Harvest for Gastineau at al 2022 Created 31 Jan 12:02

Stage: completed
Fetched: 31 Jan 12:02
Validated: 31 Jan 12:02
Deltas Created 31 Jan 12:02
Units Normalized: 31 Jan 12:02
Ancestry Built: 31 Jan 12:02
Nodes Matched: 31 Jan 12:02
Names Parsed: 31 Jan 12:02
New Models Stored: 31 Jan 12:02
Indexed: 31 Jan 12:02
Completed: 31 Jan 12:03
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2023-01-31 12:02:22] Created harvest instance #4286
[STOP] [2023-01-31 12:02:22] create_harvest_instance
[START] [2023-01-31 12:02:22] fetch_files
[STOP] [2023-01-31 12:02:22] fetch_files
[START] [2023-01-31 12:02:22] validate_each_file
[INFO] [2023-01-31 12:02:22] Looping over 3 formats...
[INFO] [2023-01-31 12:02:22] ...nodes (/app/public/data/gastineau_at_al_/taxa.tsv)
[INFO] [2023-01-31 12:02:22] Valid: /app/public/data/gastineau_at_al_/converted_csv/gastineau_at_al__nodes_30156.csv (2 lines)
[INFO] [2023-01-31 12:02:22] ...occurrences (/app/public/data/gastineau_at_al_/occurrences.tsv)
[INFO] [2023-01-31 12:02:22] Valid: /app/public/data/gastineau_at_al_/converted_csv/gastineau_at_al__occurrences_30157.csv (2 lines)
[INFO] [2023-01-31 12:02:22] ...measurements (/app/public/data/gastineau_at_al_/measurementOrFact.tsv)
[INFO] [2023-01-31 12:02:22] Valid: /app/public/data/gastineau_at_al_/converted_csv/gastineau_at_al__measurements_30158.csv (4 lines)
[STOP] [2023-01-31 12:02:22] validate_each_file
[START] [2023-01-31 12:02:22] convert_to_csv
[INFO] [2023-01-31 12:02:22] Looping over 3 formats...
[INFO] [2023-01-31 12:02:22] ...nodes (/app/public/data/gastineau_at_al_/taxa.tsv)
[CMD] [2023-01-31 12:02:22] /usr/bin/sort /app/public/data/gastineau_at_al_/converted_csv/gastineau_at_al__nodes_30156.csv > /app/public/data/gastineau_at_al_/converted_csv/gastineau_at_al__nodes_30156.csv_sorted
[INFO] [2023-01-31 12:02:22] Converted: /app/public/data/gastineau_at_al_/converted_csv/gastineau_at_al__nodes_30156.csv (2 lines)
[INFO] [2023-01-31 12:02:22] ...occurrences (/app/public/data/gastineau_at_al_/occurrences.tsv)
[CMD] [2023-01-31 12:02:22] /usr/bin/sort /app/public/data/gastineau_at_al_/converted_csv/gastineau_at_al__occurrences_30157.csv > /app/public/data/gastineau_at_al_/converted_csv/gastineau_at_al__occurrences_30157.csv_sorted
[INFO] [2023-01-31 12:02:22] Converted: /app/public/data/gastineau_at_al_/converted_csv/gastineau_at_al__occurrences_30157.csv (2 lines)
[INFO] [2023-01-31 12:02:22] ...measurements (/app/public/data/gastineau_at_al_/measurementOrFact.tsv)
[CMD] [2023-01-31 12:02:22] /usr/bin/sort /app/public/data/gastineau_at_al_/converted_csv/gastineau_at_al__measurements_30158.csv > /app/public/data/gastineau_at_al_/converted_csv/gastineau_at_al__measurements_30158.csv_sorted
[INFO] [2023-01-31 12:02:22] Converted: /app/public/data/gastineau_at_al_/converted_csv/gastineau_at_al__measurements_30158.csv (4 lines)
[STOP] [2023-01-31 12:02:22] convert_to_csv
[START] [2023-01-31 12:02:22] calculate_delta
[INFO] [2023-01-31 12:02:22] Looping over 3 formats...
[INFO] [2023-01-31 12:02:22] ...nodes (/app/public/data/gastineau_at_al_/taxa.tsv)
[CMD] [2023-01-31 12:02:22] echo "0a" > /app/public/data/gastineau_at_al_/diff/gastineau_at_al__nodes_30156.diff
[CMD] [2023-01-31 12:02:22] tail -n +1 /app/public/data/gastineau_at_al_/converted_csv/gastineau_at_al__nodes_30156.csv >> /app/public/data/gastineau_at_al_/diff/gastineau_at_al__nodes_30156.diff
[CMD] [2023-01-31 12:02:22] echo "." >> /app/public/data/gastineau_at_al_/diff/gastineau_at_al__nodes_30156.diff
[INFO] [2023-01-31 12:02:22] Created diff: /app/public/data/gastineau_at_al_/diff/gastineau_at_al__nodes_30156.diff (4 lines)
[INFO] [2023-01-31 12:02:22] ...occurrences (/app/public/data/gastineau_at_al_/occurrences.tsv)
[CMD] [2023-01-31 12:02:22] echo "0a" > /app/public/data/gastineau_at_al_/diff/gastineau_at_al__occurrences_30157.diff
[CMD] [2023-01-31 12:02:22] tail -n +1 /app/public/data/gastineau_at_al_/converted_csv/gastineau_at_al__occurrences_30157.csv >> /app/public/data/gastineau_at_al_/diff/gastineau_at_al__occurrences_30157.diff
[CMD] [2023-01-31 12:02:22] echo "." >> /app/public/data/gastineau_at_al_/diff/gastineau_at_al__occurrences_30157.diff
[INFO] [2023-01-31 12:02:22] Created diff: /app/public/data/gastineau_at_al_/diff/gastineau_at_al__occurrences_30157.diff (4 lines)
[INFO] [2023-01-31 12:02:22] ...measurements (/app/public/data/gastineau_at_al_/measurementOrFact.tsv)
[CMD] [2023-01-31 12:02:22] echo "0a" > /app/public/data/gastineau_at_al_/diff/gastineau_at_al__measurements_30158.diff
[CMD] [2023-01-31 12:02:22] tail -n +1 /app/public/data/gastineau_at_al_/converted_csv/gastineau_at_al__measurements_30158.csv >> /app/public/data/gastineau_at_al_/diff/gastineau_at_al__measurements_30158.diff
[CMD] [2023-01-31 12:02:22] echo "." >> /app/public/data/gastineau_at_al_/diff/gastineau_at_al__measurements_30158.diff
[INFO] [2023-01-31 12:02:22] Created diff: /app/public/data/gastineau_at_al_/diff/gastineau_at_al__measurements_30158.diff (6 lines)
[STOP] [2023-01-31 12:02:22] calculate_delta
[START] [2023-01-31 12:02:22] parse_diff_and_store
[INFO] [2023-01-31 12:02:22] Handling diff: /app/public/data/gastineau_at_al_/diff/gastineau_at_al__nodes_30156.diff (4 lines)
[INFO] [2023-01-31 12:02:22] Loading nodes diff file into memory (4 lines)...
[INFO] [2023-01-31 12:02:22] Storing 2 ScientificNames (4/2/4)
[INFO] [2023-01-31 12:02:22] Storing 2 Nodes (4/2/4)
[INFO] [2023-01-31 12:02:22] Handling diff: /app/public/data/gastineau_at_al_/diff/gastineau_at_al__occurrences_30157.diff (4 lines)
[INFO] [2023-01-31 12:02:22] Loading occurrences diff file into memory (4 lines)...
[INFO] [2023-01-31 12:02:22] Storing 2 Occurrences (2/2/4)
[INFO] [2023-01-31 12:02:22] Handling diff: /app/public/data/gastineau_at_al_/diff/gastineau_at_al__measurements_30158.diff (6 lines)
[INFO] [2023-01-31 12:02:22] Loading measurements diff file into memory (6 lines)...
[INFO] [2023-01-31 12:02:22] Storing 4 Traits (8/4/6)
[INFO] [2023-01-31 12:02:22] Storing 4 MetaTraits (8/4/6)
[STOP] [2023-01-31 12:02:22] parse_diff_and_store
[START] [2023-01-31 12:02:22] resolve_keys
[2023-01-31 12:02:22] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-01-31 12:02:29] Occurrences to nodes (through scientific_names)...
[INFO] [2023-01-31 12:02:29] traits to occurrences...
[INFO] [2023-01-31 12:02:29] traits to nodes (through occurrences)...
[INFO] [2023-01-31 12:02:29] Traits to sex term...
[INFO] [2023-01-31 12:02:29] Traits to lifestage term...
[INFO] [2023-01-31 12:02:29] MetaTraits to traits...
[INFO] [2023-01-31 12:02:29] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-01-31 12:02:29] Assocs to occurrences...
[INFO] [2023-01-31 12:02:29] Assocs to nodes...
[INFO] [2023-01-31 12:02:29] Assoc to sex term...
[INFO] [2023-01-31 12:02:29] Assoc to lifestage term...
[INFO] [2023-01-31 12:02:29] MetaAssoc to assocs...
[STOP] [2023-01-31 12:02:29] resolve_keys
[START] [2023-01-31 12:02:30] hold_for_later_1
[STOP] [2023-01-31 12:02:30] hold_for_later_1
[START] [2023-01-31 12:02:30] hold_for_later_2
[STOP] [2023-01-31 12:02:30] hold_for_later_2
[START] [2023-01-31 12:02:30] resolve_missing_parents
[STOP] [2023-01-31 12:02:30] resolve_missing_parents
[START] [2023-01-31 12:02:30] rebuild_nodes
[START] [2023-01-31 12:02:30] Flattener#flatten
[START] [2023-01-31 12:02:30] Flattener#study_resource
[START] [2023-01-31 12:02:30] Flattener#build_ancestry
[STOP] [2023-01-31 12:02:30] Flattener#build_ancestry
[INFO] [2023-01-31 12:02:30] 2 ancestry keys
[START] [2023-01-31 12:02:30] build_node_ancestors
[INFO] [2023-01-31 12:02:30] old ancestors deleted.
[STOP] [2023-01-31 12:02:30] build_node_ancestors
[WARN] [2023-01-31 12:02:30] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-01-31 12:02:30] Flattener#flatten
[STOP] [2023-01-31 12:02:30] rebuild_nodes
[START] [2023-01-31 12:02:30] resolve_missing_media_owners
[STOP] [2023-01-31 12:02:30] resolve_missing_media_owners
[START] [2023-01-31 12:02:30] sanitize_media_verbatims
[STOP] [2023-01-31 12:02:30] sanitize_media_verbatims
[START] [2023-01-31 12:02:30] queue_downloads
[STOP] [2023-01-31 12:02:30] queue_downloads
[START] [2023-01-31 12:02:30] parse_names
[WARN] [2023-01-31 12:02:30] I see 2 names which still need to be parsed.
[WARN] [2023-01-31 12:02:30] Names to parse: 2 formatted: 2 learned: 2 parsed: 2
[STOP] [2023-01-31 12:02:31] parse_names
[START] [2023-01-31 12:02:31] denormalize_canonical_names_to_nodes
[STOP] [2023-01-31 12:02:31] denormalize_canonical_names_to_nodes
[START] [2023-01-31 12:02:31] match_nodes
[START] [2023-01-31 12:02:31] map_all_nodes_to_pages
[STOP] [2023-01-31 12:02:31] map_all_nodes_to_pages
[INFO] [2023-01-31 12:02:31] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2023-01-31 12:02:31] update_nodes
[STOP] [2023-01-31 12:02:31] update_nodes
[STOP] [2023-01-31 12:02:31] match_nodes
[START] [2023-01-31 12:02:31] reindex_search
[STOP] [2023-01-31 12:02:31] reindex_search
[START] [2023-01-31 12:02:31] normalize_units
[STOP] [2023-01-31 12:02:31] normalize_units
[START] [2023-01-31 12:02:31] calculate_statistics
[2023-01-31 12:02:31] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-01-31 12:02:31] Duplicate page_id count: 0
[STOP] [2023-01-31 12:02:31] calculate_statistics
[START] [2023-01-31 12:02:31] complete_harvest_instance
[START] [2023-01-31 12:02:31] overall_tsv_creation
[INFO] [2023-01-31 12:02:31] Exporting 2 nodes as TSV in batches of 10000...
[INFO] [2023-01-31 12:02:31] Processing group of 2 in 1 batches of 10000
[INFO] [2023-01-31 12:02:31] 4 Traits (unfiltered) and 0 associations...
[INFO] [2023-01-31 12:02:31] Building Traits map for 2 nodes (this can take a while)...
[INFO] [2023-01-31 12:02:31] Mapped 4 traits (4 meta) for 2 nodes.
[INFO] [2023-01-31 12:02:31] Building Associations map (this can take a while)...
[INFO] [2023-01-31 12:02:31] Done. 0 assocs mapped (0 meta).
[INFO] [2023-01-31 12:02:31] Adding 4 traits...
[INFO] [2023-01-31 12:02:31] 0 metadata added.
[INFO] [2023-01-31 12:02:31] Adding 0 assocs...
[INFO] [2023-01-31 12:02:31] 0 metadata added.
[INFO] [2023-01-31 12:03:15] Processed 2/2 nodes
[INFO] [2023-01-31 12:03:15] Average Time: 44.31
[INFO] [2023-01-31 12:03:15] Total Time: 45s
[STOP] [2023-01-31 12:03:15] overall_tsv_creation
[INFO] [2023-01-31 12:03:15] Done. Check your files:
[INFO] [2023-01-31 12:03:15] (2 lines) /app/public/data/gastineau_at_al_/publish_nodes.tsv
[INFO] [2023-01-31 12:03:15] (2 lines) /app/public/data/gastineau_at_al_/publish_scientific_names.tsv
[INFO] [2023-01-31 12:03:15] (5 lines) /app/public/data/gastineau_at_al_/publish_traits.tsv
[INFO] [2023-01-31 12:03:15] (1 lines) /app/public/data/gastineau_at_al_/publish_metadata.tsv
[STOP] [2023-01-31 12:03:15] complete_harvest_instance
[START] [2023-01-31 12:03:15] completed
[STOP] [2023-01-31 12:03:15] completed
[STOP] [2023-01-31 12:03:15] logged process, took 53.78
Latest Process

31 Jan 11:58 EXITED currently processing 0