Harvest for Hunt 2007 Created 19 Apr 14:44

Harvesting Log

# Logfile created on 2020-08-27 15:17:20 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:17:20] logged process
[START] [2020-08-27 15:17:20] Creating resource from OpenData
[START] [2020-08-27 15:17:20] logged process
[START] [2020-08-27 15:17:20] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:17:20] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:17:20] Creating resource from OpenData
[INFO] [2020-11-16 09:02:04] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-11-16 09:02:05] ## remove_type: ScientificName
[INFO] [2020-11-16 09:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-16 09:02:05] [09:02:05.216] Removed 0 Scientificnames
[INFO] [2020-11-16 09:02:05] ## remove_type: Vernacular
[INFO] [2020-11-16 09:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-16 09:02:05] [09:02:05.219] Removed 0 Vernaculars
[INFO] [2020-11-16 09:02:05] ## remove_type: Article
[INFO] [2020-11-16 09:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-16 09:02:05] [09:02:05.222] Removed 0 Articles
[INFO] [2020-11-16 09:02:05] ## remove_type: Medium
[INFO] [2020-11-16 09:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-16 09:02:05] [09:02:05.225] Removed 0 Media
[INFO] [2020-11-16 09:02:05] ## remove_type: Trait
[INFO] [2020-11-16 09:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-16 09:02:05] [09:02:05.228] Removed 0 Traits
[INFO] [2020-11-16 09:02:05] ## remove_type: MetaTrait
[INFO] [2020-11-16 09:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-16 09:02:05] [09:02:05.230] Removed 0 Metatraits
[INFO] [2020-11-16 09:02:05] ## remove_type: OccurrenceMetadatum
[INFO] [2020-11-16 09:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-16 09:02:05] [09:02:05.233] Removed 0 Occurrencemetadata
[INFO] [2020-11-16 09:02:05] ## remove_type: Assoc
[INFO] [2020-11-16 09:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-16 09:02:05] [09:02:05.235] Removed 0 Assocs
[INFO] [2020-11-16 09:02:05] ## remove_type: MetaAssoc
[INFO] [2020-11-16 09:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-16 09:02:05] [09:02:05.238] Removed 0 Metaassocs
[INFO] [2020-11-16 09:02:05] ## remove_type: Identifier
[INFO] [2020-11-16 09:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-16 09:02:05] [09:02:05.241] Removed 0 Identifiers
[INFO] [2020-11-16 09:02:05] ## remove_type: Reference
[INFO] [2020-11-16 09:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-16 09:02:05] [09:02:05.243] Removed 0 References
[INFO] [2020-11-16 09:02:05] ## remove_type: Node
[INFO] [2020-11-16 09:02:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-16 09:02:05] [09:02:05.479] Removed 0 Nodes
[START] [2020-11-16 09:02:05] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-16 09:02:05] Creating resource from OpenData
[START] [2020-11-16 09:02:05] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-16 09:02:05] Parse meta.xml file and create formats with fields
[STOP] [2020-11-16 09:02:06] Parse meta.xml file and create formats with fields
[STOP] [2020-11-16 09:02:06] Creating resource from OpenData
[START] [2020-11-16 09:02:06] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-16 09:02:06] create_harvest_instance
[STOP] [2020-11-16 09:02:07] create_harvest_instance
[START] [2020-11-16 09:02:07] fetch_files
[STOP] [2020-11-16 09:02:07] fetch_files
[START] [2020-11-16 09:02:07] validate_each_file
[STOP] [2020-11-16 09:02:07] validate_each_file
[START] [2020-11-16 09:02:07] convert_to_csv
[CMD] [2020-11-16 09:02:07] /usr/bin/sort /app/public/converted_csv/hunt_hunt_2007_refs_24260.csv > /app/public/converted_csv/hunt_hunt_2007_refs_24260.csv_sorted
[CMD] [2020-11-16 09:02:07] /usr/bin/sort /app/public/converted_csv/hunt_hunt_2007_nodes_24261.csv > /app/public/converted_csv/hunt_hunt_2007_nodes_24261.csv_sorted
[CMD] [2020-11-16 09:02:07] /usr/bin/sort /app/public/converted_csv/hunt_hunt_2007_occurrences_24262.csv > /app/public/converted_csv/hunt_hunt_2007_occurrences_24262.csv_sorted
[CMD] [2020-11-16 09:02:07] /usr/bin/sort /app/public/converted_csv/hunt_hunt_2007_measurements_24263.csv > /app/public/converted_csv/hunt_hunt_2007_measurements_24263.csv_sorted
[STOP] [2020-11-16 09:02:07] convert_to_csv
[START] [2020-11-16 09:02:07] calculate_delta
[CMD] [2020-11-16 09:02:07] echo "0a" > /app/public/diff/hunt_hunt_2007_refs_24260.diff
[CMD] [2020-11-16 09:02:07] tail -n +1 /app/public/converted_csv/hunt_hunt_2007_refs_24260.csv >> /app/public/diff/hunt_hunt_2007_refs_24260.diff
[CMD] [2020-11-16 09:02:07] echo "." >> /app/public/diff/hunt_hunt_2007_refs_24260.diff
[CMD] [2020-11-16 09:02:07] echo "0a" > /app/public/diff/hunt_hunt_2007_nodes_24261.diff
[CMD] [2020-11-16 09:02:07] tail -n +1 /app/public/converted_csv/hunt_hunt_2007_nodes_24261.csv >> /app/public/diff/hunt_hunt_2007_nodes_24261.diff
[CMD] [2020-11-16 09:02:07] echo "." >> /app/public/diff/hunt_hunt_2007_nodes_24261.diff
[CMD] [2020-11-16 09:02:07] echo "0a" > /app/public/diff/hunt_hunt_2007_occurrences_24262.diff
[CMD] [2020-11-16 09:02:07] tail -n +1 /app/public/converted_csv/hunt_hunt_2007_occurrences_24262.csv >> /app/public/diff/hunt_hunt_2007_occurrences_24262.diff
[CMD] [2020-11-16 09:02:07] echo "." >> /app/public/diff/hunt_hunt_2007_occurrences_24262.diff
[CMD] [2020-11-16 09:02:07] echo "0a" > /app/public/diff/hunt_hunt_2007_measurements_24263.diff
[CMD] [2020-11-16 09:02:07] tail -n +1 /app/public/converted_csv/hunt_hunt_2007_measurements_24263.csv >> /app/public/diff/hunt_hunt_2007_measurements_24263.diff
[CMD] [2020-11-16 09:02:07] echo "." >> /app/public/diff/hunt_hunt_2007_measurements_24263.diff
[STOP] [2020-11-16 09:02:07] calculate_delta
[START] [2020-11-16 09:02:07] parse_diff_and_store
[INFO] [2020-11-16 09:02:07] Loading refs diff file into memory (true lines)...
[INFO] [2020-11-16 09:02:07] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-16 09:02:07] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-16 09:02:07] Loading measurements diff file into memory (true lines)...
[INFO] [2020-11-16 09:02:08] Storing 3 ScientificNames
[INFO] [2020-11-16 09:02:08] Processing group of 3 in 1 groups of 1000
[INFO] [2020-11-16 09:02:08] Average Time: 0.0
[INFO] [2020-11-16 09:02:08] Total Time: 1s
[INFO] [2020-11-16 09:02:08] Storing 3 Nodes
[INFO] [2020-11-16 09:02:08] Processing group of 3 in 1 groups of 1000
[INFO] [2020-11-16 09:02:09] Average Time: 0.0
[INFO] [2020-11-16 09:02:09] Total Time: 1s
[INFO] [2020-11-16 09:02:09] Storing 3 Occurrences
[INFO] [2020-11-16 09:02:09] Processing group of 3 in 1 groups of 1000
[INFO] [2020-11-16 09:02:09] Average Time: 0.01
[INFO] [2020-11-16 09:02:09] Total Time: 1s
[INFO] [2020-11-16 09:02:09] Storing 6 Traits
[INFO] [2020-11-16 09:02:09] Processing group of 6 in 1 groups of 1000
[INFO] [2020-11-16 09:02:09] Average Time: 0.0
[INFO] [2020-11-16 09:02:09] Total Time: 1s
[INFO] [2020-11-16 09:02:09] Storing 3 MetaTraits
[INFO] [2020-11-16 09:02:09] Processing group of 3 in 1 groups of 1000
[INFO] [2020-11-16 09:02:09] Average Time: 0.0
[INFO] [2020-11-16 09:02:09] Total Time: 1s
[STOP] [2020-11-16 09:02:09] parse_diff_and_store
[START] [2020-11-16 09:02:09] resolve_keys
[INFO] [2020-11-16 09:02:14] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-16 09:02:14] traits to occurrences...
[INFO] [2020-11-16 09:02:14] traits to nodes (through occurrences)...
[INFO] [2020-11-16 09:02:14] Traits to sex term...
[INFO] [2020-11-16 09:02:14] Traits to lifestage term...
[INFO] [2020-11-16 09:02:14] MetaTraits to traits...
[INFO] [2020-11-16 09:02:14] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-16 09:02:14] Assocs to occurrences...
[INFO] [2020-11-16 09:02:14] Assocs to nodes...
[INFO] [2020-11-16 09:02:14] Assoc to sex term...
[INFO] [2020-11-16 09:02:14] Assoc to lifestage term...
[INFO] [2020-11-16 09:02:14] MetaAssoc to assocs...
[STOP] [2020-11-16 09:02:14] resolve_keys
[START] [2020-11-16 09:02:14] hold_for_later_1
[STOP] [2020-11-16 09:02:14] hold_for_later_1
[START] [2020-11-16 09:02:14] hold_for_later_2
[STOP] [2020-11-16 09:02:14] hold_for_later_2
[START] [2020-11-16 09:02:14] resolve_missing_parents
[STOP] [2020-11-16 09:02:14] resolve_missing_parents
[START] [2020-11-16 09:02:14] rebuild_nodes
[START] [2020-11-16 09:02:14] Flattener#flatten
[START] [2020-11-16 09:02:14] Flattener#study_resource
[START] [2020-11-16 09:02:14] Flattener#build_ancestry
[STOP] [2020-11-16 09:02:14] Flattener#build_ancestry
[INFO] [2020-11-16 09:02:14] 3 ancestry keys
[START] [2020-11-16 09:02:14] build_node_ancestors
[INFO] [2020-11-16 09:02:14] old ancestors deleted.
[STOP] [2020-11-16 09:02:14] build_node_ancestors
[WARN] [2020-11-16 09:02:14] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-11-16 09:02:14] Flattener#flatten
[STOP] [2020-11-16 09:02:14] rebuild_nodes
[START] [2020-11-16 09:02:14] resolve_missing_media_owners
[STOP] [2020-11-16 09:02:14] resolve_missing_media_owners
[START] [2020-11-16 09:02:14] sanitize_media_verbatims
[STOP] [2020-11-16 09:02:14] sanitize_media_verbatims
[START] [2020-11-16 09:02:14] queue_downloads
[STOP] [2020-11-16 09:02:14] queue_downloads
[START] [2020-11-16 09:02:14] parse_names
[WARN] [2020-11-16 09:02:14] I see 3 names which still need to be parsed.
[STOP] [2020-11-16 09:02:15] parse_names
[START] [2020-11-16 09:02:15] denormalize_canonical_names_to_nodes
[STOP] [2020-11-16 09:02:15] denormalize_canonical_names_to_nodes
[START] [2020-11-16 09:02:15] match_nodes
[START] [2020-11-16 09:02:15] map_all_nodes_to_pages
[STOP] [2020-11-16 09:02:15] map_all_nodes_to_pages
[INFO] [2020-11-16 09:02:15] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2020-11-16 09:02:15] update_nodes
[STOP] [2020-11-16 09:02:15] update_nodes
[STOP] [2020-11-16 09:02:15] match_nodes
[START] [2020-11-16 09:02:15] reindex_search
[STOP] [2020-11-16 09:02:16] reindex_search
[START] [2020-11-16 09:02:16] normalize_units
[STOP] [2020-11-16 09:02:16] normalize_units
[START] [2020-11-16 09:02:16] calculate_statistics
[2020-11-16 09:02:16] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-11-16 09:02:16] calculate_statistics
[START] [2020-11-16 09:02:16] complete_harvest_instance
[START] [2020-11-16 09:02:16] overall_tsv_creation
[INFO] [2020-11-16 09:02:16] Processing group of 3 in 1 batches of 10000
[INFO] [2020-11-16 09:03:54] 3 Traits (unfiltered)...
[INFO] [2020-11-16 09:04:33] 3 Traits (filtered)...
[INFO] [2020-11-16 09:04:33] 0 Associations (filtered)...
[INFO] [2020-11-16 09:04:33] 6 metadata added.
[INFO] [2020-11-16 09:04:33] 0 metadata added.
[INFO] [2020-11-16 09:04:33] Average Time: 54.88
[INFO] [2020-11-16 09:04:33] Total Time: 2m17s
[STOP] [2020-11-16 09:04:33] overall_tsv_creation
[INFO] [2020-11-16 09:04:33] Done. Check your files:
[INFO] [2020-11-16 09:04:33] (3 lines) /app/public/data/hunt_hunt_2007/publish_nodes.tsv
[INFO] [2020-11-16 09:04:33] (3 lines) /app/public/data/hunt_hunt_2007/publish_scientific_names.tsv
[INFO] [2020-11-16 09:04:33] (4 lines) /app/public/data/hunt_hunt_2007/publish_traits.tsv
[INFO] [2020-11-16 09:04:33] (7 lines) /app/public/data/hunt_hunt_2007/publish_metadata.tsv
[STOP] [2020-11-16 09:04:33] complete_harvest_instance
[START] [2020-11-16 09:04:33] completed
[STOP] [2020-11-16 09:04:33] completed
[STOP] [2020-11-16 09:04:33] logged process, took 147.33
[INFO] [2021-04-19 14:39:33] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 14:44:33] ## remove_type: ScientificName
[INFO] [2021-04-19 14:44:33] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 14:44:33] [14:44:33.716] Removed 3 Scientificnames
[INFO] [2021-04-19 14:44:33] ## remove_type: Vernacular
[INFO] [2021-04-19 14:44:33] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:44:33] [14:44:33.718] Removed 0 Vernaculars
[INFO] [2021-04-19 14:44:33] ## remove_type: Article
[INFO] [2021-04-19 14:44:33] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:44:33] [14:44:33.720] Removed 0 Articles
[INFO] [2021-04-19 14:44:33] ## remove_type: Medium
[INFO] [2021-04-19 14:44:33] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:44:33] [14:44:33.722] Removed 0 Media
[INFO] [2021-04-19 14:44:33] ## remove_type: Trait
[INFO] [2021-04-19 14:44:33] ++ Calling delete_all on 6 instances...
[INFO] [2021-04-19 14:44:33] [14:44:33.724] Removed 6 Traits
[INFO] [2021-04-19 14:44:33] ## remove_type: MetaTrait
[INFO] [2021-04-19 14:44:33] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 14:44:33] [14:44:33.726] Removed 3 Metatraits
[INFO] [2021-04-19 14:44:33] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 14:44:33] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:44:33] [14:44:33.728] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 14:44:33] ## remove_type: Assoc
[INFO] [2021-04-19 14:44:33] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:44:33] [14:44:33.729] Removed 0 Assocs
[INFO] [2021-04-19 14:44:33] ## remove_type: MetaAssoc
[INFO] [2021-04-19 14:44:33] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:44:33] [14:44:33.731] Removed 0 Metaassocs
[INFO] [2021-04-19 14:44:33] ## remove_type: Identifier
[INFO] [2021-04-19 14:44:33] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:44:33] [14:44:33.733] Removed 0 Identifiers
[INFO] [2021-04-19 14:44:33] ## remove_type: Reference
[INFO] [2021-04-19 14:44:33] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:44:33] [14:44:33.734] Removed 0 References
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:33] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] Starting batch with ID 81660453...
[INFO] [2021-04-19 14:44:34] ## remove_type: Node
[INFO] [2021-04-19 14:44:34] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 14:44:34] [14:44:34.211] Removed 3 Nodes
[START] [2021-04-19 14:44:34] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:44:34] Creating resource from OpenData
[START] [2021-04-19 14:44:34] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:44:34] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 14:44:34] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 14:44:34] Creating resource from OpenData
[START] [2021-04-19 14:44:34] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:44:34] create_harvest_instance
[INFO] [2021-04-19 14:44:34] Created harvest instance #3749
[STOP] [2021-04-19 14:44:34] create_harvest_instance
[START] [2021-04-19 14:44:34] fetch_files
[STOP] [2021-04-19 14:44:34] fetch_files
[START] [2021-04-19 14:44:34] validate_each_file
[INFO] [2021-04-19 14:44:34] Looping over 4 formats...
[INFO] [2021-04-19 14:44:34] ...refs (/app/public/data/hunt_hunt_2007/references.tsv)
[INFO] [2021-04-19 14:44:34] Valid: /app/public/converted_csv/hunt_hunt_2007_refs_3749.csv (0 lines)
[INFO] [2021-04-19 14:44:34] ...nodes (/app/public/data/hunt_hunt_2007/taxa.txt)
[INFO] [2021-04-19 14:44:34] Valid: /app/public/converted_csv/hunt_hunt_2007_nodes_3749.csv (3 lines)
[INFO] [2021-04-19 14:44:34] ...occurrences (/app/public/data/hunt_hunt_2007/occurrences.txt)
[INFO] [2021-04-19 14:44:34] Valid: /app/public/converted_csv/hunt_hunt_2007_occurrences_3749.csv (3 lines)
[INFO] [2021-04-19 14:44:34] ...measurements (/app/public/data/hunt_hunt_2007/measurementsorfacts.txt)
[INFO] [2021-04-19 14:44:34] Valid: /app/public/converted_csv/hunt_hunt_2007_measurements_3749.csv (6 lines)
[STOP] [2021-04-19 14:44:34] validate_each_file
[START] [2021-04-19 14:44:34] convert_to_csv
[INFO] [2021-04-19 14:44:34] Looping over 4 formats...
[INFO] [2021-04-19 14:44:34] ...refs (/app/public/data/hunt_hunt_2007/references.tsv)
[CMD] [2021-04-19 14:44:34] /usr/bin/sort /app/public/converted_csv/hunt_hunt_2007_refs_3749.csv > /app/public/converted_csv/hunt_hunt_2007_refs_3749.csv_sorted
[INFO] [2021-04-19 14:44:34] Converted: /app/public/converted_csv/hunt_hunt_2007_refs_3749.csv (0 lines)
[INFO] [2021-04-19 14:44:34] ...nodes (/app/public/data/hunt_hunt_2007/taxa.txt)
[CMD] [2021-04-19 14:44:34] /usr/bin/sort /app/public/converted_csv/hunt_hunt_2007_nodes_3749.csv > /app/public/converted_csv/hunt_hunt_2007_nodes_3749.csv_sorted
[INFO] [2021-04-19 14:44:34] Converted: /app/public/converted_csv/hunt_hunt_2007_nodes_3749.csv (3 lines)
[INFO] [2021-04-19 14:44:34] ...occurrences (/app/public/data/hunt_hunt_2007/occurrences.txt)
[CMD] [2021-04-19 14:44:34] /usr/bin/sort /app/public/converted_csv/hunt_hunt_2007_occurrences_3749.csv > /app/public/converted_csv/hunt_hunt_2007_occurrences_3749.csv_sorted
[INFO] [2021-04-19 14:44:34] Converted: /app/public/converted_csv/hunt_hunt_2007_occurrences_3749.csv (3 lines)
[INFO] [2021-04-19 14:44:34] ...measurements (/app/public/data/hunt_hunt_2007/measurementsorfacts.txt)
[CMD] [2021-04-19 14:44:34] /usr/bin/sort /app/public/converted_csv/hunt_hunt_2007_measurements_3749.csv > /app/public/converted_csv/hunt_hunt_2007_measurements_3749.csv_sorted
[INFO] [2021-04-19 14:44:34] Converted: /app/public/converted_csv/hunt_hunt_2007_measurements_3749.csv (6 lines)
[STOP] [2021-04-19 14:44:34] convert_to_csv
[START] [2021-04-19 14:44:34] calculate_delta
[INFO] [2021-04-19 14:44:34] Looping over 4 formats...
[INFO] [2021-04-19 14:44:34] ...refs (/app/public/data/hunt_hunt_2007/references.tsv)
[CMD] [2021-04-19 14:44:34] echo "0a" > /app/public/diff/hunt_hunt_2007_refs_3749.diff
[CMD] [2021-04-19 14:44:34] tail -n +1 /app/public/converted_csv/hunt_hunt_2007_refs_3749.csv >> /app/public/diff/hunt_hunt_2007_refs_3749.diff
[CMD] [2021-04-19 14:44:34] echo "." >> /app/public/diff/hunt_hunt_2007_refs_3749.diff
[INFO] [2021-04-19 14:44:34] Created diff: /app/public/diff/hunt_hunt_2007_refs_3749.diff (2 lines)
[INFO] [2021-04-19 14:44:34] ...nodes (/app/public/data/hunt_hunt_2007/taxa.txt)
[CMD] [2021-04-19 14:44:34] echo "0a" > /app/public/diff/hunt_hunt_2007_nodes_3749.diff
[CMD] [2021-04-19 14:44:34] tail -n +1 /app/public/converted_csv/hunt_hunt_2007_nodes_3749.csv >> /app/public/diff/hunt_hunt_2007_nodes_3749.diff
[CMD] [2021-04-19 14:44:34] echo "." >> /app/public/diff/hunt_hunt_2007_nodes_3749.diff
[INFO] [2021-04-19 14:44:34] Created diff: /app/public/diff/hunt_hunt_2007_nodes_3749.diff (5 lines)
[INFO] [2021-04-19 14:44:34] ...occurrences (/app/public/data/hunt_hunt_2007/occurrences.txt)
[CMD] [2021-04-19 14:44:34] echo "0a" > /app/public/diff/hunt_hunt_2007_occurrences_3749.diff
[CMD] [2021-04-19 14:44:34] tail -n +1 /app/public/converted_csv/hunt_hunt_2007_occurrences_3749.csv >> /app/public/diff/hunt_hunt_2007_occurrences_3749.diff
[CMD] [2021-04-19 14:44:34] echo "." >> /app/public/diff/hunt_hunt_2007_occurrences_3749.diff
[INFO] [2021-04-19 14:44:34] Created diff: /app/public/diff/hunt_hunt_2007_occurrences_3749.diff (5 lines)
[INFO] [2021-04-19 14:44:34] ...measurements (/app/public/data/hunt_hunt_2007/measurementsorfacts.txt)
[CMD] [2021-04-19 14:44:34] echo "0a" > /app/public/diff/hunt_hunt_2007_measurements_3749.diff
[CMD] [2021-04-19 14:44:34] tail -n +1 /app/public/converted_csv/hunt_hunt_2007_measurements_3749.csv >> /app/public/diff/hunt_hunt_2007_measurements_3749.diff
[CMD] [2021-04-19 14:44:34] echo "." >> /app/public/diff/hunt_hunt_2007_measurements_3749.diff
[INFO] [2021-04-19 14:44:34] Created diff: /app/public/diff/hunt_hunt_2007_measurements_3749.diff (8 lines)
[STOP] [2021-04-19 14:44:34] calculate_delta
[START] [2021-04-19 14:44:34] parse_diff_and_store
[INFO] [2021-04-19 14:44:34] Handling diff: /app/public/diff/hunt_hunt_2007_refs_3749.diff (2 lines)
[INFO] [2021-04-19 14:44:34] Loading refs diff file into memory (2 /app/public/diff/hunt_hunt_2007_refs_3749.diff lines)...
[INFO] [2021-04-19 14:44:34] Handling diff: /app/public/diff/hunt_hunt_2007_nodes_3749.diff (5 lines)
[INFO] [2021-04-19 14:44:34] Loading nodes diff file into memory (5 /app/public/diff/hunt_hunt_2007_nodes_3749.diff lines)...
[INFO] [2021-04-19 14:44:34] Handling diff: /app/public/diff/hunt_hunt_2007_occurrences_3749.diff (5 lines)
[INFO] [2021-04-19 14:44:34] Loading occurrences diff file into memory (5 /app/public/diff/hunt_hunt_2007_occurrences_3749.diff lines)...
[INFO] [2021-04-19 14:44:34] Handling diff: /app/public/diff/hunt_hunt_2007_measurements_3749.diff (8 lines)
[INFO] [2021-04-19 14:44:34] Loading measurements diff file into memory (8 /app/public/diff/hunt_hunt_2007_measurements_3749.diff lines)...
[INFO] [2021-04-19 14:44:34] Storing 3 ScientificNames
[INFO] [2021-04-19 14:44:34] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 14:44:34] Average Time: 0.01
[INFO] [2021-04-19 14:44:34] Total Time: 1s
[INFO] [2021-04-19 14:44:34] Storing 3 Nodes
[INFO] [2021-04-19 14:44:34] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 14:44:34] Average Time: 0.0
[INFO] [2021-04-19 14:44:34] Total Time: 1s
[INFO] [2021-04-19 14:44:34] Storing 3 Occurrences
[INFO] [2021-04-19 14:44:34] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 14:44:35] Average Time: 0.0
[INFO] [2021-04-19 14:44:35] Total Time: 1s
[INFO] [2021-04-19 14:44:35] Storing 6 Traits
[INFO] [2021-04-19 14:44:35] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 14:44:35] Average Time: 0.0
[INFO] [2021-04-19 14:44:35] Total Time: 1s
[INFO] [2021-04-19 14:44:35] Storing 3 MetaTraits
[INFO] [2021-04-19 14:44:35] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 14:44:35] Average Time: 0.0
[INFO] [2021-04-19 14:44:35] Total Time: 1s
[STOP] [2021-04-19 14:44:35] parse_diff_and_store
[START] [2021-04-19 14:44:35] resolve_keys
[INFO] [2021-04-19 14:44:40] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 14:44:40] traits to occurrences...
[INFO] [2021-04-19 14:44:40] traits to nodes (through occurrences)...
[INFO] [2021-04-19 14:44:40] Traits to sex term...
[INFO] [2021-04-19 14:44:40] Traits to lifestage term...
[INFO] [2021-04-19 14:44:40] MetaTraits to traits...
[INFO] [2021-04-19 14:44:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 14:44:40] Assocs to occurrences...
[INFO] [2021-04-19 14:44:40] Assocs to nodes...
[INFO] [2021-04-19 14:44:40] Assoc to sex term...
[INFO] [2021-04-19 14:44:40] Assoc to lifestage term...
[INFO] [2021-04-19 14:44:40] MetaAssoc to assocs...
[STOP] [2021-04-19 14:44:40] resolve_keys
[START] [2021-04-19 14:44:40] hold_for_later_1
[STOP] [2021-04-19 14:44:40] hold_for_later_1
[START] [2021-04-19 14:44:40] hold_for_later_2
[STOP] [2021-04-19 14:44:40] hold_for_later_2
[START] [2021-04-19 14:44:40] resolve_missing_parents
[STOP] [2021-04-19 14:44:40] resolve_missing_parents
[START] [2021-04-19 14:44:40] rebuild_nodes
[START] [2021-04-19 14:44:40] Flattener#flatten
[START] [2021-04-19 14:44:40] Flattener#study_resource
[START] [2021-04-19 14:44:40] Flattener#build_ancestry
[STOP] [2021-04-19 14:44:40] Flattener#build_ancestry
[INFO] [2021-04-19 14:44:40] 3 ancestry keys
[START] [2021-04-19 14:44:40] build_node_ancestors
[INFO] [2021-04-19 14:44:40] old ancestors deleted.
[STOP] [2021-04-19 14:44:40] build_node_ancestors
[WARN] [2021-04-19 14:44:40] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 14:44:40] Flattener#flatten
[STOP] [2021-04-19 14:44:40] rebuild_nodes
[START] [2021-04-19 14:44:41] resolve_missing_media_owners
[STOP] [2021-04-19 14:44:41] resolve_missing_media_owners
[START] [2021-04-19 14:44:41] sanitize_media_verbatims
[STOP] [2021-04-19 14:44:41] sanitize_media_verbatims
[START] [2021-04-19 14:44:41] queue_downloads
[STOP] [2021-04-19 14:44:41] queue_downloads
[START] [2021-04-19 14:44:41] parse_names
[WARN] [2021-04-19 14:44:41] I see 3 names which still need to be parsed.
[STOP] [2021-04-19 14:44:42] parse_names
[START] [2021-04-19 14:44:42] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 14:44:42] denormalize_canonical_names_to_nodes
[START] [2021-04-19 14:44:42] match_nodes
[START] [2021-04-19 14:44:42] map_all_nodes_to_pages
[STOP] [2021-04-19 14:44:42] map_all_nodes_to_pages
[INFO] [2021-04-19 14:44:42] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2021-04-19 14:44:42] update_nodes
[STOP] [2021-04-19 14:44:42] update_nodes
[STOP] [2021-04-19 14:44:42] match_nodes
[START] [2021-04-19 14:44:42] reindex_search
[STOP] [2021-04-19 14:44:42] reindex_search
[START] [2021-04-19 14:44:42] normalize_units
[STOP] [2021-04-19 14:44:42] normalize_units
[START] [2021-04-19 14:44:42] calculate_statistics
[2021-04-19 14:44:42] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 14:44:42] calculate_statistics
[START] [2021-04-19 14:44:42] complete_harvest_instance
[START] [2021-04-19 14:44:42] overall_tsv_creation
[INFO] [2021-04-19 14:44:42] Processing group of 3 in 1 batches of 10000
[INFO] [2021-04-19 14:45:18] 3 Traits (unfiltered)...
[INFO] [2021-04-19 14:45:51] 3 Traits (filtered)...
[INFO] [2021-04-19 14:45:51] 0 Associations (filtered)...
[INFO] [2021-04-19 14:45:51] 3 metadata added.
[INFO] [2021-04-19 14:45:51] 0 metadata added.
[INFO] [2021-04-19 14:46:18] Average Time: 71.69
[INFO] [2021-04-19 14:46:18] Total Time: 1m36s
[STOP] [2021-04-19 14:46:18] overall_tsv_creation
[INFO] [2021-04-19 14:46:18] Done. Check your files:
[INFO] [2021-04-19 14:46:18] (3 lines) /app/public/data/hunt_hunt_2007/publish_nodes.tsv
[INFO] [2021-04-19 14:46:18] (3 lines) /app/public/data/hunt_hunt_2007/publish_scientific_names.tsv
[INFO] [2021-04-19 14:46:18] (4 lines) /app/public/data/hunt_hunt_2007/publish_traits.tsv
[INFO] [2021-04-19 14:46:18] (4 lines) /app/public/data/hunt_hunt_2007/publish_metadata.tsv
[STOP] [2021-04-19 14:46:18] complete_harvest_instance
[START] [2021-04-19 14:46:18] completed
[STOP] [2021-04-19 14:46:18] completed
[STOP] [2021-04-19 14:46:18] logged process, took 103.62

Latest Process

19 Apr 14:44 EXITED currently processing 0