Harvest for Nussbaum 1985 Created 19 Apr 16:23

Harvesting Log

# Logfile created on 2020-09-24 09:03:15 -0400 by logger.rb/v1.4.2
[START] [2020-09-24 09:03:16] logged process
[START] [2020-09-24 09:03:16] Creating resource from OpenData
[START] [2020-09-24 09:03:16] logged process
[START] [2020-09-24 09:03:16] Parse meta.xml file and create formats with fields
[STOP] [2020-09-24 09:03:16] Parse meta.xml file and create formats with fields
[STOP] [2020-09-24 09:03:16] Creating resource from OpenData
[INFO] [2020-12-03 14:25:12] ## HARVEST: type = -harvest
[START] [2020-12-03 14:25:13] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-03 14:25:13] create_harvest_instance
[STOP] [2020-12-03 14:25:14] create_harvest_instance
[START] [2020-12-03 14:25:14] fetch_files
[STOP] [2020-12-03 14:25:14] fetch_files
[START] [2020-12-03 14:25:14] validate_each_file
[STOP] [2020-12-03 14:25:15] validate_each_file
[START] [2020-12-03 14:25:15] convert_to_csv
[CMD] [2020-12-03 14:25:15] /usr/bin/sort /app/public/converted_csv/nussbaum_nussbau_nodes_24952.csv > /app/public/converted_csv/nussbaum_nussbau_nodes_24952.csv_sorted
[CMD] [2020-12-03 14:25:15] /usr/bin/sort /app/public/converted_csv/nussbaum_nussbau_occurrences_24953.csv > /app/public/converted_csv/nussbaum_nussbau_occurrences_24953.csv_sorted
[CMD] [2020-12-03 14:25:15] /usr/bin/sort /app/public/converted_csv/nussbaum_nussbau_measurements_24954.csv > /app/public/converted_csv/nussbaum_nussbau_measurements_24954.csv_sorted
[STOP] [2020-12-03 14:25:15] convert_to_csv
[START] [2020-12-03 14:25:15] calculate_delta
[CMD] [2020-12-03 14:25:15] echo "0a" > /app/public/diff/nussbaum_nussbau_nodes_24952.diff
[CMD] [2020-12-03 14:25:15] tail -n +1 /app/public/converted_csv/nussbaum_nussbau_nodes_24952.csv >> /app/public/diff/nussbaum_nussbau_nodes_24952.diff
[CMD] [2020-12-03 14:25:15] echo "." >> /app/public/diff/nussbaum_nussbau_nodes_24952.diff
[CMD] [2020-12-03 14:25:15] echo "0a" > /app/public/diff/nussbaum_nussbau_occurrences_24953.diff
[CMD] [2020-12-03 14:25:15] tail -n +1 /app/public/converted_csv/nussbaum_nussbau_occurrences_24953.csv >> /app/public/diff/nussbaum_nussbau_occurrences_24953.diff
[CMD] [2020-12-03 14:25:15] echo "." >> /app/public/diff/nussbaum_nussbau_occurrences_24953.diff
[CMD] [2020-12-03 14:25:15] echo "0a" > /app/public/diff/nussbaum_nussbau_measurements_24954.diff
[CMD] [2020-12-03 14:25:15] tail -n +1 /app/public/converted_csv/nussbaum_nussbau_measurements_24954.csv >> /app/public/diff/nussbaum_nussbau_measurements_24954.diff
[CMD] [2020-12-03 14:25:15] echo "." >> /app/public/diff/nussbaum_nussbau_measurements_24954.diff
[STOP] [2020-12-03 14:25:15] calculate_delta
[START] [2020-12-03 14:25:15] parse_diff_and_store
[INFO] [2020-12-03 14:25:15] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 14:25:15] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 14:25:15] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 14:25:16] Storing 1 ScientificNames
[INFO] [2020-12-03 14:25:16] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 14:25:16] Average Time: 0.0
[INFO] [2020-12-03 14:25:16] Total Time: 1s
[INFO] [2020-12-03 14:25:16] Storing 1 Nodes
[INFO] [2020-12-03 14:25:16] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 14:25:16] Average Time: 0.0
[INFO] [2020-12-03 14:25:16] Total Time: 1s
[INFO] [2020-12-03 14:25:16] Storing 1 Occurrences
[INFO] [2020-12-03 14:25:16] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 14:25:16] Average Time: 0.0
[INFO] [2020-12-03 14:25:16] Total Time: 1s
[INFO] [2020-12-03 14:25:16] Storing 2 Traits
[INFO] [2020-12-03 14:25:16] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 14:25:16] Average Time: 0.0
[INFO] [2020-12-03 14:25:16] Total Time: 1s
[INFO] [2020-12-03 14:25:16] Storing 2 MetaTraits
[INFO] [2020-12-03 14:25:16] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 14:25:16] Average Time: 0.0
[INFO] [2020-12-03 14:25:16] Total Time: 1s
[STOP] [2020-12-03 14:25:16] parse_diff_and_store
[START] [2020-12-03 14:25:16] resolve_keys
[INFO] [2020-12-03 14:25:21] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 14:25:21] traits to occurrences...
[INFO] [2020-12-03 14:25:21] traits to nodes (through occurrences)...
[INFO] [2020-12-03 14:25:21] Traits to sex term...
[INFO] [2020-12-03 14:25:21] Traits to lifestage term...
[INFO] [2020-12-03 14:25:21] MetaTraits to traits...
[INFO] [2020-12-03 14:25:21] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 14:25:21] Assocs to occurrences...
[INFO] [2020-12-03 14:25:21] Assocs to nodes...
[INFO] [2020-12-03 14:25:21] Assoc to sex term...
[INFO] [2020-12-03 14:25:21] Assoc to lifestage term...
[INFO] [2020-12-03 14:25:21] MetaAssoc to assocs...
[STOP] [2020-12-03 14:25:21] resolve_keys
[START] [2020-12-03 14:25:21] hold_for_later_1
[STOP] [2020-12-03 14:25:21] hold_for_later_1
[START] [2020-12-03 14:25:21] hold_for_later_2
[STOP] [2020-12-03 14:25:21] hold_for_later_2
[START] [2020-12-03 14:25:21] resolve_missing_parents
[STOP] [2020-12-03 14:25:21] resolve_missing_parents
[START] [2020-12-03 14:25:21] rebuild_nodes
[START] [2020-12-03 14:25:21] Flattener#flatten
[START] [2020-12-03 14:25:21] Flattener#study_resource
[START] [2020-12-03 14:25:21] Flattener#build_ancestry
[STOP] [2020-12-03 14:25:21] Flattener#build_ancestry
[INFO] [2020-12-03 14:25:21] 1 ancestry keys
[START] [2020-12-03 14:25:21] build_node_ancestors
[INFO] [2020-12-03 14:25:21] old ancestors deleted.
[STOP] [2020-12-03 14:25:21] build_node_ancestors
[WARN] [2020-12-03 14:25:21] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 14:25:21] Flattener#flatten
[STOP] [2020-12-03 14:25:21] rebuild_nodes
[START] [2020-12-03 14:25:21] resolve_missing_media_owners
[STOP] [2020-12-03 14:25:21] resolve_missing_media_owners
[START] [2020-12-03 14:25:21] sanitize_media_verbatims
[STOP] [2020-12-03 14:25:21] sanitize_media_verbatims
[START] [2020-12-03 14:25:21] queue_downloads
[STOP] [2020-12-03 14:25:21] queue_downloads
[START] [2020-12-03 14:25:21] parse_names
[WARN] [2020-12-03 14:25:21] I see 1 names which still need to be parsed.
[STOP] [2020-12-03 14:25:22] parse_names
[START] [2020-12-03 14:25:22] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 14:25:22] denormalize_canonical_names_to_nodes
[START] [2020-12-03 14:25:22] match_nodes
[START] [2020-12-03 14:25:22] map_all_nodes_to_pages
[STOP] [2020-12-03 14:25:22] map_all_nodes_to_pages
[INFO] [2020-12-03 14:25:22] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-12-03 14:25:22] update_nodes
[STOP] [2020-12-03 14:25:22] update_nodes
[STOP] [2020-12-03 14:25:22] match_nodes
[START] [2020-12-03 14:25:22] reindex_search
[STOP] [2020-12-03 14:25:22] reindex_search
[START] [2020-12-03 14:25:22] normalize_units
[STOP] [2020-12-03 14:25:22] normalize_units
[START] [2020-12-03 14:25:22] calculate_statistics
[2020-12-03 14:25:22] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 14:25:22] calculate_statistics
[START] [2020-12-03 14:25:22] complete_harvest_instance
[START] [2020-12-03 14:25:22] overall_tsv_creation
[INFO] [2020-12-03 14:25:22] Processing group of 1 in 1 batches of 10000
[INFO] [2020-12-03 14:26:01] 1 Traits (unfiltered)...
[INFO] [2020-12-03 14:26:38] 1 Traits (filtered)...
[INFO] [2020-12-03 14:26:38] 0 Associations (filtered)...
[INFO] [2020-12-03 14:26:38] 3 metadata added.
[INFO] [2020-12-03 14:26:38] 0 metadata added.
[INFO] [2020-12-03 14:26:38] Average Time: 52.81
[INFO] [2020-12-03 14:26:38] Total Time: 1m16s
[STOP] [2020-12-03 14:26:38] overall_tsv_creation
[INFO] [2020-12-03 14:26:38] Done. Check your files:
[INFO] [2020-12-03 14:26:38] (1 lines) /app/public/data/nussbaum_nussbau/publish_nodes.tsv
[INFO] [2020-12-03 14:26:38] (1 lines) /app/public/data/nussbaum_nussbau/publish_scientific_names.tsv
[INFO] [2020-12-03 14:26:38] (2 lines) /app/public/data/nussbaum_nussbau/publish_traits.tsv
[INFO] [2020-12-03 14:26:38] (4 lines) /app/public/data/nussbaum_nussbau/publish_metadata.tsv
[STOP] [2020-12-03 14:26:38] complete_harvest_instance
[START] [2020-12-03 14:26:38] completed
[STOP] [2020-12-03 14:26:38] completed
[STOP] [2020-12-03 14:26:38] logged process, took 85.09
[INFO] [2021-04-19 16:20:28] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 16:23:52] ## remove_type: ScientificName
[INFO] [2021-04-19 16:23:52] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 16:23:52] [16:23:52.585] Removed 1 Scientificnames
[INFO] [2021-04-19 16:23:52] ## remove_type: Vernacular
[INFO] [2021-04-19 16:23:52] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:23:52] [16:23:52.586] Removed 0 Vernaculars
[INFO] [2021-04-19 16:23:52] ## remove_type: Article
[INFO] [2021-04-19 16:23:52] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:23:52] [16:23:52.588] Removed 0 Articles
[INFO] [2021-04-19 16:23:52] ## remove_type: Medium
[INFO] [2021-04-19 16:23:52] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:23:52] [16:23:52.590] Removed 0 Media
[INFO] [2021-04-19 16:23:52] ## remove_type: Trait
[INFO] [2021-04-19 16:23:52] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 16:23:52] [16:23:52.592] Removed 2 Traits
[INFO] [2021-04-19 16:23:52] ## remove_type: MetaTrait
[INFO] [2021-04-19 16:23:52] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 16:23:52] [16:23:52.594] Removed 2 Metatraits
[INFO] [2021-04-19 16:23:52] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 16:23:52] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:23:52] [16:23:52.595] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 16:23:52] ## remove_type: Assoc
[INFO] [2021-04-19 16:23:52] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:23:52] [16:23:52.597] Removed 0 Assocs
[INFO] [2021-04-19 16:23:52] ## remove_type: MetaAssoc
[INFO] [2021-04-19 16:23:52] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:23:52] [16:23:52.598] Removed 0 Metaassocs
[INFO] [2021-04-19 16:23:52] ## remove_type: Identifier
[INFO] [2021-04-19 16:23:52] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:23:52] [16:23:52.599] Removed 0 Identifiers
[INFO] [2021-04-19 16:23:52] ## remove_type: Reference
[INFO] [2021-04-19 16:23:52] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:23:52] [16:23:52.600] Removed 0 References
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] Starting batch with ID 86116298...
[INFO] [2021-04-19 16:23:52] ## remove_type: Node
[INFO] [2021-04-19 16:23:52] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 16:23:52] [16:23:52.937] Removed 1 Nodes
[START] [2021-04-19 16:23:53] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:23:53] Creating resource from OpenData
[START] [2021-04-19 16:23:53] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:23:53] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:23:53] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:23:53] Creating resource from OpenData
[START] [2021-04-19 16:23:53] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:23:53] create_harvest_instance
[INFO] [2021-04-19 16:23:53] Created harvest instance #3792
[STOP] [2021-04-19 16:23:53] create_harvest_instance
[START] [2021-04-19 16:23:53] fetch_files
[STOP] [2021-04-19 16:23:53] fetch_files
[START] [2021-04-19 16:23:53] validate_each_file
[INFO] [2021-04-19 16:23:53] Looping over 3 formats...
[INFO] [2021-04-19 16:23:53] ...nodes (/app/public/data/nussbaum_nussbau/taxa.txt)
[INFO] [2021-04-19 16:23:53] Valid: /app/public/converted_csv/nussbaum_nussbau_nodes_3792.csv (1 lines)
[INFO] [2021-04-19 16:23:53] ...occurrences (/app/public/data/nussbaum_nussbau/occurrences.txt)
[INFO] [2021-04-19 16:23:53] Valid: /app/public/converted_csv/nussbaum_nussbau_occurrences_3792.csv (1 lines)
[INFO] [2021-04-19 16:23:53] ...measurements (/app/public/data/nussbaum_nussbau/measurementsorfacts.txt)
[INFO] [2021-04-19 16:23:53] Valid: /app/public/converted_csv/nussbaum_nussbau_measurements_3792.csv (2 lines)
[STOP] [2021-04-19 16:23:53] validate_each_file
[START] [2021-04-19 16:23:53] convert_to_csv
[INFO] [2021-04-19 16:23:53] Looping over 3 formats...
[INFO] [2021-04-19 16:23:53] ...nodes (/app/public/data/nussbaum_nussbau/taxa.txt)
[CMD] [2021-04-19 16:23:53] /usr/bin/sort /app/public/converted_csv/nussbaum_nussbau_nodes_3792.csv > /app/public/converted_csv/nussbaum_nussbau_nodes_3792.csv_sorted
[INFO] [2021-04-19 16:23:53] Converted: /app/public/converted_csv/nussbaum_nussbau_nodes_3792.csv (1 lines)
[INFO] [2021-04-19 16:23:53] ...occurrences (/app/public/data/nussbaum_nussbau/occurrences.txt)
[CMD] [2021-04-19 16:23:53] /usr/bin/sort /app/public/converted_csv/nussbaum_nussbau_occurrences_3792.csv > /app/public/converted_csv/nussbaum_nussbau_occurrences_3792.csv_sorted
[INFO] [2021-04-19 16:23:53] Converted: /app/public/converted_csv/nussbaum_nussbau_occurrences_3792.csv (1 lines)
[INFO] [2021-04-19 16:23:53] ...measurements (/app/public/data/nussbaum_nussbau/measurementsorfacts.txt)
[CMD] [2021-04-19 16:23:53] /usr/bin/sort /app/public/converted_csv/nussbaum_nussbau_measurements_3792.csv > /app/public/converted_csv/nussbaum_nussbau_measurements_3792.csv_sorted
[INFO] [2021-04-19 16:23:53] Converted: /app/public/converted_csv/nussbaum_nussbau_measurements_3792.csv (2 lines)
[STOP] [2021-04-19 16:23:53] convert_to_csv
[START] [2021-04-19 16:23:53] calculate_delta
[INFO] [2021-04-19 16:23:53] Looping over 3 formats...
[INFO] [2021-04-19 16:23:53] ...nodes (/app/public/data/nussbaum_nussbau/taxa.txt)
[CMD] [2021-04-19 16:23:53] echo "0a" > /app/public/diff/nussbaum_nussbau_nodes_3792.diff
[CMD] [2021-04-19 16:23:53] tail -n +1 /app/public/converted_csv/nussbaum_nussbau_nodes_3792.csv >> /app/public/diff/nussbaum_nussbau_nodes_3792.diff
[CMD] [2021-04-19 16:23:53] echo "." >> /app/public/diff/nussbaum_nussbau_nodes_3792.diff
[INFO] [2021-04-19 16:23:53] Created diff: /app/public/diff/nussbaum_nussbau_nodes_3792.diff (3 lines)
[INFO] [2021-04-19 16:23:53] ...occurrences (/app/public/data/nussbaum_nussbau/occurrences.txt)
[CMD] [2021-04-19 16:23:53] echo "0a" > /app/public/diff/nussbaum_nussbau_occurrences_3792.diff
[CMD] [2021-04-19 16:23:53] tail -n +1 /app/public/converted_csv/nussbaum_nussbau_occurrences_3792.csv >> /app/public/diff/nussbaum_nussbau_occurrences_3792.diff
[CMD] [2021-04-19 16:23:53] echo "." >> /app/public/diff/nussbaum_nussbau_occurrences_3792.diff
[INFO] [2021-04-19 16:23:53] Created diff: /app/public/diff/nussbaum_nussbau_occurrences_3792.diff (3 lines)
[INFO] [2021-04-19 16:23:53] ...measurements (/app/public/data/nussbaum_nussbau/measurementsorfacts.txt)
[CMD] [2021-04-19 16:23:53] echo "0a" > /app/public/diff/nussbaum_nussbau_measurements_3792.diff
[CMD] [2021-04-19 16:23:53] tail -n +1 /app/public/converted_csv/nussbaum_nussbau_measurements_3792.csv >> /app/public/diff/nussbaum_nussbau_measurements_3792.diff
[CMD] [2021-04-19 16:23:53] echo "." >> /app/public/diff/nussbaum_nussbau_measurements_3792.diff
[INFO] [2021-04-19 16:23:53] Created diff: /app/public/diff/nussbaum_nussbau_measurements_3792.diff (4 lines)
[STOP] [2021-04-19 16:23:53] calculate_delta
[START] [2021-04-19 16:23:53] parse_diff_and_store
[INFO] [2021-04-19 16:23:53] Handling diff: /app/public/diff/nussbaum_nussbau_nodes_3792.diff (3 lines)
[INFO] [2021-04-19 16:23:53] Loading nodes diff file into memory (3 /app/public/diff/nussbaum_nussbau_nodes_3792.diff lines)...
[INFO] [2021-04-19 16:23:53] Handling diff: /app/public/diff/nussbaum_nussbau_occurrences_3792.diff (3 lines)
[INFO] [2021-04-19 16:23:53] Loading occurrences diff file into memory (3 /app/public/diff/nussbaum_nussbau_occurrences_3792.diff lines)...
[INFO] [2021-04-19 16:23:53] Handling diff: /app/public/diff/nussbaum_nussbau_measurements_3792.diff (4 lines)
[INFO] [2021-04-19 16:23:53] Loading measurements diff file into memory (4 /app/public/diff/nussbaum_nussbau_measurements_3792.diff lines)...
[INFO] [2021-04-19 16:23:53] Storing 1 ScientificNames
[INFO] [2021-04-19 16:23:53] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:23:53] Average Time: 0.0
[INFO] [2021-04-19 16:23:53] Total Time: 1s
[INFO] [2021-04-19 16:23:53] Storing 1 Nodes
[INFO] [2021-04-19 16:23:53] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:23:53] Average Time: 0.0
[INFO] [2021-04-19 16:23:53] Total Time: 1s
[INFO] [2021-04-19 16:23:53] Storing 1 Occurrences
[INFO] [2021-04-19 16:23:53] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:23:53] Average Time: 0.0
[INFO] [2021-04-19 16:23:53] Total Time: 1s
[INFO] [2021-04-19 16:23:53] Storing 2 Traits
[INFO] [2021-04-19 16:23:53] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 16:23:53] Average Time: 0.0
[INFO] [2021-04-19 16:23:53] Total Time: 1s
[INFO] [2021-04-19 16:23:53] Storing 2 MetaTraits
[INFO] [2021-04-19 16:23:53] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 16:23:53] Average Time: 0.0
[INFO] [2021-04-19 16:23:53] Total Time: 1s
[STOP] [2021-04-19 16:23:53] parse_diff_and_store
[START] [2021-04-19 16:23:53] resolve_keys
[INFO] [2021-04-19 16:23:59] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 16:23:59] traits to occurrences...
[INFO] [2021-04-19 16:23:59] traits to nodes (through occurrences)...
[INFO] [2021-04-19 16:23:59] Traits to sex term...
[INFO] [2021-04-19 16:23:59] Traits to lifestage term...
[INFO] [2021-04-19 16:23:59] MetaTraits to traits...
[INFO] [2021-04-19 16:23:59] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 16:23:59] Assocs to occurrences...
[INFO] [2021-04-19 16:23:59] Assocs to nodes...
[INFO] [2021-04-19 16:23:59] Assoc to sex term...
[INFO] [2021-04-19 16:23:59] Assoc to lifestage term...
[INFO] [2021-04-19 16:23:59] MetaAssoc to assocs...
[STOP] [2021-04-19 16:23:59] resolve_keys
[START] [2021-04-19 16:23:59] hold_for_later_1
[STOP] [2021-04-19 16:23:59] hold_for_later_1
[START] [2021-04-19 16:23:59] hold_for_later_2
[STOP] [2021-04-19 16:23:59] hold_for_later_2
[START] [2021-04-19 16:23:59] resolve_missing_parents
[STOP] [2021-04-19 16:23:59] resolve_missing_parents
[START] [2021-04-19 16:23:59] rebuild_nodes
[START] [2021-04-19 16:23:59] Flattener#flatten
[START] [2021-04-19 16:23:59] Flattener#study_resource
[START] [2021-04-19 16:23:59] Flattener#build_ancestry
[STOP] [2021-04-19 16:23:59] Flattener#build_ancestry
[INFO] [2021-04-19 16:23:59] 1 ancestry keys
[START] [2021-04-19 16:23:59] build_node_ancestors
[INFO] [2021-04-19 16:23:59] old ancestors deleted.
[STOP] [2021-04-19 16:23:59] build_node_ancestors
[WARN] [2021-04-19 16:23:59] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 16:23:59] Flattener#flatten
[STOP] [2021-04-19 16:23:59] rebuild_nodes
[START] [2021-04-19 16:23:59] resolve_missing_media_owners
[STOP] [2021-04-19 16:23:59] resolve_missing_media_owners
[START] [2021-04-19 16:23:59] sanitize_media_verbatims
[STOP] [2021-04-19 16:23:59] sanitize_media_verbatims
[START] [2021-04-19 16:23:59] queue_downloads
[STOP] [2021-04-19 16:23:59] queue_downloads
[START] [2021-04-19 16:23:59] parse_names
[WARN] [2021-04-19 16:23:59] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 16:24:00] parse_names
[START] [2021-04-19 16:24:00] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 16:24:00] denormalize_canonical_names_to_nodes
[START] [2021-04-19 16:24:00] match_nodes
[START] [2021-04-19 16:24:00] map_all_nodes_to_pages
[STOP] [2021-04-19 16:24:00] map_all_nodes_to_pages
[INFO] [2021-04-19 16:24:00] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 16:24:00] update_nodes
[STOP] [2021-04-19 16:24:00] update_nodes
[STOP] [2021-04-19 16:24:00] match_nodes
[START] [2021-04-19 16:24:00] reindex_search
[STOP] [2021-04-19 16:24:00] reindex_search
[START] [2021-04-19 16:24:00] normalize_units
[STOP] [2021-04-19 16:24:00] normalize_units
[START] [2021-04-19 16:24:00] calculate_statistics
[2021-04-19 16:24:00] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 16:24:00] calculate_statistics
[START] [2021-04-19 16:24:00] complete_harvest_instance
[START] [2021-04-19 16:24:00] overall_tsv_creation
[INFO] [2021-04-19 16:24:00] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 16:24:35] 1 Traits (unfiltered)...
[INFO] [2021-04-19 16:25:07] 1 Traits (filtered)...
[INFO] [2021-04-19 16:25:07] 0 Associations (filtered)...
[INFO] [2021-04-19 16:25:07] 1 metadata added.
[INFO] [2021-04-19 16:25:07] 0 metadata added.
[INFO] [2021-04-19 16:25:33] Average Time: 69.39
[INFO] [2021-04-19 16:25:33] Total Time: 1m33s
[STOP] [2021-04-19 16:25:33] overall_tsv_creation
[INFO] [2021-04-19 16:25:33] Done. Check your files:
[INFO] [2021-04-19 16:25:33] (1 lines) /app/public/data/nussbaum_nussbau/publish_nodes.tsv
[INFO] [2021-04-19 16:25:33] (1 lines) /app/public/data/nussbaum_nussbau/publish_scientific_names.tsv
[INFO] [2021-04-19 16:25:33] (2 lines) /app/public/data/nussbaum_nussbau/publish_traits.tsv
[INFO] [2021-04-19 16:25:33] (2 lines) /app/public/data/nussbaum_nussbau/publish_metadata.tsv
[STOP] [2021-04-19 16:25:33] complete_harvest_instance
[START] [2021-04-19 16:25:33] completed
[STOP] [2021-04-19 16:25:33] completed
[STOP] [2021-04-19 16:25:33] logged process, took 100.49

Latest Process

19 Apr 16:23 EXITED currently processing 0