Harvest for von Reumont et al 2014 Created 19 Apr 14:46

Harvesting Log

# Logfile created on 2020-08-27 15:20:24 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:20:24] logged process
[START] [2020-08-27 15:20:24] Creating resource from OpenData
[START] [2020-08-27 15:20:24] logged process
[START] [2020-08-27 15:20:24] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:20:24] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:20:24] Creating resource from OpenData
[INFO] [2020-11-19 12:43:29] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-11-19 12:43:30] ## remove_type: ScientificName
[INFO] [2020-11-19 12:43:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:43:30] [12:43:30.718] Removed 0 Scientificnames
[INFO] [2020-11-19 12:43:30] ## remove_type: Vernacular
[INFO] [2020-11-19 12:43:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:43:30] [12:43:30.721] Removed 0 Vernaculars
[INFO] [2020-11-19 12:43:30] ## remove_type: Article
[INFO] [2020-11-19 12:43:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:43:30] [12:43:30.724] Removed 0 Articles
[INFO] [2020-11-19 12:43:30] ## remove_type: Medium
[INFO] [2020-11-19 12:43:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:43:30] [12:43:30.727] Removed 0 Media
[INFO] [2020-11-19 12:43:30] ## remove_type: Trait
[INFO] [2020-11-19 12:43:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:43:30] [12:43:30.730] Removed 0 Traits
[INFO] [2020-11-19 12:43:30] ## remove_type: MetaTrait
[INFO] [2020-11-19 12:43:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:43:30] [12:43:30.733] Removed 0 Metatraits
[INFO] [2020-11-19 12:43:30] ## remove_type: OccurrenceMetadatum
[INFO] [2020-11-19 12:43:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:43:30] [12:43:30.736] Removed 0 Occurrencemetadata
[INFO] [2020-11-19 12:43:30] ## remove_type: Assoc
[INFO] [2020-11-19 12:43:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:43:30] [12:43:30.739] Removed 0 Assocs
[INFO] [2020-11-19 12:43:30] ## remove_type: MetaAssoc
[INFO] [2020-11-19 12:43:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:43:30] [12:43:30.742] Removed 0 Metaassocs
[INFO] [2020-11-19 12:43:30] ## remove_type: Identifier
[INFO] [2020-11-19 12:43:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:43:30] [12:43:30.744] Removed 0 Identifiers
[INFO] [2020-11-19 12:43:30] ## remove_type: Reference
[INFO] [2020-11-19 12:43:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:43:30] [12:43:30.747] Removed 0 References
[INFO] [2020-11-19 12:43:30] ## remove_type: Node
[INFO] [2020-11-19 12:43:30] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:43:30] [12:43:30.768] Removed 0 Nodes
[START] [2020-11-19 12:43:30] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 12:43:30] Creating resource from OpenData
[START] [2020-11-19 12:43:30] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 12:43:30] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 12:43:31] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 12:43:31] Creating resource from OpenData
[START] [2020-11-19 12:43:31] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 12:43:31] create_harvest_instance
[STOP] [2020-11-19 12:43:32] create_harvest_instance
[START] [2020-11-19 12:43:32] fetch_files
[STOP] [2020-11-19 12:43:32] fetch_files
[START] [2020-11-19 12:43:32] validate_each_file
[STOP] [2020-11-19 12:43:32] validate_each_file
[START] [2020-11-19 12:43:32] convert_to_csv
[CMD] [2020-11-19 12:43:32] /usr/bin/sort /app/public/converted_csv/vreav_refs_24398.csv > /app/public/converted_csv/vreav_refs_24398.csv_sorted
[CMD] [2020-11-19 12:43:32] /usr/bin/sort /app/public/converted_csv/vreav_nodes_24399.csv > /app/public/converted_csv/vreav_nodes_24399.csv_sorted
[CMD] [2020-11-19 12:43:32] /usr/bin/sort /app/public/converted_csv/vreav_occurrences_24400.csv > /app/public/converted_csv/vreav_occurrences_24400.csv_sorted
[CMD] [2020-11-19 12:43:32] /usr/bin/sort /app/public/converted_csv/vreav_measurements_24401.csv > /app/public/converted_csv/vreav_measurements_24401.csv_sorted
[STOP] [2020-11-19 12:43:32] convert_to_csv
[START] [2020-11-19 12:43:32] calculate_delta
[CMD] [2020-11-19 12:43:32] echo "0a" > /app/public/diff/vreav_refs_24398.diff
[CMD] [2020-11-19 12:43:32] tail -n +1 /app/public/converted_csv/vreav_refs_24398.csv >> /app/public/diff/vreav_refs_24398.diff
[CMD] [2020-11-19 12:43:32] echo "." >> /app/public/diff/vreav_refs_24398.diff
[CMD] [2020-11-19 12:43:32] echo "0a" > /app/public/diff/vreav_nodes_24399.diff
[CMD] [2020-11-19 12:43:32] tail -n +1 /app/public/converted_csv/vreav_nodes_24399.csv >> /app/public/diff/vreav_nodes_24399.diff
[CMD] [2020-11-19 12:43:32] echo "." >> /app/public/diff/vreav_nodes_24399.diff
[CMD] [2020-11-19 12:43:32] echo "0a" > /app/public/diff/vreav_occurrences_24400.diff
[CMD] [2020-11-19 12:43:32] tail -n +1 /app/public/converted_csv/vreav_occurrences_24400.csv >> /app/public/diff/vreav_occurrences_24400.diff
[CMD] [2020-11-19 12:43:32] echo "." >> /app/public/diff/vreav_occurrences_24400.diff
[CMD] [2020-11-19 12:43:32] echo "0a" > /app/public/diff/vreav_measurements_24401.diff
[CMD] [2020-11-19 12:43:32] tail -n +1 /app/public/converted_csv/vreav_measurements_24401.csv >> /app/public/diff/vreav_measurements_24401.diff
[CMD] [2020-11-19 12:43:32] echo "." >> /app/public/diff/vreav_measurements_24401.diff
[STOP] [2020-11-19 12:43:32] calculate_delta
[START] [2020-11-19 12:43:32] parse_diff_and_store
[INFO] [2020-11-19 12:43:32] Loading refs diff file into memory (true lines)...
[INFO] [2020-11-19 12:43:32] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-19 12:43:32] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-19 12:43:33] Loading measurements diff file into memory (true lines)...
[INFO] [2020-11-19 12:43:34] Storing 1 ScientificNames
[INFO] [2020-11-19 12:43:34] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 12:43:34] Average Time: 0.01
[INFO] [2020-11-19 12:43:34] Total Time: 1s
[INFO] [2020-11-19 12:43:34] Storing 1 Nodes
[INFO] [2020-11-19 12:43:34] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 12:43:34] Average Time: 0.0
[INFO] [2020-11-19 12:43:34] Total Time: 1s
[INFO] [2020-11-19 12:43:34] Storing 1 Occurrences
[INFO] [2020-11-19 12:43:34] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 12:43:34] Average Time: 0.0
[INFO] [2020-11-19 12:43:34] Total Time: 1s
[INFO] [2020-11-19 12:43:34] Storing 6 Traits
[INFO] [2020-11-19 12:43:34] Processing group of 6 in 1 groups of 1000
[INFO] [2020-11-19 12:43:34] Average Time: 0.01
[INFO] [2020-11-19 12:43:34] Total Time: 1s
[INFO] [2020-11-19 12:43:34] Storing 3 MetaTraits
[INFO] [2020-11-19 12:43:34] Processing group of 3 in 1 groups of 1000
[INFO] [2020-11-19 12:43:34] Average Time: 0.0
[INFO] [2020-11-19 12:43:34] Total Time: 1s
[STOP] [2020-11-19 12:43:34] parse_diff_and_store
[START] [2020-11-19 12:43:34] resolve_keys
[INFO] [2020-11-19 12:43:40] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-19 12:43:40] traits to occurrences...
[INFO] [2020-11-19 12:43:40] traits to nodes (through occurrences)...
[INFO] [2020-11-19 12:43:40] Traits to sex term...
[INFO] [2020-11-19 12:43:40] Traits to lifestage term...
[INFO] [2020-11-19 12:43:40] MetaTraits to traits...
[INFO] [2020-11-19 12:43:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-19 12:43:40] Assocs to occurrences...
[INFO] [2020-11-19 12:43:40] Assocs to nodes...
[INFO] [2020-11-19 12:43:40] Assoc to sex term...
[INFO] [2020-11-19 12:43:40] Assoc to lifestage term...
[INFO] [2020-11-19 12:43:40] MetaAssoc to assocs...
[STOP] [2020-11-19 12:43:40] resolve_keys
[START] [2020-11-19 12:43:40] hold_for_later_1
[STOP] [2020-11-19 12:43:40] hold_for_later_1
[START] [2020-11-19 12:43:40] hold_for_later_2
[STOP] [2020-11-19 12:43:40] hold_for_later_2
[START] [2020-11-19 12:43:40] resolve_missing_parents
[STOP] [2020-11-19 12:43:40] resolve_missing_parents
[START] [2020-11-19 12:43:40] rebuild_nodes
[START] [2020-11-19 12:43:40] Flattener#flatten
[START] [2020-11-19 12:43:40] Flattener#study_resource
[START] [2020-11-19 12:43:40] Flattener#build_ancestry
[STOP] [2020-11-19 12:43:40] Flattener#build_ancestry
[INFO] [2020-11-19 12:43:40] 1 ancestry keys
[START] [2020-11-19 12:43:40] build_node_ancestors
[INFO] [2020-11-19 12:43:40] old ancestors deleted.
[STOP] [2020-11-19 12:43:40] build_node_ancestors
[WARN] [2020-11-19 12:43:40] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-11-19 12:43:40] Flattener#flatten
[STOP] [2020-11-19 12:43:40] rebuild_nodes
[START] [2020-11-19 12:43:40] resolve_missing_media_owners
[STOP] [2020-11-19 12:43:40] resolve_missing_media_owners
[START] [2020-11-19 12:43:40] sanitize_media_verbatims
[STOP] [2020-11-19 12:43:40] sanitize_media_verbatims
[START] [2020-11-19 12:43:40] queue_downloads
[STOP] [2020-11-19 12:43:40] queue_downloads
[START] [2020-11-19 12:43:40] parse_names
[WARN] [2020-11-19 12:43:40] I see 1 names which still need to be parsed.
[STOP] [2020-11-19 12:43:41] parse_names
[START] [2020-11-19 12:43:41] denormalize_canonical_names_to_nodes
[STOP] [2020-11-19 12:43:41] denormalize_canonical_names_to_nodes
[START] [2020-11-19 12:43:41] match_nodes
[START] [2020-11-19 12:43:41] map_all_nodes_to_pages
[STOP] [2020-11-19 12:43:41] map_all_nodes_to_pages
[INFO] [2020-11-19 12:43:41] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-11-19 12:43:41] update_nodes
[STOP] [2020-11-19 12:43:41] update_nodes
[STOP] [2020-11-19 12:43:41] match_nodes
[START] [2020-11-19 12:43:41] reindex_search
[STOP] [2020-11-19 12:43:41] reindex_search
[START] [2020-11-19 12:43:41] normalize_units
[STOP] [2020-11-19 12:43:41] normalize_units
[START] [2020-11-19 12:43:41] calculate_statistics
[2020-11-19 12:43:41] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-11-19 12:43:41] calculate_statistics
[START] [2020-11-19 12:43:41] complete_harvest_instance
[START] [2020-11-19 12:43:41] overall_tsv_creation
[INFO] [2020-11-19 12:43:41] Processing group of 1 in 1 batches of 10000
[INFO] [2020-11-19 12:44:24] 3 Traits (unfiltered)...
[INFO] [2020-11-19 12:45:06] 3 Traits (filtered)...
[INFO] [2020-11-19 12:45:06] 0 Associations (filtered)...
[INFO] [2020-11-19 12:45:06] 6 metadata added.
[INFO] [2020-11-19 12:45:06] 0 metadata added.
[INFO] [2020-11-19 12:45:06] Average Time: 65.95
[INFO] [2020-11-19 12:45:06] Total Time: 1m26s
[STOP] [2020-11-19 12:45:06] overall_tsv_creation
[INFO] [2020-11-19 12:45:06] Done. Check your files:
[INFO] [2020-11-19 12:45:06] (1 lines) /app/public/data/vreav/publish_nodes.tsv
[INFO] [2020-11-19 12:45:06] (1 lines) /app/public/data/vreav/publish_scientific_names.tsv
[INFO] [2020-11-19 12:45:06] (4 lines) /app/public/data/vreav/publish_traits.tsv
[INFO] [2020-11-19 12:45:06] (7 lines) /app/public/data/vreav/publish_metadata.tsv
[STOP] [2020-11-19 12:45:06] complete_harvest_instance
[START] [2020-11-19 12:45:06] completed
[STOP] [2020-11-19 12:45:06] completed
[STOP] [2020-11-19 12:45:06] logged process, took 95.87
[INFO] [2021-04-19 14:39:36] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 14:46:18] ## remove_type: ScientificName
[INFO] [2021-04-19 14:46:18] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 14:46:18] [14:46:18.251] Removed 1 Scientificnames
[INFO] [2021-04-19 14:46:18] ## remove_type: Vernacular
[INFO] [2021-04-19 14:46:18] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:46:18] [14:46:18.253] Removed 0 Vernaculars
[INFO] [2021-04-19 14:46:18] ## remove_type: Article
[INFO] [2021-04-19 14:46:18] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:46:18] [14:46:18.254] Removed 0 Articles
[INFO] [2021-04-19 14:46:18] ## remove_type: Medium
[INFO] [2021-04-19 14:46:18] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:46:18] [14:46:18.256] Removed 0 Media
[INFO] [2021-04-19 14:46:18] ## remove_type: Trait
[INFO] [2021-04-19 14:46:18] ++ Calling delete_all on 6 instances...
[INFO] [2021-04-19 14:46:18] [14:46:18.258] Removed 6 Traits
[INFO] [2021-04-19 14:46:18] ## remove_type: MetaTrait
[INFO] [2021-04-19 14:46:18] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 14:46:18] [14:46:18.259] Removed 3 Metatraits
[INFO] [2021-04-19 14:46:18] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 14:46:18] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:46:18] [14:46:18.261] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 14:46:18] ## remove_type: Assoc
[INFO] [2021-04-19 14:46:18] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:46:18] [14:46:18.262] Removed 0 Assocs
[INFO] [2021-04-19 14:46:18] ## remove_type: MetaAssoc
[INFO] [2021-04-19 14:46:18] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:46:18] [14:46:18.264] Removed 0 Metaassocs
[INFO] [2021-04-19 14:46:18] ## remove_type: Identifier
[INFO] [2021-04-19 14:46:18] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:46:18] [14:46:18.265] Removed 0 Identifiers
[INFO] [2021-04-19 14:46:18] ## remove_type: Reference
[INFO] [2021-04-19 14:46:18] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:46:18] [14:46:18.266] Removed 0 References
[INFO] [2021-04-19 14:46:18] Starting batch with ID 84620777...
[INFO] [2021-04-19 14:46:18] Starting batch with ID 84620777...
[INFO] [2021-04-19 14:46:18] Starting batch with ID 84620777...
[INFO] [2021-04-19 14:46:18] Starting batch with ID 84620777...
[INFO] [2021-04-19 14:46:18] Starting batch with ID 84620777...
[INFO] [2021-04-19 14:46:18] ## remove_type: Node
[INFO] [2021-04-19 14:46:18] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 14:46:18] [14:46:18.313] Removed 1 Nodes
[START] [2021-04-19 14:46:18] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:46:18] Creating resource from OpenData
[START] [2021-04-19 14:46:18] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:46:18] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 14:46:18] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 14:46:18] Creating resource from OpenData
[START] [2021-04-19 14:46:18] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:46:18] create_harvest_instance
[INFO] [2021-04-19 14:46:18] Created harvest instance #3750
[STOP] [2021-04-19 14:46:18] create_harvest_instance
[START] [2021-04-19 14:46:18] fetch_files
[STOP] [2021-04-19 14:46:18] fetch_files
[START] [2021-04-19 14:46:18] validate_each_file
[INFO] [2021-04-19 14:46:18] Looping over 4 formats...
[INFO] [2021-04-19 14:46:18] ...refs (/app/public/data/vreav/references.tsv)
[INFO] [2021-04-19 14:46:18] Valid: /app/public/converted_csv/vreav_refs_3750.csv (0 lines)
[INFO] [2021-04-19 14:46:18] ...nodes (/app/public/data/vreav/taxa.txt)
[INFO] [2021-04-19 14:46:18] Valid: /app/public/converted_csv/vreav_nodes_3750.csv (1 lines)
[INFO] [2021-04-19 14:46:18] ...occurrences (/app/public/data/vreav/occurrences.txt)
[INFO] [2021-04-19 14:46:18] Valid: /app/public/converted_csv/vreav_occurrences_3750.csv (1 lines)
[INFO] [2021-04-19 14:46:18] ...measurements (/app/public/data/vreav/measurementsorfacts.txt)
[INFO] [2021-04-19 14:46:18] Valid: /app/public/converted_csv/vreav_measurements_3750.csv (6 lines)
[STOP] [2021-04-19 14:46:18] validate_each_file
[START] [2021-04-19 14:46:18] convert_to_csv
[INFO] [2021-04-19 14:46:18] Looping over 4 formats...
[INFO] [2021-04-19 14:46:18] ...refs (/app/public/data/vreav/references.tsv)
[CMD] [2021-04-19 14:46:18] /usr/bin/sort /app/public/converted_csv/vreav_refs_3750.csv > /app/public/converted_csv/vreav_refs_3750.csv_sorted
[INFO] [2021-04-19 14:46:18] Converted: /app/public/converted_csv/vreav_refs_3750.csv (0 lines)
[INFO] [2021-04-19 14:46:18] ...nodes (/app/public/data/vreav/taxa.txt)
[CMD] [2021-04-19 14:46:18] /usr/bin/sort /app/public/converted_csv/vreav_nodes_3750.csv > /app/public/converted_csv/vreav_nodes_3750.csv_sorted
[INFO] [2021-04-19 14:46:18] Converted: /app/public/converted_csv/vreav_nodes_3750.csv (1 lines)
[INFO] [2021-04-19 14:46:18] ...occurrences (/app/public/data/vreav/occurrences.txt)
[CMD] [2021-04-19 14:46:18] /usr/bin/sort /app/public/converted_csv/vreav_occurrences_3750.csv > /app/public/converted_csv/vreav_occurrences_3750.csv_sorted
[INFO] [2021-04-19 14:46:18] Converted: /app/public/converted_csv/vreav_occurrences_3750.csv (1 lines)
[INFO] [2021-04-19 14:46:18] ...measurements (/app/public/data/vreav/measurementsorfacts.txt)
[CMD] [2021-04-19 14:46:18] /usr/bin/sort /app/public/converted_csv/vreav_measurements_3750.csv > /app/public/converted_csv/vreav_measurements_3750.csv_sorted
[INFO] [2021-04-19 14:46:18] Converted: /app/public/converted_csv/vreav_measurements_3750.csv (6 lines)
[STOP] [2021-04-19 14:46:18] convert_to_csv
[START] [2021-04-19 14:46:18] calculate_delta
[INFO] [2021-04-19 14:46:18] Looping over 4 formats...
[INFO] [2021-04-19 14:46:18] ...refs (/app/public/data/vreav/references.tsv)
[CMD] [2021-04-19 14:46:18] echo "0a" > /app/public/diff/vreav_refs_3750.diff
[CMD] [2021-04-19 14:46:18] tail -n +1 /app/public/converted_csv/vreav_refs_3750.csv >> /app/public/diff/vreav_refs_3750.diff
[CMD] [2021-04-19 14:46:18] echo "." >> /app/public/diff/vreav_refs_3750.diff
[INFO] [2021-04-19 14:46:18] Created diff: /app/public/diff/vreav_refs_3750.diff (2 lines)
[INFO] [2021-04-19 14:46:18] ...nodes (/app/public/data/vreav/taxa.txt)
[CMD] [2021-04-19 14:46:18] echo "0a" > /app/public/diff/vreav_nodes_3750.diff
[CMD] [2021-04-19 14:46:18] tail -n +1 /app/public/converted_csv/vreav_nodes_3750.csv >> /app/public/diff/vreav_nodes_3750.diff
[CMD] [2021-04-19 14:46:18] echo "." >> /app/public/diff/vreav_nodes_3750.diff
[INFO] [2021-04-19 14:46:18] Created diff: /app/public/diff/vreav_nodes_3750.diff (3 lines)
[INFO] [2021-04-19 14:46:18] ...occurrences (/app/public/data/vreav/occurrences.txt)
[CMD] [2021-04-19 14:46:18] echo "0a" > /app/public/diff/vreav_occurrences_3750.diff
[CMD] [2021-04-19 14:46:18] tail -n +1 /app/public/converted_csv/vreav_occurrences_3750.csv >> /app/public/diff/vreav_occurrences_3750.diff
[CMD] [2021-04-19 14:46:18] echo "." >> /app/public/diff/vreav_occurrences_3750.diff
[INFO] [2021-04-19 14:46:18] Created diff: /app/public/diff/vreav_occurrences_3750.diff (3 lines)
[INFO] [2021-04-19 14:46:18] ...measurements (/app/public/data/vreav/measurementsorfacts.txt)
[CMD] [2021-04-19 14:46:18] echo "0a" > /app/public/diff/vreav_measurements_3750.diff
[CMD] [2021-04-19 14:46:18] tail -n +1 /app/public/converted_csv/vreav_measurements_3750.csv >> /app/public/diff/vreav_measurements_3750.diff
[CMD] [2021-04-19 14:46:18] echo "." >> /app/public/diff/vreav_measurements_3750.diff
[INFO] [2021-04-19 14:46:18] Created diff: /app/public/diff/vreav_measurements_3750.diff (8 lines)
[STOP] [2021-04-19 14:46:18] calculate_delta
[START] [2021-04-19 14:46:18] parse_diff_and_store
[INFO] [2021-04-19 14:46:18] Handling diff: /app/public/diff/vreav_refs_3750.diff (2 lines)
[INFO] [2021-04-19 14:46:18] Loading refs diff file into memory (2 /app/public/diff/vreav_refs_3750.diff lines)...
[INFO] [2021-04-19 14:46:18] Handling diff: /app/public/diff/vreav_nodes_3750.diff (3 lines)
[INFO] [2021-04-19 14:46:18] Loading nodes diff file into memory (3 /app/public/diff/vreav_nodes_3750.diff lines)...
[INFO] [2021-04-19 14:46:19] Handling diff: /app/public/diff/vreav_occurrences_3750.diff (3 lines)
[INFO] [2021-04-19 14:46:19] Loading occurrences diff file into memory (3 /app/public/diff/vreav_occurrences_3750.diff lines)...
[INFO] [2021-04-19 14:46:19] Handling diff: /app/public/diff/vreav_measurements_3750.diff (8 lines)
[INFO] [2021-04-19 14:46:19] Loading measurements diff file into memory (8 /app/public/diff/vreav_measurements_3750.diff lines)...
[INFO] [2021-04-19 14:46:19] Storing 1 ScientificNames
[INFO] [2021-04-19 14:46:19] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:46:19] Average Time: 0.0
[INFO] [2021-04-19 14:46:19] Total Time: 1s
[INFO] [2021-04-19 14:46:19] Storing 1 Nodes
[INFO] [2021-04-19 14:46:19] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:46:19] Average Time: 0.0
[INFO] [2021-04-19 14:46:19] Total Time: 1s
[INFO] [2021-04-19 14:46:19] Storing 1 Occurrences
[INFO] [2021-04-19 14:46:19] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:46:19] Average Time: 0.0
[INFO] [2021-04-19 14:46:19] Total Time: 1s
[INFO] [2021-04-19 14:46:19] Storing 6 Traits
[INFO] [2021-04-19 14:46:19] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 14:46:19] Average Time: 0.0
[INFO] [2021-04-19 14:46:19] Total Time: 1s
[INFO] [2021-04-19 14:46:19] Storing 3 MetaTraits
[INFO] [2021-04-19 14:46:19] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 14:46:19] Average Time: 0.0
[INFO] [2021-04-19 14:46:19] Total Time: 1s
[STOP] [2021-04-19 14:46:19] parse_diff_and_store
[START] [2021-04-19 14:46:19] resolve_keys
[INFO] [2021-04-19 14:46:25] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 14:46:25] traits to occurrences...
[INFO] [2021-04-19 14:46:25] traits to nodes (through occurrences)...
[INFO] [2021-04-19 14:46:25] Traits to sex term...
[INFO] [2021-04-19 14:46:25] Traits to lifestage term...
[INFO] [2021-04-19 14:46:25] MetaTraits to traits...
[INFO] [2021-04-19 14:46:25] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 14:46:25] Assocs to occurrences...
[INFO] [2021-04-19 14:46:25] Assocs to nodes...
[INFO] [2021-04-19 14:46:25] Assoc to sex term...
[INFO] [2021-04-19 14:46:25] Assoc to lifestage term...
[INFO] [2021-04-19 14:46:25] MetaAssoc to assocs...
[STOP] [2021-04-19 14:46:25] resolve_keys
[START] [2021-04-19 14:46:25] hold_for_later_1
[STOP] [2021-04-19 14:46:25] hold_for_later_1
[START] [2021-04-19 14:46:25] hold_for_later_2
[STOP] [2021-04-19 14:46:25] hold_for_later_2
[START] [2021-04-19 14:46:25] resolve_missing_parents
[STOP] [2021-04-19 14:46:25] resolve_missing_parents
[START] [2021-04-19 14:46:25] rebuild_nodes
[START] [2021-04-19 14:46:25] Flattener#flatten
[START] [2021-04-19 14:46:25] Flattener#study_resource
[START] [2021-04-19 14:46:25] Flattener#build_ancestry
[STOP] [2021-04-19 14:46:25] Flattener#build_ancestry
[INFO] [2021-04-19 14:46:25] 1 ancestry keys
[START] [2021-04-19 14:46:25] build_node_ancestors
[INFO] [2021-04-19 14:46:25] old ancestors deleted.
[STOP] [2021-04-19 14:46:25] build_node_ancestors
[WARN] [2021-04-19 14:46:25] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 14:46:25] Flattener#flatten
[STOP] [2021-04-19 14:46:25] rebuild_nodes
[START] [2021-04-19 14:46:25] resolve_missing_media_owners
[STOP] [2021-04-19 14:46:25] resolve_missing_media_owners
[START] [2021-04-19 14:46:25] sanitize_media_verbatims
[STOP] [2021-04-19 14:46:25] sanitize_media_verbatims
[START] [2021-04-19 14:46:25] queue_downloads
[STOP] [2021-04-19 14:46:25] queue_downloads
[START] [2021-04-19 14:46:25] parse_names
[WARN] [2021-04-19 14:46:25] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 14:46:26] parse_names
[START] [2021-04-19 14:46:26] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 14:46:26] denormalize_canonical_names_to_nodes
[START] [2021-04-19 14:46:26] match_nodes
[START] [2021-04-19 14:46:26] map_all_nodes_to_pages
[STOP] [2021-04-19 14:46:26] map_all_nodes_to_pages
[INFO] [2021-04-19 14:46:26] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 14:46:26] update_nodes
[STOP] [2021-04-19 14:46:26] update_nodes
[STOP] [2021-04-19 14:46:26] match_nodes
[START] [2021-04-19 14:46:26] reindex_search
[STOP] [2021-04-19 14:46:26] reindex_search
[START] [2021-04-19 14:46:26] normalize_units
[STOP] [2021-04-19 14:46:26] normalize_units
[START] [2021-04-19 14:46:26] calculate_statistics
[2021-04-19 14:46:26] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 14:46:26] calculate_statistics
[START] [2021-04-19 14:46:26] complete_harvest_instance
[START] [2021-04-19 14:46:26] overall_tsv_creation
[INFO] [2021-04-19 14:46:26] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 14:47:02] 3 Traits (unfiltered)...
[INFO] [2021-04-19 14:47:33] 3 Traits (filtered)...
[INFO] [2021-04-19 14:47:33] 0 Associations (filtered)...
[INFO] [2021-04-19 14:47:33] 3 metadata added.
[INFO] [2021-04-19 14:47:33] 0 metadata added.
[INFO] [2021-04-19 14:47:59] Average Time: 69.01
[INFO] [2021-04-19 14:47:59] Total Time: 1m33s
[STOP] [2021-04-19 14:47:59] overall_tsv_creation
[INFO] [2021-04-19 14:47:59] Done. Check your files:
[INFO] [2021-04-19 14:47:59] (1 lines) /app/public/data/vreav/publish_nodes.tsv
[INFO] [2021-04-19 14:47:59] (1 lines) /app/public/data/vreav/publish_scientific_names.tsv
[INFO] [2021-04-19 14:47:59] (4 lines) /app/public/data/vreav/publish_traits.tsv
[INFO] [2021-04-19 14:47:59] (4 lines) /app/public/data/vreav/publish_metadata.tsv
[STOP] [2021-04-19 14:47:59] complete_harvest_instance
[START] [2021-04-19 14:47:59] completed
[STOP] [2021-04-19 14:47:59] completed
[STOP] [2021-04-19 14:47:59] logged process, took 100.58

Latest Process

19 Apr 14:46 EXITED currently processing 0