Stage:
completed
Fetched:
19 Apr 15:59
Validated:
19 Apr 15:59
Deltas Created
19 Apr 15:59
Units Normalized:
19 Apr 15:59
Ancestry Built:
19 Apr 15:59
Nodes Matched:
19 Apr 15:59
Names Parsed:
19 Apr 15:59
New Models Stored:
19 Apr 15:59
Indexed:
19 Apr 15:59
Completed:
19 Apr 16:00
Time to Harvest:
less than a minute
Harvesting Log
(494 lines)
# Logfile created on 2020-08-27 15:49:09 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:49:09] logged process
[START] [2020-08-27 15:49:09] Creating resource from OpenData
[START] [2020-08-27 15:49:09] logged process
[START] [2020-08-27 15:49:09] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:49:10] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:49:10] Creating resource from OpenData
[INFO] [2020-12-03 12:08:48] ## HARVEST: type = -harvest
[START] [2020-12-03 12:08:53] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-12-03 12:08:53] create_harvest_instance
[STOP] [2020-12-03 12:08:55] create_harvest_instance
[START] [2020-12-03 12:08:55] fetch_files
[STOP] [2020-12-03 12:08:55] fetch_files
[START] [2020-12-03 12:08:55] validate_each_file
[STOP] [2020-12-03 12:08:55] validate_each_file
[START] [2020-12-03 12:08:55] convert_to_csv
[CMD] [2020-12-03 12:08:55] /usr/bin/sort /app/public/converted_csv/daniels_et_al_da_refs_24880.csv > /app/public/converted_csv/daniels_et_al_da_refs_24880.csv_sorted
[CMD] [2020-12-03 12:08:55] /usr/bin/sort /app/public/converted_csv/daniels_et_al_da_nodes_24881.csv > /app/public/converted_csv/daniels_et_al_da_nodes_24881.csv_sorted
[CMD] [2020-12-03 12:08:55] /usr/bin/sort /app/public/converted_csv/daniels_et_al_da_occurrences_24882.csv > /app/public/converted_csv/daniels_et_al_da_occurrences_24882.csv_sorted
[CMD] [2020-12-03 12:08:55] /usr/bin/sort /app/public/converted_csv/daniels_et_al_da_measurements_24883.csv > /app/public/converted_csv/daniels_et_al_da_measurements_24883.csv_sorted
[STOP] [2020-12-03 12:08:55] convert_to_csv
[START] [2020-12-03 12:08:55] calculate_delta
[CMD] [2020-12-03 12:08:55] echo "0a" > /app/public/diff/daniels_et_al_da_refs_24880.diff
[CMD] [2020-12-03 12:08:55] tail -n +1 /app/public/converted_csv/daniels_et_al_da_refs_24880.csv >> /app/public/diff/daniels_et_al_da_refs_24880.diff
[CMD] [2020-12-03 12:08:55] echo "." >> /app/public/diff/daniels_et_al_da_refs_24880.diff
[CMD] [2020-12-03 12:08:55] echo "0a" > /app/public/diff/daniels_et_al_da_nodes_24881.diff
[CMD] [2020-12-03 12:08:55] tail -n +1 /app/public/converted_csv/daniels_et_al_da_nodes_24881.csv >> /app/public/diff/daniels_et_al_da_nodes_24881.diff
[CMD] [2020-12-03 12:08:55] echo "." >> /app/public/diff/daniels_et_al_da_nodes_24881.diff
[CMD] [2020-12-03 12:08:55] echo "0a" > /app/public/diff/daniels_et_al_da_occurrences_24882.diff
[CMD] [2020-12-03 12:08:55] tail -n +1 /app/public/converted_csv/daniels_et_al_da_occurrences_24882.csv >> /app/public/diff/daniels_et_al_da_occurrences_24882.diff
[CMD] [2020-12-03 12:08:55] echo "." >> /app/public/diff/daniels_et_al_da_occurrences_24882.diff
[CMD] [2020-12-03 12:08:55] echo "0a" > /app/public/diff/daniels_et_al_da_measurements_24883.diff
[CMD] [2020-12-03 12:08:55] tail -n +1 /app/public/converted_csv/daniels_et_al_da_measurements_24883.csv >> /app/public/diff/daniels_et_al_da_measurements_24883.diff
[CMD] [2020-12-03 12:08:55] echo "." >> /app/public/diff/daniels_et_al_da_measurements_24883.diff
[STOP] [2020-12-03 12:08:55] calculate_delta
[START] [2020-12-03 12:08:55] parse_diff_and_store
[INFO] [2020-12-03 12:08:55] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 12:08:55] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 12:08:55] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 12:08:55] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 12:08:56] Storing 1 ScientificNames
[INFO] [2020-12-03 12:08:56] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 12:08:56] Average Time: 0.0
[INFO] [2020-12-03 12:08:56] Total Time: 1s
[INFO] [2020-12-03 12:08:56] Storing 1 Nodes
[INFO] [2020-12-03 12:08:56] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 12:08:56] Average Time: 0.0
[INFO] [2020-12-03 12:08:56] Total Time: 1s
[INFO] [2020-12-03 12:08:56] Storing 1 Occurrences
[INFO] [2020-12-03 12:08:56] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 12:08:56] Average Time: 0.0
[INFO] [2020-12-03 12:08:56] Total Time: 1s
[INFO] [2020-12-03 12:08:56] Storing 2 Traits
[INFO] [2020-12-03 12:08:56] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 12:08:56] Average Time: 0.0
[INFO] [2020-12-03 12:08:56] Total Time: 1s
[INFO] [2020-12-03 12:08:56] Storing 2 MetaTraits
[INFO] [2020-12-03 12:08:56] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 12:08:56] Average Time: 0.0
[INFO] [2020-12-03 12:08:56] Total Time: 1s
[STOP] [2020-12-03 12:08:56] parse_diff_and_store
[START] [2020-12-03 12:08:56] resolve_keys
[INFO] [2020-12-03 12:09:01] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 12:09:01] traits to occurrences...
[INFO] [2020-12-03 12:09:01] traits to nodes (through occurrences)...
[INFO] [2020-12-03 12:09:01] Traits to sex term...
[INFO] [2020-12-03 12:09:01] Traits to lifestage term...
[INFO] [2020-12-03 12:09:01] MetaTraits to traits...
[INFO] [2020-12-03 12:09:01] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 12:09:01] Assocs to occurrences...
[INFO] [2020-12-03 12:09:02] Assocs to nodes...
[INFO] [2020-12-03 12:09:02] Assoc to sex term...
[INFO] [2020-12-03 12:09:02] Assoc to lifestage term...
[INFO] [2020-12-03 12:09:02] MetaAssoc to assocs...
[STOP] [2020-12-03 12:09:02] resolve_keys
[START] [2020-12-03 12:09:02] hold_for_later_1
[STOP] [2020-12-03 12:09:02] hold_for_later_1
[START] [2020-12-03 12:09:02] hold_for_later_2
[STOP] [2020-12-03 12:09:02] hold_for_later_2
[START] [2020-12-03 12:09:02] resolve_missing_parents
[STOP] [2020-12-03 12:09:02] resolve_missing_parents
[START] [2020-12-03 12:09:02] rebuild_nodes
[START] [2020-12-03 12:09:02] Flattener#flatten
[START] [2020-12-03 12:09:02] Flattener#study_resource
[START] [2020-12-03 12:09:02] Flattener#build_ancestry
[STOP] [2020-12-03 12:09:02] Flattener#build_ancestry
[INFO] [2020-12-03 12:09:02] 1 ancestry keys
[START] [2020-12-03 12:09:02] build_node_ancestors
[INFO] [2020-12-03 12:09:02] old ancestors deleted.
[STOP] [2020-12-03 12:09:02] build_node_ancestors
[WARN] [2020-12-03 12:09:02] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 12:09:02] Flattener#flatten
[STOP] [2020-12-03 12:09:02] rebuild_nodes
[START] [2020-12-03 12:09:02] resolve_missing_media_owners
[STOP] [2020-12-03 12:09:02] resolve_missing_media_owners
[START] [2020-12-03 12:09:02] sanitize_media_verbatims
[STOP] [2020-12-03 12:09:02] sanitize_media_verbatims
[START] [2020-12-03 12:09:02] queue_downloads
[STOP] [2020-12-03 12:09:02] queue_downloads
[START] [2020-12-03 12:09:02] parse_names
[WARN] [2020-12-03 12:09:02] I see 1 names which still need to be parsed.
[STOP] [2020-12-03 12:09:03] parse_names
[START] [2020-12-03 12:09:03] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 12:09:03] denormalize_canonical_names_to_nodes
[START] [2020-12-03 12:09:03] match_nodes
[START] [2020-12-03 12:09:03] map_all_nodes_to_pages
[STOP] [2020-12-03 12:09:03] map_all_nodes_to_pages
[INFO] [2020-12-03 12:09:03] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-12-03 12:09:03] update_nodes
[STOP] [2020-12-03 12:09:03] update_nodes
[STOP] [2020-12-03 12:09:03] match_nodes
[START] [2020-12-03 12:09:03] reindex_search
[STOP] [2020-12-03 12:09:03] reindex_search
[START] [2020-12-03 12:09:03] normalize_units
[STOP] [2020-12-03 12:09:03] normalize_units
[START] [2020-12-03 12:09:03] calculate_statistics
[2020-12-03 12:09:03] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 12:09:03] calculate_statistics
[START] [2020-12-03 12:09:03] complete_harvest_instance
[START] [2020-12-03 12:09:03] overall_tsv_creation
[INFO] [2020-12-03 12:09:03] Processing group of 1 in 1 batches of 10000
[INFO] [2020-12-03 12:09:41] 1 Traits (unfiltered)...
[INFO] [2020-12-03 12:10:17] 1 Traits (filtered)...
[INFO] [2020-12-03 12:10:17] 0 Associations (filtered)...
[INFO] [2020-12-03 12:10:17] 3 metadata added.
[INFO] [2020-12-03 12:10:17] 0 metadata added.
[INFO] [2020-12-03 12:10:17] Average Time: 51.18
[INFO] [2020-12-03 12:10:17] Total Time: 1m14s
[STOP] [2020-12-03 12:10:17] overall_tsv_creation
[INFO] [2020-12-03 12:10:17] Done. Check your files:
[INFO] [2020-12-03 12:10:17] (1 lines) /app/public/data/daniels_et_al_da/publish_nodes.tsv
[INFO] [2020-12-03 12:10:17] (1 lines) /app/public/data/daniels_et_al_da/publish_scientific_names.tsv
[INFO] [2020-12-03 12:10:17] (2 lines) /app/public/data/daniels_et_al_da/publish_traits.tsv
[INFO] [2020-12-03 12:10:17] (4 lines) /app/public/data/daniels_et_al_da/publish_metadata.tsv
[STOP] [2020-12-03 12:10:17] complete_harvest_instance
[START] [2020-12-03 12:10:17] completed
[STOP] [2020-12-03 12:10:17] completed
[STOP] [2020-12-03 12:10:17] logged process, took 83.73
[INFO] [2021-04-19 15:57:53] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:59:08] ## remove_type: ScientificName
[INFO] [2021-04-19 15:59:08] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:59:08] [15:59:08.803] Removed 1 Scientificnames
[INFO] [2021-04-19 15:59:08] ## remove_type: Vernacular
[INFO] [2021-04-19 15:59:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:59:08] [15:59:08.804] Removed 0 Vernaculars
[INFO] [2021-04-19 15:59:08] ## remove_type: Article
[INFO] [2021-04-19 15:59:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:59:08] [15:59:08.806] Removed 0 Articles
[INFO] [2021-04-19 15:59:08] ## remove_type: Medium
[INFO] [2021-04-19 15:59:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:59:08] [15:59:08.807] Removed 0 Media
[INFO] [2021-04-19 15:59:08] ## remove_type: Trait
[INFO] [2021-04-19 15:59:08] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:59:08] [15:59:08.809] Removed 2 Traits
[INFO] [2021-04-19 15:59:08] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:59:08] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:59:08] [15:59:08.811] Removed 2 Metatraits
[INFO] [2021-04-19 15:59:08] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:59:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:59:08] [15:59:08.812] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 15:59:08] ## remove_type: Assoc
[INFO] [2021-04-19 15:59:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:59:08] [15:59:08.814] Removed 0 Assocs
[INFO] [2021-04-19 15:59:08] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:59:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:59:08] [15:59:08.815] Removed 0 Metaassocs
[INFO] [2021-04-19 15:59:08] ## remove_type: Identifier
[INFO] [2021-04-19 15:59:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:59:08] [15:59:08.817] Removed 0 Identifiers
[INFO] [2021-04-19 15:59:08] ## remove_type: Reference
[INFO] [2021-04-19 15:59:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:59:08] [15:59:08.818] Removed 0 References
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:08] Starting batch with ID 86116213...
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[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
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[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
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[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
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[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
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[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
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[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] Starting batch with ID 86116213...
[INFO] [2021-04-19 15:59:09] ## remove_type: Node
[INFO] [2021-04-19 15:59:09] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:59:09] [15:59:09.785] Removed 1 Nodes
[START] [2021-04-19 15:59:09] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:59:09] Creating resource from OpenData
[START] [2021-04-19 15:59:09] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:59:09] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:59:10] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:59:10] Creating resource from OpenData
[START] [2021-04-19 15:59:10] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:59:10] create_harvest_instance
[INFO] [2021-04-19 15:59:10] Created harvest instance #3783
[STOP] [2021-04-19 15:59:10] create_harvest_instance
[START] [2021-04-19 15:59:10] fetch_files
[STOP] [2021-04-19 15:59:10] fetch_files
[START] [2021-04-19 15:59:10] validate_each_file
[INFO] [2021-04-19 15:59:10] Looping over 4 formats...
[INFO] [2021-04-19 15:59:10] ...refs (/app/public/data/daniels_et_al_da/references.tsv)
[INFO] [2021-04-19 15:59:10] Valid: /app/public/converted_csv/daniels_et_al_da_refs_3783.csv (0 lines)
[INFO] [2021-04-19 15:59:10] ...nodes (/app/public/data/daniels_et_al_da/taxa.txt)
[INFO] [2021-04-19 15:59:10] Valid: /app/public/converted_csv/daniels_et_al_da_nodes_3783.csv (1 lines)
[INFO] [2021-04-19 15:59:10] ...occurrences (/app/public/data/daniels_et_al_da/occurrences.txt)
[INFO] [2021-04-19 15:59:10] Valid: /app/public/converted_csv/daniels_et_al_da_occurrences_3783.csv (1 lines)
[INFO] [2021-04-19 15:59:10] ...measurements (/app/public/data/daniels_et_al_da/measurementsorfacts.txt)
[INFO] [2021-04-19 15:59:10] Valid: /app/public/converted_csv/daniels_et_al_da_measurements_3783.csv (2 lines)
[STOP] [2021-04-19 15:59:10] validate_each_file
[START] [2021-04-19 15:59:10] convert_to_csv
[INFO] [2021-04-19 15:59:10] Looping over 4 formats...
[INFO] [2021-04-19 15:59:10] ...refs (/app/public/data/daniels_et_al_da/references.tsv)
[CMD] [2021-04-19 15:59:10] /usr/bin/sort /app/public/converted_csv/daniels_et_al_da_refs_3783.csv > /app/public/converted_csv/daniels_et_al_da_refs_3783.csv_sorted
[INFO] [2021-04-19 15:59:10] Converted: /app/public/converted_csv/daniels_et_al_da_refs_3783.csv (0 lines)
[INFO] [2021-04-19 15:59:10] ...nodes (/app/public/data/daniels_et_al_da/taxa.txt)
[CMD] [2021-04-19 15:59:10] /usr/bin/sort /app/public/converted_csv/daniels_et_al_da_nodes_3783.csv > /app/public/converted_csv/daniels_et_al_da_nodes_3783.csv_sorted
[INFO] [2021-04-19 15:59:10] Converted: /app/public/converted_csv/daniels_et_al_da_nodes_3783.csv (1 lines)
[INFO] [2021-04-19 15:59:10] ...occurrences (/app/public/data/daniels_et_al_da/occurrences.txt)
[CMD] [2021-04-19 15:59:10] /usr/bin/sort /app/public/converted_csv/daniels_et_al_da_occurrences_3783.csv > /app/public/converted_csv/daniels_et_al_da_occurrences_3783.csv_sorted
[INFO] [2021-04-19 15:59:10] Converted: /app/public/converted_csv/daniels_et_al_da_occurrences_3783.csv (1 lines)
[INFO] [2021-04-19 15:59:10] ...measurements (/app/public/data/daniels_et_al_da/measurementsorfacts.txt)
[CMD] [2021-04-19 15:59:10] /usr/bin/sort /app/public/converted_csv/daniels_et_al_da_measurements_3783.csv > /app/public/converted_csv/daniels_et_al_da_measurements_3783.csv_sorted
[INFO] [2021-04-19 15:59:10] Converted: /app/public/converted_csv/daniels_et_al_da_measurements_3783.csv (2 lines)
[STOP] [2021-04-19 15:59:10] convert_to_csv
[START] [2021-04-19 15:59:10] calculate_delta
[INFO] [2021-04-19 15:59:10] Looping over 4 formats...
[INFO] [2021-04-19 15:59:10] ...refs (/app/public/data/daniels_et_al_da/references.tsv)
[CMD] [2021-04-19 15:59:10] echo "0a" > /app/public/diff/daniels_et_al_da_refs_3783.diff
[CMD] [2021-04-19 15:59:10] tail -n +1 /app/public/converted_csv/daniels_et_al_da_refs_3783.csv >> /app/public/diff/daniels_et_al_da_refs_3783.diff
[CMD] [2021-04-19 15:59:10] echo "." >> /app/public/diff/daniels_et_al_da_refs_3783.diff
[INFO] [2021-04-19 15:59:10] Created diff: /app/public/diff/daniels_et_al_da_refs_3783.diff (2 lines)
[INFO] [2021-04-19 15:59:10] ...nodes (/app/public/data/daniels_et_al_da/taxa.txt)
[CMD] [2021-04-19 15:59:10] echo "0a" > /app/public/diff/daniels_et_al_da_nodes_3783.diff
[CMD] [2021-04-19 15:59:10] tail -n +1 /app/public/converted_csv/daniels_et_al_da_nodes_3783.csv >> /app/public/diff/daniels_et_al_da_nodes_3783.diff
[CMD] [2021-04-19 15:59:10] echo "." >> /app/public/diff/daniels_et_al_da_nodes_3783.diff
[INFO] [2021-04-19 15:59:10] Created diff: /app/public/diff/daniels_et_al_da_nodes_3783.diff (3 lines)
[INFO] [2021-04-19 15:59:10] ...occurrences (/app/public/data/daniels_et_al_da/occurrences.txt)
[CMD] [2021-04-19 15:59:10] echo "0a" > /app/public/diff/daniels_et_al_da_occurrences_3783.diff
[CMD] [2021-04-19 15:59:10] tail -n +1 /app/public/converted_csv/daniels_et_al_da_occurrences_3783.csv >> /app/public/diff/daniels_et_al_da_occurrences_3783.diff
[CMD] [2021-04-19 15:59:10] echo "." >> /app/public/diff/daniels_et_al_da_occurrences_3783.diff
[INFO] [2021-04-19 15:59:10] Created diff: /app/public/diff/daniels_et_al_da_occurrences_3783.diff (3 lines)
[INFO] [2021-04-19 15:59:10] ...measurements (/app/public/data/daniels_et_al_da/measurementsorfacts.txt)
[CMD] [2021-04-19 15:59:10] echo "0a" > /app/public/diff/daniels_et_al_da_measurements_3783.diff
[CMD] [2021-04-19 15:59:10] tail -n +1 /app/public/converted_csv/daniels_et_al_da_measurements_3783.csv >> /app/public/diff/daniels_et_al_da_measurements_3783.diff
[CMD] [2021-04-19 15:59:10] echo "." >> /app/public/diff/daniels_et_al_da_measurements_3783.diff
[INFO] [2021-04-19 15:59:10] Created diff: /app/public/diff/daniels_et_al_da_measurements_3783.diff (4 lines)
[STOP] [2021-04-19 15:59:10] calculate_delta
[START] [2021-04-19 15:59:10] parse_diff_and_store
[INFO] [2021-04-19 15:59:10] Handling diff: /app/public/diff/daniels_et_al_da_refs_3783.diff (2 lines)
[INFO] [2021-04-19 15:59:10] Loading refs diff file into memory (2 /app/public/diff/daniels_et_al_da_refs_3783.diff lines)...
[INFO] [2021-04-19 15:59:10] Handling diff: /app/public/diff/daniels_et_al_da_nodes_3783.diff (3 lines)
[INFO] [2021-04-19 15:59:10] Loading nodes diff file into memory (3 /app/public/diff/daniels_et_al_da_nodes_3783.diff lines)...
[INFO] [2021-04-19 15:59:10] Handling diff: /app/public/diff/daniels_et_al_da_occurrences_3783.diff (3 lines)
[INFO] [2021-04-19 15:59:10] Loading occurrences diff file into memory (3 /app/public/diff/daniels_et_al_da_occurrences_3783.diff lines)...
[INFO] [2021-04-19 15:59:10] Handling diff: /app/public/diff/daniels_et_al_da_measurements_3783.diff (4 lines)
[INFO] [2021-04-19 15:59:10] Loading measurements diff file into memory (4 /app/public/diff/daniels_et_al_da_measurements_3783.diff lines)...
[INFO] [2021-04-19 15:59:10] Storing 1 ScientificNames
[INFO] [2021-04-19 15:59:10] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:59:10] Average Time: 0.0
[INFO] [2021-04-19 15:59:10] Total Time: 1s
[INFO] [2021-04-19 15:59:10] Storing 1 Nodes
[INFO] [2021-04-19 15:59:10] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:59:10] Average Time: 0.0
[INFO] [2021-04-19 15:59:10] Total Time: 1s
[INFO] [2021-04-19 15:59:10] Storing 1 Occurrences
[INFO] [2021-04-19 15:59:10] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:59:10] Average Time: 0.0
[INFO] [2021-04-19 15:59:10] Total Time: 1s
[INFO] [2021-04-19 15:59:10] Storing 2 Traits
[INFO] [2021-04-19 15:59:10] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:59:10] Average Time: 0.0
[INFO] [2021-04-19 15:59:10] Total Time: 1s
[INFO] [2021-04-19 15:59:10] Storing 2 MetaTraits
[INFO] [2021-04-19 15:59:10] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:59:10] Average Time: 0.0
[INFO] [2021-04-19 15:59:10] Total Time: 1s
[STOP] [2021-04-19 15:59:10] parse_diff_and_store
[START] [2021-04-19 15:59:10] resolve_keys
[INFO] [2021-04-19 15:59:16] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:59:16] traits to occurrences...
[INFO] [2021-04-19 15:59:16] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:59:16] Traits to sex term...
[INFO] [2021-04-19 15:59:16] Traits to lifestage term...
[INFO] [2021-04-19 15:59:16] MetaTraits to traits...
[INFO] [2021-04-19 15:59:16] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:59:16] Assocs to occurrences...
[INFO] [2021-04-19 15:59:16] Assocs to nodes...
[INFO] [2021-04-19 15:59:16] Assoc to sex term...
[INFO] [2021-04-19 15:59:16] Assoc to lifestage term...
[INFO] [2021-04-19 15:59:16] MetaAssoc to assocs...
[STOP] [2021-04-19 15:59:16] resolve_keys
[START] [2021-04-19 15:59:16] hold_for_later_1
[STOP] [2021-04-19 15:59:16] hold_for_later_1
[START] [2021-04-19 15:59:16] hold_for_later_2
[STOP] [2021-04-19 15:59:16] hold_for_later_2
[START] [2021-04-19 15:59:16] resolve_missing_parents
[STOP] [2021-04-19 15:59:16] resolve_missing_parents
[START] [2021-04-19 15:59:16] rebuild_nodes
[START] [2021-04-19 15:59:16] Flattener#flatten
[START] [2021-04-19 15:59:16] Flattener#study_resource
[START] [2021-04-19 15:59:16] Flattener#build_ancestry
[STOP] [2021-04-19 15:59:16] Flattener#build_ancestry
[INFO] [2021-04-19 15:59:16] 1 ancestry keys
[START] [2021-04-19 15:59:16] build_node_ancestors
[INFO] [2021-04-19 15:59:16] old ancestors deleted.
[STOP] [2021-04-19 15:59:16] build_node_ancestors
[WARN] [2021-04-19 15:59:16] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:59:16] Flattener#flatten
[STOP] [2021-04-19 15:59:16] rebuild_nodes
[START] [2021-04-19 15:59:16] resolve_missing_media_owners
[STOP] [2021-04-19 15:59:16] resolve_missing_media_owners
[START] [2021-04-19 15:59:16] sanitize_media_verbatims
[STOP] [2021-04-19 15:59:16] sanitize_media_verbatims
[START] [2021-04-19 15:59:16] queue_downloads
[STOP] [2021-04-19 15:59:16] queue_downloads
[START] [2021-04-19 15:59:16] parse_names
[WARN] [2021-04-19 15:59:16] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 15:59:17] parse_names
[START] [2021-04-19 15:59:17] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:59:17] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:59:17] match_nodes
[START] [2021-04-19 15:59:17] map_all_nodes_to_pages
[STOP] [2021-04-19 15:59:17] map_all_nodes_to_pages
[INFO] [2021-04-19 15:59:17] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 15:59:17] update_nodes
[STOP] [2021-04-19 15:59:17] update_nodes
[STOP] [2021-04-19 15:59:17] match_nodes
[START] [2021-04-19 15:59:17] reindex_search
[STOP] [2021-04-19 15:59:17] reindex_search
[START] [2021-04-19 15:59:17] normalize_units
[STOP] [2021-04-19 15:59:17] normalize_units
[START] [2021-04-19 15:59:17] calculate_statistics
[2021-04-19 15:59:17] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:59:17] calculate_statistics
[START] [2021-04-19 15:59:17] complete_harvest_instance
[START] [2021-04-19 15:59:17] overall_tsv_creation
[INFO] [2021-04-19 15:59:17] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 15:59:52] 1 Traits (unfiltered)...
[INFO] [2021-04-19 16:00:24] 1 Traits (filtered)...
[INFO] [2021-04-19 16:00:24] 0 Associations (filtered)...
[INFO] [2021-04-19 16:00:24] 1 metadata added.
[INFO] [2021-04-19 16:00:24] 0 metadata added.
[INFO] [2021-04-19 16:00:51] Average Time: 70.48
[INFO] [2021-04-19 16:00:51] Total Time: 1m35s
[STOP] [2021-04-19 16:00:51] overall_tsv_creation
[INFO] [2021-04-19 16:00:51] Done. Check your files:
[INFO] [2021-04-19 16:00:51] (1 lines) /app/public/data/daniels_et_al_da/publish_nodes.tsv
[INFO] [2021-04-19 16:00:51] (1 lines) /app/public/data/daniels_et_al_da/publish_scientific_names.tsv
[INFO] [2021-04-19 16:00:51] (2 lines) /app/public/data/daniels_et_al_da/publish_traits.tsv
[INFO] [2021-04-19 16:00:51] (2 lines) /app/public/data/daniels_et_al_da/publish_metadata.tsv
[STOP] [2021-04-19 16:00:51] complete_harvest_instance
[START] [2021-04-19 16:00:51] completed
[STOP] [2021-04-19 16:00:51] completed
[STOP] [2021-04-19 16:00:51] logged process, took 101.61
Latest Process