Harvest for Land 1980 Created 19 Apr 15:49

Stage: completed
Fetched: 19 Apr 15:49
Validated: 19 Apr 15:49
Deltas Created 19 Apr 15:49
Units Normalized: 19 Apr 15:49
Ancestry Built: 19 Apr 15:49
Nodes Matched: 19 Apr 15:49
Names Parsed: 19 Apr 15:49
New Models Stored: 19 Apr 15:49
Indexed: 19 Apr 15:49
Completed: 19 Apr 15:51
Time to Harvest: less than a minute

Harvesting Log

(380 lines)
# Logfile created on 2020-08-27 15:46:36 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:46:36] logged process
[START] [2020-08-27 15:46:36] Creating resource from OpenData
[START] [2020-08-27 15:46:36] logged process
[START] [2020-08-27 15:46:36] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:46:36] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:46:36] Creating resource from OpenData
[INFO] [2020-12-03 11:59:53] ## HARVEST: type = -harvest
[START] [2020-12-03 11:59:56] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-03 11:59:56] create_harvest_instance
[STOP] [2020-12-03 11:59:58] create_harvest_instance
[START] [2020-12-03 11:59:58] fetch_files
[STOP] [2020-12-03 11:59:58] fetch_files
[START] [2020-12-03 11:59:58] validate_each_file
[STOP] [2020-12-03 11:59:58] validate_each_file
[START] [2020-12-03 11:59:58] convert_to_csv
[CMD] [2020-12-03 11:59:58] /usr/bin/sort /app/public/converted_csv/land_land_1980_refs_24856.csv > /app/public/converted_csv/land_land_1980_refs_24856.csv_sorted
[CMD] [2020-12-03 11:59:58] /usr/bin/sort /app/public/converted_csv/land_land_1980_nodes_24857.csv > /app/public/converted_csv/land_land_1980_nodes_24857.csv_sorted
[CMD] [2020-12-03 11:59:58] /usr/bin/sort /app/public/converted_csv/land_land_1980_occurrences_24858.csv > /app/public/converted_csv/land_land_1980_occurrences_24858.csv_sorted
[CMD] [2020-12-03 11:59:58] /usr/bin/sort /app/public/converted_csv/land_land_1980_measurements_24859.csv > /app/public/converted_csv/land_land_1980_measurements_24859.csv_sorted
[STOP] [2020-12-03 11:59:58] convert_to_csv
[START] [2020-12-03 11:59:58] calculate_delta
[CMD] [2020-12-03 11:59:58] echo "0a" > /app/public/diff/land_land_1980_refs_24856.diff
[CMD] [2020-12-03 11:59:58] tail -n +1 /app/public/converted_csv/land_land_1980_refs_24856.csv >> /app/public/diff/land_land_1980_refs_24856.diff
[CMD] [2020-12-03 11:59:58] echo "." >> /app/public/diff/land_land_1980_refs_24856.diff
[CMD] [2020-12-03 11:59:58] echo "0a" > /app/public/diff/land_land_1980_nodes_24857.diff
[CMD] [2020-12-03 11:59:58] tail -n +1 /app/public/converted_csv/land_land_1980_nodes_24857.csv >> /app/public/diff/land_land_1980_nodes_24857.diff
[CMD] [2020-12-03 11:59:58] echo "." >> /app/public/diff/land_land_1980_nodes_24857.diff
[CMD] [2020-12-03 11:59:58] echo "0a" > /app/public/diff/land_land_1980_occurrences_24858.diff
[CMD] [2020-12-03 11:59:58] tail -n +1 /app/public/converted_csv/land_land_1980_occurrences_24858.csv >> /app/public/diff/land_land_1980_occurrences_24858.diff
[CMD] [2020-12-03 11:59:58] echo "." >> /app/public/diff/land_land_1980_occurrences_24858.diff
[CMD] [2020-12-03 11:59:58] echo "0a" > /app/public/diff/land_land_1980_measurements_24859.diff
[CMD] [2020-12-03 11:59:58] tail -n +1 /app/public/converted_csv/land_land_1980_measurements_24859.csv >> /app/public/diff/land_land_1980_measurements_24859.diff
[CMD] [2020-12-03 11:59:58] echo "." >> /app/public/diff/land_land_1980_measurements_24859.diff
[STOP] [2020-12-03 11:59:58] calculate_delta
[START] [2020-12-03 11:59:58] parse_diff_and_store
[INFO] [2020-12-03 11:59:58] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 11:59:58] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 11:59:58] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 11:59:58] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 11:59:59] Storing 1 ScientificNames
[INFO] [2020-12-03 11:59:59] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:59:59] Average Time: 0.0
[INFO] [2020-12-03 11:59:59] Total Time: 1s
[INFO] [2020-12-03 11:59:59] Storing 1 Nodes
[INFO] [2020-12-03 11:59:59] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:59:59] Average Time: 0.0
[INFO] [2020-12-03 11:59:59] Total Time: 1s
[INFO] [2020-12-03 11:59:59] Storing 1 Occurrences
[INFO] [2020-12-03 11:59:59] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:59:59] Average Time: 0.0
[INFO] [2020-12-03 11:59:59] Total Time: 1s
[INFO] [2020-12-03 11:59:59] Storing 2 Traits
[INFO] [2020-12-03 11:59:59] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 11:59:59] Average Time: 0.0
[INFO] [2020-12-03 11:59:59] Total Time: 1s
[INFO] [2020-12-03 11:59:59] Storing 1 MetaTraits
[INFO] [2020-12-03 11:59:59] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:59:59] Average Time: 0.0
[INFO] [2020-12-03 11:59:59] Total Time: 1s
[STOP] [2020-12-03 11:59:59] parse_diff_and_store
[START] [2020-12-03 11:59:59] resolve_keys
[INFO] [2020-12-03 12:00:04] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 12:00:04] traits to occurrences...
[INFO] [2020-12-03 12:00:04] traits to nodes (through occurrences)...
[INFO] [2020-12-03 12:00:04] Traits to sex term...
[INFO] [2020-12-03 12:00:04] Traits to lifestage term...
[INFO] [2020-12-03 12:00:04] MetaTraits to traits...
[INFO] [2020-12-03 12:00:04] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 12:00:04] Assocs to occurrences...
[INFO] [2020-12-03 12:00:04] Assocs to nodes...
[INFO] [2020-12-03 12:00:04] Assoc to sex term...
[INFO] [2020-12-03 12:00:04] Assoc to lifestage term...
[INFO] [2020-12-03 12:00:04] MetaAssoc to assocs...
[STOP] [2020-12-03 12:00:04] resolve_keys
[START] [2020-12-03 12:00:04] hold_for_later_1
[STOP] [2020-12-03 12:00:04] hold_for_later_1
[START] [2020-12-03 12:00:04] hold_for_later_2
[STOP] [2020-12-03 12:00:04] hold_for_later_2
[START] [2020-12-03 12:00:04] resolve_missing_parents
[STOP] [2020-12-03 12:00:04] resolve_missing_parents
[START] [2020-12-03 12:00:04] rebuild_nodes
[START] [2020-12-03 12:00:04] Flattener#flatten
[START] [2020-12-03 12:00:04] Flattener#study_resource
[START] [2020-12-03 12:00:04] Flattener#build_ancestry
[STOP] [2020-12-03 12:00:04] Flattener#build_ancestry
[INFO] [2020-12-03 12:00:04] 1 ancestry keys
[START] [2020-12-03 12:00:04] build_node_ancestors
[INFO] [2020-12-03 12:00:04] old ancestors deleted.
[STOP] [2020-12-03 12:00:04] build_node_ancestors
[WARN] [2020-12-03 12:00:04] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 12:00:04] Flattener#flatten
[STOP] [2020-12-03 12:00:04] rebuild_nodes
[START] [2020-12-03 12:00:04] resolve_missing_media_owners
[STOP] [2020-12-03 12:00:04] resolve_missing_media_owners
[START] [2020-12-03 12:00:04] sanitize_media_verbatims
[STOP] [2020-12-03 12:00:04] sanitize_media_verbatims
[START] [2020-12-03 12:00:04] queue_downloads
[STOP] [2020-12-03 12:00:04] queue_downloads
[START] [2020-12-03 12:00:04] parse_names
[WARN] [2020-12-03 12:00:04] I see 1 names which still need to be parsed.
[STOP] [2020-12-03 12:00:06] parse_names
[START] [2020-12-03 12:00:06] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 12:00:06] denormalize_canonical_names_to_nodes
[START] [2020-12-03 12:00:06] match_nodes
[START] [2020-12-03 12:00:06] map_all_nodes_to_pages
[STOP] [2020-12-03 12:00:06] map_all_nodes_to_pages
[INFO] [2020-12-03 12:00:06] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-12-03 12:00:06] update_nodes
[STOP] [2020-12-03 12:00:06] update_nodes
[STOP] [2020-12-03 12:00:06] match_nodes
[START] [2020-12-03 12:00:06] reindex_search
[STOP] [2020-12-03 12:00:06] reindex_search
[START] [2020-12-03 12:00:06] normalize_units
[STOP] [2020-12-03 12:00:06] normalize_units
[START] [2020-12-03 12:00:06] calculate_statistics
[2020-12-03 12:00:06] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 12:00:06] calculate_statistics
[START] [2020-12-03 12:00:06] complete_harvest_instance
[START] [2020-12-03 12:00:06] overall_tsv_creation
[INFO] [2020-12-03 12:00:06] Processing group of 1 in 1 batches of 10000
[INFO] [2020-12-03 12:00:44] 1 Traits (unfiltered)...
[INFO] [2020-12-03 12:01:20] 1 Traits (filtered)...
[INFO] [2020-12-03 12:01:20] 0 Associations (filtered)...
[INFO] [2020-12-03 12:01:20] 2 metadata added.
[INFO] [2020-12-03 12:01:20] 0 metadata added.
[INFO] [2020-12-03 12:01:20] Average Time: 52.2
[INFO] [2020-12-03 12:01:20] Total Time: 1m15s
[STOP] [2020-12-03 12:01:20] overall_tsv_creation
[INFO] [2020-12-03 12:01:20] Done. Check your files:
[INFO] [2020-12-03 12:01:20] (1 lines) /app/public/data/land_land_1980/publish_nodes.tsv
[INFO] [2020-12-03 12:01:20] (1 lines) /app/public/data/land_land_1980/publish_scientific_names.tsv
[INFO] [2020-12-03 12:01:20] (2 lines) /app/public/data/land_land_1980/publish_traits.tsv
[INFO] [2020-12-03 12:01:20] (3 lines) /app/public/data/land_land_1980/publish_metadata.tsv
[STOP] [2020-12-03 12:01:20] complete_harvest_instance
[START] [2020-12-03 12:01:20] completed
[STOP] [2020-12-03 12:01:20] completed
[STOP] [2020-12-03 12:01:20] logged process, took 84.52
[INFO] [2021-04-19 15:36:28] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:49:24] ## remove_type: ScientificName
[INFO] [2021-04-19 15:49:24] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:49:24] [15:49:24.222] Removed 1 Scientificnames
[INFO] [2021-04-19 15:49:24] ## remove_type: Vernacular
[INFO] [2021-04-19 15:49:24] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:49:24] [15:49:24.224] Removed 0 Vernaculars
[INFO] [2021-04-19 15:49:24] ## remove_type: Article
[INFO] [2021-04-19 15:49:24] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:49:24] [15:49:24.225] Removed 0 Articles
[INFO] [2021-04-19 15:49:24] ## remove_type: Medium
[INFO] [2021-04-19 15:49:24] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:49:24] [15:49:24.227] Removed 0 Media
[INFO] [2021-04-19 15:49:24] ## remove_type: Trait
[INFO] [2021-04-19 15:49:24] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:49:24] [15:49:24.229] Removed 2 Traits
[INFO] [2021-04-19 15:49:24] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:49:24] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:49:24] [15:49:24.232] Removed 1 Metatraits
[INFO] [2021-04-19 15:49:24] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:49:24] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:49:24] [15:49:24.234] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 15:49:24] ## remove_type: Assoc
[INFO] [2021-04-19 15:49:24] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:49:24] [15:49:24.235] Removed 0 Assocs
[INFO] [2021-04-19 15:49:24] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:49:24] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:49:24] [15:49:24.237] Removed 0 Metaassocs
[INFO] [2021-04-19 15:49:24] ## remove_type: Identifier
[INFO] [2021-04-19 15:49:24] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:49:24] [15:49:24.238] Removed 0 Identifiers
[INFO] [2021-04-19 15:49:24] ## remove_type: Reference
[INFO] [2021-04-19 15:49:24] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:49:24] [15:49:24.240] Removed 0 References
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] Starting batch with ID 86116208...
[INFO] [2021-04-19 15:49:24] ## remove_type: Node
[INFO] [2021-04-19 15:49:24] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:49:24] [15:49:24.483] Removed 1 Nodes
[START] [2021-04-19 15:49:24] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:49:24] Creating resource from OpenData
[START] [2021-04-19 15:49:24] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:49:24] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:49:24] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:49:24] Creating resource from OpenData
[START] [2021-04-19 15:49:24] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:49:24] create_harvest_instance
[INFO] [2021-04-19 15:49:24] Created harvest instance #3779
[STOP] [2021-04-19 15:49:24] create_harvest_instance
[START] [2021-04-19 15:49:24] fetch_files
[STOP] [2021-04-19 15:49:24] fetch_files
[START] [2021-04-19 15:49:24] validate_each_file
[INFO] [2021-04-19 15:49:24] Looping over 4 formats...
[INFO] [2021-04-19 15:49:24] ...refs (/app/public/data/land_land_1980/references.tsv)
[INFO] [2021-04-19 15:49:24] Valid: /app/public/converted_csv/land_land_1980_refs_3779.csv (0 lines)
[INFO] [2021-04-19 15:49:24] ...nodes (/app/public/data/land_land_1980/taxa.txt)
[INFO] [2021-04-19 15:49:24] Valid: /app/public/converted_csv/land_land_1980_nodes_3779.csv (1 lines)
[INFO] [2021-04-19 15:49:24] ...occurrences (/app/public/data/land_land_1980/occurrences.txt)
[INFO] [2021-04-19 15:49:24] Valid: /app/public/converted_csv/land_land_1980_occurrences_3779.csv (1 lines)
[INFO] [2021-04-19 15:49:24] ...measurements (/app/public/data/land_land_1980/measurementsorfacts.txt)
[INFO] [2021-04-19 15:49:24] Valid: /app/public/converted_csv/land_land_1980_measurements_3779.csv (2 lines)
[STOP] [2021-04-19 15:49:24] validate_each_file
[START] [2021-04-19 15:49:24] convert_to_csv
[INFO] [2021-04-19 15:49:24] Looping over 4 formats...
[INFO] [2021-04-19 15:49:24] ...refs (/app/public/data/land_land_1980/references.tsv)
[CMD] [2021-04-19 15:49:24] /usr/bin/sort /app/public/converted_csv/land_land_1980_refs_3779.csv > /app/public/converted_csv/land_land_1980_refs_3779.csv_sorted
[INFO] [2021-04-19 15:49:24] Converted: /app/public/converted_csv/land_land_1980_refs_3779.csv (0 lines)
[INFO] [2021-04-19 15:49:24] ...nodes (/app/public/data/land_land_1980/taxa.txt)
[CMD] [2021-04-19 15:49:24] /usr/bin/sort /app/public/converted_csv/land_land_1980_nodes_3779.csv > /app/public/converted_csv/land_land_1980_nodes_3779.csv_sorted
[INFO] [2021-04-19 15:49:25] Converted: /app/public/converted_csv/land_land_1980_nodes_3779.csv (1 lines)
[INFO] [2021-04-19 15:49:25] ...occurrences (/app/public/data/land_land_1980/occurrences.txt)
[CMD] [2021-04-19 15:49:25] /usr/bin/sort /app/public/converted_csv/land_land_1980_occurrences_3779.csv > /app/public/converted_csv/land_land_1980_occurrences_3779.csv_sorted
[INFO] [2021-04-19 15:49:25] Converted: /app/public/converted_csv/land_land_1980_occurrences_3779.csv (1 lines)
[INFO] [2021-04-19 15:49:25] ...measurements (/app/public/data/land_land_1980/measurementsorfacts.txt)
[CMD] [2021-04-19 15:49:25] /usr/bin/sort /app/public/converted_csv/land_land_1980_measurements_3779.csv > /app/public/converted_csv/land_land_1980_measurements_3779.csv_sorted
[INFO] [2021-04-19 15:49:25] Converted: /app/public/converted_csv/land_land_1980_measurements_3779.csv (2 lines)
[STOP] [2021-04-19 15:49:25] convert_to_csv
[START] [2021-04-19 15:49:25] calculate_delta
[INFO] [2021-04-19 15:49:25] Looping over 4 formats...
[INFO] [2021-04-19 15:49:25] ...refs (/app/public/data/land_land_1980/references.tsv)
[CMD] [2021-04-19 15:49:25] echo "0a" > /app/public/diff/land_land_1980_refs_3779.diff
[CMD] [2021-04-19 15:49:25] tail -n +1 /app/public/converted_csv/land_land_1980_refs_3779.csv >> /app/public/diff/land_land_1980_refs_3779.diff
[CMD] [2021-04-19 15:49:25] echo "." >> /app/public/diff/land_land_1980_refs_3779.diff
[INFO] [2021-04-19 15:49:25] Created diff: /app/public/diff/land_land_1980_refs_3779.diff (2 lines)
[INFO] [2021-04-19 15:49:25] ...nodes (/app/public/data/land_land_1980/taxa.txt)
[CMD] [2021-04-19 15:49:25] echo "0a" > /app/public/diff/land_land_1980_nodes_3779.diff
[CMD] [2021-04-19 15:49:25] tail -n +1 /app/public/converted_csv/land_land_1980_nodes_3779.csv >> /app/public/diff/land_land_1980_nodes_3779.diff
[CMD] [2021-04-19 15:49:25] echo "." >> /app/public/diff/land_land_1980_nodes_3779.diff
[INFO] [2021-04-19 15:49:25] Created diff: /app/public/diff/land_land_1980_nodes_3779.diff (3 lines)
[INFO] [2021-04-19 15:49:25] ...occurrences (/app/public/data/land_land_1980/occurrences.txt)
[CMD] [2021-04-19 15:49:25] echo "0a" > /app/public/diff/land_land_1980_occurrences_3779.diff
[CMD] [2021-04-19 15:49:25] tail -n +1 /app/public/converted_csv/land_land_1980_occurrences_3779.csv >> /app/public/diff/land_land_1980_occurrences_3779.diff
[CMD] [2021-04-19 15:49:25] echo "." >> /app/public/diff/land_land_1980_occurrences_3779.diff
[INFO] [2021-04-19 15:49:25] Created diff: /app/public/diff/land_land_1980_occurrences_3779.diff (3 lines)
[INFO] [2021-04-19 15:49:25] ...measurements (/app/public/data/land_land_1980/measurementsorfacts.txt)
[CMD] [2021-04-19 15:49:25] echo "0a" > /app/public/diff/land_land_1980_measurements_3779.diff
[CMD] [2021-04-19 15:49:25] tail -n +1 /app/public/converted_csv/land_land_1980_measurements_3779.csv >> /app/public/diff/land_land_1980_measurements_3779.diff
[CMD] [2021-04-19 15:49:25] echo "." >> /app/public/diff/land_land_1980_measurements_3779.diff
[INFO] [2021-04-19 15:49:25] Created diff: /app/public/diff/land_land_1980_measurements_3779.diff (4 lines)
[STOP] [2021-04-19 15:49:25] calculate_delta
[START] [2021-04-19 15:49:25] parse_diff_and_store
[INFO] [2021-04-19 15:49:25] Handling diff: /app/public/diff/land_land_1980_refs_3779.diff (2 lines)
[INFO] [2021-04-19 15:49:25] Loading refs diff file into memory (2 /app/public/diff/land_land_1980_refs_3779.diff lines)...
[INFO] [2021-04-19 15:49:25] Handling diff: /app/public/diff/land_land_1980_nodes_3779.diff (3 lines)
[INFO] [2021-04-19 15:49:25] Loading nodes diff file into memory (3 /app/public/diff/land_land_1980_nodes_3779.diff lines)...
[INFO] [2021-04-19 15:49:25] Handling diff: /app/public/diff/land_land_1980_occurrences_3779.diff (3 lines)
[INFO] [2021-04-19 15:49:25] Loading occurrences diff file into memory (3 /app/public/diff/land_land_1980_occurrences_3779.diff lines)...
[INFO] [2021-04-19 15:49:25] Handling diff: /app/public/diff/land_land_1980_measurements_3779.diff (4 lines)
[INFO] [2021-04-19 15:49:25] Loading measurements diff file into memory (4 /app/public/diff/land_land_1980_measurements_3779.diff lines)...
[INFO] [2021-04-19 15:49:25] Storing 1 ScientificNames
[INFO] [2021-04-19 15:49:25] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:49:25] Average Time: 0.0
[INFO] [2021-04-19 15:49:25] Total Time: 1s
[INFO] [2021-04-19 15:49:25] Storing 1 Nodes
[INFO] [2021-04-19 15:49:25] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:49:25] Average Time: 0.0
[INFO] [2021-04-19 15:49:25] Total Time: 1s
[INFO] [2021-04-19 15:49:25] Storing 1 Occurrences
[INFO] [2021-04-19 15:49:25] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:49:25] Average Time: 0.0
[INFO] [2021-04-19 15:49:25] Total Time: 1s
[INFO] [2021-04-19 15:49:25] Storing 2 Traits
[INFO] [2021-04-19 15:49:25] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:49:25] Average Time: 0.0
[INFO] [2021-04-19 15:49:25] Total Time: 1s
[INFO] [2021-04-19 15:49:25] Storing 1 MetaTraits
[INFO] [2021-04-19 15:49:25] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:49:25] Average Time: 0.0
[INFO] [2021-04-19 15:49:25] Total Time: 1s
[STOP] [2021-04-19 15:49:25] parse_diff_and_store
[START] [2021-04-19 15:49:25] resolve_keys
[INFO] [2021-04-19 15:49:31] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:49:31] traits to occurrences...
[INFO] [2021-04-19 15:49:31] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:49:31] Traits to sex term...
[INFO] [2021-04-19 15:49:31] Traits to lifestage term...
[INFO] [2021-04-19 15:49:31] MetaTraits to traits...
[INFO] [2021-04-19 15:49:31] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:49:31] Assocs to occurrences...
[INFO] [2021-04-19 15:49:31] Assocs to nodes...
[INFO] [2021-04-19 15:49:31] Assoc to sex term...
[INFO] [2021-04-19 15:49:31] Assoc to lifestage term...
[INFO] [2021-04-19 15:49:31] MetaAssoc to assocs...
[STOP] [2021-04-19 15:49:31] resolve_keys
[START] [2021-04-19 15:49:31] hold_for_later_1
[STOP] [2021-04-19 15:49:31] hold_for_later_1
[START] [2021-04-19 15:49:31] hold_for_later_2
[STOP] [2021-04-19 15:49:31] hold_for_later_2
[START] [2021-04-19 15:49:31] resolve_missing_parents
[STOP] [2021-04-19 15:49:31] resolve_missing_parents
[START] [2021-04-19 15:49:31] rebuild_nodes
[START] [2021-04-19 15:49:31] Flattener#flatten
[START] [2021-04-19 15:49:31] Flattener#study_resource
[START] [2021-04-19 15:49:31] Flattener#build_ancestry
[STOP] [2021-04-19 15:49:31] Flattener#build_ancestry
[INFO] [2021-04-19 15:49:31] 1 ancestry keys
[START] [2021-04-19 15:49:31] build_node_ancestors
[INFO] [2021-04-19 15:49:31] old ancestors deleted.
[STOP] [2021-04-19 15:49:31] build_node_ancestors
[WARN] [2021-04-19 15:49:31] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:49:31] Flattener#flatten
[STOP] [2021-04-19 15:49:31] rebuild_nodes
[START] [2021-04-19 15:49:31] resolve_missing_media_owners
[STOP] [2021-04-19 15:49:31] resolve_missing_media_owners
[START] [2021-04-19 15:49:31] sanitize_media_verbatims
[STOP] [2021-04-19 15:49:31] sanitize_media_verbatims
[START] [2021-04-19 15:49:31] queue_downloads
[STOP] [2021-04-19 15:49:31] queue_downloads
[START] [2021-04-19 15:49:31] parse_names
[WARN] [2021-04-19 15:49:31] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 15:49:32] parse_names
[START] [2021-04-19 15:49:32] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:49:32] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:49:32] match_nodes
[START] [2021-04-19 15:49:32] map_all_nodes_to_pages
[STOP] [2021-04-19 15:49:32] map_all_nodes_to_pages
[INFO] [2021-04-19 15:49:32] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 15:49:32] update_nodes
[STOP] [2021-04-19 15:49:32] update_nodes
[STOP] [2021-04-19 15:49:32] match_nodes
[START] [2021-04-19 15:49:32] reindex_search
[STOP] [2021-04-19 15:49:32] reindex_search
[START] [2021-04-19 15:49:32] normalize_units
[STOP] [2021-04-19 15:49:32] normalize_units
[START] [2021-04-19 15:49:32] calculate_statistics
[2021-04-19 15:49:32] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:49:32] calculate_statistics
[START] [2021-04-19 15:49:32] complete_harvest_instance
[START] [2021-04-19 15:49:32] overall_tsv_creation
[INFO] [2021-04-19 15:49:32] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 15:50:07] 1 Traits (unfiltered)...
[INFO] [2021-04-19 15:50:39] 1 Traits (filtered)...
[INFO] [2021-04-19 15:50:39] 0 Associations (filtered)...
[INFO] [2021-04-19 15:50:39] 1 metadata added.
[INFO] [2021-04-19 15:50:39] 0 metadata added.
[INFO] [2021-04-19 15:51:05] Average Time: 69.36
[INFO] [2021-04-19 15:51:05] Total Time: 1m33s
[STOP] [2021-04-19 15:51:05] overall_tsv_creation
[INFO] [2021-04-19 15:51:05] Done. Check your files:
[INFO] [2021-04-19 15:51:05] (1 lines) /app/public/data/land_land_1980/publish_nodes.tsv
[INFO] [2021-04-19 15:51:05] (1 lines) /app/public/data/land_land_1980/publish_scientific_names.tsv
[INFO] [2021-04-19 15:51:05] (2 lines) /app/public/data/land_land_1980/publish_traits.tsv
[INFO] [2021-04-19 15:51:05] (2 lines) /app/public/data/land_land_1980/publish_metadata.tsv
[STOP] [2021-04-19 15:51:05] complete_harvest_instance
[START] [2021-04-19 15:51:05] completed
[STOP] [2021-04-19 15:51:05] completed
[STOP] [2021-04-19 15:51:05] logged process, took 100.35

Latest Process