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Harvest for Coe 1927 Created 19 Apr 16:54

Stage: completed
Fetched: 19 Apr 16:54
Validated: 19 Apr 16:54
Deltas Created 19 Apr 16:54
Units Normalized: 19 Apr 16:54
Ancestry Built: 19 Apr 16:54
Nodes Matched: 19 Apr 16:54
Names Parsed: 19 Apr 16:54
New Models Stored: 19 Apr 16:54
Indexed: 19 Apr 16:54
Completed: 19 Apr 16:56
Time to Harvest: less than a minute

Harvesting Log

(453 lines) 
# Logfile created on 2020-09-28 09:00:18 -0400 by logger.rb/v1.4.2
[START] [2020-09-28 09:00:18] logged process
[START] [2020-09-28 09:00:18] Creating resource from OpenData
[START] [2020-09-28 09:00:18] logged process
[START] [2020-09-28 09:00:18] Parse meta.xml file and create formats with fields
[STOP] [2020-09-28 09:00:18] Parse meta.xml file and create formats with fields
[STOP] [2020-09-28 09:00:18] Creating resource from OpenData
[INFO] [2020-12-04 08:14:11] ## HARVEST: type = -harvest
[START] [2020-12-04 08:14:13] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-04 08:14:13] create_harvest_instance
[STOP] [2020-12-04 08:14:14] create_harvest_instance
[START] [2020-12-04 08:14:14] fetch_files
[STOP] [2020-12-04 08:14:14] fetch_files
[START] [2020-12-04 08:14:14] validate_each_file
[STOP] [2020-12-04 08:14:14] validate_each_file
[START] [2020-12-04 08:14:14] convert_to_csv
[CMD] [2020-12-04 08:14:14] /usr/bin/sort /app/public/converted_csv/coe_coe_1927_nodes_25073.csv > /app/public/converted_csv/coe_coe_1927_nodes_25073.csv_sorted
[CMD] [2020-12-04 08:14:14] /usr/bin/sort /app/public/converted_csv/coe_coe_1927_occurrences_25074.csv > /app/public/converted_csv/coe_coe_1927_occurrences_25074.csv_sorted
[CMD] [2020-12-04 08:14:14] /usr/bin/sort /app/public/converted_csv/coe_coe_1927_measurements_25075.csv > /app/public/converted_csv/coe_coe_1927_measurements_25075.csv_sorted
[STOP] [2020-12-04 08:14:14] convert_to_csv
[START] [2020-12-04 08:14:14] calculate_delta
[CMD] [2020-12-04 08:14:14] echo "0a" > /app/public/diff/coe_coe_1927_nodes_25073.diff
[CMD] [2020-12-04 08:14:14] tail -n +1 /app/public/converted_csv/coe_coe_1927_nodes_25073.csv >> /app/public/diff/coe_coe_1927_nodes_25073.diff
[CMD] [2020-12-04 08:14:14] echo "." >> /app/public/diff/coe_coe_1927_nodes_25073.diff
[CMD] [2020-12-04 08:14:14] echo "0a" > /app/public/diff/coe_coe_1927_occurrences_25074.diff
[CMD] [2020-12-04 08:14:14] tail -n +1 /app/public/converted_csv/coe_coe_1927_occurrences_25074.csv >> /app/public/diff/coe_coe_1927_occurrences_25074.diff
[CMD] [2020-12-04 08:14:14] echo "." >> /app/public/diff/coe_coe_1927_occurrences_25074.diff
[CMD] [2020-12-04 08:14:14] echo "0a" > /app/public/diff/coe_coe_1927_measurements_25075.diff
[CMD] [2020-12-04 08:14:14] tail -n +1 /app/public/converted_csv/coe_coe_1927_measurements_25075.csv >> /app/public/diff/coe_coe_1927_measurements_25075.diff
[CMD] [2020-12-04 08:14:14] echo "." >> /app/public/diff/coe_coe_1927_measurements_25075.diff
[STOP] [2020-12-04 08:14:14] calculate_delta
[START] [2020-12-04 08:14:14] parse_diff_and_store
[INFO] [2020-12-04 08:14:14] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-04 08:14:14] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-04 08:14:14] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-04 08:14:15] Storing 2 ScientificNames
[INFO] [2020-12-04 08:14:15] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-04 08:14:15] Average Time: 0.0
[INFO] [2020-12-04 08:14:15] Total Time: 1s
[INFO] [2020-12-04 08:14:15] Storing 2 Nodes
[INFO] [2020-12-04 08:14:15] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-04 08:14:15] Average Time: 0.0
[INFO] [2020-12-04 08:14:15] Total Time: 1s
[INFO] [2020-12-04 08:14:15] Storing 2 Occurrences
[INFO] [2020-12-04 08:14:15] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-04 08:14:15] Average Time: 0.0
[INFO] [2020-12-04 08:14:15] Total Time: 1s
[INFO] [2020-12-04 08:14:15] Storing 31 Traits
[INFO] [2020-12-04 08:14:15] Processing group of 31 in 1 groups of 1000
[INFO] [2020-12-04 08:14:15] Average Time: 0.01
[INFO] [2020-12-04 08:14:15] Total Time: 1s
[INFO] [2020-12-04 08:14:15] Storing 3 MetaTraits
[INFO] [2020-12-04 08:14:15] Processing group of 3 in 1 groups of 1000
[INFO] [2020-12-04 08:14:15] Average Time: 0.0
[INFO] [2020-12-04 08:14:15] Total Time: 1s
[STOP] [2020-12-04 08:14:15] parse_diff_and_store
[START] [2020-12-04 08:14:15] resolve_keys
[INFO] [2020-12-04 08:14:21] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-04 08:14:21] traits to occurrences...
[INFO] [2020-12-04 08:14:21] traits to nodes (through occurrences)...
[INFO] [2020-12-04 08:14:21] Traits to sex term...
[INFO] [2020-12-04 08:14:21] Traits to lifestage term...
[INFO] [2020-12-04 08:14:21] MetaTraits to traits...
[INFO] [2020-12-04 08:14:21] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-04 08:14:21] Assocs to occurrences...
[INFO] [2020-12-04 08:14:21] Assocs to nodes...
[INFO] [2020-12-04 08:14:21] Assoc to sex term...
[INFO] [2020-12-04 08:14:21] Assoc to lifestage term...
[INFO] [2020-12-04 08:14:21] MetaAssoc to assocs...
[STOP] [2020-12-04 08:14:21] resolve_keys
[START] [2020-12-04 08:14:21] hold_for_later_1
[STOP] [2020-12-04 08:14:21] hold_for_later_1
[START] [2020-12-04 08:14:21] hold_for_later_2
[STOP] [2020-12-04 08:14:21] hold_for_later_2
[START] [2020-12-04 08:14:21] resolve_missing_parents
[STOP] [2020-12-04 08:14:21] resolve_missing_parents
[START] [2020-12-04 08:14:21] rebuild_nodes
[START] [2020-12-04 08:14:21] Flattener#flatten
[START] [2020-12-04 08:14:21] Flattener#study_resource
[START] [2020-12-04 08:14:21] Flattener#build_ancestry
[STOP] [2020-12-04 08:14:21] Flattener#build_ancestry
[INFO] [2020-12-04 08:14:21] 2 ancestry keys
[START] [2020-12-04 08:14:21] build_node_ancestors
[INFO] [2020-12-04 08:14:21] old ancestors deleted.
[STOP] [2020-12-04 08:14:21] build_node_ancestors
[WARN] [2020-12-04 08:14:21] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-04 08:14:21] Flattener#flatten
[STOP] [2020-12-04 08:14:21] rebuild_nodes
[START] [2020-12-04 08:14:21] resolve_missing_media_owners
[STOP] [2020-12-04 08:14:21] resolve_missing_media_owners
[START] [2020-12-04 08:14:21] sanitize_media_verbatims
[STOP] [2020-12-04 08:14:21] sanitize_media_verbatims
[START] [2020-12-04 08:14:21] queue_downloads
[STOP] [2020-12-04 08:14:21] queue_downloads
[START] [2020-12-04 08:14:21] parse_names
[WARN] [2020-12-04 08:14:21] I see 2 names which still need to be parsed.
[STOP] [2020-12-04 08:14:22] parse_names
[START] [2020-12-04 08:14:22] denormalize_canonical_names_to_nodes
[STOP] [2020-12-04 08:14:22] denormalize_canonical_names_to_nodes
[START] [2020-12-04 08:14:22] match_nodes
[START] [2020-12-04 08:14:22] map_all_nodes_to_pages
[STOP] [2020-12-04 08:14:22] map_all_nodes_to_pages
[INFO] [2020-12-04 08:14:22] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2020-12-04 08:14:22] update_nodes
[STOP] [2020-12-04 08:14:22] update_nodes
[STOP] [2020-12-04 08:14:22] match_nodes
[START] [2020-12-04 08:14:22] reindex_search
[STOP] [2020-12-04 08:14:22] reindex_search
[START] [2020-12-04 08:14:22] normalize_units
[STOP] [2020-12-04 08:14:22] normalize_units
[START] [2020-12-04 08:14:22] calculate_statistics
[2020-12-04 08:14:22] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-04 08:14:22] calculate_statistics
[START] [2020-12-04 08:14:22] complete_harvest_instance
[START] [2020-12-04 08:14:22] overall_tsv_creation
[INFO] [2020-12-04 08:14:22] Processing group of 2 in 1 batches of 10000
[INFO] [2020-12-04 08:15:01] 2 Traits (unfiltered)...
[INFO] [2020-12-04 08:15:38] 2 Traits (filtered)...
[INFO] [2020-12-04 08:15:38] 0 Associations (filtered)...
[INFO] [2020-12-04 08:15:38] 28 metadata added.
[INFO] [2020-12-04 08:15:38] 0 metadata added.
[INFO] [2020-12-04 08:15:38] Average Time: 53.16
[INFO] [2020-12-04 08:15:38] Total Time: 1m17s
[STOP] [2020-12-04 08:15:38] overall_tsv_creation
[INFO] [2020-12-04 08:15:38] Done. Check your files:
[INFO] [2020-12-04 08:15:38] (2 lines) /app/public/data/coe_coe_1927/publish_nodes.tsv
[INFO] [2020-12-04 08:15:38] (2 lines) /app/public/data/coe_coe_1927/publish_scientific_names.tsv
[INFO] [2020-12-04 08:15:38] (3 lines) /app/public/data/coe_coe_1927/publish_traits.tsv
[INFO] [2020-12-04 08:15:38] (29 lines) /app/public/data/coe_coe_1927/publish_metadata.tsv
[STOP] [2020-12-04 08:15:38] complete_harvest_instance
[START] [2020-12-04 08:15:38] completed
[STOP] [2020-12-04 08:15:38] completed
[STOP] [2020-12-04 08:15:38] logged process, took 85.59
[INFO] [2021-04-19 16:47:38] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 16:54:38] ## remove_type: ScientificName
[INFO] [2021-04-19 16:54:38] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 16:54:38] [16:54:38.503] Removed 2 Scientificnames
[INFO] [2021-04-19 16:54:38] ## remove_type: Vernacular
[INFO] [2021-04-19 16:54:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:54:38] [16:54:38.504] Removed 0 Vernaculars
[INFO] [2021-04-19 16:54:38] ## remove_type: Article
[INFO] [2021-04-19 16:54:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:54:38] [16:54:38.506] Removed 0 Articles
[INFO] [2021-04-19 16:54:38] ## remove_type: Medium
[INFO] [2021-04-19 16:54:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:54:38] [16:54:38.507] Removed 0 Media
[INFO] [2021-04-19 16:54:38] ## remove_type: Trait
[INFO] [2021-04-19 16:54:38] ++ Calling delete_all on 31 instances...
[INFO] [2021-04-19 16:54:38] [16:54:38.511] Removed 31 Traits
[INFO] [2021-04-19 16:54:38] ## remove_type: MetaTrait
[INFO] [2021-04-19 16:54:38] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 16:54:38] [16:54:38.513] Removed 3 Metatraits
[INFO] [2021-04-19 16:54:38] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 16:54:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:54:38] [16:54:38.514] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 16:54:38] ## remove_type: Assoc
[INFO] [2021-04-19 16:54:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:54:38] [16:54:38.516] Removed 0 Assocs
[INFO] [2021-04-19 16:54:38] ## remove_type: MetaAssoc
[INFO] [2021-04-19 16:54:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:54:38] [16:54:38.518] Removed 0 Metaassocs
[INFO] [2021-04-19 16:54:38] ## remove_type: Identifier
[INFO] [2021-04-19 16:54:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:54:38] [16:54:38.519] Removed 0 Identifiers
[INFO] [2021-04-19 16:54:38] ## remove_type: Reference
[INFO] [2021-04-19 16:54:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:54:38] [16:54:38.521] Removed 0 References
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:38] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
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[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] Starting batch with ID 86116361...
[INFO] [2021-04-19 16:54:39] ## remove_type: Node
[INFO] [2021-04-19 16:54:39] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 16:54:39] [16:54:39.357] Removed 2 Nodes
[START] [2021-04-19 16:54:39] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:54:39] Creating resource from OpenData
[START] [2021-04-19 16:54:39] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:54:39] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:54:39] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:54:39] Creating resource from OpenData
[START] [2021-04-19 16:54:39] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:54:39] create_harvest_instance
[INFO] [2021-04-19 16:54:39] Created harvest instance #3809
[STOP] [2021-04-19 16:54:39] create_harvest_instance
[START] [2021-04-19 16:54:39] fetch_files
[STOP] [2021-04-19 16:54:39] fetch_files
[START] [2021-04-19 16:54:39] validate_each_file
[INFO] [2021-04-19 16:54:39] Looping over 3 formats...
[INFO] [2021-04-19 16:54:39] ...nodes (/app/public/data/coe_coe_1927/taxa.txt)
[INFO] [2021-04-19 16:54:39] Valid: /app/public/converted_csv/coe_coe_1927_nodes_3809.csv (2 lines)
[INFO] [2021-04-19 16:54:39] ...occurrences (/app/public/data/coe_coe_1927/occurrences.txt)
[INFO] [2021-04-19 16:54:39] Valid: /app/public/converted_csv/coe_coe_1927_occurrences_3809.csv (2 lines)
[INFO] [2021-04-19 16:54:39] ...measurements (/app/public/data/coe_coe_1927/measurementsorfacts.txt)
[INFO] [2021-04-19 16:54:39] Valid: /app/public/converted_csv/coe_coe_1927_measurements_3809.csv (31 lines)
[STOP] [2021-04-19 16:54:39] validate_each_file
[START] [2021-04-19 16:54:39] convert_to_csv
[INFO] [2021-04-19 16:54:39] Looping over 3 formats...
[INFO] [2021-04-19 16:54:39] ...nodes (/app/public/data/coe_coe_1927/taxa.txt)
[CMD] [2021-04-19 16:54:39] /usr/bin/sort /app/public/converted_csv/coe_coe_1927_nodes_3809.csv > /app/public/converted_csv/coe_coe_1927_nodes_3809.csv_sorted
[INFO] [2021-04-19 16:54:39] Converted: /app/public/converted_csv/coe_coe_1927_nodes_3809.csv (2 lines)
[INFO] [2021-04-19 16:54:39] ...occurrences (/app/public/data/coe_coe_1927/occurrences.txt)
[CMD] [2021-04-19 16:54:39] /usr/bin/sort /app/public/converted_csv/coe_coe_1927_occurrences_3809.csv > /app/public/converted_csv/coe_coe_1927_occurrences_3809.csv_sorted
[INFO] [2021-04-19 16:54:39] Converted: /app/public/converted_csv/coe_coe_1927_occurrences_3809.csv (2 lines)
[INFO] [2021-04-19 16:54:39] ...measurements (/app/public/data/coe_coe_1927/measurementsorfacts.txt)
[CMD] [2021-04-19 16:54:39] /usr/bin/sort /app/public/converted_csv/coe_coe_1927_measurements_3809.csv > /app/public/converted_csv/coe_coe_1927_measurements_3809.csv_sorted
[INFO] [2021-04-19 16:54:39] Converted: /app/public/converted_csv/coe_coe_1927_measurements_3809.csv (31 lines)
[STOP] [2021-04-19 16:54:39] convert_to_csv
[START] [2021-04-19 16:54:39] calculate_delta
[INFO] [2021-04-19 16:54:39] Looping over 3 formats...
[INFO] [2021-04-19 16:54:39] ...nodes (/app/public/data/coe_coe_1927/taxa.txt)
[CMD] [2021-04-19 16:54:39] echo "0a" > /app/public/diff/coe_coe_1927_nodes_3809.diff
[CMD] [2021-04-19 16:54:39] tail -n +1 /app/public/converted_csv/coe_coe_1927_nodes_3809.csv >> /app/public/diff/coe_coe_1927_nodes_3809.diff
[CMD] [2021-04-19 16:54:39] echo "." >> /app/public/diff/coe_coe_1927_nodes_3809.diff
[INFO] [2021-04-19 16:54:39] Created diff: /app/public/diff/coe_coe_1927_nodes_3809.diff (4 lines)
[INFO] [2021-04-19 16:54:39] ...occurrences (/app/public/data/coe_coe_1927/occurrences.txt)
[CMD] [2021-04-19 16:54:39] echo "0a" > /app/public/diff/coe_coe_1927_occurrences_3809.diff
[CMD] [2021-04-19 16:54:39] tail -n +1 /app/public/converted_csv/coe_coe_1927_occurrences_3809.csv >> /app/public/diff/coe_coe_1927_occurrences_3809.diff
[CMD] [2021-04-19 16:54:39] echo "." >> /app/public/diff/coe_coe_1927_occurrences_3809.diff
[INFO] [2021-04-19 16:54:39] Created diff: /app/public/diff/coe_coe_1927_occurrences_3809.diff (4 lines)
[INFO] [2021-04-19 16:54:39] ...measurements (/app/public/data/coe_coe_1927/measurementsorfacts.txt)
[CMD] [2021-04-19 16:54:39] echo "0a" > /app/public/diff/coe_coe_1927_measurements_3809.diff
[CMD] [2021-04-19 16:54:39] tail -n +1 /app/public/converted_csv/coe_coe_1927_measurements_3809.csv >> /app/public/diff/coe_coe_1927_measurements_3809.diff
[CMD] [2021-04-19 16:54:39] echo "." >> /app/public/diff/coe_coe_1927_measurements_3809.diff
[INFO] [2021-04-19 16:54:39] Created diff: /app/public/diff/coe_coe_1927_measurements_3809.diff (33 lines)
[STOP] [2021-04-19 16:54:39] calculate_delta
[START] [2021-04-19 16:54:39] parse_diff_and_store
[INFO] [2021-04-19 16:54:39] Handling diff: /app/public/diff/coe_coe_1927_nodes_3809.diff (4 lines)
[INFO] [2021-04-19 16:54:39] Loading nodes diff file into memory (4 /app/public/diff/coe_coe_1927_nodes_3809.diff lines)...
[INFO] [2021-04-19 16:54:39] Handling diff: /app/public/diff/coe_coe_1927_occurrences_3809.diff (4 lines)
[INFO] [2021-04-19 16:54:39] Loading occurrences diff file into memory (4 /app/public/diff/coe_coe_1927_occurrences_3809.diff lines)...
[INFO] [2021-04-19 16:54:39] Handling diff: /app/public/diff/coe_coe_1927_measurements_3809.diff (33 lines)
[INFO] [2021-04-19 16:54:39] Loading measurements diff file into memory (33 /app/public/diff/coe_coe_1927_measurements_3809.diff lines)...
[INFO] [2021-04-19 16:54:40] Storing 2 ScientificNames
[INFO] [2021-04-19 16:54:40] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 16:54:40] Average Time: 0.0
[INFO] [2021-04-19 16:54:40] Total Time: 1s
[INFO] [2021-04-19 16:54:40] Storing 2 Nodes
[INFO] [2021-04-19 16:54:40] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 16:54:40] Average Time: 0.0
[INFO] [2021-04-19 16:54:40] Total Time: 1s
[INFO] [2021-04-19 16:54:40] Storing 2 Occurrences
[INFO] [2021-04-19 16:54:40] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 16:54:40] Average Time: 0.0
[INFO] [2021-04-19 16:54:40] Total Time: 1s
[INFO] [2021-04-19 16:54:40] Storing 31 Traits
[INFO] [2021-04-19 16:54:40] Processing group of 31 in 1 groups of 1000
[INFO] [2021-04-19 16:54:40] Average Time: 0.01
[INFO] [2021-04-19 16:54:40] Total Time: 1s
[INFO] [2021-04-19 16:54:40] Storing 3 MetaTraits
[INFO] [2021-04-19 16:54:40] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 16:54:40] Average Time: 0.0
[INFO] [2021-04-19 16:54:40] Total Time: 1s
[STOP] [2021-04-19 16:54:40] parse_diff_and_store
[START] [2021-04-19 16:54:40] resolve_keys
[INFO] [2021-04-19 16:54:45] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 16:54:45] traits to occurrences...
[INFO] [2021-04-19 16:54:45] traits to nodes (through occurrences)...
[INFO] [2021-04-19 16:54:45] Traits to sex term...
[INFO] [2021-04-19 16:54:45] Traits to lifestage term...
[INFO] [2021-04-19 16:54:45] MetaTraits to traits...
[INFO] [2021-04-19 16:54:45] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 16:54:45] Assocs to occurrences...
[INFO] [2021-04-19 16:54:45] Assocs to nodes...
[INFO] [2021-04-19 16:54:45] Assoc to sex term...
[INFO] [2021-04-19 16:54:45] Assoc to lifestage term...
[INFO] [2021-04-19 16:54:45] MetaAssoc to assocs...
[STOP] [2021-04-19 16:54:45] resolve_keys
[START] [2021-04-19 16:54:45] hold_for_later_1
[STOP] [2021-04-19 16:54:45] hold_for_later_1
[START] [2021-04-19 16:54:45] hold_for_later_2
[STOP] [2021-04-19 16:54:45] hold_for_later_2
[START] [2021-04-19 16:54:45] resolve_missing_parents
[STOP] [2021-04-19 16:54:45] resolve_missing_parents
[START] [2021-04-19 16:54:45] rebuild_nodes
[START] [2021-04-19 16:54:45] Flattener#flatten
[START] [2021-04-19 16:54:45] Flattener#study_resource
[START] [2021-04-19 16:54:45] Flattener#build_ancestry
[STOP] [2021-04-19 16:54:45] Flattener#build_ancestry
[INFO] [2021-04-19 16:54:45] 2 ancestry keys
[START] [2021-04-19 16:54:45] build_node_ancestors
[INFO] [2021-04-19 16:54:45] old ancestors deleted.
[STOP] [2021-04-19 16:54:46] build_node_ancestors
[WARN] [2021-04-19 16:54:46] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 16:54:46] Flattener#flatten
[STOP] [2021-04-19 16:54:46] rebuild_nodes
[START] [2021-04-19 16:54:46] resolve_missing_media_owners
[STOP] [2021-04-19 16:54:46] resolve_missing_media_owners
[START] [2021-04-19 16:54:46] sanitize_media_verbatims
[STOP] [2021-04-19 16:54:46] sanitize_media_verbatims
[START] [2021-04-19 16:54:46] queue_downloads
[STOP] [2021-04-19 16:54:46] queue_downloads
[START] [2021-04-19 16:54:46] parse_names
[WARN] [2021-04-19 16:54:46] I see 2 names which still need to be parsed.
[STOP] [2021-04-19 16:54:47] parse_names
[START] [2021-04-19 16:54:47] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 16:54:47] denormalize_canonical_names_to_nodes
[START] [2021-04-19 16:54:47] match_nodes
[START] [2021-04-19 16:54:47] map_all_nodes_to_pages
[STOP] [2021-04-19 16:54:47] map_all_nodes_to_pages
[INFO] [2021-04-19 16:54:47] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2021-04-19 16:54:47] update_nodes
[STOP] [2021-04-19 16:54:47] update_nodes
[STOP] [2021-04-19 16:54:47] match_nodes
[START] [2021-04-19 16:54:47] reindex_search
[STOP] [2021-04-19 16:54:47] reindex_search
[START] [2021-04-19 16:54:47] normalize_units
[STOP] [2021-04-19 16:54:47] normalize_units
[START] [2021-04-19 16:54:47] calculate_statistics
[2021-04-19 16:54:47] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 16:54:47] calculate_statistics
[START] [2021-04-19 16:54:47] complete_harvest_instance
[START] [2021-04-19 16:54:47] overall_tsv_creation
[INFO] [2021-04-19 16:54:47] Processing group of 2 in 1 batches of 10000
[INFO] [2021-04-19 16:55:23] 2 Traits (unfiltered)...
[INFO] [2021-04-19 16:55:56] 2 Traits (filtered)...
[INFO] [2021-04-19 16:55:56] 0 Associations (filtered)...
[INFO] [2021-04-19 16:55:56] 27 metadata added.
[INFO] [2021-04-19 16:55:56] 0 metadata added.
[INFO] [2021-04-19 16:56:22] Average Time: 71.45
[INFO] [2021-04-19 16:56:22] Total Time: 1m36s
[STOP] [2021-04-19 16:56:22] overall_tsv_creation
[INFO] [2021-04-19 16:56:22] Done. Check your files:
[INFO] [2021-04-19 16:56:22] (2 lines) /app/public/data/coe_coe_1927/publish_nodes.tsv
[INFO] [2021-04-19 16:56:22] (2 lines) /app/public/data/coe_coe_1927/publish_scientific_names.tsv
[INFO] [2021-04-19 16:56:22] (3 lines) /app/public/data/coe_coe_1927/publish_traits.tsv
[INFO] [2021-04-19 16:56:22] (28 lines) /app/public/data/coe_coe_1927/publish_metadata.tsv
[STOP] [2021-04-19 16:56:22] complete_harvest_instance
[START] [2021-04-19 16:56:22] completed
[STOP] [2021-04-19 16:56:22] completed
[STOP] [2021-04-19 16:56:22] logged process, took 102.8

Latest Process