Harvest for Vater et al 2004 Created 19 Apr 16:35

Harvesting Log

# Logfile created on 2020-09-25 16:37:19 -0400 by logger.rb/v1.4.2
[START] [2020-09-25 16:37:19] logged process
[START] [2020-09-25 16:37:19] Creating resource from OpenData
[START] [2020-09-25 16:37:20] logged process
[START] [2020-09-25 16:37:20] Parse meta.xml file and create formats with fields
[STOP] [2020-09-25 16:37:20] Parse meta.xml file and create formats with fields
[STOP] [2020-09-25 16:37:20] Creating resource from OpenData
[INFO] [2020-12-03 16:16:28] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-12-03 16:16:32] ## remove_type: ScientificName
[INFO] [2020-12-03 16:16:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 16:16:32] [16:16:32.109] Removed 0 Scientificnames
[INFO] [2020-12-03 16:16:32] ## remove_type: Vernacular
[INFO] [2020-12-03 16:16:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 16:16:32] [16:16:32.112] Removed 0 Vernaculars
[INFO] [2020-12-03 16:16:32] ## remove_type: Article
[INFO] [2020-12-03 16:16:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 16:16:32] [16:16:32.114] Removed 0 Articles
[INFO] [2020-12-03 16:16:32] ## remove_type: Medium
[INFO] [2020-12-03 16:16:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 16:16:32] [16:16:32.118] Removed 0 Media
[INFO] [2020-12-03 16:16:32] ## remove_type: Trait
[INFO] [2020-12-03 16:16:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 16:16:32] [16:16:32.120] Removed 0 Traits
[INFO] [2020-12-03 16:16:32] ## remove_type: MetaTrait
[INFO] [2020-12-03 16:16:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 16:16:32] [16:16:32.123] Removed 0 Metatraits
[INFO] [2020-12-03 16:16:32] ## remove_type: OccurrenceMetadatum
[INFO] [2020-12-03 16:16:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 16:16:32] [16:16:32.125] Removed 0 Occurrencemetadata
[INFO] [2020-12-03 16:16:32] ## remove_type: Assoc
[INFO] [2020-12-03 16:16:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 16:16:32] [16:16:32.128] Removed 0 Assocs
[INFO] [2020-12-03 16:16:32] ## remove_type: MetaAssoc
[INFO] [2020-12-03 16:16:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 16:16:32] [16:16:32.130] Removed 0 Metaassocs
[INFO] [2020-12-03 16:16:32] ## remove_type: Identifier
[INFO] [2020-12-03 16:16:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 16:16:32] [16:16:32.132] Removed 0 Identifiers
[INFO] [2020-12-03 16:16:32] ## remove_type: Reference
[INFO] [2020-12-03 16:16:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 16:16:32] [16:16:32.135] Removed 0 References
[INFO] [2020-12-03 16:16:32] ## remove_type: Node
[INFO] [2020-12-03 16:16:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-12-03 16:16:32] [16:16:32.155] Removed 0 Nodes
[START] [2020-12-03 16:16:32] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-03 16:16:32] Creating resource from OpenData
[START] [2020-12-03 16:16:32] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-03 16:16:32] Parse meta.xml file and create formats with fields
[STOP] [2020-12-03 16:16:32] Parse meta.xml file and create formats with fields
[STOP] [2020-12-03 16:16:32] Creating resource from OpenData
[START] [2020-12-03 16:16:32] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-03 16:16:32] create_harvest_instance
[STOP] [2020-12-03 16:16:34] create_harvest_instance
[START] [2020-12-03 16:16:34] fetch_files
[STOP] [2020-12-03 16:16:34] fetch_files
[START] [2020-12-03 16:16:34] validate_each_file
[STOP] [2020-12-03 16:16:34] validate_each_file
[START] [2020-12-03 16:16:34] convert_to_csv
[CMD] [2020-12-03 16:16:34] /usr/bin/sort /app/public/converted_csv/vater_et_al_vate_refs_25057.csv > /app/public/converted_csv/vater_et_al_vate_refs_25057.csv_sorted
[CMD] [2020-12-03 16:16:34] /usr/bin/sort /app/public/converted_csv/vater_et_al_vate_nodes_25058.csv > /app/public/converted_csv/vater_et_al_vate_nodes_25058.csv_sorted
[CMD] [2020-12-03 16:16:34] /usr/bin/sort /app/public/converted_csv/vater_et_al_vate_occurrences_25059.csv > /app/public/converted_csv/vater_et_al_vate_occurrences_25059.csv_sorted
[CMD] [2020-12-03 16:16:34] /usr/bin/sort /app/public/converted_csv/vater_et_al_vate_measurements_25060.csv > /app/public/converted_csv/vater_et_al_vate_measurements_25060.csv_sorted
[STOP] [2020-12-03 16:16:34] convert_to_csv
[START] [2020-12-03 16:16:34] calculate_delta
[CMD] [2020-12-03 16:16:34] echo "0a" > /app/public/diff/vater_et_al_vate_refs_25057.diff
[CMD] [2020-12-03 16:16:34] tail -n +1 /app/public/converted_csv/vater_et_al_vate_refs_25057.csv >> /app/public/diff/vater_et_al_vate_refs_25057.diff
[CMD] [2020-12-03 16:16:34] echo "." >> /app/public/diff/vater_et_al_vate_refs_25057.diff
[CMD] [2020-12-03 16:16:34] echo "0a" > /app/public/diff/vater_et_al_vate_nodes_25058.diff
[CMD] [2020-12-03 16:16:34] tail -n +1 /app/public/converted_csv/vater_et_al_vate_nodes_25058.csv >> /app/public/diff/vater_et_al_vate_nodes_25058.diff
[CMD] [2020-12-03 16:16:34] echo "." >> /app/public/diff/vater_et_al_vate_nodes_25058.diff
[CMD] [2020-12-03 16:16:34] echo "0a" > /app/public/diff/vater_et_al_vate_occurrences_25059.diff
[CMD] [2020-12-03 16:16:34] tail -n +1 /app/public/converted_csv/vater_et_al_vate_occurrences_25059.csv >> /app/public/diff/vater_et_al_vate_occurrences_25059.diff
[CMD] [2020-12-03 16:16:34] echo "." >> /app/public/diff/vater_et_al_vate_occurrences_25059.diff
[CMD] [2020-12-03 16:16:34] echo "0a" > /app/public/diff/vater_et_al_vate_measurements_25060.diff
[CMD] [2020-12-03 16:16:34] tail -n +1 /app/public/converted_csv/vater_et_al_vate_measurements_25060.csv >> /app/public/diff/vater_et_al_vate_measurements_25060.diff
[CMD] [2020-12-03 16:16:34] echo "." >> /app/public/diff/vater_et_al_vate_measurements_25060.diff
[STOP] [2020-12-03 16:16:34] calculate_delta
[START] [2020-12-03 16:16:34] parse_diff_and_store
[INFO] [2020-12-03 16:16:34] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 16:16:34] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 16:16:34] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 16:16:34] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 16:16:35] Storing 3 ScientificNames
[INFO] [2020-12-03 16:16:35] Processing group of 3 in 1 groups of 1000
[INFO] [2020-12-03 16:16:35] Average Time: 0.0
[INFO] [2020-12-03 16:16:35] Total Time: 1s
[INFO] [2020-12-03 16:16:35] Storing 3 Nodes
[INFO] [2020-12-03 16:16:35] Processing group of 3 in 1 groups of 1000
[INFO] [2020-12-03 16:16:35] Average Time: 0.0
[INFO] [2020-12-03 16:16:35] Total Time: 1s
[INFO] [2020-12-03 16:16:35] Storing 3 Occurrences
[INFO] [2020-12-03 16:16:35] Processing group of 3 in 1 groups of 1000
[INFO] [2020-12-03 16:16:35] Average Time: 0.0
[INFO] [2020-12-03 16:16:35] Total Time: 1s
[INFO] [2020-12-03 16:16:35] Storing 6 Traits
[INFO] [2020-12-03 16:16:35] Processing group of 6 in 1 groups of 1000
[INFO] [2020-12-03 16:16:35] Average Time: 0.0
[INFO] [2020-12-03 16:16:35] Total Time: 1s
[INFO] [2020-12-03 16:16:35] Storing 9 MetaTraits
[INFO] [2020-12-03 16:16:35] Processing group of 9 in 1 groups of 1000
[INFO] [2020-12-03 16:16:35] Average Time: 0.0
[INFO] [2020-12-03 16:16:35] Total Time: 1s
[STOP] [2020-12-03 16:16:35] parse_diff_and_store
[START] [2020-12-03 16:16:35] resolve_keys
[INFO] [2020-12-03 16:16:40] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 16:16:40] traits to occurrences...
[INFO] [2020-12-03 16:16:40] traits to nodes (through occurrences)...
[INFO] [2020-12-03 16:16:40] Traits to sex term...
[INFO] [2020-12-03 16:16:40] Traits to lifestage term...
[INFO] [2020-12-03 16:16:40] MetaTraits to traits...
[INFO] [2020-12-03 16:16:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 16:16:40] Assocs to occurrences...
[INFO] [2020-12-03 16:16:40] Assocs to nodes...
[INFO] [2020-12-03 16:16:40] Assoc to sex term...
[INFO] [2020-12-03 16:16:40] Assoc to lifestage term...
[INFO] [2020-12-03 16:16:40] MetaAssoc to assocs...
[STOP] [2020-12-03 16:16:40] resolve_keys
[START] [2020-12-03 16:16:40] hold_for_later_1
[STOP] [2020-12-03 16:16:41] hold_for_later_1
[START] [2020-12-03 16:16:41] hold_for_later_2
[STOP] [2020-12-03 16:16:41] hold_for_later_2
[START] [2020-12-03 16:16:41] resolve_missing_parents
[STOP] [2020-12-03 16:16:41] resolve_missing_parents
[START] [2020-12-03 16:16:41] rebuild_nodes
[START] [2020-12-03 16:16:41] Flattener#flatten
[START] [2020-12-03 16:16:41] Flattener#study_resource
[START] [2020-12-03 16:16:41] Flattener#build_ancestry
[STOP] [2020-12-03 16:16:41] Flattener#build_ancestry
[INFO] [2020-12-03 16:16:41] 3 ancestry keys
[START] [2020-12-03 16:16:41] build_node_ancestors
[INFO] [2020-12-03 16:16:41] old ancestors deleted.
[STOP] [2020-12-03 16:16:41] build_node_ancestors
[WARN] [2020-12-03 16:16:41] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 16:16:41] Flattener#flatten
[STOP] [2020-12-03 16:16:41] rebuild_nodes
[START] [2020-12-03 16:16:41] resolve_missing_media_owners
[STOP] [2020-12-03 16:16:41] resolve_missing_media_owners
[START] [2020-12-03 16:16:41] sanitize_media_verbatims
[STOP] [2020-12-03 16:16:41] sanitize_media_verbatims
[START] [2020-12-03 16:16:41] queue_downloads
[STOP] [2020-12-03 16:16:41] queue_downloads
[START] [2020-12-03 16:16:41] parse_names
[WARN] [2020-12-03 16:16:41] I see 3 names which still need to be parsed.
[STOP] [2020-12-03 16:16:42] parse_names
[START] [2020-12-03 16:16:42] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 16:16:42] denormalize_canonical_names_to_nodes
[START] [2020-12-03 16:16:42] match_nodes
[START] [2020-12-03 16:16:42] map_all_nodes_to_pages
[STOP] [2020-12-03 16:16:42] map_all_nodes_to_pages
[INFO] [2020-12-03 16:16:42] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2020-12-03 16:16:42] update_nodes
[STOP] [2020-12-03 16:16:42] update_nodes
[STOP] [2020-12-03 16:16:42] match_nodes
[START] [2020-12-03 16:16:42] reindex_search
[STOP] [2020-12-03 16:16:42] reindex_search
[START] [2020-12-03 16:16:42] normalize_units
[STOP] [2020-12-03 16:16:42] normalize_units
[START] [2020-12-03 16:16:42] calculate_statistics
[2020-12-03 16:16:42] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 16:16:42] calculate_statistics
[START] [2020-12-03 16:16:42] complete_harvest_instance
[START] [2020-12-03 16:16:42] overall_tsv_creation
[INFO] [2020-12-03 16:16:42] Processing group of 3 in 1 batches of 10000
[INFO] [2020-12-03 16:17:21] 3 Traits (unfiltered)...
[INFO] [2020-12-03 16:17:58] 3 Traits (filtered)...
[INFO] [2020-12-03 16:17:58] 0 Associations (filtered)...
[INFO] [2020-12-03 16:17:58] 12 metadata added.
[INFO] [2020-12-03 16:17:58] 0 metadata added.
[INFO] [2020-12-03 16:17:58] Average Time: 53.77
[INFO] [2020-12-03 16:17:58] Total Time: 1m17s
[STOP] [2020-12-03 16:17:58] overall_tsv_creation
[INFO] [2020-12-03 16:17:58] Done. Check your files:
[INFO] [2020-12-03 16:17:58] (3 lines) /app/public/data/vater_et_al_vate/publish_nodes.tsv
[INFO] [2020-12-03 16:17:58] (3 lines) /app/public/data/vater_et_al_vate/publish_scientific_names.tsv
[INFO] [2020-12-03 16:17:58] (4 lines) /app/public/data/vater_et_al_vate/publish_traits.tsv
[INFO] [2020-12-03 16:17:58] (13 lines) /app/public/data/vater_et_al_vate/publish_metadata.tsv
[STOP] [2020-12-03 16:17:58] complete_harvest_instance
[START] [2020-12-03 16:17:58] completed
[STOP] [2020-12-03 16:17:58] completed
[STOP] [2020-12-03 16:17:58] logged process, took 86.44
[INFO] [2021-04-19 16:21:03] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 16:35:53] ## remove_type: ScientificName
[INFO] [2021-04-19 16:35:53] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 16:35:53] [16:35:53.748] Removed 3 Scientificnames
[INFO] [2021-04-19 16:35:53] ## remove_type: Vernacular
[INFO] [2021-04-19 16:35:53] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:35:53] [16:35:53.749] Removed 0 Vernaculars
[INFO] [2021-04-19 16:35:53] ## remove_type: Article
[INFO] [2021-04-19 16:35:53] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:35:53] [16:35:53.751] Removed 0 Articles
[INFO] [2021-04-19 16:35:53] ## remove_type: Medium
[INFO] [2021-04-19 16:35:53] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:35:53] [16:35:53.752] Removed 0 Media
[INFO] [2021-04-19 16:35:53] ## remove_type: Trait
[INFO] [2021-04-19 16:35:53] ++ Calling delete_all on 6 instances...
[INFO] [2021-04-19 16:35:53] [16:35:53.754] Removed 6 Traits
[INFO] [2021-04-19 16:35:53] ## remove_type: MetaTrait
[INFO] [2021-04-19 16:35:53] ++ Calling delete_all on 9 instances...
[INFO] [2021-04-19 16:35:53] [16:35:53.756] Removed 9 Metatraits
[INFO] [2021-04-19 16:35:53] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 16:35:53] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:35:53] [16:35:53.758] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 16:35:53] ## remove_type: Assoc
[INFO] [2021-04-19 16:35:53] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:35:53] [16:35:53.759] Removed 0 Assocs
[INFO] [2021-04-19 16:35:53] ## remove_type: MetaAssoc
[INFO] [2021-04-19 16:35:53] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:35:53] [16:35:53.761] Removed 0 Metaassocs
[INFO] [2021-04-19 16:35:53] ## remove_type: Identifier
[INFO] [2021-04-19 16:35:53] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:35:53] [16:35:53.762] Removed 0 Identifiers
[INFO] [2021-04-19 16:35:53] ## remove_type: Reference
[INFO] [2021-04-19 16:35:53] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:35:53] [16:35:53.764] Removed 0 References
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:53] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116320...
[INFO] [2021-04-19 16:35:54] Starting batch with ID 86116321...
[INFO] [2021-04-19 16:35:54] ## remove_type: Node
[INFO] [2021-04-19 16:35:54] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 16:35:54] [16:35:54.568] Removed 3 Nodes
[START] [2021-04-19 16:35:54] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:35:54] Creating resource from OpenData
[START] [2021-04-19 16:35:54] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:35:54] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:35:54] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:35:54] Creating resource from OpenData
[START] [2021-04-19 16:35:54] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:35:54] create_harvest_instance
[INFO] [2021-04-19 16:35:54] Created harvest instance #3799
[STOP] [2021-04-19 16:35:54] create_harvest_instance
[START] [2021-04-19 16:35:55] fetch_files
[STOP] [2021-04-19 16:35:55] fetch_files
[START] [2021-04-19 16:35:55] validate_each_file
[INFO] [2021-04-19 16:35:55] Looping over 4 formats...
[INFO] [2021-04-19 16:35:55] ...refs (/app/public/data/vater_et_al_vate/references.txt)
[INFO] [2021-04-19 16:35:55] Valid: /app/public/converted_csv/vater_et_al_vate_refs_3799.csv (0 lines)
[INFO] [2021-04-19 16:35:55] ...nodes (/app/public/data/vater_et_al_vate/taxa.txt)
[INFO] [2021-04-19 16:35:55] Valid: /app/public/converted_csv/vater_et_al_vate_nodes_3799.csv (3 lines)
[INFO] [2021-04-19 16:35:55] ...occurrences (/app/public/data/vater_et_al_vate/occurrences.txt)
[INFO] [2021-04-19 16:35:55] Valid: /app/public/converted_csv/vater_et_al_vate_occurrences_3799.csv (3 lines)
[INFO] [2021-04-19 16:35:55] ...measurements (/app/public/data/vater_et_al_vate/measurementsorfacts.txt)
[INFO] [2021-04-19 16:35:55] Valid: /app/public/converted_csv/vater_et_al_vate_measurements_3799.csv (6 lines)
[STOP] [2021-04-19 16:35:55] validate_each_file
[START] [2021-04-19 16:35:55] convert_to_csv
[INFO] [2021-04-19 16:35:55] Looping over 4 formats...
[INFO] [2021-04-19 16:35:55] ...refs (/app/public/data/vater_et_al_vate/references.txt)
[CMD] [2021-04-19 16:35:55] /usr/bin/sort /app/public/converted_csv/vater_et_al_vate_refs_3799.csv > /app/public/converted_csv/vater_et_al_vate_refs_3799.csv_sorted
[INFO] [2021-04-19 16:35:55] Converted: /app/public/converted_csv/vater_et_al_vate_refs_3799.csv (0 lines)
[INFO] [2021-04-19 16:35:55] ...nodes (/app/public/data/vater_et_al_vate/taxa.txt)
[CMD] [2021-04-19 16:35:55] /usr/bin/sort /app/public/converted_csv/vater_et_al_vate_nodes_3799.csv > /app/public/converted_csv/vater_et_al_vate_nodes_3799.csv_sorted
[INFO] [2021-04-19 16:35:55] Converted: /app/public/converted_csv/vater_et_al_vate_nodes_3799.csv (3 lines)
[INFO] [2021-04-19 16:35:55] ...occurrences (/app/public/data/vater_et_al_vate/occurrences.txt)
[CMD] [2021-04-19 16:35:55] /usr/bin/sort /app/public/converted_csv/vater_et_al_vate_occurrences_3799.csv > /app/public/converted_csv/vater_et_al_vate_occurrences_3799.csv_sorted
[INFO] [2021-04-19 16:35:55] Converted: /app/public/converted_csv/vater_et_al_vate_occurrences_3799.csv (3 lines)
[INFO] [2021-04-19 16:35:55] ...measurements (/app/public/data/vater_et_al_vate/measurementsorfacts.txt)
[CMD] [2021-04-19 16:35:55] /usr/bin/sort /app/public/converted_csv/vater_et_al_vate_measurements_3799.csv > /app/public/converted_csv/vater_et_al_vate_measurements_3799.csv_sorted
[INFO] [2021-04-19 16:35:55] Converted: /app/public/converted_csv/vater_et_al_vate_measurements_3799.csv (6 lines)
[STOP] [2021-04-19 16:35:55] convert_to_csv
[START] [2021-04-19 16:35:55] calculate_delta
[INFO] [2021-04-19 16:35:55] Looping over 4 formats...
[INFO] [2021-04-19 16:35:55] ...refs (/app/public/data/vater_et_al_vate/references.txt)
[CMD] [2021-04-19 16:35:55] echo "0a" > /app/public/diff/vater_et_al_vate_refs_3799.diff
[CMD] [2021-04-19 16:35:55] tail -n +1 /app/public/converted_csv/vater_et_al_vate_refs_3799.csv >> /app/public/diff/vater_et_al_vate_refs_3799.diff
[CMD] [2021-04-19 16:35:55] echo "." >> /app/public/diff/vater_et_al_vate_refs_3799.diff
[INFO] [2021-04-19 16:35:55] Created diff: /app/public/diff/vater_et_al_vate_refs_3799.diff (2 lines)
[INFO] [2021-04-19 16:35:55] ...nodes (/app/public/data/vater_et_al_vate/taxa.txt)
[CMD] [2021-04-19 16:35:55] echo "0a" > /app/public/diff/vater_et_al_vate_nodes_3799.diff
[CMD] [2021-04-19 16:35:55] tail -n +1 /app/public/converted_csv/vater_et_al_vate_nodes_3799.csv >> /app/public/diff/vater_et_al_vate_nodes_3799.diff
[CMD] [2021-04-19 16:35:55] echo "." >> /app/public/diff/vater_et_al_vate_nodes_3799.diff
[INFO] [2021-04-19 16:35:55] Created diff: /app/public/diff/vater_et_al_vate_nodes_3799.diff (5 lines)
[INFO] [2021-04-19 16:35:55] ...occurrences (/app/public/data/vater_et_al_vate/occurrences.txt)
[CMD] [2021-04-19 16:35:55] echo "0a" > /app/public/diff/vater_et_al_vate_occurrences_3799.diff
[CMD] [2021-04-19 16:35:55] tail -n +1 /app/public/converted_csv/vater_et_al_vate_occurrences_3799.csv >> /app/public/diff/vater_et_al_vate_occurrences_3799.diff
[CMD] [2021-04-19 16:35:55] echo "." >> /app/public/diff/vater_et_al_vate_occurrences_3799.diff
[INFO] [2021-04-19 16:35:55] Created diff: /app/public/diff/vater_et_al_vate_occurrences_3799.diff (5 lines)
[INFO] [2021-04-19 16:35:55] ...measurements (/app/public/data/vater_et_al_vate/measurementsorfacts.txt)
[CMD] [2021-04-19 16:35:55] echo "0a" > /app/public/diff/vater_et_al_vate_measurements_3799.diff
[CMD] [2021-04-19 16:35:55] tail -n +1 /app/public/converted_csv/vater_et_al_vate_measurements_3799.csv >> /app/public/diff/vater_et_al_vate_measurements_3799.diff
[CMD] [2021-04-19 16:35:55] echo "." >> /app/public/diff/vater_et_al_vate_measurements_3799.diff
[INFO] [2021-04-19 16:35:55] Created diff: /app/public/diff/vater_et_al_vate_measurements_3799.diff (8 lines)
[STOP] [2021-04-19 16:35:55] calculate_delta
[START] [2021-04-19 16:35:55] parse_diff_and_store
[INFO] [2021-04-19 16:35:55] Handling diff: /app/public/diff/vater_et_al_vate_refs_3799.diff (2 lines)
[INFO] [2021-04-19 16:35:55] Loading refs diff file into memory (2 /app/public/diff/vater_et_al_vate_refs_3799.diff lines)...
[INFO] [2021-04-19 16:35:55] Handling diff: /app/public/diff/vater_et_al_vate_nodes_3799.diff (5 lines)
[INFO] [2021-04-19 16:35:55] Loading nodes diff file into memory (5 /app/public/diff/vater_et_al_vate_nodes_3799.diff lines)...
[INFO] [2021-04-19 16:35:55] Handling diff: /app/public/diff/vater_et_al_vate_occurrences_3799.diff (5 lines)
[INFO] [2021-04-19 16:35:55] Loading occurrences diff file into memory (5 /app/public/diff/vater_et_al_vate_occurrences_3799.diff lines)...
[INFO] [2021-04-19 16:35:55] Handling diff: /app/public/diff/vater_et_al_vate_measurements_3799.diff (8 lines)
[INFO] [2021-04-19 16:35:55] Loading measurements diff file into memory (8 /app/public/diff/vater_et_al_vate_measurements_3799.diff lines)...
[INFO] [2021-04-19 16:35:55] Storing 3 ScientificNames
[INFO] [2021-04-19 16:35:55] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 16:35:55] Average Time: 0.0
[INFO] [2021-04-19 16:35:55] Total Time: 1s
[INFO] [2021-04-19 16:35:55] Storing 3 Nodes
[INFO] [2021-04-19 16:35:55] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 16:35:55] Average Time: 0.0
[INFO] [2021-04-19 16:35:55] Total Time: 1s
[INFO] [2021-04-19 16:35:55] Storing 3 Occurrences
[INFO] [2021-04-19 16:35:55] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 16:35:55] Average Time: 0.0
[INFO] [2021-04-19 16:35:55] Total Time: 1s
[INFO] [2021-04-19 16:35:55] Storing 6 Traits
[INFO] [2021-04-19 16:35:55] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 16:35:55] Average Time: 0.0
[INFO] [2021-04-19 16:35:55] Total Time: 1s
[INFO] [2021-04-19 16:35:55] Storing 9 MetaTraits
[INFO] [2021-04-19 16:35:55] Processing group of 9 in 1 groups of 1000
[INFO] [2021-04-19 16:35:55] Average Time: 0.0
[INFO] [2021-04-19 16:35:55] Total Time: 1s
[STOP] [2021-04-19 16:35:55] parse_diff_and_store
[START] [2021-04-19 16:35:55] resolve_keys
[INFO] [2021-04-19 16:36:01] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 16:36:01] traits to occurrences...
[INFO] [2021-04-19 16:36:01] traits to nodes (through occurrences)...
[INFO] [2021-04-19 16:36:01] Traits to sex term...
[INFO] [2021-04-19 16:36:01] Traits to lifestage term...
[INFO] [2021-04-19 16:36:01] MetaTraits to traits...
[INFO] [2021-04-19 16:36:01] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 16:36:01] Assocs to occurrences...
[INFO] [2021-04-19 16:36:01] Assocs to nodes...
[INFO] [2021-04-19 16:36:01] Assoc to sex term...
[INFO] [2021-04-19 16:36:01] Assoc to lifestage term...
[INFO] [2021-04-19 16:36:01] MetaAssoc to assocs...
[STOP] [2021-04-19 16:36:01] resolve_keys
[START] [2021-04-19 16:36:01] hold_for_later_1
[STOP] [2021-04-19 16:36:01] hold_for_later_1
[START] [2021-04-19 16:36:01] hold_for_later_2
[STOP] [2021-04-19 16:36:01] hold_for_later_2
[START] [2021-04-19 16:36:01] resolve_missing_parents
[STOP] [2021-04-19 16:36:01] resolve_missing_parents
[START] [2021-04-19 16:36:01] rebuild_nodes
[START] [2021-04-19 16:36:01] Flattener#flatten
[START] [2021-04-19 16:36:01] Flattener#study_resource
[START] [2021-04-19 16:36:01] Flattener#build_ancestry
[STOP] [2021-04-19 16:36:01] Flattener#build_ancestry
[INFO] [2021-04-19 16:36:01] 3 ancestry keys
[START] [2021-04-19 16:36:01] build_node_ancestors
[INFO] [2021-04-19 16:36:01] old ancestors deleted.
[STOP] [2021-04-19 16:36:01] build_node_ancestors
[WARN] [2021-04-19 16:36:01] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 16:36:01] Flattener#flatten
[STOP] [2021-04-19 16:36:01] rebuild_nodes
[START] [2021-04-19 16:36:01] resolve_missing_media_owners
[STOP] [2021-04-19 16:36:01] resolve_missing_media_owners
[START] [2021-04-19 16:36:01] sanitize_media_verbatims
[STOP] [2021-04-19 16:36:01] sanitize_media_verbatims
[START] [2021-04-19 16:36:01] queue_downloads
[STOP] [2021-04-19 16:36:01] queue_downloads
[START] [2021-04-19 16:36:01] parse_names
[WARN] [2021-04-19 16:36:01] I see 3 names which still need to be parsed.
[STOP] [2021-04-19 16:36:02] parse_names
[START] [2021-04-19 16:36:02] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 16:36:02] denormalize_canonical_names_to_nodes
[START] [2021-04-19 16:36:02] match_nodes
[START] [2021-04-19 16:36:02] map_all_nodes_to_pages
[STOP] [2021-04-19 16:36:02] map_all_nodes_to_pages
[INFO] [2021-04-19 16:36:02] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2021-04-19 16:36:02] update_nodes
[STOP] [2021-04-19 16:36:02] update_nodes
[STOP] [2021-04-19 16:36:02] match_nodes
[START] [2021-04-19 16:36:02] reindex_search
[STOP] [2021-04-19 16:36:02] reindex_search
[START] [2021-04-19 16:36:02] normalize_units
[STOP] [2021-04-19 16:36:02] normalize_units
[START] [2021-04-19 16:36:02] calculate_statistics
[2021-04-19 16:36:02] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 16:36:02] calculate_statistics
[START] [2021-04-19 16:36:02] complete_harvest_instance
[START] [2021-04-19 16:36:02] overall_tsv_creation
[INFO] [2021-04-19 16:36:02] Processing group of 3 in 1 batches of 10000
[INFO] [2021-04-19 16:36:38] 3 Traits (unfiltered)...
[INFO] [2021-04-19 16:37:10] 3 Traits (filtered)...
[INFO] [2021-04-19 16:37:10] 0 Associations (filtered)...
[INFO] [2021-04-19 16:37:11] 3 metadata added.
[INFO] [2021-04-19 16:37:11] 0 metadata added.
[INFO] [2021-04-19 16:37:36] Average Time: 70.64
[INFO] [2021-04-19 16:37:36] Total Time: 1m35s
[STOP] [2021-04-19 16:37:36] overall_tsv_creation
[INFO] [2021-04-19 16:37:36] Done. Check your files:
[INFO] [2021-04-19 16:37:36] (3 lines) /app/public/data/vater_et_al_vate/publish_nodes.tsv
[INFO] [2021-04-19 16:37:36] (3 lines) /app/public/data/vater_et_al_vate/publish_scientific_names.tsv
[INFO] [2021-04-19 16:37:36] (4 lines) /app/public/data/vater_et_al_vate/publish_traits.tsv
[INFO] [2021-04-19 16:37:36] (4 lines) /app/public/data/vater_et_al_vate/publish_metadata.tsv
[STOP] [2021-04-19 16:37:37] complete_harvest_instance
[START] [2021-04-19 16:37:37] completed
[STOP] [2021-04-19 16:37:37] completed
[STOP] [2021-04-19 16:37:37] logged process, took 102.06

Latest Process

19 Apr 16:35 EXITED currently processing 0