Harvest for
Bruce 1988
Created
19 Apr 15:38
Stage:
completed
Fetched:
19 Apr 15:38
Validated:
19 Apr 15:38
Deltas Created
19 Apr 15:38
Units Normalized:
19 Apr 15:39
Ancestry Built:
19 Apr 15:38
Nodes Matched:
19 Apr 15:39
Names Parsed:
19 Apr 15:39
New Models Stored:
19 Apr 15:38
Indexed:
19 Apr 15:39
Completed:
19 Apr 15:40
Time to Harvest:
less than a minute
Harvesting Log
(495 lines)
# Logfile created on 2020-08-27 15:43:44 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:43:44] logged process
[START] [2020-08-27 15:43:44] Creating resource from OpenData
[START] [2020-08-27 15:43:44] logged process
[START] [2020-08-27 15:43:44] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:43:44] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:43:44] Creating resource from OpenData
[INFO] [2020-12-03 11:33:47] ## HARVEST: type = -harvest
[START] [2020-12-03 11:33:50] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-12-03 11:33:50] create_harvest_instance
[STOP] [2020-12-03 11:33:51] create_harvest_instance
[START] [2020-12-03 11:33:51] fetch_files
[STOP] [2020-12-03 11:33:51] fetch_files
[START] [2020-12-03 11:33:51] validate_each_file
[STOP] [2020-12-03 11:33:52] validate_each_file
[START] [2020-12-03 11:33:52] convert_to_csv
[CMD] [2020-12-03 11:33:52] /usr/bin/sort /app/public/converted_csv/bruce_bruce_1988_refs_24824.csv > /app/public/converted_csv/bruce_bruce_1988_refs_24824.csv_sorted
[CMD] [2020-12-03 11:33:52] /usr/bin/sort /app/public/converted_csv/bruce_bruce_1988_nodes_24825.csv > /app/public/converted_csv/bruce_bruce_1988_nodes_24825.csv_sorted
[CMD] [2020-12-03 11:33:52] /usr/bin/sort /app/public/converted_csv/bruce_bruce_1988_occurrences_24826.csv > /app/public/converted_csv/bruce_bruce_1988_occurrences_24826.csv_sorted
[CMD] [2020-12-03 11:33:52] /usr/bin/sort /app/public/converted_csv/bruce_bruce_1988_measurements_24827.csv > /app/public/converted_csv/bruce_bruce_1988_measurements_24827.csv_sorted
[STOP] [2020-12-03 11:33:52] convert_to_csv
[START] [2020-12-03 11:33:52] calculate_delta
[CMD] [2020-12-03 11:33:52] echo "0a" > /app/public/diff/bruce_bruce_1988_refs_24824.diff
[CMD] [2020-12-03 11:33:52] tail -n +1 /app/public/converted_csv/bruce_bruce_1988_refs_24824.csv >> /app/public/diff/bruce_bruce_1988_refs_24824.diff
[CMD] [2020-12-03 11:33:52] echo "." >> /app/public/diff/bruce_bruce_1988_refs_24824.diff
[CMD] [2020-12-03 11:33:52] echo "0a" > /app/public/diff/bruce_bruce_1988_nodes_24825.diff
[CMD] [2020-12-03 11:33:52] tail -n +1 /app/public/converted_csv/bruce_bruce_1988_nodes_24825.csv >> /app/public/diff/bruce_bruce_1988_nodes_24825.diff
[CMD] [2020-12-03 11:33:52] echo "." >> /app/public/diff/bruce_bruce_1988_nodes_24825.diff
[CMD] [2020-12-03 11:33:52] echo "0a" > /app/public/diff/bruce_bruce_1988_occurrences_24826.diff
[CMD] [2020-12-03 11:33:52] tail -n +1 /app/public/converted_csv/bruce_bruce_1988_occurrences_24826.csv >> /app/public/diff/bruce_bruce_1988_occurrences_24826.diff
[CMD] [2020-12-03 11:33:52] echo "." >> /app/public/diff/bruce_bruce_1988_occurrences_24826.diff
[CMD] [2020-12-03 11:33:52] echo "0a" > /app/public/diff/bruce_bruce_1988_measurements_24827.diff
[CMD] [2020-12-03 11:33:52] tail -n +1 /app/public/converted_csv/bruce_bruce_1988_measurements_24827.csv >> /app/public/diff/bruce_bruce_1988_measurements_24827.diff
[CMD] [2020-12-03 11:33:52] echo "." >> /app/public/diff/bruce_bruce_1988_measurements_24827.diff
[STOP] [2020-12-03 11:33:52] calculate_delta
[START] [2020-12-03 11:33:52] parse_diff_and_store
[INFO] [2020-12-03 11:33:52] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 11:33:52] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 11:33:52] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 11:33:52] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 11:33:53] Storing 1 ScientificNames
[INFO] [2020-12-03 11:33:53] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:33:53] Average Time: 0.0
[INFO] [2020-12-03 11:33:53] Total Time: 1s
[INFO] [2020-12-03 11:33:53] Storing 1 Nodes
[INFO] [2020-12-03 11:33:53] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:33:53] Average Time: 0.0
[INFO] [2020-12-03 11:33:53] Total Time: 1s
[INFO] [2020-12-03 11:33:53] Storing 1 Occurrences
[INFO] [2020-12-03 11:33:53] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:33:53] Average Time: 0.0
[INFO] [2020-12-03 11:33:53] Total Time: 1s
[INFO] [2020-12-03 11:33:53] Storing 2 Traits
[INFO] [2020-12-03 11:33:53] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 11:33:53] Average Time: 0.0
[INFO] [2020-12-03 11:33:53] Total Time: 1s
[INFO] [2020-12-03 11:33:53] Storing 1 MetaTraits
[INFO] [2020-12-03 11:33:53] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:33:53] Average Time: 0.0
[INFO] [2020-12-03 11:33:53] Total Time: 1s
[STOP] [2020-12-03 11:33:53] parse_diff_and_store
[START] [2020-12-03 11:33:53] resolve_keys
[INFO] [2020-12-03 11:33:58] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 11:33:58] traits to occurrences...
[INFO] [2020-12-03 11:33:58] traits to nodes (through occurrences)...
[INFO] [2020-12-03 11:33:58] Traits to sex term...
[INFO] [2020-12-03 11:33:58] Traits to lifestage term...
[INFO] [2020-12-03 11:33:58] MetaTraits to traits...
[INFO] [2020-12-03 11:33:58] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 11:33:58] Assocs to occurrences...
[INFO] [2020-12-03 11:33:58] Assocs to nodes...
[INFO] [2020-12-03 11:33:58] Assoc to sex term...
[INFO] [2020-12-03 11:33:58] Assoc to lifestage term...
[INFO] [2020-12-03 11:33:58] MetaAssoc to assocs...
[STOP] [2020-12-03 11:33:58] resolve_keys
[START] [2020-12-03 11:33:58] hold_for_later_1
[STOP] [2020-12-03 11:33:58] hold_for_later_1
[START] [2020-12-03 11:33:58] hold_for_later_2
[STOP] [2020-12-03 11:33:58] hold_for_later_2
[START] [2020-12-03 11:33:58] resolve_missing_parents
[STOP] [2020-12-03 11:33:58] resolve_missing_parents
[START] [2020-12-03 11:33:58] rebuild_nodes
[START] [2020-12-03 11:33:58] Flattener#flatten
[START] [2020-12-03 11:33:58] Flattener#study_resource
[START] [2020-12-03 11:33:58] Flattener#build_ancestry
[STOP] [2020-12-03 11:33:58] Flattener#build_ancestry
[INFO] [2020-12-03 11:33:58] 1 ancestry keys
[START] [2020-12-03 11:33:58] build_node_ancestors
[INFO] [2020-12-03 11:33:58] old ancestors deleted.
[STOP] [2020-12-03 11:33:58] build_node_ancestors
[WARN] [2020-12-03 11:33:58] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 11:33:58] Flattener#flatten
[STOP] [2020-12-03 11:33:58] rebuild_nodes
[START] [2020-12-03 11:33:58] resolve_missing_media_owners
[STOP] [2020-12-03 11:33:58] resolve_missing_media_owners
[START] [2020-12-03 11:33:58] sanitize_media_verbatims
[STOP] [2020-12-03 11:33:58] sanitize_media_verbatims
[START] [2020-12-03 11:33:58] queue_downloads
[STOP] [2020-12-03 11:33:58] queue_downloads
[START] [2020-12-03 11:33:58] parse_names
[WARN] [2020-12-03 11:33:58] I see 1 names which still need to be parsed.
[STOP] [2020-12-03 11:33:59] parse_names
[START] [2020-12-03 11:33:59] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 11:33:59] denormalize_canonical_names_to_nodes
[START] [2020-12-03 11:33:59] match_nodes
[START] [2020-12-03 11:33:59] map_all_nodes_to_pages
[STOP] [2020-12-03 11:33:59] map_all_nodes_to_pages
[INFO] [2020-12-03 11:33:59] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-12-03 11:33:59] update_nodes
[STOP] [2020-12-03 11:33:59] update_nodes
[STOP] [2020-12-03 11:33:59] match_nodes
[START] [2020-12-03 11:33:59] reindex_search
[STOP] [2020-12-03 11:33:59] reindex_search
[START] [2020-12-03 11:33:59] normalize_units
[STOP] [2020-12-03 11:34:00] normalize_units
[START] [2020-12-03 11:34:00] calculate_statistics
[2020-12-03 11:34:00] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 11:34:00] calculate_statistics
[START] [2020-12-03 11:34:00] complete_harvest_instance
[START] [2020-12-03 11:34:00] overall_tsv_creation
[INFO] [2020-12-03 11:34:00] Processing group of 1 in 1 batches of 10000
[INFO] [2020-12-03 11:34:39] 1 Traits (unfiltered)...
[INFO] [2020-12-03 11:35:14] 1 Traits (filtered)...
[INFO] [2020-12-03 11:35:14] 0 Associations (filtered)...
[INFO] [2020-12-03 11:35:14] 2 metadata added.
[INFO] [2020-12-03 11:35:14] 0 metadata added.
[INFO] [2020-12-03 11:35:14] Average Time: 51.74
[INFO] [2020-12-03 11:35:14] Total Time: 1m15s
[STOP] [2020-12-03 11:35:14] overall_tsv_creation
[INFO] [2020-12-03 11:35:14] Done. Check your files:
[INFO] [2020-12-03 11:35:14] (1 lines) /app/public/data/bruce_bruce_1988/publish_nodes.tsv
[INFO] [2020-12-03 11:35:14] (1 lines) /app/public/data/bruce_bruce_1988/publish_scientific_names.tsv
[INFO] [2020-12-03 11:35:14] (2 lines) /app/public/data/bruce_bruce_1988/publish_traits.tsv
[INFO] [2020-12-03 11:35:14] (3 lines) /app/public/data/bruce_bruce_1988/publish_metadata.tsv
[STOP] [2020-12-03 11:35:14] complete_harvest_instance
[START] [2020-12-03 11:35:14] completed
[STOP] [2020-12-03 11:35:14] completed
[STOP] [2020-12-03 11:35:14] logged process, took 84.1
[INFO] [2021-04-19 15:36:03] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:38:51] ## remove_type: ScientificName
[INFO] [2021-04-19 15:38:51] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:38:51] [15:38:51.463] Removed 1 Scientificnames
[INFO] [2021-04-19 15:38:51] ## remove_type: Vernacular
[INFO] [2021-04-19 15:38:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:38:51] [15:38:51.464] Removed 0 Vernaculars
[INFO] [2021-04-19 15:38:51] ## remove_type: Article
[INFO] [2021-04-19 15:38:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:38:51] [15:38:51.466] Removed 0 Articles
[INFO] [2021-04-19 15:38:51] ## remove_type: Medium
[INFO] [2021-04-19 15:38:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:38:51] [15:38:51.467] Removed 0 Media
[INFO] [2021-04-19 15:38:51] ## remove_type: Trait
[INFO] [2021-04-19 15:38:51] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:38:51] [15:38:51.469] Removed 2 Traits
[INFO] [2021-04-19 15:38:51] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:38:51] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:38:51] [15:38:51.471] Removed 1 Metatraits
[INFO] [2021-04-19 15:38:51] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:38:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:38:51] [15:38:51.472] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 15:38:51] ## remove_type: Assoc
[INFO] [2021-04-19 15:38:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:38:51] [15:38:51.474] Removed 0 Assocs
[INFO] [2021-04-19 15:38:51] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:38:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:38:51] [15:38:51.475] Removed 0 Metaassocs
[INFO] [2021-04-19 15:38:51] ## remove_type: Identifier
[INFO] [2021-04-19 15:38:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:38:51] [15:38:51.476] Removed 0 Identifiers
[INFO] [2021-04-19 15:38:51] ## remove_type: Reference
[INFO] [2021-04-19 15:38:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:38:51] [15:38:51.478] Removed 0 References
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:51] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] Starting batch with ID 86115922...
[INFO] [2021-04-19 15:38:52] ## remove_type: Node
[INFO] [2021-04-19 15:38:52] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:38:52] [15:38:52.469] Removed 1 Nodes
[START] [2021-04-19 15:38:52] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:38:52] Creating resource from OpenData
[START] [2021-04-19 15:38:52] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:38:52] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:38:52] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:38:52] Creating resource from OpenData
[START] [2021-04-19 15:38:52] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:38:52] create_harvest_instance
[INFO] [2021-04-19 15:38:52] Created harvest instance #3773
[STOP] [2021-04-19 15:38:52] create_harvest_instance
[START] [2021-04-19 15:38:52] fetch_files
[STOP] [2021-04-19 15:38:52] fetch_files
[START] [2021-04-19 15:38:52] validate_each_file
[INFO] [2021-04-19 15:38:52] Looping over 4 formats...
[INFO] [2021-04-19 15:38:52] ...refs (/app/public/data/bruce_bruce_1988/references.tsv)
[INFO] [2021-04-19 15:38:52] Valid: /app/public/converted_csv/bruce_bruce_1988_refs_3773.csv (0 lines)
[INFO] [2021-04-19 15:38:52] ...nodes (/app/public/data/bruce_bruce_1988/taxa.txt)
[INFO] [2021-04-19 15:38:52] Valid: /app/public/converted_csv/bruce_bruce_1988_nodes_3773.csv (1 lines)
[INFO] [2021-04-19 15:38:52] ...occurrences (/app/public/data/bruce_bruce_1988/occurrences.txt)
[INFO] [2021-04-19 15:38:52] Valid: /app/public/converted_csv/bruce_bruce_1988_occurrences_3773.csv (1 lines)
[INFO] [2021-04-19 15:38:52] ...measurements (/app/public/data/bruce_bruce_1988/measurementsorfacts.txt)
[INFO] [2021-04-19 15:38:52] Valid: /app/public/converted_csv/bruce_bruce_1988_measurements_3773.csv (2 lines)
[STOP] [2021-04-19 15:38:52] validate_each_file
[START] [2021-04-19 15:38:52] convert_to_csv
[INFO] [2021-04-19 15:38:52] Looping over 4 formats...
[INFO] [2021-04-19 15:38:52] ...refs (/app/public/data/bruce_bruce_1988/references.tsv)
[CMD] [2021-04-19 15:38:52] /usr/bin/sort /app/public/converted_csv/bruce_bruce_1988_refs_3773.csv > /app/public/converted_csv/bruce_bruce_1988_refs_3773.csv_sorted
[INFO] [2021-04-19 15:38:52] Converted: /app/public/converted_csv/bruce_bruce_1988_refs_3773.csv (0 lines)
[INFO] [2021-04-19 15:38:52] ...nodes (/app/public/data/bruce_bruce_1988/taxa.txt)
[CMD] [2021-04-19 15:38:52] /usr/bin/sort /app/public/converted_csv/bruce_bruce_1988_nodes_3773.csv > /app/public/converted_csv/bruce_bruce_1988_nodes_3773.csv_sorted
[INFO] [2021-04-19 15:38:53] Converted: /app/public/converted_csv/bruce_bruce_1988_nodes_3773.csv (1 lines)
[INFO] [2021-04-19 15:38:53] ...occurrences (/app/public/data/bruce_bruce_1988/occurrences.txt)
[CMD] [2021-04-19 15:38:53] /usr/bin/sort /app/public/converted_csv/bruce_bruce_1988_occurrences_3773.csv > /app/public/converted_csv/bruce_bruce_1988_occurrences_3773.csv_sorted
[INFO] [2021-04-19 15:38:53] Converted: /app/public/converted_csv/bruce_bruce_1988_occurrences_3773.csv (1 lines)
[INFO] [2021-04-19 15:38:53] ...measurements (/app/public/data/bruce_bruce_1988/measurementsorfacts.txt)
[CMD] [2021-04-19 15:38:53] /usr/bin/sort /app/public/converted_csv/bruce_bruce_1988_measurements_3773.csv > /app/public/converted_csv/bruce_bruce_1988_measurements_3773.csv_sorted
[INFO] [2021-04-19 15:38:53] Converted: /app/public/converted_csv/bruce_bruce_1988_measurements_3773.csv (2 lines)
[STOP] [2021-04-19 15:38:53] convert_to_csv
[START] [2021-04-19 15:38:53] calculate_delta
[INFO] [2021-04-19 15:38:53] Looping over 4 formats...
[INFO] [2021-04-19 15:38:53] ...refs (/app/public/data/bruce_bruce_1988/references.tsv)
[CMD] [2021-04-19 15:38:53] echo "0a" > /app/public/diff/bruce_bruce_1988_refs_3773.diff
[CMD] [2021-04-19 15:38:53] tail -n +1 /app/public/converted_csv/bruce_bruce_1988_refs_3773.csv >> /app/public/diff/bruce_bruce_1988_refs_3773.diff
[CMD] [2021-04-19 15:38:53] echo "." >> /app/public/diff/bruce_bruce_1988_refs_3773.diff
[INFO] [2021-04-19 15:38:53] Created diff: /app/public/diff/bruce_bruce_1988_refs_3773.diff (2 lines)
[INFO] [2021-04-19 15:38:53] ...nodes (/app/public/data/bruce_bruce_1988/taxa.txt)
[CMD] [2021-04-19 15:38:53] echo "0a" > /app/public/diff/bruce_bruce_1988_nodes_3773.diff
[CMD] [2021-04-19 15:38:53] tail -n +1 /app/public/converted_csv/bruce_bruce_1988_nodes_3773.csv >> /app/public/diff/bruce_bruce_1988_nodes_3773.diff
[CMD] [2021-04-19 15:38:53] echo "." >> /app/public/diff/bruce_bruce_1988_nodes_3773.diff
[INFO] [2021-04-19 15:38:53] Created diff: /app/public/diff/bruce_bruce_1988_nodes_3773.diff (3 lines)
[INFO] [2021-04-19 15:38:53] ...occurrences (/app/public/data/bruce_bruce_1988/occurrences.txt)
[CMD] [2021-04-19 15:38:53] echo "0a" > /app/public/diff/bruce_bruce_1988_occurrences_3773.diff
[CMD] [2021-04-19 15:38:53] tail -n +1 /app/public/converted_csv/bruce_bruce_1988_occurrences_3773.csv >> /app/public/diff/bruce_bruce_1988_occurrences_3773.diff
[CMD] [2021-04-19 15:38:53] echo "." >> /app/public/diff/bruce_bruce_1988_occurrences_3773.diff
[INFO] [2021-04-19 15:38:53] Created diff: /app/public/diff/bruce_bruce_1988_occurrences_3773.diff (3 lines)
[INFO] [2021-04-19 15:38:53] ...measurements (/app/public/data/bruce_bruce_1988/measurementsorfacts.txt)
[CMD] [2021-04-19 15:38:53] echo "0a" > /app/public/diff/bruce_bruce_1988_measurements_3773.diff
[CMD] [2021-04-19 15:38:53] tail -n +1 /app/public/converted_csv/bruce_bruce_1988_measurements_3773.csv >> /app/public/diff/bruce_bruce_1988_measurements_3773.diff
[CMD] [2021-04-19 15:38:53] echo "." >> /app/public/diff/bruce_bruce_1988_measurements_3773.diff
[INFO] [2021-04-19 15:38:53] Created diff: /app/public/diff/bruce_bruce_1988_measurements_3773.diff (4 lines)
[STOP] [2021-04-19 15:38:53] calculate_delta
[START] [2021-04-19 15:38:53] parse_diff_and_store
[INFO] [2021-04-19 15:38:53] Handling diff: /app/public/diff/bruce_bruce_1988_refs_3773.diff (2 lines)
[INFO] [2021-04-19 15:38:53] Loading refs diff file into memory (2 /app/public/diff/bruce_bruce_1988_refs_3773.diff lines)...
[INFO] [2021-04-19 15:38:53] Handling diff: /app/public/diff/bruce_bruce_1988_nodes_3773.diff (3 lines)
[INFO] [2021-04-19 15:38:53] Loading nodes diff file into memory (3 /app/public/diff/bruce_bruce_1988_nodes_3773.diff lines)...
[INFO] [2021-04-19 15:38:53] Handling diff: /app/public/diff/bruce_bruce_1988_occurrences_3773.diff (3 lines)
[INFO] [2021-04-19 15:38:53] Loading occurrences diff file into memory (3 /app/public/diff/bruce_bruce_1988_occurrences_3773.diff lines)...
[INFO] [2021-04-19 15:38:53] Handling diff: /app/public/diff/bruce_bruce_1988_measurements_3773.diff (4 lines)
[INFO] [2021-04-19 15:38:53] Loading measurements diff file into memory (4 /app/public/diff/bruce_bruce_1988_measurements_3773.diff lines)...
[INFO] [2021-04-19 15:38:53] Storing 1 ScientificNames
[INFO] [2021-04-19 15:38:53] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:38:53] Average Time: 0.0
[INFO] [2021-04-19 15:38:53] Total Time: 1s
[INFO] [2021-04-19 15:38:53] Storing 1 Nodes
[INFO] [2021-04-19 15:38:53] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:38:53] Average Time: 0.0
[INFO] [2021-04-19 15:38:53] Total Time: 1s
[INFO] [2021-04-19 15:38:53] Storing 1 Occurrences
[INFO] [2021-04-19 15:38:53] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:38:53] Average Time: 0.0
[INFO] [2021-04-19 15:38:53] Total Time: 1s
[INFO] [2021-04-19 15:38:53] Storing 2 Traits
[INFO] [2021-04-19 15:38:53] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:38:53] Average Time: 0.0
[INFO] [2021-04-19 15:38:53] Total Time: 1s
[INFO] [2021-04-19 15:38:53] Storing 1 MetaTraits
[INFO] [2021-04-19 15:38:53] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:38:53] Average Time: 0.0
[INFO] [2021-04-19 15:38:53] Total Time: 1s
[STOP] [2021-04-19 15:38:53] parse_diff_and_store
[START] [2021-04-19 15:38:53] resolve_keys
[INFO] [2021-04-19 15:38:59] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:38:59] traits to occurrences...
[INFO] [2021-04-19 15:38:59] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:38:59] Traits to sex term...
[INFO] [2021-04-19 15:38:59] Traits to lifestage term...
[INFO] [2021-04-19 15:38:59] MetaTraits to traits...
[INFO] [2021-04-19 15:38:59] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:38:59] Assocs to occurrences...
[INFO] [2021-04-19 15:38:59] Assocs to nodes...
[INFO] [2021-04-19 15:38:59] Assoc to sex term...
[INFO] [2021-04-19 15:38:59] Assoc to lifestage term...
[INFO] [2021-04-19 15:38:59] MetaAssoc to assocs...
[STOP] [2021-04-19 15:38:59] resolve_keys
[START] [2021-04-19 15:38:59] hold_for_later_1
[STOP] [2021-04-19 15:38:59] hold_for_later_1
[START] [2021-04-19 15:38:59] hold_for_later_2
[STOP] [2021-04-19 15:38:59] hold_for_later_2
[START] [2021-04-19 15:38:59] resolve_missing_parents
[STOP] [2021-04-19 15:38:59] resolve_missing_parents
[START] [2021-04-19 15:38:59] rebuild_nodes
[START] [2021-04-19 15:38:59] Flattener#flatten
[START] [2021-04-19 15:38:59] Flattener#study_resource
[START] [2021-04-19 15:38:59] Flattener#build_ancestry
[STOP] [2021-04-19 15:38:59] Flattener#build_ancestry
[INFO] [2021-04-19 15:38:59] 1 ancestry keys
[START] [2021-04-19 15:38:59] build_node_ancestors
[INFO] [2021-04-19 15:38:59] old ancestors deleted.
[STOP] [2021-04-19 15:38:59] build_node_ancestors
[WARN] [2021-04-19 15:38:59] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:38:59] Flattener#flatten
[STOP] [2021-04-19 15:38:59] rebuild_nodes
[START] [2021-04-19 15:38:59] resolve_missing_media_owners
[STOP] [2021-04-19 15:38:59] resolve_missing_media_owners
[START] [2021-04-19 15:38:59] sanitize_media_verbatims
[STOP] [2021-04-19 15:38:59] sanitize_media_verbatims
[START] [2021-04-19 15:38:59] queue_downloads
[STOP] [2021-04-19 15:38:59] queue_downloads
[START] [2021-04-19 15:38:59] parse_names
[WARN] [2021-04-19 15:38:59] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 15:39:00] parse_names
[START] [2021-04-19 15:39:00] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:39:00] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:39:00] match_nodes
[START] [2021-04-19 15:39:00] map_all_nodes_to_pages
[STOP] [2021-04-19 15:39:00] map_all_nodes_to_pages
[INFO] [2021-04-19 15:39:00] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 15:39:00] update_nodes
[STOP] [2021-04-19 15:39:00] update_nodes
[STOP] [2021-04-19 15:39:00] match_nodes
[START] [2021-04-19 15:39:00] reindex_search
[STOP] [2021-04-19 15:39:00] reindex_search
[START] [2021-04-19 15:39:00] normalize_units
[STOP] [2021-04-19 15:39:00] normalize_units
[START] [2021-04-19 15:39:00] calculate_statistics
[2021-04-19 15:39:00] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:39:00] calculate_statistics
[START] [2021-04-19 15:39:00] complete_harvest_instance
[START] [2021-04-19 15:39:00] overall_tsv_creation
[INFO] [2021-04-19 15:39:00] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 15:39:35] 1 Traits (unfiltered)...
[INFO] [2021-04-19 15:40:07] 1 Traits (filtered)...
[INFO] [2021-04-19 15:40:07] 0 Associations (filtered)...
[INFO] [2021-04-19 15:40:07] 1 metadata added.
[INFO] [2021-04-19 15:40:07] 0 metadata added.
[INFO] [2021-04-19 15:40:34] Average Time: 69.71
[INFO] [2021-04-19 15:40:34] Total Time: 1m34s
[STOP] [2021-04-19 15:40:34] overall_tsv_creation
[INFO] [2021-04-19 15:40:34] Done. Check your files:
[INFO] [2021-04-19 15:40:34] (1 lines) /app/public/data/bruce_bruce_1988/publish_nodes.tsv
[INFO] [2021-04-19 15:40:34] (1 lines) /app/public/data/bruce_bruce_1988/publish_scientific_names.tsv
[INFO] [2021-04-19 15:40:34] (2 lines) /app/public/data/bruce_bruce_1988/publish_traits.tsv
[INFO] [2021-04-19 15:40:34] (2 lines) /app/public/data/bruce_bruce_1988/publish_metadata.tsv
[STOP] [2021-04-19 15:40:34] complete_harvest_instance
[START] [2021-04-19 15:40:34] completed
[STOP] [2021-04-19 15:40:34] completed
[STOP] [2021-04-19 15:40:34] logged process, took 101.24
Latest Process