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Harvest for Moore and Gibson 1981 Created 19 Apr 16:51

Stage: completed
Fetched: 19 Apr 16:51
Validated: 19 Apr 16:51
Deltas Created 19 Apr 16:51
Units Normalized: 19 Apr 16:51
Ancestry Built: 19 Apr 16:51
Nodes Matched: 19 Apr 16:51
Names Parsed: 19 Apr 16:51
New Models Stored: 19 Apr 16:51
Indexed: 19 Apr 16:51
Completed: 19 Apr 16:52
Time to Harvest: less than a minute

Harvesting Log

(358 lines) 
# Logfile created on 2020-09-28 08:58:46 -0400 by logger.rb/v1.4.2
[START] [2020-09-28 08:58:46] logged process
[START] [2020-09-28 08:58:46] Creating resource from OpenData
[START] [2020-09-28 08:58:46] logged process
[START] [2020-09-28 08:58:46] Parse meta.xml file and create formats with fields
[STOP] [2020-09-28 08:58:46] Parse meta.xml file and create formats with fields
[STOP] [2020-09-28 08:58:46] Creating resource from OpenData
[INFO] [2020-12-04 08:08:08] ## HARVEST: type = -harvest
[START] [2020-12-04 08:08:12] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-04 08:08:12] create_harvest_instance
[STOP] [2020-12-04 08:08:13] create_harvest_instance
[START] [2020-12-04 08:08:13] fetch_files
[STOP] [2020-12-04 08:08:13] fetch_files
[START] [2020-12-04 08:08:13] validate_each_file
[STOP] [2020-12-04 08:08:14] validate_each_file
[START] [2020-12-04 08:08:14] convert_to_csv
[CMD] [2020-12-04 08:08:14] /usr/bin/sort /app/public/converted_csv/moore_gibson_mo2_nodes_25064.csv > /app/public/converted_csv/moore_gibson_mo2_nodes_25064.csv_sorted
[CMD] [2020-12-04 08:08:14] /usr/bin/sort /app/public/converted_csv/moore_gibson_mo2_occurrences_25065.csv > /app/public/converted_csv/moore_gibson_mo2_occurrences_25065.csv_sorted
[CMD] [2020-12-04 08:08:14] /usr/bin/sort /app/public/converted_csv/moore_gibson_mo2_measurements_25066.csv > /app/public/converted_csv/moore_gibson_mo2_measurements_25066.csv_sorted
[STOP] [2020-12-04 08:08:14] convert_to_csv
[START] [2020-12-04 08:08:14] calculate_delta
[CMD] [2020-12-04 08:08:14] echo "0a" > /app/public/diff/moore_gibson_mo2_nodes_25064.diff
[CMD] [2020-12-04 08:08:14] tail -n +1 /app/public/converted_csv/moore_gibson_mo2_nodes_25064.csv >> /app/public/diff/moore_gibson_mo2_nodes_25064.diff
[CMD] [2020-12-04 08:08:14] echo "." >> /app/public/diff/moore_gibson_mo2_nodes_25064.diff
[CMD] [2020-12-04 08:08:14] echo "0a" > /app/public/diff/moore_gibson_mo2_occurrences_25065.diff
[CMD] [2020-12-04 08:08:14] tail -n +1 /app/public/converted_csv/moore_gibson_mo2_occurrences_25065.csv >> /app/public/diff/moore_gibson_mo2_occurrences_25065.diff
[CMD] [2020-12-04 08:08:14] echo "." >> /app/public/diff/moore_gibson_mo2_occurrences_25065.diff
[CMD] [2020-12-04 08:08:14] echo "0a" > /app/public/diff/moore_gibson_mo2_measurements_25066.diff
[CMD] [2020-12-04 08:08:14] tail -n +1 /app/public/converted_csv/moore_gibson_mo2_measurements_25066.csv >> /app/public/diff/moore_gibson_mo2_measurements_25066.diff
[CMD] [2020-12-04 08:08:14] echo "." >> /app/public/diff/moore_gibson_mo2_measurements_25066.diff
[STOP] [2020-12-04 08:08:14] calculate_delta
[START] [2020-12-04 08:08:14] parse_diff_and_store
[INFO] [2020-12-04 08:08:14] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-04 08:08:14] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-04 08:08:14] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-04 08:08:15] Storing 3 ScientificNames
[INFO] [2020-12-04 08:08:15] Processing group of 3 in 1 groups of 1000
[INFO] [2020-12-04 08:08:15] Average Time: 0.0
[INFO] [2020-12-04 08:08:15] Total Time: 1s
[INFO] [2020-12-04 08:08:15] Storing 3 Nodes
[INFO] [2020-12-04 08:08:15] Processing group of 3 in 1 groups of 1000
[INFO] [2020-12-04 08:08:15] Average Time: 0.02
[INFO] [2020-12-04 08:08:15] Total Time: 1s
[INFO] [2020-12-04 08:08:15] Storing 3 Occurrences
[INFO] [2020-12-04 08:08:15] Processing group of 3 in 1 groups of 1000
[INFO] [2020-12-04 08:08:15] Average Time: 0.0
[INFO] [2020-12-04 08:08:15] Total Time: 1s
[INFO] [2020-12-04 08:08:15] Storing 4 Traits
[INFO] [2020-12-04 08:08:15] Processing group of 4 in 1 groups of 1000
[INFO] [2020-12-04 08:08:15] Average Time: 0.0
[INFO] [2020-12-04 08:08:15] Total Time: 1s
[INFO] [2020-12-04 08:08:15] Storing 3 MetaTraits
[INFO] [2020-12-04 08:08:15] Processing group of 3 in 1 groups of 1000
[INFO] [2020-12-04 08:08:15] Average Time: 0.0
[INFO] [2020-12-04 08:08:15] Total Time: 1s
[STOP] [2020-12-04 08:08:15] parse_diff_and_store
[START] [2020-12-04 08:08:15] resolve_keys
[INFO] [2020-12-04 08:08:20] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-04 08:08:20] traits to occurrences...
[INFO] [2020-12-04 08:08:20] traits to nodes (through occurrences)...
[INFO] [2020-12-04 08:08:20] Traits to sex term...
[INFO] [2020-12-04 08:08:20] Traits to lifestage term...
[INFO] [2020-12-04 08:08:20] MetaTraits to traits...
[INFO] [2020-12-04 08:08:20] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-04 08:08:20] Assocs to occurrences...
[INFO] [2020-12-04 08:08:20] Assocs to nodes...
[INFO] [2020-12-04 08:08:20] Assoc to sex term...
[INFO] [2020-12-04 08:08:20] Assoc to lifestage term...
[INFO] [2020-12-04 08:08:20] MetaAssoc to assocs...
[STOP] [2020-12-04 08:08:20] resolve_keys
[START] [2020-12-04 08:08:20] hold_for_later_1
[STOP] [2020-12-04 08:08:20] hold_for_later_1
[START] [2020-12-04 08:08:20] hold_for_later_2
[STOP] [2020-12-04 08:08:20] hold_for_later_2
[START] [2020-12-04 08:08:20] resolve_missing_parents
[STOP] [2020-12-04 08:08:20] resolve_missing_parents
[START] [2020-12-04 08:08:20] rebuild_nodes
[START] [2020-12-04 08:08:20] Flattener#flatten
[START] [2020-12-04 08:08:20] Flattener#study_resource
[START] [2020-12-04 08:08:20] Flattener#build_ancestry
[STOP] [2020-12-04 08:08:20] Flattener#build_ancestry
[INFO] [2020-12-04 08:08:20] 3 ancestry keys
[START] [2020-12-04 08:08:20] build_node_ancestors
[INFO] [2020-12-04 08:08:20] old ancestors deleted.
[STOP] [2020-12-04 08:08:20] build_node_ancestors
[WARN] [2020-12-04 08:08:20] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-04 08:08:20] Flattener#flatten
[STOP] [2020-12-04 08:08:20] rebuild_nodes
[START] [2020-12-04 08:08:20] resolve_missing_media_owners
[STOP] [2020-12-04 08:08:20] resolve_missing_media_owners
[START] [2020-12-04 08:08:20] sanitize_media_verbatims
[STOP] [2020-12-04 08:08:20] sanitize_media_verbatims
[START] [2020-12-04 08:08:20] queue_downloads
[STOP] [2020-12-04 08:08:20] queue_downloads
[START] [2020-12-04 08:08:20] parse_names
[WARN] [2020-12-04 08:08:20] I see 3 names which still need to be parsed.
[STOP] [2020-12-04 08:08:21] parse_names
[START] [2020-12-04 08:08:21] denormalize_canonical_names_to_nodes
[STOP] [2020-12-04 08:08:21] denormalize_canonical_names_to_nodes
[START] [2020-12-04 08:08:21] match_nodes
[START] [2020-12-04 08:08:21] map_all_nodes_to_pages
[STOP] [2020-12-04 08:08:21] map_all_nodes_to_pages
[INFO] [2020-12-04 08:08:21] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2020-12-04 08:08:21] update_nodes
[STOP] [2020-12-04 08:08:21] update_nodes
[STOP] [2020-12-04 08:08:21] match_nodes
[START] [2020-12-04 08:08:21] reindex_search
[STOP] [2020-12-04 08:08:21] reindex_search
[START] [2020-12-04 08:08:22] normalize_units
[STOP] [2020-12-04 08:08:22] normalize_units
[START] [2020-12-04 08:08:22] calculate_statistics
[2020-12-04 08:08:22] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-04 08:08:22] calculate_statistics
[START] [2020-12-04 08:08:22] complete_harvest_instance
[START] [2020-12-04 08:08:22] overall_tsv_creation
[INFO] [2020-12-04 08:08:22] Processing group of 3 in 1 batches of 10000
[INFO] [2020-12-04 08:09:24] 3 Traits (unfiltered)...
[INFO] [2020-12-04 08:10:02] 3 Traits (filtered)...
[INFO] [2020-12-04 08:10:02] 0 Associations (filtered)...
[INFO] [2020-12-04 08:10:02] 4 metadata added.
[INFO] [2020-12-04 08:10:02] 0 metadata added.
[INFO] [2020-12-04 08:10:02] Average Time: 61.21
[INFO] [2020-12-04 08:10:02] Total Time: 1m41s
[STOP] [2020-12-04 08:10:02] overall_tsv_creation
[INFO] [2020-12-04 08:10:02] Done. Check your files:
[INFO] [2020-12-04 08:10:02] (3 lines) /app/public/data/moore_gibson_mo2/publish_nodes.tsv
[INFO] [2020-12-04 08:10:02] (3 lines) /app/public/data/moore_gibson_mo2/publish_scientific_names.tsv
[INFO] [2020-12-04 08:10:02] (4 lines) /app/public/data/moore_gibson_mo2/publish_traits.tsv
[INFO] [2020-12-04 08:10:02] (5 lines) /app/public/data/moore_gibson_mo2/publish_metadata.tsv
[STOP] [2020-12-04 08:10:02] complete_harvest_instance
[START] [2020-12-04 08:10:02] completed
[STOP] [2020-12-04 08:10:02] completed
[STOP] [2020-12-04 08:10:02] logged process, took 110.02
[INFO] [2021-04-19 16:47:29] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 16:51:12] ## remove_type: ScientificName
[INFO] [2021-04-19 16:51:12] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 16:51:12] [16:51:12.934] Removed 3 Scientificnames
[INFO] [2021-04-19 16:51:12] ## remove_type: Vernacular
[INFO] [2021-04-19 16:51:12] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:51:12] [16:51:12.935] Removed 0 Vernaculars
[INFO] [2021-04-19 16:51:12] ## remove_type: Article
[INFO] [2021-04-19 16:51:12] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:51:12] [16:51:12.936] Removed 0 Articles
[INFO] [2021-04-19 16:51:12] ## remove_type: Medium
[INFO] [2021-04-19 16:51:12] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:51:12] [16:51:12.938] Removed 0 Media
[INFO] [2021-04-19 16:51:12] ## remove_type: Trait
[INFO] [2021-04-19 16:51:12] ++ Calling delete_all on 4 instances...
[INFO] [2021-04-19 16:51:12] [16:51:12.940] Removed 4 Traits
[INFO] [2021-04-19 16:51:12] ## remove_type: MetaTrait
[INFO] [2021-04-19 16:51:12] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 16:51:12] [16:51:12.942] Removed 3 Metatraits
[INFO] [2021-04-19 16:51:12] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 16:51:12] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:51:12] [16:51:12.944] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 16:51:12] ## remove_type: Assoc
[INFO] [2021-04-19 16:51:12] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:51:12] [16:51:12.945] Removed 0 Assocs
[INFO] [2021-04-19 16:51:12] ## remove_type: MetaAssoc
[INFO] [2021-04-19 16:51:12] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:51:12] [16:51:12.947] Removed 0 Metaassocs
[INFO] [2021-04-19 16:51:12] ## remove_type: Identifier
[INFO] [2021-04-19 16:51:12] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:51:12] [16:51:12.949] Removed 0 Identifiers
[INFO] [2021-04-19 16:51:12] ## remove_type: Reference
[INFO] [2021-04-19 16:51:12] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:51:12] [16:51:12.950] Removed 0 References
[INFO] [2021-04-19 16:51:12] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:12] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:12] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:12] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:12] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:12] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116348...
[INFO] [2021-04-19 16:51:13] Starting batch with ID 86116347...
[INFO] [2021-04-19 16:51:13] ## remove_type: Node
[INFO] [2021-04-19 16:51:13] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 16:51:13] [16:51:13.176] Removed 3 Nodes
[START] [2021-04-19 16:51:13] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:51:13] Creating resource from OpenData
[START] [2021-04-19 16:51:13] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:51:13] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:51:13] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:51:13] Creating resource from OpenData
[START] [2021-04-19 16:51:13] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:51:13] create_harvest_instance
[INFO] [2021-04-19 16:51:13] Created harvest instance #3807
[STOP] [2021-04-19 16:51:13] create_harvest_instance
[START] [2021-04-19 16:51:13] fetch_files
[STOP] [2021-04-19 16:51:13] fetch_files
[START] [2021-04-19 16:51:13] validate_each_file
[INFO] [2021-04-19 16:51:13] Looping over 3 formats...
[INFO] [2021-04-19 16:51:13] ...nodes (/app/public/data/moore_gibson_mo2/taxa.txt)
[INFO] [2021-04-19 16:51:13] Valid: /app/public/converted_csv/moore_gibson_mo2_nodes_3807.csv (3 lines)
[INFO] [2021-04-19 16:51:13] ...occurrences (/app/public/data/moore_gibson_mo2/occurrences.txt)
[INFO] [2021-04-19 16:51:13] Valid: /app/public/converted_csv/moore_gibson_mo2_occurrences_3807.csv (3 lines)
[INFO] [2021-04-19 16:51:13] ...measurements (/app/public/data/moore_gibson_mo2/measurementsorfacts.txt)
[INFO] [2021-04-19 16:51:13] Valid: /app/public/converted_csv/moore_gibson_mo2_measurements_3807.csv (4 lines)
[STOP] [2021-04-19 16:51:13] validate_each_file
[START] [2021-04-19 16:51:13] convert_to_csv
[INFO] [2021-04-19 16:51:13] Looping over 3 formats...
[INFO] [2021-04-19 16:51:13] ...nodes (/app/public/data/moore_gibson_mo2/taxa.txt)
[CMD] [2021-04-19 16:51:13] /usr/bin/sort /app/public/converted_csv/moore_gibson_mo2_nodes_3807.csv > /app/public/converted_csv/moore_gibson_mo2_nodes_3807.csv_sorted
[INFO] [2021-04-19 16:51:13] Converted: /app/public/converted_csv/moore_gibson_mo2_nodes_3807.csv (3 lines)
[INFO] [2021-04-19 16:51:13] ...occurrences (/app/public/data/moore_gibson_mo2/occurrences.txt)
[CMD] [2021-04-19 16:51:13] /usr/bin/sort /app/public/converted_csv/moore_gibson_mo2_occurrences_3807.csv > /app/public/converted_csv/moore_gibson_mo2_occurrences_3807.csv_sorted
[INFO] [2021-04-19 16:51:13] Converted: /app/public/converted_csv/moore_gibson_mo2_occurrences_3807.csv (3 lines)
[INFO] [2021-04-19 16:51:13] ...measurements (/app/public/data/moore_gibson_mo2/measurementsorfacts.txt)
[CMD] [2021-04-19 16:51:13] /usr/bin/sort /app/public/converted_csv/moore_gibson_mo2_measurements_3807.csv > /app/public/converted_csv/moore_gibson_mo2_measurements_3807.csv_sorted
[INFO] [2021-04-19 16:51:13] Converted: /app/public/converted_csv/moore_gibson_mo2_measurements_3807.csv (4 lines)
[STOP] [2021-04-19 16:51:13] convert_to_csv
[START] [2021-04-19 16:51:13] calculate_delta
[INFO] [2021-04-19 16:51:13] Looping over 3 formats...
[INFO] [2021-04-19 16:51:13] ...nodes (/app/public/data/moore_gibson_mo2/taxa.txt)
[CMD] [2021-04-19 16:51:13] echo "0a" > /app/public/diff/moore_gibson_mo2_nodes_3807.diff
[CMD] [2021-04-19 16:51:13] tail -n +1 /app/public/converted_csv/moore_gibson_mo2_nodes_3807.csv >> /app/public/diff/moore_gibson_mo2_nodes_3807.diff
[CMD] [2021-04-19 16:51:13] echo "." >> /app/public/diff/moore_gibson_mo2_nodes_3807.diff
[INFO] [2021-04-19 16:51:13] Created diff: /app/public/diff/moore_gibson_mo2_nodes_3807.diff (5 lines)
[INFO] [2021-04-19 16:51:13] ...occurrences (/app/public/data/moore_gibson_mo2/occurrences.txt)
[CMD] [2021-04-19 16:51:13] echo "0a" > /app/public/diff/moore_gibson_mo2_occurrences_3807.diff
[CMD] [2021-04-19 16:51:13] tail -n +1 /app/public/converted_csv/moore_gibson_mo2_occurrences_3807.csv >> /app/public/diff/moore_gibson_mo2_occurrences_3807.diff
[CMD] [2021-04-19 16:51:13] echo "." >> /app/public/diff/moore_gibson_mo2_occurrences_3807.diff
[INFO] [2021-04-19 16:51:13] Created diff: /app/public/diff/moore_gibson_mo2_occurrences_3807.diff (5 lines)
[INFO] [2021-04-19 16:51:13] ...measurements (/app/public/data/moore_gibson_mo2/measurementsorfacts.txt)
[CMD] [2021-04-19 16:51:13] echo "0a" > /app/public/diff/moore_gibson_mo2_measurements_3807.diff
[CMD] [2021-04-19 16:51:13] tail -n +1 /app/public/converted_csv/moore_gibson_mo2_measurements_3807.csv >> /app/public/diff/moore_gibson_mo2_measurements_3807.diff
[CMD] [2021-04-19 16:51:13] echo "." >> /app/public/diff/moore_gibson_mo2_measurements_3807.diff
[INFO] [2021-04-19 16:51:13] Created diff: /app/public/diff/moore_gibson_mo2_measurements_3807.diff (6 lines)
[STOP] [2021-04-19 16:51:13] calculate_delta
[START] [2021-04-19 16:51:13] parse_diff_and_store
[INFO] [2021-04-19 16:51:13] Handling diff: /app/public/diff/moore_gibson_mo2_nodes_3807.diff (5 lines)
[INFO] [2021-04-19 16:51:13] Loading nodes diff file into memory (5 /app/public/diff/moore_gibson_mo2_nodes_3807.diff lines)...
[INFO] [2021-04-19 16:51:13] Handling diff: /app/public/diff/moore_gibson_mo2_occurrences_3807.diff (5 lines)
[INFO] [2021-04-19 16:51:13] Loading occurrences diff file into memory (5 /app/public/diff/moore_gibson_mo2_occurrences_3807.diff lines)...
[INFO] [2021-04-19 16:51:13] Handling diff: /app/public/diff/moore_gibson_mo2_measurements_3807.diff (6 lines)
[INFO] [2021-04-19 16:51:13] Loading measurements diff file into memory (6 /app/public/diff/moore_gibson_mo2_measurements_3807.diff lines)...
[INFO] [2021-04-19 16:51:13] Storing 3 ScientificNames
[INFO] [2021-04-19 16:51:13] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 16:51:13] Average Time: 0.0
[INFO] [2021-04-19 16:51:13] Total Time: 1s
[INFO] [2021-04-19 16:51:13] Storing 3 Nodes
[INFO] [2021-04-19 16:51:13] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 16:51:13] Average Time: 0.0
[INFO] [2021-04-19 16:51:13] Total Time: 1s
[INFO] [2021-04-19 16:51:13] Storing 3 Occurrences
[INFO] [2021-04-19 16:51:13] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 16:51:13] Average Time: 0.0
[INFO] [2021-04-19 16:51:13] Total Time: 1s
[INFO] [2021-04-19 16:51:13] Storing 4 Traits
[INFO] [2021-04-19 16:51:13] Processing group of 4 in 1 groups of 1000
[INFO] [2021-04-19 16:51:13] Average Time: 0.0
[INFO] [2021-04-19 16:51:13] Total Time: 1s
[INFO] [2021-04-19 16:51:13] Storing 3 MetaTraits
[INFO] [2021-04-19 16:51:13] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 16:51:13] Average Time: 0.0
[INFO] [2021-04-19 16:51:13] Total Time: 1s
[STOP] [2021-04-19 16:51:13] parse_diff_and_store
[START] [2021-04-19 16:51:13] resolve_keys
[INFO] [2021-04-19 16:51:19] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 16:51:19] traits to occurrences...
[INFO] [2021-04-19 16:51:19] traits to nodes (through occurrences)...
[INFO] [2021-04-19 16:51:19] Traits to sex term...
[INFO] [2021-04-19 16:51:19] Traits to lifestage term...
[INFO] [2021-04-19 16:51:19] MetaTraits to traits...
[INFO] [2021-04-19 16:51:19] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 16:51:19] Assocs to occurrences...
[INFO] [2021-04-19 16:51:19] Assocs to nodes...
[INFO] [2021-04-19 16:51:19] Assoc to sex term...
[INFO] [2021-04-19 16:51:19] Assoc to lifestage term...
[INFO] [2021-04-19 16:51:19] MetaAssoc to assocs...
[STOP] [2021-04-19 16:51:19] resolve_keys
[START] [2021-04-19 16:51:19] hold_for_later_1
[STOP] [2021-04-19 16:51:19] hold_for_later_1
[START] [2021-04-19 16:51:19] hold_for_later_2
[STOP] [2021-04-19 16:51:19] hold_for_later_2
[START] [2021-04-19 16:51:19] resolve_missing_parents
[STOP] [2021-04-19 16:51:19] resolve_missing_parents
[START] [2021-04-19 16:51:19] rebuild_nodes
[START] [2021-04-19 16:51:19] Flattener#flatten
[START] [2021-04-19 16:51:19] Flattener#study_resource
[START] [2021-04-19 16:51:19] Flattener#build_ancestry
[STOP] [2021-04-19 16:51:19] Flattener#build_ancestry
[INFO] [2021-04-19 16:51:19] 3 ancestry keys
[START] [2021-04-19 16:51:19] build_node_ancestors
[INFO] [2021-04-19 16:51:19] old ancestors deleted.
[STOP] [2021-04-19 16:51:19] build_node_ancestors
[WARN] [2021-04-19 16:51:19] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 16:51:19] Flattener#flatten
[STOP] [2021-04-19 16:51:19] rebuild_nodes
[START] [2021-04-19 16:51:19] resolve_missing_media_owners
[STOP] [2021-04-19 16:51:19] resolve_missing_media_owners
[START] [2021-04-19 16:51:19] sanitize_media_verbatims
[STOP] [2021-04-19 16:51:19] sanitize_media_verbatims
[START] [2021-04-19 16:51:19] queue_downloads
[STOP] [2021-04-19 16:51:19] queue_downloads
[START] [2021-04-19 16:51:19] parse_names
[WARN] [2021-04-19 16:51:19] I see 3 names which still need to be parsed.
[STOP] [2021-04-19 16:51:20] parse_names
[START] [2021-04-19 16:51:20] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 16:51:20] denormalize_canonical_names_to_nodes
[START] [2021-04-19 16:51:20] match_nodes
[START] [2021-04-19 16:51:20] map_all_nodes_to_pages
[STOP] [2021-04-19 16:51:20] map_all_nodes_to_pages
[INFO] [2021-04-19 16:51:20] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2021-04-19 16:51:20] update_nodes
[STOP] [2021-04-19 16:51:20] update_nodes
[STOP] [2021-04-19 16:51:20] match_nodes
[START] [2021-04-19 16:51:20] reindex_search
[STOP] [2021-04-19 16:51:21] reindex_search
[START] [2021-04-19 16:51:21] normalize_units
[STOP] [2021-04-19 16:51:21] normalize_units
[START] [2021-04-19 16:51:21] calculate_statistics
[2021-04-19 16:51:21] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 16:51:21] calculate_statistics
[START] [2021-04-19 16:51:21] complete_harvest_instance
[START] [2021-04-19 16:51:21] overall_tsv_creation
[INFO] [2021-04-19 16:51:21] Processing group of 3 in 1 batches of 10000
[INFO] [2021-04-19 16:51:56] 3 Traits (unfiltered)...
[INFO] [2021-04-19 16:52:30] 3 Traits (filtered)...
[INFO] [2021-04-19 16:52:30] 0 Associations (filtered)...
[INFO] [2021-04-19 16:52:30] 1 metadata added.
[INFO] [2021-04-19 16:52:30] 0 metadata added.
[INFO] [2021-04-19 16:52:55] Average Time: 71.17
[INFO] [2021-04-19 16:52:55] Total Time: 1m35s
[STOP] [2021-04-19 16:52:55] overall_tsv_creation
[INFO] [2021-04-19 16:52:55] Done. Check your files:
[INFO] [2021-04-19 16:52:55] (3 lines) /app/public/data/moore_gibson_mo2/publish_nodes.tsv
[INFO] [2021-04-19 16:52:56] (3 lines) /app/public/data/moore_gibson_mo2/publish_scientific_names.tsv
[INFO] [2021-04-19 16:52:56] (4 lines) /app/public/data/moore_gibson_mo2/publish_traits.tsv
[INFO] [2021-04-19 16:52:56] (2 lines) /app/public/data/moore_gibson_mo2/publish_metadata.tsv
[STOP] [2021-04-19 16:52:56] complete_harvest_instance
[START] [2021-04-19 16:52:56] completed
[STOP] [2021-04-19 16:52:56] completed
[STOP] [2021-04-19 16:52:56] logged process, took 102.54

Latest Process