Harvest for Moore and Gibson 1985 Created 19 Apr 11:23

Stage: completed
Fetched: 19 Apr 11:23
Validated: 19 Apr 11:23
Deltas Created 19 Apr 11:23
Units Normalized: 19 Apr 11:23
Ancestry Built: 19 Apr 11:23
Nodes Matched: 19 Apr 11:23
Names Parsed: 19 Apr 11:23
New Models Stored: 19 Apr 11:23
Indexed: 19 Apr 11:23
Completed: 19 Apr 11:25
Time to Harvest: less than a minute
Harvesting Log

(442 lines)
# Logfile created on 2020-09-28 08:57:57 -0400 by logger.rb/v1.4.2
[START] [2020-09-28 08:57:57] logged process
[START] [2020-09-28 08:57:57] Creating resource from OpenData
[START] [2020-09-28 08:57:58] logged process
[START] [2020-09-28 08:57:58] Parse meta.xml file and create formats with fields
[STOP] [2020-09-28 08:57:58] Parse meta.xml file and create formats with fields
[STOP] [2020-09-28 08:57:58] Creating resource from OpenData
[INFO] [2020-12-04 08:03:14] ## HARVEST: type = -harvest
[START] [2020-12-04 08:03:17] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-04 08:03:17] create_harvest_instance
[STOP] [2020-12-04 08:03:18] create_harvest_instance
[START] [2020-12-04 08:03:18] fetch_files
[STOP] [2020-12-04 08:03:18] fetch_files
[START] [2020-12-04 08:03:18] validate_each_file
[STOP] [2020-12-04 08:03:18] validate_each_file
[START] [2020-12-04 08:03:18] convert_to_csv
[CMD] [2020-12-04 08:03:18] /usr/bin/sort /app/public/converted_csv/moore_gibson_moo_nodes_25061.csv > /app/public/converted_csv/moore_gibson_moo_nodes_25061.csv_sorted
[CMD] [2020-12-04 08:03:18] /usr/bin/sort /app/public/converted_csv/moore_gibson_moo_occurrences_25062.csv > /app/public/converted_csv/moore_gibson_moo_occurrences_25062.csv_sorted
[CMD] [2020-12-04 08:03:18] /usr/bin/sort /app/public/converted_csv/moore_gibson_moo_measurements_25063.csv > /app/public/converted_csv/moore_gibson_moo_measurements_25063.csv_sorted
[STOP] [2020-12-04 08:03:18] convert_to_csv
[START] [2020-12-04 08:03:19] calculate_delta
[CMD] [2020-12-04 08:03:19] echo "0a" > /app/public/diff/moore_gibson_moo_nodes_25061.diff
[CMD] [2020-12-04 08:03:19] tail -n +1 /app/public/converted_csv/moore_gibson_moo_nodes_25061.csv >> /app/public/diff/moore_gibson_moo_nodes_25061.diff
[CMD] [2020-12-04 08:03:19] echo "." >> /app/public/diff/moore_gibson_moo_nodes_25061.diff
[CMD] [2020-12-04 08:03:19] echo "0a" > /app/public/diff/moore_gibson_moo_occurrences_25062.diff
[CMD] [2020-12-04 08:03:19] tail -n +1 /app/public/converted_csv/moore_gibson_moo_occurrences_25062.csv >> /app/public/diff/moore_gibson_moo_occurrences_25062.diff
[CMD] [2020-12-04 08:03:19] echo "." >> /app/public/diff/moore_gibson_moo_occurrences_25062.diff
[CMD] [2020-12-04 08:03:19] echo "0a" > /app/public/diff/moore_gibson_moo_measurements_25063.diff
[CMD] [2020-12-04 08:03:19] tail -n +1 /app/public/converted_csv/moore_gibson_moo_measurements_25063.csv >> /app/public/diff/moore_gibson_moo_measurements_25063.diff
[CMD] [2020-12-04 08:03:19] echo "." >> /app/public/diff/moore_gibson_moo_measurements_25063.diff
[STOP] [2020-12-04 08:03:19] calculate_delta
[START] [2020-12-04 08:03:19] parse_diff_and_store
[INFO] [2020-12-04 08:03:19] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-04 08:03:19] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-04 08:03:19] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-04 08:03:19] Storing 23 ScientificNames
[INFO] [2020-12-04 08:03:19] Processing group of 23 in 1 groups of 1000
[INFO] [2020-12-04 08:03:20] Average Time: 0.04
[INFO] [2020-12-04 08:03:20] Total Time: 1s
[INFO] [2020-12-04 08:03:20] Storing 23 Nodes
[INFO] [2020-12-04 08:03:20] Processing group of 23 in 1 groups of 1000
[INFO] [2020-12-04 08:03:20] Average Time: 0.03
[INFO] [2020-12-04 08:03:20] Total Time: 1s
[INFO] [2020-12-04 08:03:20] Storing 23 Occurrences
[INFO] [2020-12-04 08:03:20] Processing group of 23 in 1 groups of 1000
[INFO] [2020-12-04 08:03:20] Average Time: 0.06
[INFO] [2020-12-04 08:03:20] Total Time: 1s
[INFO] [2020-12-04 08:03:20] Storing 26 Traits
[INFO] [2020-12-04 08:03:20] Processing group of 26 in 1 groups of 1000
[INFO] [2020-12-04 08:03:20] Average Time: 0.01
[INFO] [2020-12-04 08:03:20] Total Time: 1s
[INFO] [2020-12-04 08:03:20] Storing 23 MetaTraits
[INFO] [2020-12-04 08:03:20] Processing group of 23 in 1 groups of 1000
[INFO] [2020-12-04 08:03:20] Average Time: 0.0
[INFO] [2020-12-04 08:03:20] Total Time: 1s
[STOP] [2020-12-04 08:03:20] parse_diff_and_store
[START] [2020-12-04 08:03:20] resolve_keys
[INFO] [2020-12-04 08:03:25] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-04 08:03:25] traits to occurrences...
[INFO] [2020-12-04 08:03:25] traits to nodes (through occurrences)...
[INFO] [2020-12-04 08:03:25] Traits to sex term...
[INFO] [2020-12-04 08:03:25] Traits to lifestage term...
[INFO] [2020-12-04 08:03:25] MetaTraits to traits...
[INFO] [2020-12-04 08:03:25] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-04 08:03:25] Assocs to occurrences...
[INFO] [2020-12-04 08:03:25] Assocs to nodes...
[INFO] [2020-12-04 08:03:25] Assoc to sex term...
[INFO] [2020-12-04 08:03:25] Assoc to lifestage term...
[INFO] [2020-12-04 08:03:25] MetaAssoc to assocs...
[STOP] [2020-12-04 08:03:25] resolve_keys
[START] [2020-12-04 08:03:25] hold_for_later_1
[STOP] [2020-12-04 08:03:25] hold_for_later_1
[START] [2020-12-04 08:03:25] hold_for_later_2
[STOP] [2020-12-04 08:03:25] hold_for_later_2
[START] [2020-12-04 08:03:25] resolve_missing_parents
[STOP] [2020-12-04 08:03:25] resolve_missing_parents
[START] [2020-12-04 08:03:25] rebuild_nodes
[START] [2020-12-04 08:03:25] Flattener#flatten
[START] [2020-12-04 08:03:25] Flattener#study_resource
[START] [2020-12-04 08:03:26] Flattener#build_ancestry
[STOP] [2020-12-04 08:03:26] Flattener#build_ancestry
[INFO] [2020-12-04 08:03:26] 23 ancestry keys
[START] [2020-12-04 08:03:26] build_node_ancestors
[INFO] [2020-12-04 08:03:26] old ancestors deleted.
[STOP] [2020-12-04 08:03:26] build_node_ancestors
[WARN] [2020-12-04 08:03:26] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-04 08:03:26] Flattener#flatten
[STOP] [2020-12-04 08:03:26] rebuild_nodes
[START] [2020-12-04 08:03:26] resolve_missing_media_owners
[STOP] [2020-12-04 08:03:26] resolve_missing_media_owners
[START] [2020-12-04 08:03:26] sanitize_media_verbatims
[STOP] [2020-12-04 08:03:26] sanitize_media_verbatims
[START] [2020-12-04 08:03:26] queue_downloads
[STOP] [2020-12-04 08:03:26] queue_downloads
[START] [2020-12-04 08:03:26] parse_names
[WARN] [2020-12-04 08:03:26] I see 23 names which still need to be parsed.
[WARN] [2020-12-04 08:03:27] I see 4 names which still need to be parsed.
[STOP] [2020-12-04 08:03:28] parse_names
[START] [2020-12-04 08:03:28] denormalize_canonical_names_to_nodes
[STOP] [2020-12-04 08:03:28] denormalize_canonical_names_to_nodes
[START] [2020-12-04 08:03:28] match_nodes
[START] [2020-12-04 08:03:28] map_all_nodes_to_pages
[STOP] [2020-12-04 08:03:28] map_all_nodes_to_pages
[INFO] [2020-12-04 08:03:28] ZERO unmatched nodes (of 23)! Nicely done.
[START] [2020-12-04 08:03:28] update_nodes
[STOP] [2020-12-04 08:03:28] update_nodes
[STOP] [2020-12-04 08:03:28] match_nodes
[START] [2020-12-04 08:03:28] reindex_search
[STOP] [2020-12-04 08:03:28] reindex_search
[START] [2020-12-04 08:03:28] normalize_units
[STOP] [2020-12-04 08:03:28] normalize_units
[START] [2020-12-04 08:03:28] calculate_statistics
[2020-12-04 08:03:28] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-04 08:03:28] calculate_statistics
[START] [2020-12-04 08:03:28] complete_harvest_instance
[START] [2020-12-04 08:03:28] overall_tsv_creation
[INFO] [2020-12-04 08:03:28] Processing group of 23 in 1 batches of 10000
[INFO] [2020-12-04 08:05:55] 23 Traits (unfiltered)...
[INFO] [2020-12-04 08:06:32] 23 Traits (filtered)...
[INFO] [2020-12-04 08:06:32] 0 Associations (filtered)...
[INFO] [2020-12-04 08:06:32] 26 metadata added.
[INFO] [2020-12-04 08:06:32] 0 metadata added.
[INFO] [2020-12-04 08:06:32] Average Time: 54.68
[INFO] [2020-12-04 08:06:32] Total Time: 3m5s
[STOP] [2020-12-04 08:06:32] overall_tsv_creation
[INFO] [2020-12-04 08:06:32] Done. Check your files:
[INFO] [2020-12-04 08:06:32] (19 lines) /app/public/data/moore_gibson_moo/publish_nodes.tsv
[INFO] [2020-12-04 08:06:32] (23 lines) /app/public/data/moore_gibson_moo/publish_scientific_names.tsv
[INFO] [2020-12-04 08:06:32] (24 lines) /app/public/data/moore_gibson_moo/publish_traits.tsv
[INFO] [2020-12-04 08:06:32] (27 lines) /app/public/data/moore_gibson_moo/publish_metadata.tsv
[STOP] [2020-12-04 08:06:32] complete_harvest_instance
[START] [2020-12-04 08:06:32] completed
[STOP] [2020-12-04 08:06:32] completed
[STOP] [2020-12-04 08:06:32] logged process, took 195.34
[INFO] [2021-04-19 11:19:28] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 11:23:31] ## remove_type: ScientificName
[INFO] [2021-04-19 11:23:31] ++ Calling delete_all on 23 instances...
[INFO] [2021-04-19 11:23:31] [11:23:31.312] Removed 23 Scientificnames
[INFO] [2021-04-19 11:23:31] ## remove_type: Vernacular
[INFO] [2021-04-19 11:23:31] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:23:31] [11:23:31.313] Removed 0 Vernaculars
[INFO] [2021-04-19 11:23:31] ## remove_type: Article
[INFO] [2021-04-19 11:23:31] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:23:31] [11:23:31.315] Removed 0 Articles
[INFO] [2021-04-19 11:23:31] ## remove_type: Medium
[INFO] [2021-04-19 11:23:31] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:23:31] [11:23:31.317] Removed 0 Media
[INFO] [2021-04-19 11:23:31] ## remove_type: Trait
[INFO] [2021-04-19 11:23:31] ++ Calling delete_all on 26 instances...
[INFO] [2021-04-19 11:23:31] [11:23:31.319] Removed 26 Traits
[INFO] [2021-04-19 11:23:31] ## remove_type: MetaTrait
[INFO] [2021-04-19 11:23:31] ++ Calling delete_all on 23 instances...
[INFO] [2021-04-19 11:23:31] [11:23:31.322] Removed 23 Metatraits
[INFO] [2021-04-19 11:23:31] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 11:23:31] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:23:31] [11:23:31.323] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 11:23:31] ## remove_type: Assoc
[INFO] [2021-04-19 11:23:31] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:23:31] [11:23:31.325] Removed 0 Assocs
[INFO] [2021-04-19 11:23:31] ## remove_type: MetaAssoc
[INFO] [2021-04-19 11:23:31] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:23:31] [11:23:31.326] Removed 0 Metaassocs
[INFO] [2021-04-19 11:23:31] ## remove_type: Identifier
[INFO] [2021-04-19 11:23:31] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:23:31] [11:23:31.328] Removed 0 Identifiers
[INFO] [2021-04-19 11:23:31] ## remove_type: Reference
[INFO] [2021-04-19 11:23:31] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:23:31] [11:23:31.329] Removed 0 References
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
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[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
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[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
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[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
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[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
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[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
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[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
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[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
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[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
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[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:31] Starting batch with ID 86116330...
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[INFO] [2021-04-19 11:23:32] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:32] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:32] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:32] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:32] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:32] Starting batch with ID 86116330...
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[INFO] [2021-04-19 11:23:32] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:32] Starting batch with ID 86116330...
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[INFO] [2021-04-19 11:23:32] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:32] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:32] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:32] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:32] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:32] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:32] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:32] Starting batch with ID 86116330...
[INFO] [2021-04-19 11:23:32] ## remove_type: Node
[INFO] [2021-04-19 11:23:32] ++ Calling delete_all on 23 instances...
[INFO] [2021-04-19 11:23:32] [11:23:32.353] Removed 23 Nodes
[START] [2021-04-19 11:23:32] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 11:23:32] Creating resource from OpenData
[START] [2021-04-19 11:23:33] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 11:23:33] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 11:23:37] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 11:23:37] Creating resource from OpenData
[START] [2021-04-19 11:23:37] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 11:23:37] create_harvest_instance
[INFO] [2021-04-19 11:23:37] Created harvest instance #3737
[STOP] [2021-04-19 11:23:37] create_harvest_instance
[START] [2021-04-19 11:23:37] fetch_files
[STOP] [2021-04-19 11:23:37] fetch_files
[START] [2021-04-19 11:23:37] validate_each_file
[INFO] [2021-04-19 11:23:37] Looping over 3 formats...
[INFO] [2021-04-19 11:23:37] ...nodes (/app/public/data/moore_gibson_moo/taxa.txt)
[INFO] [2021-04-19 11:23:37] Valid: /app/public/converted_csv/moore_gibson_moo_nodes_3737.csv (23 lines)
[INFO] [2021-04-19 11:23:37] ...occurrences (/app/public/data/moore_gibson_moo/occurrences.txt)
[INFO] [2021-04-19 11:23:37] Valid: /app/public/converted_csv/moore_gibson_moo_occurrences_3737.csv (23 lines)
[INFO] [2021-04-19 11:23:37] ...measurements (/app/public/data/moore_gibson_moo/measurementsorfacts.txt)
[INFO] [2021-04-19 11:23:37] Valid: /app/public/converted_csv/moore_gibson_moo_measurements_3737.csv (26 lines)
[STOP] [2021-04-19 11:23:37] validate_each_file
[START] [2021-04-19 11:23:37] convert_to_csv
[INFO] [2021-04-19 11:23:37] Looping over 3 formats...
[INFO] [2021-04-19 11:23:37] ...nodes (/app/public/data/moore_gibson_moo/taxa.txt)
[CMD] [2021-04-19 11:23:37] /usr/bin/sort /app/public/converted_csv/moore_gibson_moo_nodes_3737.csv > /app/public/converted_csv/moore_gibson_moo_nodes_3737.csv_sorted
[INFO] [2021-04-19 11:23:38] Converted: /app/public/converted_csv/moore_gibson_moo_nodes_3737.csv (23 lines)
[INFO] [2021-04-19 11:23:38] ...occurrences (/app/public/data/moore_gibson_moo/occurrences.txt)
[CMD] [2021-04-19 11:23:38] /usr/bin/sort /app/public/converted_csv/moore_gibson_moo_occurrences_3737.csv > /app/public/converted_csv/moore_gibson_moo_occurrences_3737.csv_sorted
[INFO] [2021-04-19 11:23:38] Converted: /app/public/converted_csv/moore_gibson_moo_occurrences_3737.csv (23 lines)
[INFO] [2021-04-19 11:23:38] ...measurements (/app/public/data/moore_gibson_moo/measurementsorfacts.txt)
[CMD] [2021-04-19 11:23:38] /usr/bin/sort /app/public/converted_csv/moore_gibson_moo_measurements_3737.csv > /app/public/converted_csv/moore_gibson_moo_measurements_3737.csv_sorted
[INFO] [2021-04-19 11:23:39] Converted: /app/public/converted_csv/moore_gibson_moo_measurements_3737.csv (26 lines)
[STOP] [2021-04-19 11:23:39] convert_to_csv
[START] [2021-04-19 11:23:39] calculate_delta
[INFO] [2021-04-19 11:23:39] Looping over 3 formats...
[INFO] [2021-04-19 11:23:39] ...nodes (/app/public/data/moore_gibson_moo/taxa.txt)
[CMD] [2021-04-19 11:23:39] echo "0a" > /app/public/diff/moore_gibson_moo_nodes_3737.diff
[CMD] [2021-04-19 11:23:39] tail -n +1 /app/public/converted_csv/moore_gibson_moo_nodes_3737.csv >> /app/public/diff/moore_gibson_moo_nodes_3737.diff
[CMD] [2021-04-19 11:23:39] echo "." >> /app/public/diff/moore_gibson_moo_nodes_3737.diff
[INFO] [2021-04-19 11:23:40] Created diff: /app/public/diff/moore_gibson_moo_nodes_3737.diff (25 lines)
[INFO] [2021-04-19 11:23:40] ...occurrences (/app/public/data/moore_gibson_moo/occurrences.txt)
[CMD] [2021-04-19 11:23:40] echo "0a" > /app/public/diff/moore_gibson_moo_occurrences_3737.diff
[CMD] [2021-04-19 11:23:40] tail -n +1 /app/public/converted_csv/moore_gibson_moo_occurrences_3737.csv >> /app/public/diff/moore_gibson_moo_occurrences_3737.diff
[CMD] [2021-04-19 11:23:40] echo "." >> /app/public/diff/moore_gibson_moo_occurrences_3737.diff
[INFO] [2021-04-19 11:23:41] Created diff: /app/public/diff/moore_gibson_moo_occurrences_3737.diff (25 lines)
[INFO] [2021-04-19 11:23:41] ...measurements (/app/public/data/moore_gibson_moo/measurementsorfacts.txt)
[CMD] [2021-04-19 11:23:41] echo "0a" > /app/public/diff/moore_gibson_moo_measurements_3737.diff
[CMD] [2021-04-19 11:23:41] tail -n +1 /app/public/converted_csv/moore_gibson_moo_measurements_3737.csv >> /app/public/diff/moore_gibson_moo_measurements_3737.diff
[CMD] [2021-04-19 11:23:42] echo "." >> /app/public/diff/moore_gibson_moo_measurements_3737.diff
[INFO] [2021-04-19 11:23:42] Created diff: /app/public/diff/moore_gibson_moo_measurements_3737.diff (28 lines)
[STOP] [2021-04-19 11:23:42] calculate_delta
[START] [2021-04-19 11:23:42] parse_diff_and_store
[INFO] [2021-04-19 11:23:42] Handling diff: /app/public/diff/moore_gibson_moo_nodes_3737.diff (25 lines)
[INFO] [2021-04-19 11:23:42] Loading nodes diff file into memory (25 /app/public/diff/moore_gibson_moo_nodes_3737.diff lines)...
[INFO] [2021-04-19 11:23:43] Handling diff: /app/public/diff/moore_gibson_moo_occurrences_3737.diff (25 lines)
[INFO] [2021-04-19 11:23:43] Loading occurrences diff file into memory (25 /app/public/diff/moore_gibson_moo_occurrences_3737.diff lines)...
[INFO] [2021-04-19 11:23:44] Handling diff: /app/public/diff/moore_gibson_moo_measurements_3737.diff (28 lines)
[INFO] [2021-04-19 11:23:44] Loading measurements diff file into memory (28 /app/public/diff/moore_gibson_moo_measurements_3737.diff lines)...
[INFO] [2021-04-19 11:23:44] Storing 23 ScientificNames
[INFO] [2021-04-19 11:23:44] Processing group of 23 in 1 groups of 1000
[INFO] [2021-04-19 11:23:44] Average Time: 0.01
[INFO] [2021-04-19 11:23:44] Total Time: 1s
[INFO] [2021-04-19 11:23:44] Storing 23 Nodes
[INFO] [2021-04-19 11:23:44] Processing group of 23 in 1 groups of 1000
[INFO] [2021-04-19 11:23:44] Average Time: 0.01
[INFO] [2021-04-19 11:23:44] Total Time: 1s
[INFO] [2021-04-19 11:23:44] Storing 23 Occurrences
[INFO] [2021-04-19 11:23:44] Processing group of 23 in 1 groups of 1000
[INFO] [2021-04-19 11:23:44] Average Time: 0.0
[INFO] [2021-04-19 11:23:44] Total Time: 1s
[INFO] [2021-04-19 11:23:44] Storing 26 Traits
[INFO] [2021-04-19 11:23:44] Processing group of 26 in 1 groups of 1000
[INFO] [2021-04-19 11:23:44] Average Time: 0.01
[INFO] [2021-04-19 11:23:44] Total Time: 1s
[INFO] [2021-04-19 11:23:44] Storing 23 MetaTraits
[INFO] [2021-04-19 11:23:44] Processing group of 23 in 1 groups of 1000
[INFO] [2021-04-19 11:23:44] Average Time: 0.0
[INFO] [2021-04-19 11:23:44] Total Time: 1s
[STOP] [2021-04-19 11:23:44] parse_diff_and_store
[START] [2021-04-19 11:23:44] resolve_keys
[INFO] [2021-04-19 11:23:50] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 11:23:50] traits to occurrences...
[INFO] [2021-04-19 11:23:50] traits to nodes (through occurrences)...
[INFO] [2021-04-19 11:23:50] Traits to sex term...
[INFO] [2021-04-19 11:23:50] Traits to lifestage term...
[INFO] [2021-04-19 11:23:50] MetaTraits to traits...
[INFO] [2021-04-19 11:23:50] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 11:23:50] Assocs to occurrences...
[INFO] [2021-04-19 11:23:50] Assocs to nodes...
[INFO] [2021-04-19 11:23:50] Assoc to sex term...
[INFO] [2021-04-19 11:23:50] Assoc to lifestage term...
[INFO] [2021-04-19 11:23:50] MetaAssoc to assocs...
[STOP] [2021-04-19 11:23:50] resolve_keys
[START] [2021-04-19 11:23:50] hold_for_later_1
[STOP] [2021-04-19 11:23:50] hold_for_later_1
[START] [2021-04-19 11:23:50] hold_for_later_2
[STOP] [2021-04-19 11:23:50] hold_for_later_2
[START] [2021-04-19 11:23:50] resolve_missing_parents
[STOP] [2021-04-19 11:23:50] resolve_missing_parents
[START] [2021-04-19 11:23:51] rebuild_nodes
[START] [2021-04-19 11:23:51] Flattener#flatten
[START] [2021-04-19 11:23:51] Flattener#study_resource
[START] [2021-04-19 11:23:51] Flattener#build_ancestry
[STOP] [2021-04-19 11:23:51] Flattener#build_ancestry
[INFO] [2021-04-19 11:23:51] 23 ancestry keys
[START] [2021-04-19 11:23:51] build_node_ancestors
[INFO] [2021-04-19 11:23:51] old ancestors deleted.
[STOP] [2021-04-19 11:23:51] build_node_ancestors
[WARN] [2021-04-19 11:23:51] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 11:23:51] Flattener#flatten
[STOP] [2021-04-19 11:23:51] rebuild_nodes
[START] [2021-04-19 11:23:51] resolve_missing_media_owners
[STOP] [2021-04-19 11:23:51] resolve_missing_media_owners
[START] [2021-04-19 11:23:51] sanitize_media_verbatims
[STOP] [2021-04-19 11:23:51] sanitize_media_verbatims
[START] [2021-04-19 11:23:51] queue_downloads
[STOP] [2021-04-19 11:23:51] queue_downloads
[START] [2021-04-19 11:23:51] parse_names
[WARN] [2021-04-19 11:23:51] I see 23 names which still need to be parsed.
[WARN] [2021-04-19 11:23:52] I see 4 names which still need to be parsed.
[STOP] [2021-04-19 11:23:53] parse_names
[START] [2021-04-19 11:23:53] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 11:23:53] denormalize_canonical_names_to_nodes
[START] [2021-04-19 11:23:53] match_nodes
[START] [2021-04-19 11:23:53] map_all_nodes_to_pages
[STOP] [2021-04-19 11:23:53] map_all_nodes_to_pages
[INFO] [2021-04-19 11:23:53] ZERO unmatched nodes (of 23)! Nicely done.
[START] [2021-04-19 11:23:53] update_nodes
[STOP] [2021-04-19 11:23:53] update_nodes
[STOP] [2021-04-19 11:23:53] match_nodes
[START] [2021-04-19 11:23:53] reindex_search
[STOP] [2021-04-19 11:23:53] reindex_search
[START] [2021-04-19 11:23:53] normalize_units
[STOP] [2021-04-19 11:23:53] normalize_units
[START] [2021-04-19 11:23:53] calculate_statistics
[2021-04-19 11:23:53] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 11:23:53] calculate_statistics
[START] [2021-04-19 11:23:53] complete_harvest_instance
[START] [2021-04-19 11:23:53] overall_tsv_creation
[INFO] [2021-04-19 11:23:53] Processing group of 23 in 1 batches of 10000
[INFO] [2021-04-19 11:24:29] 23 Traits (unfiltered)...
[INFO] [2021-04-19 11:25:03] 23 Traits (filtered)...
[INFO] [2021-04-19 11:25:03] 0 Associations (filtered)...
[INFO] [2021-04-19 11:25:03] 3 metadata added.
[INFO] [2021-04-19 11:25:03] 0 metadata added.
[INFO] [2021-04-19 11:25:30] Average Time: 72.23
[INFO] [2021-04-19 11:25:30] Total Time: 1m37s
[STOP] [2021-04-19 11:25:30] overall_tsv_creation
[INFO] [2021-04-19 11:25:30] Done. Check your files:
[INFO] [2021-04-19 11:25:30] (19 lines) /app/public/data/moore_gibson_moo/publish_nodes.tsv
[INFO] [2021-04-19 11:25:30] (23 lines) /app/public/data/moore_gibson_moo/publish_scientific_names.tsv
[INFO] [2021-04-19 11:25:31] (24 lines) /app/public/data/moore_gibson_moo/publish_traits.tsv
[INFO] [2021-04-19 11:25:31] (4 lines) /app/public/data/moore_gibson_moo/publish_metadata.tsv
[STOP] [2021-04-19 11:25:31] complete_harvest_instance
[START] [2021-04-19 11:25:31] completed
[STOP] [2021-04-19 11:25:31] completed
[STOP] [2021-04-19 11:25:31] logged process, took 114.14
Latest Process

19 Apr 11:23 EXITED currently processing 0