Harvest for Morton 2000 Created 19 Apr 15:30

Harvesting Log

# Logfile created on 2020-08-27 15:41:29 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:41:29] logged process
[START] [2020-08-27 15:41:29] Creating resource from OpenData
[START] [2020-08-27 15:41:29] logged process
[START] [2020-08-27 15:41:29] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:41:29] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:41:29] Creating resource from OpenData
[INFO] [2020-12-03 11:17:49] ## HARVEST: type = -harvest
[START] [2020-12-03 11:17:50] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-03 11:17:50] create_harvest_instance
[STOP] [2020-12-03 11:17:52] create_harvest_instance
[START] [2020-12-03 11:17:52] fetch_files
[STOP] [2020-12-03 11:17:52] fetch_files
[START] [2020-12-03 11:17:52] validate_each_file
[STOP] [2020-12-03 11:17:52] validate_each_file
[START] [2020-12-03 11:17:52] convert_to_csv
[CMD] [2020-12-03 11:17:52] /usr/bin/sort /app/public/converted_csv/morton_morton_20_refs_24804.csv > /app/public/converted_csv/morton_morton_20_refs_24804.csv_sorted
[CMD] [2020-12-03 11:17:52] /usr/bin/sort /app/public/converted_csv/morton_morton_20_nodes_24805.csv > /app/public/converted_csv/morton_morton_20_nodes_24805.csv_sorted
[CMD] [2020-12-03 11:17:52] /usr/bin/sort /app/public/converted_csv/morton_morton_20_occurrences_24806.csv > /app/public/converted_csv/morton_morton_20_occurrences_24806.csv_sorted
[CMD] [2020-12-03 11:17:52] /usr/bin/sort /app/public/converted_csv/morton_morton_20_measurements_24807.csv > /app/public/converted_csv/morton_morton_20_measurements_24807.csv_sorted
[STOP] [2020-12-03 11:17:52] convert_to_csv
[START] [2020-12-03 11:17:52] calculate_delta
[CMD] [2020-12-03 11:17:52] echo "0a" > /app/public/diff/morton_morton_20_refs_24804.diff
[CMD] [2020-12-03 11:17:52] tail -n +1 /app/public/converted_csv/morton_morton_20_refs_24804.csv >> /app/public/diff/morton_morton_20_refs_24804.diff
[CMD] [2020-12-03 11:17:52] echo "." >> /app/public/diff/morton_morton_20_refs_24804.diff
[CMD] [2020-12-03 11:17:52] echo "0a" > /app/public/diff/morton_morton_20_nodes_24805.diff
[CMD] [2020-12-03 11:17:52] tail -n +1 /app/public/converted_csv/morton_morton_20_nodes_24805.csv >> /app/public/diff/morton_morton_20_nodes_24805.diff
[CMD] [2020-12-03 11:17:52] echo "." >> /app/public/diff/morton_morton_20_nodes_24805.diff
[CMD] [2020-12-03 11:17:52] echo "0a" > /app/public/diff/morton_morton_20_occurrences_24806.diff
[CMD] [2020-12-03 11:17:52] tail -n +1 /app/public/converted_csv/morton_morton_20_occurrences_24806.csv >> /app/public/diff/morton_morton_20_occurrences_24806.diff
[CMD] [2020-12-03 11:17:52] echo "." >> /app/public/diff/morton_morton_20_occurrences_24806.diff
[CMD] [2020-12-03 11:17:52] echo "0a" > /app/public/diff/morton_morton_20_measurements_24807.diff
[CMD] [2020-12-03 11:17:52] tail -n +1 /app/public/converted_csv/morton_morton_20_measurements_24807.csv >> /app/public/diff/morton_morton_20_measurements_24807.diff
[CMD] [2020-12-03 11:17:52] echo "." >> /app/public/diff/morton_morton_20_measurements_24807.diff
[STOP] [2020-12-03 11:17:52] calculate_delta
[START] [2020-12-03 11:17:52] parse_diff_and_store
[INFO] [2020-12-03 11:17:52] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 11:17:52] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 11:17:52] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 11:17:52] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 11:17:53] Storing 1 ScientificNames
[INFO] [2020-12-03 11:17:53] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:17:53] Average Time: 0.0
[INFO] [2020-12-03 11:17:53] Total Time: 1s
[INFO] [2020-12-03 11:17:53] Storing 1 Nodes
[INFO] [2020-12-03 11:17:53] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:17:53] Average Time: 0.0
[INFO] [2020-12-03 11:17:53] Total Time: 1s
[INFO] [2020-12-03 11:17:53] Storing 1 Occurrences
[INFO] [2020-12-03 11:17:53] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:17:53] Average Time: 0.0
[INFO] [2020-12-03 11:17:53] Total Time: 1s
[INFO] [2020-12-03 11:17:53] Storing 3 Traits
[INFO] [2020-12-03 11:17:53] Processing group of 3 in 1 groups of 1000
[INFO] [2020-12-03 11:17:53] Average Time: 0.0
[INFO] [2020-12-03 11:17:53] Total Time: 1s
[INFO] [2020-12-03 11:17:53] Storing 2 MetaTraits
[INFO] [2020-12-03 11:17:53] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 11:17:53] Average Time: 0.0
[INFO] [2020-12-03 11:17:53] Total Time: 1s
[STOP] [2020-12-03 11:17:53] parse_diff_and_store
[START] [2020-12-03 11:17:53] resolve_keys
[INFO] [2020-12-03 11:17:58] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 11:17:59] traits to occurrences...
[INFO] [2020-12-03 11:17:59] traits to nodes (through occurrences)...
[INFO] [2020-12-03 11:17:59] Traits to sex term...
[INFO] [2020-12-03 11:17:59] Traits to lifestage term...
[INFO] [2020-12-03 11:17:59] MetaTraits to traits...
[INFO] [2020-12-03 11:17:59] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 11:17:59] Assocs to occurrences...
[INFO] [2020-12-03 11:17:59] Assocs to nodes...
[INFO] [2020-12-03 11:17:59] Assoc to sex term...
[INFO] [2020-12-03 11:17:59] Assoc to lifestage term...
[INFO] [2020-12-03 11:17:59] MetaAssoc to assocs...
[STOP] [2020-12-03 11:17:59] resolve_keys
[START] [2020-12-03 11:17:59] hold_for_later_1
[STOP] [2020-12-03 11:17:59] hold_for_later_1
[START] [2020-12-03 11:17:59] hold_for_later_2
[STOP] [2020-12-03 11:17:59] hold_for_later_2
[START] [2020-12-03 11:17:59] resolve_missing_parents
[STOP] [2020-12-03 11:17:59] resolve_missing_parents
[START] [2020-12-03 11:17:59] rebuild_nodes
[START] [2020-12-03 11:17:59] Flattener#flatten
[START] [2020-12-03 11:17:59] Flattener#study_resource
[START] [2020-12-03 11:17:59] Flattener#build_ancestry
[STOP] [2020-12-03 11:17:59] Flattener#build_ancestry
[INFO] [2020-12-03 11:17:59] 1 ancestry keys
[START] [2020-12-03 11:17:59] build_node_ancestors
[INFO] [2020-12-03 11:17:59] old ancestors deleted.
[STOP] [2020-12-03 11:17:59] build_node_ancestors
[WARN] [2020-12-03 11:17:59] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 11:17:59] Flattener#flatten
[STOP] [2020-12-03 11:17:59] rebuild_nodes
[START] [2020-12-03 11:17:59] resolve_missing_media_owners
[STOP] [2020-12-03 11:17:59] resolve_missing_media_owners
[START] [2020-12-03 11:17:59] sanitize_media_verbatims
[STOP] [2020-12-03 11:17:59] sanitize_media_verbatims
[START] [2020-12-03 11:17:59] queue_downloads
[STOP] [2020-12-03 11:17:59] queue_downloads
[START] [2020-12-03 11:17:59] parse_names
[WARN] [2020-12-03 11:17:59] I see 1 names which still need to be parsed.
[STOP] [2020-12-03 11:18:00] parse_names
[START] [2020-12-03 11:18:00] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 11:18:00] denormalize_canonical_names_to_nodes
[START] [2020-12-03 11:18:00] match_nodes
[START] [2020-12-03 11:18:00] map_all_nodes_to_pages
[STOP] [2020-12-03 11:18:00] map_all_nodes_to_pages
[INFO] [2020-12-03 11:18:00] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-12-03 11:18:00] update_nodes
[STOP] [2020-12-03 11:18:00] update_nodes
[STOP] [2020-12-03 11:18:00] match_nodes
[START] [2020-12-03 11:18:00] reindex_search
[STOP] [2020-12-03 11:18:00] reindex_search
[START] [2020-12-03 11:18:00] normalize_units
[STOP] [2020-12-03 11:18:00] normalize_units
[START] [2020-12-03 11:18:00] calculate_statistics
[2020-12-03 11:18:00] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 11:18:00] calculate_statistics
[START] [2020-12-03 11:18:00] complete_harvest_instance
[START] [2020-12-03 11:18:00] overall_tsv_creation
[INFO] [2020-12-03 11:18:00] Processing group of 1 in 1 batches of 10000
[INFO] [2020-12-03 11:18:38] 1 Traits (unfiltered)...
[INFO] [2020-12-03 11:19:15] 1 Traits (filtered)...
[INFO] [2020-12-03 11:19:15] 0 Associations (filtered)...
[INFO] [2020-12-03 11:19:15] 4 metadata added.
[INFO] [2020-12-03 11:19:15] 0 metadata added.
[INFO] [2020-12-03 11:19:15] Average Time: 52.18
[INFO] [2020-12-03 11:19:15] Total Time: 1m15s
[STOP] [2020-12-03 11:19:15] overall_tsv_creation
[INFO] [2020-12-03 11:19:15] Done. Check your files:
[INFO] [2020-12-03 11:19:15] (1 lines) /app/public/data/morton_morton_20/publish_nodes.tsv
[INFO] [2020-12-03 11:19:15] (1 lines) /app/public/data/morton_morton_20/publish_scientific_names.tsv
[INFO] [2020-12-03 11:19:15] (2 lines) /app/public/data/morton_morton_20/publish_traits.tsv
[INFO] [2020-12-03 11:19:15] (5 lines) /app/public/data/morton_morton_20/publish_metadata.tsv
[STOP] [2020-12-03 11:19:15] complete_harvest_instance
[START] [2020-12-03 11:19:15] completed
[STOP] [2020-12-03 11:19:15] completed
[STOP] [2020-12-03 11:19:15] logged process, took 84.71
[INFO] [2021-04-19 15:17:10] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:30:10] ## remove_type: ScientificName
[INFO] [2021-04-19 15:30:10] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:30:10] [15:30:10.821] Removed 1 Scientificnames
[INFO] [2021-04-19 15:30:10] ## remove_type: Vernacular
[INFO] [2021-04-19 15:30:10] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:30:10] [15:30:10.823] Removed 0 Vernaculars
[INFO] [2021-04-19 15:30:10] ## remove_type: Article
[INFO] [2021-04-19 15:30:10] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:30:10] [15:30:10.824] Removed 0 Articles
[INFO] [2021-04-19 15:30:10] ## remove_type: Medium
[INFO] [2021-04-19 15:30:10] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:30:10] [15:30:10.826] Removed 0 Media
[INFO] [2021-04-19 15:30:10] ## remove_type: Trait
[INFO] [2021-04-19 15:30:10] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 15:30:10] [15:30:10.828] Removed 3 Traits
[INFO] [2021-04-19 15:30:10] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:30:10] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:30:10] [15:30:10.830] Removed 2 Metatraits
[INFO] [2021-04-19 15:30:10] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:30:10] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:30:10] [15:30:10.831] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 15:30:10] ## remove_type: Assoc
[INFO] [2021-04-19 15:30:10] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:30:10] [15:30:10.833] Removed 0 Assocs
[INFO] [2021-04-19 15:30:10] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:30:10] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:30:10] [15:30:10.835] Removed 0 Metaassocs
[INFO] [2021-04-19 15:30:10] ## remove_type: Identifier
[INFO] [2021-04-19 15:30:10] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:30:10] [15:30:10.836] Removed 0 Identifiers
[INFO] [2021-04-19 15:30:10] ## remove_type: Reference
[INFO] [2021-04-19 15:30:10] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:30:10] [15:30:10.838] Removed 0 References
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] Starting batch with ID 86115907...
[INFO] [2021-04-19 15:30:10] ## remove_type: Node
[INFO] [2021-04-19 15:30:10] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:30:10] [15:30:10.973] Removed 1 Nodes
[START] [2021-04-19 15:30:11] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:30:11] Creating resource from OpenData
[START] [2021-04-19 15:30:11] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:30:11] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:30:11] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:30:11] Creating resource from OpenData
[START] [2021-04-19 15:30:11] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:30:11] create_harvest_instance
[INFO] [2021-04-19 15:30:11] Created harvest instance #3768
[STOP] [2021-04-19 15:30:11] create_harvest_instance
[START] [2021-04-19 15:30:11] fetch_files
[STOP] [2021-04-19 15:30:11] fetch_files
[START] [2021-04-19 15:30:11] validate_each_file
[INFO] [2021-04-19 15:30:11] Looping over 4 formats...
[INFO] [2021-04-19 15:30:11] ...refs (/app/public/data/morton_morton_20/references.tsv)
[INFO] [2021-04-19 15:30:11] Valid: /app/public/converted_csv/morton_morton_20_refs_3768.csv (0 lines)
[INFO] [2021-04-19 15:30:11] ...nodes (/app/public/data/morton_morton_20/taxa.txt)
[INFO] [2021-04-19 15:30:11] Valid: /app/public/converted_csv/morton_morton_20_nodes_3768.csv (1 lines)
[INFO] [2021-04-19 15:30:11] ...occurrences (/app/public/data/morton_morton_20/occurrences.txt)
[INFO] [2021-04-19 15:30:11] Valid: /app/public/converted_csv/morton_morton_20_occurrences_3768.csv (1 lines)
[INFO] [2021-04-19 15:30:11] ...measurements (/app/public/data/morton_morton_20/measurementsorfacts.txt)
[INFO] [2021-04-19 15:30:11] Valid: /app/public/converted_csv/morton_morton_20_measurements_3768.csv (3 lines)
[STOP] [2021-04-19 15:30:11] validate_each_file
[START] [2021-04-19 15:30:11] convert_to_csv
[INFO] [2021-04-19 15:30:11] Looping over 4 formats...
[INFO] [2021-04-19 15:30:11] ...refs (/app/public/data/morton_morton_20/references.tsv)
[CMD] [2021-04-19 15:30:11] /usr/bin/sort /app/public/converted_csv/morton_morton_20_refs_3768.csv > /app/public/converted_csv/morton_morton_20_refs_3768.csv_sorted
[INFO] [2021-04-19 15:30:11] Converted: /app/public/converted_csv/morton_morton_20_refs_3768.csv (0 lines)
[INFO] [2021-04-19 15:30:11] ...nodes (/app/public/data/morton_morton_20/taxa.txt)
[CMD] [2021-04-19 15:30:11] /usr/bin/sort /app/public/converted_csv/morton_morton_20_nodes_3768.csv > /app/public/converted_csv/morton_morton_20_nodes_3768.csv_sorted
[INFO] [2021-04-19 15:30:11] Converted: /app/public/converted_csv/morton_morton_20_nodes_3768.csv (1 lines)
[INFO] [2021-04-19 15:30:11] ...occurrences (/app/public/data/morton_morton_20/occurrences.txt)
[CMD] [2021-04-19 15:30:11] /usr/bin/sort /app/public/converted_csv/morton_morton_20_occurrences_3768.csv > /app/public/converted_csv/morton_morton_20_occurrences_3768.csv_sorted
[INFO] [2021-04-19 15:30:11] Converted: /app/public/converted_csv/morton_morton_20_occurrences_3768.csv (1 lines)
[INFO] [2021-04-19 15:30:11] ...measurements (/app/public/data/morton_morton_20/measurementsorfacts.txt)
[CMD] [2021-04-19 15:30:11] /usr/bin/sort /app/public/converted_csv/morton_morton_20_measurements_3768.csv > /app/public/converted_csv/morton_morton_20_measurements_3768.csv_sorted
[INFO] [2021-04-19 15:30:11] Converted: /app/public/converted_csv/morton_morton_20_measurements_3768.csv (3 lines)
[STOP] [2021-04-19 15:30:11] convert_to_csv
[START] [2021-04-19 15:30:11] calculate_delta
[INFO] [2021-04-19 15:30:11] Looping over 4 formats...
[INFO] [2021-04-19 15:30:11] ...refs (/app/public/data/morton_morton_20/references.tsv)
[CMD] [2021-04-19 15:30:11] echo "0a" > /app/public/diff/morton_morton_20_refs_3768.diff
[CMD] [2021-04-19 15:30:11] tail -n +1 /app/public/converted_csv/morton_morton_20_refs_3768.csv >> /app/public/diff/morton_morton_20_refs_3768.diff
[CMD] [2021-04-19 15:30:11] echo "." >> /app/public/diff/morton_morton_20_refs_3768.diff
[INFO] [2021-04-19 15:30:11] Created diff: /app/public/diff/morton_morton_20_refs_3768.diff (2 lines)
[INFO] [2021-04-19 15:30:11] ...nodes (/app/public/data/morton_morton_20/taxa.txt)
[CMD] [2021-04-19 15:30:11] echo "0a" > /app/public/diff/morton_morton_20_nodes_3768.diff
[CMD] [2021-04-19 15:30:11] tail -n +1 /app/public/converted_csv/morton_morton_20_nodes_3768.csv >> /app/public/diff/morton_morton_20_nodes_3768.diff
[CMD] [2021-04-19 15:30:11] echo "." >> /app/public/diff/morton_morton_20_nodes_3768.diff
[INFO] [2021-04-19 15:30:11] Created diff: /app/public/diff/morton_morton_20_nodes_3768.diff (3 lines)
[INFO] [2021-04-19 15:30:11] ...occurrences (/app/public/data/morton_morton_20/occurrences.txt)
[CMD] [2021-04-19 15:30:11] echo "0a" > /app/public/diff/morton_morton_20_occurrences_3768.diff
[CMD] [2021-04-19 15:30:11] tail -n +1 /app/public/converted_csv/morton_morton_20_occurrences_3768.csv >> /app/public/diff/morton_morton_20_occurrences_3768.diff
[CMD] [2021-04-19 15:30:11] echo "." >> /app/public/diff/morton_morton_20_occurrences_3768.diff
[INFO] [2021-04-19 15:30:11] Created diff: /app/public/diff/morton_morton_20_occurrences_3768.diff (3 lines)
[INFO] [2021-04-19 15:30:11] ...measurements (/app/public/data/morton_morton_20/measurementsorfacts.txt)
[CMD] [2021-04-19 15:30:11] echo "0a" > /app/public/diff/morton_morton_20_measurements_3768.diff
[CMD] [2021-04-19 15:30:11] tail -n +1 /app/public/converted_csv/morton_morton_20_measurements_3768.csv >> /app/public/diff/morton_morton_20_measurements_3768.diff
[CMD] [2021-04-19 15:30:11] echo "." >> /app/public/diff/morton_morton_20_measurements_3768.diff
[INFO] [2021-04-19 15:30:11] Created diff: /app/public/diff/morton_morton_20_measurements_3768.diff (5 lines)
[STOP] [2021-04-19 15:30:11] calculate_delta
[START] [2021-04-19 15:30:11] parse_diff_and_store
[INFO] [2021-04-19 15:30:11] Handling diff: /app/public/diff/morton_morton_20_refs_3768.diff (2 lines)
[INFO] [2021-04-19 15:30:11] Loading refs diff file into memory (2 /app/public/diff/morton_morton_20_refs_3768.diff lines)...
[INFO] [2021-04-19 15:30:11] Handling diff: /app/public/diff/morton_morton_20_nodes_3768.diff (3 lines)
[INFO] [2021-04-19 15:30:11] Loading nodes diff file into memory (3 /app/public/diff/morton_morton_20_nodes_3768.diff lines)...
[INFO] [2021-04-19 15:30:11] Handling diff: /app/public/diff/morton_morton_20_occurrences_3768.diff (3 lines)
[INFO] [2021-04-19 15:30:11] Loading occurrences diff file into memory (3 /app/public/diff/morton_morton_20_occurrences_3768.diff lines)...
[INFO] [2021-04-19 15:30:11] Handling diff: /app/public/diff/morton_morton_20_measurements_3768.diff (5 lines)
[INFO] [2021-04-19 15:30:11] Loading measurements diff file into memory (5 /app/public/diff/morton_morton_20_measurements_3768.diff lines)...
[INFO] [2021-04-19 15:30:11] Storing 1 ScientificNames
[INFO] [2021-04-19 15:30:11] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:30:11] Average Time: 0.0
[INFO] [2021-04-19 15:30:11] Total Time: 1s
[INFO] [2021-04-19 15:30:11] Storing 1 Nodes
[INFO] [2021-04-19 15:30:11] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:30:11] Average Time: 0.0
[INFO] [2021-04-19 15:30:11] Total Time: 1s
[INFO] [2021-04-19 15:30:11] Storing 1 Occurrences
[INFO] [2021-04-19 15:30:11] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:30:11] Average Time: 0.0
[INFO] [2021-04-19 15:30:11] Total Time: 1s
[INFO] [2021-04-19 15:30:11] Storing 3 Traits
[INFO] [2021-04-19 15:30:11] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 15:30:11] Average Time: 0.0
[INFO] [2021-04-19 15:30:11] Total Time: 1s
[INFO] [2021-04-19 15:30:11] Storing 2 MetaTraits
[INFO] [2021-04-19 15:30:11] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:30:11] Average Time: 0.0
[INFO] [2021-04-19 15:30:11] Total Time: 1s
[STOP] [2021-04-19 15:30:11] parse_diff_and_store
[START] [2021-04-19 15:30:11] resolve_keys
[INFO] [2021-04-19 15:30:17] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:30:17] traits to occurrences...
[INFO] [2021-04-19 15:30:17] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:30:17] Traits to sex term...
[INFO] [2021-04-19 15:30:17] Traits to lifestage term...
[INFO] [2021-04-19 15:30:17] MetaTraits to traits...
[INFO] [2021-04-19 15:30:17] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:30:17] Assocs to occurrences...
[INFO] [2021-04-19 15:30:17] Assocs to nodes...
[INFO] [2021-04-19 15:30:17] Assoc to sex term...
[INFO] [2021-04-19 15:30:17] Assoc to lifestage term...
[INFO] [2021-04-19 15:30:17] MetaAssoc to assocs...
[STOP] [2021-04-19 15:30:17] resolve_keys
[START] [2021-04-19 15:30:17] hold_for_later_1
[STOP] [2021-04-19 15:30:17] hold_for_later_1
[START] [2021-04-19 15:30:17] hold_for_later_2
[STOP] [2021-04-19 15:30:17] hold_for_later_2
[START] [2021-04-19 15:30:17] resolve_missing_parents
[STOP] [2021-04-19 15:30:17] resolve_missing_parents
[START] [2021-04-19 15:30:17] rebuild_nodes
[START] [2021-04-19 15:30:17] Flattener#flatten
[START] [2021-04-19 15:30:17] Flattener#study_resource
[START] [2021-04-19 15:30:17] Flattener#build_ancestry
[STOP] [2021-04-19 15:30:17] Flattener#build_ancestry
[INFO] [2021-04-19 15:30:17] 1 ancestry keys
[START] [2021-04-19 15:30:17] build_node_ancestors
[INFO] [2021-04-19 15:30:17] old ancestors deleted.
[STOP] [2021-04-19 15:30:17] build_node_ancestors
[WARN] [2021-04-19 15:30:17] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:30:17] Flattener#flatten
[STOP] [2021-04-19 15:30:17] rebuild_nodes
[START] [2021-04-19 15:30:17] resolve_missing_media_owners
[STOP] [2021-04-19 15:30:17] resolve_missing_media_owners
[START] [2021-04-19 15:30:17] sanitize_media_verbatims
[STOP] [2021-04-19 15:30:17] sanitize_media_verbatims
[START] [2021-04-19 15:30:17] queue_downloads
[STOP] [2021-04-19 15:30:17] queue_downloads
[START] [2021-04-19 15:30:17] parse_names
[WARN] [2021-04-19 15:30:17] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 15:30:18] parse_names
[START] [2021-04-19 15:30:18] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:30:18] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:30:18] match_nodes
[START] [2021-04-19 15:30:18] map_all_nodes_to_pages
[STOP] [2021-04-19 15:30:18] map_all_nodes_to_pages
[INFO] [2021-04-19 15:30:18] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 15:30:18] update_nodes
[STOP] [2021-04-19 15:30:18] update_nodes
[STOP] [2021-04-19 15:30:18] match_nodes
[START] [2021-04-19 15:30:18] reindex_search
[STOP] [2021-04-19 15:30:18] reindex_search
[START] [2021-04-19 15:30:18] normalize_units
[STOP] [2021-04-19 15:30:18] normalize_units
[START] [2021-04-19 15:30:18] calculate_statistics
[2021-04-19 15:30:18] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:30:18] calculate_statistics
[START] [2021-04-19 15:30:18] complete_harvest_instance
[START] [2021-04-19 15:30:18] overall_tsv_creation
[INFO] [2021-04-19 15:30:18] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 15:30:54] 1 Traits (unfiltered)...
[INFO] [2021-04-19 15:31:27] 1 Traits (filtered)...
[INFO] [2021-04-19 15:31:27] 0 Associations (filtered)...
[INFO] [2021-04-19 15:31:27] 2 metadata added.
[INFO] [2021-04-19 15:31:27] 0 metadata added.
[INFO] [2021-04-19 15:31:53] Average Time: 71.01
[INFO] [2021-04-19 15:31:53] Total Time: 1m35s
[STOP] [2021-04-19 15:31:53] overall_tsv_creation
[INFO] [2021-04-19 15:31:53] Done. Check your files:
[INFO] [2021-04-19 15:31:53] (1 lines) /app/public/data/morton_morton_20/publish_nodes.tsv
[INFO] [2021-04-19 15:31:53] (1 lines) /app/public/data/morton_morton_20/publish_scientific_names.tsv
[INFO] [2021-04-19 15:31:53] (2 lines) /app/public/data/morton_morton_20/publish_traits.tsv
[INFO] [2021-04-19 15:31:53] (3 lines) /app/public/data/morton_morton_20/publish_metadata.tsv
[STOP] [2021-04-19 15:31:53] complete_harvest_instance
[START] [2021-04-19 15:31:53] completed
[STOP] [2021-04-19 15:31:53] completed
[STOP] [2021-04-19 15:31:53] logged process, took 102.34

Latest Process

19 Apr 15:30 EXITED currently processing 0