Harvest for Roscito and Rodrigues 2012 Created 19 Apr 15:57

Harvesting Log

# Logfile created on 2020-08-27 15:48:42 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:48:42] logged process
[START] [2020-08-27 15:48:42] Creating resource from OpenData
[START] [2020-08-27 15:48:42] logged process
[START] [2020-08-27 15:48:42] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:48:43] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:48:43] Creating resource from OpenData
[INFO] [2020-12-03 12:06:16] ## HARVEST: type = -harvest
[START] [2020-12-03 12:06:20] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-03 12:06:20] create_harvest_instance
[STOP] [2020-12-03 12:06:22] create_harvest_instance
[START] [2020-12-03 12:06:22] fetch_files
[STOP] [2020-12-03 12:06:22] fetch_files
[START] [2020-12-03 12:06:22] validate_each_file
[STOP] [2020-12-03 12:06:22] validate_each_file
[START] [2020-12-03 12:06:22] convert_to_csv
[CMD] [2020-12-03 12:06:22] /usr/bin/sort /app/public/converted_csv/roscito_rodrigue_refs_24876.csv > /app/public/converted_csv/roscito_rodrigue_refs_24876.csv_sorted
[CMD] [2020-12-03 12:06:22] /usr/bin/sort /app/public/converted_csv/roscito_rodrigue_nodes_24877.csv > /app/public/converted_csv/roscito_rodrigue_nodes_24877.csv_sorted
[CMD] [2020-12-03 12:06:22] /usr/bin/sort /app/public/converted_csv/roscito_rodrigue_occurrences_24878.csv > /app/public/converted_csv/roscito_rodrigue_occurrences_24878.csv_sorted
[CMD] [2020-12-03 12:06:22] /usr/bin/sort /app/public/converted_csv/roscito_rodrigue_measurements_24879.csv > /app/public/converted_csv/roscito_rodrigue_measurements_24879.csv_sorted
[STOP] [2020-12-03 12:06:22] convert_to_csv
[START] [2020-12-03 12:06:22] calculate_delta
[CMD] [2020-12-03 12:06:22] echo "0a" > /app/public/diff/roscito_rodrigue_refs_24876.diff
[CMD] [2020-12-03 12:06:22] tail -n +1 /app/public/converted_csv/roscito_rodrigue_refs_24876.csv >> /app/public/diff/roscito_rodrigue_refs_24876.diff
[CMD] [2020-12-03 12:06:22] echo "." >> /app/public/diff/roscito_rodrigue_refs_24876.diff
[CMD] [2020-12-03 12:06:22] echo "0a" > /app/public/diff/roscito_rodrigue_nodes_24877.diff
[CMD] [2020-12-03 12:06:22] tail -n +1 /app/public/converted_csv/roscito_rodrigue_nodes_24877.csv >> /app/public/diff/roscito_rodrigue_nodes_24877.diff
[CMD] [2020-12-03 12:06:22] echo "." >> /app/public/diff/roscito_rodrigue_nodes_24877.diff
[CMD] [2020-12-03 12:06:22] echo "0a" > /app/public/diff/roscito_rodrigue_occurrences_24878.diff
[CMD] [2020-12-03 12:06:22] tail -n +1 /app/public/converted_csv/roscito_rodrigue_occurrences_24878.csv >> /app/public/diff/roscito_rodrigue_occurrences_24878.diff
[CMD] [2020-12-03 12:06:22] echo "." >> /app/public/diff/roscito_rodrigue_occurrences_24878.diff
[CMD] [2020-12-03 12:06:22] echo "0a" > /app/public/diff/roscito_rodrigue_measurements_24879.diff
[CMD] [2020-12-03 12:06:22] tail -n +1 /app/public/converted_csv/roscito_rodrigue_measurements_24879.csv >> /app/public/diff/roscito_rodrigue_measurements_24879.diff
[CMD] [2020-12-03 12:06:22] echo "." >> /app/public/diff/roscito_rodrigue_measurements_24879.diff
[STOP] [2020-12-03 12:06:22] calculate_delta
[START] [2020-12-03 12:06:22] parse_diff_and_store
[INFO] [2020-12-03 12:06:22] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 12:06:22] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 12:06:22] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 12:06:22] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 12:06:23] Storing 1 ScientificNames
[INFO] [2020-12-03 12:06:23] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 12:06:23] Average Time: 0.0
[INFO] [2020-12-03 12:06:23] Total Time: 1s
[INFO] [2020-12-03 12:06:23] Storing 1 Nodes
[INFO] [2020-12-03 12:06:23] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 12:06:23] Average Time: 0.0
[INFO] [2020-12-03 12:06:23] Total Time: 1s
[INFO] [2020-12-03 12:06:23] Storing 1 Occurrences
[INFO] [2020-12-03 12:06:23] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 12:06:23] Average Time: 0.0
[INFO] [2020-12-03 12:06:23] Total Time: 1s
[INFO] [2020-12-03 12:06:23] Storing 1 Traits
[INFO] [2020-12-03 12:06:23] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 12:06:23] Average Time: 0.0
[INFO] [2020-12-03 12:06:23] Total Time: 1s
[INFO] [2020-12-03 12:06:23] Storing 2 MetaTraits
[INFO] [2020-12-03 12:06:23] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 12:06:23] Average Time: 0.0
[INFO] [2020-12-03 12:06:23] Total Time: 1s
[STOP] [2020-12-03 12:06:23] parse_diff_and_store
[START] [2020-12-03 12:06:23] resolve_keys
[INFO] [2020-12-03 12:06:29] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 12:06:29] traits to occurrences...
[INFO] [2020-12-03 12:06:29] traits to nodes (through occurrences)...
[INFO] [2020-12-03 12:06:29] Traits to sex term...
[INFO] [2020-12-03 12:06:29] Traits to lifestage term...
[INFO] [2020-12-03 12:06:29] MetaTraits to traits...
[INFO] [2020-12-03 12:06:29] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 12:06:29] Assocs to occurrences...
[INFO] [2020-12-03 12:06:29] Assocs to nodes...
[INFO] [2020-12-03 12:06:29] Assoc to sex term...
[INFO] [2020-12-03 12:06:29] Assoc to lifestage term...
[INFO] [2020-12-03 12:06:29] MetaAssoc to assocs...
[STOP] [2020-12-03 12:06:29] resolve_keys
[START] [2020-12-03 12:06:29] hold_for_later_1
[STOP] [2020-12-03 12:06:29] hold_for_later_1
[START] [2020-12-03 12:06:29] hold_for_later_2
[STOP] [2020-12-03 12:06:29] hold_for_later_2
[START] [2020-12-03 12:06:29] resolve_missing_parents
[STOP] [2020-12-03 12:06:29] resolve_missing_parents
[START] [2020-12-03 12:06:29] rebuild_nodes
[START] [2020-12-03 12:06:29] Flattener#flatten
[START] [2020-12-03 12:06:29] Flattener#study_resource
[START] [2020-12-03 12:06:29] Flattener#build_ancestry
[STOP] [2020-12-03 12:06:29] Flattener#build_ancestry
[INFO] [2020-12-03 12:06:29] 1 ancestry keys
[START] [2020-12-03 12:06:29] build_node_ancestors
[INFO] [2020-12-03 12:06:29] old ancestors deleted.
[STOP] [2020-12-03 12:06:29] build_node_ancestors
[WARN] [2020-12-03 12:06:29] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 12:06:29] Flattener#flatten
[STOP] [2020-12-03 12:06:29] rebuild_nodes
[START] [2020-12-03 12:06:29] resolve_missing_media_owners
[STOP] [2020-12-03 12:06:29] resolve_missing_media_owners
[START] [2020-12-03 12:06:29] sanitize_media_verbatims
[STOP] [2020-12-03 12:06:29] sanitize_media_verbatims
[START] [2020-12-03 12:06:29] queue_downloads
[STOP] [2020-12-03 12:06:29] queue_downloads
[START] [2020-12-03 12:06:29] parse_names
[WARN] [2020-12-03 12:06:29] I see 1 names which still need to be parsed.
[STOP] [2020-12-03 12:06:30] parse_names
[START] [2020-12-03 12:06:30] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 12:06:30] denormalize_canonical_names_to_nodes
[START] [2020-12-03 12:06:30] match_nodes
[START] [2020-12-03 12:06:30] map_all_nodes_to_pages
[STOP] [2020-12-03 12:06:30] map_all_nodes_to_pages
[INFO] [2020-12-03 12:06:30] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-12-03 12:06:30] update_nodes
[STOP] [2020-12-03 12:06:30] update_nodes
[STOP] [2020-12-03 12:06:30] match_nodes
[START] [2020-12-03 12:06:30] reindex_search
[STOP] [2020-12-03 12:06:30] reindex_search
[START] [2020-12-03 12:06:30] normalize_units
[STOP] [2020-12-03 12:06:30] normalize_units
[START] [2020-12-03 12:06:30] calculate_statistics
[2020-12-03 12:06:30] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 12:06:30] calculate_statistics
[START] [2020-12-03 12:06:30] complete_harvest_instance
[START] [2020-12-03 12:06:30] overall_tsv_creation
[INFO] [2020-12-03 12:06:30] Processing group of 1 in 1 batches of 10000
[INFO] [2020-12-03 12:07:09] 1 Traits (unfiltered)...
[INFO] [2020-12-03 12:07:44] 1 Traits (filtered)...
[INFO] [2020-12-03 12:07:44] 0 Associations (filtered)...
[INFO] [2020-12-03 12:07:44] 2 metadata added.
[INFO] [2020-12-03 12:07:44] 0 metadata added.
[INFO] [2020-12-03 12:07:44] Average Time: 51.59
[INFO] [2020-12-03 12:07:44] Total Time: 1m15s
[STOP] [2020-12-03 12:07:44] overall_tsv_creation
[INFO] [2020-12-03 12:07:44] Done. Check your files:
[INFO] [2020-12-03 12:07:44] (1 lines) /app/public/data/roscito_rodrigue/publish_nodes.tsv
[INFO] [2020-12-03 12:07:44] (1 lines) /app/public/data/roscito_rodrigue/publish_scientific_names.tsv
[INFO] [2020-12-03 12:07:44] (2 lines) /app/public/data/roscito_rodrigue/publish_traits.tsv
[INFO] [2020-12-03 12:07:44] (3 lines) /app/public/data/roscito_rodrigue/publish_metadata.tsv
[STOP] [2020-12-03 12:07:44] complete_harvest_instance
[START] [2020-12-03 12:07:44] completed
[STOP] [2020-12-03 12:07:44] completed
[STOP] [2020-12-03 12:07:44] logged process, took 84.16
[INFO] [2021-04-19 15:57:20] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:57:25] ## remove_type: ScientificName
[INFO] [2021-04-19 15:57:25] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:57:25] [15:57:25.113] Removed 1 Scientificnames
[INFO] [2021-04-19 15:57:25] ## remove_type: Vernacular
[INFO] [2021-04-19 15:57:25] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:57:25] [15:57:25.114] Removed 0 Vernaculars
[INFO] [2021-04-19 15:57:25] ## remove_type: Article
[INFO] [2021-04-19 15:57:25] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:57:25] [15:57:25.116] Removed 0 Articles
[INFO] [2021-04-19 15:57:25] ## remove_type: Medium
[INFO] [2021-04-19 15:57:25] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:57:25] [15:57:25.117] Removed 0 Media
[INFO] [2021-04-19 15:57:25] ## remove_type: Trait
[INFO] [2021-04-19 15:57:25] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:57:25] [15:57:25.119] Removed 1 Traits
[INFO] [2021-04-19 15:57:25] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:57:25] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:57:25] [15:57:25.121] Removed 2 Metatraits
[INFO] [2021-04-19 15:57:25] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:57:25] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:57:25] [15:57:25.122] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 15:57:25] ## remove_type: Assoc
[INFO] [2021-04-19 15:57:25] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:57:25] [15:57:25.124] Removed 0 Assocs
[INFO] [2021-04-19 15:57:25] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:57:25] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:57:25] [15:57:25.125] Removed 0 Metaassocs
[INFO] [2021-04-19 15:57:25] ## remove_type: Identifier
[INFO] [2021-04-19 15:57:25] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:57:25] [15:57:25.127] Removed 0 Identifiers
[INFO] [2021-04-19 15:57:25] ## remove_type: Reference
[INFO] [2021-04-19 15:57:25] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:57:25] [15:57:25.129] Removed 0 References
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] Starting batch with ID 86116212...
[INFO] [2021-04-19 15:57:25] ## remove_type: Node
[INFO] [2021-04-19 15:57:25] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:57:25] [15:57:25.734] Removed 1 Nodes
[START] [2021-04-19 15:57:25] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:57:25] Creating resource from OpenData
[START] [2021-04-19 15:57:25] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:57:25] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:57:26] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:57:26] Creating resource from OpenData
[START] [2021-04-19 15:57:26] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:57:26] create_harvest_instance
[INFO] [2021-04-19 15:57:26] Created harvest instance #3782
[STOP] [2021-04-19 15:57:26] create_harvest_instance
[START] [2021-04-19 15:57:26] fetch_files
[STOP] [2021-04-19 15:57:26] fetch_files
[START] [2021-04-19 15:57:26] validate_each_file
[INFO] [2021-04-19 15:57:26] Looping over 4 formats...
[INFO] [2021-04-19 15:57:26] ...refs (/app/public/data/roscito_rodrigue/references.tsv)
[INFO] [2021-04-19 15:57:26] Valid: /app/public/converted_csv/roscito_rodrigue_refs_3782.csv (0 lines)
[INFO] [2021-04-19 15:57:26] ...nodes (/app/public/data/roscito_rodrigue/taxa.txt)
[INFO] [2021-04-19 15:57:26] Valid: /app/public/converted_csv/roscito_rodrigue_nodes_3782.csv (1 lines)
[INFO] [2021-04-19 15:57:26] ...occurrences (/app/public/data/roscito_rodrigue/occurrences.txt)
[INFO] [2021-04-19 15:57:26] Valid: /app/public/converted_csv/roscito_rodrigue_occurrences_3782.csv (1 lines)
[INFO] [2021-04-19 15:57:26] ...measurements (/app/public/data/roscito_rodrigue/measurementsorfacts.txt)
[INFO] [2021-04-19 15:57:26] Valid: /app/public/converted_csv/roscito_rodrigue_measurements_3782.csv (1 lines)
[STOP] [2021-04-19 15:57:26] validate_each_file
[START] [2021-04-19 15:57:26] convert_to_csv
[INFO] [2021-04-19 15:57:26] Looping over 4 formats...
[INFO] [2021-04-19 15:57:26] ...refs (/app/public/data/roscito_rodrigue/references.tsv)
[CMD] [2021-04-19 15:57:26] /usr/bin/sort /app/public/converted_csv/roscito_rodrigue_refs_3782.csv > /app/public/converted_csv/roscito_rodrigue_refs_3782.csv_sorted
[INFO] [2021-04-19 15:57:26] Converted: /app/public/converted_csv/roscito_rodrigue_refs_3782.csv (0 lines)
[INFO] [2021-04-19 15:57:26] ...nodes (/app/public/data/roscito_rodrigue/taxa.txt)
[CMD] [2021-04-19 15:57:26] /usr/bin/sort /app/public/converted_csv/roscito_rodrigue_nodes_3782.csv > /app/public/converted_csv/roscito_rodrigue_nodes_3782.csv_sorted
[INFO] [2021-04-19 15:57:26] Converted: /app/public/converted_csv/roscito_rodrigue_nodes_3782.csv (1 lines)
[INFO] [2021-04-19 15:57:26] ...occurrences (/app/public/data/roscito_rodrigue/occurrences.txt)
[CMD] [2021-04-19 15:57:26] /usr/bin/sort /app/public/converted_csv/roscito_rodrigue_occurrences_3782.csv > /app/public/converted_csv/roscito_rodrigue_occurrences_3782.csv_sorted
[INFO] [2021-04-19 15:57:26] Converted: /app/public/converted_csv/roscito_rodrigue_occurrences_3782.csv (1 lines)
[INFO] [2021-04-19 15:57:26] ...measurements (/app/public/data/roscito_rodrigue/measurementsorfacts.txt)
[CMD] [2021-04-19 15:57:26] /usr/bin/sort /app/public/converted_csv/roscito_rodrigue_measurements_3782.csv > /app/public/converted_csv/roscito_rodrigue_measurements_3782.csv_sorted
[INFO] [2021-04-19 15:57:26] Converted: /app/public/converted_csv/roscito_rodrigue_measurements_3782.csv (1 lines)
[STOP] [2021-04-19 15:57:26] convert_to_csv
[START] [2021-04-19 15:57:26] calculate_delta
[INFO] [2021-04-19 15:57:26] Looping over 4 formats...
[INFO] [2021-04-19 15:57:26] ...refs (/app/public/data/roscito_rodrigue/references.tsv)
[CMD] [2021-04-19 15:57:26] echo "0a" > /app/public/diff/roscito_rodrigue_refs_3782.diff
[CMD] [2021-04-19 15:57:26] tail -n +1 /app/public/converted_csv/roscito_rodrigue_refs_3782.csv >> /app/public/diff/roscito_rodrigue_refs_3782.diff
[CMD] [2021-04-19 15:57:26] echo "." >> /app/public/diff/roscito_rodrigue_refs_3782.diff
[INFO] [2021-04-19 15:57:26] Created diff: /app/public/diff/roscito_rodrigue_refs_3782.diff (2 lines)
[INFO] [2021-04-19 15:57:26] ...nodes (/app/public/data/roscito_rodrigue/taxa.txt)
[CMD] [2021-04-19 15:57:26] echo "0a" > /app/public/diff/roscito_rodrigue_nodes_3782.diff
[CMD] [2021-04-19 15:57:26] tail -n +1 /app/public/converted_csv/roscito_rodrigue_nodes_3782.csv >> /app/public/diff/roscito_rodrigue_nodes_3782.diff
[CMD] [2021-04-19 15:57:26] echo "." >> /app/public/diff/roscito_rodrigue_nodes_3782.diff
[INFO] [2021-04-19 15:57:26] Created diff: /app/public/diff/roscito_rodrigue_nodes_3782.diff (3 lines)
[INFO] [2021-04-19 15:57:26] ...occurrences (/app/public/data/roscito_rodrigue/occurrences.txt)
[CMD] [2021-04-19 15:57:26] echo "0a" > /app/public/diff/roscito_rodrigue_occurrences_3782.diff
[CMD] [2021-04-19 15:57:26] tail -n +1 /app/public/converted_csv/roscito_rodrigue_occurrences_3782.csv >> /app/public/diff/roscito_rodrigue_occurrences_3782.diff
[CMD] [2021-04-19 15:57:26] echo "." >> /app/public/diff/roscito_rodrigue_occurrences_3782.diff
[INFO] [2021-04-19 15:57:26] Created diff: /app/public/diff/roscito_rodrigue_occurrences_3782.diff (3 lines)
[INFO] [2021-04-19 15:57:26] ...measurements (/app/public/data/roscito_rodrigue/measurementsorfacts.txt)
[CMD] [2021-04-19 15:57:26] echo "0a" > /app/public/diff/roscito_rodrigue_measurements_3782.diff
[CMD] [2021-04-19 15:57:26] tail -n +1 /app/public/converted_csv/roscito_rodrigue_measurements_3782.csv >> /app/public/diff/roscito_rodrigue_measurements_3782.diff
[CMD] [2021-04-19 15:57:26] echo "." >> /app/public/diff/roscito_rodrigue_measurements_3782.diff
[INFO] [2021-04-19 15:57:26] Created diff: /app/public/diff/roscito_rodrigue_measurements_3782.diff (3 lines)
[STOP] [2021-04-19 15:57:26] calculate_delta
[START] [2021-04-19 15:57:26] parse_diff_and_store
[INFO] [2021-04-19 15:57:26] Handling diff: /app/public/diff/roscito_rodrigue_refs_3782.diff (2 lines)
[INFO] [2021-04-19 15:57:26] Loading refs diff file into memory (2 /app/public/diff/roscito_rodrigue_refs_3782.diff lines)...
[INFO] [2021-04-19 15:57:26] Handling diff: /app/public/diff/roscito_rodrigue_nodes_3782.diff (3 lines)
[INFO] [2021-04-19 15:57:26] Loading nodes diff file into memory (3 /app/public/diff/roscito_rodrigue_nodes_3782.diff lines)...
[INFO] [2021-04-19 15:57:26] Handling diff: /app/public/diff/roscito_rodrigue_occurrences_3782.diff (3 lines)
[INFO] [2021-04-19 15:57:26] Loading occurrences diff file into memory (3 /app/public/diff/roscito_rodrigue_occurrences_3782.diff lines)...
[INFO] [2021-04-19 15:57:26] Handling diff: /app/public/diff/roscito_rodrigue_measurements_3782.diff (3 lines)
[INFO] [2021-04-19 15:57:26] Loading measurements diff file into memory (3 /app/public/diff/roscito_rodrigue_measurements_3782.diff lines)...
[INFO] [2021-04-19 15:57:26] Storing 1 ScientificNames
[INFO] [2021-04-19 15:57:26] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:57:26] Average Time: 0.0
[INFO] [2021-04-19 15:57:26] Total Time: 1s
[INFO] [2021-04-19 15:57:26] Storing 1 Nodes
[INFO] [2021-04-19 15:57:26] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:57:26] Average Time: 0.0
[INFO] [2021-04-19 15:57:26] Total Time: 1s
[INFO] [2021-04-19 15:57:26] Storing 1 Occurrences
[INFO] [2021-04-19 15:57:26] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:57:26] Average Time: 0.0
[INFO] [2021-04-19 15:57:26] Total Time: 1s
[INFO] [2021-04-19 15:57:26] Storing 1 Traits
[INFO] [2021-04-19 15:57:26] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:57:26] Average Time: 0.0
[INFO] [2021-04-19 15:57:26] Total Time: 1s
[INFO] [2021-04-19 15:57:26] Storing 2 MetaTraits
[INFO] [2021-04-19 15:57:26] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:57:26] Average Time: 0.0
[INFO] [2021-04-19 15:57:26] Total Time: 1s
[STOP] [2021-04-19 15:57:26] parse_diff_and_store
[START] [2021-04-19 15:57:26] resolve_keys
[INFO] [2021-04-19 15:57:32] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:57:32] traits to occurrences...
[INFO] [2021-04-19 15:57:32] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:57:32] Traits to sex term...
[INFO] [2021-04-19 15:57:32] Traits to lifestage term...
[INFO] [2021-04-19 15:57:32] MetaTraits to traits...
[INFO] [2021-04-19 15:57:32] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:57:32] Assocs to occurrences...
[INFO] [2021-04-19 15:57:32] Assocs to nodes...
[INFO] [2021-04-19 15:57:32] Assoc to sex term...
[INFO] [2021-04-19 15:57:32] Assoc to lifestage term...
[INFO] [2021-04-19 15:57:32] MetaAssoc to assocs...
[STOP] [2021-04-19 15:57:32] resolve_keys
[START] [2021-04-19 15:57:32] hold_for_later_1
[STOP] [2021-04-19 15:57:32] hold_for_later_1
[START] [2021-04-19 15:57:32] hold_for_later_2
[STOP] [2021-04-19 15:57:32] hold_for_later_2
[START] [2021-04-19 15:57:32] resolve_missing_parents
[STOP] [2021-04-19 15:57:32] resolve_missing_parents
[START] [2021-04-19 15:57:32] rebuild_nodes
[START] [2021-04-19 15:57:32] Flattener#flatten
[START] [2021-04-19 15:57:32] Flattener#study_resource
[START] [2021-04-19 15:57:32] Flattener#build_ancestry
[STOP] [2021-04-19 15:57:32] Flattener#build_ancestry
[INFO] [2021-04-19 15:57:32] 1 ancestry keys
[START] [2021-04-19 15:57:32] build_node_ancestors
[INFO] [2021-04-19 15:57:32] old ancestors deleted.
[STOP] [2021-04-19 15:57:32] build_node_ancestors
[WARN] [2021-04-19 15:57:32] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:57:32] Flattener#flatten
[STOP] [2021-04-19 15:57:32] rebuild_nodes
[START] [2021-04-19 15:57:32] resolve_missing_media_owners
[STOP] [2021-04-19 15:57:32] resolve_missing_media_owners
[START] [2021-04-19 15:57:32] sanitize_media_verbatims
[STOP] [2021-04-19 15:57:32] sanitize_media_verbatims
[START] [2021-04-19 15:57:32] queue_downloads
[STOP] [2021-04-19 15:57:32] queue_downloads
[START] [2021-04-19 15:57:32] parse_names
[WARN] [2021-04-19 15:57:32] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 15:57:33] parse_names
[START] [2021-04-19 15:57:33] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:57:33] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:57:33] match_nodes
[START] [2021-04-19 15:57:33] map_all_nodes_to_pages
[STOP] [2021-04-19 15:57:33] map_all_nodes_to_pages
[INFO] [2021-04-19 15:57:33] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 15:57:33] update_nodes
[STOP] [2021-04-19 15:57:33] update_nodes
[STOP] [2021-04-19 15:57:33] match_nodes
[START] [2021-04-19 15:57:33] reindex_search
[STOP] [2021-04-19 15:57:33] reindex_search
[START] [2021-04-19 15:57:33] normalize_units
[STOP] [2021-04-19 15:57:33] normalize_units
[START] [2021-04-19 15:57:33] calculate_statistics
[2021-04-19 15:57:33] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:57:33] calculate_statistics
[START] [2021-04-19 15:57:33] complete_harvest_instance
[START] [2021-04-19 15:57:33] overall_tsv_creation
[INFO] [2021-04-19 15:57:33] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 15:58:09] 1 Traits (unfiltered)...
[INFO] [2021-04-19 15:58:41] 1 Traits (filtered)...
[INFO] [2021-04-19 15:58:41] 0 Associations (filtered)...
[INFO] [2021-04-19 15:58:41] 0 metadata added.
[INFO] [2021-04-19 15:58:41] 0 metadata added.
[INFO] [2021-04-19 15:59:08] Average Time: 71.31
[INFO] [2021-04-19 15:59:08] Total Time: 1m36s
[STOP] [2021-04-19 15:59:08] overall_tsv_creation
[INFO] [2021-04-19 15:59:08] Done. Check your files:
[INFO] [2021-04-19 15:59:08] (1 lines) /app/public/data/roscito_rodrigue/publish_nodes.tsv
[INFO] [2021-04-19 15:59:08] (1 lines) /app/public/data/roscito_rodrigue/publish_scientific_names.tsv
[INFO] [2021-04-19 15:59:08] (2 lines) /app/public/data/roscito_rodrigue/publish_traits.tsv
[INFO] [2021-04-19 15:59:08] (1 lines) /app/public/data/roscito_rodrigue/publish_metadata.tsv
[STOP] [2021-04-19 15:59:08] complete_harvest_instance
[START] [2021-04-19 15:59:08] completed
[STOP] [2021-04-19 15:59:08] completed
[STOP] [2021-04-19 15:59:08] logged process, took 102.67

Latest Process

19 Apr 15:57 EXITED currently processing 0