Harvest for
Tsurnamal 2008
Created
19 Apr 15:37
Stage:
completed
Fetched:
19 Apr 15:37
Validated:
19 Apr 15:37
Deltas Created
19 Apr 15:37
Units Normalized:
19 Apr 15:37
Ancestry Built:
19 Apr 15:37
Nodes Matched:
19 Apr 15:37
Names Parsed:
19 Apr 15:37
New Models Stored:
19 Apr 15:37
Indexed:
19 Apr 15:37
Completed:
19 Apr 15:38
Time to Harvest:
less than a minute
Harvesting Log
(431 lines)
# Logfile created on 2020-08-27 15:43:13 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:43:13] logged process
[START] [2020-08-27 15:43:13] Creating resource from OpenData
[START] [2020-08-27 15:43:13] logged process
[START] [2020-08-27 15:43:13] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:43:14] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:43:14] Creating resource from OpenData
[INFO] [2020-12-03 11:31:15] ## HARVEST: type = -harvest
[START] [2020-12-03 11:31:17] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-12-03 11:31:17] create_harvest_instance
[STOP] [2020-12-03 11:31:18] create_harvest_instance
[START] [2020-12-03 11:31:18] fetch_files
[STOP] [2020-12-03 11:31:18] fetch_files
[START] [2020-12-03 11:31:18] validate_each_file
[STOP] [2020-12-03 11:31:19] validate_each_file
[START] [2020-12-03 11:31:19] convert_to_csv
[CMD] [2020-12-03 11:31:19] /usr/bin/sort /app/public/converted_csv/tsurnamal_tsurna_refs_24820.csv > /app/public/converted_csv/tsurnamal_tsurna_refs_24820.csv_sorted
[CMD] [2020-12-03 11:31:19] /usr/bin/sort /app/public/converted_csv/tsurnamal_tsurna_nodes_24821.csv > /app/public/converted_csv/tsurnamal_tsurna_nodes_24821.csv_sorted
[CMD] [2020-12-03 11:31:19] /usr/bin/sort /app/public/converted_csv/tsurnamal_tsurna_occurrences_24822.csv > /app/public/converted_csv/tsurnamal_tsurna_occurrences_24822.csv_sorted
[CMD] [2020-12-03 11:31:19] /usr/bin/sort /app/public/converted_csv/tsurnamal_tsurna_measurements_24823.csv > /app/public/converted_csv/tsurnamal_tsurna_measurements_24823.csv_sorted
[STOP] [2020-12-03 11:31:19] convert_to_csv
[START] [2020-12-03 11:31:19] calculate_delta
[CMD] [2020-12-03 11:31:19] echo "0a" > /app/public/diff/tsurnamal_tsurna_refs_24820.diff
[CMD] [2020-12-03 11:31:19] tail -n +1 /app/public/converted_csv/tsurnamal_tsurna_refs_24820.csv >> /app/public/diff/tsurnamal_tsurna_refs_24820.diff
[CMD] [2020-12-03 11:31:19] echo "." >> /app/public/diff/tsurnamal_tsurna_refs_24820.diff
[CMD] [2020-12-03 11:31:19] echo "0a" > /app/public/diff/tsurnamal_tsurna_nodes_24821.diff
[CMD] [2020-12-03 11:31:19] tail -n +1 /app/public/converted_csv/tsurnamal_tsurna_nodes_24821.csv >> /app/public/diff/tsurnamal_tsurna_nodes_24821.diff
[CMD] [2020-12-03 11:31:19] echo "." >> /app/public/diff/tsurnamal_tsurna_nodes_24821.diff
[CMD] [2020-12-03 11:31:19] echo "0a" > /app/public/diff/tsurnamal_tsurna_occurrences_24822.diff
[CMD] [2020-12-03 11:31:19] tail -n +1 /app/public/converted_csv/tsurnamal_tsurna_occurrences_24822.csv >> /app/public/diff/tsurnamal_tsurna_occurrences_24822.diff
[CMD] [2020-12-03 11:31:19] echo "." >> /app/public/diff/tsurnamal_tsurna_occurrences_24822.diff
[CMD] [2020-12-03 11:31:19] echo "0a" > /app/public/diff/tsurnamal_tsurna_measurements_24823.diff
[CMD] [2020-12-03 11:31:19] tail -n +1 /app/public/converted_csv/tsurnamal_tsurna_measurements_24823.csv >> /app/public/diff/tsurnamal_tsurna_measurements_24823.diff
[CMD] [2020-12-03 11:31:19] echo "." >> /app/public/diff/tsurnamal_tsurna_measurements_24823.diff
[STOP] [2020-12-03 11:31:19] calculate_delta
[START] [2020-12-03 11:31:19] parse_diff_and_store
[INFO] [2020-12-03 11:31:19] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 11:31:19] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 11:31:19] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 11:31:19] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 11:31:20] Storing 1 ScientificNames
[INFO] [2020-12-03 11:31:20] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:31:20] Average Time: 0.0
[INFO] [2020-12-03 11:31:20] Total Time: 1s
[INFO] [2020-12-03 11:31:20] Storing 1 Nodes
[INFO] [2020-12-03 11:31:20] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:31:20] Average Time: 0.0
[INFO] [2020-12-03 11:31:20] Total Time: 1s
[INFO] [2020-12-03 11:31:20] Storing 1 Occurrences
[INFO] [2020-12-03 11:31:20] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:31:20] Average Time: 0.0
[INFO] [2020-12-03 11:31:20] Total Time: 1s
[INFO] [2020-12-03 11:31:20] Storing 2 Traits
[INFO] [2020-12-03 11:31:20] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 11:31:20] Average Time: 0.0
[INFO] [2020-12-03 11:31:20] Total Time: 1s
[INFO] [2020-12-03 11:31:20] Storing 1 MetaTraits
[INFO] [2020-12-03 11:31:20] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:31:20] Average Time: 0.0
[INFO] [2020-12-03 11:31:20] Total Time: 1s
[STOP] [2020-12-03 11:31:20] parse_diff_and_store
[START] [2020-12-03 11:31:20] resolve_keys
[INFO] [2020-12-03 11:31:25] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 11:31:25] traits to occurrences...
[INFO] [2020-12-03 11:31:25] traits to nodes (through occurrences)...
[INFO] [2020-12-03 11:31:25] Traits to sex term...
[INFO] [2020-12-03 11:31:25] Traits to lifestage term...
[INFO] [2020-12-03 11:31:25] MetaTraits to traits...
[INFO] [2020-12-03 11:31:25] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 11:31:25] Assocs to occurrences...
[INFO] [2020-12-03 11:31:25] Assocs to nodes...
[INFO] [2020-12-03 11:31:25] Assoc to sex term...
[INFO] [2020-12-03 11:31:25] Assoc to lifestage term...
[INFO] [2020-12-03 11:31:25] MetaAssoc to assocs...
[STOP] [2020-12-03 11:31:25] resolve_keys
[START] [2020-12-03 11:31:25] hold_for_later_1
[STOP] [2020-12-03 11:31:25] hold_for_later_1
[START] [2020-12-03 11:31:25] hold_for_later_2
[STOP] [2020-12-03 11:31:25] hold_for_later_2
[START] [2020-12-03 11:31:25] resolve_missing_parents
[STOP] [2020-12-03 11:31:25] resolve_missing_parents
[START] [2020-12-03 11:31:25] rebuild_nodes
[START] [2020-12-03 11:31:25] Flattener#flatten
[START] [2020-12-03 11:31:25] Flattener#study_resource
[START] [2020-12-03 11:31:25] Flattener#build_ancestry
[STOP] [2020-12-03 11:31:25] Flattener#build_ancestry
[INFO] [2020-12-03 11:31:25] 1 ancestry keys
[START] [2020-12-03 11:31:25] build_node_ancestors
[INFO] [2020-12-03 11:31:25] old ancestors deleted.
[STOP] [2020-12-03 11:31:25] build_node_ancestors
[WARN] [2020-12-03 11:31:25] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 11:31:25] Flattener#flatten
[STOP] [2020-12-03 11:31:25] rebuild_nodes
[START] [2020-12-03 11:31:25] resolve_missing_media_owners
[STOP] [2020-12-03 11:31:25] resolve_missing_media_owners
[START] [2020-12-03 11:31:25] sanitize_media_verbatims
[STOP] [2020-12-03 11:31:25] sanitize_media_verbatims
[START] [2020-12-03 11:31:25] queue_downloads
[STOP] [2020-12-03 11:31:25] queue_downloads
[START] [2020-12-03 11:31:25] parse_names
[WARN] [2020-12-03 11:31:25] I see 1 names which still need to be parsed.
[STOP] [2020-12-03 11:31:27] parse_names
[START] [2020-12-03 11:31:27] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 11:31:27] denormalize_canonical_names_to_nodes
[START] [2020-12-03 11:31:27] match_nodes
[START] [2020-12-03 11:31:27] map_all_nodes_to_pages
[STOP] [2020-12-03 11:31:27] map_all_nodes_to_pages
[INFO] [2020-12-03 11:31:27] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-12-03 11:31:27] update_nodes
[STOP] [2020-12-03 11:31:27] update_nodes
[STOP] [2020-12-03 11:31:27] match_nodes
[START] [2020-12-03 11:31:27] reindex_search
[STOP] [2020-12-03 11:31:27] reindex_search
[START] [2020-12-03 11:31:27] normalize_units
[STOP] [2020-12-03 11:31:27] normalize_units
[START] [2020-12-03 11:31:27] calculate_statistics
[2020-12-03 11:31:27] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 11:31:27] calculate_statistics
[START] [2020-12-03 11:31:27] complete_harvest_instance
[START] [2020-12-03 11:31:27] overall_tsv_creation
[INFO] [2020-12-03 11:31:27] Processing group of 1 in 1 batches of 10000
[INFO] [2020-12-03 11:32:05] 1 Traits (unfiltered)...
[INFO] [2020-12-03 11:32:41] 1 Traits (filtered)...
[INFO] [2020-12-03 11:32:41] 0 Associations (filtered)...
[INFO] [2020-12-03 11:32:41] 2 metadata added.
[INFO] [2020-12-03 11:32:41] 0 metadata added.
[INFO] [2020-12-03 11:32:41] Average Time: 51.92
[INFO] [2020-12-03 11:32:41] Total Time: 1m15s
[STOP] [2020-12-03 11:32:41] overall_tsv_creation
[INFO] [2020-12-03 11:32:41] Done. Check your files:
[INFO] [2020-12-03 11:32:41] (1 lines) /app/public/data/tsurnamal_tsurna/publish_nodes.tsv
[INFO] [2020-12-03 11:32:41] (1 lines) /app/public/data/tsurnamal_tsurna/publish_scientific_names.tsv
[INFO] [2020-12-03 11:32:41] (2 lines) /app/public/data/tsurnamal_tsurna/publish_traits.tsv
[INFO] [2020-12-03 11:32:41] (3 lines) /app/public/data/tsurnamal_tsurna/publish_metadata.tsv
[STOP] [2020-12-03 11:32:41] complete_harvest_instance
[START] [2020-12-03 11:32:41] completed
[STOP] [2020-12-03 11:32:41] completed
[STOP] [2020-12-03 11:32:41] logged process, took 84.26
[INFO] [2021-04-19 15:35:59] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:37:06] ## remove_type: ScientificName
[INFO] [2021-04-19 15:37:06] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:37:06] [15:37:06.802] Removed 1 Scientificnames
[INFO] [2021-04-19 15:37:06] ## remove_type: Vernacular
[INFO] [2021-04-19 15:37:06] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:37:06] [15:37:06.803] Removed 0 Vernaculars
[INFO] [2021-04-19 15:37:06] ## remove_type: Article
[INFO] [2021-04-19 15:37:06] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:37:06] [15:37:06.805] Removed 0 Articles
[INFO] [2021-04-19 15:37:06] ## remove_type: Medium
[INFO] [2021-04-19 15:37:06] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:37:06] [15:37:06.806] Removed 0 Media
[INFO] [2021-04-19 15:37:06] ## remove_type: Trait
[INFO] [2021-04-19 15:37:06] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:37:06] [15:37:06.808] Removed 2 Traits
[INFO] [2021-04-19 15:37:06] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:37:06] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:37:06] [15:37:06.810] Removed 1 Metatraits
[INFO] [2021-04-19 15:37:06] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:37:06] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:37:06] [15:37:06.811] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 15:37:06] ## remove_type: Assoc
[INFO] [2021-04-19 15:37:06] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:37:06] [15:37:06.813] Removed 0 Assocs
[INFO] [2021-04-19 15:37:06] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:37:06] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:37:06] [15:37:06.814] Removed 0 Metaassocs
[INFO] [2021-04-19 15:37:06] ## remove_type: Identifier
[INFO] [2021-04-19 15:37:06] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:37:06] [15:37:06.816] Removed 0 Identifiers
[INFO] [2021-04-19 15:37:06] ## remove_type: Reference
[INFO] [2021-04-19 15:37:06] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:37:06] [15:37:06.817] Removed 0 References
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:06] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] Starting batch with ID 86115921...
[INFO] [2021-04-19 15:37:07] ## remove_type: Node
[INFO] [2021-04-19 15:37:07] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:37:07] [15:37:07.393] Removed 1 Nodes
[START] [2021-04-19 15:37:07] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:37:07] Creating resource from OpenData
[START] [2021-04-19 15:37:07] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:37:07] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:37:07] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:37:07] Creating resource from OpenData
[START] [2021-04-19 15:37:07] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:37:07] create_harvest_instance
[INFO] [2021-04-19 15:37:07] Created harvest instance #3772
[STOP] [2021-04-19 15:37:07] create_harvest_instance
[START] [2021-04-19 15:37:07] fetch_files
[STOP] [2021-04-19 15:37:07] fetch_files
[START] [2021-04-19 15:37:07] validate_each_file
[INFO] [2021-04-19 15:37:07] Looping over 4 formats...
[INFO] [2021-04-19 15:37:07] ...refs (/app/public/data/tsurnamal_tsurna/references.tsv)
[INFO] [2021-04-19 15:37:07] Valid: /app/public/converted_csv/tsurnamal_tsurna_refs_3772.csv (0 lines)
[INFO] [2021-04-19 15:37:07] ...nodes (/app/public/data/tsurnamal_tsurna/taxa.txt)
[INFO] [2021-04-19 15:37:07] Valid: /app/public/converted_csv/tsurnamal_tsurna_nodes_3772.csv (1 lines)
[INFO] [2021-04-19 15:37:07] ...occurrences (/app/public/data/tsurnamal_tsurna/occurrences.txt)
[INFO] [2021-04-19 15:37:07] Valid: /app/public/converted_csv/tsurnamal_tsurna_occurrences_3772.csv (1 lines)
[INFO] [2021-04-19 15:37:07] ...measurements (/app/public/data/tsurnamal_tsurna/measurementsorfacts.txt)
[INFO] [2021-04-19 15:37:07] Valid: /app/public/converted_csv/tsurnamal_tsurna_measurements_3772.csv (2 lines)
[STOP] [2021-04-19 15:37:07] validate_each_file
[START] [2021-04-19 15:37:07] convert_to_csv
[INFO] [2021-04-19 15:37:07] Looping over 4 formats...
[INFO] [2021-04-19 15:37:07] ...refs (/app/public/data/tsurnamal_tsurna/references.tsv)
[CMD] [2021-04-19 15:37:07] /usr/bin/sort /app/public/converted_csv/tsurnamal_tsurna_refs_3772.csv > /app/public/converted_csv/tsurnamal_tsurna_refs_3772.csv_sorted
[INFO] [2021-04-19 15:37:07] Converted: /app/public/converted_csv/tsurnamal_tsurna_refs_3772.csv (0 lines)
[INFO] [2021-04-19 15:37:07] ...nodes (/app/public/data/tsurnamal_tsurna/taxa.txt)
[CMD] [2021-04-19 15:37:07] /usr/bin/sort /app/public/converted_csv/tsurnamal_tsurna_nodes_3772.csv > /app/public/converted_csv/tsurnamal_tsurna_nodes_3772.csv_sorted
[INFO] [2021-04-19 15:37:07] Converted: /app/public/converted_csv/tsurnamal_tsurna_nodes_3772.csv (1 lines)
[INFO] [2021-04-19 15:37:07] ...occurrences (/app/public/data/tsurnamal_tsurna/occurrences.txt)
[CMD] [2021-04-19 15:37:07] /usr/bin/sort /app/public/converted_csv/tsurnamal_tsurna_occurrences_3772.csv > /app/public/converted_csv/tsurnamal_tsurna_occurrences_3772.csv_sorted
[INFO] [2021-04-19 15:37:07] Converted: /app/public/converted_csv/tsurnamal_tsurna_occurrences_3772.csv (1 lines)
[INFO] [2021-04-19 15:37:07] ...measurements (/app/public/data/tsurnamal_tsurna/measurementsorfacts.txt)
[CMD] [2021-04-19 15:37:07] /usr/bin/sort /app/public/converted_csv/tsurnamal_tsurna_measurements_3772.csv > /app/public/converted_csv/tsurnamal_tsurna_measurements_3772.csv_sorted
[INFO] [2021-04-19 15:37:07] Converted: /app/public/converted_csv/tsurnamal_tsurna_measurements_3772.csv (2 lines)
[STOP] [2021-04-19 15:37:07] convert_to_csv
[START] [2021-04-19 15:37:08] calculate_delta
[INFO] [2021-04-19 15:37:08] Looping over 4 formats...
[INFO] [2021-04-19 15:37:08] ...refs (/app/public/data/tsurnamal_tsurna/references.tsv)
[CMD] [2021-04-19 15:37:08] echo "0a" > /app/public/diff/tsurnamal_tsurna_refs_3772.diff
[CMD] [2021-04-19 15:37:08] tail -n +1 /app/public/converted_csv/tsurnamal_tsurna_refs_3772.csv >> /app/public/diff/tsurnamal_tsurna_refs_3772.diff
[CMD] [2021-04-19 15:37:08] echo "." >> /app/public/diff/tsurnamal_tsurna_refs_3772.diff
[INFO] [2021-04-19 15:37:08] Created diff: /app/public/diff/tsurnamal_tsurna_refs_3772.diff (2 lines)
[INFO] [2021-04-19 15:37:08] ...nodes (/app/public/data/tsurnamal_tsurna/taxa.txt)
[CMD] [2021-04-19 15:37:08] echo "0a" > /app/public/diff/tsurnamal_tsurna_nodes_3772.diff
[CMD] [2021-04-19 15:37:08] tail -n +1 /app/public/converted_csv/tsurnamal_tsurna_nodes_3772.csv >> /app/public/diff/tsurnamal_tsurna_nodes_3772.diff
[CMD] [2021-04-19 15:37:08] echo "." >> /app/public/diff/tsurnamal_tsurna_nodes_3772.diff
[INFO] [2021-04-19 15:37:08] Created diff: /app/public/diff/tsurnamal_tsurna_nodes_3772.diff (3 lines)
[INFO] [2021-04-19 15:37:08] ...occurrences (/app/public/data/tsurnamal_tsurna/occurrences.txt)
[CMD] [2021-04-19 15:37:08] echo "0a" > /app/public/diff/tsurnamal_tsurna_occurrences_3772.diff
[CMD] [2021-04-19 15:37:08] tail -n +1 /app/public/converted_csv/tsurnamal_tsurna_occurrences_3772.csv >> /app/public/diff/tsurnamal_tsurna_occurrences_3772.diff
[CMD] [2021-04-19 15:37:08] echo "." >> /app/public/diff/tsurnamal_tsurna_occurrences_3772.diff
[INFO] [2021-04-19 15:37:08] Created diff: /app/public/diff/tsurnamal_tsurna_occurrences_3772.diff (3 lines)
[INFO] [2021-04-19 15:37:08] ...measurements (/app/public/data/tsurnamal_tsurna/measurementsorfacts.txt)
[CMD] [2021-04-19 15:37:08] echo "0a" > /app/public/diff/tsurnamal_tsurna_measurements_3772.diff
[CMD] [2021-04-19 15:37:08] tail -n +1 /app/public/converted_csv/tsurnamal_tsurna_measurements_3772.csv >> /app/public/diff/tsurnamal_tsurna_measurements_3772.diff
[CMD] [2021-04-19 15:37:08] echo "." >> /app/public/diff/tsurnamal_tsurna_measurements_3772.diff
[INFO] [2021-04-19 15:37:08] Created diff: /app/public/diff/tsurnamal_tsurna_measurements_3772.diff (4 lines)
[STOP] [2021-04-19 15:37:08] calculate_delta
[START] [2021-04-19 15:37:08] parse_diff_and_store
[INFO] [2021-04-19 15:37:08] Handling diff: /app/public/diff/tsurnamal_tsurna_refs_3772.diff (2 lines)
[INFO] [2021-04-19 15:37:08] Loading refs diff file into memory (2 /app/public/diff/tsurnamal_tsurna_refs_3772.diff lines)...
[INFO] [2021-04-19 15:37:08] Handling diff: /app/public/diff/tsurnamal_tsurna_nodes_3772.diff (3 lines)
[INFO] [2021-04-19 15:37:08] Loading nodes diff file into memory (3 /app/public/diff/tsurnamal_tsurna_nodes_3772.diff lines)...
[INFO] [2021-04-19 15:37:08] Handling diff: /app/public/diff/tsurnamal_tsurna_occurrences_3772.diff (3 lines)
[INFO] [2021-04-19 15:37:08] Loading occurrences diff file into memory (3 /app/public/diff/tsurnamal_tsurna_occurrences_3772.diff lines)...
[INFO] [2021-04-19 15:37:08] Handling diff: /app/public/diff/tsurnamal_tsurna_measurements_3772.diff (4 lines)
[INFO] [2021-04-19 15:37:08] Loading measurements diff file into memory (4 /app/public/diff/tsurnamal_tsurna_measurements_3772.diff lines)...
[INFO] [2021-04-19 15:37:08] Storing 1 ScientificNames
[INFO] [2021-04-19 15:37:08] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:37:08] Average Time: 0.0
[INFO] [2021-04-19 15:37:08] Total Time: 1s
[INFO] [2021-04-19 15:37:08] Storing 1 Nodes
[INFO] [2021-04-19 15:37:08] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:37:08] Average Time: 0.0
[INFO] [2021-04-19 15:37:08] Total Time: 1s
[INFO] [2021-04-19 15:37:08] Storing 1 Occurrences
[INFO] [2021-04-19 15:37:08] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:37:08] Average Time: 0.0
[INFO] [2021-04-19 15:37:08] Total Time: 1s
[INFO] [2021-04-19 15:37:08] Storing 2 Traits
[INFO] [2021-04-19 15:37:08] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:37:08] Average Time: 0.0
[INFO] [2021-04-19 15:37:08] Total Time: 1s
[INFO] [2021-04-19 15:37:08] Storing 1 MetaTraits
[INFO] [2021-04-19 15:37:08] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:37:08] Average Time: 0.0
[INFO] [2021-04-19 15:37:08] Total Time: 1s
[STOP] [2021-04-19 15:37:08] parse_diff_and_store
[START] [2021-04-19 15:37:08] resolve_keys
[INFO] [2021-04-19 15:37:14] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:37:14] traits to occurrences...
[INFO] [2021-04-19 15:37:14] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:37:14] Traits to sex term...
[INFO] [2021-04-19 15:37:14] Traits to lifestage term...
[INFO] [2021-04-19 15:37:14] MetaTraits to traits...
[INFO] [2021-04-19 15:37:14] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:37:14] Assocs to occurrences...
[INFO] [2021-04-19 15:37:14] Assocs to nodes...
[INFO] [2021-04-19 15:37:14] Assoc to sex term...
[INFO] [2021-04-19 15:37:14] Assoc to lifestage term...
[INFO] [2021-04-19 15:37:14] MetaAssoc to assocs...
[STOP] [2021-04-19 15:37:14] resolve_keys
[START] [2021-04-19 15:37:14] hold_for_later_1
[STOP] [2021-04-19 15:37:14] hold_for_later_1
[START] [2021-04-19 15:37:14] hold_for_later_2
[STOP] [2021-04-19 15:37:14] hold_for_later_2
[START] [2021-04-19 15:37:14] resolve_missing_parents
[STOP] [2021-04-19 15:37:14] resolve_missing_parents
[START] [2021-04-19 15:37:14] rebuild_nodes
[START] [2021-04-19 15:37:14] Flattener#flatten
[START] [2021-04-19 15:37:14] Flattener#study_resource
[START] [2021-04-19 15:37:14] Flattener#build_ancestry
[STOP] [2021-04-19 15:37:14] Flattener#build_ancestry
[INFO] [2021-04-19 15:37:14] 1 ancestry keys
[START] [2021-04-19 15:37:14] build_node_ancestors
[INFO] [2021-04-19 15:37:14] old ancestors deleted.
[STOP] [2021-04-19 15:37:14] build_node_ancestors
[WARN] [2021-04-19 15:37:14] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:37:14] Flattener#flatten
[STOP] [2021-04-19 15:37:14] rebuild_nodes
[START] [2021-04-19 15:37:14] resolve_missing_media_owners
[STOP] [2021-04-19 15:37:14] resolve_missing_media_owners
[START] [2021-04-19 15:37:14] sanitize_media_verbatims
[STOP] [2021-04-19 15:37:14] sanitize_media_verbatims
[START] [2021-04-19 15:37:14] queue_downloads
[STOP] [2021-04-19 15:37:14] queue_downloads
[START] [2021-04-19 15:37:14] parse_names
[WARN] [2021-04-19 15:37:14] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 15:37:15] parse_names
[START] [2021-04-19 15:37:15] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:37:15] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:37:15] match_nodes
[START] [2021-04-19 15:37:15] map_all_nodes_to_pages
[STOP] [2021-04-19 15:37:15] map_all_nodes_to_pages
[INFO] [2021-04-19 15:37:15] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 15:37:15] update_nodes
[STOP] [2021-04-19 15:37:15] update_nodes
[STOP] [2021-04-19 15:37:15] match_nodes
[START] [2021-04-19 15:37:15] reindex_search
[STOP] [2021-04-19 15:37:15] reindex_search
[START] [2021-04-19 15:37:15] normalize_units
[STOP] [2021-04-19 15:37:15] normalize_units
[START] [2021-04-19 15:37:15] calculate_statistics
[2021-04-19 15:37:15] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:37:15] calculate_statistics
[START] [2021-04-19 15:37:15] complete_harvest_instance
[START] [2021-04-19 15:37:15] overall_tsv_creation
[INFO] [2021-04-19 15:37:15] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 15:37:51] 1 Traits (unfiltered)...
[INFO] [2021-04-19 15:38:24] 1 Traits (filtered)...
[INFO] [2021-04-19 15:38:24] 0 Associations (filtered)...
[INFO] [2021-04-19 15:38:24] 1 metadata added.
[INFO] [2021-04-19 15:38:24] 0 metadata added.
[INFO] [2021-04-19 15:38:51] Average Time: 71.7
[INFO] [2021-04-19 15:38:51] Total Time: 1m36s
[STOP] [2021-04-19 15:38:51] overall_tsv_creation
[INFO] [2021-04-19 15:38:51] Done. Check your files:
[INFO] [2021-04-19 15:38:51] (1 lines) /app/public/data/tsurnamal_tsurna/publish_nodes.tsv
[INFO] [2021-04-19 15:38:51] (1 lines) /app/public/data/tsurnamal_tsurna/publish_scientific_names.tsv
[INFO] [2021-04-19 15:38:51] (2 lines) /app/public/data/tsurnamal_tsurna/publish_traits.tsv
[INFO] [2021-04-19 15:38:51] (2 lines) /app/public/data/tsurnamal_tsurna/publish_metadata.tsv
[STOP] [2021-04-19 15:38:51] complete_harvest_instance
[START] [2021-04-19 15:38:51] completed
[STOP] [2021-04-19 15:38:51] completed
[STOP] [2021-04-19 15:38:51] logged process, took 103.59
Latest Process