Stage:
completed
Fetched:
06 Apr 20:35
Validated:
06 Apr 20:35
Deltas Created
06 Apr 20:35
Units Normalized:
06 Apr 20:35
Ancestry Built:
06 Apr 20:35
Nodes Matched:
06 Apr 20:35
Names Parsed:
06 Apr 20:35
New Models Stored:
06 Apr 20:35
Indexed:
06 Apr 20:35
Completed:
06 Apr 20:36
Time to Harvest:
less than a minute
Harvesting Log
(375 lines)
# Logfile created on 2021-02-03 11:09:56 -0500 by logger.rb/v1.4.2
[START] [2021-02-03 11:09:56] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 11:09:56] Creating resource from OpenData
[START] [2021-02-03 11:09:56] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 11:09:56] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:09:56] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:09:56] Creating resource from OpenData
[INFO] [2021-02-03 11:10:27] ## HARVEST: type = -harvest
[START] [2021-02-03 11:10:28] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 11:10:28] create_harvest_instance
[STOP] [2021-02-03 11:10:29] create_harvest_instance
[START] [2021-02-03 11:10:29] fetch_files
[STOP] [2021-02-03 11:10:29] fetch_files
[START] [2021-02-03 11:10:29] validate_each_file
[STOP] [2021-02-03 11:10:29] validate_each_file
[START] [2021-02-03 11:10:29] convert_to_csv
[CMD] [2021-02-03 11:10:29] /usr/bin/sort /app/public/converted_csv/schmitz_motani_s_nodes_26647.csv > /app/public/converted_csv/schmitz_motani_s_nodes_26647.csv_sorted
[CMD] [2021-02-03 11:10:29] /usr/bin/sort /app/public/converted_csv/schmitz_motani_s_occurrences_26648.csv > /app/public/converted_csv/schmitz_motani_s_occurrences_26648.csv_sorted
[CMD] [2021-02-03 11:10:29] /usr/bin/sort /app/public/converted_csv/schmitz_motani_s_measurements_26649.csv > /app/public/converted_csv/schmitz_motani_s_measurements_26649.csv_sorted
[STOP] [2021-02-03 11:10:29] convert_to_csv
[START] [2021-02-03 11:10:29] calculate_delta
[CMD] [2021-02-03 11:10:29] echo "0a" > /app/public/diff/schmitz_motani_s_nodes_26647.diff
[CMD] [2021-02-03 11:10:29] tail -n +1 /app/public/converted_csv/schmitz_motani_s_nodes_26647.csv >> /app/public/diff/schmitz_motani_s_nodes_26647.diff
[CMD] [2021-02-03 11:10:29] echo "." >> /app/public/diff/schmitz_motani_s_nodes_26647.diff
[CMD] [2021-02-03 11:10:29] echo "0a" > /app/public/diff/schmitz_motani_s_occurrences_26648.diff
[CMD] [2021-02-03 11:10:29] tail -n +1 /app/public/converted_csv/schmitz_motani_s_occurrences_26648.csv >> /app/public/diff/schmitz_motani_s_occurrences_26648.diff
[CMD] [2021-02-03 11:10:29] echo "." >> /app/public/diff/schmitz_motani_s_occurrences_26648.diff
[CMD] [2021-02-03 11:10:29] echo "0a" > /app/public/diff/schmitz_motani_s_measurements_26649.diff
[CMD] [2021-02-03 11:10:29] tail -n +1 /app/public/converted_csv/schmitz_motani_s_measurements_26649.csv >> /app/public/diff/schmitz_motani_s_measurements_26649.diff
[CMD] [2021-02-03 11:10:29] echo "." >> /app/public/diff/schmitz_motani_s_measurements_26649.diff
[STOP] [2021-02-03 11:10:29] calculate_delta
[START] [2021-02-03 11:10:29] parse_diff_and_store
[INFO] [2021-02-03 11:10:29] Loading nodes diff file into memory (true lines)...
[INFO] [2021-02-03 11:10:29] Loading occurrences diff file into memory (true lines)...
[INFO] [2021-02-03 11:10:29] Loading measurements diff file into memory (true lines)...
[INFO] [2021-02-03 11:10:30] Storing 32 ScientificNames
[INFO] [2021-02-03 11:10:30] Processing group of 32 in 1 groups of 1000
[INFO] [2021-02-03 11:10:30] Average Time: 0.01
[INFO] [2021-02-03 11:10:30] Total Time: 1s
[INFO] [2021-02-03 11:10:30] Storing 32 Nodes
[INFO] [2021-02-03 11:10:30] Processing group of 32 in 1 groups of 1000
[INFO] [2021-02-03 11:10:30] Average Time: 0.02
[INFO] [2021-02-03 11:10:30] Total Time: 1s
[INFO] [2021-02-03 11:10:30] Storing 32 Occurrences
[INFO] [2021-02-03 11:10:30] Processing group of 32 in 1 groups of 1000
[INFO] [2021-02-03 11:10:30] Average Time: 0.01
[INFO] [2021-02-03 11:10:30] Total Time: 1s
[INFO] [2021-02-03 11:10:30] Storing 34 Traits
[INFO] [2021-02-03 11:10:30] Processing group of 34 in 1 groups of 1000
[INFO] [2021-02-03 11:10:30] Average Time: 0.02
[INFO] [2021-02-03 11:10:30] Total Time: 1s
[INFO] [2021-02-03 11:10:30] Storing 64 MetaTraits
[INFO] [2021-02-03 11:10:30] Processing group of 64 in 1 groups of 1000
[INFO] [2021-02-03 11:10:30] Average Time: 0.01
[INFO] [2021-02-03 11:10:30] Total Time: 1s
[STOP] [2021-02-03 11:10:30] parse_diff_and_store
[START] [2021-02-03 11:10:30] resolve_keys
[INFO] [2021-02-03 11:10:36] Occurrences to nodes (through scientific_names)...
[INFO] [2021-02-03 11:10:36] traits to occurrences...
[INFO] [2021-02-03 11:10:36] traits to nodes (through occurrences)...
[INFO] [2021-02-03 11:10:36] Traits to sex term...
[INFO] [2021-02-03 11:10:36] Traits to lifestage term...
[INFO] [2021-02-03 11:10:36] MetaTraits to traits...
[INFO] [2021-02-03 11:10:36] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-02-03 11:10:36] Assocs to occurrences...
[INFO] [2021-02-03 11:10:36] Assocs to nodes...
[INFO] [2021-02-03 11:10:36] Assoc to sex term...
[INFO] [2021-02-03 11:10:36] Assoc to lifestage term...
[INFO] [2021-02-03 11:10:36] MetaAssoc to assocs...
[STOP] [2021-02-03 11:10:36] resolve_keys
[START] [2021-02-03 11:10:36] hold_for_later_1
[STOP] [2021-02-03 11:10:36] hold_for_later_1
[START] [2021-02-03 11:10:36] hold_for_later_2
[STOP] [2021-02-03 11:10:36] hold_for_later_2
[START] [2021-02-03 11:10:36] resolve_missing_parents
[STOP] [2021-02-03 11:10:36] resolve_missing_parents
[START] [2021-02-03 11:10:36] rebuild_nodes
[START] [2021-02-03 11:10:36] Flattener#flatten
[START] [2021-02-03 11:10:36] Flattener#study_resource
[START] [2021-02-03 11:10:36] Flattener#build_ancestry
[STOP] [2021-02-03 11:10:36] Flattener#build_ancestry
[INFO] [2021-02-03 11:10:36] 32 ancestry keys
[START] [2021-02-03 11:10:36] build_node_ancestors
[INFO] [2021-02-03 11:10:36] old ancestors deleted.
[STOP] [2021-02-03 11:10:36] build_node_ancestors
[WARN] [2021-02-03 11:10:36] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-02-03 11:10:36] Flattener#flatten
[STOP] [2021-02-03 11:10:36] rebuild_nodes
[START] [2021-02-03 11:10:36] resolve_missing_media_owners
[STOP] [2021-02-03 11:10:36] resolve_missing_media_owners
[START] [2021-02-03 11:10:36] sanitize_media_verbatims
[STOP] [2021-02-03 11:10:36] sanitize_media_verbatims
[START] [2021-02-03 11:10:36] queue_downloads
[STOP] [2021-02-03 11:10:36] queue_downloads
[START] [2021-02-03 11:10:36] parse_names
[WARN] [2021-02-03 11:10:36] I see 32 names which still need to be parsed.
[STOP] [2021-02-03 11:10:37] parse_names
[START] [2021-02-03 11:10:37] denormalize_canonical_names_to_nodes
[STOP] [2021-02-03 11:10:37] denormalize_canonical_names_to_nodes
[START] [2021-02-03 11:10:37] match_nodes
[START] [2021-02-03 11:10:37] map_all_nodes_to_pages
[STOP] [2021-02-03 11:10:38] map_all_nodes_to_pages
[INFO] [2021-02-03 11:10:38] Unmatched nodes (2 of 32): Euparkeria capensis (#87728822); Megapnosaurus kayentakatae (#87728827)
[START] [2021-02-03 11:10:38] update_nodes
[STOP] [2021-02-03 11:10:38] update_nodes
[STOP] [2021-02-03 11:10:38] match_nodes
[START] [2021-02-03 11:10:38] reindex_search
[STOP] [2021-02-03 11:10:38] reindex_search
[START] [2021-02-03 11:10:38] normalize_units
[STOP] [2021-02-03 11:10:38] normalize_units
[START] [2021-02-03 11:10:38] calculate_statistics
[2021-02-03 11:10:38] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-02-03 11:10:38] calculate_statistics
[START] [2021-02-03 11:10:38] complete_harvest_instance
[START] [2021-02-03 11:10:38] overall_tsv_creation
[INFO] [2021-02-03 11:10:38] Processing group of 32 in 1 batches of 10000
[INFO] [2021-02-03 11:11:18] 32 Traits (unfiltered)...
[INFO] [2021-02-03 11:11:55] 32 Traits (filtered)...
[INFO] [2021-02-03 11:11:55] 0 Associations (filtered)...
[INFO] [2021-02-03 11:11:55] 66 metadata added.
[INFO] [2021-02-03 11:11:55] 0 metadata added.
[INFO] [2021-02-03 11:12:27] Average Time: 82.5
[INFO] [2021-02-03 11:12:27] Total Time: 1m49s
[STOP] [2021-02-03 11:12:27] overall_tsv_creation
[INFO] [2021-02-03 11:12:27] Done. Check your files:
[INFO] [2021-02-03 11:12:27] (32 lines) /app/public/data/schmitz_motani_s/publish_nodes.tsv
[INFO] [2021-02-03 11:12:27] (32 lines) /app/public/data/schmitz_motani_s/publish_scientific_names.tsv
[INFO] [2021-02-03 11:12:27] (33 lines) /app/public/data/schmitz_motani_s/publish_traits.tsv
[INFO] [2021-02-03 11:12:27] (67 lines) /app/public/data/schmitz_motani_s/publish_metadata.tsv
[STOP] [2021-02-03 11:12:27] complete_harvest_instance
[START] [2021-02-03 11:12:27] completed
[STOP] [2021-02-03 11:12:27] completed
[STOP] [2021-02-03 11:12:27] logged process, took 118.9
[INFO] [2021-04-06 20:28:01] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-06 20:35:05] ## remove_type: ScientificName
[INFO] [2021-04-06 20:35:05] ++ Calling delete_all on 32 instances...
[INFO] [2021-04-06 20:35:05] [20:35:05.322] Removed 32 Scientificnames
[INFO] [2021-04-06 20:35:05] ## remove_type: Vernacular
[INFO] [2021-04-06 20:35:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-06 20:35:05] [20:35:05.323] Removed 0 Vernaculars
[INFO] [2021-04-06 20:35:05] ## remove_type: Article
[INFO] [2021-04-06 20:35:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-06 20:35:05] [20:35:05.324] Removed 0 Articles
[INFO] [2021-04-06 20:35:05] ## remove_type: Medium
[INFO] [2021-04-06 20:35:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-06 20:35:05] [20:35:05.326] Removed 0 Media
[INFO] [2021-04-06 20:35:05] ## remove_type: Trait
[INFO] [2021-04-06 20:35:05] ++ Calling delete_all on 34 instances...
[INFO] [2021-04-06 20:35:05] [20:35:05.328] Removed 34 Traits
[INFO] [2021-04-06 20:35:05] ## remove_type: MetaTrait
[INFO] [2021-04-06 20:35:05] ++ Calling delete_all on 64 instances...
[INFO] [2021-04-06 20:35:05] [20:35:05.333] Removed 64 Metatraits
[INFO] [2021-04-06 20:35:05] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-06 20:35:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-06 20:35:05] [20:35:05.335] Removed 0 Occurrencemetadata
[INFO] [2021-04-06 20:35:05] ## remove_type: Assoc
[INFO] [2021-04-06 20:35:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-06 20:35:05] [20:35:05.337] Removed 0 Assocs
[INFO] [2021-04-06 20:35:05] ## remove_type: MetaAssoc
[INFO] [2021-04-06 20:35:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-06 20:35:05] [20:35:05.343] Removed 0 Metaassocs
[INFO] [2021-04-06 20:35:05] ## remove_type: Identifier
[INFO] [2021-04-06 20:35:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-06 20:35:05] [20:35:05.345] Removed 0 Identifiers
[INFO] [2021-04-06 20:35:05] ## remove_type: Reference
[INFO] [2021-04-06 20:35:05] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-06 20:35:05] [20:35:05.346] Removed 0 References
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] Starting batch with ID 87728815...
[INFO] [2021-04-06 20:35:05] ## remove_type: Node
[INFO] [2021-04-06 20:35:05] ++ Calling delete_all on 32 instances...
[INFO] [2021-04-06 20:35:05] [20:35:05.806] Removed 32 Nodes
[START] [2021-04-06 20:35:05] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-06 20:35:05] Creating resource from OpenData
[START] [2021-04-06 20:35:06] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-06 20:35:06] Parse meta.xml file and create formats with fields
[STOP] [2021-04-06 20:35:06] Parse meta.xml file and create formats with fields
[STOP] [2021-04-06 20:35:06] Creating resource from OpenData
[START] [2021-04-06 20:35:06] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-06 20:35:06] create_harvest_instance
[INFO] [2021-04-06 20:35:06] Created harvest instance #3660
[STOP] [2021-04-06 20:35:06] create_harvest_instance
[START] [2021-04-06 20:35:06] fetch_files
[STOP] [2021-04-06 20:35:06] fetch_files
[START] [2021-04-06 20:35:06] validate_each_file
[INFO] [2021-04-06 20:35:06] Looping over 3 formats...
[INFO] [2021-04-06 20:35:06] ...nodes (/app/public/data/schmitz_motani_s/taxa.txt)
[INFO] [2021-04-06 20:35:06] Valid: /app/public/converted_csv/schmitz_motani_s_nodes_3660.csv (32 lines)
[INFO] [2021-04-06 20:35:06] ...occurrences (/app/public/data/schmitz_motani_s/occurrences.txt)
[INFO] [2021-04-06 20:35:06] Valid: /app/public/converted_csv/schmitz_motani_s_occurrences_3660.csv (32 lines)
[INFO] [2021-04-06 20:35:06] ...measurements (/app/public/data/schmitz_motani_s/measurementsorfacts.txt)
[INFO] [2021-04-06 20:35:06] Valid: /app/public/converted_csv/schmitz_motani_s_measurements_3660.csv (34 lines)
[STOP] [2021-04-06 20:35:06] validate_each_file
[START] [2021-04-06 20:35:06] convert_to_csv
[INFO] [2021-04-06 20:35:06] Looping over 3 formats...
[INFO] [2021-04-06 20:35:06] ...nodes (/app/public/data/schmitz_motani_s/taxa.txt)
[CMD] [2021-04-06 20:35:06] /usr/bin/sort /app/public/converted_csv/schmitz_motani_s_nodes_3660.csv > /app/public/converted_csv/schmitz_motani_s_nodes_3660.csv_sorted
[INFO] [2021-04-06 20:35:06] Converted: /app/public/converted_csv/schmitz_motani_s_nodes_3660.csv (32 lines)
[INFO] [2021-04-06 20:35:06] ...occurrences (/app/public/data/schmitz_motani_s/occurrences.txt)
[CMD] [2021-04-06 20:35:06] /usr/bin/sort /app/public/converted_csv/schmitz_motani_s_occurrences_3660.csv > /app/public/converted_csv/schmitz_motani_s_occurrences_3660.csv_sorted
[INFO] [2021-04-06 20:35:06] Converted: /app/public/converted_csv/schmitz_motani_s_occurrences_3660.csv (32 lines)
[INFO] [2021-04-06 20:35:06] ...measurements (/app/public/data/schmitz_motani_s/measurementsorfacts.txt)
[CMD] [2021-04-06 20:35:06] /usr/bin/sort /app/public/converted_csv/schmitz_motani_s_measurements_3660.csv > /app/public/converted_csv/schmitz_motani_s_measurements_3660.csv_sorted
[INFO] [2021-04-06 20:35:06] Converted: /app/public/converted_csv/schmitz_motani_s_measurements_3660.csv (34 lines)
[STOP] [2021-04-06 20:35:06] convert_to_csv
[START] [2021-04-06 20:35:06] calculate_delta
[INFO] [2021-04-06 20:35:06] Looping over 3 formats...
[INFO] [2021-04-06 20:35:06] ...nodes (/app/public/data/schmitz_motani_s/taxa.txt)
[CMD] [2021-04-06 20:35:06] echo "0a" > /app/public/diff/schmitz_motani_s_nodes_3660.diff
[CMD] [2021-04-06 20:35:06] tail -n +1 /app/public/converted_csv/schmitz_motani_s_nodes_3660.csv >> /app/public/diff/schmitz_motani_s_nodes_3660.diff
[CMD] [2021-04-06 20:35:06] echo "." >> /app/public/diff/schmitz_motani_s_nodes_3660.diff
[INFO] [2021-04-06 20:35:06] Created diff: /app/public/diff/schmitz_motani_s_nodes_3660.diff (34 lines)
[INFO] [2021-04-06 20:35:06] ...occurrences (/app/public/data/schmitz_motani_s/occurrences.txt)
[CMD] [2021-04-06 20:35:06] echo "0a" > /app/public/diff/schmitz_motani_s_occurrences_3660.diff
[CMD] [2021-04-06 20:35:06] tail -n +1 /app/public/converted_csv/schmitz_motani_s_occurrences_3660.csv >> /app/public/diff/schmitz_motani_s_occurrences_3660.diff
[CMD] [2021-04-06 20:35:06] echo "." >> /app/public/diff/schmitz_motani_s_occurrences_3660.diff
[INFO] [2021-04-06 20:35:06] Created diff: /app/public/diff/schmitz_motani_s_occurrences_3660.diff (34 lines)
[INFO] [2021-04-06 20:35:06] ...measurements (/app/public/data/schmitz_motani_s/measurementsorfacts.txt)
[CMD] [2021-04-06 20:35:06] echo "0a" > /app/public/diff/schmitz_motani_s_measurements_3660.diff
[CMD] [2021-04-06 20:35:06] tail -n +1 /app/public/converted_csv/schmitz_motani_s_measurements_3660.csv >> /app/public/diff/schmitz_motani_s_measurements_3660.diff
[CMD] [2021-04-06 20:35:06] echo "." >> /app/public/diff/schmitz_motani_s_measurements_3660.diff
[INFO] [2021-04-06 20:35:06] Created diff: /app/public/diff/schmitz_motani_s_measurements_3660.diff (36 lines)
[STOP] [2021-04-06 20:35:06] calculate_delta
[START] [2021-04-06 20:35:06] parse_diff_and_store
[INFO] [2021-04-06 20:35:06] Handling diff: /app/public/diff/schmitz_motani_s_nodes_3660.diff (34 lines)
[INFO] [2021-04-06 20:35:06] Loading nodes diff file into memory (34 /app/public/diff/schmitz_motani_s_nodes_3660.diff lines)...
[INFO] [2021-04-06 20:35:06] Handling diff: /app/public/diff/schmitz_motani_s_occurrences_3660.diff (34 lines)
[INFO] [2021-04-06 20:35:06] Loading occurrences diff file into memory (34 /app/public/diff/schmitz_motani_s_occurrences_3660.diff lines)...
[INFO] [2021-04-06 20:35:06] Handling diff: /app/public/diff/schmitz_motani_s_measurements_3660.diff (36 lines)
[INFO] [2021-04-06 20:35:06] Loading measurements diff file into memory (36 /app/public/diff/schmitz_motani_s_measurements_3660.diff lines)...
[INFO] [2021-04-06 20:35:06] Storing 32 ScientificNames
[INFO] [2021-04-06 20:35:06] Processing group of 32 in 1 groups of 1000
[INFO] [2021-04-06 20:35:06] Average Time: 0.01
[INFO] [2021-04-06 20:35:06] Total Time: 1s
[INFO] [2021-04-06 20:35:06] Storing 32 Nodes
[INFO] [2021-04-06 20:35:06] Processing group of 32 in 1 groups of 1000
[INFO] [2021-04-06 20:35:06] Average Time: 0.01
[INFO] [2021-04-06 20:35:06] Total Time: 1s
[INFO] [2021-04-06 20:35:06] Storing 32 Occurrences
[INFO] [2021-04-06 20:35:06] Processing group of 32 in 1 groups of 1000
[INFO] [2021-04-06 20:35:06] Average Time: 0.0
[INFO] [2021-04-06 20:35:06] Total Time: 1s
[INFO] [2021-04-06 20:35:06] Storing 34 Traits
[INFO] [2021-04-06 20:35:06] Processing group of 34 in 1 groups of 1000
[INFO] [2021-04-06 20:35:06] Average Time: 0.01
[INFO] [2021-04-06 20:35:06] Total Time: 1s
[INFO] [2021-04-06 20:35:06] Storing 64 MetaTraits
[INFO] [2021-04-06 20:35:06] Processing group of 64 in 1 groups of 1000
[INFO] [2021-04-06 20:35:06] Average Time: 0.01
[INFO] [2021-04-06 20:35:06] Total Time: 1s
[STOP] [2021-04-06 20:35:06] parse_diff_and_store
[START] [2021-04-06 20:35:06] resolve_keys
[INFO] [2021-04-06 20:35:12] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-06 20:35:12] traits to occurrences...
[INFO] [2021-04-06 20:35:12] traits to nodes (through occurrences)...
[INFO] [2021-04-06 20:35:12] Traits to sex term...
[INFO] [2021-04-06 20:35:12] Traits to lifestage term...
[INFO] [2021-04-06 20:35:12] MetaTraits to traits...
[INFO] [2021-04-06 20:35:12] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-06 20:35:12] Assocs to occurrences...
[INFO] [2021-04-06 20:35:12] Assocs to nodes...
[INFO] [2021-04-06 20:35:12] Assoc to sex term...
[INFO] [2021-04-06 20:35:12] Assoc to lifestage term...
[INFO] [2021-04-06 20:35:12] MetaAssoc to assocs...
[STOP] [2021-04-06 20:35:12] resolve_keys
[START] [2021-04-06 20:35:12] hold_for_later_1
[STOP] [2021-04-06 20:35:12] hold_for_later_1
[START] [2021-04-06 20:35:12] hold_for_later_2
[STOP] [2021-04-06 20:35:12] hold_for_later_2
[START] [2021-04-06 20:35:12] resolve_missing_parents
[STOP] [2021-04-06 20:35:12] resolve_missing_parents
[START] [2021-04-06 20:35:12] rebuild_nodes
[START] [2021-04-06 20:35:12] Flattener#flatten
[START] [2021-04-06 20:35:12] Flattener#study_resource
[START] [2021-04-06 20:35:12] Flattener#build_ancestry
[STOP] [2021-04-06 20:35:12] Flattener#build_ancestry
[INFO] [2021-04-06 20:35:12] 32 ancestry keys
[START] [2021-04-06 20:35:12] build_node_ancestors
[INFO] [2021-04-06 20:35:12] old ancestors deleted.
[STOP] [2021-04-06 20:35:12] build_node_ancestors
[WARN] [2021-04-06 20:35:12] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-06 20:35:12] Flattener#flatten
[STOP] [2021-04-06 20:35:12] rebuild_nodes
[START] [2021-04-06 20:35:12] resolve_missing_media_owners
[STOP] [2021-04-06 20:35:12] resolve_missing_media_owners
[START] [2021-04-06 20:35:12] sanitize_media_verbatims
[STOP] [2021-04-06 20:35:12] sanitize_media_verbatims
[START] [2021-04-06 20:35:12] queue_downloads
[STOP] [2021-04-06 20:35:12] queue_downloads
[START] [2021-04-06 20:35:12] parse_names
[WARN] [2021-04-06 20:35:12] I see 32 names which still need to be parsed.
[STOP] [2021-04-06 20:35:13] parse_names
[START] [2021-04-06 20:35:13] denormalize_canonical_names_to_nodes
[STOP] [2021-04-06 20:35:13] denormalize_canonical_names_to_nodes
[START] [2021-04-06 20:35:13] match_nodes
[START] [2021-04-06 20:35:13] map_all_nodes_to_pages
[STOP] [2021-04-06 20:35:13] map_all_nodes_to_pages
[INFO] [2021-04-06 20:35:13] Unmatched nodes (2 of 32): Euparkeria capensis (#92627118); Megapnosaurus kayentakatae (#92627123)
[START] [2021-04-06 20:35:13] update_nodes
[STOP] [2021-04-06 20:35:13] update_nodes
[STOP] [2021-04-06 20:35:13] match_nodes
[START] [2021-04-06 20:35:13] reindex_search
[STOP] [2021-04-06 20:35:13] reindex_search
[START] [2021-04-06 20:35:13] normalize_units
[STOP] [2021-04-06 20:35:13] normalize_units
[START] [2021-04-06 20:35:13] calculate_statistics
[2021-04-06 20:35:13] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-06 20:35:13] calculate_statistics
[START] [2021-04-06 20:35:13] complete_harvest_instance
[START] [2021-04-06 20:35:13] overall_tsv_creation
[INFO] [2021-04-06 20:35:13] Processing group of 32 in 1 batches of 10000
[INFO] [2021-04-06 20:35:50] 32 Traits (unfiltered)...
[INFO] [2021-04-06 20:36:23] 32 Traits (filtered)...
[INFO] [2021-04-06 20:36:23] 0 Associations (filtered)...
[INFO] [2021-04-06 20:36:23] 2 metadata added.
[INFO] [2021-04-06 20:36:23] 0 metadata added.
[INFO] [2021-04-06 20:36:49] Average Time: 71.52
[INFO] [2021-04-06 20:36:49] Total Time: 1m36s
[STOP] [2021-04-06 20:36:49] overall_tsv_creation
[INFO] [2021-04-06 20:36:49] Done. Check your files:
[INFO] [2021-04-06 20:36:49] (32 lines) /app/public/data/schmitz_motani_s/publish_nodes.tsv
[INFO] [2021-04-06 20:36:49] (32 lines) /app/public/data/schmitz_motani_s/publish_scientific_names.tsv
[INFO] [2021-04-06 20:36:49] (33 lines) /app/public/data/schmitz_motani_s/publish_traits.tsv
[INFO] [2021-04-06 20:36:49] (3 lines) /app/public/data/schmitz_motani_s/publish_metadata.tsv
[STOP] [2021-04-06 20:36:49] complete_harvest_instance
[START] [2021-04-06 20:36:49] completed
[STOP] [2021-04-06 20:36:49] completed
[STOP] [2021-04-06 20:36:49] logged process, took 103.8
Latest Process