Stage:
completed
Fetched:
19 Apr 16:22
Validated:
19 Apr 16:22
Deltas Created
19 Apr 16:22
Units Normalized:
19 Apr 16:22
Ancestry Built:
19 Apr 16:22
Nodes Matched:
19 Apr 16:22
Names Parsed:
19 Apr 16:22
New Models Stored:
19 Apr 16:22
Indexed:
19 Apr 16:22
Completed:
19 Apr 16:23
Time to Harvest:
less than a minute
Harvesting Log
(392 lines)
# Logfile created on 2020-08-27 15:54:52 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:54:52] logged process
[START] [2020-08-27 15:54:52] Creating resource from OpenData
[START] [2020-08-27 15:54:53] logged process
[START] [2020-08-27 15:54:53] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:54:53] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:54:53] Creating resource from OpenData
[INFO] [2020-12-03 14:21:33] ## HARVEST: type = -harvest
[START] [2020-12-03 14:21:37] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-12-03 14:21:37] create_harvest_instance
[STOP] [2020-12-03 14:21:38] create_harvest_instance
[START] [2020-12-03 14:21:38] fetch_files
[STOP] [2020-12-03 14:21:38] fetch_files
[START] [2020-12-03 14:21:38] validate_each_file
[STOP] [2020-12-03 14:21:38] validate_each_file
[START] [2020-12-03 14:21:38] convert_to_csv
[CMD] [2020-12-03 14:21:38] /usr/bin/sort /app/public/converted_csv/suschenko_pursch_refs_24940.csv > /app/public/converted_csv/suschenko_pursch_refs_24940.csv_sorted
[CMD] [2020-12-03 14:21:38] /usr/bin/sort /app/public/converted_csv/suschenko_pursch_nodes_24941.csv > /app/public/converted_csv/suschenko_pursch_nodes_24941.csv_sorted
[CMD] [2020-12-03 14:21:38] /usr/bin/sort /app/public/converted_csv/suschenko_pursch_occurrences_24942.csv > /app/public/converted_csv/suschenko_pursch_occurrences_24942.csv_sorted
[CMD] [2020-12-03 14:21:38] /usr/bin/sort /app/public/converted_csv/suschenko_pursch_measurements_24943.csv > /app/public/converted_csv/suschenko_pursch_measurements_24943.csv_sorted
[STOP] [2020-12-03 14:21:38] convert_to_csv
[START] [2020-12-03 14:21:38] calculate_delta
[CMD] [2020-12-03 14:21:38] echo "0a" > /app/public/diff/suschenko_pursch_refs_24940.diff
[CMD] [2020-12-03 14:21:38] tail -n +1 /app/public/converted_csv/suschenko_pursch_refs_24940.csv >> /app/public/diff/suschenko_pursch_refs_24940.diff
[CMD] [2020-12-03 14:21:38] echo "." >> /app/public/diff/suschenko_pursch_refs_24940.diff
[CMD] [2020-12-03 14:21:38] echo "0a" > /app/public/diff/suschenko_pursch_nodes_24941.diff
[CMD] [2020-12-03 14:21:38] tail -n +1 /app/public/converted_csv/suschenko_pursch_nodes_24941.csv >> /app/public/diff/suschenko_pursch_nodes_24941.diff
[CMD] [2020-12-03 14:21:38] echo "." >> /app/public/diff/suschenko_pursch_nodes_24941.diff
[CMD] [2020-12-03 14:21:38] echo "0a" > /app/public/diff/suschenko_pursch_occurrences_24942.diff
[CMD] [2020-12-03 14:21:38] tail -n +1 /app/public/converted_csv/suschenko_pursch_occurrences_24942.csv >> /app/public/diff/suschenko_pursch_occurrences_24942.diff
[CMD] [2020-12-03 14:21:38] echo "." >> /app/public/diff/suschenko_pursch_occurrences_24942.diff
[CMD] [2020-12-03 14:21:38] echo "0a" > /app/public/diff/suschenko_pursch_measurements_24943.diff
[CMD] [2020-12-03 14:21:38] tail -n +1 /app/public/converted_csv/suschenko_pursch_measurements_24943.csv >> /app/public/diff/suschenko_pursch_measurements_24943.diff
[CMD] [2020-12-03 14:21:38] echo "." >> /app/public/diff/suschenko_pursch_measurements_24943.diff
[STOP] [2020-12-03 14:21:38] calculate_delta
[START] [2020-12-03 14:21:38] parse_diff_and_store
[INFO] [2020-12-03 14:21:38] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 14:21:38] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 14:21:39] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 14:21:39] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 14:21:39] Storing 2 ScientificNames
[INFO] [2020-12-03 14:21:39] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 14:21:39] Average Time: 0.0
[INFO] [2020-12-03 14:21:39] Total Time: 1s
[INFO] [2020-12-03 14:21:39] Storing 2 Nodes
[INFO] [2020-12-03 14:21:39] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 14:21:39] Average Time: 0.01
[INFO] [2020-12-03 14:21:39] Total Time: 1s
[INFO] [2020-12-03 14:21:39] Storing 2 Occurrences
[INFO] [2020-12-03 14:21:39] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 14:21:39] Average Time: 0.0
[INFO] [2020-12-03 14:21:39] Total Time: 1s
[INFO] [2020-12-03 14:21:39] Storing 4 Traits
[INFO] [2020-12-03 14:21:39] Processing group of 4 in 1 groups of 1000
[INFO] [2020-12-03 14:21:39] Average Time: 0.01
[INFO] [2020-12-03 14:21:39] Total Time: 1s
[INFO] [2020-12-03 14:21:39] Storing 4 MetaTraits
[INFO] [2020-12-03 14:21:39] Processing group of 4 in 1 groups of 1000
[INFO] [2020-12-03 14:21:39] Average Time: 0.0
[INFO] [2020-12-03 14:21:39] Total Time: 1s
[STOP] [2020-12-03 14:21:39] parse_diff_and_store
[START] [2020-12-03 14:21:40] resolve_keys
[INFO] [2020-12-03 14:21:45] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 14:21:45] traits to occurrences...
[INFO] [2020-12-03 14:21:45] traits to nodes (through occurrences)...
[INFO] [2020-12-03 14:21:45] Traits to sex term...
[INFO] [2020-12-03 14:21:45] Traits to lifestage term...
[INFO] [2020-12-03 14:21:45] MetaTraits to traits...
[INFO] [2020-12-03 14:21:45] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 14:21:45] Assocs to occurrences...
[INFO] [2020-12-03 14:21:45] Assocs to nodes...
[INFO] [2020-12-03 14:21:45] Assoc to sex term...
[INFO] [2020-12-03 14:21:45] Assoc to lifestage term...
[INFO] [2020-12-03 14:21:45] MetaAssoc to assocs...
[STOP] [2020-12-03 14:21:45] resolve_keys
[START] [2020-12-03 14:21:45] hold_for_later_1
[STOP] [2020-12-03 14:21:45] hold_for_later_1
[START] [2020-12-03 14:21:45] hold_for_later_2
[STOP] [2020-12-03 14:21:45] hold_for_later_2
[START] [2020-12-03 14:21:45] resolve_missing_parents
[STOP] [2020-12-03 14:21:45] resolve_missing_parents
[START] [2020-12-03 14:21:45] rebuild_nodes
[START] [2020-12-03 14:21:45] Flattener#flatten
[START] [2020-12-03 14:21:45] Flattener#study_resource
[START] [2020-12-03 14:21:45] Flattener#build_ancestry
[STOP] [2020-12-03 14:21:45] Flattener#build_ancestry
[INFO] [2020-12-03 14:21:45] 2 ancestry keys
[START] [2020-12-03 14:21:45] build_node_ancestors
[INFO] [2020-12-03 14:21:45] old ancestors deleted.
[STOP] [2020-12-03 14:21:45] build_node_ancestors
[WARN] [2020-12-03 14:21:45] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 14:21:45] Flattener#flatten
[STOP] [2020-12-03 14:21:45] rebuild_nodes
[START] [2020-12-03 14:21:45] resolve_missing_media_owners
[STOP] [2020-12-03 14:21:45] resolve_missing_media_owners
[START] [2020-12-03 14:21:45] sanitize_media_verbatims
[STOP] [2020-12-03 14:21:45] sanitize_media_verbatims
[START] [2020-12-03 14:21:45] queue_downloads
[STOP] [2020-12-03 14:21:45] queue_downloads
[START] [2020-12-03 14:21:45] parse_names
[WARN] [2020-12-03 14:21:45] I see 2 names which still need to be parsed.
[STOP] [2020-12-03 14:21:46] parse_names
[START] [2020-12-03 14:21:46] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 14:21:46] denormalize_canonical_names_to_nodes
[START] [2020-12-03 14:21:46] match_nodes
[START] [2020-12-03 14:21:46] map_all_nodes_to_pages
[STOP] [2020-12-03 14:21:46] map_all_nodes_to_pages
[INFO] [2020-12-03 14:21:46] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2020-12-03 14:21:46] update_nodes
[STOP] [2020-12-03 14:21:46] update_nodes
[STOP] [2020-12-03 14:21:46] match_nodes
[START] [2020-12-03 14:21:46] reindex_search
[STOP] [2020-12-03 14:21:46] reindex_search
[START] [2020-12-03 14:21:46] normalize_units
[STOP] [2020-12-03 14:21:46] normalize_units
[START] [2020-12-03 14:21:46] calculate_statistics
[2020-12-03 14:21:46] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 14:21:46] calculate_statistics
[START] [2020-12-03 14:21:46] complete_harvest_instance
[START] [2020-12-03 14:21:46] overall_tsv_creation
[INFO] [2020-12-03 14:21:46] Processing group of 2 in 1 batches of 10000
[INFO] [2020-12-03 14:22:25] 2 Traits (unfiltered)...
[INFO] [2020-12-03 14:23:03] 2 Traits (filtered)...
[INFO] [2020-12-03 14:23:03] 0 Associations (filtered)...
[INFO] [2020-12-03 14:23:03] 6 metadata added.
[INFO] [2020-12-03 14:23:03] 0 metadata added.
[INFO] [2020-12-03 14:23:03] Average Time: 53.47
[INFO] [2020-12-03 14:23:03] Total Time: 1m17s
[STOP] [2020-12-03 14:23:03] overall_tsv_creation
[INFO] [2020-12-03 14:23:03] Done. Check your files:
[INFO] [2020-12-03 14:23:03] (2 lines) /app/public/data/suschenko_pursch/publish_nodes.tsv
[INFO] [2020-12-03 14:23:03] (2 lines) /app/public/data/suschenko_pursch/publish_scientific_names.tsv
[INFO] [2020-12-03 14:23:03] (3 lines) /app/public/data/suschenko_pursch/publish_traits.tsv
[INFO] [2020-12-03 14:23:03] (7 lines) /app/public/data/suschenko_pursch/publish_metadata.tsv
[STOP] [2020-12-03 14:23:03] complete_harvest_instance
[START] [2020-12-03 14:23:03] completed
[STOP] [2020-12-03 14:23:03] completed
[STOP] [2020-12-03 14:23:03] logged process, took 85.94
[INFO] [2021-04-19 16:20:24] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 16:22:08] ## remove_type: ScientificName
[INFO] [2021-04-19 16:22:08] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 16:22:08] [16:22:08.484] Removed 2 Scientificnames
[INFO] [2021-04-19 16:22:08] ## remove_type: Vernacular
[INFO] [2021-04-19 16:22:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:22:08] [16:22:08.485] Removed 0 Vernaculars
[INFO] [2021-04-19 16:22:08] ## remove_type: Article
[INFO] [2021-04-19 16:22:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:22:08] [16:22:08.486] Removed 0 Articles
[INFO] [2021-04-19 16:22:08] ## remove_type: Medium
[INFO] [2021-04-19 16:22:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:22:08] [16:22:08.488] Removed 0 Media
[INFO] [2021-04-19 16:22:08] ## remove_type: Trait
[INFO] [2021-04-19 16:22:08] ++ Calling delete_all on 4 instances...
[INFO] [2021-04-19 16:22:08] [16:22:08.490] Removed 4 Traits
[INFO] [2021-04-19 16:22:08] ## remove_type: MetaTrait
[INFO] [2021-04-19 16:22:08] ++ Calling delete_all on 4 instances...
[INFO] [2021-04-19 16:22:08] [16:22:08.492] Removed 4 Metatraits
[INFO] [2021-04-19 16:22:08] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 16:22:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:22:08] [16:22:08.493] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 16:22:08] ## remove_type: Assoc
[INFO] [2021-04-19 16:22:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:22:08] [16:22:08.495] Removed 0 Assocs
[INFO] [2021-04-19 16:22:08] ## remove_type: MetaAssoc
[INFO] [2021-04-19 16:22:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:22:08] [16:22:08.496] Removed 0 Metaassocs
[INFO] [2021-04-19 16:22:08] ## remove_type: Identifier
[INFO] [2021-04-19 16:22:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:22:08] [16:22:08.498] Removed 0 Identifiers
[INFO] [2021-04-19 16:22:08] ## remove_type: Reference
[INFO] [2021-04-19 16:22:08] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:22:08] [16:22:08.500] Removed 0 References
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116281...
[INFO] [2021-04-19 16:22:08] Starting batch with ID 86116280...
[INFO] [2021-04-19 16:22:08] ## remove_type: Node
[INFO] [2021-04-19 16:22:08] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 16:22:08] [16:22:08.828] Removed 2 Nodes
[START] [2021-04-19 16:22:08] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:22:08] Creating resource from OpenData
[START] [2021-04-19 16:22:09] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:22:09] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:22:09] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:22:09] Creating resource from OpenData
[START] [2021-04-19 16:22:09] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:22:09] create_harvest_instance
[INFO] [2021-04-19 16:22:09] Created harvest instance #3791
[STOP] [2021-04-19 16:22:09] create_harvest_instance
[START] [2021-04-19 16:22:09] fetch_files
[STOP] [2021-04-19 16:22:09] fetch_files
[START] [2021-04-19 16:22:09] validate_each_file
[INFO] [2021-04-19 16:22:09] Looping over 4 formats...
[INFO] [2021-04-19 16:22:09] ...refs (/app/public/data/suschenko_pursch/references.tsv)
[INFO] [2021-04-19 16:22:09] Valid: /app/public/converted_csv/suschenko_pursch_refs_3791.csv (0 lines)
[INFO] [2021-04-19 16:22:09] ...nodes (/app/public/data/suschenko_pursch/taxa.txt)
[INFO] [2021-04-19 16:22:09] Valid: /app/public/converted_csv/suschenko_pursch_nodes_3791.csv (2 lines)
[INFO] [2021-04-19 16:22:09] ...occurrences (/app/public/data/suschenko_pursch/occurrences.txt)
[INFO] [2021-04-19 16:22:09] Valid: /app/public/converted_csv/suschenko_pursch_occurrences_3791.csv (2 lines)
[INFO] [2021-04-19 16:22:09] ...measurements (/app/public/data/suschenko_pursch/measurementsorfacts.txt)
[INFO] [2021-04-19 16:22:09] Valid: /app/public/converted_csv/suschenko_pursch_measurements_3791.csv (4 lines)
[STOP] [2021-04-19 16:22:09] validate_each_file
[START] [2021-04-19 16:22:09] convert_to_csv
[INFO] [2021-04-19 16:22:09] Looping over 4 formats...
[INFO] [2021-04-19 16:22:09] ...refs (/app/public/data/suschenko_pursch/references.tsv)
[CMD] [2021-04-19 16:22:09] /usr/bin/sort /app/public/converted_csv/suschenko_pursch_refs_3791.csv > /app/public/converted_csv/suschenko_pursch_refs_3791.csv_sorted
[INFO] [2021-04-19 16:22:09] Converted: /app/public/converted_csv/suschenko_pursch_refs_3791.csv (0 lines)
[INFO] [2021-04-19 16:22:09] ...nodes (/app/public/data/suschenko_pursch/taxa.txt)
[CMD] [2021-04-19 16:22:09] /usr/bin/sort /app/public/converted_csv/suschenko_pursch_nodes_3791.csv > /app/public/converted_csv/suschenko_pursch_nodes_3791.csv_sorted
[INFO] [2021-04-19 16:22:09] Converted: /app/public/converted_csv/suschenko_pursch_nodes_3791.csv (2 lines)
[INFO] [2021-04-19 16:22:09] ...occurrences (/app/public/data/suschenko_pursch/occurrences.txt)
[CMD] [2021-04-19 16:22:09] /usr/bin/sort /app/public/converted_csv/suschenko_pursch_occurrences_3791.csv > /app/public/converted_csv/suschenko_pursch_occurrences_3791.csv_sorted
[INFO] [2021-04-19 16:22:09] Converted: /app/public/converted_csv/suschenko_pursch_occurrences_3791.csv (2 lines)
[INFO] [2021-04-19 16:22:09] ...measurements (/app/public/data/suschenko_pursch/measurementsorfacts.txt)
[CMD] [2021-04-19 16:22:09] /usr/bin/sort /app/public/converted_csv/suschenko_pursch_measurements_3791.csv > /app/public/converted_csv/suschenko_pursch_measurements_3791.csv_sorted
[INFO] [2021-04-19 16:22:09] Converted: /app/public/converted_csv/suschenko_pursch_measurements_3791.csv (4 lines)
[STOP] [2021-04-19 16:22:09] convert_to_csv
[START] [2021-04-19 16:22:09] calculate_delta
[INFO] [2021-04-19 16:22:09] Looping over 4 formats...
[INFO] [2021-04-19 16:22:09] ...refs (/app/public/data/suschenko_pursch/references.tsv)
[CMD] [2021-04-19 16:22:09] echo "0a" > /app/public/diff/suschenko_pursch_refs_3791.diff
[CMD] [2021-04-19 16:22:09] tail -n +1 /app/public/converted_csv/suschenko_pursch_refs_3791.csv >> /app/public/diff/suschenko_pursch_refs_3791.diff
[CMD] [2021-04-19 16:22:09] echo "." >> /app/public/diff/suschenko_pursch_refs_3791.diff
[INFO] [2021-04-19 16:22:09] Created diff: /app/public/diff/suschenko_pursch_refs_3791.diff (2 lines)
[INFO] [2021-04-19 16:22:09] ...nodes (/app/public/data/suschenko_pursch/taxa.txt)
[CMD] [2021-04-19 16:22:09] echo "0a" > /app/public/diff/suschenko_pursch_nodes_3791.diff
[CMD] [2021-04-19 16:22:09] tail -n +1 /app/public/converted_csv/suschenko_pursch_nodes_3791.csv >> /app/public/diff/suschenko_pursch_nodes_3791.diff
[CMD] [2021-04-19 16:22:09] echo "." >> /app/public/diff/suschenko_pursch_nodes_3791.diff
[INFO] [2021-04-19 16:22:09] Created diff: /app/public/diff/suschenko_pursch_nodes_3791.diff (4 lines)
[INFO] [2021-04-19 16:22:09] ...occurrences (/app/public/data/suschenko_pursch/occurrences.txt)
[CMD] [2021-04-19 16:22:09] echo "0a" > /app/public/diff/suschenko_pursch_occurrences_3791.diff
[CMD] [2021-04-19 16:22:09] tail -n +1 /app/public/converted_csv/suschenko_pursch_occurrences_3791.csv >> /app/public/diff/suschenko_pursch_occurrences_3791.diff
[CMD] [2021-04-19 16:22:09] echo "." >> /app/public/diff/suschenko_pursch_occurrences_3791.diff
[INFO] [2021-04-19 16:22:09] Created diff: /app/public/diff/suschenko_pursch_occurrences_3791.diff (4 lines)
[INFO] [2021-04-19 16:22:09] ...measurements (/app/public/data/suschenko_pursch/measurementsorfacts.txt)
[CMD] [2021-04-19 16:22:09] echo "0a" > /app/public/diff/suschenko_pursch_measurements_3791.diff
[CMD] [2021-04-19 16:22:09] tail -n +1 /app/public/converted_csv/suschenko_pursch_measurements_3791.csv >> /app/public/diff/suschenko_pursch_measurements_3791.diff
[CMD] [2021-04-19 16:22:09] echo "." >> /app/public/diff/suschenko_pursch_measurements_3791.diff
[INFO] [2021-04-19 16:22:09] Created diff: /app/public/diff/suschenko_pursch_measurements_3791.diff (6 lines)
[STOP] [2021-04-19 16:22:09] calculate_delta
[START] [2021-04-19 16:22:09] parse_diff_and_store
[INFO] [2021-04-19 16:22:09] Handling diff: /app/public/diff/suschenko_pursch_refs_3791.diff (2 lines)
[INFO] [2021-04-19 16:22:09] Loading refs diff file into memory (2 /app/public/diff/suschenko_pursch_refs_3791.diff lines)...
[INFO] [2021-04-19 16:22:09] Handling diff: /app/public/diff/suschenko_pursch_nodes_3791.diff (4 lines)
[INFO] [2021-04-19 16:22:09] Loading nodes diff file into memory (4 /app/public/diff/suschenko_pursch_nodes_3791.diff lines)...
[INFO] [2021-04-19 16:22:09] Handling diff: /app/public/diff/suschenko_pursch_occurrences_3791.diff (4 lines)
[INFO] [2021-04-19 16:22:09] Loading occurrences diff file into memory (4 /app/public/diff/suschenko_pursch_occurrences_3791.diff lines)...
[INFO] [2021-04-19 16:22:09] Handling diff: /app/public/diff/suschenko_pursch_measurements_3791.diff (6 lines)
[INFO] [2021-04-19 16:22:09] Loading measurements diff file into memory (6 /app/public/diff/suschenko_pursch_measurements_3791.diff lines)...
[INFO] [2021-04-19 16:22:09] Storing 2 ScientificNames
[INFO] [2021-04-19 16:22:09] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 16:22:09] Average Time: 0.0
[INFO] [2021-04-19 16:22:09] Total Time: 1s
[INFO] [2021-04-19 16:22:09] Storing 2 Nodes
[INFO] [2021-04-19 16:22:09] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 16:22:09] Average Time: 0.0
[INFO] [2021-04-19 16:22:09] Total Time: 1s
[INFO] [2021-04-19 16:22:09] Storing 2 Occurrences
[INFO] [2021-04-19 16:22:09] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 16:22:09] Average Time: 0.0
[INFO] [2021-04-19 16:22:09] Total Time: 1s
[INFO] [2021-04-19 16:22:09] Storing 4 Traits
[INFO] [2021-04-19 16:22:09] Processing group of 4 in 1 groups of 1000
[INFO] [2021-04-19 16:22:09] Average Time: 0.0
[INFO] [2021-04-19 16:22:09] Total Time: 1s
[INFO] [2021-04-19 16:22:09] Storing 4 MetaTraits
[INFO] [2021-04-19 16:22:09] Processing group of 4 in 1 groups of 1000
[INFO] [2021-04-19 16:22:09] Average Time: 0.0
[INFO] [2021-04-19 16:22:09] Total Time: 1s
[STOP] [2021-04-19 16:22:09] parse_diff_and_store
[START] [2021-04-19 16:22:09] resolve_keys
[INFO] [2021-04-19 16:22:15] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 16:22:15] traits to occurrences...
[INFO] [2021-04-19 16:22:15] traits to nodes (through occurrences)...
[INFO] [2021-04-19 16:22:15] Traits to sex term...
[INFO] [2021-04-19 16:22:15] Traits to lifestage term...
[INFO] [2021-04-19 16:22:15] MetaTraits to traits...
[INFO] [2021-04-19 16:22:15] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 16:22:15] Assocs to occurrences...
[INFO] [2021-04-19 16:22:15] Assocs to nodes...
[INFO] [2021-04-19 16:22:15] Assoc to sex term...
[INFO] [2021-04-19 16:22:15] Assoc to lifestage term...
[INFO] [2021-04-19 16:22:15] MetaAssoc to assocs...
[STOP] [2021-04-19 16:22:15] resolve_keys
[START] [2021-04-19 16:22:15] hold_for_later_1
[STOP] [2021-04-19 16:22:15] hold_for_later_1
[START] [2021-04-19 16:22:15] hold_for_later_2
[STOP] [2021-04-19 16:22:15] hold_for_later_2
[START] [2021-04-19 16:22:15] resolve_missing_parents
[STOP] [2021-04-19 16:22:15] resolve_missing_parents
[START] [2021-04-19 16:22:15] rebuild_nodes
[START] [2021-04-19 16:22:15] Flattener#flatten
[START] [2021-04-19 16:22:15] Flattener#study_resource
[START] [2021-04-19 16:22:15] Flattener#build_ancestry
[STOP] [2021-04-19 16:22:15] Flattener#build_ancestry
[INFO] [2021-04-19 16:22:15] 2 ancestry keys
[START] [2021-04-19 16:22:15] build_node_ancestors
[INFO] [2021-04-19 16:22:15] old ancestors deleted.
[STOP] [2021-04-19 16:22:15] build_node_ancestors
[WARN] [2021-04-19 16:22:15] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 16:22:15] Flattener#flatten
[STOP] [2021-04-19 16:22:15] rebuild_nodes
[START] [2021-04-19 16:22:15] resolve_missing_media_owners
[STOP] [2021-04-19 16:22:15] resolve_missing_media_owners
[START] [2021-04-19 16:22:15] sanitize_media_verbatims
[STOP] [2021-04-19 16:22:15] sanitize_media_verbatims
[START] [2021-04-19 16:22:15] queue_downloads
[STOP] [2021-04-19 16:22:15] queue_downloads
[START] [2021-04-19 16:22:15] parse_names
[WARN] [2021-04-19 16:22:15] I see 2 names which still need to be parsed.
[STOP] [2021-04-19 16:22:16] parse_names
[START] [2021-04-19 16:22:16] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 16:22:16] denormalize_canonical_names_to_nodes
[START] [2021-04-19 16:22:16] match_nodes
[START] [2021-04-19 16:22:16] map_all_nodes_to_pages
[STOP] [2021-04-19 16:22:16] map_all_nodes_to_pages
[INFO] [2021-04-19 16:22:16] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2021-04-19 16:22:16] update_nodes
[STOP] [2021-04-19 16:22:16] update_nodes
[STOP] [2021-04-19 16:22:16] match_nodes
[START] [2021-04-19 16:22:16] reindex_search
[STOP] [2021-04-19 16:22:16] reindex_search
[START] [2021-04-19 16:22:16] normalize_units
[STOP] [2021-04-19 16:22:16] normalize_units
[START] [2021-04-19 16:22:16] calculate_statistics
[2021-04-19 16:22:16] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 16:22:16] calculate_statistics
[START] [2021-04-19 16:22:16] complete_harvest_instance
[START] [2021-04-19 16:22:16] overall_tsv_creation
[INFO] [2021-04-19 16:22:16] Processing group of 2 in 1 batches of 10000
[INFO] [2021-04-19 16:22:52] 2 Traits (unfiltered)...
[INFO] [2021-04-19 16:23:26] 2 Traits (filtered)...
[INFO] [2021-04-19 16:23:26] 0 Associations (filtered)...
[INFO] [2021-04-19 16:23:26] 2 metadata added.
[INFO] [2021-04-19 16:23:26] 0 metadata added.
[INFO] [2021-04-19 16:23:52] Average Time: 71.83
[INFO] [2021-04-19 16:23:52] Total Time: 1m36s
[STOP] [2021-04-19 16:23:52] overall_tsv_creation
[INFO] [2021-04-19 16:23:52] Done. Check your files:
[INFO] [2021-04-19 16:23:52] (2 lines) /app/public/data/suschenko_pursch/publish_nodes.tsv
[INFO] [2021-04-19 16:23:52] (2 lines) /app/public/data/suschenko_pursch/publish_scientific_names.tsv
[INFO] [2021-04-19 16:23:52] (3 lines) /app/public/data/suschenko_pursch/publish_traits.tsv
[INFO] [2021-04-19 16:23:52] (3 lines) /app/public/data/suschenko_pursch/publish_metadata.tsv
[STOP] [2021-04-19 16:23:52] complete_harvest_instance
[START] [2021-04-19 16:23:52] completed
[STOP] [2021-04-19 16:23:52] completed
[STOP] [2021-04-19 16:23:52] logged process, took 103.38
Latest Process