2021-04-19 15:32:00] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:32:00] Flattener#flatten
[STOP] [2021-04-19 15:32:00] rebuild_nodes
[START] [2021-04-19 15:32:00] resolve_missing_media_owners
[STOP] [2021-04-19 15:32:00] resolve_missing_media_owners
[START] [2021-04-19 15:32:00] sanitize_media_verbatims
[STOP] [2021-04-19 15:32:00] sanitize_media_verbatims
[START] [2021-04-19 15:32:00] queue_downloads
[STOP] [2021-04-19 15:32:00] queue_downloads
[START] [2021-04-19 15:32:00] parse_names
[WARN] [2021-04-19 15:32:00] I see 7 names which still need to be parsed.
[STOP] [2021-04-19 15:32:02] parse_names
[START] [2021-04-19 15:32:02] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:32:02] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:32:02] match_nodes
[START] [2021-04-19 15:32:02] map_all_nodes_to_pages
[STOP] [2021-04-19 15:32:02] map_all_nodes_to_pages
[INFO] [2021-04-19 15:32:02] ZERO unmatched nodes (of 7)! Nicely done.
[START] [2021-04-19 15:32:02] update_nodes
[STOP] [2021-04-19 15:32:02] update_nodes
[STOP] [2021-04-19 15:32:02] match_nodes
[START] [2021-04-19 15:32:02] reindex_search
[STOP] [2021-04-19 15:32:02] reindex_search
[START] [2021-04-19 15:32:02] normalize_units
[STOP] [2021-04-19 15:32:02] normalize_units
[START] [2021-04-19 15:32:02] calculate_statistics
[2021-04-19 15:32:02] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:32:02] calculate_statistics
[START] [2021-04-19 15:32:02] complete_harvest_instance
[START] [2021-04-19 15:32:02] overall_tsv_creation
[INFO] [2021-04-19 15:32:02] Processing group of 7 in 1 batches of 10000
[INFO] [2021-04-19 15:32:38] 7 Traits (unfiltered)...
[INFO] [2021-04-19 15:33:11] 7 Traits (filtered)...
[INFO] [2021-04-19 15:33:11] 0 Associations (filtered)...
[INFO] [2021-04-19 15:33:11] 9 metadata added.
[INFO] [2021-04-19 15:33:11] 0 metadata added.
[INFO] [2021-04-19 15:33:38] Average Time: 71.94
[INFO] [2021-04-19 15:33:38] Total Time: 1m37s
[STOP] [2021-04-19 15:33:38] overall_tsv_creation
[INFO] [2021-04-19 15:33:38] Done. Check your files:
[INFO] [2021-04-19 15:33:38] (7 lines) /app/public/data/nilsson_nilsson_/publish_nodes.tsv
[INFO] [2021-04-19 15:33:38] (7 lines) /app/public/data/nilsson_nilsson_/publish_scientific_names.tsv
[INFO] [2021-04-19 15:33:38] (8 lines) /app/public/data/nilsson_nilsson_/publish_traits.tsv
[INFO] [2021-04-19 15:33:38] (10 lines) /app/public/data/nilsson_nilsson_/publish_metadata.tsv
[STOP] [2021-04-19 15:33:38] complete_harvest_instance
[START] [2021-04-19 15:33:38] completed
[STOP] [2021-04-19 15:33:38] completed
[STOP] [2021-04-19 15:33:38] logged process, took 103.92

Latest Process

19 Apr 15:31 EXITED currently processing 0