Stage:
completed
Fetched:
19 Apr 15:23
Validated:
19 Apr 15:23
Deltas Created
19 Apr 15:23
Units Normalized:
19 Apr 15:23
Ancestry Built:
19 Apr 15:23
Nodes Matched:
19 Apr 15:23
Names Parsed:
19 Apr 15:23
New Models Stored:
19 Apr 15:23
Indexed:
19 Apr 15:23
Completed:
19 Apr 15:24
Time to Harvest:
less than a minute
Harvesting Log
(532 lines)
# Logfile created on 2020-08-27 15:39:18 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:39:18] logged process
[START] [2020-08-27 15:39:18] Creating resource from OpenData
[START] [2020-08-27 15:39:19] logged process
[START] [2020-08-27 15:39:19] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:39:19] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:39:19] Creating resource from OpenData
[INFO] [2020-11-19 14:13:12] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-11-19 14:13:14] ## remove_type: ScientificName
[INFO] [2020-11-19 14:13:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:13:14] [14:13:14.709] Removed 0 Scientificnames
[INFO] [2020-11-19 14:13:14] ## remove_type: Vernacular
[INFO] [2020-11-19 14:13:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:13:14] [14:13:14.712] Removed 0 Vernaculars
[INFO] [2020-11-19 14:13:14] ## remove_type: Article
[INFO] [2020-11-19 14:13:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:13:14] [14:13:14.715] Removed 0 Articles
[INFO] [2020-11-19 14:13:14] ## remove_type: Medium
[INFO] [2020-11-19 14:13:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:13:14] [14:13:14.718] Removed 0 Media
[INFO] [2020-11-19 14:13:14] ## remove_type: Trait
[INFO] [2020-11-19 14:13:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:13:14] [14:13:14.720] Removed 0 Traits
[INFO] [2020-11-19 14:13:14] ## remove_type: MetaTrait
[INFO] [2020-11-19 14:13:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:13:14] [14:13:14.723] Removed 0 Metatraits
[INFO] [2020-11-19 14:13:14] ## remove_type: OccurrenceMetadatum
[INFO] [2020-11-19 14:13:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:13:14] [14:13:14.725] Removed 0 Occurrencemetadata
[INFO] [2020-11-19 14:13:14] ## remove_type: Assoc
[INFO] [2020-11-19 14:13:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:13:14] [14:13:14.728] Removed 0 Assocs
[INFO] [2020-11-19 14:13:14] ## remove_type: MetaAssoc
[INFO] [2020-11-19 14:13:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:13:14] [14:13:14.730] Removed 0 Metaassocs
[INFO] [2020-11-19 14:13:14] ## remove_type: Identifier
[INFO] [2020-11-19 14:13:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:13:14] [14:13:14.732] Removed 0 Identifiers
[INFO] [2020-11-19 14:13:14] ## remove_type: Reference
[INFO] [2020-11-19 14:13:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:13:14] [14:13:14.735] Removed 0 References
[INFO] [2020-11-19 14:13:14] ## remove_type: Node
[INFO] [2020-11-19 14:13:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:13:14] [14:13:14.755] Removed 0 Nodes
[START] [2020-11-19 14:13:14] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 14:13:14] Creating resource from OpenData
[START] [2020-11-19 14:13:14] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 14:13:14] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 14:13:15] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 14:13:15] Creating resource from OpenData
[START] [2020-11-19 14:13:15] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 14:13:15] create_harvest_instance
[STOP] [2020-11-19 14:13:16] create_harvest_instance
[START] [2020-11-19 14:13:16] fetch_files
[STOP] [2020-11-19 14:13:16] fetch_files
[START] [2020-11-19 14:13:16] validate_each_file
[STOP] [2020-11-19 14:13:16] validate_each_file
[START] [2020-11-19 14:13:16] convert_to_csv
[CMD] [2020-11-19 14:13:16] /usr/bin/sort /app/public/converted_csv/sreas_refs_24550.csv > /app/public/converted_csv/sreas_refs_24550.csv_sorted
[CMD] [2020-11-19 14:13:16] /usr/bin/sort /app/public/converted_csv/sreas_nodes_24551.csv > /app/public/converted_csv/sreas_nodes_24551.csv_sorted
[CMD] [2020-11-19 14:13:16] /usr/bin/sort /app/public/converted_csv/sreas_occurrences_24552.csv > /app/public/converted_csv/sreas_occurrences_24552.csv_sorted
[CMD] [2020-11-19 14:13:16] /usr/bin/sort /app/public/converted_csv/sreas_measurements_24553.csv > /app/public/converted_csv/sreas_measurements_24553.csv_sorted
[STOP] [2020-11-19 14:13:16] convert_to_csv
[START] [2020-11-19 14:13:16] calculate_delta
[CMD] [2020-11-19 14:13:16] echo "0a" > /app/public/diff/sreas_refs_24550.diff
[CMD] [2020-11-19 14:13:16] tail -n +1 /app/public/converted_csv/sreas_refs_24550.csv >> /app/public/diff/sreas_refs_24550.diff
[CMD] [2020-11-19 14:13:16] echo "." >> /app/public/diff/sreas_refs_24550.diff
[CMD] [2020-11-19 14:13:16] echo "0a" > /app/public/diff/sreas_nodes_24551.diff
[CMD] [2020-11-19 14:13:16] tail -n +1 /app/public/converted_csv/sreas_nodes_24551.csv >> /app/public/diff/sreas_nodes_24551.diff
[CMD] [2020-11-19 14:13:16] echo "." >> /app/public/diff/sreas_nodes_24551.diff
[CMD] [2020-11-19 14:13:16] echo "0a" > /app/public/diff/sreas_occurrences_24552.diff
[CMD] [2020-11-19 14:13:16] tail -n +1 /app/public/converted_csv/sreas_occurrences_24552.csv >> /app/public/diff/sreas_occurrences_24552.diff
[CMD] [2020-11-19 14:13:16] echo "." >> /app/public/diff/sreas_occurrences_24552.diff
[CMD] [2020-11-19 14:13:16] echo "0a" > /app/public/diff/sreas_measurements_24553.diff
[CMD] [2020-11-19 14:13:16] tail -n +1 /app/public/converted_csv/sreas_measurements_24553.csv >> /app/public/diff/sreas_measurements_24553.diff
[CMD] [2020-11-19 14:13:16] echo "." >> /app/public/diff/sreas_measurements_24553.diff
[STOP] [2020-11-19 14:13:16] calculate_delta
[START] [2020-11-19 14:13:16] parse_diff_and_store
[INFO] [2020-11-19 14:13:16] Loading refs diff file into memory (true lines)...
[INFO] [2020-11-19 14:13:16] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-19 14:13:16] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-19 14:13:17] Loading measurements diff file into memory (true lines)...
[INFO] [2020-11-19 14:13:18] Storing 1 ScientificNames
[INFO] [2020-11-19 14:13:18] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 14:13:18] Average Time: 0.0
[INFO] [2020-11-19 14:13:18] Total Time: 1s
[INFO] [2020-11-19 14:13:18] Storing 1 Nodes
[INFO] [2020-11-19 14:13:18] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 14:13:18] Average Time: 0.0
[INFO] [2020-11-19 14:13:18] Total Time: 1s
[INFO] [2020-11-19 14:13:18] Storing 1 Occurrences
[INFO] [2020-11-19 14:13:18] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 14:13:18] Average Time: 0.01
[INFO] [2020-11-19 14:13:18] Total Time: 1s
[INFO] [2020-11-19 14:13:18] Storing 2 Traits
[INFO] [2020-11-19 14:13:18] Processing group of 2 in 1 groups of 1000
[INFO] [2020-11-19 14:13:18] Average Time: 0.01
[INFO] [2020-11-19 14:13:18] Total Time: 1s
[INFO] [2020-11-19 14:13:18] Storing 2 MetaTraits
[INFO] [2020-11-19 14:13:18] Processing group of 2 in 1 groups of 1000
[INFO] [2020-11-19 14:13:18] Average Time: 0.0
[INFO] [2020-11-19 14:13:18] Total Time: 1s
[STOP] [2020-11-19 14:13:18] parse_diff_and_store
[START] [2020-11-19 14:13:18] resolve_keys
[INFO] [2020-11-19 14:13:24] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-19 14:13:24] traits to occurrences...
[INFO] [2020-11-19 14:13:24] traits to nodes (through occurrences)...
[INFO] [2020-11-19 14:13:24] Traits to sex term...
[INFO] [2020-11-19 14:13:24] Traits to lifestage term...
[INFO] [2020-11-19 14:13:24] MetaTraits to traits...
[INFO] [2020-11-19 14:13:24] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-19 14:13:24] Assocs to occurrences...
[INFO] [2020-11-19 14:13:24] Assocs to nodes...
[INFO] [2020-11-19 14:13:24] Assoc to sex term...
[INFO] [2020-11-19 14:13:24] Assoc to lifestage term...
[INFO] [2020-11-19 14:13:24] MetaAssoc to assocs...
[STOP] [2020-11-19 14:13:24] resolve_keys
[START] [2020-11-19 14:13:24] hold_for_later_1
[STOP] [2020-11-19 14:13:24] hold_for_later_1
[START] [2020-11-19 14:13:24] hold_for_later_2
[STOP] [2020-11-19 14:13:24] hold_for_later_2
[START] [2020-11-19 14:13:24] resolve_missing_parents
[STOP] [2020-11-19 14:13:24] resolve_missing_parents
[START] [2020-11-19 14:13:24] rebuild_nodes
[START] [2020-11-19 14:13:24] Flattener#flatten
[START] [2020-11-19 14:13:24] Flattener#study_resource
[START] [2020-11-19 14:13:24] Flattener#build_ancestry
[STOP] [2020-11-19 14:13:24] Flattener#build_ancestry
[INFO] [2020-11-19 14:13:24] 1 ancestry keys
[START] [2020-11-19 14:13:24] build_node_ancestors
[INFO] [2020-11-19 14:13:24] old ancestors deleted.
[STOP] [2020-11-19 14:13:24] build_node_ancestors
[WARN] [2020-11-19 14:13:24] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-11-19 14:13:24] Flattener#flatten
[STOP] [2020-11-19 14:13:24] rebuild_nodes
[START] [2020-11-19 14:13:24] resolve_missing_media_owners
[STOP] [2020-11-19 14:13:24] resolve_missing_media_owners
[START] [2020-11-19 14:13:24] sanitize_media_verbatims
[STOP] [2020-11-19 14:13:24] sanitize_media_verbatims
[START] [2020-11-19 14:13:24] queue_downloads
[STOP] [2020-11-19 14:13:24] queue_downloads
[START] [2020-11-19 14:13:24] parse_names
[WARN] [2020-11-19 14:13:24] I see 1 names which still need to be parsed.
[STOP] [2020-11-19 14:13:25] parse_names
[START] [2020-11-19 14:13:25] denormalize_canonical_names_to_nodes
[STOP] [2020-11-19 14:13:25] denormalize_canonical_names_to_nodes
[START] [2020-11-19 14:13:25] match_nodes
[START] [2020-11-19 14:13:25] map_all_nodes_to_pages
[STOP] [2020-11-19 14:13:25] map_all_nodes_to_pages
[INFO] [2020-11-19 14:13:25] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-11-19 14:13:25] update_nodes
[STOP] [2020-11-19 14:13:25] update_nodes
[STOP] [2020-11-19 14:13:25] match_nodes
[START] [2020-11-19 14:13:25] reindex_search
[STOP] [2020-11-19 14:13:25] reindex_search
[START] [2020-11-19 14:13:25] normalize_units
[STOP] [2020-11-19 14:13:25] normalize_units
[START] [2020-11-19 14:13:25] calculate_statistics
[2020-11-19 14:13:25] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-11-19 14:13:25] calculate_statistics
[START] [2020-11-19 14:13:25] complete_harvest_instance
[START] [2020-11-19 14:13:25] overall_tsv_creation
[INFO] [2020-11-19 14:13:25] Processing group of 1 in 1 batches of 10000
[INFO] [2020-11-19 14:14:08] 1 Traits (unfiltered)...
[INFO] [2020-11-19 14:14:50] 1 Traits (filtered)...
[INFO] [2020-11-19 14:14:50] 0 Associations (filtered)...
[INFO] [2020-11-19 14:14:50] 3 metadata added.
[INFO] [2020-11-19 14:14:50] 0 metadata added.
[INFO] [2020-11-19 14:14:50] Average Time: 65.4
[INFO] [2020-11-19 14:14:50] Total Time: 1m26s
[STOP] [2020-11-19 14:14:50] overall_tsv_creation
[INFO] [2020-11-19 14:14:50] Done. Check your files:
[INFO] [2020-11-19 14:14:50] (1 lines) /app/public/data/sreas/publish_nodes.tsv
[INFO] [2020-11-19 14:14:50] (1 lines) /app/public/data/sreas/publish_scientific_names.tsv
[INFO] [2020-11-19 14:14:50] (2 lines) /app/public/data/sreas/publish_traits.tsv
[INFO] [2020-11-19 14:14:50] (4 lines) /app/public/data/sreas/publish_metadata.tsv
[STOP] [2020-11-19 14:14:50] complete_harvest_instance
[START] [2020-11-19 14:14:50] completed
[STOP] [2020-11-19 14:14:50] completed
[STOP] [2020-11-19 14:14:50] logged process, took 95.43
[INFO] [2021-04-19 15:16:08] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:23:16] ## remove_type: ScientificName
[INFO] [2021-04-19 15:23:16] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:23:16] [15:23:16.718] Removed 1 Scientificnames
[INFO] [2021-04-19 15:23:16] ## remove_type: Vernacular
[INFO] [2021-04-19 15:23:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:23:16] [15:23:16.719] Removed 0 Vernaculars
[INFO] [2021-04-19 15:23:16] ## remove_type: Article
[INFO] [2021-04-19 15:23:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:23:16] [15:23:16.721] Removed 0 Articles
[INFO] [2021-04-19 15:23:16] ## remove_type: Medium
[INFO] [2021-04-19 15:23:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:23:16] [15:23:16.722] Removed 0 Media
[INFO] [2021-04-19 15:23:16] ## remove_type: Trait
[INFO] [2021-04-19 15:23:16] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:23:16] [15:23:16.724] Removed 2 Traits
[INFO] [2021-04-19 15:23:16] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:23:16] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:23:16] [15:23:16.726] Removed 2 Metatraits
[INFO] [2021-04-19 15:23:16] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:23:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:23:16] [15:23:16.728] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 15:23:16] ## remove_type: Assoc
[INFO] [2021-04-19 15:23:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:23:16] [15:23:16.729] Removed 0 Assocs
[INFO] [2021-04-19 15:23:16] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:23:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:23:16] [15:23:16.731] Removed 0 Metaassocs
[INFO] [2021-04-19 15:23:16] ## remove_type: Identifier
[INFO] [2021-04-19 15:23:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:23:16] [15:23:16.732] Removed 0 Identifiers
[INFO] [2021-04-19 15:23:16] ## remove_type: Reference
[INFO] [2021-04-19 15:23:16] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:23:16] [15:23:16.734] Removed 0 References
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:16] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
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[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] Starting batch with ID 84620951...
[INFO] [2021-04-19 15:23:17] ## remove_type: Node
[INFO] [2021-04-19 15:23:17] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:23:17] [15:23:17.670] Removed 1 Nodes
[START] [2021-04-19 15:23:17] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:23:17] Creating resource from OpenData
[START] [2021-04-19 15:23:17] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:23:17] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:23:18] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:23:18] Creating resource from OpenData
[START] [2021-04-19 15:23:18] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:23:18] create_harvest_instance
[INFO] [2021-04-19 15:23:18] Created harvest instance #3764
[STOP] [2021-04-19 15:23:18] create_harvest_instance
[START] [2021-04-19 15:23:18] fetch_files
[STOP] [2021-04-19 15:23:18] fetch_files
[START] [2021-04-19 15:23:18] validate_each_file
[INFO] [2021-04-19 15:23:18] Looping over 4 formats...
[INFO] [2021-04-19 15:23:18] ...refs (/app/public/data/sreas/references.tsv)
[INFO] [2021-04-19 15:23:18] Valid: /app/public/converted_csv/sreas_refs_3764.csv (0 lines)
[INFO] [2021-04-19 15:23:18] ...nodes (/app/public/data/sreas/taxa.txt)
[INFO] [2021-04-19 15:23:18] Valid: /app/public/converted_csv/sreas_nodes_3764.csv (1 lines)
[INFO] [2021-04-19 15:23:18] ...occurrences (/app/public/data/sreas/occurrences.txt)
[INFO] [2021-04-19 15:23:18] Valid: /app/public/converted_csv/sreas_occurrences_3764.csv (1 lines)
[INFO] [2021-04-19 15:23:18] ...measurements (/app/public/data/sreas/measurementsorfacts.txt)
[INFO] [2021-04-19 15:23:18] Valid: /app/public/converted_csv/sreas_measurements_3764.csv (2 lines)
[STOP] [2021-04-19 15:23:18] validate_each_file
[START] [2021-04-19 15:23:18] convert_to_csv
[INFO] [2021-04-19 15:23:18] Looping over 4 formats...
[INFO] [2021-04-19 15:23:18] ...refs (/app/public/data/sreas/references.tsv)
[CMD] [2021-04-19 15:23:18] /usr/bin/sort /app/public/converted_csv/sreas_refs_3764.csv > /app/public/converted_csv/sreas_refs_3764.csv_sorted
[INFO] [2021-04-19 15:23:18] Converted: /app/public/converted_csv/sreas_refs_3764.csv (0 lines)
[INFO] [2021-04-19 15:23:18] ...nodes (/app/public/data/sreas/taxa.txt)
[CMD] [2021-04-19 15:23:18] /usr/bin/sort /app/public/converted_csv/sreas_nodes_3764.csv > /app/public/converted_csv/sreas_nodes_3764.csv_sorted
[INFO] [2021-04-19 15:23:18] Converted: /app/public/converted_csv/sreas_nodes_3764.csv (1 lines)
[INFO] [2021-04-19 15:23:18] ...occurrences (/app/public/data/sreas/occurrences.txt)
[CMD] [2021-04-19 15:23:18] /usr/bin/sort /app/public/converted_csv/sreas_occurrences_3764.csv > /app/public/converted_csv/sreas_occurrences_3764.csv_sorted
[INFO] [2021-04-19 15:23:18] Converted: /app/public/converted_csv/sreas_occurrences_3764.csv (1 lines)
[INFO] [2021-04-19 15:23:18] ...measurements (/app/public/data/sreas/measurementsorfacts.txt)
[CMD] [2021-04-19 15:23:18] /usr/bin/sort /app/public/converted_csv/sreas_measurements_3764.csv > /app/public/converted_csv/sreas_measurements_3764.csv_sorted
[INFO] [2021-04-19 15:23:18] Converted: /app/public/converted_csv/sreas_measurements_3764.csv (2 lines)
[STOP] [2021-04-19 15:23:18] convert_to_csv
[START] [2021-04-19 15:23:18] calculate_delta
[INFO] [2021-04-19 15:23:18] Looping over 4 formats...
[INFO] [2021-04-19 15:23:18] ...refs (/app/public/data/sreas/references.tsv)
[CMD] [2021-04-19 15:23:18] echo "0a" > /app/public/diff/sreas_refs_3764.diff
[CMD] [2021-04-19 15:23:18] tail -n +1 /app/public/converted_csv/sreas_refs_3764.csv >> /app/public/diff/sreas_refs_3764.diff
[CMD] [2021-04-19 15:23:18] echo "." >> /app/public/diff/sreas_refs_3764.diff
[INFO] [2021-04-19 15:23:18] Created diff: /app/public/diff/sreas_refs_3764.diff (2 lines)
[INFO] [2021-04-19 15:23:18] ...nodes (/app/public/data/sreas/taxa.txt)
[CMD] [2021-04-19 15:23:18] echo "0a" > /app/public/diff/sreas_nodes_3764.diff
[CMD] [2021-04-19 15:23:18] tail -n +1 /app/public/converted_csv/sreas_nodes_3764.csv >> /app/public/diff/sreas_nodes_3764.diff
[CMD] [2021-04-19 15:23:18] echo "." >> /app/public/diff/sreas_nodes_3764.diff
[INFO] [2021-04-19 15:23:18] Created diff: /app/public/diff/sreas_nodes_3764.diff (3 lines)
[INFO] [2021-04-19 15:23:18] ...occurrences (/app/public/data/sreas/occurrences.txt)
[CMD] [2021-04-19 15:23:18] echo "0a" > /app/public/diff/sreas_occurrences_3764.diff
[CMD] [2021-04-19 15:23:18] tail -n +1 /app/public/converted_csv/sreas_occurrences_3764.csv >> /app/public/diff/sreas_occurrences_3764.diff
[CMD] [2021-04-19 15:23:18] echo "." >> /app/public/diff/sreas_occurrences_3764.diff
[INFO] [2021-04-19 15:23:18] Created diff: /app/public/diff/sreas_occurrences_3764.diff (3 lines)
[INFO] [2021-04-19 15:23:18] ...measurements (/app/public/data/sreas/measurementsorfacts.txt)
[CMD] [2021-04-19 15:23:18] echo "0a" > /app/public/diff/sreas_measurements_3764.diff
[CMD] [2021-04-19 15:23:18] tail -n +1 /app/public/converted_csv/sreas_measurements_3764.csv >> /app/public/diff/sreas_measurements_3764.diff
[CMD] [2021-04-19 15:23:18] echo "." >> /app/public/diff/sreas_measurements_3764.diff
[INFO] [2021-04-19 15:23:18] Created diff: /app/public/diff/sreas_measurements_3764.diff (4 lines)
[STOP] [2021-04-19 15:23:18] calculate_delta
[START] [2021-04-19 15:23:18] parse_diff_and_store
[INFO] [2021-04-19 15:23:18] Handling diff: /app/public/diff/sreas_refs_3764.diff (2 lines)
[INFO] [2021-04-19 15:23:18] Loading refs diff file into memory (2 /app/public/diff/sreas_refs_3764.diff lines)...
[INFO] [2021-04-19 15:23:18] Handling diff: /app/public/diff/sreas_nodes_3764.diff (3 lines)
[INFO] [2021-04-19 15:23:18] Loading nodes diff file into memory (3 /app/public/diff/sreas_nodes_3764.diff lines)...
[INFO] [2021-04-19 15:23:18] Handling diff: /app/public/diff/sreas_occurrences_3764.diff (3 lines)
[INFO] [2021-04-19 15:23:18] Loading occurrences diff file into memory (3 /app/public/diff/sreas_occurrences_3764.diff lines)...
[INFO] [2021-04-19 15:23:18] Handling diff: /app/public/diff/sreas_measurements_3764.diff (4 lines)
[INFO] [2021-04-19 15:23:18] Loading measurements diff file into memory (4 /app/public/diff/sreas_measurements_3764.diff lines)...
[INFO] [2021-04-19 15:23:18] Storing 1 ScientificNames
[INFO] [2021-04-19 15:23:18] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:23:18] Average Time: 0.0
[INFO] [2021-04-19 15:23:18] Total Time: 1s
[INFO] [2021-04-19 15:23:18] Storing 1 Nodes
[INFO] [2021-04-19 15:23:18] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:23:18] Average Time: 0.0
[INFO] [2021-04-19 15:23:18] Total Time: 1s
[INFO] [2021-04-19 15:23:18] Storing 1 Occurrences
[INFO] [2021-04-19 15:23:18] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:23:18] Average Time: 0.0
[INFO] [2021-04-19 15:23:18] Total Time: 1s
[INFO] [2021-04-19 15:23:18] Storing 2 Traits
[INFO] [2021-04-19 15:23:18] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:23:18] Average Time: 0.0
[INFO] [2021-04-19 15:23:18] Total Time: 1s
[INFO] [2021-04-19 15:23:18] Storing 2 MetaTraits
[INFO] [2021-04-19 15:23:18] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:23:18] Average Time: 0.0
[INFO] [2021-04-19 15:23:18] Total Time: 1s
[STOP] [2021-04-19 15:23:18] parse_diff_and_store
[START] [2021-04-19 15:23:18] resolve_keys
[INFO] [2021-04-19 15:23:24] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:23:24] traits to occurrences...
[INFO] [2021-04-19 15:23:24] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:23:24] Traits to sex term...
[INFO] [2021-04-19 15:23:24] Traits to lifestage term...
[INFO] [2021-04-19 15:23:24] MetaTraits to traits...
[INFO] [2021-04-19 15:23:24] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:23:24] Assocs to occurrences...
[INFO] [2021-04-19 15:23:24] Assocs to nodes...
[INFO] [2021-04-19 15:23:24] Assoc to sex term...
[INFO] [2021-04-19 15:23:24] Assoc to lifestage term...
[INFO] [2021-04-19 15:23:24] MetaAssoc to assocs...
[STOP] [2021-04-19 15:23:24] resolve_keys
[START] [2021-04-19 15:23:24] hold_for_later_1
[STOP] [2021-04-19 15:23:24] hold_for_later_1
[START] [2021-04-19 15:23:24] hold_for_later_2
[STOP] [2021-04-19 15:23:24] hold_for_later_2
[START] [2021-04-19 15:23:24] resolve_missing_parents
[STOP] [2021-04-19 15:23:24] resolve_missing_parents
[START] [2021-04-19 15:23:24] rebuild_nodes
[START] [2021-04-19 15:23:24] Flattener#flatten
[START] [2021-04-19 15:23:24] Flattener#study_resource
[START] [2021-04-19 15:23:24] Flattener#build_ancestry
[STOP] [2021-04-19 15:23:24] Flattener#build_ancestry
[INFO] [2021-04-19 15:23:24] 1 ancestry keys
[START] [2021-04-19 15:23:24] build_node_ancestors
[INFO] [2021-04-19 15:23:24] old ancestors deleted.
[STOP] [2021-04-19 15:23:24] build_node_ancestors
[WARN] [2021-04-19 15:23:24] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:23:24] Flattener#flatten
[STOP] [2021-04-19 15:23:24] rebuild_nodes
[START] [2021-04-19 15:23:24] resolve_missing_media_owners
[STOP] [2021-04-19 15:23:24] resolve_missing_media_owners
[START] [2021-04-19 15:23:24] sanitize_media_verbatims
[STOP] [2021-04-19 15:23:24] sanitize_media_verbatims
[START] [2021-04-19 15:23:24] queue_downloads
[STOP] [2021-04-19 15:23:24] queue_downloads
[START] [2021-04-19 15:23:24] parse_names
[WARN] [2021-04-19 15:23:24] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 15:23:25] parse_names
[START] [2021-04-19 15:23:25] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:23:25] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:23:25] match_nodes
[START] [2021-04-19 15:23:25] map_all_nodes_to_pages
[STOP] [2021-04-19 15:23:25] map_all_nodes_to_pages
[INFO] [2021-04-19 15:23:25] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 15:23:25] update_nodes
[STOP] [2021-04-19 15:23:25] update_nodes
[STOP] [2021-04-19 15:23:25] match_nodes
[START] [2021-04-19 15:23:25] reindex_search
[STOP] [2021-04-19 15:23:25] reindex_search
[START] [2021-04-19 15:23:25] normalize_units
[STOP] [2021-04-19 15:23:25] normalize_units
[START] [2021-04-19 15:23:25] calculate_statistics
[2021-04-19 15:23:25] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:23:25] calculate_statistics
[START] [2021-04-19 15:23:25] complete_harvest_instance
[START] [2021-04-19 15:23:25] overall_tsv_creation
[INFO] [2021-04-19 15:23:25] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 15:24:00] 1 Traits (unfiltered)...
[INFO] [2021-04-19 15:24:32] 1 Traits (filtered)...
[INFO] [2021-04-19 15:24:32] 0 Associations (filtered)...
[INFO] [2021-04-19 15:24:32] 1 metadata added.
[INFO] [2021-04-19 15:24:32] 0 metadata added.
[INFO] [2021-04-19 15:24:58] Average Time: 69.58
[INFO] [2021-04-19 15:24:58] Total Time: 1m34s
[STOP] [2021-04-19 15:24:58] overall_tsv_creation
[INFO] [2021-04-19 15:24:58] Done. Check your files:
[INFO] [2021-04-19 15:24:58] (1 lines) /app/public/data/sreas/publish_nodes.tsv
[INFO] [2021-04-19 15:24:58] (1 lines) /app/public/data/sreas/publish_scientific_names.tsv
[INFO] [2021-04-19 15:24:58] (2 lines) /app/public/data/sreas/publish_traits.tsv
[INFO] [2021-04-19 15:24:58] (2 lines) /app/public/data/sreas/publish_metadata.tsv
[STOP] [2021-04-19 15:24:58] complete_harvest_instance
[START] [2021-04-19 15:24:58] completed
[STOP] [2021-04-19 15:24:58] completed
[STOP] [2021-04-19 15:24:58] logged process, took 100.92
Latest Process