Harvest for
Kornicker 1991
Created
19 Apr 14:57
Stage:
completed
Fetched:
19 Apr 14:57
Validated:
19 Apr 14:57
Deltas Created
19 Apr 14:57
Units Normalized:
19 Apr 14:57
Ancestry Built:
19 Apr 14:57
Nodes Matched:
19 Apr 14:57
Names Parsed:
19 Apr 14:57
New Models Stored:
19 Apr 14:57
Indexed:
19 Apr 14:57
Completed:
19 Apr 14:58
Time to Harvest:
less than a minute
Harvesting Log
(476 lines)
# Logfile created on 2020-08-27 15:23:26 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:23:26] logged process
[START] [2020-08-27 15:23:26] Creating resource from OpenData
[START] [2020-08-27 15:23:26] logged process
[START] [2020-08-27 15:23:26] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:23:26] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:23:26] Creating resource from OpenData
[INFO] [2020-11-19 13:34:25] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-11-19 13:34:25] ## remove_type: ScientificName
[INFO] [2020-11-19 13:34:25] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:34:25] [13:34:25.744] Removed 0 Scientificnames
[INFO] [2020-11-19 13:34:25] ## remove_type: Vernacular
[INFO] [2020-11-19 13:34:25] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:34:25] [13:34:25.746] Removed 0 Vernaculars
[INFO] [2020-11-19 13:34:25] ## remove_type: Article
[INFO] [2020-11-19 13:34:25] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:34:25] [13:34:25.750] Removed 0 Articles
[INFO] [2020-11-19 13:34:25] ## remove_type: Medium
[INFO] [2020-11-19 13:34:25] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:34:25] [13:34:25.753] Removed 0 Media
[INFO] [2020-11-19 13:34:25] ## remove_type: Trait
[INFO] [2020-11-19 13:34:25] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:34:25] [13:34:25.756] Removed 0 Traits
[INFO] [2020-11-19 13:34:25] ## remove_type: MetaTrait
[INFO] [2020-11-19 13:34:25] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:34:25] [13:34:25.759] Removed 0 Metatraits
[INFO] [2020-11-19 13:34:25] ## remove_type: OccurrenceMetadatum
[INFO] [2020-11-19 13:34:25] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:34:25] [13:34:25.762] Removed 0 Occurrencemetadata
[INFO] [2020-11-19 13:34:25] ## remove_type: Assoc
[INFO] [2020-11-19 13:34:25] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:34:25] [13:34:25.765] Removed 0 Assocs
[INFO] [2020-11-19 13:34:25] ## remove_type: MetaAssoc
[INFO] [2020-11-19 13:34:25] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:34:25] [13:34:25.768] Removed 0 Metaassocs
[INFO] [2020-11-19 13:34:25] ## remove_type: Identifier
[INFO] [2020-11-19 13:34:25] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:34:25] [13:34:25.770] Removed 0 Identifiers
[INFO] [2020-11-19 13:34:25] ## remove_type: Reference
[INFO] [2020-11-19 13:34:25] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:34:25] [13:34:25.772] Removed 0 References
[INFO] [2020-11-19 13:34:25] ## remove_type: Node
[INFO] [2020-11-19 13:34:25] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:34:25] [13:34:25.794] Removed 0 Nodes
[START] [2020-11-19 13:34:25] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 13:34:25] Creating resource from OpenData
[START] [2020-11-19 13:34:25] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 13:34:25] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 13:34:26] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 13:34:26] Creating resource from OpenData
[START] [2020-11-19 13:34:26] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 13:34:26] create_harvest_instance
[STOP] [2020-11-19 13:34:27] create_harvest_instance
[START] [2020-11-19 13:34:27] fetch_files
[STOP] [2020-11-19 13:34:27] fetch_files
[START] [2020-11-19 13:34:27] validate_each_file
[STOP] [2020-11-19 13:34:27] validate_each_file
[START] [2020-11-19 13:34:27] convert_to_csv
[CMD] [2020-11-19 13:34:27] /usr/bin/sort /app/public/converted_csv/kornicker_kornic_refs_24430.csv > /app/public/converted_csv/kornicker_kornic_refs_24430.csv_sorted
[CMD] [2020-11-19 13:34:27] /usr/bin/sort /app/public/converted_csv/kornicker_kornic_nodes_24431.csv > /app/public/converted_csv/kornicker_kornic_nodes_24431.csv_sorted
[CMD] [2020-11-19 13:34:27] /usr/bin/sort /app/public/converted_csv/kornicker_kornic_occurrences_24432.csv > /app/public/converted_csv/kornicker_kornic_occurrences_24432.csv_sorted
[CMD] [2020-11-19 13:34:27] /usr/bin/sort /app/public/converted_csv/kornicker_kornic_measurements_24433.csv > /app/public/converted_csv/kornicker_kornic_measurements_24433.csv_sorted
[STOP] [2020-11-19 13:34:27] convert_to_csv
[START] [2020-11-19 13:34:27] calculate_delta
[CMD] [2020-11-19 13:34:27] echo "0a" > /app/public/diff/kornicker_kornic_refs_24430.diff
[CMD] [2020-11-19 13:34:27] tail -n +1 /app/public/converted_csv/kornicker_kornic_refs_24430.csv >> /app/public/diff/kornicker_kornic_refs_24430.diff
[CMD] [2020-11-19 13:34:27] echo "." >> /app/public/diff/kornicker_kornic_refs_24430.diff
[CMD] [2020-11-19 13:34:27] echo "0a" > /app/public/diff/kornicker_kornic_nodes_24431.diff
[CMD] [2020-11-19 13:34:27] tail -n +1 /app/public/converted_csv/kornicker_kornic_nodes_24431.csv >> /app/public/diff/kornicker_kornic_nodes_24431.diff
[CMD] [2020-11-19 13:34:27] echo "." >> /app/public/diff/kornicker_kornic_nodes_24431.diff
[CMD] [2020-11-19 13:34:27] echo "0a" > /app/public/diff/kornicker_kornic_occurrences_24432.diff
[CMD] [2020-11-19 13:34:27] tail -n +1 /app/public/converted_csv/kornicker_kornic_occurrences_24432.csv >> /app/public/diff/kornicker_kornic_occurrences_24432.diff
[CMD] [2020-11-19 13:34:27] echo "." >> /app/public/diff/kornicker_kornic_occurrences_24432.diff
[CMD] [2020-11-19 13:34:27] echo "0a" > /app/public/diff/kornicker_kornic_measurements_24433.diff
[CMD] [2020-11-19 13:34:27] tail -n +1 /app/public/converted_csv/kornicker_kornic_measurements_24433.csv >> /app/public/diff/kornicker_kornic_measurements_24433.diff
[CMD] [2020-11-19 13:34:27] echo "." >> /app/public/diff/kornicker_kornic_measurements_24433.diff
[STOP] [2020-11-19 13:34:27] calculate_delta
[START] [2020-11-19 13:34:27] parse_diff_and_store
[INFO] [2020-11-19 13:34:27] Loading refs diff file into memory (true lines)...
[INFO] [2020-11-19 13:34:27] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-19 13:34:27] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-19 13:34:27] Loading measurements diff file into memory (true lines)...
[INFO] [2020-11-19 13:34:29] Storing 1 ScientificNames
[INFO] [2020-11-19 13:34:29] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 13:34:29] Average Time: 0.0
[INFO] [2020-11-19 13:34:29] Total Time: 1s
[INFO] [2020-11-19 13:34:29] Storing 1 Nodes
[INFO] [2020-11-19 13:34:29] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 13:34:29] Average Time: 0.0
[INFO] [2020-11-19 13:34:29] Total Time: 1s
[INFO] [2020-11-19 13:34:29] Storing 1 Occurrences
[INFO] [2020-11-19 13:34:29] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 13:34:29] Average Time: 0.0
[INFO] [2020-11-19 13:34:29] Total Time: 1s
[INFO] [2020-11-19 13:34:29] Storing 2 Traits
[INFO] [2020-11-19 13:34:29] Processing group of 2 in 1 groups of 1000
[INFO] [2020-11-19 13:34:29] Average Time: 0.01
[INFO] [2020-11-19 13:34:29] Total Time: 1s
[INFO] [2020-11-19 13:34:29] Storing 1 MetaTraits
[INFO] [2020-11-19 13:34:29] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 13:34:29] Average Time: 0.0
[INFO] [2020-11-19 13:34:29] Total Time: 1s
[STOP] [2020-11-19 13:34:29] parse_diff_and_store
[START] [2020-11-19 13:34:29] resolve_keys
[INFO] [2020-11-19 13:34:35] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-19 13:34:35] traits to occurrences...
[INFO] [2020-11-19 13:34:35] traits to nodes (through occurrences)...
[INFO] [2020-11-19 13:34:35] Traits to sex term...
[INFO] [2020-11-19 13:34:35] Traits to lifestage term...
[INFO] [2020-11-19 13:34:35] MetaTraits to traits...
[INFO] [2020-11-19 13:34:35] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-19 13:34:35] Assocs to occurrences...
[INFO] [2020-11-19 13:34:35] Assocs to nodes...
[INFO] [2020-11-19 13:34:35] Assoc to sex term...
[INFO] [2020-11-19 13:34:35] Assoc to lifestage term...
[INFO] [2020-11-19 13:34:35] MetaAssoc to assocs...
[STOP] [2020-11-19 13:34:35] resolve_keys
[START] [2020-11-19 13:34:35] hold_for_later_1
[STOP] [2020-11-19 13:34:35] hold_for_later_1
[START] [2020-11-19 13:34:35] hold_for_later_2
[STOP] [2020-11-19 13:34:35] hold_for_later_2
[START] [2020-11-19 13:34:35] resolve_missing_parents
[STOP] [2020-11-19 13:34:35] resolve_missing_parents
[START] [2020-11-19 13:34:35] rebuild_nodes
[START] [2020-11-19 13:34:35] Flattener#flatten
[START] [2020-11-19 13:34:35] Flattener#study_resource
[START] [2020-11-19 13:34:35] Flattener#build_ancestry
[STOP] [2020-11-19 13:34:35] Flattener#build_ancestry
[INFO] [2020-11-19 13:34:35] 1 ancestry keys
[START] [2020-11-19 13:34:35] build_node_ancestors
[INFO] [2020-11-19 13:34:35] old ancestors deleted.
[STOP] [2020-11-19 13:34:35] build_node_ancestors
[WARN] [2020-11-19 13:34:35] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-11-19 13:34:35] Flattener#flatten
[STOP] [2020-11-19 13:34:35] rebuild_nodes
[START] [2020-11-19 13:34:35] resolve_missing_media_owners
[STOP] [2020-11-19 13:34:35] resolve_missing_media_owners
[START] [2020-11-19 13:34:35] sanitize_media_verbatims
[STOP] [2020-11-19 13:34:35] sanitize_media_verbatims
[START] [2020-11-19 13:34:35] queue_downloads
[STOP] [2020-11-19 13:34:35] queue_downloads
[START] [2020-11-19 13:34:35] parse_names
[WARN] [2020-11-19 13:34:35] I see 1 names which still need to be parsed.
[STOP] [2020-11-19 13:34:36] parse_names
[START] [2020-11-19 13:34:36] denormalize_canonical_names_to_nodes
[STOP] [2020-11-19 13:34:36] denormalize_canonical_names_to_nodes
[START] [2020-11-19 13:34:36] match_nodes
[START] [2020-11-19 13:34:36] map_all_nodes_to_pages
[STOP] [2020-11-19 13:34:36] map_all_nodes_to_pages
[INFO] [2020-11-19 13:34:36] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-11-19 13:34:36] update_nodes
[STOP] [2020-11-19 13:34:36] update_nodes
[STOP] [2020-11-19 13:34:36] match_nodes
[START] [2020-11-19 13:34:36] reindex_search
[STOP] [2020-11-19 13:34:36] reindex_search
[START] [2020-11-19 13:34:36] normalize_units
[STOP] [2020-11-19 13:34:36] normalize_units
[START] [2020-11-19 13:34:36] calculate_statistics
[2020-11-19 13:34:36] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-11-19 13:34:36] calculate_statistics
[START] [2020-11-19 13:34:36] complete_harvest_instance
[START] [2020-11-19 13:34:36] overall_tsv_creation
[INFO] [2020-11-19 13:34:36] Processing group of 1 in 1 batches of 10000
[INFO] [2020-11-19 13:35:19] 1 Traits (unfiltered)...
[INFO] [2020-11-19 13:36:01] 1 Traits (filtered)...
[INFO] [2020-11-19 13:36:01] 0 Associations (filtered)...
[INFO] [2020-11-19 13:36:01] 2 metadata added.
[INFO] [2020-11-19 13:36:01] 0 metadata added.
[INFO] [2020-11-19 13:36:01] Average Time: 65.22
[INFO] [2020-11-19 13:36:01] Total Time: 1m26s
[STOP] [2020-11-19 13:36:01] overall_tsv_creation
[INFO] [2020-11-19 13:36:01] Done. Check your files:
[INFO] [2020-11-19 13:36:01] (1 lines) /app/public/data/kornicker_kornic/publish_nodes.tsv
[INFO] [2020-11-19 13:36:01] (1 lines) /app/public/data/kornicker_kornic/publish_scientific_names.tsv
[INFO] [2020-11-19 13:36:01] (2 lines) /app/public/data/kornicker_kornic/publish_traits.tsv
[INFO] [2020-11-19 13:36:01] (3 lines) /app/public/data/kornicker_kornic/publish_metadata.tsv
[STOP] [2020-11-19 13:36:01] complete_harvest_instance
[START] [2020-11-19 13:36:01] completed
[STOP] [2020-11-19 13:36:01] completed
[STOP] [2020-11-19 13:36:01] logged process, took 95.59
[INFO] [2021-04-19 14:52:06] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 14:56:59] ## remove_type: ScientificName
[INFO] [2021-04-19 14:56:59] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 14:56:59] [14:56:59.060] Removed 1 Scientificnames
[INFO] [2021-04-19 14:56:59] ## remove_type: Vernacular
[INFO] [2021-04-19 14:56:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:56:59] [14:56:59.061] Removed 0 Vernaculars
[INFO] [2021-04-19 14:56:59] ## remove_type: Article
[INFO] [2021-04-19 14:56:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:56:59] [14:56:59.063] Removed 0 Articles
[INFO] [2021-04-19 14:56:59] ## remove_type: Medium
[INFO] [2021-04-19 14:56:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:56:59] [14:56:59.064] Removed 0 Media
[INFO] [2021-04-19 14:56:59] ## remove_type: Trait
[INFO] [2021-04-19 14:56:59] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 14:56:59] [14:56:59.066] Removed 2 Traits
[INFO] [2021-04-19 14:56:59] ## remove_type: MetaTrait
[INFO] [2021-04-19 14:56:59] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 14:56:59] [14:56:59.068] Removed 1 Metatraits
[INFO] [2021-04-19 14:56:59] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 14:56:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:56:59] [14:56:59.070] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 14:56:59] ## remove_type: Assoc
[INFO] [2021-04-19 14:56:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:56:59] [14:56:59.071] Removed 0 Assocs
[INFO] [2021-04-19 14:56:59] ## remove_type: MetaAssoc
[INFO] [2021-04-19 14:56:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:56:59] [14:56:59.072] Removed 0 Metaassocs
[INFO] [2021-04-19 14:56:59] ## remove_type: Identifier
[INFO] [2021-04-19 14:56:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:56:59] [14:56:59.074] Removed 0 Identifiers
[INFO] [2021-04-19 14:56:59] ## remove_type: Reference
[INFO] [2021-04-19 14:56:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:56:59] [14:56:59.076] Removed 0 References
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
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[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
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[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] Starting batch with ID 84620781...
[INFO] [2021-04-19 14:56:59] ## remove_type: Node
[INFO] [2021-04-19 14:56:59] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 14:56:59] [14:56:59.666] Removed 1 Nodes
[START] [2021-04-19 14:56:59] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:56:59] Creating resource from OpenData
[START] [2021-04-19 14:56:59] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:56:59] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 14:57:00] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 14:57:00] Creating resource from OpenData
[START] [2021-04-19 14:57:00] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:57:00] create_harvest_instance
[INFO] [2021-04-19 14:57:00] Created harvest instance #3755
[STOP] [2021-04-19 14:57:00] create_harvest_instance
[START] [2021-04-19 14:57:00] fetch_files
[STOP] [2021-04-19 14:57:00] fetch_files
[START] [2021-04-19 14:57:00] validate_each_file
[INFO] [2021-04-19 14:57:00] Looping over 4 formats...
[INFO] [2021-04-19 14:57:00] ...refs (/app/public/data/kornicker_kornic/references.tsv)
[INFO] [2021-04-19 14:57:00] Valid: /app/public/converted_csv/kornicker_kornic_refs_3755.csv (0 lines)
[INFO] [2021-04-19 14:57:00] ...nodes (/app/public/data/kornicker_kornic/taxa.txt)
[INFO] [2021-04-19 14:57:00] Valid: /app/public/converted_csv/kornicker_kornic_nodes_3755.csv (1 lines)
[INFO] [2021-04-19 14:57:00] ...occurrences (/app/public/data/kornicker_kornic/occurrences.txt)
[INFO] [2021-04-19 14:57:00] Valid: /app/public/converted_csv/kornicker_kornic_occurrences_3755.csv (1 lines)
[INFO] [2021-04-19 14:57:00] ...measurements (/app/public/data/kornicker_kornic/measurementsorfacts.txt)
[INFO] [2021-04-19 14:57:00] Valid: /app/public/converted_csv/kornicker_kornic_measurements_3755.csv (2 lines)
[STOP] [2021-04-19 14:57:00] validate_each_file
[START] [2021-04-19 14:57:00] convert_to_csv
[INFO] [2021-04-19 14:57:00] Looping over 4 formats...
[INFO] [2021-04-19 14:57:00] ...refs (/app/public/data/kornicker_kornic/references.tsv)
[CMD] [2021-04-19 14:57:00] /usr/bin/sort /app/public/converted_csv/kornicker_kornic_refs_3755.csv > /app/public/converted_csv/kornicker_kornic_refs_3755.csv_sorted
[INFO] [2021-04-19 14:57:00] Converted: /app/public/converted_csv/kornicker_kornic_refs_3755.csv (0 lines)
[INFO] [2021-04-19 14:57:00] ...nodes (/app/public/data/kornicker_kornic/taxa.txt)
[CMD] [2021-04-19 14:57:00] /usr/bin/sort /app/public/converted_csv/kornicker_kornic_nodes_3755.csv > /app/public/converted_csv/kornicker_kornic_nodes_3755.csv_sorted
[INFO] [2021-04-19 14:57:00] Converted: /app/public/converted_csv/kornicker_kornic_nodes_3755.csv (1 lines)
[INFO] [2021-04-19 14:57:00] ...occurrences (/app/public/data/kornicker_kornic/occurrences.txt)
[CMD] [2021-04-19 14:57:00] /usr/bin/sort /app/public/converted_csv/kornicker_kornic_occurrences_3755.csv > /app/public/converted_csv/kornicker_kornic_occurrences_3755.csv_sorted
[INFO] [2021-04-19 14:57:00] Converted: /app/public/converted_csv/kornicker_kornic_occurrences_3755.csv (1 lines)
[INFO] [2021-04-19 14:57:00] ...measurements (/app/public/data/kornicker_kornic/measurementsorfacts.txt)
[CMD] [2021-04-19 14:57:00] /usr/bin/sort /app/public/converted_csv/kornicker_kornic_measurements_3755.csv > /app/public/converted_csv/kornicker_kornic_measurements_3755.csv_sorted
[INFO] [2021-04-19 14:57:00] Converted: /app/public/converted_csv/kornicker_kornic_measurements_3755.csv (2 lines)
[STOP] [2021-04-19 14:57:00] convert_to_csv
[START] [2021-04-19 14:57:00] calculate_delta
[INFO] [2021-04-19 14:57:00] Looping over 4 formats...
[INFO] [2021-04-19 14:57:00] ...refs (/app/public/data/kornicker_kornic/references.tsv)
[CMD] [2021-04-19 14:57:00] echo "0a" > /app/public/diff/kornicker_kornic_refs_3755.diff
[CMD] [2021-04-19 14:57:00] tail -n +1 /app/public/converted_csv/kornicker_kornic_refs_3755.csv >> /app/public/diff/kornicker_kornic_refs_3755.diff
[CMD] [2021-04-19 14:57:00] echo "." >> /app/public/diff/kornicker_kornic_refs_3755.diff
[INFO] [2021-04-19 14:57:00] Created diff: /app/public/diff/kornicker_kornic_refs_3755.diff (2 lines)
[INFO] [2021-04-19 14:57:00] ...nodes (/app/public/data/kornicker_kornic/taxa.txt)
[CMD] [2021-04-19 14:57:00] echo "0a" > /app/public/diff/kornicker_kornic_nodes_3755.diff
[CMD] [2021-04-19 14:57:00] tail -n +1 /app/public/converted_csv/kornicker_kornic_nodes_3755.csv >> /app/public/diff/kornicker_kornic_nodes_3755.diff
[CMD] [2021-04-19 14:57:00] echo "." >> /app/public/diff/kornicker_kornic_nodes_3755.diff
[INFO] [2021-04-19 14:57:00] Created diff: /app/public/diff/kornicker_kornic_nodes_3755.diff (3 lines)
[INFO] [2021-04-19 14:57:00] ...occurrences (/app/public/data/kornicker_kornic/occurrences.txt)
[CMD] [2021-04-19 14:57:00] echo "0a" > /app/public/diff/kornicker_kornic_occurrences_3755.diff
[CMD] [2021-04-19 14:57:00] tail -n +1 /app/public/converted_csv/kornicker_kornic_occurrences_3755.csv >> /app/public/diff/kornicker_kornic_occurrences_3755.diff
[CMD] [2021-04-19 14:57:00] echo "." >> /app/public/diff/kornicker_kornic_occurrences_3755.diff
[INFO] [2021-04-19 14:57:00] Created diff: /app/public/diff/kornicker_kornic_occurrences_3755.diff (3 lines)
[INFO] [2021-04-19 14:57:00] ...measurements (/app/public/data/kornicker_kornic/measurementsorfacts.txt)
[CMD] [2021-04-19 14:57:00] echo "0a" > /app/public/diff/kornicker_kornic_measurements_3755.diff
[CMD] [2021-04-19 14:57:00] tail -n +1 /app/public/converted_csv/kornicker_kornic_measurements_3755.csv >> /app/public/diff/kornicker_kornic_measurements_3755.diff
[CMD] [2021-04-19 14:57:00] echo "." >> /app/public/diff/kornicker_kornic_measurements_3755.diff
[INFO] [2021-04-19 14:57:00] Created diff: /app/public/diff/kornicker_kornic_measurements_3755.diff (4 lines)
[STOP] [2021-04-19 14:57:00] calculate_delta
[START] [2021-04-19 14:57:00] parse_diff_and_store
[INFO] [2021-04-19 14:57:00] Handling diff: /app/public/diff/kornicker_kornic_refs_3755.diff (2 lines)
[INFO] [2021-04-19 14:57:00] Loading refs diff file into memory (2 /app/public/diff/kornicker_kornic_refs_3755.diff lines)...
[INFO] [2021-04-19 14:57:00] Handling diff: /app/public/diff/kornicker_kornic_nodes_3755.diff (3 lines)
[INFO] [2021-04-19 14:57:00] Loading nodes diff file into memory (3 /app/public/diff/kornicker_kornic_nodes_3755.diff lines)...
[INFO] [2021-04-19 14:57:00] Handling diff: /app/public/diff/kornicker_kornic_occurrences_3755.diff (3 lines)
[INFO] [2021-04-19 14:57:00] Loading occurrences diff file into memory (3 /app/public/diff/kornicker_kornic_occurrences_3755.diff lines)...
[INFO] [2021-04-19 14:57:00] Handling diff: /app/public/diff/kornicker_kornic_measurements_3755.diff (4 lines)
[INFO] [2021-04-19 14:57:00] Loading measurements diff file into memory (4 /app/public/diff/kornicker_kornic_measurements_3755.diff lines)...
[INFO] [2021-04-19 14:57:00] Storing 1 ScientificNames
[INFO] [2021-04-19 14:57:00] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:57:00] Average Time: 0.0
[INFO] [2021-04-19 14:57:00] Total Time: 1s
[INFO] [2021-04-19 14:57:00] Storing 1 Nodes
[INFO] [2021-04-19 14:57:00] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:57:00] Average Time: 0.0
[INFO] [2021-04-19 14:57:00] Total Time: 1s
[INFO] [2021-04-19 14:57:00] Storing 1 Occurrences
[INFO] [2021-04-19 14:57:00] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:57:00] Average Time: 0.0
[INFO] [2021-04-19 14:57:00] Total Time: 1s
[INFO] [2021-04-19 14:57:00] Storing 2 Traits
[INFO] [2021-04-19 14:57:00] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 14:57:00] Average Time: 0.0
[INFO] [2021-04-19 14:57:00] Total Time: 1s
[INFO] [2021-04-19 14:57:00] Storing 1 MetaTraits
[INFO] [2021-04-19 14:57:00] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:57:00] Average Time: 0.0
[INFO] [2021-04-19 14:57:00] Total Time: 1s
[STOP] [2021-04-19 14:57:00] parse_diff_and_store
[START] [2021-04-19 14:57:00] resolve_keys
[INFO] [2021-04-19 14:57:06] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 14:57:06] traits to occurrences...
[INFO] [2021-04-19 14:57:06] traits to nodes (through occurrences)...
[INFO] [2021-04-19 14:57:06] Traits to sex term...
[INFO] [2021-04-19 14:57:06] Traits to lifestage term...
[INFO] [2021-04-19 14:57:06] MetaTraits to traits...
[INFO] [2021-04-19 14:57:06] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 14:57:06] Assocs to occurrences...
[INFO] [2021-04-19 14:57:06] Assocs to nodes...
[INFO] [2021-04-19 14:57:06] Assoc to sex term...
[INFO] [2021-04-19 14:57:06] Assoc to lifestage term...
[INFO] [2021-04-19 14:57:06] MetaAssoc to assocs...
[STOP] [2021-04-19 14:57:06] resolve_keys
[START] [2021-04-19 14:57:06] hold_for_later_1
[STOP] [2021-04-19 14:57:06] hold_for_later_1
[START] [2021-04-19 14:57:06] hold_for_later_2
[STOP] [2021-04-19 14:57:06] hold_for_later_2
[START] [2021-04-19 14:57:06] resolve_missing_parents
[STOP] [2021-04-19 14:57:06] resolve_missing_parents
[START] [2021-04-19 14:57:06] rebuild_nodes
[START] [2021-04-19 14:57:06] Flattener#flatten
[START] [2021-04-19 14:57:06] Flattener#study_resource
[START] [2021-04-19 14:57:06] Flattener#build_ancestry
[STOP] [2021-04-19 14:57:06] Flattener#build_ancestry
[INFO] [2021-04-19 14:57:06] 1 ancestry keys
[START] [2021-04-19 14:57:06] build_node_ancestors
[INFO] [2021-04-19 14:57:06] old ancestors deleted.
[STOP] [2021-04-19 14:57:06] build_node_ancestors
[WARN] [2021-04-19 14:57:06] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 14:57:06] Flattener#flatten
[STOP] [2021-04-19 14:57:06] rebuild_nodes
[START] [2021-04-19 14:57:06] resolve_missing_media_owners
[STOP] [2021-04-19 14:57:06] resolve_missing_media_owners
[START] [2021-04-19 14:57:06] sanitize_media_verbatims
[STOP] [2021-04-19 14:57:06] sanitize_media_verbatims
[START] [2021-04-19 14:57:06] queue_downloads
[STOP] [2021-04-19 14:57:06] queue_downloads
[START] [2021-04-19 14:57:06] parse_names
[WARN] [2021-04-19 14:57:06] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 14:57:07] parse_names
[START] [2021-04-19 14:57:07] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 14:57:07] denormalize_canonical_names_to_nodes
[START] [2021-04-19 14:57:07] match_nodes
[START] [2021-04-19 14:57:07] map_all_nodes_to_pages
[STOP] [2021-04-19 14:57:07] map_all_nodes_to_pages
[INFO] [2021-04-19 14:57:07] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 14:57:07] update_nodes
[STOP] [2021-04-19 14:57:07] update_nodes
[STOP] [2021-04-19 14:57:07] match_nodes
[START] [2021-04-19 14:57:07] reindex_search
[STOP] [2021-04-19 14:57:07] reindex_search
[START] [2021-04-19 14:57:07] normalize_units
[STOP] [2021-04-19 14:57:07] normalize_units
[START] [2021-04-19 14:57:07] calculate_statistics
[2021-04-19 14:57:07] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 14:57:07] calculate_statistics
[START] [2021-04-19 14:57:07] complete_harvest_instance
[START] [2021-04-19 14:57:07] overall_tsv_creation
[INFO] [2021-04-19 14:57:07] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 14:57:43] 1 Traits (unfiltered)...
[INFO] [2021-04-19 14:58:15] 1 Traits (filtered)...
[INFO] [2021-04-19 14:58:15] 0 Associations (filtered)...
[INFO] [2021-04-19 14:58:15] 1 metadata added.
[INFO] [2021-04-19 14:58:15] 0 metadata added.
[INFO] [2021-04-19 14:58:41] Average Time: 70.21
[INFO] [2021-04-19 14:58:41] Total Time: 1m35s
[STOP] [2021-04-19 14:58:41] overall_tsv_creation
[INFO] [2021-04-19 14:58:41] Done. Check your files:
[INFO] [2021-04-19 14:58:41] (1 lines) /app/public/data/kornicker_kornic/publish_nodes.tsv
[INFO] [2021-04-19 14:58:41] (1 lines) /app/public/data/kornicker_kornic/publish_scientific_names.tsv
[INFO] [2021-04-19 14:58:41] (2 lines) /app/public/data/kornicker_kornic/publish_traits.tsv
[INFO] [2021-04-19 14:58:41] (2 lines) /app/public/data/kornicker_kornic/publish_metadata.tsv
[STOP] [2021-04-19 14:58:41] complete_harvest_instance
[START] [2021-04-19 14:58:41] completed
[STOP] [2021-04-19 14:58:41] completed
[STOP] [2021-04-19 14:58:41] logged process, took 101.63
Latest Process