Stage:
completed
Fetched:
19 Apr 11:25
Validated:
19 Apr 11:25
Deltas Created
19 Apr 11:25
Units Normalized:
19 Apr 11:25
Ancestry Built:
19 Apr 11:25
Nodes Matched:
19 Apr 11:25
Names Parsed:
19 Apr 11:25
New Models Stored:
19 Apr 11:25
Indexed:
19 Apr 11:25
Completed:
19 Apr 11:27
Time to Harvest:
less than a minute
Harvesting Log
(424 lines)
# Logfile created on 2020-09-28 08:59:16 -0400 by logger.rb/v1.4.2
[START] [2020-09-28 08:59:16] logged process
[START] [2020-09-28 08:59:16] Creating resource from OpenData
[START] [2020-09-28 08:59:17] logged process
[START] [2020-09-28 08:59:17] Parse meta.xml file and create formats with fields
[STOP] [2020-09-28 08:59:17] Parse meta.xml file and create formats with fields
[STOP] [2020-09-28 08:59:17] Creating resource from OpenData
[INFO] [2020-12-04 08:10:40] ## HARVEST: type = -harvest
[START] [2020-12-04 08:10:44] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-12-04 08:10:44] create_harvest_instance
[STOP] [2020-12-04 08:10:45] create_harvest_instance
[START] [2020-12-04 08:10:45] fetch_files
[STOP] [2020-12-04 08:10:45] fetch_files
[START] [2020-12-04 08:10:45] validate_each_file
[STOP] [2020-12-04 08:10:45] validate_each_file
[START] [2020-12-04 08:10:45] convert_to_csv
[CMD] [2020-12-04 08:10:45] /usr/bin/sort /app/public/converted_csv/sundberg_gibson__nodes_25067.csv > /app/public/converted_csv/sundberg_gibson__nodes_25067.csv_sorted
[CMD] [2020-12-04 08:10:45] /usr/bin/sort /app/public/converted_csv/sundberg_gibson__occurrences_25068.csv > /app/public/converted_csv/sundberg_gibson__occurrences_25068.csv_sorted
[CMD] [2020-12-04 08:10:45] /usr/bin/sort /app/public/converted_csv/sundberg_gibson__measurements_25069.csv > /app/public/converted_csv/sundberg_gibson__measurements_25069.csv_sorted
[STOP] [2020-12-04 08:10:45] convert_to_csv
[START] [2020-12-04 08:10:45] calculate_delta
[CMD] [2020-12-04 08:10:45] echo "0a" > /app/public/diff/sundberg_gibson__nodes_25067.diff
[CMD] [2020-12-04 08:10:45] tail -n +1 /app/public/converted_csv/sundberg_gibson__nodes_25067.csv >> /app/public/diff/sundberg_gibson__nodes_25067.diff
[CMD] [2020-12-04 08:10:45] echo "." >> /app/public/diff/sundberg_gibson__nodes_25067.diff
[CMD] [2020-12-04 08:10:45] echo "0a" > /app/public/diff/sundberg_gibson__occurrences_25068.diff
[CMD] [2020-12-04 08:10:45] tail -n +1 /app/public/converted_csv/sundberg_gibson__occurrences_25068.csv >> /app/public/diff/sundberg_gibson__occurrences_25068.diff
[CMD] [2020-12-04 08:10:45] echo "." >> /app/public/diff/sundberg_gibson__occurrences_25068.diff
[CMD] [2020-12-04 08:10:45] echo "0a" > /app/public/diff/sundberg_gibson__measurements_25069.diff
[CMD] [2020-12-04 08:10:45] tail -n +1 /app/public/converted_csv/sundberg_gibson__measurements_25069.csv >> /app/public/diff/sundberg_gibson__measurements_25069.diff
[CMD] [2020-12-04 08:10:45] echo "." >> /app/public/diff/sundberg_gibson__measurements_25069.diff
[STOP] [2020-12-04 08:10:45] calculate_delta
[START] [2020-12-04 08:10:45] parse_diff_and_store
[INFO] [2020-12-04 08:10:46] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-04 08:10:46] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-04 08:10:46] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-04 08:10:46] Storing 11 ScientificNames
[INFO] [2020-12-04 08:10:46] Processing group of 11 in 1 groups of 1000
[INFO] [2020-12-04 08:10:46] Average Time: 0.03
[INFO] [2020-12-04 08:10:46] Total Time: 1s
[INFO] [2020-12-04 08:10:46] Storing 11 Nodes
[INFO] [2020-12-04 08:10:46] Processing group of 11 in 1 groups of 1000
[INFO] [2020-12-04 08:10:47] Average Time: 0.07
[INFO] [2020-12-04 08:10:47] Total Time: 1s
[INFO] [2020-12-04 08:10:47] Storing 11 Occurrences
[INFO] [2020-12-04 08:10:47] Processing group of 11 in 1 groups of 1000
[INFO] [2020-12-04 08:10:47] Average Time: 0.06
[INFO] [2020-12-04 08:10:47] Total Time: 1s
[INFO] [2020-12-04 08:10:47] Storing 21 Traits
[INFO] [2020-12-04 08:10:47] Processing group of 21 in 1 groups of 1000
[INFO] [2020-12-04 08:10:47] Average Time: 0.01
[INFO] [2020-12-04 08:10:47] Total Time: 1s
[INFO] [2020-12-04 08:10:47] Storing 11 MetaTraits
[INFO] [2020-12-04 08:10:47] Processing group of 11 in 1 groups of 1000
[INFO] [2020-12-04 08:10:47] Average Time: 0.0
[INFO] [2020-12-04 08:10:47] Total Time: 1s
[STOP] [2020-12-04 08:10:47] parse_diff_and_store
[START] [2020-12-04 08:10:47] resolve_keys
[INFO] [2020-12-04 08:10:53] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-04 08:10:53] traits to occurrences...
[INFO] [2020-12-04 08:10:53] traits to nodes (through occurrences)...
[INFO] [2020-12-04 08:10:53] Traits to sex term...
[INFO] [2020-12-04 08:10:53] Traits to lifestage term...
[INFO] [2020-12-04 08:10:53] MetaTraits to traits...
[INFO] [2020-12-04 08:10:53] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-04 08:10:53] Assocs to occurrences...
[INFO] [2020-12-04 08:10:53] Assocs to nodes...
[INFO] [2020-12-04 08:10:53] Assoc to sex term...
[INFO] [2020-12-04 08:10:53] Assoc to lifestage term...
[INFO] [2020-12-04 08:10:53] MetaAssoc to assocs...
[STOP] [2020-12-04 08:10:53] resolve_keys
[START] [2020-12-04 08:10:53] hold_for_later_1
[STOP] [2020-12-04 08:10:53] hold_for_later_1
[START] [2020-12-04 08:10:53] hold_for_later_2
[STOP] [2020-12-04 08:10:53] hold_for_later_2
[START] [2020-12-04 08:10:53] resolve_missing_parents
[STOP] [2020-12-04 08:10:53] resolve_missing_parents
[START] [2020-12-04 08:10:53] rebuild_nodes
[START] [2020-12-04 08:10:53] Flattener#flatten
[START] [2020-12-04 08:10:53] Flattener#study_resource
[START] [2020-12-04 08:10:53] Flattener#build_ancestry
[STOP] [2020-12-04 08:10:53] Flattener#build_ancestry
[INFO] [2020-12-04 08:10:53] 11 ancestry keys
[START] [2020-12-04 08:10:53] build_node_ancestors
[INFO] [2020-12-04 08:10:53] old ancestors deleted.
[STOP] [2020-12-04 08:10:53] build_node_ancestors
[WARN] [2020-12-04 08:10:53] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-04 08:10:53] Flattener#flatten
[STOP] [2020-12-04 08:10:53] rebuild_nodes
[START] [2020-12-04 08:10:53] resolve_missing_media_owners
[STOP] [2020-12-04 08:10:53] resolve_missing_media_owners
[START] [2020-12-04 08:10:53] sanitize_media_verbatims
[STOP] [2020-12-04 08:10:53] sanitize_media_verbatims
[START] [2020-12-04 08:10:53] queue_downloads
[STOP] [2020-12-04 08:10:53] queue_downloads
[START] [2020-12-04 08:10:53] parse_names
[WARN] [2020-12-04 08:10:53] I see 11 names which still need to be parsed.
[STOP] [2020-12-04 08:10:54] parse_names
[START] [2020-12-04 08:10:54] denormalize_canonical_names_to_nodes
[STOP] [2020-12-04 08:10:54] denormalize_canonical_names_to_nodes
[START] [2020-12-04 08:10:54] match_nodes
[START] [2020-12-04 08:10:54] map_all_nodes_to_pages
[STOP] [2020-12-04 08:10:54] map_all_nodes_to_pages
[INFO] [2020-12-04 08:10:54] ZERO unmatched nodes (of 11)! Nicely done.
[START] [2020-12-04 08:10:54] update_nodes
[STOP] [2020-12-04 08:10:54] update_nodes
[STOP] [2020-12-04 08:10:54] match_nodes
[START] [2020-12-04 08:10:54] reindex_search
[STOP] [2020-12-04 08:10:54] reindex_search
[START] [2020-12-04 08:10:54] normalize_units
[STOP] [2020-12-04 08:10:54] normalize_units
[START] [2020-12-04 08:10:54] calculate_statistics
[2020-12-04 08:10:54] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-04 08:10:54] calculate_statistics
[START] [2020-12-04 08:10:54] complete_harvest_instance
[START] [2020-12-04 08:10:54] overall_tsv_creation
[INFO] [2020-12-04 08:10:54] Processing group of 11 in 1 batches of 10000
[INFO] [2020-12-04 08:11:34] 11 Traits (unfiltered)...
[INFO] [2020-12-04 08:12:12] 11 Traits (filtered)...
[INFO] [2020-12-04 08:12:12] 0 Associations (filtered)...
[INFO] [2020-12-04 08:12:12] 21 metadata added.
[INFO] [2020-12-04 08:12:12] 0 metadata added.
[INFO] [2020-12-04 08:12:12] Average Time: 54.79
[INFO] [2020-12-04 08:12:12] Total Time: 1m19s
[STOP] [2020-12-04 08:12:12] overall_tsv_creation
[INFO] [2020-12-04 08:12:12] Done. Check your files:
[INFO] [2020-12-04 08:12:12] (11 lines) /app/public/data/sundberg_gibson_/publish_nodes.tsv
[INFO] [2020-12-04 08:12:12] (11 lines) /app/public/data/sundberg_gibson_/publish_scientific_names.tsv
[INFO] [2020-12-04 08:12:12] (12 lines) /app/public/data/sundberg_gibson_/publish_traits.tsv
[INFO] [2020-12-04 08:12:12] (22 lines) /app/public/data/sundberg_gibson_/publish_metadata.tsv
[STOP] [2020-12-04 08:12:12] complete_harvest_instance
[START] [2020-12-04 08:12:12] completed
[STOP] [2020-12-04 08:12:12] completed
[STOP] [2020-12-04 08:12:12] logged process, took 88.16
[INFO] [2021-04-19 11:19:31] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 11:25:31] ## remove_type: ScientificName
[INFO] [2021-04-19 11:25:31] ++ Calling delete_all on 11 instances...
[INFO] [2021-04-19 11:25:31] [11:25:31.602] Removed 11 Scientificnames
[INFO] [2021-04-19 11:25:31] ## remove_type: Vernacular
[INFO] [2021-04-19 11:25:31] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:25:31] [11:25:31.603] Removed 0 Vernaculars
[INFO] [2021-04-19 11:25:31] ## remove_type: Article
[INFO] [2021-04-19 11:25:31] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:25:31] [11:25:31.604] Removed 0 Articles
[INFO] [2021-04-19 11:25:31] ## remove_type: Medium
[INFO] [2021-04-19 11:25:31] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:25:31] [11:25:31.606] Removed 0 Media
[INFO] [2021-04-19 11:25:31] ## remove_type: Trait
[INFO] [2021-04-19 11:25:31] ++ Calling delete_all on 21 instances...
[INFO] [2021-04-19 11:25:31] [11:25:31.608] Removed 21 Traits
[INFO] [2021-04-19 11:25:31] ## remove_type: MetaTrait
[INFO] [2021-04-19 11:25:31] ++ Calling delete_all on 11 instances...
[INFO] [2021-04-19 11:25:31] [11:25:31.610] Removed 11 Metatraits
[INFO] [2021-04-19 11:25:31] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 11:25:31] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:25:31] [11:25:31.611] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 11:25:31] ## remove_type: Assoc
[INFO] [2021-04-19 11:25:31] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:25:31] [11:25:31.612] Removed 0 Assocs
[INFO] [2021-04-19 11:25:31] ## remove_type: MetaAssoc
[INFO] [2021-04-19 11:25:31] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:25:31] [11:25:31.614] Removed 0 Metaassocs
[INFO] [2021-04-19 11:25:31] ## remove_type: Identifier
[INFO] [2021-04-19 11:25:31] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:25:31] [11:25:31.615] Removed 0 Identifiers
[INFO] [2021-04-19 11:25:31] ## remove_type: Reference
[INFO] [2021-04-19 11:25:31] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 11:25:31] [11:25:31.617] Removed 0 References
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:31] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] Starting batch with ID 86116351...
[INFO] [2021-04-19 11:25:32] ## remove_type: Node
[INFO] [2021-04-19 11:25:32] ++ Calling delete_all on 11 instances...
[INFO] [2021-04-19 11:25:32] [11:25:32.542] Removed 11 Nodes
[START] [2021-04-19 11:25:33] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 11:25:33] Creating resource from OpenData
[START] [2021-04-19 11:25:33] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 11:25:33] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 11:25:37] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 11:25:37] Creating resource from OpenData
[START] [2021-04-19 11:25:37] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 11:25:37] create_harvest_instance
[INFO] [2021-04-19 11:25:37] Created harvest instance #3738
[STOP] [2021-04-19 11:25:37] create_harvest_instance
[START] [2021-04-19 11:25:37] fetch_files
[STOP] [2021-04-19 11:25:37] fetch_files
[START] [2021-04-19 11:25:37] validate_each_file
[INFO] [2021-04-19 11:25:37] Looping over 3 formats...
[INFO] [2021-04-19 11:25:37] ...nodes (/app/public/data/sundberg_gibson_/taxa.txt)
[INFO] [2021-04-19 11:25:37] Valid: /app/public/converted_csv/sundberg_gibson__nodes_3738.csv (11 lines)
[INFO] [2021-04-19 11:25:37] ...occurrences (/app/public/data/sundberg_gibson_/occurrences.txt)
[INFO] [2021-04-19 11:25:37] Valid: /app/public/converted_csv/sundberg_gibson__occurrences_3738.csv (11 lines)
[INFO] [2021-04-19 11:25:37] ...measurements (/app/public/data/sundberg_gibson_/measurementsorfacts.txt)
[INFO] [2021-04-19 11:25:37] Valid: /app/public/converted_csv/sundberg_gibson__measurements_3738.csv (21 lines)
[STOP] [2021-04-19 11:25:37] validate_each_file
[START] [2021-04-19 11:25:37] convert_to_csv
[INFO] [2021-04-19 11:25:37] Looping over 3 formats...
[INFO] [2021-04-19 11:25:37] ...nodes (/app/public/data/sundberg_gibson_/taxa.txt)
[CMD] [2021-04-19 11:25:37] /usr/bin/sort /app/public/converted_csv/sundberg_gibson__nodes_3738.csv > /app/public/converted_csv/sundberg_gibson__nodes_3738.csv_sorted
[INFO] [2021-04-19 11:25:38] Converted: /app/public/converted_csv/sundberg_gibson__nodes_3738.csv (11 lines)
[INFO] [2021-04-19 11:25:38] ...occurrences (/app/public/data/sundberg_gibson_/occurrences.txt)
[CMD] [2021-04-19 11:25:38] /usr/bin/sort /app/public/converted_csv/sundberg_gibson__occurrences_3738.csv > /app/public/converted_csv/sundberg_gibson__occurrences_3738.csv_sorted
[INFO] [2021-04-19 11:25:38] Converted: /app/public/converted_csv/sundberg_gibson__occurrences_3738.csv (11 lines)
[INFO] [2021-04-19 11:25:38] ...measurements (/app/public/data/sundberg_gibson_/measurementsorfacts.txt)
[CMD] [2021-04-19 11:25:38] /usr/bin/sort /app/public/converted_csv/sundberg_gibson__measurements_3738.csv > /app/public/converted_csv/sundberg_gibson__measurements_3738.csv_sorted
[INFO] [2021-04-19 11:25:38] Converted: /app/public/converted_csv/sundberg_gibson__measurements_3738.csv (21 lines)
[STOP] [2021-04-19 11:25:38] convert_to_csv
[START] [2021-04-19 11:25:38] calculate_delta
[INFO] [2021-04-19 11:25:38] Looping over 3 formats...
[INFO] [2021-04-19 11:25:38] ...nodes (/app/public/data/sundberg_gibson_/taxa.txt)
[CMD] [2021-04-19 11:25:38] echo "0a" > /app/public/diff/sundberg_gibson__nodes_3738.diff
[CMD] [2021-04-19 11:25:39] tail -n +1 /app/public/converted_csv/sundberg_gibson__nodes_3738.csv >> /app/public/diff/sundberg_gibson__nodes_3738.diff
[CMD] [2021-04-19 11:25:39] echo "." >> /app/public/diff/sundberg_gibson__nodes_3738.diff
[INFO] [2021-04-19 11:25:40] Created diff: /app/public/diff/sundberg_gibson__nodes_3738.diff (13 lines)
[INFO] [2021-04-19 11:25:40] ...occurrences (/app/public/data/sundberg_gibson_/occurrences.txt)
[CMD] [2021-04-19 11:25:40] echo "0a" > /app/public/diff/sundberg_gibson__occurrences_3738.diff
[CMD] [2021-04-19 11:25:40] tail -n +1 /app/public/converted_csv/sundberg_gibson__occurrences_3738.csv >> /app/public/diff/sundberg_gibson__occurrences_3738.diff
[CMD] [2021-04-19 11:25:40] echo "." >> /app/public/diff/sundberg_gibson__occurrences_3738.diff
[INFO] [2021-04-19 11:25:41] Created diff: /app/public/diff/sundberg_gibson__occurrences_3738.diff (13 lines)
[INFO] [2021-04-19 11:25:41] ...measurements (/app/public/data/sundberg_gibson_/measurementsorfacts.txt)
[CMD] [2021-04-19 11:25:41] echo "0a" > /app/public/diff/sundberg_gibson__measurements_3738.diff
[CMD] [2021-04-19 11:25:41] tail -n +1 /app/public/converted_csv/sundberg_gibson__measurements_3738.csv >> /app/public/diff/sundberg_gibson__measurements_3738.diff
[CMD] [2021-04-19 11:25:41] echo "." >> /app/public/diff/sundberg_gibson__measurements_3738.diff
[INFO] [2021-04-19 11:25:42] Created diff: /app/public/diff/sundberg_gibson__measurements_3738.diff (23 lines)
[STOP] [2021-04-19 11:25:42] calculate_delta
[START] [2021-04-19 11:25:42] parse_diff_and_store
[INFO] [2021-04-19 11:25:42] Handling diff: /app/public/diff/sundberg_gibson__nodes_3738.diff (13 lines)
[INFO] [2021-04-19 11:25:42] Loading nodes diff file into memory (13 /app/public/diff/sundberg_gibson__nodes_3738.diff lines)...
[INFO] [2021-04-19 11:25:43] Handling diff: /app/public/diff/sundberg_gibson__occurrences_3738.diff (13 lines)
[INFO] [2021-04-19 11:25:43] Loading occurrences diff file into memory (13 /app/public/diff/sundberg_gibson__occurrences_3738.diff lines)...
[INFO] [2021-04-19 11:25:43] Handling diff: /app/public/diff/sundberg_gibson__measurements_3738.diff (23 lines)
[INFO] [2021-04-19 11:25:44] Loading measurements diff file into memory (23 /app/public/diff/sundberg_gibson__measurements_3738.diff lines)...
[INFO] [2021-04-19 11:25:44] Storing 11 ScientificNames
[INFO] [2021-04-19 11:25:44] Processing group of 11 in 1 groups of 1000
[INFO] [2021-04-19 11:25:44] Average Time: 0.01
[INFO] [2021-04-19 11:25:44] Total Time: 1s
[INFO] [2021-04-19 11:25:44] Storing 11 Nodes
[INFO] [2021-04-19 11:25:44] Processing group of 11 in 1 groups of 1000
[INFO] [2021-04-19 11:25:44] Average Time: 0.0
[INFO] [2021-04-19 11:25:44] Total Time: 1s
[INFO] [2021-04-19 11:25:44] Storing 11 Occurrences
[INFO] [2021-04-19 11:25:44] Processing group of 11 in 1 groups of 1000
[INFO] [2021-04-19 11:25:44] Average Time: 0.0
[INFO] [2021-04-19 11:25:44] Total Time: 1s
[INFO] [2021-04-19 11:25:44] Storing 21 Traits
[INFO] [2021-04-19 11:25:44] Processing group of 21 in 1 groups of 1000
[INFO] [2021-04-19 11:25:44] Average Time: 0.01
[INFO] [2021-04-19 11:25:44] Total Time: 1s
[INFO] [2021-04-19 11:25:44] Storing 11 MetaTraits
[INFO] [2021-04-19 11:25:44] Processing group of 11 in 1 groups of 1000
[INFO] [2021-04-19 11:25:44] Average Time: 0.0
[INFO] [2021-04-19 11:25:44] Total Time: 1s
[STOP] [2021-04-19 11:25:44] parse_diff_and_store
[START] [2021-04-19 11:25:44] resolve_keys
[INFO] [2021-04-19 11:25:50] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 11:25:50] traits to occurrences...
[INFO] [2021-04-19 11:25:50] traits to nodes (through occurrences)...
[INFO] [2021-04-19 11:25:50] Traits to sex term...
[INFO] [2021-04-19 11:25:50] Traits to lifestage term...
[INFO] [2021-04-19 11:25:50] MetaTraits to traits...
[INFO] [2021-04-19 11:25:50] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 11:25:50] Assocs to occurrences...
[INFO] [2021-04-19 11:25:50] Assocs to nodes...
[INFO] [2021-04-19 11:25:50] Assoc to sex term...
[INFO] [2021-04-19 11:25:50] Assoc to lifestage term...
[INFO] [2021-04-19 11:25:50] MetaAssoc to assocs...
[STOP] [2021-04-19 11:25:50] resolve_keys
[START] [2021-04-19 11:25:50] hold_for_later_1
[STOP] [2021-04-19 11:25:50] hold_for_later_1
[START] [2021-04-19 11:25:50] hold_for_later_2
[STOP] [2021-04-19 11:25:50] hold_for_later_2
[START] [2021-04-19 11:25:50] resolve_missing_parents
[STOP] [2021-04-19 11:25:50] resolve_missing_parents
[START] [2021-04-19 11:25:50] rebuild_nodes
[START] [2021-04-19 11:25:50] Flattener#flatten
[START] [2021-04-19 11:25:50] Flattener#study_resource
[START] [2021-04-19 11:25:50] Flattener#build_ancestry
[STOP] [2021-04-19 11:25:50] Flattener#build_ancestry
[INFO] [2021-04-19 11:25:50] 11 ancestry keys
[START] [2021-04-19 11:25:50] build_node_ancestors
[INFO] [2021-04-19 11:25:50] old ancestors deleted.
[STOP] [2021-04-19 11:25:50] build_node_ancestors
[WARN] [2021-04-19 11:25:50] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 11:25:50] Flattener#flatten
[STOP] [2021-04-19 11:25:50] rebuild_nodes
[START] [2021-04-19 11:25:50] resolve_missing_media_owners
[STOP] [2021-04-19 11:25:50] resolve_missing_media_owners
[START] [2021-04-19 11:25:50] sanitize_media_verbatims
[STOP] [2021-04-19 11:25:50] sanitize_media_verbatims
[START] [2021-04-19 11:25:50] queue_downloads
[STOP] [2021-04-19 11:25:50] queue_downloads
[START] [2021-04-19 11:25:50] parse_names
[WARN] [2021-04-19 11:25:50] I see 11 names which still need to be parsed.
[STOP] [2021-04-19 11:25:51] parse_names
[START] [2021-04-19 11:25:51] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 11:25:51] denormalize_canonical_names_to_nodes
[START] [2021-04-19 11:25:51] match_nodes
[START] [2021-04-19 11:25:51] map_all_nodes_to_pages
[STOP] [2021-04-19 11:25:51] map_all_nodes_to_pages
[INFO] [2021-04-19 11:25:51] ZERO unmatched nodes (of 11)! Nicely done.
[START] [2021-04-19 11:25:51] update_nodes
[STOP] [2021-04-19 11:25:51] update_nodes
[STOP] [2021-04-19 11:25:51] match_nodes
[START] [2021-04-19 11:25:51] reindex_search
[STOP] [2021-04-19 11:25:51] reindex_search
[START] [2021-04-19 11:25:51] normalize_units
[STOP] [2021-04-19 11:25:51] normalize_units
[START] [2021-04-19 11:25:51] calculate_statistics
[2021-04-19 11:25:52] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 11:25:52] calculate_statistics
[START] [2021-04-19 11:25:52] complete_harvest_instance
[START] [2021-04-19 11:25:52] overall_tsv_creation
[INFO] [2021-04-19 11:25:52] Processing group of 11 in 1 batches of 10000
[INFO] [2021-04-19 11:26:28] 11 Traits (unfiltered)...
[INFO] [2021-04-19 11:27:02] 11 Traits (filtered)...
[INFO] [2021-04-19 11:27:02] 0 Associations (filtered)...
[INFO] [2021-04-19 11:27:02] 10 metadata added.
[INFO] [2021-04-19 11:27:02] 0 metadata added.
[INFO] [2021-04-19 11:27:29] Average Time: 72.7
[INFO] [2021-04-19 11:27:29] Total Time: 1m37s
[STOP] [2021-04-19 11:27:29] overall_tsv_creation
[INFO] [2021-04-19 11:27:29] Done. Check your files:
[INFO] [2021-04-19 11:27:29] (11 lines) /app/public/data/sundberg_gibson_/publish_nodes.tsv
[INFO] [2021-04-19 11:27:29] (11 lines) /app/public/data/sundberg_gibson_/publish_scientific_names.tsv
[INFO] [2021-04-19 11:27:30] (12 lines) /app/public/data/sundberg_gibson_/publish_traits.tsv
[INFO] [2021-04-19 11:27:30] (11 lines) /app/public/data/sundberg_gibson_/publish_metadata.tsv
[STOP] [2021-04-19 11:27:30] complete_harvest_instance
[START] [2021-04-19 11:27:30] completed
[STOP] [2021-04-19 11:27:30] completed
[STOP] [2021-04-19 11:27:30] logged process, took 113.29
Latest Process