Harvest for Vodopyanov and Purschke 2017 Created 19 Apr 15:02

Harvesting Log

# Logfile created on 2020-08-27 15:25:32 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:25:32] logged process
[START] [2020-08-27 15:25:32] Creating resource from OpenData
[START] [2020-08-27 15:25:32] logged process
[START] [2020-08-27 15:25:32] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:25:32] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:25:32] Creating resource from OpenData
[INFO] [2020-11-19 13:44:27] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-11-19 13:44:30] ## remove_type: ScientificName
[INFO] [2020-11-19 13:44:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:44:30] [13:44:30.903] Removed 0 Scientificnames
[INFO] [2020-11-19 13:44:30] ## remove_type: Vernacular
[INFO] [2020-11-19 13:44:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:44:30] [13:44:30.905] Removed 0 Vernaculars
[INFO] [2020-11-19 13:44:30] ## remove_type: Article
[INFO] [2020-11-19 13:44:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:44:30] [13:44:30.908] Removed 0 Articles
[INFO] [2020-11-19 13:44:30] ## remove_type: Medium
[INFO] [2020-11-19 13:44:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:44:30] [13:44:30.912] Removed 0 Media
[INFO] [2020-11-19 13:44:30] ## remove_type: Trait
[INFO] [2020-11-19 13:44:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:44:30] [13:44:30.915] Removed 0 Traits
[INFO] [2020-11-19 13:44:30] ## remove_type: MetaTrait
[INFO] [2020-11-19 13:44:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:44:30] [13:44:30.918] Removed 0 Metatraits
[INFO] [2020-11-19 13:44:30] ## remove_type: OccurrenceMetadatum
[INFO] [2020-11-19 13:44:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:44:30] [13:44:30.920] Removed 0 Occurrencemetadata
[INFO] [2020-11-19 13:44:30] ## remove_type: Assoc
[INFO] [2020-11-19 13:44:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:44:30] [13:44:30.923] Removed 0 Assocs
[INFO] [2020-11-19 13:44:30] ## remove_type: MetaAssoc
[INFO] [2020-11-19 13:44:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:44:30] [13:44:30.925] Removed 0 Metaassocs
[INFO] [2020-11-19 13:44:30] ## remove_type: Identifier
[INFO] [2020-11-19 13:44:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:44:30] [13:44:30.928] Removed 0 Identifiers
[INFO] [2020-11-19 13:44:30] ## remove_type: Reference
[INFO] [2020-11-19 13:44:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:44:30] [13:44:30.930] Removed 0 References
[INFO] [2020-11-19 13:44:30] ## remove_type: Node
[INFO] [2020-11-19 13:44:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:44:30] [13:44:30.953] Removed 0 Nodes
[START] [2020-11-19 13:44:31] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 13:44:31] Creating resource from OpenData
[START] [2020-11-19 13:44:31] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 13:44:31] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 13:44:31] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 13:44:31] Creating resource from OpenData
[START] [2020-11-19 13:44:31] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 13:44:31] create_harvest_instance
[STOP] [2020-11-19 13:44:32] create_harvest_instance
[START] [2020-11-19 13:44:32] fetch_files
[STOP] [2020-11-19 13:44:32] fetch_files
[START] [2020-11-19 13:44:32] validate_each_file
[STOP] [2020-11-19 13:44:32] validate_each_file
[START] [2020-11-19 13:44:32] convert_to_csv
[CMD] [2020-11-19 13:44:32] /usr/bin/sort /app/public/converted_csv/vodopyanov_pursc_refs_24454.csv > /app/public/converted_csv/vodopyanov_pursc_refs_24454.csv_sorted
[CMD] [2020-11-19 13:44:32] /usr/bin/sort /app/public/converted_csv/vodopyanov_pursc_nodes_24455.csv > /app/public/converted_csv/vodopyanov_pursc_nodes_24455.csv_sorted
[CMD] [2020-11-19 13:44:32] /usr/bin/sort /app/public/converted_csv/vodopyanov_pursc_occurrences_24456.csv > /app/public/converted_csv/vodopyanov_pursc_occurrences_24456.csv_sorted
[CMD] [2020-11-19 13:44:32] /usr/bin/sort /app/public/converted_csv/vodopyanov_pursc_measurements_24457.csv > /app/public/converted_csv/vodopyanov_pursc_measurements_24457.csv_sorted
[STOP] [2020-11-19 13:44:32] convert_to_csv
[START] [2020-11-19 13:44:32] calculate_delta
[CMD] [2020-11-19 13:44:32] echo "0a" > /app/public/diff/vodopyanov_pursc_refs_24454.diff
[CMD] [2020-11-19 13:44:32] tail -n +1 /app/public/converted_csv/vodopyanov_pursc_refs_24454.csv >> /app/public/diff/vodopyanov_pursc_refs_24454.diff
[CMD] [2020-11-19 13:44:33] echo "." >> /app/public/diff/vodopyanov_pursc_refs_24454.diff
[CMD] [2020-11-19 13:44:33] echo "0a" > /app/public/diff/vodopyanov_pursc_nodes_24455.diff
[CMD] [2020-11-19 13:44:33] tail -n +1 /app/public/converted_csv/vodopyanov_pursc_nodes_24455.csv >> /app/public/diff/vodopyanov_pursc_nodes_24455.diff
[CMD] [2020-11-19 13:44:33] echo "." >> /app/public/diff/vodopyanov_pursc_nodes_24455.diff
[CMD] [2020-11-19 13:44:33] echo "0a" > /app/public/diff/vodopyanov_pursc_occurrences_24456.diff
[CMD] [2020-11-19 13:44:33] tail -n +1 /app/public/converted_csv/vodopyanov_pursc_occurrences_24456.csv >> /app/public/diff/vodopyanov_pursc_occurrences_24456.diff
[CMD] [2020-11-19 13:44:33] echo "." >> /app/public/diff/vodopyanov_pursc_occurrences_24456.diff
[CMD] [2020-11-19 13:44:33] echo "0a" > /app/public/diff/vodopyanov_pursc_measurements_24457.diff
[CMD] [2020-11-19 13:44:33] tail -n +1 /app/public/converted_csv/vodopyanov_pursc_measurements_24457.csv >> /app/public/diff/vodopyanov_pursc_measurements_24457.diff
[CMD] [2020-11-19 13:44:33] echo "." >> /app/public/diff/vodopyanov_pursc_measurements_24457.diff
[STOP] [2020-11-19 13:44:33] calculate_delta
[START] [2020-11-19 13:44:33] parse_diff_and_store
[INFO] [2020-11-19 13:44:33] Loading refs diff file into memory (true lines)...
[INFO] [2020-11-19 13:44:33] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-19 13:44:33] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-19 13:44:33] Loading measurements diff file into memory (true lines)...
[INFO] [2020-11-19 13:44:34] Storing 1 ScientificNames
[INFO] [2020-11-19 13:44:34] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 13:44:34] Average Time: 0.0
[INFO] [2020-11-19 13:44:34] Total Time: 1s
[INFO] [2020-11-19 13:44:34] Storing 1 Nodes
[INFO] [2020-11-19 13:44:34] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 13:44:34] Average Time: 0.0
[INFO] [2020-11-19 13:44:34] Total Time: 1s
[INFO] [2020-11-19 13:44:34] Storing 1 Occurrences
[INFO] [2020-11-19 13:44:34] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 13:44:34] Average Time: 0.0
[INFO] [2020-11-19 13:44:34] Total Time: 1s
[INFO] [2020-11-19 13:44:34] Storing 2 Traits
[INFO] [2020-11-19 13:44:34] Processing group of 2 in 1 groups of 1000
[INFO] [2020-11-19 13:44:34] Average Time: 0.0
[INFO] [2020-11-19 13:44:34] Total Time: 1s
[INFO] [2020-11-19 13:44:34] Storing 2 MetaTraits
[INFO] [2020-11-19 13:44:34] Processing group of 2 in 1 groups of 1000
[INFO] [2020-11-19 13:44:34] Average Time: 0.0
[INFO] [2020-11-19 13:44:34] Total Time: 1s
[STOP] [2020-11-19 13:44:34] parse_diff_and_store
[START] [2020-11-19 13:44:34] resolve_keys
[INFO] [2020-11-19 13:44:40] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-19 13:44:40] traits to occurrences...
[INFO] [2020-11-19 13:44:40] traits to nodes (through occurrences)...
[INFO] [2020-11-19 13:44:40] Traits to sex term...
[INFO] [2020-11-19 13:44:40] Traits to lifestage term...
[INFO] [2020-11-19 13:44:40] MetaTraits to traits...
[INFO] [2020-11-19 13:44:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-19 13:44:40] Assocs to occurrences...
[INFO] [2020-11-19 13:44:40] Assocs to nodes...
[INFO] [2020-11-19 13:44:40] Assoc to sex term...
[INFO] [2020-11-19 13:44:40] Assoc to lifestage term...
[INFO] [2020-11-19 13:44:40] MetaAssoc to assocs...
[STOP] [2020-11-19 13:44:40] resolve_keys
[START] [2020-11-19 13:44:40] hold_for_later_1
[STOP] [2020-11-19 13:44:40] hold_for_later_1
[START] [2020-11-19 13:44:40] hold_for_later_2
[STOP] [2020-11-19 13:44:40] hold_for_later_2
[START] [2020-11-19 13:44:40] resolve_missing_parents
[STOP] [2020-11-19 13:44:40] resolve_missing_parents
[START] [2020-11-19 13:44:40] rebuild_nodes
[START] [2020-11-19 13:44:40] Flattener#flatten
[START] [2020-11-19 13:44:40] Flattener#study_resource
[START] [2020-11-19 13:44:40] Flattener#build_ancestry
[STOP] [2020-11-19 13:44:40] Flattener#build_ancestry
[INFO] [2020-11-19 13:44:40] 1 ancestry keys
[START] [2020-11-19 13:44:40] build_node_ancestors
[INFO] [2020-11-19 13:44:40] old ancestors deleted.
[STOP] [2020-11-19 13:44:40] build_node_ancestors
[WARN] [2020-11-19 13:44:40] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-11-19 13:44:40] Flattener#flatten
[STOP] [2020-11-19 13:44:40] rebuild_nodes
[START] [2020-11-19 13:44:40] resolve_missing_media_owners
[STOP] [2020-11-19 13:44:40] resolve_missing_media_owners
[START] [2020-11-19 13:44:40] sanitize_media_verbatims
[STOP] [2020-11-19 13:44:40] sanitize_media_verbatims
[START] [2020-11-19 13:44:40] queue_downloads
[STOP] [2020-11-19 13:44:40] queue_downloads
[START] [2020-11-19 13:44:40] parse_names
[WARN] [2020-11-19 13:44:40] I see 1 names which still need to be parsed.
[STOP] [2020-11-19 13:44:41] parse_names
[START] [2020-11-19 13:44:41] denormalize_canonical_names_to_nodes
[STOP] [2020-11-19 13:44:41] denormalize_canonical_names_to_nodes
[START] [2020-11-19 13:44:41] match_nodes
[START] [2020-11-19 13:44:41] map_all_nodes_to_pages
[STOP] [2020-11-19 13:44:41] map_all_nodes_to_pages
[INFO] [2020-11-19 13:44:41] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-11-19 13:44:41] update_nodes
[STOP] [2020-11-19 13:44:41] update_nodes
[STOP] [2020-11-19 13:44:41] match_nodes
[START] [2020-11-19 13:44:41] reindex_search
[STOP] [2020-11-19 13:44:41] reindex_search
[START] [2020-11-19 13:44:41] normalize_units
[STOP] [2020-11-19 13:44:41] normalize_units
[START] [2020-11-19 13:44:41] calculate_statistics
[2020-11-19 13:44:41] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-11-19 13:44:41] calculate_statistics
[START] [2020-11-19 13:44:41] complete_harvest_instance
[START] [2020-11-19 13:44:41] overall_tsv_creation
[INFO] [2020-11-19 13:44:41] Processing group of 1 in 1 batches of 10000
[INFO] [2020-11-19 13:45:24] 1 Traits (unfiltered)...
[INFO] [2020-11-19 13:46:06] 1 Traits (filtered)...
[INFO] [2020-11-19 13:46:06] 0 Associations (filtered)...
[INFO] [2020-11-19 13:46:06] 3 metadata added.
[INFO] [2020-11-19 13:46:06] 0 metadata added.
[INFO] [2020-11-19 13:46:06] Average Time: 65.35
[INFO] [2020-11-19 13:46:06] Total Time: 1m25s
[STOP] [2020-11-19 13:46:06] overall_tsv_creation
[INFO] [2020-11-19 13:46:06] Done. Check your files:
[INFO] [2020-11-19 13:46:06] (1 lines) /app/public/data/vodopyanov_pursc/publish_nodes.tsv
[INFO] [2020-11-19 13:46:06] (1 lines) /app/public/data/vodopyanov_pursc/publish_scientific_names.tsv
[INFO] [2020-11-19 13:46:06] (2 lines) /app/public/data/vodopyanov_pursc/publish_traits.tsv
[INFO] [2020-11-19 13:46:06] (4 lines) /app/public/data/vodopyanov_pursc/publish_metadata.tsv
[STOP] [2020-11-19 13:46:06] complete_harvest_instance
[START] [2020-11-19 13:46:06] completed
[STOP] [2020-11-19 13:46:06] completed
[STOP] [2020-11-19 13:46:06] logged process, took 95.26
[INFO] [2021-04-19 14:52:14] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:02:05] ## remove_type: ScientificName
[INFO] [2021-04-19 15:02:05] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:02:05] [15:02:05.702] Removed 1 Scientificnames
[INFO] [2021-04-19 15:02:05] ## remove_type: Vernacular
[INFO] [2021-04-19 15:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:02:05] [15:02:05.704] Removed 0 Vernaculars
[INFO] [2021-04-19 15:02:05] ## remove_type: Article
[INFO] [2021-04-19 15:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:02:05] [15:02:05.705] Removed 0 Articles
[INFO] [2021-04-19 15:02:05] ## remove_type: Medium
[INFO] [2021-04-19 15:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:02:05] [15:02:05.707] Removed 0 Media
[INFO] [2021-04-19 15:02:05] ## remove_type: Trait
[INFO] [2021-04-19 15:02:05] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:02:05] [15:02:05.709] Removed 2 Traits
[INFO] [2021-04-19 15:02:05] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:02:05] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:02:05] [15:02:05.710] Removed 2 Metatraits
[INFO] [2021-04-19 15:02:05] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:02:05] [15:02:05.712] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 15:02:05] ## remove_type: Assoc
[INFO] [2021-04-19 15:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:02:05] [15:02:05.714] Removed 0 Assocs
[INFO] [2021-04-19 15:02:05] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:02:05] [15:02:05.715] Removed 0 Metaassocs
[INFO] [2021-04-19 15:02:05] ## remove_type: Identifier
[INFO] [2021-04-19 15:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:02:05] [15:02:05.717] Removed 0 Identifiers
[INFO] [2021-04-19 15:02:05] ## remove_type: Reference
[INFO] [2021-04-19 15:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:02:05] [15:02:05.719] Removed 0 References
[INFO] [2021-04-19 15:02:05] Starting batch with ID 84620785...
[INFO] [2021-04-19 15:02:05] Starting batch with ID 84620785...
[INFO] [2021-04-19 15:02:05] Starting batch with ID 84620785...
[INFO] [2021-04-19 15:02:05] Starting batch with ID 84620785...
[INFO] [2021-04-19 15:02:05] Starting batch with ID 84620785...
[INFO] [2021-04-19 15:02:05] Starting batch with ID 84620785...
[INFO] [2021-04-19 15:02:05] Starting batch with ID 84620785...
[INFO] [2021-04-19 15:02:05] Starting batch with ID 84620785...
[INFO] [2021-04-19 15:02:05] Starting batch with ID 84620785...
[INFO] [2021-04-19 15:02:05] Starting batch with ID 84620785...
[INFO] [2021-04-19 15:02:05] Starting batch with ID 84620785...
[INFO] [2021-04-19 15:02:05] Starting batch with ID 84620785...
[INFO] [2021-04-19 15:02:05] Starting batch with ID 84620785...
[INFO] [2021-04-19 15:02:05] Starting batch with ID 84620785...
[INFO] [2021-04-19 15:02:05] Starting batch with ID 84620785...
[INFO] [2021-04-19 15:02:05] ## remove_type: Node
[INFO] [2021-04-19 15:02:05] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:02:05] [15:02:05.833] Removed 1 Nodes
[START] [2021-04-19 15:02:05] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:02:05] Creating resource from OpenData
[START] [2021-04-19 15:02:06] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:02:06] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:02:06] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:02:06] Creating resource from OpenData
[START] [2021-04-19 15:02:06] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:02:06] create_harvest_instance
[INFO] [2021-04-19 15:02:06] Created harvest instance #3758
[STOP] [2021-04-19 15:02:06] create_harvest_instance
[START] [2021-04-19 15:02:06] fetch_files
[STOP] [2021-04-19 15:02:06] fetch_files
[START] [2021-04-19 15:02:06] validate_each_file
[INFO] [2021-04-19 15:02:06] Looping over 4 formats...
[INFO] [2021-04-19 15:02:06] ...refs (/app/public/data/vodopyanov_pursc/references.tsv)
[INFO] [2021-04-19 15:02:06] Valid: /app/public/converted_csv/vodopyanov_pursc_refs_3758.csv (0 lines)
[INFO] [2021-04-19 15:02:06] ...nodes (/app/public/data/vodopyanov_pursc/taxa.txt)
[INFO] [2021-04-19 15:02:06] Valid: /app/public/converted_csv/vodopyanov_pursc_nodes_3758.csv (1 lines)
[INFO] [2021-04-19 15:02:06] ...occurrences (/app/public/data/vodopyanov_pursc/occurrences.txt)
[INFO] [2021-04-19 15:02:06] Valid: /app/public/converted_csv/vodopyanov_pursc_occurrences_3758.csv (1 lines)
[INFO] [2021-04-19 15:02:06] ...measurements (/app/public/data/vodopyanov_pursc/measurementsorfacts.txt)
[INFO] [2021-04-19 15:02:06] Valid: /app/public/converted_csv/vodopyanov_pursc_measurements_3758.csv (2 lines)
[STOP] [2021-04-19 15:02:06] validate_each_file
[START] [2021-04-19 15:02:06] convert_to_csv
[INFO] [2021-04-19 15:02:06] Looping over 4 formats...
[INFO] [2021-04-19 15:02:06] ...refs (/app/public/data/vodopyanov_pursc/references.tsv)
[CMD] [2021-04-19 15:02:06] /usr/bin/sort /app/public/converted_csv/vodopyanov_pursc_refs_3758.csv > /app/public/converted_csv/vodopyanov_pursc_refs_3758.csv_sorted
[INFO] [2021-04-19 15:02:06] Converted: /app/public/converted_csv/vodopyanov_pursc_refs_3758.csv (0 lines)
[INFO] [2021-04-19 15:02:06] ...nodes (/app/public/data/vodopyanov_pursc/taxa.txt)
[CMD] [2021-04-19 15:02:06] /usr/bin/sort /app/public/converted_csv/vodopyanov_pursc_nodes_3758.csv > /app/public/converted_csv/vodopyanov_pursc_nodes_3758.csv_sorted
[INFO] [2021-04-19 15:02:06] Converted: /app/public/converted_csv/vodopyanov_pursc_nodes_3758.csv (1 lines)
[INFO] [2021-04-19 15:02:06] ...occurrences (/app/public/data/vodopyanov_pursc/occurrences.txt)
[CMD] [2021-04-19 15:02:06] /usr/bin/sort /app/public/converted_csv/vodopyanov_pursc_occurrences_3758.csv > /app/public/converted_csv/vodopyanov_pursc_occurrences_3758.csv_sorted
[INFO] [2021-04-19 15:02:06] Converted: /app/public/converted_csv/vodopyanov_pursc_occurrences_3758.csv (1 lines)
[INFO] [2021-04-19 15:02:06] ...measurements (/app/public/data/vodopyanov_pursc/measurementsorfacts.txt)
[CMD] [2021-04-19 15:02:06] /usr/bin/sort /app/public/converted_csv/vodopyanov_pursc_measurements_3758.csv > /app/public/converted_csv/vodopyanov_pursc_measurements_3758.csv_sorted
[INFO] [2021-04-19 15:02:06] Converted: /app/public/converted_csv/vodopyanov_pursc_measurements_3758.csv (2 lines)
[STOP] [2021-04-19 15:02:06] convert_to_csv
[START] [2021-04-19 15:02:06] calculate_delta
[INFO] [2021-04-19 15:02:06] Looping over 4 formats...
[INFO] [2021-04-19 15:02:06] ...refs (/app/public/data/vodopyanov_pursc/references.tsv)
[CMD] [2021-04-19 15:02:06] echo "0a" > /app/public/diff/vodopyanov_pursc_refs_3758.diff
[CMD] [2021-04-19 15:02:06] tail -n +1 /app/public/converted_csv/vodopyanov_pursc_refs_3758.csv >> /app/public/diff/vodopyanov_pursc_refs_3758.diff
[CMD] [2021-04-19 15:02:06] echo "." >> /app/public/diff/vodopyanov_pursc_refs_3758.diff
[INFO] [2021-04-19 15:02:06] Created diff: /app/public/diff/vodopyanov_pursc_refs_3758.diff (2 lines)
[INFO] [2021-04-19 15:02:06] ...nodes (/app/public/data/vodopyanov_pursc/taxa.txt)
[CMD] [2021-04-19 15:02:06] echo "0a" > /app/public/diff/vodopyanov_pursc_nodes_3758.diff
[CMD] [2021-04-19 15:02:06] tail -n +1 /app/public/converted_csv/vodopyanov_pursc_nodes_3758.csv >> /app/public/diff/vodopyanov_pursc_nodes_3758.diff
[CMD] [2021-04-19 15:02:06] echo "." >> /app/public/diff/vodopyanov_pursc_nodes_3758.diff
[INFO] [2021-04-19 15:02:06] Created diff: /app/public/diff/vodopyanov_pursc_nodes_3758.diff (3 lines)
[INFO] [2021-04-19 15:02:06] ...occurrences (/app/public/data/vodopyanov_pursc/occurrences.txt)
[CMD] [2021-04-19 15:02:06] echo "0a" > /app/public/diff/vodopyanov_pursc_occurrences_3758.diff
[CMD] [2021-04-19 15:02:06] tail -n +1 /app/public/converted_csv/vodopyanov_pursc_occurrences_3758.csv >> /app/public/diff/vodopyanov_pursc_occurrences_3758.diff
[CMD] [2021-04-19 15:02:06] echo "." >> /app/public/diff/vodopyanov_pursc_occurrences_3758.diff
[INFO] [2021-04-19 15:02:06] Created diff: /app/public/diff/vodopyanov_pursc_occurrences_3758.diff (3 lines)
[INFO] [2021-04-19 15:02:06] ...measurements (/app/public/data/vodopyanov_pursc/measurementsorfacts.txt)
[CMD] [2021-04-19 15:02:06] echo "0a" > /app/public/diff/vodopyanov_pursc_measurements_3758.diff
[CMD] [2021-04-19 15:02:06] tail -n +1 /app/public/converted_csv/vodopyanov_pursc_measurements_3758.csv >> /app/public/diff/vodopyanov_pursc_measurements_3758.diff
[CMD] [2021-04-19 15:02:06] echo "." >> /app/public/diff/vodopyanov_pursc_measurements_3758.diff
[INFO] [2021-04-19 15:02:06] Created diff: /app/public/diff/vodopyanov_pursc_measurements_3758.diff (4 lines)
[STOP] [2021-04-19 15:02:06] calculate_delta
[START] [2021-04-19 15:02:06] parse_diff_and_store
[INFO] [2021-04-19 15:02:06] Handling diff: /app/public/diff/vodopyanov_pursc_refs_3758.diff (2 lines)
[INFO] [2021-04-19 15:02:06] Loading refs diff file into memory (2 /app/public/diff/vodopyanov_pursc_refs_3758.diff lines)...
[INFO] [2021-04-19 15:02:06] Handling diff: /app/public/diff/vodopyanov_pursc_nodes_3758.diff (3 lines)
[INFO] [2021-04-19 15:02:06] Loading nodes diff file into memory (3 /app/public/diff/vodopyanov_pursc_nodes_3758.diff lines)...
[INFO] [2021-04-19 15:02:06] Handling diff: /app/public/diff/vodopyanov_pursc_occurrences_3758.diff (3 lines)
[INFO] [2021-04-19 15:02:06] Loading occurrences diff file into memory (3 /app/public/diff/vodopyanov_pursc_occurrences_3758.diff lines)...
[INFO] [2021-04-19 15:02:06] Handling diff: /app/public/diff/vodopyanov_pursc_measurements_3758.diff (4 lines)
[INFO] [2021-04-19 15:02:06] Loading measurements diff file into memory (4 /app/public/diff/vodopyanov_pursc_measurements_3758.diff lines)...
[INFO] [2021-04-19 15:02:06] Storing 1 ScientificNames
[INFO] [2021-04-19 15:02:06] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:02:06] Average Time: 0.0
[INFO] [2021-04-19 15:02:06] Total Time: 1s
[INFO] [2021-04-19 15:02:06] Storing 1 Nodes
[INFO] [2021-04-19 15:02:06] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:02:06] Average Time: 0.0
[INFO] [2021-04-19 15:02:06] Total Time: 1s
[INFO] [2021-04-19 15:02:06] Storing 1 Occurrences
[INFO] [2021-04-19 15:02:06] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:02:06] Average Time: 0.0
[INFO] [2021-04-19 15:02:06] Total Time: 1s
[INFO] [2021-04-19 15:02:06] Storing 2 Traits
[INFO] [2021-04-19 15:02:06] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:02:06] Average Time: 0.0
[INFO] [2021-04-19 15:02:06] Total Time: 1s
[INFO] [2021-04-19 15:02:06] Storing 2 MetaTraits
[INFO] [2021-04-19 15:02:06] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:02:06] Average Time: 0.0
[INFO] [2021-04-19 15:02:06] Total Time: 1s
[STOP] [2021-04-19 15:02:06] parse_diff_and_store
[START] [2021-04-19 15:02:06] resolve_keys
[INFO] [2021-04-19 15:02:12] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:02:12] traits to occurrences...
[INFO] [2021-04-19 15:02:12] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:02:12] Traits to sex term...
[INFO] [2021-04-19 15:02:12] Traits to lifestage term...
[INFO] [2021-04-19 15:02:12] MetaTraits to traits...
[INFO] [2021-04-19 15:02:12] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:02:12] Assocs to occurrences...
[INFO] [2021-04-19 15:02:12] Assocs to nodes...
[INFO] [2021-04-19 15:02:12] Assoc to sex term...
[INFO] [2021-04-19 15:02:12] Assoc to lifestage term...
[INFO] [2021-04-19 15:02:12] MetaAssoc to assocs...
[STOP] [2021-04-19 15:02:12] resolve_keys
[START] [2021-04-19 15:02:12] hold_for_later_1
[STOP] [2021-04-19 15:02:12] hold_for_later_1
[START] [2021-04-19 15:02:12] hold_for_later_2
[STOP] [2021-04-19 15:02:12] hold_for_later_2
[START] [2021-04-19 15:02:12] resolve_missing_parents
[STOP] [2021-04-19 15:02:12] resolve_missing_parents
[START] [2021-04-19 15:02:12] rebuild_nodes
[START] [2021-04-19 15:02:12] Flattener#flatten
[START] [2021-04-19 15:02:12] Flattener#study_resource
[START] [2021-04-19 15:02:12] Flattener#build_ancestry
[STOP] [2021-04-19 15:02:12] Flattener#build_ancestry
[INFO] [2021-04-19 15:02:12] 1 ancestry keys
[START] [2021-04-19 15:02:12] build_node_ancestors
[INFO] [2021-04-19 15:02:12] old ancestors deleted.
[STOP] [2021-04-19 15:02:12] build_node_ancestors
[WARN] [2021-04-19 15:02:12] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:02:12] Flattener#flatten
[STOP] [2021-04-19 15:02:12] rebuild_nodes
[START] [2021-04-19 15:02:12] resolve_missing_media_owners
[STOP] [2021-04-19 15:02:12] resolve_missing_media_owners
[START] [2021-04-19 15:02:12] sanitize_media_verbatims
[STOP] [2021-04-19 15:02:12] sanitize_media_verbatims
[START] [2021-04-19 15:02:12] queue_downloads
[STOP] [2021-04-19 15:02:12] queue_downloads
[START] [2021-04-19 15:02:12] parse_names
[WARN] [2021-04-19 15:02:12] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 15:02:13] parse_names
[START] [2021-04-19 15:02:13] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:02:13] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:02:13] match_nodes
[START] [2021-04-19 15:02:13] map_all_nodes_to_pages
[STOP] [2021-04-19 15:02:13] map_all_nodes_to_pages
[INFO] [2021-04-19 15:02:13] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 15:02:13] update_nodes
[STOP] [2021-04-19 15:02:13] update_nodes
[STOP] [2021-04-19 15:02:13] match_nodes
[START] [2021-04-19 15:02:13] reindex_search
[STOP] [2021-04-19 15:02:13] reindex_search
[START] [2021-04-19 15:02:13] normalize_units
[STOP] [2021-04-19 15:02:13] normalize_units
[START] [2021-04-19 15:02:13] calculate_statistics
[2021-04-19 15:02:13] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:02:13] calculate_statistics
[START] [2021-04-19 15:02:13] complete_harvest_instance
[START] [2021-04-19 15:02:13] overall_tsv_creation
[INFO] [2021-04-19 15:02:13] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 15:02:49] 1 Traits (unfiltered)...
[INFO] [2021-04-19 15:03:20] 1 Traits (filtered)...
[INFO] [2021-04-19 15:03:20] 0 Associations (filtered)...
[INFO] [2021-04-19 15:03:20] 1 metadata added.
[INFO] [2021-04-19 15:03:20] 0 metadata added.
[INFO] [2021-04-19 15:03:46] Average Time: 69.42
[INFO] [2021-04-19 15:03:46] Total Time: 1m34s
[STOP] [2021-04-19 15:03:46] overall_tsv_creation
[INFO] [2021-04-19 15:03:46] Done. Check your files:
[INFO] [2021-04-19 15:03:46] (1 lines) /app/public/data/vodopyanov_pursc/publish_nodes.tsv
[INFO] [2021-04-19 15:03:46] (1 lines) /app/public/data/vodopyanov_pursc/publish_scientific_names.tsv
[INFO] [2021-04-19 15:03:47] (2 lines) /app/public/data/vodopyanov_pursc/publish_traits.tsv
[INFO] [2021-04-19 15:03:47] (2 lines) /app/public/data/vodopyanov_pursc/publish_metadata.tsv
[STOP] [2021-04-19 15:03:47] complete_harvest_instance
[START] [2021-04-19 15:03:47] completed
[STOP] [2021-04-19 15:03:47] completed
[STOP] [2021-04-19 15:03:47] logged process, took 100.82

Latest Process

19 Apr 15:02 EXITED currently processing 0