Harvest for Yager 1981 Created 19 Apr 14:53

Harvesting Log

# Logfile created on 2020-08-27 15:22:19 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:22:19] logged process
[START] [2020-08-27 15:22:19] Creating resource from OpenData
[START] [2020-08-27 15:22:19] logged process
[START] [2020-08-27 15:22:19] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:22:20] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:22:20] Creating resource from OpenData
[INFO] [2020-11-19 12:47:52] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-11-19 12:47:56] ## remove_type: ScientificName
[INFO] [2020-11-19 12:47:56] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:47:56] [12:47:56.422] Removed 0 Scientificnames
[INFO] [2020-11-19 12:47:56] ## remove_type: Vernacular
[INFO] [2020-11-19 12:47:56] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:47:56] [12:47:56.425] Removed 0 Vernaculars
[INFO] [2020-11-19 12:47:56] ## remove_type: Article
[INFO] [2020-11-19 12:47:56] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:47:56] [12:47:56.428] Removed 0 Articles
[INFO] [2020-11-19 12:47:56] ## remove_type: Medium
[INFO] [2020-11-19 12:47:56] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:47:56] [12:47:56.432] Removed 0 Media
[INFO] [2020-11-19 12:47:56] ## remove_type: Trait
[INFO] [2020-11-19 12:47:56] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:47:56] [12:47:56.435] Removed 0 Traits
[INFO] [2020-11-19 12:47:56] ## remove_type: MetaTrait
[INFO] [2020-11-19 12:47:56] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:47:56] [12:47:56.437] Removed 0 Metatraits
[INFO] [2020-11-19 12:47:56] ## remove_type: OccurrenceMetadatum
[INFO] [2020-11-19 12:47:56] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:47:56] [12:47:56.440] Removed 0 Occurrencemetadata
[INFO] [2020-11-19 12:47:56] ## remove_type: Assoc
[INFO] [2020-11-19 12:47:56] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:47:56] [12:47:56.442] Removed 0 Assocs
[INFO] [2020-11-19 12:47:56] ## remove_type: MetaAssoc
[INFO] [2020-11-19 12:47:56] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:47:56] [12:47:56.445] Removed 0 Metaassocs
[INFO] [2020-11-19 12:47:56] ## remove_type: Identifier
[INFO] [2020-11-19 12:47:56] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:47:56] [12:47:56.447] Removed 0 Identifiers
[INFO] [2020-11-19 12:47:56] ## remove_type: Reference
[INFO] [2020-11-19 12:47:56] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:47:56] [12:47:56.449] Removed 0 References
[INFO] [2020-11-19 12:47:56] ## remove_type: Node
[INFO] [2020-11-19 12:47:56] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:47:56] [12:47:56.471] Removed 0 Nodes
[START] [2020-11-19 12:47:56] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 12:47:56] Creating resource from OpenData
[START] [2020-11-19 12:47:56] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 12:47:56] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 12:47:56] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 12:47:56] Creating resource from OpenData
[START] [2020-11-19 12:47:56] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 12:47:56] create_harvest_instance
[STOP] [2020-11-19 12:47:58] create_harvest_instance
[START] [2020-11-19 12:47:58] fetch_files
[STOP] [2020-11-19 12:47:58] fetch_files
[START] [2020-11-19 12:47:58] validate_each_file
[STOP] [2020-11-19 12:47:58] validate_each_file
[START] [2020-11-19 12:47:58] convert_to_csv
[CMD] [2020-11-19 12:47:58] /usr/bin/sort /app/public/converted_csv/yager_yager_1981_refs_24414.csv > /app/public/converted_csv/yager_yager_1981_refs_24414.csv_sorted
[CMD] [2020-11-19 12:47:58] /usr/bin/sort /app/public/converted_csv/yager_yager_1981_nodes_24415.csv > /app/public/converted_csv/yager_yager_1981_nodes_24415.csv_sorted
[CMD] [2020-11-19 12:47:58] /usr/bin/sort /app/public/converted_csv/yager_yager_1981_occurrences_24416.csv > /app/public/converted_csv/yager_yager_1981_occurrences_24416.csv_sorted
[CMD] [2020-11-19 12:47:58] /usr/bin/sort /app/public/converted_csv/yager_yager_1981_measurements_24417.csv > /app/public/converted_csv/yager_yager_1981_measurements_24417.csv_sorted
[STOP] [2020-11-19 12:47:58] convert_to_csv
[START] [2020-11-19 12:47:58] calculate_delta
[CMD] [2020-11-19 12:47:58] echo "0a" > /app/public/diff/yager_yager_1981_refs_24414.diff
[CMD] [2020-11-19 12:47:58] tail -n +1 /app/public/converted_csv/yager_yager_1981_refs_24414.csv >> /app/public/diff/yager_yager_1981_refs_24414.diff
[CMD] [2020-11-19 12:47:58] echo "." >> /app/public/diff/yager_yager_1981_refs_24414.diff
[CMD] [2020-11-19 12:47:58] echo "0a" > /app/public/diff/yager_yager_1981_nodes_24415.diff
[CMD] [2020-11-19 12:47:58] tail -n +1 /app/public/converted_csv/yager_yager_1981_nodes_24415.csv >> /app/public/diff/yager_yager_1981_nodes_24415.diff
[CMD] [2020-11-19 12:47:58] echo "." >> /app/public/diff/yager_yager_1981_nodes_24415.diff
[CMD] [2020-11-19 12:47:58] echo "0a" > /app/public/diff/yager_yager_1981_occurrences_24416.diff
[CMD] [2020-11-19 12:47:58] tail -n +1 /app/public/converted_csv/yager_yager_1981_occurrences_24416.csv >> /app/public/diff/yager_yager_1981_occurrences_24416.diff
[CMD] [2020-11-19 12:47:58] echo "." >> /app/public/diff/yager_yager_1981_occurrences_24416.diff
[CMD] [2020-11-19 12:47:58] echo "0a" > /app/public/diff/yager_yager_1981_measurements_24417.diff
[CMD] [2020-11-19 12:47:58] tail -n +1 /app/public/converted_csv/yager_yager_1981_measurements_24417.csv >> /app/public/diff/yager_yager_1981_measurements_24417.diff
[CMD] [2020-11-19 12:47:58] echo "." >> /app/public/diff/yager_yager_1981_measurements_24417.diff
[STOP] [2020-11-19 12:47:58] calculate_delta
[START] [2020-11-19 12:47:58] parse_diff_and_store
[INFO] [2020-11-19 12:47:58] Loading refs diff file into memory (true lines)...
[INFO] [2020-11-19 12:47:58] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-19 12:47:58] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-19 12:47:58] Loading measurements diff file into memory (true lines)...
[INFO] [2020-11-19 12:47:59] Storing 1 ScientificNames
[INFO] [2020-11-19 12:47:59] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 12:47:59] Average Time: 0.0
[INFO] [2020-11-19 12:47:59] Total Time: 1s
[INFO] [2020-11-19 12:47:59] Storing 1 Nodes
[INFO] [2020-11-19 12:47:59] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 12:47:59] Average Time: 0.0
[INFO] [2020-11-19 12:47:59] Total Time: 1s
[INFO] [2020-11-19 12:47:59] Storing 1 Occurrences
[INFO] [2020-11-19 12:47:59] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 12:47:59] Average Time: 0.0
[INFO] [2020-11-19 12:47:59] Total Time: 1s
[INFO] [2020-11-19 12:47:59] Storing 2 Traits
[INFO] [2020-11-19 12:47:59] Processing group of 2 in 1 groups of 1000
[INFO] [2020-11-19 12:47:59] Average Time: 0.0
[INFO] [2020-11-19 12:47:59] Total Time: 1s
[INFO] [2020-11-19 12:47:59] Storing 1 MetaTraits
[INFO] [2020-11-19 12:47:59] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 12:47:59] Average Time: 0.0
[INFO] [2020-11-19 12:47:59] Total Time: 1s
[STOP] [2020-11-19 12:47:59] parse_diff_and_store
[START] [2020-11-19 12:47:59] resolve_keys
[INFO] [2020-11-19 12:48:05] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-19 12:48:05] traits to occurrences...
[INFO] [2020-11-19 12:48:05] traits to nodes (through occurrences)...
[INFO] [2020-11-19 12:48:05] Traits to sex term...
[INFO] [2020-11-19 12:48:05] Traits to lifestage term...
[INFO] [2020-11-19 12:48:05] MetaTraits to traits...
[INFO] [2020-11-19 12:48:05] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-19 12:48:05] Assocs to occurrences...
[INFO] [2020-11-19 12:48:05] Assocs to nodes...
[INFO] [2020-11-19 12:48:05] Assoc to sex term...
[INFO] [2020-11-19 12:48:05] Assoc to lifestage term...
[INFO] [2020-11-19 12:48:05] MetaAssoc to assocs...
[STOP] [2020-11-19 12:48:05] resolve_keys
[START] [2020-11-19 12:48:05] hold_for_later_1
[STOP] [2020-11-19 12:48:05] hold_for_later_1
[START] [2020-11-19 12:48:05] hold_for_later_2
[STOP] [2020-11-19 12:48:05] hold_for_later_2
[START] [2020-11-19 12:48:05] resolve_missing_parents
[STOP] [2020-11-19 12:48:05] resolve_missing_parents
[START] [2020-11-19 12:48:05] rebuild_nodes
[START] [2020-11-19 12:48:05] Flattener#flatten
[START] [2020-11-19 12:48:05] Flattener#study_resource
[START] [2020-11-19 12:48:05] Flattener#build_ancestry
[STOP] [2020-11-19 12:48:05] Flattener#build_ancestry
[INFO] [2020-11-19 12:48:05] 1 ancestry keys
[START] [2020-11-19 12:48:05] build_node_ancestors
[INFO] [2020-11-19 12:48:05] old ancestors deleted.
[STOP] [2020-11-19 12:48:05] build_node_ancestors
[WARN] [2020-11-19 12:48:05] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-11-19 12:48:05] Flattener#flatten
[STOP] [2020-11-19 12:48:05] rebuild_nodes
[START] [2020-11-19 12:48:05] resolve_missing_media_owners
[STOP] [2020-11-19 12:48:05] resolve_missing_media_owners
[START] [2020-11-19 12:48:05] sanitize_media_verbatims
[STOP] [2020-11-19 12:48:05] sanitize_media_verbatims
[START] [2020-11-19 12:48:05] queue_downloads
[STOP] [2020-11-19 12:48:05] queue_downloads
[START] [2020-11-19 12:48:05] parse_names
[WARN] [2020-11-19 12:48:05] I see 1 names which still need to be parsed.
[STOP] [2020-11-19 12:48:06] parse_names
[START] [2020-11-19 12:48:06] denormalize_canonical_names_to_nodes
[STOP] [2020-11-19 12:48:06] denormalize_canonical_names_to_nodes
[START] [2020-11-19 12:48:06] match_nodes
[START] [2020-11-19 12:48:06] map_all_nodes_to_pages
[STOP] [2020-11-19 12:48:06] map_all_nodes_to_pages
[INFO] [2020-11-19 12:48:06] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-11-19 12:48:06] update_nodes
[STOP] [2020-11-19 12:48:06] update_nodes
[STOP] [2020-11-19 12:48:06] match_nodes
[START] [2020-11-19 12:48:06] reindex_search
[STOP] [2020-11-19 12:48:07] reindex_search
[START] [2020-11-19 12:48:07] normalize_units
[STOP] [2020-11-19 12:48:07] normalize_units
[START] [2020-11-19 12:48:07] calculate_statistics
[2020-11-19 12:48:07] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-11-19 12:48:07] calculate_statistics
[START] [2020-11-19 12:48:07] complete_harvest_instance
[START] [2020-11-19 12:48:07] overall_tsv_creation
[INFO] [2020-11-19 12:48:07] Processing group of 1 in 1 batches of 10000
[INFO] [2020-11-19 12:48:49] 1 Traits (unfiltered)...
[INFO] [2020-11-19 12:49:33] 1 Traits (filtered)...
[INFO] [2020-11-19 12:49:33] 0 Associations (filtered)...
[INFO] [2020-11-19 12:49:33] 2 metadata added.
[INFO] [2020-11-19 12:49:33] 0 metadata added.
[INFO] [2020-11-19 12:49:33] Average Time: 66.53
[INFO] [2020-11-19 12:49:33] Total Time: 1m27s
[STOP] [2020-11-19 12:49:33] overall_tsv_creation
[INFO] [2020-11-19 12:49:33] Done. Check your files:
[INFO] [2020-11-19 12:49:33] (1 lines) /app/public/data/yager_yager_1981/publish_nodes.tsv
[INFO] [2020-11-19 12:49:33] (1 lines) /app/public/data/yager_yager_1981/publish_scientific_names.tsv
[INFO] [2020-11-19 12:49:33] (2 lines) /app/public/data/yager_yager_1981/publish_traits.tsv
[INFO] [2020-11-19 12:49:33] (3 lines) /app/public/data/yager_yager_1981/publish_metadata.tsv
[STOP] [2020-11-19 12:49:33] complete_harvest_instance
[START] [2020-11-19 12:49:33] completed
[STOP] [2020-11-19 12:49:33] completed
[STOP] [2020-11-19 12:49:33] logged process, took 96.39
[INFO] [2021-04-19 14:51:58] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 14:53:38] ## remove_type: ScientificName
[INFO] [2021-04-19 14:53:38] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 14:53:38] [14:53:38.214] Removed 1 Scientificnames
[INFO] [2021-04-19 14:53:38] ## remove_type: Vernacular
[INFO] [2021-04-19 14:53:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:53:38] [14:53:38.215] Removed 0 Vernaculars
[INFO] [2021-04-19 14:53:38] ## remove_type: Article
[INFO] [2021-04-19 14:53:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:53:38] [14:53:38.216] Removed 0 Articles
[INFO] [2021-04-19 14:53:38] ## remove_type: Medium
[INFO] [2021-04-19 14:53:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:53:38] [14:53:38.218] Removed 0 Media
[INFO] [2021-04-19 14:53:38] ## remove_type: Trait
[INFO] [2021-04-19 14:53:38] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 14:53:38] [14:53:38.220] Removed 2 Traits
[INFO] [2021-04-19 14:53:38] ## remove_type: MetaTrait
[INFO] [2021-04-19 14:53:38] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 14:53:38] [14:53:38.221] Removed 1 Metatraits
[INFO] [2021-04-19 14:53:38] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 14:53:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:53:38] [14:53:38.223] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 14:53:38] ## remove_type: Assoc
[INFO] [2021-04-19 14:53:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:53:38] [14:53:38.224] Removed 0 Assocs
[INFO] [2021-04-19 14:53:38] ## remove_type: MetaAssoc
[INFO] [2021-04-19 14:53:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:53:38] [14:53:38.226] Removed 0 Metaassocs
[INFO] [2021-04-19 14:53:38] ## remove_type: Identifier
[INFO] [2021-04-19 14:53:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:53:38] [14:53:38.227] Removed 0 Identifiers
[INFO] [2021-04-19 14:53:38] ## remove_type: Reference
[INFO] [2021-04-19 14:53:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:53:38] [14:53:38.228] Removed 0 References
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] Starting batch with ID 84620779...
[INFO] [2021-04-19 14:53:38] ## remove_type: Node
[INFO] [2021-04-19 14:53:38] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 14:53:38] [14:53:38.557] Removed 1 Nodes
[START] [2021-04-19 14:53:38] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:53:38] Creating resource from OpenData
[START] [2021-04-19 14:53:38] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:53:38] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 14:53:38] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 14:53:38] Creating resource from OpenData
[START] [2021-04-19 14:53:38] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:53:38] create_harvest_instance
[INFO] [2021-04-19 14:53:38] Created harvest instance #3753
[STOP] [2021-04-19 14:53:38] create_harvest_instance
[START] [2021-04-19 14:53:38] fetch_files
[STOP] [2021-04-19 14:53:38] fetch_files
[START] [2021-04-19 14:53:38] validate_each_file
[INFO] [2021-04-19 14:53:38] Looping over 4 formats...
[INFO] [2021-04-19 14:53:38] ...refs (/app/public/data/yager_yager_1981/references.tsv)
[INFO] [2021-04-19 14:53:38] Valid: /app/public/converted_csv/yager_yager_1981_refs_3753.csv (0 lines)
[INFO] [2021-04-19 14:53:38] ...nodes (/app/public/data/yager_yager_1981/taxa.txt)
[INFO] [2021-04-19 14:53:38] Valid: /app/public/converted_csv/yager_yager_1981_nodes_3753.csv (1 lines)
[INFO] [2021-04-19 14:53:38] ...occurrences (/app/public/data/yager_yager_1981/occurrences.txt)
[INFO] [2021-04-19 14:53:39] Valid: /app/public/converted_csv/yager_yager_1981_occurrences_3753.csv (1 lines)
[INFO] [2021-04-19 14:53:39] ...measurements (/app/public/data/yager_yager_1981/measurementsorfacts.txt)
[INFO] [2021-04-19 14:53:39] Valid: /app/public/converted_csv/yager_yager_1981_measurements_3753.csv (2 lines)
[STOP] [2021-04-19 14:53:39] validate_each_file
[START] [2021-04-19 14:53:39] convert_to_csv
[INFO] [2021-04-19 14:53:39] Looping over 4 formats...
[INFO] [2021-04-19 14:53:39] ...refs (/app/public/data/yager_yager_1981/references.tsv)
[CMD] [2021-04-19 14:53:39] /usr/bin/sort /app/public/converted_csv/yager_yager_1981_refs_3753.csv > /app/public/converted_csv/yager_yager_1981_refs_3753.csv_sorted
[INFO] [2021-04-19 14:53:39] Converted: /app/public/converted_csv/yager_yager_1981_refs_3753.csv (0 lines)
[INFO] [2021-04-19 14:53:39] ...nodes (/app/public/data/yager_yager_1981/taxa.txt)
[CMD] [2021-04-19 14:53:39] /usr/bin/sort /app/public/converted_csv/yager_yager_1981_nodes_3753.csv > /app/public/converted_csv/yager_yager_1981_nodes_3753.csv_sorted
[INFO] [2021-04-19 14:53:39] Converted: /app/public/converted_csv/yager_yager_1981_nodes_3753.csv (1 lines)
[INFO] [2021-04-19 14:53:39] ...occurrences (/app/public/data/yager_yager_1981/occurrences.txt)
[CMD] [2021-04-19 14:53:39] /usr/bin/sort /app/public/converted_csv/yager_yager_1981_occurrences_3753.csv > /app/public/converted_csv/yager_yager_1981_occurrences_3753.csv_sorted
[INFO] [2021-04-19 14:53:39] Converted: /app/public/converted_csv/yager_yager_1981_occurrences_3753.csv (1 lines)
[INFO] [2021-04-19 14:53:39] ...measurements (/app/public/data/yager_yager_1981/measurementsorfacts.txt)
[CMD] [2021-04-19 14:53:39] /usr/bin/sort /app/public/converted_csv/yager_yager_1981_measurements_3753.csv > /app/public/converted_csv/yager_yager_1981_measurements_3753.csv_sorted
[INFO] [2021-04-19 14:53:39] Converted: /app/public/converted_csv/yager_yager_1981_measurements_3753.csv (2 lines)
[STOP] [2021-04-19 14:53:39] convert_to_csv
[START] [2021-04-19 14:53:39] calculate_delta
[INFO] [2021-04-19 14:53:39] Looping over 4 formats...
[INFO] [2021-04-19 14:53:39] ...refs (/app/public/data/yager_yager_1981/references.tsv)
[CMD] [2021-04-19 14:53:39] echo "0a" > /app/public/diff/yager_yager_1981_refs_3753.diff
[CMD] [2021-04-19 14:53:39] tail -n +1 /app/public/converted_csv/yager_yager_1981_refs_3753.csv >> /app/public/diff/yager_yager_1981_refs_3753.diff
[CMD] [2021-04-19 14:53:39] echo "." >> /app/public/diff/yager_yager_1981_refs_3753.diff
[INFO] [2021-04-19 14:53:39] Created diff: /app/public/diff/yager_yager_1981_refs_3753.diff (2 lines)
[INFO] [2021-04-19 14:53:39] ...nodes (/app/public/data/yager_yager_1981/taxa.txt)
[CMD] [2021-04-19 14:53:39] echo "0a" > /app/public/diff/yager_yager_1981_nodes_3753.diff
[CMD] [2021-04-19 14:53:39] tail -n +1 /app/public/converted_csv/yager_yager_1981_nodes_3753.csv >> /app/public/diff/yager_yager_1981_nodes_3753.diff
[CMD] [2021-04-19 14:53:39] echo "." >> /app/public/diff/yager_yager_1981_nodes_3753.diff
[INFO] [2021-04-19 14:53:39] Created diff: /app/public/diff/yager_yager_1981_nodes_3753.diff (3 lines)
[INFO] [2021-04-19 14:53:39] ...occurrences (/app/public/data/yager_yager_1981/occurrences.txt)
[CMD] [2021-04-19 14:53:39] echo "0a" > /app/public/diff/yager_yager_1981_occurrences_3753.diff
[CMD] [2021-04-19 14:53:39] tail -n +1 /app/public/converted_csv/yager_yager_1981_occurrences_3753.csv >> /app/public/diff/yager_yager_1981_occurrences_3753.diff
[CMD] [2021-04-19 14:53:39] echo "." >> /app/public/diff/yager_yager_1981_occurrences_3753.diff
[INFO] [2021-04-19 14:53:39] Created diff: /app/public/diff/yager_yager_1981_occurrences_3753.diff (3 lines)
[INFO] [2021-04-19 14:53:39] ...measurements (/app/public/data/yager_yager_1981/measurementsorfacts.txt)
[CMD] [2021-04-19 14:53:39] echo "0a" > /app/public/diff/yager_yager_1981_measurements_3753.diff
[CMD] [2021-04-19 14:53:39] tail -n +1 /app/public/converted_csv/yager_yager_1981_measurements_3753.csv >> /app/public/diff/yager_yager_1981_measurements_3753.diff
[CMD] [2021-04-19 14:53:39] echo "." >> /app/public/diff/yager_yager_1981_measurements_3753.diff
[INFO] [2021-04-19 14:53:39] Created diff: /app/public/diff/yager_yager_1981_measurements_3753.diff (4 lines)
[STOP] [2021-04-19 14:53:39] calculate_delta
[START] [2021-04-19 14:53:39] parse_diff_and_store
[INFO] [2021-04-19 14:53:39] Handling diff: /app/public/diff/yager_yager_1981_refs_3753.diff (2 lines)
[INFO] [2021-04-19 14:53:39] Loading refs diff file into memory (2 /app/public/diff/yager_yager_1981_refs_3753.diff lines)...
[INFO] [2021-04-19 14:53:39] Handling diff: /app/public/diff/yager_yager_1981_nodes_3753.diff (3 lines)
[INFO] [2021-04-19 14:53:39] Loading nodes diff file into memory (3 /app/public/diff/yager_yager_1981_nodes_3753.diff lines)...
[INFO] [2021-04-19 14:53:39] Handling diff: /app/public/diff/yager_yager_1981_occurrences_3753.diff (3 lines)
[INFO] [2021-04-19 14:53:39] Loading occurrences diff file into memory (3 /app/public/diff/yager_yager_1981_occurrences_3753.diff lines)...
[INFO] [2021-04-19 14:53:39] Handling diff: /app/public/diff/yager_yager_1981_measurements_3753.diff (4 lines)
[INFO] [2021-04-19 14:53:39] Loading measurements diff file into memory (4 /app/public/diff/yager_yager_1981_measurements_3753.diff lines)...
[INFO] [2021-04-19 14:53:39] Storing 1 ScientificNames
[INFO] [2021-04-19 14:53:39] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:53:39] Average Time: 0.0
[INFO] [2021-04-19 14:53:39] Total Time: 1s
[INFO] [2021-04-19 14:53:39] Storing 1 Nodes
[INFO] [2021-04-19 14:53:39] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:53:39] Average Time: 0.0
[INFO] [2021-04-19 14:53:39] Total Time: 1s
[INFO] [2021-04-19 14:53:39] Storing 1 Occurrences
[INFO] [2021-04-19 14:53:39] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:53:39] Average Time: 0.0
[INFO] [2021-04-19 14:53:39] Total Time: 1s
[INFO] [2021-04-19 14:53:39] Storing 2 Traits
[INFO] [2021-04-19 14:53:39] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 14:53:39] Average Time: 0.0
[INFO] [2021-04-19 14:53:39] Total Time: 1s
[INFO] [2021-04-19 14:53:39] Storing 1 MetaTraits
[INFO] [2021-04-19 14:53:39] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:53:39] Average Time: 0.0
[INFO] [2021-04-19 14:53:39] Total Time: 1s
[STOP] [2021-04-19 14:53:39] parse_diff_and_store
[START] [2021-04-19 14:53:39] resolve_keys
[INFO] [2021-04-19 14:53:45] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 14:53:45] traits to occurrences...
[INFO] [2021-04-19 14:53:45] traits to nodes (through occurrences)...
[INFO] [2021-04-19 14:53:45] Traits to sex term...
[INFO] [2021-04-19 14:53:45] Traits to lifestage term...
[INFO] [2021-04-19 14:53:45] MetaTraits to traits...
[INFO] [2021-04-19 14:53:45] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 14:53:45] Assocs to occurrences...
[INFO] [2021-04-19 14:53:45] Assocs to nodes...
[INFO] [2021-04-19 14:53:45] Assoc to sex term...
[INFO] [2021-04-19 14:53:45] Assoc to lifestage term...
[INFO] [2021-04-19 14:53:45] MetaAssoc to assocs...
[STOP] [2021-04-19 14:53:45] resolve_keys
[START] [2021-04-19 14:53:45] hold_for_later_1
[STOP] [2021-04-19 14:53:45] hold_for_later_1
[START] [2021-04-19 14:53:45] hold_for_later_2
[STOP] [2021-04-19 14:53:45] hold_for_later_2
[START] [2021-04-19 14:53:45] resolve_missing_parents
[STOP] [2021-04-19 14:53:45] resolve_missing_parents
[START] [2021-04-19 14:53:45] rebuild_nodes
[START] [2021-04-19 14:53:45] Flattener#flatten
[START] [2021-04-19 14:53:45] Flattener#study_resource
[START] [2021-04-19 14:53:45] Flattener#build_ancestry
[STOP] [2021-04-19 14:53:45] Flattener#build_ancestry
[INFO] [2021-04-19 14:53:45] 1 ancestry keys
[START] [2021-04-19 14:53:45] build_node_ancestors
[INFO] [2021-04-19 14:53:45] old ancestors deleted.
[STOP] [2021-04-19 14:53:45] build_node_ancestors
[WARN] [2021-04-19 14:53:45] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 14:53:45] Flattener#flatten
[STOP] [2021-04-19 14:53:45] rebuild_nodes
[START] [2021-04-19 14:53:45] resolve_missing_media_owners
[STOP] [2021-04-19 14:53:45] resolve_missing_media_owners
[START] [2021-04-19 14:53:45] sanitize_media_verbatims
[STOP] [2021-04-19 14:53:45] sanitize_media_verbatims
[START] [2021-04-19 14:53:45] queue_downloads
[STOP] [2021-04-19 14:53:45] queue_downloads
[START] [2021-04-19 14:53:45] parse_names
[WARN] [2021-04-19 14:53:45] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 14:53:46] parse_names
[START] [2021-04-19 14:53:46] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 14:53:46] denormalize_canonical_names_to_nodes
[START] [2021-04-19 14:53:46] match_nodes
[START] [2021-04-19 14:53:46] map_all_nodes_to_pages
[STOP] [2021-04-19 14:53:46] map_all_nodes_to_pages
[INFO] [2021-04-19 14:53:46] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 14:53:46] update_nodes
[STOP] [2021-04-19 14:53:46] update_nodes
[STOP] [2021-04-19 14:53:46] match_nodes
[START] [2021-04-19 14:53:46] reindex_search
[STOP] [2021-04-19 14:53:46] reindex_search
[START] [2021-04-19 14:53:46] normalize_units
[STOP] [2021-04-19 14:53:46] normalize_units
[START] [2021-04-19 14:53:46] calculate_statistics
[2021-04-19 14:53:46] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 14:53:46] calculate_statistics
[START] [2021-04-19 14:53:46] complete_harvest_instance
[START] [2021-04-19 14:53:46] overall_tsv_creation
[INFO] [2021-04-19 14:53:46] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 14:54:21] 1 Traits (unfiltered)...
[INFO] [2021-04-19 14:54:53] 1 Traits (filtered)...
[INFO] [2021-04-19 14:54:53] 0 Associations (filtered)...
[INFO] [2021-04-19 14:54:53] 1 metadata added.
[INFO] [2021-04-19 14:54:53] 0 metadata added.
[INFO] [2021-04-19 14:55:19] Average Time: 69.03
[INFO] [2021-04-19 14:55:19] Total Time: 1m33s
[STOP] [2021-04-19 14:55:19] overall_tsv_creation
[INFO] [2021-04-19 14:55:19] Done. Check your files:
[INFO] [2021-04-19 14:55:19] (1 lines) /app/public/data/yager_yager_1981/publish_nodes.tsv
[INFO] [2021-04-19 14:55:19] (1 lines) /app/public/data/yager_yager_1981/publish_scientific_names.tsv
[INFO] [2021-04-19 14:55:19] (2 lines) /app/public/data/yager_yager_1981/publish_traits.tsv
[INFO] [2021-04-19 14:55:19] (2 lines) /app/public/data/yager_yager_1981/publish_metadata.tsv
[STOP] [2021-04-19 14:55:19] complete_harvest_instance
[START] [2021-04-19 14:55:19] completed
[STOP] [2021-04-19 14:55:19] completed
[STOP] [2021-04-19 14:55:19] logged process, took 100.31

Latest Process

19 Apr 14:53 EXITED currently processing 0