Harvest for
Mayer 2006
Created
19 Apr 16:09
Stage:
completed
Fetched:
19 Apr 16:09
Validated:
19 Apr 16:09
Deltas Created
19 Apr 16:09
Units Normalized:
19 Apr 16:09
Ancestry Built:
19 Apr 16:09
Nodes Matched:
19 Apr 16:09
Names Parsed:
19 Apr 16:09
New Models Stored:
19 Apr 16:09
Indexed:
19 Apr 16:09
Completed:
19 Apr 16:11
Time to Harvest:
less than a minute
Harvesting Log
(432 lines)
# Logfile created on 2020-08-27 15:53:34 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:53:34] logged process
[START] [2020-08-27 15:53:34] Creating resource from OpenData
[START] [2020-08-27 15:53:34] logged process
[START] [2020-08-27 15:53:34] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:53:34] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:53:34] Creating resource from OpenData
[INFO] [2020-12-03 14:16:21] ## HARVEST: type = -harvest
[START] [2020-12-03 14:16:23] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-12-03 14:16:23] create_harvest_instance
[STOP] [2020-12-03 14:16:25] create_harvest_instance
[START] [2020-12-03 14:16:25] fetch_files
[STOP] [2020-12-03 14:16:25] fetch_files
[START] [2020-12-03 14:16:25] validate_each_file
[STOP] [2020-12-03 14:16:25] validate_each_file
[START] [2020-12-03 14:16:25] convert_to_csv
[CMD] [2020-12-03 14:16:25] /usr/bin/sort /app/public/converted_csv/mayer_mayer_2006_refs_24928.csv > /app/public/converted_csv/mayer_mayer_2006_refs_24928.csv_sorted
[CMD] [2020-12-03 14:16:25] /usr/bin/sort /app/public/converted_csv/mayer_mayer_2006_nodes_24929.csv > /app/public/converted_csv/mayer_mayer_2006_nodes_24929.csv_sorted
[CMD] [2020-12-03 14:16:25] /usr/bin/sort /app/public/converted_csv/mayer_mayer_2006_occurrences_24930.csv > /app/public/converted_csv/mayer_mayer_2006_occurrences_24930.csv_sorted
[CMD] [2020-12-03 14:16:25] /usr/bin/sort /app/public/converted_csv/mayer_mayer_2006_measurements_24931.csv > /app/public/converted_csv/mayer_mayer_2006_measurements_24931.csv_sorted
[STOP] [2020-12-03 14:16:25] convert_to_csv
[START] [2020-12-03 14:16:25] calculate_delta
[CMD] [2020-12-03 14:16:25] echo "0a" > /app/public/diff/mayer_mayer_2006_refs_24928.diff
[CMD] [2020-12-03 14:16:25] tail -n +1 /app/public/converted_csv/mayer_mayer_2006_refs_24928.csv >> /app/public/diff/mayer_mayer_2006_refs_24928.diff
[CMD] [2020-12-03 14:16:25] echo "." >> /app/public/diff/mayer_mayer_2006_refs_24928.diff
[CMD] [2020-12-03 14:16:25] echo "0a" > /app/public/diff/mayer_mayer_2006_nodes_24929.diff
[CMD] [2020-12-03 14:16:25] tail -n +1 /app/public/converted_csv/mayer_mayer_2006_nodes_24929.csv >> /app/public/diff/mayer_mayer_2006_nodes_24929.diff
[CMD] [2020-12-03 14:16:25] echo "." >> /app/public/diff/mayer_mayer_2006_nodes_24929.diff
[CMD] [2020-12-03 14:16:25] echo "0a" > /app/public/diff/mayer_mayer_2006_occurrences_24930.diff
[CMD] [2020-12-03 14:16:25] tail -n +1 /app/public/converted_csv/mayer_mayer_2006_occurrences_24930.csv >> /app/public/diff/mayer_mayer_2006_occurrences_24930.diff
[CMD] [2020-12-03 14:16:25] echo "." >> /app/public/diff/mayer_mayer_2006_occurrences_24930.diff
[CMD] [2020-12-03 14:16:25] echo "0a" > /app/public/diff/mayer_mayer_2006_measurements_24931.diff
[CMD] [2020-12-03 14:16:25] tail -n +1 /app/public/converted_csv/mayer_mayer_2006_measurements_24931.csv >> /app/public/diff/mayer_mayer_2006_measurements_24931.diff
[CMD] [2020-12-03 14:16:25] echo "." >> /app/public/diff/mayer_mayer_2006_measurements_24931.diff
[STOP] [2020-12-03 14:16:25] calculate_delta
[START] [2020-12-03 14:16:25] parse_diff_and_store
[INFO] [2020-12-03 14:16:25] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 14:16:25] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 14:16:25] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 14:16:25] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 14:16:26] Storing 1 ScientificNames
[INFO] [2020-12-03 14:16:26] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 14:16:26] Average Time: 0.0
[INFO] [2020-12-03 14:16:26] Total Time: 1s
[INFO] [2020-12-03 14:16:26] Storing 1 Nodes
[INFO] [2020-12-03 14:16:26] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 14:16:26] Average Time: 0.0
[INFO] [2020-12-03 14:16:26] Total Time: 1s
[INFO] [2020-12-03 14:16:26] Storing 1 Occurrences
[INFO] [2020-12-03 14:16:26] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 14:16:26] Average Time: 0.0
[INFO] [2020-12-03 14:16:26] Total Time: 1s
[INFO] [2020-12-03 14:16:26] Storing 7 Traits
[INFO] [2020-12-03 14:16:26] Processing group of 7 in 1 groups of 1000
[INFO] [2020-12-03 14:16:26] Average Time: 0.0
[INFO] [2020-12-03 14:16:26] Total Time: 1s
[INFO] [2020-12-03 14:16:26] Storing 1 MetaTraits
[INFO] [2020-12-03 14:16:26] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 14:16:26] Average Time: 0.0
[INFO] [2020-12-03 14:16:26] Total Time: 1s
[STOP] [2020-12-03 14:16:26] parse_diff_and_store
[START] [2020-12-03 14:16:26] resolve_keys
[INFO] [2020-12-03 14:16:31] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 14:16:31] traits to occurrences...
[INFO] [2020-12-03 14:16:31] traits to nodes (through occurrences)...
[INFO] [2020-12-03 14:16:31] Traits to sex term...
[INFO] [2020-12-03 14:16:31] Traits to lifestage term...
[INFO] [2020-12-03 14:16:31] MetaTraits to traits...
[INFO] [2020-12-03 14:16:31] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 14:16:31] Assocs to occurrences...
[INFO] [2020-12-03 14:16:31] Assocs to nodes...
[INFO] [2020-12-03 14:16:31] Assoc to sex term...
[INFO] [2020-12-03 14:16:31] Assoc to lifestage term...
[INFO] [2020-12-03 14:16:31] MetaAssoc to assocs...
[STOP] [2020-12-03 14:16:31] resolve_keys
[START] [2020-12-03 14:16:31] hold_for_later_1
[STOP] [2020-12-03 14:16:31] hold_for_later_1
[START] [2020-12-03 14:16:32] hold_for_later_2
[STOP] [2020-12-03 14:16:32] hold_for_later_2
[START] [2020-12-03 14:16:32] resolve_missing_parents
[STOP] [2020-12-03 14:16:32] resolve_missing_parents
[START] [2020-12-03 14:16:32] rebuild_nodes
[START] [2020-12-03 14:16:32] Flattener#flatten
[START] [2020-12-03 14:16:32] Flattener#study_resource
[START] [2020-12-03 14:16:32] Flattener#build_ancestry
[STOP] [2020-12-03 14:16:32] Flattener#build_ancestry
[INFO] [2020-12-03 14:16:32] 1 ancestry keys
[START] [2020-12-03 14:16:32] build_node_ancestors
[INFO] [2020-12-03 14:16:32] old ancestors deleted.
[STOP] [2020-12-03 14:16:32] build_node_ancestors
[WARN] [2020-12-03 14:16:32] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 14:16:32] Flattener#flatten
[STOP] [2020-12-03 14:16:32] rebuild_nodes
[START] [2020-12-03 14:16:32] resolve_missing_media_owners
[STOP] [2020-12-03 14:16:32] resolve_missing_media_owners
[START] [2020-12-03 14:16:32] sanitize_media_verbatims
[STOP] [2020-12-03 14:16:32] sanitize_media_verbatims
[START] [2020-12-03 14:16:32] queue_downloads
[STOP] [2020-12-03 14:16:32] queue_downloads
[START] [2020-12-03 14:16:32] parse_names
[WARN] [2020-12-03 14:16:32] I see 1 names which still need to be parsed.
[STOP] [2020-12-03 14:16:33] parse_names
[START] [2020-12-03 14:16:33] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 14:16:33] denormalize_canonical_names_to_nodes
[START] [2020-12-03 14:16:33] match_nodes
[START] [2020-12-03 14:16:33] map_all_nodes_to_pages
[STOP] [2020-12-03 14:16:33] map_all_nodes_to_pages
[INFO] [2020-12-03 14:16:33] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-12-03 14:16:33] update_nodes
[STOP] [2020-12-03 14:16:33] update_nodes
[STOP] [2020-12-03 14:16:33] match_nodes
[START] [2020-12-03 14:16:33] reindex_search
[STOP] [2020-12-03 14:16:33] reindex_search
[START] [2020-12-03 14:16:33] normalize_units
[STOP] [2020-12-03 14:16:33] normalize_units
[START] [2020-12-03 14:16:33] calculate_statistics
[2020-12-03 14:16:33] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 14:16:33] calculate_statistics
[START] [2020-12-03 14:16:33] complete_harvest_instance
[START] [2020-12-03 14:16:33] overall_tsv_creation
[INFO] [2020-12-03 14:16:33] Processing group of 1 in 1 batches of 10000
[INFO] [2020-12-03 14:17:11] 1 Traits (unfiltered)...
[INFO] [2020-12-03 14:17:47] 1 Traits (filtered)...
[INFO] [2020-12-03 14:17:47] 0 Associations (filtered)...
[INFO] [2020-12-03 14:17:47] 7 metadata added.
[INFO] [2020-12-03 14:17:47] 0 metadata added.
[INFO] [2020-12-03 14:17:47] Average Time: 51.76
[INFO] [2020-12-03 14:17:47] Total Time: 1m15s
[STOP] [2020-12-03 14:17:47] overall_tsv_creation
[INFO] [2020-12-03 14:17:47] Done. Check your files:
[INFO] [2020-12-03 14:17:47] (1 lines) /app/public/data/mayer_mayer_2006/publish_nodes.tsv
[INFO] [2020-12-03 14:17:47] (1 lines) /app/public/data/mayer_mayer_2006/publish_scientific_names.tsv
[INFO] [2020-12-03 14:17:47] (2 lines) /app/public/data/mayer_mayer_2006/publish_traits.tsv
[INFO] [2020-12-03 14:17:47] (8 lines) /app/public/data/mayer_mayer_2006/publish_metadata.tsv
[STOP] [2020-12-03 14:17:47] complete_harvest_instance
[START] [2020-12-03 14:17:47] completed
[STOP] [2020-12-03 14:17:47] completed
[STOP] [2020-12-03 14:17:47] logged process, took 84.37
[INFO] [2021-04-19 15:58:24] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 16:09:25] ## remove_type: ScientificName
[INFO] [2021-04-19 16:09:25] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 16:09:25] [16:09:25.920] Removed 1 Scientificnames
[INFO] [2021-04-19 16:09:25] ## remove_type: Vernacular
[INFO] [2021-04-19 16:09:25] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:09:25] [16:09:25.922] Removed 0 Vernaculars
[INFO] [2021-04-19 16:09:25] ## remove_type: Article
[INFO] [2021-04-19 16:09:25] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:09:25] [16:09:25.923] Removed 0 Articles
[INFO] [2021-04-19 16:09:25] ## remove_type: Medium
[INFO] [2021-04-19 16:09:25] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:09:25] [16:09:25.925] Removed 0 Media
[INFO] [2021-04-19 16:09:25] ## remove_type: Trait
[INFO] [2021-04-19 16:09:25] ++ Calling delete_all on 7 instances...
[INFO] [2021-04-19 16:09:25] [16:09:25.927] Removed 7 Traits
[INFO] [2021-04-19 16:09:25] ## remove_type: MetaTrait
[INFO] [2021-04-19 16:09:25] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 16:09:25] [16:09:25.929] Removed 1 Metatraits
[INFO] [2021-04-19 16:09:25] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 16:09:25] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:09:25] [16:09:25.931] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 16:09:25] ## remove_type: Assoc
[INFO] [2021-04-19 16:09:25] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:09:25] [16:09:25.932] Removed 0 Assocs
[INFO] [2021-04-19 16:09:25] ## remove_type: MetaAssoc
[INFO] [2021-04-19 16:09:25] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:09:25] [16:09:25.933] Removed 0 Metaassocs
[INFO] [2021-04-19 16:09:25] ## remove_type: Identifier
[INFO] [2021-04-19 16:09:25] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:09:25] [16:09:25.935] Removed 0 Identifiers
[INFO] [2021-04-19 16:09:25] ## remove_type: Reference
[INFO] [2021-04-19 16:09:25] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:09:25] [16:09:25.937] Removed 0 References
[INFO] [2021-04-19 16:09:25] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:25] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:25] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:25] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:25] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:25] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:25] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:25] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] Starting batch with ID 86116275...
[INFO] [2021-04-19 16:09:26] ## remove_type: Node
[INFO] [2021-04-19 16:09:26] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 16:09:26] [16:09:26.513] Removed 1 Nodes
[START] [2021-04-19 16:09:26] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:09:26] Creating resource from OpenData
[START] [2021-04-19 16:09:26] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:09:26] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:09:26] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:09:26] Creating resource from OpenData
[START] [2021-04-19 16:09:26] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:09:26] create_harvest_instance
[INFO] [2021-04-19 16:09:26] Created harvest instance #3789
[STOP] [2021-04-19 16:09:26] create_harvest_instance
[START] [2021-04-19 16:09:26] fetch_files
[STOP] [2021-04-19 16:09:26] fetch_files
[START] [2021-04-19 16:09:26] validate_each_file
[INFO] [2021-04-19 16:09:26] Looping over 4 formats...
[INFO] [2021-04-19 16:09:27] ...refs (/app/public/data/mayer_mayer_2006/references.tsv)
[INFO] [2021-04-19 16:09:27] Valid: /app/public/converted_csv/mayer_mayer_2006_refs_3789.csv (0 lines)
[INFO] [2021-04-19 16:09:27] ...nodes (/app/public/data/mayer_mayer_2006/taxa.txt)
[INFO] [2021-04-19 16:09:27] Valid: /app/public/converted_csv/mayer_mayer_2006_nodes_3789.csv (1 lines)
[INFO] [2021-04-19 16:09:27] ...occurrences (/app/public/data/mayer_mayer_2006/occurrences.txt)
[INFO] [2021-04-19 16:09:27] Valid: /app/public/converted_csv/mayer_mayer_2006_occurrences_3789.csv (1 lines)
[INFO] [2021-04-19 16:09:27] ...measurements (/app/public/data/mayer_mayer_2006/measurementsorfacts.txt)
[INFO] [2021-04-19 16:09:27] Valid: /app/public/converted_csv/mayer_mayer_2006_measurements_3789.csv (7 lines)
[STOP] [2021-04-19 16:09:27] validate_each_file
[START] [2021-04-19 16:09:27] convert_to_csv
[INFO] [2021-04-19 16:09:27] Looping over 4 formats...
[INFO] [2021-04-19 16:09:27] ...refs (/app/public/data/mayer_mayer_2006/references.tsv)
[CMD] [2021-04-19 16:09:27] /usr/bin/sort /app/public/converted_csv/mayer_mayer_2006_refs_3789.csv > /app/public/converted_csv/mayer_mayer_2006_refs_3789.csv_sorted
[INFO] [2021-04-19 16:09:27] Converted: /app/public/converted_csv/mayer_mayer_2006_refs_3789.csv (0 lines)
[INFO] [2021-04-19 16:09:27] ...nodes (/app/public/data/mayer_mayer_2006/taxa.txt)
[CMD] [2021-04-19 16:09:27] /usr/bin/sort /app/public/converted_csv/mayer_mayer_2006_nodes_3789.csv > /app/public/converted_csv/mayer_mayer_2006_nodes_3789.csv_sorted
[INFO] [2021-04-19 16:09:27] Converted: /app/public/converted_csv/mayer_mayer_2006_nodes_3789.csv (1 lines)
[INFO] [2021-04-19 16:09:27] ...occurrences (/app/public/data/mayer_mayer_2006/occurrences.txt)
[CMD] [2021-04-19 16:09:27] /usr/bin/sort /app/public/converted_csv/mayer_mayer_2006_occurrences_3789.csv > /app/public/converted_csv/mayer_mayer_2006_occurrences_3789.csv_sorted
[INFO] [2021-04-19 16:09:27] Converted: /app/public/converted_csv/mayer_mayer_2006_occurrences_3789.csv (1 lines)
[INFO] [2021-04-19 16:09:27] ...measurements (/app/public/data/mayer_mayer_2006/measurementsorfacts.txt)
[CMD] [2021-04-19 16:09:27] /usr/bin/sort /app/public/converted_csv/mayer_mayer_2006_measurements_3789.csv > /app/public/converted_csv/mayer_mayer_2006_measurements_3789.csv_sorted
[INFO] [2021-04-19 16:09:27] Converted: /app/public/converted_csv/mayer_mayer_2006_measurements_3789.csv (7 lines)
[STOP] [2021-04-19 16:09:27] convert_to_csv
[START] [2021-04-19 16:09:27] calculate_delta
[INFO] [2021-04-19 16:09:27] Looping over 4 formats...
[INFO] [2021-04-19 16:09:27] ...refs (/app/public/data/mayer_mayer_2006/references.tsv)
[CMD] [2021-04-19 16:09:27] echo "0a" > /app/public/diff/mayer_mayer_2006_refs_3789.diff
[CMD] [2021-04-19 16:09:27] tail -n +1 /app/public/converted_csv/mayer_mayer_2006_refs_3789.csv >> /app/public/diff/mayer_mayer_2006_refs_3789.diff
[CMD] [2021-04-19 16:09:27] echo "." >> /app/public/diff/mayer_mayer_2006_refs_3789.diff
[INFO] [2021-04-19 16:09:27] Created diff: /app/public/diff/mayer_mayer_2006_refs_3789.diff (2 lines)
[INFO] [2021-04-19 16:09:27] ...nodes (/app/public/data/mayer_mayer_2006/taxa.txt)
[CMD] [2021-04-19 16:09:27] echo "0a" > /app/public/diff/mayer_mayer_2006_nodes_3789.diff
[CMD] [2021-04-19 16:09:27] tail -n +1 /app/public/converted_csv/mayer_mayer_2006_nodes_3789.csv >> /app/public/diff/mayer_mayer_2006_nodes_3789.diff
[CMD] [2021-04-19 16:09:27] echo "." >> /app/public/diff/mayer_mayer_2006_nodes_3789.diff
[INFO] [2021-04-19 16:09:27] Created diff: /app/public/diff/mayer_mayer_2006_nodes_3789.diff (3 lines)
[INFO] [2021-04-19 16:09:27] ...occurrences (/app/public/data/mayer_mayer_2006/occurrences.txt)
[CMD] [2021-04-19 16:09:27] echo "0a" > /app/public/diff/mayer_mayer_2006_occurrences_3789.diff
[CMD] [2021-04-19 16:09:27] tail -n +1 /app/public/converted_csv/mayer_mayer_2006_occurrences_3789.csv >> /app/public/diff/mayer_mayer_2006_occurrences_3789.diff
[CMD] [2021-04-19 16:09:27] echo "." >> /app/public/diff/mayer_mayer_2006_occurrences_3789.diff
[INFO] [2021-04-19 16:09:27] Created diff: /app/public/diff/mayer_mayer_2006_occurrences_3789.diff (3 lines)
[INFO] [2021-04-19 16:09:27] ...measurements (/app/public/data/mayer_mayer_2006/measurementsorfacts.txt)
[CMD] [2021-04-19 16:09:27] echo "0a" > /app/public/diff/mayer_mayer_2006_measurements_3789.diff
[CMD] [2021-04-19 16:09:27] tail -n +1 /app/public/converted_csv/mayer_mayer_2006_measurements_3789.csv >> /app/public/diff/mayer_mayer_2006_measurements_3789.diff
[CMD] [2021-04-19 16:09:27] echo "." >> /app/public/diff/mayer_mayer_2006_measurements_3789.diff
[INFO] [2021-04-19 16:09:27] Created diff: /app/public/diff/mayer_mayer_2006_measurements_3789.diff (9 lines)
[STOP] [2021-04-19 16:09:27] calculate_delta
[START] [2021-04-19 16:09:27] parse_diff_and_store
[INFO] [2021-04-19 16:09:27] Handling diff: /app/public/diff/mayer_mayer_2006_refs_3789.diff (2 lines)
[INFO] [2021-04-19 16:09:27] Loading refs diff file into memory (2 /app/public/diff/mayer_mayer_2006_refs_3789.diff lines)...
[INFO] [2021-04-19 16:09:27] Handling diff: /app/public/diff/mayer_mayer_2006_nodes_3789.diff (3 lines)
[INFO] [2021-04-19 16:09:27] Loading nodes diff file into memory (3 /app/public/diff/mayer_mayer_2006_nodes_3789.diff lines)...
[INFO] [2021-04-19 16:09:27] Handling diff: /app/public/diff/mayer_mayer_2006_occurrences_3789.diff (3 lines)
[INFO] [2021-04-19 16:09:27] Loading occurrences diff file into memory (3 /app/public/diff/mayer_mayer_2006_occurrences_3789.diff lines)...
[INFO] [2021-04-19 16:09:27] Handling diff: /app/public/diff/mayer_mayer_2006_measurements_3789.diff (9 lines)
[INFO] [2021-04-19 16:09:27] Loading measurements diff file into memory (9 /app/public/diff/mayer_mayer_2006_measurements_3789.diff lines)...
[INFO] [2021-04-19 16:09:27] Storing 1 ScientificNames
[INFO] [2021-04-19 16:09:27] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:09:27] Average Time: 0.0
[INFO] [2021-04-19 16:09:27] Total Time: 1s
[INFO] [2021-04-19 16:09:27] Storing 1 Nodes
[INFO] [2021-04-19 16:09:27] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:09:27] Average Time: 0.0
[INFO] [2021-04-19 16:09:27] Total Time: 1s
[INFO] [2021-04-19 16:09:27] Storing 1 Occurrences
[INFO] [2021-04-19 16:09:27] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:09:27] Average Time: 0.0
[INFO] [2021-04-19 16:09:27] Total Time: 1s
[INFO] [2021-04-19 16:09:27] Storing 7 Traits
[INFO] [2021-04-19 16:09:27] Processing group of 7 in 1 groups of 1000
[INFO] [2021-04-19 16:09:27] Average Time: 0.0
[INFO] [2021-04-19 16:09:27] Total Time: 1s
[INFO] [2021-04-19 16:09:27] Storing 1 MetaTraits
[INFO] [2021-04-19 16:09:27] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 16:09:27] Average Time: 0.0
[INFO] [2021-04-19 16:09:27] Total Time: 1s
[STOP] [2021-04-19 16:09:27] parse_diff_and_store
[START] [2021-04-19 16:09:27] resolve_keys
[INFO] [2021-04-19 16:09:33] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 16:09:33] traits to occurrences...
[INFO] [2021-04-19 16:09:33] traits to nodes (through occurrences)...
[INFO] [2021-04-19 16:09:33] Traits to sex term...
[INFO] [2021-04-19 16:09:33] Traits to lifestage term...
[INFO] [2021-04-19 16:09:33] MetaTraits to traits...
[INFO] [2021-04-19 16:09:33] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 16:09:33] Assocs to occurrences...
[INFO] [2021-04-19 16:09:33] Assocs to nodes...
[INFO] [2021-04-19 16:09:33] Assoc to sex term...
[INFO] [2021-04-19 16:09:33] Assoc to lifestage term...
[INFO] [2021-04-19 16:09:33] MetaAssoc to assocs...
[STOP] [2021-04-19 16:09:33] resolve_keys
[START] [2021-04-19 16:09:33] hold_for_later_1
[STOP] [2021-04-19 16:09:33] hold_for_later_1
[START] [2021-04-19 16:09:33] hold_for_later_2
[STOP] [2021-04-19 16:09:33] hold_for_later_2
[START] [2021-04-19 16:09:33] resolve_missing_parents
[STOP] [2021-04-19 16:09:33] resolve_missing_parents
[START] [2021-04-19 16:09:33] rebuild_nodes
[START] [2021-04-19 16:09:33] Flattener#flatten
[START] [2021-04-19 16:09:33] Flattener#study_resource
[START] [2021-04-19 16:09:33] Flattener#build_ancestry
[STOP] [2021-04-19 16:09:33] Flattener#build_ancestry
[INFO] [2021-04-19 16:09:33] 1 ancestry keys
[START] [2021-04-19 16:09:33] build_node_ancestors
[INFO] [2021-04-19 16:09:33] old ancestors deleted.
[STOP] [2021-04-19 16:09:33] build_node_ancestors
[WARN] [2021-04-19 16:09:33] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 16:09:33] Flattener#flatten
[STOP] [2021-04-19 16:09:33] rebuild_nodes
[START] [2021-04-19 16:09:33] resolve_missing_media_owners
[STOP] [2021-04-19 16:09:33] resolve_missing_media_owners
[START] [2021-04-19 16:09:33] sanitize_media_verbatims
[STOP] [2021-04-19 16:09:33] sanitize_media_verbatims
[START] [2021-04-19 16:09:33] queue_downloads
[STOP] [2021-04-19 16:09:33] queue_downloads
[START] [2021-04-19 16:09:33] parse_names
[WARN] [2021-04-19 16:09:33] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 16:09:34] parse_names
[START] [2021-04-19 16:09:34] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 16:09:34] denormalize_canonical_names_to_nodes
[START] [2021-04-19 16:09:34] match_nodes
[START] [2021-04-19 16:09:34] map_all_nodes_to_pages
[STOP] [2021-04-19 16:09:34] map_all_nodes_to_pages
[INFO] [2021-04-19 16:09:34] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 16:09:34] update_nodes
[STOP] [2021-04-19 16:09:34] update_nodes
[STOP] [2021-04-19 16:09:34] match_nodes
[START] [2021-04-19 16:09:34] reindex_search
[STOP] [2021-04-19 16:09:34] reindex_search
[START] [2021-04-19 16:09:34] normalize_units
[STOP] [2021-04-19 16:09:34] normalize_units
[START] [2021-04-19 16:09:34] calculate_statistics
[2021-04-19 16:09:34] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 16:09:34] calculate_statistics
[START] [2021-04-19 16:09:34] complete_harvest_instance
[START] [2021-04-19 16:09:34] overall_tsv_creation
[INFO] [2021-04-19 16:09:34] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 16:10:10] 1 Traits (unfiltered)...
[INFO] [2021-04-19 16:10:42] 1 Traits (filtered)...
[INFO] [2021-04-19 16:10:42] 0 Associations (filtered)...
[INFO] [2021-04-19 16:10:42] 6 metadata added.
[INFO] [2021-04-19 16:10:42] 0 metadata added.
[INFO] [2021-04-19 16:11:08] Average Time: 69.78
[INFO] [2021-04-19 16:11:08] Total Time: 1m35s
[STOP] [2021-04-19 16:11:08] overall_tsv_creation
[INFO] [2021-04-19 16:11:08] Done. Check your files:
[INFO] [2021-04-19 16:11:08] (1 lines) /app/public/data/mayer_mayer_2006/publish_nodes.tsv
[INFO] [2021-04-19 16:11:08] (1 lines) /app/public/data/mayer_mayer_2006/publish_scientific_names.tsv
[INFO] [2021-04-19 16:11:08] (2 lines) /app/public/data/mayer_mayer_2006/publish_traits.tsv
[INFO] [2021-04-19 16:11:08] (7 lines) /app/public/data/mayer_mayer_2006/publish_metadata.tsv
[STOP] [2021-04-19 16:11:08] complete_harvest_instance
[START] [2021-04-19 16:11:08] completed
[STOP] [2021-04-19 16:11:08] completed
[STOP] [2021-04-19 16:11:08] logged process, took 101.86
Latest Process