Stage:
completed
Fetched:
19 Apr 15:51
Validated:
19 Apr 15:51
Deltas Created
19 Apr 15:51
Units Normalized:
19 Apr 15:51
Ancestry Built:
19 Apr 15:51
Nodes Matched:
19 Apr 15:51
Names Parsed:
19 Apr 15:51
New Models Stored:
19 Apr 15:51
Indexed:
19 Apr 15:51
Completed:
19 Apr 15:52
Time to Harvest:
less than a minute
Harvesting Log
(384 lines)
# Logfile created on 2020-08-27 15:47:18 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:47:18] logged process
[START] [2020-08-27 15:47:18] Creating resource from OpenData
[START] [2020-08-27 15:47:18] logged process
[START] [2020-08-27 15:47:18] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:47:18] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:47:18] Creating resource from OpenData
[INFO] [2020-12-03 12:02:22] ## HARVEST: type = -harvest
[START] [2020-12-03 12:02:24] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-12-03 12:02:24] create_harvest_instance
[STOP] [2020-12-03 12:02:25] create_harvest_instance
[START] [2020-12-03 12:02:25] fetch_files
[STOP] [2020-12-03 12:02:26] fetch_files
[START] [2020-12-03 12:02:26] validate_each_file
[STOP] [2020-12-03 12:02:26] validate_each_file
[START] [2020-12-03 12:02:26] convert_to_csv
[CMD] [2020-12-03 12:02:26] /usr/bin/sort /app/public/converted_csv/koppetsch_et_al__refs_24860.csv > /app/public/converted_csv/koppetsch_et_al__refs_24860.csv_sorted
[CMD] [2020-12-03 12:02:26] /usr/bin/sort /app/public/converted_csv/koppetsch_et_al__nodes_24861.csv > /app/public/converted_csv/koppetsch_et_al__nodes_24861.csv_sorted
[CMD] [2020-12-03 12:02:26] /usr/bin/sort /app/public/converted_csv/koppetsch_et_al__occurrences_24862.csv > /app/public/converted_csv/koppetsch_et_al__occurrences_24862.csv_sorted
[CMD] [2020-12-03 12:02:26] /usr/bin/sort /app/public/converted_csv/koppetsch_et_al__measurements_24863.csv > /app/public/converted_csv/koppetsch_et_al__measurements_24863.csv_sorted
[STOP] [2020-12-03 12:02:26] convert_to_csv
[START] [2020-12-03 12:02:26] calculate_delta
[CMD] [2020-12-03 12:02:26] echo "0a" > /app/public/diff/koppetsch_et_al__refs_24860.diff
[CMD] [2020-12-03 12:02:26] tail -n +1 /app/public/converted_csv/koppetsch_et_al__refs_24860.csv >> /app/public/diff/koppetsch_et_al__refs_24860.diff
[CMD] [2020-12-03 12:02:26] echo "." >> /app/public/diff/koppetsch_et_al__refs_24860.diff
[CMD] [2020-12-03 12:02:26] echo "0a" > /app/public/diff/koppetsch_et_al__nodes_24861.diff
[CMD] [2020-12-03 12:02:26] tail -n +1 /app/public/converted_csv/koppetsch_et_al__nodes_24861.csv >> /app/public/diff/koppetsch_et_al__nodes_24861.diff
[CMD] [2020-12-03 12:02:26] echo "." >> /app/public/diff/koppetsch_et_al__nodes_24861.diff
[CMD] [2020-12-03 12:02:26] echo "0a" > /app/public/diff/koppetsch_et_al__occurrences_24862.diff
[CMD] [2020-12-03 12:02:26] tail -n +1 /app/public/converted_csv/koppetsch_et_al__occurrences_24862.csv >> /app/public/diff/koppetsch_et_al__occurrences_24862.diff
[CMD] [2020-12-03 12:02:26] echo "." >> /app/public/diff/koppetsch_et_al__occurrences_24862.diff
[CMD] [2020-12-03 12:02:26] echo "0a" > /app/public/diff/koppetsch_et_al__measurements_24863.diff
[CMD] [2020-12-03 12:02:26] tail -n +1 /app/public/converted_csv/koppetsch_et_al__measurements_24863.csv >> /app/public/diff/koppetsch_et_al__measurements_24863.diff
[CMD] [2020-12-03 12:02:26] echo "." >> /app/public/diff/koppetsch_et_al__measurements_24863.diff
[STOP] [2020-12-03 12:02:26] calculate_delta
[START] [2020-12-03 12:02:26] parse_diff_and_store
[INFO] [2020-12-03 12:02:26] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 12:02:26] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 12:02:26] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 12:02:26] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 12:02:27] Storing 1 ScientificNames
[INFO] [2020-12-03 12:02:27] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 12:02:27] Average Time: 0.0
[INFO] [2020-12-03 12:02:27] Total Time: 1s
[INFO] [2020-12-03 12:02:27] Storing 1 Nodes
[INFO] [2020-12-03 12:02:27] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 12:02:27] Average Time: 0.0
[INFO] [2020-12-03 12:02:27] Total Time: 1s
[INFO] [2020-12-03 12:02:27] Storing 1 Occurrences
[INFO] [2020-12-03 12:02:27] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 12:02:27] Average Time: 0.0
[INFO] [2020-12-03 12:02:27] Total Time: 1s
[INFO] [2020-12-03 12:02:27] Storing 2 Traits
[INFO] [2020-12-03 12:02:27] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 12:02:27] Average Time: 0.0
[INFO] [2020-12-03 12:02:27] Total Time: 1s
[INFO] [2020-12-03 12:02:27] Storing 2 MetaTraits
[INFO] [2020-12-03 12:02:27] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 12:02:27] Average Time: 0.0
[INFO] [2020-12-03 12:02:27] Total Time: 1s
[STOP] [2020-12-03 12:02:27] parse_diff_and_store
[START] [2020-12-03 12:02:27] resolve_keys
[INFO] [2020-12-03 12:02:32] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 12:02:32] traits to occurrences...
[INFO] [2020-12-03 12:02:32] traits to nodes (through occurrences)...
[INFO] [2020-12-03 12:02:32] Traits to sex term...
[INFO] [2020-12-03 12:02:32] Traits to lifestage term...
[INFO] [2020-12-03 12:02:32] MetaTraits to traits...
[INFO] [2020-12-03 12:02:32] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 12:02:32] Assocs to occurrences...
[INFO] [2020-12-03 12:02:32] Assocs to nodes...
[INFO] [2020-12-03 12:02:32] Assoc to sex term...
[INFO] [2020-12-03 12:02:32] Assoc to lifestage term...
[INFO] [2020-12-03 12:02:32] MetaAssoc to assocs...
[STOP] [2020-12-03 12:02:32] resolve_keys
[START] [2020-12-03 12:02:32] hold_for_later_1
[STOP] [2020-12-03 12:02:32] hold_for_later_1
[START] [2020-12-03 12:02:32] hold_for_later_2
[STOP] [2020-12-03 12:02:32] hold_for_later_2
[START] [2020-12-03 12:02:32] resolve_missing_parents
[STOP] [2020-12-03 12:02:32] resolve_missing_parents
[START] [2020-12-03 12:02:32] rebuild_nodes
[START] [2020-12-03 12:02:32] Flattener#flatten
[START] [2020-12-03 12:02:32] Flattener#study_resource
[START] [2020-12-03 12:02:32] Flattener#build_ancestry
[STOP] [2020-12-03 12:02:32] Flattener#build_ancestry
[INFO] [2020-12-03 12:02:32] 1 ancestry keys
[START] [2020-12-03 12:02:32] build_node_ancestors
[INFO] [2020-12-03 12:02:32] old ancestors deleted.
[STOP] [2020-12-03 12:02:32] build_node_ancestors
[WARN] [2020-12-03 12:02:32] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 12:02:32] Flattener#flatten
[STOP] [2020-12-03 12:02:32] rebuild_nodes
[START] [2020-12-03 12:02:32] resolve_missing_media_owners
[STOP] [2020-12-03 12:02:32] resolve_missing_media_owners
[START] [2020-12-03 12:02:32] sanitize_media_verbatims
[STOP] [2020-12-03 12:02:32] sanitize_media_verbatims
[START] [2020-12-03 12:02:32] queue_downloads
[STOP] [2020-12-03 12:02:32] queue_downloads
[START] [2020-12-03 12:02:32] parse_names
[WARN] [2020-12-03 12:02:32] I see 1 names which still need to be parsed.
[STOP] [2020-12-03 12:02:34] parse_names
[START] [2020-12-03 12:02:34] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 12:02:34] denormalize_canonical_names_to_nodes
[START] [2020-12-03 12:02:34] match_nodes
[START] [2020-12-03 12:02:34] map_all_nodes_to_pages
[STOP] [2020-12-03 12:02:34] map_all_nodes_to_pages
[INFO] [2020-12-03 12:02:34] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-12-03 12:02:34] update_nodes
[STOP] [2020-12-03 12:02:34] update_nodes
[STOP] [2020-12-03 12:02:34] match_nodes
[START] [2020-12-03 12:02:34] reindex_search
[STOP] [2020-12-03 12:02:34] reindex_search
[START] [2020-12-03 12:02:34] normalize_units
[STOP] [2020-12-03 12:02:34] normalize_units
[START] [2020-12-03 12:02:34] calculate_statistics
[2020-12-03 12:02:34] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 12:02:34] calculate_statistics
[START] [2020-12-03 12:02:34] complete_harvest_instance
[START] [2020-12-03 12:02:34] overall_tsv_creation
[INFO] [2020-12-03 12:02:34] Processing group of 1 in 1 batches of 10000
[INFO] [2020-12-03 12:03:12] 1 Traits (unfiltered)...
[INFO] [2020-12-03 12:03:49] 1 Traits (filtered)...
[INFO] [2020-12-03 12:03:49] 0 Associations (filtered)...
[INFO] [2020-12-03 12:03:49] 3 metadata added.
[INFO] [2020-12-03 12:03:49] 0 metadata added.
[INFO] [2020-12-03 12:03:49] Average Time: 52.24
[INFO] [2020-12-03 12:03:49] Total Time: 1m16s
[STOP] [2020-12-03 12:03:49] overall_tsv_creation
[INFO] [2020-12-03 12:03:49] Done. Check your files:
[INFO] [2020-12-03 12:03:49] (1 lines) /app/public/data/koppetsch_et_al_/publish_nodes.tsv
[INFO] [2020-12-03 12:03:49] (1 lines) /app/public/data/koppetsch_et_al_/publish_scientific_names.tsv
[INFO] [2020-12-03 12:03:49] (2 lines) /app/public/data/koppetsch_et_al_/publish_traits.tsv
[INFO] [2020-12-03 12:03:49] (4 lines) /app/public/data/koppetsch_et_al_/publish_metadata.tsv
[STOP] [2020-12-03 12:03:49] complete_harvest_instance
[START] [2020-12-03 12:03:49] completed
[STOP] [2020-12-03 12:03:49] completed
[STOP] [2020-12-03 12:03:49] logged process, took 84.87
[INFO] [2021-04-19 15:36:32] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:51:05] ## remove_type: ScientificName
[INFO] [2021-04-19 15:51:05] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:51:05] [15:51:05.249] Removed 1 Scientificnames
[INFO] [2021-04-19 15:51:05] ## remove_type: Vernacular
[INFO] [2021-04-19 15:51:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:51:05] [15:51:05.250] Removed 0 Vernaculars
[INFO] [2021-04-19 15:51:05] ## remove_type: Article
[INFO] [2021-04-19 15:51:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:51:05] [15:51:05.252] Removed 0 Articles
[INFO] [2021-04-19 15:51:05] ## remove_type: Medium
[INFO] [2021-04-19 15:51:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:51:05] [15:51:05.254] Removed 0 Media
[INFO] [2021-04-19 15:51:05] ## remove_type: Trait
[INFO] [2021-04-19 15:51:05] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:51:05] [15:51:05.256] Removed 2 Traits
[INFO] [2021-04-19 15:51:05] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:51:05] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:51:05] [15:51:05.258] Removed 2 Metatraits
[INFO] [2021-04-19 15:51:05] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:51:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:51:05] [15:51:05.260] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 15:51:05] ## remove_type: Assoc
[INFO] [2021-04-19 15:51:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:51:05] [15:51:05.262] Removed 0 Assocs
[INFO] [2021-04-19 15:51:05] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:51:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:51:05] [15:51:05.263] Removed 0 Metaassocs
[INFO] [2021-04-19 15:51:05] ## remove_type: Identifier
[INFO] [2021-04-19 15:51:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:51:05] [15:51:05.265] Removed 0 Identifiers
[INFO] [2021-04-19 15:51:05] ## remove_type: Reference
[INFO] [2021-04-19 15:51:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:51:05] [15:51:05.266] Removed 0 References
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] Starting batch with ID 86116209...
[INFO] [2021-04-19 15:51:05] ## remove_type: Node
[INFO] [2021-04-19 15:51:05] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:51:05] [15:51:05.537] Removed 1 Nodes
[START] [2021-04-19 15:51:05] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:51:05] Creating resource from OpenData
[START] [2021-04-19 15:51:05] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:51:05] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:51:05] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:51:05] Creating resource from OpenData
[START] [2021-04-19 15:51:05] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:51:05] create_harvest_instance
[INFO] [2021-04-19 15:51:05] Created harvest instance #3780
[STOP] [2021-04-19 15:51:05] create_harvest_instance
[START] [2021-04-19 15:51:05] fetch_files
[STOP] [2021-04-19 15:51:05] fetch_files
[START] [2021-04-19 15:51:05] validate_each_file
[INFO] [2021-04-19 15:51:05] Looping over 4 formats...
[INFO] [2021-04-19 15:51:05] ...refs (/app/public/data/koppetsch_et_al_/references.tsv)
[INFO] [2021-04-19 15:51:05] Valid: /app/public/converted_csv/koppetsch_et_al__refs_3780.csv (0 lines)
[INFO] [2021-04-19 15:51:05] ...nodes (/app/public/data/koppetsch_et_al_/taxa.txt)
[INFO] [2021-04-19 15:51:05] Valid: /app/public/converted_csv/koppetsch_et_al__nodes_3780.csv (1 lines)
[INFO] [2021-04-19 15:51:05] ...occurrences (/app/public/data/koppetsch_et_al_/occurrences.txt)
[INFO] [2021-04-19 15:51:05] Valid: /app/public/converted_csv/koppetsch_et_al__occurrences_3780.csv (1 lines)
[INFO] [2021-04-19 15:51:05] ...measurements (/app/public/data/koppetsch_et_al_/measurementsorfacts.txt)
[INFO] [2021-04-19 15:51:05] Valid: /app/public/converted_csv/koppetsch_et_al__measurements_3780.csv (2 lines)
[STOP] [2021-04-19 15:51:05] validate_each_file
[START] [2021-04-19 15:51:05] convert_to_csv
[INFO] [2021-04-19 15:51:05] Looping over 4 formats...
[INFO] [2021-04-19 15:51:05] ...refs (/app/public/data/koppetsch_et_al_/references.tsv)
[CMD] [2021-04-19 15:51:05] /usr/bin/sort /app/public/converted_csv/koppetsch_et_al__refs_3780.csv > /app/public/converted_csv/koppetsch_et_al__refs_3780.csv_sorted
[INFO] [2021-04-19 15:51:05] Converted: /app/public/converted_csv/koppetsch_et_al__refs_3780.csv (0 lines)
[INFO] [2021-04-19 15:51:05] ...nodes (/app/public/data/koppetsch_et_al_/taxa.txt)
[CMD] [2021-04-19 15:51:05] /usr/bin/sort /app/public/converted_csv/koppetsch_et_al__nodes_3780.csv > /app/public/converted_csv/koppetsch_et_al__nodes_3780.csv_sorted
[INFO] [2021-04-19 15:51:06] Converted: /app/public/converted_csv/koppetsch_et_al__nodes_3780.csv (1 lines)
[INFO] [2021-04-19 15:51:06] ...occurrences (/app/public/data/koppetsch_et_al_/occurrences.txt)
[CMD] [2021-04-19 15:51:06] /usr/bin/sort /app/public/converted_csv/koppetsch_et_al__occurrences_3780.csv > /app/public/converted_csv/koppetsch_et_al__occurrences_3780.csv_sorted
[INFO] [2021-04-19 15:51:06] Converted: /app/public/converted_csv/koppetsch_et_al__occurrences_3780.csv (1 lines)
[INFO] [2021-04-19 15:51:06] ...measurements (/app/public/data/koppetsch_et_al_/measurementsorfacts.txt)
[CMD] [2021-04-19 15:51:06] /usr/bin/sort /app/public/converted_csv/koppetsch_et_al__measurements_3780.csv > /app/public/converted_csv/koppetsch_et_al__measurements_3780.csv_sorted
[INFO] [2021-04-19 15:51:06] Converted: /app/public/converted_csv/koppetsch_et_al__measurements_3780.csv (2 lines)
[STOP] [2021-04-19 15:51:06] convert_to_csv
[START] [2021-04-19 15:51:06] calculate_delta
[INFO] [2021-04-19 15:51:06] Looping over 4 formats...
[INFO] [2021-04-19 15:51:06] ...refs (/app/public/data/koppetsch_et_al_/references.tsv)
[CMD] [2021-04-19 15:51:06] echo "0a" > /app/public/diff/koppetsch_et_al__refs_3780.diff
[CMD] [2021-04-19 15:51:06] tail -n +1 /app/public/converted_csv/koppetsch_et_al__refs_3780.csv >> /app/public/diff/koppetsch_et_al__refs_3780.diff
[CMD] [2021-04-19 15:51:06] echo "." >> /app/public/diff/koppetsch_et_al__refs_3780.diff
[INFO] [2021-04-19 15:51:06] Created diff: /app/public/diff/koppetsch_et_al__refs_3780.diff (2 lines)
[INFO] [2021-04-19 15:51:06] ...nodes (/app/public/data/koppetsch_et_al_/taxa.txt)
[CMD] [2021-04-19 15:51:06] echo "0a" > /app/public/diff/koppetsch_et_al__nodes_3780.diff
[CMD] [2021-04-19 15:51:06] tail -n +1 /app/public/converted_csv/koppetsch_et_al__nodes_3780.csv >> /app/public/diff/koppetsch_et_al__nodes_3780.diff
[CMD] [2021-04-19 15:51:06] echo "." >> /app/public/diff/koppetsch_et_al__nodes_3780.diff
[INFO] [2021-04-19 15:51:06] Created diff: /app/public/diff/koppetsch_et_al__nodes_3780.diff (3 lines)
[INFO] [2021-04-19 15:51:06] ...occurrences (/app/public/data/koppetsch_et_al_/occurrences.txt)
[CMD] [2021-04-19 15:51:06] echo "0a" > /app/public/diff/koppetsch_et_al__occurrences_3780.diff
[CMD] [2021-04-19 15:51:06] tail -n +1 /app/public/converted_csv/koppetsch_et_al__occurrences_3780.csv >> /app/public/diff/koppetsch_et_al__occurrences_3780.diff
[CMD] [2021-04-19 15:51:06] echo "." >> /app/public/diff/koppetsch_et_al__occurrences_3780.diff
[INFO] [2021-04-19 15:51:06] Created diff: /app/public/diff/koppetsch_et_al__occurrences_3780.diff (3 lines)
[INFO] [2021-04-19 15:51:06] ...measurements (/app/public/data/koppetsch_et_al_/measurementsorfacts.txt)
[CMD] [2021-04-19 15:51:06] echo "0a" > /app/public/diff/koppetsch_et_al__measurements_3780.diff
[CMD] [2021-04-19 15:51:06] tail -n +1 /app/public/converted_csv/koppetsch_et_al__measurements_3780.csv >> /app/public/diff/koppetsch_et_al__measurements_3780.diff
[CMD] [2021-04-19 15:51:06] echo "." >> /app/public/diff/koppetsch_et_al__measurements_3780.diff
[INFO] [2021-04-19 15:51:06] Created diff: /app/public/diff/koppetsch_et_al__measurements_3780.diff (4 lines)
[STOP] [2021-04-19 15:51:06] calculate_delta
[START] [2021-04-19 15:51:06] parse_diff_and_store
[INFO] [2021-04-19 15:51:06] Handling diff: /app/public/diff/koppetsch_et_al__refs_3780.diff (2 lines)
[INFO] [2021-04-19 15:51:06] Loading refs diff file into memory (2 /app/public/diff/koppetsch_et_al__refs_3780.diff lines)...
[INFO] [2021-04-19 15:51:06] Handling diff: /app/public/diff/koppetsch_et_al__nodes_3780.diff (3 lines)
[INFO] [2021-04-19 15:51:06] Loading nodes diff file into memory (3 /app/public/diff/koppetsch_et_al__nodes_3780.diff lines)...
[INFO] [2021-04-19 15:51:06] Handling diff: /app/public/diff/koppetsch_et_al__occurrences_3780.diff (3 lines)
[INFO] [2021-04-19 15:51:06] Loading occurrences diff file into memory (3 /app/public/diff/koppetsch_et_al__occurrences_3780.diff lines)...
[INFO] [2021-04-19 15:51:06] Handling diff: /app/public/diff/koppetsch_et_al__measurements_3780.diff (4 lines)
[INFO] [2021-04-19 15:51:06] Loading measurements diff file into memory (4 /app/public/diff/koppetsch_et_al__measurements_3780.diff lines)...
[INFO] [2021-04-19 15:51:06] Storing 1 ScientificNames
[INFO] [2021-04-19 15:51:06] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:51:06] Average Time: 0.0
[INFO] [2021-04-19 15:51:06] Total Time: 1s
[INFO] [2021-04-19 15:51:06] Storing 1 Nodes
[INFO] [2021-04-19 15:51:06] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:51:06] Average Time: 0.0
[INFO] [2021-04-19 15:51:06] Total Time: 1s
[INFO] [2021-04-19 15:51:06] Storing 1 Occurrences
[INFO] [2021-04-19 15:51:06] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:51:06] Average Time: 0.0
[INFO] [2021-04-19 15:51:06] Total Time: 1s
[INFO] [2021-04-19 15:51:06] Storing 2 Traits
[INFO] [2021-04-19 15:51:06] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:51:06] Average Time: 0.0
[INFO] [2021-04-19 15:51:06] Total Time: 1s
[INFO] [2021-04-19 15:51:06] Storing 2 MetaTraits
[INFO] [2021-04-19 15:51:06] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:51:06] Average Time: 0.0
[INFO] [2021-04-19 15:51:06] Total Time: 1s
[STOP] [2021-04-19 15:51:06] parse_diff_and_store
[START] [2021-04-19 15:51:06] resolve_keys
[INFO] [2021-04-19 15:51:12] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:51:12] traits to occurrences...
[INFO] [2021-04-19 15:51:12] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:51:12] Traits to sex term...
[INFO] [2021-04-19 15:51:12] Traits to lifestage term...
[INFO] [2021-04-19 15:51:12] MetaTraits to traits...
[INFO] [2021-04-19 15:51:12] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:51:12] Assocs to occurrences...
[INFO] [2021-04-19 15:51:12] Assocs to nodes...
[INFO] [2021-04-19 15:51:12] Assoc to sex term...
[INFO] [2021-04-19 15:51:12] Assoc to lifestage term...
[INFO] [2021-04-19 15:51:12] MetaAssoc to assocs...
[STOP] [2021-04-19 15:51:12] resolve_keys
[START] [2021-04-19 15:51:12] hold_for_later_1
[STOP] [2021-04-19 15:51:12] hold_for_later_1
[START] [2021-04-19 15:51:12] hold_for_later_2
[STOP] [2021-04-19 15:51:12] hold_for_later_2
[START] [2021-04-19 15:51:12] resolve_missing_parents
[STOP] [2021-04-19 15:51:12] resolve_missing_parents
[START] [2021-04-19 15:51:12] rebuild_nodes
[START] [2021-04-19 15:51:12] Flattener#flatten
[START] [2021-04-19 15:51:12] Flattener#study_resource
[START] [2021-04-19 15:51:12] Flattener#build_ancestry
[STOP] [2021-04-19 15:51:12] Flattener#build_ancestry
[INFO] [2021-04-19 15:51:12] 1 ancestry keys
[START] [2021-04-19 15:51:12] build_node_ancestors
[INFO] [2021-04-19 15:51:12] old ancestors deleted.
[STOP] [2021-04-19 15:51:12] build_node_ancestors
[WARN] [2021-04-19 15:51:12] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:51:12] Flattener#flatten
[STOP] [2021-04-19 15:51:12] rebuild_nodes
[START] [2021-04-19 15:51:12] resolve_missing_media_owners
[STOP] [2021-04-19 15:51:12] resolve_missing_media_owners
[START] [2021-04-19 15:51:12] sanitize_media_verbatims
[STOP] [2021-04-19 15:51:12] sanitize_media_verbatims
[START] [2021-04-19 15:51:12] queue_downloads
[STOP] [2021-04-19 15:51:12] queue_downloads
[START] [2021-04-19 15:51:12] parse_names
[WARN] [2021-04-19 15:51:12] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 15:51:13] parse_names
[START] [2021-04-19 15:51:13] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:51:13] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:51:13] match_nodes
[START] [2021-04-19 15:51:13] map_all_nodes_to_pages
[STOP] [2021-04-19 15:51:13] map_all_nodes_to_pages
[INFO] [2021-04-19 15:51:13] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 15:51:13] update_nodes
[STOP] [2021-04-19 15:51:13] update_nodes
[STOP] [2021-04-19 15:51:13] match_nodes
[START] [2021-04-19 15:51:13] reindex_search
[STOP] [2021-04-19 15:51:13] reindex_search
[START] [2021-04-19 15:51:13] normalize_units
[STOP] [2021-04-19 15:51:13] normalize_units
[START] [2021-04-19 15:51:13] calculate_statistics
[2021-04-19 15:51:13] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:51:13] calculate_statistics
[START] [2021-04-19 15:51:13] complete_harvest_instance
[START] [2021-04-19 15:51:13] overall_tsv_creation
[INFO] [2021-04-19 15:51:13] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 15:51:48] 1 Traits (unfiltered)...
[INFO] [2021-04-19 15:52:20] 1 Traits (filtered)...
[INFO] [2021-04-19 15:52:20] 0 Associations (filtered)...
[INFO] [2021-04-19 15:52:20] 1 metadata added.
[INFO] [2021-04-19 15:52:20] 0 metadata added.
[INFO] [2021-04-19 15:52:47] Average Time: 69.96
[INFO] [2021-04-19 15:52:47] Total Time: 1m34s
[STOP] [2021-04-19 15:52:47] overall_tsv_creation
[INFO] [2021-04-19 15:52:47] Done. Check your files:
[INFO] [2021-04-19 15:52:47] (1 lines) /app/public/data/koppetsch_et_al_/publish_nodes.tsv
[INFO] [2021-04-19 15:52:47] (1 lines) /app/public/data/koppetsch_et_al_/publish_scientific_names.tsv
[INFO] [2021-04-19 15:52:47] (2 lines) /app/public/data/koppetsch_et_al_/publish_traits.tsv
[INFO] [2021-04-19 15:52:47] (2 lines) /app/public/data/koppetsch_et_al_/publish_metadata.tsv
[STOP] [2021-04-19 15:52:47] complete_harvest_instance
[START] [2021-04-19 15:52:47] completed
[STOP] [2021-04-19 15:52:47] completed
[STOP] [2021-04-19 15:52:47] logged process, took 101.36
Latest Process