Harvest for Dittami et al, 2017 Created 19 Apr 11:27

Harvesting Log

# Logfile created on 2020-12-08 15:19:19 -0500 by logger.rb/v1.4.2
[START] [2020-12-08 15:19:19] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-08 15:19:19] Creating resource from OpenData
[START] [2020-12-08 15:19:19] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-08 15:19:19] Parse meta.xml file and create formats with fields
[STOP] [2020-12-08 15:19:19] Parse meta.xml file and create formats with fields
[STOP] [2020-12-08 15:19:19] Creating resource from OpenData
[INFO] [2020-12-08 15:19:36] ## HARVEST: type = -harvest
[START] [2020-12-08 15:19:40] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-08 15:19:40] create_harvest_instance
[STOP] [2020-12-08 15:19:41] create_harvest_instance
[START] [2020-12-08 15:19:41] fetch_files
[STOP] [2020-12-08 15:19:41] fetch_files
[START] [2020-12-08 15:19:41] validate_each_file
[STOP] [2020-12-08 15:19:42] validate_each_file
[START] [2020-12-08 15:19:42] convert_to_csv
[CMD] [2020-12-08 15:19:42] /usr/bin/sort /app/public/converted_csv/dittami_et_al_di_nodes_25297.csv > /app/public/converted_csv/dittami_et_al_di_nodes_25297.csv_sorted
[CMD] [2020-12-08 15:19:42] /usr/bin/sort /app/public/converted_csv/dittami_et_al_di_occurrences_25298.csv > /app/public/converted_csv/dittami_et_al_di_occurrences_25298.csv_sorted
[CMD] [2020-12-08 15:19:42] /usr/bin/sort /app/public/converted_csv/dittami_et_al_di_measurements_25299.csv > /app/public/converted_csv/dittami_et_al_di_measurements_25299.csv_sorted
[STOP] [2020-12-08 15:19:42] convert_to_csv
[START] [2020-12-08 15:19:42] calculate_delta
[CMD] [2020-12-08 15:19:42] echo "0a" > /app/public/diff/dittami_et_al_di_nodes_25297.diff
[CMD] [2020-12-08 15:19:42] tail -n +1 /app/public/converted_csv/dittami_et_al_di_nodes_25297.csv >> /app/public/diff/dittami_et_al_di_nodes_25297.diff
[CMD] [2020-12-08 15:19:42] echo "." >> /app/public/diff/dittami_et_al_di_nodes_25297.diff
[CMD] [2020-12-08 15:19:42] echo "0a" > /app/public/diff/dittami_et_al_di_occurrences_25298.diff
[CMD] [2020-12-08 15:19:42] tail -n +1 /app/public/converted_csv/dittami_et_al_di_occurrences_25298.csv >> /app/public/diff/dittami_et_al_di_occurrences_25298.diff
[CMD] [2020-12-08 15:19:42] echo "." >> /app/public/diff/dittami_et_al_di_occurrences_25298.diff
[CMD] [2020-12-08 15:19:42] echo "0a" > /app/public/diff/dittami_et_al_di_measurements_25299.diff
[CMD] [2020-12-08 15:19:42] tail -n +1 /app/public/converted_csv/dittami_et_al_di_measurements_25299.csv >> /app/public/diff/dittami_et_al_di_measurements_25299.diff
[CMD] [2020-12-08 15:19:42] echo "." >> /app/public/diff/dittami_et_al_di_measurements_25299.diff
[STOP] [2020-12-08 15:19:42] calculate_delta
[START] [2020-12-08 15:19:42] parse_diff_and_store
[INFO] [2020-12-08 15:19:42] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-08 15:19:42] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-08 15:19:42] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-08 15:19:43] Storing 22 ScientificNames
[INFO] [2020-12-08 15:19:43] Processing group of 22 in 1 groups of 1000
[INFO] [2020-12-08 15:19:43] Average Time: 0.02
[INFO] [2020-12-08 15:19:43] Total Time: 1s
[INFO] [2020-12-08 15:19:43] Storing 22 Nodes
[INFO] [2020-12-08 15:19:43] Processing group of 22 in 1 groups of 1000
[INFO] [2020-12-08 15:19:43] Average Time: 0.01
[INFO] [2020-12-08 15:19:43] Total Time: 1s
[INFO] [2020-12-08 15:19:43] Storing 22 Occurrences
[INFO] [2020-12-08 15:19:43] Processing group of 22 in 1 groups of 1000
[INFO] [2020-12-08 15:19:43] Average Time: 0.0
[INFO] [2020-12-08 15:19:43] Total Time: 1s
[INFO] [2020-12-08 15:19:43] Storing 43 Traits
[INFO] [2020-12-08 15:19:43] Processing group of 43 in 1 groups of 1000
[INFO] [2020-12-08 15:19:43] Average Time: 0.04
[INFO] [2020-12-08 15:19:43] Total Time: 1s
[INFO] [2020-12-08 15:19:43] Storing 22 MetaTraits
[INFO] [2020-12-08 15:19:43] Processing group of 22 in 1 groups of 1000
[INFO] [2020-12-08 15:19:43] Average Time: 0.01
[INFO] [2020-12-08 15:19:43] Total Time: 1s
[STOP] [2020-12-08 15:19:43] parse_diff_and_store
[START] [2020-12-08 15:19:43] resolve_keys
[INFO] [2020-12-08 15:19:49] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-08 15:19:49] traits to occurrences...
[INFO] [2020-12-08 15:19:49] traits to nodes (through occurrences)...
[INFO] [2020-12-08 15:19:49] Traits to sex term...
[INFO] [2020-12-08 15:19:49] Traits to lifestage term...
[INFO] [2020-12-08 15:19:49] MetaTraits to traits...
[INFO] [2020-12-08 15:19:49] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-08 15:19:49] Assocs to occurrences...
[INFO] [2020-12-08 15:19:49] Assocs to nodes...
[INFO] [2020-12-08 15:19:49] Assoc to sex term...
[INFO] [2020-12-08 15:19:49] Assoc to lifestage term...
[INFO] [2020-12-08 15:19:49] MetaAssoc to assocs...
[STOP] [2020-12-08 15:19:49] resolve_keys
[START] [2020-12-08 15:19:49] hold_for_later_1
[STOP] [2020-12-08 15:19:49] hold_for_later_1
[START] [2020-12-08 15:19:49] hold_for_later_2
[STOP] [2020-12-08 15:19:49] hold_for_later_2
[START] [2020-12-08 15:19:49] resolve_missing_parents
[STOP] [2020-12-08 15:19:49] resolve_missing_parents
[START] [2020-12-08 15:19:49] rebuild_nodes
[START] [2020-12-08 15:19:49] Flattener#flatten
[START] [2020-12-08 15:19:49] Flattener#study_resource
[START] [2020-12-08 15:19:49] Flattener#build_ancestry
[STOP] [2020-12-08 15:19:49] Flattener#build_ancestry
[INFO] [2020-12-08 15:19:49] 22 ancestry keys
[START] [2020-12-08 15:19:49] build_node_ancestors
[INFO] [2020-12-08 15:19:49] old ancestors deleted.
[STOP] [2020-12-08 15:19:49] build_node_ancestors
[WARN] [2020-12-08 15:19:49] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-08 15:19:49] Flattener#flatten
[STOP] [2020-12-08 15:19:49] rebuild_nodes
[START] [2020-12-08 15:19:49] resolve_missing_media_owners
[STOP] [2020-12-08 15:19:49] resolve_missing_media_owners
[START] [2020-12-08 15:19:49] sanitize_media_verbatims
[STOP] [2020-12-08 15:19:49] sanitize_media_verbatims
[START] [2020-12-08 15:19:49] queue_downloads
[STOP] [2020-12-08 15:19:49] queue_downloads
[START] [2020-12-08 15:19:49] parse_names
[WARN] [2020-12-08 15:19:49] I see 22 names which still need to be parsed.
[STOP] [2020-12-08 15:19:50] parse_names
[START] [2020-12-08 15:19:50] denormalize_canonical_names_to_nodes
[STOP] [2020-12-08 15:19:50] denormalize_canonical_names_to_nodes
[START] [2020-12-08 15:19:50] match_nodes
[START] [2020-12-08 15:19:50] map_all_nodes_to_pages
[STOP] [2020-12-08 15:19:50] map_all_nodes_to_pages
[INFO] [2020-12-08 15:19:50] Unmatched nodes (1 of 22): Arnodiella (#86121246)
[START] [2020-12-08 15:19:50] update_nodes
[STOP] [2020-12-08 15:19:50] update_nodes
[STOP] [2020-12-08 15:19:50] match_nodes
[START] [2020-12-08 15:19:50] reindex_search
[STOP] [2020-12-08 15:19:50] reindex_search
[START] [2020-12-08 15:19:50] normalize_units
[STOP] [2020-12-08 15:19:50] normalize_units
[START] [2020-12-08 15:19:50] calculate_statistics
[2020-12-08 15:19:50] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-08 15:19:50] calculate_statistics
[START] [2020-12-08 15:19:50] complete_harvest_instance
[START] [2020-12-08 15:19:50] overall_tsv_creation
[INFO] [2020-12-08 15:19:50] Processing group of 22 in 1 batches of 10000
[INFO] [2020-12-08 15:20:30] 21 Traits (unfiltered)...
[INFO] [2020-12-08 15:21:09] 21 Traits (filtered)...
[INFO] [2020-12-08 15:21:09] 0 Associations (filtered)...
[INFO] [2020-12-08 15:21:09] 39 metadata added.
[INFO] [2020-12-08 15:21:09] 0 metadata added.
[INFO] [2020-12-08 15:21:09] Average Time: 55.07
[INFO] [2020-12-08 15:21:09] Total Time: 1m19s
[STOP] [2020-12-08 15:21:09] overall_tsv_creation
[INFO] [2020-12-08 15:21:09] Done. Check your files:
[INFO] [2020-12-08 15:21:09] (22 lines) /app/public/data/dittami_et_al_di/publish_nodes.tsv
[INFO] [2020-12-08 15:21:09] (22 lines) /app/public/data/dittami_et_al_di/publish_scientific_names.tsv
[INFO] [2020-12-08 15:21:09] (22 lines) /app/public/data/dittami_et_al_di/publish_traits.tsv
[INFO] [2020-12-08 15:21:09] (40 lines) /app/public/data/dittami_et_al_di/publish_metadata.tsv
[STOP] [2020-12-08 15:21:09] complete_harvest_instance
[START] [2020-12-08 15:21:09] completed
[STOP] [2020-12-08 15:21:09] completed
[STOP] [2020-12-08 15:21:09] logged process, took 88.26
[INFO] [2021-04-19 11:19:34] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 11:27:30] ## remove_type: ScientificName
[INFO] [2021-04-19 11:27:30] ++ Calling delete_all on 22 instances...
[INFO] [2021-04-19 11:27:30] [11:27:30.626] Removed 22 Scientificnames
[INFO] [2021-04-19 11:27:30] ## remove_type: Vernacular
[INFO] [2021-04-19 11:27:30] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:27:30] [11:27:30.627] Removed 0 Vernaculars
[INFO] [2021-04-19 11:27:30] ## remove_type: Article
[INFO] [2021-04-19 11:27:30] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:27:30] [11:27:30.628] Removed 0 Articles
[INFO] [2021-04-19 11:27:30] ## remove_type: Medium
[INFO] [2021-04-19 11:27:30] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:27:30] [11:27:30.630] Removed 0 Media
[INFO] [2021-04-19 11:27:30] ## remove_type: Trait
[INFO] [2021-04-19 11:27:30] ++ Calling delete_all on 43 instances...
[INFO] [2021-04-19 11:27:30] [11:27:30.633] Removed 43 Traits
[INFO] [2021-04-19 11:27:30] ## remove_type: MetaTrait
[INFO] [2021-04-19 11:27:30] ++ Calling delete_all on 22 instances...
[INFO] [2021-04-19 11:27:30] [11:27:30.635] Removed 22 Metatraits
[INFO] [2021-04-19 11:27:30] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 11:27:30] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:27:30] [11:27:30.637] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 11:27:30] ## remove_type: Assoc
[INFO] [2021-04-19 11:27:30] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:27:30] [11:27:30.638] Removed 0 Assocs
[INFO] [2021-04-19 11:27:30] ## remove_type: MetaAssoc
[INFO] [2021-04-19 11:27:30] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:27:30] [11:27:30.640] Removed 0 Metaassocs
[INFO] [2021-04-19 11:27:30] ## remove_type: Identifier
[INFO] [2021-04-19 11:27:30] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:27:30] [11:27:30.641] Removed 0 Identifiers
[INFO] [2021-04-19 11:27:30] ## remove_type: Reference
[INFO] [2021-04-19 11:27:30] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:27:30] [11:27:30.643] Removed 0 References
[INFO] [2021-04-19 11:27:30] Starting batch with ID 86121249...
[INFO] [2021-04-19 11:27:30] Starting batch with ID 86121249...
[INFO] [2021-04-19 11:27:30] Starting batch with ID 86121249...
[INFO] [2021-04-19 11:27:30] Starting batch with ID 86121249...
[INFO] [2021-04-19 11:27:30] Starting batch with ID 86121249...
[INFO] [2021-04-19 11:27:30] Starting batch with ID 86121249...
[INFO] [2021-04-19 11:27:30] Starting batch with ID 86121249...
[INFO] [2021-04-19 11:27:30] Starting batch with ID 86121249...
[INFO] [2021-04-19 11:27:30] ## remove_type: Node
[INFO] [2021-04-19 11:27:30] ++ Calling delete_all on 22 instances...
[INFO] [2021-04-19 11:27:30] [11:27:30.731] Removed 22 Nodes
[START] [2021-04-19 11:27:31] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 11:27:31] Creating resource from OpenData
[START] [2021-04-19 11:27:32] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 11:27:32] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 11:27:35] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 11:27:35] Creating resource from OpenData
[START] [2021-04-19 11:27:36] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 11:27:36] create_harvest_instance
[INFO] [2021-04-19 11:27:36] Created harvest instance #3739
[STOP] [2021-04-19 11:27:36] create_harvest_instance
[START] [2021-04-19 11:27:36] fetch_files
[STOP] [2021-04-19 11:27:36] fetch_files
[START] [2021-04-19 11:27:36] validate_each_file
[INFO] [2021-04-19 11:27:36] Looping over 3 formats...
[INFO] [2021-04-19 11:27:36] ...nodes (/app/public/data/dittami_et_al_di/taxa.txt)
[INFO] [2021-04-19 11:27:36] Valid: /app/public/converted_csv/dittami_et_al_di_nodes_3739.csv (22 lines)
[INFO] [2021-04-19 11:27:36] ...occurrences (/app/public/data/dittami_et_al_di/occurrences.txt)
[INFO] [2021-04-19 11:27:36] Valid: /app/public/converted_csv/dittami_et_al_di_occurrences_3739.csv (22 lines)
[INFO] [2021-04-19 11:27:36] ...measurements (/app/public/data/dittami_et_al_di/measurementsorfacts.txt)
[INFO] [2021-04-19 11:27:36] Valid: /app/public/converted_csv/dittami_et_al_di_measurements_3739.csv (43 lines)
[STOP] [2021-04-19 11:27:36] validate_each_file
[START] [2021-04-19 11:27:36] convert_to_csv
[INFO] [2021-04-19 11:27:36] Looping over 3 formats...
[INFO] [2021-04-19 11:27:36] ...nodes (/app/public/data/dittami_et_al_di/taxa.txt)
[CMD] [2021-04-19 11:27:36] /usr/bin/sort /app/public/converted_csv/dittami_et_al_di_nodes_3739.csv > /app/public/converted_csv/dittami_et_al_di_nodes_3739.csv_sorted
[INFO] [2021-04-19 11:27:36] Converted: /app/public/converted_csv/dittami_et_al_di_nodes_3739.csv (22 lines)
[INFO] [2021-04-19 11:27:36] ...occurrences (/app/public/data/dittami_et_al_di/occurrences.txt)
[CMD] [2021-04-19 11:27:36] /usr/bin/sort /app/public/converted_csv/dittami_et_al_di_occurrences_3739.csv > /app/public/converted_csv/dittami_et_al_di_occurrences_3739.csv_sorted
[INFO] [2021-04-19 11:27:37] Converted: /app/public/converted_csv/dittami_et_al_di_occurrences_3739.csv (22 lines)
[INFO] [2021-04-19 11:27:37] ...measurements (/app/public/data/dittami_et_al_di/measurementsorfacts.txt)
[CMD] [2021-04-19 11:27:37] /usr/bin/sort /app/public/converted_csv/dittami_et_al_di_measurements_3739.csv > /app/public/converted_csv/dittami_et_al_di_measurements_3739.csv_sorted
[INFO] [2021-04-19 11:27:37] Converted: /app/public/converted_csv/dittami_et_al_di_measurements_3739.csv (43 lines)
[STOP] [2021-04-19 11:27:37] convert_to_csv
[START] [2021-04-19 11:27:37] calculate_delta
[INFO] [2021-04-19 11:27:37] Looping over 3 formats...
[INFO] [2021-04-19 11:27:37] ...nodes (/app/public/data/dittami_et_al_di/taxa.txt)
[CMD] [2021-04-19 11:27:37] echo "0a" > /app/public/diff/dittami_et_al_di_nodes_3739.diff
[CMD] [2021-04-19 11:27:37] tail -n +1 /app/public/converted_csv/dittami_et_al_di_nodes_3739.csv >> /app/public/diff/dittami_et_al_di_nodes_3739.diff
[CMD] [2021-04-19 11:27:38] echo "." >> /app/public/diff/dittami_et_al_di_nodes_3739.diff
[INFO] [2021-04-19 11:27:38] Created diff: /app/public/diff/dittami_et_al_di_nodes_3739.diff (24 lines)
[INFO] [2021-04-19 11:27:38] ...occurrences (/app/public/data/dittami_et_al_di/occurrences.txt)
[CMD] [2021-04-19 11:27:38] echo "0a" > /app/public/diff/dittami_et_al_di_occurrences_3739.diff
[CMD] [2021-04-19 11:27:39] tail -n +1 /app/public/converted_csv/dittami_et_al_di_occurrences_3739.csv >> /app/public/diff/dittami_et_al_di_occurrences_3739.diff
[CMD] [2021-04-19 11:27:39] echo "." >> /app/public/diff/dittami_et_al_di_occurrences_3739.diff
[INFO] [2021-04-19 11:27:39] Created diff: /app/public/diff/dittami_et_al_di_occurrences_3739.diff (24 lines)
[INFO] [2021-04-19 11:27:39] ...measurements (/app/public/data/dittami_et_al_di/measurementsorfacts.txt)
[CMD] [2021-04-19 11:27:39] echo "0a" > /app/public/diff/dittami_et_al_di_measurements_3739.diff
[CMD] [2021-04-19 11:27:40] tail -n +1 /app/public/converted_csv/dittami_et_al_di_measurements_3739.csv >> /app/public/diff/dittami_et_al_di_measurements_3739.diff
[CMD] [2021-04-19 11:27:40] echo "." >> /app/public/diff/dittami_et_al_di_measurements_3739.diff
[INFO] [2021-04-19 11:27:40] Created diff: /app/public/diff/dittami_et_al_di_measurements_3739.diff (45 lines)
[STOP] [2021-04-19 11:27:40] calculate_delta
[START] [2021-04-19 11:27:40] parse_diff_and_store
[INFO] [2021-04-19 11:27:40] Handling diff: /app/public/diff/dittami_et_al_di_nodes_3739.diff (24 lines)
[INFO] [2021-04-19 11:27:41] Loading nodes diff file into memory (24 /app/public/diff/dittami_et_al_di_nodes_3739.diff lines)...
[INFO] [2021-04-19 11:27:41] Handling diff: /app/public/diff/dittami_et_al_di_occurrences_3739.diff (24 lines)
[INFO] [2021-04-19 11:27:42] Loading occurrences diff file into memory (24 /app/public/diff/dittami_et_al_di_occurrences_3739.diff lines)...
[INFO] [2021-04-19 11:27:42] Handling diff: /app/public/diff/dittami_et_al_di_measurements_3739.diff (45 lines)
[INFO] [2021-04-19 11:27:42] Loading measurements diff file into memory (45 /app/public/diff/dittami_et_al_di_measurements_3739.diff lines)...
[INFO] [2021-04-19 11:27:43] Storing 22 ScientificNames
[INFO] [2021-04-19 11:27:43] Processing group of 22 in 1 groups of 1000
[INFO] [2021-04-19 11:27:43] Average Time: 0.01
[INFO] [2021-04-19 11:27:43] Total Time: 1s
[INFO] [2021-04-19 11:27:43] Storing 22 Nodes
[INFO] [2021-04-19 11:27:43] Processing group of 22 in 1 groups of 1000
[INFO] [2021-04-19 11:27:43] Average Time: 0.01
[INFO] [2021-04-19 11:27:43] Total Time: 1s
[INFO] [2021-04-19 11:27:43] Storing 22 Occurrences
[INFO] [2021-04-19 11:27:43] Processing group of 22 in 1 groups of 1000
[INFO] [2021-04-19 11:27:43] Average Time: 0.0
[INFO] [2021-04-19 11:27:43] Total Time: 1s
[INFO] [2021-04-19 11:27:43] Storing 43 Traits
[INFO] [2021-04-19 11:27:43] Processing group of 43 in 1 groups of 1000
[INFO] [2021-04-19 11:27:43] Average Time: 0.01
[INFO] [2021-04-19 11:27:43] Total Time: 1s
[INFO] [2021-04-19 11:27:43] Storing 22 MetaTraits
[INFO] [2021-04-19 11:27:43] Processing group of 22 in 1 groups of 1000
[INFO] [2021-04-19 11:27:43] Average Time: 0.0
[INFO] [2021-04-19 11:27:43] Total Time: 1s
[STOP] [2021-04-19 11:27:43] parse_diff_and_store
[START] [2021-04-19 11:27:43] resolve_keys
[INFO] [2021-04-19 11:27:49] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 11:27:49] traits to occurrences...
[INFO] [2021-04-19 11:27:49] traits to nodes (through occurrences)...
[INFO] [2021-04-19 11:27:49] Traits to sex term...
[INFO] [2021-04-19 11:27:49] Traits to lifestage term...
[INFO] [2021-04-19 11:27:49] MetaTraits to traits...
[INFO] [2021-04-19 11:27:49] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 11:27:49] Assocs to occurrences...
[INFO] [2021-04-19 11:27:49] Assocs to nodes...
[INFO] [2021-04-19 11:27:49] Assoc to sex term...
[INFO] [2021-04-19 11:27:49] Assoc to lifestage term...
[INFO] [2021-04-19 11:27:49] MetaAssoc to assocs...
[STOP] [2021-04-19 11:27:49] resolve_keys
[START] [2021-04-19 11:27:49] hold_for_later_1
[STOP] [2021-04-19 11:27:49] hold_for_later_1
[START] [2021-04-19 11:27:49] hold_for_later_2
[STOP] [2021-04-19 11:27:49] hold_for_later_2
[START] [2021-04-19 11:27:49] resolve_missing_parents
[STOP] [2021-04-19 11:27:49] resolve_missing_parents
[START] [2021-04-19 11:27:49] rebuild_nodes
[START] [2021-04-19 11:27:49] Flattener#flatten
[START] [2021-04-19 11:27:49] Flattener#study_resource
[START] [2021-04-19 11:27:49] Flattener#build_ancestry
[STOP] [2021-04-19 11:27:49] Flattener#build_ancestry
[INFO] [2021-04-19 11:27:49] 22 ancestry keys
[START] [2021-04-19 11:27:49] build_node_ancestors
[INFO] [2021-04-19 11:27:49] old ancestors deleted.
[STOP] [2021-04-19 11:27:49] build_node_ancestors
[WARN] [2021-04-19 11:27:49] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 11:27:49] Flattener#flatten
[STOP] [2021-04-19 11:27:49] rebuild_nodes
[START] [2021-04-19 11:27:49] resolve_missing_media_owners
[STOP] [2021-04-19 11:27:49] resolve_missing_media_owners
[START] [2021-04-19 11:27:49] sanitize_media_verbatims
[STOP] [2021-04-19 11:27:49] sanitize_media_verbatims
[START] [2021-04-19 11:27:49] queue_downloads
[STOP] [2021-04-19 11:27:49] queue_downloads
[START] [2021-04-19 11:27:49] parse_names
[WARN] [2021-04-19 11:27:49] I see 22 names which still need to be parsed.
[STOP] [2021-04-19 11:27:50] parse_names
[START] [2021-04-19 11:27:50] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 11:27:50] denormalize_canonical_names_to_nodes
[START] [2021-04-19 11:27:50] match_nodes
[START] [2021-04-19 11:27:50] map_all_nodes_to_pages
[STOP] [2021-04-19 11:27:50] map_all_nodes_to_pages
[INFO] [2021-04-19 11:27:50] Unmatched nodes (1 of 22): Arnodiella (#92873303)
[START] [2021-04-19 11:27:50] update_nodes
[STOP] [2021-04-19 11:27:50] update_nodes
[STOP] [2021-04-19 11:27:50] match_nodes
[START] [2021-04-19 11:27:50] reindex_search
[STOP] [2021-04-19 11:27:50] reindex_search
[START] [2021-04-19 11:27:50] normalize_units
[STOP] [2021-04-19 11:27:50] normalize_units
[START] [2021-04-19 11:27:50] calculate_statistics
[2021-04-19 11:27:50] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 11:27:50] calculate_statistics
[START] [2021-04-19 11:27:50] complete_harvest_instance
[START] [2021-04-19 11:27:50] overall_tsv_creation
[INFO] [2021-04-19 11:27:50] Processing group of 22 in 1 batches of 10000
[INFO] [2021-04-19 11:28:26] 21 Traits (unfiltered)...
[INFO] [2021-04-19 11:29:01] 21 Traits (filtered)...
[INFO] [2021-04-19 11:29:01] 0 Associations (filtered)...
[INFO] [2021-04-19 11:29:01] 18 metadata added.
[INFO] [2021-04-19 11:29:01] 0 metadata added.
[INFO] [2021-04-19 11:29:28] Average Time: 73.74
[INFO] [2021-04-19 11:29:28] Total Time: 1m38s
[STOP] [2021-04-19 11:29:28] overall_tsv_creation
[INFO] [2021-04-19 11:29:28] Done. Check your files:
[INFO] [2021-04-19 11:29:28] (22 lines) /app/public/data/dittami_et_al_di/publish_nodes.tsv
[INFO] [2021-04-19 11:29:29] (22 lines) /app/public/data/dittami_et_al_di/publish_scientific_names.tsv
[INFO] [2021-04-19 11:29:29] (22 lines) /app/public/data/dittami_et_al_di/publish_traits.tsv
[INFO] [2021-04-19 11:29:30] (19 lines) /app/public/data/dittami_et_al_di/publish_metadata.tsv
[STOP] [2021-04-19 11:29:30] complete_harvest_instance
[START] [2021-04-19 11:29:30] completed
[STOP] [2021-04-19 11:29:30] completed
[STOP] [2021-04-19 11:29:30] logged process, took 114.31

Latest Process

19 Apr 11:27 EXITED currently processing 0