Harvest for Norenburg 1985 Created 19 Apr 16:52

Harvesting Log

# Logfile created on 2020-09-28 08:59:45 -0400 by logger.rb/v1.4.2
[START] [2020-09-28 08:59:45] logged process
[START] [2020-09-28 08:59:45] Creating resource from OpenData
[START] [2020-09-28 08:59:46] logged process
[START] [2020-09-28 08:59:46] Parse meta.xml file and create formats with fields
[STOP] [2020-09-28 08:59:46] Parse meta.xml file and create formats with fields
[STOP] [2020-09-28 08:59:46] Creating resource from OpenData
[INFO] [2020-12-04 08:12:25] ## HARVEST: type = -harvest
[START] [2020-12-04 08:12:25] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-04 08:12:25] create_harvest_instance
[STOP] [2020-12-04 08:12:26] create_harvest_instance
[START] [2020-12-04 08:12:26] fetch_files
[STOP] [2020-12-04 08:12:26] fetch_files
[START] [2020-12-04 08:12:26] validate_each_file
[STOP] [2020-12-04 08:12:26] validate_each_file
[START] [2020-12-04 08:12:26] convert_to_csv
[CMD] [2020-12-04 08:12:26] /usr/bin/sort /app/public/converted_csv/norenburg_norenb_nodes_25070.csv > /app/public/converted_csv/norenburg_norenb_nodes_25070.csv_sorted
[CMD] [2020-12-04 08:12:26] /usr/bin/sort /app/public/converted_csv/norenburg_norenb_occurrences_25071.csv > /app/public/converted_csv/norenburg_norenb_occurrences_25071.csv_sorted
[CMD] [2020-12-04 08:12:26] /usr/bin/sort /app/public/converted_csv/norenburg_norenb_measurements_25072.csv > /app/public/converted_csv/norenburg_norenb_measurements_25072.csv_sorted
[STOP] [2020-12-04 08:12:26] convert_to_csv
[START] [2020-12-04 08:12:26] calculate_delta
[CMD] [2020-12-04 08:12:26] echo "0a" > /app/public/diff/norenburg_norenb_nodes_25070.diff
[CMD] [2020-12-04 08:12:26] tail -n +1 /app/public/converted_csv/norenburg_norenb_nodes_25070.csv >> /app/public/diff/norenburg_norenb_nodes_25070.diff
[CMD] [2020-12-04 08:12:26] echo "." >> /app/public/diff/norenburg_norenb_nodes_25070.diff
[CMD] [2020-12-04 08:12:26] echo "0a" > /app/public/diff/norenburg_norenb_occurrences_25071.diff
[CMD] [2020-12-04 08:12:26] tail -n +1 /app/public/converted_csv/norenburg_norenb_occurrences_25071.csv >> /app/public/diff/norenburg_norenb_occurrences_25071.diff
[CMD] [2020-12-04 08:12:26] echo "." >> /app/public/diff/norenburg_norenb_occurrences_25071.diff
[CMD] [2020-12-04 08:12:26] echo "0a" > /app/public/diff/norenburg_norenb_measurements_25072.diff
[CMD] [2020-12-04 08:12:26] tail -n +1 /app/public/converted_csv/norenburg_norenb_measurements_25072.csv >> /app/public/diff/norenburg_norenb_measurements_25072.diff
[CMD] [2020-12-04 08:12:26] echo "." >> /app/public/diff/norenburg_norenb_measurements_25072.diff
[STOP] [2020-12-04 08:12:26] calculate_delta
[START] [2020-12-04 08:12:26] parse_diff_and_store
[INFO] [2020-12-04 08:12:26] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-04 08:12:26] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-04 08:12:26] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-04 08:12:27] Storing 1 ScientificNames
[INFO] [2020-12-04 08:12:27] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-04 08:12:27] Average Time: 0.0
[INFO] [2020-12-04 08:12:27] Total Time: 1s
[INFO] [2020-12-04 08:12:27] Storing 1 Nodes
[INFO] [2020-12-04 08:12:27] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-04 08:12:27] Average Time: 0.0
[INFO] [2020-12-04 08:12:27] Total Time: 1s
[INFO] [2020-12-04 08:12:27] Storing 1 Occurrences
[INFO] [2020-12-04 08:12:27] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-04 08:12:27] Average Time: 0.0
[INFO] [2020-12-04 08:12:27] Total Time: 1s
[INFO] [2020-12-04 08:12:27] Storing 3 Traits
[INFO] [2020-12-04 08:12:27] Processing group of 3 in 1 groups of 1000
[INFO] [2020-12-04 08:12:27] Average Time: 0.0
[INFO] [2020-12-04 08:12:27] Total Time: 1s
[INFO] [2020-12-04 08:12:27] Storing 1 MetaTraits
[INFO] [2020-12-04 08:12:27] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-04 08:12:27] Average Time: 0.0
[INFO] [2020-12-04 08:12:27] Total Time: 1s
[STOP] [2020-12-04 08:12:27] parse_diff_and_store
[START] [2020-12-04 08:12:27] resolve_keys
[INFO] [2020-12-04 08:12:33] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-04 08:12:33] traits to occurrences...
[INFO] [2020-12-04 08:12:33] traits to nodes (through occurrences)...
[INFO] [2020-12-04 08:12:33] Traits to sex term...
[INFO] [2020-12-04 08:12:33] Traits to lifestage term...
[INFO] [2020-12-04 08:12:33] MetaTraits to traits...
[INFO] [2020-12-04 08:12:33] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-04 08:12:33] Assocs to occurrences...
[INFO] [2020-12-04 08:12:33] Assocs to nodes...
[INFO] [2020-12-04 08:12:33] Assoc to sex term...
[INFO] [2020-12-04 08:12:33] Assoc to lifestage term...
[INFO] [2020-12-04 08:12:33] MetaAssoc to assocs...
[STOP] [2020-12-04 08:12:33] resolve_keys
[START] [2020-12-04 08:12:33] hold_for_later_1
[STOP] [2020-12-04 08:12:33] hold_for_later_1
[START] [2020-12-04 08:12:33] hold_for_later_2
[STOP] [2020-12-04 08:12:33] hold_for_later_2
[START] [2020-12-04 08:12:33] resolve_missing_parents
[STOP] [2020-12-04 08:12:33] resolve_missing_parents
[START] [2020-12-04 08:12:33] rebuild_nodes
[START] [2020-12-04 08:12:33] Flattener#flatten
[START] [2020-12-04 08:12:33] Flattener#study_resource
[START] [2020-12-04 08:12:33] Flattener#build_ancestry
[STOP] [2020-12-04 08:12:33] Flattener#build_ancestry
[INFO] [2020-12-04 08:12:33] 1 ancestry keys
[START] [2020-12-04 08:12:33] build_node_ancestors
[INFO] [2020-12-04 08:12:33] old ancestors deleted.
[STOP] [2020-12-04 08:12:33] build_node_ancestors
[WARN] [2020-12-04 08:12:33] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-04 08:12:33] Flattener#flatten
[STOP] [2020-12-04 08:12:33] rebuild_nodes
[START] [2020-12-04 08:12:33] resolve_missing_media_owners
[STOP] [2020-12-04 08:12:33] resolve_missing_media_owners
[START] [2020-12-04 08:12:33] sanitize_media_verbatims
[STOP] [2020-12-04 08:12:33] sanitize_media_verbatims
[START] [2020-12-04 08:12:33] queue_downloads
[STOP] [2020-12-04 08:12:33] queue_downloads
[START] [2020-12-04 08:12:33] parse_names
[WARN] [2020-12-04 08:12:33] I see 1 names which still need to be parsed.
[STOP] [2020-12-04 08:12:34] parse_names
[START] [2020-12-04 08:12:34] denormalize_canonical_names_to_nodes
[STOP] [2020-12-04 08:12:34] denormalize_canonical_names_to_nodes
[START] [2020-12-04 08:12:34] match_nodes
[START] [2020-12-04 08:12:34] map_all_nodes_to_pages
[STOP] [2020-12-04 08:12:34] map_all_nodes_to_pages
[INFO] [2020-12-04 08:12:34] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-12-04 08:12:34] update_nodes
[STOP] [2020-12-04 08:12:34] update_nodes
[STOP] [2020-12-04 08:12:34] match_nodes
[START] [2020-12-04 08:12:34] reindex_search
[STOP] [2020-12-04 08:12:34] reindex_search
[START] [2020-12-04 08:12:34] normalize_units
[STOP] [2020-12-04 08:12:34] normalize_units
[START] [2020-12-04 08:12:34] calculate_statistics
[2020-12-04 08:12:34] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-04 08:12:34] calculate_statistics
[START] [2020-12-04 08:12:34] complete_harvest_instance
[START] [2020-12-04 08:12:34] overall_tsv_creation
[INFO] [2020-12-04 08:12:34] Processing group of 1 in 1 batches of 10000
[INFO] [2020-12-04 08:13:13] 1 Traits (unfiltered)...
[INFO] [2020-12-04 08:13:49] 1 Traits (filtered)...
[INFO] [2020-12-04 08:13:49] 0 Associations (filtered)...
[INFO] [2020-12-04 08:13:49] 3 metadata added.
[INFO] [2020-12-04 08:13:49] 0 metadata added.
[INFO] [2020-12-04 08:13:49] Average Time: 51.47
[INFO] [2020-12-04 08:13:49] Total Time: 1m15s
[STOP] [2020-12-04 08:13:49] overall_tsv_creation
[INFO] [2020-12-04 08:13:49] Done. Check your files:
[INFO] [2020-12-04 08:13:49] (1 lines) /app/public/data/norenburg_norenb/publish_nodes.tsv
[INFO] [2020-12-04 08:13:49] (1 lines) /app/public/data/norenburg_norenb/publish_scientific_names.tsv
[INFO] [2020-12-04 08:13:49] (2 lines) /app/public/data/norenburg_norenb/publish_traits.tsv
[INFO] [2020-12-04 08:13:49] (4 lines) /app/public/data/norenburg_norenb/publish_metadata.tsv
[STOP] [2020-12-04 08:13:49] complete_harvest_instance
[START] [2020-12-04 08:13:49] completed
[STOP] [2020-12-04 08:13:49] completed
[STOP] [2020-12-04 08:13:49] logged process, took 83.72
[INFO] [2021-04-19 16:47:33] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 16:52:56] ## remove_type: ScientificName
[INFO] [2021-04-19 16:52:56] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 16:52:56] [16:52:56.068] Removed 1 Scientificnames
[INFO] [2021-04-19 16:52:56] ## remove_type: Vernacular
[INFO] [2021-04-19 16:52:56] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:52:56] [16:52:56.070] Removed 0 Vernaculars
[INFO] [2021-04-19 16:52:56] ## remove_type: Article
[INFO] [2021-04-19 16:52:56] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:52:56] [16:52:56.072] Removed 0 Articles
[INFO] [2021-04-19 16:52:56] ## remove_type: Medium
[INFO] [2021-04-19 16:52:56] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:52:56] [16:52:56.074] Removed 0 Media
[INFO] [2021-04-19 16:52:56] ## remove_type: Trait
[INFO] [2021-04-19 16:52:56] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 16:52:56] [16:52:56.076] Removed 3 Traits
[INFO] [2021-04-19 16:52:56] ## remove_type: MetaTrait
[INFO] [2021-04-19 16:52:56] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 16:52:56] [16:52:56.078] Removed 1 Metatraits
[INFO] [2021-04-19 16:52:56] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 16:52:56] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:52:56] [16:52:56.080] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 16:52:56] ## remove_type: Assoc
[INFO] [2021-04-19 16:52:56] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:52:56] [16:52:56.082] Removed 0 Assocs
[INFO] [2021-04-19 16:52:56] ## remove_type: MetaAssoc
[INFO] [2021-04-19 16:52:56] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:52:56] [16:52:56.083] Removed 0 Metaassocs
[INFO] [2021-04-19 16:52:56] ## remove_type: Identifier
[INFO] [2021-04-19 16:52:56] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:52:56] [16:52:56.085] Removed 0 Identifiers
[INFO] [2021-04-19 16:52:56] ## remove_type: Reference
[INFO] [2021-04-19 16:52:56] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:52:56] [16:52:56.086] Removed 0 References
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] Starting batch with ID 86116360...
[INFO] [2021-04-19 16:52:56] ## remove_type: Node
[INFO] [2021-04-19 16:52:56] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 16:52:56] [16:52:56.299] Removed 1 Nodes
[START] [2021-04-19 16:52:56] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:52:56] Creating resource from OpenData
[START] [2021-04-19 16:52:56] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:52:56] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:52:56] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:52:56] Creating resource from OpenData
[START] [2021-04-19 16:52:56] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:52:56] create_harvest_instance
[INFO] [2021-04-19 16:52:56] Created harvest instance #3808
[STOP] [2021-04-19 16:52:56] create_harvest_instance
[START] [2021-04-19 16:52:56] fetch_files
[STOP] [2021-04-19 16:52:56] fetch_files
[START] [2021-04-19 16:52:56] validate_each_file
[INFO] [2021-04-19 16:52:56] Looping over 3 formats...
[INFO] [2021-04-19 16:52:56] ...nodes (/app/public/data/norenburg_norenb/taxa.txt)
[INFO] [2021-04-19 16:52:56] Valid: /app/public/converted_csv/norenburg_norenb_nodes_3808.csv (1 lines)
[INFO] [2021-04-19 16:52:56] ...occurrences (/app/public/data/norenburg_norenb/occurrences.txt)
[INFO] [2021-04-19 16:52:56] Valid: /app/public/converted_csv/norenburg_norenb_occurrences_3808.csv (1 lines)
[INFO] [2021-04-19 16:52:56] ...measurements (/app/public/data/norenburg_norenb/measurementsorfacts.txt)
[INFO] [2021-04-19 16:52:56] Valid: /app/public/converted_csv/norenburg_norenb_measurements_3808.csv (3 lines)
[STOP] [2021-04-19 16:52:56] validate_each_file
[START] [2021-04-19 16:52:56] convert_to_csv
[INFO] [2021-04-19 16:52:56] Looping over 3 formats...
[INFO] [2021-04-19 16:52:56] ...nodes (/app/public/data/norenburg_norenb/taxa.txt)
[CMD] [2021-04-19 16:52:56] /usr/bin/sort /app/public/converted_csv/norenburg_norenb_nodes_3808.csv > /app/public/converted_csv/norenburg_norenb_nodes_3808.csv_sorted
[INFO] [2021-04-19 16:52:56] Converted: /app/public/converted_csv/norenburg_norenb_nodes_3808.csv (1 lines)
[INFO] [2021-04-19 16:52:56] ...occurrences (/app/public/data/norenburg_norenb/occurrences.txt)
[CMD] [2021-04-19 16:52:56] /usr/bin/sort /app/public/converted_csv/norenburg_norenb_occurrences_3808.csv > /app/public/converted_csv/norenburg_norenb_occurrences_3808.csv_sorted
[INFO] [2021-04-19 16:52:56] Converted: /app/public/converted_csv/norenburg_norenb_occurrences_3808.csv (1 lines)
[INFO] [2021-04-19 16:52:56] ...measurements (/app/public/data/norenburg_norenb/measurementsorfacts.txt)
[CMD] [2021-04-19 16:52:56] /usr/bin/sort /app/public/converted_csv/norenburg_norenb_measurements_3808.csv > /app/public/converted_csv/norenburg_norenb_measurements_3808.csv_sorted
[INFO] [2021-04-19 16:52:56] Converted: /app/public/converted_csv/norenburg_norenb_measurements_3808.csv (3 lines)
[STOP] [2021-04-19 16:52:56] convert_to_csv
[START] [2021-04-19 16:52:56] calculate_delta
[INFO] [2021-04-19 16:52:56] Looping over 3 formats...
[INFO] [2021-04-19 16:52:56] ...nodes (/app/public/data/norenburg_norenb/taxa.txt)
[CMD] [2021-04-19 16:52:56] echo "0a" > /app/public/diff/norenburg_norenb_nodes_3808.diff
[CMD] [2021-04-19 16:52:56] tail -n +1 /app/public/converted_csv/norenburg_norenb_nodes_3808.csv >> /app/public/diff/norenburg_norenb_nodes_3808.diff
[CMD] [2021-04-19 16:52:56] echo "." >> /app/public/diff/norenburg_norenb_nodes_3808.diff
[INFO] [2021-04-19 16:52:56] Created diff: /app/public/diff/norenburg_norenb_nodes_3808.diff (3 lines)
[INFO] [2021-04-19 16:52:56] ...occurrences (/app/public/data/norenburg_norenb/occurrences.txt)
[CMD] [2021-04-19 16:52:56] echo "0a" > /app/public/diff/norenburg_norenb_occurrences_3808.diff
[CMD] [2021-04-19 16:52:56] tail -n +1 /app/public/converted_csv/norenburg_norenb_occurrences_3808.csv >> /app/public/diff/norenburg_norenb_occurrences_3808.diff
[CMD] [2021-04-19 16:52:56] echo "." >> /app/public/diff/norenburg_norenb_occurrences_3808.diff
[INFO] [2021-04-19 16:52:56] Created diff: /app/public/diff/norenburg_norenb_occurrences_3808.diff (3 lines)
[INFO] [2021-04-19 16:52:56] ...measurements (/app/public/data/norenburg_norenb/measurementsorfacts.txt)
[CMD] [2021-04-19 16:52:56] echo "0a" > /app/public/diff/norenburg_norenb_measurements_3808.diff
[CMD] [2021-04-19 16:52:56] tail -n +1 /app/public/converted_csv/norenburg_norenb_measurements_3808.csv >> /app/public/diff/norenburg_norenb_measurements_3808.diff
[CMD] [2021-04-19 16:52:56] echo "." >> /app/public/diff/norenburg_norenb_measurements_3808.diff
[INFO] [2021-04-19 16:52:56] Created diff: /app/public/diff/norenburg_norenb_measurements_3808.diff (5 lines)
[STOP] [2021-04-19 16:52:56] calculate_delta
[START] [2021-04-19 16:52:56] parse_diff_and_store
[INFO] [2021-04-19 16:52:56] Handling diff: /app/public/diff/norenburg_norenb_nodes_3808.diff (3 lines)
[INFO] [2021-04-19 16:52:56] Loading nodes diff file into memory (3 /app/public/diff/norenburg_norenb_nodes_3808.diff lines)...
[INFO] [2021-04-19 16:52:56] Handling diff: /app/public/diff/norenburg_norenb_occurrences_3808.diff (3 lines)
[INFO] [2021-04-19 16:52:56] Loading occurrences diff file into memory (3 /app/public/diff/norenburg_norenb_occurrences_3808.diff lines)...
[INFO] [2021-04-19 16:52:56] Handling diff: /app/public/diff/norenburg_norenb_measurements_3808.diff (5 lines)
[INFO] [2021-04-19 16:52:56] Loading measurements diff file into memory (5 /app/public/diff/norenburg_norenb_measurements_3808.diff lines)...
[INFO] [2021-04-19 16:52:56] Storing 1 ScientificNames
[INFO] [2021-04-19 16:52:56] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:52:56] Average Time: 0.0
[INFO] [2021-04-19 16:52:56] Total Time: 1s
[INFO] [2021-04-19 16:52:56] Storing 1 Nodes
[INFO] [2021-04-19 16:52:56] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:52:56] Average Time: 0.0
[INFO] [2021-04-19 16:52:56] Total Time: 1s
[INFO] [2021-04-19 16:52:56] Storing 1 Occurrences
[INFO] [2021-04-19 16:52:56] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:52:56] Average Time: 0.0
[INFO] [2021-04-19 16:52:56] Total Time: 1s
[INFO] [2021-04-19 16:52:56] Storing 3 Traits
[INFO] [2021-04-19 16:52:56] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 16:52:57] Average Time: 0.0
[INFO] [2021-04-19 16:52:57] Total Time: 1s
[INFO] [2021-04-19 16:52:57] Storing 1 MetaTraits
[INFO] [2021-04-19 16:52:57] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:52:57] Average Time: 0.0
[INFO] [2021-04-19 16:52:57] Total Time: 1s
[STOP] [2021-04-19 16:52:57] parse_diff_and_store
[START] [2021-04-19 16:52:57] resolve_keys
[INFO] [2021-04-19 16:53:02] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 16:53:02] traits to occurrences...
[INFO] [2021-04-19 16:53:02] traits to nodes (through occurrences)...
[INFO] [2021-04-19 16:53:02] Traits to sex term...
[INFO] [2021-04-19 16:53:02] Traits to lifestage term...
[INFO] [2021-04-19 16:53:02] MetaTraits to traits...
[INFO] [2021-04-19 16:53:02] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 16:53:02] Assocs to occurrences...
[INFO] [2021-04-19 16:53:02] Assocs to nodes...
[INFO] [2021-04-19 16:53:02] Assoc to sex term...
[INFO] [2021-04-19 16:53:02] Assoc to lifestage term...
[INFO] [2021-04-19 16:53:02] MetaAssoc to assocs...
[STOP] [2021-04-19 16:53:02] resolve_keys
[START] [2021-04-19 16:53:02] hold_for_later_1
[STOP] [2021-04-19 16:53:02] hold_for_later_1
[START] [2021-04-19 16:53:02] hold_for_later_2
[STOP] [2021-04-19 16:53:02] hold_for_later_2
[START] [2021-04-19 16:53:02] resolve_missing_parents
[STOP] [2021-04-19 16:53:02] resolve_missing_parents
[START] [2021-04-19 16:53:02] rebuild_nodes
[START] [2021-04-19 16:53:02] Flattener#flatten
[START] [2021-04-19 16:53:02] Flattener#study_resource
[START] [2021-04-19 16:53:02] Flattener#build_ancestry
[STOP] [2021-04-19 16:53:02] Flattener#build_ancestry
[INFO] [2021-04-19 16:53:02] 1 ancestry keys
[START] [2021-04-19 16:53:02] build_node_ancestors
[INFO] [2021-04-19 16:53:02] old ancestors deleted.
[STOP] [2021-04-19 16:53:02] build_node_ancestors
[WARN] [2021-04-19 16:53:02] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 16:53:02] Flattener#flatten
[STOP] [2021-04-19 16:53:02] rebuild_nodes
[START] [2021-04-19 16:53:02] resolve_missing_media_owners
[STOP] [2021-04-19 16:53:02] resolve_missing_media_owners
[START] [2021-04-19 16:53:02] sanitize_media_verbatims
[STOP] [2021-04-19 16:53:02] sanitize_media_verbatims
[START] [2021-04-19 16:53:02] queue_downloads
[STOP] [2021-04-19 16:53:02] queue_downloads
[START] [2021-04-19 16:53:02] parse_names
[WARN] [2021-04-19 16:53:02] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 16:53:04] parse_names
[START] [2021-04-19 16:53:04] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 16:53:04] denormalize_canonical_names_to_nodes
[START] [2021-04-19 16:53:04] match_nodes
[START] [2021-04-19 16:53:04] map_all_nodes_to_pages
[STOP] [2021-04-19 16:53:04] map_all_nodes_to_pages
[INFO] [2021-04-19 16:53:04] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 16:53:04] update_nodes
[STOP] [2021-04-19 16:53:04] update_nodes
[STOP] [2021-04-19 16:53:04] match_nodes
[START] [2021-04-19 16:53:04] reindex_search
[STOP] [2021-04-19 16:53:04] reindex_search
[START] [2021-04-19 16:53:04] normalize_units
[STOP] [2021-04-19 16:53:04] normalize_units
[START] [2021-04-19 16:53:04] calculate_statistics
[2021-04-19 16:53:04] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 16:53:04] calculate_statistics
[START] [2021-04-19 16:53:04] complete_harvest_instance
[START] [2021-04-19 16:53:04] overall_tsv_creation
[INFO] [2021-04-19 16:53:04] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 16:53:39] 1 Traits (unfiltered)...
[INFO] [2021-04-19 16:54:11] 1 Traits (filtered)...
[INFO] [2021-04-19 16:54:11] 0 Associations (filtered)...
[INFO] [2021-04-19 16:54:11] 2 metadata added.
[INFO] [2021-04-19 16:54:11] 0 metadata added.
[INFO] [2021-04-19 16:54:38] Average Time: 70.32
[INFO] [2021-04-19 16:54:38] Total Time: 1m35s
[STOP] [2021-04-19 16:54:38] overall_tsv_creation
[INFO] [2021-04-19 16:54:38] Done. Check your files:
[INFO] [2021-04-19 16:54:38] (1 lines) /app/public/data/norenburg_norenb/publish_nodes.tsv
[INFO] [2021-04-19 16:54:38] (1 lines) /app/public/data/norenburg_norenb/publish_scientific_names.tsv
[INFO] [2021-04-19 16:54:38] (2 lines) /app/public/data/norenburg_norenb/publish_traits.tsv
[INFO] [2021-04-19 16:54:38] (3 lines) /app/public/data/norenburg_norenb/publish_metadata.tsv
[STOP] [2021-04-19 16:54:38] complete_harvest_instance
[START] [2021-04-19 16:54:38] completed
[STOP] [2021-04-19 16:54:38] completed
[STOP] [2021-04-19 16:54:38] logged process, took 101.83

Latest Process

19 Apr 16:52 EXITED currently processing 0