Harvest for Body Size Data for North American Orthopteroid Created 30 Mar 11:59

Stage: completed
Fetched: 30 Mar 11:59
Validated: 30 Mar 11:59
Deltas Created 30 Mar 11:59
Units Normalized: 30 Mar 11:59
Ancestry Built: 30 Mar 11:59
Nodes Matched: 30 Mar 11:59
Names Parsed: 30 Mar 11:59
New Models Stored: 30 Mar 11:59
Indexed: 30 Mar 11:59
Completed: 30 Mar 12:00
Time to Harvest: less than a minute
Harvesting Log

(144 lines)
[INFO] [2023-03-30 11:59:16] Created harvest instance #4324
[STOP] [2023-03-30 11:59:16] create_harvest_instance
[START] [2023-03-30 11:59:16] fetch_files
[STOP] [2023-03-30 11:59:16] fetch_files
[START] [2023-03-30 11:59:16] validate_each_file
[INFO] [2023-03-30 11:59:16] Looping over 3 formats...
[INFO] [2023-03-30 11:59:16] ...nodes (/app/public/data/bsdnao/taxon.tab)
[INFO] [2023-03-30 11:59:16] Valid: /app/public/data/bsdnao/converted_csv/bsdnao_nodes_30257.csv (222 lines)
[INFO] [2023-03-30 11:59:16] ...occurrences (/app/public/data/bsdnao/occurrence_specific.tab)
[INFO] [2023-03-30 11:59:16] Valid: /app/public/data/bsdnao/converted_csv/bsdnao_occurrences_30258.csv (810 lines)
[INFO] [2023-03-30 11:59:16] ...measurements (/app/public/data/bsdnao/measurement_or_fact_specific.tab)
[INFO] [2023-03-30 11:59:16] Valid: /app/public/data/bsdnao/converted_csv/bsdnao_measurements_30259.csv (810 lines)
[STOP] [2023-03-30 11:59:16] validate_each_file
[START] [2023-03-30 11:59:16] convert_to_csv
[INFO] [2023-03-30 11:59:16] Looping over 3 formats...
[INFO] [2023-03-30 11:59:16] ...nodes (/app/public/data/bsdnao/taxon.tab)
[CMD] [2023-03-30 11:59:16] /usr/bin/sort /app/public/data/bsdnao/converted_csv/bsdnao_nodes_30257.csv > /app/public/data/bsdnao/converted_csv/bsdnao_nodes_30257.csv_sorted
[INFO] [2023-03-30 11:59:16] Converted: /app/public/data/bsdnao/converted_csv/bsdnao_nodes_30257.csv (222 lines)
[INFO] [2023-03-30 11:59:16] ...occurrences (/app/public/data/bsdnao/occurrence_specific.tab)
[CMD] [2023-03-30 11:59:16] /usr/bin/sort /app/public/data/bsdnao/converted_csv/bsdnao_occurrences_30258.csv > /app/public/data/bsdnao/converted_csv/bsdnao_occurrences_30258.csv_sorted
[INFO] [2023-03-30 11:59:16] Converted: /app/public/data/bsdnao/converted_csv/bsdnao_occurrences_30258.csv (810 lines)
[INFO] [2023-03-30 11:59:16] ...measurements (/app/public/data/bsdnao/measurement_or_fact_specific.tab)
[CMD] [2023-03-30 11:59:16] /usr/bin/sort /app/public/data/bsdnao/converted_csv/bsdnao_measurements_30259.csv > /app/public/data/bsdnao/converted_csv/bsdnao_measurements_30259.csv_sorted
[INFO] [2023-03-30 11:59:16] Converted: /app/public/data/bsdnao/converted_csv/bsdnao_measurements_30259.csv (810 lines)
[STOP] [2023-03-30 11:59:16] convert_to_csv
[START] [2023-03-30 11:59:16] calculate_delta
[INFO] [2023-03-30 11:59:16] Looping over 3 formats...
[INFO] [2023-03-30 11:59:16] ...nodes (/app/public/data/bsdnao/taxon.tab)
[CMD] [2023-03-30 11:59:16] echo "0a" > /app/public/data/bsdnao/diff/bsdnao_nodes_30257.diff
[CMD] [2023-03-30 11:59:16] tail -n +1 /app/public/data/bsdnao/converted_csv/bsdnao_nodes_30257.csv >> /app/public/data/bsdnao/diff/bsdnao_nodes_30257.diff
[CMD] [2023-03-30 11:59:17] echo "." >> /app/public/data/bsdnao/diff/bsdnao_nodes_30257.diff
[INFO] [2023-03-30 11:59:17] Created diff: /app/public/data/bsdnao/diff/bsdnao_nodes_30257.diff (224 lines)
[INFO] [2023-03-30 11:59:17] ...occurrences (/app/public/data/bsdnao/occurrence_specific.tab)
[CMD] [2023-03-30 11:59:17] echo "0a" > /app/public/data/bsdnao/diff/bsdnao_occurrences_30258.diff
[CMD] [2023-03-30 11:59:17] tail -n +1 /app/public/data/bsdnao/converted_csv/bsdnao_occurrences_30258.csv >> /app/public/data/bsdnao/diff/bsdnao_occurrences_30258.diff
[CMD] [2023-03-30 11:59:17] echo "." >> /app/public/data/bsdnao/diff/bsdnao_occurrences_30258.diff
[INFO] [2023-03-30 11:59:17] Created diff: /app/public/data/bsdnao/diff/bsdnao_occurrences_30258.diff (812 lines)
[INFO] [2023-03-30 11:59:17] ...measurements (/app/public/data/bsdnao/measurement_or_fact_specific.tab)
[CMD] [2023-03-30 11:59:17] echo "0a" > /app/public/data/bsdnao/diff/bsdnao_measurements_30259.diff
[CMD] [2023-03-30 11:59:17] tail -n +1 /app/public/data/bsdnao/converted_csv/bsdnao_measurements_30259.csv >> /app/public/data/bsdnao/diff/bsdnao_measurements_30259.diff
[CMD] [2023-03-30 11:59:18] echo "." >> /app/public/data/bsdnao/diff/bsdnao_measurements_30259.diff
[INFO] [2023-03-30 11:59:18] Created diff: /app/public/data/bsdnao/diff/bsdnao_measurements_30259.diff (812 lines)
[STOP] [2023-03-30 11:59:18] calculate_delta
[START] [2023-03-30 11:59:18] parse_diff_and_store
[INFO] [2023-03-30 11:59:18] Handling diff: /app/public/data/bsdnao/diff/bsdnao_nodes_30257.diff (224 lines)
[INFO] [2023-03-30 11:59:18] Loading nodes diff file into memory (224 lines)...
[INFO] [2023-03-30 11:59:18] Storing 224 ScientificNames (448/222/224)
[INFO] [2023-03-30 11:59:18] Storing 224 Nodes (448/222/224)
[INFO] [2023-03-30 11:59:18] Handling diff: /app/public/data/bsdnao/diff/bsdnao_occurrences_30258.diff (812 lines)
[INFO] [2023-03-30 11:59:18] Loading occurrences diff file into memory (812 lines)...
[INFO] [2023-03-30 11:59:19] Storing 810 Occurrences (2280/810/812)
[INFO] [2023-03-30 11:59:19] Storing 1470 OccurrenceMetadata (2280/810/812)
[INFO] [2023-03-30 11:59:19] Handling diff: /app/public/data/bsdnao/diff/bsdnao_measurements_30259.diff (812 lines)
[INFO] [2023-03-30 11:59:19] Loading measurements diff file into memory (812 lines)...
[INFO] [2023-03-30 11:59:19] Storing 810 Traits (1632/810/812)
[INFO] [2023-03-30 11:59:20] Storing 822 MetaTraits (1632/810/812)
[STOP] [2023-03-30 11:59:20] parse_diff_and_store
[START] [2023-03-30 11:59:20] resolve_keys
[2023-03-30 11:59:20] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-03-30 11:59:27] Occurrences to nodes (through scientific_names)...
[INFO] [2023-03-30 11:59:27] traits to occurrences...
[INFO] [2023-03-30 11:59:27] traits to nodes (through occurrences)...
[INFO] [2023-03-30 11:59:27] Traits to sex term...
[INFO] [2023-03-30 11:59:27] Traits to lifestage term...
[INFO] [2023-03-30 11:59:27] MetaTraits to traits...
[INFO] [2023-03-30 11:59:27] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-03-30 11:59:27] Assocs to occurrences...
[INFO] [2023-03-30 11:59:27] Assocs to nodes...
[INFO] [2023-03-30 11:59:27] Assoc to sex term...
[INFO] [2023-03-30 11:59:27] Assoc to lifestage term...
[INFO] [2023-03-30 11:59:27] MetaAssoc to assocs...
[STOP] [2023-03-30 11:59:27] resolve_keys
[START] [2023-03-30 11:59:27] hold_for_later_1
[STOP] [2023-03-30 11:59:27] hold_for_later_1
[START] [2023-03-30 11:59:27] hold_for_later_2
[STOP] [2023-03-30 11:59:27] hold_for_later_2
[START] [2023-03-30 11:59:27] resolve_missing_parents
[STOP] [2023-03-30 11:59:27] resolve_missing_parents
[START] [2023-03-30 11:59:27] rebuild_nodes
[START] [2023-03-30 11:59:27] Flattener#flatten
[START] [2023-03-30 11:59:27] Flattener#study_resource
[START] [2023-03-30 11:59:27] Flattener#build_ancestry
[STOP] [2023-03-30 11:59:27] Flattener#build_ancestry
[INFO] [2023-03-30 11:59:27] 224 ancestry keys
[START] [2023-03-30 11:59:27] build_node_ancestors
[INFO] [2023-03-30 11:59:27] old ancestors deleted.
[STOP] [2023-03-30 11:59:27] build_node_ancestors
[START] [2023-03-30 11:59:28] Flattener#propagate_ancestor_ids
[STOP] [2023-03-30 11:59:28] Flattener#propagate_ancestor_ids
[STOP] [2023-03-30 11:59:28] Flattener#flatten
[STOP] [2023-03-30 11:59:28] rebuild_nodes
[START] [2023-03-30 11:59:28] resolve_missing_media_owners
[STOP] [2023-03-30 11:59:28] resolve_missing_media_owners
[START] [2023-03-30 11:59:28] sanitize_media_verbatims
[STOP] [2023-03-30 11:59:28] sanitize_media_verbatims
[START] [2023-03-30 11:59:28] queue_downloads
[STOP] [2023-03-30 11:59:28] queue_downloads
[START] [2023-03-30 11:59:28] parse_names
[WARN] [2023-03-30 11:59:28] I see 224 names which still need to be parsed.
[WARN] [2023-03-30 11:59:28] Names to parse: 224 formatted: 224 learned: 224 parsed: 224
[STOP] [2023-03-30 11:59:29] parse_names
[START] [2023-03-30 11:59:29] denormalize_canonical_names_to_nodes
[STOP] [2023-03-30 11:59:29] denormalize_canonical_names_to_nodes
[START] [2023-03-30 11:59:29] match_nodes
[START] [2023-03-30 11:59:29] map_all_nodes_to_pages
[STOP] [2023-03-30 11:59:39] map_all_nodes_to_pages
[INFO] [2023-03-30 11:59:39] ZERO unmatched nodes (of 224)! Nicely done.
[START] [2023-03-30 11:59:39] update_nodes
[STOP] [2023-03-30 11:59:39] update_nodes
[STOP] [2023-03-30 11:59:39] match_nodes
[START] [2023-03-30 11:59:39] reindex_search
[STOP] [2023-03-30 11:59:40] reindex_search
[START] [2023-03-30 11:59:40] normalize_units
[STOP] [2023-03-30 11:59:43] normalize_units
[START] [2023-03-30 11:59:43] calculate_statistics
[INFO] [2023-03-30 11:59:43] Duplicate page_id count: 8
[STOP] [2023-03-30 11:59:43] calculate_statistics
[START] [2023-03-30 11:59:43] complete_harvest_instance
[START] [2023-03-30 11:59:43] overall_tsv_creation
[INFO] [2023-03-30 11:59:43] Exporting 224 nodes as TSV in batches of 10000...
[INFO] [2023-03-30 11:59:43] Processing group of 224 in 1 batches of 10000
[INFO] [2023-03-30 11:59:43] 810 Traits (unfiltered) and 0 associations...
[INFO] [2023-03-30 11:59:43] Building Traits map for 224 nodes (this can take a while)...
[INFO] [2023-03-30 11:59:43] Mapped 810 traits (822 meta) for 224 nodes.
[INFO] [2023-03-30 11:59:43] Building Associations map (this can take a while)...
[INFO] [2023-03-30 11:59:43] Done. 0 assocs mapped (0 meta).
[INFO] [2023-03-30 11:59:43] Adding 810 traits...
[INFO] [2023-03-30 11:59:44] 0 metadata added.
[INFO] [2023-03-30 11:59:44] Adding 0 assocs...
[INFO] [2023-03-30 11:59:44] 0 metadata added.
[INFO] [2023-03-30 12:00:38] Processed 224/224 nodes
[INFO] [2023-03-30 12:00:38] Average Time: 55.58
[INFO] [2023-03-30 12:00:38] Total Time: 56s
[STOP] [2023-03-30 12:00:38] overall_tsv_creation
[INFO] [2023-03-30 12:00:38] Done. Check your files:
[INFO] [2023-03-30 12:00:39] (224 lines) /app/public/data/bsdnao/publish_nodes.tsv
[INFO] [2023-03-30 12:00:39] (445 lines) /app/public/data/bsdnao/publish_node_ancestors.tsv
[INFO] [2023-03-30 12:00:39] (224 lines) /app/public/data/bsdnao/publish_scientific_names.tsv
[INFO] [2023-03-30 12:00:39] (811 lines) /app/public/data/bsdnao/publish_traits.tsv
[INFO] [2023-03-30 12:00:39] (1 lines) /app/public/data/bsdnao/publish_metadata.tsv
[STOP] [2023-03-30 12:00:39] complete_harvest_instance
[START] [2023-03-30 12:00:39] completed
[STOP] [2023-03-30 12:00:39] completed
[STOP] [2023-03-30 12:00:39] logged process, took 83.87
Latest Process

30 Mar 11:59 EXITED currently processing 0