Harvest for Insect Wings Created 05 May 15:21

Stage: completed
Fetched: 05 May 15:21
Validated: 05 May 15:21
Deltas Created 05 May 15:21
Units Normalized: 05 May 15:21
Ancestry Built: 05 May 15:21
Nodes Matched: 05 May 15:21
Names Parsed: 05 May 15:21
New Models Stored: 05 May 15:21
Indexed: 05 May 15:21
Completed: 05 May 15:22
Time to Harvest: less than a minute
Harvesting Log

(143 lines)
[INFO] [2023-05-05 15:21:37] Created harvest instance #4344
[STOP] [2023-05-05 15:21:37] create_harvest_instance
[START] [2023-05-05 15:21:37] fetch_files
[STOP] [2023-05-05 15:21:37] fetch_files
[START] [2023-05-05 15:21:37] validate_each_file
[INFO] [2023-05-05 15:21:37] Looping over 3 formats...
[INFO] [2023-05-05 15:21:37] ...nodes (/app/public/data/insect_wings/taxa.txt)
[INFO] [2023-05-05 15:21:37] Valid: /app/public/data/insect_wings/converted_csv/insect_wings_nodes_30335.csv (311 lines)
[INFO] [2023-05-05 15:21:37] ...occurrences (/app/public/data/insect_wings/occurrences.txt)
[INFO] [2023-05-05 15:21:37] Valid: /app/public/data/insect_wings/converted_csv/insect_wings_occurrences_30336.csv (326 lines)
[INFO] [2023-05-05 15:21:37] ...measurements (/app/public/data/insect_wings/measurementsorfacts.txt)
[INFO] [2023-05-05 15:21:37] Valid: /app/public/data/insect_wings/converted_csv/insect_wings_measurements_30337.csv (530 lines)
[STOP] [2023-05-05 15:21:37] validate_each_file
[START] [2023-05-05 15:21:37] convert_to_csv
[INFO] [2023-05-05 15:21:37] Looping over 3 formats...
[INFO] [2023-05-05 15:21:37] ...nodes (/app/public/data/insect_wings/taxa.txt)
[CMD] [2023-05-05 15:21:37] /usr/bin/sort /app/public/data/insect_wings/converted_csv/insect_wings_nodes_30335.csv > /app/public/data/insect_wings/converted_csv/insect_wings_nodes_30335.csv_sorted
[INFO] [2023-05-05 15:21:37] Converted: /app/public/data/insect_wings/converted_csv/insect_wings_nodes_30335.csv (311 lines)
[INFO] [2023-05-05 15:21:37] ...occurrences (/app/public/data/insect_wings/occurrences.txt)
[CMD] [2023-05-05 15:21:37] /usr/bin/sort /app/public/data/insect_wings/converted_csv/insect_wings_occurrences_30336.csv > /app/public/data/insect_wings/converted_csv/insect_wings_occurrences_30336.csv_sorted
[INFO] [2023-05-05 15:21:37] Converted: /app/public/data/insect_wings/converted_csv/insect_wings_occurrences_30336.csv (326 lines)
[INFO] [2023-05-05 15:21:37] ...measurements (/app/public/data/insect_wings/measurementsorfacts.txt)
[CMD] [2023-05-05 15:21:37] /usr/bin/sort /app/public/data/insect_wings/converted_csv/insect_wings_measurements_30337.csv > /app/public/data/insect_wings/converted_csv/insect_wings_measurements_30337.csv_sorted
[INFO] [2023-05-05 15:21:37] Converted: /app/public/data/insect_wings/converted_csv/insect_wings_measurements_30337.csv (530 lines)
[STOP] [2023-05-05 15:21:37] convert_to_csv
[START] [2023-05-05 15:21:37] calculate_delta
[INFO] [2023-05-05 15:21:37] Looping over 3 formats...
[INFO] [2023-05-05 15:21:37] ...nodes (/app/public/data/insect_wings/taxa.txt)
[CMD] [2023-05-05 15:21:37] echo "0a" > /app/public/data/insect_wings/diff/insect_wings_nodes_30335.diff
[CMD] [2023-05-05 15:21:37] tail -n +1 /app/public/data/insect_wings/converted_csv/insect_wings_nodes_30335.csv >> /app/public/data/insect_wings/diff/insect_wings_nodes_30335.diff
[CMD] [2023-05-05 15:21:37] echo "." >> /app/public/data/insect_wings/diff/insect_wings_nodes_30335.diff
[INFO] [2023-05-05 15:21:37] Created diff: /app/public/data/insect_wings/diff/insect_wings_nodes_30335.diff (313 lines)
[INFO] [2023-05-05 15:21:37] ...occurrences (/app/public/data/insect_wings/occurrences.txt)
[CMD] [2023-05-05 15:21:37] echo "0a" > /app/public/data/insect_wings/diff/insect_wings_occurrences_30336.diff
[CMD] [2023-05-05 15:21:37] tail -n +1 /app/public/data/insect_wings/converted_csv/insect_wings_occurrences_30336.csv >> /app/public/data/insect_wings/diff/insect_wings_occurrences_30336.diff
[CMD] [2023-05-05 15:21:37] echo "." >> /app/public/data/insect_wings/diff/insect_wings_occurrences_30336.diff
[INFO] [2023-05-05 15:21:38] Created diff: /app/public/data/insect_wings/diff/insect_wings_occurrences_30336.diff (328 lines)
[INFO] [2023-05-05 15:21:38] ...measurements (/app/public/data/insect_wings/measurementsorfacts.txt)
[CMD] [2023-05-05 15:21:38] echo "0a" > /app/public/data/insect_wings/diff/insect_wings_measurements_30337.diff
[CMD] [2023-05-05 15:21:38] tail -n +1 /app/public/data/insect_wings/converted_csv/insect_wings_measurements_30337.csv >> /app/public/data/insect_wings/diff/insect_wings_measurements_30337.diff
[CMD] [2023-05-05 15:21:38] echo "." >> /app/public/data/insect_wings/diff/insect_wings_measurements_30337.diff
[INFO] [2023-05-05 15:21:38] Created diff: /app/public/data/insect_wings/diff/insect_wings_measurements_30337.diff (532 lines)
[STOP] [2023-05-05 15:21:38] calculate_delta
[START] [2023-05-05 15:21:38] parse_diff_and_store
[INFO] [2023-05-05 15:21:38] Handling diff: /app/public/data/insect_wings/diff/insect_wings_nodes_30335.diff (313 lines)
[INFO] [2023-05-05 15:21:38] Loading nodes diff file into memory (313 lines)...
[INFO] [2023-05-05 15:21:38] Storing 311 ScientificNames (622/311/313)
[INFO] [2023-05-05 15:21:38] Storing 311 Nodes (622/311/313)
[INFO] [2023-05-05 15:21:38] Handling diff: /app/public/data/insect_wings/diff/insect_wings_occurrences_30336.diff (328 lines)
[INFO] [2023-05-05 15:21:38] Loading occurrences diff file into memory (328 lines)...
[INFO] [2023-05-05 15:21:40] Storing 326 Occurrences (857/326/328)
[INFO] [2023-05-05 15:21:40] Storing 531 OccurrenceMetadata (857/326/328)
[INFO] [2023-05-05 15:21:40] Handling diff: /app/public/data/insect_wings/diff/insect_wings_measurements_30337.diff (532 lines)
[INFO] [2023-05-05 15:21:40] Loading measurements diff file into memory (532 lines)...
[INFO] [2023-05-05 15:21:40] Storing 530 Traits (860/530/532)
[INFO] [2023-05-05 15:21:40] Storing 330 MetaTraits (860/530/532)
[STOP] [2023-05-05 15:21:40] parse_diff_and_store
[START] [2023-05-05 15:21:41] resolve_keys
[2023-05-05 15:21:41] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-05-05 15:21:50] Occurrences to nodes (through scientific_names)...
[INFO] [2023-05-05 15:21:50] traits to occurrences...
[INFO] [2023-05-05 15:21:50] traits to nodes (through occurrences)...
[INFO] [2023-05-05 15:21:50] Traits to sex term...
[INFO] [2023-05-05 15:21:50] Traits to lifestage term...
[INFO] [2023-05-05 15:21:50] MetaTraits to traits...
[INFO] [2023-05-05 15:21:50] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-05-05 15:21:50] Assocs to occurrences...
[INFO] [2023-05-05 15:21:50] Assocs to nodes...
[INFO] [2023-05-05 15:21:50] Assoc to sex term...
[INFO] [2023-05-05 15:21:50] Assoc to lifestage term...
[INFO] [2023-05-05 15:21:50] MetaAssoc to assocs...
[STOP] [2023-05-05 15:21:50] resolve_keys
[START] [2023-05-05 15:21:50] hold_for_later_1
[STOP] [2023-05-05 15:21:50] hold_for_later_1
[START] [2023-05-05 15:21:50] hold_for_later_2
[STOP] [2023-05-05 15:21:50] hold_for_later_2
[START] [2023-05-05 15:21:50] resolve_missing_parents
[STOP] [2023-05-05 15:21:50] resolve_missing_parents
[START] [2023-05-05 15:21:50] rebuild_nodes
[START] [2023-05-05 15:21:50] Flattener#flatten
[START] [2023-05-05 15:21:50] Flattener#study_resource
[START] [2023-05-05 15:21:50] Flattener#build_ancestry
[STOP] [2023-05-05 15:21:50] Flattener#build_ancestry
[INFO] [2023-05-05 15:21:50] 311 ancestry keys
[START] [2023-05-05 15:21:50] build_node_ancestors
[INFO] [2023-05-05 15:21:50] old ancestors deleted.
[STOP] [2023-05-05 15:21:50] build_node_ancestors
[WARN] [2023-05-05 15:21:50] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-05-05 15:21:50] Flattener#flatten
[STOP] [2023-05-05 15:21:50] rebuild_nodes
[START] [2023-05-05 15:21:50] resolve_missing_media_owners
[STOP] [2023-05-05 15:21:50] resolve_missing_media_owners
[START] [2023-05-05 15:21:50] sanitize_media_verbatims
[STOP] [2023-05-05 15:21:50] sanitize_media_verbatims
[START] [2023-05-05 15:21:50] queue_downloads
[STOP] [2023-05-05 15:21:50] queue_downloads
[START] [2023-05-05 15:21:50] parse_names
[WARN] [2023-05-05 15:21:50] I see 311 names which still need to be parsed.
[WARN] [2023-05-05 15:21:50] Names to parse: 311 formatted: 311 learned: 311 parsed: 311
[STOP] [2023-05-05 15:21:51] parse_names
[START] [2023-05-05 15:21:51] denormalize_canonical_names_to_nodes
[STOP] [2023-05-05 15:21:51] denormalize_canonical_names_to_nodes
[START] [2023-05-05 15:21:51] match_nodes
[START] [2023-05-05 15:21:51] map_all_nodes_to_pages
[STOP] [2023-05-05 15:21:52] map_all_nodes_to_pages
[INFO] [2023-05-05 15:21:52] ZERO unmatched nodes (of 311)! Nicely done.
[START] [2023-05-05 15:21:52] update_nodes
[STOP] [2023-05-05 15:21:52] update_nodes
[STOP] [2023-05-05 15:21:52] match_nodes
[START] [2023-05-05 15:21:52] reindex_search
[STOP] [2023-05-05 15:21:55] reindex_search
[START] [2023-05-05 15:21:55] normalize_units
[STOP] [2023-05-05 15:21:55] normalize_units
[START] [2023-05-05 15:21:55] calculate_statistics
[2023-05-05 15:21:55] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-05-05 15:22:05] Duplicate page_id count: 0
[STOP] [2023-05-05 15:22:05] calculate_statistics
[START] [2023-05-05 15:22:05] complete_harvest_instance
[START] [2023-05-05 15:22:05] overall_tsv_creation
[INFO] [2023-05-05 15:22:05] Exporting 311 nodes as TSV in batches of 10000...
[INFO] [2023-05-05 15:22:05] Processing group of 311 in 1 batches of 10000
[INFO] [2023-05-05 15:22:05] 329 Traits (unfiltered) and 0 associations...
[INFO] [2023-05-05 15:22:05] Building Traits map for 311 nodes (this can take a while)...
[INFO] [2023-05-05 15:22:05] Mapped 329 traits (329 meta) for 311 nodes.
[INFO] [2023-05-05 15:22:05] Building Associations map (this can take a while)...
[INFO] [2023-05-05 15:22:05] Done. 0 assocs mapped (0 meta).
[INFO] [2023-05-05 15:22:05] Adding 329 traits...
[INFO] [2023-05-05 15:22:05] 217 metadata added.
[INFO] [2023-05-05 15:22:05] Adding 0 assocs...
[INFO] [2023-05-05 15:22:05] 0 metadata added.
[INFO] [2023-05-05 15:22:58] Processed 311/311 nodes
[INFO] [2023-05-05 15:22:58] Average Time: 53.31
[INFO] [2023-05-05 15:22:58] Total Time: 54s
[STOP] [2023-05-05 15:22:58] overall_tsv_creation
[INFO] [2023-05-05 15:22:58] Done. Check your files:
[INFO] [2023-05-05 15:22:58] (311 lines) /app/public/data/insect_wings/publish_nodes.tsv
[INFO] [2023-05-05 15:22:58] (311 lines) /app/public/data/insect_wings/publish_scientific_names.tsv
[INFO] [2023-05-05 15:22:58] (330 lines) /app/public/data/insect_wings/publish_traits.tsv
[INFO] [2023-05-05 15:22:58] (218 lines) /app/public/data/insect_wings/publish_metadata.tsv
[STOP] [2023-05-05 15:22:58] complete_harvest_instance
[START] [2023-05-05 15:22:58] completed
[STOP] [2023-05-05 15:22:58] completed
[STOP] [2023-05-05 15:22:58] logged process, took 81.16
Latest Process

05 May 15:21 EXITED currently processing 0